From 46921669cd06e701e80a8f4fefbeac317abe86de Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 31 Oct 2023 18:08:04 +0000 Subject: [PATCH 001/468] Added a GridForce as a CustomCPPForce. This links in and works well. There is about a 10% speed drop from copying the coordinates / forces from GPU to CPU. Also made the std::exception errors RuntimeErrors rather than UserWarnings, as this was confusing (they are errors). Also detected a std::bad_alloc and convert this to MemoryError with a useful message. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 23 +++++++ wrapper/Convert/SireOpenMM/customforce.cpp | 79 ++++++++++++++++++++++ wrapper/Convert/SireOpenMM/customforce.h | 25 +++++++ wrapper/Error/wrap_exceptions.cpp | 22 +++++- 4 files changed, 146 insertions(+), 3 deletions(-) create mode 100644 wrapper/Convert/SireOpenMM/customforce.cpp create mode 100644 wrapper/Convert/SireOpenMM/customforce.h diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index bee36a1f6..85dec066b 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -24,11 +24,34 @@ if (${SIRE_USE_OPENMM}) # Other python wrapping directories include_directories(${CMAKE_SOURCE_DIR}) + include(CheckCXXSourceRuns) + + # Whether or not we have CustomCPPForceImpl (OpenMM 8.1+) + CHECK_CXX_SOURCE_RUNS(" + #include \"openmm/internal/ContextImpl.h\" + #include \"openmm/internal/CustomCPPForceImpl.h\" + + int main() + { + OpenMM::ContextImpl* context = NULL; + OpenMM::CustomCPPForceImpl* force = NULL; + return 0; + }" + CAN_USE_CUSTOMCPPFORCE) + + if (CAN_USE_CUSTOMCPPFORCE) + message(STATUS "OpenMM version supports CustomCPPForce") + add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") + else() + message(STATUS "OpenMM version does not support CustomCPPForce") + endif() + # Define the sources in SireOpenMM set ( SIREOPENMM_SOURCES _SireOpenMM.main.cpp + customforce.cpp lambdalever.cpp openmmminimise.cpp openmmmolecule.cpp diff --git a/wrapper/Convert/SireOpenMM/customforce.cpp b/wrapper/Convert/SireOpenMM/customforce.cpp new file mode 100644 index 000000000..450ec5ca5 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/customforce.cpp @@ -0,0 +1,79 @@ + +#include "customforce.h" + +#ifdef SIRE_USE_CUSTOMCPPFORCE +#include "openmm/internal/ContextImpl.h" +#include "openmm/internal/CustomCPPForceImpl.h" +#endif + +#include "SireError/errors.h" + +#include + +using namespace SireOpenMM; + +#ifdef SIRE_USE_CUSTOMCPPFORCE +class GridForceImpl : public OpenMM::CustomCPPForceImpl +{ +public: + GridForceImpl(const GridForce &owner) + : OpenMM::CustomCPPForceImpl(owner), + owner(owner) + { + } + + ~GridForceImpl() + { + } + + double computeForce(OpenMM::ContextImpl &context, + const std::vector &positions, + std::vector &forces) + { + // Compute the forces and energy here. Store the forces into the + // vector and return the energy. + + // we can get the platform using + // const auto platform = context.getPlatform().getName(); + // so we could have custom code for different platforms if we wanted + + // return the potential energy + return 0; + } + + const GridForce &getOwner() const + { + return owner; + } + +private: + const GridForce &owner; +}; +#endif + +GridForce::GridForce() : OpenMM::Force() +{ +#ifndef SIRE_USE_CUSTOMCPPFORCE + throw SireError::unsupported(QObject::tr( + "Unable to create a GridForce because OpenMM::CustomCPPForceImpl " + "is not available. You need to use OpenMM 8.1 or later."), + CODELOC); +#endif +} + +GridForce::~GridForce() +{ +} + +OpenMM::ForceImpl *GridForce::createImpl() const +{ +#ifdef SIRE_USE_CUSTOMCPPFORCE + return new GridForceImpl(*this); +#else + throw SireError::unsupported(QObject::tr( + "Unable to create a GridForce because OpenMM::CustomCPPForceImpl " + "is not available. You need to use OpenMM 8.1 or later."), + CODELOC); + return 0; +#endif +} diff --git a/wrapper/Convert/SireOpenMM/customforce.h b/wrapper/Convert/SireOpenMM/customforce.h new file mode 100644 index 000000000..72ee81d17 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/customforce.h @@ -0,0 +1,25 @@ +#ifndef SIRE_OPENMM_CUSTOMFORCE_H +#define SIRE_OPENMM_CUSTOMFORCE_H + +#include "openmm/Force.h" + +#include "sireglobal.h" + +SIRE_BEGIN_HEADER + +namespace SireOpenMM +{ + class GridForce : public OpenMM::Force + { + public: + GridForce(); + ~GridForce(); + + protected: + OpenMM::ForceImpl *createImpl() const; + }; +} + +SIRE_END_HEADER + +#endif diff --git a/wrapper/Error/wrap_exceptions.cpp b/wrapper/Error/wrap_exceptions.cpp index fc366336d..3b9fb8b55 100644 --- a/wrapper/Error/wrap_exceptions.cpp +++ b/wrapper/Error/wrap_exceptions.cpp @@ -152,17 +152,33 @@ namespace SireError void exception_translator(const SireError::exception &ex) { boost::python::release_gil_policy::acquire_gil_no_raii(); - PyErr_SetString(PyExc_UserWarning, + PyErr_SetString(PyExc_RuntimeError, get_exception_string(ex).toUtf8()); } - void std_exception_translator(const std::exception &ex) + void bad_alloc_exception_translator(const std::bad_alloc &ex) { boost::python::release_gil_policy::acquire_gil_no_raii(); - PyErr_SetString(PyExc_UserWarning, + PyErr_SetString(PyExc_MemoryError, QString("%1").arg(ex.what()).toUtf8()); } + void std_exception_translator(const std::exception &ex) + { + boost::python::release_gil_policy::acquire_gil_no_raii(); + + if (dynamic_cast(&ex) != 0) + { + PyErr_SetString(PyExc_MemoryError, + "Memory error - out of memory?"); + } + else + { + PyErr_SetString(PyExc_RuntimeError, + QString("%1").arg(ex.what()).toUtf8()); + } + } + SireError::FastExceptionFlag *fast_exception_flag(0); void enable_backtrace_exceptions() From 9ba807cfcb777e278b2ec500a6c7d0342c9adc45 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 2 Nov 2023 00:35:57 +0000 Subject: [PATCH 002/468] Beginning to think about what data is needed for GridForce --- wrapper/Convert/SireOpenMM/customforce.h | 33 ++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/customforce.h b/wrapper/Convert/SireOpenMM/customforce.h index 72ee81d17..03b756421 100644 --- a/wrapper/Convert/SireOpenMM/customforce.h +++ b/wrapper/Convert/SireOpenMM/customforce.h @@ -1,6 +1,7 @@ #ifndef SIRE_OPENMM_CUSTOMFORCE_H #define SIRE_OPENMM_CUSTOMFORCE_H +#include "openmm.h" #include "openmm/Force.h" #include "sireglobal.h" @@ -15,8 +16,40 @@ namespace SireOpenMM GridForce(); ~GridForce(); + int addFixedAtom(const OpenMM::Vec3 &position, + float charge, float sigma, float epsilon); + + void getFixedAtom(int idx, OpenMM::Vec3 &position, + float &charge, float &sigma, float &epsilon) const; + + void updateFixedAtom(int idx, const OpenMM::Vec3 &position, + float charge, float sigma, float epsilon); + protected: OpenMM::ForceImpl *createImpl() const; + + private: + /** All of the data for the fixed atoms */ + std::vector> fixed_atoms; + + /** The coulomb potential grid */ + std::vector coulomb_grid; + + /** The center of the grid */ + OpenMM::Vec3 grid_center; + + /** The half-extents of this grid (plus or minus this to + get the grid boundaries) */ + OpenMM::Vec3 grid_half_extents; + + /** The coulomb cutoff (applies from the center of the grid) */ + double coulomb_cutoff; + + /** The grid spacing */ + double grid_spacing; + + /** The number of grid points along x, y and z */ + unsigned int dimx, dimy, dimz; }; } From c71630e25b02ffd980bdcb445ca2003c21aa4b2b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 2 Nov 2023 10:57:04 +0000 Subject: [PATCH 003/468] Working out how to specify field atoms (those that can be represented on a potential grid) and how they are managed in OpenMMMolecule WIP! --- src/sire/mol/_dynamics.py | 4 +- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 110 ++++++++++++++++++ wrapper/Convert/SireOpenMM/openmmmolecule.h | 13 +++ 3 files changed, 125 insertions(+), 2 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index c1bf10d17..326747975 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -596,7 +596,7 @@ def run( energy_frequency = u(energy_frequency) if lambda_windows is not None: - if type(lambda_windows) is not list: + if isinstance(lambda_windows, list): lambda_windows = [lambda_windows] try: @@ -1314,7 +1314,7 @@ def current_potential_energy(self, lambda_values=None): if lambda_values is None: return self._d.current_potential_energy() else: - if not type(lambda_values) is list: + if not isinstance(lambda_values, list): lambda_values = [lambda_values] # save the current value of lambda so we diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 07083cc04..81f2e392f 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -161,6 +161,26 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, perturbable_constraint_type = constraint_type; } + // extract out the indicies of any field atoms, if there are any. + // Field atoms are those that only exist via the interaction field + // they produce (i.e. their potentials are combined into a grid, + // which affects the energy/forces of other particles that are + // on that grid) + const auto field_atom_prop = map["is_field_atom"]; + + if (mol.hasProperty(field_atom_prop)) + { + const auto atoms = mol.atoms("atom property is_field_atom == True"); + + for (int i = 0; i < atoms.count(); ++i) + { + field_atoms.append(atoms(i).index().value()); + } + + // should not need to sort it, but just in case + qSort(field_atoms); + } + if (ffinfo.isAmberStyle()) { if (is_perturbable) @@ -222,6 +242,11 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, .arg(ffinfo.toString()), CODELOC); } + + if (this->hasFieldAtoms()) + { + this->processFieldAtoms(); + } } OpenMMMolecule::~OpenMMMolecule() @@ -248,6 +273,21 @@ bool OpenMMMolecule::isGhostAtom(int atom) const return from_ghost_idxs.contains(atom) or to_ghost_idxs.contains(atom); } +bool OpenMMMolecule::isFieldAtom(int atom) const +{ + return field_atoms.contains(atom); +} + +bool OpenMMMolecule::isFieldMolecule() const +{ + return field_atoms.count() == atoms.count(); +} + +bool OpenMMMolecule::hasFieldAtoms() const +{ + return not field_atoms.isEmpty(); +} + OpenMM::Vec3 to_vec3(const SireMaths::Vector &coords) { const double internal_to_nm = (1 * SireUnits::angstrom).to(SireUnits::nanometer); @@ -1373,6 +1413,76 @@ void OpenMMMolecule::copyInCoordsAndVelocities(OpenMM::Vec3 *c, OpenMM::Vec3 *v) } } +/** Process this molecule to remove unnecessary parameters associated + * with field atoms. Field atoms are massless atoms that are not + * bonded to any other atom + */ +void OpenMMMolecule::processFieldAtoms() +{ + if (not this->hasFieldAtoms()) + return; + + if (this->isPerturbable()) + throw SireError::incompatible_error(QObject::tr( + "We cannot (yet) support perturbable molecules that also " + "contain field atoms. Please raise an issue if you would " + "like us to write the code to do this."), + CODELOC); + + if (this->isFieldMolecule()) + { + qDebug() << "This is a field molecule"; + + // very easy case - all atoms are field atoms + field_points.reserve(field_atoms.count()); + + for (int i = 0; i < this->atoms.count(); ++i) + { + const auto &clj = cljs.at(i); + field_points.append(std::make_tuple(coords[i], + std::get<0>(clj), + std::get<1>(clj), + std::get<2>(clj))); + } + + coords.clear(); + vels.clear(); + masses.clear(); + light_atoms.clear(); + virtual_sites.clear(); + cljs.clear(); + exception_params.clear(); + bond_params.clear(); + ang_params.clear(); + dih_params.clear(); + constraints.clear(); + perturbed.reset(); + exception_idxs.clear(); + unbonded_atoms.clear(); + alphas.clear(); + to_ghost_idxs.clear(); + from_ghost_idxs.clear(); + + return; + } + + // more difficult case - a mixture of field and non-field atoms. + // This is almost certainly a protein or similar + + // to start, the easiest is to create a bitmask to indicate + // which atoms are field atoms - we can then go through the + // atoms in sequence and then sort them into the appropriate + // bins + field_points.reserve(field_atoms.count()); + + QVector is_field_atom(this->atoms.count(), false); + + for (const auto &atom : field_atoms) + { + is_field_atom[atom] = true; + } +} + /** Return the alpha parameters of all atoms in atom order for * this molecule */ diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 5241dc8ff..d00552867 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -73,6 +73,11 @@ namespace SireOpenMM bool isGhostAtom(int atom) const; + bool isFieldAtom(int atom) const; + bool isFieldMolecule() const; + + bool hasFieldAtoms() const; + std::tuple getException(int atom0, int atom1, int start_index, @@ -113,6 +118,12 @@ namespace SireOpenMM /** Indexes of virtual sites */ QList virtual_sites; + /** Indexes of all of the field atoms */ + QList field_atoms; + + /** All of the field points with their parameters */ + QVector> field_points; + /** Charge and LJ parameters (sigma / epsilon) */ QVector> cljs; @@ -181,6 +192,8 @@ namespace SireOpenMM const SireBase::PropertyMap &map); void alignInternals(const SireBase::PropertyMap &map); + + void processFieldAtoms(); }; /** This class holds all of the information of an OpenMM molecule From 504f3108485eb7cde27d19f0fab099877e5e2b9e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 3 Nov 2023 19:35:31 +0000 Subject: [PATCH 004/468] Fixed bug introduced by poorly fixing a lint error --- src/sire/mol/_dynamics.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 326747975..d9cdc89a4 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -596,7 +596,7 @@ def run( energy_frequency = u(energy_frequency) if lambda_windows is not None: - if isinstance(lambda_windows, list): + if not isinstance(lambda_windows, list): lambda_windows = [lambda_windows] try: From 4f44ec365a921ce74871ffc5896dfdca411e460d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 5 Nov 2023 22:37:40 +0000 Subject: [PATCH 005/468] Making progress separating out the mobile atoms and the field atoms. Still very WIP --- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 305 ++++++++++-------- wrapper/Convert/SireOpenMM/openmmmolecule.h | 49 ++- .../SireOpenMM/sire_to_openmm_system.cpp | 33 +- 3 files changed, 241 insertions(+), 146 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 81f2e392f..b591a6488 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -40,6 +40,113 @@ using namespace SireMM; using namespace SireMol; using namespace SireBase; +/////// +/////// Helper functions +/////// + +OpenMM::Vec3 to_vec3(const SireMaths::Vector &coords) +{ + const double internal_to_nm = (1 * SireUnits::angstrom).to(SireUnits::nanometer); + + return OpenMM::Vec3(internal_to_nm * coords.x(), + internal_to_nm * coords.y(), + internal_to_nm * coords.z()); +} + +OpenMM::Vec3 to_vec3(const SireMol::Velocity3D &vel) +{ + return OpenMM::Vec3(vel.x().to(SireUnits::nanometers_per_ps), + vel.y().to(SireUnits::nanometers_per_ps), + vel.z().to(SireUnits::nanometers_per_ps)); +} + +inline qint64 to_pair(qint64 x, qint64 y) +{ + if (y < x) + return to_pair(y, x); + else + return x << 32 | y & 0x00000000FFFFFFFF; +} + +//////// +//////// Implementation of FieldMolecule +//////// + +FieldMolecule::FieldMolecule(const Selector &atoms, + const PropertyMap &map) +{ + const int nats = atoms.count(); + + const auto coords_prop = map["coordinates"]; + const auto charge_prop = map["charge"]; + const auto lj_prop = map["LJ"]; + + coords = QVector(nats, OpenMM::Vec3(0, 0, 0)); + charges = QVector(nats, 0.0); + sigmas = QVector(nats, 0.0); + epsilons = QVector(nats, 0.0); + + auto coords_data = coords.data(); + auto charges_data = charges.data(); + auto sigmas_data = sigmas.data(); + auto epsilons_data = epsilons.data(); + + for (int i = 0; i < nats; ++i) + { + const auto &atom = atoms(i); + + coords_data[i] = to_vec3(atom.property(coords_prop)); + charges_data[i] = atom.property(charge_prop).to(SireUnits::mod_electron); + + const auto &lj = atom.property(lj_prop); + + const double sig = lj.sigma().to(SireUnits::nanometer); + const double eps = lj.epsilon().to(SireUnits::kJ_per_mol); + } +} + +FieldMolecule::~FieldMolecule() +{ +} + +int FieldMolecule::nAtoms() const +{ + return coords.count(); +} + +QVector FieldMolecule::getCoords() const +{ + return coords; +} + +QVector FieldMolecule::getCharges() const +{ + return charges; +} + +QVector FieldMolecule::getSigmas() const +{ + return sigmas; +} + +QVector FieldMolecule::getEpsilons() const +{ + return epsilons; +} + +bool FieldMolecule::isFieldAtom(int atomidx) const +{ + return this->atomidx_to_fieldidx.isEmpty() or this->atomidx_to_fieldidx.contains(atomidx); +} + +int FieldMolecule::getAtomFieldIndex(int atomidx) const +{ + if (this->atomidx_to_fieldidx.isEmpty()) + return atomidx; + else + return this->atomidx_to_fieldidx.value(atomidx, -1); +} + //////// //////// Implementation of OpenMMMolecule //////// @@ -172,13 +279,8 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, { const auto atoms = mol.atoms("atom property is_field_atom == True"); - for (int i = 0; i < atoms.count(); ++i) - { - field_atoms.append(atoms(i).index().value()); - } - - // should not need to sort it, but just in case - qSort(field_atoms); + if (not atoms.isEmpty()) + field_mol.reset(new FieldMolecule(atoms, map)); } if (ffinfo.isAmberStyle()) @@ -242,11 +344,6 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, .arg(ffinfo.toString()), CODELOC); } - - if (this->hasFieldAtoms()) - { - this->processFieldAtoms(); - } } OpenMMMolecule::~OpenMMMolecule() @@ -263,53 +360,34 @@ bool OpenMMMolecule::operator!=(const OpenMMMolecule &other) const return not this->operator==(other); } -bool OpenMMMolecule::isPerturbable() const +/** The number of non-field atoms */ +int OpenMMMolecule::nAtoms() const { - return perturbed.get() != 0; + return coords.count(); } -bool OpenMMMolecule::isGhostAtom(int atom) const +/** The number of field atoms */ +int OpenMMMolecule::nFieldAtoms() const { - return from_ghost_idxs.contains(atom) or to_ghost_idxs.contains(atom); + if (field_mol.get() != 0) + return field_mol->nAtoms(); + else + return 0; } -bool OpenMMMolecule::isFieldAtom(int atom) const +bool OpenMMMolecule::isPerturbable() const { - return field_atoms.contains(atom); + return perturbed.get() != 0; } -bool OpenMMMolecule::isFieldMolecule() const +bool OpenMMMolecule::isGhostAtom(int atom) const { - return field_atoms.count() == atoms.count(); + return from_ghost_idxs.contains(atom) or to_ghost_idxs.contains(atom); } bool OpenMMMolecule::hasFieldAtoms() const { - return not field_atoms.isEmpty(); -} - -OpenMM::Vec3 to_vec3(const SireMaths::Vector &coords) -{ - const double internal_to_nm = (1 * SireUnits::angstrom).to(SireUnits::nanometer); - - return OpenMM::Vec3(internal_to_nm * coords.x(), - internal_to_nm * coords.y(), - internal_to_nm * coords.z()); -} - -OpenMM::Vec3 to_vec3(const SireMol::Velocity3D &vel) -{ - return OpenMM::Vec3(vel.x().to(SireUnits::nanometers_per_ps), - vel.y().to(SireUnits::nanometers_per_ps), - vel.z().to(SireUnits::nanometers_per_ps)); -} - -inline qint64 to_pair(qint64 x, qint64 y) -{ - if (y < x) - return to_pair(y, x); - else - return x << 32 | y & 0x00000000FFFFFFFF; + return field_mol.get() != 0; } std::tuple OpenMMMolecule::getException( @@ -414,7 +492,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, { const auto &moldata = mol.data(); atoms = mol.atoms(); - const int nats = atoms.count(); + const int nats = atoms.count() - this->nFieldAtoms(); if (nats <= 0) { @@ -422,13 +500,37 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } // look up the CGAtomIdx of each atom - this is because we - // will use AtomIdx for the ordering and atom identifiers + // will use AtomIdx for the ordering and atom identifiers, + // and also we may be skipping some atoms if they are field + // atoms auto idx_to_cgatomidx = QVector(nats); auto idx_to_cgatomidx_data = idx_to_cgatomidx.data(); - for (int i = 0; i < nats; ++i) + auto atomidx_to_idx = QVector(atoms.count(), 0); + auto atomidx_to_idx_data = atomidx_to_idx.data(); + + if (this->hasFieldAtoms()) { - idx_to_cgatomidx_data[i] = molinfo.cgAtomIdx(SireMol::AtomIdx(i)); + const int natoms = atoms.count(); + int idx = 0; + + for (int i = 0; i < natoms; ++i) + { + if (not field_mol->isFieldAtom(i)) + { + idx_to_cgatomidx_data[idx] = molinfo.cgAtomIdx(SireMol::AtomIdx(i)); + atomidx_to_idx_data[i] = idx; + idx += 1; + } + } + } + else + { + for (int i = 0; i < nats; ++i) + { + idx_to_cgatomidx_data[i] = molinfo.cgAtomIdx(SireMol::AtomIdx(i)); + atomidx_to_idx_data[i] = i; + } } // extract the coordinates and convert to OpenMM units @@ -545,7 +647,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, for (int i = 0; i < nats; ++i) { - this->unbonded_atoms.insert(i); + this->unbonded_atoms.insert(atomidx_to_idx_data[i]); } // now the bonds @@ -568,8 +670,8 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const auto bondid = it.key().map(molinfo); const auto &bondparam = it.value().first; - int atom0 = bondid.get<0>().value(); - int atom1 = bondid.get<1>().value(); + int atom0 = atomidx_to_idx_data[bondid.get<0>().value()]; + int atom1 = atomidx_to_idx_data[bondid.get<1>().value()]; if (atom0 > atom1) std::swap(atom0, atom1); @@ -631,9 +733,9 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const auto angid = it.key().map(molinfo); const auto &angparam = it.value().first; - int atom0 = angid.get<0>().value(); - int atom1 = angid.get<1>().value(); - int atom2 = angid.get<2>().value(); + int atom0 = atomidx_to_idx_data[angid.get<0>().value()]; + int atom1 = atomidx_to_idx_data[angid.get<1>().value()]; + int atom2 = atomidx_to_idx_data[angid.get<2>().value()]; if (atom0 > atom2) std::swap(atom0, atom2); @@ -699,10 +801,10 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const auto dihid = it.key().map(molinfo); const auto &dihparam = it.value().first; - int atom0 = dihid.get<0>().value(); - int atom1 = dihid.get<1>().value(); - int atom2 = dihid.get<2>().value(); - int atom3 = dihid.get<3>().value(); + int atom0 = atomidx_to_idx_data[dihid.get<0>().value()]; + int atom1 = atomidx_to_idx_data[dihid.get<1>().value()]; + int atom2 = atomidx_to_idx_data[dihid.get<2>().value()]; + int atom3 = atomidx_to_idx_data[dihid.get<3>().value()]; if (atom0 > atom3) { @@ -745,10 +847,10 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const auto impid = it.key().map(molinfo); const auto &impparam = it.value().first; - const int atom0 = impid.get<0>().value(); - const int atom1 = impid.get<1>().value(); - const int atom2 = impid.get<2>().value(); - const int atom3 = impid.get<3>().value(); + const int atom0 = atomidx_to_idx_data[impid.get<0>().value()]; + const int atom1 = atomidx_to_idx_data[impid.get<1>().value()]; + const int atom2 = atomidx_to_idx_data[impid.get<2>().value()]; + const int atom3 = atomidx_to_idx_data[impid.get<3>().value()]; for (const auto &term : impparam.terms()) { @@ -777,7 +879,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } } - this->buildExceptions(mol, constrained_pairs, map); + this->buildExceptions(mol, atomidx_to_idx, constrained_pairs, map); } bool is_ghost(const std::tuple &clj) @@ -1136,6 +1238,7 @@ void OpenMMMolecule::alignInternals(const PropertyMap &map) atoms in the molecule */ void OpenMMMolecule::buildExceptions(const Molecule &mol, + const QVector &atomidx_to_idx, QSet &constrained_pairs, const PropertyMap &map) { @@ -1159,8 +1262,8 @@ void OpenMMMolecule::buildExceptions(const Molecule &mol, { if (cscl != 1 or ljscl != 1) { - const int i = atom0.value(); - const int j = atom1.value(); + const int i = atomidx_to_idx[atom0.value()]; + const int j = atomidx_to_idx[atom1.value()]; exception_params.append(std::make_tuple(i, j, cscl, ljscl)); @@ -1413,76 +1516,6 @@ void OpenMMMolecule::copyInCoordsAndVelocities(OpenMM::Vec3 *c, OpenMM::Vec3 *v) } } -/** Process this molecule to remove unnecessary parameters associated - * with field atoms. Field atoms are massless atoms that are not - * bonded to any other atom - */ -void OpenMMMolecule::processFieldAtoms() -{ - if (not this->hasFieldAtoms()) - return; - - if (this->isPerturbable()) - throw SireError::incompatible_error(QObject::tr( - "We cannot (yet) support perturbable molecules that also " - "contain field atoms. Please raise an issue if you would " - "like us to write the code to do this."), - CODELOC); - - if (this->isFieldMolecule()) - { - qDebug() << "This is a field molecule"; - - // very easy case - all atoms are field atoms - field_points.reserve(field_atoms.count()); - - for (int i = 0; i < this->atoms.count(); ++i) - { - const auto &clj = cljs.at(i); - field_points.append(std::make_tuple(coords[i], - std::get<0>(clj), - std::get<1>(clj), - std::get<2>(clj))); - } - - coords.clear(); - vels.clear(); - masses.clear(); - light_atoms.clear(); - virtual_sites.clear(); - cljs.clear(); - exception_params.clear(); - bond_params.clear(); - ang_params.clear(); - dih_params.clear(); - constraints.clear(); - perturbed.reset(); - exception_idxs.clear(); - unbonded_atoms.clear(); - alphas.clear(); - to_ghost_idxs.clear(); - from_ghost_idxs.clear(); - - return; - } - - // more difficult case - a mixture of field and non-field atoms. - // This is almost certainly a protein or similar - - // to start, the easiest is to create a bitmask to indicate - // which atoms are field atoms - we can then go through the - // atoms in sequence and then sort them into the appropriate - // bins - field_points.reserve(field_atoms.count()); - - QVector is_field_atom(this->atoms.count(), false); - - for (const auto &atom : field_atoms) - { - is_field_atom[atom] = true; - } -} - /** Return the alpha parameters of all atoms in atom order for * this molecule */ diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index d00552867..4f410ec15 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -16,6 +16,37 @@ SIRE_BEGIN_HEADER namespace SireOpenMM { + /** Internal class used to hold information about field molecules + * + * These are either entire or parts of molecules that contribute + * to a fixed potential field + */ + class FieldMolecule + { + public: + FieldMolecule(const SireMol::Selector &atoms, + const SireBase::PropertyMap &map); + ~FieldMolecule(); + + int nAtoms() const; + + QVector getCoords() const; + QVector getCharges() const; + QVector getSigmas() const; + QVector getEpsilons() const; + + bool isFieldAtom(int atom) const; + + int getAtomFieldIndex(int atom) const; + + private: + QVector coords; + QVector charges; + QVector sigmas; + QVector epsilons; + + QHash atomidx_to_fieldidx; + }; /** Internal class used to hold all of the extracted information * of an OpenMM Molecule. You should not use this outside @@ -51,6 +82,8 @@ namespace SireOpenMM bool isPerturbable() const; + int nAtoms() const; + QVector getCharges() const; QVector getSigmas() const; QVector getEpsilons() const; @@ -73,11 +106,13 @@ namespace SireOpenMM bool isGhostAtom(int atom) const; - bool isFieldAtom(int atom) const; bool isFieldMolecule() const; - bool hasFieldAtoms() const; + int nFieldAtoms() const; + + std::shared_ptr getFieldMolecule() const; + std::tuple getException(int atom0, int atom1, int start_index, @@ -118,12 +153,6 @@ namespace SireOpenMM /** Indexes of virtual sites */ QList virtual_sites; - /** Indexes of all of the field atoms */ - QList field_atoms; - - /** All of the field points with their parameters */ - QVector> field_points; - /** Charge and LJ parameters (sigma / epsilon) */ QVector> cljs; @@ -146,6 +175,9 @@ namespace SireOpenMM /** The molecule perturbed molecule, if this is perturbable */ std::shared_ptr perturbed; + /** The field atoms for the molecule, if this has field atoms */ + std::shared_ptr field_mol; + /** The indicies of the added exceptions - only populated * if this is a peturbable molecule */ QHash>> exception_idxs; @@ -188,6 +220,7 @@ namespace SireOpenMM bool is_perturbable); void buildExceptions(const SireMol::Molecule &mol, + const QVector &atomidx_to_idx, QSet &constrained_pairs, const SireBase::PropertyMap &map); diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index a7c7f47e4..f9f4cc6bb 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -46,6 +46,7 @@ #include "tostring.h" #include "openmmmolecule.h" +#include "customforce.h" #include @@ -660,6 +661,18 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } } + // check to see if there are any field molecules + bool any_field_mols = false; + + for (int i = 0; i < nmols; ++i) + { + if (openmm_mols_data[i].hasFieldAtoms()) + { + any_field_mols = true; + break; + } + } + QSet fixed_atoms; if (map.specified("fixed")) @@ -714,6 +727,14 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, OpenMM::HarmonicAngleForce *angff = new OpenMM::HarmonicAngleForce(); OpenMM::PeriodicTorsionForce *dihff = new OpenMM::PeriodicTorsionForce(); + // now create the grid potential for field atoms + GridForce *gridff = 0; + + if (any_field_mols) + { + gridff = new GridForce(); + } + // end of stage 2 - we now have the base forces /// @@ -769,6 +790,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, lambda_lever.addLever("torsion_phase"); lambda_lever.addLever("torsion_k"); + if (gridff != 0) + { + lambda_lever.setForceIndex("field", system.addForce(gridff)); + lambda_lever.addLever("field_scale"); + } + /// /// Stage 4 - define the forces for ghost atoms /// @@ -1126,7 +1153,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (any_perturbable and mol.isPerturbable()) { // This is a perturbable molecule and we're modelling perturbations - for (int j = 0; j < mol.molinfo.nAtoms(); ++j) + for (int j = 0; j < mol.nAtoms(); ++j) { const bool is_from_ghost = mol.from_ghost_idxs.contains(j); const bool is_to_ghost = mol.to_ghost_idxs.contains(j); @@ -1136,6 +1163,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // masses is used const int atom_index = start_index + j; + // NEED TO UPDATE FIXED ATOMS WITH FIELD ATOMS INDEXES!!! if (fixed_atoms.contains(atom_index)) { // this is a fixed (zero mass) atom @@ -1191,11 +1219,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { // Code path if this isn't a perturbable molecule or // we don't want to model perturbations - for (int j = 0; j < mol.molinfo.nAtoms(); ++j) + for (int j = 0; j < mol.nAtoms(); ++j) { // Add the particle to the system const int atom_index = start_index + j; + // NEED TO UPDATE FIXED ATOMS WITH FIELD ATOMS INDEXES!!! if (fixed_atoms.contains(atom_index)) { // this is a fixed (zero mass) atom From 4dc1b31560be0852edc03af3aa9ed6a49fb7d894 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 7 Nov 2023 22:33:32 +0000 Subject: [PATCH 006/468] Still working on the field atoms - updating the code so that we can extract coordinates from a context that does not contain all of the atoms in the molecules. Still very WIP --- corelib/src/libs/SireMol/selectorm.hpp | 21 +++ src/sire/mol/_dynamics.py | 84 +++------ .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 44 ++++- wrapper/Convert/SireOpenMM/sire_openmm.cpp | 178 ++++++++++++++++++ wrapper/Convert/SireOpenMM/sire_openmm.h | 10 + .../SireOpenMM/sire_to_openmm_system.cpp | 13 +- 6 files changed, 290 insertions(+), 60 deletions(-) diff --git a/corelib/src/libs/SireMol/selectorm.hpp b/corelib/src/libs/SireMol/selectorm.hpp index 1372c4553..594900ba8 100644 --- a/corelib/src/libs/SireMol/selectorm.hpp +++ b/corelib/src/libs/SireMol/selectorm.hpp @@ -326,6 +326,9 @@ namespace SireMol template QList metadata(const PropertyName &key, const PropertyName &metakey) const; + QList> toSelectorList() const; + QVector> toSelectorVector() const; + protected: void _append(const T &view); void _append(const Selector &views); @@ -2859,6 +2862,24 @@ namespace SireMol return ret; } + /** Return a QList containing all of the underlying Selector + * objects that make up this container + */ + template + SIRE_OUTOFLINE_TEMPLATE QList> SelectorM::toSelectorList() const + { + return vws; + } + + /** Return a QVector containing all of the underlying Selector + * objects that make up this container + */ + template + SIRE_OUTOFLINE_TEMPLATE QVector> SelectorM::toSelectorVector() const + { + return vws.toVector(); + } + template SIRE_OUTOFLINE_TEMPLATE QString SelectorM::toString() const { diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index d9cdc89a4..065c7537d 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -45,12 +45,8 @@ def __init__(self, mols=None, map=None, **kwargs): else: # create a system to work on self._sire_mols = System() - self._sire_mols._system.add( - mols.molecules().to_molecule_group() - ) - self._sire_mols._system.set_property( - "space", self._ffinfo.space() - ) + self._sire_mols._system.add(mols.molecules().to_molecule_group()) + self._sire_mols._system.set_property("space", self._ffinfo.space()) # find the existing energy trajectory - we will build on this self._energy_trajectory = self._sire_mols.energy_trajectory( @@ -120,19 +116,22 @@ def _update_from(self, state, state_has_cv, nsteps_completed): openmm_extract_space, ) + atoms = self._omm_mols.get_atom_index().clone() + atoms.update(self._sire_mols.molecules()) + if state_has_cv[1]: # get velocities too - mols = openmm_extract_coordinates_and_velocities( + atoms = openmm_extract_coordinates_and_velocities( state, - self._sire_mols.molecules(), + self._omm_mols.get_atom_index(), # black auto-formats this to a long line perturbable_maps=self._omm_mols.get_lambda_lever().get_perturbable_molecule_maps(), # noqa: E501 map=self._map, ) else: - mols = openmm_extract_coordinates( + atoms = openmm_extract_coordinates( state, - self._sire_mols.molecules(), + self._omm_mols.get_atom_index(), # black auto-formats this to a long line perturbable_maps=self._omm_mols.get_lambda_lever().get_perturbable_molecule_maps(), # noqa: E501 map=self._map, @@ -140,7 +139,7 @@ def _update_from(self, state, state_has_cv, nsteps_completed): self._current_step = nsteps_completed - self._sire_mols.update(mols.to_molecules()) + self._sire_mols.update(atoms.to_molecules()) if self._ffinfo.space().is_periodic(): # don't change the space if it is infinite - this @@ -154,9 +153,7 @@ def _update_from(self, state, state_has_cv, nsteps_completed): def _enter_dynamics_block(self): if self._is_running: - raise SystemError( - "Cannot start dynamics while it is already running!" - ) + raise SystemError("Cannot start dynamics while it is already running!") self._is_running = True self._omm_state = None @@ -189,8 +186,7 @@ def _exit_dynamics_block( self._omm_state_has_cv = (False, False) current_time = ( - self._omm_state.getTime().value_in_unit(openmm.unit.nanosecond) - * nanosecond + self._omm_state.getTime().value_in_unit(openmm.unit.nanosecond) * nanosecond ) delta = current_time - self._elapsed_time @@ -358,9 +354,7 @@ def set_temperature(self, temperature, rescale_velocities: bool = True): ensemble.set_temperature(temperature) - self.set_ensemble( - ensemble=ensemble, rescale_velocities=rescale_velocities - ) + self.set_ensemble(ensemble=ensemble, rescale_velocities=rescale_velocities) def set_pressure(self, pressure): """ @@ -600,9 +594,7 @@ def run( lambda_windows = [lambda_windows] try: - steps_to_run = int( - time.to(picosecond) / self.timestep().to(picosecond) - ) + steps_to_run = int(time.to(picosecond) / self.timestep().to(picosecond)) except Exception: # passed in the number of steps instead steps_to_run = int(time) @@ -617,9 +609,7 @@ def run( if save_frequency != 0: if save_frequency is None: if self._map.specified("save_frequency"): - save_frequency = ( - self._map["save_frequency"].value().to(picosecond) - ) + save_frequency = self._map["save_frequency"].value().to(picosecond) else: save_frequency = 25 else: @@ -672,13 +662,9 @@ def process_block(state, state_has_cv, nsteps_completed): completed = 0 - frame_frequency_steps = int( - frame_frequency / self.timestep().to(picosecond) - ) + frame_frequency_steps = int(frame_frequency / self.timestep().to(picosecond)) - energy_frequency_steps = int( - energy_frequency / self.timestep().to(picosecond) - ) + energy_frequency_steps = int(energy_frequency / self.timestep().to(picosecond)) def get_steps_till_save(completed: int, total: int): """Internal function to calculate the number of steps @@ -703,8 +689,7 @@ def get_steps_till_save(completed: int, total: int): if frame_frequency_steps > 0: n_to_frame = min( - frame_frequency_steps - - (completed % frame_frequency_steps), + frame_frequency_steps - (completed % frame_frequency_steps), n_to_end, ) else: @@ -712,8 +697,7 @@ def get_steps_till_save(completed: int, total: int): if energy_frequency_steps > 0: n_to_energy = min( - energy_frequency_steps - - (completed % energy_frequency_steps), + energy_frequency_steps - (completed % energy_frequency_steps), n_to_end, ) else: @@ -829,10 +813,8 @@ class NeedsMinimiseError(Exception): saved_last_frame = False - kinetic_energy = ( - state.getKineticEnergy().value_in_unit( - openmm.unit.kilocalorie_per_mole - ) + kinetic_energy = state.getKineticEnergy().value_in_unit( + openmm.unit.kilocalorie_per_mole ) ke_per_atom = kinetic_energy / self._num_atoms @@ -855,9 +837,7 @@ class NeedsMinimiseError(Exception): "and run again." ) - self._walltime += ( - datetime.now() - start_time - ).total_seconds() * second + self._walltime += (datetime.now() - start_time).total_seconds() * second if state is not None and not saved_last_frame: # we can process the last block in the main thread @@ -883,16 +863,12 @@ def commit(self): return self._update_from( - state=self._get_current_state( - include_coords=True, include_velocities=True - ), + state=self._get_current_state(include_coords=True, include_velocities=True), state_has_cv=(True, True), nsteps_completed=self._current_step, ) - self._sire_mols.set_energy_trajectory( - self._energy_trajectory, map=self._map - ) + self._sire_mols.set_energy_trajectory(self._energy_trajectory, map=self._map) self._sire_mols.set_ensemble(self.ensemble()) @@ -1080,9 +1056,7 @@ def run( if not self._d.is_null(): if save_velocities is None: if self._d._map.specified("save_velocities"): - save_velocities = ( - self._d._map["save_velocities"].value().as_bool() - ) + save_velocities = self._d._map["save_velocities"].value().as_bool() else: save_velocities = False @@ -1180,9 +1154,7 @@ def randomise_velocities(self, temperature=None, random_seed: int = None): - random_seed (int): The random seed to use. If None, then a random seed will be generated """ - self._d.randomise_velocities( - temperature=temperature, random_seed=random_seed - ) + self._d.randomise_velocities(temperature=temperature, random_seed=random_seed) def constraint(self): """ @@ -1341,9 +1313,7 @@ def current_kinetic_energy(self): """ return self._d.current_kinetic_energy() - def energy_trajectory( - self, to_pandas: bool = False, to_alchemlyb: bool = False - ): + def energy_trajectory(self, to_pandas: bool = False, to_alchemlyb: bool = False): """ Return the energy trajectory. This is the trajectory of energy values that have been captured during dynamics. diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 0757bc9bc..faa684a84 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -97,16 +97,56 @@ BOOST_PYTHON_MODULE(_SireOpenMM) (bp::arg("context"), bp::arg("coords_and_velocities")), "Set the coordinates and velocities in a context"); + typedef SireMol::SelectorMol (*extract_coordinates_function_type1)( + const OpenMM::State &, + const SireMol::SelectorMol &, + const QHash &, + const SireBase::PropertyMap &); + + typedef SireMol::SelectorM (*extract_coordinates_function_type2)( + const OpenMM::State &, + const SireMol::SelectorM &, + const QHash &, + const SireBase::PropertyMap &); + + extract_coordinates_function_type1 extract_coordinates_value1(&extract_coordinates); + extract_coordinates_function_type2 extract_coordinates_value2(&extract_coordinates); + bp::def("_openmm_extract_coordinates", - &extract_coordinates, + extract_coordinates_value1, (bp::arg("state"), bp::arg("mols"), bp::arg("perturbable_maps"), bp::arg("map")), "Extract the coordinates from 'state' and copy then into the passed 'mols'"); + bp::def("_openmm_extract_coordinates", + extract_coordinates_value2, + (bp::arg("state"), bp::arg("atoms"), bp::arg("perturbable_maps"), bp::arg("map")), + "Extract the coordinates from 'state' and copy then into the passed 'atoms'"); + + typedef SireMol::SelectorMol (*extract_coordinates_and_velocities_function_type1)( + const OpenMM::State &, + const SireMol::SelectorMol &, + const QHash &, + const SireBase::PropertyMap &); + + typedef SireMol::SelectorM (*extract_coordinates_and_velocities_function_type2)( + const OpenMM::State &, + const SireMol::SelectorM &, + const QHash &, + const SireBase::PropertyMap &); + + extract_coordinates_and_velocities_function_type1 extract_coordinates_and_velocities_value1(&extract_coordinates_and_velocities); + extract_coordinates_and_velocities_function_type2 extract_coordinates_and_velocities_value2(&extract_coordinates_and_velocities); + bp::def("_openmm_extract_coordinates_and_velocities", - &extract_coordinates_and_velocities, + extract_coordinates_and_velocities_value1, (bp::arg("state"), bp::arg("mols"), bp::arg("perturbable_maps"), bp::arg("map")), "Extract the coordinates and velocities from 'state' and copy then into the passed 'mols'"); + bp::def("_openmm_extract_coordinates_and_velocities", + extract_coordinates_and_velocities_value2, + (bp::arg("state"), bp::arg("atoms"), bp::arg("perturbable_maps"), bp::arg("map")), + "Extract the coordinates and velocities from 'state' and copy then into the passed 'atoms'"); + bp::def("_openmm_extract_space", &extract_space, (bp::arg("state")), diff --git a/wrapper/Convert/SireOpenMM/sire_openmm.cpp b/wrapper/Convert/SireOpenMM/sire_openmm.cpp index f2f58de39..db10a6b74 100644 --- a/wrapper/Convert/SireOpenMM/sire_openmm.cpp +++ b/wrapper/Convert/SireOpenMM/sire_openmm.cpp @@ -19,6 +19,7 @@ #include "SireMol/bondid.h" #include "SireMol/bondorder.h" #include "SireMol/atomvelocities.h" +#include "SireMol/selectorm.hpp" #include "SireMM/atomljs.h" #include "SireMM/selectorbond.h" @@ -46,8 +47,10 @@ using SireBase::PropertyMap; using SireCAS::LambdaSchedule; +using SireMol::Atom; using SireMol::Molecule; using SireMol::MolNum; +using SireMol::SelectorM; using SireMol::SelectorMol; using SireSystem::ForceFieldInfo; @@ -275,6 +278,173 @@ namespace SireOpenMM CODELOC); } + SelectorM extract_coordinates(const OpenMM::State &state, + const SireMol::SelectorM &atoms, + const QHash &perturbable_maps, + const SireBase::PropertyMap &map) + { + const auto positions = state.getPositions(); + + const int natoms = positions.size(); + const auto positions_data = positions.data(); + + if (atoms.count() > natoms) + { + throw SireError::incompatible_error(QObject::tr( + "Different number of atoms from OpenMM and sire. " + "%1 versus %2. Cannot extract the coordinates.") + .arg(natoms) + .arg(atoms.count()), + CODELOC); + } + + const auto mols = atoms.toSelectorVector(); + const auto mols_data = mols.constData(); + const int nmols = mols.count(); + + QVector> ret(nmols); + auto ret_data = ret.data(); + + const auto coords_prop = map["coordinates"]; + + QVector offsets(nmols); + + int offset = 0; + + for (int i = 0; i < nmols; ++i) + { + offsets[i] = offset; + offset += mols_data[i].count(); + } + + const auto offsets_data = offsets.constData(); + + if (SireBase::should_run_in_parallel(nmols, map)) + { + tbb::parallel_for(tbb::blocked_range(0, nmols), [&](const tbb::blocked_range &r) + { + QVector converted_coords; + + for (int i=r.begin(); i(my_coords_prop, + converted_coords, false)) + { + SireMol::AtomCoords c(mol.data().info()); + c.copyFrom(converted_coords); + molecule.setProperty(my_coords_prop, c); + } + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + else + { + auto molecule = mol.molecule().edit(); + + SireMol::AtomCoords atomcoords; + + if (molecule.hasProperty(coords_prop)) + { + atomcoords = molecule.property(coords_prop).asA(); + } + else + { + atomcoords = SireMol::AtomCoords(molecule.data().info()); + } + + atomcoords.copyFrom(converted_coords, mol.selection()); + + molecule.setProperty(coords_prop, atomcoords); + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + } }); + } + else + { + QVector converted_coords; + + for (int i = 0; i < nmols; ++i) + { + const auto &mol = mols_data[i]; + const int mol_natoms = mol.count(); + + if (mol_natoms == 0) + continue; + + _populate_coords(converted_coords, positions_data + offsets_data[i], mol_natoms); + + auto my_coords_prop = coords_prop.source(); + + if (perturbable_maps.contains(mol.data().number())) + { + my_coords_prop = perturbable_maps[mol.data().number()]["coordinates"].source(); + } + + if (mol.selectedAll()) + { + auto molecule = mol.molecule().edit(); + + if (not molecule.updatePropertyFrom(my_coords_prop, + converted_coords, false)) + { + SireMol::AtomCoords c(mol.data().info()); + c.copyFrom(converted_coords); + molecule.setProperty(my_coords_prop, c); + } + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + else + { + auto molecule = mol.molecule().edit(); + + SireMol::AtomCoords atomcoords; + + if (molecule.hasProperty(coords_prop)) + { + atomcoords = molecule.property(coords_prop).asA(); + } + else + { + atomcoords = SireMol::AtomCoords(molecule.data().info()); + } + + atomcoords.copyFrom(converted_coords, mol.selection()); + + molecule.setProperty(coords_prop, atomcoords); + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + } + } + + return SelectorM(ret.toList()); + } + SelectorMol extract_coordinates(const OpenMM::State &state, const SireMol::SelectorMol &mols, const QHash &perturbable_maps, @@ -378,6 +548,14 @@ namespace SireOpenMM return SelectorMol(ret); } + SelectorM extract_coordinates_and_velocities(const OpenMM::State &state, + const SireMol::SelectorM &atoms, + const QHash &perturbable_maps, + const SireBase::PropertyMap &map) + { + return atoms; + } + SelectorMol extract_coordinates_and_velocities(const OpenMM::State &state, const SireMol::SelectorMol &mols, const QHash &perturbable_maps, diff --git a/wrapper/Convert/SireOpenMM/sire_openmm.h b/wrapper/Convert/SireOpenMM/sire_openmm.h index 9e9dbd760..d57eff446 100644 --- a/wrapper/Convert/SireOpenMM/sire_openmm.h +++ b/wrapper/Convert/SireOpenMM/sire_openmm.h @@ -81,11 +81,21 @@ namespace SireOpenMM SireUnits::Dimension::MolarEnergy get_potential_energy(OpenMM::Context &context); + SireMol::SelectorM extract_coordinates(const OpenMM::State &state, + const SireMol::SelectorM &mols, + const QHash &perturbable_maps, + const SireBase::PropertyMap &map); + SireMol::SelectorMol extract_coordinates(const OpenMM::State &state, const SireMol::SelectorMol &mols, const QHash &perturbable_maps, const SireBase::PropertyMap &map); + SireMol::SelectorM extract_coordinates_and_velocities(const OpenMM::State &state, + const SireMol::SelectorM &mols, + const QHash &perturbable_maps, + const SireBase::PropertyMap &map); + SireMol::SelectorMol extract_coordinates_and_velocities(const OpenMM::State &state, const SireMol::SelectorMol &mols, const QHash &perturbable_maps, diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index f9f4cc6bb..47411f825 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1569,5 +1569,16 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // All done - we can return the metadata (atoms are always added in // molidx/atomidx order) - return OpenMMMetaData(mols.atoms(), coords, vels, boxvecs, lambda_lever); + SireMol::SelectorM atom_indexes; + + if (any_field_mols) + { + atom_indexes = mols.atoms("not atom property is_field_atom"); + } + else + { + atom_indexes = mols.atoms(); + } + + return OpenMMMetaData(atom_indexes, coords, vels, boxvecs, lambda_lever); } From 90ccbde782ac4d48545459b263fdf81334084f5f Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 8 Nov 2023 21:47:22 +0000 Subject: [PATCH 007/468] Can now separate out atoms that should not be simulated using OpenMM from those that should. This way, field atoms can be separated out. The atom_index in the SOMMContext is now accurate, containing the list of atoms that are in the context --- src/sire/mol/_dynamics.py | 21 +- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 4 +- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 37 +-- wrapper/Convert/SireOpenMM/sire_openmm.cpp | 215 +++++++++++++++++- .../SireOpenMM/sire_to_openmm_system.cpp | 22 +- wrapper/Convert/__init__.py | 18 +- 6 files changed, 266 insertions(+), 51 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 065c7537d..3e98a3cdd 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -116,22 +116,29 @@ def _update_from(self, state, state_has_cv, nsteps_completed): openmm_extract_space, ) - atoms = self._omm_mols.get_atom_index().clone() - atoms.update(self._sire_mols.molecules()) + if self._sire_mols.num_atoms() == self._omm_mols.get_atom_index().count(): + # all of the atoms in all molecules are in the context, + # and we can assume they are in atom index order + mols_to_update = self._sire_mols.molecules() + else: + # some of the atoms aren't in the context, and they may be + # in a different order + mols_to_update = self._omm_mols.get_atom_index().atoms() + mols_to_update.update(self._sire_mols.molecules()) if state_has_cv[1]: # get velocities too - atoms = openmm_extract_coordinates_and_velocities( + mols_to_update = openmm_extract_coordinates_and_velocities( state, - self._omm_mols.get_atom_index(), + mols_to_update, # black auto-formats this to a long line perturbable_maps=self._omm_mols.get_lambda_lever().get_perturbable_molecule_maps(), # noqa: E501 map=self._map, ) else: - atoms = openmm_extract_coordinates( + mols_to_update = openmm_extract_coordinates( state, - self._omm_mols.get_atom_index(), + mols_to_update, # black auto-formats this to a long line perturbable_maps=self._omm_mols.get_lambda_lever().get_perturbable_molecule_maps(), # noqa: E501 map=self._map, @@ -139,7 +146,7 @@ def _update_from(self, state, state_has_cv, nsteps_completed): self._current_step = nsteps_completed - self._sire_mols.update(atoms.to_molecules()) + self._sire_mols.update(mols_to_update.molecules()) if self._ffinfo.space().is_periodic(): # don't change the space if it is infinite - this diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index faa684a84..6216e7cfa 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -119,7 +119,7 @@ BOOST_PYTHON_MODULE(_SireOpenMM) bp::def("_openmm_extract_coordinates", extract_coordinates_value2, - (bp::arg("state"), bp::arg("atoms"), bp::arg("perturbable_maps"), bp::arg("map")), + (bp::arg("state"), bp::arg("mols"), bp::arg("perturbable_maps"), bp::arg("map")), "Extract the coordinates from 'state' and copy then into the passed 'atoms'"); typedef SireMol::SelectorMol (*extract_coordinates_and_velocities_function_type1)( @@ -144,7 +144,7 @@ BOOST_PYTHON_MODULE(_SireOpenMM) bp::def("_openmm_extract_coordinates_and_velocities", extract_coordinates_and_velocities_value2, - (bp::arg("state"), bp::arg("atoms"), bp::arg("perturbable_maps"), bp::arg("map")), + (bp::arg("state"), bp::arg("mols"), bp::arg("perturbable_maps"), bp::arg("map")), "Extract the coordinates and velocities from 'state' and copy then into the passed 'atoms'"); bp::def("_openmm_extract_space", diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index b591a6488..cd6820229 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -491,8 +491,23 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, bool is_perturbable) { const auto &moldata = mol.data(); - atoms = mol.atoms(); - const int nats = atoms.count() - this->nFieldAtoms(); + + if (this->hasFieldAtoms()) + { + if (this->nFieldAtoms() == molinfo.nAtoms()) + { + // this is a field molecule, so we don't need to do anything + return; + } + + atoms = mol.atoms("atom property is_field_atom == False"); + } + else + { + atoms = mol.atoms(); + } + + const int nats = atoms.count(); if (nats <= 0) { @@ -506,22 +521,16 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, auto idx_to_cgatomidx = QVector(nats); auto idx_to_cgatomidx_data = idx_to_cgatomidx.data(); - auto atomidx_to_idx = QVector(atoms.count(), 0); + auto atomidx_to_idx = QVector(molinfo.nAtoms(), 0); auto atomidx_to_idx_data = atomidx_to_idx.data(); if (this->hasFieldAtoms()) { - const int natoms = atoms.count(); - int idx = 0; - - for (int i = 0; i < natoms; ++i) + for (int i = 0; i < nats; ++i) { - if (not field_mol->isFieldAtom(i)) - { - idx_to_cgatomidx_data[idx] = molinfo.cgAtomIdx(SireMol::AtomIdx(i)); - atomidx_to_idx_data[i] = idx; - idx += 1; - } + const auto &atom = atoms(i); + idx_to_cgatomidx_data[i] = molinfo.cgAtomIdx(atom.index()); + atomidx_to_idx_data[atom.index().value()] = i; } } else @@ -537,7 +546,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const auto &c = moldata.property(map["coordinates"]).asA(); this->coords = QVector(nats, OpenMM::Vec3(0, 0, 0)); - auto coords_data = coords.data(); + auto coords_data = this->coords.data(); for (int i = 0; i < nats; ++i) { diff --git a/wrapper/Convert/SireOpenMM/sire_openmm.cpp b/wrapper/Convert/SireOpenMM/sire_openmm.cpp index db10a6b74..a75638aba 100644 --- a/wrapper/Convert/SireOpenMM/sire_openmm.cpp +++ b/wrapper/Convert/SireOpenMM/sire_openmm.cpp @@ -553,7 +553,220 @@ namespace SireOpenMM const QHash &perturbable_maps, const SireBase::PropertyMap &map) { - return atoms; + const auto positions = state.getPositions(); + const auto velocities = state.getVelocities(); + + const int natoms = positions.size(); + const auto positions_data = positions.data(); + const auto velocities_data = velocities.data(); + + if (atoms.count() > natoms) + { + throw SireError::incompatible_error(QObject::tr( + "Different number of atoms from OpenMM and sire. " + "%1 versus %2. Cannot extract the coordinates.") + .arg(natoms) + .arg(atoms.count()), + CODELOC); + } + + const auto mols = atoms.toSelectorVector(); + const auto mols_data = mols.constData(); + const int nmols = mols.count(); + + QVector> ret(nmols); + auto ret_data = ret.data(); + + const auto coords_prop = map["coordinates"]; + const auto vels_prop = map["velocity"]; + + QVector offsets(nmols); + + int offset = 0; + + for (int i = 0; i < nmols; ++i) + { + offsets[i] = offset; + offset += mols_data[i].count(); + } + + const auto offsets_data = offsets.constData(); + + if (SireBase::should_run_in_parallel(nmols, map)) + { + tbb::parallel_for(tbb::blocked_range(0, nmols), [&](const tbb::blocked_range &r) + { + QVector converted_coords; + QVector converted_vels; + + for (int i=r.begin(); i(my_coords_prop, + converted_coords, false)) + { + SireMol::AtomCoords c(mol.data().info()); + c.copyFrom(converted_coords); + molecule.setProperty(my_coords_prop, c); + } + + if (not molecule.updatePropertyFrom(my_vels_prop, + converted_vels, false)) + { + SireMol::AtomVelocities v(mol.data().info()); + v.copyFrom(converted_vels); + molecule.setProperty(my_vels_prop, v); + } + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + else + { + auto molecule = mol.molecule().edit(); + + SireMol::AtomCoords atomcoords; + + if (molecule.hasProperty(coords_prop)) + { + atomcoords = molecule.property(coords_prop).asA(); + } + else + { + atomcoords = SireMol::AtomCoords(molecule.data().info()); + } + + atomcoords.copyFrom(converted_coords, mol.selection()); + + SireMol::AtomVelocities atomvels; + + if (molecule.hasProperty(vels_prop)) + { + atomvels = molecule.property(vels_prop).asA(); + } + else + { + atomvels = SireMol::AtomVelocities(molecule.data().info()); + } + + atomvels.copyFrom(converted_vels, mol.selection()); + + molecule.setProperty(coords_prop, atomcoords); + molecule.setProperty(vels_prop, atomvels); + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + } }); + } + else + { + QVector converted_coords; + QVector converted_vels; + + for (int i = 0; i < nmols; ++i) + { + const auto &mol = mols_data[i]; + const int mol_natoms = mol.count(); + + if (mol_natoms == 0) + continue; + + _populate_coords(converted_coords, positions_data + offsets_data[i], mol_natoms); + _populate_vels(converted_vels, velocities_data + offsets_data[i], mol_natoms); + + auto my_coords_prop = coords_prop.source(); + auto my_vels_prop = vels_prop.source(); + + if (perturbable_maps.contains(mol.data().number())) + { + my_coords_prop = perturbable_maps[mol.data().number()]["coordinates"].source(); + my_vels_prop = perturbable_maps[mol.data().number()]["velocity"].source(); + } + + if (mol.selectedAll()) + { + auto molecule = mol.molecule().edit(); + + if (not molecule.updatePropertyFrom(my_coords_prop, + converted_coords, false)) + { + SireMol::AtomCoords c(mol.data().info()); + c.copyFrom(converted_coords); + molecule.setProperty(my_coords_prop, c); + } + + if (not molecule.updatePropertyFrom(my_vels_prop, + converted_vels, false)) + { + SireMol::AtomVelocities v(mol.data().info()); + v.copyFrom(converted_vels); + molecule.setProperty(my_vels_prop, v); + } + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + else + { + auto molecule = mol.molecule().edit(); + + SireMol::AtomCoords atomcoords; + SireMol::AtomVelocities atomvels; + + if (molecule.hasProperty(coords_prop)) + { + atomcoords = molecule.property(coords_prop).asA(); + } + else + { + atomcoords = SireMol::AtomCoords(molecule.data().info()); + } + + atomcoords.copyFrom(converted_coords, mol.selection()); + + if (molecule.hasProperty(vels_prop)) + { + atomvels = molecule.property(vels_prop).asA(); + } + else + { + atomvels = SireMol::AtomVelocities(molecule.data().info()); + } + + atomvels.copyFrom(converted_vels, mol.selection()); + + molecule.setProperty(coords_prop, atomcoords); + molecule.setProperty(vels_prop, atomvels); + + ret_data[i] = mol; + ret_data[i].update(molecule.commit().data()); + } + } + } + + return SelectorM(ret.toList()); } SelectorMol extract_coordinates_and_velocities(const OpenMM::State &state, diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 47411f825..cfc6afdfa 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1055,6 +1055,9 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // start_index keeps track of the index of the first atom in each molecule int start_index = 0; + // this is the list of atoms added, in atom order + QList> order_of_added_atoms; + // get the 1-4 scaling factors from the first molecule const double coul_14_scl = openmm_mols_data[0].ffinfo.electrostatic14ScaleFactor(); const double lj_14_scl = openmm_mols_data[0].ffinfo.vdw14ScaleFactor(); @@ -1088,6 +1091,8 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, start_indexes[i] = start_index; const auto &mol = openmm_mols_data[i]; + order_of_added_atoms.append(mol.atoms); + // double-check that the molecule has a compatible forcefield with // the other molecules in this system if (std::abs(mol.ffinfo.electrostatic14ScaleFactor() - coul_14_scl) > 0.001 or @@ -1567,18 +1572,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } } - // All done - we can return the metadata (atoms are always added in - // molidx/atomidx order) - SireMol::SelectorM atom_indexes; - - if (any_field_mols) - { - atom_indexes = mols.atoms("not atom property is_field_atom"); - } - else - { - atom_indexes = mols.atoms(); - } - - return OpenMMMetaData(atom_indexes, coords, vels, boxvecs, lambda_lever); + // All done - we can return the metadata + return OpenMMMetaData(SireMol::SelectorM(order_of_added_atoms), + coords, vels, boxvecs, lambda_lever); } diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 2ef5d2e16..c23b60322 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -162,16 +162,13 @@ def sire_to_openmm(mols, map): if integrator == "verlet" or integrator == "leapfrog": if not ensemble.is_nve(): raise ValueError( - "You cannot use a verlet integrator with the " - f"{ensemble}" + "You cannot use a verlet integrator with the " f"{ensemble}" ) integrator = openmm.VerletIntegrator(timestep) elif integrator != "auto": - temperature = ( - ensemble.temperature().to(kelvin) * openmm.unit.kelvin - ) + temperature = ensemble.temperature().to(kelvin) * openmm.unit.kelvin if ensemble.is_nve(): raise ValueError( @@ -218,9 +215,7 @@ def sire_to_openmm(mols, map): timestep, ) - temperature = ( - ensemble.temperature().to(kelvin) * openmm.unit.kelvin - ) + temperature = ensemble.temperature().to(kelvin) * openmm.unit.kelvin elif openmm.Integrator not in type(integrator).mro(): raise TypeError( f"Cannot cast the integrator {integrator} to the correct " @@ -298,8 +293,7 @@ def sire_to_openmm(mols, map): p = openmm.Platform.getPlatform(i) if (p.getName().lower() == desired_platform.lower()) or ( - p.getName() == "HIP" - and desired_platform.lower() == "metal" + p.getName() == "HIP" and desired_platform.lower() == "metal" ): platform = p break @@ -398,9 +392,7 @@ def sire_to_openmm(mols, map): return context - def openmm_extract_coordinates( - state, mols, perturbable_maps=None, map=None - ): + def openmm_extract_coordinates(state, mols, perturbable_maps=None, map=None): from ...base import create_map map = create_map(map) From 5e3c09f1302727660f44fe458e19b37c396a7011 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 8 Nov 2023 22:30:14 +0000 Subject: [PATCH 008/468] Have now added the particle parameters to the GridForce. --- wrapper/Convert/SireOpenMM/customforce.cpp | 88 +++++++++++++++++++ wrapper/Convert/SireOpenMM/customforce.h | 39 +++----- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 69 ++++++++++----- wrapper/Convert/SireOpenMM/openmmmolecule.h | 22 ++--- .../SireOpenMM/sire_to_openmm_system.cpp | 18 ++++ 5 files changed, 176 insertions(+), 60 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/customforce.cpp b/wrapper/Convert/SireOpenMM/customforce.cpp index 450ec5ca5..909c4e618 100644 --- a/wrapper/Convert/SireOpenMM/customforce.cpp +++ b/wrapper/Convert/SireOpenMM/customforce.cpp @@ -6,6 +6,8 @@ #include "openmm/internal/CustomCPPForceImpl.h" #endif +#include "openmmmolecule.h" + #include "SireError/errors.h" #include @@ -37,6 +39,23 @@ class GridForceImpl : public OpenMM::CustomCPPForceImpl // const auto platform = context.getPlatform().getName(); // so we could have custom code for different platforms if we wanted + if (fixed_atoms.empty()) + rebuild_fixed_atoms(); + + // now need to calculate the coulomb and LJ forces and energy... + const auto ¶ms = owner.getParticleParameters(); + + const int natoms = positions.size(); + + if (natoms != params.count()) + throw SireError::incompatible_error(QObject::tr( + "Incorrect number of atoms in the grid force. Expected %1, got %2") + .arg(params.count()) + .arg(natoms), + CODELOC); + + const auto ¶ms_data = params.constData(); + // return the potential energy return 0; } @@ -47,6 +66,55 @@ class GridForceImpl : public OpenMM::CustomCPPForceImpl } private: + void rebuild_fixed_atoms() + { + fixed_atoms.clear(); + + const auto &atoms = owner.getFieldAtoms(); + + const int natoms = atoms.count(); + + if (natoms == 0) + return; + + fixed_atoms = std::vector>(natoms); + + const auto &coords = atoms.getCoords().data(); + const auto &charges = atoms.getCharges().data(); + const auto &sigmas = atoms.getSigmas().data(); + const auto &epsilons = atoms.getEpsilons().data(); + + for (int i = 0; i < natoms; ++i) + { + fixed_atoms.push_back(std::make_tuple(coords[i], + charges[i], + sigmas[i], + epsilons[i])); + } + } + + void rebuild_grid() + { + } + + /** All of the atoms data */ + std::vector> fixed_atoms; + + /** The coulomb potential grid */ + std::vector coulomb_grid; + + /** Information about the grid dimensions */ + SireVol::AABox grid_box; + + /** The coulomb cutoff (applies from the center of the grid) */ + double coulomb_cutoff; + + /** The grid spacing */ + double grid_spacing; + + /** The number of grid points along x, y and z */ + unsigned int dimx, dimy, dimz; + const GridForce &owner; }; #endif @@ -77,3 +145,23 @@ OpenMM::ForceImpl *GridForce::createImpl() const return 0; #endif } + +void GridForce::addFieldAtoms(const FieldAtoms &atoms) +{ + field_atoms += atoms; +} + +const FieldAtoms &GridForce::getFieldAtoms() const +{ + return field_atoms; +} + +void GridForce::addParticle(double charge, double sigma, double epsilon) +{ + params.push_back(std::make_tuple(charge, sigma, epsilon)); +} + +const QVector> &GridForce::getParticleParameters() const +{ + return params; +} diff --git a/wrapper/Convert/SireOpenMM/customforce.h b/wrapper/Convert/SireOpenMM/customforce.h index 03b756421..8e988784f 100644 --- a/wrapper/Convert/SireOpenMM/customforce.h +++ b/wrapper/Convert/SireOpenMM/customforce.h @@ -4,7 +4,9 @@ #include "openmm.h" #include "openmm/Force.h" -#include "sireglobal.h" +#include "openmmmolecule.h" + +#include "SireVol/aabox.h" SIRE_BEGIN_HEADER @@ -16,40 +18,23 @@ namespace SireOpenMM GridForce(); ~GridForce(); - int addFixedAtom(const OpenMM::Vec3 &position, - float charge, float sigma, float epsilon); + void addFieldAtoms(const FieldAtoms &atoms); + + const FieldAtoms &getFieldAtoms() const; - void getFixedAtom(int idx, OpenMM::Vec3 &position, - float &charge, float &sigma, float &epsilon) const; + void addParticle(double charge, double sigma, double epsilon); - void updateFixedAtom(int idx, const OpenMM::Vec3 &position, - float charge, float sigma, float epsilon); + const QVector> &getParticleParameters() const; protected: OpenMM::ForceImpl *createImpl() const; private: - /** All of the data for the fixed atoms */ - std::vector> fixed_atoms; - - /** The coulomb potential grid */ - std::vector coulomb_grid; - - /** The center of the grid */ - OpenMM::Vec3 grid_center; - - /** The half-extents of this grid (plus or minus this to - get the grid boundaries) */ - OpenMM::Vec3 grid_half_extents; - - /** The coulomb cutoff (applies from the center of the grid) */ - double coulomb_cutoff; - - /** The grid spacing */ - double grid_spacing; + /** All of the field atoms */ + FieldAtoms field_atoms; - /** The number of grid points along x, y and z */ - unsigned int dimx, dimy, dimz; + /** All of the particle parameters */ + QVector> params; }; } diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index cd6820229..43e2db976 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -69,11 +69,15 @@ inline qint64 to_pair(qint64 x, qint64 y) } //////// -//////// Implementation of FieldMolecule +//////// Implementation of FieldAtoms //////// -FieldMolecule::FieldMolecule(const Selector &atoms, - const PropertyMap &map) +FieldAtoms::FieldAtoms() +{ +} + +FieldAtoms::FieldAtoms(const Selector &atoms, + const PropertyMap &map) { const int nats = atoms.count(); @@ -105,46 +109,52 @@ FieldMolecule::FieldMolecule(const Selector &atoms, } } -FieldMolecule::~FieldMolecule() +FieldAtoms::~FieldAtoms() { } -int FieldMolecule::nAtoms() const +int FieldAtoms::nAtoms() const { return coords.count(); } -QVector FieldMolecule::getCoords() const +int FieldAtoms::count() const +{ + return this->nAtoms(); +} + +QVector FieldAtoms::getCoords() const { return coords; } -QVector FieldMolecule::getCharges() const +QVector FieldAtoms::getCharges() const { return charges; } -QVector FieldMolecule::getSigmas() const +QVector FieldAtoms::getSigmas() const { return sigmas; } -QVector FieldMolecule::getEpsilons() const +QVector FieldAtoms::getEpsilons() const { return epsilons; } -bool FieldMolecule::isFieldAtom(int atomidx) const +void FieldAtoms::append(const FieldAtoms &other) { - return this->atomidx_to_fieldidx.isEmpty() or this->atomidx_to_fieldidx.contains(atomidx); + coords += other.coords; + charges += other.charges; + sigmas += other.sigmas; + epsilons += other.epsilons; } -int FieldMolecule::getAtomFieldIndex(int atomidx) const +FieldAtoms &FieldAtoms::operator+=(const FieldAtoms &other) { - if (this->atomidx_to_fieldidx.isEmpty()) - return atomidx; - else - return this->atomidx_to_fieldidx.value(atomidx, -1); + this->append(other); + return *this; } //////// @@ -277,10 +287,10 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, if (mol.hasProperty(field_atom_prop)) { - const auto atoms = mol.atoms("atom property is_field_atom == True"); + const auto atms = mol.atoms("atom property is_field_atom == True"); - if (not atoms.isEmpty()) - field_mol.reset(new FieldMolecule(atoms, map)); + if (not atms.isEmpty()) + field_atoms.reset(new FieldAtoms(atms, map)); } if (ffinfo.isAmberStyle()) @@ -369,12 +379,24 @@ int OpenMMMolecule::nAtoms() const /** The number of field atoms */ int OpenMMMolecule::nFieldAtoms() const { - if (field_mol.get() != 0) - return field_mol->nAtoms(); + if (field_atoms.get() != 0) + return field_atoms->nAtoms(); else return 0; } +/** Return the field atoms */ +const FieldAtoms &OpenMMMolecule::getFieldAtoms() const +{ + if (field_atoms.get() != 0) + return *field_atoms; + else + { + static const FieldAtoms empty; + return empty; + } +} + bool OpenMMMolecule::isPerturbable() const { return perturbed.get() != 0; @@ -387,7 +409,10 @@ bool OpenMMMolecule::isGhostAtom(int atom) const bool OpenMMMolecule::hasFieldAtoms() const { - return field_mol.get() != 0; + if (field_atoms.get() != 0) + return field_atoms->nAtoms() > 0; + else + return false; } std::tuple OpenMMMolecule::getException( diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 4f410ec15..72398c247 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -21,31 +21,31 @@ namespace SireOpenMM * These are either entire or parts of molecules that contribute * to a fixed potential field */ - class FieldMolecule + class FieldAtoms { public: - FieldMolecule(const SireMol::Selector &atoms, - const SireBase::PropertyMap &map); - ~FieldMolecule(); + FieldAtoms(); + FieldAtoms(const SireMol::Selector &atoms, + const SireBase::PropertyMap &map); + ~FieldAtoms(); int nAtoms() const; + int count() const; QVector getCoords() const; QVector getCharges() const; QVector getSigmas() const; QVector getEpsilons() const; - bool isFieldAtom(int atom) const; + void append(const FieldAtoms &other); - int getAtomFieldIndex(int atom) const; + FieldAtoms &operator+=(const FieldAtoms &other); private: QVector coords; QVector charges; QVector sigmas; QVector epsilons; - - QHash atomidx_to_fieldidx; }; /** Internal class used to hold all of the extracted information @@ -106,12 +106,12 @@ namespace SireOpenMM bool isGhostAtom(int atom) const; - bool isFieldMolecule() const; + bool isFieldAtoms() const; bool hasFieldAtoms() const; int nFieldAtoms() const; - std::shared_ptr getFieldMolecule() const; + const FieldAtoms &getFieldAtoms() const; std::tuple getException(int atom0, int atom1, @@ -176,7 +176,7 @@ namespace SireOpenMM std::shared_ptr perturbed; /** The field atoms for the molecule, if this has field atoms */ - std::shared_ptr field_mol; + std::shared_ptr field_atoms; /** The indicies of the added exceptions - only populated * if this is a peturbable molecule */ diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index cfc6afdfa..0b7c8857e 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1218,6 +1218,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, std::get<2>(clj)); non_ghost_atoms.insert(atom_index); } + + if (gridff != 0) + { + gridff->addParticle(std::get<0>(clj), std::get<1>(clj), + std::get<2>(clj)); + } } } else @@ -1263,6 +1269,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, ghost_nonghostff->addParticle(custom_params); non_ghost_atoms.insert(atom_index); } + + if (gridff != 0) + { + gridff->addParticle(std::get<0>(clj), std::get<1>(clj), + std::get<2>(clj)); + } } } @@ -1312,6 +1324,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // involving fixed atoms. Could we fix the other atom too? } + // add any field atoms + if (gridff != 0 and mol.hasFieldAtoms()) + { + gridff->addFieldAtoms(mol.getFieldAtoms()); + } + start_index += mol.masses.count(); } From 58f3774e273e7cc5d3b59ed739f51e5856842d82 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 15 Nov 2023 13:29:03 +0000 Subject: [PATCH 009/468] Fix name of OpenMM.h header. --- wrapper/Convert/SireOpenMM/customforce.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/customforce.h b/wrapper/Convert/SireOpenMM/customforce.h index 8e988784f..b2b82f9c3 100644 --- a/wrapper/Convert/SireOpenMM/customforce.h +++ b/wrapper/Convert/SireOpenMM/customforce.h @@ -1,7 +1,7 @@ #ifndef SIRE_OPENMM_CUSTOMFORCE_H #define SIRE_OPENMM_CUSTOMFORCE_H -#include "openmm.h" +#include "OpenMM.h" #include "openmm/Force.h" #include "openmmmolecule.h" From d9363264bf52ef028eb97798fffb73d01ba98eb6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 16 Nov 2023 15:49:37 +0000 Subject: [PATCH 010/468] Added class to enable call of Python function or method from C++. --- tests/convert/test_emle.py | 70 +++++++++++++++ wrapper/Convert/SireOpenMM/CMakeLists.txt | 1 + .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 11 ++- wrapper/Convert/SireOpenMM/emlecallback.cpp | 46 ++++++++++ wrapper/Convert/SireOpenMM/emlecallback.h | 89 +++++++++++++++++++ 5 files changed, 216 insertions(+), 1 deletion(-) create mode 100644 tests/convert/test_emle.py create mode 100644 wrapper/Convert/SireOpenMM/emlecallback.cpp create mode 100644 wrapper/Convert/SireOpenMM/emlecallback.h diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py new file mode 100644 index 000000000..74d69280e --- /dev/null +++ b/tests/convert/test_emle.py @@ -0,0 +1,70 @@ +from functools import partialmethod + +from sire.legacy.Convert._SireOpenMM import EMLECallback + +# Create some lists to hold test data. +a = [1, 2, 3, 4] +b = [5, 6, 7, 8] +c = [9, 10, 11, 12] +d = [13, 14, 15, 16] + + +def callback(a, b, c, d): + # Zip lists together and return the sum. + result = [] + for aa, bb, cc, dd in zip(a, b, c, d): + result.append(aa + bb + cc + dd) + return result + + +def callback_wrapper(obj, a, b, c, d): + """A callback wrapper function""" + # No object, compute the result directly. + if obj is None: + return callback(a, b, c, d) + # Object, call the method. + else: + return obj._callback(a, b, c, d) + + +def test_callback_function(): + """Makes sure that a callback function works correctly""" + + # Create a callback object. + cb = EMLECallback(None, callback_wrapper) + + # Call the callback. + result = cb.call(a, b, c, d) + + # Make sure the result is correct. + assert ( + result + == [28, 32, 36, 40] + == callback_wrapper(None, a, b, c, d) + == callback(a, b, c, d) + ) + + +def test_callback_method(): + """Makes sure that a callback method works correctly""" + + class Test: + def _callback(self, a, b, c, d): + return callback(a, b, c, d) + + # Instantiate the class. + test = Test() + + # Create a callback object. + cb = EMLECallback(test, callback_wrapper) + + # Call the callback. + result = cb.call(a, b, c, d) + + # Make sure the result is correct. + assert ( + result + == [28, 32, 36, 40] + == callback_wrapper(test, a, b, c, d) + == callback(a, b, c, d) + ) diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 85dec066b..93868446f 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -52,6 +52,7 @@ if (${SIRE_USE_OPENMM}) _SireOpenMM.main.cpp customforce.cpp + emlecallback.cpp lambdalever.cpp openmmminimise.cpp openmmmolecule.cpp diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 6216e7cfa..6fa732380 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -5,6 +5,8 @@ #include "sire_openmm.h" +#include "emlecallback.h" + #include "lambdalever.h" #include "openmmminimise.h" @@ -48,7 +50,6 @@ BOOST_PYTHON_MODULE(_SireOpenMM) { bp::class_ OpenMMMetaData_exposer_t("OpenMMMetaData", "Internal class used to hold OpenMM coordinates and velocities data"); - OpenMMMetaData_exposer_t.def( "index", &OpenMMMetaData::index, "Return the index used to locate atoms in the OpenMM system"); @@ -58,6 +59,14 @@ BOOST_PYTHON_MODULE(_SireOpenMM) "Return the lambda lever used to update the parameters in the " "OpenMM system according to lambda"); + bp::class_("EMLECallback", + bp::init( + "Constructor: A callback wrapper class to enable electrostatic embedding" + "of machine learning potentials via emle-engine." + ) + ) + .def("call", &EMLECallback::call, "Call the callback"); + bp::class_> LambdaLever_exposer_t( "LambdaLever", "A lever that can be used to change the parameters in an OpenMM system " diff --git a/wrapper/Convert/SireOpenMM/emlecallback.cpp b/wrapper/Convert/SireOpenMM/emlecallback.cpp new file mode 100644 index 000000000..a42dce1f4 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/emlecallback.cpp @@ -0,0 +1,46 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2023 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "emlecallback.h" + +using namespace SireOpenMM; + +EMLECallback::EMLECallback(bp::object py_object, bp::object callback) : + py_object(py_object), callback(callback) +{ +} + +QVector EMLECallback::call( + QVector numbers_qm, + QVector charges_mm, + QVector xyz_qm, + QVector xyz_mm) +{ + bp::object result = this->callback(this->py_object, numbers_qm, charges_mm, xyz_qm, xyz_mm); + return bp::extract>(result); +} diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h new file mode 100644 index 000000000..fdd5df55c --- /dev/null +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -0,0 +1,89 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2023 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREOPENMM_EMLECALLBACK_H +#define SIREOPENMM_EMLECALLBACK_H + +#include "boost/python.hpp" + +#include "openmmmolecule.h" + +namespace bp = boost::python; + +SIRE_BEGIN_HEADER + +namespace SireOpenMM +{ + // A callback wrapper class to allow use of electrostatic embedding of + // machine learning potentials via emle-engine. + class EMLECallback + { + public: + //! Constructor + /*! \param py_object + A Python object that contains the callback function. + + \param callback + A Python function that takes the following arguments: + - numbers_qm: A list of atomic numbers for the atoms in the ML region. + - charges_mm: A list of the MM charges. + - xyz_qm: A flattened list of the QM coordinates of the atoms in the ML region. + - xyz_mm: A flattened list of the MM coordinates of the point charges. + */ + EMLECallback(bp::object object, bp::object callback); + + //! Constructor + /*! \param numbers_qm + A vector of atomic numbers for the atoms in the ML region. + + \param charges_mm + A vector of the MM charges. + + \param xyz_qm + A flattened vector of the QM coordinates of the atoms in the ML region. + + \param xyz_mm + A flattened vector of the MM coordinates of the point charges. + + \returns + A flattened vector of forces for the QM and MM atoms. + */ + QVector call(QVector numbers_qm, + QVector charges_mm, + QVector xyz_qm, + QVector xyz_mm); + + private: + bp::object py_object; + bp::object callback; + }; +} + +SIRE_END_HEADER + +#endif From 6bc2c473c2e4d45371cffa72ff0ade64ceeb0908 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 16 Nov 2023 16:17:35 +0000 Subject: [PATCH 011/468] Remove redundant import. --- tests/convert/test_emle.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py index 74d69280e..d8df8dc7e 100644 --- a/tests/convert/test_emle.py +++ b/tests/convert/test_emle.py @@ -1,5 +1,3 @@ -from functools import partialmethod - from sire.legacy.Convert._SireOpenMM import EMLECallback # Create some lists to hold test data. From 36ae91a548a3dafb3ec5cf79f3170137250ad866 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 11:00:37 +0000 Subject: [PATCH 012/468] Switch to using call_method. --- tests/convert/test_emle.py | 63 ++++--------------- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 4 +- wrapper/Convert/SireOpenMM/emlecallback.cpp | 12 +++- wrapper/Convert/SireOpenMM/emlecallback.h | 8 +-- 4 files changed, 26 insertions(+), 61 deletions(-) diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py index d8df8dc7e..9e4cb1471 100644 --- a/tests/convert/test_emle.py +++ b/tests/convert/test_emle.py @@ -1,68 +1,27 @@ from sire.legacy.Convert._SireOpenMM import EMLECallback -# Create some lists to hold test data. -a = [1, 2, 3, 4] -b = [5, 6, 7, 8] -c = [9, 10, 11, 12] -d = [13, 14, 15, 16] - -def callback(a, b, c, d): - # Zip lists together and return the sum. - result = [] - for aa, bb, cc, dd in zip(a, b, c, d): - result.append(aa + bb + cc + dd) - return result - - -def callback_wrapper(obj, a, b, c, d): - """A callback wrapper function""" - # No object, compute the result directly. - if obj is None: - return callback(a, b, c, d) - # Object, call the method. - else: - return obj._callback(a, b, c, d) - - -def test_callback_function(): - """Makes sure that a callback function works correctly""" - - # Create a callback object. - cb = EMLECallback(None, callback_wrapper) - - # Call the callback. - result = cb.call(a, b, c, d) - - # Make sure the result is correct. - assert ( - result - == [28, 32, 36, 40] - == callback_wrapper(None, a, b, c, d) - == callback(a, b, c, d) - ) - - -def test_callback_method(): +def test_callback(): """Makes sure that a callback method works correctly""" class Test: - def _callback(self, a, b, c, d): - return callback(a, b, c, d) + def callback(self, a, b, c, d): + return [sum(x) for x in zip(a, b, c, d)] # Instantiate the class. test = Test() # Create a callback object. - cb = EMLECallback(test, callback_wrapper) + cb = EMLECallback(test, "callback") + + # Create some lists to hold test data. + a = [1, 2, 3, 4] + b = [5, 6, 7, 8] + c = [9, 10, 11, 12] + d = [13, 14, 15, 16] # Call the callback. result = cb.call(a, b, c, d) # Make sure the result is correct. - assert ( - result - == [28, 32, 36, 40] - == callback_wrapper(test, a, b, c, d) - == callback(a, b, c, d) - ) + assert result == [28, 32, 36, 40] == test.callback(a, b, c, d) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 6fa732380..f4b2dbb8e 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -59,8 +59,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) "Return the lambda lever used to update the parameters in the " "OpenMM system according to lambda"); - bp::class_("EMLECallback", - bp::init( + bp::class_("EMLECallback", + bp::init( "Constructor: A callback wrapper class to enable electrostatic embedding" "of machine learning potentials via emle-engine." ) diff --git a/wrapper/Convert/SireOpenMM/emlecallback.cpp b/wrapper/Convert/SireOpenMM/emlecallback.cpp index a42dce1f4..b69c6db7a 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.cpp +++ b/wrapper/Convert/SireOpenMM/emlecallback.cpp @@ -30,7 +30,7 @@ using namespace SireOpenMM; -EMLECallback::EMLECallback(bp::object py_object, bp::object callback) : +EMLECallback::EMLECallback(bp::object py_object, QString callback) : py_object(py_object), callback(callback) { } @@ -41,6 +41,12 @@ QVector EMLECallback::call( QVector xyz_qm, QVector xyz_mm) { - bp::object result = this->callback(this->py_object, numbers_qm, charges_mm, xyz_qm, xyz_mm); - return bp::extract>(result); + return bp::call_method>( + this->py_object.ptr(), + this->callback.toStdString().c_str(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm + ); } diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index fdd5df55c..f761cfaae 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -46,16 +46,16 @@ namespace SireOpenMM public: //! Constructor /*! \param py_object - A Python object that contains the callback function. + A Python object that contains the callback function. \param callback - A Python function that takes the following arguments: + The name of a callback method that take the following arguments: - numbers_qm: A list of atomic numbers for the atoms in the ML region. - charges_mm: A list of the MM charges. - xyz_qm: A flattened list of the QM coordinates of the atoms in the ML region. - xyz_mm: A flattened list of the MM coordinates of the point charges. */ - EMLECallback(bp::object object, bp::object callback); + EMLECallback(bp::object object, QString callback); //! Constructor /*! \param numbers_qm @@ -80,7 +80,7 @@ namespace SireOpenMM private: bp::object py_object; - bp::object callback; + QString callback; }; } From c347bb92e5e4374f6607eef9298de605da414440 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 12:15:36 +0000 Subject: [PATCH 013/468] Callback now returns a tuple. --- tests/convert/test_emle.py | 8 ++++++-- wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 12 ++++++++++-- wrapper/Convert/SireOpenMM/emlecallback.cpp | 4 ++-- wrapper/Convert/SireOpenMM/emlecallback.h | 11 +++++++---- 4 files changed, 25 insertions(+), 10 deletions(-) diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py index 9e4cb1471..35de64a5e 100644 --- a/tests/convert/test_emle.py +++ b/tests/convert/test_emle.py @@ -6,7 +6,11 @@ def test_callback(): class Test: def callback(self, a, b, c, d): - return [sum(x) for x in zip(a, b, c, d)] + return ( + sum(a + b + c + d), + [sum(x) for x in zip(a, b)], + [sum(x) for x in zip(c, d)], + ) # Instantiate the class. test = Test() @@ -24,4 +28,4 @@ def callback(self, a, b, c, d): result = cb.call(a, b, c, d) # Make sure the result is correct. - assert result == [28, 32, 36, 40] == test.callback(a, b, c, d) + assert result == (136, [6, 8, 10, 12], [22, 24, 26, 28]) == test.callback(a, b, c, d) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index f4b2dbb8e..8b29c4489 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -2,6 +2,7 @@ // (C) Christopher Woods, GPL >= 3 License #include "boost/python.hpp" +#include #include "sire_openmm.h" @@ -12,13 +13,17 @@ #include "openmmminimise.h" #include "Helpers/convertlist.hpp" +#include "Helpers/tuples.hpp" #include - -namespace bp = boost::python; +#include using namespace SireOpenMM; +using boost::python::register_tuple; + +namespace bp = boost::python; + /** Thanks to this page for instructions on how to convert from SWIG to Boost * https://wiki.python.org/moin/boost.python/HowTo */ @@ -59,6 +64,9 @@ BOOST_PYTHON_MODULE(_SireOpenMM) "Return the lambda lever used to update the parameters in the " "OpenMM system according to lambda"); + // Return container for EMLECallback. + register_tuple, QVector>>(); + bp::class_("EMLECallback", bp::init( "Constructor: A callback wrapper class to enable electrostatic embedding" diff --git a/wrapper/Convert/SireOpenMM/emlecallback.cpp b/wrapper/Convert/SireOpenMM/emlecallback.cpp index b69c6db7a..cd6f6bc6a 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.cpp +++ b/wrapper/Convert/SireOpenMM/emlecallback.cpp @@ -35,13 +35,13 @@ EMLECallback::EMLECallback(bp::object py_object, QString callback) : { } -QVector EMLECallback::call( +boost::tuple, QVector> EMLECallback::call( QVector numbers_qm, QVector charges_mm, QVector xyz_qm, QVector xyz_mm) { - return bp::call_method>( + return bp::call_method, QVector>>( this->py_object.ptr(), this->callback.toStdString().c_str(), numbers_qm, diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index f761cfaae..41197e816 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -30,6 +30,7 @@ #define SIREOPENMM_EMLECALLBACK_H #include "boost/python.hpp" +#include #include "openmmmolecule.h" @@ -73,10 +74,12 @@ namespace SireOpenMM \returns A flattened vector of forces for the QM and MM atoms. */ - QVector call(QVector numbers_qm, - QVector charges_mm, - QVector xyz_qm, - QVector xyz_mm); + boost::tuple, QVector> call( + QVector numbers_qm, + QVector charges_mm, + QVector xyz_qm, + QVector xyz_mm + ); private: bp::object py_object; From 9d639f9fb747f6cc4c7cf734ed5c0d2226c21f5d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 12:25:32 +0000 Subject: [PATCH 014/468] Handle forces as a two dimensional vector. --- tests/convert/test_emle.py | 12 ++++++------ wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 4 ++-- wrapper/Convert/SireOpenMM/emlecallback.cpp | 5 +++-- wrapper/Convert/SireOpenMM/emlecallback.h | 2 +- 4 files changed, 12 insertions(+), 11 deletions(-) diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py index 35de64a5e..9ceb2fb9b 100644 --- a/tests/convert/test_emle.py +++ b/tests/convert/test_emle.py @@ -6,11 +6,7 @@ def test_callback(): class Test: def callback(self, a, b, c, d): - return ( - sum(a + b + c + d), - [sum(x) for x in zip(a, b)], - [sum(x) for x in zip(c, d)], - ) + return (sum(a + b + c + d), [a, b], [c, d]) # Instantiate the class. test = Test() @@ -28,4 +24,8 @@ def callback(self, a, b, c, d): result = cb.call(a, b, c, d) # Make sure the result is correct. - assert result == (136, [6, 8, 10, 12], [22, 24, 26, 28]) == test.callback(a, b, c, d) + assert ( + result + == (136, [[1, 2, 3, 4], [5, 6, 7, 8]], [[9, 10, 11, 12], [13, 14, 15, 16]]) + == test.callback(a, b, c, d) + ) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 8b29c4489..9d2c1a803 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -64,8 +64,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) "Return the lambda lever used to update the parameters in the " "OpenMM system according to lambda"); - // Return container for EMLECallback. - register_tuple, QVector>>(); + // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) + register_tuple>, QVector>>>(); bp::class_("EMLECallback", bp::init( diff --git a/wrapper/Convert/SireOpenMM/emlecallback.cpp b/wrapper/Convert/SireOpenMM/emlecallback.cpp index cd6f6bc6a..08b77db30 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.cpp +++ b/wrapper/Convert/SireOpenMM/emlecallback.cpp @@ -35,13 +35,14 @@ EMLECallback::EMLECallback(bp::object py_object, QString callback) : { } -boost::tuple, QVector> EMLECallback::call( +boost::tuple>, QVector>> +EMLECallback::call( QVector numbers_qm, QVector charges_mm, QVector xyz_qm, QVector xyz_mm) { - return bp::call_method, QVector>>( + return bp::call_method>, QVector>>>( this->py_object.ptr(), this->callback.toStdString().c_str(), numbers_qm, diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index 41197e816..deda74f09 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -74,7 +74,7 @@ namespace SireOpenMM \returns A flattened vector of forces for the QM and MM atoms. */ - boost::tuple, QVector> call( + boost::tuple>, QVector>> call( QVector numbers_qm, QVector charges_mm, QVector xyz_qm, From 26d29bc8b37a99de542fe14e12c4c22ceae345e9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 12:33:47 +0000 Subject: [PATCH 015/468] Refactor include directives. --- wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 1 - wrapper/Convert/SireOpenMM/emlecallback.h | 4 +++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 9d2c1a803..1cdc5854c 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -15,7 +15,6 @@ #include "Helpers/convertlist.hpp" #include "Helpers/tuples.hpp" -#include #include using namespace SireOpenMM; diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index deda74f09..ddfeb2dd4 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -32,7 +32,9 @@ #include "boost/python.hpp" #include -#include "openmmmolecule.h" +#include + +#include "sireglobal.h" namespace bp = boost::python; From 003c0b0a842a4a70ec3774250fc914b97424c0b0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 12:43:32 +0000 Subject: [PATCH 016/468] Callback now takes vector of positions. --- tests/convert/test_emle.py | 16 ++++++---------- wrapper/Convert/SireOpenMM/emlecallback.cpp | 4 ++-- wrapper/Convert/SireOpenMM/emlecallback.h | 8 ++++---- 3 files changed, 12 insertions(+), 16 deletions(-) diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py index 9ceb2fb9b..581526ae8 100644 --- a/tests/convert/test_emle.py +++ b/tests/convert/test_emle.py @@ -6,7 +6,7 @@ def test_callback(): class Test: def callback(self, a, b, c, d): - return (sum(a + b + c + d), [a, b], [c, d]) + return (42, d, c) # Instantiate the class. test = Test() @@ -15,17 +15,13 @@ def callback(self, a, b, c, d): cb = EMLECallback(test, "callback") # Create some lists to hold test data. - a = [1, 2, 3, 4] - b = [5, 6, 7, 8] - c = [9, 10, 11, 12] - d = [13, 14, 15, 16] + a = [1, 2] + b = [3, 4] + c = [a, b] + d = [b, a] # Call the callback. result = cb.call(a, b, c, d) # Make sure the result is correct. - assert ( - result - == (136, [[1, 2, 3, 4], [5, 6, 7, 8]], [[9, 10, 11, 12], [13, 14, 15, 16]]) - == test.callback(a, b, c, d) - ) + assert result == (42, d, c) == test.callback(a, b, c, d) diff --git a/wrapper/Convert/SireOpenMM/emlecallback.cpp b/wrapper/Convert/SireOpenMM/emlecallback.cpp index 08b77db30..19979a201 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.cpp +++ b/wrapper/Convert/SireOpenMM/emlecallback.cpp @@ -39,8 +39,8 @@ boost::tuple>, QVector>> EMLECallback::call( QVector numbers_qm, QVector charges_mm, - QVector xyz_qm, - QVector xyz_mm) + QVector> xyz_qm, + QVector> xyz_mm) { return bp::call_method>, QVector>>>( this->py_object.ptr(), diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index ddfeb2dd4..96a61c85d 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -55,8 +55,8 @@ namespace SireOpenMM The name of a callback method that take the following arguments: - numbers_qm: A list of atomic numbers for the atoms in the ML region. - charges_mm: A list of the MM charges. - - xyz_qm: A flattened list of the QM coordinates of the atoms in the ML region. - - xyz_mm: A flattened list of the MM coordinates of the point charges. + - xyz_qm: A vector of positions for the atoms in the ML region. + - xyz_mm: A vector of positions for the atoms in the MM region.. */ EMLECallback(bp::object object, QString callback); @@ -79,8 +79,8 @@ namespace SireOpenMM boost::tuple>, QVector>> call( QVector numbers_qm, QVector charges_mm, - QVector xyz_qm, - QVector xyz_mm + QVector> xyz_qm, + QVector> xyz_mm ); private: From 401e130573e0bfa5b5be32ca32f6c167c6f966e1 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 12:45:56 +0000 Subject: [PATCH 017/468] Fix docstring. --- wrapper/Convert/SireOpenMM/emlecallback.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index 96a61c85d..8a354241e 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -56,7 +56,7 @@ namespace SireOpenMM - numbers_qm: A list of atomic numbers for the atoms in the ML region. - charges_mm: A list of the MM charges. - xyz_qm: A vector of positions for the atoms in the ML region. - - xyz_mm: A vector of positions for the atoms in the MM region.. + - xyz_mm: A vector of positions for the atoms in the MM region. */ EMLECallback(bp::object object, QString callback); @@ -65,13 +65,13 @@ namespace SireOpenMM A vector of atomic numbers for the atoms in the ML region. \param charges_mm - A vector of the MM charges. + A vector of the charges on the MM atoms. \param xyz_qm - A flattened vector of the QM coordinates of the atoms in the ML region. + A vector of positions for the atoms in the ML region. \param xyz_mm - A flattened vector of the MM coordinates of the point charges. + A vector of positions for the atoms in the MM region. \returns A flattened vector of forces for the QM and MM atoms. From fec75f16624f1751ec78d2c9855a9aa3ee9ec30e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 17 Nov 2023 14:28:40 +0000 Subject: [PATCH 018/468] Add default callback function name. --- wrapper/Convert/SireOpenMM/emlecallback.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emlecallback.h index 8a354241e..368c70834 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emlecallback.h @@ -58,7 +58,7 @@ namespace SireOpenMM - xyz_qm: A vector of positions for the atoms in the ML region. - xyz_mm: A vector of positions for the atoms in the MM region. */ - EMLECallback(bp::object object, QString callback); + EMLECallback(bp::object object, QString callback="_sire_callback"); //! Constructor /*! \param numbers_qm @@ -74,7 +74,7 @@ namespace SireOpenMM A vector of positions for the atoms in the MM region. \returns - A flattened vector of forces for the QM and MM atoms. + A vector of forces for the QM and MM atoms. */ boost::tuple>, QVector>> call( QVector numbers_qm, From 5baf85884a0e4dfbf1336fd216e0e9c6b22f11d2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 20 Nov 2023 10:20:35 +0000 Subject: [PATCH 019/468] Refactor to add abstract QMMEngine interface and derived EMLEEngine. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 3 +- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 39 ++++-- wrapper/Convert/SireOpenMM/emle.cpp | 126 ++++++++++++++++++ .../SireOpenMM/{emlecallback.h => emle.h} | 97 +++++++++++++- .../SireOpenMM/{emlecallback.cpp => qmmm.cpp} | 22 +-- wrapper/Convert/SireOpenMM/qmmm.h | 53 ++++++++ 6 files changed, 304 insertions(+), 36 deletions(-) create mode 100644 wrapper/Convert/SireOpenMM/emle.cpp rename wrapper/Convert/SireOpenMM/{emlecallback.h => emle.h} (53%) rename wrapper/Convert/SireOpenMM/{emlecallback.cpp => qmmm.cpp} (64%) create mode 100644 wrapper/Convert/SireOpenMM/qmmm.h diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 93868446f..b5a74bc05 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -52,10 +52,11 @@ if (${SIRE_USE_OPENMM}) _SireOpenMM.main.cpp customforce.cpp - emlecallback.cpp + emle.cpp lambdalever.cpp openmmminimise.cpp openmmmolecule.cpp + qmmm.cpp sire_openmm.cpp sire_to_openmm_system.cpp diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 1cdc5854c..fd5d250d3 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -6,7 +6,7 @@ #include "sire_openmm.h" -#include "emlecallback.h" +#include "emle.h" #include "lambdalever.h" @@ -63,17 +63,6 @@ BOOST_PYTHON_MODULE(_SireOpenMM) "Return the lambda lever used to update the parameters in the " "OpenMM system according to lambda"); - // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) - register_tuple>, QVector>>>(); - - bp::class_("EMLECallback", - bp::init( - "Constructor: A callback wrapper class to enable electrostatic embedding" - "of machine learning potentials via emle-engine." - ) - ) - .def("call", &EMLECallback::call, "Call the callback"); - bp::class_> LambdaLever_exposer_t( "LambdaLever", "A lever that can be used to change the parameters in an OpenMM system " @@ -182,4 +171,30 @@ BOOST_PYTHON_MODULE(_SireOpenMM) bp::converter::registry::insert(&extract_swig_wrapped_pointer, bp::type_id()); bp::converter::registry::insert(&extract_swig_wrapped_pointer, bp::type_id()); bp::converter::registry::insert(&extract_swig_wrapped_pointer, bp::type_id()); + + // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) + register_tuple>, QVector>>>(); + + bp::class_("EMLEEngine", + bp::init( + ( + bp::arg("py_object"), bp::arg("cutoff")=SireUnits::Dimension::Length(8.0), bp::arg("lambda")=1.0 + ), + "Constructor: An engine that can be used to enable electrostatic embedding" + "of machine learning potentials via emle-engine." + ) + ) + .def("getLambda", &EMLEEngine::getLambda, "Get the lambda value") + .def("setLambda", &EMLEEngine::setLambda, "Set the lambda value") + .def("getCutoff", &EMLEEngine::getCutoff, "Get the cutoff value") + .def("setCutoff", &EMLEEngine::setCutoff, "Set the cutoff value") + .def("call", &EMLEEngine::call, "Call the callback"); + + bp::class_("EMLECallback", + bp::init( + "Constructor: A callback wrapper class to enable electrostatic embedding" + "of machine learning potentials via emle-engine." + ) + ) + .def("call", &EMLECallback::call, "Call the callback"); } diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp new file mode 100644 index 000000000..ca4f4f764 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -0,0 +1,126 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2023 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "emle.h" + +using namespace SireOpenMM; + +EMLECallback::EMLECallback(bp::object py_object, QString callback) : + py_object(py_object), callback(callback) +{ +} + +boost::tuple>, QVector>> +EMLECallback::call( + QVector numbers_qm, + QVector charges_mm, + QVector> xyz_qm, + QVector> xyz_mm) +{ + return bp::call_method>, QVector>>>( + this->py_object.ptr(), + this->callback.toStdString().c_str(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm + ); +} + +EMLEEngine::EMLEEngine(bp::object py_object, SireUnits::Dimension::Length cutoff, double lambda) : + callback(py_object, "_sire_callback"), + cutoff(cutoff), + lambda(lambda) +{ +} + +void EMLEEngine::setLambda(double lambda) +{ + this->lambda = lambda; +} + +double EMLEEngine::getLambda() const +{ + return this->lambda; +} + +void EMLEEngine::setCutoff(SireUnits::Dimension::Length cutoff) +{ + this->cutoff = cutoff; +} + +SireUnits::Dimension::Length EMLEEngine::getCutoff() const +{ + return this->cutoff; +} + +OpenMM::ForceImpl *EMLEEngine::createImpl() const +{ +#ifdef SIRE_USE_CUSTOMCPPFORCE + return new EMLEEngineImpl(*this); +#else + throw SireError::unsupported(QObject::tr( + "Unable to create a EMLEEngine because OpenMM::CustomCPPForceImpl " + "is not available. You need to use OpenMM 8.1 or later."), + CODELOC); + return 0; +#endif +} + +EMLEEngineImpl::EMLEEngineImpl(const EMLEEngine &owner) : + OpenMM::CustomCPPForceImpl(owner), + owner(owner) +{ +} + +EMLEEngineImpl::~EMLEEngineImpl() +{ +} + +const EMLEEngine &EMLEEngineImpl::getOwner() const +{ + return this->owner; +} + +double EMLEEngineImpl::computeForce( + OpenMM::ContextImpl &context, + const std::vector &positions, + std::vector &forces) +{ + return 0; +} + +boost::tuple>, QVector>> +EMLEEngine::call( + QVector numbers_qm, + QVector charges_mm, + QVector> xyz_qm, + QVector> xyz_mm) +{ + return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); +} diff --git a/wrapper/Convert/SireOpenMM/emlecallback.h b/wrapper/Convert/SireOpenMM/emle.h similarity index 53% rename from wrapper/Convert/SireOpenMM/emlecallback.h rename to wrapper/Convert/SireOpenMM/emle.h index 368c70834..406af3637 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -26,8 +26,15 @@ * \*********************************************/ -#ifndef SIREOPENMM_EMLECALLBACK_H -#define SIREOPENMM_EMLECALLBACK_H +#ifndef SIREOPENMM_EMLE_H +#define SIREOPENMM_EMLE_H + +#include "OpenMM.h" +#include "openmm/Force.h" +#ifdef SIRE_USE_CUSTOMCPPFORCE +#include "openmm/internal/ContextImpl.h" +#include "openmm/internal/CustomCPPForceImpl.h" +#endif #include "boost/python.hpp" #include @@ -36,6 +43,11 @@ #include "sireglobal.h" +#include "SireUnits/dimensions.h" +#include "SireUnits/units.h" + +#include "qmmm.h" + namespace bp = boost::python; SIRE_BEGIN_HEADER @@ -58,7 +70,7 @@ namespace SireOpenMM - xyz_qm: A vector of positions for the atoms in the ML region. - xyz_mm: A vector of positions for the atoms in the MM region. */ - EMLECallback(bp::object object, QString callback="_sire_callback"); + EMLECallback(bp::object, QString callback="_sire_callback"); //! Constructor /*! \param numbers_qm @@ -87,6 +99,85 @@ namespace SireOpenMM bp::object py_object; QString callback; }; + + class EMLEEngine : public QMMMEngine + { + public: + //! Constructor + /*! \param py_object + An EMLECalculator Python object. + + \param cutoff + The ML cutoff distance. + + \param lambda + The lambda weighting factor. This can be used to interpolate between + potentials for end-state correction calculations. + */ + EMLEEngine( + bp::object, + SireUnits::Dimension::Length cutoff=8.0*SireUnits::angstrom, + double lambda=1.0 + ); + + double getLambda() const; + + void setLambda(double lambda); + + SireUnits::Dimension::Length getCutoff() const; + + void setCutoff(SireUnits::Dimension::Length cutoff); + + //! Constructor + /*! \param numbers_qm + A vector of atomic numbers for the atoms in the ML region. + + \param charges_mm + A vector of the charges on the MM atoms. + + \param xyz_qm + A vector of positions for the atoms in the ML region. + + \param xyz_mm + A vector of positions for the atoms in the MM region. + + \returns + A vector of forces for the QM and MM atoms. + */ + boost::tuple>, QVector>> call( + QVector numbers_qm, + QVector charges_mm, + QVector> xyz_qm, + QVector> xyz_mm + ); + + protected: + OpenMM::ForceImpl *createImpl() const; + + private: + EMLECallback callback; + SireUnits::Dimension::Length cutoff; + double lambda; + }; + +#ifdef SIRE_USE_CUSTOMCPPFORCE + class EMLEEngineImpl : public OpenMM::CustomCPPForceImpl + { + public: + EMLEEngineImpl(const EMLEEngine &owner); + + ~EMLEEngineImpl(); + + double computeForce(OpenMM::ContextImpl &context, + const std::vector &positions, + std::vector &forces); + + const EMLEEngine &getOwner() const; + + private: + const EMLEEngine &owner; + }; +#endif } SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/emlecallback.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp similarity index 64% rename from wrapper/Convert/SireOpenMM/emlecallback.cpp rename to wrapper/Convert/SireOpenMM/qmmm.cpp index 19979a201..510639620 100644 --- a/wrapper/Convert/SireOpenMM/emlecallback.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -26,28 +26,10 @@ * \*********************************************/ -#include "emlecallback.h" +#include "qmmm.h" using namespace SireOpenMM; -EMLECallback::EMLECallback(bp::object py_object, QString callback) : - py_object(py_object), callback(callback) +QMMMEngine::QMMMEngine() { } - -boost::tuple>, QVector>> -EMLECallback::call( - QVector numbers_qm, - QVector charges_mm, - QVector> xyz_qm, - QVector> xyz_mm) -{ - return bp::call_method>, QVector>>>( - this->py_object.ptr(), - this->callback.toStdString().c_str(), - numbers_qm, - charges_mm, - xyz_qm, - xyz_mm - ); -} diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h new file mode 100644 index 000000000..4d86bc74a --- /dev/null +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -0,0 +1,53 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2023 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREOPENMM_QMMM_H +#define SIREOPENMM_QMMM_H + +#include "OpenMM.h" +#include "openmm/Force.h" + +#include "sireglobal.h" + +SIRE_BEGIN_HEADER + +namespace SireOpenMM +{ + class QMMMEngine : public OpenMM::Force + { + public: + QMMMEngine(); + + protected: + virtual OpenMM::ForceImpl *createImpl() const = 0; + }; +} + +SIRE_END_HEADER + +#endif From 5904286b871af76eff42dd97a077d39fb09ad7f8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 20 Nov 2023 21:09:46 +0000 Subject: [PATCH 020/468] Don't use slots keywords from Qt signals. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 1 + wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 1 + 2 files changed, 2 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index b5a74bc05..314e2d32f 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -17,6 +17,7 @@ if (${SIRE_USE_OPENMM}) # Third Party dependencies of this module include_directories( ${OpenMM_INCLUDE_DIR} ) add_definitions("-DSIRE_USE_OPENMM") + add_definitions(-DQT_NO_SIGNALS_SLOTS_KEYWORDS) # Sire include paths include_directories( BEFORE ${SIRE_INCLUDE_DIR} ) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 0b7c8857e..1e9d08668 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -47,6 +47,7 @@ #include "openmmmolecule.h" #include "customforce.h" +#include "emle.h" #include From 582e7c5533f0c2ff18780b0bdcbebee73cfaab33 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 20 Nov 2023 22:16:40 +0000 Subject: [PATCH 021/468] SireBase::Property inheritance now working. --- src/sire/mol/__init__.py | 2 ++ src/sire/mol/_dynamics.py | 2 ++ src/sire/system/_system.py | 4 +++ .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 6 ++++- wrapper/Convert/SireOpenMM/emle.cpp | 23 ++++++++++++++++ wrapper/Convert/SireOpenMM/emle.h | 26 +++++++++++++++++-- wrapper/Convert/SireOpenMM/qmmm.cpp | 2 +- wrapper/Convert/SireOpenMM/qmmm.h | 13 ++++++++-- 8 files changed, 72 insertions(+), 6 deletions(-) diff --git a/src/sire/mol/__init__.py b/src/sire/mol/__init__.py index a6420383f..cb6afca0f 100644 --- a/src/sire/mol/__init__.py +++ b/src/sire/mol/__init__.py @@ -1600,6 +1600,7 @@ def _dynamics( platform=None, device=None, precision=None, + qm_engine=None, map=None, ): """ @@ -1864,6 +1865,7 @@ def _dynamics( ignore_perturbations=ignore_perturbations, restraints=restraints, fixed=fixed, + qm_engine=qm_engine, map=map, ) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 3e98a3cdd..c7e28a2bc 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -910,6 +910,7 @@ def __init__( coulomb_power=None, restraints=None, fixed=None, + qm_engine=None, ): from ..base import create_map from .. import u @@ -935,6 +936,7 @@ def __init__( _add_extra(extras, "coulomb_power", coulomb_power) _add_extra(extras, "restraints", restraints) _add_extra(extras, "fixed", fixed) + _add_extra(extras, "qm_engine", qm_engine) map = create_map(map, extras) diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index 419577c19..dcef328e5 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -594,6 +594,10 @@ def dynamics(self, *args, **kwargs): that should be fixed in place during the simulation. These atoms will not be moved by dynamics. + qm_engine: + A QMMMEngine object to used to compute QM/MM forces and energies + on a subset of the atoms in the system. + platform: str The name of the OpenMM platform on which to run the dynamics, e.g. "CUDA", "OpenCL", "Metal" etc. diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index fd5d250d3..145307b37 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -175,7 +175,9 @@ BOOST_PYTHON_MODULE(_SireOpenMM) // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) register_tuple>, QVector>>>(); - bp::class_("EMLEEngine", + bp::class_, boost::noncopyable>("QMMMEngine", bp::no_init); + + bp::class_>("EMLEEngine", bp::init( ( bp::arg("py_object"), bp::arg("cutoff")=SireUnits::Dimension::Length(8.0), bp::arg("lambda")=1.0 @@ -188,6 +190,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setLambda", &EMLEEngine::setLambda, "Set the lambda value") .def("getCutoff", &EMLEEngine::getCutoff, "Get the cutoff value") .def("setCutoff", &EMLEEngine::setCutoff, "Set the cutoff value") + .def("what", &EMLEEngine::what, "Call the callback") + .def("typeName", &EMLEEngine::typeName, "Call the callback") .def("call", &EMLEEngine::call, "Call the callback"); bp::class_("EMLECallback", diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index ca4f4f764..f45a49a01 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -30,6 +30,10 @@ using namespace SireOpenMM; +EMLECallback::EMLECallback() +{ +} + EMLECallback::EMLECallback(bp::object py_object, QString callback) : py_object(py_object), callback(callback) { @@ -52,6 +56,10 @@ EMLECallback::call( ); } +EMLEEngine::EMLEEngine() +{ +} + EMLEEngine::EMLEEngine(bp::object py_object, SireUnits::Dimension::Length cutoff, double lambda) : callback(py_object, "_sire_callback"), cutoff(cutoff), @@ -79,6 +87,21 @@ SireUnits::Dimension::Length EMLEEngine::getCutoff() const return this->cutoff; } +void EMLEEngine::setAtoms(QVector ml_indices) +{ + this->ml_indices = ml_indices; +} + +const char *EMLEEngine::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *EMLEEngine::what() const +{ + return EMLEEngine::typeName(); +} + OpenMM::ForceImpl *EMLEEngine::createImpl() const { #ifdef SIRE_USE_CUSTOMCPPFORCE diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 406af3637..643760bf0 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -59,6 +59,9 @@ namespace SireOpenMM class EMLECallback { public: + //! Default constructor. + EMLECallback(); + //! Constructor /*! \param py_object A Python object that contains the callback function. @@ -100,9 +103,12 @@ namespace SireOpenMM QString callback; }; - class EMLEEngine : public QMMMEngine + class EMLEEngine : public SireBase::ConcreteProperty { public: + //! Default constructor. + EMLEEngine(); + //! Constructor /*! \param py_object An EMLECalculator Python object. @@ -116,18 +122,31 @@ namespace SireOpenMM */ EMLEEngine( bp::object, - SireUnits::Dimension::Length cutoff=8.0*SireUnits::angstrom, + SireUnits::Dimension::Length cutoff=8.0*SireUnits::angstrom, double lambda=1.0 ); + //! Get the lambda weighting factor. double getLambda() const; + //! Set the lambda weighting factor. void setLambda(double lambda); + //! Get the QM cutoff distance. SireUnits::Dimension::Length getCutoff() const; + //! Set the QM cutoff distance. void setCutoff(SireUnits::Dimension::Length cutoff); + //! Set the list of atom indices for the QM region. + void setAtoms(QVector ml_indices); + + //! Return the C++ name for this class. + static const char *typeName(); + + //! Return the C++ name for this class. + const char *what() const; + //! Constructor /*! \param numbers_qm A vector of atomic numbers for the atoms in the ML region. @@ -158,6 +177,7 @@ namespace SireOpenMM EMLECallback callback; SireUnits::Dimension::Length cutoff; double lambda; + QVector ml_indices; }; #ifdef SIRE_USE_CUSTOMCPPFORCE @@ -180,6 +200,8 @@ namespace SireOpenMM #endif } +Q_DECLARE_METATYPE(SireOpenMM::EMLEEngine) + SIRE_END_HEADER #endif diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index 510639620..7f2b6680a 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -30,6 +30,6 @@ using namespace SireOpenMM; -QMMMEngine::QMMMEngine() +QMMMEngine::~QMMMEngine() { } diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 4d86bc74a..31d37a3ed 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -34,14 +34,23 @@ #include "sireglobal.h" +#include "SireBase/property.h" + SIRE_BEGIN_HEADER namespace SireOpenMM { - class QMMMEngine : public OpenMM::Force + class QMMMEngine; +} + +namespace SireOpenMM +{ + typedef SireBase::PropPtr QMMEnginePtr; + + class QMMMEngine : public SireBase::Property, public OpenMM::Force { public: - QMMMEngine(); + virtual ~QMMMEngine(); protected: virtual OpenMM::ForceImpl *createImpl() const = 0; From bb5031072278b4780793313ea02db91a04c4abea Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 10:52:36 +0000 Subject: [PATCH 022/468] Get qm_engine from the map. --- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 1e9d08668..225f9d5b5 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -736,6 +736,14 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, gridff = new GridForce(); } + // now create the engine for computing QM or ML forces on atoms + QMMMEngine *qmff = 0; + + if (map.specified("qm_engine")) + { + auto &qmff = map["qm_engine"].value().asA(); + } + // end of stage 2 - we now have the base forces /// From 7b5b24651f775c4d7f0b74cbc6ec2dd9e38043fc Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 11:57:14 +0000 Subject: [PATCH 023/468] Add convenience functions for setting/unsetting QM molecules. --- src/sire/system/_system.py | 50 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index dcef328e5..5f003bb4d 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -869,6 +869,56 @@ def set_energy_trajectory(self, trajectory, map=None): self._system.set_property(traj_propname.source(), trajectory) + def set_qm_molecule(self, index, map=None): + """ + Set the specified molecule to be a QM molecule. + """ + if index < 0 or index > self.num_molecules()-1: + raise ValueError( + f"Index {index} is out of range for the number of " + f"molecules in this system ({self.num_molecules()})" + ) + + # Check for existing QM molecules. Currently we only support a single + # molecule. + try: + qm_mols = self["property is_qm"].molecules() + except: + qm_mols = [] + + if len(qm_mols) > 0: + raise ValueError( + "This system already contains a QM molecule!" + ) + + # Extract the molecule. + mol = self[index] + + # Create a cursor. + c = mol.cursor() + + # Flag the molecule as QM. + c["is_qm"] = True + + # Commit the changes and update. + mol = c.commit() + self.update(mol) + + def unset_qm_molecule(self, map=None): + """ + Unset the QM molecule. + """ + try: + # Loop over the QM molecules and unset them. + qm_mols = self["property is_qm"].molecules() + for mol in qm_mols: + c = mol.cursor() + c["is_qm"] = False + mol = c.commit() + self.update(mol) + except: + pass + def clear_energy_trajectory(self, map=None): """ Completely clear any existing energy trajectory From 5b682e52bb7c8a82c10ad8b9591ba08be6b706d7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 11:58:06 +0000 Subject: [PATCH 024/468] Add code for adding QM force to the system. --- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 60 +++++++++++++++---- wrapper/Convert/SireOpenMM/openmmmolecule.h | 3 +- .../SireOpenMM/sire_to_openmm_system.cpp | 6 ++ 3 files changed, 57 insertions(+), 12 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 43e2db976..1c1ef37db 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -179,6 +179,7 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, } bool is_perturbable = false; + bool is_qm = false; bool swap_end_states = false; if (mol.hasProperty(map["is_perturbable"])) @@ -191,6 +192,11 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, } } + if (mol.hasProperty(map["is_qm"])) + { + is_qm = mol.property(map["is_qm"]).asABoolean(); + } + if (is_perturbable) { ffinfo = mol.property(map["forcefield0"]).asA(); @@ -293,6 +299,22 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, field_atoms.reset(new FieldAtoms(atms, map)); } + if (mol.hasProperty(map["is_qm"])) + { + if (mol.property(map["is_qm"]).asABoolean()) + { + // remove all internal terms + bond_params.clear(); + ang_params.clear(); + dih_params.clear(); + constraints.clear(); + virtual_sites.clear(); + light_atoms.clear(); + unbonded_atoms.clear(); + perturbed.reset(); + } + } + if (ffinfo.isAmberStyle()) { if (is_perturbable) @@ -331,16 +353,21 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, const auto params1 = SireMM::AmberParams(mol, map1); perturbed.reset(new OpenMMMolecule(*this)); - perturbed->constructFromAmber(mol, params1, params, map1, true); + perturbed->constructFromAmber(mol, params1, params, map1, true, false); - this->constructFromAmber(mol, params, params1, map0, true); + this->constructFromAmber(mol, params, params1, map0, true, false); this->alignInternals(map); } + else if (is_qm) + { + const auto params = SireMM::AmberParams(mol, map); + this->constructFromAmber(mol, params, params, map, false, true); + } else { const auto params = SireMM::AmberParams(mol, map); - this->constructFromAmber(mol, params, params, map, false); + this->constructFromAmber(mol, params, params, map, false, false); } } else @@ -513,8 +540,15 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const AmberParams ¶ms, const AmberParams ¶ms1, const PropertyMap &map, - bool is_perturbable) + bool is_perturbable, + bool is_qm) { + if (is_perturbable and is_qm) + { + throw SireError::invalid_key(QObject::tr( + "We currently do not support perturbable QM molecules."), CODELOC); + } + const auto &moldata = mol.data(); if (this->hasFieldAtoms()) @@ -660,17 +694,21 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, this->cljs = QVector>(nats, std::make_tuple(0.0, 0.0, 0.0)); auto cljs_data = cljs.data(); - for (int i = 0; i < nats; ++i) + // cljs are zeroed for QM molecules + if (not is_qm) { - const auto &cgatomidx = idx_to_cgatomidx_data[i]; + for (int i = 0; i < nats; ++i) + { + const auto &cgatomidx = idx_to_cgatomidx_data[i]; - const double chg = params_charges.at(idx_to_cgatomidx_data[i]).to(SireUnits::mod_electron); + const double chg = params_charges.at(idx_to_cgatomidx_data[i]).to(SireUnits::mod_electron); - const auto &lj = params_ljs.at(idx_to_cgatomidx_data[i]); - const double sig = lj.sigma().to(SireUnits::nanometer); - const double eps = lj.epsilon().to(SireUnits::kJ_per_mol); + const auto &lj = params_ljs.at(idx_to_cgatomidx_data[i]); + const double sig = lj.sigma().to(SireUnits::nanometer); + const double eps = lj.epsilon().to(SireUnits::kJ_per_mol); - cljs_data[i] = std::make_tuple(chg, sig, eps); + cljs_data[i] = std::make_tuple(chg, sig, eps); + } } this->bond_params.clear(); diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 72398c247..b78a85571 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -217,7 +217,8 @@ namespace SireOpenMM const SireMM::AmberParams ¶ms, const SireMM::AmberParams ¶ms1, const SireBase::PropertyMap &map, - bool is_perturbable); + bool is_perturbable=false, + bool is_qm=false); void buildExceptions(const SireMol::Molecule &mol, const QVector &atomidx_to_idx, diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 225f9d5b5..5ff466230 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -805,6 +805,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, lambda_lever.addLever("field_scale"); } + if (qmff != 0) + { + lambda_lever.setForceIndex("qm", system.addForce(qmff)); + lambda_lever.addLever("qm_scale"); + } + /// /// Stage 4 - define the forces for ghost atoms /// From 8c4a24f478debeb1b0aae102e29b8196167315d9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 12:19:34 +0000 Subject: [PATCH 025/468] Add sr.qm Python module. --- src/sire/CMakeLists.txt | 1 + src/sire/__init__.py | 1 + src/sire/qm/CMakeLists.txt | 13 +++++++++++++ src/sire/qm/__init__.py | 9 +++++++++ 4 files changed, 24 insertions(+) create mode 100644 src/sire/qm/CMakeLists.txt create mode 100644 src/sire/qm/__init__.py diff --git a/src/sire/CMakeLists.txt b/src/sire/CMakeLists.txt index c152f4342..db12d268b 100644 --- a/src/sire/CMakeLists.txt +++ b/src/sire/CMakeLists.txt @@ -104,6 +104,7 @@ add_subdirectory (mol) add_subdirectory (morph) add_subdirectory (move) add_subdirectory (options) +add_subdirectory (qm) add_subdirectory (restraints) add_subdirectory (search) add_subdirectory (stream) diff --git a/src/sire/__init__.py b/src/sire/__init__.py index 02b97fb7a..bdde34ea7 100644 --- a/src/sire/__init__.py +++ b/src/sire/__init__.py @@ -698,6 +698,7 @@ def _convert(id): morph = _lazy_import.lazy_module("sire.morph") move = _lazy_import.lazy_module("sire.move") options = _lazy_import.lazy_module("sire.options") + qm = _lazy_import.lazy_module("sire.qm") qt = _lazy_import.lazy_module("sire.qt") restraints = _lazy_import.lazy_module("sire.restraints") search = _lazy_import.lazy_module("sire.search") diff --git a/src/sire/qm/CMakeLists.txt b/src/sire/qm/CMakeLists.txt new file mode 100644 index 000000000..89cd53fb2 --- /dev/null +++ b/src/sire/qm/CMakeLists.txt @@ -0,0 +1,13 @@ +######################################## +# +# sire.qm +# +######################################## + +# Add your script to this list +set ( SCRIPTS + __init__.py + ) + +# installation +install( FILES ${SCRIPTS} DESTINATION ${SIRE_PYTHON}/sire/qm ) diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py new file mode 100644 index 000000000..6f7e2f1b8 --- /dev/null +++ b/src/sire/qm/__init__.py @@ -0,0 +1,9 @@ +__all__ = ["EMLEEngine"] + +from ..legacy import Convert as _Convert + +from .. import use_new_api as _use_new_api + +_use_new_api() + +EMLEEngine = _Convert._SireOpenMM.EMLEEngine From ebb659bea2adc65dc2002bacfabb3533f3f07542 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 12:39:36 +0000 Subject: [PATCH 026/468] Add virtual methods to QMMMEngine base class. --- wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 2 ++ wrapper/Convert/SireOpenMM/emle.cpp | 9 +++++++-- wrapper/Convert/SireOpenMM/emle.h | 7 +++++-- wrapper/Convert/SireOpenMM/qmmm.h | 14 ++++++++++++++ 4 files changed, 28 insertions(+), 4 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 145307b37..dd2c8616a 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -190,6 +190,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setLambda", &EMLEEngine::setLambda, "Set the lambda value") .def("getCutoff", &EMLEEngine::getCutoff, "Get the cutoff value") .def("setCutoff", &EMLEEngine::setCutoff, "Set the cutoff value") + .def("getAtoms", &EMLEEngine::getAtoms, "Get QM atom indices") + .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") .def("what", &EMLEEngine::what, "Call the callback") .def("typeName", &EMLEEngine::typeName, "Call the callback") .def("call", &EMLEEngine::call, "Call the callback"); diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index f45a49a01..3304b0860 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -87,9 +87,14 @@ SireUnits::Dimension::Length EMLEEngine::getCutoff() const return this->cutoff; } -void EMLEEngine::setAtoms(QVector ml_indices) +QVector EMLEEngine::getAtoms() const { - this->ml_indices = ml_indices; + return this->atoms; +} + +void EMLEEngine::setAtoms(QVector atoms) +{ + this->atoms = atoms; } const char *EMLEEngine::typeName() diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 643760bf0..54b36d30b 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -138,8 +138,11 @@ namespace SireOpenMM //! Set the QM cutoff distance. void setCutoff(SireUnits::Dimension::Length cutoff); + //! Get the indices of the atoms in the QM region. + QVector getAtoms() const; + //! Set the list of atom indices for the QM region. - void setAtoms(QVector ml_indices); + void setAtoms(QVector atoms); //! Return the C++ name for this class. static const char *typeName(); @@ -177,7 +180,7 @@ namespace SireOpenMM EMLECallback callback; SireUnits::Dimension::Length cutoff; double lambda; - QVector ml_indices; + QVector atoms; }; #ifdef SIRE_USE_CUSTOMCPPFORCE diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 31d37a3ed..47e90518b 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -36,6 +36,8 @@ #include "SireBase/property.h" +#include "SireUnits/dimensions.h" + SIRE_BEGIN_HEADER namespace SireOpenMM @@ -52,6 +54,18 @@ namespace SireOpenMM public: virtual ~QMMMEngine(); + //! Get the QM cutoff distance. + virtual SireUnits::Dimension::Length getCutoff() const = 0; + + //! Set the QM cutoff distance. + virtual void setCutoff(SireUnits::Dimension::Length cutoff) = 0; + + //! Get the indices of the atoms in the QM region. + virtual QVector getAtoms() const = 0; + + //! Set the list of atom indices for the QM region. + virtual void setAtoms(QVector) = 0; + protected: virtual OpenMM::ForceImpl *createImpl() const = 0; }; From a925b1fab610243ebab816bc9022d87bde59f29b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 12:48:04 +0000 Subject: [PATCH 027/468] Add code to set the QM atoms. (Need to work out why old API is needed.) --- src/sire/mol/_dynamics.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index c7e28a2bc..1921dec55 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -915,6 +915,15 @@ def __init__( from ..base import create_map from .. import u + # Set the global indices of the QM atoms in the engine. + if qm_engine is not None and mols is not None: + try: + atoms_to_find = mols["property is_qm"].atoms() + idxs = mols.atoms().find(atoms_to_find) + qm_engine.setAtoms(idxs) + except: + raise ValueError("Unable to set QM atoms in the engine.") + extras = {} _add_extra(extras, "cutoff", cutoff) From a44dc9aaa3a4065399eeddfc4c8cccecdd225cbd Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 13:46:24 +0000 Subject: [PATCH 028/468] Use map to get property name. --- src/sire/system/_system.py | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index 5f003bb4d..f5cac4a8d 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -879,10 +879,16 @@ def set_qm_molecule(self, index, map=None): f"molecules in this system ({self.num_molecules()})" ) + from ..base import create_map + + map = create_map(map) + + qm_propname = map["is_qm"] + # Check for existing QM molecules. Currently we only support a single # molecule. try: - qm_mols = self["property is_qm"].molecules() + qm_mols = self[f"property {qm_propname}"].molecules() except: qm_mols = [] @@ -898,7 +904,7 @@ def set_qm_molecule(self, index, map=None): c = mol.cursor() # Flag the molecule as QM. - c["is_qm"] = True + c[qm_propname] = True # Commit the changes and update. mol = c.commit() @@ -909,11 +915,17 @@ def unset_qm_molecule(self, map=None): Unset the QM molecule. """ try: + from ..base import create_map + + map = create_map(map) + + qm_propname = map["is_qm"] + # Loop over the QM molecules and unset them. - qm_mols = self["property is_qm"].molecules() + qm_mols = self[f"property {qm_propname}"].molecules() for mol in qm_mols: c = mol.cursor() - c["is_qm"] = False + c[qm_propname] = False mol = c.commit() self.update(mol) except: From 3c9aa136311bb8b34291b5b5b4ac60d529f714e6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 15:42:01 +0000 Subject: [PATCH 029/468] Improve error message. --- src/sire/mol/_dynamics.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 1921dec55..3b28c10c4 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -922,7 +922,10 @@ def __init__( idxs = mols.atoms().find(atoms_to_find) qm_engine.setAtoms(idxs) except: - raise ValueError("Unable to set QM atoms in the engine.") + raise ValueError( + "Unable to set QM atoms in the engine. " + "Have you set a QM molecule?" + ) extras = {} From dfd928d68ac78666ddf74fe33d205b5727331e11 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 15:42:21 +0000 Subject: [PATCH 030/468] Blacken. --- src/sire/system/_system.py | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index f5cac4a8d..a150e8a29 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -825,9 +825,7 @@ def energy_trajectory( # we need to create this trajectory from ..maths import EnergyTrajectory - self._system.set_property( - traj_propname.source(), EnergyTrajectory() - ) + self._system.set_property(traj_propname.source(), EnergyTrajectory()) traj = self._system.property(traj_propname) @@ -863,8 +861,7 @@ def set_energy_trajectory(self, trajectory, map=None): if trajectory.what() != "SireMaths::EnergyTrajectory": raise TypeError( - f"You cannot set a {type(trajectory)} as an " - "energy trajectory!" + f"You cannot set a {type(trajectory)} as an " "energy trajectory!" ) self._system.set_property(traj_propname.source(), trajectory) @@ -873,7 +870,7 @@ def set_qm_molecule(self, index, map=None): """ Set the specified molecule to be a QM molecule. """ - if index < 0 or index > self.num_molecules()-1: + if index < 0 or index > self.num_molecules() - 1: raise ValueError( f"Index {index} is out of range for the number of " f"molecules in this system ({self.num_molecules()})" @@ -893,9 +890,7 @@ def set_qm_molecule(self, index, map=None): qm_mols = [] if len(qm_mols) > 0: - raise ValueError( - "This system already contains a QM molecule!" - ) + raise ValueError("This system already contains a QM molecule!") # Extract the molecule. mol = self[index] From c21e54933d16ed8d6c29743373d55f6bcc269b62 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 16:06:07 +0000 Subject: [PATCH 031/468] Need to make qmff non-const. Will figure out better way to do this. --- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 5ff466230..d54949ee6 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -741,7 +741,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (map.specified("qm_engine")) { - auto &qmff = map["qm_engine"].value().asA(); + qmff = const_cast(&map["qm_engine"].value().asA()); } // end of stage 2 - we now have the base forces From e4cc7f2fdb5927f5e959a8ee550d99df4523aec8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 16:16:26 +0000 Subject: [PATCH 032/468] Make call methods const. --- wrapper/Convert/SireOpenMM/emle.cpp | 4 ++-- wrapper/Convert/SireOpenMM/emle.h | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 3304b0860..b00aa1336 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -44,7 +44,7 @@ EMLECallback::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm) + QVector> xyz_mm) const { return bp::call_method>, QVector>>>( this->py_object.ptr(), @@ -148,7 +148,7 @@ EMLEEngine::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm) + QVector> xyz_mm) const { return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); } diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 54b36d30b..893f2c058 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -96,7 +96,7 @@ namespace SireOpenMM QVector charges_mm, QVector> xyz_qm, QVector> xyz_mm - ); + ) const; private: bp::object py_object; @@ -171,7 +171,7 @@ namespace SireOpenMM QVector charges_mm, QVector> xyz_qm, QVector> xyz_mm - ); + ) const; protected: OpenMM::ForceImpl *createImpl() const; From 12dc3be5f4b90c689184b042dff485a213e6da96 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 16:36:34 +0000 Subject: [PATCH 033/468] Remove redundant forward declaration. --- wrapper/Convert/SireOpenMM/qmmm.h | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 47e90518b..d8ee99350 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -42,13 +42,6 @@ SIRE_BEGIN_HEADER namespace SireOpenMM { - class QMMMEngine; -} - -namespace SireOpenMM -{ - typedef SireBase::PropPtr QMMEnginePtr; - class QMMMEngine : public SireBase::Property, public OpenMM::Force { public: @@ -69,6 +62,8 @@ namespace SireOpenMM protected: virtual OpenMM::ForceImpl *createImpl() const = 0; }; + + typedef SireBase::PropPtr QMMEnginePtr; } SIRE_END_HEADER From 4b788c89551d680dbfe6260024f2576e2b512eae Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 20:42:04 +0000 Subject: [PATCH 034/468] Acquire GIL before invoking Python callback. --- wrapper/Convert/SireOpenMM/emle.cpp | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index b00aa1336..cf7086e4e 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -30,6 +30,15 @@ using namespace SireOpenMM; +class GILLock +{ +public: + GILLock() { state_ = PyGILState_Ensure(); } + ~GILLock() { PyGILState_Release(state_); } +private: + PyGILState_STATE state_; +}; + EMLECallback::EMLECallback() { } @@ -46,13 +55,16 @@ EMLECallback::call( QVector> xyz_qm, QVector> xyz_mm) const { + // Acquire GIL before calling Python code. + GILLock lock; + return bp::call_method>, QVector>>>( - this->py_object.ptr(), - this->callback.toStdString().c_str(), - numbers_qm, - charges_mm, - xyz_qm, - xyz_mm + this->py_object.ptr(), + this->callback.toStdString().c_str(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm ); } From e607087cda230aa07a10039959d30853f4d762c0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 21 Nov 2023 21:41:09 +0000 Subject: [PATCH 035/468] Standardise add_definitions formatting. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 314e2d32f..530f50cde 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -17,7 +17,7 @@ if (${SIRE_USE_OPENMM}) # Third Party dependencies of this module include_directories( ${OpenMM_INCLUDE_DIR} ) add_definitions("-DSIRE_USE_OPENMM") - add_definitions(-DQT_NO_SIGNALS_SLOTS_KEYWORDS) + add_definitions("-DQT_NO_SIGNALS_SLOTS_KEYWORDS") # Sire include paths include_directories( BEFORE ${SIRE_INCLUDE_DIR} ) From f2552e659f35167e221957e165e1a48dba4383ab Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 09:13:18 +0000 Subject: [PATCH 036/468] Add comment regarding need for const_cast. --- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index d54949ee6..0640a1723 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -741,6 +741,8 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (map.specified("qm_engine")) { + // we need to cast away constness since the OpenMM::System::addForce + // method expects a non-const pointer. qmff = const_cast(&map["qm_engine"].value().asA()); } From 1c2101d4570126ec4e4f091d607e335073b64d1c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 09:47:40 +0000 Subject: [PATCH 037/468] Add full getters and setters and a copy constructor. --- wrapper/Convert/SireOpenMM/emle.cpp | 34 +++++++++++++++++++++++++++++ wrapper/Convert/SireOpenMM/emle.h | 12 ++++++++++ 2 files changed, 46 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index cf7086e4e..d4badb273 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -79,6 +79,31 @@ EMLEEngine::EMLEEngine(bp::object py_object, SireUnits::Dimension::Length cutoff { } +EMLEEngine::EMLEEngine(const EMLEEngine &other) : + callback(other.callback), + cutoff(other.cutoff), + lambda(other.lambda) +{ +} + +EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) +{ + this->callback = other.callback; + this->cutoff = other.cutoff; + this->lambda = other.lambda; + return *this; +} + +void EMLEEngine::setCallback(EMLECallback callback) +{ + this->callback = callback; +} + +EMLECallback EMLEEngine::getCallback() const +{ + return this->callback; +} + void EMLEEngine::setLambda(double lambda) { this->lambda = lambda; @@ -152,6 +177,15 @@ double EMLEEngineImpl::computeForce( const std::vector &positions, std::vector &forces) { + qDebug() << "Hello from C++!"; + + // Create some dummy data so that we can test the Python callback. + QVector a = {1, 2, 3}; + QVector b = {1.0, 2.0, 3.0}; + QVector> c = {{1.0, 2.0, 3.0}, {4.0, 5.0, 6.0}}; + QVector> d = {{1.0, 2.0, 3.0}, {4.0, 5.0, 6.0}}; + auto result = this->owner.call(a, b, c, d); + return 0; } diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 893f2c058..c2958540c 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -126,6 +126,18 @@ namespace SireOpenMM double lambda=1.0 ); + //! Copy constructor. + EMLEEngine(const EMLEEngine &other); + + //! Assignment operator. + EMLEEngine &operator=(const EMLEEngine &other); + + //! Set the callback object. + void setCallback(EMLECallback callback); + + //! Get the callback object. + EMLECallback getCallback() const; + //! Get the lambda weighting factor. double getLambda() const; From a2f8afe30542d9919d0fcd43586b6108840e2b9d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 10:01:32 +0000 Subject: [PATCH 038/468] Expose copy constructor. --- wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index dd2c8616a..cb6e01831 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -50,6 +50,9 @@ void *extract_swig_wrapped_pointer(PyObject *obj) return pointer; } +// Copy constructor for Python bindings. +SireOpenMM::EMLEEngine __copy__(const SireOpenMM::EMLEEngine &other){ return SireOpenMM::EMLEEngine(other); } + BOOST_PYTHON_MODULE(_SireOpenMM) { bp::class_ OpenMMMetaData_exposer_t("OpenMMMetaData", @@ -194,7 +197,10 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") .def("what", &EMLEEngine::what, "Call the callback") .def("typeName", &EMLEEngine::typeName, "Call the callback") - .def("call", &EMLEEngine::call, "Call the callback"); + .def("call", &EMLEEngine::call, "Call the callback") + .def( "__copy__", &__copy__) + .def( "__deepcopy__", &__copy__) + .def( "clone", &__copy__); bp::class_("EMLECallback", bp::init( From eb68d321c9e8a769902ccd105919e2814a086751 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 10:02:07 +0000 Subject: [PATCH 039/468] Create intstance of concrete class. --- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 0640a1723..f878e785b 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -741,9 +741,15 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (map.specified("qm_engine")) { - // we need to cast away constness since the OpenMM::System::addForce - // method expects a non-const pointer. - qmff = const_cast(&map["qm_engine"].value().asA()); + try + { + auto &engine = map["qm_engine"].value().asA(); + qmff = new EMLEEngine(engine); + } + catch (...) + { + throw SireError::incompatible_error(QObject::tr("Invalid QM engine!"), CODELOC); + } } // end of stage 2 - we now have the base forces From cd745ccac2cb4b1526863ea31cacee599fb8b3b5 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 11:28:55 +0000 Subject: [PATCH 040/468] Pythonize the EMLEEngine class. --- src/sire/_pythonize.py | 3 +++ src/sire/mol/_dynamics.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index 231ea05fb..1b71bd9e7 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -224,6 +224,9 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): delete_old=delete_old, ) + # Pythonize the EMLEEngine class. + _pythonize(Convert._SireOpenMM.EMLEEngine, delete_old=delete_old) + try: import lazy_import diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 3b28c10c4..875554817 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -920,7 +920,7 @@ def __init__( try: atoms_to_find = mols["property is_qm"].atoms() idxs = mols.atoms().find(atoms_to_find) - qm_engine.setAtoms(idxs) + qm_engine.set_atoms(idxs) except: raise ValueError( "Unable to set QM atoms in the engine. " From 04e7642f04642f4ef682b56c35a542bf0c710433 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 12:33:50 +0000 Subject: [PATCH 041/468] Add functionality to set atomic numbers for the QM region. --- src/sire/mol/_dynamics.py | 6 +++++ .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 2 ++ wrapper/Convert/SireOpenMM/emle.cpp | 22 ++++++++++++++++++- wrapper/Convert/SireOpenMM/emle.h | 7 ++++++ 4 files changed, 36 insertions(+), 1 deletion(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 875554817..f59a4def4 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -918,9 +918,15 @@ def __init__( # Set the global indices of the QM atoms in the engine. if qm_engine is not None and mols is not None: try: + # Work out the indices of the QM atoms. atoms_to_find = mols["property is_qm"].atoms() idxs = mols.atoms().find(atoms_to_find) qm_engine.set_atoms(idxs) + + # Work out the atomic numbers of the QM atoms. + elem_prop = map["element"] + numbers = [atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find] + qm_engine.set_numbers(numbers) except: raise ValueError( "Unable to set QM atoms in the engine. " diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index cb6e01831..b955013cb 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -195,6 +195,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setCutoff", &EMLEEngine::setCutoff, "Set the cutoff value") .def("getAtoms", &EMLEEngine::getAtoms, "Get QM atom indices") .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") + .def("getNumbers", &EMLEEngine::getNumbers, "Get QM atomic numbers") + .def("setNumbers", &EMLEEngine::setNumbers, "Set the QM atomic numbers") .def("what", &EMLEEngine::what, "Call the callback") .def("typeName", &EMLEEngine::typeName, "Call the callback") .def("call", &EMLEEngine::call, "Call the callback") diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index d4badb273..bad467723 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -82,7 +82,9 @@ EMLEEngine::EMLEEngine(bp::object py_object, SireUnits::Dimension::Length cutoff EMLEEngine::EMLEEngine(const EMLEEngine &other) : callback(other.callback), cutoff(other.cutoff), - lambda(other.lambda) + lambda(other.lambda), + atoms(other.atoms), + numbers(other.numbers) { } @@ -91,6 +93,8 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) this->callback = other.callback; this->cutoff = other.cutoff; this->lambda = other.lambda; + this->atoms = other.atoms; + this->numbers = other.numbers; return *this; } @@ -134,6 +138,16 @@ void EMLEEngine::setAtoms(QVector atoms) this->atoms = atoms; } +QVector EMLEEngine::getNumbers() const +{ + return this->numbers; +} + +void EMLEEngine::setNumbers(QVector numbers) +{ + this->numbers = numbers; +} + const char *EMLEEngine::typeName() { return QMetaType::typeName(qMetaTypeId()); @@ -186,6 +200,12 @@ double EMLEEngineImpl::computeForce( QVector> d = {{1.0, 2.0, 3.0}, {4.0, 5.0, 6.0}}; auto result = this->owner.call(a, b, c, d); + const auto ref_pos = positions[this->owner.getAtoms()[0]]; + + qDebug() << "Reference position:" << ref_pos[0] << ref_pos[1] << ref_pos[2]; + qDebug() << this->owner.getAtoms(); + qDebug() << this->owner.getNumbers(); + return 0; } diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index c2958540c..183a181e0 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -156,6 +156,12 @@ namespace SireOpenMM //! Set the list of atom indices for the QM region. void setAtoms(QVector atoms); + //! Get the atomic numbers for the atoms in the QM region. + QVector getNumbers() const; + + //! Set the atomic numbers for the atoms in the QM region. + void setNumbers(QVector numbers); + //! Return the C++ name for this class. static const char *typeName(); @@ -193,6 +199,7 @@ namespace SireOpenMM SireUnits::Dimension::Length cutoff; double lambda; QVector atoms; + QVector numbers; }; #ifdef SIRE_USE_CUSTOMCPPFORCE From 96fcf3d48778b4cf57a085b8de97ae38b3273a25 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 14:02:06 +0000 Subject: [PATCH 042/468] Add more virtual setters/getters to the base class. --- wrapper/Convert/SireOpenMM/qmmm.h | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index d8ee99350..fc9bf93f1 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -59,6 +59,12 @@ namespace SireOpenMM //! Set the list of atom indices for the QM region. virtual void setAtoms(QVector) = 0; + //! Get the atomic numbers of the atoms in the QM region. + virtual QVector getNumbers() const = 0; + + //! Set the list of atomic numbers for the QM region. + virtual void setNumbers(QVector) = 0; + protected: virtual OpenMM::ForceImpl *createImpl() const = 0; }; From 845a733c7581b5da41b92ba5411827e84539b3d0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 15:21:38 +0000 Subject: [PATCH 043/468] Add computeForce implementation. --- src/sire/mol/_dynamics.py | 5 + .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 2 + wrapper/Convert/SireOpenMM/emle.cpp | 164 ++++++++++++++++-- wrapper/Convert/SireOpenMM/emle.h | 7 + wrapper/Convert/SireOpenMM/qmmm.h | 6 + 5 files changed, 171 insertions(+), 13 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index f59a4def4..bc37060b0 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -927,6 +927,11 @@ def __init__( elem_prop = map["element"] numbers = [atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find] qm_engine.set_numbers(numbers) + + # Work out the atomic charge for all atoms in the system. + charge_prop = map["charge"] + charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] + qm_engine.set_charges(charges) except: raise ValueError( "Unable to set QM atoms in the engine. " diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index b955013cb..4cf1e3323 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -197,6 +197,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") .def("getNumbers", &EMLEEngine::getNumbers, "Get QM atomic numbers") .def("setNumbers", &EMLEEngine::setNumbers, "Set the QM atomic numbers") + .def("getCharges", &EMLEEngine::getCharges, "Get the atomic charges") + .def("setCharges", &EMLEEngine::setCharges, "Set the atomic charges") .def("what", &EMLEEngine::what, "Call the callback") .def("typeName", &EMLEEngine::typeName, "Call the callback") .def("call", &EMLEEngine::call, "Call the callback") diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index bad467723..28a167375 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -26,9 +26,14 @@ * \*********************************************/ +#include "SireMaths/vector.h" +#include "SireVol/triclinicbox.h" + #include "emle.h" +using namespace SireMaths; using namespace SireOpenMM; +using namespace SireVol; class GILLock { @@ -84,7 +89,8 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : cutoff(other.cutoff), lambda(other.lambda), atoms(other.atoms), - numbers(other.numbers) + numbers(other.numbers), + charges(other.charges) { } @@ -95,6 +101,7 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) this->lambda = other.lambda; this->atoms = other.atoms; this->numbers = other.numbers; + this->charges = other.charges; return *this; } @@ -148,6 +155,16 @@ void EMLEEngine::setNumbers(QVector numbers) this->numbers = numbers; } +QVector EMLEEngine::getCharges() const +{ + return this->charges; +} + +void EMLEEngine::setCharges(QVector charges) +{ + this->charges = charges; +} + const char *EMLEEngine::typeName() { return QMetaType::typeName(qMetaTypeId()); @@ -191,22 +208,143 @@ double EMLEEngineImpl::computeForce( const std::vector &positions, std::vector &forces) { - qDebug() << "Hello from C++!"; + // Get the current box vectors. (OpenMM units, i.e. nm) + OpenMM::Vec3 omm_box_x, omm_box_y, omm_box_z; + context.getPeriodicBoxVectors(omm_box_x, omm_box_y, omm_box_z); + + // Convert to Sire vectors. (Sire units, i.e. Angstrom) + Vector box_x(0.1*omm_box_x[0], 0.1*omm_box_x[1], 0.1*omm_box_x[2]); + Vector box_y(0.1*omm_box_y[0], 0.1*omm_box_y[1], 0.1*omm_box_y[2]); + Vector box_z(0.1*omm_box_z[0], 0.1*omm_box_z[1], 0.1*omm_box_z[2]); + + // Create a triclinic space. + TriclinicBox space(box_x, box_y, box_z); + + // Initialise a vector to hold the current positions for the QM atoms. + QVector> xyz_qm(this->owner.getAtoms().size()); + QVector xyz_qm_vec(this->owner.getAtoms().size()); + + // Loop over all atoms in the QM region, get the OpenMM posistion, + // then store it in Angstroms. We also store in Sire Vector format + // so that we can use the Sire space to compute the distances. + int i = 0; + for (const auto &idx : this->owner.getAtoms()) + { + const auto &omm_pos = positions[idx]; + QVector pos = {0.1*omm_pos[0], 0.1*omm_pos[1], 0.1*omm_pos[2]}; + Vector vec(pos[0], pos[1], pos[2]); + xyz_qm[i] = pos; + xyz_qm_vec[i] = vec; + i++; + } + + // Next we need to work out the position of the MM atoms within the cutoff, + // along with their charges. Here the cutoff is applied by including MM atoms + // within the cutoff distance from any QM atom. + + // Initialise a vector to hold the current positions for the MM atoms. + QVector> xyz_mm; + + // Initialise a vector to hold the charges for the MM atoms. + QVector charges_mm; + + // Initialise a list to hold the indices of the MM atoms. + QVector idx_mm; + + // Store the cutoff as a double. + const auto cutoff = this->owner.getCutoff().value(); + + // Loop over all of the OpenMM positions. + i = 0; + for (const auto &pos : positions) + { + // Exclude QM atoms. + if (not this->owner.getAtoms().contains(i)) + { + // Whether to add the atom, i.e. it is an MM atom and is + // within the cutoff. + bool to_add = false; + + // Store the position as a Vector. + const Vector mm_vec(0.1*pos[0], 0.1*pos[1], 0.1*pos[2]); + + // Loop over all of the QM atoms. + for (const auto &qm_vec : xyz_qm_vec) + { + if (space.calcDist(mm_vec, qm_vec) < cutoff) + { + // The current MM atom is within the cutoff, add it. + to_add = true; + break; + } + } + + // Store the MM atom information. + if (to_add) + { + QVector xyz = {mm_vec[0], mm_vec[1], mm_vec[2]}; + xyz_mm.append(xyz); + charges_mm.append(this->owner.getCharges()[i]); + idx_mm.append(i); + } + } + + // Update the atom index. + i++; + } + + // Call the callback. + auto result = this->owner.call( + this->owner.getNumbers(), + charges_mm, + xyz_qm, + xyz_mm + ); - // Create some dummy data so that we can test the Python callback. - QVector a = {1, 2, 3}; - QVector b = {1.0, 2.0, 3.0}; - QVector> c = {{1.0, 2.0, 3.0}, {4.0, 5.0, 6.0}}; - QVector> d = {{1.0, 2.0, 3.0}, {4.0, 5.0, 6.0}}; - auto result = this->owner.call(a, b, c, d); + // Extract the results. This will automatically be returned in + // OpenMM units. + auto energy = result.get<0>(); + auto forces_qm = result.get<1>(); + auto forces_mm = result.get<2>(); - const auto ref_pos = positions[this->owner.getAtoms()[0]]; + // Now update the force vector. - qDebug() << "Reference position:" << ref_pos[0] << ref_pos[1] << ref_pos[2]; - qDebug() << this->owner.getAtoms(); - qDebug() << this->owner.getNumbers(); + // First the QM atoms. + i = 0; + for (const auto &force : forces_qm) + { + // Get the index of the atom. + const auto idx = this->owner.getAtoms()[i]; - return 0; + // Convert to OpenMM format. + OpenMM::Vec3 omm_force(force[0], force[1], force[2]); + + // Update the force vector. + forces[idx] = omm_force; + + // Update the atom index. + i++; + } + + // Now the MM atoms. + i = 0; + for (const auto &force : forces_mm) + { + // Get the index of the atom. + const auto idx = idx_mm[i]; + + // Convert to OpenMM format. + OpenMM::Vec3 omm_force(force[0], force[1], force[2]); + + // Update the force vector. + forces[idx] = omm_force; + + // Update the atom index. + i++; + } + + // Finally, return the energy. + return energy; } boost::tuple>, QVector>> diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 183a181e0..6f872a6bf 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -162,6 +162,12 @@ namespace SireOpenMM //! Set the atomic numbers for the atoms in the QM region. void setNumbers(QVector numbers); + //! Get the atomic charges of all atoms in the system. + QVector getCharges() const; + + //! Set the atomic charges of all atoms in the system. + void setCharges(QVector charges); + //! Return the C++ name for this class. static const char *typeName(); @@ -200,6 +206,7 @@ namespace SireOpenMM double lambda; QVector atoms; QVector numbers; + QVector charges; }; #ifdef SIRE_USE_CUSTOMCPPFORCE diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index fc9bf93f1..5d1bc6b28 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -65,6 +65,12 @@ namespace SireOpenMM //! Set the list of atomic numbers for the QM region. virtual void setNumbers(QVector) = 0; + //! Get the atomic charges of all atoms in the system. + virtual QVector getCharges() const = 0; + + //! Set the atomic charges of all atoms in the system. + virtual void setCharges(QVector) = 0; + protected: virtual OpenMM::ForceImpl *createImpl() const = 0; }; From b8a3b0c075f79305feb0f24e66775bcee36affd0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 22 Nov 2023 16:13:09 +0000 Subject: [PATCH 044/468] Blacken. --- src/sire/mol/_dynamics.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index bc37060b0..253da0362 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -925,12 +925,17 @@ def __init__( # Work out the atomic numbers of the QM atoms. elem_prop = map["element"] - numbers = [atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find] + numbers = [ + atom.property(f"{elem_prop}").num_protons() + for atom in atoms_to_find + ] qm_engine.set_numbers(numbers) # Work out the atomic charge for all atoms in the system. charge_prop = map["charge"] - charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] + charges = [ + atom.property(f"{charge_prop}").value() for atom in mols.atoms() + ] qm_engine.set_charges(charges) except: raise ValueError( From e79ebd8b0dc2d63c57c5c4eba3d2a28702d98bd6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 23 Nov 2023 09:34:44 +0000 Subject: [PATCH 045/468] Clarify units in docstrings and apply minor optimisations. --- wrapper/Convert/SireOpenMM/emle.cpp | 31 +++++++++++++++-------------- wrapper/Convert/SireOpenMM/emle.h | 28 ++++++++++++++++---------- 2 files changed, 33 insertions(+), 26 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 28a167375..024af90f3 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -33,6 +33,7 @@ using namespace SireMaths; using namespace SireOpenMM; +using namespace SireUnits; using namespace SireVol; class GILLock @@ -209,16 +210,17 @@ double EMLEEngineImpl::computeForce( std::vector &forces) { // Get the current box vectors. (OpenMM units, i.e. nm) - OpenMM::Vec3 omm_box_x, omm_box_y, omm_box_z; - context.getPeriodicBoxVectors(omm_box_x, omm_box_y, omm_box_z); - - // Convert to Sire vectors. (Sire units, i.e. Angstrom) - Vector box_x(0.1*omm_box_x[0], 0.1*omm_box_x[1], 0.1*omm_box_x[2]); - Vector box_y(0.1*omm_box_y[0], 0.1*omm_box_y[1], 0.1*omm_box_y[2]); - Vector box_z(0.1*omm_box_z[0], 0.1*omm_box_z[1], 0.1*omm_box_z[2]); - - // Create a triclinic space. - TriclinicBox space(box_x, box_y, box_z); + OpenMM::Vec3 box_x, box_y, box_z; + context.getPeriodicBoxVectors(box_x, box_y, box_z); + + // Create a triclinic space. Internally, Sire would assume lengths are in + // Angstroms, but we will just convert the cutoff when comparing distances + // in this space. + TriclinicBox space( + Vector(box_x[0], box_x[1], box_x[2]), + Vector(box_y[0], box_y[1], box_y[2]), + Vector(box_z[0], box_z[1], box_z[2]) + ); // Initialise a vector to hold the current positions for the QM atoms. QVector> xyz_qm(this->owner.getAtoms().size()); @@ -231,7 +233,7 @@ double EMLEEngineImpl::computeForce( for (const auto &idx : this->owner.getAtoms()) { const auto &omm_pos = positions[idx]; - QVector pos = {0.1*omm_pos[0], 0.1*omm_pos[1], 0.1*omm_pos[2]}; + QVector pos = {omm_pos[0], omm_pos[1], omm_pos[2]}; Vector vec(pos[0], pos[1], pos[2]); xyz_qm[i] = pos; xyz_qm_vec[i] = vec; @@ -251,8 +253,8 @@ double EMLEEngineImpl::computeForce( // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; - // Store the cutoff as a double. - const auto cutoff = this->owner.getCutoff().value(); + // Store the cutoff as a double in nanometers. + const auto cutoff = this->owner.getCutoff().to(nanometer); // Loop over all of the OpenMM positions. i = 0; @@ -265,8 +267,7 @@ double EMLEEngineImpl::computeForce( // within the cutoff. bool to_add = false; - // Store the position as a Vector. - const Vector mm_vec(0.1*pos[0], 0.1*pos[1], 0.1*pos[2]); + const Vector mm_vec(pos[0], pos[1], pos[2]); // Loop over all of the QM atoms. for (const auto &qm_vec : xyz_qm_vec) diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 6f872a6bf..b45996e4f 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -69,9 +69,9 @@ namespace SireOpenMM \param callback The name of a callback method that take the following arguments: - numbers_qm: A list of atomic numbers for the atoms in the ML region. - - charges_mm: A list of the MM charges. - - xyz_qm: A vector of positions for the atoms in the ML region. - - xyz_mm: A vector of positions for the atoms in the MM region. + - charges_mm: A list of the MM charges in mod electron charge. + - xyz_qm: A vector of positions for the atoms in the ML region in nanometers. + - xyz_mm: A vector of positions for the atoms in the MM region in nanometers. */ EMLECallback(bp::object, QString callback="_sire_callback"); @@ -80,16 +80,19 @@ namespace SireOpenMM A vector of atomic numbers for the atoms in the ML region. \param charges_mm - A vector of the charges on the MM atoms. + A vector of the charges on the MM atoms in mod electron charge. \param xyz_qm - A vector of positions for the atoms in the ML region. + A vector of positions for the atoms in the ML region in nanometers. \param xyz_mm - A vector of positions for the atoms in the MM region. + A vector of positions for the atoms in the MM region in nanometers. \returns - A vector of forces for the QM and MM atoms. + A tuple containing: + - The energy in kJ/mol. + - A vector of forces for the QM atoms in kJ/mol/nm. + - A vector of forces for the MM atoms in kJ/mol/nm. */ boost::tuple>, QVector>> call( QVector numbers_qm, @@ -179,16 +182,19 @@ namespace SireOpenMM A vector of atomic numbers for the atoms in the ML region. \param charges_mm - A vector of the charges on the MM atoms. + A vector of the charges on the MM atoms in mod electron charge. \param xyz_qm - A vector of positions for the atoms in the ML region. + A vector of positions for the atoms in the ML region in nanometers. \param xyz_mm - A vector of positions for the atoms in the MM region. + A vector of positions for the atoms in the MM region in nanometers. \returns - A vector of forces for the QM and MM atoms. + A tuple containing: + - The energy in kJ/mol. + - A vector of forces for the QM atoms in kJ/mol/nm. + - A vector of forces for the MM atoms in kJ/mol/nm. */ boost::tuple>, QVector>> call( QVector numbers_qm, From 90197f78a42d5d3d6f5d72778c1220b8895b681f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 23 Nov 2023 10:46:16 +0000 Subject: [PATCH 046/468] Add functionality for building sire-emle package. --- .github/workflows/emle.yaml | 72 +++++++++++++++++++++++ actions/update_recipe.py | 13 ++++- requirements_emle.txt | 13 +++++ setup.py | 111 ++++++++++++++++++++++++------------ 4 files changed, 169 insertions(+), 40 deletions(-) create mode 100644 .github/workflows/emle.yaml create mode 100644 requirements_emle.txt diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml new file mode 100644 index 000000000..b61365b7a --- /dev/null +++ b/.github/workflows/emle.yaml @@ -0,0 +1,72 @@ +name: Release sire-emle + +# Note that push and pull-request builds are automatically +# now skipped by GitHub if +# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip] +# are in the commit message. We don't need to check for this ourselves. + +# Only allow this action to run on a manual run. +# We should specify when run whether or not we want +# to upload the packages at the end. +on: + workflow_dispatch: + inputs: + upload_packages: + description: "Upload packages to anaconda (yes/no)?" + required: true + default: "no" +jobs: + build: + name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) + runs-on: ${{ matrix.platform.os }} + strategy: + max-parallel: 9 + fail-fast: false + matrix: + python-version: ["3.10"] + platform: + - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } + - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + environment: + name: sire-build + defaults: + run: + shell: ${{ matrix.platform.shell }} + env: + SIRE_DONT_PHONEHOME: 1 + SIRE_SILENT_PHONEHOME: 1 + SIRE_EMLE: 1 + REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" + steps: + # + - uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + python-version: ${{ matrix.python-version }} + activate-environment: sire_build + miniforge-version: latest + miniforge-variant: Mambaforge + use-mamba: true + # + - name: Clone the feature_emle branch + run: git clone -b feature_emle https://github.com/openbiosim/sire sire + # + - name: Setup Conda + run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + # + - name: Update Conda recipe + run: python ${{ github.workspace }}/sire/actions/update_recipe.py + # + - name: Prepare build location + run: mkdir ${{ github.workspace }}/build + # + - name: Build Conda package using mamba build + run: conda mambabuild -c conda-forge -c conda-forge/label/openmm_rc -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + # + - name: Upload Conda package + # upload to the 'test' channel + run: python ${{ github.workspace }}/sire/actions/upload_package.py emle + env: + SRC_DIR: ${{ github.workspace }}/sire + ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} + if: github.event.inputs.upload_packages == 'yes' diff --git a/actions/update_recipe.py b/actions/update_recipe.py index 41e93d5cf..deade331f 100644 --- a/actions/update_recipe.py +++ b/actions/update_recipe.py @@ -9,6 +9,9 @@ from parse_requirements import parse_requirements +# Check whether we are building a sire-emle package. +is_emle = os.environ.get("SIRE_EMLE", "False") + # has the user supplied an environment.yml file? if len(sys.argv) > 1: from pathlib import Path @@ -44,8 +47,13 @@ print(host_reqs) run_reqs = parse_requirements(os.path.join(srcdir, "requirements_run.txt")) print(run_reqs) -bss_reqs = parse_requirements(os.path.join(srcdir, "requirements_bss.txt")) -print(bss_reqs) +if not is_emle: + bss_reqs = parse_requirements(os.path.join(srcdir, "requirements_bss.txt")) + print(bss_reqs) + emle_reqs = [] +else: + emle_reqs = parse_requirements(os.path.join(srcdir, "requirements_emle.txt")) + print(emle_reqs) test_reqs = parse_requirements(os.path.join(srcdir, "requirements_test.txt")) @@ -222,6 +230,7 @@ def check_reqs(reqs0, reqs1): build_reqs = dep_lines(check_reqs(build_reqs, env_reqs)) host_reqs = combine(host_reqs, bss_reqs) +host_reqs = combine(host_reqs, emle_reqs) host_reqs = dep_lines(combine(host_reqs, env_reqs)) run_reqs = dep_lines(check_reqs(run_reqs, env_reqs)) test_reqs = dep_lines(check_reqs(test_reqs, env_reqs)) diff --git a/requirements_emle.txt b/requirements_emle.txt new file mode 100644 index 000000000..1eb7109b6 --- /dev/null +++ b/requirements_emle.txt @@ -0,0 +1,13 @@ +ambertools +ase +deepmd-kit +eigen +pip +pybind11 +pytorch +python < 3.11 +torchani +xtb-python + +gcc< 13 ; sys_platform == "linux" +gxx< 13 ; sys_platform == "linux" diff --git a/setup.py b/setup.py index de547447a..17537e862 100644 --- a/setup.py +++ b/setup.py @@ -261,6 +261,12 @@ def parse_args(): help="Install BioSimSpace's dependencies too. This helps ensure " "compatibility between Sire's and BioSimSpace's dependencies.", ) + parser.add_argument( + "--install-emle-deps", + action="store_true", + default=False, + help="Install emle-engine's dependencies too.", + ) parser.add_argument( "--skip-deps", action="store_true", @@ -323,7 +329,7 @@ def _add_to_dependencies(dependencies, lines): _is_conda_prepped = False -def conda_install(dependencies, install_bss_reqs=False): +def conda_install(dependencies, install_bss_reqs=False, install_emle_reqs=False): """Install the passed list of dependencies using conda""" conda_exe = conda @@ -332,9 +338,7 @@ def conda_install(dependencies, install_bss_reqs=False): if not _is_conda_prepped: if install_bss_reqs: - cmd = ( - "%s config --prepend channels openbiosim/label/dev" % conda_exe - ) + cmd = "%s config --prepend channels openbiosim/label/dev" % conda_exe print("Activating openbiosim channel channel using: '%s'" % cmd) status = subprocess.run(cmd.split()) if status.returncode != 0: @@ -384,8 +388,46 @@ def conda_install(dependencies, install_bss_reqs=False): print("from running again. Please re-execute this script.") sys.exit(-1) + # Install additional requirements for EMLE. + if install_emle_reqs: + # OpenMM 8.1.0beta. + cmd = [ + "mamba", + "install", + "--yes", + "-c", + "conda-forge/label/openmm_rc", + "openmm=8.1.0beta", + ] + status = subprocess.run(cmd) + if status.returncode != 0: + print("Something went wrong installing OpenMM 8.1.0beta!") + sys.exit(-1) + + # librascal. + cmd = [ + "pip", + "install", + "git+https://github.com/lab-cosmo/librascal.git", + ] + status = subprocess.run(cmd) + if status.returncode != 0: + print("Something went wrong installing librascal!") + sys.exit(-1) + + # emle-engine. + cmd = [ + "pip", + "install", + "git+https://github.com/chemle/emle-engine.git", + ] + status = subprocess.run(cmd) + if status.returncode != 0: + print("Something went wrong installing emle-engine!") + sys.exit(-1) + -def install_requires(install_bss_reqs=False): +def install_requires(install_bss_reqs=False, install_emle_reqs=False): """Installs all of the dependencies. This can safely be called multiple times, as it will cache the result to prevent future installs taking too long @@ -393,9 +435,7 @@ def install_requires(install_bss_reqs=False): print(f"Installing requirements for {platform_string}") if not os.path.exists(conda): - print( - "\nSire can only be installed into a conda or miniconda environment." - ) + print("\nSire can only be installed into a conda or miniconda environment.") print( "Please install conda, miniconda, miniforge or similar, then " "activate the conda environment, then rerun this installation " @@ -408,7 +448,7 @@ def install_requires(install_bss_reqs=False): if mamba is None: # install mamba first! - conda_install(["mamba"], install_bss_reqs) + conda_install(["mamba"], install_bss_reqs, install_emle_reqs) mamba = find_mamba() try: @@ -417,14 +457,14 @@ def install_requires(install_bss_reqs=False): except Exception: # this didn't import - maybe we are missing pip-requirements-parser print("Installing pip-requirements-parser") - conda_install(["pip-requirements-parser"], install_bss_reqs) + conda_install( + ["pip-requirements-parser"], install_bss_reqs, install_emle_reqs=False + ) try: from parse_requirements import parse_requirements except ImportError as e: print("\n\n[ERROR] ** You need to install pip-requirements-parser") - print( - "Run `conda install -c conda-forge pip-requirements-parser\n\n" - ) + print("Run `conda install -c conda-forge pip-requirements-parser\n\n") raise e reqs = parse_requirements("requirements_host.txt") @@ -434,8 +474,12 @@ def install_requires(install_bss_reqs=False): bss_reqs = parse_requirements("requirements_bss.txt") reqs = reqs + bss_reqs + if install_emle_reqs: + emle_reqs = parse_requirements("requirements_emle.txt") + reqs = reqs + emle_reqs + dependencies = build_reqs + reqs - conda_install(dependencies, install_bss_reqs) + conda_install(dependencies, install_bss_reqs, install_emle_reqs) def add_default_cmake_defs(cmake_defs, ncores): @@ -481,10 +525,7 @@ def _get_build_ext(): else: ext = "" - return ( - os.path.basename(conda_base.replace(" ", "_").replace(".", "_")) - + ext - ) + return os.path.basename(conda_base.replace(" ", "_").replace(".", "_")) + ext def _get_bin_dir(): @@ -533,12 +574,8 @@ def build(ncores: int = 1, npycores: int = 1, coredefs=[], pydefs=[]): print(f"{CC} => {CC_bin}") if CXX_bin is None or CC_bin is None: - print( - "Cannot find the compilers requested by conda-build in the PATH" - ) - print( - "Please check that the compilers are installed and available." - ) + print("Cannot find the compilers requested by conda-build in the PATH") + print("Please check that the compilers are installed and available.") sys.exit(-1) # use the full paths, in case CMake struggles @@ -669,9 +706,7 @@ def build(ncores: int = 1, npycores: int = 1, coredefs=[], pydefs=[]): # Compile and install, as need to install to compile the wrappers make_args = make_cmd(ncores, True) - print( - 'NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args)) - ) + print('NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args))) sys.stdout.flush() status = subprocess.run([cmake, "--build", ".", "--target", *make_args]) @@ -735,9 +770,7 @@ def build(ncores: int = 1, npycores: int = 1, coredefs=[], pydefs=[]): # Just compile the wrappers make_args = make_cmd(npycores, False) - print( - 'NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args)) - ) + print('NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args))) sys.stdout.flush() status = subprocess.run([cmake, "--build", ".", "--target", *make_args]) @@ -810,9 +843,7 @@ def install_module(ncores: int = 1): make_args = make_cmd(ncores, True) # Now that cmake has run, we can compile and install wrapper - print( - 'NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args)) - ) + print('NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args))) sys.stdout.flush() status = subprocess.run([cmake, "--build", ".", "--target", *make_args]) @@ -852,9 +883,7 @@ def install(ncores: int = 1, npycores: int = 1): # Now install the wrappers make_args = make_cmd(npycores, True) - print( - 'NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args)) - ) + print('NOW RUNNING "%s" --build . --target %s' % (cmake, " ".join(make_args))) sys.stdout.flush() status = subprocess.run([cmake, "--build", ".", "--target", *make_args]) @@ -875,6 +904,10 @@ def install(ncores: int = 1, npycores: int = 1): sys.exit(-1) install_bss = args.install_bss_deps + install_emle = args.install_emle_deps + + if install_emle and is_windows: + raise NotImplementedError("EMLE is current not supported on Windows") action = args.action[0] @@ -890,7 +923,9 @@ def install(ncores: int = 1, npycores: int = 1): if action == "install": if not (args.skip_deps or args.skip_build): - install_requires(install_bss_reqs=install_bss) + install_requires( + install_bss_reqs=install_bss, install_emle_reqs=install_emle + ) if not args.skip_build: build( @@ -914,7 +949,7 @@ def install(ncores: int = 1, npycores: int = 1): ) elif action == "install_requires": - install_requires(install_bss_reqs=install_bss) + install_requires(install_bss_reqs=install_bss, install_emle_reqs=install_emle) elif action == "install_module": install_module(ncores=args.ncores[0]) From f5bd7c11f21bb7a7d08e8ecfdcc35c64eaec9752 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 23 Nov 2023 12:20:46 +0000 Subject: [PATCH 047/468] Pass positions to emle-engine in Angstrom. --- wrapper/Convert/SireOpenMM/emle.cpp | 21 +++++++++------------ wrapper/Convert/SireOpenMM/emle.h | 12 ++++++------ 2 files changed, 15 insertions(+), 18 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 024af90f3..519b592a9 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -33,7 +33,6 @@ using namespace SireMaths; using namespace SireOpenMM; -using namespace SireUnits; using namespace SireVol; class GILLock @@ -209,17 +208,15 @@ double EMLEEngineImpl::computeForce( const std::vector &positions, std::vector &forces) { - // Get the current box vectors. (OpenMM units, i.e. nm) + // Get the current box vectors in nanometers. OpenMM::Vec3 box_x, box_y, box_z; context.getPeriodicBoxVectors(box_x, box_y, box_z); - // Create a triclinic space. Internally, Sire would assume lengths are in - // Angstroms, but we will just convert the cutoff when comparing distances - // in this space. + // Create a triclinic space, converting to Angstrom. TriclinicBox space( - Vector(box_x[0], box_x[1], box_x[2]), - Vector(box_y[0], box_y[1], box_y[2]), - Vector(box_z[0], box_z[1], box_z[2]) + Vector(0.1*box_x[0], 0.1*box_x[1], 0.1*box_x[2]), + Vector(0.1*box_y[0], 0.1*box_y[1], 0.1*box_y[2]), + Vector(0.1*box_z[0], 0.1*box_z[1], 0.1*box_z[2]) ); // Initialise a vector to hold the current positions for the QM atoms. @@ -233,7 +230,7 @@ double EMLEEngineImpl::computeForce( for (const auto &idx : this->owner.getAtoms()) { const auto &omm_pos = positions[idx]; - QVector pos = {omm_pos[0], omm_pos[1], omm_pos[2]}; + QVector pos = {0.1*omm_pos[0], 0.1*omm_pos[1], 0.1*omm_pos[2]}; Vector vec(pos[0], pos[1], pos[2]); xyz_qm[i] = pos; xyz_qm_vec[i] = vec; @@ -253,8 +250,8 @@ double EMLEEngineImpl::computeForce( // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; - // Store the cutoff as a double in nanometers. - const auto cutoff = this->owner.getCutoff().to(nanometer); + // Store the cutoff as a double in Angstom. + const auto cutoff = this->owner.getCutoff().value(); // Loop over all of the OpenMM positions. i = 0; @@ -267,7 +264,7 @@ double EMLEEngineImpl::computeForce( // within the cutoff. bool to_add = false; - const Vector mm_vec(pos[0], pos[1], pos[2]); + const Vector mm_vec(0.1*pos[0], 0.1*pos[1], 0.1*pos[2]); // Loop over all of the QM atoms. for (const auto &qm_vec : xyz_qm_vec) diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index b45996e4f..f9100b313 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -70,8 +70,8 @@ namespace SireOpenMM The name of a callback method that take the following arguments: - numbers_qm: A list of atomic numbers for the atoms in the ML region. - charges_mm: A list of the MM charges in mod electron charge. - - xyz_qm: A vector of positions for the atoms in the ML region in nanometers. - - xyz_mm: A vector of positions for the atoms in the MM region in nanometers. + - xyz_qm: A vector of positions for the atoms in the ML region in Angstrom. + - xyz_mm: A vector of positions for the atoms in the MM region in Angstrom. */ EMLECallback(bp::object, QString callback="_sire_callback"); @@ -83,10 +83,10 @@ namespace SireOpenMM A vector of the charges on the MM atoms in mod electron charge. \param xyz_qm - A vector of positions for the atoms in the ML region in nanometers. + A vector of positions for the atoms in the ML region in Angstrom. \param xyz_mm - A vector of positions for the atoms in the MM region in nanometers. + A vector of positions for the atoms in the MM region in Angstrom. \returns A tuple containing: @@ -185,10 +185,10 @@ namespace SireOpenMM A vector of the charges on the MM atoms in mod electron charge. \param xyz_qm - A vector of positions for the atoms in the ML region in nanometers. + A vector of positions for the atoms in the ML region in Angstrom. \param xyz_mm - A vector of positions for the atoms in the MM region in nanometers. + A vector of positions for the atoms in the MM region in Angstrom. \returns A tuple containing: From db0f0d281abf714588032b455b7e28226ac7d464 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 23 Nov 2023 15:45:08 +0000 Subject: [PATCH 048/468] Fix unit conversion. --- wrapper/Convert/SireOpenMM/emle.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 519b592a9..0992cb8e7 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -214,9 +214,9 @@ double EMLEEngineImpl::computeForce( // Create a triclinic space, converting to Angstrom. TriclinicBox space( - Vector(0.1*box_x[0], 0.1*box_x[1], 0.1*box_x[2]), - Vector(0.1*box_y[0], 0.1*box_y[1], 0.1*box_y[2]), - Vector(0.1*box_z[0], 0.1*box_z[1], 0.1*box_z[2]) + Vector(10*box_x[0], 10*box_x[1], 10*box_x[2]), + Vector(10*box_y[0], 10*box_y[1], 10*box_y[2]), + Vector(10*box_z[0], 10*box_z[1], 10*box_z[2]) ); // Initialise a vector to hold the current positions for the QM atoms. @@ -230,7 +230,7 @@ double EMLEEngineImpl::computeForce( for (const auto &idx : this->owner.getAtoms()) { const auto &omm_pos = positions[idx]; - QVector pos = {0.1*omm_pos[0], 0.1*omm_pos[1], 0.1*omm_pos[2]}; + QVector pos = {10*omm_pos[0], 10*omm_pos[1], 10*omm_pos[2]}; Vector vec(pos[0], pos[1], pos[2]); xyz_qm[i] = pos; xyz_qm_vec[i] = vec; @@ -264,7 +264,7 @@ double EMLEEngineImpl::computeForce( // within the cutoff. bool to_add = false; - const Vector mm_vec(0.1*pos[0], 0.1*pos[1], 0.1*pos[2]); + const Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); // Loop over all of the QM atoms. for (const auto &qm_vec : xyz_qm_vec) From 7441408761132e1ba492183869feffe412016681 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 23 Nov 2023 16:24:12 +0000 Subject: [PATCH 049/468] Use minimum image position with respect to reference QM atom. --- wrapper/Convert/SireOpenMM/emle.cpp | 37 +++++++++++++++++++++-------- 1 file changed, 27 insertions(+), 10 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 0992cb8e7..3a7a93e21 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -223,23 +223,35 @@ double EMLEEngineImpl::computeForce( QVector> xyz_qm(this->owner.getAtoms().size()); QVector xyz_qm_vec(this->owner.getAtoms().size()); - // Loop over all atoms in the QM region, get the OpenMM posistion, - // then store it in Angstroms. We also store in Sire Vector format - // so that we can use the Sire space to compute the distances. + // Loop over all atoms in the QM region, get the OpenMM position, then + // store it in Angstroms. We also store in Sire Vector format so that + // we can use the Sire space to compute the distances. Positions are + // stored using the minimum image conventin with respect to the first + // QM atom. + + // Get the reference position. + const auto ref_omm_pos = positions[this->owner.getAtoms()[0]]; + + // Convert to Sire Vector format. + const Vector ref_vec(10*ref_omm_pos[0], 10*ref_omm_pos[1], 10*ref_omm_pos[2]); + + // Loop over all of the QM atoms and store the positions with respect to + // the reference position. int i = 0; for (const auto &idx : this->owner.getAtoms()) { - const auto &omm_pos = positions[idx]; - QVector pos = {10*omm_pos[0], 10*omm_pos[1], 10*omm_pos[2]}; - Vector vec(pos[0], pos[1], pos[2]); - xyz_qm[i] = pos; - xyz_qm_vec[i] = vec; + const auto &pos = positions[idx]; + const Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + const auto qm_vec_min = space.getMinimumImage(qm_vec, ref_vec); + xyz_qm[i] = QVector({qm_vec_min[0], qm_vec_min[1], qm_vec_min[2]}); + xyz_qm_vec[i] = qm_vec_min; i++; } // Next we need to work out the position of the MM atoms within the cutoff, // along with their charges. Here the cutoff is applied by including MM atoms - // within the cutoff distance from any QM atom. + // within the cutoff distance from any QM atom. Again we store the positions + // using the minimum image with respect to the reference position. // Initialise a vector to hold the current positions for the MM atoms. QVector> xyz_mm; @@ -280,8 +292,13 @@ double EMLEEngineImpl::computeForce( // Store the MM atom information. if (to_add) { - QVector xyz = {mm_vec[0], mm_vec[1], mm_vec[2]}; + // Work out the minimum image position with respect to the + // first QM atom and append to the vector. + const auto mm_vec_min = space.getMinimumImage(mm_vec, ref_vec); + QVector xyz = {mm_vec_min[0], mm_vec_min[1], mm_vec_min[2]}; xyz_mm.append(xyz); + + // Add the charge and index. charges_mm.append(this->owner.getCharges()[i]); idx_mm.append(i); } From 5aef3d362fba33716e59885f7f980c701ed266e0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 24 Nov 2023 11:01:01 +0000 Subject: [PATCH 050/468] Fix wrapping of atomic positions. --- wrapper/Convert/SireOpenMM/emle.cpp | 42 ++++++++++++++++++++--------- 1 file changed, 29 insertions(+), 13 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 3a7a93e21..345251590 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -219,30 +219,45 @@ double EMLEEngineImpl::computeForce( Vector(10*box_z[0], 10*box_z[1], 10*box_z[2]) ); + // Store the QM atom indices. + const auto qm_atoms = this->owner.getAtoms(); + // Initialise a vector to hold the current positions for the QM atoms. - QVector> xyz_qm(this->owner.getAtoms().size()); - QVector xyz_qm_vec(this->owner.getAtoms().size()); + QVector> xyz_qm(qm_atoms.size()); + QVector xyz_qm_vec(qm_atoms.size()); // Loop over all atoms in the QM region, get the OpenMM position, then // store it in Angstroms. We also store in Sire Vector format so that // we can use the Sire space to compute the distances. Positions are - // stored using the minimum image conventin with respect to the first - // QM atom. + // stored using the minimum image convention with respect to the center + // of geometry of the QM atoms. - // Get the reference position. + // Get the reference position. (First QM atom.) const auto ref_omm_pos = positions[this->owner.getAtoms()[0]]; // Convert to Sire Vector format. - const Vector ref_vec(10*ref_omm_pos[0], 10*ref_omm_pos[1], 10*ref_omm_pos[2]); + Vector ref_vec(10*ref_omm_pos[0], 10*ref_omm_pos[1], 10*ref_omm_pos[2]); + + // Work out the center of geometry of the QM atoms. + int i = 0; + Vector center; + for (const auto &idx : qm_atoms) + { + const auto &pos = positions[idx]; + Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + center += space.getMinimumImage(qm_vec, ref_vec); + i++; + } + center /= i; // Loop over all of the QM atoms and store the positions with respect to // the reference position. - int i = 0; - for (const auto &idx : this->owner.getAtoms()) + i = 0; + for (const auto &idx : qm_atoms) { const auto &pos = positions[idx]; - const Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); - const auto qm_vec_min = space.getMinimumImage(qm_vec, ref_vec); + Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + const auto qm_vec_min = space.getMinimumImage(qm_vec, center); xyz_qm[i] = QVector({qm_vec_min[0], qm_vec_min[1], qm_vec_min[2]}); xyz_qm_vec[i] = qm_vec_min; i++; @@ -270,12 +285,13 @@ double EMLEEngineImpl::computeForce( for (const auto &pos : positions) { // Exclude QM atoms. - if (not this->owner.getAtoms().contains(i)) + if (not qm_atoms.contains(i)) { // Whether to add the atom, i.e. it is an MM atom and is // within the cutoff. bool to_add = false; + // Current MM atom position in Sire Vector format. const Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); // Loop over all of the QM atoms. @@ -293,8 +309,8 @@ double EMLEEngineImpl::computeForce( if (to_add) { // Work out the minimum image position with respect to the - // first QM atom and append to the vector. - const auto mm_vec_min = space.getMinimumImage(mm_vec, ref_vec); + // reference positions and add to the vector. + const auto mm_vec_min = space.getMinimumImage(mm_vec, center); QVector xyz = {mm_vec_min[0], mm_vec_min[1], mm_vec_min[2]}; xyz_mm.append(xyz); From 862ae2984e9abb0cc6614c4f4dd35f23c40c9f03 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 24 Nov 2023 11:09:31 +0000 Subject: [PATCH 051/468] Use local copy of vector. --- wrapper/Convert/SireOpenMM/emle.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 345251590..730048e44 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -345,7 +345,7 @@ double EMLEEngineImpl::computeForce( for (const auto &force : forces_qm) { // Get the index of the atom. - const auto idx = this->owner.getAtoms()[i]; + const auto idx = qm_atoms[i]; // Convert to OpenMM format. OpenMM::Vec3 omm_force(force[0], force[1], force[2]); From c605a48b6ebd9fa27f3b40f84c2a6f52244a57ce Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 24 Nov 2023 20:08:18 +0000 Subject: [PATCH 052/468] Make sure QM atoms are whole. (Not necessary, but worth checking.) --- wrapper/Convert/SireOpenMM/emle.cpp | 60 ++++++++++------------------- 1 file changed, 20 insertions(+), 40 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 730048e44..a4e4d5973 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -226,47 +226,30 @@ double EMLEEngineImpl::computeForce( QVector> xyz_qm(qm_atoms.size()); QVector xyz_qm_vec(qm_atoms.size()); - // Loop over all atoms in the QM region, get the OpenMM position, then - // store it in Angstroms. We also store in Sire Vector format so that - // we can use the Sire space to compute the distances. Positions are - // stored using the minimum image convention with respect to the center - // of geometry of the QM atoms. - - // Get the reference position. (First QM atom.) - const auto ref_omm_pos = positions[this->owner.getAtoms()[0]]; - - // Convert to Sire Vector format. - Vector ref_vec(10*ref_omm_pos[0], 10*ref_omm_pos[1], 10*ref_omm_pos[2]); - - // Work out the center of geometry of the QM atoms. + // First loop over all QM atoms and store the positions. int i = 0; - Vector center; for (const auto &idx : qm_atoms) { const auto &pos = positions[idx]; Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); - center += space.getMinimumImage(qm_vec, ref_vec); + xyz_qm_vec[i] = qm_vec; i++; } - center /= i; - // Loop over all of the QM atoms and store the positions with respect to - // the reference position. + // Next sure that the QM atoms are whole (unwrapped). + xyz_qm_vec = space.makeWhole(xyz_qm_vec); + + // Get the center of the QM atoms. We will use this as a reference when + // re-imaging the MM atoms. Also store the QM atoms in the xyz_qm vector. + Vector center; i = 0; - for (const auto &idx : qm_atoms) + for (const auto &qm_vec : xyz_qm_vec) { - const auto &pos = positions[idx]; - Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); - const auto qm_vec_min = space.getMinimumImage(qm_vec, center); - xyz_qm[i] = QVector({qm_vec_min[0], qm_vec_min[1], qm_vec_min[2]}); - xyz_qm_vec[i] = qm_vec_min; + xyz_qm[i] = QVector({qm_vec[0], qm_vec[1], qm_vec[2]}); + center += qm_vec; i++; } - - // Next we need to work out the position of the MM atoms within the cutoff, - // along with their charges. Here the cutoff is applied by including MM atoms - // within the cutoff distance from any QM atom. Again we store the positions - // using the minimum image with respect to the reference position. + center /= i; // Initialise a vector to hold the current positions for the MM atoms. QVector> xyz_mm; @@ -287,19 +270,18 @@ double EMLEEngineImpl::computeForce( // Exclude QM atoms. if (not qm_atoms.contains(i)) { - // Whether to add the atom, i.e. it is an MM atom and is - // within the cutoff. + // Initialise a flag for whether to add the atom. bool to_add = false; - // Current MM atom position in Sire Vector format. - const Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + // Store the MM atom position in Sire Vector format. + Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); // Loop over all of the QM atoms. for (const auto &qm_vec : xyz_qm_vec) { + // The current MM atom is within the cutoff, add it. if (space.calcDist(mm_vec, qm_vec) < cutoff) { - // The current MM atom is within the cutoff, add it. to_add = true; break; } @@ -309,10 +291,9 @@ double EMLEEngineImpl::computeForce( if (to_add) { // Work out the minimum image position with respect to the - // reference positions and add to the vector. - const auto mm_vec_min = space.getMinimumImage(mm_vec, center); - QVector xyz = {mm_vec_min[0], mm_vec_min[1], mm_vec_min[2]}; - xyz_mm.append(xyz); + // reference position and add to the vector. + mm_vec = space.getMinimumImage(mm_vec, center); + xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); // Add the charge and index. charges_mm.append(this->owner.getCharges()[i]); @@ -332,8 +313,7 @@ double EMLEEngineImpl::computeForce( xyz_mm ); - // Extract the results. This will automatically be returned in - // OpenMM units. + // Extract the results. This will automatically be returned in OpenMM units. auto energy = result.get<0>(); auto forces_qm = result.get<1>(); auto forces_mm = result.get<2>(); From b5630a40310cef96f44ca034b0c773abe30de166 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 27 Nov 2023 12:11:26 +0000 Subject: [PATCH 053/468] We need VdW interactions for the QM molecule. --- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 28 +++++++++++-------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 1c1ef37db..aff420b9e 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -694,21 +694,27 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, this->cljs = QVector>(nats, std::make_tuple(0.0, 0.0, 0.0)); auto cljs_data = cljs.data(); - // cljs are zeroed for QM molecules - if (not is_qm) + for (int i = 0; i < nats; ++i) { - for (int i = 0; i < nats; ++i) - { - const auto &cgatomidx = idx_to_cgatomidx_data[i]; + const auto &cgatomidx = idx_to_cgatomidx_data[i]; - const double chg = params_charges.at(idx_to_cgatomidx_data[i]).to(SireUnits::mod_electron); + double chg; + + // No Coulomb interactions for QM atoms. + if (is_qm) + { + chg = 0; + } + else + { + chg = params_charges.at(idx_to_cgatomidx_data[i]).to(SireUnits::mod_electron); + } - const auto &lj = params_ljs.at(idx_to_cgatomidx_data[i]); - const double sig = lj.sigma().to(SireUnits::nanometer); - const double eps = lj.epsilon().to(SireUnits::kJ_per_mol); + const auto &lj = params_ljs.at(idx_to_cgatomidx_data[i]); + const double sig = lj.sigma().to(SireUnits::nanometer); + const double eps = lj.epsilon().to(SireUnits::kJ_per_mol); - cljs_data[i] = std::make_tuple(chg, sig, eps); - } + cljs_data[i] = std::make_tuple(chg, sig, eps); } this->bond_params.clear(); From 3d5a519689dca96cc0a4ce950d3fa2a97eea539c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 29 Nov 2023 14:37:12 +0000 Subject: [PATCH 054/468] Add support for lambda interpolation between MM and EMLE potential. --- tests/convert/test_emle.py | 27 - tests/qm/test_emle.py | 89 ++ wrapper/Convert/SireOpenMM/_sommcontext.py | 5 + wrapper/Convert/SireOpenMM/emle.cpp | 9 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 795 ++++++++++++------ wrapper/Convert/SireOpenMM/lambdalever.h | 26 +- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 81 +- wrapper/Convert/SireOpenMM/openmmmolecule.h | 27 +- wrapper/Convert/SireOpenMM/qmmm.h | 6 + .../SireOpenMM/sire_to_openmm_system.cpp | 84 +- 10 files changed, 776 insertions(+), 373 deletions(-) delete mode 100644 tests/convert/test_emle.py create mode 100644 tests/qm/test_emle.py diff --git a/tests/convert/test_emle.py b/tests/convert/test_emle.py deleted file mode 100644 index 581526ae8..000000000 --- a/tests/convert/test_emle.py +++ /dev/null @@ -1,27 +0,0 @@ -from sire.legacy.Convert._SireOpenMM import EMLECallback - - -def test_callback(): - """Makes sure that a callback method works correctly""" - - class Test: - def callback(self, a, b, c, d): - return (42, d, c) - - # Instantiate the class. - test = Test() - - # Create a callback object. - cb = EMLECallback(test, "callback") - - # Create some lists to hold test data. - a = [1, 2] - b = [3, 4] - c = [a, b] - d = [b, a] - - # Call the callback. - result = cb.call(a, b, c, d) - - # Make sure the result is correct. - assert result == (42, d, c) == test.callback(a, b, c, d) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py new file mode 100644 index 000000000..189328d61 --- /dev/null +++ b/tests/qm/test_emle.py @@ -0,0 +1,89 @@ +import math +import pytest +import tempfile + +from sire.legacy.Convert._SireOpenMM import EMLECallback + +from sire.qm import EMLEEngine + +try: + from emle.emle import EMLECalculator + + has_emle = True +except: + has_emle = False + + +def test_callback(): + """Makes sure that a callback method works correctly""" + + class Test: + def callback(self, a, b, c, d): + return (42, d, c) + + # Instantiate the class. + test = Test() + + # Create a callback object. + cb = EMLECallback(test, "callback") + + # Create some lists to hold test data. + a = [1, 2] + b = [3, 4] + c = [a, b] + d = [b, a] + + # Call the callback. + result = cb.call(a, b, c, d) + + # Make sure the result is correct. + assert result == (42, d, c) == test.callback(a, b, c, d) + + +@pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") +def test_interpolate(ala_mols): + """ + Make sure that lambda interpolation between pure MM and EMLE potentials works. + """ + + # Create a local copy of the test system. + mols = ala_mols + + # Create an EMLE calculator. + calculator = EMLECalculator(device="cpu", log=0, save_settings=False) + + # Create an EMLEE engine bound to the calculator. + engine = EMLEEngine(calculator) + + # Create a dynamics object. + d = mols.dynamics(timestep="1fs", constraint="none", platform="cpu") + + # Get the pure MM energy. + nrg_mm = d.current_potential_energy() + + # Set the first molecule as QM. + mols.set_qm_molecule(0) + + # Create a QM/MM capable dynamics object. + d = mols.dynamics( + timestep="1fs", constraint="none", qm_engine=engine, platform="cpu" + ) + + # Get the pure EMLE energy. + nrq_emle = d.current_potential_energy() + + # Get interpolated MM energy. + d.set_lambda(0.0) + nrg_mm_interp = d.current_potential_energy() + + # Make sure this agrees with the standard MM energy. + assert math.isclose(nrg_mm_interp.value(), nrg_mm.value(), rel_tol=1e-4) + + # Now get the interpolated energy at lambda = 0.5. + d.set_lambda(0.5) + nrg_interp = d.current_potential_energy() + + # Make sure the interpolated energy is correct. + assert math.isclose( + nrg_interp.value(), 0.5 * (nrg_mm + nrq_emle).value(), rel_tol=1e-4 + ) diff --git a/wrapper/Convert/SireOpenMM/_sommcontext.py b/wrapper/Convert/SireOpenMM/_sommcontext.py index 74d64f4d6..641b1d0d8 100644 --- a/wrapper/Convert/SireOpenMM/_sommcontext.py +++ b/wrapper/Convert/SireOpenMM/_sommcontext.py @@ -45,6 +45,11 @@ def __init__( lambda_value = map["lambda"].value().as_double() elif map.specified("lambda_value"): lambda_value = map["lambda_value"].value().as_double() + elif map.specified("qm_engine"): + # If there is a QM engine then default lambda = 1.0 unless + # explcitly specified. This means that the QM region will + # be modelled with full QM. + lambda_value = 1.0 else: lambda_value = 0.0 diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index a4e4d5973..374f24054 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -318,6 +318,9 @@ double EMLEEngineImpl::computeForce( auto forces_qm = result.get<1>(); auto forces_mm = result.get<2>(); + // Store the current lambda weighting factor. + const auto lambda = this->owner.getLambda(); + // Now update the force vector. // First the QM atoms. @@ -331,7 +334,7 @@ double EMLEEngineImpl::computeForce( OpenMM::Vec3 omm_force(force[0], force[1], force[2]); // Update the force vector. - forces[idx] = omm_force; + forces[idx] = lambda * omm_force; // Update the atom index. i++; @@ -348,14 +351,14 @@ double EMLEEngineImpl::computeForce( OpenMM::Vec3 omm_force(force[0], force[1], force[2]); // Update the force vector. - forces[idx] = omm_force; + forces[idx] = lambda * omm_force; // Update the atom index. i++; } // Finally, return the energy. - return energy; + return lambda * energy; } boost::tuple>, QVector>> diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 0f014f58f..afb537d33 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -26,6 +26,7 @@ * \*********************************************/ +#include "emle.h" #include "lambdalever.h" #include "SireCAS/values.h" @@ -45,8 +46,11 @@ LambdaLever::LambdaLever(const LambdaLever &other) name_to_restraintidx(other.name_to_restraintidx), lambda_schedule(other.lambda_schedule), perturbable_mols(other.perturbable_mols), - start_indicies(other.start_indicies), - perturbable_maps(other.perturbable_maps) + qm_mols(other.qm_mols), + start_indices_pert(other.start_indices_pert), + start_indices_qm(other.start_indices_qm), + perturbable_maps(other.perturbable_maps), + qm_maps(other.qm_maps) { } @@ -62,8 +66,11 @@ LambdaLever &LambdaLever::operator=(const LambdaLever &other) name_to_restraintidx = other.name_to_restraintidx; lambda_schedule = other.lambda_schedule; perturbable_mols = other.perturbable_mols; - start_indicies = other.start_indicies; + qm_mols = other.qm_mols; + start_indices_pert = other.start_indices_pert; + start_indices_qm = other.start_indices_qm; perturbable_maps = other.perturbable_maps; + qm_maps = other.qm_maps; Property::operator=(other); } @@ -76,8 +83,11 @@ bool LambdaLever::operator==(const LambdaLever &other) const name_to_restraintidx == other.name_to_restraintidx and lambda_schedule == other.lambda_schedule and perturbable_mols == other.perturbable_mols and - start_indicies == other.start_indicies and - perturbable_maps == other.perturbable_maps; + qm_mols == other.qm_mols and + start_indices_pert == other.start_indices_pert and + start_indices_qm == other.start_indices_qm and + perturbable_maps == other.perturbable_maps and + qm_maps == other.qm_maps; } bool LambdaLever::operator!=(const LambdaLever &other) const @@ -239,339 +249,550 @@ double LambdaLever::setLambda(OpenMM::Context &context, // pointers to the forces... OpenMM::System &system = const_cast(context.getSystem()); - // get copies of the forcefields in which the parameters will be changed - auto cljff = this->getForce("clj", system); - auto ghost_ghostff = this->getForce("ghost/ghost", system); - auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); - auto ghost_14ff = this->getForce("ghost-14", system); - auto bondff = this->getForce("bond", system); - auto angff = this->getForce("angle", system); - auto dihff = this->getForce("torsion", system); + // First try to get the QM forcefield. If it exists, then we will updated the + // forcefield parameters and set the lambda value in the customCCPForce. + if (this->getForceIndex("emle") != -1) + { + // First update the lambda value in the QM/MM engine. + auto qmff = this->getForce("emle", system); + qmff->setLambda(lambda_value); + + // get copies of the forcefields in which the parameters will be changed + auto cljff = this->getForce("clj", system); + auto bondff = this->getForce("bond", system); + auto angff = this->getForce("angle", system); + auto dihff = this->getForce("torsion", system); + + // Now scale the MM contributions to QM molecules by 1.0 - lambda. + // This allows the use of lambda interpolation for end-state correction + // simulations. + const auto lam = 1.0 - lambda_value; + + // Change the parameters for all of the QM molecules. We only change the + // force constant of bonded terms and update the charge scale factor for + // the Coulomb interaction. The LJ parameters are not changed. + for (int i = 0; i < this->qm_mols.size(); ++i) + { + const auto &qm_mol = this->qm_mols[i]; + const auto &start_idxs = this->start_indices_qm[i]; - // we know if we have peturbable ghost atoms if we have the ghost forcefields - const bool have_ghost_atoms = (ghost_ghostff != 0 or ghost_nonghostff != 0); + // calculate the new parameters for this lambda value - std::vector custom_params = {0.0, 0.0, 0.0, 0.0}; + const auto morphed_charges = this->lambda_schedule.morph( + "charge", + QVector(qm_mol.getCharges().size(), 0.0), + qm_mol.getCharges(), + lam); - // change the parameters for all of the perturbable molecules - for (int i = 0; i < this->perturbable_mols.count(); ++i) - { - const auto &perturbable_mol = this->perturbable_mols[i]; - const auto &start_idxs = this->start_indicies[i]; - - // calculate the new parameters for this lambda value - const auto morphed_charges = this->lambda_schedule.morph( - "charge", - perturbable_mol.getCharges0(), - perturbable_mol.getCharges1(), - lambda_value); - - const auto morphed_sigmas = this->lambda_schedule.morph( - "sigma", - perturbable_mol.getSigmas0(), - perturbable_mol.getSigmas1(), - lambda_value); - - const auto morphed_epsilons = this->lambda_schedule.morph( - "epsilon", - perturbable_mol.getEpsilons0(), - perturbable_mol.getEpsilons1(), - lambda_value); - - const auto morphed_alphas = this->lambda_schedule.morph( - "alpha", - perturbable_mol.getAlphas0(), - perturbable_mol.getAlphas1(), - lambda_value); - - const auto morphed_bond_k = this->lambda_schedule.morph( - "bond_k", - perturbable_mol.getBondKs0(), - perturbable_mol.getBondKs1(), - lambda_value); - - const auto morphed_bond_length = this->lambda_schedule.morph( - "bond_length", - perturbable_mol.getBondLengths0(), - perturbable_mol.getBondLengths1(), - lambda_value); - - const auto morphed_angle_k = this->lambda_schedule.morph( - "angle_k", - perturbable_mol.getAngleKs0(), - perturbable_mol.getAngleKs1(), - lambda_value); - - const auto morphed_angle_size = this->lambda_schedule.morph( - "angle_size", - perturbable_mol.getAngleSizes0(), - perturbable_mol.getAngleSizes1(), - lambda_value); - - const auto morphed_torsion_phase = this->lambda_schedule.morph( - "torsion_phase", - perturbable_mol.getTorsionPhases0(), - perturbable_mol.getTorsionPhases1(), - lambda_value); - - const auto morphed_torsion_k = this->lambda_schedule.morph( - "torsion_k", - perturbable_mol.getTorsionKs0(), - perturbable_mol.getTorsionKs1(), - lambda_value); - - const auto morphed_charge_scale = this->lambda_schedule.morph( - "charge_scale", - perturbable_mol.getChargeScales0(), - perturbable_mol.getChargeScales1(), - lambda_value); - - const auto morphed_lj_scale = this->lambda_schedule.morph( - "lj_scale", - perturbable_mol.getLJScales0(), - perturbable_mol.getLJScales1(), - lambda_value); - - // now update the forcefields - int start_index = start_idxs.value("clj", -1); - - if (start_index != -1 and cljff != 0) - { - const int nparams = morphed_charges.count(); + const auto sigmas = qm_mol.getSigmas(); + + const auto epsilons = qm_mol.getEpsilons(); + + const auto alphas = qm_mol.getAlphas(); + + const auto morphed_bond_k = this->lambda_schedule.morph( + "bond_k", + QVector(qm_mol.getBondKs().size(), 0.0), + qm_mol.getBondKs(), + lam); + + const auto bond_length = qm_mol.getBondLengths(); + + const auto morphed_angle_k = this->lambda_schedule.morph( + "angle_k", + QVector(qm_mol.getAngleKs().size(), 0.0), + qm_mol.getAngleKs(), + lam); - if (have_ghost_atoms) + const auto angle_size = qm_mol.getAngleSizes(); + + const auto torsion_phase = qm_mol.getTorsionPhases(); + + const auto morphed_torsion_k = this->lambda_schedule.morph( + "torsion_k", + QVector(qm_mol.getTorsionKs().size(), 0.0), + qm_mol.getTorsionKs(), + lam); + + const auto morphed_charge_scale = this->lambda_schedule.morph( + "charge_scale", + QVector(qm_mol.getChargeScales().size(), 0.0), + qm_mol.getChargeScales(), + lam); + + const auto lj_scale = qm_mol.getLJScales(); + + // now update the forcefields + int start_index = start_idxs.value("clj", -1); + + if (start_index != -1 and cljff != 0) { + const int nparams = morphed_charges.count(); + for (int j = 0; j < nparams; ++j) { - const bool is_from_ghost = perturbable_mol.getFromGhostIdxs().contains(j); - const bool is_to_ghost = perturbable_mol.getToGhostIdxs().contains(j); - - // reduced charge - custom_params[0] = morphed_charges[j]; - // half_sigma - custom_params[1] = 0.5 * morphed_sigmas[j]; - // two_sqrt_epsilon - custom_params[2] = 2.0 * std::sqrt(morphed_epsilons[j]); - // alpha - custom_params[3] = morphed_alphas[j]; - - // clamp alpha between 0 and 1 - if (custom_params[3] < 0) - custom_params[3] = 0; - else if (custom_params[3] > 1) - custom_params[3] = 1; - - ghost_ghostff->setParticleParameters(start_index + j, custom_params); - ghost_nonghostff->setParticleParameters(start_index + j, custom_params); - - if (is_from_ghost or is_to_ghost) - { - // don't set the LJ parameters in the cljff - cljff->setParticleParameters(start_index + j, morphed_charges[j], 0.0, 0.0); - } - else + cljff->setParticleParameters(start_index + j, morphed_charges[j], sigmas[j], epsilons[j]); + } + + const auto idxs = qm_mol.getExceptionIndices("clj"); + + if (not idxs.isEmpty()) + { + const auto exception_atoms = qm_mol.getExceptionAtoms(); + + for (int j = 0; j < exception_atoms.count(); ++j) { - cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); + const auto &atoms = exception_atoms[j]; + + const auto atom0 = std::get<0>(atoms); + const auto atom1 = std::get<1>(atoms); + + const auto coul_14_scale = morphed_charge_scale[j]; + const auto lj_14_scale = lj_scale[j]; + + const auto p = get_exception(atom0, atom1, + start_index, coul_14_scale, lj_14_scale, + morphed_charges, sigmas, epsilons, alphas); + + cljff->setExceptionParameters( + std::get<0>(idxs[j]), + std::get<0>(p), std::get<1>(p), + std::get<2>(p), std::get<3>(p), + std::get<4>(p)); } } } - else + + start_index = start_idxs.value("bond", -1); + + if (start_index != -1 and bondff != 0) { + const int nparams = morphed_bond_k.count(); + for (int j = 0; j < nparams; ++j) { - cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); + const int index = start_index + j; + + int particle1, particle2; + double length, k; + + bondff->getBondParameters(index, particle1, particle2, + length, k); + + bondff->setBondParameters(index, particle1, particle2, + bond_length[j], + morphed_bond_k[j]); } } - const auto idxs = perturbable_mol.getExceptionIndicies("clj"); + start_index = start_idxs.value("angle", -1); - if (not idxs.isEmpty()) + if (start_index != -1 and angff != 0) { - const auto exception_atoms = perturbable_mol.getExceptionAtoms(); + const int nparams = morphed_angle_k.count(); - for (int j = 0; j < exception_atoms.count(); ++j) + for (int j = 0; j < nparams; ++j) { - const auto &atoms = exception_atoms[j]; + const int index = start_index + j; - const auto atom0 = std::get<0>(atoms); - const auto atom1 = std::get<1>(atoms); + int particle1, particle2, particle3; + double size, k; - const auto coul_14_scale = morphed_charge_scale[j]; - const auto lj_14_scale = morphed_lj_scale[j]; + angff->getAngleParameters(index, + particle1, particle2, particle3, + size, k); - const bool atom0_is_ghost = perturbable_mol.isGhostAtom(atom0); - const bool atom1_is_ghost = perturbable_mol.isGhostAtom(atom1); + angff->setAngleParameters(index, + particle1, particle2, particle3, + angle_size[j], + morphed_angle_k[j]); + } + } - const auto p = get_exception(atom0, atom1, - start_index, coul_14_scale, lj_14_scale, - morphed_charges, morphed_sigmas, morphed_epsilons, - morphed_alphas); + start_index = start_idxs.value("torsion", -1); - // don't set LJ terms for ghost atoms - if (atom0_is_ghost or atom1_is_ghost) - { - cljff->setExceptionParameters( - std::get<0>(idxs[j]), - std::get<0>(p), std::get<1>(p), - std::get<2>(p), 1e-9, 1e-9); + if (start_index != -1 and dihff != 0) + { + const int nparams = morphed_torsion_k.count(); - if (coul_14_scale != 0 or lj_14_scale != 0) + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; + + int particle1, particle2, particle3, particle4; + double phase, k; + int periodicity; + + dihff->getTorsionParameters(index, + particle1, particle2, + particle3, particle4, + periodicity, phase, k); + + dihff->setTorsionParameters(index, + particle1, particle2, + particle3, particle4, + periodicity, + torsion_phase[j], + morphed_torsion_k[j]); + } + } + } + + // update the parameters in the context + if (cljff) + cljff->updateParametersInContext(context); + + // in OpenMM 8.1beta updating the bond parameters past lambda=0.25 + // causes a "All Forces must have identical exclusions" error, + // when running minimisation without h-bond constraints... + if (bondff) + bondff->updateParametersInContext(context); + + if (angff) + angff->updateParametersInContext(context); + + if (dihff) + dihff->updateParametersInContext(context); + + return lambda_value; + } + + else + { + // get copies of the forcefields in which the parameters will be changed + auto cljff = this->getForce("clj", system); + auto ghost_ghostff = this->getForce("ghost/ghost", system); + auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); + auto ghost_14ff = this->getForce("ghost-14", system); + auto bondff = this->getForce("bond", system); + auto angff = this->getForce("angle", system); + auto dihff = this->getForce("torsion", system); + + // we know if we have peturbable ghost atoms if we have the ghost forcefields + const bool have_ghost_atoms = (ghost_ghostff != 0 or ghost_nonghostff != 0); + + std::vector custom_params = {0.0, 0.0, 0.0, 0.0}; + + // change the parameters for all of the perturbable molecules + for (int i = 0; i < this->perturbable_mols.count(); ++i) + { + const auto &perturbable_mol = this->perturbable_mols[i]; + const auto &start_idxs = this->start_indices_pert[i]; + + // calculate the new parameters for this lambda value + const auto morphed_charges = this->lambda_schedule.morph( + "charge", + perturbable_mol.getCharges0(), + perturbable_mol.getCharges1(), + lambda_value); + + const auto morphed_sigmas = this->lambda_schedule.morph( + "sigma", + perturbable_mol.getSigmas0(), + perturbable_mol.getSigmas1(), + lambda_value); + + const auto morphed_epsilons = this->lambda_schedule.morph( + "epsilon", + perturbable_mol.getEpsilons0(), + perturbable_mol.getEpsilons1(), + lambda_value); + + const auto morphed_alphas = this->lambda_schedule.morph( + "alpha", + perturbable_mol.getAlphas0(), + perturbable_mol.getAlphas1(), + lambda_value); + + const auto morphed_bond_k = this->lambda_schedule.morph( + "bond_k", + perturbable_mol.getBondKs0(), + perturbable_mol.getBondKs1(), + lambda_value); + + const auto morphed_bond_length = this->lambda_schedule.morph( + "bond_length", + perturbable_mol.getBondLengths0(), + perturbable_mol.getBondLengths1(), + lambda_value); + + const auto morphed_angle_k = this->lambda_schedule.morph( + "angle_k", + perturbable_mol.getAngleKs0(), + perturbable_mol.getAngleKs1(), + lambda_value); + + const auto morphed_angle_size = this->lambda_schedule.morph( + "angle_size", + perturbable_mol.getAngleSizes0(), + perturbable_mol.getAngleSizes1(), + lambda_value); + + const auto morphed_torsion_phase = this->lambda_schedule.morph( + "torsion_phase", + perturbable_mol.getTorsionPhases0(), + perturbable_mol.getTorsionPhases1(), + lambda_value); + + const auto morphed_torsion_k = this->lambda_schedule.morph( + "torsion_k", + perturbable_mol.getTorsionKs0(), + perturbable_mol.getTorsionKs1(), + lambda_value); + + const auto morphed_charge_scale = this->lambda_schedule.morph( + "charge_scale", + perturbable_mol.getChargeScales0(), + perturbable_mol.getChargeScales1(), + lambda_value); + + const auto morphed_lj_scale = this->lambda_schedule.morph( + "lj_scale", + perturbable_mol.getLJScales0(), + perturbable_mol.getLJScales1(), + lambda_value); + + // now update the forcefields + int start_index = start_idxs.value("clj", -1); + + if (start_index != -1 and cljff != 0) + { + const int nparams = morphed_charges.count(); + + if (have_ghost_atoms) + { + for (int j = 0; j < nparams; ++j) + { + const bool is_from_ghost = perturbable_mol.getFromGhostIdxs().contains(j); + const bool is_to_ghost = perturbable_mol.getToGhostIdxs().contains(j); + + // reduced charge + custom_params[0] = morphed_charges[j]; + // half_sigma + custom_params[1] = 0.5 * morphed_sigmas[j]; + // two_sqrt_epsilon + custom_params[2] = 2.0 * std::sqrt(morphed_epsilons[j]); + // alpha + custom_params[3] = morphed_alphas[j]; + + // clamp alpha between 0 and 1 + if (custom_params[3] < 0) + custom_params[3] = 0; + else if (custom_params[3] > 1) + custom_params[3] = 1; + + ghost_ghostff->setParticleParameters(start_index + j, custom_params); + ghost_nonghostff->setParticleParameters(start_index + j, custom_params); + + if (is_from_ghost or is_to_ghost) { - // this is a 1-4 parameter - need to update - // the ghost 1-4 forcefield - int nbidx = std::get<1>(idxs[j]); + // don't set the LJ parameters in the cljff + cljff->setParticleParameters(start_index + j, morphed_charges[j], 0.0, 0.0); + } + else + { + cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); + } + } + } + else + { + for (int j = 0; j < nparams; ++j) + { + cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); + } + } + + const auto idxs = perturbable_mol.getExceptionIndices("clj"); + + if (not idxs.isEmpty()) + { + const auto exception_atoms = perturbable_mol.getExceptionAtoms(); + + for (int j = 0; j < exception_atoms.count(); ++j) + { + const auto &atoms = exception_atoms[j]; + + const auto atom0 = std::get<0>(atoms); + const auto atom1 = std::get<1>(atoms); + + const auto coul_14_scale = morphed_charge_scale[j]; + const auto lj_14_scale = morphed_lj_scale[j]; + + const bool atom0_is_ghost = perturbable_mol.isGhostAtom(atom0); + const bool atom1_is_ghost = perturbable_mol.isGhostAtom(atom1); - if (nbidx < 0) - throw SireError::program_bug(QObject::tr( - "Unset NB14 index for a ghost atom?"), - CODELOC); + const auto p = get_exception(atom0, atom1, + start_index, coul_14_scale, lj_14_scale, + morphed_charges, morphed_sigmas, morphed_epsilons, + morphed_alphas); - if (ghost_14ff != 0) + // don't set LJ terms for ghost atoms + if (atom0_is_ghost or atom1_is_ghost) + { + cljff->setExceptionParameters( + std::get<0>(idxs[j]), + std::get<0>(p), std::get<1>(p), + std::get<2>(p), 1e-9, 1e-9); + + if (coul_14_scale != 0 or lj_14_scale != 0) { - // parameters are q, sigma, four_epsilon and alpha - std::vector params14 = - {std::get<2>(p), std::get<3>(p), - 4.0 * std::get<4>(p), std::get<5>(p)}; - - ghost_14ff->setBondParameters(nbidx, - std::get<0>(p), - std::get<1>(p), - params14); + // this is a 1-4 parameter - need to update + // the ghost 1-4 forcefield + int nbidx = std::get<1>(idxs[j]); + + if (nbidx < 0) + throw SireError::program_bug(QObject::tr( + "Unset NB14 index for a ghost atom?"), + CODELOC); + + if (ghost_14ff != 0) + { + // parameters are q, sigma, four_epsilon and alpha + std::vector params14 = + {std::get<2>(p), std::get<3>(p), + 4.0 * std::get<4>(p), std::get<5>(p)}; + + ghost_14ff->setBondParameters(nbidx, + std::get<0>(p), + std::get<1>(p), + params14); + } } } - } - else - { - cljff->setExceptionParameters( - std::get<0>(idxs[j]), - std::get<0>(p), std::get<1>(p), - std::get<2>(p), std::get<3>(p), - std::get<4>(p)); + else + { + cljff->setExceptionParameters( + std::get<0>(idxs[j]), + std::get<0>(p), std::get<1>(p), + std::get<2>(p), std::get<3>(p), + std::get<4>(p)); + } } } } - } - start_index = start_idxs.value("bond", -1); + start_index = start_idxs.value("bond", -1); - if (start_index != -1 and bondff != 0) - { - const int nparams = morphed_bond_k.count(); - - for (int j = 0; j < nparams; ++j) + if (start_index != -1 and bondff != 0) { - const int index = start_index + j; + const int nparams = morphed_bond_k.count(); + + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; - int particle1, particle2; - double length, k; + int particle1, particle2; + double length, k; - bondff->getBondParameters(index, particle1, particle2, - length, k); + bondff->getBondParameters(index, particle1, particle2, + length, k); - bondff->setBondParameters(index, particle1, particle2, - morphed_bond_length[j], - morphed_bond_k[j]); + bondff->setBondParameters(index, particle1, particle2, + morphed_bond_length[j], + morphed_bond_k[j]); + } } - } - start_index = start_idxs.value("angle", -1); - - if (start_index != -1 and angff != 0) - { - const int nparams = morphed_angle_k.count(); + start_index = start_idxs.value("angle", -1); - for (int j = 0; j < nparams; ++j) + if (start_index != -1 and angff != 0) { - const int index = start_index + j; + const int nparams = morphed_angle_k.count(); - int particle1, particle2, particle3; - double size, k; + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; - angff->getAngleParameters(index, - particle1, particle2, particle3, - size, k); + int particle1, particle2, particle3; + double size, k; - angff->setAngleParameters(index, - particle1, particle2, particle3, - morphed_angle_size[j], - morphed_angle_k[j]); - } - } + angff->getAngleParameters(index, + particle1, particle2, particle3, + size, k); - start_index = start_idxs.value("torsion", -1); + angff->setAngleParameters(index, + particle1, particle2, particle3, + morphed_angle_size[j], + morphed_angle_k[j]); + } + } - if (start_index != -1 and dihff != 0) - { - const int nparams = morphed_torsion_k.count(); + start_index = start_idxs.value("torsion", -1); - for (int j = 0; j < nparams; ++j) + if (start_index != -1 and dihff != 0) { - const int index = start_index + j; - - int particle1, particle2, particle3, particle4; - double phase, k; - int periodicity; - - dihff->getTorsionParameters(index, - particle1, particle2, - particle3, particle4, - periodicity, phase, k); - - dihff->setTorsionParameters(index, - particle1, particle2, - particle3, particle4, - periodicity, - morphed_torsion_phase[j], - morphed_torsion_k[j]); + const int nparams = morphed_torsion_k.count(); + + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; + + int particle1, particle2, particle3, particle4; + double phase, k; + int periodicity; + + dihff->getTorsionParameters(index, + particle1, particle2, + particle3, particle4, + periodicity, phase, k); + + dihff->setTorsionParameters(index, + particle1, particle2, + particle3, particle4, + periodicity, + morphed_torsion_phase[j], + morphed_torsion_k[j]); + } } } - } - // update the parameters in the context - if (cljff) - cljff->updateParametersInContext(context); + // update the parameters in the context + if (cljff) + cljff->updateParametersInContext(context); - if (ghost_ghostff) - ghost_ghostff->updateParametersInContext(context); + if (ghost_ghostff) + ghost_ghostff->updateParametersInContext(context); - if (ghost_nonghostff) - ghost_nonghostff->updateParametersInContext(context); + if (ghost_nonghostff) + ghost_nonghostff->updateParametersInContext(context); - if (ghost_14ff) - ghost_14ff->updateParametersInContext(context); + if (ghost_14ff) + ghost_14ff->updateParametersInContext(context); - // in OpenMM 8.1beta updating the bond parameters past lambda=0.25 - // causes a "All Forces must have identical exclusions" error, - // when running minimisation without h-bond constraints... - if (bondff) - bondff->updateParametersInContext(context); + // in OpenMM 8.1beta updating the bond parameters past lambda=0.25 + // causes a "All Forces must have identical exclusions" error, + // when running minimisation without h-bond constraints... + if (bondff) + bondff->updateParametersInContext(context); - if (angff) - angff->updateParametersInContext(context); + if (angff) + angff->updateParametersInContext(context); - if (dihff) - dihff->updateParametersInContext(context); + if (dihff) + dihff->updateParametersInContext(context); - // now update any restraints that are scaled - for (const auto &restraint : this->name_to_restraintidx.keys()) - { - // restraints always morph between 1 and 1 (i.e. they fully - // follow whatever is set by lambda, e.g. 'initial*lambda' - // to switch them on, or `final*lambda` to switch them off) - const double rho = lambda_schedule.morph(restraint, - 1.0, 1.0, - lambda_value); - - for (auto &ff : this->getRestraints(restraint, system)) + // now update any restraints that are scaled + for (const auto &restraint : this->name_to_restraintidx.keys()) { - if (ff != 0) + // restraints always morph between 1 and 1 (i.e. they fully + // follow whatever is set by lambda, e.g. 'initial*lambda' + // to switch them on, or `final*lambda` to switch them off) + const double rho = lambda_schedule.morph(restraint, + 1.0, 1.0, + lambda_value); + + for (auto &ff : this->getRestraints(restraint, system)) { - this->updateRestraintInContext(*ff, rho, context); + if (ff != 0) + { + this->updateRestraintInContext(*ff, rho, context); + } } } - } - return lambda_value; + return lambda_value; + } } /** Update the parameters for a CustomCompoundBondForce for scale factor 'rho' @@ -765,21 +986,41 @@ int LambdaLever::addPerturbableMolecule(const OpenMMMolecule &molecule, { // should add in some sanity checks for these inputs this->perturbable_mols.append(PerturbableOpenMMMolecule(molecule)); - this->start_indicies.append(starts); + this->start_indices_pert.append(starts); this->perturbable_maps.insert(molecule.number, molecule.perturtable_map); return this->perturbable_mols.count() - 1; } +/** Add infor for the passed OpenMMMolecule, returning its index + * in the list of QM molecules + */ +int LambdaLever::addQMMolecule(const OpenMMMolecule &molecule, + const QHash &starts) +{ + // should add in some sanity checks for these inputs + this->qm_mols.append(molecule); + this->start_indices_qm.append(starts); + return this->qm_mols.count() - 1; +} + /** Set the exception indices for the perturbable molecule at * index 'mol_idx' */ -void LambdaLever::setExceptionIndicies(int mol_idx, - const QString &name, - const QVector> &exception_idxs) +void LambdaLever::setExceptionIndices(int mol_idx, + const QString &name, + const QVector> &exception_idxs, + bool is_qm) { - mol_idx = SireID::Index(mol_idx).map(this->perturbable_mols.count()); - - this->perturbable_mols[mol_idx].setExceptionIndicies(name, exception_idxs); + if (is_qm) + { + mol_idx = SireID::Index(mol_idx).map(this->qm_mols.count()); + this->qm_mols[mol_idx].setExceptionIndices(name, exception_idxs); + } + else + { + mol_idx = SireID::Index(mol_idx).map(this->perturbable_mols.count()); + this->perturbable_mols[mol_idx].setExceptionIndices(name, exception_idxs); + } } /** Return all of the property maps used to find the perturbable properties diff --git a/wrapper/Convert/SireOpenMM/lambdalever.h b/wrapper/Convert/SireOpenMM/lambdalever.h index ee158ce25..4f7445b44 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.h +++ b/wrapper/Convert/SireOpenMM/lambdalever.h @@ -69,10 +69,14 @@ namespace SireOpenMM void addRestraintIndex(const QString &force, int index); int addPerturbableMolecule(const OpenMMMolecule &molecule, - const QHash &start_indicies); + const QHash &start_indices); - void setExceptionIndicies(int idx, const QString &ff, - const QVector> &exception_idxs); + int addQMMolecule(const OpenMMMolecule &molecule, + const QHash &start_indices); + + void setExceptionIndices(int idx, const QString &ff, + const QVector> &exception_idxs, + bool is_qm = false); void setSchedule(const SireCAS::LambdaSchedule &schedule); @@ -111,12 +115,22 @@ namespace SireOpenMM /** The list of perturbable molecules */ QVector perturbable_mols; - /** The start indicies of the parameters in each named - forcefield for each perturbable moleucle */ - QVector> start_indicies; + /** The list of QM molecules */ + QVector qm_mols; + + /** The start indices of the parameters in each named + forcefield for each perturbable molecule */ + QVector> start_indices_pert; + + /** The start indices of the parameters in each named + forcefield for each QM molecule */ + QVector> start_indices_qm; /** All of the property maps for the perturbable molecules */ QHash perturbable_maps; + + /** All of the property maps for the QM molecules */ + QHash qm_maps; }; #ifndef SIRE_SKIP_INLINE_FUNCTION diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index aff420b9e..9896a6359 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -194,7 +194,7 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, if (mol.hasProperty(map["is_qm"])) { - is_qm = mol.property(map["is_qm"]).asABoolean(); + this->is_qm = mol.property(map["is_qm"]).asABoolean(); } if (is_perturbable) @@ -299,22 +299,6 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, field_atoms.reset(new FieldAtoms(atms, map)); } - if (mol.hasProperty(map["is_qm"])) - { - if (mol.property(map["is_qm"]).asABoolean()) - { - // remove all internal terms - bond_params.clear(); - ang_params.clear(); - dih_params.clear(); - constraints.clear(); - virtual_sites.clear(); - light_atoms.clear(); - unbonded_atoms.clear(); - perturbed.reset(); - } - } - if (ffinfo.isAmberStyle()) { if (is_perturbable) @@ -359,15 +343,10 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, this->alignInternals(map); } - else if (is_qm) - { - const auto params = SireMM::AmberParams(mol, map); - this->constructFromAmber(mol, params, params, map, false, true); - } else { const auto params = SireMM::AmberParams(mol, map); - this->constructFromAmber(mol, params, params, map, false, false); + this->constructFromAmber(mol, params, params, map, false, this->isQM()); } } else @@ -429,6 +408,11 @@ bool OpenMMMolecule::isPerturbable() const return perturbed.get() != 0; } +bool OpenMMMolecule::isQM() const +{ + return this->is_qm; +} + bool OpenMMMolecule::isGhostAtom(int atom) const { return from_ghost_idxs.contains(atom) or to_ghost_idxs.contains(atom); @@ -466,7 +450,7 @@ std::tuple OpenMMMolecule::getException( epsilon = lj_14_scl * std::sqrt(std::get<2>(clj0) * std::get<2>(clj1)); } - if (this->isPerturbable() and charge == 0 and epsilon == 0) + if ((this->isPerturbable() or this->isQM()) and charge == 0 and epsilon == 0) { // openmm tries to optimise away zero parameters - this is an issue // as perturbation requires that we don't remove them! @@ -482,6 +466,30 @@ std::tuple OpenMMMolecule::getException( charge, sigma, epsilon); } +/** Return the global indexes of the exceptions in the non-bonded and + * ghost-14 forces + */ +QVector> OpenMMMolecule::getExceptionIndices(const QString &name) const +{ + return this->exception_idxs.value(name); +} + +/** Set the global indexes of the exceptions in the non-bonded and + * ghost-14 forces + */ +void OpenMMMolecule::setExceptionIndices(const QString &name, + const QVector> &exception_idxs) +{ + if (exception_idxs.count() != this->exception_atoms.count()) + throw SireError::incompatible_error(QObject::tr( + "The number of exception indicies (%1) does not match the number of exceptions (%2)") + .arg(exception_idxs.count()) + .arg(this->exception_atoms.count()), + CODELOC); + + this->exception_idxs.insert(name, exception_idxs); +} + /** Return closest constraint length to 'length' based on what * we have seen before and the constraint_length_tolerance */ @@ -698,18 +706,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, { const auto &cgatomidx = idx_to_cgatomidx_data[i]; - double chg; - - // No Coulomb interactions for QM atoms. - if (is_qm) - { - chg = 0; - } - else - { - chg = params_charges.at(idx_to_cgatomidx_data[i]).to(SireUnits::mod_electron); - } - + const auto chg = params_charges.at(idx_to_cgatomidx_data[i]).to(SireUnits::mod_electron); const auto &lj = params_ljs.at(idx_to_cgatomidx_data[i]); const double sig = lj.sigma().to(SireUnits::nanometer); const double eps = lj.epsilon().to(SireUnits::kJ_per_mol); @@ -958,6 +955,12 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } this->buildExceptions(mol, atomidx_to_idx, constrained_pairs, map); + + // Set the exception indices for this molecule. + if (is_qm) + { + this->exception_atoms = this->getExceptionAtoms(); + } } bool is_ghost(const std::tuple &clj) @@ -2143,7 +2146,7 @@ QVector> PerturbableOpenMMMolecule::getExceptionAtoms() cons /** Return the global indexes of the exceptions in the non-bonded and * ghost-14 forces */ -QVector> PerturbableOpenMMMolecule::getExceptionIndicies(const QString &name) const +QVector> PerturbableOpenMMMolecule::getExceptionIndices(const QString &name) const { return this->exception_idxs.value(name); } @@ -2151,8 +2154,8 @@ QVector> PerturbableOpenMMMolecule::getExceptionIndicies(con /** Set the global indexes of the exceptions in the non-bonded and * ghost-14 forces */ -void PerturbableOpenMMMolecule::setExceptionIndicies(const QString &name, - const QVector> &exception_idxs) +void PerturbableOpenMMMolecule::setExceptionIndices(const QString &name, + const QVector> &exception_idxs) { if (exception_idxs.count() != this->exception_atoms.count()) throw SireError::incompatible_error(QObject::tr( diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index b78a85571..a4b0067ee 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -81,6 +81,7 @@ namespace SireOpenMM OpenMM::Vec3 *velocities) const; bool isPerturbable() const; + bool isQM() const; int nAtoms() const; @@ -119,6 +120,11 @@ namespace SireOpenMM double coul_14_scl, double lj_14_scl) const; + QVector> getExceptionIndices(const QString &name) const; + + void setExceptionIndices(const QString &name, + const QVector> &exception_idxs); + /** All the member data is public as this is an internal * class. This class should not be used outside of * this SireOpenMM converter library. @@ -178,10 +184,6 @@ namespace SireOpenMM /** The field atoms for the molecule, if this has field atoms */ std::shared_ptr field_atoms; - /** The indicies of the added exceptions - only populated - * if this is a peturbable molecule */ - QHash>> exception_idxs; - /** The property map used to get the perturbable properties - * this is only non-default if the molecule is perturbable */ @@ -228,6 +230,16 @@ namespace SireOpenMM void alignInternals(const SireBase::PropertyMap &map); void processFieldAtoms(); + + /** Whether this is a QM molecule. */ + bool is_qm = false; + + /** The indicies of the atoms in the exceptions, in exception order */ + QVector> exception_atoms; + + /** The indicies of the added exceptions - only populated + * if this is a QM molecule */ + QHash>> exception_idxs; }; /** This class holds all of the information of an OpenMM molecule @@ -288,10 +300,10 @@ namespace SireOpenMM QVector> getExceptionAtoms() const; - QVector> getExceptionIndicies(const QString &name) const; + QVector> getExceptionIndices(const QString &name) const; - void setExceptionIndicies(const QString &name, - const QVector> &exception_idxs); + void setExceptionIndices(const QString &name, + const QVector> &exception_idxs); private: /** The array of parameters for the two end states, aligned @@ -328,7 +340,6 @@ namespace SireOpenMM * if this is a peturbable molecule */ QHash>> exception_idxs; }; - } SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 5d1bc6b28..06c750fb5 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -47,6 +47,12 @@ namespace SireOpenMM public: virtual ~QMMMEngine(); + //! Get the lambda weighting factor. + virtual double getLambda() const = 0; + + //! Set the lambda weighting factor. + virtual void setLambda(double lambda) = 0; + //! Get the QM cutoff distance. virtual SireUnits::Dimension::Length getCutoff() const = 0; diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index f878e785b..368cb7251 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -621,6 +621,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // should we just ignore perturbations? bool ignore_perturbations = false; bool any_perturbable = false; + bool is_qm = false; if (map.specified("ignore_perturbations")) { @@ -738,6 +739,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // now create the engine for computing QM or ML forces on atoms QMMMEngine *qmff = 0; + QString qm_engine; if (map.specified("qm_engine")) { @@ -745,6 +747,8 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { auto &engine = map["qm_engine"].value().asA(); qmff = new EMLEEngine(engine); + qm_engine = "emle"; + is_qm = true; } catch (...) { @@ -772,7 +776,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, lambda_lever.setSchedule( map["schedule"].value().asA()); } - else if (any_perturbable) + else if (any_perturbable or is_qm) { // use a standard morph if we have an alchemical perturbation lambda_lever.setSchedule( @@ -815,7 +819,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (qmff != 0) { - lambda_lever.setForceIndex("qm", system.addForce(qmff)); + lambda_lever.setForceIndex(qm_engine, system.addForce(qmff)); lambda_lever.addLever("qm_scale"); } @@ -1089,9 +1093,10 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // particle in that molecule QVector start_indexes(nmols); - // the index to the perturbable molecule for the specified molecule + // the index to the perturbable or QM molecule for the specified molecule // (i.e. the 5th perturbable molecule is the 10th molecule in the System) QHash idx_to_pert_idx; + QHash idx_to_qm_idx; // just a holder for all of the custom parameters for the // ghost forces (prevents us having to continually re-allocate it) @@ -1132,14 +1137,13 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, CODELOC); } - // this hash holds the start indicies for the various - // parameters for this molecule (e.g. bond, angle, CLJ parameters) - // We only need to record this if this is a perturbable molecule - QHash start_indicies; - // is this a perturbable molecule (and we haven't disabled perturbations)? if (any_perturbable and mol.isPerturbable()) { + // this hash holds the start indicies for the various + // parameters for this molecule (e.g. bond, angle, CLJ parameters) + QHash start_indicies; + // add a perturbable molecule, recording the start index // for each of the forcefields start_indicies.reserve(7); @@ -1169,6 +1173,39 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, idx_to_pert_idx.insert(i, pert_idx); } + if (mol.isQM()) + { + // this hash holds the start indicies for the various + // parameters for this molecule (e.g. bond, angle, CLJ parameters) + QHash start_indicies; + + // add a QM molecule, recording the start index + // for each of the forcefields + start_indicies.reserve(4); + + start_indicies.insert("clj", start_index); + + // the start index for this molecules first bond, angle or + // torsion parameters will be however many of these + // parameters exist already (parameters are added + // contiguously for each molecule) + start_indicies.insert("bond", bondff->getNumBonds()); + start_indicies.insert("angle", angff->getNumAngles()); + start_indicies.insert("torsion", dihff->getNumTorsions()); + + // we can now record this as a perturbable molecule + // in the lambda lever. The returned index is the + // index of this perturbable molecule in the list + // of perturbable molecules (e.g. the first perturbable + // molecule we find has index 0) + auto qm_idx = lambda_lever.addQMMolecule(mol, + start_indicies); + + // and we can record the map from the molecule index + // to the perturbable molecule index + idx_to_qm_idx.insert(i, qm_idx); + } + // Copy in all of the atom (particle) parameters. These // are the masses, charge and LJ parameters. // There is a different code path depending on whether @@ -1399,13 +1436,20 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, int start_index = start_indexes[i]; const auto &mol = openmm_mols_data[i]; - QVector> exception_idxs; + QVector> perturbable_exception_idxs; + QVector> qm_exception_idxs; const bool is_perturbable = any_perturbable and mol.isPerturbable(); if (is_perturbable) { - exception_idxs = QVector>(mol.exception_params.count(), + perturbable_exception_idxs = QVector>(mol.exception_params.count(), + std::make_pair(-1, -1)); + } + + if (is_qm) + { + qm_exception_idxs = QVector>(mol.exception_params.count(), std::make_pair(-1, -1)); } @@ -1475,7 +1519,14 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // these are the indexes of the exception in the // non-bonded forcefields and also the ghost-14 forcefield - exception_idxs[j] = std::make_pair(idx, nbidx); + perturbable_exception_idxs[j] = std::make_pair(idx, nbidx); + } + else if (mol.isQM()) + { + const auto idx = cljff->addException(std::get<0>(p), std::get<1>(p), + std::get<2>(p), std::get<3>(p), + std::get<4>(p), true); + qm_exception_idxs[j] = std::make_pair(idx, -1); } else { @@ -1496,8 +1547,15 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (is_perturbable) { auto pert_idx = idx_to_pert_idx.value(i, openmm_mols.count() + 1); - lambda_lever.setExceptionIndicies(pert_idx, - "clj", exception_idxs); + lambda_lever.setExceptionIndices(pert_idx, + "clj", perturbable_exception_idxs); + } + + if (mol.isQM()) + { + auto qm_idx = idx_to_qm_idx.value(i, openmm_mols.count() + 1); + lambda_lever.setExceptionIndices(qm_idx, + "clj", qm_exception_idxs, true); } } From 550d92edf1261cdb99d1e6f7a9db8f4bfda836a9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 29 Nov 2023 15:07:27 +0000 Subject: [PATCH 055/468] Refactor and improve detection of QM molecules. --- .../SireOpenMM/sire_to_openmm_system.cpp | 20 ++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 368cb7251..bc63f2b38 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -663,6 +663,16 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } } + // check to see if there are any QM molecules. + for (int i = 0; i < nmols; ++i) + { + if (openmm_mols_data[i].isQM()) + { + is_qm = true; + break; + } + } + // check to see if there are any field molecules bool any_field_mols = false; @@ -748,13 +758,21 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, auto &engine = map["qm_engine"].value().asA(); qmff = new EMLEEngine(engine); qm_engine = "emle"; - is_qm = true; } catch (...) { throw SireError::incompatible_error(QObject::tr("Invalid QM engine!"), CODELOC); } } + else + { + if (is_qm) + { + throw SireError::incompatible_error( + QObject::tr("The system contains QM molecules but no QM engine is specified!"), + CODELOC); + } + } // end of stage 2 - we now have the base forces From 57b2b14f1594ebdd204610689fcc04ce70b07bd2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 30 Nov 2023 11:28:32 +0000 Subject: [PATCH 056/468] Fix typo. --- tests/qm/test_emle.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 189328d61..a4e026242 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -70,7 +70,7 @@ def test_interpolate(ala_mols): ) # Get the pure EMLE energy. - nrq_emle = d.current_potential_energy() + nrg_emle = d.current_potential_energy() # Get interpolated MM energy. d.set_lambda(0.0) @@ -85,5 +85,5 @@ def test_interpolate(ala_mols): # Make sure the interpolated energy is correct. assert math.isclose( - nrg_interp.value(), 0.5 * (nrg_mm + nrq_emle).value(), rel_tol=1e-4 + nrg_interp.value(), 0.5 * (nrg_mm + nrg_emle).value(), rel_tol=1e-4 ) From 51c8d4f6d7710ffadde32cd85e897c64497a71e5 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 1 Dec 2023 10:52:32 +0000 Subject: [PATCH 057/468] Add rudimentary neighbour list support. --- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 9 +- wrapper/Convert/SireOpenMM/emle.cpp | 159 +++++++++++++++--- wrapper/Convert/SireOpenMM/emle.h | 18 ++ 3 files changed, 156 insertions(+), 30 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 4cf1e3323..e46415190 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -181,9 +181,12 @@ BOOST_PYTHON_MODULE(_SireOpenMM) bp::class_, boost::noncopyable>("QMMMEngine", bp::no_init); bp::class_>("EMLEEngine", - bp::init( + bp::init( ( - bp::arg("py_object"), bp::arg("cutoff")=SireUnits::Dimension::Length(8.0), bp::arg("lambda")=1.0 + bp::arg("py_object"), + bp::arg("cutoff")=SireUnits::Dimension::Length(8.0), + bp::arg("neighbour_list_frequency")=20, + bp::arg("lambda")=1.0 ), "Constructor: An engine that can be used to enable electrostatic embedding" "of machine learning potentials via emle-engine." @@ -193,6 +196,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setLambda", &EMLEEngine::setLambda, "Set the lambda value") .def("getCutoff", &EMLEEngine::getCutoff, "Get the cutoff value") .def("setCutoff", &EMLEEngine::setCutoff, "Set the cutoff value") + .def("getNeighbourListFrequency", &EMLEEngine::getNeighbourListFrequency, "Get the neighbour list frequency") + .def("setNeighbourListFrequency", &EMLEEngine::setNeighbourListFrequency, "Set the neighbour list frequency") .def("getAtoms", &EMLEEngine::getAtoms, "Get QM atom indices") .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") .def("getNumbers", &EMLEEngine::getNumbers, "Get QM atomic numbers") diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 374f24054..92bb3ee11 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -77,16 +77,34 @@ EMLEEngine::EMLEEngine() { } -EMLEEngine::EMLEEngine(bp::object py_object, SireUnits::Dimension::Length cutoff, double lambda) : +EMLEEngine::EMLEEngine( + bp::object py_object, + SireUnits::Dimension::Length cutoff, + int neighbour_list_frequency, + double lambda) : callback(py_object, "_sire_callback"), cutoff(cutoff), + neighbour_list_frequency(neighbour_list_frequency), lambda(lambda) { + if (this->neighbour_list_frequency < 0) + { + neighbour_list_frequency = 0; + } + if (this->lambda < 0.0) + { + this->lambda = 0.0; + } + else if (this->lambda > 1.0) + { + this->lambda = 1.0; + } } EMLEEngine::EMLEEngine(const EMLEEngine &other) : callback(other.callback), cutoff(other.cutoff), + neighbour_list_frequency(other.neighbour_list_frequency), lambda(other.lambda), atoms(other.atoms), numbers(other.numbers), @@ -98,6 +116,7 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) { this->callback = other.callback; this->cutoff = other.cutoff; + this->neighbour_list_frequency = other.neighbour_list_frequency; this->lambda = other.lambda; this->atoms = other.atoms; this->numbers = other.numbers; @@ -117,6 +136,15 @@ EMLECallback EMLEEngine::getCallback() const void EMLEEngine::setLambda(double lambda) { + // Clamp the lambda value. + if (lambda < 0.0) + { + lambda = 0.0; + } + else if (lambda > 1.0) + { + lambda = 1.0; + } this->lambda = lambda; } @@ -135,6 +163,21 @@ SireUnits::Dimension::Length EMLEEngine::getCutoff() const return this->cutoff; } +int EMLEEngine::getNeighbourListFrequency() const +{ + return this->neighbour_list_frequency; +} + +void EMLEEngine::setNeighbourListFrequency(int neighbour_list_frequency) +{ + // Assume anything less than zero means no neighbour list. + if (neighbour_list_frequency < 0) + { + neighbour_list_frequency = 0; + } + this->neighbour_list_frequency = neighbour_list_frequency; +} + QVector EMLEEngine::getAtoms() const { return this->atoms; @@ -208,6 +251,22 @@ double EMLEEngineImpl::computeForce( const std::vector &positions, std::vector &forces) { + // If this is the first step, then setup information for the neighbour list. + if (this->step_count == 0) + { + // Store the cutoff as a double in Angstom. + this->cutoff = this->owner.getCutoff().value(); + + // The neighbour list cutoff is 20% larger than the cutoff. + this->neighbour_list_cutoff = 1.2*this->cutoff; + + // Store the neighbour list update frequency. + this->neighbour_list_frequency = this->owner.getNeighbourListFrequency(); + + // Flag whether a neighbour list is used. + this->is_neighbour_list = this->neighbour_list_frequency > 0; + } + // Get the current box vectors in nanometers. OpenMM::Vec3 box_x, box_y, box_z; context.getPeriodicBoxVectors(box_x, box_y, box_z); @@ -260,21 +319,68 @@ double EMLEEngineImpl::computeForce( // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; - // Store the cutoff as a double in Angstom. - const auto cutoff = this->owner.getCutoff().value(); - - // Loop over all of the OpenMM positions. - i = 0; - for (const auto &pos : positions) + // Manually work out the MM point charges and build the neigbour list. + if (not this->is_neighbour_list or this->step_count % this->neighbour_list_frequency == 0) { - // Exclude QM atoms. - if (not qm_atoms.contains(i)) + // Clear the neighbour list. + if (this->is_neighbour_list) + { + this->neighbour_list.clear(); + } + + i = 0; + // Loop over all of the OpenMM positions. + for (const auto &pos : positions) { - // Initialise a flag for whether to add the atom. - bool to_add = false; + // Exclude QM atoms. + if (not qm_atoms.contains(i)) + { + // Store the MM atom position in Sire Vector format. + Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + + // Loop over all of the QM atoms. + for (const auto &qm_vec : xyz_qm_vec) + { + // Work out the distance between the current MM atom and QM atoms. + const auto dist = space.calcDist(mm_vec, qm_vec); + + // The current MM atom is within the neighbour list cutoff. + if (this->is_neighbour_list and dist < this->neighbour_list_cutoff) + { + // Insert the MM atom index into the neighbour list. + this->neighbour_list.insert(i); + } + + // The current MM atom is within the cutoff, add it. + if (dist < cutoff) + { + // Work out the minimum image position with respect to the + // reference position and add to the vector. + mm_vec = space.getMinimumImage(mm_vec, center); + xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[i]); + idx_mm.append(i); + + // Exit the inner loop. + break; + } + } + } + // Update the atom index. + i++; + } + } + // Use the neighbour list. + else + { + // Loop over the MM atoms in the neighbour list. + for (const auto &idx : this->neighbour_list) + { // Store the MM atom position in Sire Vector format. - Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + Vector mm_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); // Loop over all of the QM atoms. for (const auto &qm_vec : xyz_qm_vec) @@ -282,27 +388,21 @@ double EMLEEngineImpl::computeForce( // The current MM atom is within the cutoff, add it. if (space.calcDist(mm_vec, qm_vec) < cutoff) { - to_add = true; + // Work out the minimum image position with respect to the + // reference position and add to the vector. + mm_vec = space.getMinimumImage(mm_vec, center); + xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[idx]); + idx_mm.append(idx); + + // Exit the inner loop. break; } } - // Store the MM atom information. - if (to_add) - { - // Work out the minimum image position with respect to the - // reference position and add to the vector. - mm_vec = space.getMinimumImage(mm_vec, center); - xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); - - // Add the charge and index. - charges_mm.append(this->owner.getCharges()[i]); - idx_mm.append(i); - } } - - // Update the atom index. - i++; } // Call the callback. @@ -357,6 +457,9 @@ double EMLEEngineImpl::computeForce( i++; } + // Update the step count. + this->step_count++; + // Finally, return the energy. return lambda * energy; } diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index f9100b313..64d294f3d 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -119,6 +119,10 @@ namespace SireOpenMM \param cutoff The ML cutoff distance. + \param neighbour_list_frequency + The frequency at which the neighbour list is updated. (Number of steps.) + If zero, then no neighbour list is used. + \param lambda The lambda weighting factor. This can be used to interpolate between potentials for end-state correction calculations. @@ -126,6 +130,7 @@ namespace SireOpenMM EMLEEngine( bp::object, SireUnits::Dimension::Length cutoff=8.0*SireUnits::angstrom, + int neighbour_list_frequency=20, double lambda=1.0 ); @@ -153,6 +158,12 @@ namespace SireOpenMM //! Set the QM cutoff distance. void setCutoff(SireUnits::Dimension::Length cutoff); + //! Get the neighbour list frequency. + int getNeighbourListFrequency() const; + + //! Set the neighbour list frequency. + void setNeighbourListFrequency(int neighbour_list_frequency); + //! Get the indices of the atoms in the QM region. QVector getAtoms() const; @@ -209,6 +220,7 @@ namespace SireOpenMM private: EMLECallback callback; SireUnits::Dimension::Length cutoff; + int neighbour_list_frequency; double lambda; QVector atoms; QVector numbers; @@ -231,6 +243,12 @@ namespace SireOpenMM private: const EMLEEngine &owner; + unsigned long long step_count=0; + double cutoff; + bool is_neighbour_list; + int neighbour_list_frequency; + double neighbour_list_cutoff; + QSet neighbour_list; }; #endif } From 9a6b63eebe2754dd71c0af2a16f05b183cb0c336 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 1 Dec 2023 12:09:22 +0000 Subject: [PATCH 058/468] Typo. --- wrapper/Convert/SireOpenMM/emle.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 92bb3ee11..8b173a22b 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -413,7 +413,7 @@ double EMLEEngineImpl::computeForce( xyz_mm ); - // Extract the results. This will automatically be returned in OpenMM units. + // Extract the results. These will automatically be returned in OpenMM units. auto energy = result.get<0>(); auto forces_qm = result.get<1>(); auto forces_mm = result.get<2>(); From c95e32fca300fa8230cc06086378738cc344f527 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 4 Dec 2023 14:43:39 +0000 Subject: [PATCH 059/468] Add support for storing interpolation energy trajectory. --- src/sire/mol/__init__.py | 67 +++++++----------- src/sire/mol/_dynamics.py | 141 ++++++++++++++++++++++++++++++------- src/sire/system/_system.py | 12 +++- 3 files changed, 151 insertions(+), 69 deletions(-) diff --git a/src/sire/mol/__init__.py b/src/sire/mol/__init__.py index cb6afca0f..da56b24fb 100644 --- a/src/sire/mol/__init__.py +++ b/src/sire/mol/__init__.py @@ -226,9 +226,7 @@ def is_water(mol, map=None): if hasattr(type(mol), "molecules"): return _Mol.is_water(mol.molecules(), map) - raise TypeError( - f"Cannot convert {mol} to a molecule view or molecule collection." - ) + raise TypeError(f"Cannot convert {mol} to a molecule view or molecule collection.") # Here I will define some functions that make accessing @@ -280,9 +278,7 @@ def __is_atom_class(obj): def __is_residue_class(obj): mro = type(obj).mro() - return ( - Residue in mro or Selector_Residue_ in mro or SelectorM_Residue_ in mro - ) + return Residue in mro or Selector_Residue_ in mro or SelectorM_Residue_ in mro def __is_chain_class(obj): @@ -294,28 +290,19 @@ def __is_chain_class(obj): def __is_segment_class(obj): mro = type(obj).mro() - return ( - Segment in mro or Selector_Segment_ in mro or SelectorM_Segment_ in mro - ) + return Segment in mro or Selector_Segment_ in mro or SelectorM_Segment_ in mro def __is_cutgroup_class(obj): mro = type(obj).mro() - return ( - CutGroup in mro - or Selector_CutGroup_ in mro - or SelectorM_CutGroup_ in mro - ) + return CutGroup in mro or Selector_CutGroup_ in mro or SelectorM_CutGroup_ in mro def __is_selector_class(obj): try: t = obj.what() - return ( - t.find("SireMol::Selector") != -1 - or t.find("SireMM::Selector") != -1 - ) + return t.find("SireMol::Selector") != -1 or t.find("SireMM::Selector") != -1 except Exception: return False @@ -963,9 +950,7 @@ def __fixed__bond__(obj, idx=None, idx1=None, map=None): def __fixed__angle__(obj, idx=None, idx1=None, idx2=None, map=None): - angles = __fixed__angles__( - obj, idx, idx1, idx2, auto_reduce=False, map=map - ) + angles = __fixed__angles__(obj, idx, idx1, idx2, auto_reduce=False, map=map) if len(angles) == 0: raise KeyError("There is no matching angle in this view.") @@ -977,9 +962,7 @@ def __fixed__angle__(obj, idx=None, idx1=None, idx2=None, map=None): return angles[0] -def __fixed__dihedral__( - obj, idx=None, idx1=None, idx2=None, idx3=None, map=None -): +def __fixed__dihedral__(obj, idx=None, idx1=None, idx2=None, idx3=None, map=None): dihedrals = __fixed__dihedrals__( obj, idx, idx1, idx2, idx3, auto_reduce=False, map=map ) @@ -988,16 +971,13 @@ def __fixed__dihedral__( raise KeyError("There is no matching dihedral in this view.") elif len(dihedrals) > 1: raise KeyError( - "More than one dihedral matches. Number of " - f"matches is {len(dihedrals)}." + "More than one dihedral matches. Number of " f"matches is {len(dihedrals)}." ) return dihedrals[0] -def __fixed__improper__( - obj, idx=None, idx1=None, idx2=None, idx3=None, map=None -): +def __fixed__improper__(obj, idx=None, idx1=None, idx2=None, idx3=None, map=None): impropers = __fixed__impropers__( obj, idx, idx1, idx2, idx3, auto_reduce=False, map=map ) @@ -1006,8 +986,7 @@ def __fixed__improper__( raise KeyError("There is no matching improper in this view.") elif len(impropers) > 1: raise KeyError( - "More than one improper matches. Number of " - f"matches is {len(impropers)}." + "More than one improper matches. Number of " f"matches is {len(impropers)}." ) return impropers[0] @@ -1361,18 +1340,14 @@ def _apply(objs, func, *args, **kwargs): if str(func) == func: # we calling a named function - with ProgressBar( - total=len(objs), text="Looping through views" - ) as progress: + with ProgressBar(total=len(objs), text="Looping through views") as progress: for i, obj in enumerate(objs): result.append(getattr(obj, func)(*args, **kwargs)) progress.set_progress(i + 1) else: # we have been passed the function to call - with ProgressBar( - total=len(objs), text="Looping through views" - ) as progress: + with ProgressBar(total=len(objs), text="Looping through views") as progress: for i, obj in enumerate(objs): result.append(func(obj, *args, **kwargs)) progress.set_progress(i + 1) @@ -1601,6 +1576,7 @@ def _dynamics( device=None, precision=None, qm_engine=None, + lambda_interpolate=None, map=None, ): """ @@ -1746,6 +1722,18 @@ def _dynamics( The desired precision for the simulation (e.g. `single`, `mixed` or `double`) + qm_engine: + A sire.qm.QMMMEngine object to used to compute QM/MM forces + and energies on a subset of the atoms in the system. + + lambda_interpolate: float + The lambda value at which to interpolate the QM/MM forces and + energies, which can be used to perform end-state correction + simulations. A value of 1.0 is full QM, whereas a value of 0.0 is + full MM. If two values are specified, then lambda will be linearly + interpolated between the two values over the course of the + simulation, which lambda updated at the energy_frequency. + map: dict A dictionary of additional options. Note that any options set in this dictionary that are also specified via one of @@ -1866,6 +1854,7 @@ def _dynamics( restraints=restraints, fixed=fixed, qm_engine=qm_engine, + lambda_interpolate=lambda_interpolate, map=map, ) @@ -2328,9 +2317,7 @@ def _total_energy(obj, other=None, map=None): elif other is None: return calculate_energy(mols.molecules(), map=map) else: - return calculate_energy( - mols.molecules(), _to_molecules(other), map=map - ) + return calculate_energy(mols.molecules(), _to_molecules(other), map=map) Atom.energy = _atom_energy diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 253da0362..c9602dca9 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -31,6 +31,33 @@ def __init__(self, mols=None, map=None, **kwargs): mols.atoms().find(selection_to_atoms(mols, fixed_atoms)), ) + # see if this is an interpolation simulation + if map.specified("lambda_interpolate"): + if map["lambda_interpolate"].has_value(): + lambda_interpolate = map["lambda_interpolate"].value() + else: + lambda_interpolate = map["lambda_interpolate"].source() + + # Single lambda value. + try: + lambda_interpolate = float(lambda_interpolate) + map.set("lambda_value", lambda_interpolate) + # Two lambda values. + except: + try: + if not len(lambda_interpolate) == 2: + raise + lambda_interpolate = [float(x) for x in lambda_interpolate] + map.set("lambda_value", lambda_interpolate[0]) + except: + raise ValueError( + "'lambda_interpolate' must be a float or a list of two floats" + ) + self._is_interpolate = True + self._lambda_interpolate = lambda_interpolate + else: + self._is_interpolate = False + # get the forcefield info from the passed parameters # and from whatever we can glean from the molecules from ..system import ForceFieldInfo, System @@ -172,6 +199,7 @@ def _exit_dynamics_block( save_energy: bool = False, lambda_windows=[], save_velocities: bool = False, + delta_lambda: float = None, ): if not self._is_running: raise SystemError("Cannot stop dynamics that is not running!") @@ -220,24 +248,66 @@ def _exit_dynamics_block( ) sim_lambda_value = self._omm_mols.get_lambda() - nrgs[str(sim_lambda_value)] = nrgs["potential"] - if lambda_windows is not None: - for lambda_value in lambda_windows: - if lambda_value != sim_lambda_value: - self._omm_mols.set_lambda(lambda_value) - nrgs[str(lambda_value)] = ( - self._omm_mols.get_potential_energy( - to_sire_units=False - ).value_in_unit(openmm.unit.kilocalorie_per_mole) - * kcal_per_mol - ) + if self._is_interpolate: + nrgs["E(lambda)"] = nrgs["potential"] + nrgs.pop("potential") + if sim_lambda_value != 0.0: + self._omm_mols.set_lambda(0.0) + nrgs["E(lambda=0)"] = ( + self._omm_mols.get_potential_energy( + to_sire_units=False + ).value_in_unit(openmm.unit.kilocalorie_per_mole) + * kcal_per_mol + ) + else: + nrgs["E(lambda=0)"] = nrgs["E(lambda)"] + if sim_lambda_value != 1.0: + self._omm_mols.set_lambda(1.0) + nrgs["E(lambda=1)"] = ( + self._omm_mols.get_potential_energy( + to_sire_units=False + ).value_in_unit(openmm.unit.kilocalorie_per_mole) + * kcal_per_mol + ) + else: + nrgs["E(lambda=1)"] = nrgs["E(lambda)"] + + else: + nrgs[str(sim_lambda_value)] = nrgs["potential"] + + if lambda_windows is not None: + for lambda_value in lambda_windows: + if lambda_value != sim_lambda_value: + self._omm_mols.set_lambda(lambda_value) + nrgs[str(lambda_value)] = ( + self._omm_mols.get_potential_energy( + to_sire_units=False + ).value_in_unit(openmm.unit.kilocalorie_per_mole) + * kcal_per_mol + ) self._omm_mols.set_lambda(sim_lambda_value) - self._energy_trajectory.set( - self._current_time, nrgs, {"lambda": str(sim_lambda_value)} - ) + if self._is_interpolate: + self._energy_trajectory.set( + self._current_time, nrgs, {"lambda": f"{sim_lambda_value:.8f}"} + ) + else: + self._energy_trajectory.set( + self._current_time, nrgs, {"lambda": str(sim_lambda_value)} + ) + + # update the interpolation lambda value + if self._is_interpolate: + if delta_lambda: + sim_lambda_value += delta_lambda + # clamp to [0, 1] + if sim_lambda_value < 0.0: + sim_lambda_value = 0.0 + elif sim_lambda_value > 1.0: + sim_lambda_value = 1.0 + self._omm_mols.set_lambda(sim_lambda_value) self._is_running = False @@ -596,10 +666,6 @@ def run( if energy_frequency is not None: energy_frequency = u(energy_frequency) - if lambda_windows is not None: - if not isinstance(lambda_windows, list): - lambda_windows = [lambda_windows] - try: steps_to_run = int(time.to(picosecond) / self.timestep().to(picosecond)) except Exception: @@ -644,9 +710,33 @@ def run( else: frame_frequency = frame_frequency.to(picosecond) - if lambda_windows is None: - if self._map.specified("lambda_windows"): - lambda_windows = self._map["lambda_windows"].value() + completed = 0 + + frame_frequency_steps = int(frame_frequency / self.timestep().to(picosecond)) + + energy_frequency_steps = int(energy_frequency / self.timestep().to(picosecond)) + + # If performing QM/MM lambda interpolation, then we just compute energies + # for the pure MM (0.0) and QM (1.0) potentials. + if self._is_interpolate: + lambda_windows = [0.0, 1.0] + # Work out the lambda increment. + if isinstance(self._lambda_interpolate, list): + divisor = (steps_to_run / energy_frequency_steps) - 1.0 + delta_lambda = ( + self._lambda_interpolate[1] - self._lambda_interpolate[0] + ) / divisor + # Fixed lambda value. + else: + delta_lambda = None + else: + delta_lambda = None + if lambda_windows is not None: + if not isinstance(lambda_windows, list): + lambda_windows = [lambda_windows] + else: + if self._map.specified("lambda_windows"): + lambda_windows = self._map["lambda_windows"].value() def runfunc(num_steps): try: @@ -667,12 +757,6 @@ def process_block(state, state_has_cv, nsteps_completed): } ) - completed = 0 - - frame_frequency_steps = int(frame_frequency / self.timestep().to(picosecond)) - - energy_frequency_steps = int(energy_frequency / self.timestep().to(picosecond)) - def get_steps_till_save(completed: int, total: int): """Internal function to calculate the number of steps to run before the next save. This returns a tuple @@ -816,6 +900,7 @@ class NeedsMinimiseError(Exception): save_energy=save_energy, lambda_windows=lambda_windows, save_velocities=save_velocities, + delta_lambda=delta_lambda, ) saved_last_frame = False @@ -911,6 +996,7 @@ def __init__( restraints=None, fixed=None, qm_engine=None, + lambda_interpolate=None, ): from ..base import create_map from .. import u @@ -965,6 +1051,7 @@ def __init__( _add_extra(extras, "restraints", restraints) _add_extra(extras, "fixed", fixed) _add_extra(extras, "qm_engine", qm_engine) + _add_extra(extras, "lambda_interpolate", lambda_interpolate) map = create_map(map, extras) diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index a150e8a29..ce70e3e9a 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -595,8 +595,16 @@ def dynamics(self, *args, **kwargs): atoms will not be moved by dynamics. qm_engine: - A QMMMEngine object to used to compute QM/MM forces and energies - on a subset of the atoms in the system. + A sire.qm.QMMMEngine object to used to compute QM/MM forces + and energies on a subset of the atoms in the system. + + lambda_interpolate: float + The lambda value at which to interpolate the QM/MM forces and + energies, which can be used to perform end-state correction + simulations. A value of 1.0 is full QM, whereas a value of 0.0 is + full MM. If two values are specified, then lambda will be linearly + interpolated between the two values over the course of the + simulation, which lambda updated at the energy_frequency. platform: str The name of the OpenMM platform on which to run the dynamics, From 4b7cafe1d34f0d72939ae25abcb347e46c432c38 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 5 Dec 2023 09:23:18 +0000 Subject: [PATCH 060/468] Improve formatting of interpolation energy trajectory. --- src/sire/mol/_dynamics.py | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index c9602dca9..ab5831737 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -233,7 +233,12 @@ def _exit_dynamics_block( # should save energy here nrgs = {} - nrgs["kinetic"] = ( + if self._is_interpolate: + ke = "KE" + else: + ke = "kinetic" + + nrgs[ke] = ( self._omm_state.getKineticEnergy().value_in_unit( openmm.unit.kilocalorie_per_mole ) @@ -250,28 +255,28 @@ def _exit_dynamics_block( sim_lambda_value = self._omm_mols.get_lambda() if self._is_interpolate: - nrgs["E(lambda)"] = nrgs["potential"] + nrgs["PE(lambda)"] = nrgs["potential"] nrgs.pop("potential") if sim_lambda_value != 0.0: self._omm_mols.set_lambda(0.0) - nrgs["E(lambda=0)"] = ( + nrgs["PE(lambda=0)"] = ( self._omm_mols.get_potential_energy( to_sire_units=False ).value_in_unit(openmm.unit.kilocalorie_per_mole) * kcal_per_mol ) else: - nrgs["E(lambda=0)"] = nrgs["E(lambda)"] + nrgs["PE(lambda=0)"] = nrgs["PE(lambda)"] if sim_lambda_value != 1.0: self._omm_mols.set_lambda(1.0) - nrgs["E(lambda=1)"] = ( + nrgs["PE(lambda=1)"] = ( self._omm_mols.get_potential_energy( to_sire_units=False ).value_in_unit(openmm.unit.kilocalorie_per_mole) * kcal_per_mol ) else: - nrgs["E(lambda=1)"] = nrgs["E(lambda)"] + nrgs["PE(lambda=1)"] = nrgs["PE(lambda)"] else: nrgs[str(sim_lambda_value)] = nrgs["potential"] From d5b61b241f9bb178aefc52b5303be3ef6b3135ed Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 6 Dec 2023 08:47:03 +0000 Subject: [PATCH 061/468] Switch to OpenMM 8.1 conda-forge release. --- requirements_run.txt | 2 +- setup.py | 14 -------------- 2 files changed, 1 insertion(+), 15 deletions(-) diff --git a/requirements_run.txt b/requirements_run.txt index 802a78db6..c27ff5ae9 100644 --- a/requirements_run.txt +++ b/requirements_run.txt @@ -4,7 +4,7 @@ boost gsl lazy_import libnetcdf -openmm +openmm>=8.1 pandas python qt-main diff --git a/setup.py b/setup.py index 17537e862..c6d499341 100644 --- a/setup.py +++ b/setup.py @@ -390,20 +390,6 @@ def conda_install(dependencies, install_bss_reqs=False, install_emle_reqs=False) # Install additional requirements for EMLE. if install_emle_reqs: - # OpenMM 8.1.0beta. - cmd = [ - "mamba", - "install", - "--yes", - "-c", - "conda-forge/label/openmm_rc", - "openmm=8.1.0beta", - ] - status = subprocess.run(cmd) - if status.returncode != 0: - print("Something went wrong installing OpenMM 8.1.0beta!") - sys.exit(-1) - # librascal. cmd = [ "pip", From 8f71c368712385055bde026d52fe1d35b4e2559a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 6 Dec 2023 09:09:32 +0000 Subject: [PATCH 062/468] No need to pin OpenMM. --- requirements_run.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_run.txt b/requirements_run.txt index c27ff5ae9..802a78db6 100644 --- a/requirements_run.txt +++ b/requirements_run.txt @@ -4,7 +4,7 @@ boost gsl lazy_import libnetcdf -openmm>=8.1 +openmm pandas python qt-main From 7d6350dc03e713cad307b12b786d0b7c559eae33 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 19 Dec 2023 13:14:52 +0000 Subject: [PATCH 063/468] Try adding push trigger. --- .github/workflows/emle.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index b61365b7a..5f7824565 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -15,6 +15,9 @@ on: description: "Upload packages to anaconda (yes/no)?" required: true default: "no" + push: + branches: [feature_emle] + jobs: build: name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) From 3832d692ce5be8adf8c4725a62d2e1588b30ae71 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 19 Dec 2023 13:23:58 +0000 Subject: [PATCH 064/468] Add empty bss_reqs list. --- actions/update_recipe.py | 1 + 1 file changed, 1 insertion(+) diff --git a/actions/update_recipe.py b/actions/update_recipe.py index deade331f..b2c8ae768 100644 --- a/actions/update_recipe.py +++ b/actions/update_recipe.py @@ -54,6 +54,7 @@ else: emle_reqs = parse_requirements(os.path.join(srcdir, "requirements_emle.txt")) print(emle_reqs) + bss_reqs = [] test_reqs = parse_requirements(os.path.join(srcdir, "requirements_test.txt")) From c0910ec8e489bd046b38ba52ba067306c475fd1a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 19 Dec 2023 13:30:31 +0000 Subject: [PATCH 065/468] Remove push trigger. [ci skip] --- .github/workflows/emle.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 5f7824565..154d0d503 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -15,8 +15,6 @@ on: description: "Upload packages to anaconda (yes/no)?" required: true default: "no" - push: - branches: [feature_emle] jobs: build: From 40d5c66c80f06d59fc2ae6fb618d504068bb7323 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 19 Dec 2023 16:26:07 +0000 Subject: [PATCH 066/468] Include SireError header. [ci skip] --- wrapper/Convert/SireOpenMM/emle.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 8b173a22b..7713f4dc3 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -26,6 +26,7 @@ * \*********************************************/ +#include "SireError/errors.h" #include "SireMaths/vector.h" #include "SireVol/triclinicbox.h" From 9e2e947fb1381a2254f173ec1789c5be6a28d8ac Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 19 Dec 2023 20:15:55 +0000 Subject: [PATCH 067/468] Set CMAKE_REQUIRED_INCLUDES to include OpenMM_INCLUDE_DIR. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 530f50cde..8584049fb 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -27,6 +27,10 @@ if (${SIRE_USE_OPENMM}) include(CheckCXXSourceRuns) + # Temporarily add OpenMM include directory to CMAKE_REQUIRED_INCLUDES. + set(CMAKE_OLD_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES}) + set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${OpenMM_INCLUDE_DIR}) + # Whether or not we have CustomCPPForceImpl (OpenMM 8.1+) CHECK_CXX_SOURCE_RUNS(" #include \"openmm/internal/ContextImpl.h\" @@ -40,6 +44,9 @@ if (${SIRE_USE_OPENMM}) }" CAN_USE_CUSTOMCPPFORCE) + # Restore CMAKE_REQUIRED_INCLUDES. + set(CMAKE_REQUIRED_INCLUDES ${CMAKE_OLD_REQUIRED_INCLUDES}) + if (CAN_USE_CUSTOMCPPFORCE) message(STATUS "OpenMM version supports CustomCPPForce") add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") From 1fe153323e3f251b6ba561afc131b3a3e955d10b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 21 Dec 2023 11:08:55 +0000 Subject: [PATCH 068/468] Install BioSimSpace requirements too. --- actions/update_recipe.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/actions/update_recipe.py b/actions/update_recipe.py index b2c8ae768..1cf4355e3 100644 --- a/actions/update_recipe.py +++ b/actions/update_recipe.py @@ -47,14 +47,13 @@ print(host_reqs) run_reqs = parse_requirements(os.path.join(srcdir, "requirements_run.txt")) print(run_reqs) -if not is_emle: - bss_reqs = parse_requirements(os.path.join(srcdir, "requirements_bss.txt")) - print(bss_reqs) - emle_reqs = [] -else: +bss_reqs = parse_requirements(os.path.join(srcdir, "requirements_bss.txt")) +print(bss_reqs) +if is_emle: emle_reqs = parse_requirements(os.path.join(srcdir, "requirements_emle.txt")) print(emle_reqs) - bss_reqs = [] +else: + emle_reqs = [] test_reqs = parse_requirements(os.path.join(srcdir, "requirements_test.txt")) From 15f57b7f627ba31c7b152ca97348d49f03a5a799 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 21 Dec 2023 11:09:13 +0000 Subject: [PATCH 069/468] No need to use openmm_rc label. --- .github/workflows/emle.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 154d0d503..987f676c2 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -62,7 +62,7 @@ jobs: run: mkdir ${{ github.workspace }}/build # - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c conda-forge/label/openmm_rc -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # upload to the 'test' channel From a319dc99d16675c91c99e70523fa0b267ef070af Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 8 Jan 2024 11:48:27 +0000 Subject: [PATCH 070/468] Guard EMLEEngineImpl::computeForce against missing CustomCPPForceImpl. --- wrapper/Convert/SireOpenMM/emle.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 7713f4dc3..2fdf5d16a 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -252,6 +252,7 @@ double EMLEEngineImpl::computeForce( const std::vector &positions, std::vector &forces) { +#ifdef SIRE_USE_CUSTOMCPPFORCE // If this is the first step, then setup information for the neighbour list. if (this->step_count == 0) { @@ -463,6 +464,7 @@ double EMLEEngineImpl::computeForce( // Finally, return the energy. return lambda * energy; +#endif } boost::tuple>, QVector>> From 7af6298bef71afc946f1edcfeebaf0e591c7df4f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 8 Jan 2024 11:50:41 +0000 Subject: [PATCH 071/468] Force use of CustomCPPForceImpl until we figure out build issue. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 30 +++++++++++------------ 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 8584049fb..8edf61462 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -28,31 +28,31 @@ if (${SIRE_USE_OPENMM}) include(CheckCXXSourceRuns) # Temporarily add OpenMM include directory to CMAKE_REQUIRED_INCLUDES. - set(CMAKE_OLD_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES}) - set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${OpenMM_INCLUDE_DIR}) + #set(CMAKE_OLD_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES}) + #set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${OpenMM_INCLUDE_DIR}) # Whether or not we have CustomCPPForceImpl (OpenMM 8.1+) - CHECK_CXX_SOURCE_RUNS(" + #CHECK_CXX_SOURCE_RUNS(" #include \"openmm/internal/ContextImpl.h\" #include \"openmm/internal/CustomCPPForceImpl.h\" - int main() - { - OpenMM::ContextImpl* context = NULL; - OpenMM::CustomCPPForceImpl* force = NULL; - return 0; - }" - CAN_USE_CUSTOMCPPFORCE) + # int main() + #{ + # OpenMM::ContextImpl* context = NULL; + # OpenMM::CustomCPPForceImpl* force = NULL; + # return 0; + #}" + #CAN_USE_CUSTOMCPPFORCE) # Restore CMAKE_REQUIRED_INCLUDES. - set(CMAKE_REQUIRED_INCLUDES ${CMAKE_OLD_REQUIRED_INCLUDES}) + #set(CMAKE_REQUIRED_INCLUDES ${CMAKE_OLD_REQUIRED_INCLUDES}) - if (CAN_USE_CUSTOMCPPFORCE) + #if (CAN_USE_CUSTOMCPPFORCE) message(STATUS "OpenMM version supports CustomCPPForce") add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") - else() - message(STATUS "OpenMM version does not support CustomCPPForce") - endif() + #else() + #message(STATUS "OpenMM version does not support CustomCPPForce") + #endif() # Define the sources in SireOpenMM set ( SIREOPENMM_SOURCES From f38c16f3f734095fb4617f0211eb1af0e52c4da3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 9 Jan 2024 16:14:41 +0000 Subject: [PATCH 072/468] Refactor EMLEEngine setup into sire.qm.emle function. --- src/sire/mol/_dynamics.py | 28 ---- src/sire/qm/CMakeLists.txt | 1 + src/sire/qm/__init__.py | 10 +- src/sire/qm/_emle.py | 160 +++++++++++++++++++++ src/sire/system/_system.py | 60 -------- tests/qm/test_emle.py | 11 +- wrapper/Convert/SireOpenMM/CMakeLists.txt | 2 +- wrapper/Convert/SireOpenMM/emle.h | 2 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 7 + 9 files changed, 176 insertions(+), 105 deletions(-) create mode 100644 src/sire/qm/_emle.py diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index ab5831737..1da9586ad 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -1006,34 +1006,6 @@ def __init__( from ..base import create_map from .. import u - # Set the global indices of the QM atoms in the engine. - if qm_engine is not None and mols is not None: - try: - # Work out the indices of the QM atoms. - atoms_to_find = mols["property is_qm"].atoms() - idxs = mols.atoms().find(atoms_to_find) - qm_engine.set_atoms(idxs) - - # Work out the atomic numbers of the QM atoms. - elem_prop = map["element"] - numbers = [ - atom.property(f"{elem_prop}").num_protons() - for atom in atoms_to_find - ] - qm_engine.set_numbers(numbers) - - # Work out the atomic charge for all atoms in the system. - charge_prop = map["charge"] - charges = [ - atom.property(f"{charge_prop}").value() for atom in mols.atoms() - ] - qm_engine.set_charges(charges) - except: - raise ValueError( - "Unable to set QM atoms in the engine. " - "Have you set a QM molecule?" - ) - extras = {} _add_extra(extras, "cutoff", cutoff) diff --git a/src/sire/qm/CMakeLists.txt b/src/sire/qm/CMakeLists.txt index 89cd53fb2..8c1057b00 100644 --- a/src/sire/qm/CMakeLists.txt +++ b/src/sire/qm/CMakeLists.txt @@ -7,6 +7,7 @@ # Add your script to this list set ( SCRIPTS __init__.py + _emle.py ) # installation diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index 6f7e2f1b8..a677d3e0a 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -1,9 +1,3 @@ -__all__ = ["EMLEEngine"] +__all__ = ["emle"] -from ..legacy import Convert as _Convert - -from .. import use_new_api as _use_new_api - -_use_new_api() - -EMLEEngine = _Convert._SireOpenMM.EMLEEngine +from ._emle import emle diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py new file mode 100644 index 000000000..6fd49b193 --- /dev/null +++ b/src/sire/qm/_emle.py @@ -0,0 +1,160 @@ +__all__ = ["emle"] + +from ..legacy import Convert as _Convert + +from .. import use_new_api as _use_new_api + +_use_new_api() + +_EMLEEngine = _Convert._SireOpenMM.EMLEEngine + +try: + from emle.emle import EMLECalculator as _EMLECalculator + + _has_emle = True +except: + _has_emle = False + + +def emle( + mols, + calculator, + qm_index, + cutoff="7.5A", + neighbourlist_update_frequency=20, + map=None, +): + """ + Create an EMLEEngine object to allow QM/MM simulations using sire.mol.dynamics. + + Parameters + ---------- + + mols : sire.system.System + The molecular system. + + calculator : emle.emle.EMLECalculator + The EMLECalculator object to use for elecotrostatic embedding calculations. + + qm_index : int + The index of the QM molecule in the system. + + cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" + The cutoff to use for the QM/MM calculation. + + neighbourlist_update_frequency : int, optional, default=20 + The frequency with which to update the neighbourlist. + + Returns + ------- + + engine : sire.legacy.Convert._SireOpenMM.EMLEEngine + The EMLEEngine object. + """ + if not _has_emle: + raise ImportError( + "Could not import emle. Please install emle-egine and try again." + ) + + from ..base import create_map as _create_map + from ..system import System as _System + from ..legacy import Units as _Units + from ..units import angstrom as _angstrom + from .. import u as _u + + if not isinstance(mols, _System): + raise TypeError("mols must be a of type 'sire.System'") + + if not isinstance(calculator, _EMLECalculator): + raise TypeError("'calculator' must be a of type 'emle.emle.EMLECalculator'") + + if not isinstance(qm_index, int): + raise TypeError("'qm_index' must be of type 'int'") + + try: + qm_mol = mols[qm_index] + except: + raise ValueError(f"qm_index must be in range [0, {len(mols)})") + + if not isinstance(cutoff, (str, _Units.GeneralUnit)): + raise TypeError( + "cutoff must be of type 'str' or 'sire.legacy.Units.GeneralUnit'" + ) + + if isinstance(cutoff, str): + try: + cutoff = _u(cutoff) + except: + raise ValueError("Unable to parse cutoff as a GeneralUnit") + + if not cutoff.has_same_units(_angstrom): + raise ValueError("'cutoff' must be in units of length") + + if not isinstance(neighbourlist_update_frequency, int): + raise TypeError("'neighbourlist_update_frequency' must be of type 'int'") + + if neighbourlist_update_frequency < 0: + raise ValueError("'neighbourlist_update_frequency' must be >= 0") + + if map is not None: + if not isinstance(map, dict): + raise TypeError("'map' must be of type 'dict'") + map = _create_map(map) + + # Create the EMLEEngine. + engine = _EMLEEngine( + calculator, + cutoff, + neighbourlist_update_frequency, + ) + + # Work out the indices of the QM atoms. + try: + atoms_to_find = qm_mol.atoms() + idxs = mols.atoms().find(atoms_to_find) + engine.set_atoms(idxs) + except: + raise Exception("Unable to set atom indices for the QM region.") + + # Work out the atomic numbers of the QM atoms. + try: + elem_prop = map["element"] + numbers = [ + atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find + ] + engine.set_numbers(numbers) + except: + raise Exception("Unable to set atomic numbers for the QM region.") + + # Work out the atomic charge for all atoms in the system. + try: + charge_prop = map["charge"] + charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] + engine.set_charges(charges) + except: + raise Exception("Unable to set atomic charges for the system.") + + # Get the QM property flag. + qm_propname = map["is_qm"] + + # Check for existing QM molecules. Currently we only support a single + # molecule. + try: + qm_mols = mols[f"property {qm_propname}"].molecules() + except: + qm_mols = [] + + if len(qm_mols) > 0: + raise ValueError("This system already contains a QM molecule!") + + # Create a cursor. + c = qm_mol.cursor() + + # Flag the molecule as QM. + c[qm_propname] = True + + # Commit the changes and update. + qm_mol = c.commit() + mols.update(qm_mol) + + return engine diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index ce70e3e9a..9a7fe6ac9 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -874,66 +874,6 @@ def set_energy_trajectory(self, trajectory, map=None): self._system.set_property(traj_propname.source(), trajectory) - def set_qm_molecule(self, index, map=None): - """ - Set the specified molecule to be a QM molecule. - """ - if index < 0 or index > self.num_molecules() - 1: - raise ValueError( - f"Index {index} is out of range for the number of " - f"molecules in this system ({self.num_molecules()})" - ) - - from ..base import create_map - - map = create_map(map) - - qm_propname = map["is_qm"] - - # Check for existing QM molecules. Currently we only support a single - # molecule. - try: - qm_mols = self[f"property {qm_propname}"].molecules() - except: - qm_mols = [] - - if len(qm_mols) > 0: - raise ValueError("This system already contains a QM molecule!") - - # Extract the molecule. - mol = self[index] - - # Create a cursor. - c = mol.cursor() - - # Flag the molecule as QM. - c[qm_propname] = True - - # Commit the changes and update. - mol = c.commit() - self.update(mol) - - def unset_qm_molecule(self, map=None): - """ - Unset the QM molecule. - """ - try: - from ..base import create_map - - map = create_map(map) - - qm_propname = map["is_qm"] - - # Loop over the QM molecules and unset them. - qm_mols = self[f"property {qm_propname}"].molecules() - for mol in qm_mols: - c = mol.cursor() - c[qm_propname] = False - mol = c.commit() - self.update(mol) - except: - pass - def clear_energy_trajectory(self, map=None): """ Completely clear any existing energy trajectory diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index a4e026242..88bd70b20 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -2,9 +2,9 @@ import pytest import tempfile -from sire.legacy.Convert._SireOpenMM import EMLECallback +from sire.legacy.Convert._SireOpenMM import EMLECallback, EMLEEngine -from sire.qm import EMLEEngine +from sire.qm import emle try: from emle.emle import EMLECalculator @@ -52,17 +52,14 @@ def test_interpolate(ala_mols): # Create an EMLE calculator. calculator = EMLECalculator(device="cpu", log=0, save_settings=False) - # Create an EMLEE engine bound to the calculator. - engine = EMLEEngine(calculator) - # Create a dynamics object. d = mols.dynamics(timestep="1fs", constraint="none", platform="cpu") # Get the pure MM energy. nrg_mm = d.current_potential_energy() - # Set the first molecule as QM. - mols.set_qm_molecule(0) + # Create an EMLE engine bound to the calculator. + engine = emle(mols, calculator, 0) # Create a QM/MM capable dynamics object. d = mols.dynamics( diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 8edf61462..88ba4f630 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -25,7 +25,7 @@ if (${SIRE_USE_OPENMM}) # Other python wrapping directories include_directories(${CMAKE_SOURCE_DIR}) - include(CheckCXXSourceRuns) + #include(CheckCXXSourceRuns) # Temporarily add OpenMM include directory to CMAKE_REQUIRED_INCLUDES. #set(CMAKE_OLD_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES}) diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 64d294f3d..db57e83fd 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -129,7 +129,7 @@ namespace SireOpenMM */ EMLEEngine( bp::object, - SireUnits::Dimension::Length cutoff=8.0*SireUnits::angstrom, + SireUnits::Dimension::Length cutoff=7.5*SireUnits::angstrom, int neighbour_list_frequency=20, double lambda=1.0 ); diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index afb537d33..2ce84c5fd 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -460,6 +460,7 @@ double LambdaLever::setLambda(OpenMM::Context &context, else { // get copies of the forcefields in which the parameters will be changed + //auto qmff = this->getForce("qmmm", system); auto cljff = this->getForce("clj", system); auto ghost_ghostff = this->getForce("ghost/ghost", system); auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); @@ -473,6 +474,12 @@ double LambdaLever::setLambda(OpenMM::Context &context, std::vector custom_params = {0.0, 0.0, 0.0, 0.0}; + /*if (qmff != 0) + { + double lam = this->lambda_schedule.morph("qm", 1.0, 0.0, lambda_value); + qmff->setLambda(lam); + }*/ + // change the parameters for all of the perturbable molecules for (int i = 0; i < this->perturbable_mols.count(); ++i) { From ef702864318b73e22c6c2edc98fa153f6e7f8d71 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jan 2024 08:52:38 +0000 Subject: [PATCH 073/468] Switch to QMMMForce and add LamdaLever template specialisation. --- wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 4 ++-- wrapper/Convert/SireOpenMM/emle.h | 2 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 6 +++--- wrapper/Convert/SireOpenMM/lambdalever.h | 7 +++++++ wrapper/Convert/SireOpenMM/qmmm.cpp | 2 +- wrapper/Convert/SireOpenMM/qmmm.h | 6 +++--- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 2 +- 7 files changed, 18 insertions(+), 11 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index e46415190..cdf93bdb3 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -178,9 +178,9 @@ BOOST_PYTHON_MODULE(_SireOpenMM) // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) register_tuple>, QVector>>>(); - bp::class_, boost::noncopyable>("QMMMEngine", bp::no_init); + bp::class_, boost::noncopyable>("QMMMForce", bp::no_init); - bp::class_>("EMLEEngine", + bp::class_>("EMLEEngine", bp::init( ( bp::arg("py_object"), diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index db57e83fd..4163d5a5a 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -106,7 +106,7 @@ namespace SireOpenMM QString callback; }; - class EMLEEngine : public SireBase::ConcreteProperty + class EMLEEngine : public SireBase::ConcreteProperty { public: //! Default constructor. diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 2ce84c5fd..e8d87ab5b 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -460,7 +460,7 @@ double LambdaLever::setLambda(OpenMM::Context &context, else { // get copies of the forcefields in which the parameters will be changed - //auto qmff = this->getForce("qmmm", system); + auto qmff = this->getForce("qmmm", system); auto cljff = this->getForce("clj", system); auto ghost_ghostff = this->getForce("ghost/ghost", system); auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); @@ -474,11 +474,11 @@ double LambdaLever::setLambda(OpenMM::Context &context, std::vector custom_params = {0.0, 0.0, 0.0, 0.0}; - /*if (qmff != 0) + if (qmff != 0) { double lam = this->lambda_schedule.morph("qm", 1.0, 0.0, lambda_value); qmff->setLambda(lam); - }*/ + } // change the parameters for all of the perturbable molecules for (int i = 0; i < this->perturbable_mols.count(); ++i) diff --git a/wrapper/Convert/SireOpenMM/lambdalever.h b/wrapper/Convert/SireOpenMM/lambdalever.h index 4f7445b44..cc3cbeff9 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.h +++ b/wrapper/Convert/SireOpenMM/lambdalever.h @@ -30,6 +30,7 @@ #define SIREOPENMM_LAMBDALEVER_H #include "openmmmolecule.h" +#include "qmmm.h" #include "SireCAS/lambdaschedule.h" @@ -153,6 +154,12 @@ namespace SireOpenMM return "OpenMM::CustomBondForce"; } + template <> + inline QString _get_typename() + { + return "SireOpenMM::QMMMForce"; + } + /** Return the OpenMM::Force (of type T) that is called 'name' * from the passed OpenMM::System. This returns 0 if the force * doesn't exist diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index 7f2b6680a..83cc8bf50 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -30,6 +30,6 @@ using namespace SireOpenMM; -QMMMEngine::~QMMMEngine() +QMMMForce::~QMMMForce() { } diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 06c750fb5..ef1f549af 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -42,10 +42,10 @@ SIRE_BEGIN_HEADER namespace SireOpenMM { - class QMMMEngine : public SireBase::Property, public OpenMM::Force + class QMMMForce : public SireBase::Property, public OpenMM::Force { public: - virtual ~QMMMEngine(); + virtual ~QMMMForce(); //! Get the lambda weighting factor. virtual double getLambda() const = 0; @@ -81,7 +81,7 @@ namespace SireOpenMM virtual OpenMM::ForceImpl *createImpl() const = 0; }; - typedef SireBase::PropPtr QMMEnginePtr; + typedef SireBase::PropPtr QMMEnginePtr; } SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index bc63f2b38..e08b42a48 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -748,7 +748,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } // now create the engine for computing QM or ML forces on atoms - QMMMEngine *qmff = 0; + QMMMForce *qmff = 0; QString qm_engine; if (map.specified("qm_engine")) From d9aa605408c5643275fc907fe371a8c70647e104 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jan 2024 08:58:43 +0000 Subject: [PATCH 074/468] Refactor common QM utility functions into utility module. --- src/sire/qm/CMakeLists.txt | 1 + src/sire/qm/_emle.py | 29 ++++------------------------- src/sire/qm/_utils.py | 38 ++++++++++++++++++++++++++++++++++++++ tests/qm/test_emle.py | 2 +- 4 files changed, 44 insertions(+), 26 deletions(-) create mode 100644 src/sire/qm/_utils.py diff --git a/src/sire/qm/CMakeLists.txt b/src/sire/qm/CMakeLists.txt index 8c1057b00..d2a02efb8 100644 --- a/src/sire/qm/CMakeLists.txt +++ b/src/sire/qm/CMakeLists.txt @@ -8,6 +8,7 @@ set ( SCRIPTS __init__.py _emle.py + _utils.py ) # installation diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 6fd49b193..eedbdc138 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -108,31 +108,10 @@ def emle( neighbourlist_update_frequency, ) - # Work out the indices of the QM atoms. - try: - atoms_to_find = qm_mol.atoms() - idxs = mols.atoms().find(atoms_to_find) - engine.set_atoms(idxs) - except: - raise Exception("Unable to set atom indices for the QM region.") + from ._utils import _configure_engine - # Work out the atomic numbers of the QM atoms. - try: - elem_prop = map["element"] - numbers = [ - atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find - ] - engine.set_numbers(numbers) - except: - raise Exception("Unable to set atomic numbers for the QM region.") - - # Work out the atomic charge for all atoms in the system. - try: - charge_prop = map["charge"] - charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] - engine.set_charges(charges) - except: - raise Exception("Unable to set atomic charges for the system.") + # Configure the engine. + engine = _configure_engine(engine, mols, qm_mol, map) # Get the QM property flag. qm_propname = map["is_qm"] @@ -157,4 +136,4 @@ def emle( qm_mol = c.commit() mols.update(qm_mol) - return engine + return mols, engine diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py new file mode 100644 index 000000000..688b6bce3 --- /dev/null +++ b/src/sire/qm/_utils.py @@ -0,0 +1,38 @@ +def _configure_engine(engine, mols, qm_mol, map): + """ + Internal helper function to configure a QM engine ready for dynamics. + """ + + # Work out the indices of the QM atoms. + try: + atoms_to_find = qm_mol.atoms() + idxs = mols.atoms().find(atoms_to_find) + engine.set_atoms(idxs) + except: + raise Exception("Unable to set atom indices for the QM region.") + + # Work out the atomic numbers of the QM atoms. + try: + elem_prop = map["element"] + numbers = [ + atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find + ] + engine.set_numbers(numbers) + except: + raise Exception("Unable to set atomic numbers for the QM region.") + + # Work out the atomic charge for all atoms in the system. + try: + charge_prop = map["charge"] + charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] + engine.set_charges(charges) + except: + raise Exception("Unable to set atomic charges for the system.") + + return engine + + +def _create_merged_mol(qm_mol, map): + """ + Internal helper function to create a merged molecule from the QM molecule. + """ diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 88bd70b20..71025e8f7 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -59,7 +59,7 @@ def test_interpolate(ala_mols): nrg_mm = d.current_potential_energy() # Create an EMLE engine bound to the calculator. - engine = emle(mols, calculator, 0) + mols, engine = emle(mols, calculator, 0) # Create a QM/MM capable dynamics object. d = mols.dynamics( From bb787304d342d790c784bb85065f6f89e9f6c103 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jan 2024 10:17:05 +0000 Subject: [PATCH 075/468] Switch to using existing perturbable molecule functionality. --- src/sire/qm/_emle.py | 25 +- src/sire/qm/_utils.py | 208 +++++ tests/qm/test_emle.py | 2 +- wrapper/Convert/SireOpenMM/_sommcontext.py | 5 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 757 +++++++----------- .../SireOpenMM/sire_to_openmm_system.cpp | 4 +- 6 files changed, 488 insertions(+), 513 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index eedbdc138..bfca6ac5d 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -108,32 +108,15 @@ def emle( neighbourlist_update_frequency, ) - from ._utils import _configure_engine + from ._utils import _configure_engine, _create_merged_mol # Configure the engine. engine = _configure_engine(engine, mols, qm_mol, map) - # Get the QM property flag. - qm_propname = map["is_qm"] + # Create the merged molecule. + qm_mol = _create_merged_mol(qm_mol, map) - # Check for existing QM molecules. Currently we only support a single - # molecule. - try: - qm_mols = mols[f"property {qm_propname}"].molecules() - except: - qm_mols = [] - - if len(qm_mols) > 0: - raise ValueError("This system already contains a QM molecule!") - - # Create a cursor. - c = qm_mol.cursor() - - # Flag the molecule as QM. - c[qm_propname] = True - - # Commit the changes and update. - qm_mol = c.commit() + # Update the molecule in the system. mols.update(qm_mol) return mols, engine diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 688b6bce3..a3a725d84 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -36,3 +36,211 @@ def _create_merged_mol(qm_mol, map): """ Internal helper function to create a merged molecule from the QM molecule. """ + + from ..legacy import CAS as _CAS + from ..legacy import Mol as _Mol + from ..legacy import MM as _MM + + # Get the user defined names for the properties that we need to + # merge. + bond_prop = map["bond"] + angle_prop = map["angle"] + dihedral_prop = map["dihedral"] + improper_prop = map["improper"] + charge_prop = map["charge"] + connectivity_prop = map["connectivity"] + + # Get the molecular info object. + info = qm_mol.info() + + # Make an editable version of the molecule. + edit_mol = qm_mol.edit() + + for prop in qm_mol.property_keys(): + # Bonds. + if prop == bond_prop: + # Copy the bonds to the lambda = 1 state. + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() + + # Create an equivalent set of bonds for the lambda = 0 state with + # zeroed force constants. + + bonds = _MM.TwoAtomFunctions(info) + + for bond in qm_mol.property(prop).potentials(): + # Extract the atoms involved in the bond.:w + atom0 = info.atom_idx(bond.atom0()) + atom1 = info.atom_idx(bond.atom1()) + + # CAS variable for the bond. + r = _CAS.Symbol("r") + + # Create a null AmberBond. + amber_bond = _MM.AmberBond(0, r) + + # Set the new bond. + bonds.set(atom0, atom1, amber_bond.to_expression(r)) + + # Set the bonds for the lambda = 0 state. + edit_mol = edit_mol.set_property(prop + "0", bonds).molecule() + + # Finally, delete the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + + # Angles. + elif prop == angle_prop: + # Copy the angles to the lambda = 1 state. + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() + + # Create an equivalent set of angles for the lambda = 0 state with + # zeroed force constants. + + angles = _MM.ThreeAtomFunctions(info) + + for angle in qm_mol.property(prop).potentials(): + # Extract the atoms involved in the angle. + atom0 = info.atom_idx(angle.atom0()) + atom1 = info.atom_idx(angle.atom1()) + atom2 = info.atom_idx(angle.atom2()) + + # CAS variable for the angle. + theta = _CAS.Symbol("theta") + + # Create a null AmberAngle. + amber_angle = _MM.AmberAngle(0.0, theta) + + # Set the new angle. + angles.set(atom0, atom1, atom2, amber_angle.to_expression(theta)) + + # Set the angles for the lambda = 0 state. + edit_mol = edit_mol.set_property(prop + "0", angles).molecule() + + # Finally, delete the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + + # Dihedrals. + elif prop == dihedral_prop: + # Copy the dihedrals to the lambda = 1 state. + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() + + # Create an equivalent set of dihedrals for the lambda = 0 state + # with zeroed force constants. + + dihedrals = _MM.FourAtomFunctions(info) + + for dihedral in qm_mol.property(prop).potentials(): + # Extract the atoms involved in the dihedral. + atom0 = info.atom_idx(dihedral.atom0()) + atom1 = info.atom_idx(dihedral.atom1()) + atom2 = info.atom_idx(dihedral.atom2()) + atom3 = info.atom_idx(dihedral.atom3()) + + # CAS varialbe for the dihedral. + phi = _CAS.Symbol("phi") + + # Create a hull AmberDihedral. + amber_dihedral = _MM.AmberDihedral(0, phi) + + # Set the new dihedral. + dihedrals.set( + atom0, + atom1, + atom2, + atom3, + amber_dihedral.to_expression(phi), + ) + + # Set the dihedrals for the lambda = 0 state. + edit_mol = edit_mol.set_property(prop + "0", dihedrals).molecule() + + # Finally, delete the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + + # Impropers. + elif prop == improper_prop: + # Copy the impropers to the lambda = 1 state. + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() + + # Create an equivalent set of impropers for the lambda = 0 state + # with zeroed force constants. + + impropers = _MM.FourAtomFunctions(info) + + for improper in qm_mol.property(prop).potentials(): + # Extract the atoms involved in the improper. + atom0 = info.atom_idx(improper.atom0()) + atom1 = info.atom_idx(improper.atom1()) + atom2 = info.atom_idx(improper.atom2()) + atom3 = info.atom_idx(improper.atom3()) + + # CAS variable for the improper. + psi = _CAS.Symbol("psi") + + # Create a null AmberDihedral. + amber_improper = _MM.AmberDihedral(0, psi) + + # Set the new improper. + impropers.set( + atom0, + atom1, + atom2, + atom3, + amber_improper.to_expression(psi), + ) + + # Set the impropers for the lambda = 0 state. + edit_mol = edit_mol.set_property(prop + "0", impropers).molecule() + + # Finally, delete the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + + # Charge. + elif prop == charge_prop: + # Copy the charges to the lambda = 1 state. + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() + + # Create a set of null charges for the lambda = 0 state. + charges = _Mol.AtomCharges(info) + edit_mol = edit_mol.set_property(prop + "0", charges).molecule() + + # Finally, delete the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + + # Connectivity. + elif prop == connectivity_prop: + pass + + # Everything else. + else: + # All other properties remain the same in both end states. + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() + + # Delete the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + + # Flag the molecule as perturbable. + edit_mol = edit_mol.set_property(map["is_perturbable"], True).molecule() + + # Commit the changes. + qm_mol = edit_mol.commit() + + # Link to the perturbation to the reference state. + qm_mol = qm_mol.perturbation().link_to_reference().commit() + + # Return the merged molecule. + return qm_mol diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 71025e8f7..d50c43d34 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -70,7 +70,7 @@ def test_interpolate(ala_mols): nrg_emle = d.current_potential_energy() # Get interpolated MM energy. - d.set_lambda(0.0) + d.set_lambda(1.0) nrg_mm_interp = d.current_potential_energy() # Make sure this agrees with the standard MM energy. diff --git a/wrapper/Convert/SireOpenMM/_sommcontext.py b/wrapper/Convert/SireOpenMM/_sommcontext.py index 641b1d0d8..a138052ac 100644 --- a/wrapper/Convert/SireOpenMM/_sommcontext.py +++ b/wrapper/Convert/SireOpenMM/_sommcontext.py @@ -46,10 +46,7 @@ def __init__( elif map.specified("lambda_value"): lambda_value = map["lambda_value"].value().as_double() elif map.specified("qm_engine"): - # If there is a QM engine then default lambda = 1.0 unless - # explcitly specified. This means that the QM region will - # be modelled with full QM. - lambda_value = 1.0 + lambda_value = 0.0 else: lambda_value = 0.0 diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index e8d87ab5b..0ce8a79c3 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -249,557 +249,346 @@ double LambdaLever::setLambda(OpenMM::Context &context, // pointers to the forces... OpenMM::System &system = const_cast(context.getSystem()); - // First try to get the QM forcefield. If it exists, then we will updated the - // forcefield parameters and set the lambda value in the customCCPForce. - if (this->getForceIndex("emle") != -1) + // get copies of the forcefields in which the parameters will be changed + auto qmff = this->getForce("qmff", system); + auto cljff = this->getForce("clj", system); + auto ghost_ghostff = this->getForce("ghost/ghost", system); + auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); + auto ghost_14ff = this->getForce("ghost-14", system); + auto bondff = this->getForce("bond", system); + auto angff = this->getForce("angle", system); + auto dihff = this->getForce("torsion", system); + + // we know if we have peturbable ghost atoms if we have the ghost forcefields + const bool have_ghost_atoms = (ghost_ghostff != 0 or ghost_nonghostff != 0); + + std::vector custom_params = {0.0, 0.0, 0.0, 0.0}; + + if (qmff != 0) { - // First update the lambda value in the QM/MM engine. - auto qmff = this->getForce("emle", system); - qmff->setLambda(lambda_value); - - // get copies of the forcefields in which the parameters will be changed - auto cljff = this->getForce("clj", system); - auto bondff = this->getForce("bond", system); - auto angff = this->getForce("angle", system); - auto dihff = this->getForce("torsion", system); - - // Now scale the MM contributions to QM molecules by 1.0 - lambda. - // This allows the use of lambda interpolation for end-state correction - // simulations. - const auto lam = 1.0 - lambda_value; - - // Change the parameters for all of the QM molecules. We only change the - // force constant of bonded terms and update the charge scale factor for - // the Coulomb interaction. The LJ parameters are not changed. - for (int i = 0; i < this->qm_mols.size(); ++i) - { - const auto &qm_mol = this->qm_mols[i]; - const auto &start_idxs = this->start_indices_qm[i]; - - // calculate the new parameters for this lambda value - - const auto morphed_charges = this->lambda_schedule.morph( - "charge", - QVector(qm_mol.getCharges().size(), 0.0), - qm_mol.getCharges(), - lam); - - const auto sigmas = qm_mol.getSigmas(); - - const auto epsilons = qm_mol.getEpsilons(); - - const auto alphas = qm_mol.getAlphas(); - - const auto morphed_bond_k = this->lambda_schedule.morph( - "bond_k", - QVector(qm_mol.getBondKs().size(), 0.0), - qm_mol.getBondKs(), - lam); - - const auto bond_length = qm_mol.getBondLengths(); - - const auto morphed_angle_k = this->lambda_schedule.morph( - "angle_k", - QVector(qm_mol.getAngleKs().size(), 0.0), - qm_mol.getAngleKs(), - lam); - - const auto angle_size = qm_mol.getAngleSizes(); - - const auto torsion_phase = qm_mol.getTorsionPhases(); - - const auto morphed_torsion_k = this->lambda_schedule.morph( - "torsion_k", - QVector(qm_mol.getTorsionKs().size(), 0.0), - qm_mol.getTorsionKs(), - lam); - - const auto morphed_charge_scale = this->lambda_schedule.morph( - "charge_scale", - QVector(qm_mol.getChargeScales().size(), 0.0), - qm_mol.getChargeScales(), - lam); - - const auto lj_scale = qm_mol.getLJScales(); + double lam = this->lambda_schedule.morph("qmff", 1.0, 0.0, lambda_value); + qmff->setLambda(lam); + } - // now update the forcefields - int start_index = start_idxs.value("clj", -1); + // change the parameters for all of the perturbable molecules + for (int i = 0; i < this->perturbable_mols.count(); ++i) + { + const auto &perturbable_mol = this->perturbable_mols[i]; + const auto &start_idxs = this->start_indices_pert[i]; + + // calculate the new parameters for this lambda value + const auto morphed_charges = this->lambda_schedule.morph( + "charge", + perturbable_mol.getCharges0(), + perturbable_mol.getCharges1(), + lambda_value); + + const auto morphed_sigmas = this->lambda_schedule.morph( + "sigma", + perturbable_mol.getSigmas0(), + perturbable_mol.getSigmas1(), + lambda_value); + + const auto morphed_epsilons = this->lambda_schedule.morph( + "epsilon", + perturbable_mol.getEpsilons0(), + perturbable_mol.getEpsilons1(), + lambda_value); + + const auto morphed_alphas = this->lambda_schedule.morph( + "alpha", + perturbable_mol.getAlphas0(), + perturbable_mol.getAlphas1(), + lambda_value); + + const auto morphed_bond_k = this->lambda_schedule.morph( + "bond_k", + perturbable_mol.getBondKs0(), + perturbable_mol.getBondKs1(), + lambda_value); + + const auto morphed_bond_length = this->lambda_schedule.morph( + "bond_length", + perturbable_mol.getBondLengths0(), + perturbable_mol.getBondLengths1(), + lambda_value); + + const auto morphed_angle_k = this->lambda_schedule.morph( + "angle_k", + perturbable_mol.getAngleKs0(), + perturbable_mol.getAngleKs1(), + lambda_value); + + const auto morphed_angle_size = this->lambda_schedule.morph( + "angle_size", + perturbable_mol.getAngleSizes0(), + perturbable_mol.getAngleSizes1(), + lambda_value); + + const auto morphed_torsion_phase = this->lambda_schedule.morph( + "torsion_phase", + perturbable_mol.getTorsionPhases0(), + perturbable_mol.getTorsionPhases1(), + lambda_value); + + const auto morphed_torsion_k = this->lambda_schedule.morph( + "torsion_k", + perturbable_mol.getTorsionKs0(), + perturbable_mol.getTorsionKs1(), + lambda_value); + + const auto morphed_charge_scale = this->lambda_schedule.morph( + "charge_scale", + perturbable_mol.getChargeScales0(), + perturbable_mol.getChargeScales1(), + lambda_value); + + const auto morphed_lj_scale = this->lambda_schedule.morph( + "lj_scale", + perturbable_mol.getLJScales0(), + perturbable_mol.getLJScales1(), + lambda_value); + + // now update the forcefields + int start_index = start_idxs.value("clj", -1); + + if (start_index != -1 and cljff != 0) + { + const int nparams = morphed_charges.count(); - if (start_index != -1 and cljff != 0) + if (have_ghost_atoms) { - const int nparams = morphed_charges.count(); - for (int j = 0; j < nparams; ++j) { - cljff->setParticleParameters(start_index + j, morphed_charges[j], sigmas[j], epsilons[j]); - } - - const auto idxs = qm_mol.getExceptionIndices("clj"); - - if (not idxs.isEmpty()) - { - const auto exception_atoms = qm_mol.getExceptionAtoms(); - - for (int j = 0; j < exception_atoms.count(); ++j) + const bool is_from_ghost = perturbable_mol.getFromGhostIdxs().contains(j); + const bool is_to_ghost = perturbable_mol.getToGhostIdxs().contains(j); + + // reduced charge + custom_params[0] = morphed_charges[j]; + // half_sigma + custom_params[1] = 0.5 * morphed_sigmas[j]; + // two_sqrt_epsilon + custom_params[2] = 2.0 * std::sqrt(morphed_epsilons[j]); + // alpha + custom_params[3] = morphed_alphas[j]; + + // clamp alpha between 0 and 1 + if (custom_params[3] < 0) + custom_params[3] = 0; + else if (custom_params[3] > 1) + custom_params[3] = 1; + + ghost_ghostff->setParticleParameters(start_index + j, custom_params); + ghost_nonghostff->setParticleParameters(start_index + j, custom_params); + + if (is_from_ghost or is_to_ghost) { - const auto &atoms = exception_atoms[j]; - - const auto atom0 = std::get<0>(atoms); - const auto atom1 = std::get<1>(atoms); - - const auto coul_14_scale = morphed_charge_scale[j]; - const auto lj_14_scale = lj_scale[j]; - - const auto p = get_exception(atom0, atom1, - start_index, coul_14_scale, lj_14_scale, - morphed_charges, sigmas, epsilons, alphas); - - cljff->setExceptionParameters( - std::get<0>(idxs[j]), - std::get<0>(p), std::get<1>(p), - std::get<2>(p), std::get<3>(p), - std::get<4>(p)); + // don't set the LJ parameters in the cljff + cljff->setParticleParameters(start_index + j, morphed_charges[j], 0.0, 0.0); + } + else + { + cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); } } } - - start_index = start_idxs.value("bond", -1); - - if (start_index != -1 and bondff != 0) - { - const int nparams = morphed_bond_k.count(); - - for (int j = 0; j < nparams; ++j) - { - const int index = start_index + j; - - int particle1, particle2; - double length, k; - - bondff->getBondParameters(index, particle1, particle2, - length, k); - - bondff->setBondParameters(index, particle1, particle2, - bond_length[j], - morphed_bond_k[j]); - } - } - - start_index = start_idxs.value("angle", -1); - - if (start_index != -1 and angff != 0) + else { - const int nparams = morphed_angle_k.count(); - for (int j = 0; j < nparams; ++j) { - const int index = start_index + j; - - int particle1, particle2, particle3; - double size, k; - - angff->getAngleParameters(index, - particle1, particle2, particle3, - size, k); - - angff->setAngleParameters(index, - particle1, particle2, particle3, - angle_size[j], - morphed_angle_k[j]); + cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); } } - start_index = start_idxs.value("torsion", -1); + const auto idxs = perturbable_mol.getExceptionIndices("clj"); - if (start_index != -1 and dihff != 0) + if (not idxs.isEmpty()) { - const int nparams = morphed_torsion_k.count(); + const auto exception_atoms = perturbable_mol.getExceptionAtoms(); - for (int j = 0; j < nparams; ++j) + for (int j = 0; j < exception_atoms.count(); ++j) { - const int index = start_index + j; - - int particle1, particle2, particle3, particle4; - double phase, k; - int periodicity; - - dihff->getTorsionParameters(index, - particle1, particle2, - particle3, particle4, - periodicity, phase, k); - - dihff->setTorsionParameters(index, - particle1, particle2, - particle3, particle4, - periodicity, - torsion_phase[j], - morphed_torsion_k[j]); - } - } - } + const auto &atoms = exception_atoms[j]; - // update the parameters in the context - if (cljff) - cljff->updateParametersInContext(context); + const auto atom0 = std::get<0>(atoms); + const auto atom1 = std::get<1>(atoms); - // in OpenMM 8.1beta updating the bond parameters past lambda=0.25 - // causes a "All Forces must have identical exclusions" error, - // when running minimisation without h-bond constraints... - if (bondff) - bondff->updateParametersInContext(context); + const auto coul_14_scale = morphed_charge_scale[j]; + const auto lj_14_scale = morphed_lj_scale[j]; - if (angff) - angff->updateParametersInContext(context); + const bool atom0_is_ghost = perturbable_mol.isGhostAtom(atom0); + const bool atom1_is_ghost = perturbable_mol.isGhostAtom(atom1); - if (dihff) - dihff->updateParametersInContext(context); + const auto p = get_exception(atom0, atom1, + start_index, coul_14_scale, lj_14_scale, + morphed_charges, morphed_sigmas, morphed_epsilons, + morphed_alphas); - return lambda_value; - } - - else - { - // get copies of the forcefields in which the parameters will be changed - auto qmff = this->getForce("qmmm", system); - auto cljff = this->getForce("clj", system); - auto ghost_ghostff = this->getForce("ghost/ghost", system); - auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); - auto ghost_14ff = this->getForce("ghost-14", system); - auto bondff = this->getForce("bond", system); - auto angff = this->getForce("angle", system); - auto dihff = this->getForce("torsion", system); - - // we know if we have peturbable ghost atoms if we have the ghost forcefields - const bool have_ghost_atoms = (ghost_ghostff != 0 or ghost_nonghostff != 0); - - std::vector custom_params = {0.0, 0.0, 0.0, 0.0}; - - if (qmff != 0) - { - double lam = this->lambda_schedule.morph("qm", 1.0, 0.0, lambda_value); - qmff->setLambda(lam); - } - - // change the parameters for all of the perturbable molecules - for (int i = 0; i < this->perturbable_mols.count(); ++i) - { - const auto &perturbable_mol = this->perturbable_mols[i]; - const auto &start_idxs = this->start_indices_pert[i]; - - // calculate the new parameters for this lambda value - const auto morphed_charges = this->lambda_schedule.morph( - "charge", - perturbable_mol.getCharges0(), - perturbable_mol.getCharges1(), - lambda_value); - - const auto morphed_sigmas = this->lambda_schedule.morph( - "sigma", - perturbable_mol.getSigmas0(), - perturbable_mol.getSigmas1(), - lambda_value); - - const auto morphed_epsilons = this->lambda_schedule.morph( - "epsilon", - perturbable_mol.getEpsilons0(), - perturbable_mol.getEpsilons1(), - lambda_value); - - const auto morphed_alphas = this->lambda_schedule.morph( - "alpha", - perturbable_mol.getAlphas0(), - perturbable_mol.getAlphas1(), - lambda_value); - - const auto morphed_bond_k = this->lambda_schedule.morph( - "bond_k", - perturbable_mol.getBondKs0(), - perturbable_mol.getBondKs1(), - lambda_value); - - const auto morphed_bond_length = this->lambda_schedule.morph( - "bond_length", - perturbable_mol.getBondLengths0(), - perturbable_mol.getBondLengths1(), - lambda_value); - - const auto morphed_angle_k = this->lambda_schedule.morph( - "angle_k", - perturbable_mol.getAngleKs0(), - perturbable_mol.getAngleKs1(), - lambda_value); - - const auto morphed_angle_size = this->lambda_schedule.morph( - "angle_size", - perturbable_mol.getAngleSizes0(), - perturbable_mol.getAngleSizes1(), - lambda_value); - - const auto morphed_torsion_phase = this->lambda_schedule.morph( - "torsion_phase", - perturbable_mol.getTorsionPhases0(), - perturbable_mol.getTorsionPhases1(), - lambda_value); - - const auto morphed_torsion_k = this->lambda_schedule.morph( - "torsion_k", - perturbable_mol.getTorsionKs0(), - perturbable_mol.getTorsionKs1(), - lambda_value); - - const auto morphed_charge_scale = this->lambda_schedule.morph( - "charge_scale", - perturbable_mol.getChargeScales0(), - perturbable_mol.getChargeScales1(), - lambda_value); - - const auto morphed_lj_scale = this->lambda_schedule.morph( - "lj_scale", - perturbable_mol.getLJScales0(), - perturbable_mol.getLJScales1(), - lambda_value); - - // now update the forcefields - int start_index = start_idxs.value("clj", -1); - - if (start_index != -1 and cljff != 0) - { - const int nparams = morphed_charges.count(); - - if (have_ghost_atoms) - { - for (int j = 0; j < nparams; ++j) - { - const bool is_from_ghost = perturbable_mol.getFromGhostIdxs().contains(j); - const bool is_to_ghost = perturbable_mol.getToGhostIdxs().contains(j); - - // reduced charge - custom_params[0] = morphed_charges[j]; - // half_sigma - custom_params[1] = 0.5 * morphed_sigmas[j]; - // two_sqrt_epsilon - custom_params[2] = 2.0 * std::sqrt(morphed_epsilons[j]); - // alpha - custom_params[3] = morphed_alphas[j]; - - // clamp alpha between 0 and 1 - if (custom_params[3] < 0) - custom_params[3] = 0; - else if (custom_params[3] > 1) - custom_params[3] = 1; - - ghost_ghostff->setParticleParameters(start_index + j, custom_params); - ghost_nonghostff->setParticleParameters(start_index + j, custom_params); - - if (is_from_ghost or is_to_ghost) - { - // don't set the LJ parameters in the cljff - cljff->setParticleParameters(start_index + j, morphed_charges[j], 0.0, 0.0); - } - else - { - cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); - } - } - } - else - { - for (int j = 0; j < nparams; ++j) - { - cljff->setParticleParameters(start_index + j, morphed_charges[j], morphed_sigmas[j], morphed_epsilons[j]); - } - } - - const auto idxs = perturbable_mol.getExceptionIndices("clj"); - - if (not idxs.isEmpty()) - { - const auto exception_atoms = perturbable_mol.getExceptionAtoms(); - - for (int j = 0; j < exception_atoms.count(); ++j) + // don't set LJ terms for ghost atoms + if (atom0_is_ghost or atom1_is_ghost) { - const auto &atoms = exception_atoms[j]; - - const auto atom0 = std::get<0>(atoms); - const auto atom1 = std::get<1>(atoms); - - const auto coul_14_scale = morphed_charge_scale[j]; - const auto lj_14_scale = morphed_lj_scale[j]; - - const bool atom0_is_ghost = perturbable_mol.isGhostAtom(atom0); - const bool atom1_is_ghost = perturbable_mol.isGhostAtom(atom1); - - const auto p = get_exception(atom0, atom1, - start_index, coul_14_scale, lj_14_scale, - morphed_charges, morphed_sigmas, morphed_epsilons, - morphed_alphas); + cljff->setExceptionParameters( + std::get<0>(idxs[j]), + std::get<0>(p), std::get<1>(p), + std::get<2>(p), 1e-9, 1e-9); - // don't set LJ terms for ghost atoms - if (atom0_is_ghost or atom1_is_ghost) + if (coul_14_scale != 0 or lj_14_scale != 0) { - cljff->setExceptionParameters( - std::get<0>(idxs[j]), - std::get<0>(p), std::get<1>(p), - std::get<2>(p), 1e-9, 1e-9); + // this is a 1-4 parameter - need to update + // the ghost 1-4 forcefield + int nbidx = std::get<1>(idxs[j]); - if (coul_14_scale != 0 or lj_14_scale != 0) + if (nbidx < 0) + throw SireError::program_bug(QObject::tr( + "Unset NB14 index for a ghost atom?"), + CODELOC); + + if (ghost_14ff != 0) { - // this is a 1-4 parameter - need to update - // the ghost 1-4 forcefield - int nbidx = std::get<1>(idxs[j]); - - if (nbidx < 0) - throw SireError::program_bug(QObject::tr( - "Unset NB14 index for a ghost atom?"), - CODELOC); - - if (ghost_14ff != 0) - { - // parameters are q, sigma, four_epsilon and alpha - std::vector params14 = - {std::get<2>(p), std::get<3>(p), - 4.0 * std::get<4>(p), std::get<5>(p)}; - - ghost_14ff->setBondParameters(nbidx, - std::get<0>(p), - std::get<1>(p), - params14); - } + // parameters are q, sigma, four_epsilon and alpha + std::vector params14 = + {std::get<2>(p), std::get<3>(p), + 4.0 * std::get<4>(p), std::get<5>(p)}; + + ghost_14ff->setBondParameters(nbidx, + std::get<0>(p), + std::get<1>(p), + params14); } } - else - { - cljff->setExceptionParameters( - std::get<0>(idxs[j]), - std::get<0>(p), std::get<1>(p), - std::get<2>(p), std::get<3>(p), - std::get<4>(p)); - } + } + else + { + cljff->setExceptionParameters( + std::get<0>(idxs[j]), + std::get<0>(p), std::get<1>(p), + std::get<2>(p), std::get<3>(p), + std::get<4>(p)); } } } + } - start_index = start_idxs.value("bond", -1); + start_index = start_idxs.value("bond", -1); - if (start_index != -1 and bondff != 0) - { - const int nparams = morphed_bond_k.count(); + if (start_index != -1 and bondff != 0) + { + const int nparams = morphed_bond_k.count(); - for (int j = 0; j < nparams; ++j) - { - const int index = start_index + j; + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; - int particle1, particle2; - double length, k; + int particle1, particle2; + double length, k; - bondff->getBondParameters(index, particle1, particle2, - length, k); + bondff->getBondParameters(index, particle1, particle2, + length, k); - bondff->setBondParameters(index, particle1, particle2, - morphed_bond_length[j], - morphed_bond_k[j]); - } + bondff->setBondParameters(index, particle1, particle2, + morphed_bond_length[j], + morphed_bond_k[j]); } + } - start_index = start_idxs.value("angle", -1); + start_index = start_idxs.value("angle", -1); - if (start_index != -1 and angff != 0) - { - const int nparams = morphed_angle_k.count(); + if (start_index != -1 and angff != 0) + { + const int nparams = morphed_angle_k.count(); - for (int j = 0; j < nparams; ++j) - { - const int index = start_index + j; + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; - int particle1, particle2, particle3; - double size, k; + int particle1, particle2, particle3; + double size, k; - angff->getAngleParameters(index, - particle1, particle2, particle3, - size, k); + angff->getAngleParameters(index, + particle1, particle2, particle3, + size, k); - angff->setAngleParameters(index, - particle1, particle2, particle3, - morphed_angle_size[j], - morphed_angle_k[j]); - } + angff->setAngleParameters(index, + particle1, particle2, particle3, + morphed_angle_size[j], + morphed_angle_k[j]); } + } - start_index = start_idxs.value("torsion", -1); + start_index = start_idxs.value("torsion", -1); - if (start_index != -1 and dihff != 0) - { - const int nparams = morphed_torsion_k.count(); + if (start_index != -1 and dihff != 0) + { + const int nparams = morphed_torsion_k.count(); - for (int j = 0; j < nparams; ++j) - { - const int index = start_index + j; - - int particle1, particle2, particle3, particle4; - double phase, k; - int periodicity; - - dihff->getTorsionParameters(index, - particle1, particle2, - particle3, particle4, - periodicity, phase, k); - - dihff->setTorsionParameters(index, - particle1, particle2, - particle3, particle4, - periodicity, - morphed_torsion_phase[j], - morphed_torsion_k[j]); - } + for (int j = 0; j < nparams; ++j) + { + const int index = start_index + j; + + int particle1, particle2, particle3, particle4; + double phase, k; + int periodicity; + + dihff->getTorsionParameters(index, + particle1, particle2, + particle3, particle4, + periodicity, phase, k); + + dihff->setTorsionParameters(index, + particle1, particle2, + particle3, particle4, + periodicity, + morphed_torsion_phase[j], + morphed_torsion_k[j]); } } + } - // update the parameters in the context - if (cljff) - cljff->updateParametersInContext(context); + // update the parameters in the context + if (cljff) + cljff->updateParametersInContext(context); - if (ghost_ghostff) - ghost_ghostff->updateParametersInContext(context); + if (ghost_ghostff) + ghost_ghostff->updateParametersInContext(context); - if (ghost_nonghostff) - ghost_nonghostff->updateParametersInContext(context); + if (ghost_nonghostff) + ghost_nonghostff->updateParametersInContext(context); - if (ghost_14ff) - ghost_14ff->updateParametersInContext(context); + if (ghost_14ff) + ghost_14ff->updateParametersInContext(context); - // in OpenMM 8.1beta updating the bond parameters past lambda=0.25 - // causes a "All Forces must have identical exclusions" error, - // when running minimisation without h-bond constraints... - if (bondff) - bondff->updateParametersInContext(context); + // in OpenMM 8.1beta updating the bond parameters past lambda=0.25 + // causes a "All Forces must have identical exclusions" error, + // when running minimisation without h-bond constraints... + if (bondff) + bondff->updateParametersInContext(context); - if (angff) - angff->updateParametersInContext(context); + if (angff) + angff->updateParametersInContext(context); - if (dihff) - dihff->updateParametersInContext(context); + if (dihff) + dihff->updateParametersInContext(context); - // now update any restraints that are scaled - for (const auto &restraint : this->name_to_restraintidx.keys()) + // now update any restraints that are scaled + for (const auto &restraint : this->name_to_restraintidx.keys()) + { + // restraints always morph between 1 and 1 (i.e. they fully + // follow whatever is set by lambda, e.g. 'initial*lambda' + // to switch them on, or `final*lambda` to switch them off) + const double rho = lambda_schedule.morph(restraint, + 1.0, 1.0, + lambda_value); + + for (auto &ff : this->getRestraints(restraint, system)) { - // restraints always morph between 1 and 1 (i.e. they fully - // follow whatever is set by lambda, e.g. 'initial*lambda' - // to switch them on, or `final*lambda` to switch them off) - const double rho = lambda_schedule.morph(restraint, - 1.0, 1.0, - lambda_value); - - for (auto &ff : this->getRestraints(restraint, system)) + if (ff != 0) { - if (ff != 0) - { - this->updateRestraintInContext(*ff, rho, context); - } + this->updateRestraintInContext(*ff, rho, context); } } - - return lambda_value; } + + return lambda_value; } /** Update the parameters for a CustomCompoundBondForce for scale factor 'rho' diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index e08b42a48..fa6ac84fe 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -749,7 +749,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // now create the engine for computing QM or ML forces on atoms QMMMForce *qmff = 0; - QString qm_engine; if (map.specified("qm_engine")) { @@ -757,7 +756,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { auto &engine = map["qm_engine"].value().asA(); qmff = new EMLEEngine(engine); - qm_engine = "emle"; } catch (...) { @@ -837,7 +835,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, if (qmff != 0) { - lambda_lever.setForceIndex(qm_engine, system.addForce(qmff)); + lambda_lever.setForceIndex("qmff", system.addForce(qmff)); lambda_lever.addLever("qm_scale"); } From 9eaa1bae876a709c884e0907c58c42d67dd520e6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jan 2024 11:15:34 +0000 Subject: [PATCH 076/468] Remove redundant QM molecule boilerplate. --- wrapper/Convert/SireOpenMM/lambdalever.cpp | 39 ++------- wrapper/Convert/SireOpenMM/lambdalever.h | 16 +--- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 58 ++------------ wrapper/Convert/SireOpenMM/openmmmolecule.h | 19 +---- .../SireOpenMM/sire_to_openmm_system.cpp | 79 +------------------ 5 files changed, 15 insertions(+), 196 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 0ce8a79c3..25891819e 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -46,11 +46,8 @@ LambdaLever::LambdaLever(const LambdaLever &other) name_to_restraintidx(other.name_to_restraintidx), lambda_schedule(other.lambda_schedule), perturbable_mols(other.perturbable_mols), - qm_mols(other.qm_mols), start_indices_pert(other.start_indices_pert), - start_indices_qm(other.start_indices_qm), - perturbable_maps(other.perturbable_maps), - qm_maps(other.qm_maps) + perturbable_maps(other.perturbable_maps) { } @@ -66,11 +63,8 @@ LambdaLever &LambdaLever::operator=(const LambdaLever &other) name_to_restraintidx = other.name_to_restraintidx; lambda_schedule = other.lambda_schedule; perturbable_mols = other.perturbable_mols; - qm_mols = other.qm_mols; start_indices_pert = other.start_indices_pert; - start_indices_qm = other.start_indices_qm; perturbable_maps = other.perturbable_maps; - qm_maps = other.qm_maps; Property::operator=(other); } @@ -83,11 +77,8 @@ bool LambdaLever::operator==(const LambdaLever &other) const name_to_restraintidx == other.name_to_restraintidx and lambda_schedule == other.lambda_schedule and perturbable_mols == other.perturbable_mols and - qm_mols == other.qm_mols and start_indices_pert == other.start_indices_pert and - start_indices_qm == other.start_indices_qm and - perturbable_maps == other.perturbable_maps and - qm_maps == other.qm_maps; + perturbable_maps == other.perturbable_maps; } bool LambdaLever::operator!=(const LambdaLever &other) const @@ -787,36 +778,16 @@ int LambdaLever::addPerturbableMolecule(const OpenMMMolecule &molecule, return this->perturbable_mols.count() - 1; } -/** Add infor for the passed OpenMMMolecule, returning its index - * in the list of QM molecules - */ -int LambdaLever::addQMMolecule(const OpenMMMolecule &molecule, - const QHash &starts) -{ - // should add in some sanity checks for these inputs - this->qm_mols.append(molecule); - this->start_indices_qm.append(starts); - return this->qm_mols.count() - 1; -} /** Set the exception indices for the perturbable molecule at * index 'mol_idx' */ void LambdaLever::setExceptionIndices(int mol_idx, const QString &name, - const QVector> &exception_idxs, - bool is_qm) + const QVector> &exception_idxs) { - if (is_qm) - { - mol_idx = SireID::Index(mol_idx).map(this->qm_mols.count()); - this->qm_mols[mol_idx].setExceptionIndices(name, exception_idxs); - } - else - { - mol_idx = SireID::Index(mol_idx).map(this->perturbable_mols.count()); - this->perturbable_mols[mol_idx].setExceptionIndices(name, exception_idxs); - } + mol_idx = SireID::Index(mol_idx).map(this->perturbable_mols.count()); + this->perturbable_mols[mol_idx].setExceptionIndices(name, exception_idxs); } /** Return all of the property maps used to find the perturbable properties diff --git a/wrapper/Convert/SireOpenMM/lambdalever.h b/wrapper/Convert/SireOpenMM/lambdalever.h index cc3cbeff9..981971980 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.h +++ b/wrapper/Convert/SireOpenMM/lambdalever.h @@ -72,12 +72,8 @@ namespace SireOpenMM int addPerturbableMolecule(const OpenMMMolecule &molecule, const QHash &start_indices); - int addQMMolecule(const OpenMMMolecule &molecule, - const QHash &start_indices); - void setExceptionIndices(int idx, const QString &ff, - const QVector> &exception_idxs, - bool is_qm = false); + const QVector> &exception_idxs); void setSchedule(const SireCAS::LambdaSchedule &schedule); @@ -116,22 +112,12 @@ namespace SireOpenMM /** The list of perturbable molecules */ QVector perturbable_mols; - /** The list of QM molecules */ - QVector qm_mols; - /** The start indices of the parameters in each named forcefield for each perturbable molecule */ QVector> start_indices_pert; - /** The start indices of the parameters in each named - forcefield for each QM molecule */ - QVector> start_indices_qm; - /** All of the property maps for the perturbable molecules */ QHash perturbable_maps; - - /** All of the property maps for the QM molecules */ - QHash qm_maps; }; #ifndef SIRE_SKIP_INLINE_FUNCTION diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 8f6903dc0..989353786 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -179,7 +179,6 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, } bool is_perturbable = false; - bool is_qm = false; bool swap_end_states = false; if (mol.hasProperty(map["is_perturbable"])) @@ -192,11 +191,6 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, } } - if (mol.hasProperty(map["is_qm"])) - { - this->is_qm = mol.property(map["is_qm"]).asABoolean(); - } - if (is_perturbable) { ffinfo = mol.property(map["forcefield0"]).asA(); @@ -337,16 +331,16 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, const auto params1 = SireMM::AmberParams(mol, map1); perturbed.reset(new OpenMMMolecule(*this)); - perturbed->constructFromAmber(mol, params1, params, map1, true, false); + perturbed->constructFromAmber(mol, params1, params, map1, true); - this->constructFromAmber(mol, params, params1, map0, true, false); + this->constructFromAmber(mol, params, params1, map0, true); this->alignInternals(map); } else { const auto params = SireMM::AmberParams(mol, map); - this->constructFromAmber(mol, params, params, map, false, this->isQM()); + this->constructFromAmber(mol, params, params, map, false); } } else @@ -408,11 +402,6 @@ bool OpenMMMolecule::isPerturbable() const return perturbed.get() != 0; } -bool OpenMMMolecule::isQM() const -{ - return this->is_qm; -} - bool OpenMMMolecule::isGhostAtom(int atom) const { return from_ghost_idxs.contains(atom) or to_ghost_idxs.contains(atom); @@ -450,7 +439,7 @@ std::tuple OpenMMMolecule::getException( epsilon = lj_14_scl * std::sqrt(std::get<2>(clj0) * std::get<2>(clj1)); } - if ((this->isPerturbable() or this->isQM()) and charge == 0 and std::abs(epsilon) < 1e-9) + if (this->isPerturbable() and charge == 0 and std::abs(epsilon) < 1e-9) { // openmm tries to optimise away zero parameters - this is an issue // as perturbation requires that we don't remove them! @@ -472,30 +461,6 @@ std::tuple OpenMMMolecule::getException( charge, sigma, epsilon); } -/** Return the global indexes of the exceptions in the non-bonded and - * ghost-14 forces - */ -QVector> OpenMMMolecule::getExceptionIndices(const QString &name) const -{ - return this->exception_idxs.value(name); -} - -/** Set the global indexes of the exceptions in the non-bonded and - * ghost-14 forces - */ -void OpenMMMolecule::setExceptionIndices(const QString &name, - const QVector> &exception_idxs) -{ - if (exception_idxs.count() != this->exception_atoms.count()) - throw SireError::incompatible_error(QObject::tr( - "The number of exception indicies (%1) does not match the number of exceptions (%2)") - .arg(exception_idxs.count()) - .arg(this->exception_atoms.count()), - CODELOC); - - this->exception_idxs.insert(name, exception_idxs); -} - /** Return closest constraint length to 'length' based on what * we have seen before and the constraint_length_tolerance */ @@ -554,15 +519,8 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const AmberParams ¶ms, const AmberParams ¶ms1, const PropertyMap &map, - bool is_perturbable, - bool is_qm) + bool is_perturbable) { - if (is_perturbable and is_qm) - { - throw SireError::invalid_key(QObject::tr( - "We currently do not support perturbable QM molecules."), CODELOC); - } - const auto &moldata = mol.data(); if (this->hasFieldAtoms()) @@ -968,12 +926,6 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } this->buildExceptions(mol, atomidx_to_idx, constrained_pairs, map); - - // Set the exception indices for this molecule. - if (is_qm) - { - this->exception_atoms = this->getExceptionAtoms(); - } } bool is_ghost(const std::tuple &clj) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index a4b0067ee..f421e01be 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -81,7 +81,6 @@ namespace SireOpenMM OpenMM::Vec3 *velocities) const; bool isPerturbable() const; - bool isQM() const; int nAtoms() const; @@ -120,11 +119,6 @@ namespace SireOpenMM double coul_14_scl, double lj_14_scl) const; - QVector> getExceptionIndices(const QString &name) const; - - void setExceptionIndices(const QString &name, - const QVector> &exception_idxs); - /** All the member data is public as this is an internal * class. This class should not be used outside of * this SireOpenMM converter library. @@ -219,8 +213,7 @@ namespace SireOpenMM const SireMM::AmberParams ¶ms, const SireMM::AmberParams ¶ms1, const SireBase::PropertyMap &map, - bool is_perturbable=false, - bool is_qm=false); + bool is_perturbable=false); void buildExceptions(const SireMol::Molecule &mol, const QVector &atomidx_to_idx, @@ -230,16 +223,6 @@ namespace SireOpenMM void alignInternals(const SireBase::PropertyMap &map); void processFieldAtoms(); - - /** Whether this is a QM molecule. */ - bool is_qm = false; - - /** The indicies of the atoms in the exceptions, in exception order */ - QVector> exception_atoms; - - /** The indicies of the added exceptions - only populated - * if this is a QM molecule */ - QHash>> exception_idxs; }; /** This class holds all of the information of an OpenMM molecule diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index fa6ac84fe..c2211c20f 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -621,7 +621,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // should we just ignore perturbations? bool ignore_perturbations = false; bool any_perturbable = false; - bool is_qm = false; if (map.specified("ignore_perturbations")) { @@ -663,16 +662,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } } - // check to see if there are any QM molecules. - for (int i = 0; i < nmols; ++i) - { - if (openmm_mols_data[i].isQM()) - { - is_qm = true; - break; - } - } - // check to see if there are any field molecules bool any_field_mols = false; @@ -747,7 +736,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, gridff = new GridForce(); } - // now create the engine for computing QM or ML forces on atoms + // now create the engine for computing QM forces on atoms QMMMForce *qmff = 0; if (map.specified("qm_engine")) @@ -762,15 +751,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, throw SireError::incompatible_error(QObject::tr("Invalid QM engine!"), CODELOC); } } - else - { - if (is_qm) - { - throw SireError::incompatible_error( - QObject::tr("The system contains QM molecules but no QM engine is specified!"), - CODELOC); - } - } // end of stage 2 - we now have the base forces @@ -792,9 +772,9 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, lambda_lever.setSchedule( map["schedule"].value().asA()); } - else if (any_perturbable or is_qm) + else if (any_perturbable) { - // use a standard morph if we have an alchemical perturbation + // use a standard morph if we have an alchemical or QM perturbation lambda_lever.setSchedule( LambdaSchedule::standard_morph()); } @@ -1189,39 +1169,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, idx_to_pert_idx.insert(i, pert_idx); } - if (mol.isQM()) - { - // this hash holds the start indicies for the various - // parameters for this molecule (e.g. bond, angle, CLJ parameters) - QHash start_indicies; - - // add a QM molecule, recording the start index - // for each of the forcefields - start_indicies.reserve(4); - - start_indicies.insert("clj", start_index); - - // the start index for this molecules first bond, angle or - // torsion parameters will be however many of these - // parameters exist already (parameters are added - // contiguously for each molecule) - start_indicies.insert("bond", bondff->getNumBonds()); - start_indicies.insert("angle", angff->getNumAngles()); - start_indicies.insert("torsion", dihff->getNumTorsions()); - - // we can now record this as a perturbable molecule - // in the lambda lever. The returned index is the - // index of this perturbable molecule in the list - // of perturbable molecules (e.g. the first perturbable - // molecule we find has index 0) - auto qm_idx = lambda_lever.addQMMolecule(mol, - start_indicies); - - // and we can record the map from the molecule index - // to the perturbable molecule index - idx_to_qm_idx.insert(i, qm_idx); - } - // Copy in all of the atom (particle) parameters. These // are the masses, charge and LJ parameters. // There is a different code path depending on whether @@ -1463,12 +1410,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, std::make_pair(-1, -1)); } - if (is_qm) - { - qm_exception_idxs = QVector>(mol.exception_params.count(), - std::make_pair(-1, -1)); - } - for (int j = 0; j < mol.exception_params.count(); ++j) { const auto ¶m = mol.exception_params[j]; @@ -1537,13 +1478,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // non-bonded forcefields and also the ghost-14 forcefield perturbable_exception_idxs[j] = std::make_pair(idx, nbidx); } - else if (mol.isQM()) - { - const auto idx = cljff->addException(std::get<0>(p), std::get<1>(p), - std::get<2>(p), std::get<3>(p), - std::get<4>(p), true); - qm_exception_idxs[j] = std::make_pair(idx, -1); - } else { cljff->addException(std::get<0>(p), std::get<1>(p), @@ -1566,13 +1500,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, lambda_lever.setExceptionIndices(pert_idx, "clj", perturbable_exception_idxs); } - - if (mol.isQM()) - { - auto qm_idx = idx_to_qm_idx.value(i, openmm_mols.count() + 1); - lambda_lever.setExceptionIndices(qm_idx, - "clj", qm_exception_idxs, true); - } } // Stage 6 is complete. We have set up all of the exceptions. The From 3ffdaacf66441371dadb57f15289d4e5c5f1501e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jan 2024 14:48:05 +0000 Subject: [PATCH 077/468] Invert direction of perturbation for consistency with other codes. --- src/sire/qm/_utils.py | 48 +++++++++++----------- tests/qm/test_emle.py | 2 +- wrapper/Convert/SireOpenMM/_sommcontext.py | 3 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 2 +- 4 files changed, 28 insertions(+), 27 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index a3a725d84..66eeb7283 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -59,12 +59,12 @@ def _create_merged_mol(qm_mol, map): for prop in qm_mol.property_keys(): # Bonds. if prop == bond_prop: - # Copy the bonds to the lambda = 1 state. + # Copy the bonds to the lambda = 0 state. edit_mol = edit_mol.set_property( - prop + "1", qm_mol.property(prop) + prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of bonds for the lambda = 0 state with + # Create an equivalent set of bonds for the lambda = 1 state with # zeroed force constants. bonds = _MM.TwoAtomFunctions(info) @@ -83,20 +83,20 @@ def _create_merged_mol(qm_mol, map): # Set the new bond. bonds.set(atom0, atom1, amber_bond.to_expression(r)) - # Set the bonds for the lambda = 0 state. - edit_mol = edit_mol.set_property(prop + "0", bonds).molecule() + # Set the bonds for the lambda = 1 state. + edit_mol = edit_mol.set_property(prop + "1", bonds).molecule() # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Angles. elif prop == angle_prop: - # Copy the angles to the lambda = 1 state. + # Copy the angles to the lambda = 0 state. edit_mol = edit_mol.set_property( - prop + "1", qm_mol.property(prop) + prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of angles for the lambda = 0 state with + # Create an equivalent set of angles for the lambda = 1 state with # zeroed force constants. angles = _MM.ThreeAtomFunctions(info) @@ -116,20 +116,20 @@ def _create_merged_mol(qm_mol, map): # Set the new angle. angles.set(atom0, atom1, atom2, amber_angle.to_expression(theta)) - # Set the angles for the lambda = 0 state. - edit_mol = edit_mol.set_property(prop + "0", angles).molecule() + # Set the angles for the lambda = 1 state. + edit_mol = edit_mol.set_property(prop + "1", angles).molecule() # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Dihedrals. elif prop == dihedral_prop: - # Copy the dihedrals to the lambda = 1 state. + # Copy the dihedrals to the lambda = 0 state. edit_mol = edit_mol.set_property( - prop + "1", qm_mol.property(prop) + prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of dihedrals for the lambda = 0 state + # Create an equivalent set of dihedrals for the lambda = 1 state # with zeroed force constants. dihedrals = _MM.FourAtomFunctions(info) @@ -156,20 +156,20 @@ def _create_merged_mol(qm_mol, map): amber_dihedral.to_expression(phi), ) - # Set the dihedrals for the lambda = 0 state. - edit_mol = edit_mol.set_property(prop + "0", dihedrals).molecule() + # Set the dihedrals for the lambda = 1 state. + edit_mol = edit_mol.set_property(prop + "1", dihedrals).molecule() # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Impropers. elif prop == improper_prop: - # Copy the impropers to the lambda = 1 state. + # Copy the impropers to the lambda = 0 state. edit_mol = edit_mol.set_property( - prop + "1", qm_mol.property(prop) + prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of impropers for the lambda = 0 state + # Create an equivalent set of impropers for the lambda = 1 state # with zeroed force constants. impropers = _MM.FourAtomFunctions(info) @@ -196,22 +196,22 @@ def _create_merged_mol(qm_mol, map): amber_improper.to_expression(psi), ) - # Set the impropers for the lambda = 0 state. - edit_mol = edit_mol.set_property(prop + "0", impropers).molecule() + # Set the impropers for the lambda = 1 state. + edit_mol = edit_mol.set_property(prop + "1", impropers).molecule() # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Charge. elif prop == charge_prop: - # Copy the charges to the lambda = 1 state. + # Copy the charges to the lambda = 0 state. edit_mol = edit_mol.set_property( - prop + "1", qm_mol.property(prop) + prop + "0", qm_mol.property(prop) ).molecule() - # Create a set of null charges for the lambda = 0 state. + # Create a set of null charges for the lambda = 1 state. charges = _Mol.AtomCharges(info) - edit_mol = edit_mol.set_property(prop + "0", charges).molecule() + edit_mol = edit_mol.set_property(prop + "1", charges).molecule() # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index d50c43d34..71025e8f7 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -70,7 +70,7 @@ def test_interpolate(ala_mols): nrg_emle = d.current_potential_energy() # Get interpolated MM energy. - d.set_lambda(1.0) + d.set_lambda(0.0) nrg_mm_interp = d.current_potential_energy() # Make sure this agrees with the standard MM energy. diff --git a/wrapper/Convert/SireOpenMM/_sommcontext.py b/wrapper/Convert/SireOpenMM/_sommcontext.py index a138052ac..9aea3379b 100644 --- a/wrapper/Convert/SireOpenMM/_sommcontext.py +++ b/wrapper/Convert/SireOpenMM/_sommcontext.py @@ -46,7 +46,8 @@ def __init__( elif map.specified("lambda_value"): lambda_value = map["lambda_value"].value().as_double() elif map.specified("qm_engine"): - lambda_value = 0.0 + # Default to full QM. + lambda_value = 1.0 else: lambda_value = 0.0 diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 25891819e..a70076adb 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -257,7 +257,7 @@ double LambdaLever::setLambda(OpenMM::Context &context, if (qmff != 0) { - double lam = this->lambda_schedule.morph("qmff", 1.0, 0.0, lambda_value); + double lam = this->lambda_schedule.morph("qmff", 0.0, 1.0, lambda_value); qmff->setLambda(lam); } From c8a442fefa47aabe2536c8bb3bda339841f6af8a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jan 2024 16:26:22 +0000 Subject: [PATCH 078/468] Refactor comments. --- src/sire/qm/_utils.py | 62 +++++-------------------------------------- 1 file changed, 7 insertions(+), 55 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 66eeb7283..d2413f9f5 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -57,97 +57,70 @@ def _create_merged_mol(qm_mol, map): edit_mol = qm_mol.edit() for prop in qm_mol.property_keys(): + # For all bonded properties we copy the MM terms to the lambda = 0 + # (MM) end state, create a null set of terms for the lambda = 1 (QM) + # end state, then remove the existing property. Charges also zeroed + # for the MM end state. All other properties remain the same in both + # states. + # Bonds. if prop == bond_prop: - # Copy the bonds to the lambda = 0 state. edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of bonds for the lambda = 1 state with - # zeroed force constants. - bonds = _MM.TwoAtomFunctions(info) for bond in qm_mol.property(prop).potentials(): - # Extract the atoms involved in the bond.:w atom0 = info.atom_idx(bond.atom0()) atom1 = info.atom_idx(bond.atom1()) - # CAS variable for the bond. r = _CAS.Symbol("r") - - # Create a null AmberBond. amber_bond = _MM.AmberBond(0, r) - # Set the new bond. bonds.set(atom0, atom1, amber_bond.to_expression(r)) - # Set the bonds for the lambda = 1 state. edit_mol = edit_mol.set_property(prop + "1", bonds).molecule() - - # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Angles. elif prop == angle_prop: - # Copy the angles to the lambda = 0 state. edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of angles for the lambda = 1 state with - # zeroed force constants. - angles = _MM.ThreeAtomFunctions(info) for angle in qm_mol.property(prop).potentials(): - # Extract the atoms involved in the angle. atom0 = info.atom_idx(angle.atom0()) atom1 = info.atom_idx(angle.atom1()) atom2 = info.atom_idx(angle.atom2()) - # CAS variable for the angle. theta = _CAS.Symbol("theta") - - # Create a null AmberAngle. amber_angle = _MM.AmberAngle(0.0, theta) - # Set the new angle. angles.set(atom0, atom1, atom2, amber_angle.to_expression(theta)) - # Set the angles for the lambda = 1 state. edit_mol = edit_mol.set_property(prop + "1", angles).molecule() - - # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Dihedrals. elif prop == dihedral_prop: - # Copy the dihedrals to the lambda = 0 state. edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of dihedrals for the lambda = 1 state - # with zeroed force constants. - dihedrals = _MM.FourAtomFunctions(info) for dihedral in qm_mol.property(prop).potentials(): - # Extract the atoms involved in the dihedral. atom0 = info.atom_idx(dihedral.atom0()) atom1 = info.atom_idx(dihedral.atom1()) atom2 = info.atom_idx(dihedral.atom2()) atom3 = info.atom_idx(dihedral.atom3()) - # CAS varialbe for the dihedral. phi = _CAS.Symbol("phi") - - # Create a hull AmberDihedral. amber_dihedral = _MM.AmberDihedral(0, phi) - # Set the new dihedral. dihedrals.set( atom0, atom1, @@ -156,38 +129,26 @@ def _create_merged_mol(qm_mol, map): amber_dihedral.to_expression(phi), ) - # Set the dihedrals for the lambda = 1 state. edit_mol = edit_mol.set_property(prop + "1", dihedrals).molecule() - - # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Impropers. elif prop == improper_prop: - # Copy the impropers to the lambda = 0 state. edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() - # Create an equivalent set of impropers for the lambda = 1 state - # with zeroed force constants. - impropers = _MM.FourAtomFunctions(info) for improper in qm_mol.property(prop).potentials(): - # Extract the atoms involved in the improper. atom0 = info.atom_idx(improper.atom0()) atom1 = info.atom_idx(improper.atom1()) atom2 = info.atom_idx(improper.atom2()) atom3 = info.atom_idx(improper.atom3()) - # CAS variable for the improper. psi = _CAS.Symbol("psi") - - # Create a null AmberDihedral. amber_improper = _MM.AmberDihedral(0, psi) - # Set the new improper. impropers.set( atom0, atom1, @@ -196,33 +157,25 @@ def _create_merged_mol(qm_mol, map): amber_improper.to_expression(psi), ) - # Set the impropers for the lambda = 1 state. edit_mol = edit_mol.set_property(prop + "1", impropers).molecule() - - # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Charge. elif prop == charge_prop: - # Copy the charges to the lambda = 0 state. edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() - # Create a set of null charges for the lambda = 1 state. charges = _Mol.AtomCharges(info) edit_mol = edit_mol.set_property(prop + "1", charges).molecule() - - # Finally, delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Connectivity. elif prop == connectivity_prop: pass - # Everything else. + # All other properties remain the same in both end states. else: - # All other properties remain the same in both end states. edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() @@ -230,7 +183,6 @@ def _create_merged_mol(qm_mol, map): prop + "1", qm_mol.property(prop) ).molecule() - # Delete the existing property. edit_mol = edit_mol.remove_property(prop).molecule() # Flag the molecule as perturbable. From 8a4fef8ef5aca88d6636f9766ab52b7458ca20ac Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 11 Jan 2024 12:46:55 +0000 Subject: [PATCH 079/468] Use updated emle-engine API. --- src/sire/qm/_emle.py | 8 ++++---- tests/qm/test_emle.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index bfca6ac5d..336c4438b 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -9,7 +9,7 @@ _EMLEEngine = _Convert._SireOpenMM.EMLEEngine try: - from emle.emle import EMLECalculator as _EMLECalculator + from emle.calculator import EMLECalculator as _EMLECalculator _has_emle = True except: @@ -33,7 +33,7 @@ def emle( mols : sire.system.System The molecular system. - calculator : emle.emle.EMLECalculator + calculator : emle.calculator.EMLECalculator The EMLECalculator object to use for elecotrostatic embedding calculations. qm_index : int @@ -53,7 +53,7 @@ def emle( """ if not _has_emle: raise ImportError( - "Could not import emle. Please install emle-egine and try again." + "Could not import emle. Please install emle-engine and try again." ) from ..base import create_map as _create_map @@ -66,7 +66,7 @@ def emle( raise TypeError("mols must be a of type 'sire.System'") if not isinstance(calculator, _EMLECalculator): - raise TypeError("'calculator' must be a of type 'emle.emle.EMLECalculator'") + raise TypeError("'calculator' must be a of type 'emle.calculator.EMLECalculator'") if not isinstance(qm_index, int): raise TypeError("'qm_index' must be of type 'int'") diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 71025e8f7..ed2339d5d 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -7,7 +7,7 @@ from sire.qm import emle try: - from emle.emle import EMLECalculator + from emle.calculator import EMLECalculator has_emle = True except: From 52da1b876c8eb43bd609cdc6bd606b6ea02eea1e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 11 Jan 2024 13:29:18 +0000 Subject: [PATCH 080/468] Add first pass of QM/MM docs. --- doc/source/tutorial/index.rst | 1 + doc/source/tutorial/index_part07.rst | 18 ++++ doc/source/tutorial/part07/01_emle.rst | 143 +++++++++++++++++++++++++ 3 files changed, 162 insertions(+) create mode 100644 doc/source/tutorial/index_part07.rst create mode 100644 doc/source/tutorial/part07/01_emle.rst diff --git a/doc/source/tutorial/index.rst b/doc/source/tutorial/index.rst index 232078d85..bcb473c25 100644 --- a/doc/source/tutorial/index.rst +++ b/doc/source/tutorial/index.rst @@ -27,3 +27,4 @@ please :doc:`ask for support. <../support>` index_part04 index_part05 index_part06 + index_part07 diff --git a/doc/source/tutorial/index_part07.rst b/doc/source/tutorial/index_part07.rst new file mode 100644 index 000000000..a6ae74262 --- /dev/null +++ b/doc/source/tutorial/index_part07.rst @@ -0,0 +1,18 @@ +============== +Part 7 - QM/MM +============== + +QM/MM is a method that combines the accuracy of quantum mechanics with the +speed of molecular mechanics. In QM/MM, a small region of the system is treated +at the quantum mechanical level, while the rest of the system is treated at the +molecular mechanical level. This allows us to perform accurate calculations on +the region of interest, while still being able to simulate the rest of the system +at a much lower computational cost. Due to the recent development of cheap and +accurate machine learning based QM models, there has been a resurgence of +interest in QM/MM methods. In this tutorial we will show how to perform +QM/MM simulations using ``sire``. + +.. toctree:: + :maxdepth: 1 + + part07/01_emle diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst new file mode 100644 index 000000000..6decacc28 --- /dev/null +++ b/doc/source/tutorial/part07/01_emle.rst @@ -0,0 +1,143 @@ +========= +Sire-EMLE +========= + +The ``sire`` QM/MM implementation takes advantage of the new means of writing +`platform independent force calculations `_ +introduced in `OpenMM `_ 8.1. This allows us to interface +with any external package to modify atomic forces within the ``OpenMM`` context. +While OpenMM already directly supports ML/MM simulations via the `OpenMM-ML `_ +package, it is currently limited to specific backends and only supports mechanical +embedding. The ``sire`` QM/MM implementation performs the QM calculation using +the `emle-engine `_ package, which has +support for a wide range of backends and embedding models, importantly providing +a simple and efficient ML model for electrostatic embedding. + +In order to use QM/MM functionality within ``sire`` you will first need to +create the following ``conda`` environment: + +.. code-block:: bash + + $ git clone https://github.com/chemle/emle-engine.git + $ cd emle-engine + $ conda env create -f environment_sire.yaml + $ conda activate emle-sire + $ pip install -e . + +In this tutorial, we will perform a short ML/MM simulation of alanine dipeptide +in water. First, let us load the molecular system: + +>>> import sire as sr +>>> mols = sr.load_test_files("ala.crd", "ala.top") + +Next we will create an ``emle-engine`` calculator to perform the QM (or ML) calculation +for the dipeptide along with the ML electrostatic embedding. Since this is a small molecule +it isn't beneficial to perform the calculation on a GPU, so we will use the CPU instead. +We will also disable logging to file to improve performance. + +>>> from emle.calculator import EMLECalculator +>>> calculator = EMLECalculator(device="cpu", log=0) + +By default, ``emle-engine`` will use `TorchANI `_ +as the backend for in vacuo calculation of energies and gradients. However, +it is possible to use a wide variety of other backends, including your own +as long as it supports the standand `Atomic Simulation Environment (ASE) `_ +`calculator `_ interface. +For details, see the `backends `_ +section of the ``emle-engine`` documentation. At present, the default embedding +model provided with ``emle-engine`` supports only the elements H, C, N, O, and S. +We plan on adding support for other elements in the near future. + +We now need to set up the molecular system for the QM/MM simulation and create +an engine to perform the calculation: + +>>> mols, engine = sr.qm.emle(mols, calculator, 0, "7.5A", 20) + +Here the first argument is the molecules that we are simulating, the second +is the calculator, and the third is the index of the molecule that we want to +treat at the QM level. The fourth and fith arguments are optional, and specify +the QM cutoff distance and the neigbour list update frequency respectively. +(Shown are the default values.) The function returns a modified version of +the molecules containing a "merged" dipeptide that can be interpolated between +QM and MM levels of theory, along with an engine. The engine registers a Python +callback that uses ``emle-engine`` to perform the QM calculation. + +.. note:: + + Currently we only support QM/MM where an *entire* molecule is treated + at the QM level. We plan to add support for partial molecules via the + link atom and charge shifting approach in a future release. + +Next we need to create a dynamics object to perform the simulation. For QM/MM +simulations it is recommended to use a 1 femtosecond timestep and no constraints. +In this example we will use the ``lambda_interpolate`` keyword to interpolate +the dipeptide potential between pure MM (λ=0) and QM (λ=1) over the course of +the simulation, which can be used for end-state correction of binding free +energy calculations. + +>>> d = mols.dynamics(timestep="1fs", constraint="none", qm_engine=engine, lambda_interpolate=[0, 1]) + +We can now run the simulation. The options below specify the run time, the +frequency at which trajectory frames are saved, and the frequency at which +energies are recorded. The ``energy_frequency`` also specifies the frequency +at which the λ value is updated. + +>>> d.run("1ps", frame_frequency="0.05ps", energy_frequency="0.05ps") + +.. note:: + + Updating λ requires the updating of force field parameters in the ``OpenMM`` + context. For large systems, this can be quite slow so it isn't recommended + to set the ``energy_frequency`` to a value that is too small. We have a custom + `fork `_ of ``OpenMM`` that provides a + significant speedup for this operation by only updating a subset of the parameters. + Installation instructions can be provided on request. + +.. note:: + + If you don't require a trajectory file, then better performance can be achieved + leaving the ``frame_frequency`` keyword argument unset. + +.. note:: + + ``emle-engine`` currently requires the use of `librascal `_ + for the calculation of SOAP (Smooth Overlap of Atomic Positions) descriptors. + This is a serial code, so you may see better performance by restricting the + number of ``OpenMP`` threads to 1, e.g. by setting the ``OMP_NUM_THREADS`` + environment variable. + +Once the simulation has finished we can get back the trajectory of energy values. +This can be obtained as a `pandas `_ ``DataFrame``, +allowing for easy plotting and analysis. The table below shows the instantaneous +kintetic and potential energies as a function of λ, along with the pure MM and +QM potential energies. (Times are in picoseconds and energies are in kcal/mol.) + +>>> nrg_traj = d.energy_trajectory(to_pandas=True) +>>> print(nrg_traj) + lambda KE PE(lambda) PE(lambda=0) PE(lambda=1) +time +6000.05 0.000000 980.181564 -6954.938694 -6954.938694 -318014.135823 +6000.10 0.052632 871.904630 -23214.139963 -6843.385099 -317910.734657 +6000.15 0.105263 1074.693130 -39796.029943 -7056.370765 -318111.343285 +6000.20 0.157895 979.813677 -56061.595767 -6952.183998 -318008.475588 +6000.25 0.210526 1009.571276 -72462.277097 -6981.451657 -318040.986409 +6000.30 0.263158 1016.026458 -88842.745858 -6991.337337 -318046.238677 +6000.35 0.315789 1003.273813 -105199.347795 -6976.690749 -318031.016925 +6000.40 0.368421 1021.295211 -121583.564572 -6991.838146 -318041.438719 +6000.45 0.421053 1027.366329 -137961.602333 -7000.530076 -318049.949920 +6000.50 0.473684 1049.387973 -154355.318394 -7023.254018 -318072.387286 +6000.55 0.526316 1040.626785 -170718.777695 -7016.367279 -318066.329145 +6000.60 0.578947 1047.005579 -187097.460730 -7015.987089 -318076.072803 +6000.65 0.631579 1030.218148 -203453.572350 -6997.132190 -318063.875864 +6000.70 0.684211 1022.362023 -219819.959312 -6994.205184 -318058.533453 +6000.75 0.736842 1044.950320 -236216.451165 -7012.311296 -318084.096807 +6000.80 0.789474 1024.087813 -252561.720268 -6985.090189 -318055.746705 +6000.85 0.842105 1056.241205 -268962.249393 -7016.702075 -318082.555659 +6000.90 0.894737 1053.591066 -285328.646842 -7013.509852 -318075.626766 +6000.95 0.947368 1033.013716 -301672.026582 -6986.164439 -318045.397622 +6001.00 1.000000 1045.687318 -318056.550581 -6991.865785 -318056.550599 + +.. note:: + + In the table above, the time doesn't start from zero because the example + molecular system was loaded from an existing trajectory restart file. From 2bffe81891be2b4f73825290e348aa4881a92927 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 17 Jan 2024 10:19:43 +0000 Subject: [PATCH 081/468] Add boilerplate for handling partial QM molecules and link atoms. --- doc/source/tutorial/part07/01_emle.rst | 23 +-- src/sire/qm/_emle.py | 44 ++-- src/sire/qm/_utils.py | 193 ++++++++++++++---- tests/qm/test_emle.py | 2 +- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 7 + wrapper/Convert/SireOpenMM/emle.cpp | 21 ++ wrapper/Convert/SireOpenMM/emle.h | 59 ++++++ wrapper/Convert/SireOpenMM/qmmm.h | 9 + 8 files changed, 290 insertions(+), 68 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index 6decacc28..3463bc351 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -51,22 +51,17 @@ We plan on adding support for other elements in the near future. We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation: ->>> mols, engine = sr.qm.emle(mols, calculator, 0, "7.5A", 20) +>>> mols, engine = sr.qm.emle(mols, mols[0], calculator, 0, "7.5A", 20) Here the first argument is the molecules that we are simulating, the second -is the calculator, and the third is the index of the molecule that we want to -treat at the QM level. The fourth and fith arguments are optional, and specify -the QM cutoff distance and the neigbour list update frequency respectively. -(Shown are the default values.) The function returns a modified version of -the molecules containing a "merged" dipeptide that can be interpolated between -QM and MM levels of theory, along with an engine. The engine registers a Python -callback that uses ``emle-engine`` to perform the QM calculation. - -.. note:: - - Currently we only support QM/MM where an *entire* molecule is treated - at the QM level. We plan to add support for partial molecules via the - link atom and charge shifting approach in a future release. +selection coresponding to the QM region (here this is the first molecule), and +the third is calculator that was created above. The fourth and fifth arguments +are optional, and specify the QM cutoff distance and the neigbour list update +frequency respectively. (Shown are the default values.) The function returns a +modified version of the molecules containing a "merged" dipeptide that can be +interpolated between QM and MM levels of theory, along with an engine. The +engine registers a Python callback that uses ``emle-engine`` to perform the QM +calculation. Next we need to create a dynamics object to perform the simulation. For QM/MM simulations it is recommended to use a 1 femtosecond timestep and no constraints. diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 336c4438b..be7252039 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -18,8 +18,8 @@ def emle( mols, + qm_atoms, calculator, - qm_index, cutoff="7.5A", neighbourlist_update_frequency=20, map=None, @@ -33,12 +33,14 @@ def emle( mols : sire.system.System The molecular system. + qm_atoms : str, int, list, molecule view/collection etc. + Any valid search string, atom index, list of atom indicies, + or molecule view/container that can be used to select + qm_atoms from 'mols'. + calculator : emle.calculator.EMLECalculator The EMLECalculator object to use for elecotrostatic embedding calculations. - qm_index : int - The index of the QM molecule in the system. - cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. @@ -57,6 +59,7 @@ def emle( ) from ..base import create_map as _create_map + from ..mol import selection_to_atoms as _selection_to_atoms from ..system import System as _System from ..legacy import Units as _Units from ..units import angstrom as _angstrom @@ -65,16 +68,23 @@ def emle( if not isinstance(mols, _System): raise TypeError("mols must be a of type 'sire.System'") - if not isinstance(calculator, _EMLECalculator): - raise TypeError("'calculator' must be a of type 'emle.calculator.EMLECalculator'") - - if not isinstance(qm_index, int): - raise TypeError("'qm_index' must be of type 'int'") - try: - qm_mol = mols[qm_index] + qm_atoms = _selection_to_atoms(mols, qm_atoms) except: - raise ValueError(f"qm_index must be in range [0, {len(mols)})") + raise ValueError("Unable to select 'qm_atoms' from 'mols'") + + # Get the molecule containing the qm_atoms. + qm_mol = qm_atoms[0].molecule() + + # Make sure all of the atoms are in the same molecule. + for atom in qm_atoms[1:]: + if not atom.molecule() == qm_mol: + raise ValueError("'qm_atoms' must all be in the same molecule") + + if not isinstance(calculator, _EMLECalculator): + raise TypeError( + "'calculator' must be a of type 'emle.calculator.EMLECalculator'" + ) if not isinstance(cutoff, (str, _Units.GeneralUnit)): raise TypeError( @@ -108,13 +118,17 @@ def emle( neighbourlist_update_frequency, ) - from ._utils import _configure_engine, _create_merged_mol + from ._utils import _configure_engine, _create_merged_mol, _get_link_atoms + + # Get dictionary of link atoms for each QM atom (mm1_atoms) and the + # dictionary of bonded MM atoms for each link atom (mm2_atoms). + mm1_atoms, mm2_atoms = _get_link_atoms(mols, qm_mol, qm_atoms, map) # Configure the engine. - engine = _configure_engine(engine, mols, qm_mol, map) + engine = _configure_engine(engine, mols, qm_atoms, mm2_atoms, map) # Create the merged molecule. - qm_mol = _create_merged_mol(qm_mol, map) + qm_mol = _create_merged_mol(qm_mol, qm_atoms, map) # Update the molecule in the system. mols.update(qm_mol) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index d2413f9f5..3fccb001a 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,12 +1,11 @@ -def _configure_engine(engine, mols, qm_mol, map): +def _configure_engine(engine, mols, qm_atoms, link_atoms, map): """ Internal helper function to configure a QM engine ready for dynamics. """ # Work out the indices of the QM atoms. try: - atoms_to_find = qm_mol.atoms() - idxs = mols.atoms().find(atoms_to_find) + idxs = mols.atoms().find(qm_atoms) engine.set_atoms(idxs) except: raise Exception("Unable to set atom indices for the QM region.") @@ -14,9 +13,7 @@ def _configure_engine(engine, mols, qm_mol, map): # Work out the atomic numbers of the QM atoms. try: elem_prop = map["element"] - numbers = [ - atom.property(f"{elem_prop}").num_protons() for atom in atoms_to_find - ] + numbers = [atom.property(f"{elem_prop}").num_protons() for atom in qm_atoms] engine.set_numbers(numbers) except: raise Exception("Unable to set atomic numbers for the QM region.") @@ -29,10 +26,16 @@ def _configure_engine(engine, mols, qm_mol, map): except: raise Exception("Unable to set atomic charges for the system.") + # Set the link atom information. + try: + engine.set_link_atoms(link_atoms) + except: + raise Exception("Unable to set link atom information.") + return engine -def _create_merged_mol(qm_mol, map): +def _create_merged_mol(qm_mol, qm_atoms, map): """ Internal helper function to create a merged molecule from the QM molecule. """ @@ -41,6 +44,9 @@ def _create_merged_mol(qm_mol, map): from ..legacy import Mol as _Mol from ..legacy import MM as _MM + # Store the indices of the QM atoms. + qm_idxs = [atom.index() for atom in qm_atoms] + # Get the user defined names for the properties that we need to # merge. bond_prop = map["bond"] @@ -59,9 +65,9 @@ def _create_merged_mol(qm_mol, map): for prop in qm_mol.property_keys(): # For all bonded properties we copy the MM terms to the lambda = 0 # (MM) end state, create a null set of terms for the lambda = 1 (QM) - # end state, then remove the existing property. Charges also zeroed - # for the MM end state. All other properties remain the same in both - # states. + # end state for any terms that only involve QM atoms, then remove + # the existing property. Charges also zeroed for the MM end state. + # All other properties remain the same in both states. # Bonds. if prop == bond_prop: @@ -75,10 +81,12 @@ def _create_merged_mol(qm_mol, map): atom0 = info.atom_idx(bond.atom0()) atom1 = info.atom_idx(bond.atom1()) - r = _CAS.Symbol("r") - amber_bond = _MM.AmberBond(0, r) - - bonds.set(atom0, atom1, amber_bond.to_expression(r)) + if atom0 in qm_idxs and atom1 in qm_idxs: + r = _CAS.Symbol("r") + amber_bond = _MM.AmberBond(0, r) + bonds.set(atom0, atom1, amber_bond.to_expression(r)) + else: + bonds.set(atom0, atom1, bond.function()) edit_mol = edit_mol.set_property(prop + "1", bonds).molecule() edit_mol = edit_mol.remove_property(prop).molecule() @@ -96,10 +104,12 @@ def _create_merged_mol(qm_mol, map): atom1 = info.atom_idx(angle.atom1()) atom2 = info.atom_idx(angle.atom2()) - theta = _CAS.Symbol("theta") - amber_angle = _MM.AmberAngle(0.0, theta) - - angles.set(atom0, atom1, atom2, amber_angle.to_expression(theta)) + if atom0 in qm_idxs and atom1 in qm_idxs and atom2 in qm_idxs: + theta = _CAS.Symbol("theta") + amber_angle = _MM.AmberAngle(0.0, theta) + angles.set(atom0, atom1, atom2, amber_angle.to_expression(theta)) + else: + angles.set(atom0, atom1, atom2, angle.function()) edit_mol = edit_mol.set_property(prop + "1", angles).molecule() edit_mol = edit_mol.remove_property(prop).molecule() @@ -118,16 +128,23 @@ def _create_merged_mol(qm_mol, map): atom2 = info.atom_idx(dihedral.atom2()) atom3 = info.atom_idx(dihedral.atom3()) - phi = _CAS.Symbol("phi") - amber_dihedral = _MM.AmberDihedral(0, phi) - - dihedrals.set( - atom0, - atom1, - atom2, - atom3, - amber_dihedral.to_expression(phi), - ) + if ( + atom0 in qm_idxs + and atom1 in qm_idxs + and atom2 in qm_idxs + and atom3 in qm_idxs + ): + phi = _CAS.Symbol("phi") + amber_dihedral = _MM.AmberDihedral(0, phi) + dihedrals.set( + atom0, + atom1, + atom2, + atom3, + amber_dihedral.to_expression(phi), + ) + else: + dihedrals.set(atom0, atom1, atom2, atom3, dihedral.function()) edit_mol = edit_mol.set_property(prop + "1", dihedrals).molecule() edit_mol = edit_mol.remove_property(prop).molecule() @@ -146,16 +163,23 @@ def _create_merged_mol(qm_mol, map): atom2 = info.atom_idx(improper.atom2()) atom3 = info.atom_idx(improper.atom3()) - psi = _CAS.Symbol("psi") - amber_improper = _MM.AmberDihedral(0, psi) - - impropers.set( - atom0, - atom1, - atom2, - atom3, - amber_improper.to_expression(psi), - ) + if ( + atom0 in qm_idxs + and atom1 in qm_idxs + and atom2 in qm_idxs + and atom3 in qm_idxs + ): + psi = _CAS.Symbol("psi") + amber_improper = _MM.AmberDihedral(0, psi) + impropers.set( + atom0, + atom1, + atom2, + atom3, + amber_improper.to_expression(psi), + ) + else: + impropers.set(atom0, atom1, atom2, atom3, improper.function()) edit_mol = edit_mol.set_property(prop + "1", impropers).molecule() edit_mol = edit_mol.remove_property(prop).molecule() @@ -196,3 +220,96 @@ def _create_merged_mol(qm_mol, map): # Return the merged molecule. return qm_mol + + +def _get_link_atoms(mols, qm_mol, qm_atoms, map): + """ + Internal helper function to get a dictionary with link atoms for each QM atom. + """ + + from ..legacy.Mol import Connectivity as _Connectivity + from ..legacy.Mol import CovalentBondHunter as _CovalentBondHunter + + # Store the indices of the QM atoms. + qm_idxs = [atom.index() for atom in qm_atoms] + + # Create a connectivity object. + connectivity = _Connectivity(qm_mol, _CovalentBondHunter(), map) + + mm1_atoms = {} + + # Loop over the QM atoms and find any MM atoms that are bonded to them. + for atom in qm_atoms: + # Store the atom index. + idx = atom.index() + + # Get the bonds for the atom. + bonds = connectivity.get_bonds(idx) + + # A list to hold MM atoms involved in the bonds. + mm_bonds = [] + + # A flag to indicate if the atom has a bond to another QM atom. + has_qm_bond = False + + # Loop over the bonds and find the MM atoms. + for bond in bonds: + # Get the indices of the two atoms in the bond. + idx0 = bond.atom0() + idx1 = bond.atom1() + + # Work out which atom isn't the current QM atom. + if idx0 != idx: + bond_idx = idx0 + else: + bond_idx = idx1 + + # If the atom is not in the QM region, add it to the list. + if bond_idx not in qm_idxs: + mm_bonds.append(bond_idx) + else: + has_qm_bond = True + + # If there are no QM bonds for this atom, raise an exception. + if not has_qm_bond: + raise ValueError( + f"Atom {idx} in the QM region has no bonds to other QM atoms!" + ) + + # Store the list of MM atoms. + if len(mm_bonds) > 0: + mm1_atoms[idx] = mm_bonds + + # Now work out the MM atoms that are bonded to the link atoms. + mm2_atoms = {} + for k, v in mm1_atoms.items(): + for idx in v: + if idx not in mm2_atoms: + bonds = connectivity.get_bonds(idx) + mm_bonds = [] + for bond in bonds: + idx0 = bond.atom0() + idx1 = bond.atom1() + if idx0 != idx: + bond_idx = idx0 + else: + bond_idx = idx1 + if bond_idx not in qm_idxs: + mm_bonds.append(bond_idx) + mm2_atoms[idx] = mm_bonds + + # Convert MM1 atoms dictionary to absolute indices. + abs_mm1_atoms = {} + for k, v in mm1_atoms.items(): + qm_idx = mols.atoms().find(qm_mol.atoms()[k]) + link_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] + abs_mm1_atoms[qm_idx] = link_idx + + # Convert MM2 atoms dictionary to absolute indices. + abs_mm2_atoms = {} + for k, v in mm2_atoms.items(): + link_idx = mols.atoms().find(qm_mol.atoms()[k]) + mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] + abs_mm2_atoms[link_idx] = mm_idx + + return abs_mm1_atoms, abs_mm2_atoms diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index ed2339d5d..98ed54f07 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -59,7 +59,7 @@ def test_interpolate(ala_mols): nrg_mm = d.current_potential_energy() # Create an EMLE engine bound to the calculator. - mols, engine = emle(mols, calculator, 0) + mols, engine = emle(mols, mols[0], calculator) # Create a QM/MM capable dynamics object. d = mols.dynamics( diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index cdf93bdb3..566cb7ec1 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -12,9 +12,11 @@ #include "openmmminimise.h" +#include "Helpers/convertdict.hpp" #include "Helpers/convertlist.hpp" #include "Helpers/tuples.hpp" +#include #include using namespace SireOpenMM; @@ -178,6 +180,9 @@ BOOST_PYTHON_MODULE(_SireOpenMM) // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) register_tuple>, QVector>>>(); + // A dictionary mapping link atoms (MM1) to the other MM atoms to which they are bonded (MM2). + register_dict>>(); + bp::class_, boost::noncopyable>("QMMMForce", bp::no_init); bp::class_>("EMLEEngine", @@ -200,6 +205,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM) .def("setNeighbourListFrequency", &EMLEEngine::setNeighbourListFrequency, "Set the neighbour list frequency") .def("getAtoms", &EMLEEngine::getAtoms, "Get QM atom indices") .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") + .def("getLinkAtoms", &EMLEEngine::getLinkAtoms, "Get the link atoms") + .def("setLinkAtoms", &EMLEEngine::setLinkAtoms, "Set the link atoms") .def("getNumbers", &EMLEEngine::getNumbers, "Get QM atomic numbers") .def("setNumbers", &EMLEEngine::setNumbers, "Set the QM atomic numbers") .def("getCharges", &EMLEEngine::getCharges, "Get the atomic charges") diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 2fdf5d16a..41db90fb6 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -108,6 +108,8 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : neighbour_list_frequency(other.neighbour_list_frequency), lambda(other.lambda), atoms(other.atoms), + link_atoms(other.link_atoms), + mm2_atoms(other.mm2_atoms), numbers(other.numbers), charges(other.charges) { @@ -120,6 +122,8 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) this->neighbour_list_frequency = other.neighbour_list_frequency; this->lambda = other.lambda; this->atoms = other.atoms; + this->link_atoms = other.link_atoms; + this->mm2_atoms = other.mm2_atoms; this->numbers = other.numbers; this->charges = other.charges; return *this; @@ -189,6 +193,23 @@ void EMLEEngine::setAtoms(QVector atoms) this->atoms = atoms; } +QHash> EMLEEngine::getLinkAtoms() const +{ + return this->link_atoms; +} + +void EMLEEngine::setLinkAtoms(QHash> link_atoms) +{ + this->link_atoms = link_atoms; + + // Build a vector of all of the MM2 atoms. + this->mm2_atoms.clear(); + for (const auto &mm2 : this->link_atoms.values()) + { + this->mm2_atoms.append(mm2); + } +} + QVector EMLEEngine::getNumbers() const { return this->numbers; diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 4163d5a5a..f3c3f5a6d 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -39,6 +39,7 @@ #include "boost/python.hpp" #include +#include #include #include "sireglobal.h" @@ -141,45 +142,101 @@ namespace SireOpenMM EMLEEngine &operator=(const EMLEEngine &other); //! Set the callback object. + /*! \param callback + A Python object that contains the callback function. + */ void setCallback(EMLECallback callback); //! Get the callback object. + /*! \returns + A Python object that contains the callback function. + */ EMLECallback getCallback() const; //! Get the lambda weighting factor. + /*! \returns + The lambda weighting factor. + */ double getLambda() const; //! Set the lambda weighting factor. + /*! \param lambda + The lambda weighting factor. + */ void setLambda(double lambda); //! Get the QM cutoff distance. + /*! \returns + The QM cutoff distance. + */ SireUnits::Dimension::Length getCutoff() const; //! Set the QM cutoff distance. + /*! \param cutoff + The QM cutoff distance. + */ void setCutoff(SireUnits::Dimension::Length cutoff); //! Get the neighbour list frequency. + /*! \returns + The neighbour list frequency. + */ int getNeighbourListFrequency() const; //! Set the neighbour list frequency. + /*! \param neighbour_list_frequency + The neighbour list frequency. + */ void setNeighbourListFrequency(int neighbour_list_frequency); //! Get the indices of the atoms in the QM region. + /*! \returns + A vector of atom indices for the QM region. + */ QVector getAtoms() const; //! Set the list of atom indices for the QM region. + /*! \param atoms + A vector of atom indices for the QM region. + */ void setAtoms(QVector atoms); + //! Get the link atoms associated with each QM atom. + /*! \returns + A dictionary of link atom indices (MM1) to a list of MM + atom indices to which they are bonded (MM2 atoms). + */ + QHash> getLinkAtoms() const; + + //! Set the link atoms associated with each QM atom. + /*! \param link_atoms + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + */ + void setLinkAtoms(QHash> link_atoms); + //! Get the atomic numbers for the atoms in the QM region. + /*! \returns + A vector of atomic numbers for the atoms in the QM region. + */ QVector getNumbers() const; //! Set the atomic numbers for the atoms in the QM region. + /*! \param numbers + A vector of atomic numbers for the atoms in the QM region. + */ void setNumbers(QVector numbers); //! Get the atomic charges of all atoms in the system. + /*! \returns + A vector of atomic charges for all atoms in the system. + */ QVector getCharges() const; //! Set the atomic charges of all atoms in the system. + /*! \param charges + A vector of atomic charges for all atoms in the system. + */ void setCharges(QVector charges); //! Return the C++ name for this class. @@ -223,6 +280,8 @@ namespace SireOpenMM int neighbour_list_frequency; double lambda; QVector atoms; + QHash> link_atoms; + QVector mm2_atoms; QVector numbers; QVector charges; }; diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index ef1f549af..bb79d25f8 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -32,6 +32,9 @@ #include "OpenMM.h" #include "openmm/Force.h" +#include +#include + #include "sireglobal.h" #include "SireBase/property.h" @@ -65,6 +68,12 @@ namespace SireOpenMM //! Set the list of atom indices for the QM region. virtual void setAtoms(QVector) = 0; + //! Get the link atoms associated with each QM atom. + QHash> getLinkAtoms() const; + + //! Set the link atoms associated with each QM atom. + virtual void setLinkAtoms(QHash>) = 0; + //! Get the atomic numbers of the atoms in the QM region. virtual QVector getNumbers() const = 0; From 4c66aa54a764bc6ca10ea8ebc883052910726c34 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 17 Jan 2024 16:18:51 +0000 Subject: [PATCH 082/468] Add link atom implementation using charge shifting method. --- doc/source/tutorial/part07/01_emle.rst | 8 + src/sire/qm/_emle.py | 9 +- src/sire/qm/_utils.py | 138 +++++++++++++---- tests/qm/test_emle.py | 7 +- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 11 +- wrapper/Convert/SireOpenMM/emle.cpp | 143 ++++++++++++++++-- wrapper/Convert/SireOpenMM/emle.h | 42 ++++- wrapper/Convert/SireOpenMM/qmmm.h | 8 +- 8 files changed, 306 insertions(+), 60 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index 3463bc351..d4ba55150 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -63,6 +63,14 @@ interpolated between QM and MM levels of theory, along with an engine. The engine registers a Python callback that uses ``emle-engine`` to perform the QM calculation. +The selection syntax for QM atoms is extremely flexible. Any valid search string, +atom index, list of atom indicies, or molecule view/container that can be used. +The only constraint is that the atoms are bonded to each other, i.e. they are +part of the same molecule. Support for modelling partial molecules at the QM +level is provided via the link atom approach, via the charge shifting method. +For details of this implementation, see, e.g., the NAMD user guide +`here `_. + Next we need to create a dynamics object to perform the simulation. For QM/MM simulations it is recommended to use a 1 femtosecond timestep and no constraints. In this example we will use the ``lambda_interpolate`` keyword to interpolate diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index be7252039..a771583bb 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -120,12 +120,13 @@ def emle( from ._utils import _configure_engine, _create_merged_mol, _get_link_atoms - # Get dictionary of link atoms for each QM atom (mm1_atoms) and the - # dictionary of bonded MM atoms for each link atom (mm2_atoms). - mm1_atoms, mm2_atoms = _get_link_atoms(mols, qm_mol, qm_atoms, map) + # Get link atom information. + mm1_to_qm, mm1_to_mm2, bond_lengths = _get_link_atoms(mols, qm_mol, qm_atoms, map) # Configure the engine. - engine = _configure_engine(engine, mols, qm_atoms, mm2_atoms, map) + engine = _configure_engine( + engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map + ) # Create the merged molecule. qm_mol = _create_merged_mol(qm_mol, qm_atoms, map) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 3fccb001a..1237ea76e 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,4 +1,4 @@ -def _configure_engine(engine, mols, qm_atoms, link_atoms, map): +def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map): """ Internal helper function to configure a QM engine ready for dynamics. """ @@ -28,7 +28,7 @@ def _configure_engine(engine, mols, qm_atoms, link_atoms, map): # Set the link atom information. try: - engine.set_link_atoms(link_atoms) + engine.set_link_atoms(mm1_to_qm, mm1_to_mm2, bond_lengths) except: raise Exception("Unable to set link atom information.") @@ -227,14 +227,15 @@ def _get_link_atoms(mols, qm_mol, qm_atoms, map): Internal helper function to get a dictionary with link atoms for each QM atom. """ - from ..legacy.Mol import Connectivity as _Connectivity - from ..legacy.Mol import CovalentBondHunter as _CovalentBondHunter + from ..legacy import CAS as _CAS + from ..legacy import Mol as _Mol + from ..legacy import MM as _MM # Store the indices of the QM atoms. qm_idxs = [atom.index() for atom in qm_atoms] # Create a connectivity object. - connectivity = _Connectivity(qm_mol, _CovalentBondHunter(), map) + connectivity = _Mol.Connectivity(qm_mol, _Mol.CovalentBondHunter(), map) mm1_atoms = {} @@ -278,38 +279,121 @@ def _get_link_atoms(mols, qm_mol, qm_atoms, map): # Store the list of MM atoms. if len(mm_bonds) > 0: - mm1_atoms[idx] = mm_bonds + if len(mm_bonds) > 1: + raise Exception(f"QM atom {idx} has more than one MM bond!") + else: + mm1_atoms[idx] = mm_bonds[0] # Now work out the MM atoms that are bonded to the link atoms. mm2_atoms = {} - for k, v in mm1_atoms.items(): - for idx in v: - if idx not in mm2_atoms: - bonds = connectivity.get_bonds(idx) - mm_bonds = [] - for bond in bonds: - idx0 = bond.atom0() - idx1 = bond.atom1() - if idx0 != idx: - bond_idx = idx0 - else: - bond_idx = idx1 - if bond_idx not in qm_idxs: - mm_bonds.append(bond_idx) - mm2_atoms[idx] = mm_bonds + for qm_idx, mm1_idx in mm1_atoms.items(): + if mm1_idx not in mm2_atoms: + bonds = connectivity.get_bonds(mm1_idx) + mm_bonds = [] + for bond in bonds: + idx0 = bond.atom0() + idx1 = bond.atom1() + if idx0 != mm1_idx: + bond_idx = idx0 + else: + bond_idx = idx1 + if bond_idx not in qm_idxs: + mm_bonds.append(bond_idx) + mm2_atoms[mm1_idx] = mm_bonds # Convert MM1 atoms dictionary to absolute indices. - abs_mm1_atoms = {} + mm1_to_qm = {} for k, v in mm1_atoms.items(): qm_idx = mols.atoms().find(qm_mol.atoms()[k]) - link_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] - abs_mm1_atoms[qm_idx] = link_idx + link_idx = mols.atoms().find(qm_mol.atoms()[v]) + mm1_to_qm[link_idx] = qm_idx # Convert MM2 atoms dictionary to absolute indices. - abs_mm2_atoms = {} + mm1_to_mm2 = {} for k, v in mm2_atoms.items(): link_idx = mols.atoms().find(qm_mol.atoms()[k]) mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] - abs_mm2_atoms[link_idx] = mm_idx + mm1_to_mm2[link_idx] = mm_idx + + # Now work out the QM-MM1 bond distances based on the equilibrium + # MM bond lengths. + + # A dictionary to store the bond lengths. + bond_lengths = {} + link_bond_lengths = {} + + # Get the MM bond potentials. + bonds = qm_mol.property(map["bond"]).potentials() + + # Store the info for the QM molecule. + info = qm_mol.info() + + # Store the bond potential symbol. + r = _CAS.Symbol("r") + + # Loop over the link atoms. + for qm_idx, mm1_idx in mm1_atoms.items(): + # Convert to cg_atom_idx objects. + cg_qm_idx = info.cg_atom_idx(qm_idx) + cg_mm1_idx = info.cg_atom_idx(mm1_idx) + + # Store the element of the QM atom. + qm_elem = qm_mol[cg_qm_idx].element() + hydrogen = _Mol.Element("H") + + qm_m1_bond_found = False + qm_link_bond_found = False + + # Loop over the bonds. + for bond in bonds: + # Get the indices of the atoms in the bond. + bond_idx0 = bond.atom0() + bond_idx1 = bond.atom1() + + # If the bond is between the QM atom and the MM atom, store the + # bond length. + if ( + not qm_m1_bond_found + and cg_qm_idx == bond_idx0 + and cg_mm1_idx == bond_idx1 + or cg_qm_idx == bond_idx1 + and cg_mm1_idx == bond_idx0 + ): + # Cast as an AmberBond. + ab = _MM.AmberBond(bond.function(), r) + bond_lengths[mm1_idx] = ab.r0() + qm_m1_bond_found = True + if qm_link_bond_found: + break + else: + # Check to see if this bond is between a hydrogen and and the + # same element as the QM atom. + elem0 = qm_mol[bond_idx0].element() + elem1 = qm_mol[bond_idx1].element() + + if ( + not qm_link_bond_found + and elem0 == hydrogen + and elem1 == qm_elem + or elem0 == qm_elem + and elem1 == hydrogen + ): + # Cast as an AmberBond. + ab = _MM.AmberBond(bond.function(), r) + link_bond_lengths[mm1_idx] = ab.r0() + qm_link_bond_found = True + if qm_m1_bond_found: + break + + # Work out the rescaled bond length: R0(Q-H) / R0(Q-MM1) + try: + scaled_bond_lengths = {} + for idx in bond_lengths: + abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) + scaled_bond_lengths[abs_idx] = link_bond_lengths[idx] / bond_lengths[idx] + except: + raise Exception( + f"Unable to compute the scaled the QM-MM1 bond lengths for MM1 atom {idx}!" + ) - return abs_mm1_atoms, abs_mm2_atoms + return mm1_to_qm, mm1_to_mm2, scaled_bond_lengths diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 98ed54f07..6f33fb1d4 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -41,13 +41,14 @@ def callback(self, a, b, c, d): @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") -def test_interpolate(ala_mols): +@pytest.mark.parametrize("selection", ["molidx 0", "resname ALA"]) +def test_interpolate(ala_mols, selection): """ Make sure that lambda interpolation between pure MM and EMLE potentials works. """ # Create a local copy of the test system. - mols = ala_mols + mols = ala_mols.__copy__() # Create an EMLE calculator. calculator = EMLECalculator(device="cpu", log=0, save_settings=False) @@ -59,7 +60,7 @@ def test_interpolate(ala_mols): nrg_mm = d.current_potential_energy() # Create an EMLE engine bound to the calculator. - mols, engine = emle(mols, mols[0], calculator) + mols, engine = emle(mols, selection, calculator) # Create a QM/MM capable dynamics object. d = mols.dynamics( diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 566cb7ec1..e0aece7ff 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -16,7 +16,7 @@ #include "Helpers/convertlist.hpp" #include "Helpers/tuples.hpp" -#include +#include #include using namespace SireOpenMM; @@ -180,8 +180,13 @@ BOOST_PYTHON_MODULE(_SireOpenMM) // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) register_tuple>, QVector>>>(); - // A dictionary mapping link atoms (MM1) to the other MM atoms to which they are bonded (MM2). - register_dict>>(); + // Dictionary for mapping link atoms to QM and MM2 atoms. + register_dict>(); + register_dict>(); + register_dict>>(); + + // A tuple for passing link atom information to EMLEEngine. + register_tuple, QMap>>>(); bp::class_, boost::noncopyable>("QMMMForce", bp::no_init); diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 41db90fb6..c23e57db7 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -108,8 +108,10 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : neighbour_list_frequency(other.neighbour_list_frequency), lambda(other.lambda), atoms(other.atoms), - link_atoms(other.link_atoms), + mm1_to_qm(other.mm1_to_qm), + mm1_to_mm2(other.mm1_to_mm2), mm2_atoms(other.mm2_atoms), + bond_lengths(other.bond_lengths), numbers(other.numbers), charges(other.charges) { @@ -122,8 +124,10 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) this->neighbour_list_frequency = other.neighbour_list_frequency; this->lambda = other.lambda; this->atoms = other.atoms; - this->link_atoms = other.link_atoms; + this->mm1_to_qm = other.mm1_to_qm; + this->mm1_to_mm2 = other.mm1_to_mm2; this->mm2_atoms = other.mm2_atoms; + this->bond_lengths = other.bond_lengths; this->numbers = other.numbers; this->charges = other.charges; return *this; @@ -193,23 +197,33 @@ void EMLEEngine::setAtoms(QVector atoms) this->atoms = atoms; } -QHash> EMLEEngine::getLinkAtoms() const +boost::tuple, QMap>, QMap> EMLEEngine::getLinkAtoms() const { - return this->link_atoms; + return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_lengths); } -void EMLEEngine::setLinkAtoms(QHash> link_atoms) +void EMLEEngine::setLinkAtoms( + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_lengths) { - this->link_atoms = link_atoms; - + this->mm1_to_qm = mm1_to_qm; + this->mm1_to_mm2 = mm1_to_mm2; + this->bond_lengths = bond_lengths; + // Build a vector of all of the MM2 atoms. this->mm2_atoms.clear(); - for (const auto &mm2 : this->link_atoms.values()) + for (const auto &mm2 : this->mm1_to_mm2.values()) { this->mm2_atoms.append(mm2); } } +QVector EMLEEngine::getMM2Atoms() const +{ + return this->mm2_atoms; +} + QVector EMLEEngine::getNumbers() const { return this->numbers; @@ -301,8 +315,16 @@ double EMLEEngineImpl::computeForce( Vector(10*box_z[0], 10*box_z[1], 10*box_z[2]) ); - // Store the QM atom indices. + // Store the QM atomic indices and numbers. const auto qm_atoms = this->owner.getAtoms(); + auto numbers = this->owner.getNumbers(); + + // Store the link atom info. + const auto link_atoms = this->owner.getLinkAtoms(); + const auto mm1_to_qm = link_atoms.get<0>(); + const auto mm1_to_mm2 = link_atoms.get<1>(); + const auto bond_lengths = link_atoms.get<2>(); + const auto mm2_atoms = this->owner.getMM2Atoms(); // Initialise a vector to hold the current positions for the QM atoms. QVector> xyz_qm(qm_atoms.size()); @@ -334,10 +356,13 @@ double EMLEEngineImpl::computeForce( center /= i; // Initialise a vector to hold the current positions for the MM atoms. + // and dipoles. QVector> xyz_mm; + QVector> xyz_dipole; - // Initialise a vector to hold the charges for the MM atoms. + // Initialise a vector to hold the charges for the MM atoms and dipoles. QVector charges_mm; + QVector charges_dipole; // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; @@ -355,8 +380,10 @@ double EMLEEngineImpl::computeForce( // Loop over all of the OpenMM positions. for (const auto &pos : positions) { - // Exclude QM atoms. - if (not qm_atoms.contains(i)) + // Exclude QM atoms or link atoms, which are handled later. + if (not qm_atoms.contains(i) and + not mm1_to_mm2.contains(i) and + not mm2_atoms.contains(i)) { // Store the MM atom position in Sire Vector format. Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); @@ -424,13 +451,91 @@ double EMLEEngineImpl::computeForce( break; } } + } + } + + // Store the current number of QM. + const auto num_qm = xyz_qm.size(); + + // Handle link atoms. + for (const auto &idx: mm1_to_mm2.keys()) + { + // Get the QM atom to which the current MM atom is bonded. + const auto qm_idx = mm1_to_qm[idx]; + + // Store the MM1 position in Sire Vector format, along with the + // position of the QM atom to which it is bonded. + Vector mm1_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); + Vector qm_vec(10*positions[qm_idx][0], 10*positions[qm_idx][1], 10*positions[qm_idx][2]); + + // Work out the minimum image positions with respect to the reference position. + mm1_vec = space.getMinimumImage(mm1_vec, center); + qm_vec = space.getMinimumImage(qm_vec, center); + + // Work out the normal vector between the MM1 and QM atoms. + const auto normal = (qm_vec - mm1_vec).normalise(); + + // Work out the position of the link atom. + const auto link_vec = mm1_vec + 10*bond_lengths[idx]*normal; + + // Add to the QM positions. + xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); + + // Append a hydrogen element to the numbers vector. + numbers.append(1); + + // Store the number of MM2 atoms. + const auto num_mm2 = mm1_to_mm2[idx].size(); + + // Store the fractional charge contribution to the MM2 atoms and dipoles. + const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; + // Loop over the MM2 atoms. + for (const auto& mm2_idx : mm1_to_mm2[idx]) + { + // Store the MM2 position in Sire Vector format. + Vector mm2_vec(10*positions[mm2_idx][0], 10*positions[mm2_idx][1], 10*positions[mm2_idx][2]); + + // Work out the minimum image position with respect to the reference position. + mm2_vec = space.getMinimumImage(mm2_vec, center); + + // Add to the MM positions. + xyz_mm.append(QVector({mm2_vec[0], mm2_vec[1], mm2_vec[2]})); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); + idx_mm.append(mm2_idx); + + // Now add the dipoles. + + // Compute the normal vector from the MM1 to MM2 atom. + const auto normal = (mm2_vec - mm1_vec).normalise(); + + // Positive direction. (Away from MM1 atom.) + auto xyz = mm2_vec + 0.01*normal; + xyz_dipole.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_dipole.append(-frac_charge); + + // Negative direction (Towards MM1 atom.) + xyz = mm2_vec - 0.01*normal; + xyz_dipole.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_dipole.append(frac_charge); } } + // Store the current number of MM atoms. + const auto num_mm = xyz_mm.size(); + + // If there are any dipoles, then add to the MM positions and charges. + if (xyz_dipole.size() > 0) + { + xyz_mm.append(xyz_dipole); + charges_mm.append(charges_dipole); + } + // Call the callback. auto result = this->owner.call( - this->owner.getNumbers(), + numbers, charges_mm, xyz_qm, xyz_mm @@ -461,6 +566,12 @@ double EMLEEngineImpl::computeForce( // Update the atom index. i++; + + // Exit if we have reached the end of the QM atoms, i.e. ignore link atoms. + if (i == num_qm) + { + break; + } } // Now the MM atoms. @@ -478,6 +589,12 @@ double EMLEEngineImpl::computeForce( // Update the atom index. i++; + + // Exit if we have reached the end of the MM atoms, i.e. ignore dipoles. + if (i == num_mm) + { + break; + } } // Update the step count. diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index f3c3f5a6d..4a0bf9a09 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -39,7 +39,7 @@ #include "boost/python.hpp" #include -#include +#include #include #include "sireglobal.h" @@ -203,17 +203,43 @@ namespace SireOpenMM //! Get the link atoms associated with each QM atom. /*! \returns - A dictionary of link atom indices (MM1) to a list of MM - atom indices to which they are bonded (MM2 atoms). + A tuple containing: + + mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + bond_lengths + A dictionary of link atom indices (MM1) to a list of the bond + lengths between the MM1 and QM atoms. */ - QHash> getLinkAtoms() const; + boost::tuple, QMap>, QMap> getLinkAtoms() const; //! Set the link atoms associated with each QM atom. - /*! \param link_atoms + /*! \param mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + \param mm1_to_mm2 A dictionary of link atoms indices (MM1) to a list of the MM atoms to which they are bonded (MM2). + + \param bond_lengths + A dictionary of link atom indices (MM1) to a list of the bond + lengths between the MM1 and QM atoms. + */ - void setLinkAtoms(QHash> link_atoms); + void setLinkAtoms(QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_lengths); + + //! Get the vector of MM2 atoms. + /*! \returns + A vector of MM2 atom indices. + */ + QVector getMM2Atoms() const; //! Get the atomic numbers for the atoms in the QM region. /*! \returns @@ -280,7 +306,9 @@ namespace SireOpenMM int neighbour_list_frequency; double lambda; QVector atoms; - QHash> link_atoms; + QMap mm1_to_qm; + QMap> mm1_to_mm2; + QMap bond_lengths; QVector mm2_atoms; QVector numbers; QVector charges; diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index bb79d25f8..d43ef81e1 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -32,7 +32,9 @@ #include "OpenMM.h" #include "openmm/Force.h" -#include +#include + +#include #include #include "sireglobal.h" @@ -69,10 +71,10 @@ namespace SireOpenMM virtual void setAtoms(QVector) = 0; //! Get the link atoms associated with each QM atom. - QHash> getLinkAtoms() const; + boost::tuple, QMap>, QMap> getLinkAtoms() const; //! Set the link atoms associated with each QM atom. - virtual void setLinkAtoms(QHash>) = 0; + virtual void setLinkAtoms(QMap, QMap>, QMap) = 0; //! Get the atomic numbers of the atoms in the QM region. virtual QVector getNumbers() const = 0; From 7c4493fc25e3d49f8e6a3921537d95ca25044198 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 18 Jan 2024 10:56:09 +0000 Subject: [PATCH 083/468] Add support for multiple QM regions. --- doc/source/tutorial/part07/01_emle.rst | 10 +- src/sire/qm/_emle.py | 23 +- src/sire/qm/_utils.py | 643 +++++++++++++------------ 3 files changed, 355 insertions(+), 321 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index d4ba55150..2584b1954 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -65,11 +65,11 @@ calculation. The selection syntax for QM atoms is extremely flexible. Any valid search string, atom index, list of atom indicies, or molecule view/container that can be used. -The only constraint is that the atoms are bonded to each other, i.e. they are -part of the same molecule. Support for modelling partial molecules at the QM -level is provided via the link atom approach, via the charge shifting method. -For details of this implementation, see, e.g., the NAMD user guide -`here `_. +Support for modelling partial molecules at the QM level is provided via the link +atom approach, via the charge shifting method. For details of this implementation, +see, e.g., the NAMD user guide `here `_. +While we support multiple QM regions, we do not currently support multiple +*independent* QM regions. We plan on adding support for this in the near future. Next we need to create a dynamics object to perform the simulation. For QM/MM simulations it is recommended to use a 1 femtosecond timestep and no constraints. diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index a771583bb..8699c4055 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -73,13 +73,14 @@ def emle( except: raise ValueError("Unable to select 'qm_atoms' from 'mols'") - # Get the molecule containing the qm_atoms. - qm_mol = qm_atoms[0].molecule() - - # Make sure all of the atoms are in the same molecule. - for atom in qm_atoms[1:]: - if not atom.molecule() == qm_mol: - raise ValueError("'qm_atoms' must all be in the same molecule") + # Create a dictionary mapping molecule numbers to a list of QM atoms. + qm_mol_to_atoms = {} + for atom in qm_atoms: + mol_num = atom.molecule().number() + if mol_num not in qm_mol_to_atoms: + qm_mol_to_atoms[mol_num] = [atom] + else: + qm_mol_to_atoms[mol_num].append(atom) if not isinstance(calculator, _EMLECalculator): raise TypeError( @@ -118,10 +119,10 @@ def emle( neighbourlist_update_frequency, ) - from ._utils import _configure_engine, _create_merged_mol, _get_link_atoms + from ._utils import _configure_engine, _create_merged_mols, _get_link_atoms # Get link atom information. - mm1_to_qm, mm1_to_mm2, bond_lengths = _get_link_atoms(mols, qm_mol, qm_atoms, map) + mm1_to_qm, mm1_to_mm2, bond_lengths = _get_link_atoms(mols, qm_mol_to_atoms, map) # Configure the engine. engine = _configure_engine( @@ -129,9 +130,9 @@ def emle( ) # Create the merged molecule. - qm_mol = _create_merged_mol(qm_mol, qm_atoms, map) + qm_mols = _create_merged_mols(qm_mol_to_atoms, map) # Update the molecule in the system. - mols.update(qm_mol) + mols.update(qm_mols) return mols, engine diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 1237ea76e..d67f0cb25 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -35,7 +35,7 @@ def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_length return engine -def _create_merged_mol(qm_mol, qm_atoms, map): +def _create_merged_mols(qm_mol_to_atoms, map): """ Internal helper function to create a merged molecule from the QM molecule. """ @@ -44,185 +44,195 @@ def _create_merged_mol(qm_mol, qm_atoms, map): from ..legacy import Mol as _Mol from ..legacy import MM as _MM - # Store the indices of the QM atoms. - qm_idxs = [atom.index() for atom in qm_atoms] - - # Get the user defined names for the properties that we need to - # merge. - bond_prop = map["bond"] - angle_prop = map["angle"] - dihedral_prop = map["dihedral"] - improper_prop = map["improper"] - charge_prop = map["charge"] - connectivity_prop = map["connectivity"] - - # Get the molecular info object. - info = qm_mol.info() - - # Make an editable version of the molecule. - edit_mol = qm_mol.edit() - - for prop in qm_mol.property_keys(): - # For all bonded properties we copy the MM terms to the lambda = 0 - # (MM) end state, create a null set of terms for the lambda = 1 (QM) - # end state for any terms that only involve QM atoms, then remove - # the existing property. Charges also zeroed for the MM end state. - # All other properties remain the same in both states. - - # Bonds. - if prop == bond_prop: - edit_mol = edit_mol.set_property( - prop + "0", qm_mol.property(prop) - ).molecule() - - bonds = _MM.TwoAtomFunctions(info) - - for bond in qm_mol.property(prop).potentials(): - atom0 = info.atom_idx(bond.atom0()) - atom1 = info.atom_idx(bond.atom1()) - - if atom0 in qm_idxs and atom1 in qm_idxs: - r = _CAS.Symbol("r") - amber_bond = _MM.AmberBond(0, r) - bonds.set(atom0, atom1, amber_bond.to_expression(r)) - else: - bonds.set(atom0, atom1, bond.function()) - - edit_mol = edit_mol.set_property(prop + "1", bonds).molecule() - edit_mol = edit_mol.remove_property(prop).molecule() - - # Angles. - elif prop == angle_prop: - edit_mol = edit_mol.set_property( - prop + "0", qm_mol.property(prop) - ).molecule() - - angles = _MM.ThreeAtomFunctions(info) - - for angle in qm_mol.property(prop).potentials(): - atom0 = info.atom_idx(angle.atom0()) - atom1 = info.atom_idx(angle.atom1()) - atom2 = info.atom_idx(angle.atom2()) - - if atom0 in qm_idxs and atom1 in qm_idxs and atom2 in qm_idxs: - theta = _CAS.Symbol("theta") - amber_angle = _MM.AmberAngle(0.0, theta) - angles.set(atom0, atom1, atom2, amber_angle.to_expression(theta)) - else: - angles.set(atom0, atom1, atom2, angle.function()) - - edit_mol = edit_mol.set_property(prop + "1", angles).molecule() - edit_mol = edit_mol.remove_property(prop).molecule() - - # Dihedrals. - elif prop == dihedral_prop: - edit_mol = edit_mol.set_property( - prop + "0", qm_mol.property(prop) - ).molecule() - - dihedrals = _MM.FourAtomFunctions(info) - - for dihedral in qm_mol.property(prop).potentials(): - atom0 = info.atom_idx(dihedral.atom0()) - atom1 = info.atom_idx(dihedral.atom1()) - atom2 = info.atom_idx(dihedral.atom2()) - atom3 = info.atom_idx(dihedral.atom3()) - - if ( - atom0 in qm_idxs - and atom1 in qm_idxs - and atom2 in qm_idxs - and atom3 in qm_idxs - ): - phi = _CAS.Symbol("phi") - amber_dihedral = _MM.AmberDihedral(0, phi) - dihedrals.set( - atom0, - atom1, - atom2, - atom3, - amber_dihedral.to_expression(phi), - ) - else: - dihedrals.set(atom0, atom1, atom2, atom3, dihedral.function()) - - edit_mol = edit_mol.set_property(prop + "1", dihedrals).molecule() - edit_mol = edit_mol.remove_property(prop).molecule() - - # Impropers. - elif prop == improper_prop: - edit_mol = edit_mol.set_property( - prop + "0", qm_mol.property(prop) - ).molecule() - - impropers = _MM.FourAtomFunctions(info) - - for improper in qm_mol.property(prop).potentials(): - atom0 = info.atom_idx(improper.atom0()) - atom1 = info.atom_idx(improper.atom1()) - atom2 = info.atom_idx(improper.atom2()) - atom3 = info.atom_idx(improper.atom3()) - - if ( - atom0 in qm_idxs - and atom1 in qm_idxs - and atom2 in qm_idxs - and atom3 in qm_idxs - ): - psi = _CAS.Symbol("psi") - amber_improper = _MM.AmberDihedral(0, psi) - impropers.set( - atom0, - atom1, - atom2, - atom3, - amber_improper.to_expression(psi), - ) - else: - impropers.set(atom0, atom1, atom2, atom3, improper.function()) - - edit_mol = edit_mol.set_property(prop + "1", impropers).molecule() - edit_mol = edit_mol.remove_property(prop).molecule() - - # Charge. - elif prop == charge_prop: - edit_mol = edit_mol.set_property( - prop + "0", qm_mol.property(prop) - ).molecule() + # Initialise a list to store the merged molecules. + qm_mols = [] - charges = _Mol.AtomCharges(info) - edit_mol = edit_mol.set_property(prop + "1", charges).molecule() - edit_mol = edit_mol.remove_property(prop).molecule() + # Loop over all molecules containing QM atoms. + for mol_num, qm_atoms in qm_mol_to_atoms.items(): + # Get the molecule. + qm_mol = qm_atoms[0].molecule() - # Connectivity. - elif prop == connectivity_prop: - pass + # Store the indices of the QM atoms. + qm_idxs = [atom.index() for atom in qm_atoms] - # All other properties remain the same in both end states. - else: - edit_mol = edit_mol.set_property( - prop + "0", qm_mol.property(prop) - ).molecule() - edit_mol = edit_mol.set_property( - prop + "1", qm_mol.property(prop) - ).molecule() + # Get the user defined names for the properties that we need to + # merge. + bond_prop = map["bond"] + angle_prop = map["angle"] + dihedral_prop = map["dihedral"] + improper_prop = map["improper"] + charge_prop = map["charge"] + connectivity_prop = map["connectivity"] + + # Get the molecular info object. + info = qm_mol.info() + + # Make an editable version of the molecule. + edit_mol = qm_mol.edit() + + for prop in qm_mol.property_keys(): + # For all bonded properties we copy the MM terms to the lambda = 0 + # (MM) end state, create a null set of terms for the lambda = 1 (QM) + # end state for any terms that only involve QM atoms, then remove + # the existing property. Charges also zeroed for the MM end state. + # All other properties remain the same in both states. + + # Bonds. + if prop == bond_prop: + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + + bonds = _MM.TwoAtomFunctions(info) + + for bond in qm_mol.property(prop).potentials(): + atom0 = info.atom_idx(bond.atom0()) + atom1 = info.atom_idx(bond.atom1()) + + if atom0 in qm_idxs and atom1 in qm_idxs: + r = _CAS.Symbol("r") + amber_bond = _MM.AmberBond(0, r) + bonds.set(atom0, atom1, amber_bond.to_expression(r)) + else: + bonds.set(atom0, atom1, bond.function()) + + edit_mol = edit_mol.set_property(prop + "1", bonds).molecule() + edit_mol = edit_mol.remove_property(prop).molecule() + + # Angles. + elif prop == angle_prop: + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + + angles = _MM.ThreeAtomFunctions(info) + + for angle in qm_mol.property(prop).potentials(): + atom0 = info.atom_idx(angle.atom0()) + atom1 = info.atom_idx(angle.atom1()) + atom2 = info.atom_idx(angle.atom2()) + + if atom0 in qm_idxs and atom1 in qm_idxs and atom2 in qm_idxs: + theta = _CAS.Symbol("theta") + amber_angle = _MM.AmberAngle(0.0, theta) + angles.set( + atom0, atom1, atom2, amber_angle.to_expression(theta) + ) + else: + angles.set(atom0, atom1, atom2, angle.function()) + + edit_mol = edit_mol.set_property(prop + "1", angles).molecule() + edit_mol = edit_mol.remove_property(prop).molecule() + + # Dihedrals. + elif prop == dihedral_prop: + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + + dihedrals = _MM.FourAtomFunctions(info) + + for dihedral in qm_mol.property(prop).potentials(): + atom0 = info.atom_idx(dihedral.atom0()) + atom1 = info.atom_idx(dihedral.atom1()) + atom2 = info.atom_idx(dihedral.atom2()) + atom3 = info.atom_idx(dihedral.atom3()) + + if ( + atom0 in qm_idxs + and atom1 in qm_idxs + and atom2 in qm_idxs + and atom3 in qm_idxs + ): + phi = _CAS.Symbol("phi") + amber_dihedral = _MM.AmberDihedral(0, phi) + dihedrals.set( + atom0, + atom1, + atom2, + atom3, + amber_dihedral.to_expression(phi), + ) + else: + dihedrals.set(atom0, atom1, atom2, atom3, dihedral.function()) + + edit_mol = edit_mol.set_property(prop + "1", dihedrals).molecule() + edit_mol = edit_mol.remove_property(prop).molecule() + + # Impropers. + elif prop == improper_prop: + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + + impropers = _MM.FourAtomFunctions(info) + + for improper in qm_mol.property(prop).potentials(): + atom0 = info.atom_idx(improper.atom0()) + atom1 = info.atom_idx(improper.atom1()) + atom2 = info.atom_idx(improper.atom2()) + atom3 = info.atom_idx(improper.atom3()) + + if ( + atom0 in qm_idxs + and atom1 in qm_idxs + and atom2 in qm_idxs + and atom3 in qm_idxs + ): + psi = _CAS.Symbol("psi") + amber_improper = _MM.AmberDihedral(0, psi) + impropers.set( + atom0, + atom1, + atom2, + atom3, + amber_improper.to_expression(psi), + ) + else: + impropers.set(atom0, atom1, atom2, atom3, improper.function()) + + edit_mol = edit_mol.set_property(prop + "1", impropers).molecule() + edit_mol = edit_mol.remove_property(prop).molecule() + + # Charge. + elif prop == charge_prop: + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + + charges = _Mol.AtomCharges(info) + edit_mol = edit_mol.set_property(prop + "1", charges).molecule() + edit_mol = edit_mol.remove_property(prop).molecule() + + # Connectivity. + elif prop == connectivity_prop: + pass + + # All other properties remain the same in both end states. + else: + edit_mol = edit_mol.set_property( + prop + "0", qm_mol.property(prop) + ).molecule() + edit_mol = edit_mol.set_property( + prop + "1", qm_mol.property(prop) + ).molecule() - edit_mol = edit_mol.remove_property(prop).molecule() + edit_mol = edit_mol.remove_property(prop).molecule() - # Flag the molecule as perturbable. - edit_mol = edit_mol.set_property(map["is_perturbable"], True).molecule() + # Flag the molecule as perturbable. + edit_mol = edit_mol.set_property(map["is_perturbable"], True).molecule() - # Commit the changes. - qm_mol = edit_mol.commit() + # Commit the changes. + qm_mol = edit_mol.commit() - # Link to the perturbation to the reference state. - qm_mol = qm_mol.perturbation().link_to_reference().commit() + # Link to the perturbation to the reference state. + qm_mol = qm_mol.perturbation().link_to_reference().commit() # Return the merged molecule. return qm_mol -def _get_link_atoms(mols, qm_mol, qm_atoms, map): +def _get_link_atoms(mols, qm_mol_to_atoms, map): """ Internal helper function to get a dictionary with link atoms for each QM atom. """ @@ -231,169 +241,192 @@ def _get_link_atoms(mols, qm_mol, qm_atoms, map): from ..legacy import Mol as _Mol from ..legacy import MM as _MM - # Store the indices of the QM atoms. - qm_idxs = [atom.index() for atom in qm_atoms] + # Initialise the dictionaries. - # Create a connectivity object. - connectivity = _Mol.Connectivity(qm_mol, _Mol.CovalentBondHunter(), map) + # Link atoms to QM atoms. + mm1_to_qm = {} - mm1_atoms = {} + # Link atoms to MM atoms. + mm1_to_mm2 = {} - # Loop over the QM atoms and find any MM atoms that are bonded to them. - for atom in qm_atoms: - # Store the atom index. - idx = atom.index() + # Rescaled QM -- link atom bond lengths. + scaled_bond_lengths = {} - # Get the bonds for the atom. - bonds = connectivity.get_bonds(idx) + # Loop over all molecules containing QM atoms. + for mol_num, qm_atoms in qm_mol_to_atoms.items(): + # Get the molecule. + qm_mol = qm_atoms[0].molecule() - # A list to hold MM atoms involved in the bonds. - mm_bonds = [] + # Store the indices of the QM atoms. + qm_idxs = [atom.index() for atom in qm_atoms] - # A flag to indicate if the atom has a bond to another QM atom. - has_qm_bond = False + # Create a connectivity object. + connectivity = _Mol.Connectivity(qm_mol, _Mol.CovalentBondHunter(), map) - # Loop over the bonds and find the MM atoms. - for bond in bonds: - # Get the indices of the two atoms in the bond. - idx0 = bond.atom0() - idx1 = bond.atom1() + mm1_atoms = {} - # Work out which atom isn't the current QM atom. - if idx0 != idx: - bond_idx = idx0 - else: - bond_idx = idx1 + # Loop over the QM atoms and find any MM atoms that are bonded to them. + for atom in qm_atoms: + # Store the atom index. + idx = atom.index() - # If the atom is not in the QM region, add it to the list. - if bond_idx not in qm_idxs: - mm_bonds.append(bond_idx) - else: - has_qm_bond = True + # Get the bonds for the atom. + bonds = connectivity.get_bonds(idx) - # If there are no QM bonds for this atom, raise an exception. - if not has_qm_bond: - raise ValueError( - f"Atom {idx} in the QM region has no bonds to other QM atoms!" - ) + # A list to hold MM atoms involved in the bonds. + mm_bonds = [] - # Store the list of MM atoms. - if len(mm_bonds) > 0: - if len(mm_bonds) > 1: - raise Exception(f"QM atom {idx} has more than one MM bond!") - else: - mm1_atoms[idx] = mm_bonds[0] + # A flag to indicate if the atom has a bond to another QM atom. + has_qm_bond = False - # Now work out the MM atoms that are bonded to the link atoms. - mm2_atoms = {} - for qm_idx, mm1_idx in mm1_atoms.items(): - if mm1_idx not in mm2_atoms: - bonds = connectivity.get_bonds(mm1_idx) - mm_bonds = [] + # Loop over the bonds and find the MM atoms. for bond in bonds: + # Get the indices of the two atoms in the bond. idx0 = bond.atom0() idx1 = bond.atom1() - if idx0 != mm1_idx: + + # Work out which atom isn't the current QM atom. + if idx0 != idx: bond_idx = idx0 else: bond_idx = idx1 + + # If the atom is not in the QM region, add it to the list. if bond_idx not in qm_idxs: mm_bonds.append(bond_idx) - mm2_atoms[mm1_idx] = mm_bonds - - # Convert MM1 atoms dictionary to absolute indices. - mm1_to_qm = {} - for k, v in mm1_atoms.items(): - qm_idx = mols.atoms().find(qm_mol.atoms()[k]) - link_idx = mols.atoms().find(qm_mol.atoms()[v]) - mm1_to_qm[link_idx] = qm_idx - - # Convert MM2 atoms dictionary to absolute indices. - mm1_to_mm2 = {} - for k, v in mm2_atoms.items(): - link_idx = mols.atoms().find(qm_mol.atoms()[k]) - mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] - mm1_to_mm2[link_idx] = mm_idx - - # Now work out the QM-MM1 bond distances based on the equilibrium - # MM bond lengths. - - # A dictionary to store the bond lengths. - bond_lengths = {} - link_bond_lengths = {} - - # Get the MM bond potentials. - bonds = qm_mol.property(map["bond"]).potentials() - - # Store the info for the QM molecule. - info = qm_mol.info() - - # Store the bond potential symbol. - r = _CAS.Symbol("r") - - # Loop over the link atoms. - for qm_idx, mm1_idx in mm1_atoms.items(): - # Convert to cg_atom_idx objects. - cg_qm_idx = info.cg_atom_idx(qm_idx) - cg_mm1_idx = info.cg_atom_idx(mm1_idx) - - # Store the element of the QM atom. - qm_elem = qm_mol[cg_qm_idx].element() - hydrogen = _Mol.Element("H") - - qm_m1_bond_found = False - qm_link_bond_found = False - - # Loop over the bonds. - for bond in bonds: - # Get the indices of the atoms in the bond. - bond_idx0 = bond.atom0() - bond_idx1 = bond.atom1() - - # If the bond is between the QM atom and the MM atom, store the - # bond length. - if ( - not qm_m1_bond_found - and cg_qm_idx == bond_idx0 - and cg_mm1_idx == bond_idx1 - or cg_qm_idx == bond_idx1 - and cg_mm1_idx == bond_idx0 - ): - # Cast as an AmberBond. - ab = _MM.AmberBond(bond.function(), r) - bond_lengths[mm1_idx] = ab.r0() - qm_m1_bond_found = True - if qm_link_bond_found: - break - else: - # Check to see if this bond is between a hydrogen and and the - # same element as the QM atom. - elem0 = qm_mol[bond_idx0].element() - elem1 = qm_mol[bond_idx1].element() + else: + has_qm_bond = True + + # If there are no QM bonds for this atom, raise an exception. + if not has_qm_bond: + raise ValueError( + f"Atom {idx} in the QM region has no bonds to other QM atoms!" + ) + + # Store the list of MM atoms. + if len(mm_bonds) > 0: + if len(mm_bonds) > 1: + raise Exception(f"QM atom {idx} has more than one MM bond!") + else: + mm1_atoms[idx] = mm_bonds[0] + + # Now work out the MM atoms that are bonded to the link atoms. + mm2_atoms = {} + for qm_idx, mm1_idx in mm1_atoms.items(): + if mm1_idx not in mm2_atoms: + bonds = connectivity.get_bonds(mm1_idx) + mm_bonds = [] + for bond in bonds: + idx0 = bond.atom0() + idx1 = bond.atom1() + if idx0 != mm1_idx: + bond_idx = idx0 + else: + bond_idx = idx1 + if bond_idx not in qm_idxs: + mm_bonds.append(bond_idx) + mm2_atoms[mm1_idx] = mm_bonds + + # Convert MM1 atoms dictionary to absolute indices. + mm1_to_qm_local = {} + for k, v in mm1_atoms.items(): + qm_idx = mols.atoms().find(qm_mol.atoms()[k]) + link_idx = mols.atoms().find(qm_mol.atoms()[v]) + mm1_to_qm_local[link_idx] = qm_idx + + # Convert MM2 atoms dictionary to absolute indices. + mm1_to_mm2_local = {} + for k, v in mm2_atoms.items(): + link_idx = mols.atoms().find(qm_mol.atoms()[k]) + mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] + mm1_to_mm2_local[link_idx] = mm_idx + + # Now work out the QM-MM1 bond distances based on the equilibrium + # MM bond lengths. + + # A dictionary to store the bond lengths. + bond_lengths = {} + link_bond_lengths = {} + + # Get the MM bond potentials. + bonds = qm_mol.property(map["bond"]).potentials() + + # Store the info for the QM molecule. + info = qm_mol.info() + + # Store the bond potential symbol. + r = _CAS.Symbol("r") + + # Loop over the link atoms. + for qm_idx, mm1_idx in mm1_atoms.items(): + # Convert to cg_atom_idx objects. + cg_qm_idx = info.cg_atom_idx(qm_idx) + cg_mm1_idx = info.cg_atom_idx(mm1_idx) + + # Store the element of the QM atom. + qm_elem = qm_mol[cg_qm_idx].element() + hydrogen = _Mol.Element("H") + + qm_m1_bond_found = False + qm_link_bond_found = False + + # Loop over the bonds. + for bond in bonds: + # Get the indices of the atoms in the bond. + bond_idx0 = bond.atom0() + bond_idx1 = bond.atom1() + # If the bond is between the QM atom and the MM atom, store the + # bond length. if ( - not qm_link_bond_found - and elem0 == hydrogen - and elem1 == qm_elem - or elem0 == qm_elem - and elem1 == hydrogen + not qm_m1_bond_found + and cg_qm_idx == bond_idx0 + and cg_mm1_idx == bond_idx1 + or cg_qm_idx == bond_idx1 + and cg_mm1_idx == bond_idx0 ): # Cast as an AmberBond. ab = _MM.AmberBond(bond.function(), r) - link_bond_lengths[mm1_idx] = ab.r0() - qm_link_bond_found = True - if qm_m1_bond_found: + bond_lengths[mm1_idx] = ab.r0() + qm_m1_bond_found = True + if qm_link_bond_found: break + else: + # Check to see if this bond is between a hydrogen and and the + # same element as the QM atom. + elem0 = qm_mol[bond_idx0].element() + elem1 = qm_mol[bond_idx1].element() + + if ( + not qm_link_bond_found + and elem0 == hydrogen + and elem1 == qm_elem + or elem0 == qm_elem + and elem1 == hydrogen + ): + # Cast as an AmberBond. + ab = _MM.AmberBond(bond.function(), r) + link_bond_lengths[mm1_idx] = ab.r0() + qm_link_bond_found = True + if qm_m1_bond_found: + break + + # Work out the rescaled bond length: R0(Q-H) / R0(Q-MM1) + try: + scaled_bond_lengths_local = {} + for idx in bond_lengths: + abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) + scaled_bond_lengths_local[abs_idx] = ( + link_bond_lengths[idx] / bond_lengths[idx] + ) + except: + raise Exception( + f"Unable to compute the scaled the QM-MM1 bond lengths for MM1 atom {idx}!" + ) - # Work out the rescaled bond length: R0(Q-H) / R0(Q-MM1) - try: - scaled_bond_lengths = {} - for idx in bond_lengths: - abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) - scaled_bond_lengths[abs_idx] = link_bond_lengths[idx] / bond_lengths[idx] - except: - raise Exception( - f"Unable to compute the scaled the QM-MM1 bond lengths for MM1 atom {idx}!" - ) + # Update the dictionaries. + mm1_to_qm.update(mm1_to_qm_local) + mm1_to_mm2.update(mm1_to_mm2_local) + scaled_bond_lengths.update(scaled_bond_lengths_local) return mm1_to_qm, mm1_to_mm2, scaled_bond_lengths From d4d769b8cd4b23660d5c1b32789697693bb81f27 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 18 Jan 2024 13:29:25 +0000 Subject: [PATCH 084/468] Fix Q1-MM1 bond length scaling factor implementation. --- src/sire/qm/_emle.py | 6 ++++-- src/sire/qm/_utils.py | 12 ++++++------ wrapper/Convert/SireOpenMM/emle.cpp | 17 +++++++---------- wrapper/Convert/SireOpenMM/emle.h | 16 ++++++++-------- 4 files changed, 25 insertions(+), 26 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 8699c4055..fa6116b86 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -122,11 +122,13 @@ def emle( from ._utils import _configure_engine, _create_merged_mols, _get_link_atoms # Get link atom information. - mm1_to_qm, mm1_to_mm2, bond_lengths = _get_link_atoms(mols, qm_mol_to_atoms, map) + mm1_to_qm, mm1_to_mm2, bond_scaling_factors = _get_link_atoms( + mols, qm_mol_to_atoms, map + ) # Configure the engine. engine = _configure_engine( - engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map + engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_scaling_factors, map ) # Create the merged molecule. diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index d67f0cb25..13a803f1b 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -249,8 +249,8 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Link atoms to MM atoms. mm1_to_mm2 = {} - # Rescaled QM -- link atom bond lengths. - scaled_bond_lengths = {} + # Rescaled QM -- link atom bond length scaling factors. + bond_scaling_factors = {} # Loop over all molecules containing QM atoms. for mol_num, qm_atoms in qm_mol_to_atoms.items(): @@ -413,10 +413,10 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Work out the rescaled bond length: R0(Q-H) / R0(Q-MM1) try: - scaled_bond_lengths_local = {} + bond_scaling_factors_local = {} for idx in bond_lengths: abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) - scaled_bond_lengths_local[abs_idx] = ( + bond_scaling_factors_local[abs_idx] = ( link_bond_lengths[idx] / bond_lengths[idx] ) except: @@ -427,6 +427,6 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Update the dictionaries. mm1_to_qm.update(mm1_to_qm_local) mm1_to_mm2.update(mm1_to_mm2_local) - scaled_bond_lengths.update(scaled_bond_lengths_local) + bond_scaling_factors.update(bond_scaling_factors_local) - return mm1_to_qm, mm1_to_mm2, scaled_bond_lengths + return mm1_to_qm, mm1_to_mm2, bond_scaling_factors diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index c23e57db7..8c0702dac 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -111,7 +111,7 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : mm1_to_qm(other.mm1_to_qm), mm1_to_mm2(other.mm1_to_mm2), mm2_atoms(other.mm2_atoms), - bond_lengths(other.bond_lengths), + bond_scaling_factors(other.bond_scaling_factors), numbers(other.numbers), charges(other.charges) { @@ -127,7 +127,7 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) this->mm1_to_qm = other.mm1_to_qm; this->mm1_to_mm2 = other.mm1_to_mm2; this->mm2_atoms = other.mm2_atoms; - this->bond_lengths = other.bond_lengths; + this->bond_scaling_factors = other.bond_scaling_factors; this->numbers = other.numbers; this->charges = other.charges; return *this; @@ -199,17 +199,17 @@ void EMLEEngine::setAtoms(QVector atoms) boost::tuple, QMap>, QMap> EMLEEngine::getLinkAtoms() const { - return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_lengths); + return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scaling_factors); } void EMLEEngine::setLinkAtoms( QMap mm1_to_qm, QMap> mm1_to_mm2, - QMap bond_lengths) + QMap bond_scaling_factors) { this->mm1_to_qm = mm1_to_qm; this->mm1_to_mm2 = mm1_to_mm2; - this->bond_lengths = bond_lengths; + this->bond_scaling_factors = bond_scaling_factors; // Build a vector of all of the MM2 atoms. this->mm2_atoms.clear(); @@ -323,7 +323,7 @@ double EMLEEngineImpl::computeForce( const auto link_atoms = this->owner.getLinkAtoms(); const auto mm1_to_qm = link_atoms.get<0>(); const auto mm1_to_mm2 = link_atoms.get<1>(); - const auto bond_lengths = link_atoms.get<2>(); + const auto bond_scaling_factors = link_atoms.get<2>(); const auto mm2_atoms = this->owner.getMM2Atoms(); // Initialise a vector to hold the current positions for the QM atoms. @@ -472,11 +472,8 @@ double EMLEEngineImpl::computeForce( mm1_vec = space.getMinimumImage(mm1_vec, center); qm_vec = space.getMinimumImage(qm_vec, center); - // Work out the normal vector between the MM1 and QM atoms. - const auto normal = (qm_vec - mm1_vec).normalise(); - // Work out the position of the link atom. - const auto link_vec = mm1_vec + 10*bond_lengths[idx]*normal; + const auto link_vec = qm_vec + bond_scaling_factors[idx]*(qm_vec - mm1_vec); // Add to the QM positions. xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 4a0bf9a09..7e44f6f12 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -208,14 +208,14 @@ namespace SireOpenMM mm1_to_qm A dictionary mapping link atom (MM1) indices to the QM atoms to which they are bonded. - + mm1_to_mm2 A dictionary of link atoms indices (MM1) to a list of the MM atoms to which they are bonded (MM2). - bond_lengths + bond_scaling_factors A dictionary of link atom indices (MM1) to a list of the bond - lengths between the MM1 and QM atoms. + length scaling factors between the MM1 and QM atoms. */ boost::tuple, QMap>, QMap> getLinkAtoms() const; @@ -223,17 +223,17 @@ namespace SireOpenMM /*! \param mm1_to_qm A dictionary mapping link atom (MM1) indices to the QM atoms to which they are bonded. - + \param mm1_to_mm2 A dictionary of link atoms indices (MM1) to a list of the MM atoms to which they are bonded (MM2). - \param bond_lengths + \param bond_scaling_factors A dictionary of link atom indices (MM1) to a list of the bond - lengths between the MM1 and QM atoms. + length scaling factors between the MM1 and QM atoms. */ - void setLinkAtoms(QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_lengths); + void setLinkAtoms(QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_scaling_factors); //! Get the vector of MM2 atoms. /*! \returns @@ -308,7 +308,7 @@ namespace SireOpenMM QVector atoms; QMap mm1_to_qm; QMap> mm1_to_mm2; - QMap bond_lengths; + QMap bond_scaling_factors; QVector mm2_atoms; QVector numbers; QVector charges; From 9f8b3a8c08abaae01eb1b8522bb189d2a586a01f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 09:04:41 +0000 Subject: [PATCH 085/468] Improve documention of methodology and fix some terminology. --- doc/source/tutorial/part07/01_emle.rst | 2 +- src/sire/qm/_emle.py | 4 +- src/sire/qm/_utils.py | 17 +++++--- wrapper/Convert/SireOpenMM/emle.cpp | 59 +++++++++++++++----------- wrapper/Convert/SireOpenMM/emle.h | 19 ++++++--- 5 files changed, 61 insertions(+), 40 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index 2584b1954..1653a58b8 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -68,7 +68,7 @@ atom index, list of atom indicies, or molecule view/container that can be used. Support for modelling partial molecules at the QM level is provided via the link atom approach, via the charge shifting method. For details of this implementation, see, e.g., the NAMD user guide `here `_. -While we support multiple QM regions, we do not currently support multiple +While we support multiple QM fragments, we do not currently support multiple *independent* QM regions. We plan on adding support for this in the near future. Next we need to create a dynamics object to perform the simulation. For QM/MM diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index fa6116b86..dbe48aceb 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -122,13 +122,13 @@ def emle( from ._utils import _configure_engine, _create_merged_mols, _get_link_atoms # Get link atom information. - mm1_to_qm, mm1_to_mm2, bond_scaling_factors = _get_link_atoms( + mm1_to_qm, mm1_to_mm2, bond_scale_factors = _get_link_atoms( mols, qm_mol_to_atoms, map ) # Configure the engine. engine = _configure_engine( - engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_scaling_factors, map + engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_scale_factors, map ) # Create the merged molecule. diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 13a803f1b..a76e15280 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -250,7 +250,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): mm1_to_mm2 = {} # Rescaled QM -- link atom bond length scaling factors. - bond_scaling_factors = {} + bond_scale_factors = {} # Loop over all molecules containing QM atoms. for mol_num, qm_atoms in qm_mol_to_atoms.items(): @@ -344,7 +344,10 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Now work out the QM-MM1 bond distances based on the equilibrium # MM bond lengths. - # A dictionary to store the bond lengths. + # A dictionary to store the bond lengths. Here 'bond_lengths' are the + # equilibrium bond lengths for the QM-MM1 bonds, and 'link_bond_lengths', + # are the equilibrium bond lengths for the QM-L (QM-link) bonds. Both of + # these are evaluated from the MM bond potentials. bond_lengths = {} link_bond_lengths = {} @@ -411,12 +414,12 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): if qm_m1_bond_found: break - # Work out the rescaled bond length: R0(Q-H) / R0(Q-MM1) + # Work out the bond scale factors: R0(QM-L) / R0(QM-MM1) try: - bond_scaling_factors_local = {} + bond_scale_factors_local = {} for idx in bond_lengths: abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) - bond_scaling_factors_local[abs_idx] = ( + bond_scale_factors_local[abs_idx] = ( link_bond_lengths[idx] / bond_lengths[idx] ) except: @@ -427,6 +430,6 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Update the dictionaries. mm1_to_qm.update(mm1_to_qm_local) mm1_to_mm2.update(mm1_to_mm2_local) - bond_scaling_factors.update(bond_scaling_factors_local) + bond_scale_factors.update(bond_scale_factors_local) - return mm1_to_qm, mm1_to_mm2, bond_scaling_factors + return mm1_to_qm, mm1_to_mm2, bond_scale_factors diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 8c0702dac..84cc82011 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -36,6 +36,10 @@ using namespace SireMaths; using namespace SireOpenMM; using namespace SireVol; +// The delta used to place virtual point charges either side of the MM2 +// atoms, in nanometers. +static const double VIRTUAL_PC_DELTA = 0.01; + class GILLock { public: @@ -111,7 +115,7 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : mm1_to_qm(other.mm1_to_qm), mm1_to_mm2(other.mm1_to_mm2), mm2_atoms(other.mm2_atoms), - bond_scaling_factors(other.bond_scaling_factors), + bond_scale_factors(other.bond_scale_factors), numbers(other.numbers), charges(other.charges) { @@ -127,7 +131,7 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) this->mm1_to_qm = other.mm1_to_qm; this->mm1_to_mm2 = other.mm1_to_mm2; this->mm2_atoms = other.mm2_atoms; - this->bond_scaling_factors = other.bond_scaling_factors; + this->bond_scale_factors = other.bond_scale_factors; this->numbers = other.numbers; this->charges = other.charges; return *this; @@ -199,17 +203,17 @@ void EMLEEngine::setAtoms(QVector atoms) boost::tuple, QMap>, QMap> EMLEEngine::getLinkAtoms() const { - return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scaling_factors); + return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); } void EMLEEngine::setLinkAtoms( QMap mm1_to_qm, QMap> mm1_to_mm2, - QMap bond_scaling_factors) + QMap bond_scale_factors) { this->mm1_to_qm = mm1_to_qm; this->mm1_to_mm2 = mm1_to_mm2; - this->bond_scaling_factors = bond_scaling_factors; + this->bond_scale_factors = bond_scale_factors; // Build a vector of all of the MM2 atoms. this->mm2_atoms.clear(); @@ -323,7 +327,7 @@ double EMLEEngineImpl::computeForce( const auto link_atoms = this->owner.getLinkAtoms(); const auto mm1_to_qm = link_atoms.get<0>(); const auto mm1_to_mm2 = link_atoms.get<1>(); - const auto bond_scaling_factors = link_atoms.get<2>(); + const auto bond_scale_factors = link_atoms.get<2>(); const auto mm2_atoms = this->owner.getMM2Atoms(); // Initialise a vector to hold the current positions for the QM atoms. @@ -356,13 +360,14 @@ double EMLEEngineImpl::computeForce( center /= i; // Initialise a vector to hold the current positions for the MM atoms. - // and dipoles. + // and virtual point charges. QVector> xyz_mm; - QVector> xyz_dipole; + QVector> xyz_virtual; - // Initialise a vector to hold the charges for the MM atoms and dipoles. + // Initialise a vector to hold the charges for the MM atoms and virtual + // point charges. QVector charges_mm; - QVector charges_dipole; + QVector charges_virtual; // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; @@ -473,7 +478,7 @@ double EMLEEngineImpl::computeForce( qm_vec = space.getMinimumImage(qm_vec, center); // Work out the position of the link atom. - const auto link_vec = qm_vec + bond_scaling_factors[idx]*(qm_vec - mm1_vec); + const auto link_vec = qm_vec + bond_scale_factors[idx]*(qm_vec - mm1_vec); // Add to the QM positions. xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); @@ -484,10 +489,14 @@ double EMLEEngineImpl::computeForce( // Store the number of MM2 atoms. const auto num_mm2 = mm1_to_mm2[idx].size(); - // Store the fractional charge contribution to the MM2 atoms and dipoles. + // Store the fractional charge contribution to the MM2 atoms and + // virtual point charges. const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; - // Loop over the MM2 atoms. + // Loop over the MM2 atoms to and perform charge shifting. Here the + // MM1 charge is redistributed over the MM2 atoms and two virtual point + // charges are added either side of the MM2 atoms in order to preserve + // the MM1-MM2 dipole. for (const auto& mm2_idx : mm1_to_mm2[idx]) { // Store the MM2 position in Sire Vector format. @@ -503,31 +512,32 @@ double EMLEEngineImpl::computeForce( charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); idx_mm.append(mm2_idx); - // Now add the dipoles. + // Now add the virtual point charges. // Compute the normal vector from the MM1 to MM2 atom. const auto normal = (mm2_vec - mm1_vec).normalise(); // Positive direction. (Away from MM1 atom.) - auto xyz = mm2_vec + 0.01*normal; - xyz_dipole.append(QVector({xyz[0], xyz[1], xyz[2]})); - charges_dipole.append(-frac_charge); + auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; + xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_virtual.append(-frac_charge); // Negative direction (Towards MM1 atom.) xyz = mm2_vec - 0.01*normal; - xyz_dipole.append(QVector({xyz[0], xyz[1], xyz[2]})); - charges_dipole.append(frac_charge); + xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_virtual.append(frac_charge); } } // Store the current number of MM atoms. const auto num_mm = xyz_mm.size(); - // If there are any dipoles, then add to the MM positions and charges. - if (xyz_dipole.size() > 0) + // If there are any virtual point charges, then add to the MM positions + // and charges. + if (xyz_virtual.size() > 0) { - xyz_mm.append(xyz_dipole); - charges_mm.append(charges_dipole); + xyz_mm.append(xyz_virtual); + charges_mm.append(charges_virtual); } // Call the callback. @@ -587,7 +597,8 @@ double EMLEEngineImpl::computeForce( // Update the atom index. i++; - // Exit if we have reached the end of the MM atoms, i.e. ignore dipoles. + // Exit if we have reached the end of the MM atoms, i.e. ignore virtual + // point charges. if (i == num_mm) { break; diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 7e44f6f12..3a5fd5881 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -213,9 +213,13 @@ namespace SireOpenMM A dictionary of link atoms indices (MM1) to a list of the MM atoms to which they are bonded (MM2). - bond_scaling_factors + bond_scale_factors A dictionary of link atom indices (MM1) to a list of the bond - length scaling factors between the MM1 and QM atoms. + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + */ boost::tuple, QMap>, QMap> getLinkAtoms() const; @@ -228,12 +232,15 @@ namespace SireOpenMM A dictionary of link atoms indices (MM1) to a list of the MM atoms to which they are bonded (MM2). - \param bond_scaling_factors + \param bond_scale_factors A dictionary of link atom indices (MM1) to a list of the bond - length scaling factors between the MM1 and QM atoms. + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. */ - void setLinkAtoms(QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_scaling_factors); + void setLinkAtoms(QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_scale_factors); //! Get the vector of MM2 atoms. /*! \returns @@ -308,7 +315,7 @@ namespace SireOpenMM QVector atoms; QMap mm1_to_qm; QMap> mm1_to_mm2; - QMap bond_scaling_factors; + QMap bond_scale_factors; QVector mm2_atoms; QVector numbers; QVector charges; From 4a91a15522eed6b4fe5f1b3d035e37a1ebf2e866 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 09:40:10 +0000 Subject: [PATCH 086/468] Expose argument names to Python wrapper docstrings. --- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 74 ++++++++++++++----- wrapper/Convert/SireOpenMM/emle.cpp | 6 +- 2 files changed, 59 insertions(+), 21 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index e0aece7ff..c676ab3fc 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -198,27 +198,65 @@ BOOST_PYTHON_MODULE(_SireOpenMM) bp::arg("neighbour_list_frequency")=20, bp::arg("lambda")=1.0 ), - "Constructor: An engine that can be used to enable electrostatic embedding" + "Constructor: An engine that can be used to enable electrostatic embedding " "of machine learning potentials via emle-engine." ) ) - .def("getLambda", &EMLEEngine::getLambda, "Get the lambda value") - .def("setLambda", &EMLEEngine::setLambda, "Set the lambda value") - .def("getCutoff", &EMLEEngine::getCutoff, "Get the cutoff value") - .def("setCutoff", &EMLEEngine::setCutoff, "Set the cutoff value") - .def("getNeighbourListFrequency", &EMLEEngine::getNeighbourListFrequency, "Get the neighbour list frequency") - .def("setNeighbourListFrequency", &EMLEEngine::setNeighbourListFrequency, "Set the neighbour list frequency") - .def("getAtoms", &EMLEEngine::getAtoms, "Get QM atom indices") - .def("setAtoms", &EMLEEngine::setAtoms, "Set the QM atom indices") - .def("getLinkAtoms", &EMLEEngine::getLinkAtoms, "Get the link atoms") - .def("setLinkAtoms", &EMLEEngine::setLinkAtoms, "Set the link atoms") - .def("getNumbers", &EMLEEngine::getNumbers, "Get QM atomic numbers") - .def("setNumbers", &EMLEEngine::setNumbers, "Set the QM atomic numbers") - .def("getCharges", &EMLEEngine::getCharges, "Get the atomic charges") - .def("setCharges", &EMLEEngine::setCharges, "Set the atomic charges") - .def("what", &EMLEEngine::what, "Call the callback") - .def("typeName", &EMLEEngine::typeName, "Call the callback") - .def("call", &EMLEEngine::call, "Call the callback") + .def("getLambda", + &EMLEEngine::getLambda, + "Get the lambda value") + .def("setLambda", + &EMLEEngine::setLambda, + bp::arg("lambda"), + "Set the lambda value") + .def("getCutoff", + &EMLEEngine::getCutoff, + "Get the cutoff value") + .def("setCutoff", + &EMLEEngine::setCutoff, + bp::arg("cutoff"), + "Set the cutoff value") + .def("getNeighbourListFrequency", + &EMLEEngine::getNeighbourListFrequency, + "Get the neighbour list frequency") + .def("setNeighbourListFrequency", + &EMLEEngine::setNeighbourListFrequency, + bp::arg("neighbour_list_frequency"), + "Set the neighbour list frequency") + .def("getAtoms", + &EMLEEngine::getAtoms, + "Get QM atom indices") + .def("setAtoms", + &EMLEEngine::setAtoms, + bp::arg("atoms"), + "Set the QM atom indices") + .def("getLinkAtoms", + &EMLEEngine::getLinkAtoms, + "Get the link atoms") + .def("setLinkAtoms", + &EMLEEngine::setLinkAtoms, + (bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors")), + "Set the link atoms") + .def("getNumbers", + &EMLEEngine::getNumbers, + "Get QM atomic numbers") + .def("setNumbers", + &EMLEEngine::setNumbers, + bp::arg("numbers"), + "Set the QM atomic numbers") + .def("getCharges", + &EMLEEngine::getCharges, + "Get the atomic charges") + .def("setCharges", + &EMLEEngine::setCharges, + bp::arg("charges"), + "Set the atomic charges") + .def("call", + &EMLEEngine::call, + (bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm")), + "Call the callback") + .def("what", &EMLEEngine::what, "Return type name") + .def("typeName", &EMLEEngine::typeName, "Return type name") .def( "__copy__", &__copy__) .def( "__deepcopy__", &__copy__) .def( "clone", &__copy__); diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 84cc82011..30f8827fc 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -493,8 +493,8 @@ double EMLEEngineImpl::computeForce( // virtual point charges. const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; - // Loop over the MM2 atoms to and perform charge shifting. Here the - // MM1 charge is redistributed over the MM2 atoms and two virtual point + // Loop over the MM2 atoms and perform charge shifting. Here the MM1 + // charge is redistributed over the MM2 atoms and two virtual point // charges are added either side of the MM2 atoms in order to preserve // the MM1-MM2 dipole. for (const auto& mm2_idx : mm1_to_mm2[idx]) @@ -523,7 +523,7 @@ double EMLEEngineImpl::computeForce( charges_virtual.append(-frac_charge); // Negative direction (Towards MM1 atom.) - xyz = mm2_vec - 0.01*normal; + xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); charges_virtual.append(frac_charge); } From a201f7b473ce5be4212f691728f146f7c5784063 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 12:14:28 +0000 Subject: [PATCH 087/468] More clarifications in comments. --- src/sire/qm/_utils.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index a76e15280..8c739889c 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -249,7 +249,9 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Link atoms to MM atoms. mm1_to_mm2 = {} - # Rescaled QM -- link atom bond length scaling factors. + # QM to link atom bond scale factors. These are the ratios of the equilibrium + # bond lengths for the QM-L bonds and the QM-MM1 bonds, taken from the MM + # bond potentials, i.e. R0(QM-L) / R0(QM-MM1). bond_scale_factors = {} # Loop over all molecules containing QM atoms. @@ -263,6 +265,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Create a connectivity object. connectivity = _Mol.Connectivity(qm_mol, _Mol.CovalentBondHunter(), map) + # Dictionary to store the MM1 atoms. mm1_atoms = {} # Loop over the QM atoms and find any MM atoms that are bonded to them. @@ -310,7 +313,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): else: mm1_atoms[idx] = mm_bonds[0] - # Now work out the MM atoms that are bonded to the link atoms. + # Now work out the MM atoms that are bonded to the link atoms. (MM2 atoms.) mm2_atoms = {} for qm_idx, mm1_idx in mm1_atoms.items(): if mm1_idx not in mm2_atoms: @@ -327,14 +330,14 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): mm_bonds.append(bond_idx) mm2_atoms[mm1_idx] = mm_bonds - # Convert MM1 atoms dictionary to absolute indices. + # Convert MM1 to QM atom dictionary to absolute indices. mm1_to_qm_local = {} for k, v in mm1_atoms.items(): qm_idx = mols.atoms().find(qm_mol.atoms()[k]) link_idx = mols.atoms().find(qm_mol.atoms()[v]) mm1_to_qm_local[link_idx] = qm_idx - # Convert MM2 atoms dictionary to absolute indices. + # Convert MM1 to MM2 atom dictionary to absolute indices. mm1_to_mm2_local = {} for k, v in mm2_atoms.items(): link_idx = mols.atoms().find(qm_mol.atoms()[k]) @@ -395,11 +398,11 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): if qm_link_bond_found: break else: - # Check to see if this bond is between a hydrogen and and the - # same element as the QM atom. elem0 = qm_mol[bond_idx0].element() elem1 = qm_mol[bond_idx1].element() + # Is this bond is between a hydrogen and and the same element + # as the QM atom? If so, store the bond length. if ( not qm_link_bond_found and elem0 == hydrogen From 40a233e90c533e786684c7fd6d8c7ac4517c2db8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 12:22:36 +0000 Subject: [PATCH 088/468] Refactor qm_mol_to_atoms dictionary creation into utility function. --- src/sire/qm/_emle.py | 19 +- src/sire/qm/_utils.py | 466 ++++++++++++++++++++++-------------------- 2 files changed, 250 insertions(+), 235 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index dbe48aceb..6743b3ffe 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -73,15 +73,6 @@ def emle( except: raise ValueError("Unable to select 'qm_atoms' from 'mols'") - # Create a dictionary mapping molecule numbers to a list of QM atoms. - qm_mol_to_atoms = {} - for atom in qm_atoms: - mol_num = atom.molecule().number() - if mol_num not in qm_mol_to_atoms: - qm_mol_to_atoms[mol_num] = [atom] - else: - qm_mol_to_atoms[mol_num].append(atom) - if not isinstance(calculator, _EMLECalculator): raise TypeError( "'calculator' must be a of type 'emle.calculator.EMLECalculator'" @@ -119,7 +110,15 @@ def emle( neighbourlist_update_frequency, ) - from ._utils import _configure_engine, _create_merged_mols, _get_link_atoms + from ._utils import ( + _create_qm_mol_to_atoms, + _configure_engine, + _create_merged_mols, + _get_link_atoms, + ) + + # Get the mapping between molecule numbers and QM atoms. + qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) # Get link atom information. mm1_to_qm, mm1_to_mm2, bond_scale_factors = _get_link_atoms( diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 8c739889c..cc2dae0c4 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,38 +1,223 @@ -def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map): +def _create_qm_mol_to_atoms(qm_atoms): """ - Internal helper function to configure a QM engine ready for dynamics. + Internal helper function to create a mapping between molecule numbers and + a list of QM atoms. """ + qm_mol_to_atoms = {} + for atom in qm_atoms: + mol_num = atom.molecule().number() + if mol_num not in qm_mol_to_atoms: + qm_mol_to_atoms[mol_num] = [atom] + else: + qm_mol_to_atoms[mol_num].append(atom) - # Work out the indices of the QM atoms. - try: - idxs = mols.atoms().find(qm_atoms) - engine.set_atoms(idxs) - except: - raise Exception("Unable to set atom indices for the QM region.") + return qm_mol_to_atoms - # Work out the atomic numbers of the QM atoms. - try: - elem_prop = map["element"] - numbers = [atom.property(f"{elem_prop}").num_protons() for atom in qm_atoms] - engine.set_numbers(numbers) - except: - raise Exception("Unable to set atomic numbers for the QM region.") - # Work out the atomic charge for all atoms in the system. - try: - charge_prop = map["charge"] - charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] - engine.set_charges(charges) - except: - raise Exception("Unable to set atomic charges for the system.") +def _get_link_atoms(mols, qm_mol_to_atoms, map): + """ + Internal helper function to get a dictionary with link atoms for each QM atom. + """ - # Set the link atom information. - try: - engine.set_link_atoms(mm1_to_qm, mm1_to_mm2, bond_lengths) - except: - raise Exception("Unable to set link atom information.") + from ..legacy import CAS as _CAS + from ..legacy import Mol as _Mol + from ..legacy import MM as _MM - return engine + # Initialise the dictionaries. + + # Link atoms to QM atoms. + mm1_to_qm = {} + + # Link atoms to MM atoms. + mm1_to_mm2 = {} + + # QM to link atom bond scale factors. These are the ratios of the equilibrium + # bond lengths for the QM-L bonds and the QM-MM1 bonds, taken from the MM + # bond potentials, i.e. R0(QM-L) / R0(QM-MM1). + bond_scale_factors = {} + + # Loop over all molecules containing QM atoms. + for mol_num, qm_atoms in qm_mol_to_atoms.items(): + # Get the molecule. + qm_mol = qm_atoms[0].molecule() + + # Store the indices of the QM atoms. + qm_idxs = [atom.index() for atom in qm_atoms] + + # Create a connectivity object. + connectivity = _Mol.Connectivity(qm_mol, _Mol.CovalentBondHunter(), map) + + # Dictionary to store the MM1 atoms. + mm1_atoms = {} + + # Loop over the QM atoms and find any MM atoms that are bonded to them. + for atom in qm_atoms: + # Store the atom index. + idx = atom.index() + + # Get the bonds for the atom. + bonds = connectivity.get_bonds(idx) + + # A list to hold MM atoms involved in the bonds. + mm_bonds = [] + + # A flag to indicate if the atom has a bond to another QM atom. + has_qm_bond = False + + # Loop over the bonds and find the MM atoms. + for bond in bonds: + # Get the indices of the two atoms in the bond. + idx0 = bond.atom0() + idx1 = bond.atom1() + + # Work out which atom isn't the current QM atom. + if idx0 != idx: + bond_idx = idx0 + else: + bond_idx = idx1 + + # If the atom is not in the QM region, add it to the list. + if bond_idx not in qm_idxs: + mm_bonds.append(bond_idx) + else: + has_qm_bond = True + + # If there are no QM bonds for this atom, raise an exception. + if not has_qm_bond: + raise ValueError( + f"Atom {idx} in the QM region has no bonds to other QM atoms!" + ) + + # Store the list of MM atoms. + if len(mm_bonds) > 0: + if len(mm_bonds) > 1: + raise Exception(f"QM atom {idx} has more than one MM bond!") + else: + mm1_atoms[idx] = mm_bonds[0] + + # Now work out the MM atoms that are bonded to the link atoms. (MM2 atoms.) + mm2_atoms = {} + for qm_idx, mm1_idx in mm1_atoms.items(): + if mm1_idx not in mm2_atoms: + bonds = connectivity.get_bonds(mm1_idx) + mm_bonds = [] + for bond in bonds: + idx0 = bond.atom0() + idx1 = bond.atom1() + if idx0 != mm1_idx: + bond_idx = idx0 + else: + bond_idx = idx1 + if bond_idx not in qm_idxs: + mm_bonds.append(bond_idx) + mm2_atoms[mm1_idx] = mm_bonds + + # Convert MM1 to QM atom dictionary to absolute indices. + mm1_to_qm_local = {} + for k, v in mm1_atoms.items(): + qm_idx = mols.atoms().find(qm_mol.atoms()[k]) + link_idx = mols.atoms().find(qm_mol.atoms()[v]) + mm1_to_qm_local[link_idx] = qm_idx + + # Convert MM1 to MM2 atom dictionary to absolute indices. + mm1_to_mm2_local = {} + for k, v in mm2_atoms.items(): + link_idx = mols.atoms().find(qm_mol.atoms()[k]) + mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] + mm1_to_mm2_local[link_idx] = mm_idx + + # Now work out the QM-MM1 bond distances based on the equilibrium + # MM bond lengths. + + # A dictionary to store the bond lengths. Here 'bond_lengths' are the + # equilibrium bond lengths for the QM-MM1 bonds, and 'link_bond_lengths', + # are the equilibrium bond lengths for the QM-L (QM-link) bonds. Both of + # these are evaluated from the MM bond potentials. + bond_lengths = {} + link_bond_lengths = {} + + # Get the MM bond potentials. + bonds = qm_mol.property(map["bond"]).potentials() + + # Store the info for the QM molecule. + info = qm_mol.info() + + # Store the bond potential symbol. + r = _CAS.Symbol("r") + + # Loop over the link atoms. + for qm_idx, mm1_idx in mm1_atoms.items(): + # Convert to cg_atom_idx objects. + cg_qm_idx = info.cg_atom_idx(qm_idx) + cg_mm1_idx = info.cg_atom_idx(mm1_idx) + + # Store the element of the QM atom. + qm_elem = qm_mol[cg_qm_idx].element() + hydrogen = _Mol.Element("H") + + qm_m1_bond_found = False + qm_link_bond_found = False + + # Loop over the bonds. + for bond in bonds: + # Get the indices of the atoms in the bond. + bond_idx0 = bond.atom0() + bond_idx1 = bond.atom1() + + # If the bond is between the QM atom and the MM atom, store the + # bond length. + if ( + not qm_m1_bond_found + and cg_qm_idx == bond_idx0 + and cg_mm1_idx == bond_idx1 + or cg_qm_idx == bond_idx1 + and cg_mm1_idx == bond_idx0 + ): + # Cast as an AmberBond. + ab = _MM.AmberBond(bond.function(), r) + bond_lengths[mm1_idx] = ab.r0() + qm_m1_bond_found = True + if qm_link_bond_found: + break + else: + elem0 = qm_mol[bond_idx0].element() + elem1 = qm_mol[bond_idx1].element() + + # Is this bond is between a hydrogen and and the same element + # as the QM atom? If so, store the bond length. + if ( + not qm_link_bond_found + and elem0 == hydrogen + and elem1 == qm_elem + or elem0 == qm_elem + and elem1 == hydrogen + ): + # Cast as an AmberBond. + ab = _MM.AmberBond(bond.function(), r) + link_bond_lengths[mm1_idx] = ab.r0() + qm_link_bond_found = True + if qm_m1_bond_found: + break + + # Work out the bond scale factors: R0(QM-L) / R0(QM-MM1) + try: + bond_scale_factors_local = {} + for idx in bond_lengths: + abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) + bond_scale_factors_local[abs_idx] = ( + link_bond_lengths[idx] / bond_lengths[idx] + ) + except: + raise Exception( + f"Unable to compute the scaled the QM-MM1 bond lengths for MM1 atom {idx}!" + ) + + # Update the dictionaries. + mm1_to_qm.update(mm1_to_qm_local) + mm1_to_mm2.update(mm1_to_mm2_local) + bond_scale_factors.update(bond_scale_factors_local) + + return mm1_to_qm, mm1_to_mm2, bond_scale_factors def _create_merged_mols(qm_mol_to_atoms, map): @@ -232,207 +417,38 @@ def _create_merged_mols(qm_mol_to_atoms, map): return qm_mol -def _get_link_atoms(mols, qm_mol_to_atoms, map): +def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map): """ - Internal helper function to get a dictionary with link atoms for each QM atom. + Internal helper function to configure a QM engine ready for dynamics. """ - from ..legacy import CAS as _CAS - from ..legacy import Mol as _Mol - from ..legacy import MM as _MM - - # Initialise the dictionaries. - - # Link atoms to QM atoms. - mm1_to_qm = {} - - # Link atoms to MM atoms. - mm1_to_mm2 = {} - - # QM to link atom bond scale factors. These are the ratios of the equilibrium - # bond lengths for the QM-L bonds and the QM-MM1 bonds, taken from the MM - # bond potentials, i.e. R0(QM-L) / R0(QM-MM1). - bond_scale_factors = {} - - # Loop over all molecules containing QM atoms. - for mol_num, qm_atoms in qm_mol_to_atoms.items(): - # Get the molecule. - qm_mol = qm_atoms[0].molecule() - - # Store the indices of the QM atoms. - qm_idxs = [atom.index() for atom in qm_atoms] - - # Create a connectivity object. - connectivity = _Mol.Connectivity(qm_mol, _Mol.CovalentBondHunter(), map) - - # Dictionary to store the MM1 atoms. - mm1_atoms = {} - - # Loop over the QM atoms and find any MM atoms that are bonded to them. - for atom in qm_atoms: - # Store the atom index. - idx = atom.index() - - # Get the bonds for the atom. - bonds = connectivity.get_bonds(idx) - - # A list to hold MM atoms involved in the bonds. - mm_bonds = [] - - # A flag to indicate if the atom has a bond to another QM atom. - has_qm_bond = False - - # Loop over the bonds and find the MM atoms. - for bond in bonds: - # Get the indices of the two atoms in the bond. - idx0 = bond.atom0() - idx1 = bond.atom1() - - # Work out which atom isn't the current QM atom. - if idx0 != idx: - bond_idx = idx0 - else: - bond_idx = idx1 - - # If the atom is not in the QM region, add it to the list. - if bond_idx not in qm_idxs: - mm_bonds.append(bond_idx) - else: - has_qm_bond = True - - # If there are no QM bonds for this atom, raise an exception. - if not has_qm_bond: - raise ValueError( - f"Atom {idx} in the QM region has no bonds to other QM atoms!" - ) - - # Store the list of MM atoms. - if len(mm_bonds) > 0: - if len(mm_bonds) > 1: - raise Exception(f"QM atom {idx} has more than one MM bond!") - else: - mm1_atoms[idx] = mm_bonds[0] - - # Now work out the MM atoms that are bonded to the link atoms. (MM2 atoms.) - mm2_atoms = {} - for qm_idx, mm1_idx in mm1_atoms.items(): - if mm1_idx not in mm2_atoms: - bonds = connectivity.get_bonds(mm1_idx) - mm_bonds = [] - for bond in bonds: - idx0 = bond.atom0() - idx1 = bond.atom1() - if idx0 != mm1_idx: - bond_idx = idx0 - else: - bond_idx = idx1 - if bond_idx not in qm_idxs: - mm_bonds.append(bond_idx) - mm2_atoms[mm1_idx] = mm_bonds - - # Convert MM1 to QM atom dictionary to absolute indices. - mm1_to_qm_local = {} - for k, v in mm1_atoms.items(): - qm_idx = mols.atoms().find(qm_mol.atoms()[k]) - link_idx = mols.atoms().find(qm_mol.atoms()[v]) - mm1_to_qm_local[link_idx] = qm_idx - - # Convert MM1 to MM2 atom dictionary to absolute indices. - mm1_to_mm2_local = {} - for k, v in mm2_atoms.items(): - link_idx = mols.atoms().find(qm_mol.atoms()[k]) - mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] - mm1_to_mm2_local[link_idx] = mm_idx - - # Now work out the QM-MM1 bond distances based on the equilibrium - # MM bond lengths. - - # A dictionary to store the bond lengths. Here 'bond_lengths' are the - # equilibrium bond lengths for the QM-MM1 bonds, and 'link_bond_lengths', - # are the equilibrium bond lengths for the QM-L (QM-link) bonds. Both of - # these are evaluated from the MM bond potentials. - bond_lengths = {} - link_bond_lengths = {} - - # Get the MM bond potentials. - bonds = qm_mol.property(map["bond"]).potentials() - - # Store the info for the QM molecule. - info = qm_mol.info() - - # Store the bond potential symbol. - r = _CAS.Symbol("r") - - # Loop over the link atoms. - for qm_idx, mm1_idx in mm1_atoms.items(): - # Convert to cg_atom_idx objects. - cg_qm_idx = info.cg_atom_idx(qm_idx) - cg_mm1_idx = info.cg_atom_idx(mm1_idx) - - # Store the element of the QM atom. - qm_elem = qm_mol[cg_qm_idx].element() - hydrogen = _Mol.Element("H") - - qm_m1_bond_found = False - qm_link_bond_found = False - - # Loop over the bonds. - for bond in bonds: - # Get the indices of the atoms in the bond. - bond_idx0 = bond.atom0() - bond_idx1 = bond.atom1() - - # If the bond is between the QM atom and the MM atom, store the - # bond length. - if ( - not qm_m1_bond_found - and cg_qm_idx == bond_idx0 - and cg_mm1_idx == bond_idx1 - or cg_qm_idx == bond_idx1 - and cg_mm1_idx == bond_idx0 - ): - # Cast as an AmberBond. - ab = _MM.AmberBond(bond.function(), r) - bond_lengths[mm1_idx] = ab.r0() - qm_m1_bond_found = True - if qm_link_bond_found: - break - else: - elem0 = qm_mol[bond_idx0].element() - elem1 = qm_mol[bond_idx1].element() + # Work out the indices of the QM atoms. + try: + idxs = mols.atoms().find(qm_atoms) + engine.set_atoms(idxs) + except: + raise Exception("Unable to set atom indices for the QM region.") - # Is this bond is between a hydrogen and and the same element - # as the QM atom? If so, store the bond length. - if ( - not qm_link_bond_found - and elem0 == hydrogen - and elem1 == qm_elem - or elem0 == qm_elem - and elem1 == hydrogen - ): - # Cast as an AmberBond. - ab = _MM.AmberBond(bond.function(), r) - link_bond_lengths[mm1_idx] = ab.r0() - qm_link_bond_found = True - if qm_m1_bond_found: - break + # Work out the atomic numbers of the QM atoms. + try: + elem_prop = map["element"] + numbers = [atom.property(f"{elem_prop}").num_protons() for atom in qm_atoms] + engine.set_numbers(numbers) + except: + raise Exception("Unable to set atomic numbers for the QM region.") - # Work out the bond scale factors: R0(QM-L) / R0(QM-MM1) - try: - bond_scale_factors_local = {} - for idx in bond_lengths: - abs_idx = mols.atoms().find(qm_mol.atoms()[idx]) - bond_scale_factors_local[abs_idx] = ( - link_bond_lengths[idx] / bond_lengths[idx] - ) - except: - raise Exception( - f"Unable to compute the scaled the QM-MM1 bond lengths for MM1 atom {idx}!" - ) + # Work out the atomic charge for all atoms in the system. + try: + charge_prop = map["charge"] + charges = [atom.property(f"{charge_prop}").value() for atom in mols.atoms()] + engine.set_charges(charges) + except: + raise Exception("Unable to set atomic charges for the system.") - # Update the dictionaries. - mm1_to_qm.update(mm1_to_qm_local) - mm1_to_mm2.update(mm1_to_mm2_local) - bond_scale_factors.update(bond_scale_factors_local) + # Set the link atom information. + try: + engine.set_link_atoms(mm1_to_qm, mm1_to_mm2, bond_lengths) + except: + raise Exception("Unable to set link atom information.") - return mm1_to_qm, mm1_to_mm2, bond_scale_factors + return engine From 651d949b0b9cd4eb74b20131d1fcee98d9e1dd21 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 12:47:19 +0000 Subject: [PATCH 089/468] Add test for link atom detection. --- tests/qm/test_emle.py | 56 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 6f33fb1d4..855df318a 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -40,6 +40,62 @@ def callback(self, a, b, c, d): assert result == (42, d, c) == test.callback(a, b, c, d) +@pytest.mark.parametrize( + "selection, expected", + [ + ( + "residx 0", + ( + {6: 4}, + {6: [7, 8]}, + {6: 0.8164794007490638}, + ), + ), + ( + "residx 1", + ( + {4: 6, 16: 14}, + {4: [1, 5], 16: [17, 18]}, + {4: 0.7565543071161049, 16: 0.8164794007490638}, + ), + ), + ( + "residx 2", + ( + {14: 16}, + {14: [8, 15]}, + {14: 0.7565543071161049}, + ), + ), + ], +) +def test_link_atoms(ala_mols, selection, expected): + """ + Make sure that the link atoms are correctly identified. + """ + + from sire.base import create_map as _create_map + from sire.qm._utils import _create_qm_mol_to_atoms, _get_link_atoms + + # Create a local copy of the test system. + mols = ala_mols + + # Extract the QM atom selection. + qm_atoms = mols[selection].atoms() + + # Create the mapping between molecule numbers and QM atoms. + qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) + + # Get link atom information. + mm1_to_qm, mm1_to_mm2, bond_scale_factors = _get_link_atoms( + mols, qm_mol_to_atoms, _create_map({}) + ) + + assert mm1_to_qm == expected[0] + assert mm1_to_mm2 == expected[1] + assert bond_scale_factors == expected[2] + + @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") @pytest.mark.parametrize("selection", ["molidx 0", "resname ALA"]) def test_interpolate(ala_mols, selection): From be4227ef96e3b2aeb2bc3dcd96ca41089a3dbd98 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 15:56:23 +0000 Subject: [PATCH 090/468] Make sure selection is applied to the first molecule. --- tests/qm/test_emle.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 855df318a..6a261544f 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -81,13 +81,13 @@ def test_link_atoms(ala_mols, selection, expected): mols = ala_mols # Extract the QM atom selection. - qm_atoms = mols[selection].atoms() + qm_atoms = mols[0][selection].atoms() # Create the mapping between molecule numbers and QM atoms. qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) # Get link atom information. - mm1_to_qm, mm1_to_mm2, bond_scale_factors = _get_link_atoms( + mm1_to_qm, mm1_to_mm2, bond_scale_factors, mm1_indices = _get_link_atoms( mols, qm_mol_to_atoms, _create_map({}) ) From 789f735f281fa979b2b44658afb149d4223ad224 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 16:57:50 +0000 Subject: [PATCH 091/468] Switch to using sander link atom approach. --- doc/source/tutorial/part07/01_emle.rst | 4 +- src/sire/qm/_emle.py | 4 +- src/sire/qm/_utils.py | 67 +++++++++- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 7 + wrapper/Convert/SireOpenMM/emle.cpp | 123 ++++++------------ wrapper/Convert/SireOpenMM/emle.h | 13 ++ wrapper/Convert/SireOpenMM/qmmm.h | 6 + 7 files changed, 131 insertions(+), 93 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index 1653a58b8..69775e55c 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -66,8 +66,8 @@ calculation. The selection syntax for QM atoms is extremely flexible. Any valid search string, atom index, list of atom indicies, or molecule view/container that can be used. Support for modelling partial molecules at the QM level is provided via the link -atom approach, via the charge shifting method. For details of this implementation, -see, e.g., the NAMD user guide `here `_. +atom approach, using the same method as the ``sander`` QM/MM implementation. +See `here `_ for details. While we support multiple QM fragments, we do not currently support multiple *independent* QM regions. We plan on adding support for this in the near future. diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 6743b3ffe..8cfa77760 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -121,7 +121,7 @@ def emle( qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) # Get link atom information. - mm1_to_qm, mm1_to_mm2, bond_scale_factors = _get_link_atoms( + mm1_to_qm, mm1_to_mm2, bond_scale_factors, mm1_indices = _get_link_atoms( mols, qm_mol_to_atoms, map ) @@ -131,7 +131,7 @@ def emle( ) # Create the merged molecule. - qm_mols = _create_merged_mols(qm_mol_to_atoms, map) + qm_mols = _create_merged_mols(qm_mol_to_atoms, mm1_indices, map) # Update the molecule in the system. mols.update(qm_mols) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index cc2dae0c4..2ed4eabc1 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -25,6 +25,9 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Initialise the dictionaries. + # List of MM1 atom indices as sire.legacy.Mol.AtomIdx objects. + mm1_indices = [] + # Link atoms to QM atoms. mm1_to_qm = {} @@ -126,6 +129,9 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): mm_idx = [mols.atoms().find(qm_mol.atoms()[x]) for x in v] mm1_to_mm2_local[link_idx] = mm_idx + # Store the MM1 atom indices. + mm1_indices.append(list(mm1_atoms.values())) + # Now work out the QM-MM1 bond distances based on the equilibrium # MM bond lengths. @@ -217,10 +223,44 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): mm1_to_mm2.update(mm1_to_mm2_local) bond_scale_factors.update(bond_scale_factors_local) - return mm1_to_qm, mm1_to_mm2, bond_scale_factors + return mm1_to_qm, mm1_to_mm2, bond_scale_factors, mm1_indices + + +def _get_charge_shift(mols, qm_atoms, mm1_to_mm2): + """ + Internal helper function to compute the charge shift for MM atoms + when link atoms are present. + """ + + from ..units import e_charge as _e_charge + + # Store the atoms. + atoms = mols.atoms() + + # First work out the charge of the QM atoms. + qm_charge = 0 * _e_charge + for atom in qm_atoms: + qm_charge += atom.charge() + + # Now work out the charge of any link atoms. + link_charge = 0 * _e_charge + num_mm2 = 0 + for mm1_idx, mm2_idx in mm1_to_mm2.items(): + link_charge += atoms[mm1_idx].charge() + num_mm2 += len(mm2_idx) + + # Compute the charge shift. + if qm_charge != link_charge: + charge_shift = (link_charge - qm_charge) / ( + len(atoms) - len(qm_atoms) - len(mm1_to_mm2) - num_mm2 + ) + else: + charge_shift = 0 * _e_charge + + return charge_shift -def _create_merged_mols(qm_mol_to_atoms, map): +def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): """ Internal helper function to create a merged molecule from the QM molecule. """ @@ -233,7 +273,7 @@ def _create_merged_mols(qm_mol_to_atoms, map): qm_mols = [] # Loop over all molecules containing QM atoms. - for mol_num, qm_atoms in qm_mol_to_atoms.items(): + for (mol_num, qm_atoms), mm1_idxs in zip(qm_mol_to_atoms.items(), mm1_indices): # Get the molecule. qm_mol = qm_atoms[0].molecule() @@ -386,6 +426,15 @@ def _create_merged_mols(qm_mol_to_atoms, map): ).molecule() charges = _Mol.AtomCharges(info) + + # Set the charge for all non-QM atoms (including link atoms) + # to the MM value. + for atom in qm_mol.atoms(): + idx = info.atom_idx(atom.index()) + if idx not in qm_idxs and idx not in mm1_idxs: + idx = info.cg_atom_idx(idx) + charges.set(idx, atom.property(prop)) + edit_mol = edit_mol.set_property(prop + "1", charges).molecule() edit_mol = edit_mol.remove_property(prop).molecule() @@ -413,8 +462,11 @@ def _create_merged_mols(qm_mol_to_atoms, map): # Link to the perturbation to the reference state. qm_mol = qm_mol.perturbation().link_to_reference().commit() + # Add the molecule to the list. + qm_mols.append(qm_mol) + # Return the merged molecule. - return qm_mol + return qm_mols def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map): @@ -451,4 +503,11 @@ def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_length except: raise Exception("Unable to set link atom information.") + # Set the MM charge shift. + try: + charge_shift = _get_charge_shift(mols, qm_atoms, mm1_to_mm2) + engine.set_charge_shift(_get_charge_shift(mols, qm_atoms, mm1_to_mm2)) + except: + raise Exception("Unable to set the MM charge shift.") + return engine diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index c676ab3fc..206da00c4 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -251,6 +251,13 @@ BOOST_PYTHON_MODULE(_SireOpenMM) &EMLEEngine::setCharges, bp::arg("charges"), "Set the atomic charges") + .def("getChargeShift", + &EMLEEngine::getChargeShift, + "Get the charge shift") + .def("setChargeShift", + &EMLEEngine::setChargeShift, + bp::arg("charge_shift"), + "Set the charge shift") .def("call", &EMLEEngine::call, (bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm")), diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 30f8827fc..6b98b8df8 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -36,10 +36,6 @@ using namespace SireMaths; using namespace SireOpenMM; using namespace SireVol; -// The delta used to place virtual point charges either side of the MM2 -// atoms, in nanometers. -static const double VIRTUAL_PC_DELTA = 0.01; - class GILLock { public: @@ -248,6 +244,16 @@ void EMLEEngine::setCharges(QVector charges) this->charges = charges; } +SireUnits::Dimension::Charge EMLEEngine::getChargeShift() const +{ + return this->charge_shift; +} + +void EMLEEngine::setChargeShift(SireUnits::Dimension::Charge charge_shift) +{ + this->charge_shift = charge_shift; +} + const char *EMLEEngine::typeName() { return QMetaType::typeName(qMetaTypeId()); @@ -320,16 +326,20 @@ double EMLEEngineImpl::computeForce( ); // Store the QM atomic indices and numbers. - const auto qm_atoms = this->owner.getAtoms(); + auto qm_atoms = this->owner.getAtoms(); auto numbers = this->owner.getNumbers(); - // Store the link atom info. + // Store the link atom info. Link atoms are handled using the same approach + // as sander, as described here: https://onlinelibrary.wiley.com/doi/10.1002/jcc.20857 const auto link_atoms = this->owner.getLinkAtoms(); const auto mm1_to_qm = link_atoms.get<0>(); const auto mm1_to_mm2 = link_atoms.get<1>(); const auto bond_scale_factors = link_atoms.get<2>(); const auto mm2_atoms = this->owner.getMM2Atoms(); + // Store the MM charge shift when link atoms are present. + const double delta_charge = this->owner.getChargeShift().value(); + // Initialise a vector to hold the current positions for the QM atoms. QVector> xyz_qm(qm_atoms.size()); QVector xyz_qm_vec(qm_atoms.size()); @@ -360,14 +370,10 @@ double EMLEEngineImpl::computeForce( center /= i; // Initialise a vector to hold the current positions for the MM atoms. - // and virtual point charges. QVector> xyz_mm; - QVector> xyz_virtual; - // Initialise a vector to hold the charges for the MM atoms and virtual - // point charges. + // Initialise a vector to hold the charges for the MM atoms. QVector charges_mm; - QVector charges_virtual; // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; @@ -387,8 +393,7 @@ double EMLEEngineImpl::computeForce( { // Exclude QM atoms or link atoms, which are handled later. if (not qm_atoms.contains(i) and - not mm1_to_mm2.contains(i) and - not mm2_atoms.contains(i)) + not mm1_to_mm2.contains(i)) { // Store the MM atom position in Sire Vector format. Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); @@ -415,7 +420,14 @@ double EMLEEngineImpl::computeForce( xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); // Add the charge and index. - charges_mm.append(this->owner.getCharges()[i]); + if (not mm2_atoms.contains(i)) + { + charges_mm.append(this->owner.getCharges()[i]); + } + else + { + charges_mm.append(this->owner.getCharges()[i] + delta_charge); + } idx_mm.append(i); // Exit the inner loop. @@ -449,7 +461,14 @@ double EMLEEngineImpl::computeForce( xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); // Add the charge and index. - charges_mm.append(this->owner.getCharges()[idx]); + if (not mm2_atoms.contains(idx)) + { + charges_mm.append(this->owner.getCharges()[idx]); + } + else + { + charges_mm.append(this->owner.getCharges()[idx] + delta_charge); + } idx_mm.append(idx); // Exit the inner loop. @@ -459,9 +478,6 @@ double EMLEEngineImpl::computeForce( } } - // Store the current number of QM. - const auto num_qm = xyz_qm.size(); - // Handle link atoms. for (const auto &idx: mm1_to_mm2.keys()) { @@ -478,66 +494,16 @@ double EMLEEngineImpl::computeForce( qm_vec = space.getMinimumImage(qm_vec, center); // Work out the position of the link atom. - const auto link_vec = qm_vec + bond_scale_factors[idx]*(qm_vec - mm1_vec); + const auto link_vec = qm_vec + bond_scale_factors[idx]*(mm1_vec - qm_vec); // Add to the QM positions. xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); + // Append the index to the qm_atoms vector. + qm_atoms.append(idx); + // Append a hydrogen element to the numbers vector. numbers.append(1); - - // Store the number of MM2 atoms. - const auto num_mm2 = mm1_to_mm2[idx].size(); - - // Store the fractional charge contribution to the MM2 atoms and - // virtual point charges. - const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; - - // Loop over the MM2 atoms and perform charge shifting. Here the MM1 - // charge is redistributed over the MM2 atoms and two virtual point - // charges are added either side of the MM2 atoms in order to preserve - // the MM1-MM2 dipole. - for (const auto& mm2_idx : mm1_to_mm2[idx]) - { - // Store the MM2 position in Sire Vector format. - Vector mm2_vec(10*positions[mm2_idx][0], 10*positions[mm2_idx][1], 10*positions[mm2_idx][2]); - - // Work out the minimum image position with respect to the reference position. - mm2_vec = space.getMinimumImage(mm2_vec, center); - - // Add to the MM positions. - xyz_mm.append(QVector({mm2_vec[0], mm2_vec[1], mm2_vec[2]})); - - // Add the charge and index. - charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); - idx_mm.append(mm2_idx); - - // Now add the virtual point charges. - - // Compute the normal vector from the MM1 to MM2 atom. - const auto normal = (mm2_vec - mm1_vec).normalise(); - - // Positive direction. (Away from MM1 atom.) - auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; - xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); - charges_virtual.append(-frac_charge); - - // Negative direction (Towards MM1 atom.) - xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; - xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); - charges_virtual.append(frac_charge); - } - } - - // Store the current number of MM atoms. - const auto num_mm = xyz_mm.size(); - - // If there are any virtual point charges, then add to the MM positions - // and charges. - if (xyz_virtual.size() > 0) - { - xyz_mm.append(xyz_virtual); - charges_mm.append(charges_virtual); } // Call the callback. @@ -573,12 +539,6 @@ double EMLEEngineImpl::computeForce( // Update the atom index. i++; - - // Exit if we have reached the end of the QM atoms, i.e. ignore link atoms. - if (i == num_qm) - { - break; - } } // Now the MM atoms. @@ -596,13 +556,6 @@ double EMLEEngineImpl::computeForce( // Update the atom index. i++; - - // Exit if we have reached the end of the MM atoms, i.e. ignore virtual - // point charges. - if (i == num_mm) - { - break; - } } // Update the step count. diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 3a5fd5881..6d315254c 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -272,6 +272,18 @@ namespace SireOpenMM */ void setCharges(QVector charges); + //! Get the MM atom charge shift when link atoms are present. + /*! \returns + The MM atom charge shift. + */ + SireUnits::Dimension::Charge getChargeShift() const; + + //! Set the MM atom charge shift when link atoms are present. + /*! \param charge_shift + The MM atom charge shift. + */ + void setChargeShift(SireUnits::Dimension::Charge charge_shift); + //! Return the C++ name for this class. static const char *typeName(); @@ -310,6 +322,7 @@ namespace SireOpenMM private: EMLECallback callback; SireUnits::Dimension::Length cutoff; + SireUnits::Dimension::Charge charge_shift; int neighbour_list_frequency; double lambda; QVector atoms; diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index d43ef81e1..db0807f2a 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -88,6 +88,12 @@ namespace SireOpenMM //! Set the atomic charges of all atoms in the system. virtual void setCharges(QVector) = 0; + //! Get charge shift. + virtual SireUnits::Dimension::Charge getChargeShift() const = 0; + + //! Set charge shift. + virtual void setChargeShift(SireUnits::Dimension::Charge) = 0; + protected: virtual OpenMM::ForceImpl *createImpl() const = 0; }; From f429fa3ef359557c6c03fdd15b8a800972ef3c1e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Jan 2024 20:55:20 +0000 Subject: [PATCH 092/468] Check for multiple assigment of the same link atom. --- src/sire/qm/_utils.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 2ed4eabc1..23d7b7839 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -120,6 +120,12 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): for k, v in mm1_atoms.items(): qm_idx = mols.atoms().find(qm_mol.atoms()[k]) link_idx = mols.atoms().find(qm_mol.atoms()[v]) + # Make sure that we haven't assigned this link atom already. + if link_idx in mm1_to_qm_local or link_idx in mm1_to_qm: + raise Exception( + f"Cannot substitue the same MM atom (index {link_idx}) " + "for more than one link atom!" + ) mm1_to_qm_local[link_idx] = qm_idx # Convert MM1 to MM2 atom dictionary to absolute indices. From aeed4cbb268209ac0f791547463bc3a8c62a1269 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Jan 2024 10:31:33 +0000 Subject: [PATCH 093/468] Switch back to CS method to avoid system wide MM charge perturbation. --- doc/source/tutorial/part07/01_emle.rst | 4 +- src/sire/qm/_emle.py | 6 +- src/sire/qm/_utils.py | 82 ++++++------- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 7 -- wrapper/Convert/SireOpenMM/emle.cpp | 109 ++++++++++++------ wrapper/Convert/SireOpenMM/emle.h | 13 --- wrapper/Convert/SireOpenMM/qmmm.h | 6 - 7 files changed, 119 insertions(+), 108 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index 69775e55c..1653a58b8 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -66,8 +66,8 @@ calculation. The selection syntax for QM atoms is extremely flexible. Any valid search string, atom index, list of atom indicies, or molecule view/container that can be used. Support for modelling partial molecules at the QM level is provided via the link -atom approach, using the same method as the ``sander`` QM/MM implementation. -See `here `_ for details. +atom approach, via the charge shifting method. For details of this implementation, +see, e.g., the NAMD user guide `here `_. While we support multiple QM fragments, we do not currently support multiple *independent* QM regions. We plan on adding support for this in the near future. diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 8cfa77760..a0d025e5a 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -111,12 +111,16 @@ def emle( ) from ._utils import ( + _check_charge, _create_qm_mol_to_atoms, _configure_engine, _create_merged_mols, _get_link_atoms, ) + # Check that the charge of the QM region is integer valued. + _check_charge(qm_atoms, map) + # Get the mapping between molecule numbers and QM atoms. qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) @@ -136,4 +140,4 @@ def emle( # Update the molecule in the system. mols.update(qm_mols) - return mols, engine + return engine diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 23d7b7839..eba292009 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,3 +1,23 @@ +def _check_charge(qm_atoms, map, tol=1e-6): + """ + Internal helper function to check that the QM region has integer charge. + """ + + import math as _math + + # Get the charge property. + charge_prop = map["charge"] + + # Work out the charge of the QM atoms. + qm_charge = 0 + for atom in qm_atoms: + qm_charge += atom.property(charge_prop).value() + + # Check that the charge is an integer. + if not _math.isclose(qm_charge, round(qm_charge), abs_tol=tol): + raise Exception(f"Charge of the QM region ({qm_charge}) is not an integer!") + + def _create_qm_mol_to_atoms(qm_atoms): """ Internal helper function to create a mapping between molecule numbers and @@ -39,6 +59,12 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # bond potentials, i.e. R0(QM-L) / R0(QM-MM1). bond_scale_factors = {} + # Store a hydrogen element. + hydrogen = _Mol.Element("H") + + # Store the element property. + elem_prop = map["element"] + # Loop over all molecules containing QM atoms. for mol_num, qm_atoms in qm_mol_to_atoms.items(): # Get the molecule. @@ -96,6 +122,16 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): if len(mm_bonds) > 1: raise Exception(f"QM atom {idx} has more than one MM bond!") else: + # Get the element of the cut atom. + elem = qm_mol[mm_bonds[0]].property(elem_prop) + + # If the element is hydrogen, raise an exception. + if elem == hydrogen: + raise Exception( + f"Attempting replace a hydrogen with a link atom (index {mm_bonds[0]})!" + ) + + # Store the link (MM1) atom. mm1_atoms[idx] = mm_bonds[0] # Now work out the MM atoms that are bonded to the link atoms. (MM2 atoms.) @@ -232,40 +268,6 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): return mm1_to_qm, mm1_to_mm2, bond_scale_factors, mm1_indices -def _get_charge_shift(mols, qm_atoms, mm1_to_mm2): - """ - Internal helper function to compute the charge shift for MM atoms - when link atoms are present. - """ - - from ..units import e_charge as _e_charge - - # Store the atoms. - atoms = mols.atoms() - - # First work out the charge of the QM atoms. - qm_charge = 0 * _e_charge - for atom in qm_atoms: - qm_charge += atom.charge() - - # Now work out the charge of any link atoms. - link_charge = 0 * _e_charge - num_mm2 = 0 - for mm1_idx, mm2_idx in mm1_to_mm2.items(): - link_charge += atoms[mm1_idx].charge() - num_mm2 += len(mm2_idx) - - # Compute the charge shift. - if qm_charge != link_charge: - charge_shift = (link_charge - qm_charge) / ( - len(atoms) - len(qm_atoms) - len(mm1_to_mm2) - num_mm2 - ) - else: - charge_shift = 0 * _e_charge - - return charge_shift - - def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): """ Internal helper function to create a merged molecule from the QM molecule. @@ -433,8 +435,7 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): charges = _Mol.AtomCharges(info) - # Set the charge for all non-QM atoms (including link atoms) - # to the MM value. + # Set the charge for all non-QM and non-MM1 atoms to the MM value. for atom in qm_mol.atoms(): idx = info.atom_idx(atom.index()) if idx not in qm_idxs and idx not in mm1_idxs: @@ -509,11 +510,4 @@ def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_length except: raise Exception("Unable to set link atom information.") - # Set the MM charge shift. - try: - charge_shift = _get_charge_shift(mols, qm_atoms, mm1_to_mm2) - engine.set_charge_shift(_get_charge_shift(mols, qm_atoms, mm1_to_mm2)) - except: - raise Exception("Unable to set the MM charge shift.") - - return engine + return mols, engine diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 206da00c4..c676ab3fc 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -251,13 +251,6 @@ BOOST_PYTHON_MODULE(_SireOpenMM) &EMLEEngine::setCharges, bp::arg("charges"), "Set the atomic charges") - .def("getChargeShift", - &EMLEEngine::getChargeShift, - "Get the charge shift") - .def("setChargeShift", - &EMLEEngine::setChargeShift, - bp::arg("charge_shift"), - "Set the charge shift") .def("call", &EMLEEngine::call, (bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm")), diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 6b98b8df8..744582d5a 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -36,6 +36,10 @@ using namespace SireMaths; using namespace SireOpenMM; using namespace SireVol; +// The delta used to place virtual point charges either side of the MM2 +// atoms, in nanometers. +static const double VIRTUAL_PC_DELTA = 0.01; + class GILLock { public: @@ -244,16 +248,6 @@ void EMLEEngine::setCharges(QVector charges) this->charges = charges; } -SireUnits::Dimension::Charge EMLEEngine::getChargeShift() const -{ - return this->charge_shift; -} - -void EMLEEngine::setChargeShift(SireUnits::Dimension::Charge charge_shift) -{ - this->charge_shift = charge_shift; -} - const char *EMLEEngine::typeName() { return QMetaType::typeName(qMetaTypeId()); @@ -337,9 +331,6 @@ double EMLEEngineImpl::computeForce( const auto bond_scale_factors = link_atoms.get<2>(); const auto mm2_atoms = this->owner.getMM2Atoms(); - // Store the MM charge shift when link atoms are present. - const double delta_charge = this->owner.getChargeShift().value(); - // Initialise a vector to hold the current positions for the QM atoms. QVector> xyz_qm(qm_atoms.size()); QVector xyz_qm_vec(qm_atoms.size()); @@ -370,10 +361,14 @@ double EMLEEngineImpl::computeForce( center /= i; // Initialise a vector to hold the current positions for the MM atoms. + // and virtual point charges. QVector> xyz_mm; + QVector> xyz_virtual; - // Initialise a vector to hold the charges for the MM atoms. + // Initialise a vector to hold the charges for the MM atoms and virtual + // point charges. QVector charges_mm; + QVector charges_virtual; // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; @@ -393,7 +388,8 @@ double EMLEEngineImpl::computeForce( { // Exclude QM atoms or link atoms, which are handled later. if (not qm_atoms.contains(i) and - not mm1_to_mm2.contains(i)) + not mm1_to_mm2.contains(i) and + not mm2_atoms.contains(i)) { // Store the MM atom position in Sire Vector format. Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); @@ -420,14 +416,7 @@ double EMLEEngineImpl::computeForce( xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); // Add the charge and index. - if (not mm2_atoms.contains(i)) - { - charges_mm.append(this->owner.getCharges()[i]); - } - else - { - charges_mm.append(this->owner.getCharges()[i] + delta_charge); - } + charges_mm.append(this->owner.getCharges()[i]); idx_mm.append(i); // Exit the inner loop. @@ -461,14 +450,7 @@ double EMLEEngineImpl::computeForce( xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); // Add the charge and index. - if (not mm2_atoms.contains(idx)) - { - charges_mm.append(this->owner.getCharges()[idx]); - } - else - { - charges_mm.append(this->owner.getCharges()[idx] + delta_charge); - } + charges_mm.append(this->owner.getCharges()[idx]); idx_mm.append(idx); // Exit the inner loop. @@ -478,7 +460,7 @@ double EMLEEngineImpl::computeForce( } } - // Handle link atoms. + // Handle link atoms via the Charge Shift method. for (const auto &idx: mm1_to_mm2.keys()) { // Get the QM atom to which the current MM atom is bonded. @@ -499,11 +481,61 @@ double EMLEEngineImpl::computeForce( // Add to the QM positions. xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); - // Append the index to the qm_atoms vector. - qm_atoms.append(idx); - // Append a hydrogen element to the numbers vector. numbers.append(1); + + // Store the number of MM2 atoms. + const auto num_mm2 = mm1_to_mm2[idx].size(); + + // Store the fractional charge contribution to the MM2 atoms and + // virtual point charges. + const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; + + // Loop over the MM2 atoms and perform charge shifting. Here the MM1 + // charge is redistributed over the MM2 atoms and two virtual point + // charges are added either side of the MM2 atoms in order to preserve + // the MM1-MM2 dipole. + for (const auto& mm2_idx : mm1_to_mm2[idx]) + { + // Store the MM2 position in Sire Vector format. + Vector mm2_vec(10*positions[mm2_idx][0], 10*positions[mm2_idx][1], 10*positions[mm2_idx][2]); + + // Work out the minimum image position with respect to the reference position. + mm2_vec = space.getMinimumImage(mm2_vec, center); + + // Add to the MM positions. + xyz_mm.append(QVector({mm2_vec[0], mm2_vec[1], mm2_vec[2]})); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); + idx_mm.append(mm2_idx); + + // Now add the virtual point charges. + + // Compute the normal vector from the MM1 to MM2 atom. + const auto normal = (mm2_vec - mm1_vec).normalise(); + + // Positive direction. (Away from MM1 atom.) + auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; + xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_virtual.append(-frac_charge); + + // Negative direction (Towards MM1 atom.) + xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; + xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_virtual.append(frac_charge); + } + } + + // Store the current number of MM atoms. + const auto num_mm = xyz_mm.size(); + + // If there are any virtual point charges, then add to the MM positions + // and charges. + if (xyz_virtual.size() > 0) + { + xyz_mm.append(xyz_virtual); + charges_mm.append(charges_virtual); } // Call the callback. @@ -556,6 +588,13 @@ double EMLEEngineImpl::computeForce( // Update the atom index. i++; + + // Exit if we have reached the end of the MM atoms, i.e. ignore virtual + // point charges. + if (i == num_mm) + { + break; + } } // Update the step count. diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 6d315254c..3a5fd5881 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -272,18 +272,6 @@ namespace SireOpenMM */ void setCharges(QVector charges); - //! Get the MM atom charge shift when link atoms are present. - /*! \returns - The MM atom charge shift. - */ - SireUnits::Dimension::Charge getChargeShift() const; - - //! Set the MM atom charge shift when link atoms are present. - /*! \param charge_shift - The MM atom charge shift. - */ - void setChargeShift(SireUnits::Dimension::Charge charge_shift); - //! Return the C++ name for this class. static const char *typeName(); @@ -322,7 +310,6 @@ namespace SireOpenMM private: EMLECallback callback; SireUnits::Dimension::Length cutoff; - SireUnits::Dimension::Charge charge_shift; int neighbour_list_frequency; double lambda; QVector atoms; diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index db0807f2a..d43ef81e1 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -88,12 +88,6 @@ namespace SireOpenMM //! Set the atomic charges of all atoms in the system. virtual void setCharges(QVector) = 0; - //! Get charge shift. - virtual SireUnits::Dimension::Charge getChargeShift() const = 0; - - //! Set charge shift. - virtual void setChargeShift(SireUnits::Dimension::Charge) = 0; - protected: virtual OpenMM::ForceImpl *createImpl() const = 0; }; From f0174e19e4814585f5c99c3a92756012aafde501 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Jan 2024 12:02:37 +0000 Subject: [PATCH 094/468] Raise warning if link atom cuts a non carbon-carbon bond. --- src/sire/qm/_utils.py | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index eba292009..917f5c604 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -39,6 +39,8 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): Internal helper function to get a dictionary with link atoms for each QM atom. """ + import warnings as _warnings + from ..legacy import CAS as _CAS from ..legacy import Mol as _Mol from ..legacy import MM as _MM @@ -59,7 +61,8 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # bond potentials, i.e. R0(QM-L) / R0(QM-MM1). bond_scale_factors = {} - # Store a hydrogen element. + # Store carbon and hydrogen elements. + carbon = _Mol.Element("C") hydrogen = _Mol.Element("H") # Store the element property. @@ -84,6 +87,9 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Store the atom index. idx = atom.index() + # Store the element of the atom. + elem = atom.property(elem_prop) + # Get the bonds for the atom. bonds = connectivity.get_bonds(idx) @@ -123,12 +129,22 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): raise Exception(f"QM atom {idx} has more than one MM bond!") else: # Get the element of the cut atom. - elem = qm_mol[mm_bonds[0]].property(elem_prop) + link_elem = qm_mol[mm_bonds[0]].property(elem_prop) # If the element is hydrogen, raise an exception. if elem == hydrogen: + abs_idx = mols.atoms().find(atom) raise Exception( - f"Attempting replace a hydrogen with a link atom (index {mm_bonds[0]})!" + "Attempting replace a hydrogen with a link atom " + f"(QM atom index {abs_idx})!" + ) + + # Warn if the link atom is not for a carbon-carbon bond. + if elem != carbon or link_elem != carbon: + abs_idx = mols.atoms().find(atom) + _warnings.warn( + "Attempting to add a link atom for a non carbon-carbon " + f"bond (QM atom index {abs_idx})!" ) # Store the link (MM1) atom. From ef83baf4a376773c91e85af6f51f150c556c13c7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Jan 2024 12:17:46 +0000 Subject: [PATCH 095/468] Add note regarding positioning of link atoms. --- wrapper/Convert/SireOpenMM/emle.cpp | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 744582d5a..bc4021636 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -323,8 +323,8 @@ double EMLEEngineImpl::computeForce( auto qm_atoms = this->owner.getAtoms(); auto numbers = this->owner.getNumbers(); - // Store the link atom info. Link atoms are handled using the same approach - // as sander, as described here: https://onlinelibrary.wiley.com/doi/10.1002/jcc.20857 + // Store the link atom info. Link atoms are handled using the Charge Shift + // method. See: https://www.ks.uiuc.edu/Research/qmmm const auto link_atoms = this->owner.getLinkAtoms(); const auto mm1_to_qm = link_atoms.get<0>(); const auto mm1_to_mm2 = link_atoms.get<1>(); @@ -461,6 +461,7 @@ double EMLEEngineImpl::computeForce( } // Handle link atoms via the Charge Shift method. + // See: https://www.ks.uiuc.edu/Research/qmmm for (const auto &idx: mm1_to_mm2.keys()) { // Get the QM atom to which the current MM atom is bonded. @@ -475,7 +476,11 @@ double EMLEEngineImpl::computeForce( mm1_vec = space.getMinimumImage(mm1_vec, center); qm_vec = space.getMinimumImage(qm_vec, center); - // Work out the position of the link atom. + // Work out the position of the link atom. Here we use a bond length + // scale factor taken from the MM bond potential, i.e. R0(QM-L) / R0(QM-MM1), + // where R0(QM-L) is the equilibrium bond length for the QM and link (L) + // elements, and R0(QM-MM1) is the equilibrium bond length for the QM + // and MM1 elements. const auto link_vec = qm_vec + bond_scale_factors[idx]*(mm1_vec - qm_vec); // Add to the QM positions. From 4289f1cf100bae50139437148fe0d0ba75e29dfe Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Jan 2024 12:46:30 +0000 Subject: [PATCH 096/468] Remove reference to QM atom in print statement. --- src/sire/qm/_utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 917f5c604..c5e4511d2 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -136,7 +136,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): abs_idx = mols.atoms().find(atom) raise Exception( "Attempting replace a hydrogen with a link atom " - f"(QM atom index {abs_idx})!" + f"(atom index {abs_idx})!" ) # Warn if the link atom is not for a carbon-carbon bond. @@ -144,7 +144,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): abs_idx = mols.atoms().find(atom) _warnings.warn( "Attempting to add a link atom for a non carbon-carbon " - f"bond (QM atom index {abs_idx})!" + f"bond (atom index {abs_idx})!" ) # Store the link (MM1) atom. From 4332bb2b0d96f058e0f25684f6f981a2e855857e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Jan 2024 15:38:35 +0000 Subject: [PATCH 097/468] Append MM1 atom index to the qm_atoms vector. --- wrapper/Convert/SireOpenMM/emle.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index bc4021636..a5d9193be 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -486,6 +486,9 @@ double EMLEEngineImpl::computeForce( // Add to the QM positions. xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); + // Add the MM1 index to the QM atoms vector. + qm_atoms.append(qm_idx); + // Append a hydrogen element to the numbers vector. numbers.append(1); From 83dcfbe0b358adb8c2d14ead4d0811c6bb11a4d7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Jan 2024 09:23:54 +0000 Subject: [PATCH 098/468] Switch to QMForce abstract base class. --- wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp | 4 ++-- wrapper/Convert/SireOpenMM/emle.h | 2 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 2 +- wrapper/Convert/SireOpenMM/lambdalever.h | 4 ++-- wrapper/Convert/SireOpenMM/qmmm.cpp | 2 +- wrapper/Convert/SireOpenMM/qmmm.h | 6 +++--- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 2 +- 7 files changed, 11 insertions(+), 11 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index c676ab3fc..5eecfed30 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -188,9 +188,9 @@ BOOST_PYTHON_MODULE(_SireOpenMM) // A tuple for passing link atom information to EMLEEngine. register_tuple, QMap>>>(); - bp::class_, boost::noncopyable>("QMMMForce", bp::no_init); + bp::class_, boost::noncopyable>("QMForce", bp::no_init); - bp::class_>("EMLEEngine", + bp::class_>("EMLEEngine", bp::init( ( bp::arg("py_object"), diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 3a5fd5881..7902059e6 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -107,7 +107,7 @@ namespace SireOpenMM QString callback; }; - class EMLEEngine : public SireBase::ConcreteProperty + class EMLEEngine : public SireBase::ConcreteProperty { public: //! Default constructor. diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 5830f6578..406d88576 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -363,7 +363,7 @@ double LambdaLever::setLambda(OpenMM::Context &context, OpenMM::System &system = const_cast(context.getSystem()); // get copies of the forcefields in which the parameters will be changed - auto qmff = this->getForce("qmff", system); + auto qmff = this->getForce("qmff", system); auto cljff = this->getForce("clj", system); auto ghost_ghostff = this->getForce("ghost/ghost", system); auto ghost_nonghostff = this->getForce("ghost/non-ghost", system); diff --git a/wrapper/Convert/SireOpenMM/lambdalever.h b/wrapper/Convert/SireOpenMM/lambdalever.h index 75d4bd7cf..2f1f8e10f 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.h +++ b/wrapper/Convert/SireOpenMM/lambdalever.h @@ -186,9 +186,9 @@ namespace SireOpenMM } template <> - inline QString _get_typename() + inline QString _get_typename() { - return "SireOpenMM::QMMMForce"; + return "SireOpenMM::QMForce"; } /** Return the OpenMM::Force (of type T) that is called 'name' diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index 83cc8bf50..d646e073e 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -30,6 +30,6 @@ using namespace SireOpenMM; -QMMMForce::~QMMMForce() +QMForce::~QMForce() { } diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index d43ef81e1..429a67e38 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -47,10 +47,10 @@ SIRE_BEGIN_HEADER namespace SireOpenMM { - class QMMMForce : public SireBase::Property, public OpenMM::Force + class QMForce : public SireBase::Property, public OpenMM::Force { public: - virtual ~QMMMForce(); + virtual ~QMForce(); //! Get the lambda weighting factor. virtual double getLambda() const = 0; @@ -92,7 +92,7 @@ namespace SireOpenMM virtual OpenMM::ForceImpl *createImpl() const = 0; }; - typedef SireBase::PropPtr QMMEnginePtr; + typedef SireBase::PropPtr QMForcePtr; } SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index d88891e7a..f897a9946 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -741,7 +741,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } // now create the engine for computing QM forces on atoms - QMMMForce *qmff = 0; + QMForce *qmff = 0; if (map.specified("qm_engine")) { From 52cf120f89ae40f32a1393205ef3201d75acd5c8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Jan 2024 09:24:21 +0000 Subject: [PATCH 099/468] Validate the qm_engine keyword argument. --- src/sire/mol/_dynamics.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 180cdaeff..c8882ab91 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -35,6 +35,17 @@ def __init__(self, mols=None, map=None, **kwargs): mols.atoms().find(selection_to_atoms(mols, fixed_atoms)), ) + # see if there is a QM/MM engine + if map.specified("qm_engine"): + qm_engine = map["qm_engine"].value() + + from ..legacy.Convert._SireOpenMM import QMForce + + if qm_engine and not isinstance(qm_engine, QMForce): + raise ValueError( + "'qm_engine' must be an instance of QMForce." + ) + # see if this is an interpolation simulation if map.specified("lambda_interpolate"): if map["lambda_interpolate"].has_value(): From 1820ff16df46b29023d076387510b248803cf3cf Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Jan 2024 14:39:38 +0000 Subject: [PATCH 100/468] emle-engine now defaults to no energy logging. --- doc/source/tutorial/part07/01_emle.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index 1653a58b8..d4973e762 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -33,10 +33,9 @@ in water. First, let us load the molecular system: Next we will create an ``emle-engine`` calculator to perform the QM (or ML) calculation for the dipeptide along with the ML electrostatic embedding. Since this is a small molecule it isn't beneficial to perform the calculation on a GPU, so we will use the CPU instead. -We will also disable logging to file to improve performance. >>> from emle.calculator import EMLECalculator ->>> calculator = EMLECalculator(device="cpu", log=0) +>>> calculator = EMLECalculator(device="cpu") By default, ``emle-engine`` will use `TorchANI `_ as the backend for in vacuo calculation of energies and gradients. However, From f90d0d333a452de3cf3ee952891ccc3c33d47e69 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Jan 2024 14:45:59 +0000 Subject: [PATCH 101/468] Add loguru and pyyaml to emle requirements. --- requirements_emle.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/requirements_emle.txt b/requirements_emle.txt index 1eb7109b6..61a260174 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -2,10 +2,12 @@ ambertools ase deepmd-kit eigen +loguru pip pybind11 pytorch python < 3.11 +pyyaml torchani xtb-python From 429c174a28bd2b826ae684f391f32ff218b84b01 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Jan 2024 15:44:05 +0000 Subject: [PATCH 102/468] Update EMLECalculator constructor arguments. --- tests/qm/test_emle.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 6a261544f..68f4c1914 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -107,7 +107,7 @@ def test_interpolate(ala_mols, selection): mols = ala_mols.__copy__() # Create an EMLE calculator. - calculator = EMLECalculator(device="cpu", log=0, save_settings=False) + calculator = EMLECalculator(device="cpu") # Create a dynamics object. d = mols.dynamics(timestep="1fs", constraint="none", platform="cpu") From 31ef0df4f5761a7c5cdf919ba4701b67b00a85e9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 29 Jan 2024 14:32:26 +0000 Subject: [PATCH 103/468] Fix emle function call following API change. [ref #153] --- doc/source/tutorial/part07/01_emle.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part07/01_emle.rst index d4973e762..13ea73b51 100644 --- a/doc/source/tutorial/part07/01_emle.rst +++ b/doc/source/tutorial/part07/01_emle.rst @@ -50,7 +50,7 @@ We plan on adding support for other elements in the near future. We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation: ->>> mols, engine = sr.qm.emle(mols, mols[0], calculator, 0, "7.5A", 20) +>>> mols, engine = sr.qm.emle(mols, mols[0], calculator, "7.5A", 20) Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule), and From 55268940fcb61ea4c07f1c4f33d8eb511f3cc5d6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 29 Jan 2024 14:33:12 +0000 Subject: [PATCH 104/468] Move emle-emle import check to avoid circular dependency. [closes #153] --- src/sire/qm/_emle.py | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index a0d025e5a..6096527a1 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -8,13 +8,6 @@ _EMLEEngine = _Convert._SireOpenMM.EMLEEngine -try: - from emle.calculator import EMLECalculator as _EMLECalculator - - _has_emle = True -except: - _has_emle = False - def emle( mols, @@ -53,7 +46,10 @@ def emle( engine : sire.legacy.Convert._SireOpenMM.EMLEEngine The EMLEEngine object. """ - if not _has_emle: + + try: + from emle.calculator import EMLECalculator as _EMLECalculator + except: raise ImportError( "Could not import emle. Please install emle-engine and try again." ) From ea4e0ed8a6ef9afc1eda41df8e709bf07b5e7119 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 12 Feb 2024 09:54:47 +0000 Subject: [PATCH 105/468] Move QM/MM tutorial to part08. --- doc/source/tutorial/index.rst | 2 +- doc/source/tutorial/{index_part07.rst => index_part08.rst} | 4 ++-- doc/source/tutorial/{part07 => part08}/01_emle.rst | 0 3 files changed, 3 insertions(+), 3 deletions(-) rename doc/source/tutorial/{index_part07.rst => index_part08.rst} (95%) rename doc/source/tutorial/{part07 => part08}/01_emle.rst (100%) diff --git a/doc/source/tutorial/index.rst b/doc/source/tutorial/index.rst index bcb473c25..758b31c07 100644 --- a/doc/source/tutorial/index.rst +++ b/doc/source/tutorial/index.rst @@ -27,4 +27,4 @@ please :doc:`ask for support. <../support>` index_part04 index_part05 index_part06 - index_part07 + index_part08 diff --git a/doc/source/tutorial/index_part07.rst b/doc/source/tutorial/index_part08.rst similarity index 95% rename from doc/source/tutorial/index_part07.rst rename to doc/source/tutorial/index_part08.rst index a6ae74262..6f9cb84c3 100644 --- a/doc/source/tutorial/index_part07.rst +++ b/doc/source/tutorial/index_part08.rst @@ -1,5 +1,5 @@ ============== -Part 7 - QM/MM +Part 8 - QM/MM ============== QM/MM is a method that combines the accuracy of quantum mechanics with the @@ -15,4 +15,4 @@ QM/MM simulations using ``sire``. .. toctree:: :maxdepth: 1 - part07/01_emle + part08/01_emle diff --git a/doc/source/tutorial/part07/01_emle.rst b/doc/source/tutorial/part08/01_emle.rst similarity index 100% rename from doc/source/tutorial/part07/01_emle.rst rename to doc/source/tutorial/part08/01_emle.rst From e3484bf56060fceeae71eef5daf5fba7e2211a2b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 13 Feb 2024 11:11:53 +0000 Subject: [PATCH 106/468] Split into QMForce and QMEngine classes. --- wrapper/Convert/SireOpenMM/emle.cpp | 353 +++++++++++++----- wrapper/Convert/SireOpenMM/emle.h | 255 +++++++++++-- wrapper/Convert/SireOpenMM/qmmm.cpp | 87 +++++ wrapper/Convert/SireOpenMM/qmmm.h | 75 ++-- .../SireOpenMM/sire_to_openmm_system.cpp | 4 +- 5 files changed, 624 insertions(+), 150 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 8afee7027..197729b29 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -49,6 +49,10 @@ class GILLock PyGILState_STATE state_; }; +///////// +///////// Implementation of EMLECallback +///////// + EMLECallback::EMLECallback() { } @@ -89,35 +93,41 @@ const char *EMLECallback::what() const return EMLECallback::typeName(); } -EMLEEngine::EMLEEngine() +///////// +///////// Implementation of EMLEForce +///////// + +EMLEForce::EMLEForce() { } -EMLEEngine::EMLEEngine( - bp::object py_object, +EMLEForce::EMLEForce( + EMLECallback callback, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, - double lambda) : - callback(py_object, "_sire_callback"), + double lambda, + QVector atoms, + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_scale_factors, + QVector mm2_atoms, + QVector numbers, + QVector charges) : + callback(callback), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), - lambda(lambda) + lambda(lambda), + atoms(atoms), + mm1_to_qm(mm1_to_qm), + mm1_to_mm2(mm1_to_mm2), + bond_scale_factors(bond_scale_factors), + mm2_atoms(mm2_atoms), + numbers(numbers), + charges(charges) { - if (this->neighbour_list_frequency < 0) - { - neighbour_list_frequency = 0; - } - if (this->lambda < 0.0) - { - this->lambda = 0.0; - } - else if (this->lambda > 1.0) - { - this->lambda = 1.0; - } } -EMLEEngine::EMLEEngine(const EMLEEngine &other) : +EMLEForce::EMLEForce(const EMLEForce &other) : callback(other.callback), cutoff(other.cutoff), neighbour_list_frequency(other.neighbour_list_frequency), @@ -132,7 +142,7 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : { } -EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) +EMLEForce &EMLEForce::operator=(const EMLEForce &other) { this->callback = other.callback; this->cutoff = other.cutoff; @@ -148,17 +158,12 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) return *this; } -void EMLEEngine::setCallback(EMLECallback callback) -{ - this->callback = callback; -} - -EMLECallback EMLEEngine::getCallback() const +EMLECallback EMLEForce::getCallback() const { return this->callback; } -void EMLEEngine::setLambda(double lambda) +void EMLEForce::setLambda(double lambda) { // Clamp the lambda value. if (lambda < 0.0) @@ -172,132 +177,99 @@ void EMLEEngine::setLambda(double lambda) this->lambda = lambda; } -double EMLEEngine::getLambda() const +double EMLEForce::getLambda() const { return this->lambda; } -void EMLEEngine::setCutoff(SireUnits::Dimension::Length cutoff) -{ - this->cutoff = cutoff; -} - -SireUnits::Dimension::Length EMLEEngine::getCutoff() const +SireUnits::Dimension::Length EMLEForce::getCutoff() const { return this->cutoff; } -int EMLEEngine::getNeighbourListFrequency() const +int EMLEForce::getNeighbourListFrequency() const { return this->neighbour_list_frequency; } -void EMLEEngine::setNeighbourListFrequency(int neighbour_list_frequency) -{ - // Assume anything less than zero means no neighbour list. - if (neighbour_list_frequency < 0) - { - neighbour_list_frequency = 0; - } - this->neighbour_list_frequency = neighbour_list_frequency; -} - -QVector EMLEEngine::getAtoms() const +QVector EMLEForce::getAtoms() const { return this->atoms; } -void EMLEEngine::setAtoms(QVector atoms) -{ - this->atoms = atoms; -} - -boost::tuple, QMap>, QMap> EMLEEngine::getLinkAtoms() const +boost::tuple, QMap>, QMap> EMLEForce::getLinkAtoms() const { return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); } -void EMLEEngine::setLinkAtoms( - QMap mm1_to_qm, - QMap> mm1_to_mm2, - QMap bond_scale_factors) -{ - this->mm1_to_qm = mm1_to_qm; - this->mm1_to_mm2 = mm1_to_mm2; - this->bond_scale_factors = bond_scale_factors; - - // Build a vector of all of the MM2 atoms. - this->mm2_atoms.clear(); - for (const auto &mm2 : this->mm1_to_mm2.values()) - { - this->mm2_atoms.append(mm2); - } -} - -QVector EMLEEngine::getMM2Atoms() const +QVector EMLEForce::getMM2Atoms() const { return this->mm2_atoms; } -QVector EMLEEngine::getNumbers() const +QVector EMLEForce::getNumbers() const { return this->numbers; } -void EMLEEngine::setNumbers(QVector numbers) -{ - this->numbers = numbers; -} - -QVector EMLEEngine::getCharges() const +QVector EMLEForce::getCharges() const { return this->charges; } -void EMLEEngine::setCharges(QVector charges) +const char *EMLEForce::typeName() { - this->charges = charges; + return QMetaType::typeName(qMetaTypeId()); } -const char *EMLEEngine::typeName() +const char *EMLEForce::what() const { - return QMetaType::typeName(qMetaTypeId()); + return EMLEForce::typeName(); } -const char *EMLEEngine::what() const +boost::tuple>, QVector>> +EMLEForce::call( + QVector numbers_qm, + QVector charges_mm, + QVector> xyz_qm, + QVector> xyz_mm) const { - return EMLEEngine::typeName(); + return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); } -OpenMM::ForceImpl *EMLEEngine::createImpl() const +///////// +///////// Implementation of EMLEForceImpl +///////// + +OpenMM::ForceImpl *EMLEForce::createImpl() const { #ifdef SIRE_USE_CUSTOMCPPFORCE - return new EMLEEngineImpl(*this); + return new EMLEForceImpl(*this); #else throw SireError::unsupported(QObject::tr( - "Unable to create a EMLEEngine because OpenMM::CustomCPPForceImpl " + "Unable to create an EMLEForceImpl because OpenMM::CustomCPPForceImpl " "is not available. You need to use OpenMM 8.1 or later."), CODELOC); return 0; #endif } -EMLEEngineImpl::EMLEEngineImpl(const EMLEEngine &owner) : +EMLEForceImpl::EMLEForceImpl(const EMLEForce &owner) : OpenMM::CustomCPPForceImpl(owner), owner(owner) { } -EMLEEngineImpl::~EMLEEngineImpl() +EMLEForceImpl::~EMLEForceImpl() { } -const EMLEEngine &EMLEEngineImpl::getOwner() const +const EMLEForce &EMLEForceImpl::getOwner() const { return this->owner; } -double EMLEEngineImpl::computeForce( +double EMLEForceImpl::computeForce( OpenMM::ContextImpl &context, const std::vector &positions, std::vector &forces) @@ -624,6 +596,190 @@ double EMLEEngineImpl::computeForce( #endif } +///////// +///////// Implementation of EMLEEngine +///////// + +EMLEEngine::EMLEEngine() +{ +} + +EMLEEngine::EMLEEngine( + bp::object py_object, + SireUnits::Dimension::Length cutoff, + int neighbour_list_frequency, + double lambda) : + callback(py_object, "_sire_callback"), + cutoff(cutoff), + neighbour_list_frequency(neighbour_list_frequency), + lambda(lambda) +{ + if (this->neighbour_list_frequency < 0) + { + neighbour_list_frequency = 0; + } + if (this->lambda < 0.0) + { + this->lambda = 0.0; + } + else if (this->lambda > 1.0) + { + this->lambda = 1.0; + } +} + +EMLEEngine::EMLEEngine(const EMLEEngine &other) : + callback(other.callback), + cutoff(other.cutoff), + neighbour_list_frequency(other.neighbour_list_frequency), + lambda(other.lambda), + atoms(other.atoms), + mm1_to_qm(other.mm1_to_qm), + mm1_to_mm2(other.mm1_to_mm2), + mm2_atoms(other.mm2_atoms), + bond_scale_factors(other.bond_scale_factors), + numbers(other.numbers), + charges(other.charges) +{ +} + +EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) +{ + this->callback = other.callback; + this->cutoff = other.cutoff; + this->neighbour_list_frequency = other.neighbour_list_frequency; + this->lambda = other.lambda; + this->atoms = other.atoms; + this->mm1_to_qm = other.mm1_to_qm; + this->mm1_to_mm2 = other.mm1_to_mm2; + this->mm2_atoms = other.mm2_atoms; + this->bond_scale_factors = other.bond_scale_factors; + this->numbers = other.numbers; + this->charges = other.charges; + return *this; +} + +void EMLEEngine::setCallback(EMLECallback callback) +{ + this->callback = callback; +} + +EMLECallback EMLEEngine::getCallback() const +{ + return this->callback; +} + +void EMLEEngine::setLambda(double lambda) +{ + // Clamp the lambda value. + if (lambda < 0.0) + { + lambda = 0.0; + } + else if (lambda > 1.0) + { + lambda = 1.0; + } + this->lambda = lambda; +} + +double EMLEEngine::getLambda() const +{ + return this->lambda; +} + +void EMLEEngine::setCutoff(SireUnits::Dimension::Length cutoff) +{ + this->cutoff = cutoff; +} + +SireUnits::Dimension::Length EMLEEngine::getCutoff() const +{ + return this->cutoff; +} + +int EMLEEngine::getNeighbourListFrequency() const +{ + return this->neighbour_list_frequency; +} + +void EMLEEngine::setNeighbourListFrequency(int neighbour_list_frequency) +{ + // Assume anything less than zero means no neighbour list. + if (neighbour_list_frequency < 0) + { + neighbour_list_frequency = 0; + } + this->neighbour_list_frequency = neighbour_list_frequency; +} + +QVector EMLEEngine::getAtoms() const +{ + return this->atoms; +} + +void EMLEEngine::setAtoms(QVector atoms) +{ + this->atoms = atoms; +} + +boost::tuple, QMap>, QMap> EMLEEngine::getLinkAtoms() const +{ + return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); +} + +void EMLEEngine::setLinkAtoms( + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_scale_factors) +{ + this->mm1_to_qm = mm1_to_qm; + this->mm1_to_mm2 = mm1_to_mm2; + this->bond_scale_factors = bond_scale_factors; + + // Build a vector of all of the MM2 atoms. + this->mm2_atoms.clear(); + for (const auto &mm2 : this->mm1_to_mm2.values()) + { + this->mm2_atoms.append(mm2); + } +} + +QVector EMLEEngine::getMM2Atoms() const +{ + return this->mm2_atoms; +} + +QVector EMLEEngine::getNumbers() const +{ + return this->numbers; +} + +void EMLEEngine::setNumbers(QVector numbers) +{ + this->numbers = numbers; +} + +QVector EMLEEngine::getCharges() const +{ + return this->charges; +} + +void EMLEEngine::setCharges(QVector charges) +{ + this->charges = charges; +} + +const char *EMLEEngine::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *EMLEEngine::what() const +{ + return EMLEEngine::typeName(); +} + boost::tuple>, QVector>> EMLEEngine::call( QVector numbers_qm, @@ -633,3 +789,20 @@ EMLEEngine::call( { return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); } + +QMForce* EMLEEngine::createForce() const +{ + return new EMLEForce( + this->callback, + this->cutoff, + this->neighbour_list_frequency, + this->lambda, + this->atoms, + this->mm1_to_qm, + this->mm1_to_mm2, + this->bond_scale_factors, + this->mm2_atoms, + this->numbers, + this->charges + ); +} diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 2fcff2087..ded7f971d 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -76,7 +76,7 @@ namespace SireOpenMM */ EMLECallback(bp::object, QString callback="_sire_callback"); - //! Constructor + //! Call the callback function. /*! \param numbers_qm A vector of atomic numbers for the atoms in the ML region. @@ -113,7 +113,225 @@ namespace SireOpenMM QString callback; }; - class EMLEEngine : public SireBase::ConcreteProperty + class EMLEForce : public QMForce + { + public: + //! Default constructor. + EMLEForce(); + + //! Constructor. + /* \param callback + The EMLECallback object. + + \param cutoff + The ML cutoff distance. + + \param neighbour_list_frequency + The frequency at which the neighbour list is updated. (Number of steps.) + If zero, then no neighbour list is used. + + \param lambda + The lambda weighting factor. This can be used to interpolate between + potentials for end-state correction calculations. + + \param atoms + A vector of atom indices for the QM region. + + \param mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + \param mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + \param bond_scale_factors + A dictionary of link atom indices (MM1) to a list of the bond + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + + \param mm2_atoms + A vector of MM2 atom indices. + + \param numbers + A vector of atomic charges for all atoms in the system. + + \param charges + A vector of atomic charges for all atoms in the system. + */ + EMLEForce( + EMLECallback callback, + SireUnits::Dimension::Length cutoff, + int neighbour_list_frequency, + double lambda, + QVector atoms, + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_scale_factors, + QVector mm2_atoms, + QVector numbers, + QVector charges + ); + + //! Copy constructor. + EMLEForce(const EMLEForce &other); + + //! Assignment operator. + EMLEForce &operator=(const EMLEForce &other); + + //! Get the callback object. + /*! \returns + A Python object that contains the callback function. + */ + EMLECallback getCallback() const; + + //! Get the lambda weighting factor. + /*! \returns + The lambda weighting factor. + */ + double getLambda() const; + + //! Set the lambda weighting factor + /* \param lambda + The lambda weighting factor. + */ + void setLambda(double lambda); + + //! Get the QM cutoff distance. + /*! \returns + The QM cutoff distance. + */ + SireUnits::Dimension::Length getCutoff() const; + + //! Get the neighbour list frequency. + /*! \returns + The neighbour list frequency. + */ + int getNeighbourListFrequency() const; + + //! Get the indices of the atoms in the QM region. + /*! \returns + A vector of atom indices for the QM region. + */ + QVector getAtoms() const; + + //! Get the link atoms associated with each QM atom. + /*! \returns + A tuple containing: + + mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + bond_scale_factors + A dictionary of link atom indices (MM1) to a list of the bond + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + + */ + boost::tuple, QMap>, QMap> getLinkAtoms() const; + + //! Get the vector of MM2 atoms. + /*! \returns + A vector of MM2 atom indices. + */ + QVector getMM2Atoms() const; + + //! Get the atomic numbers for the atoms in the QM region. + /*! \returns + A vector of atomic numbers for the atoms in the QM region. + */ + QVector getNumbers() const; + + //! Get the atomic charges of all atoms in the system. + /*! \returns + A vector of atomic charges for all atoms in the system. + */ + QVector getCharges() const; + + //! Return the C++ name for this class. + static const char *typeName(); + + //! Return the C++ name for this class. + const char *what() const; + + //! Call the callback function. + /*! \param numbers_qm + A vector of atomic numbers for the atoms in the ML region. + + \param charges_mm + A vector of the charges on the MM atoms in mod electron charge. + + \param xyz_qm + A vector of positions for the atoms in the ML region in Angstrom. + + \param xyz_mm + A vector of positions for the atoms in the MM region in Angstrom. + + \returns + A tuple containing: + - The energy in kJ/mol. + - A vector of forces for the QM atoms in kJ/mol/nm. + - A vector of forces for the MM atoms in kJ/mol/nm. + */ + boost::tuple>, QVector>> call( + QVector numbers_qm, + QVector charges_mm, + QVector> xyz_qm, + QVector> xyz_mm + ) const; + + protected: + OpenMM::ForceImpl *createImpl() const; + + private: + EMLECallback callback; + SireUnits::Dimension::Length cutoff; + int neighbour_list_frequency; + double lambda; + QVector atoms; + QMap mm1_to_qm; + QMap> mm1_to_mm2; + QMap bond_scale_factors; + QVector mm2_atoms; + QVector numbers; + QVector charges; + }; + +#ifdef SIRE_USE_CUSTOMCPPFORCE + class EMLEForceImpl : public OpenMM::CustomCPPForceImpl + { + public: + EMLEForceImpl(const EMLEForce &owner); + + ~EMLEForceImpl(); + + double computeForce(OpenMM::ContextImpl &context, + const std::vector &positions, + std::vector &forces); + + const EMLEForce &getOwner() const; + + private: + const EMLEForce &owner; + unsigned long long step_count=0; + double cutoff; + bool is_neighbour_list; + int neighbour_list_frequency; + double neighbour_list_cutoff; + QSet neighbour_list; + }; +#endif + + class EMLEEngine : public SireBase::ConcreteProperty { public: //! Default constructor. @@ -284,7 +502,7 @@ namespace SireOpenMM //! Return the C++ name for this class. const char *what() const; - //! Constructor + //! Call the callback function. /*! \param numbers_qm A vector of atomic numbers for the atoms in the ML region. @@ -310,8 +528,8 @@ namespace SireOpenMM QVector> xyz_mm ) const; - protected: - OpenMM::ForceImpl *createImpl() const; + //! Create an EMLE force object. + QMForce* createForce() const; private: EMLECallback callback; @@ -326,37 +544,14 @@ namespace SireOpenMM QVector numbers; QVector charges; }; - -#ifdef SIRE_USE_CUSTOMCPPFORCE - class EMLEEngineImpl : public OpenMM::CustomCPPForceImpl - { - public: - EMLEEngineImpl(const EMLEEngine &owner); - - ~EMLEEngineImpl(); - - double computeForce(OpenMM::ContextImpl &context, - const std::vector &positions, - std::vector &forces); - - const EMLEEngine &getOwner() const; - - private: - const EMLEEngine &owner; - unsigned long long step_count=0; - double cutoff; - bool is_neighbour_list; - int neighbour_list_frequency; - double neighbour_list_cutoff; - QSet neighbour_list; - }; -#endif } Q_DECLARE_METATYPE(SireOpenMM::EMLECallback) +Q_DECLARE_METATYPE(SireOpenMM::EMLEForce) Q_DECLARE_METATYPE(SireOpenMM::EMLEEngine) SIRE_EXPOSE_CLASS(SireOpenMM::EMLECallback) +SIRE_EXPOSE_CLASS(SireOpenMM::EMLEForce) SIRE_EXPOSE_CLASS(SireOpenMM::EMLEEngine) SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index d646e073e..feb2f3d24 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -28,8 +28,95 @@ #include "qmmm.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" + +using namespace SireBase; using namespace SireOpenMM; +using namespace SireStream; + +///////// +///////// Implementation of QMForce +///////// + +/** Constructor */ +QMForce::QMForce() : OpenMM::Force() +{ +} QMForce::~QMForce() { } + +///////// +///////// Implementation of QMEngine +///////// + +/** Constructor */ +QMEngine::QMEngine() : Property() +{ +} + +/** Destructor */ +QMEngine::~QMEngine() +{ +} + +///////// +///////// Implementation of NullQMEngine +///////// + +static const RegisterMetaType r_nullqmengine; + +/** Serialise to a binary datastream */ +QDataStream &operator<<(QDataStream &ds, const NullQMEngine &qmengine) +{ + writeHeader(ds, r_nullqmengine, 1); + + ds << static_cast(qmengine); + + return ds; +} + +/** Extract from a binary datastream */ +QDataStream &operator>>(QDataStream &ds, NullQMEngine &qmengine) +{ + VersionID v = readHeader(ds, r_nullqmengine); + + if (v == 1) + { + ds >> static_cast(qmengine); + } + else + throw version_error(v, "1", r_nullqmengine, CODELOC); + + return ds; +} + +/** Constructor */ +NullQMEngine::NullQMEngine() : ConcreteProperty() +{ +} + +/** Destructor */ +NullQMEngine::~NullQMEngine() +{ +} + +/** Return the type name */ +const char *NullQMEngine::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +/** Return the type name */ +const char *NullQMEngine::what() const +{ + return NullQMEngine::typeName(); +} + +/** Return a null QM engine */ +const NullQMEngine &QMEngine::null() +{ + return *(create_shared_null()); +} diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 1ef4fbf3f..3e0069c6a 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -47,55 +47,74 @@ SIRE_BEGIN_HEADER namespace SireOpenMM { - class QMForce : public SireBase::Property, public OpenMM::Force + class QMForce; + class QMEngine; + class NullQMEngine; + + class QMForce : public OpenMM::Force { public: - virtual ~QMForce(); + QMForce(); - //! Get the lambda weighting factor. - virtual double getLambda() const = 0; + virtual ~QMForce(); //! Set the lambda weighting factor. virtual void setLambda(double lambda) = 0; - //! Get the QM cutoff distance. - virtual SireUnits::Dimension::Length getCutoff() const = 0; + protected: + virtual OpenMM::ForceImpl *createImpl() const = 0; + }; - //! Set the QM cutoff distance. - virtual void setCutoff(SireUnits::Dimension::Length cutoff) = 0; + class QMEngine : public SireBase::Property + { + public: + QMEngine(); - //! Get the indices of the atoms in the QM region. - virtual QVector getAtoms() const = 0; + virtual ~QMEngine(); - //! Set the list of atom indices for the QM region. - virtual void setAtoms(QVector) = 0; + //! Clone the QM engine. + virtual QMEngine *clone() const = 0; - //! Get the link atoms associated with each QM atom. - virtual boost::tuple, QMap>, QMap> getLinkAtoms() const = 0; + //! Get the name of the QM engine. + static const char *typeName(); - //! Set the link atoms associated with each QM atom. - virtual void setLinkAtoms(QMap, QMap>, QMap) = 0; + //! Get the name of the QM engine. + const char *what() const; - //! Get the atomic numbers of the atoms in the QM region. - virtual QVector getNumbers() const = 0; + //! Create a QM force object. + virtual QMForce* createForce() const=0; - //! Set the list of atomic numbers for the QM region. - virtual void setNumbers(QVector) = 0; + //! Get a null QM engine. + static const NullQMEngine &null(); + }; - //! Get the atomic charges of all atoms in the system. - virtual QVector getCharges() const = 0; + typedef SireBase::PropPtr QMEnginePtr; - //! Set the atomic charges of all atoms in the system. - virtual void setCharges(QVector) = 0; + class NullQMEngine : public SireBase::ConcreteProperty + { + public: + NullQMEngine(); - protected: - virtual OpenMM::ForceImpl *createImpl() const = 0; - }; + ~NullQMEngine(); + + //! Get the name of the QM engine. + static const char *typeName(); - typedef SireBase::PropPtr QMForcePtr; + //! Get the name of the QM engine. + const char *what() const; + + //! Create a QM force object. + QMForce* createForce() const; + }; } +Q_DECLARE_METATYPE(SireOpenMM::NullQMEngine) + SIRE_EXPOSE_CLASS(SireOpenMM::QMForce) +SIRE_EXPOSE_CLASS(SireOpenMM::QMEngine) +SIRE_EXPOSE_CLASS(SireOpenMM::NullQMEngine) + +SIRE_EXPOSE_PROPERTY(SireOpenMM::QMEnginePtr, SireOpenMM::QMEngine) SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index fdef7871f..25f4a7cd5 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -727,8 +727,8 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { try { - auto &engine = map["qm_engine"].value().asA(); - qmff = new EMLEEngine(engine); + auto &engine = map["qm_engine"].value().asA(); + qmff = engine.createForce(); } catch (...) { From 9c6b0b09f4ebabe2131059115d18cd970d41e2ca Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 13 Feb 2024 11:38:20 +0000 Subject: [PATCH 107/468] Add updated wrappers. --- src/sire/mol/_dynamics.py | 6 +- .../Convert/SireOpenMM/CMakeAutogenFile.txt | 4 + .../Convert/SireOpenMM/EMLECallback.pypp.cpp | 2 +- .../Convert/SireOpenMM/EMLEEngine.pypp.cpp | 4 +- wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp | 221 ++++++++++++++++++ wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp | 10 + .../Convert/SireOpenMM/NullQMEngine.pypp.cpp | 79 +++++++ .../Convert/SireOpenMM/NullQMEngine.pypp.hpp | 10 + wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp | 92 ++++++++ wrapper/Convert/SireOpenMM/QMEngine.pypp.hpp | 10 + wrapper/Convert/SireOpenMM/QMForce.pypp.cpp | 157 +------------ .../SireOpenMM/SireOpenMM_properties.cpp | 17 ++ .../SireOpenMM/SireOpenMM_properties.h | 6 + .../SireOpenMM/SireOpenMM_registrars.cpp | 5 + .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 18 +- wrapper/Convert/SireOpenMM/qmmm.cpp | 12 +- wrapper/Convert/SireOpenMM/qmmm.h | 9 +- wrapper/Convert/__init__.py | 6 +- 18 files changed, 503 insertions(+), 165 deletions(-) create mode 100644 wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp create mode 100644 wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp create mode 100644 wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp create mode 100644 wrapper/Convert/SireOpenMM/NullQMEngine.pypp.hpp create mode 100644 wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp create mode 100644 wrapper/Convert/SireOpenMM/QMEngine.pypp.hpp create mode 100644 wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp create mode 100644 wrapper/Convert/SireOpenMM/SireOpenMM_properties.h diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index eb9431e6e..e01f107c0 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -39,11 +39,11 @@ def __init__(self, mols=None, map=None, **kwargs): if map.specified("qm_engine"): qm_engine = map["qm_engine"].value() - from ..legacy.Convert import QMForce + from ..legacy.Convert import QMEngine - if qm_engine and not isinstance(qm_engine, QMForce): + if qm_engine and not isinstance(qm_engine, QMEngine): raise ValueError( - "'qm_engine' must be an instance of QMForce." + "'qm_engine' must be an instance of 'sire.legacy.Convert.QMEngine'" ) # see if this is an interpolation simulation diff --git a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt index 7a147d97d..14b187087 100644 --- a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt +++ b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt @@ -2,11 +2,15 @@ set ( PYPP_SOURCES LambdaLever.pypp.cpp PerturbableOpenMMMolecule.pypp.cpp + QMEngine.pypp.cpp + EMLEForce.pypp.cpp EMLEEngine.pypp.cpp EMLECallback.pypp.cpp _SireOpenMM_free_functions.pypp.cpp QMForce.pypp.cpp vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp + NullQMEngine.pypp.cpp OpenMMMetaData.pypp.cpp + SireOpenMM_properties.cpp SireOpenMM_registrars.cpp ) diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp index 52a511dca..17b138b8d 100644 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp @@ -46,7 +46,7 @@ void register_EMLECallback_class(){ , call_function_value , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) , bp::release_gil_policy() - , "Constructor\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } { //::SireOpenMM::EMLECallback::typeName diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp index 6183240c6..8285d72c6 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp @@ -52,7 +52,7 @@ SireOpenMM::EMLEEngine __copy__(const SireOpenMM::EMLEEngine &other){ return Sir void register_EMLEEngine_class(){ { //::SireOpenMM::EMLEEngine - typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireOpenMM::QMForce, SireBase::Property > > EMLEEngine_exposer_t; + typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > EMLEEngine_exposer_t; EMLEEngine_exposer_t EMLEEngine_exposer = EMLEEngine_exposer_t( "EMLEEngine", "", bp::init< >("Default constructor.") ); bp::scope EMLEEngine_scope( EMLEEngine_exposer ); EMLEEngine_exposer.def( bp::init< bp::api::object, bp::optional< SireUnits::Dimension::Length, int, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nAn EMLECalculator Python object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); @@ -67,7 +67,7 @@ void register_EMLEEngine_class(){ , call_function_value , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) , bp::release_gil_policy() - , "Constructor\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } { //::SireOpenMM::EMLEEngine::getAtoms diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp new file mode 100644 index 000000000..8b10bcc4f --- /dev/null +++ b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp @@ -0,0 +1,221 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "EMLEForce.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireVol/triclinicbox.h" + +#include "emle.h" + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireVol/triclinicbox.h" + +#include "emle.h" + +SireOpenMM::EMLEForce __copy__(const SireOpenMM::EMLEForce &other){ return SireOpenMM::EMLEForce(other); } + +const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLEForce";} + +#include "Helpers/release_gil_policy.hpp" + +void register_EMLEForce_class(){ + + { //::SireOpenMM::EMLEForce + typedef bp::class_< SireOpenMM::EMLEForce, bp::bases< SireOpenMM::QMForce > > EMLEForce_exposer_t; + EMLEForce_exposer_t EMLEForce_exposer = EMLEForce_exposer_t( "EMLEForce", "", bp::init< >("Default constructor.") ); + bp::scope EMLEForce_scope( EMLEForce_exposer ); + EMLEForce_exposer.def( bp::init< SireOpenMM::EMLECallback, SireUnits::Dimension::Length, int, double, QVector< int >, QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, QVector< int >, QVector< int >, QVector< double > >(( bp::arg("callback"), bp::arg("cutoff"), bp::arg("neighbour_list_frequency"), bp::arg("lambda"), bp::arg("atoms"), bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors"), bp::arg("mm2_atoms"), bp::arg("numbers"), bp::arg("charges") ), "Constructor.\nPar:am callback\nThe EMLECallback object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n\nPar:am atoms\nA vector of atom indices for the QM region.\n\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\nPar:am mm2_atoms\nA vector of MM2 atom indices.\n\nPar:am numbers\nA vector of atomic charges for all atoms in the system.\n\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n") ); + EMLEForce_exposer.def( bp::init< SireOpenMM::EMLEForce const & >(( bp::arg("other") ), "Copy constructor.") ); + { //::SireOpenMM::EMLEForce::call + + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLEForce::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + call_function_type call_function_value( &::SireOpenMM::EMLEForce::call ); + + EMLEForce_exposer.def( + "call" + , call_function_value + , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) + , bp::release_gil_policy() + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + + } + { //::SireOpenMM::EMLEForce::getAtoms + + typedef ::QVector< int > ( ::SireOpenMM::EMLEForce::*getAtoms_function_type)( ) const; + getAtoms_function_type getAtoms_function_value( &::SireOpenMM::EMLEForce::getAtoms ); + + EMLEForce_exposer.def( + "getAtoms" + , getAtoms_function_value + , bp::release_gil_policy() + , "Get the indices of the atoms in the QM region.\nReturn:s\nA vector of atom indices for the QM region.\n" ); + + } + { //::SireOpenMM::EMLEForce::getCallback + + typedef ::SireOpenMM::EMLECallback ( ::SireOpenMM::EMLEForce::*getCallback_function_type)( ) const; + getCallback_function_type getCallback_function_value( &::SireOpenMM::EMLEForce::getCallback ); + + EMLEForce_exposer.def( + "getCallback" + , getCallback_function_value + , bp::release_gil_policy() + , "Get the callback object.\nReturn:s\nA Python object that contains the callback function.\n" ); + + } + { //::SireOpenMM::EMLEForce::getCharges + + typedef ::QVector< double > ( ::SireOpenMM::EMLEForce::*getCharges_function_type)( ) const; + getCharges_function_type getCharges_function_value( &::SireOpenMM::EMLEForce::getCharges ); + + EMLEForce_exposer.def( + "getCharges" + , getCharges_function_value + , bp::release_gil_policy() + , "Get the atomic charges of all atoms in the system.\nReturn:s\nA vector of atomic charges for all atoms in the system.\n" ); + + } + { //::SireOpenMM::EMLEForce::getCutoff + + typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::EMLEForce::*getCutoff_function_type)( ) const; + getCutoff_function_type getCutoff_function_value( &::SireOpenMM::EMLEForce::getCutoff ); + + EMLEForce_exposer.def( + "getCutoff" + , getCutoff_function_value + , bp::release_gil_policy() + , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); + + } + { //::SireOpenMM::EMLEForce::getLambda + + typedef double ( ::SireOpenMM::EMLEForce::*getLambda_function_type)( ) const; + getLambda_function_type getLambda_function_value( &::SireOpenMM::EMLEForce::getLambda ); + + EMLEForce_exposer.def( + "getLambda" + , getLambda_function_value + , bp::release_gil_policy() + , "Get the lambda weighting factor.\nReturn:s\nThe lambda weighting factor.\n" ); + + } + { //::SireOpenMM::EMLEForce::getLinkAtoms + + typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLEForce::*getLinkAtoms_function_type)( ) const; + getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::EMLEForce::getLinkAtoms ); + + EMLEForce_exposer.def( + "getLinkAtoms" + , getLinkAtoms_function_value + , bp::release_gil_policy() + , "Get the link atoms associated with each QM atom.\nReturn:s\nA tuple containing:\n\nmm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nmm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nbond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); + + } + { //::SireOpenMM::EMLEForce::getMM2Atoms + + typedef ::QVector< int > ( ::SireOpenMM::EMLEForce::*getMM2Atoms_function_type)( ) const; + getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::EMLEForce::getMM2Atoms ); + + EMLEForce_exposer.def( + "getMM2Atoms" + , getMM2Atoms_function_value + , bp::release_gil_policy() + , "Get the vector of MM2 atoms.\nReturn:s\nA vector of MM2 atom indices.\n" ); + + } + { //::SireOpenMM::EMLEForce::getNeighbourListFrequency + + typedef int ( ::SireOpenMM::EMLEForce::*getNeighbourListFrequency_function_type)( ) const; + getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::EMLEForce::getNeighbourListFrequency ); + + EMLEForce_exposer.def( + "getNeighbourListFrequency" + , getNeighbourListFrequency_function_value + , bp::release_gil_policy() + , "Get the neighbour list frequency.\nReturn:s\nThe neighbour list frequency.\n" ); + + } + { //::SireOpenMM::EMLEForce::getNumbers + + typedef ::QVector< int > ( ::SireOpenMM::EMLEForce::*getNumbers_function_type)( ) const; + getNumbers_function_type getNumbers_function_value( &::SireOpenMM::EMLEForce::getNumbers ); + + EMLEForce_exposer.def( + "getNumbers" + , getNumbers_function_value + , bp::release_gil_policy() + , "Get the atomic numbers for the atoms in the QM region.\nReturn:s\nA vector of atomic numbers for the atoms in the QM region.\n" ); + + } + { //::SireOpenMM::EMLEForce::operator= + + typedef ::SireOpenMM::EMLEForce & ( ::SireOpenMM::EMLEForce::*assign_function_type)( ::SireOpenMM::EMLEForce const & ) ; + assign_function_type assign_function_value( &::SireOpenMM::EMLEForce::operator= ); + + EMLEForce_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "Assignment operator." ); + + } + { //::SireOpenMM::EMLEForce::setLambda + + typedef void ( ::SireOpenMM::EMLEForce::*setLambda_function_type)( double ) ; + setLambda_function_type setLambda_function_value( &::SireOpenMM::EMLEForce::setLambda ); + + EMLEForce_exposer.def( + "setLambda" + , setLambda_function_value + , ( bp::arg("lambda") ) + , bp::release_gil_policy() + , "Set the lambda weighting factor\nPar:am lambda\nThe lambda weighting factor.\n" ); + + } + { //::SireOpenMM::EMLEForce::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireOpenMM::EMLEForce::typeName ); + + EMLEForce_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + { //::SireOpenMM::EMLEForce::what + + typedef char const * ( ::SireOpenMM::EMLEForce::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::EMLEForce::what ); + + EMLEForce_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + EMLEForce_exposer.staticmethod( "typeName" ); + EMLEForce_exposer.def( "__copy__", &__copy__); + EMLEForce_exposer.def( "__deepcopy__", &__copy__); + EMLEForce_exposer.def( "clone", &__copy__); + EMLEForce_exposer.def( "__str__", &pvt_get_name); + EMLEForce_exposer.def( "__repr__", &pvt_get_name); + EMLEForce_exposer.def( "__str__", &pvt_get_name); + EMLEForce_exposer.def( "__repr__", &pvt_get_name); + } + +} diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp new file mode 100644 index 000000000..05d6d9265 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef EMLEForce_hpp__pyplusplus_wrapper +#define EMLEForce_hpp__pyplusplus_wrapper + +void register_EMLEForce_class(); + +#endif//EMLEForce_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp new file mode 100644 index 000000000..3f9770a74 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp @@ -0,0 +1,79 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "NullQMEngine.pypp.hpp" + +namespace bp = boost::python; + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +void register_NullQMEngine_class(){ + + { //::SireOpenMM::NullQMEngine + typedef bp::class_< SireOpenMM::NullQMEngine, bp::bases< SireOpenMM::QMEngine >, boost::noncopyable > NullQMEngine_exposer_t; + NullQMEngine_exposer_t NullQMEngine_exposer = NullQMEngine_exposer_t( "NullQMEngine", "" ); + bp::scope NullQMEngine_scope( NullQMEngine_exposer ); + { //::SireOpenMM::NullQMEngine::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireOpenMM::NullQMEngine::typeName ); + + NullQMEngine_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "Get the name of the QM engine." ); + + } + { //::SireOpenMM::NullQMEngine::what + + typedef char const * ( ::SireOpenMM::NullQMEngine::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::NullQMEngine::what ); + + NullQMEngine_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Get the name of the QM engine." ); + + } + NullQMEngine_exposer.staticmethod( "typeName" ); + NullQMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::NullQMEngine > ); + NullQMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::NullQMEngine > ); + NullQMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::NullQMEngine > ); + NullQMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::NullQMEngine > ); + } + +} diff --git a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.hpp b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.hpp new file mode 100644 index 000000000..0c4147d7b --- /dev/null +++ b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef NullQMEngine_hpp__pyplusplus_wrapper +#define NullQMEngine_hpp__pyplusplus_wrapper + +void register_NullQMEngine_class(); + +#endif//NullQMEngine_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp new file mode 100644 index 000000000..d95fa4f11 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp @@ -0,0 +1,92 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "QMEngine.pypp.hpp" + +namespace bp = boost::python; + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "qmmm.h" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +void register_QMEngine_class(){ + + { //::SireOpenMM::QMEngine + typedef bp::class_< SireOpenMM::QMEngine, boost::noncopyable > QMEngine_exposer_t; + QMEngine_exposer_t QMEngine_exposer = QMEngine_exposer_t( "QMEngine", "", bp::no_init ); + bp::scope QMEngine_scope( QMEngine_exposer ); + { //::SireOpenMM::QMEngine::null + + typedef ::SireOpenMM::NullQMEngine const & ( *null_function_type )( ); + null_function_type null_function_value( &::SireOpenMM::QMEngine::null ); + + QMEngine_exposer.def( + "null" + , null_function_value + , bp::return_value_policy< bp::copy_const_reference >() + , "Get a null QM engine." ); + + } + { //::SireOpenMM::QMEngine::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireOpenMM::QMEngine::typeName ); + + QMEngine_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "Get the name of the QM engine." ); + + } + { //::SireOpenMM::QMEngine::what + + typedef char const * ( ::SireOpenMM::QMEngine::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::QMEngine::what ); + + QMEngine_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Get the name of the QM engine." ); + + } + QMEngine_exposer.staticmethod( "null" ); + QMEngine_exposer.staticmethod( "typeName" ); + QMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::QMEngine > ); + QMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::QMEngine > ); + QMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::QMEngine > ); + QMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::QMEngine > ); + } + +} diff --git a/wrapper/Convert/SireOpenMM/QMEngine.pypp.hpp b/wrapper/Convert/SireOpenMM/QMEngine.pypp.hpp new file mode 100644 index 000000000..bf9bd075c --- /dev/null +++ b/wrapper/Convert/SireOpenMM/QMEngine.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef QMEngine_hpp__pyplusplus_wrapper +#define QMEngine_hpp__pyplusplus_wrapper + +void register_QMEngine_class(); + +#endif//QMEngine_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp index 593b7c0f6..fda73f29f 100644 --- a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp @@ -7,19 +7,19 @@ namespace bp = boost::python; -#include "qmmm.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "Helpers/str.hpp" +#include "SireStream/datastream.h" -#include "Helpers/release_gil_policy.hpp" - -#include "qmmm.h" +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "Helpers/str.hpp" +const char* pvt_get_name(const SireOpenMM::QMForce&){ return "SireOpenMM::QMForce";} #include "Helpers/release_gil_policy.hpp" @@ -29,117 +29,6 @@ void register_QMForce_class(){ typedef bp::class_< SireOpenMM::QMForce, boost::noncopyable > QMForce_exposer_t; QMForce_exposer_t QMForce_exposer = QMForce_exposer_t( "QMForce", "", bp::no_init ); bp::scope QMForce_scope( QMForce_exposer ); - { //::SireOpenMM::QMForce::getAtoms - - typedef ::QVector< int > ( ::SireOpenMM::QMForce::*getAtoms_function_type)( ) const; - getAtoms_function_type getAtoms_function_value( &::SireOpenMM::QMForce::getAtoms ); - - QMForce_exposer.def( - "getAtoms" - , getAtoms_function_value - , bp::release_gil_policy() - , "Get the indices of the atoms in the QM region." ); - - } - { //::SireOpenMM::QMForce::getCharges - - typedef ::QVector< double > ( ::SireOpenMM::QMForce::*getCharges_function_type)( ) const; - getCharges_function_type getCharges_function_value( &::SireOpenMM::QMForce::getCharges ); - - QMForce_exposer.def( - "getCharges" - , getCharges_function_value - , bp::release_gil_policy() - , "Get the atomic charges of all atoms in the system." ); - - } - { //::SireOpenMM::QMForce::getCutoff - - typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::QMForce::*getCutoff_function_type)( ) const; - getCutoff_function_type getCutoff_function_value( &::SireOpenMM::QMForce::getCutoff ); - - QMForce_exposer.def( - "getCutoff" - , getCutoff_function_value - , bp::release_gil_policy() - , "Get the QM cutoff distance." ); - - } - { //::SireOpenMM::QMForce::getLambda - - typedef double ( ::SireOpenMM::QMForce::*getLambda_function_type)( ) const; - getLambda_function_type getLambda_function_value( &::SireOpenMM::QMForce::getLambda ); - - QMForce_exposer.def( - "getLambda" - , getLambda_function_value - , bp::release_gil_policy() - , "Get the lambda weighting factor." ); - - } - { //::SireOpenMM::QMForce::getLinkAtoms - - typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::QMForce::*getLinkAtoms_function_type)( ) const; - getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::QMForce::getLinkAtoms ); - - QMForce_exposer.def( - "getLinkAtoms" - , getLinkAtoms_function_value - , bp::release_gil_policy() - , "Get the link atoms associated with each QM atom." ); - - } - { //::SireOpenMM::QMForce::getNumbers - - typedef ::QVector< int > ( ::SireOpenMM::QMForce::*getNumbers_function_type)( ) const; - getNumbers_function_type getNumbers_function_value( &::SireOpenMM::QMForce::getNumbers ); - - QMForce_exposer.def( - "getNumbers" - , getNumbers_function_value - , bp::release_gil_policy() - , "Get the atomic numbers of the atoms in the QM region." ); - - } - { //::SireOpenMM::QMForce::setAtoms - - typedef void ( ::SireOpenMM::QMForce::*setAtoms_function_type)( ::QVector< int > ) ; - setAtoms_function_type setAtoms_function_value( &::SireOpenMM::QMForce::setAtoms ); - - QMForce_exposer.def( - "setAtoms" - , setAtoms_function_value - , ( bp::arg("arg0") ) - , bp::release_gil_policy() - , "Set the list of atom indices for the QM region." ); - - } - { //::SireOpenMM::QMForce::setCharges - - typedef void ( ::SireOpenMM::QMForce::*setCharges_function_type)( ::QVector< double > ) ; - setCharges_function_type setCharges_function_value( &::SireOpenMM::QMForce::setCharges ); - - QMForce_exposer.def( - "setCharges" - , setCharges_function_value - , ( bp::arg("arg0") ) - , bp::release_gil_policy() - , "Set the atomic charges of all atoms in the system." ); - - } - { //::SireOpenMM::QMForce::setCutoff - - typedef void ( ::SireOpenMM::QMForce::*setCutoff_function_type)( ::SireUnits::Dimension::Length ) ; - setCutoff_function_type setCutoff_function_value( &::SireOpenMM::QMForce::setCutoff ); - - QMForce_exposer.def( - "setCutoff" - , setCutoff_function_value - , ( bp::arg("cutoff") ) - , bp::release_gil_policy() - , "Set the QM cutoff distance." ); - - } { //::SireOpenMM::QMForce::setLambda typedef void ( ::SireOpenMM::QMForce::*setLambda_function_type)( double ) ; @@ -153,36 +42,10 @@ void register_QMForce_class(){ , "Set the lambda weighting factor." ); } - { //::SireOpenMM::QMForce::setLinkAtoms - - typedef void ( ::SireOpenMM::QMForce::*setLinkAtoms_function_type)( ::QMap< int, int >,::QMap< int, QVector< int > >,::QMap< int, double > ) ; - setLinkAtoms_function_type setLinkAtoms_function_value( &::SireOpenMM::QMForce::setLinkAtoms ); - - QMForce_exposer.def( - "setLinkAtoms" - , setLinkAtoms_function_value - , ( bp::arg("arg0"), bp::arg("arg1"), bp::arg("arg2") ) - , bp::release_gil_policy() - , "Set the link atoms associated with each QM atom." ); - - } - { //::SireOpenMM::QMForce::setNumbers - - typedef void ( ::SireOpenMM::QMForce::*setNumbers_function_type)( ::QVector< int > ) ; - setNumbers_function_type setNumbers_function_value( &::SireOpenMM::QMForce::setNumbers ); - - QMForce_exposer.def( - "setNumbers" - , setNumbers_function_value - , ( bp::arg("arg0") ) - , bp::release_gil_policy() - , "Set the list of atomic numbers for the QM region." ); - - } - QMForce_exposer.def( "__str__", &__str__< ::SireOpenMM::QMForce > ); - QMForce_exposer.def( "__repr__", &__str__< ::SireOpenMM::QMForce > ); - QMForce_exposer.def( "__str__", &__str__< ::SireOpenMM::QMForce > ); - QMForce_exposer.def( "__repr__", &__str__< ::SireOpenMM::QMForce > ); + QMForce_exposer.def( "__str__", &pvt_get_name); + QMForce_exposer.def( "__repr__", &pvt_get_name); + QMForce_exposer.def( "__str__", &pvt_get_name); + QMForce_exposer.def( "__repr__", &pvt_get_name); } } diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp new file mode 100644 index 000000000..c512db19a --- /dev/null +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp @@ -0,0 +1,17 @@ +#include +#include + +#include "Base/convertproperty.hpp" +#include "SireOpenMM_properties.h" + +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "qmmm.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "qmmm.h" +void register_SireOpenMM_properties() +{ + register_property_container< SireOpenMM::QMEnginePtr, SireOpenMM::QMEngine >(); + register_property_container< SireOpenMM::QMEnginePtr, SireOpenMM::QMEngine >(); +} diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.h b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.h new file mode 100644 index 000000000..346789c91 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.h @@ -0,0 +1,6 @@ +#ifndef SireOpenMM_PROPERTIES_H +#define SireOpenMM_PROPERTIES_H + +void register_SireOpenMM_properties(); + +#endif diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index 53b5d8fa1..4145761c4 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -3,6 +3,7 @@ #include "SireOpenMM_registrars.h" +#include "qmmm.h" #include "emle.h" #include "lambdalever.h" #include "openmmmolecule.h" @@ -12,9 +13,13 @@ void register_SireOpenMM_objects() { + ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); + ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::EMLECallback >(); + ObjectRegistry::registerConverterFor< SireOpenMM::EMLEForce >(); ObjectRegistry::registerConverterFor< SireOpenMM::EMLEEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::EMLECallback >(); + ObjectRegistry::registerConverterFor< SireOpenMM::EMLEForce >(); ObjectRegistry::registerConverterFor< SireOpenMM::EMLEEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 8426ac8d7..e1ac8a459 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -11,12 +11,18 @@ #include "EMLEEngine.pypp.hpp" +#include "EMLEForce.pypp.hpp" + #include "LambdaLever.pypp.hpp" +#include "NullQMEngine.pypp.hpp" + #include "OpenMMMetaData.pypp.hpp" #include "PerturbableOpenMMMolecule.pypp.hpp" +#include "QMEngine.pypp.hpp" + #include "QMForce.pypp.hpp" #include "_SireOpenMM_free_functions.pypp.hpp" @@ -27,6 +33,8 @@ namespace bp = boost::python; #include "SireOpenMM_registrars.h" +#include "SireOpenMM_properties.h" + #include "./register_extras.h" BOOST_PYTHON_MODULE(_SireOpenMM){ @@ -36,16 +44,24 @@ BOOST_PYTHON_MODULE(_SireOpenMM){ register_EMLECallback_class(); - register_QMForce_class(); + register_QMEngine_class(); register_EMLEEngine_class(); + register_QMForce_class(); + + register_EMLEForce_class(); + register_LambdaLever_class(); + register_NullQMEngine_class(); + register_OpenMMMetaData_class(); register_PerturbableOpenMMMolecule_class(); + register_SireOpenMM_properties(); + SireOpenMM::register_extras(); register_free_functions(); diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index feb2f3d24..76dd8c72b 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -62,6 +62,12 @@ QMEngine::~QMEngine() { } +/** Return a null QM engine */ +const NullQMEngine &QMEngine::null() +{ + return *(create_shared_null()); +} + ///////// ///////// Implementation of NullQMEngine ///////// @@ -115,8 +121,8 @@ const char *NullQMEngine::what() const return NullQMEngine::typeName(); } -/** Return a null QM engine */ -const NullQMEngine &QMEngine::null() +/** Create a QM force object */ +QMForce *NullQMEngine::createForce() const { - return *(create_shared_null()); + std::runtime_error("NullQMEngine::createForce() called"); } diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index 3e0069c6a..f7108c1ad 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -75,11 +75,10 @@ namespace SireOpenMM //! Clone the QM engine. virtual QMEngine *clone() const = 0; - //! Get the name of the QM engine. - static const char *typeName(); - - //! Get the name of the QM engine. - const char *what() const; + static const char *typeName() + { + return "SireOpenMM::QMEngine"; + } //! Create a QM force object. virtual QMForce* createForce() const=0; diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index ac46b196a..96e1437e8 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -18,7 +18,7 @@ "PerturbableOpenMMMolecule", "OpenMMMetaData", "SOMMContext", - "QMForce", + "QMEngine", "EMLECallback", "EMLEEngine", ] @@ -98,7 +98,7 @@ def smarts_to_rdkit(*args, **kwargs): LambdaLever, PerturbableOpenMMMolecule, OpenMMMetaData, - QMForce, + QMEngine, EMLECallback, EMLEEngine, ) @@ -110,7 +110,7 @@ def smarts_to_rdkit(*args, **kwargs): LambdaLever, PerturbableOpenMMMolecule, OpenMMMetaData, - QMForce, + QMEngine, EMLECallback, EMLEEngine, ], From 071dc829d6ab23efb447b7e3111a66d8a958e309 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 13 Feb 2024 11:56:17 +0000 Subject: [PATCH 108/468] Throw invalid_operation error. --- wrapper/Convert/SireOpenMM/qmmm.cpp | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index 76dd8c72b..ddfbbe78a 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -28,6 +28,8 @@ #include "qmmm.h" +#include "SireError/errors.h" + #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -124,5 +126,5 @@ const char *NullQMEngine::what() const /** Create a QM force object */ QMForce *NullQMEngine::createForce() const { - std::runtime_error("NullQMEngine::createForce() called"); + throw SireError::invalid_operation(QObject::tr("NullQMEngine::createForce() called"), CODELOC); } From 27d10e9c96f67b8f448d56d2f416d488cbffec52 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 13 Feb 2024 11:58:13 +0000 Subject: [PATCH 109/468] Remove streaming operators. --- wrapper/Convert/SireOpenMM/qmmm.cpp | 30 ----------------------------- 1 file changed, 30 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index ddfbbe78a..227c92695 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -30,9 +30,6 @@ #include "SireError/errors.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" - using namespace SireBase; using namespace SireOpenMM; using namespace SireStream; @@ -74,33 +71,6 @@ const NullQMEngine &QMEngine::null() ///////// Implementation of NullQMEngine ///////// -static const RegisterMetaType r_nullqmengine; - -/** Serialise to a binary datastream */ -QDataStream &operator<<(QDataStream &ds, const NullQMEngine &qmengine) -{ - writeHeader(ds, r_nullqmengine, 1); - - ds << static_cast(qmengine); - - return ds; -} - -/** Extract from a binary datastream */ -QDataStream &operator>>(QDataStream &ds, NullQMEngine &qmengine) -{ - VersionID v = readHeader(ds, r_nullqmengine); - - if (v == 1) - { - ds >> static_cast(qmengine); - } - else - throw version_error(v, "1", r_nullqmengine, CODELOC); - - return ds; -} - /** Constructor */ NullQMEngine::NullQMEngine() : ConcreteProperty() { From cdf1dda12420c1f1c22d46d4aaea0c66240f98c8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 13 Feb 2024 12:04:04 +0000 Subject: [PATCH 110/468] Update EMLEEngine constructor. --- wrapper/Convert/SireOpenMM/emle.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 197729b29..00f498547 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -600,7 +600,7 @@ double EMLEForceImpl::computeForce( ///////// Implementation of EMLEEngine ///////// -EMLEEngine::EMLEEngine() +EMLEEngine::EMLEEngine() : ConcreteProperty() { } @@ -609,6 +609,7 @@ EMLEEngine::EMLEEngine( SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, double lambda) : + ConcreteProperty(), callback(py_object, "_sire_callback"), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), From e185e1b5a84d8f8a9781252fec72285b780efd62 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 13 Feb 2024 17:27:30 +0000 Subject: [PATCH 111/468] Adding a change to create_wrappers.py so that it (should!) automatically find the directory containing pyconfig.h --- wrapper/AutoGenerate/create_wrappers.py | 3 +- .../Convert/SireOpenMM/CMakeAutogenFile.txt | 14 ++++----- .../Convert/SireOpenMM/EMLECallback.pypp.cpp | 20 +++++++++++++ .../Convert/SireOpenMM/EMLEEngine.pypp.cpp | 2 +- wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp | 20 +++++++++++++ .../Convert/SireOpenMM/NullQMEngine.pypp.cpp | 16 +++------- wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp | 30 ++++--------------- wrapper/Convert/SireOpenMM/QMForce.pypp.cpp | 16 +++++++--- .../SireOpenMM/SireOpenMM_properties.cpp | 6 ++-- .../SireOpenMM/SireOpenMM_registrars.cpp | 6 ++-- wrapper/Convert/SireOpenMM/emle.h | 1 + ...less__OpenMM_scope_Vec3__greater_.pypp.cpp | 2 -- 12 files changed, 77 insertions(+), 59 deletions(-) diff --git a/wrapper/AutoGenerate/create_wrappers.py b/wrapper/AutoGenerate/create_wrappers.py index 679c0f429..ac616a517 100644 --- a/wrapper/AutoGenerate/create_wrappers.py +++ b/wrapper/AutoGenerate/create_wrappers.py @@ -743,6 +743,7 @@ def fixMB(mb): qtdir = "%s/../include/qt" % os.path.abspath(dir) boostdir = "%s/../include" % os.path.abspath(dir) + pydir = glob("%s/../include/python3*" % os.path.abspath(dir))[0] gsldir = boostdir openmm_include_dir = boostdir @@ -776,7 +777,7 @@ def fixMB(mb): qt_include_dirs = [] qt_include_dirs = [qtdir, "%s/QtCore" % qtdir] - boost_include_dirs = [boostdir] + boost_include_dirs = [boostdir, pydir] gsl_include_dirs = [gsldir] generator_path, generator_name = pygccxml.utils.find_xml_generator() diff --git a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt index 14b187087..d39bec456 100644 --- a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt +++ b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt @@ -1,15 +1,15 @@ # WARNING - AUTOGENERATED FILE - CONTENTS WILL BE OVERWRITTEN! set ( PYPP_SOURCES - LambdaLever.pypp.cpp - PerturbableOpenMMMolecule.pypp.cpp - QMEngine.pypp.cpp - EMLEForce.pypp.cpp - EMLEEngine.pypp.cpp - EMLECallback.pypp.cpp _SireOpenMM_free_functions.pypp.cpp + LambdaLever.pypp.cpp QMForce.pypp.cpp - vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp + EMLEEngine.pypp.cpp NullQMEngine.pypp.cpp + EMLEForce.pypp.cpp + vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp + EMLECallback.pypp.cpp + PerturbableOpenMMMolecule.pypp.cpp + QMEngine.pypp.cpp OpenMMMetaData.pypp.cpp SireOpenMM_properties.cpp SireOpenMM_registrars.cpp diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp index 17b138b8d..21e7619f4 100644 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp @@ -29,6 +29,26 @@ const char* pvt_get_name(const SireOpenMM::EMLECallback&){ return "SireOpenMM::E #include "Helpers/release_gil_policy.hpp" +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireVol/triclinicbox.h" + +#include "emle.h" + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireVol/triclinicbox.h" + +#include "emle.h" + +const char* pvt_get_name(const SireOpenMM::EMLECallback&){ return "SireOpenMM::EMLECallback";} + +#include "Helpers/release_gil_policy.hpp" + void register_EMLECallback_class(){ { //::SireOpenMM::EMLECallback diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp index 8285d72c6..f39dfd9ce 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp @@ -52,7 +52,7 @@ SireOpenMM::EMLEEngine __copy__(const SireOpenMM::EMLEEngine &other){ return Sir void register_EMLEEngine_class(){ { //::SireOpenMM::EMLEEngine - typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > EMLEEngine_exposer_t; + typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireOpenMM::QMEngine > > EMLEEngine_exposer_t; EMLEEngine_exposer_t EMLEEngine_exposer = EMLEEngine_exposer_t( "EMLEEngine", "", bp::init< >("Default constructor.") ); bp::scope EMLEEngine_scope( EMLEEngine_exposer ); EMLEEngine_exposer.def( bp::init< bp::api::object, bp::optional< SireUnits::Dimension::Length, int, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nAn EMLECalculator Python object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp index 8b10bcc4f..24915ad3e 100644 --- a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp @@ -29,6 +29,26 @@ const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLE #include "Helpers/release_gil_policy.hpp" +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireVol/triclinicbox.h" + +#include "emle.h" + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireVol/triclinicbox.h" + +#include "emle.h" + +const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLEForce";} + +#include "Helpers/release_gil_policy.hpp" + void register_EMLEForce_class(){ { //::SireOpenMM::EMLEForce diff --git a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp index 3f9770a74..d0f70f96b 100644 --- a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp @@ -7,15 +7,11 @@ namespace bp = boost::python; -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" @@ -23,15 +19,11 @@ namespace bp = boost::python; #include "Helpers/release_gil_policy.hpp" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" diff --git a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp index d95fa4f11..34000ac5b 100644 --- a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp @@ -7,15 +7,11 @@ namespace bp = boost::python; -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" @@ -23,15 +19,11 @@ namespace bp = boost::python; #include "Helpers/release_gil_policy.hpp" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" @@ -66,19 +58,7 @@ void register_QMEngine_class(){ "typeName" , typeName_function_value , bp::release_gil_policy() - , "Get the name of the QM engine." ); - - } - { //::SireOpenMM::QMEngine::what - - typedef char const * ( ::SireOpenMM::QMEngine::*what_function_type)( ) const; - what_function_type what_function_value( &::SireOpenMM::QMEngine::what ); - - QMEngine_exposer.def( - "what" - , what_function_value - , bp::release_gil_policy() - , "Get the name of the QM engine." ); + , "" ); } QMEngine_exposer.staticmethod( "null" ); diff --git a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp index fda73f29f..9f3b35c53 100644 --- a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp @@ -7,15 +7,23 @@ namespace bp = boost::python; -#include "SireStream/datastream.h" +#include "SireError/errors.h" -#include "SireStream/shareddatastream.h" +#include "qmmm.h" + +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" +const char* pvt_get_name(const SireOpenMM::QMForce&){ return "SireOpenMM::QMForce";} + +#include "Helpers/release_gil_policy.hpp" + +#include "SireError/errors.h" + +#include "qmmm.h" -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp index c512db19a..1bb490cf7 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp @@ -4,11 +4,9 @@ #include "Base/convertproperty.hpp" #include "SireOpenMM_properties.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" void register_SireOpenMM_properties() { diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index 4145761c4..e99002e94 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -3,16 +3,18 @@ #include "SireOpenMM_registrars.h" +#include "openmmmolecule.h" #include "qmmm.h" #include "emle.h" #include "lambdalever.h" -#include "openmmmolecule.h" #include "Helpers/objectregistry.hpp" void register_SireOpenMM_objects() { + ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::EMLECallback >(); @@ -23,8 +25,6 @@ void register_SireOpenMM_objects() ObjectRegistry::registerConverterFor< SireOpenMM::EMLEEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); - ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); - ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); } diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index ded7f971d..552219272 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -37,6 +37,7 @@ #endif #include "boost/python.hpp" + #include #include diff --git a/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp b/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp index 9a1052cec..d54d94310 100644 --- a/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp @@ -6,8 +6,6 @@ #include "boost/python/suite/indexing/vector_indexing_suite.hpp" #include "vector_less__OpenMM_scope_Vec3__greater_.pypp.hpp" -#include - namespace bp = boost::python; void register_vector_less__OpenMM_scope_Vec3__greater__class(){ From 31912f8f9f7220325218de62b0438b56cb9f6aff Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 13 Feb 2024 17:29:40 +0000 Subject: [PATCH 112/468] Revert "Update EMLEEngine constructor." This reverts commit cdf1dda12420c1f1c22d46d4aaea0c66240f98c8. --- wrapper/Convert/SireOpenMM/emle.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 00f498547..197729b29 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -600,7 +600,7 @@ double EMLEForceImpl::computeForce( ///////// Implementation of EMLEEngine ///////// -EMLEEngine::EMLEEngine() : ConcreteProperty() +EMLEEngine::EMLEEngine() { } @@ -609,7 +609,6 @@ EMLEEngine::EMLEEngine( SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, double lambda) : - ConcreteProperty(), callback(py_object, "_sire_callback"), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), From f8ac6657d2e9c10130c101d7a0abb1ca5c204fe4 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 13 Feb 2024 17:30:15 +0000 Subject: [PATCH 113/468] Reapply "Update EMLEEngine constructor." This reverts commit 31912f8f9f7220325218de62b0438b56cb9f6aff. --- wrapper/Convert/SireOpenMM/emle.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 197729b29..00f498547 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -600,7 +600,7 @@ double EMLEForceImpl::computeForce( ///////// Implementation of EMLEEngine ///////// -EMLEEngine::EMLEEngine() +EMLEEngine::EMLEEngine() : ConcreteProperty() { } @@ -609,6 +609,7 @@ EMLEEngine::EMLEEngine( SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, double lambda) : + ConcreteProperty(), callback(py_object, "_sire_callback"), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), From d019cab1406c093fce694d0a1e1613ac227ad0eb Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 13 Feb 2024 17:30:30 +0000 Subject: [PATCH 114/468] Revert "Adding a change to create_wrappers.py so that it (should!) automatically find the" This reverts commit e185e1b5a84d8f8a9781252fec72285b780efd62. --- wrapper/AutoGenerate/create_wrappers.py | 3 +- .../Convert/SireOpenMM/CMakeAutogenFile.txt | 14 ++++----- .../Convert/SireOpenMM/EMLECallback.pypp.cpp | 20 ------------- .../Convert/SireOpenMM/EMLEEngine.pypp.cpp | 2 +- wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp | 20 ------------- .../Convert/SireOpenMM/NullQMEngine.pypp.cpp | 16 +++++++--- wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp | 30 +++++++++++++++---- wrapper/Convert/SireOpenMM/QMForce.pypp.cpp | 16 +++------- .../SireOpenMM/SireOpenMM_properties.cpp | 6 ++-- .../SireOpenMM/SireOpenMM_registrars.cpp | 6 ++-- wrapper/Convert/SireOpenMM/emle.h | 1 - ...less__OpenMM_scope_Vec3__greater_.pypp.cpp | 2 ++ 12 files changed, 59 insertions(+), 77 deletions(-) diff --git a/wrapper/AutoGenerate/create_wrappers.py b/wrapper/AutoGenerate/create_wrappers.py index ac616a517..679c0f429 100644 --- a/wrapper/AutoGenerate/create_wrappers.py +++ b/wrapper/AutoGenerate/create_wrappers.py @@ -743,7 +743,6 @@ def fixMB(mb): qtdir = "%s/../include/qt" % os.path.abspath(dir) boostdir = "%s/../include" % os.path.abspath(dir) - pydir = glob("%s/../include/python3*" % os.path.abspath(dir))[0] gsldir = boostdir openmm_include_dir = boostdir @@ -777,7 +776,7 @@ def fixMB(mb): qt_include_dirs = [] qt_include_dirs = [qtdir, "%s/QtCore" % qtdir] - boost_include_dirs = [boostdir, pydir] + boost_include_dirs = [boostdir] gsl_include_dirs = [gsldir] generator_path, generator_name = pygccxml.utils.find_xml_generator() diff --git a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt index d39bec456..14b187087 100644 --- a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt +++ b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt @@ -1,15 +1,15 @@ # WARNING - AUTOGENERATED FILE - CONTENTS WILL BE OVERWRITTEN! set ( PYPP_SOURCES - _SireOpenMM_free_functions.pypp.cpp LambdaLever.pypp.cpp - QMForce.pypp.cpp - EMLEEngine.pypp.cpp - NullQMEngine.pypp.cpp - EMLEForce.pypp.cpp - vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp - EMLECallback.pypp.cpp PerturbableOpenMMMolecule.pypp.cpp QMEngine.pypp.cpp + EMLEForce.pypp.cpp + EMLEEngine.pypp.cpp + EMLECallback.pypp.cpp + _SireOpenMM_free_functions.pypp.cpp + QMForce.pypp.cpp + vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp + NullQMEngine.pypp.cpp OpenMMMetaData.pypp.cpp SireOpenMM_properties.cpp SireOpenMM_registrars.cpp diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp index 21e7619f4..17b138b8d 100644 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp @@ -29,26 +29,6 @@ const char* pvt_get_name(const SireOpenMM::EMLECallback&){ return "SireOpenMM::E #include "Helpers/release_gil_policy.hpp" -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -const char* pvt_get_name(const SireOpenMM::EMLECallback&){ return "SireOpenMM::EMLECallback";} - -#include "Helpers/release_gil_policy.hpp" - void register_EMLECallback_class(){ { //::SireOpenMM::EMLECallback diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp index f39dfd9ce..8285d72c6 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp @@ -52,7 +52,7 @@ SireOpenMM::EMLEEngine __copy__(const SireOpenMM::EMLEEngine &other){ return Sir void register_EMLEEngine_class(){ { //::SireOpenMM::EMLEEngine - typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireOpenMM::QMEngine > > EMLEEngine_exposer_t; + typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > EMLEEngine_exposer_t; EMLEEngine_exposer_t EMLEEngine_exposer = EMLEEngine_exposer_t( "EMLEEngine", "", bp::init< >("Default constructor.") ); bp::scope EMLEEngine_scope( EMLEEngine_exposer ); EMLEEngine_exposer.def( bp::init< bp::api::object, bp::optional< SireUnits::Dimension::Length, int, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nAn EMLECalculator Python object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp index 24915ad3e..8b10bcc4f 100644 --- a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp @@ -29,26 +29,6 @@ const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLE #include "Helpers/release_gil_policy.hpp" -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLEForce";} - -#include "Helpers/release_gil_policy.hpp" - void register_EMLEForce_class(){ { //::SireOpenMM::EMLEForce diff --git a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp index d0f70f96b..3f9770a74 100644 --- a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp @@ -7,11 +7,15 @@ namespace bp = boost::python; -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" @@ -19,11 +23,15 @@ namespace bp = boost::python; #include "Helpers/release_gil_policy.hpp" -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" diff --git a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp index 34000ac5b..d95fa4f11 100644 --- a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp @@ -7,11 +7,15 @@ namespace bp = boost::python; -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" @@ -19,11 +23,15 @@ namespace bp = boost::python; #include "Helpers/release_gil_policy.hpp" -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "SireError/errors.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" #include "qmmm.h" @@ -58,7 +66,19 @@ void register_QMEngine_class(){ "typeName" , typeName_function_value , bp::release_gil_policy() - , "" ); + , "Get the name of the QM engine." ); + + } + { //::SireOpenMM::QMEngine::what + + typedef char const * ( ::SireOpenMM::QMEngine::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::QMEngine::what ); + + QMEngine_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Get the name of the QM engine." ); } QMEngine_exposer.staticmethod( "null" ); diff --git a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp index 9f3b35c53..fda73f29f 100644 --- a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp @@ -7,23 +7,15 @@ namespace bp = boost::python; -#include "SireError/errors.h" +#include "SireStream/datastream.h" -#include "qmmm.h" - -#include "SireError/errors.h" +#include "SireStream/shareddatastream.h" #include "qmmm.h" -const char* pvt_get_name(const SireOpenMM::QMForce&){ return "SireOpenMM::QMForce";} - -#include "Helpers/release_gil_policy.hpp" - -#include "SireError/errors.h" - -#include "qmmm.h" +#include "SireStream/datastream.h" -#include "SireError/errors.h" +#include "SireStream/shareddatastream.h" #include "qmmm.h" diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp index 1bb490cf7..c512db19a 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp @@ -4,9 +4,11 @@ #include "Base/convertproperty.hpp" #include "SireOpenMM_properties.h" -#include "SireError/errors.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" #include "qmmm.h" -#include "SireError/errors.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" #include "qmmm.h" void register_SireOpenMM_properties() { diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index e99002e94..4145761c4 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -3,18 +3,16 @@ #include "SireOpenMM_registrars.h" -#include "openmmmolecule.h" #include "qmmm.h" #include "emle.h" #include "lambdalever.h" +#include "openmmmolecule.h" #include "Helpers/objectregistry.hpp" void register_SireOpenMM_objects() { - ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); - ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::EMLECallback >(); @@ -25,6 +23,8 @@ void register_SireOpenMM_objects() ObjectRegistry::registerConverterFor< SireOpenMM::EMLEEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); } diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 552219272..ded7f971d 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -37,7 +37,6 @@ #endif #include "boost/python.hpp" - #include #include diff --git a/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp b/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp index d54d94310..9a1052cec 100644 --- a/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp @@ -6,6 +6,8 @@ #include "boost/python/suite/indexing/vector_indexing_suite.hpp" #include "vector_less__OpenMM_scope_Vec3__greater_.pypp.hpp" +#include + namespace bp = boost::python; void register_vector_less__OpenMM_scope_Vec3__greater__class(){ From 12413115fcccf9eca17808b659ee63356d11d84f Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 13 Feb 2024 17:32:20 +0000 Subject: [PATCH 115/468] Added back code that auto-detects directory that contains pyconfig.h --- wrapper/AutoGenerate/create_wrappers.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wrapper/AutoGenerate/create_wrappers.py b/wrapper/AutoGenerate/create_wrappers.py index 679c0f429..ac616a517 100644 --- a/wrapper/AutoGenerate/create_wrappers.py +++ b/wrapper/AutoGenerate/create_wrappers.py @@ -743,6 +743,7 @@ def fixMB(mb): qtdir = "%s/../include/qt" % os.path.abspath(dir) boostdir = "%s/../include" % os.path.abspath(dir) + pydir = glob("%s/../include/python3*" % os.path.abspath(dir))[0] gsldir = boostdir openmm_include_dir = boostdir @@ -776,7 +777,7 @@ def fixMB(mb): qt_include_dirs = [] qt_include_dirs = [qtdir, "%s/QtCore" % qtdir] - boost_include_dirs = [boostdir] + boost_include_dirs = [boostdir, pydir] gsl_include_dirs = [gsldir] generator_path, generator_name = pygccxml.utils.find_xml_generator() From 89f0712bdb4fbe761679ba5fa89ccec41c98e0b9 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 13 Feb 2024 17:49:20 +0000 Subject: [PATCH 116/468] Updated create_wrappers so that it only exports a class once --- wrapper/AutoGenerate/create_wrappers.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/wrapper/AutoGenerate/create_wrappers.py b/wrapper/AutoGenerate/create_wrappers.py index ac616a517..5665cfc72 100644 --- a/wrapper/AutoGenerate/create_wrappers.py +++ b/wrapper/AutoGenerate/create_wrappers.py @@ -373,6 +373,8 @@ def call_with_released_gil(c, func_name): _call_with_release_gil(f) +all_exported_classes = {} + def export_class( mb, classname, aliases, includes, special_code, auto_str_function=True ): @@ -381,6 +383,12 @@ def export_class( supplied special code, and adding the header files in 'includes' to the generated C++""" + if classname in all_exported_classes: + # don't export twice! + return + + all_exported_classes[classname] = 1 + # find the class in the declarations c = find_class(mb, classname) From 4895424d7fbb7fcaa791d11a5cd49ee946ae9080 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Feb 2024 09:17:41 +0000 Subject: [PATCH 117/468] Update wrappers. --- .../Convert/SireOpenMM/EMLECallback.pypp.cpp | 2 - .../Convert/SireOpenMM/EMLEEngine.pypp.cpp | 22 --- wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp | 2 - .../Convert/SireOpenMM/LambdaLever.pypp.cpp | 22 --- .../Convert/SireOpenMM/NullQMEngine.pypp.cpp | 26 +--- .../SireOpenMM/OpenMMMetaData.pypp.cpp | 130 ------------------ .../PerturbableOpenMMMolecule.pypp.cpp | 110 --------------- wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp | 40 +----- wrapper/Convert/SireOpenMM/QMForce.pypp.cpp | 10 +- .../SireOpenMM/SireOpenMM_properties.cpp | 6 +- 10 files changed, 9 insertions(+), 361 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp index 17b138b8d..c464d95e3 100644 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp @@ -79,8 +79,6 @@ void register_EMLECallback_class(){ EMLECallback_exposer.def( "clone", &__copy__); EMLECallback_exposer.def( "__str__", &pvt_get_name); EMLECallback_exposer.def( "__repr__", &pvt_get_name); - EMLECallback_exposer.def( "__str__", &pvt_get_name); - EMLECallback_exposer.def( "__repr__", &pvt_get_name); } } diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp index 8285d72c6..5c19ad65a 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp @@ -29,26 +29,6 @@ SireOpenMM::EMLEEngine __copy__(const SireOpenMM::EMLEEngine &other){ return Sir #include "Helpers/release_gil_policy.hpp" -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -#include "Helpers/str.hpp" - -#include "Helpers/release_gil_policy.hpp" - void register_EMLEEngine_class(){ { //::SireOpenMM::EMLEEngine @@ -325,8 +305,6 @@ void register_EMLEEngine_class(){ EMLEEngine_exposer.def( "clone", &__copy__); EMLEEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::EMLEEngine > ); EMLEEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::EMLEEngine > ); - EMLEEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::EMLEEngine > ); - EMLEEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::EMLEEngine > ); } } diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp index 8b10bcc4f..ac3d6bd27 100644 --- a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp @@ -214,8 +214,6 @@ void register_EMLEForce_class(){ EMLEForce_exposer.def( "clone", &__copy__); EMLEForce_exposer.def( "__str__", &pvt_get_name); EMLEForce_exposer.def( "__repr__", &pvt_get_name); - EMLEForce_exposer.def( "__str__", &pvt_get_name); - EMLEForce_exposer.def( "__repr__", &pvt_get_name); } } diff --git a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp index 1e62d36ba..63204fe7c 100644 --- a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp @@ -29,26 +29,6 @@ SireOpenMM::LambdaLever __copy__(const SireOpenMM::LambdaLever &other){ return S #include "Helpers/release_gil_policy.hpp" -#include "SireCAS/values.h" - -#include "emle.h" - -#include "lambdalever.h" - -#include "tostring.h" - -#include "SireCAS/values.h" - -#include "emle.h" - -#include "lambdalever.h" - -#include "tostring.h" - -#include "Helpers/str.hpp" - -#include "Helpers/release_gil_policy.hpp" - void register_LambdaLever_class(){ { //::SireOpenMM::LambdaLever @@ -280,8 +260,6 @@ void register_LambdaLever_class(){ LambdaLever_exposer.def( "clone", &__copy__); LambdaLever_exposer.def( "__str__", &__str__< ::SireOpenMM::LambdaLever > ); LambdaLever_exposer.def( "__repr__", &__str__< ::SireOpenMM::LambdaLever > ); - LambdaLever_exposer.def( "__str__", &__str__< ::SireOpenMM::LambdaLever > ); - LambdaLever_exposer.def( "__repr__", &__str__< ::SireOpenMM::LambdaLever > ); } } diff --git a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp index 3f9770a74..990175cda 100644 --- a/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/NullQMEngine.pypp.cpp @@ -7,31 +7,11 @@ namespace bp = boost::python; -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "qmmm.h" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "qmmm.h" - -#include "Helpers/str.hpp" - -#include "Helpers/release_gil_policy.hpp" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" @@ -72,8 +52,6 @@ void register_NullQMEngine_class(){ NullQMEngine_exposer.staticmethod( "typeName" ); NullQMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::NullQMEngine > ); NullQMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::NullQMEngine > ); - NullQMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::NullQMEngine > ); - NullQMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::NullQMEngine > ); } } diff --git a/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp b/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp index 0751f7685..af8812d9d 100644 --- a/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp @@ -137,134 +137,6 @@ SireOpenMM::OpenMMMetaData __copy__(const SireOpenMM::OpenMMMetaData &other){ re #include "Helpers/release_gil_policy.hpp" -#include "SireBase/parallel.h" - -#include "SireBase/propertylist.h" - -#include "SireCAS/lambdaschedule.h" - -#include "SireError/errors.h" - -#include "SireMM/amberparams.h" - -#include "SireMM/atomljs.h" - -#include "SireMM/selectorbond.h" - -#include "SireMaths/vector.h" - -#include "SireMol/atomcharges.h" - -#include "SireMol/atomcoords.h" - -#include "SireMol/atomelements.h" - -#include "SireMol/atommasses.h" - -#include "SireMol/atomproperty.hpp" - -#include "SireMol/atomvelocities.h" - -#include "SireMol/bondid.h" - -#include "SireMol/bondorder.h" - -#include "SireMol/connectivity.h" - -#include "SireMol/core.h" - -#include "SireMol/moleditor.h" - -#include "SireMol/selectorm.hpp" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "SireSystem/forcefieldinfo.h" - -#include "SireUnits/units.h" - -#include "SireVol/periodicbox.h" - -#include "SireVol/triclinicbox.h" - -#include "openmmmolecule.h" - -#include "sire_openmm.h" - -#include "tostring.h" - -#include - -#include - -#include "SireBase/parallel.h" - -#include "SireBase/propertylist.h" - -#include "SireCAS/lambdaschedule.h" - -#include "SireError/errors.h" - -#include "SireMM/amberparams.h" - -#include "SireMM/atomljs.h" - -#include "SireMM/selectorbond.h" - -#include "SireMaths/vector.h" - -#include "SireMol/atomcharges.h" - -#include "SireMol/atomcoords.h" - -#include "SireMol/atomelements.h" - -#include "SireMol/atommasses.h" - -#include "SireMol/atomproperty.hpp" - -#include "SireMol/atomvelocities.h" - -#include "SireMol/bondid.h" - -#include "SireMol/bondorder.h" - -#include "SireMol/connectivity.h" - -#include "SireMol/core.h" - -#include "SireMol/moleditor.h" - -#include "SireMol/selectorm.hpp" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "SireSystem/forcefieldinfo.h" - -#include "SireUnits/units.h" - -#include "SireVol/periodicbox.h" - -#include "SireVol/triclinicbox.h" - -#include "openmmmolecule.h" - -#include "sire_openmm.h" - -#include "tostring.h" - -#include - -#include - -#include "Helpers/str.hpp" - -#include "Helpers/release_gil_policy.hpp" - void register_OpenMMMetaData_class(){ { //::SireOpenMM::OpenMMMetaData @@ -410,8 +282,6 @@ void register_OpenMMMetaData_class(){ OpenMMMetaData_exposer.def( "clone", &__copy__); OpenMMMetaData_exposer.def( "__str__", &__str__< ::SireOpenMM::OpenMMMetaData > ); OpenMMMetaData_exposer.def( "__repr__", &__str__< ::SireOpenMM::OpenMMMetaData > ); - OpenMMMetaData_exposer.def( "__str__", &__str__< ::SireOpenMM::OpenMMMetaData > ); - OpenMMMetaData_exposer.def( "__repr__", &__str__< ::SireOpenMM::OpenMMMetaData > ); } } diff --git a/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp b/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp index 37e354983..b24f08114 100644 --- a/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp @@ -117,114 +117,6 @@ SireOpenMM::PerturbableOpenMMMolecule __copy__(const SireOpenMM::PerturbableOpen #include "Helpers/release_gil_policy.hpp" -#include "SireBase/parallel.h" - -#include "SireBase/propertylist.h" - -#include "SireError/errors.h" - -#include "SireMM/amberparams.h" - -#include "SireMM/atomljs.h" - -#include "SireMM/selectorbond.h" - -#include "SireMM/twoatomfunctions.h" - -#include "SireMaths/vector.h" - -#include "SireMol/atomcharges.h" - -#include "SireMol/atomcoords.h" - -#include "SireMol/atomelements.h" - -#include "SireMol/atommasses.h" - -#include "SireMol/atomproperty.hpp" - -#include "SireMol/atomvelocities.h" - -#include "SireMol/bondid.h" - -#include "SireMol/bondorder.h" - -#include "SireMol/connectivity.h" - -#include "SireMol/core.h" - -#include "SireMol/moleditor.h" - -#include "SireUnits/units.h" - -#include "openmmmolecule.h" - -#include "tostring.h" - -#include - -#include - -#include - -#include - -#include "SireBase/parallel.h" - -#include "SireBase/propertylist.h" - -#include "SireError/errors.h" - -#include "SireMM/amberparams.h" - -#include "SireMM/atomljs.h" - -#include "SireMM/selectorbond.h" - -#include "SireMM/twoatomfunctions.h" - -#include "SireMaths/vector.h" - -#include "SireMol/atomcharges.h" - -#include "SireMol/atomcoords.h" - -#include "SireMol/atomelements.h" - -#include "SireMol/atommasses.h" - -#include "SireMol/atomproperty.hpp" - -#include "SireMol/atomvelocities.h" - -#include "SireMol/bondid.h" - -#include "SireMol/bondorder.h" - -#include "SireMol/connectivity.h" - -#include "SireMol/core.h" - -#include "SireMol/moleditor.h" - -#include "SireUnits/units.h" - -#include "openmmmolecule.h" - -#include "tostring.h" - -#include - -#include - -#include - -#include - -#include "Helpers/str.hpp" - -#include "Helpers/release_gil_policy.hpp" - void register_PerturbableOpenMMMolecule_class(){ { //::SireOpenMM::PerturbableOpenMMMolecule @@ -799,8 +691,6 @@ void register_PerturbableOpenMMMolecule_class(){ PerturbableOpenMMMolecule_exposer.def( "clone", &__copy__); PerturbableOpenMMMolecule_exposer.def( "__str__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > ); PerturbableOpenMMMolecule_exposer.def( "__repr__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > ); - PerturbableOpenMMMolecule_exposer.def( "__str__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > ); - PerturbableOpenMMMolecule_exposer.def( "__repr__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > ); } } diff --git a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp index d95fa4f11..d1656fbb5 100644 --- a/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMEngine.pypp.cpp @@ -7,31 +7,11 @@ namespace bp = boost::python; -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "qmmm.h" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "qmmm.h" - -#include "Helpers/str.hpp" - -#include "Helpers/release_gil_policy.hpp" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" @@ -66,27 +46,13 @@ void register_QMEngine_class(){ "typeName" , typeName_function_value , bp::release_gil_policy() - , "Get the name of the QM engine." ); - - } - { //::SireOpenMM::QMEngine::what - - typedef char const * ( ::SireOpenMM::QMEngine::*what_function_type)( ) const; - what_function_type what_function_value( &::SireOpenMM::QMEngine::what ); - - QMEngine_exposer.def( - "what" - , what_function_value - , bp::release_gil_policy() - , "Get the name of the QM engine." ); + , "" ); } QMEngine_exposer.staticmethod( "null" ); QMEngine_exposer.staticmethod( "typeName" ); QMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::QMEngine > ); QMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::QMEngine > ); - QMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::QMEngine > ); - QMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::QMEngine > ); } } diff --git a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp index fda73f29f..6988a0647 100644 --- a/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/QMForce.pypp.cpp @@ -7,15 +7,11 @@ namespace bp = boost::python; -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" @@ -44,8 +40,6 @@ void register_QMForce_class(){ } QMForce_exposer.def( "__str__", &pvt_get_name); QMForce_exposer.def( "__repr__", &pvt_get_name); - QMForce_exposer.def( "__str__", &pvt_get_name); - QMForce_exposer.def( "__repr__", &pvt_get_name); } } diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp index c512db19a..1bb490cf7 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_properties.cpp @@ -4,11 +4,9 @@ #include "Base/convertproperty.hpp" #include "SireOpenMM_properties.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" +#include "SireError/errors.h" #include "qmmm.h" void register_SireOpenMM_properties() { From 032634432760e28335e22c2ba89b7c8e540f660c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 15 Feb 2024 13:05:14 +0000 Subject: [PATCH 118/468] Need to use bond potentials for link atom calculation. --- src/sire/qm/_utils.py | 207 ++++++++++++++++++++++++++++++++++++------ 1 file changed, 177 insertions(+), 30 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 39a0fe5f1..6544514ef 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,6 +1,24 @@ def _check_charge(qm_atoms, map, tol=1e-6): """ Internal helper function to check that the QM region has integer charge. + + Parameters + ---------- + + qm_atoms: [sire.legacy.Mol.AtomIdx] + A list of QM atoms. + + map: sire.legacy.Base.PropertyMap + The property map for the molecule. + + tol: float + The tolerance for the charge check. + + Raises + ------ + + Exception + If the charge of the QM region is not an integer. """ import math as _math @@ -22,6 +40,19 @@ def _create_qm_mol_to_atoms(qm_atoms): """ Internal helper function to create a mapping between molecule numbers and a list of QM atoms. + + Parameters + ---------- + + qm_atoms: [sire.legacy.Mol.AtomIdx] + A list of QM atoms. + + Returns + ------- + + qm_mol_to_atoms: {int: [sire.legacy.Mol.AtomIdx]} + A dictionary with molecule numbers as keys and a list of QM atoms as + values. """ qm_mol_to_atoms = {} for atom in qm_atoms: @@ -34,9 +65,106 @@ def _create_qm_mol_to_atoms(qm_atoms): return qm_mol_to_atoms +def _check_qm_atom_bonds(mol, atom, qm_idxs, map): + """ + Internal helper function to check the bonding for QM atoms. + + Parameters + ---------- + + mol: sire.legacy.Mol.Mol + The molecule containing the QM atoms. + + atom: sire.legacy.Mol.Atom + The QM atom to check the bonding for. + + qm_idxs: [sire.legacy.Mol.AtomIdx] + The indices of the QM atoms. + + map: sire.legacy.Base.PropertyMap + The property map for the molecule. + + Returns + ------- + + mm_atoms: [sire.legacy.Mol.AtomIdx] + A list of MM atoms that are bonded to the QM atom. + + has_qm_bond: bool + A flag to indicate if the QM atom has a bond to another QM atom. + """ + + # Get the bonds for the molecule. + bonds = mol.property(map["bond"]).potentials() + + # Store the info for the molecule. + info = mol.info() + + # Store the cut-group atom index pair. + cg_atom_idx = info.cg_atom_idx(atom.index()) + + # Initialise a list to store the MM atoms. + mm_atoms = [] + + # A flag to indicate if the atom has a bond to another QM atom. + has_qm_bond = False + + # Loop over all of the bonds. + for bond in bonds: + # Get the indices of the atoms in the bond. + idx0 = bond.atom0() + idx1 = bond.atom1() + + # Work out which is the other atom in the bond. + if idx0 == cg_atom_idx: + idx = idx1 + elif idx1 == cg_atom_idx: + idx = idx0 + else: + continue + + # Convert to an atom index. + idx = mol.atom(idx).index() + + # The atom is not in the QM region. + if idx not in qm_idxs: + mm_atoms.append(idx) + else: + has_qm_bond = True + + return mm_atoms, has_qm_bond + + def _get_link_atoms(mols, qm_mol_to_atoms, map): """ Internal helper function to get a dictionary with link atoms for each QM atom. + + Parameters + ---------- + + mols: sire.legacy.System.System + The Sire system containing the QM atoms. + + qm_mol_to_atoms: {sire.legacy.Mol.MolNum: [sire.legacy.Mol.AtomIdx]} + A dictionary with molecule numbers as keys and a list of QM atoms as + values. + + map: sire.legacy.Base.PropertyMap + The property map for the system. + + Returns + + mm1_to_qm: {sire.legacy.Mol.AtomIdx: sire.legacy.Mol.AtomIdx} + A dictionary with link atoms as keys and QM atoms as values. + + mm1_to_mm2: {sire.legacy.Mol.AtomIdx: [sire.legacy.Mol.AtomIdx]} + A dictionary with link atoms as keys and a list of MM atoms as values. + + bond_scale_factors: {sire.legacy.Mol.AtomIdx: float} + A dictionary with link atoms as keys and bond scale factors as values. + + mm1_indices: [[sire.legacy.Mol.AtomIdx]] + A list of lists of MM1 atom indices. """ import warnings as _warnings @@ -90,32 +218,8 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): # Store the element of the atom. elem = atom.property(elem_prop) - # Get the bonds for the atom. - bonds = connectivity.get_bonds(idx) - - # A list to hold MM atoms involved in the bonds. - mm_bonds = [] - - # A flag to indicate if the atom has a bond to another QM atom. - has_qm_bond = False - - # Loop over the bonds and find the MM atoms. - for bond in bonds: - # Get the indices of the two atoms in the bond. - idx0 = bond.atom0() - idx1 = bond.atom1() - - # Work out which atom isn't the current QM atom. - if idx0 != idx: - bond_idx = idx0 - else: - bond_idx = idx1 - - # If the atom is not in the QM region, add it to the list. - if bond_idx not in qm_idxs: - mm_bonds.append(bond_idx) - else: - has_qm_bond = True + # Check the bonding for this atom. + mm_atoms, has_qm_bond = _check_qm_atom_bonds(qm_mol, atom, qm_idxs, map) # If there are no QM bonds for this atom, raise an exception. if not has_qm_bond: @@ -124,12 +228,12 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): ) # Store the list of MM atoms. - if len(mm_bonds) > 0: - if len(mm_bonds) > 1: + if len(mm_atoms) > 0: + if len(mm_atoms) > 1: raise Exception(f"QM atom {idx} has more than one MM bond!") else: # Get the element of the cut atom. - link_elem = qm_mol[mm_bonds[0]].property(elem_prop) + link_elem = qm_mol[mm_atoms[0]].property(elem_prop) # If the element is hydrogen, raise an exception. if elem == hydrogen: @@ -148,7 +252,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): ) # Store the link (MM1) atom. - mm1_atoms[idx] = mm_bonds[0] + mm1_atoms[idx] = mm_atoms[0] # Now work out the MM atoms that are bonded to the link atoms. (MM2 atoms.) mm2_atoms = {} @@ -287,6 +391,25 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): """ Internal helper function to create a merged molecule from the QM molecule. + + Parameters + ---------- + + qm_mol_to_atoms: {sire.legacy.Mol.MolNum: [sire.legacy.Mol.AtomIdx]} + A dictionary with molecule numbers as keys and a list of QM atoms as + values. + + mm1_indices: [[sire.legacy.Mol.AtomIdx]] + A list of lists of MM1 atom indices. + + map: sire.legacy.Base.PropertyMap + The property map for the system. + + Returns + ------- + + qm_mols: [sire.legacy.Mol.Mol] + A list of merged molecules. """ from ..legacy import CAS as _CAS @@ -496,6 +619,30 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_lengths, map): """ Internal helper function to configure a QM engine ready for dynamics. + + Parameters + ---------- + + engine: sire.legacy.QM.Engine + The QM engine to configure. + + mols: sire.legacy.System.System + The Sire system containing the QM atoms. + + qm_atoms: [sire.legacy.Mol.AtomIdx] + A list of QM atoms. + + mm1_to_qm: {sire.legacy.Mol.AtomIdx: sire.legacy.Mol.AtomIdx} + A dictionary with link atoms as keys and QM atoms as values. + + mm1_to_mm2: {sire.legacy.Mol.AtomIdx: [sire.legacy.Mol.AtomIdx]} + A dictionary with link atoms as keys and a list of MM atoms as values. + + bond_lengths: {sire.legacy.Mol.AtomIdx: float} + A dictionary with link atoms as keys and bond lengths as values. + + map: sire.legacy.Base.PropertyMap + The property map for the system. """ # Work out the indices of the QM atoms. From f9ec72d90db53514088affdf4a70dfafc82d5c8c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 16 Feb 2024 12:07:09 +0000 Subject: [PATCH 119/468] Switch to using info object. [ci skip] --- src/sire/qm/_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 6544514ef..201a1c077 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -124,7 +124,7 @@ def _check_qm_atom_bonds(mol, atom, qm_idxs, map): continue # Convert to an atom index. - idx = mol.atom(idx).index() + idx = info.atom_idx(idx) # The atom is not in the QM region. if idx not in qm_idxs: From 4e4bdccf706f9b9e40aea4606955c6a3cc8fa3a8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 16 Feb 2024 13:19:09 +0000 Subject: [PATCH 120/468] Fix types in docstrings. [ci skip] --- src/sire/qm/_utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 201a1c077..5279a6e0a 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -72,7 +72,7 @@ def _check_qm_atom_bonds(mol, atom, qm_idxs, map): Parameters ---------- - mol: sire.legacy.Mol.Mol + mol: sire.legacy.Mol.Molecule The molecule containing the QM atoms. atom: sire.legacy.Mol.Atom @@ -408,7 +408,7 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): Returns ------- - qm_mols: [sire.legacy.Mol.Mol] + qm_mols: [sire.legacy.Mol.Molecule] A list of merged molecules. """ From f5a307b204a4aa28e378bbdc8b9d4e76e94b7e87 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 18 Feb 2024 17:44:39 +0000 Subject: [PATCH 121/468] WIP - adding in mutate and merge functions to make it easier to use AtomMapping objects to mutate or merge molecules. --- corelib/src/libs/SireMol/atommapping.cpp | 9 ++ corelib/src/libs/SireMol/atommapping.h | 2 + corelib/src/libs/SireSystem/CMakeLists.txt | 4 + corelib/src/libs/SireSystem/merge.cpp | 48 ++++++ corelib/src/libs/SireSystem/merge.h | 50 ++++++ corelib/src/libs/SireSystem/mutate.cpp | 153 ++++++++++++++++++ corelib/src/libs/SireSystem/mutate.h | 50 ++++++ src/sire/morph/CMakeLists.txt | 2 + src/sire/morph/__init__.py | 10 ++ src/sire/morph/_merge.py | 19 +++ src/sire/morph/_mutate.py | 19 +++ wrapper/System/CMakeAutogenFile.txt | 76 ++++----- wrapper/System/SireSystem_registrars.cpp | 96 +++++------ .../System/_System_free_functions.pypp.cpp | 34 ++++ wrapper/System/active_headers.h | 2 + 15 files changed, 488 insertions(+), 86 deletions(-) create mode 100644 corelib/src/libs/SireSystem/merge.cpp create mode 100644 corelib/src/libs/SireSystem/merge.h create mode 100644 corelib/src/libs/SireSystem/mutate.cpp create mode 100644 corelib/src/libs/SireSystem/mutate.h create mode 100644 src/sire/morph/_merge.py create mode 100644 src/sire/morph/_mutate.py diff --git a/corelib/src/libs/SireMol/atommapping.cpp b/corelib/src/libs/SireMol/atommapping.cpp index be33f0329..9ecb1a354 100644 --- a/corelib/src/libs/SireMol/atommapping.cpp +++ b/corelib/src/libs/SireMol/atommapping.cpp @@ -265,6 +265,15 @@ AtomMapping AtomMapping::swap() const return AtomMapping(this->atms1, this->atms0); } +/** Return whether or not the forward mapping contains the + * passed atom - this returns true if mapping[atom] would + * return a valid atom + */ +bool AtomMapping::contains(const Atom &atom) const +{ + return this->atms0.contains(atom); +} + /** Map from 'atom' (which must be in the reference atoms) to * the corresponding atom in the mapped atoms */ Atom AtomMapping::map(const Atom &atom, bool find_all) const diff --git a/corelib/src/libs/SireMol/atommapping.h b/corelib/src/libs/SireMol/atommapping.h index 033e6fe41..3238ceb65 100644 --- a/corelib/src/libs/SireMol/atommapping.h +++ b/corelib/src/libs/SireMol/atommapping.h @@ -99,6 +99,8 @@ namespace SireMol bool isEmpty() const; + bool contains(const Atom &atom) const; + const SelectorM &atoms0() const; const SelectorM &atoms1() const; diff --git a/corelib/src/libs/SireSystem/CMakeLists.txt b/corelib/src/libs/SireSystem/CMakeLists.txt index b490c697c..422c36b11 100644 --- a/corelib/src/libs/SireSystem/CMakeLists.txt +++ b/corelib/src/libs/SireSystem/CMakeLists.txt @@ -32,6 +32,7 @@ set ( SIRESYSTEM_HEADERS geometrycomponent.h idassigner.h identityconstraint.h + merge.h moleculeconstraint.h monitorcomponent.h monitorcomponents.h @@ -41,6 +42,7 @@ set ( SIRESYSTEM_HEADERS monitormonitor.h monitorname.h monitorproperty.h + mutate.h perturbationconstraint.h polarisecharges.h spacewrapper.h @@ -77,6 +79,7 @@ set ( SIRESYSTEM_SOURCES geometrycomponent.cpp idassigner.cpp identityconstraint.cpp + merge.cpp moleculeconstraint.cpp monitorcomponent.cpp monitorcomponents.cpp @@ -84,6 +87,7 @@ set ( SIRESYSTEM_SOURCES monitoridentifier.cpp monitormonitor.cpp monitorproperty.cpp + mutate.cpp perturbationconstraint.cpp polarisecharges.cpp spacewrapper.cpp diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp new file mode 100644 index 000000000..a9f05d6df --- /dev/null +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -0,0 +1,48 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "SireSystem/merge.h" + +using namespace SireMol; +using namespace SireBase; + +namespace SireSystem +{ + /** + * @brief Merge function that combines multiple molecules into a single molecule. + * + * @param mols The AtomMapping object that contains the molecules to be merged. + * @param as_new_molecule Flag indicating whether the merged molecule should be created as a new molecule. + * @param map The PropertyMap object that contains additional properties for the merged molecule. + * @return The merged molecule. + */ + Molecule merge(const AtomMapping &mols, bool as_new_molecule, const PropertyMap &map) + { + return mols.atoms0().molecules()[0]; + } +} diff --git a/corelib/src/libs/SireSystem/merge.h b/corelib/src/libs/SireSystem/merge.h new file mode 100644 index 000000000..c12c0a2fb --- /dev/null +++ b/corelib/src/libs/SireSystem/merge.h @@ -0,0 +1,50 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIRESYSTEM_MERGE_H +#define SIRESYSTEM_MERGE_H + +#include "SireMol/atommapping.h" +#include "SireMol/molecule.h" + +#include "SireBase/propertymap.h" + +SIRE_BEGIN_HEADER + +namespace SireSystem +{ + SIRESYSTEM_EXPORT SireMol::Molecule merge(const SireMol::AtomMapping &mols, + bool as_new_molecule = true, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); +} + +SIRE_EXPOSE_FUNCTION(SireSystem::merge); + +SIRE_END_HEADER; + +#endif diff --git a/corelib/src/libs/SireSystem/mutate.cpp b/corelib/src/libs/SireSystem/mutate.cpp new file mode 100644 index 000000000..a1aeef4ec --- /dev/null +++ b/corelib/src/libs/SireSystem/mutate.cpp @@ -0,0 +1,153 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "SireSystem/mutate.h" + +#include "SireMol/moleditor.h" +#include "SireMol/core.h" + +#include "SireError/errors.h" + +using namespace SireMol; +using namespace SireBase; + +namespace SireSystem +{ + /** + * @brief Mutate function that transforms a molecule into a new molecule. + * + * @param mols The AtomMapping object that contains the molecule to be mutated. + * @param as_new_molecule Flag indicating whether the mutated molecule should be created as a new molecule. + * @param map The PropertyMap object that contains additional properties for the mutated molecule. + * @return The mutated molecule. + */ + Molecule mutate(const AtomMapping &mols, bool as_new_molecule, const PropertyMap &map) + { + if (mols.atoms0().molecules().count() != 1 or mols.atoms1().molecules().count() != 1) + { + throw SireError::incompatible_error(QObject::tr( + "The passed mapping must contain just a single molecule to be mutated."), + CODELOC); + } + + auto mol = MolStructureEditor(mols.atoms0().molecules()[0]); + + // we will look up from mol1 to mol0 + const auto swapped_mols = mols.swap(); + + // we will match residue by residue + auto residues1 = mols.atoms1().molecules()[0].residues(); + + Residue residue0; + ResStructureEditor res; + CGStructureEditor cg; + + for (int i = 0; i < residues1.count(); ++i) + { + const auto &residue1 = residues1(i); + const auto atoms1 = residue1.atoms(); + + QSet found_atoms; + found_atoms.reserve(atoms1.count()); + + for (int j = 0; j < atoms1.count(); ++j) + { + const auto &atom1 = atoms1(j); + + AtomStructureEditor atom; + + if (swapped_mols.contains(atom1)) + { + // update the existing atom + auto atom0 = swapped_mols[atom1]; + found_atoms.insert(atom0.index()); + + if (residue0.isNull()) + { + residue0 = atom0.residue(); + qDebug() << "MUTATING" << residue0.toString() << "TO" << residue1.toString(); + + // rename the residue in the new molecule (we keep the same residue number) + res = mol.residue(residue0.index()); + res.rename(residue1.name()); + cg = res.atom(0).cutGroup(); + } + else if (residue0 != atom0.residue()) + { + throw SireError::incompatible_error(QObject::tr( + "The atoms in the mapping must belong to the same residue. " + "Currently mapping the atoms in %1 to %2, but atom %3 belongs to %4.") + .arg(residue0.toString()) + .arg(residue1.toString()) + .arg(atom0.toString()) + .arg(atom0.residue().toString()), + CODELOC); + } + + qDebug() << "UPDATING" << atom0.toString() << "TO" << atom1.toString(); + + // rename the atom in the new molecule (we keep the same atom number) + atom = mol.atom(atom0.index()); + atom.rename(atom1.name()); + } + else + { + // add the new atom + qDebug() << "ADDING" << atom1.toString() << "TO" << residue0.toString(); + atom = cg.add(atom1.name()); + atom.reparent(residue0.index()); + + // calculate the coordinates of the new atom + } + } // for each atom in residue + + // find any atoms in the residue that weren't matched, and so need to be removed + for (int j = 0; j < residue0.atoms().count(); ++j) + { + const auto &atom0 = residue0.atoms()(j); + + if (not found_atoms.contains(atom0.index())) + { + qDebug() << "REMOVING" << atom0.toString(); + mol.atom(atom0.index()).remove(); + } + } + + } // for each residue + + if (as_new_molecule) + { + qDebug() << "RENUMBER"; + mol.renumber(); + } + + qDebug() << "COMMIT"; + return mol.commit(); + } + +} // namespace SireSystem diff --git a/corelib/src/libs/SireSystem/mutate.h b/corelib/src/libs/SireSystem/mutate.h new file mode 100644 index 000000000..9377e5b88 --- /dev/null +++ b/corelib/src/libs/SireSystem/mutate.h @@ -0,0 +1,50 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIRESYSTEM_MUTATE_H +#define SIRESYSTEM_MUTATE_H + +#include "SireMol/atommapping.h" +#include "SireMol/molecule.h" + +#include "SireBase/propertymap.h" + +SIRE_BEGIN_HEADER + +namespace SireSystem +{ + SIRESYSTEM_EXPORT SireMol::Molecule mutate(const SireMol::AtomMapping &mols, + bool as_new_molecule = true, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); +} + +SIRE_EXPOSE_FUNCTION(SireSystem::mutate); + +SIRE_END_HEADER; + +#endif diff --git a/src/sire/morph/CMakeLists.txt b/src/sire/morph/CMakeLists.txt index d0ce6a852..b4e0428f5 100644 --- a/src/sire/morph/CMakeLists.txt +++ b/src/sire/morph/CMakeLists.txt @@ -10,6 +10,8 @@ set ( SCRIPTS _alchemy.py _ghost_atoms.py _hmr.py + _merge.py + _mutate.py _pertfile.py _perturbation.py _repex.py diff --git a/src/sire/morph/__init__.py b/src/sire/morph/__init__.py index d0b26373d..0cc8be327 100644 --- a/src/sire/morph/__init__.py +++ b/src/sire/morph/__init__.py @@ -8,6 +8,9 @@ "extract_perturbed", "link_to_reference", "link_to_perturbed", + "match", + "merge", + "mutate", "zero_ghost_bonds", "zero_ghost_angles", "zero_ghost_torsions", @@ -25,6 +28,9 @@ zero_ghost_torsions, ) + +from .. import match_atoms as match + from ._ghost_atoms import shrink_ghost_atoms from ._repex import replica_exchange @@ -34,3 +40,7 @@ from ._alchemy import to_alchemlyb from ._pertfile import create_from_pertfile + +from ._merge import merge + +from ._mutate import mutate diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py new file mode 100644 index 000000000..8a5163f42 --- /dev/null +++ b/src/sire/morph/_merge.py @@ -0,0 +1,19 @@ +__all__ = ["merge"] + + +from ..mol import AtomMapping as _AtomMapping + + +def _merge(mapping: _AtomMapping, map=None): + from ..legacy.System import merge as _merge + + return _merge(mapping, map) + + +def merge(mol0, mol1, map=None): + mapping = _AtomMapping(mol0.atoms(), mol1.atoms()) + return _merge(mapping, map=map) + + +if not hasattr(_AtomMapping, "merge"): + _AtomMapping.merge = _merge diff --git a/src/sire/morph/_mutate.py b/src/sire/morph/_mutate.py new file mode 100644 index 000000000..fe2107a51 --- /dev/null +++ b/src/sire/morph/_mutate.py @@ -0,0 +1,19 @@ +__all__ = ["mutate"] + + +from ..mol import AtomMapping as _AtomMapping + + +def _mutate(mapping: _AtomMapping, map=None): + from ..legacy.System import mutate as _mutate + + return _mutate(mapping, map) + + +def mutate(mol0, mol1, map=None): + mapping = _AtomMapping(mol0.atoms(), mol1.atoms()) + return _mutate(mapping, map=map) + + +if not hasattr(_AtomMapping, "mutate"): + _AtomMapping.mutate = _mutate diff --git a/wrapper/System/CMakeAutogenFile.txt b/wrapper/System/CMakeAutogenFile.txt index 32c7048c6..3ddf80616 100644 --- a/wrapper/System/CMakeAutogenFile.txt +++ b/wrapper/System/CMakeAutogenFile.txt @@ -1,53 +1,53 @@ # WARNING - AUTOGENERATED FILE - CONTENTS WILL BE OVERWRITTEN! set ( PYPP_SOURCES - AngleComponent.pypp.cpp - AssignerGroup.pypp.cpp - ChargeConstraint.pypp.cpp - CheckPoint.pypp.cpp - CloseMols.pypp.cpp ComponentConstraint.pypp.cpp - Constraint.pypp.cpp - Constraints.pypp.cpp - DihedralComponent.pypp.cpp - DistanceComponent.pypp.cpp - DoubleDistanceComponent.pypp.cpp + TripleDistanceComponent.pypp.cpp EnergyMonitor.pypp.cpp - ForceFieldInfo.pypp.cpp - FreeEnergyMonitor.pypp.cpp - GeometryComponent.pypp.cpp - IDAndSet_MonitorID_.pypp.cpp - IDAndSet_SysID_.pypp.cpp - IDAssigner.pypp.cpp - IDOrSet_MonitorID_.pypp.cpp + PropertyConstraint.pypp.cpp + PolariseCharges.pypp.cpp + NullConstraint.pypp.cpp + Specify_MonitorID_.pypp.cpp + SpaceWrapper.pypp.cpp + WindowedComponent.pypp.cpp + CloseMols.pypp.cpp + CheckPoint.pypp.cpp + MonitorMonitor.pypp.cpp + MonitorIdx.pypp.cpp + DihedralComponent.pypp.cpp + System.pypp.cpp IDOrSet_SysID_.pypp.cpp - IdentityConstraint.pypp.cpp - MoleculeConstraint.pypp.cpp + DoubleDistanceComponent.pypp.cpp + Constraints.pypp.cpp + AssignerGroup.pypp.cpp + SysID.pypp.cpp MonitorComponent.pypp.cpp + ForceFieldInfo.pypp.cpp MonitorComponents.pypp.cpp MonitorID.pypp.cpp - MonitorIdx.pypp.cpp - MonitorMonitor.pypp.cpp - MonitorName.pypp.cpp - MonitorProperty.pypp.cpp - NullConstraint.pypp.cpp + IdentityConstraint.pypp.cpp + SystemMonitors.pypp.cpp + IDOrSet_MonitorID_.pypp.cpp + _System_free_functions.pypp.cpp + SysName.pypp.cpp NullMonitor.pypp.cpp PerturbationConstraint.pypp.cpp - PolariseCharges.pypp.cpp - PolariseChargesFF.pypp.cpp - PropertyConstraint.pypp.cpp - SpaceWrapper.pypp.cpp - Specify_MonitorID_.pypp.cpp - Specify_SysID_.pypp.cpp - SysID.pypp.cpp - SysIdx.pypp.cpp - SysName.pypp.cpp - System.pypp.cpp + MonitorName.pypp.cpp + FreeEnergyMonitor.pypp.cpp SystemMonitor.pypp.cpp - SystemMonitors.pypp.cpp - TripleDistanceComponent.pypp.cpp + SysIdx.pypp.cpp + MoleculeConstraint.pypp.cpp + AngleComponent.pypp.cpp + DistanceComponent.pypp.cpp VolMapMonitor.pypp.cpp - WindowedComponent.pypp.cpp - _System_free_functions.pypp.cpp + ChargeConstraint.pypp.cpp + Specify_SysID_.pypp.cpp + Constraint.pypp.cpp + IDAndSet_MonitorID_.pypp.cpp + GeometryComponent.pypp.cpp + IDAndSet_SysID_.pypp.cpp + MonitorProperty.pypp.cpp + PolariseChargesFF.pypp.cpp + IDAssigner.pypp.cpp SireSystem_containers.cpp SireSystem_properties.cpp SireSystem_registrars.cpp diff --git a/wrapper/System/SireSystem_registrars.cpp b/wrapper/System/SireSystem_registrars.cpp index 55a0a3e82..78bae3b56 100644 --- a/wrapper/System/SireSystem_registrars.cpp +++ b/wrapper/System/SireSystem_registrars.cpp @@ -3,83 +3,83 @@ #include "SireSystem_registrars.h" -#include "anglecomponent.h" +#include "systemmonitors.h" +#include "sysidentifier.h" #include "checkpoint.h" -#include "closemols.h" -#include "constraint.h" -#include "constraints.h" +#include "monitorcomponent.h" #include "dihedralcomponent.h" -#include "distancecomponent.h" #include "energymonitor.h" -#include "forcefieldinfo.h" -#include "freeenergymonitor.h" +#include "constraints.h" +#include "perturbationconstraint.h" +#include "sysidx.h" #include "idassigner.h" -#include "identityconstraint.h" -#include "monitorcomponent.h" +#include "spacewrapper.h" +#include "freeenergymonitor.h" +#include "forcefieldinfo.h" +#include "monitormonitor.h" #include "monitorcomponents.h" -#include "monitoridentifier.h" #include "monitoridx.h" -#include "monitormonitor.h" -#include "monitorname.h" -#include "monitorproperty.h" -#include "perturbationconstraint.h" -#include "polarisecharges.h" -#include "spacewrapper.h" -#include "sysidentifier.h" -#include "sysidx.h" +#include "identityconstraint.h" +#include "monitoridentifier.h" +#include "constraint.h" +#include "anglecomponent.h" #include "sysname.h" +#include "distancecomponent.h" +#include "closemols.h" #include "system.h" -#include "systemmonitor.h" -#include "systemmonitors.h" +#include "monitorproperty.h" #include "volmapmonitor.h" +#include "monitorname.h" +#include "polarisecharges.h" +#include "systemmonitor.h" #include "Helpers/objectregistry.hpp" void register_SireSystem_objects() { - ObjectRegistry::registerConverterFor< SireSystem::AngleComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::SystemMonitors >(); + ObjectRegistry::registerConverterFor< SireID::Specify >(); + ObjectRegistry::registerConverterFor< SireID::IDAndSet >(); + ObjectRegistry::registerConverterFor< SireID::IDOrSet >(); + ObjectRegistry::registerConverterFor< SireSystem::SysIdentifier >(); ObjectRegistry::registerConverterFor< SireSystem::CheckPoint >(); - ObjectRegistry::registerConverterFor< SireSystem::CloseMols >(); - ObjectRegistry::registerConverterFor< SireSystem::NullConstraint >(); - ObjectRegistry::registerConverterFor< SireSystem::PropertyConstraint >(); - ObjectRegistry::registerConverterFor< SireSystem::ComponentConstraint >(); - ObjectRegistry::registerConverterFor< SireSystem::WindowedComponent >(); - ObjectRegistry::registerConverterFor< SireSystem::Constraints >(); + ObjectRegistry::registerConverterFor< SireSystem::MonitorComponent >(); ObjectRegistry::registerConverterFor< SireSystem::DihedralComponent >(); - ObjectRegistry::registerConverterFor< SireSystem::DistanceComponent >(); - ObjectRegistry::registerConverterFor< SireSystem::DoubleDistanceComponent >(); - ObjectRegistry::registerConverterFor< SireSystem::TripleDistanceComponent >(); ObjectRegistry::registerConverterFor< SireSystem::EnergyMonitor >(); - ObjectRegistry::registerConverterFor< SireSystem::ForceFieldInfo >(); + ObjectRegistry::registerConverterFor< SireSystem::Constraints >(); + ObjectRegistry::registerConverterFor< SireSystem::PerturbationConstraint >(); + ObjectRegistry::registerConverterFor< SireSystem::SysIdx >(); + ObjectRegistry::registerConverterFor< SireSystem::IDAssigner >(); + ObjectRegistry::registerConverterFor< SireSystem::SpaceWrapper >(); ObjectRegistry::registerConverterFor< SireSystem::FreeEnergyMonitor >(); ObjectRegistry::registerConverterFor< SireSystem::AssignerGroup >(); - ObjectRegistry::registerConverterFor< SireSystem::IDAssigner >(); - ObjectRegistry::registerConverterFor< SireSystem::IdentityConstraint >(); - ObjectRegistry::registerConverterFor< SireSystem::MonitorComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::ForceFieldInfo >(); + ObjectRegistry::registerConverterFor< SireSystem::MonitorMonitor >(); ObjectRegistry::registerConverterFor< SireSystem::MonitorComponents >(); + ObjectRegistry::registerConverterFor< SireSystem::MonitorIdx >(); + ObjectRegistry::registerConverterFor< SireSystem::IdentityConstraint >(); ObjectRegistry::registerConverterFor< SireID::Specify >(); ObjectRegistry::registerConverterFor< SireID::IDAndSet >(); ObjectRegistry::registerConverterFor< SireID::IDOrSet >(); ObjectRegistry::registerConverterFor< SireSystem::MonitorIdentifier >(); - ObjectRegistry::registerConverterFor< SireSystem::MonitorIdx >(); - ObjectRegistry::registerConverterFor< SireSystem::MonitorMonitor >(); - ObjectRegistry::registerConverterFor< SireSystem::MonitorName >(); + ObjectRegistry::registerConverterFor< SireSystem::NullConstraint >(); + ObjectRegistry::registerConverterFor< SireSystem::PropertyConstraint >(); + ObjectRegistry::registerConverterFor< SireSystem::ComponentConstraint >(); + ObjectRegistry::registerConverterFor< SireSystem::WindowedComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::AngleComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::SysName >(); + ObjectRegistry::registerConverterFor< SireSystem::DistanceComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::DoubleDistanceComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::TripleDistanceComponent >(); + ObjectRegistry::registerConverterFor< SireSystem::CloseMols >(); + ObjectRegistry::registerConverterFor< SireSystem::System >(); ObjectRegistry::registerConverterFor< SireSystem::MonitorProperty >(); - ObjectRegistry::registerConverterFor< SireSystem::PerturbationConstraint >(); + ObjectRegistry::registerConverterFor< SireSystem::VolMapMonitor >(); + ObjectRegistry::registerConverterFor< SireSystem::MonitorName >(); ObjectRegistry::registerConverterFor< SireSystem::PolariseCharges >(); ObjectRegistry::registerConverterFor< SireSystem::PolariseChargesFF >(); - ObjectRegistry::registerConverterFor< SireSystem::SpaceWrapper >(); - ObjectRegistry::registerConverterFor< SireID::Specify >(); - ObjectRegistry::registerConverterFor< SireID::IDAndSet >(); - ObjectRegistry::registerConverterFor< SireID::IDOrSet >(); - ObjectRegistry::registerConverterFor< SireSystem::SysIdentifier >(); - ObjectRegistry::registerConverterFor< SireSystem::SysIdx >(); - ObjectRegistry::registerConverterFor< SireSystem::SysName >(); - ObjectRegistry::registerConverterFor< SireSystem::System >(); ObjectRegistry::registerConverterFor< SireSystem::NullMonitor >(); - ObjectRegistry::registerConverterFor< SireSystem::SystemMonitors >(); - ObjectRegistry::registerConverterFor< SireSystem::VolMapMonitor >(); } diff --git a/wrapper/System/_System_free_functions.pypp.cpp b/wrapper/System/_System_free_functions.pypp.cpp index 51ab0031a..a5e932938 100644 --- a/wrapper/System/_System_free_functions.pypp.cpp +++ b/wrapper/System/_System_free_functions.pypp.cpp @@ -721,6 +721,14 @@ namespace bp = boost::python; #include "create_test_molecule.h" +#include "merge.h" + +#include "merge.h" + +#include "mutate.h" + +#include "mutate.h" + void register_free_functions(){ { //::SireSystem::calculate_energy @@ -969,4 +977,30 @@ void register_free_functions(){ } + { //::SireSystem::merge + + typedef ::SireMol::Molecule ( *merge_function_type )( ::SireMol::AtomMapping const &,bool,::SireBase::PropertyMap const & ); + merge_function_type merge_function_value( &::SireSystem::merge ); + + bp::def( + "merge" + , merge_function_value + , ( bp::arg("mols"), bp::arg("as_new_molecule")=(bool)(true), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + + } + + { //::SireSystem::mutate + + typedef ::SireMol::Molecule ( *mutate_function_type )( ::SireMol::AtomMapping const &,bool,::SireBase::PropertyMap const & ); + mutate_function_type mutate_function_value( &::SireSystem::mutate ); + + bp::def( + "mutate" + , mutate_function_value + , ( bp::arg("mols"), bp::arg("as_new_molecule")=(bool)(true), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + + } + } diff --git a/wrapper/System/active_headers.h b/wrapper/System/active_headers.h index 923425a8b..38978d1e6 100644 --- a/wrapper/System/active_headers.h +++ b/wrapper/System/active_headers.h @@ -19,6 +19,7 @@ #include "geometrycomponent.h" #include "idassigner.h" #include "identityconstraint.h" +#include "merge.h" #include "moleculeconstraint.h" #include "monitorcomponent.h" #include "monitorcomponents.h" @@ -28,6 +29,7 @@ #include "monitormonitor.h" #include "monitorname.h" #include "monitorproperty.h" +#include "mutate.h" #include "perturbationconstraint.h" #include "polarisecharges.h" #include "spacewrapper.h" From 5a8d34ec6924c38cfb2fa5a45434d7318cf35083 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 19 Feb 2024 19:16:26 +0000 Subject: [PATCH 122/468] Added the ability in AtomMapping to store the atoms that weren't mapped at both end states. This means we now have the full information in this object to be able to properly construct merged and mutated molecules. Added a unit test to verify this works for mapping an alanine to a lysine within a protein (mapping works on subsets of molecules, meaning we can do a region of interest mapping and merge just be passing in the residues that we want to map - see test_match.py) Also, removed the C++ code for mutate as I realised that mutation is a merge followed by extracting the perturbed state. This is still a WIP - have got matching working, and have added the necessary info to AtomMapping. The next step is to fill in the C++ code for merge based on the information in AtomMapping. --- corelib/src/libs/SireMol/atommapping.cpp | 247 ++++++++++++++++-- corelib/src/libs/SireMol/atommapping.h | 78 +++++- corelib/src/libs/SireMol/selector.hpp | 35 ++- corelib/src/libs/SireMol/selectorm.hpp | 57 ++++ corelib/src/libs/SireSystem/CMakeLists.txt | 2 - corelib/src/libs/SireSystem/mutate.cpp | 153 ----------- corelib/src/libs/SireSystem/mutate.h | 50 ---- src/sire/_match.py | 11 +- src/sire/morph/_merge.py | 30 ++- src/sire/morph/_mutate.py | 31 ++- tests/morph/test_match.py | 78 ++++++ wrapper/Mol/AtomMapping.pypp.cpp | 113 +++++++- wrapper/Mol/MoleculeView.pypp.cpp | 2 +- wrapper/Mol/SelectorM_Atom_.pypp.cpp | 39 +++ wrapper/Mol/SelectorM_Chain_.pypp.cpp | 39 +++ wrapper/Mol/SelectorM_CutGroup_.pypp.cpp | 39 +++ wrapper/Mol/SelectorM_Residue_.pypp.cpp | 39 +++ wrapper/Mol/SelectorM_Segment_.pypp.cpp | 39 +++ wrapper/Mol/Selector_Atom_.pypp.cpp | 39 +++ wrapper/Mol/Selector_Chain_.pypp.cpp | 39 +++ wrapper/Mol/Selector_CutGroup_.pypp.cpp | 39 +++ wrapper/Mol/Selector_Residue_.pypp.cpp | 39 +++ wrapper/Mol/Selector_Segment_.pypp.cpp | 39 +++ .../System/_System_free_functions.pypp.cpp | 19 +- wrapper/System/active_headers.h | 1 - 25 files changed, 1026 insertions(+), 271 deletions(-) delete mode 100644 corelib/src/libs/SireSystem/mutate.cpp delete mode 100644 corelib/src/libs/SireSystem/mutate.h create mode 100644 tests/morph/test_match.py diff --git a/corelib/src/libs/SireMol/atommapping.cpp b/corelib/src/libs/SireMol/atommapping.cpp index 9ecb1a354..12c812cb7 100644 --- a/corelib/src/libs/SireMol/atommapping.cpp +++ b/corelib/src/libs/SireMol/atommapping.cpp @@ -41,11 +41,14 @@ static const RegisterMetaType r_mapping; QDataStream &operator<<(QDataStream &ds, const AtomMapping &mapping) { - writeHeader(ds, r_mapping, 1); + writeHeader(ds, r_mapping, 2); SharedDataStream sds(ds); sds << mapping.atms0 << mapping.atms1 + << mapping.orig_atms0 << mapping.orig_atms1 + << mapping.unmapped_atms0 << mapping.unmapped_atms1 + << mapping.map0 << mapping.map1 << static_cast(mapping); return ds; @@ -55,14 +58,29 @@ QDataStream &operator>>(QDataStream &ds, AtomMapping &mapping) { VersionID v = readHeader(ds, r_mapping); - if (v == 1) + if (v == 2) + { + SharedDataStream sds(ds); + + sds >> mapping.atms0 >> mapping.atms1 >> mapping.orig_atms0 >> mapping.orig_atms1 >> mapping.unmapped_atms0 >> mapping.unmapped_atms1 >> mapping.map0 >> mapping.map1 >> static_cast(mapping); + } + else if (v == 1) { SharedDataStream sds(ds); sds >> mapping.atms0 >> mapping.atms1 >> static_cast(mapping); + + mapping.map0 = PropertyMap(); + mapping.map1 = PropertyMap(); + + mapping.orig_atms0 = mapping.atms0; + mapping.orig_atms1 = mapping.atms1; + + mapping.unmapped_atms0.clear(); + mapping.unmapped_atms1.clear(); } else - throw version_error(v, "1", r_mapping, CODELOC); + throw version_error(v, "1,2", r_mapping, CODELOC); return ds; } @@ -72,9 +90,13 @@ AtomMapping::AtomMapping() : ConcreteProperty() } AtomMapping::AtomMapping(const SelectorM &atoms0, - const SelectorM &atoms1) + const SelectorM &atoms1, + const PropertyMap &m0, + const PropertyMap &m1) : ConcreteProperty(), - atms0(atoms0), atms1(atoms1) + atms0(atoms0), atms1(atoms1), + orig_atms0(atoms0), orig_atms1(atoms1), + map0(m0), map1(m1) { if (atms0.count() != atms1.count()) { @@ -88,22 +110,100 @@ AtomMapping::AtomMapping(const SelectorM &atoms0, } } -AtomMapping::AtomMapping(const MoleculeView &mol0, const MoleculeView &mol1) +AtomMapping::AtomMapping(const SelectorM &atoms0, + const SelectorM &atoms1, + const PropertyMap &map) + : ConcreteProperty() +{ + this->operator=(AtomMapping(atoms0, atoms1, map, map)); +} + +AtomMapping::AtomMapping(const MoleculeView &mol0, const MoleculeView &mol1, + const PropertyMap &map) + : ConcreteProperty() +{ + this->operator=(AtomMapping(SelectorM(mol0.atoms()), + SelectorM(mol1.atoms()), + map)); +} + +AtomMapping::AtomMapping(const MoleculeView &mol0, const MoleculeView &mol1, + const PropertyMap &m0, const PropertyMap &m1) : ConcreteProperty() { this->operator=(AtomMapping(SelectorM(mol0.atoms()), - SelectorM(mol1.atoms()))); + SelectorM(mol1.atoms()), + m0, m1)); +} + +AtomMapping::AtomMapping(const SelectorMol &mols0, const SelectorMol &mols1, + const PropertyMap &map) + : ConcreteProperty() +{ + this->operator=(AtomMapping(mols0.atoms(), mols1.atoms(), map)); +} + +AtomMapping::AtomMapping(const SelectorMol &mols0, const SelectorMol &mols1, + const PropertyMap &m0, const PropertyMap &m1) + : ConcreteProperty() +{ + this->operator=(AtomMapping(mols0.atoms(), mols1.atoms(), m0, m1)); +} + +AtomMapping::AtomMapping(const SelectorM &atoms0, + const SelectorM &atoms1, + const SelectorM &matched_atoms0, + const SelectorM &matched_atoms1, + const SireBase::PropertyMap &m0, + const SireBase::PropertyMap &m1) + : ConcreteProperty(), + atms0(matched_atoms0), atms1(matched_atoms1), + orig_atms0(atoms0), orig_atms1(atoms1), + map0(m0), map1(m1) +{ + if (atms0.count() != atms1.count()) + { + throw SireError::incompatible_error(QObject::tr( + "The number of atoms in 'atoms0' (%1) is not equal to the " + "number of atoms in 'atoms1' (%2). You can only create a " + "mapping if the number of atoms is the same.") + .arg(atms0.count()) + .arg(atms1.count()), + CODELOC); + } + + // find the indexes of missing atoms + for (int i = 0; i < atoms0.count(); ++i) + { + if (not atms0.contains(atoms0[i])) + this->unmapped_atms0.append(i); + } + + for (int i = 0; i < atoms1.count(); ++i) + { + if (not atms1.contains(atoms1[i])) + this->unmapped_atms1.append(i); + } } -AtomMapping::AtomMapping(const SelectorMol &mols0, const SelectorMol &mols1) +AtomMapping::AtomMapping(const SelectorM &atoms0, + const SelectorM &atoms1, + const SelectorM &matched_atoms0, + const SelectorM &matched_atoms1, + const SireBase::PropertyMap &map) : ConcreteProperty() { - this->operator=(AtomMapping(mols0.atoms(), mols1.atoms())); + this->operator=(AtomMapping(atoms0, atoms1, + matched_atoms0, matched_atoms1, + map, map)); } AtomMapping::AtomMapping(const AtomMapping &other) : ConcreteProperty(other), - atms0(other.atms0), atms1(other.atms1) + atms0(other.atms0), atms1(other.atms1), + orig_atms0(other.orig_atms0), orig_atms1(other.orig_atms1), + unmapped_atms0(other.unmapped_atms0), unmapped_atms1(other.unmapped_atms1), + map0(other.map0), map1(other.map1) { } @@ -117,6 +217,13 @@ AtomMapping &AtomMapping::operator=(const AtomMapping &other) { atms0 = other.atms0; atms1 = other.atms1; + orig_atms0 = other.orig_atms0; + orig_atms1 = other.orig_atms1; + unmapped_atms0 = other.unmapped_atms0; + unmapped_atms1 = other.unmapped_atms1; + map0 = other.map0; + map1 = other.map1; + Property::operator=(other); } @@ -125,7 +232,9 @@ AtomMapping &AtomMapping::operator=(const AtomMapping &other) bool AtomMapping::operator==(const AtomMapping &other) const { - return atms0 == other.atms0 and atms1 == other.atms1; + return orig_atms0 == other.orig_atms0 and orig_atms1 == other.orig_atms1 and + atms0 == other.atms0 and atms1 == other.atms1 and + map0 == other.map0 and map1 == other.map1; } bool AtomMapping::operator!=(const AtomMapping &other) const @@ -241,37 +350,59 @@ QString AtomMapping::toString() const } } - return QObject::tr("AtomMapping( size=%1\n%2\n)").arg(n).arg(parts.join("\n")); + return QObject::tr("AtomMapping( size=%1, unmapped0=%2, unmapped1=%3\n%4\n)") + .arg(n) + .arg(this->unmapped_atms0.count()) + .arg(this->unmapped_atms1.count()) + .arg(parts.join("\n")); } } -/** Return the reference atoms. We map from these atom to - * the mapped atoms (atoms1) */ +/** Return the original reference atoms. This is the collection of both + * mapped and unmapped reference atoms + */ const SelectorM &AtomMapping::atoms0() const { - return this->atms0; + return this->orig_atms0; } -/** Return the mapped atoms. We map from the reference atoms (atoms0) - * to these atoms. */ +/** Return the original mapped atoms. This is the collection of both + * mapped and unmapped mapped atoms + */ const SelectorM &AtomMapping::atoms1() const { - return this->atms1; + return this->orig_atms1; } /** Return an AtomMapping that swaps the reference and mapped atoms */ AtomMapping AtomMapping::swap() const { - return AtomMapping(this->atms1, this->atms0); + AtomMapping ret; + + ret.orig_atms0 = this->orig_atms1; + ret.orig_atms1 = this->orig_atms0; + + ret.atms0 = this->atms1; + ret.atms1 = this->atms0; + + ret.map0 = this->map1; + ret.map1 = this->map0; + + ret.unmapped_atms0 = this->unmapped_atms1; + ret.unmapped_atms1 = this->unmapped_atms0; + + return ret; } /** Return whether or not the forward mapping contains the - * passed atom - this returns true if mapping[atom] would - * return a valid atom + * passed atom - this returns true if the atom is contained + * in the original reference atoms, i.e. it doesn't guarantee + * that the atom is mapped. Use the 'isMapped' method to + * check if the atom is mapped. */ bool AtomMapping::contains(const Atom &atom) const { - return this->atms0.contains(atom); + return this->orig_atms0.contains(atom); } /** Map from 'atom' (which must be in the reference atoms) to @@ -478,3 +609,75 @@ SelectorM AtomMapping::find(const SelectorM &atoms, return filtered; } + +/** Return all of the reference atoms that have been mapped, + * in the same order as the mapped atoms they match with + */ +SelectorM AtomMapping::mappedAtoms0() const +{ + return this->atms0; +} + +/** Return all of the mapped atoms that have been mapped, + * in the same order as the reference atoms they match with + */ +SelectorM AtomMapping::mappedAtoms1() const +{ + return this->atms1; +} + +/** Return all of the reference atoms that haven't been mapped, + * in the same order as they appear in the original reference + */ +SelectorM AtomMapping::unmappedAtoms0() const +{ + if (this->unmapped_atms0.isEmpty()) + { + return SelectorM(); + } + else + { + return this->orig_atms0[this->unmapped_atms0]; + } +} + +/** Return all of the mapped atoms that haven't been mapped, + * in the same order as they appear in the original mapped atoms + */ +SelectorM AtomMapping::unmappedAtoms1() const +{ + if (this->unmapped_atms1.isEmpty()) + { + return SelectorM(); + } + else + { + return this->orig_atms1[this->unmapped_atms1]; + } +} + +/** Return whether or not the passed reference atom has been + * mapped to a mapped atom + */ +bool AtomMapping::isMapped(const Atom &atom) const +{ + return this->atms0.contains(atom); +} + +/** Return whether or not this mapping refers to only a single molecule */ +bool AtomMapping::isSingleMolecule() const +{ + return this->orig_atms0.isSingleMolecule() and this->orig_atms1.isSingleMolecule(); +} + +/** Assert that this mapping refers only to a single molecule */ +void AtomMapping::assertSingleMolecule() const +{ + if (not this->isSingleMolecule()) + { + throw SireError::incompatible_error(QObject::tr( + "This mapping refers to more than one molecule, and so " + "cannot be used in this context."), + CODELOC); + } +} diff --git a/corelib/src/libs/SireMol/atommapping.h b/corelib/src/libs/SireMol/atommapping.h index 3238ceb65..1e6ed728c 100644 --- a/corelib/src/libs/SireMol/atommapping.h +++ b/corelib/src/libs/SireMol/atommapping.h @@ -33,6 +33,8 @@ #include "atom.h" #include "selectorm.hpp" +#include "SireBase/propertymap.h" + SIRE_BEGIN_HEADER namespace SireMol @@ -61,13 +63,44 @@ namespace SireMol public: AtomMapping(); AtomMapping(const SelectorM &atoms0, - const SelectorM &atoms1); + const SelectorM &atoms1, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); + + AtomMapping(const SelectorM &atoms0, + const SelectorM &atoms1, + const SireBase::PropertyMap &map0, + const SireBase::PropertyMap &map1); AtomMapping(const MoleculeView &mol0, - const MoleculeView &mol1); + const MoleculeView &mol1, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); + + AtomMapping(const MoleculeView &mol0, + const MoleculeView &mol1, + const SireBase::PropertyMap &map0, + const SireBase::PropertyMap &map1); + + AtomMapping(const SelectorMol &mols0, + const SelectorMol &mols1, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); AtomMapping(const SelectorMol &mols0, - const SelectorMol &mols1); + const SelectorMol &mols1, + const SireBase::PropertyMap &map0, + const SireBase::PropertyMap &map1); + + AtomMapping(const SelectorM &atoms0, + const SelectorM &atoms1, + const SelectorM &matched_atoms0, + const SelectorM &matched_atoms1, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); + + AtomMapping(const SelectorM &atoms0, + const SelectorM &atoms1, + const SelectorM &matched_atoms0, + const SelectorM &matched_atoms1, + const SireBase::PropertyMap &map0, + const SireBase::PropertyMap &map1); AtomMapping(const AtomMapping &other); @@ -104,6 +137,18 @@ namespace SireMol const SelectorM &atoms0() const; const SelectorM &atoms1() const; + SelectorM mappedAtoms0() const; + SelectorM mappedAtoms1() const; + + SelectorM unmappedAtoms0() const; + SelectorM unmappedAtoms1() const; + + bool isMapped(const Atom &atom) const; + + bool isSingleMolecule() const; + + void assertSingleMolecule() const; + AtomMapping swap() const; Atom map(const Atom &atom, bool find_all = true) const; @@ -140,8 +185,33 @@ namespace SireMol /** The mapped atoms - we map from the reference atoms to these atoms */ SelectorM atms1; - }; + /** The original set of reference atoms - this includes the atoms + * in the same order as input, including any unmatched atoms + */ + SelectorM orig_atms0; + + /** The original set of mapped atoms - this includes the atoms + * in the same order as input, including any unmatched atoms + */ + SelectorM orig_atms1; + + /** The indexes of reference atoms in `orig_atms0` that are not mapped, + * in the order they appear in `orig_atms0` + */ + QList unmapped_atms0; + + /** The indexes of mapped atoms in `orig_atms1` that are not mapped, + * in the order they appear in `orig_atms1` + */ + QList unmapped_atms1; + + /** Property map for the reference atoms */ + SireBase::PropertyMap map0; + + /** Property map for the mapped atoms */ + SireBase::PropertyMap map1; + }; } Q_DECLARE_METATYPE(SireMol::AtomMapping) diff --git a/corelib/src/libs/SireMol/selector.hpp b/corelib/src/libs/SireMol/selector.hpp index 967c937d8..c9ee1256b 100644 --- a/corelib/src/libs/SireMol/selector.hpp +++ b/corelib/src/libs/SireMol/selector.hpp @@ -114,7 +114,7 @@ namespace SireMol { friend SIREMOL_EXPORT QDataStream & ::operator<< <>(QDataStream &, const Selector &); - friend SIREMOL_EXPORT QDataStream & ::operator>><>(QDataStream &, Selector &); + friend SIREMOL_EXPORT QDataStream & ::operator>> <>(QDataStream &, Selector &); public: Selector(); @@ -206,6 +206,12 @@ namespace SireMol bool isSelector() const; + void assertSingleMolecule() const; + + bool isSingleMolecule() const; + + Selector toSingleMolecule() const; + Selector add(const Selector &other) const; Selector add(const T &view) const; Selector add(const typename T::ID &id) const; @@ -1840,6 +1846,33 @@ namespace SireMol return this->operator()(0).metadataKeys(key); } + template + SIRE_OUTOFLINE_TEMPLATE bool Selector::isSingleMolecule() const + { + if (this->isEmpty()) + return false; + else + return true; + } + + template + SIRE_OUTOFLINE_TEMPLATE void Selector::assertSingleMolecule() const + { + if (not this->isSingleMolecule()) + { + throw SireMol::duplicate_molecule(QObject::tr( + "There are no molecules represented in this object."), + CODELOC); + } + } + + template + SIRE_OUTOFLINE_TEMPLATE Selector Selector::toSingleMolecule() const + { + this->assertSingleMolecule(); + return *this; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // end of namespace SireMol diff --git a/corelib/src/libs/SireMol/selectorm.hpp b/corelib/src/libs/SireMol/selectorm.hpp index 0859fc9c7..ebf13f37d 100644 --- a/corelib/src/libs/SireMol/selectorm.hpp +++ b/corelib/src/libs/SireMol/selectorm.hpp @@ -317,6 +317,11 @@ namespace SireMol QStringList metadataKeys() const; QStringList metadataKeys(const PropertyName &key) const; + bool isSingleMolecule() const; + void assertSingleMolecule() const; + + Selector toSingleMolecule() const; + template QList property(const PropertyName &key) const; @@ -2861,6 +2866,58 @@ namespace SireMol return ret; } + template + SIRE_OUTOFLINE_TEMPLATE bool SelectorM::isSingleMolecule() const + { + if (this->isEmpty()) + return false; + else if (this->vws.count() == 1) + return true; + else + { + MolNum molnum = this->vws.at(0).data().number(); + + for (int i = 1; i < this->vws.count(); ++i) + { + if (this->vws.at(i).data().number() != molnum) + return false; + } + + return true; + } + } + + template + SIRE_OUTOFLINE_TEMPLATE void SelectorM::assertSingleMolecule() const + { + if (not this->isSingleMolecule()) + { + throw SireMol::duplicate_molecule(QObject::tr( + "There is more than one molecule represented in this object. The molecules are: %1") + .arg(this->molecules().toString()), + CODELOC); + } + } + + template + SIRE_OUTOFLINE_TEMPLATE Selector SelectorM::toSingleMolecule() const + { + this->assertSingleMolecule(); + + if (this->vws.count() == 1) + return this->vws.at(0); + + // we need to combine the matching views together into a single view + Selector ret = this->vws.at(0); + + for (int i = 1; i < this->vws.count(); ++i) + { + ret += this->vws.at(i); + } + + return ret; + } + template SIRE_OUTOFLINE_TEMPLATE QString SelectorM::toString() const { diff --git a/corelib/src/libs/SireSystem/CMakeLists.txt b/corelib/src/libs/SireSystem/CMakeLists.txt index 422c36b11..6bdea44f9 100644 --- a/corelib/src/libs/SireSystem/CMakeLists.txt +++ b/corelib/src/libs/SireSystem/CMakeLists.txt @@ -42,7 +42,6 @@ set ( SIRESYSTEM_HEADERS monitormonitor.h monitorname.h monitorproperty.h - mutate.h perturbationconstraint.h polarisecharges.h spacewrapper.h @@ -87,7 +86,6 @@ set ( SIRESYSTEM_SOURCES monitoridentifier.cpp monitormonitor.cpp monitorproperty.cpp - mutate.cpp perturbationconstraint.cpp polarisecharges.cpp spacewrapper.cpp diff --git a/corelib/src/libs/SireSystem/mutate.cpp b/corelib/src/libs/SireSystem/mutate.cpp deleted file mode 100644 index a1aeef4ec..000000000 --- a/corelib/src/libs/SireSystem/mutate.cpp +++ /dev/null @@ -1,153 +0,0 @@ -/********************************************\ - * - * Sire - Molecular Simulation Framework - * - * Copyright (C) 2024 Christopher Woods - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - * - * For full details of the license please see the COPYING file - * that should have come with this distribution. - * - * You can contact the authors via the website - * at https://sire.openbiosim.org - * -\*********************************************/ - -#include "SireSystem/mutate.h" - -#include "SireMol/moleditor.h" -#include "SireMol/core.h" - -#include "SireError/errors.h" - -using namespace SireMol; -using namespace SireBase; - -namespace SireSystem -{ - /** - * @brief Mutate function that transforms a molecule into a new molecule. - * - * @param mols The AtomMapping object that contains the molecule to be mutated. - * @param as_new_molecule Flag indicating whether the mutated molecule should be created as a new molecule. - * @param map The PropertyMap object that contains additional properties for the mutated molecule. - * @return The mutated molecule. - */ - Molecule mutate(const AtomMapping &mols, bool as_new_molecule, const PropertyMap &map) - { - if (mols.atoms0().molecules().count() != 1 or mols.atoms1().molecules().count() != 1) - { - throw SireError::incompatible_error(QObject::tr( - "The passed mapping must contain just a single molecule to be mutated."), - CODELOC); - } - - auto mol = MolStructureEditor(mols.atoms0().molecules()[0]); - - // we will look up from mol1 to mol0 - const auto swapped_mols = mols.swap(); - - // we will match residue by residue - auto residues1 = mols.atoms1().molecules()[0].residues(); - - Residue residue0; - ResStructureEditor res; - CGStructureEditor cg; - - for (int i = 0; i < residues1.count(); ++i) - { - const auto &residue1 = residues1(i); - const auto atoms1 = residue1.atoms(); - - QSet found_atoms; - found_atoms.reserve(atoms1.count()); - - for (int j = 0; j < atoms1.count(); ++j) - { - const auto &atom1 = atoms1(j); - - AtomStructureEditor atom; - - if (swapped_mols.contains(atom1)) - { - // update the existing atom - auto atom0 = swapped_mols[atom1]; - found_atoms.insert(atom0.index()); - - if (residue0.isNull()) - { - residue0 = atom0.residue(); - qDebug() << "MUTATING" << residue0.toString() << "TO" << residue1.toString(); - - // rename the residue in the new molecule (we keep the same residue number) - res = mol.residue(residue0.index()); - res.rename(residue1.name()); - cg = res.atom(0).cutGroup(); - } - else if (residue0 != atom0.residue()) - { - throw SireError::incompatible_error(QObject::tr( - "The atoms in the mapping must belong to the same residue. " - "Currently mapping the atoms in %1 to %2, but atom %3 belongs to %4.") - .arg(residue0.toString()) - .arg(residue1.toString()) - .arg(atom0.toString()) - .arg(atom0.residue().toString()), - CODELOC); - } - - qDebug() << "UPDATING" << atom0.toString() << "TO" << atom1.toString(); - - // rename the atom in the new molecule (we keep the same atom number) - atom = mol.atom(atom0.index()); - atom.rename(atom1.name()); - } - else - { - // add the new atom - qDebug() << "ADDING" << atom1.toString() << "TO" << residue0.toString(); - atom = cg.add(atom1.name()); - atom.reparent(residue0.index()); - - // calculate the coordinates of the new atom - } - } // for each atom in residue - - // find any atoms in the residue that weren't matched, and so need to be removed - for (int j = 0; j < residue0.atoms().count(); ++j) - { - const auto &atom0 = residue0.atoms()(j); - - if (not found_atoms.contains(atom0.index())) - { - qDebug() << "REMOVING" << atom0.toString(); - mol.atom(atom0.index()).remove(); - } - } - - } // for each residue - - if (as_new_molecule) - { - qDebug() << "RENUMBER"; - mol.renumber(); - } - - qDebug() << "COMMIT"; - return mol.commit(); - } - -} // namespace SireSystem diff --git a/corelib/src/libs/SireSystem/mutate.h b/corelib/src/libs/SireSystem/mutate.h deleted file mode 100644 index 9377e5b88..000000000 --- a/corelib/src/libs/SireSystem/mutate.h +++ /dev/null @@ -1,50 +0,0 @@ -/********************************************\ - * - * Sire - Molecular Simulation Framework - * - * Copyright (C) 2024 Christopher Woods - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - * - * For full details of the license please see the COPYING file - * that should have come with this distribution. - * - * You can contact the authors via the website - * at https://sire.openbiosim.org - * -\*********************************************/ - -#ifndef SIRESYSTEM_MUTATE_H -#define SIRESYSTEM_MUTATE_H - -#include "SireMol/atommapping.h" -#include "SireMol/molecule.h" - -#include "SireBase/propertymap.h" - -SIRE_BEGIN_HEADER - -namespace SireSystem -{ - SIRESYSTEM_EXPORT SireMol::Molecule mutate(const SireMol::AtomMapping &mols, - bool as_new_molecule = true, - const SireBase::PropertyMap &map = SireBase::PropertyMap()); -} - -SIRE_EXPOSE_FUNCTION(SireSystem::mutate); - -SIRE_END_HEADER; - -#endif diff --git a/src/sire/_match.py b/src/sire/_match.py index c1405a7a7..34d197af9 100644 --- a/src/sire/_match.py +++ b/src/sire/_match.py @@ -13,9 +13,7 @@ def match_atoms(mol0, mol1, match_light_atoms=False, map0=None, map1=None): map0 = create_map(map0) map1 = create_map(map1) - matcher = AtomMCSMatcher( - match_light_atoms=match_light_atoms, verbose=False - ) + matcher = AtomMCSMatcher(match_light_atoms=match_light_atoms, verbose=False) m = matcher.match(mol0, map0, mol1, map1) @@ -27,5 +25,10 @@ def match_atoms(mol0, mol1, match_light_atoms=False, map0=None, map1=None): atoms1.append(atom1.value()) return AtomMapping( - mol0.molecule().atoms()[atoms0], mol1.molecule().atoms()[atoms1] + mol0.atoms(), + mol1.atoms(), + mol0.molecule().atoms()[atoms0], + mol1.molecule().atoms()[atoms1], + map0, + map1, ) diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py index 8a5163f42..09eac236d 100644 --- a/src/sire/morph/_merge.py +++ b/src/sire/morph/_merge.py @@ -4,15 +4,35 @@ from ..mol import AtomMapping as _AtomMapping -def _merge(mapping: _AtomMapping, map=None): +def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): from ..legacy.System import merge as _merge + from ..base import create_map - return _merge(mapping, map) + map = create_map(map) + return _merge(mapping, as_new_molecule=as_new_molecule, map=map) -def merge(mol0, mol1, map=None): - mapping = _AtomMapping(mol0.atoms(), mol1.atoms()) - return _merge(mapping, map=map) + +def merge(mol0, mol1, map=None, map0=None, map1=None): + from ..base import create_map + + map = create_map(map) + + if map0 is None: + map0 = map + else: + map0 = create_map(map, map0) + + if map1 is None: + map1 = map + else: + map1 = create_map(map, map1) + + from . import match + + mapping = match(mol0=mol0, mol1=mol1, match_light_atoms=True, map0=map0, map1=map1) + + return mapping.merge(as_new_molecule=True, map=map) if not hasattr(_AtomMapping, "merge"): diff --git a/src/sire/morph/_mutate.py b/src/sire/morph/_mutate.py index fe2107a51..859c1a1e3 100644 --- a/src/sire/morph/_mutate.py +++ b/src/sire/morph/_mutate.py @@ -4,15 +4,34 @@ from ..mol import AtomMapping as _AtomMapping -def _mutate(mapping: _AtomMapping, map=None): - from ..legacy.System import mutate as _mutate +def _mutate(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): + return ( + mapping.merge(as_new_molecule=as_new_molecule, map=map) + .morph(map=map) + .extract_perturbed(remove_ghosts=True) + ) - return _mutate(mapping, map) +def mutate(mol0, mol1, map=None, map0=None, map1=None): + from ..base import create_map -def mutate(mol0, mol1, map=None): - mapping = _AtomMapping(mol0.atoms(), mol1.atoms()) - return _mutate(mapping, map=map) + map = create_map(map) + + if map0 is None: + map0 = map + else: + map0 = create_map(map, map0) + + if map1 is None: + map1 = map + else: + map1 = create_map(map, map1) + + from . import match + + mapping = match(mol0=mol0, mol1=mol1, match_light_atoms=True, map0=map0, map1=map1) + + return mapping.mutate(as_new_molecule=True, map=map) if not hasattr(_AtomMapping, "mutate"): diff --git a/tests/morph/test_match.py b/tests/morph/test_match.py new file mode 100644 index 000000000..17921d644 --- /dev/null +++ b/tests/morph/test_match.py @@ -0,0 +1,78 @@ +import sire as sr + +import pytest + + +def test_match(kigaki_mols): + mols = kigaki_mols + + mol = mols.molecule("protein") + + ala = mol.residues("ALA")[1] + phe = mol.residues("LYS")[1] + + m = sr.morph.match(ala, phe, match_light_atoms=True) + + assert m is not None + + assert len(m) == 9 + + assert len(m.mapped_atoms0()) == 9 + assert len(m.mapped_atoms1()) == 9 + + assert len(m.unmapped_atoms0().atoms()) == 1 + assert len(m.unmapped_atoms1().atoms()) == 13 + + assert len(m.atoms0()) == len(ala.atoms()) + assert len(m.atoms1()) == len(phe.atoms()) + + assert m.atoms0() == ala.atoms() + assert m.atoms1() == phe.atoms() + + assert m.is_single_molecule() + + assert not m.is_empty() + + num_unmapped = 0 + + for atom in ala.atoms(): + assert m.contains(atom) + + if atom.element().num_protons() != 1: + assert m.is_mapped(atom) + + if not m.is_mapped(atom): + num_unmapped += 1 + + assert num_unmapped == 1 + + m = m.swap() + + assert len(m) == 9 + + assert len(m.mapped_atoms0()) == 9 + assert len(m.mapped_atoms1()) == 9 + + assert len(m.unmapped_atoms0().atoms()) == 13 + assert len(m.unmapped_atoms1().atoms()) == 1 + + assert len(m.atoms0()) == len(phe.atoms()) + assert len(m.atoms1()) == len(ala.atoms()) + + assert m.atoms0() == phe.atoms() + assert m.atoms1() == ala.atoms() + + assert m.is_single_molecule() + + assert not m.is_empty() + + num_unmapped = 0 + + for atom in phe.atoms(): + assert m.contains(atom) + + if not m.is_mapped(atom): + num_unmapped += 1 + + assert m.atoms0().to_single_molecule() == phe.atoms().to_single_molecule() + assert m.atoms1().to_single_molecule() == ala.atoms().to_single_molecule() diff --git a/wrapper/Mol/AtomMapping.pypp.cpp b/wrapper/Mol/AtomMapping.pypp.cpp index ba79bd2ba..8ca2c953d 100644 --- a/wrapper/Mol/AtomMapping.pypp.cpp +++ b/wrapper/Mol/AtomMapping.pypp.cpp @@ -34,10 +34,27 @@ void register_AtomMapping_class(){ typedef bp::class_< SireMol::AtomMapping, bp::bases< SireBase::Property > > AtomMapping_exposer_t; AtomMapping_exposer_t AtomMapping_exposer = AtomMapping_exposer_t( "AtomMapping", "This class holds the mapping from one set of atoms to another.\nThis enables you associate, atom by atom, atoms in one set to\natoms in another set. This is useful, e.g. for building perturbations,\nor for specifying mappings for alignments or RMSD calculations etc.\n", bp::init< >("") ); bp::scope AtomMapping_scope( AtomMapping_exposer ); - AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const & >(( bp::arg("atoms0"), bp::arg("atoms1") ), "") ); - AtomMapping_exposer.def( bp::init< SireMol::MoleculeView const &, SireMol::MoleculeView const & >(( bp::arg("mol0"), bp::arg("mol1") ), "") ); - AtomMapping_exposer.def( bp::init< SireMol::SelectorMol const &, SireMol::SelectorMol const & >(( bp::arg("mols0"), bp::arg("mols1") ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("atoms0"), bp::arg("atoms1"), bp::arg("map")=SireBase::PropertyMap() ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireBase::PropertyMap const &, SireBase::PropertyMap const & >(( bp::arg("atoms0"), bp::arg("atoms1"), bp::arg("map0"), bp::arg("map1") ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::MoleculeView const &, SireMol::MoleculeView const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("mol0"), bp::arg("mol1"), bp::arg("map")=SireBase::PropertyMap() ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::MoleculeView const &, SireMol::MoleculeView const &, SireBase::PropertyMap const &, SireBase::PropertyMap const & >(( bp::arg("mol0"), bp::arg("mol1"), bp::arg("map0"), bp::arg("map1") ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::SelectorMol const &, SireMol::SelectorMol const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("mols0"), bp::arg("mols1"), bp::arg("map")=SireBase::PropertyMap() ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::SelectorMol const &, SireMol::SelectorMol const &, SireBase::PropertyMap const &, SireBase::PropertyMap const & >(( bp::arg("mols0"), bp::arg("mols1"), bp::arg("map0"), bp::arg("map1") ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("atoms0"), bp::arg("atoms1"), bp::arg("matched_atoms0"), bp::arg("matched_atoms1"), bp::arg("map")=SireBase::PropertyMap() ), "") ); + AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireBase::PropertyMap const &, SireBase::PropertyMap const & >(( bp::arg("atoms0"), bp::arg("atoms1"), bp::arg("matched_atoms0"), bp::arg("matched_atoms1"), bp::arg("map0"), bp::arg("map1") ), "") ); AtomMapping_exposer.def( bp::init< SireMol::AtomMapping const & >(( bp::arg("other") ), "") ); + { //::SireMol::AtomMapping::assertSingleMolecule + + typedef void ( ::SireMol::AtomMapping::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::AtomMapping::assertSingleMolecule ); + + AtomMapping_exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "Assert that this mapping refers only to a single molecule" ); + + } { //::SireMol::AtomMapping::atoms0 typedef ::SireMol::SelectorM< SireMol::Atom > const & ( ::SireMol::AtomMapping::*atoms0_function_type)( ) const; @@ -47,7 +64,7 @@ void register_AtomMapping_class(){ "atoms0" , atoms0_function_value , bp::return_value_policy() - , "Return the reference atoms. We map from these atom to\n the mapped atoms (atoms1)" ); + , "Return the original reference atoms. This is the collection of both\n mapped and unmapped reference atoms\n" ); } { //::SireMol::AtomMapping::atoms1 @@ -59,7 +76,20 @@ void register_AtomMapping_class(){ "atoms1" , atoms1_function_value , bp::return_value_policy() - , "Return the mapped atoms. We map from the reference atoms (atoms0)\n to these atoms." ); + , "Return the original mapped atoms. This is the collection of both\n mapped and unmapped mapped atoms\n" ); + + } + { //::SireMol::AtomMapping::contains + + typedef bool ( ::SireMol::AtomMapping::*contains_function_type)( ::SireMol::Atom const & ) const; + contains_function_type contains_function_value( &::SireMol::AtomMapping::contains ); + + AtomMapping_exposer.def( + "contains" + , contains_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return whether or not the forward mapping contains the\n passed atom - this returns true if the atom is contained\n in the original reference atoms, i.e. it doesnt guarantee\n that the atom is mapped. Use the isMapped method to\n check if the atom is mapped.\n" ); } { //::SireMol::AtomMapping::count @@ -157,6 +187,31 @@ void register_AtomMapping_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomMapping::isMapped + + typedef bool ( ::SireMol::AtomMapping::*isMapped_function_type)( ::SireMol::Atom const & ) const; + isMapped_function_type isMapped_function_value( &::SireMol::AtomMapping::isMapped ); + + AtomMapping_exposer.def( + "isMapped" + , isMapped_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return whether or not the passed reference atom has been\n mapped to a mapped atom\n" ); + + } + { //::SireMol::AtomMapping::isSingleMolecule + + typedef bool ( ::SireMol::AtomMapping::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::AtomMapping::isSingleMolecule ); + + AtomMapping_exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "Return whether or not this mapping refers to only a single molecule" ); + } { //::SireMol::AtomMapping::map @@ -193,6 +248,30 @@ void register_AtomMapping_class(){ , ( bp::arg("atoms"), bp::arg("find_all")=(bool)(true) ) , "Map from the passed atoms (which must all be in the reference\n atoms) to the corresponding atoms in the mapped atoms. The\n mapped atoms will be returned in the same order as the\n reference atoms appeared in atoms. If find_all` is false\n then this will use null atoms in the map when the mapped\n atom cannot be found" ); + } + { //::SireMol::AtomMapping::mappedAtoms0 + + typedef ::SireMol::SelectorM< SireMol::Atom > ( ::SireMol::AtomMapping::*mappedAtoms0_function_type)( ) const; + mappedAtoms0_function_type mappedAtoms0_function_value( &::SireMol::AtomMapping::mappedAtoms0 ); + + AtomMapping_exposer.def( + "mappedAtoms0" + , mappedAtoms0_function_value + , bp::release_gil_policy() + , "Return all of the reference atoms that have been mapped,\n in the same order as the mapped atoms they match with\n" ); + + } + { //::SireMol::AtomMapping::mappedAtoms1 + + typedef ::SireMol::SelectorM< SireMol::Atom > ( ::SireMol::AtomMapping::*mappedAtoms1_function_type)( ) const; + mappedAtoms1_function_type mappedAtoms1_function_value( &::SireMol::AtomMapping::mappedAtoms1 ); + + AtomMapping_exposer.def( + "mappedAtoms1" + , mappedAtoms1_function_value + , bp::release_gil_policy() + , "Return all of the mapped atoms that have been mapped,\n in the same order as the reference atoms they match with\n" ); + } AtomMapping_exposer.def( bp::self != bp::self ); { //::SireMol::AtomMapping::operator= @@ -328,6 +407,30 @@ void register_AtomMapping_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomMapping::unmappedAtoms0 + + typedef ::SireMol::SelectorM< SireMol::Atom > ( ::SireMol::AtomMapping::*unmappedAtoms0_function_type)( ) const; + unmappedAtoms0_function_type unmappedAtoms0_function_value( &::SireMol::AtomMapping::unmappedAtoms0 ); + + AtomMapping_exposer.def( + "unmappedAtoms0" + , unmappedAtoms0_function_value + , bp::release_gil_policy() + , "Return all of the reference atoms that havent been mapped,\n in the same order as they appear in the original reference\n" ); + + } + { //::SireMol::AtomMapping::unmappedAtoms1 + + typedef ::SireMol::SelectorM< SireMol::Atom > ( ::SireMol::AtomMapping::*unmappedAtoms1_function_type)( ) const; + unmappedAtoms1_function_type unmappedAtoms1_function_value( &::SireMol::AtomMapping::unmappedAtoms1 ); + + AtomMapping_exposer.def( + "unmappedAtoms1" + , unmappedAtoms1_function_value + , bp::release_gil_policy() + , "Return all of the mapped atoms that havent been mapped,\n in the same order as they appear in the original mapped atoms\n" ); + } { //::SireMol::AtomMapping::what diff --git a/wrapper/Mol/MoleculeView.pypp.cpp b/wrapper/Mol/MoleculeView.pypp.cpp index 5dc1e56d6..42bbd56df 100644 --- a/wrapper/Mol/MoleculeView.pypp.cpp +++ b/wrapper/Mol/MoleculeView.pypp.cpp @@ -673,7 +673,7 @@ void register_MoleculeView_class(){ "extract" , extract_function_value , ( bp::arg("to_same_molecule")=(bool)(false) ) - , "" ); + , "Extract a copy of this view which contains only the currently\nselected atoms. This allows the used to pull out parts of a larger molecule,\ne.g. if they want to have only selected residues in a protein and do not\nwant to have to store or manipulate the larger protein molecule" ); } { //::SireMol::MoleculeView::getLink diff --git a/wrapper/Mol/SelectorM_Atom_.pypp.cpp b/wrapper/Mol/SelectorM_Atom_.pypp.cpp index 4946cdbf8..438ad2b83 100644 --- a/wrapper/Mol/SelectorM_Atom_.pypp.cpp +++ b/wrapper/Mol/SelectorM_Atom_.pypp.cpp @@ -137,6 +137,19 @@ void register_SelectorM_Atom__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Atom >::assertSingleMolecule + + typedef SireMol::SelectorM< SireMol::Atom > exported_class_t; + typedef void ( ::SireMol::SelectorM< SireMol::Atom >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Atom >::assertSingleMolecule ); + + SelectorM_Atom__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Atom >::atom @@ -886,6 +899,19 @@ void register_SelectorM_Atom__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Atom >::isSingleMolecule + + typedef SireMol::SelectorM< SireMol::Atom > exported_class_t; + typedef bool ( ::SireMol::SelectorM< SireMol::Atom >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Atom >::isSingleMolecule ); + + SelectorM_Atom__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Atom >::loadFrame @@ -1780,6 +1806,19 @@ void register_SelectorM_Atom__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Atom >::toSingleMolecule + + typedef SireMol::SelectorM< SireMol::Atom > exported_class_t; + typedef ::SireMol::Selector< SireMol::Atom > ( ::SireMol::SelectorM< SireMol::Atom >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Atom >::toSingleMolecule ); + + SelectorM_Atom__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Atom >::toString diff --git a/wrapper/Mol/SelectorM_Chain_.pypp.cpp b/wrapper/Mol/SelectorM_Chain_.pypp.cpp index a3eb7da28..3e143957f 100644 --- a/wrapper/Mol/SelectorM_Chain_.pypp.cpp +++ b/wrapper/Mol/SelectorM_Chain_.pypp.cpp @@ -137,6 +137,19 @@ void register_SelectorM_Chain__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Chain >::assertSingleMolecule + + typedef SireMol::SelectorM< SireMol::Chain > exported_class_t; + typedef void ( ::SireMol::SelectorM< SireMol::Chain >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Chain >::assertSingleMolecule ); + + SelectorM_Chain__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Chain >::atom @@ -886,6 +899,19 @@ void register_SelectorM_Chain__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Chain >::isSingleMolecule + + typedef SireMol::SelectorM< SireMol::Chain > exported_class_t; + typedef bool ( ::SireMol::SelectorM< SireMol::Chain >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Chain >::isSingleMolecule ); + + SelectorM_Chain__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Chain >::loadFrame @@ -1780,6 +1806,19 @@ void register_SelectorM_Chain__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Chain >::toSingleMolecule + + typedef SireMol::SelectorM< SireMol::Chain > exported_class_t; + typedef ::SireMol::Selector< SireMol::Chain > ( ::SireMol::SelectorM< SireMol::Chain >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Chain >::toSingleMolecule ); + + SelectorM_Chain__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Chain >::toString diff --git a/wrapper/Mol/SelectorM_CutGroup_.pypp.cpp b/wrapper/Mol/SelectorM_CutGroup_.pypp.cpp index a6ff84c4e..5cdba2efd 100644 --- a/wrapper/Mol/SelectorM_CutGroup_.pypp.cpp +++ b/wrapper/Mol/SelectorM_CutGroup_.pypp.cpp @@ -137,6 +137,19 @@ void register_SelectorM_CutGroup__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::CutGroup >::assertSingleMolecule + + typedef SireMol::SelectorM< SireMol::CutGroup > exported_class_t; + typedef void ( ::SireMol::SelectorM< SireMol::CutGroup >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::CutGroup >::assertSingleMolecule ); + + SelectorM_CutGroup__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::CutGroup >::atom @@ -886,6 +899,19 @@ void register_SelectorM_CutGroup__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::CutGroup >::isSingleMolecule + + typedef SireMol::SelectorM< SireMol::CutGroup > exported_class_t; + typedef bool ( ::SireMol::SelectorM< SireMol::CutGroup >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::CutGroup >::isSingleMolecule ); + + SelectorM_CutGroup__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::CutGroup >::loadFrame @@ -1780,6 +1806,19 @@ void register_SelectorM_CutGroup__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::CutGroup >::toSingleMolecule + + typedef SireMol::SelectorM< SireMol::CutGroup > exported_class_t; + typedef ::SireMol::Selector< SireMol::CutGroup > ( ::SireMol::SelectorM< SireMol::CutGroup >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::CutGroup >::toSingleMolecule ); + + SelectorM_CutGroup__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::CutGroup >::toString diff --git a/wrapper/Mol/SelectorM_Residue_.pypp.cpp b/wrapper/Mol/SelectorM_Residue_.pypp.cpp index 2d6beff74..84f98f675 100644 --- a/wrapper/Mol/SelectorM_Residue_.pypp.cpp +++ b/wrapper/Mol/SelectorM_Residue_.pypp.cpp @@ -137,6 +137,19 @@ void register_SelectorM_Residue__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Residue >::assertSingleMolecule + + typedef SireMol::SelectorM< SireMol::Residue > exported_class_t; + typedef void ( ::SireMol::SelectorM< SireMol::Residue >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Residue >::assertSingleMolecule ); + + SelectorM_Residue__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Residue >::atom @@ -886,6 +899,19 @@ void register_SelectorM_Residue__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Residue >::isSingleMolecule + + typedef SireMol::SelectorM< SireMol::Residue > exported_class_t; + typedef bool ( ::SireMol::SelectorM< SireMol::Residue >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Residue >::isSingleMolecule ); + + SelectorM_Residue__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Residue >::loadFrame @@ -1780,6 +1806,19 @@ void register_SelectorM_Residue__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Residue >::toSingleMolecule + + typedef SireMol::SelectorM< SireMol::Residue > exported_class_t; + typedef ::SireMol::Selector< SireMol::Residue > ( ::SireMol::SelectorM< SireMol::Residue >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Residue >::toSingleMolecule ); + + SelectorM_Residue__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Residue >::toString diff --git a/wrapper/Mol/SelectorM_Segment_.pypp.cpp b/wrapper/Mol/SelectorM_Segment_.pypp.cpp index e4c006625..481aa5986 100644 --- a/wrapper/Mol/SelectorM_Segment_.pypp.cpp +++ b/wrapper/Mol/SelectorM_Segment_.pypp.cpp @@ -137,6 +137,19 @@ void register_SelectorM_Segment__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Segment >::assertSingleMolecule + + typedef SireMol::SelectorM< SireMol::Segment > exported_class_t; + typedef void ( ::SireMol::SelectorM< SireMol::Segment >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Segment >::assertSingleMolecule ); + + SelectorM_Segment__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Segment >::atom @@ -886,6 +899,19 @@ void register_SelectorM_Segment__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Segment >::isSingleMolecule + + typedef SireMol::SelectorM< SireMol::Segment > exported_class_t; + typedef bool ( ::SireMol::SelectorM< SireMol::Segment >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Segment >::isSingleMolecule ); + + SelectorM_Segment__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Segment >::loadFrame @@ -1780,6 +1806,19 @@ void register_SelectorM_Segment__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SelectorM< SireMol::Segment >::toSingleMolecule + + typedef SireMol::SelectorM< SireMol::Segment > exported_class_t; + typedef ::SireMol::Selector< SireMol::Segment > ( ::SireMol::SelectorM< SireMol::Segment >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::SelectorM< SireMol::Segment >::toSingleMolecule ); + + SelectorM_Segment__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::SelectorM< SireMol::Segment >::toString diff --git a/wrapper/Mol/Selector_Atom_.pypp.cpp b/wrapper/Mol/Selector_Atom_.pypp.cpp index d1b7ff4e4..ca3dd7ee3 100644 --- a/wrapper/Mol/Selector_Atom_.pypp.cpp +++ b/wrapper/Mol/Selector_Atom_.pypp.cpp @@ -125,6 +125,19 @@ void register_Selector_Atom__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Atom >::assertSingleMolecule + + typedef SireMol::Selector< SireMol::Atom > exported_class_t; + typedef void ( ::SireMol::Selector< SireMol::Atom >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::Selector< SireMol::Atom >::assertSingleMolecule ); + + Selector_Atom__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Atom >::contains @@ -442,6 +455,19 @@ void register_Selector_Atom__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Atom >::isSingleMolecule + + typedef SireMol::Selector< SireMol::Atom > exported_class_t; + typedef bool ( ::SireMol::Selector< SireMol::Atom >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::Selector< SireMol::Atom >::isSingleMolecule ); + + Selector_Atom__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Atom >::metadataKeys @@ -1036,6 +1062,19 @@ void register_Selector_Atom__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Atom >::toSingleMolecule + + typedef SireMol::Selector< SireMol::Atom > exported_class_t; + typedef ::SireMol::Selector< SireMol::Atom > ( ::SireMol::Selector< SireMol::Atom >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::Selector< SireMol::Atom >::toSingleMolecule ); + + Selector_Atom__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Atom >::toString diff --git a/wrapper/Mol/Selector_Chain_.pypp.cpp b/wrapper/Mol/Selector_Chain_.pypp.cpp index eb96863df..36bb2dc7d 100644 --- a/wrapper/Mol/Selector_Chain_.pypp.cpp +++ b/wrapper/Mol/Selector_Chain_.pypp.cpp @@ -117,6 +117,19 @@ void register_Selector_Chain__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Chain >::assertSingleMolecule + + typedef SireMol::Selector< SireMol::Chain > exported_class_t; + typedef void ( ::SireMol::Selector< SireMol::Chain >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::Selector< SireMol::Chain >::assertSingleMolecule ); + + Selector_Chain__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Chain >::contains @@ -434,6 +447,19 @@ void register_Selector_Chain__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Chain >::isSingleMolecule + + typedef SireMol::Selector< SireMol::Chain > exported_class_t; + typedef bool ( ::SireMol::Selector< SireMol::Chain >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::Selector< SireMol::Chain >::isSingleMolecule ); + + Selector_Chain__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Chain >::metadataKeys @@ -1028,6 +1054,19 @@ void register_Selector_Chain__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Chain >::toSingleMolecule + + typedef SireMol::Selector< SireMol::Chain > exported_class_t; + typedef ::SireMol::Selector< SireMol::Chain > ( ::SireMol::Selector< SireMol::Chain >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::Selector< SireMol::Chain >::toSingleMolecule ); + + Selector_Chain__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Chain >::toString diff --git a/wrapper/Mol/Selector_CutGroup_.pypp.cpp b/wrapper/Mol/Selector_CutGroup_.pypp.cpp index d31875923..62449a5b9 100644 --- a/wrapper/Mol/Selector_CutGroup_.pypp.cpp +++ b/wrapper/Mol/Selector_CutGroup_.pypp.cpp @@ -117,6 +117,19 @@ void register_Selector_CutGroup__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::CutGroup >::assertSingleMolecule + + typedef SireMol::Selector< SireMol::CutGroup > exported_class_t; + typedef void ( ::SireMol::Selector< SireMol::CutGroup >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::Selector< SireMol::CutGroup >::assertSingleMolecule ); + + Selector_CutGroup__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::CutGroup >::contains @@ -434,6 +447,19 @@ void register_Selector_CutGroup__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::CutGroup >::isSingleMolecule + + typedef SireMol::Selector< SireMol::CutGroup > exported_class_t; + typedef bool ( ::SireMol::Selector< SireMol::CutGroup >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::Selector< SireMol::CutGroup >::isSingleMolecule ); + + Selector_CutGroup__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::CutGroup >::metadataKeys @@ -1028,6 +1054,19 @@ void register_Selector_CutGroup__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::CutGroup >::toSingleMolecule + + typedef SireMol::Selector< SireMol::CutGroup > exported_class_t; + typedef ::SireMol::Selector< SireMol::CutGroup > ( ::SireMol::Selector< SireMol::CutGroup >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::Selector< SireMol::CutGroup >::toSingleMolecule ); + + Selector_CutGroup__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::CutGroup >::toString diff --git a/wrapper/Mol/Selector_Residue_.pypp.cpp b/wrapper/Mol/Selector_Residue_.pypp.cpp index edb91a1b1..0919f52c7 100644 --- a/wrapper/Mol/Selector_Residue_.pypp.cpp +++ b/wrapper/Mol/Selector_Residue_.pypp.cpp @@ -119,6 +119,19 @@ void register_Selector_Residue__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Residue >::assertSingleMolecule + + typedef SireMol::Selector< SireMol::Residue > exported_class_t; + typedef void ( ::SireMol::Selector< SireMol::Residue >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::Selector< SireMol::Residue >::assertSingleMolecule ); + + Selector_Residue__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Residue >::contains @@ -436,6 +449,19 @@ void register_Selector_Residue__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Residue >::isSingleMolecule + + typedef SireMol::Selector< SireMol::Residue > exported_class_t; + typedef bool ( ::SireMol::Selector< SireMol::Residue >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::Selector< SireMol::Residue >::isSingleMolecule ); + + Selector_Residue__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Residue >::metadataKeys @@ -1030,6 +1056,19 @@ void register_Selector_Residue__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Residue >::toSingleMolecule + + typedef SireMol::Selector< SireMol::Residue > exported_class_t; + typedef ::SireMol::Selector< SireMol::Residue > ( ::SireMol::Selector< SireMol::Residue >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::Selector< SireMol::Residue >::toSingleMolecule ); + + Selector_Residue__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Residue >::toString diff --git a/wrapper/Mol/Selector_Segment_.pypp.cpp b/wrapper/Mol/Selector_Segment_.pypp.cpp index 2da624c09..13a5159d7 100644 --- a/wrapper/Mol/Selector_Segment_.pypp.cpp +++ b/wrapper/Mol/Selector_Segment_.pypp.cpp @@ -113,6 +113,19 @@ void register_Selector_Segment__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Segment >::assertSingleMolecule + + typedef SireMol::Selector< SireMol::Segment > exported_class_t; + typedef void ( ::SireMol::Selector< SireMol::Segment >::*assertSingleMolecule_function_type)( ) const; + assertSingleMolecule_function_type assertSingleMolecule_function_value( &::SireMol::Selector< SireMol::Segment >::assertSingleMolecule ); + + Selector_Segment__exposer.def( + "assertSingleMolecule" + , assertSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Segment >::contains @@ -430,6 +443,19 @@ void register_Selector_Segment__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Segment >::isSingleMolecule + + typedef SireMol::Selector< SireMol::Segment > exported_class_t; + typedef bool ( ::SireMol::Selector< SireMol::Segment >::*isSingleMolecule_function_type)( ) const; + isSingleMolecule_function_type isSingleMolecule_function_value( &::SireMol::Selector< SireMol::Segment >::isSingleMolecule ); + + Selector_Segment__exposer.def( + "isSingleMolecule" + , isSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Segment >::metadataKeys @@ -1024,6 +1050,19 @@ void register_Selector_Segment__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Selector< SireMol::Segment >::toSingleMolecule + + typedef SireMol::Selector< SireMol::Segment > exported_class_t; + typedef ::SireMol::Selector< SireMol::Segment > ( ::SireMol::Selector< SireMol::Segment >::*toSingleMolecule_function_type)( ) const; + toSingleMolecule_function_type toSingleMolecule_function_value( &::SireMol::Selector< SireMol::Segment >::toSingleMolecule ); + + Selector_Segment__exposer.def( + "toSingleMolecule" + , toSingleMolecule_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Selector< SireMol::Segment >::toString diff --git a/wrapper/System/_System_free_functions.pypp.cpp b/wrapper/System/_System_free_functions.pypp.cpp index a5e932938..372b00b7c 100644 --- a/wrapper/System/_System_free_functions.pypp.cpp +++ b/wrapper/System/_System_free_functions.pypp.cpp @@ -721,13 +721,11 @@ namespace bp = boost::python; #include "create_test_molecule.h" -#include "merge.h" +#include "SireSystem/merge.h" #include "merge.h" -#include "mutate.h" - -#include "mutate.h" +#include "merge.h" void register_free_functions(){ @@ -990,17 +988,4 @@ void register_free_functions(){ } - { //::SireSystem::mutate - - typedef ::SireMol::Molecule ( *mutate_function_type )( ::SireMol::AtomMapping const &,bool,::SireBase::PropertyMap const & ); - mutate_function_type mutate_function_value( &::SireSystem::mutate ); - - bp::def( - "mutate" - , mutate_function_value - , ( bp::arg("mols"), bp::arg("as_new_molecule")=(bool)(true), bp::arg("map")=SireBase::PropertyMap() ) - , "" ); - - } - } diff --git a/wrapper/System/active_headers.h b/wrapper/System/active_headers.h index 38978d1e6..a532f983f 100644 --- a/wrapper/System/active_headers.h +++ b/wrapper/System/active_headers.h @@ -29,7 +29,6 @@ #include "monitormonitor.h" #include "monitorname.h" #include "monitorproperty.h" -#include "mutate.h" #include "perturbationconstraint.h" #include "polarisecharges.h" #include "spacewrapper.h" From 326032a7343bb0beff9403f2ae46f2f6e0172c69 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 20 Feb 2024 18:16:42 +0000 Subject: [PATCH 123/468] Added quick functions to get and set the expression used for the potential energy of internal terms via the Cursor --- doc/source/changelog.rst | 4 + src/sire/mol/_cursor.py | 157 +++++++++++++++++++++++---------------- 2 files changed, 97 insertions(+), 64 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 3db7a65de..7fe293b04 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -108,6 +108,10 @@ organisation on `GitHub `__. * Preserve user atom names when writing to PDB format. +* Updated the :class:`~sire.mol.Cursor` so that it is easier to get and + set the expression used for the potential energy (using the + ``get_potential`` and ``set_potential`` functions). + * Fixed compile error using Python 3.12. This fixes issue #147. * Optimised the OpenMM minimisation code and making it more robust. diff --git a/src/sire/mol/_cursor.py b/src/sire/mol/_cursor.py index d332d922c..26e88d1eb 100644 --- a/src/sire/mol/_cursor.py +++ b/src/sire/mol/_cursor.py @@ -46,9 +46,7 @@ def __init__(self, molecule=None, map=None): try: connectivity = hunter(self.molecule, self.map) - self.molecule.set_property( - self.connectivity_property, connectivity - ) + self.molecule.set_property(self.connectivity_property, connectivity) self.connectivity = connectivity.edit() except Exception as e: from ..utils import Console @@ -373,9 +371,7 @@ def get_length(map=None): map = self._d.merge(map) return self.view().length(map=map) - def set_length( - value, anchor=None, weighting=None, auto_align=True, map=None - ): + def set_length(value, anchor=None, weighting=None, auto_align=True, map=None): """Set the length of the bond being edited by this cursor to 'value'. This should be either a length unit, or a float (in which case it is converted into a value with default @@ -481,12 +477,34 @@ def change_length( return self + def get_potential(map=None): + """Return the energy expression for this bond""" + map = self._d.merge(map) + return self._d.molecule.property(map[self.type()]).get(self.id()) + + def set_potential(value, map=None): + """Set the energy expression for this bond to 'value'""" + from ..cas import Expression + + map = self._d.merge(map) + + internals = self._d.molecule.property(map[self.type()]) + internals.set(self.id(), Expression(value)) + + self._d.molecule.set_property(map[self.type()], internals) + + self._update() + + return self + self.length = get_length self.set_length = set_length self.change_length = change_length self.measure = get_length self.set_measure = set_length self.change_measure = change_length + self.get_potential = get_potential + self.set_potential = set_potential def _add_angle_functions(self): """Internal function used to add member functions that are @@ -624,9 +642,7 @@ def change_size( if move_all and self.is_dihedral(): from . import BondID - center_bond = BondID( - self._internal.atom1(), self._internal.atom2() - ) + center_bond = BondID(self._internal.atom1(), self._internal.atom2()) moved = view.move().change(center_bond, delta, map) else: moved = view.move().change(self._internal, delta, map) @@ -637,12 +653,35 @@ def change_size( self._d.molecule = moved.commit().molecule().edit() self._update() + def get_potential(map=None): + """Return the energy expression for this internal""" + map = self._d.merge(map) + return self._d.molecule.property(map[self.type()]).get(self.id()) + + def set_potential(value, map=None): + """Set the energy expression for this internal to 'value'""" + from ..cas import Expression + + map = self._d.merge(map) + print(map) + + internals = self._d.molecule.property(map[self.type()]) + internals.set(self.id(), Expression(value)) + + self._d.molecule.set_property(map[self.type()], internals) + + self._update() + + return self + self.size = get_size self.set_size = set_size self.change_size = change_size self.measure = get_size self.set_measure = set_size self.change_measure = change_size + self.get_potential = get_potential + self.set_potential = set_potential def _add_extra_functions(self): """Internal function that adds additional functions to this @@ -929,8 +968,7 @@ def residue(self, i=None): return c except Exception: raise TypeError( - f"There is no residue that contains {self.type()}:" - f"{self.id()}" + f"There is no residue that contains {self.type()}:" f"{self.id()}" ) self._update() @@ -957,8 +995,7 @@ def chain(self, i=None): return c except Exception: raise TypeError( - f"There is no chain that contains {self.type()}:" - f"{self.id()}" + f"There is no chain that contains {self.type()}:" f"{self.id()}" ) self._update() @@ -985,8 +1022,7 @@ def segment(self, i=None): return c except Exception: raise TypeError( - f"There is no segment that contains {self.type()}:" - f"{self.id()}" + f"There is no segment that contains {self.type()}:" f"{self.id()}" ) self._update() @@ -1019,6 +1055,12 @@ def bond(self, *args, **kwargs): c._internal = bond.id() c._add_extra_functions() + if "map" in kwargs: + raise ValueError( + "The 'map' parameter is not allowed when creating a " + "Cursor for a bond" + ) + return c def angle(self, *args, **kwargs): @@ -1031,6 +1073,12 @@ def angle(self, *args, **kwargs): c._internal = angle.id() c._add_extra_functions() + if "map" in kwargs: + raise ValueError( + "The 'map' parameter is not allowed when creating a " + "Cursor for an angle" + ) + return c def dihedral(self, *args, **kwargs): @@ -1043,6 +1091,12 @@ def dihedral(self, *args, **kwargs): c._internal = dihedral.id() c._add_extra_functions() + if "map" in kwargs: + raise ValueError( + "The 'map' parameter is not allowed when creating a " + "Cursor for a dihedral" + ) + return c def improper(self, *args, **kwargs): @@ -1055,6 +1109,12 @@ def improper(self, *args, **kwargs): c._internal = improper.id() c._add_extra_functions() + if "map" in kwargs: + raise ValueError( + "The 'map' parameter is not allowed when creating a " + "Cursor for an improper" + ) + return c def parent(self): @@ -1115,8 +1175,7 @@ def get_name(self): if self.is_internal(): raise TypeError( - "An internal (bond/angle/dihedral/improper) does not have " - "a name!" + "An internal (bond/angle/dihedral/improper) does not have " "a name!" ) return self._view.name().value() @@ -1127,8 +1186,7 @@ def set_name(self, name): if self.is_internal(): raise TypeError( - "An internal (bond/angle/dihedral/improper) does not have " - "a name!" + "An internal (bond/angle/dihedral/improper) does not have " "a name!" ) # get the type right... @@ -1151,8 +1209,7 @@ def get_number(self): if self.is_internal(): raise TypeError( - "An internal (bond/angle/dihedral/improper) does not have " - "a number!" + "An internal (bond/angle/dihedral/improper) does not have " "a number!" ) try: @@ -1166,8 +1223,7 @@ def set_number(self, number): if self.is_internal(): raise TypeError( - "An internal (bond/angle/dihedral/improper) does not have " - "a number!" + "An internal (bond/angle/dihedral/improper) does not have " "a number!" ) try: @@ -1188,8 +1244,7 @@ def get_index(self): if self.is_internal(): raise TypeError( - "An internal (bond/angle/dihedral/improper) does not have " - "an index!" + "An internal (bond/angle/dihedral/improper) does not have " "an index!" ) return self._view.index().value() @@ -1427,9 +1482,7 @@ def items(self): items = [] for key in keys: - items.append( - (key, self._d.connectivity.property(self._internal, key)) - ) + items.append((key, self._d.connectivity.property(self._internal, key))) else: keys = self._view.property_keys() items = [] @@ -1503,9 +1556,7 @@ def make_whole(self, center=None, map=None): else: from ..maths import Vector - view = ( - view.move().make_whole(center=Vector(center), map=map).commit() - ) + view = view.move().make_whole(center=Vector(center), map=map).commit() self._d.molecule = view.molecule().edit() self._update() @@ -1654,9 +1705,7 @@ def __init__(self, parent: Cursor, cursors: _List[Cursor], view): raise TypeError(f"{c} must be a Cursor object!") if c._d is not parent._d: - raise ValueError( - "The list of cursors must be created from the parent!" - ) + raise ValueError("The list of cursors must be created from the parent!") self._parent = parent self._cursors = cursors @@ -1785,9 +1834,7 @@ def get_lengths(map=None): return lengths - def set_lengths( - values, anchor=None, weighting=None, auto_align=True, map=None - ): + def set_lengths(values, anchor=None, weighting=None, auto_align=True, map=None): """ Set the lengths of the bonds being edited by this cursor to the specified @@ -1858,9 +1905,7 @@ def set_lengths( self._update() return self - def set_length( - value, anchor=None, weighting=None, auto_align=True, map=None - ): + def set_length(value, anchor=None, weighting=None, auto_align=True, map=None): """Set all bonds edited by this cursor to the supplied length. value: float or length @@ -2253,9 +2298,7 @@ def change_sizes( from . import BondID for delta, cursor in zip(deltas, self._cursors): - bond = BondID( - cursor._internal.atom0(), cursor._internal.atom1() - ) + bond = BondID(cursor._internal.atom0(), cursor._internal.atom1()) moved.change(bond, delta, map) else: for delta, cursor in zip(deltas, self._cursors): @@ -2712,9 +2755,7 @@ def __init__(self, parent=None, map=None): if molnum not in self._molcursors: self._molcursors[molnum] = child_mol.cursor(map=map) - self._cursors.append( - self._molcursors[molnum]._from_view(child) - ) + self._cursors.append(self._molcursors[molnum]._from_view(child)) self._add_extra_functions() @@ -2732,9 +2773,7 @@ def get_lengths(map=None): return lengths - def set_lengths( - values, anchor=None, weighting=None, auto_align=True, map=None - ): + def set_lengths(values, anchor=None, weighting=None, auto_align=True, map=None): """ Set the lengths of the bonds being edited by this cursor to the specified values. Note that there should be the same number of @@ -2817,9 +2856,7 @@ def set_lengths( self._update() return self - def set_length( - value, anchor=None, weighting=None, auto_align=True, map=None - ): + def set_length(value, anchor=None, weighting=None, auto_align=True, map=None): """Set the lengths of all of the bonds edited by this cursor to the passed value. @@ -3238,9 +3275,7 @@ def change_sizes( molnum = cursor._d.number() if molnum not in movers: - molecule = self._molcursors[ - molnum - ]._d.molecule.commit() + molecule = self._molcursors[molnum]._d.molecule.commit() molecules[molnum] = molecule movers[molnum] = molecule.move() maps[molnum] = self._cursors[0]._d.merge( @@ -3252,18 +3287,14 @@ def change_sizes( ) ) - bond = BondID( - cursor._internal.atom0(), cursor._internal.atom1() - ) + bond = BondID(cursor._internal.atom0(), cursor._internal.atom1()) movers[molnum].change(bond, delta, maps[molnum]) else: for delta, cursor in zip(deltas, self._cursors): molnum = cursor._d.number() if molnum not in movers: - molecule = self._molcursors[ - molnum - ]._d.molecule.commit() + molecule = self._molcursors[molnum]._d.molecule.commit() molecules[molnum] = molecule movers[molnum] = molecule.move() maps[molnum] = self._cursors[0]._d.merge( @@ -3275,9 +3306,7 @@ def change_sizes( ) ) - movers[molnum].change( - cursor._internal, delta, maps[molnum] - ) + movers[molnum].change(cursor._internal, delta, maps[molnum]) for molnum, mover in movers.items(): if auto_align and (anchor is None): From e3668f8f0476fed96b50e990da5793233649749d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 22 Feb 2024 20:07:25 +0000 Subject: [PATCH 124/468] WIP - VERY WIP Gone a little down the rabbit hole in the merge code by adding in support for alternate names for atoms and residues. This will enable the names of the perturbed end state to be saved, so that we can get something sensible out when we extract the end states. Will not compile --- corelib/src/libs/SireMol/atom.h | 2 + corelib/src/libs/SireMol/atomeditor.h | 18 ++ corelib/src/libs/SireMol/atommapping.cpp | 16 ++ corelib/src/libs/SireMol/atommapping.h | 3 + corelib/src/libs/SireMol/moleculeinfo.cpp | 36 ++++ corelib/src/libs/SireMol/moleculeinfo.h | 9 + corelib/src/libs/SireMol/moleculeinfodata.cpp | 157 ++++++++++++-- corelib/src/libs/SireMol/moleculeinfodata.h | 9 + corelib/src/libs/SireMol/moleditor.cpp | 7 + corelib/src/libs/SireMol/moleditor.h | 2 + corelib/src/libs/SireMol/reseditor.h | 19 +- corelib/src/libs/SireMol/residue.h | 2 + corelib/src/libs/SireMol/structureeditor.cpp | 147 ++++++++++++- corelib/src/libs/SireMol/structureeditor.h | 11 +- corelib/src/libs/SireSystem/merge.cpp | 196 +++++++++++++++++- corelib/src/libs/SireSystem/merge.h | 3 + wrapper/Mol/Atom.pypp.cpp | 12 ++ wrapper/Mol/AtomEditor.pypp.cpp | 77 +++++++ wrapper/Mol/AtomMapping.pypp.cpp | 24 +++ wrapper/Mol/AtomStructureEditor.pypp.cpp | 77 +++++++ wrapper/Mol/Frame.pypp.cpp | 2 +- wrapper/Mol/MolStructureEditor.pypp.cpp | 12 ++ wrapper/Mol/MoleculeInfo.pypp.cpp | 78 +++++++ wrapper/Mol/ResEditor.pypp.cpp | 78 +++++++ wrapper/Mol/ResStructureEditor.pypp.cpp | 77 +++++++ wrapper/Mol/Residue.pypp.cpp | 12 ++ .../System/_System_free_functions.pypp.cpp | 4 +- 27 files changed, 1056 insertions(+), 34 deletions(-) diff --git a/corelib/src/libs/SireMol/atom.h b/corelib/src/libs/SireMol/atom.h index a000bcf0e..084541306 100644 --- a/corelib/src/libs/SireMol/atom.h +++ b/corelib/src/libs/SireMol/atom.h @@ -130,6 +130,8 @@ namespace SireMol AtomIdx index() const; const CGAtomIdx &cgAtomIdx() const; + AtomName alternateName() const; + bool hasProperty(const PropertyName &key) const; bool hasMetadata(const PropertyName &metakey) const; bool hasMetadata(const PropertyName &key, const PropertyName &metakey) const; diff --git a/corelib/src/libs/SireMol/atomeditor.h b/corelib/src/libs/SireMol/atomeditor.h index e26044c72..371a8f3d8 100644 --- a/corelib/src/libs/SireMol/atomeditor.h +++ b/corelib/src/libs/SireMol/atomeditor.h @@ -109,7 +109,16 @@ namespace SireMol AtomEditor &rename(const AtomName &name); AtomEditor &renumber(AtomNum number); + AtomEditor &rename(const QString &name); + AtomEditor &renumber(int number); + AtomStructureEditor reindex(AtomIdx atomidx) const; + AtomStructureEditor reindex(int atomidx) const; + + AtomEditor &setAlternateName(const QString &name); + AtomEditor &setAlternateName(const AtomName &name); + + AtomName alternateName() const; MolStructureEditor remove() const; @@ -170,6 +179,10 @@ namespace SireMol AtomNum number() const; AtomIdx index() const; + AtomStructureEditor &rename(const QString &name); + AtomStructureEditor &renumber(int number); + AtomStructureEditor &reindex(int idx); + AtomStructureEditor &rename(const AtomName &name); AtomStructureEditor &renumber(AtomNum number); AtomStructureEditor &reindex(AtomIdx idx); @@ -185,6 +198,11 @@ namespace SireMol AtomStructureEditor &reparent(SegIdx segidx); AtomStructureEditor &reparent(const SegID &segid); + void setAlternateName(const QString &name); + void setAlternateName(const AtomName &name); + + const AtomName &alternateName() const; + template T property(const QString &key) const; diff --git a/corelib/src/libs/SireMol/atommapping.cpp b/corelib/src/libs/SireMol/atommapping.cpp index 12c812cb7..8e683d487 100644 --- a/corelib/src/libs/SireMol/atommapping.cpp +++ b/corelib/src/libs/SireMol/atommapping.cpp @@ -681,3 +681,19 @@ void AtomMapping::assertSingleMolecule() const CODELOC); } } + +/** Return the property map used to find properties of the + * reference molecule + */ +const PropertyMap &AtomMapping::propertyMap0() const +{ + return this->map0; +} + +/** Return the property map used to find properties of the + * mapped molecule + */ +const PropertyMap &AtomMapping::propertyMap1() const +{ + return this->map1; +} diff --git a/corelib/src/libs/SireMol/atommapping.h b/corelib/src/libs/SireMol/atommapping.h index 1e6ed728c..dc224d2f9 100644 --- a/corelib/src/libs/SireMol/atommapping.h +++ b/corelib/src/libs/SireMol/atommapping.h @@ -179,6 +179,9 @@ namespace SireMol const SelectorM &container, bool find_all = true) const; + const SireBase::PropertyMap &propertyMap0() const; + const SireBase::PropertyMap &propertyMap1() const; + private: /** The reference atoms - we map from these to the other atoms */ SelectorM atms0; diff --git a/corelib/src/libs/SireMol/moleculeinfo.cpp b/corelib/src/libs/SireMol/moleculeinfo.cpp index 2b3b70902..ec2c20442 100644 --- a/corelib/src/libs/SireMol/moleculeinfo.cpp +++ b/corelib/src/libs/SireMol/moleculeinfo.cpp @@ -1136,3 +1136,39 @@ void MoleculeInfo::assertEqualTo(const MoleculeInfoData &other) const { d->assertEqualTo(other); } + +/** Return the alternate name of the specified atom */ +const AtomName &MoleculeInfo::alternateName(const AtomID &atomid) const +{ + return d->alternateName(atomid); +} + +/** Return the alternate name of the specified atom */ +const AtomName &MoleculeInfo::alternateName(AtomIdx atomidx) const +{ + return d->alternateName(atomidx); +} + +/** Return the alternate name of the specified residue */ +const ResName &MoleculeInfo::alternateName(const ResID &resid) const +{ + return d->alternateName(resid); +} + +/** Return the alternate name of the specified residue */ +const ResName &MoleculeInfo::alternateName(ResIdx residx) const +{ + return d->alternateName(residx); +} + +/** Set the alternate name of the passed atom */ +MoleculeInfo MoleculeInfo::setAlternateName(AtomIdx atomidx, const AtomName &name) const +{ + return MoleculeInfo(d->setAlternateName(atomidx, name)); +} + +/** Set the alternate name of the passed atom */ +MoleculeInfo MoleculeInfo::setAlternateName(ResIdx residx, const ResName &name) const +{ + return MoleculeInfo(d->setAlternateName(residx, name)); +} diff --git a/corelib/src/libs/SireMol/moleculeinfo.h b/corelib/src/libs/SireMol/moleculeinfo.h index fe2695b6f..cabb09332 100644 --- a/corelib/src/libs/SireMol/moleculeinfo.h +++ b/corelib/src/libs/SireMol/moleculeinfo.h @@ -123,6 +123,15 @@ namespace SireMol const AtomName &name(const AtomID &atomid) const; const AtomName &name(AtomIdx atomidx) const; + const AtomName &alternateName(const AtomID &atomid) const; + const AtomName &alternateName(AtomIdx atomidx) const; + + const ResName &alternateName(const ResID &resid) const; + const ResName &alternateName(ResIdx residx) const; + + MoleculeInfo setAlternateName(AtomIdx atomidx, const AtomName &name) const; + MoleculeInfo setAlternateName(ResIdx residx, const ResName &name) const; + ResNum number(const ResID &resid) const; ResNum number(ResIdx residx) const; diff --git a/corelib/src/libs/SireMol/moleculeinfodata.cpp b/corelib/src/libs/SireMol/moleculeinfodata.cpp index 32db83780..39ad2ee9b 100644 --- a/corelib/src/libs/SireMol/moleculeinfodata.cpp +++ b/corelib/src/libs/SireMol/moleculeinfodata.cpp @@ -83,6 +83,9 @@ namespace SireMol /** The name of this residue */ ResName name; + /** The alternate name of this residue */ + ResName altname; + /** The number of this residue */ ResNum number; @@ -169,6 +172,9 @@ namespace SireMol /** The name of this atom */ AtomName name; + /** The alternate name of this atom */ + AtomName altname; + /** The number of this atom */ AtomNum number; @@ -206,10 +212,12 @@ QDataStream &operator>>(QDataStream &ds, AtomInfo &atominfo) { ds >> atominfo.name >> atominfo.number >> atominfo.residx >> atominfo.segidx >> atominfo.cgatomidx; + atominfo.altname = atominfo.name; + return ds; } -AtomInfo::AtomInfo() : name(QString()), number(AtomNum::null()), residx(ResIdx::null()), segidx(SegIdx::null()) +AtomInfo::AtomInfo() : name(QString()), altname(QString()), number(AtomNum::null()), residx(ResIdx::null()), segidx(SegIdx::null()) { } @@ -219,7 +227,8 @@ AtomInfo::~AtomInfo() bool AtomInfo::operator==(const AtomInfo &other) const { - return this == &other or (name == other.name and number == other.number and residx == other.residx and + return this == &other or (name == other.name and altname == other.altname and + number == other.number and residx == other.residx and segidx == other.segidx and cgatomidx == other.cgatomidx); } @@ -271,21 +280,23 @@ bool CGInfo::operator!=(const CGInfo &other) const QDataStream &operator<<(QDataStream &ds, const ResInfo &resinfo) { - ds << resinfo.name << resinfo.number << resinfo.chainidx << resinfo.atom_indicies; + ds << resinfo.name << resinfo.altname << resinfo.number << resinfo.chainidx << resinfo.atom_indicies; return ds; } QDataStream &operator>>(QDataStream &ds, ResInfo &resinfo) { - ds >> resinfo.name >> resinfo.number >> resinfo.chainidx >> resinfo.atom_indicies; + ds >> resinfo.name >> resinfo.altname >> resinfo.number >> resinfo.chainidx >> resinfo.atom_indicies; + + resinfo.altname = resinfo.name; resinfo.cgidx = CGIdx::null(); return ds; } -ResInfo::ResInfo() : name(QString()), number(ResNum::null()), chainidx(ChainIdx::null()) +ResInfo::ResInfo() : name(QString()), altname(QString()), number(ResNum::null()), chainidx(ChainIdx::null()) { } @@ -295,7 +306,8 @@ ResInfo::~ResInfo() bool ResInfo::operator==(const ResInfo &other) const { - return this == &other or (name == other.name and number == other.number and chainidx == other.chainidx and + return this == &other or (name == other.name and altname == other.altname and + number == other.number and chainidx == other.chainidx and atom_indicies == other.atom_indicies); } @@ -385,13 +397,31 @@ static const RegisterMetaType r_molinfo(NO_ROOT); /** Serialise to a binary datastream */ QDataStream &operator<<(QDataStream &ds, const MoleculeInfoData &molinfo) { - writeHeader(ds, r_molinfo, 1); + writeHeader(ds, r_molinfo, 2); SharedDataStream sds(ds); sds << molinfo.uid << molinfo.atoms_by_index << molinfo.res_by_index << molinfo.chains_by_index << molinfo.seg_by_index << molinfo.cg_by_index; + QHash alt_atomnames; + + for (int i = 0; i < molinfo.atoms_by_index.count(); ++i) + { + if (molinfo.atoms_by_index[i].name != molinfo.atoms_by_index[i].altname) + alt_atomnames.insert(i, molinfo.atoms_by_index[i].altname.value()); + } + + QHash alt_resnames; + + for (int i = 0; i < molinfo.res_by_index.count(); ++i) + { + if (molinfo.res_by_index[i].name != molinfo.res_by_index[i].altname) + alt_resnames.insert(i, molinfo.res_by_index[i].altname.value()); + } + + sds << alt_atomnames << alt_resnames; + return ds; } @@ -595,7 +625,38 @@ QDataStream &operator>>(QDataStream &ds, MoleculeInfoData &molinfo) { VersionID v = readHeader(ds, r_molinfo); - if (v == 1) + if (v == 2) + { + SharedDataStream sds(ds); + + sds >> molinfo.uid >> molinfo.atoms_by_index >> molinfo.res_by_index >> molinfo.chains_by_index >> + molinfo.seg_by_index >> molinfo.cg_by_index; + + QHash alt_atomnames; + QHash alt_resnames; + + sds >> alt_atomnames >> alt_resnames; + + for (auto it = alt_atomnames.constBegin(); it != alt_atomnames.constEnd(); ++it) + { + if (it.key() >= 0 and it.key() < molinfo.atoms_by_index.count()) + { + molinfo.atoms_by_index[it.key()].altname = AtomName(it.value()); + } + } + + for (auto it = alt_resnames.constBegin(); it != alt_resnames.constEnd(); ++it) + { + if (it.key() >= 0 and it.key() < molinfo.res_by_index.count()) + { + molinfo.res_by_index[it.key()].altname = ResName(it.value()); + } + } + + // reconstruct the name and number indexes + molinfo.rebuildNameAndNumberIndexes(); + } + else if (v == 1) { SharedDataStream sds(ds); @@ -606,7 +667,7 @@ QDataStream &operator>>(QDataStream &ds, MoleculeInfoData &molinfo) molinfo.rebuildNameAndNumberIndexes(); } else - throw version_error(v, "1", r_molinfo, CODELOC); + throw version_error(v, "1, 2", r_molinfo, CODELOC); return ds; } @@ -658,6 +719,7 @@ MoleculeInfoData::MoleculeInfoData(const QString &resname, qint64 resnum, ResInfo res; res.name = ResName(resname.simplified()); + res.altname = res.name; res.number = ResNum(resnum); res.cgidx = CGIdx(0); @@ -685,6 +747,7 @@ MoleculeInfoData::MoleculeInfoData(const QString &resname, qint64 resnum, auto &atom = atoms_by_index_data[i]; atom.name = AtomName(atomnames_data[i].simplified()); + atom.altname = atom.name; atom.number = AtomNum(atomnums_data[i]); atom.residx = ResIdx(0); atom.cgatomidx = CGAtomIdx(CGIdx(0), Index(i)); @@ -849,13 +912,14 @@ MoleculeInfoData::MoleculeInfoData(const StructureEditor &editor) : RefCountData // create the data for atom 'i' AtomInfo &atom = atoms_by_index_array[i]; - tuple atomdata = editor.getAtomData(i); + tuple atomdata = editor.getAtomData(i); atom.name = atomdata.get<0>(); - atom.number = atomdata.get<1>(); - atom.cgatomidx = atomdata.get<2>(); - atom.residx = atomdata.get<3>(); - atom.segidx = atomdata.get<4>(); + atom.altname = atomdata.get<1>(); + atom.number = atomdata.get<2>(); + atom.cgatomidx = atomdata.get<3>(); + atom.residx = atomdata.get<4>(); + atom.segidx = atomdata.get<5>(); if (atom.cgatomidx.cutGroup().isNull()) atoms_missing_cutgroups.append(i); @@ -902,12 +966,13 @@ MoleculeInfoData::MoleculeInfoData(const StructureEditor &editor) : RefCountData { ResInfo &residue = res_by_index_array[i]; - tuple> resdata = editor.getResData(i); + tuple> resdata = editor.getResData(i); residue.name = resdata.get<0>(); - residue.number = resdata.get<1>(); - residue.chainidx = resdata.get<2>(); - residue.atom_indicies = resdata.get<3>(); + residue.altname = resdata.get<1>(); + residue.number = resdata.get<2>(); + residue.chainidx = resdata.get<3>(); + residue.atom_indicies = resdata.get<4>(); if (residue.atom_indicies.isEmpty()) empty_residues.append(i); @@ -1336,6 +1401,62 @@ void remove_from_hash(QMultiHash &hash, const Key &key, const T &value) } #endif +/** Return the alternate name of the specified atom */ +const AtomName &MoleculeInfoData::alternateName(const AtomID &atomid) const +{ + return this->alternateName(this->atomIdx(atomid)); +} + +/** Return the alternate name of the specified atom */ +const AtomName &MoleculeInfoData::alternateName(AtomIdx atomidx) const +{ + atomidx = atomidx.map(this->nAtoms()); + return atoms_by_index.at(atomidx).altname; +} + +/** Return the alternate name of the specified residue */ +const ResName &MoleculeInfoData::alternateName(const ResID &resid) const +{ + return this->alternateName(this->resIdx(resid)); +} + +/** Return the alternate name of the specified residue */ +const ResName &MoleculeInfoData::alternateName(ResIdx residx) const +{ + residx = residx.map(this->nResidues()); + return res_by_index.at(residx).altname; +} + +/** Set the alternate name of the passed atom */ +MoleculeInfoData MoleculeInfoData::setAlternateName(AtomIdx atomidx, const AtomName &altname) const +{ + atomidx = atomidx.map(this->nAtoms()); + + if (atoms_by_index.at(atomidx).altname == altname) + return *this; + + // make the change in a copy of this object + MoleculeInfoData newinfo(*this); + newinfo.atoms_by_index[atomidx].altname = altname; + + return newinfo; +} + +/* Set the alternate name of the passed residue */ +MoleculeInfoData MoleculeInfoData::setAlternateName(ResIdx residx, const ResName &altname) const +{ + residx = residx.map(this->nResidues()); + + if (res_by_index.at(residx).altname == altname) + return *this; + + // make the change in a copy of this object + MoleculeInfoData newinfo(*this); + newinfo.res_by_index[residx].altname = altname; + + return newinfo; +} + /** Rename the atom at index 'atomidx' to have the new name 'newname'. \throw SireError::invalid_index diff --git a/corelib/src/libs/SireMol/moleculeinfodata.h b/corelib/src/libs/SireMol/moleculeinfodata.h index 012cc4f0b..f12cb72a9 100644 --- a/corelib/src/libs/SireMol/moleculeinfodata.h +++ b/corelib/src/libs/SireMol/moleculeinfodata.h @@ -182,6 +182,12 @@ namespace SireMol const AtomName &name(const AtomID &atomid) const; const AtomName &name(AtomIdx atomidx) const; + const AtomName &alternateName(const AtomID &atomid) const; + const AtomName &alternateName(AtomIdx atomidx) const; + + const ResName &alternateName(const ResID &resid) const; + const ResName &alternateName(ResIdx residx) const; + SegIdx number(const SegID &segid) const; SegIdx number(SegIdx segidx) const; @@ -197,6 +203,9 @@ namespace SireMol AtomNum number(const AtomID &atomid) const; AtomNum number(AtomIdx atomidx) const; + MoleculeInfoData setAlternateName(AtomIdx atomidx, const AtomName &newname) const; + MoleculeInfoData setAlternateName(ResIdx residx, const ResName &newname) const; + MoleculeInfoData rename(AtomIdx atomidx, const AtomName &newname) const; MoleculeInfoData renumber(AtomIdx atomidx, const AtomNum &newnum) const; diff --git a/corelib/src/libs/SireMol/moleditor.cpp b/corelib/src/libs/SireMol/moleditor.cpp index dd0df85e3..5089eb2c8 100644 --- a/corelib/src/libs/SireMol/moleditor.cpp +++ b/corelib/src/libs/SireMol/moleditor.cpp @@ -633,6 +633,13 @@ MolStructureEditor &MolStructureEditor::rename(const MolName &newname) return *this; } +/** Move all atoms into a single CutGroup */ +MolStructureEditor &MolStructureEditor::makeSingleCutGroup() +{ + StructureEditor::convertToSingleCutGroupMolecule(); + return *this; +} + /** Give this molecule a new, unique ID number */ MolStructureEditor &MolStructureEditor::renumber() { diff --git a/corelib/src/libs/SireMol/moleditor.h b/corelib/src/libs/SireMol/moleditor.h index ea148af4a..1843f83cb 100644 --- a/corelib/src/libs/SireMol/moleditor.h +++ b/corelib/src/libs/SireMol/moleditor.h @@ -191,6 +191,8 @@ namespace SireMol int nChains() const; int nSegments() const; + MolStructureEditor &makeSingleCutGroup(); + AtomStructureEditor select(const AtomID &atomid); CGStructureEditor select(const CGID &cgid); ResStructureEditor select(const ResID &resid); diff --git a/corelib/src/libs/SireMol/reseditor.h b/corelib/src/libs/SireMol/reseditor.h index 1029052d2..59c4adc20 100644 --- a/corelib/src/libs/SireMol/reseditor.h +++ b/corelib/src/libs/SireMol/reseditor.h @@ -101,7 +101,16 @@ namespace SireMol ResEditor &rename(const ResName &name); ResEditor &renumber(ResNum number); + ResEditor &rename(const QString &name); + ResEditor &renumber(int number); + ResStructureEditor reindex(ResIdx index) const; + ResStructureEditor &reindex(int index) const; + + ResEditor &setAlternatename(const ResName &name); + ResEditor &setAlternatename(const QString &name); + + const ResName &alternateName() const; MolStructureEditor remove() const; @@ -174,9 +183,17 @@ namespace SireMol ResStructureEditor &rename(const ResName &name); ResStructureEditor &renumber(ResNum number); - ResStructureEditor &reindex(ResIdx index); + ResStructureEditor &rename(const QString &name); + ResStructureEditor &renumber(int number); + ResStructureEditor &reindex(int index); + + ResStructureEditor &setAlternatename(const ResName &name); + ResStructureEditor &setAlternatename(const QString &name); + + const ResName &alternateName() const; + MolStructureEditor remove(); ResStructureEditor &reparent(const ChainID &chainid); diff --git a/corelib/src/libs/SireMol/residue.h b/corelib/src/libs/SireMol/residue.h index 3d6e2a39f..a130a63ab 100644 --- a/corelib/src/libs/SireMol/residue.h +++ b/corelib/src/libs/SireMol/residue.h @@ -120,6 +120,8 @@ namespace SireMol ResNum number() const; ResIdx index() const; + ResName alternateName() const; + bool hasProperty(const PropertyName &key) const; bool hasMetadata(const PropertyName &metakey) const; bool hasMetadata(const PropertyName &key, const PropertyName &metakey) const; diff --git a/corelib/src/libs/SireMol/structureeditor.cpp b/corelib/src/libs/SireMol/structureeditor.cpp index 3196b2c68..83f7e3b45 100644 --- a/corelib/src/libs/SireMol/structureeditor.cpp +++ b/corelib/src/libs/SireMol/structureeditor.cpp @@ -153,6 +153,7 @@ namespace SireMol ~EditAtomData(); AtomName name; + AtomName altname; AtomNum number; quint32 cg_parent; @@ -198,6 +199,7 @@ namespace SireMol ~EditResData(); ResName name; + ResName altname; ResNum number; quint32 chain_parent; @@ -404,6 +406,8 @@ QDataStream &operator>>(QDataStream &ds, EditAtomData &editatom) ds >> editatom.name >> editatom.number >> editatom.cg_parent >> editatom.res_parent >> editatom.seg_parent >> editatom.properties >> editatom.molecule_metadata >> editatom.property_metadata; + editatom.altname = AtomName(); + return ds; } @@ -485,6 +489,8 @@ QDataStream &operator>>(QDataStream &ds, EditResData &editres) ds >> editres.name >> editres.number >> editres.chain_parent >> editres.atoms >> editres.properties >> editres.molecule_metadata >> editres.property_metadata; + editres.altname = ResName(); + return ds; } @@ -2889,12 +2895,38 @@ static const RegisterMetaType r_editor(MAGIC_ONLY, "SireMol::St /** Serialise to a binary datastream */ QDataStream &operator<<(QDataStream &ds, const StructureEditor &editor) { - writeHeader(ds, r_editor, 1); + writeHeader(ds, r_editor, 2); SharedDataStream sds(ds); sds << editor.d; + QHash alt_atomnames; + + for (int i = 0; i < editor.d->atoms.count(); ++i) + { + const EditAtomData &atom = editor.d->atoms[i]; + + if (not atom.altname.isEmpty()) + { + alt_atomnames.insert(i, atom.altname.value()); + } + } + + QHash alt_resnames; + + for (int i = 0; i < editor.d->residues.count(); ++i) + { + const EditResData &res = editor.d->residues[i]; + + if (not res.altname.isEmpty()) + { + alt_resnames.insert(i, res.altname.value()); + } + } + + sds << alt_atomnames << alt_resnames; + return ds; } @@ -2903,10 +2935,29 @@ QDataStream &operator>>(QDataStream &ds, StructureEditor &editor) { VersionID v = readHeader(ds, r_editor); - if (v == 1) + if (v == 1 or v == 2) { SharedDataStream sds(ds); sds >> editor.d; + + if (v == 2) + { + QHash alt_atomnames, alt_resnames; + + sds >> alt_atomnames >> alt_resnames; + + for (auto it = alt_atomnames.constBegin(); it != alt_atomnames.constEnd(); ++it) + { + if (it.key() >= 0 and it.key() < editor.d->atoms.count()) + editor.d->atoms[it.key()].altname = AtomName(it.value()); + } + + for (auto it = alt_resnames.constBegin(); it != alt_resnames.constEnd(); ++it) + { + if (it.key() >= 0 and it.key() < editor.d->residues.count()) + editor.d->residues[it.key()].altname = ResName(it.value()); + } + } } else throw version_error(v, "1", r_editor, CODELOC); @@ -3002,15 +3053,15 @@ SegIdx EditMolData::segIdx(const EditAtomData &atom) const \throw SireError::invalid_index */ -tuple StructureEditor::getAtomData(AtomIdx atomidx) const +tuple StructureEditor::getAtomData(AtomIdx atomidx) const { this->assertSane(); quint32 atomuid = getUID(atomidx); const EditAtomData &atom = d->atom(atomuid); - return tuple(atom.name, atom.number, d->cgAtomIdx(atomuid, atom), - d->resIdx(atom), d->segIdx(atom)); + return tuple(atom.name, atom.altname, atom.number, d->cgAtomIdx(atomuid, atom), + d->resIdx(atom), d->segIdx(atom)); } /** Return all of the metadata about the CutGroup at index 'cgidx' @@ -3050,7 +3101,7 @@ ChainIdx EditMolData::chainIdx(const EditResData &residue) const \throw SireError::invalid_index */ -boost::tuple> StructureEditor::getResData(ResIdx residx) const +boost::tuple> StructureEditor::getResData(ResIdx residx) const { this->assertSane(); @@ -3063,8 +3114,8 @@ boost::tuple> StructureEditor::getResD atomidxs.append(AtomIdx(d->atoms_by_index.indexOf(atom))); } - return tuple>(residue.name, residue.number, d->chainIdx(residue), - atomidxs); + return tuple>(residue.name, residue.altname, residue.number, d->chainIdx(residue), + atomidxs); } /** Return the metadata for the chain at index 'chainidx' @@ -3909,6 +3960,61 @@ void StructureEditor::renumberMolecule(MolNum newnum) d->molnum = newnum; } +/** Set the alternate atom name */ +void StructureEditor::setAlternateName(quint32 uid, const AtomName &name) +{ + this->assertSane(); + + EditAtomData &atom = d->atom(uid); + + if (atom.altname != name) + { + atom.altname = AtomName(cacheName(name)); + d->cached_molinfo = 0; + } +} + +/** Set the alternate residue name */ +void StructureEditor::setAlternateName(quint32 uid, const ResName &name) +{ + this->assertSane(); + + EditResData &res = d->residue(uid); + + if (res.altname != name) + { + res.altname = ResName(cacheName(name)); + d->cached_molinfo = 0; + } +} + +/** Return the alternate atom name - this will be the atom name if + * this hasn't been set + */ +const AtomName &StructureEditor::alternateAtomName(quint32 uid) const +{ + this->assertSane(); + + EditAtomData &atom = d->atom(uid); + + if (atom.altname.isNull()) + return atom.name; + else + return atom.altname; +} + +const ResName &StructureEditor::alternateResName(quint32 uid) const +{ + this->assertSane(); + + EditResData &res = d->residue(uid); + + if (res.altname.isNull()) + return res.name; + else + return res.altname; +} + /** Rename the atom identified by 'uid' to 'newname' \throw SireMol::missing_atom @@ -4425,6 +4531,31 @@ void StructureEditor::removeAllAtoms() } } +/** Move all atoms into a single CutGroup */ +void StructureEditor::convertToSingleCutGroupMolecule() +{ + this->assertSane(); + + QList cg_by_index = d->cg_by_index; + + if (cg_by_index.count() <= 1) + { + // nothing to do + return; + } + + for (quint32 i = 0; i < this->nAtomsInMolecule(); ++i) + { + this->reparentAtom(i, CGIdx(0)); + } + + // now remove all of the other CutGroups + for (int i = cg_by_index.count() - 1; i > 0; --i) + { + this->removeCutGroup(CGIdx(i)); + } +} + /** Remove all CutGroups from this molecule */ void StructureEditor::removeAllCutGroups() { diff --git a/corelib/src/libs/SireMol/structureeditor.h b/corelib/src/libs/SireMol/structureeditor.h index 8f335b6a2..097069bfb 100644 --- a/corelib/src/libs/SireMol/structureeditor.h +++ b/corelib/src/libs/SireMol/structureeditor.h @@ -175,17 +175,18 @@ namespace SireMol const MoleculeInfoData &info() const; /// functions used by MoleculeInfoData when committing - boost::tuple getAtomData(AtomIdx atomidx) const; + boost::tuple getAtomData(AtomIdx atomidx) const; boost::tuple> getCGData(CGIdx cgidx) const; - boost::tuple> getResData(ResIdx residx) const; + boost::tuple> getResData(ResIdx residx) const; boost::tuple> getChainData(ChainIdx chainidx) const; boost::tuple> getSegData(SegIdx segidx) const; /// Functions predominantly for StructureEditor derived classes + void convertToSingleCutGroupMolecule(); quint32 getUID(AtomIdx atomidx) const; quint32 getUID(CGIdx cgidx) const; @@ -275,6 +276,12 @@ namespace SireMol void renameSegment(quint32 uid, const SegName &name); void reindexSegment(quint32 uid, SegIdx index); + void setAlternateName(quint32 uid, const AtomName &name); + void setAlternateName(quint32 uid, const ResName &name); + + const AtomName &alternateAtomName(quint32 uid) const; + const ResName &alternateResName(quint32 uid) const; + void removeAtom(quint32 uid); void removeCutGroup(quint32 uid); void removeResidue(quint32 uid); diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index a9f05d6df..ba439748c 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -28,6 +28,9 @@ #include "SireSystem/merge.h" +#include "SireMol/core.h" +#include "SireMol/moleditor.h" + using namespace SireMol; using namespace SireBase; @@ -38,11 +41,200 @@ namespace SireSystem * * @param mols The AtomMapping object that contains the molecules to be merged. * @param as_new_molecule Flag indicating whether the merged molecule should be created as a new molecule. + * @param allow_ring_breaking Whether to allow the opening/closing of rings during a merge. + * @param allow_ring_size_change Whether to allow changes in ring size. + * @param force Whether to try to force the merge, even when the molecular + * connectivity changes not as the result of a ring transformation. + * This will likely lead to an unstable perturbation. This option + * takes precedence over 'allow_ring_breaking' and + * 'allow_ring_size_change'. * @param map The PropertyMap object that contains additional properties for the merged molecule. * @return The merged molecule. */ - Molecule merge(const AtomMapping &mols, bool as_new_molecule, const PropertyMap &map) + Molecule merge(const AtomMapping &mols, bool as_new_molecule, + bool allow_ring_breaking, bool allow_ring_size_change, + bool force, const PropertyMap &map) { - return mols.atoms0().molecules()[0]; + if (not mols.isSingleMolecule()) + { + throw SireError::incompatible_error(QObject::tr( + "You can only create a merged molecule from a mapping that " + "refers to a single molecule. You cannot use:\n%1") + .arg(mols.toString())); + } + + if (map.specified("as_new_molecule")) + { + as_new_molecule = map["as_new_molecule"].value().asABoolean(); + } + + if (map.specified("allow_ring_breaking")) + { + allow_ring_breaking = map["allow_ring_breaking"].value().asABoolean(); + } + + if (map.specified("allow_ring_size_change")) + { + allow_ring_size_change = map["allow_ring_size_change"].value().asABoolean(); + } + + if (map.specified("as_new_molecule")) + { + as_new_molecule = map["as_new_molecule"].value().asABoolean(); + } + + if (map.specified("force")) + { + force = map["force"].value().asABoolean(); + } + + if (force) + { + allow_ring_breaking = true; + allow_ring_size_change = true; + } + + // get the forwards and backwards map + auto forwards_map = mols; + auto backwards_map = mols.swap(); + + // the list of mapped atoms + const auto mapped_atoms0 = mols.mappedAtoms0(); + const auto mapped_atoms1 = mols.mappedAtoms1(); + + if (mapped_atoms0.count() != mapped_atoms1.count()) + { + throw SireError::program_bug(QObject::tr( + "The number of atoms in the forward and backward mappings " + "are not the same. This is a bug!."), + CODELOC); + } + + const int nmapped = mapped_atoms0.count(); + + // get the merged maps for the reference and perturbed states + auto map0 = map.merge(mols.propertyMap0()); + auto map1 = map.merge(mols.propertyMap1()); + + // get an editable copy of the molecule to be changed + MolStructureEditor mol(mols.atoms0().toSingleMolecule().molecule()); + + // and a handle on the whole reference and perturbed molecule + const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); + const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); + + // first, check that the merge will not change any of the CutGroup assigments... + if (mol.nCutGroups() > 1) + { + bool merge_changes_cutgroups = false; + + QHash cg_map; + cg_map.reserve(mol.nCutGroups()); + + for (int i = 0; i < nmapped; ++i) + { + const auto cg0 = mapped_atoms0[i].cutGroup().index(); + const auto cg1 = mapped_atoms1[i].cutGroup().index(); + + if (cg_map.contains(cg0)) + { + if (cg_map[cg0] != cg1) + { + merge_changes_cutgroups = true; + break; + } + } + else + { + cg_map[cg0] = cg1; + } + } + + if (merge_changes_cutgroups) + { + // it is safest to move all atoms into a single cutgroup + mol.makeSingleCutGroup(); + } + } + + // copy the properties from the reference state to both states + QStringList merged_properties = {"charge", "LJ", "atomtype", "intrascale", + "coordinates", "mass", "element", + "bond", "angle", "dihedral", + "improper"}; + + for (int i = 0; i < mol.nAtoms(); ++i) + { + auto atom = mol.atom(AtomIdx(i)); + + for (const auto &prop : merged_properties) + { + if (mol0.hasProperty(map0[prop])) + { + const auto &val = mol0.property(map0[prop]); + + atom.setProperty(map[prop + "0"].source(), val); + atom.setProperty(map[prop + "1"].source(), val); + } + } + } + + QVector matched_atoms; + matched_atoms.reserve(nmapped); + + // now go through and update the values of properties for + // the atoms that mutate + ResStructureEditor last_res; + bool changed_res = false; + + for (int i = 0; i < nmapped; ++i) + { + const auto atom0 = mapped_atoms0[i]; + const auto atom1 = mapped_atoms1[i]; + + matched_atoms.append(mol.atom(atom0.index())); + auto &atom = matched_atoms.last(); + + // save the perturbed state atom and residue names into new properties, so + // that we can use these when extracting the end states + atom.setAlternateName(atom1.name()); + + try + { + auto next_res = atom.residue(); + + if (next_res != last_res) + { + changed_res = true; + last_res = next_res; + } + } + catch (...) + { + } + + if (changed_res) + { + last_res.setAlternateName(atom1.residue().name()); + } + + // check if we need to change residue + } + + if (as_new_molecule) + { + mol.renumber(); + } + + auto editmol = mol.commit().edit(); + + // add the reference and perturbed molecules as 'molecule0' and 'molecule1' + editmol.setProperty(map["molecule0"].source(), mol0); + editmol.setProperty(map["molecule1"].source(), mol1); + + // set the flag that this is a perturbable molecule + editmol.setProperty(map["is_perturbable"].source(), BooleanProperty(true)); + + return editmol.commit(); } } diff --git a/corelib/src/libs/SireSystem/merge.h b/corelib/src/libs/SireSystem/merge.h index c12c0a2fb..80592ba0c 100644 --- a/corelib/src/libs/SireSystem/merge.h +++ b/corelib/src/libs/SireSystem/merge.h @@ -40,6 +40,9 @@ namespace SireSystem { SIRESYSTEM_EXPORT SireMol::Molecule merge(const SireMol::AtomMapping &mols, bool as_new_molecule = true, + bool allow_ring_breaking = false, + bool allow_ring_size_change = false, + bool force = false, const SireBase::PropertyMap &map = SireBase::PropertyMap()); } diff --git a/wrapper/Mol/Atom.pypp.cpp b/wrapper/Mol/Atom.pypp.cpp index dc5c15bc2..0e22c4630 100644 --- a/wrapper/Mol/Atom.pypp.cpp +++ b/wrapper/Mol/Atom.pypp.cpp @@ -292,6 +292,18 @@ void register_Atom_class(){ Atom_exposer.def( bp::init< SireMol::MoleculeView const &, SireMol::AtomID const & >(( bp::arg("molview"), bp::arg("atomid") ), "Construct the atom that that is identified by ID atomid\nin the view molview - this atom must be within this view\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n") ); Atom_exposer.def( bp::init< SireMol::MoleculeData const &, SireMol::AtomID const & >(( bp::arg("moldata"), bp::arg("atomid") ), "Construct the atom that is identified by ID atomid\nin the molecule whose data is in moldata\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n") ); Atom_exposer.def( bp::init< SireMol::Atom const & >(( bp::arg("other") ), "Copy constructor") ); + { //::SireMol::Atom::alternateName + + typedef ::SireMol::AtomName ( ::SireMol::Atom::*alternateName_function_type)( ) const; + alternateName_function_type alternateName_function_value( &::SireMol::Atom::alternateName ); + + Atom_exposer.def( + "alternateName" + , alternateName_function_value + , bp::release_gil_policy() + , "" ); + + } { //::SireMol::Atom::assertContains typedef void ( ::SireMol::Atom::*assertContains_function_type)( ::SireMol::AtomIdx ) const; diff --git a/wrapper/Mol/AtomEditor.pypp.cpp b/wrapper/Mol/AtomEditor.pypp.cpp index 45bcdbb53..b7eb7d835 100644 --- a/wrapper/Mol/AtomEditor.pypp.cpp +++ b/wrapper/Mol/AtomEditor.pypp.cpp @@ -67,6 +67,18 @@ void register_AtomEditor_class(){ bp::scope AtomEditor_scope( AtomEditor_exposer ); AtomEditor_exposer.def( bp::init< SireMol::Atom const & >(( bp::arg("atom") ), "Construct an editor that edits a copy of atom") ); AtomEditor_exposer.def( bp::init< SireMol::AtomEditor const & >(( bp::arg("other") ), "Copy constructor") ); + { //::SireMol::AtomEditor::alternateName + + typedef ::SireMol::AtomName ( ::SireMol::AtomEditor::*alternateName_function_type)( ) const; + alternateName_function_type alternateName_function_value( &::SireMol::AtomEditor::alternateName ); + + AtomEditor_exposer.def( + "alternateName" + , alternateName_function_value + , bp::release_gil_policy() + , "" ); + + } { //::SireMol::AtomEditor::operator= typedef ::SireMol::AtomEditor & ( ::SireMol::AtomEditor::*assign_function_type)( ::SireMol::Atom const & ) ; @@ -105,6 +117,19 @@ void register_AtomEditor_class(){ , bp::release_gil_policy() , "Reindex this atom so that it lies at index newidx. Note\nthat if newidx is greater than the number of atoms, then\nthis will move this atom to be the last in the list" ); + } + { //::SireMol::AtomEditor::reindex + + typedef ::SireMol::AtomStructureEditor ( ::SireMol::AtomEditor::*reindex_function_type)( int ) const; + reindex_function_type reindex_function_value( &::SireMol::AtomEditor::reindex ); + + AtomEditor_exposer.def( + "reindex" + , reindex_function_value + , ( bp::arg("atomidx") ) + , bp::release_gil_policy() + , "Reindex this atom so that it lies at index newidx. Note\nthat if newidx is greater than the number of atoms, then\nthis will move this atom to be the last in the list" ); + } { //::SireMol::AtomEditor::remove @@ -130,6 +155,19 @@ void register_AtomEditor_class(){ , bp::return_self< >() , "Rename this atom so that it is called newname" ); + } + { //::SireMol::AtomEditor::rename + + typedef ::SireMol::AtomEditor & ( ::SireMol::AtomEditor::*rename_function_type)( ::QString const & ) ; + rename_function_type rename_function_value( &::SireMol::AtomEditor::rename ); + + AtomEditor_exposer.def( + "rename" + , rename_function_value + , ( bp::arg("name") ) + , bp::return_self< >() + , "Rename this atom so that it is called newname" ); + } { //::SireMol::AtomEditor::renumber @@ -143,6 +181,19 @@ void register_AtomEditor_class(){ , bp::return_self< >() , "Renumber this atom so that it has number newnum" ); + } + { //::SireMol::AtomEditor::renumber + + typedef ::SireMol::AtomEditor & ( ::SireMol::AtomEditor::*renumber_function_type)( int ) ; + renumber_function_type renumber_function_value( &::SireMol::AtomEditor::renumber ); + + AtomEditor_exposer.def( + "renumber" + , renumber_function_value + , ( bp::arg("number") ) + , bp::return_self< >() + , "Renumber this atom so that it has number newnum" ); + } { //::SireMol::AtomEditor::reparent @@ -221,6 +272,32 @@ void register_AtomEditor_class(){ , bp::release_gil_policy() , "Reparent this atom so that it will be placed into the segment\nwith ID segid - this returns the updated atom in\nan AtomStructureEditor, which is optimised for further\nediting of the molecule structure\nThrow: SireMol::missing_segment\nThrow: SireMol::duplicate_segment\nThrow: SireError::invalid_index\n" ); + } + { //::SireMol::AtomEditor::setAlternateName + + typedef ::SireMol::AtomEditor & ( ::SireMol::AtomEditor::*setAlternateName_function_type)( ::QString const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::AtomEditor::setAlternateName ); + + AtomEditor_exposer.def( + "setAlternateName" + , setAlternateName_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomEditor::setAlternateName + + typedef ::SireMol::AtomEditor & ( ::SireMol::AtomEditor::*setAlternateName_function_type)( ::SireMol::AtomName const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::AtomEditor::setAlternateName ); + + AtomEditor_exposer.def( + "setAlternateName" + , setAlternateName_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::AtomEditor::toString diff --git a/wrapper/Mol/AtomMapping.pypp.cpp b/wrapper/Mol/AtomMapping.pypp.cpp index 8ca2c953d..243bb1624 100644 --- a/wrapper/Mol/AtomMapping.pypp.cpp +++ b/wrapper/Mol/AtomMapping.pypp.cpp @@ -359,6 +359,30 @@ void register_AtomMapping_class(){ , ( bp::arg("atoms") ) , "" ); + } + { //::SireMol::AtomMapping::propertyMap0 + + typedef ::SireBase::PropertyMap const & ( ::SireMol::AtomMapping::*propertyMap0_function_type)( ) const; + propertyMap0_function_type propertyMap0_function_value( &::SireMol::AtomMapping::propertyMap0 ); + + AtomMapping_exposer.def( + "propertyMap0" + , propertyMap0_function_value + , bp::return_value_policy< bp::copy_const_reference >() + , "Return the property map used to find properties of the\n reference molecule\n" ); + + } + { //::SireMol::AtomMapping::propertyMap1 + + typedef ::SireBase::PropertyMap const & ( ::SireMol::AtomMapping::*propertyMap1_function_type)( ) const; + propertyMap1_function_type propertyMap1_function_value( &::SireMol::AtomMapping::propertyMap1 ); + + AtomMapping_exposer.def( + "propertyMap1" + , propertyMap1_function_value + , bp::return_value_policy< bp::copy_const_reference >() + , "Return the property map used to find properties of the\n mapped molecule\n" ); + } { //::SireMol::AtomMapping::size diff --git a/wrapper/Mol/AtomStructureEditor.pypp.cpp b/wrapper/Mol/AtomStructureEditor.pypp.cpp index da595f49e..785a9616b 100644 --- a/wrapper/Mol/AtomStructureEditor.pypp.cpp +++ b/wrapper/Mol/AtomStructureEditor.pypp.cpp @@ -67,6 +67,18 @@ void register_AtomStructureEditor_class(){ AtomStructureEditor_exposer.def( bp::init< SireMol::Atom const & >(( bp::arg("atom") ), "Construct from an Atom") ); AtomStructureEditor_exposer.def( bp::init< SireMol::StructureEditor const &, SireMol::AtomIdx >(( bp::arg("data"), bp::arg("atomidx") ), "Construct for the atom at index idx in the molecule whose data\nis being edited in moldata\nThrow: SireError::invalid_index\n") ); AtomStructureEditor_exposer.def( bp::init< SireMol::AtomStructureEditor const & >(( bp::arg("other") ), "Copy constructor") ); + { //::SireMol::AtomStructureEditor::alternateName + + typedef ::SireMol::AtomName const & ( ::SireMol::AtomStructureEditor::*alternateName_function_type)( ) const; + alternateName_function_type alternateName_function_value( &::SireMol::AtomStructureEditor::alternateName ); + + AtomStructureEditor_exposer.def( + "alternateName" + , alternateName_function_value + , bp::return_value_policy() + , "" ); + + } { //::SireMol::AtomStructureEditor::chain typedef ::SireMol::ChainStructureEditor ( ::SireMol::AtomStructureEditor::*chain_function_type)( ) ; @@ -176,6 +188,19 @@ void register_AtomStructureEditor_class(){ , bp::return_self< >() , "" ); + } + { //::SireMol::AtomStructureEditor::reindex + + typedef ::SireMol::AtomStructureEditor & ( ::SireMol::AtomStructureEditor::*reindex_function_type)( int ) ; + reindex_function_type reindex_function_value( &::SireMol::AtomStructureEditor::reindex ); + + AtomStructureEditor_exposer.def( + "reindex" + , reindex_function_value + , ( bp::arg("idx") ) + , bp::return_self< >() + , "Reindex this atom to newidx - this will move the atom to\nthe end if newidx is greater than the number of atoms\nin the molecule" ); + } { //::SireMol::AtomStructureEditor::reindex @@ -201,6 +226,19 @@ void register_AtomStructureEditor_class(){ , bp::release_gil_policy() , "Completely remove this atom from the molecule and return\na MolStructureEditor that can be used to continue editing\nthe molecule" ); + } + { //::SireMol::AtomStructureEditor::rename + + typedef ::SireMol::AtomStructureEditor & ( ::SireMol::AtomStructureEditor::*rename_function_type)( ::QString const & ) ; + rename_function_type rename_function_value( &::SireMol::AtomStructureEditor::rename ); + + AtomStructureEditor_exposer.def( + "rename" + , rename_function_value + , ( bp::arg("name") ) + , bp::return_self< >() + , "Rename this atom to newname" ); + } { //::SireMol::AtomStructureEditor::rename @@ -214,6 +252,19 @@ void register_AtomStructureEditor_class(){ , bp::return_self< >() , "Rename this atom to newname" ); + } + { //::SireMol::AtomStructureEditor::renumber + + typedef ::SireMol::AtomStructureEditor & ( ::SireMol::AtomStructureEditor::*renumber_function_type)( int ) ; + renumber_function_type renumber_function_value( &::SireMol::AtomStructureEditor::renumber ); + + AtomStructureEditor_exposer.def( + "renumber" + , renumber_function_value + , ( bp::arg("number") ) + , bp::return_self< >() + , "Renumber this atom to newnum" ); + } { //::SireMol::AtomStructureEditor::renumber @@ -341,6 +392,32 @@ void register_AtomStructureEditor_class(){ , bp::release_gil_policy() , "Return whether or not this contains the whole molecule" ); + } + { //::SireMol::AtomStructureEditor::setAlternateName + + typedef void ( ::SireMol::AtomStructureEditor::*setAlternateName_function_type)( ::QString const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::AtomStructureEditor::setAlternateName ); + + AtomStructureEditor_exposer.def( + "setAlternateName" + , setAlternateName_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomStructureEditor::setAlternateName + + typedef void ( ::SireMol::AtomStructureEditor::*setAlternateName_function_type)( ::SireMol::AtomName const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::AtomStructureEditor::setAlternateName ); + + AtomStructureEditor_exposer.def( + "setAlternateName" + , setAlternateName_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::AtomStructureEditor::toString diff --git a/wrapper/Mol/Frame.pypp.cpp b/wrapper/Mol/Frame.pypp.cpp index 5a817d414..1c01beb1f 100644 --- a/wrapper/Mol/Frame.pypp.cpp +++ b/wrapper/Mol/Frame.pypp.cpp @@ -268,7 +268,7 @@ void register_Frame_class(){ , reorder_function_value , ( bp::arg("order") ) , bp::release_gil_policy() - , "" ); + , "Return a copy of this frame which has been reordered according\n to order (i.e. atom i is moved to order[i]). This does nothing\n if the order is empty. It silently ignores invalid orders, and\n will leave atoms that arent referenced in their original\n positions\n" ); } { //::SireMol::Frame::reverse diff --git a/wrapper/Mol/MolStructureEditor.pypp.cpp b/wrapper/Mol/MolStructureEditor.pypp.cpp index 8430d65f2..5182545a8 100644 --- a/wrapper/Mol/MolStructureEditor.pypp.cpp +++ b/wrapper/Mol/MolStructureEditor.pypp.cpp @@ -198,6 +198,18 @@ void register_MolStructureEditor_class(){ , bp::release_gil_policy() , "Return an editor for the CutGroup at ID cgid\nThrow: SireMol::missing_cutgroup\nThrow: SireMol::duplicate_cutgroup\nThrow: SireError::invalid_index\n" ); + } + { //::SireMol::MolStructureEditor::makeSingleCutGroup + + typedef ::SireMol::MolStructureEditor & ( ::SireMol::MolStructureEditor::*makeSingleCutGroup_function_type)( ) ; + makeSingleCutGroup_function_type makeSingleCutGroup_function_value( &::SireMol::MolStructureEditor::makeSingleCutGroup ); + + MolStructureEditor_exposer.def( + "makeSingleCutGroup" + , makeSingleCutGroup_function_value + , bp::release_gil_policy() + , "Move all atoms into a single CutGroup" ); + } { //::SireMol::MolStructureEditor::nAtoms diff --git a/wrapper/Mol/MoleculeInfo.pypp.cpp b/wrapper/Mol/MoleculeInfo.pypp.cpp index 0ae183e49..2613fa2e6 100644 --- a/wrapper/Mol/MoleculeInfo.pypp.cpp +++ b/wrapper/Mol/MoleculeInfo.pypp.cpp @@ -54,6 +54,58 @@ void register_MoleculeInfo_class(){ , bp::return_value_policy< bp::copy_const_reference >() , "Return the unique ID of this layout. Each unique layout has its\nown unique ID. You can use this to quickly check if two molecules\nhave the same layout" ); + } + { //::SireMol::MoleculeInfo::alternateName + + typedef ::SireMol::AtomName const & ( ::SireMol::MoleculeInfo::*alternateName_function_type)( ::SireMol::AtomID const & ) const; + alternateName_function_type alternateName_function_value( &::SireMol::MoleculeInfo::alternateName ); + + MoleculeInfo_exposer.def( + "alternateName" + , alternateName_function_value + , ( bp::arg("atomid") ) + , bp::return_value_policy() + , "Return the alternate name of the specified atom" ); + + } + { //::SireMol::MoleculeInfo::alternateName + + typedef ::SireMol::AtomName const & ( ::SireMol::MoleculeInfo::*alternateName_function_type)( ::SireMol::AtomIdx ) const; + alternateName_function_type alternateName_function_value( &::SireMol::MoleculeInfo::alternateName ); + + MoleculeInfo_exposer.def( + "alternateName" + , alternateName_function_value + , ( bp::arg("atomidx") ) + , bp::return_value_policy() + , "Return the alternate name of the specified atom" ); + + } + { //::SireMol::MoleculeInfo::alternateName + + typedef ::SireMol::ResName const & ( ::SireMol::MoleculeInfo::*alternateName_function_type)( ::SireMol::ResID const & ) const; + alternateName_function_type alternateName_function_value( &::SireMol::MoleculeInfo::alternateName ); + + MoleculeInfo_exposer.def( + "alternateName" + , alternateName_function_value + , ( bp::arg("resid") ) + , bp::return_value_policy() + , "Return the alternate name of the specified residue" ); + + } + { //::SireMol::MoleculeInfo::alternateName + + typedef ::SireMol::ResName const & ( ::SireMol::MoleculeInfo::*alternateName_function_type)( ::SireMol::ResIdx ) const; + alternateName_function_type alternateName_function_value( &::SireMol::MoleculeInfo::alternateName ); + + MoleculeInfo_exposer.def( + "alternateName" + , alternateName_function_value + , ( bp::arg("residx") ) + , bp::return_value_policy() + , "Return the alternate name of the specified residue" ); + } { //::SireMol::MoleculeInfo::assertCompatibleWith @@ -2173,6 +2225,32 @@ void register_MoleculeInfo_class(){ , bp::release_gil_policy() , "Return the index of the identified segment" ); + } + { //::SireMol::MoleculeInfo::setAlternateName + + typedef ::SireMol::MoleculeInfo ( ::SireMol::MoleculeInfo::*setAlternateName_function_type)( ::SireMol::AtomIdx,::SireMol::AtomName const & ) const; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::MoleculeInfo::setAlternateName ); + + MoleculeInfo_exposer.def( + "setAlternateName" + , setAlternateName_function_value + , ( bp::arg("atomidx"), bp::arg("name") ) + , bp::release_gil_policy() + , "Set the alternate name of the passed atom" ); + + } + { //::SireMol::MoleculeInfo::setAlternateName + + typedef ::SireMol::MoleculeInfo ( ::SireMol::MoleculeInfo::*setAlternateName_function_type)( ::SireMol::ResIdx,::SireMol::ResName const & ) const; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::MoleculeInfo::setAlternateName ); + + MoleculeInfo_exposer.def( + "setAlternateName" + , setAlternateName_function_value + , ( bp::arg("residx"), bp::arg("name") ) + , bp::release_gil_policy() + , "Set the alternate name of the passed atom" ); + } { //::SireMol::MoleculeInfo::squeeze diff --git a/wrapper/Mol/ResEditor.pypp.cpp b/wrapper/Mol/ResEditor.pypp.cpp index 8bff8cee9..99a65c8f2 100644 --- a/wrapper/Mol/ResEditor.pypp.cpp +++ b/wrapper/Mol/ResEditor.pypp.cpp @@ -3,6 +3,7 @@ // (C) Christopher Woods, GPL >= 3 License #include "boost/python.hpp" +#include "Helpers/clone_const_reference.hpp" #include "ResEditor.pypp.hpp" namespace bp = boost::python; @@ -84,6 +85,18 @@ void register_ResEditor_class(){ , bp::release_gil_policy() , "Add a new atom with the number number to this residue - this\nreturns an editor that can be used to further edit this atom" ); + } + { //::SireMol::ResEditor::alternateName + + typedef ::SireMol::ResName const & ( ::SireMol::ResEditor::*alternateName_function_type)( ) const; + alternateName_function_type alternateName_function_value( &::SireMol::ResEditor::alternateName ); + + ResEditor_exposer.def( + "alternateName" + , alternateName_function_value + , bp::return_value_policy() + , "" ); + } { //::SireMol::ResEditor::commit @@ -135,6 +148,19 @@ void register_ResEditor_class(){ , bp::release_gil_policy() , "Change the index of this residue to newidx. If this\nis larger than the number of residues in the molecule\nthen this residue is moved to the end" ); + } + { //::SireMol::ResEditor::reindex + + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResEditor::*reindex_function_type)( int ) const; + reindex_function_type reindex_function_value( &::SireMol::ResEditor::reindex ); + + ResEditor_exposer.def( + "reindex" + , reindex_function_value + , ( bp::arg("index") ) + , bp::release_gil_policy() + , "Change the index of this residue to newidx. If this\nis larger than the number of residues in the molecule\nthen this residue is moved to the end" ); + } { //::SireMol::ResEditor::remove @@ -186,6 +212,19 @@ void register_ResEditor_class(){ , bp::return_self< >() , "Rename this residue to newname" ); + } + { //::SireMol::ResEditor::rename + + typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*rename_function_type)( ::QString const & ) ; + rename_function_type rename_function_value( &::SireMol::ResEditor::rename ); + + ResEditor_exposer.def( + "rename" + , rename_function_value + , ( bp::arg("name") ) + , bp::return_self< >() + , "Rename this residue to newname" ); + } { //::SireMol::ResEditor::renumber @@ -199,6 +238,19 @@ void register_ResEditor_class(){ , bp::return_self< >() , "Renumber this residue to newnum" ); + } + { //::SireMol::ResEditor::renumber + + typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*renumber_function_type)( int ) ; + renumber_function_type renumber_function_value( &::SireMol::ResEditor::renumber ); + + ResEditor_exposer.def( + "renumber" + , renumber_function_value + , ( bp::arg("number") ) + , bp::return_self< >() + , "Renumber this residue to newnum" ); + } { //::SireMol::ResEditor::reparent @@ -212,6 +264,32 @@ void register_ResEditor_class(){ , bp::release_gil_policy() , "Move this residue into the chain with ID chainid\nThrow: SireMol::missing_chain\nThrow: SireMol::duplicate_chain\nThrow: SireError::invalid_index\n" ); + } + { //::SireMol::ResEditor::setAlternatename + + typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*setAlternatename_function_type)( ::SireMol::ResName const & ) ; + setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResEditor::setAlternatename ); + + ResEditor_exposer.def( + "setAlternatename" + , setAlternatename_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::ResEditor::setAlternatename + + typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*setAlternatename_function_type)( ::QString const & ) ; + setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResEditor::setAlternatename ); + + ResEditor_exposer.def( + "setAlternatename" + , setAlternatename_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::ResEditor::toString diff --git a/wrapper/Mol/ResStructureEditor.pypp.cpp b/wrapper/Mol/ResStructureEditor.pypp.cpp index 2f9418ba1..2c0caef0a 100644 --- a/wrapper/Mol/ResStructureEditor.pypp.cpp +++ b/wrapper/Mol/ResStructureEditor.pypp.cpp @@ -84,6 +84,18 @@ void register_ResStructureEditor_class(){ , bp::release_gil_policy() , "Add a new atom with the number number to this residue - this\nreturns an editor that can be used to further edit this atom" ); + } + { //::SireMol::ResStructureEditor::alternateName + + typedef ::SireMol::ResName const & ( ::SireMol::ResStructureEditor::*alternateName_function_type)( ) const; + alternateName_function_type alternateName_function_value( &::SireMol::ResStructureEditor::alternateName ); + + ResStructureEditor_exposer.def( + "alternateName" + , alternateName_function_value + , bp::return_value_policy() + , "" ); + } { //::SireMol::ResStructureEditor::atom @@ -233,6 +245,19 @@ void register_ResStructureEditor_class(){ , bp::return_self< >() , "Change the index of this residue to newidx. If this\nis larger than the number of residues in the molecule\nthen this residue is moved to the end" ); + } + { //::SireMol::ResStructureEditor::reindex + + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*reindex_function_type)( int ) ; + reindex_function_type reindex_function_value( &::SireMol::ResStructureEditor::reindex ); + + ResStructureEditor_exposer.def( + "reindex" + , reindex_function_value + , ( bp::arg("index") ) + , bp::return_self< >() + , "Change the index of this residue to newidx. If this\nis larger than the number of residues in the molecule\nthen this residue is moved to the end" ); + } { //::SireMol::ResStructureEditor::remove @@ -284,6 +309,19 @@ void register_ResStructureEditor_class(){ , bp::return_self< >() , "Rename this residue to newname" ); + } + { //::SireMol::ResStructureEditor::rename + + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*rename_function_type)( ::QString const & ) ; + rename_function_type rename_function_value( &::SireMol::ResStructureEditor::rename ); + + ResStructureEditor_exposer.def( + "rename" + , rename_function_value + , ( bp::arg("name") ) + , bp::return_self< >() + , "Rename this residue to newname" ); + } { //::SireMol::ResStructureEditor::renumber @@ -297,6 +335,19 @@ void register_ResStructureEditor_class(){ , bp::return_self< >() , "Renumber this residue to newnum" ); + } + { //::SireMol::ResStructureEditor::renumber + + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*renumber_function_type)( int ) ; + renumber_function_type renumber_function_value( &::SireMol::ResStructureEditor::renumber ); + + ResStructureEditor_exposer.def( + "renumber" + , renumber_function_value + , ( bp::arg("number") ) + , bp::return_self< >() + , "Renumber this residue to newnum" ); + } { //::SireMol::ResStructureEditor::reparent @@ -348,6 +399,32 @@ void register_ResStructureEditor_class(){ , bp::release_gil_policy() , "Is this editor editing the entire molecule?" ); + } + { //::SireMol::ResStructureEditor::setAlternatename + + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*setAlternatename_function_type)( ::SireMol::ResName const & ) ; + setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResStructureEditor::setAlternatename ); + + ResStructureEditor_exposer.def( + "setAlternatename" + , setAlternatename_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::ResStructureEditor::setAlternatename + + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*setAlternatename_function_type)( ::QString const & ) ; + setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResStructureEditor::setAlternatename ); + + ResStructureEditor_exposer.def( + "setAlternatename" + , setAlternatename_function_value + , ( bp::arg("name") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::ResStructureEditor::toString diff --git a/wrapper/Mol/Residue.pypp.cpp b/wrapper/Mol/Residue.pypp.cpp index 3ccf64a64..0bd6713b9 100644 --- a/wrapper/Mol/Residue.pypp.cpp +++ b/wrapper/Mol/Residue.pypp.cpp @@ -98,6 +98,18 @@ void register_Residue_class(){ bp::scope Residue_scope( Residue_exposer ); Residue_exposer.def( bp::init< SireMol::MoleculeData const &, SireMol::ResID const & >(( bp::arg("moldata"), bp::arg("resid") ), "Construct as a specified residue") ); Residue_exposer.def( bp::init< SireMol::Residue const & >(( bp::arg("other") ), "Copy constructor") ); + { //::SireMol::Residue::alternateName + + typedef ::SireMol::ResName ( ::SireMol::Residue::*alternateName_function_type)( ) const; + alternateName_function_type alternateName_function_value( &::SireMol::Residue::alternateName ); + + Residue_exposer.def( + "alternateName" + , alternateName_function_value + , bp::release_gil_policy() + , "" ); + + } { //::SireMol::Residue::assertContainsMetadata typedef void ( ::SireMol::Residue::*assertContainsMetadata_function_type)( ::SireBase::PropertyName const & ) const; diff --git a/wrapper/System/_System_free_functions.pypp.cpp b/wrapper/System/_System_free_functions.pypp.cpp index 372b00b7c..3992360c6 100644 --- a/wrapper/System/_System_free_functions.pypp.cpp +++ b/wrapper/System/_System_free_functions.pypp.cpp @@ -977,13 +977,13 @@ void register_free_functions(){ { //::SireSystem::merge - typedef ::SireMol::Molecule ( *merge_function_type )( ::SireMol::AtomMapping const &,bool,::SireBase::PropertyMap const & ); + typedef ::SireMol::Molecule ( *merge_function_type )( ::SireMol::AtomMapping const &,bool,bool,bool,bool,::SireBase::PropertyMap const & ); merge_function_type merge_function_value( &::SireSystem::merge ); bp::def( "merge" , merge_function_value - , ( bp::arg("mols"), bp::arg("as_new_molecule")=(bool)(true), bp::arg("map")=SireBase::PropertyMap() ) + , ( bp::arg("mols"), bp::arg("as_new_molecule")=(bool)(true), bp::arg("allow_ring_breaking")=(bool)(false), bp::arg("allow_ring_size_change")=(bool)(false), bp::arg("force")=(bool)(false), bp::arg("map")=SireBase::PropertyMap() ) , "" ); } From 469e28453c822da2e3d781c8be93dc0767b0591e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 22 Feb 2024 22:43:11 +0000 Subject: [PATCH 125/468] WIP - filling in missing functions and fixing wrappers --- corelib/src/libs/SireMol/atomeditor.cpp | 79 ++++++++++++ corelib/src/libs/SireMol/atomeditor.h | 4 +- corelib/src/libs/SireMol/moleculedata.cpp | 42 +++++++ corelib/src/libs/SireMol/moleculedata.h | 6 + corelib/src/libs/SireMol/moleditor.cpp | 9 ++ corelib/src/libs/SireMol/moleditor.h | 2 + corelib/src/libs/SireMol/reseditor.cpp | 79 ++++++++++++ corelib/src/libs/SireMol/reseditor.h | 12 +- corelib/src/libs/SireMol/structureeditor.cpp | 8 +- corelib/src/libs/SireMol/structureeditor.h | 8 +- corelib/src/libs/SireSystem/merge.cpp | 126 +++++++------------ wrapper/Mol/AtomEditor.pypp.cpp | 4 +- wrapper/Mol/AtomStructureEditor.pypp.cpp | 8 +- wrapper/Mol/MolEditor.pypp.cpp | 12 ++ wrapper/Mol/MolStructureEditor.pypp.cpp | 2 +- wrapper/Mol/ResEditor.pypp.cpp | 31 +++-- wrapper/Mol/ResStructureEditor.pypp.cpp | 24 ++-- wrapper/Mol/special_code.py | 3 + 18 files changed, 329 insertions(+), 130 deletions(-) diff --git a/corelib/src/libs/SireMol/atomeditor.cpp b/corelib/src/libs/SireMol/atomeditor.cpp index 33c7de4f4..d810d4311 100644 --- a/corelib/src/libs/SireMol/atomeditor.cpp +++ b/corelib/src/libs/SireMol/atomeditor.cpp @@ -133,6 +133,30 @@ QString AtomEditor::toString() const return QObject::tr("Editor{ %1 }").arg(Atom::toString()); } +/** Return the alternate name for this atom */ +AtomName AtomEditor::alternateName() const +{ + return d->getAlternateAtomName(this->index()); +} + +/** Set the alternate name for this atom */ +AtomEditor &AtomEditor::setAlternateName(const AtomName &newname) +{ + if (newname == this->alternateName()) + // nothing needs to be done + return *this; + + d->setAlternateAtomName(this->index(), newname); + + return *this; +} + +/** Set the alternate name for this atom */ +AtomEditor &AtomEditor::setAlternateName(const QString &newname) +{ + return this->setAlternateName(AtomName(newname)); +} + /** Rename this atom so that it is called 'newname' */ AtomEditor &AtomEditor::rename(const AtomName &newname) { @@ -145,6 +169,12 @@ AtomEditor &AtomEditor::rename(const AtomName &newname) return *this; } +/** Rename this atom */ +AtomEditor &AtomEditor::rename(const QString &newname) +{ + return this->rename(AtomName(newname)); +} + /** Renumber this atom so that it has number 'newnum' */ AtomEditor &AtomEditor::renumber(AtomNum newnum) { @@ -157,6 +187,12 @@ AtomEditor &AtomEditor::renumber(AtomNum newnum) return *this; } +/** Renumber this atom */ +AtomEditor &AtomEditor::renumber(int newnum) +{ + return this->renumber(AtomNum(newnum)); +} + /** Reindex this atom so that it lies at index 'newidx'. Note that if 'newidx' is greater than the number of atoms, then this will move this atom to be the last in the list */ @@ -167,6 +203,12 @@ AtomStructureEditor AtomEditor::reindex(AtomIdx newidx) const return editor; } +/** Reindex this atom */ +AtomStructureEditor AtomEditor::reindex(int newidx) const +{ + return this->reindex(AtomIdx(newidx)); +} + /** Remove this atom from the molecule, returning an editor that can further edit the structure of the molecule */ MolStructureEditor AtomEditor::remove() const @@ -412,6 +454,25 @@ MolStructureEditor AtomStructureEditor::molecule() return MolStructureEditor(*this); } +/** Return the alternate name for this atom */ +const AtomName &AtomStructureEditor::alternateName() const +{ + return StructureEditor::getAlternateAtomName(uid); +} + +/** Set the alternate name for this atom */ +AtomStructureEditor &AtomStructureEditor::setAlternateName(const AtomName &newname) +{ + StructureEditor::setAlternateAtomName(uid, newname); + return *this; +} + +/** Set the alternate name for this atom */ +AtomStructureEditor &AtomStructureEditor::setAlternateName(const QString &newname) +{ + return this->setAlternateName(AtomName(newname)); +} + /** Rename this atom to 'newname' */ AtomStructureEditor &AtomStructureEditor::rename(const AtomName &newname) { @@ -419,6 +480,12 @@ AtomStructureEditor &AtomStructureEditor::rename(const AtomName &newname) return *this; } +/** Rename this atom */ +AtomStructureEditor &AtomStructureEditor::rename(const QString &newname) +{ + return this->rename(AtomName(newname)); +} + /** Renumber this atom to 'newnum' */ AtomStructureEditor &AtomStructureEditor::renumber(AtomNum newnum) { @@ -426,6 +493,12 @@ AtomStructureEditor &AtomStructureEditor::renumber(AtomNum newnum) return *this; } +/** Renumber this atom */ +AtomStructureEditor &AtomStructureEditor::renumber(int newnum) +{ + return this->renumber(AtomNum(newnum)); +} + /** Reindex this atom to 'newidx' - this will move the atom to the end if 'newidx' is greater than the number of atoms in the molecule */ @@ -435,6 +508,12 @@ AtomStructureEditor &AtomStructureEditor::reindex(AtomIdx newidx) return *this; } +/** Reindex this atom */ +AtomStructureEditor &AtomStructureEditor::reindex(int newidx) +{ + return this->reindex(AtomIdx(newidx)); +} + /** Completely remove this atom from the molecule and return a MolStructureEditor that can be used to continue editing the molecule */ diff --git a/corelib/src/libs/SireMol/atomeditor.h b/corelib/src/libs/SireMol/atomeditor.h index 371a8f3d8..9a3e248e9 100644 --- a/corelib/src/libs/SireMol/atomeditor.h +++ b/corelib/src/libs/SireMol/atomeditor.h @@ -198,8 +198,8 @@ namespace SireMol AtomStructureEditor &reparent(SegIdx segidx); AtomStructureEditor &reparent(const SegID &segid); - void setAlternateName(const QString &name); - void setAlternateName(const AtomName &name); + AtomStructureEditor &setAlternateName(const QString &name); + AtomStructureEditor &setAlternateName(const AtomName &name); const AtomName &alternateName() const; diff --git a/corelib/src/libs/SireMol/moleculedata.cpp b/corelib/src/libs/SireMol/moleculedata.cpp index d60133099..08cf8bab7 100644 --- a/corelib/src/libs/SireMol/moleculedata.cpp +++ b/corelib/src/libs/SireMol/moleculedata.cpp @@ -672,6 +672,48 @@ void MoleculeData::rename(const MolName &newname) } } +/** Set the alternate atom name for the specified atom */ +void MoleculeData::setAlternateAtomName(AtomIdx atomidx, const AtomName &newname) +{ + MoleculeInfoData newinfo = molinfo->setAlternateName(atomidx, newname); + + if (newinfo.UID() != molinfo.constData()->UID()) + { + SireBase::assert_true(vrsns.get() != 0, CODELOC); + + molinfo = newinfo; + updatePropertyMolInfo(); + vrsn = vrsns->increment(); + } +} + +/** Set the alternate residue name for the specified residue */ +void MoleculeData::setAlternateResName(ResIdx residx, const ResName &newname) +{ + MoleculeInfoData newinfo = molinfo->setAlternateName(residx, newname); + + if (newinfo.UID() != molinfo.constData()->UID()) + { + SireBase::assert_true(vrsns.get() != 0, CODELOC); + + molinfo = newinfo; + updatePropertyMolInfo(); + vrsn = vrsns->increment(); + } +} + +/** Return the alternate atom name for the specified atom */ +AtomName MoleculeData::getAlternateAtomName(AtomIdx atomidx) const +{ + return molinfo->alternateName(atomidx); +} + +/** Return the alternate residue name for the specified residue */ +ResName MoleculeData::getAlternateResName(ResIdx residx) const +{ + return molinfo->alternateName(residx); +} + /** Rename the atom at index 'atomidx' to 'newname' \throw SireError::invalid_index diff --git a/corelib/src/libs/SireMol/moleculedata.h b/corelib/src/libs/SireMol/moleculedata.h index b1cc92cb7..22293cbf1 100644 --- a/corelib/src/libs/SireMol/moleculedata.h +++ b/corelib/src/libs/SireMol/moleculedata.h @@ -247,6 +247,12 @@ namespace SireMol void renumber(const QHash &resnums); void renumber(const QHash &atomnums, const QHash &resnums); + void setAlternateAtomName(AtomIdx atomidx, const AtomName &newname); + void setAlternateResName(ResIdx residx, const ResName &newname); + + AtomName getAlternateAtomName(AtomIdx atomidx) const; + ResName getAlternateResName(ResIdx residx) const; + void setProperty(const QString &key, const Property &value, bool clear_metadata = false); bool updateProperty(const QString &key, const Property &value, bool auto_add = true); diff --git a/corelib/src/libs/SireMol/moleditor.cpp b/corelib/src/libs/SireMol/moleditor.cpp index 5089eb2c8..4876a08a5 100644 --- a/corelib/src/libs/SireMol/moleditor.cpp +++ b/corelib/src/libs/SireMol/moleditor.cpp @@ -189,6 +189,15 @@ MolEditor &MolEditor::renumber(const QHash &atomnums, const QH return *this; } +/** Return an editor where all atoms have been moved into a + * single cutgroup + */ +MolStructureEditor MolEditor::makeSingleCutGroup() const +{ + MolStructureEditor editor(*this); + return editor.makeSingleCutGroup(); +} + /** Add an atom called 'name' and return an editor that can be used to edit it */ AtomStructureEditor MolEditor::add(const AtomName &name) const diff --git a/corelib/src/libs/SireMol/moleditor.h b/corelib/src/libs/SireMol/moleditor.h index 1843f83cb..a2c8e759c 100644 --- a/corelib/src/libs/SireMol/moleditor.h +++ b/corelib/src/libs/SireMol/moleditor.h @@ -120,6 +120,8 @@ namespace SireMol MolEditor &removeLink(const QString &key); MolEditor &removeAllLinks(); + MolStructureEditor makeSingleCutGroup() const; + AtomStructureEditor add(const AtomName &atom) const; AtomStructureEditor add(const AtomNum &atom) const; diff --git a/corelib/src/libs/SireMol/reseditor.cpp b/corelib/src/libs/SireMol/reseditor.cpp index 86ff70e83..71c86a5f2 100644 --- a/corelib/src/libs/SireMol/reseditor.cpp +++ b/corelib/src/libs/SireMol/reseditor.cpp @@ -127,6 +127,30 @@ QString ResEditor::toString() const return QObject::tr("Editor{ %1 }").arg(Residue::toString()); } +/** Return the alternate name for this residue */ +ResName ResEditor::alternateName() const +{ + return d->getAlternateResName(this->index()); +} + +/** Set the alternate residue name for this residue */ +ResEditor &ResEditor::setAlternateName(const ResName &altname) +{ + if (altname == this->alternateName()) + // nothing to do + return *this; + + d->setAlternateResName(this->index(), altname); + + return *this; +} + +/** Set the alternate name for this residue */ +ResEditor &ResEditor::setAlternateName(const QString &altname) +{ + return this->setAlternateName(ResName(altname)); +} + /** Rename this residue to 'newname' */ ResEditor &ResEditor::rename(const ResName &newname) { @@ -139,6 +163,12 @@ ResEditor &ResEditor::rename(const ResName &newname) return *this; } +/** Rename this residue to 'newname' */ +ResEditor &ResEditor::rename(const QString &newname) +{ + return this->rename(ResName(newname)); +} + /** Renumber this residue to 'newnum' */ ResEditor &ResEditor::renumber(ResNum newnum) { @@ -151,6 +181,12 @@ ResEditor &ResEditor::renumber(ResNum newnum) return *this; } +/** Renumber this residue to 'newnum' */ +ResEditor &ResEditor::renumber(int newnum) +{ + return this->renumber(ResNum(newnum)); +} + /** Change the index of this residue to 'newidx'. If this is larger than the number of residues in the molecule then this residue is moved to the end */ @@ -162,6 +198,12 @@ ResStructureEditor ResEditor::reindex(ResIdx newidx) const return editor; } +/** Reindex this residue to 'newidx' */ +ResStructureEditor ResEditor::reindex(int newidx) const +{ + return this->reindex(ResIdx(newidx)); +} + /** Completely remove this residue from the molecule - this returns a MolStructureEditor that can be used to further edit the molecule */ MolStructureEditor ResEditor::remove() const @@ -447,6 +489,25 @@ AtomStructureEditor ResStructureEditor::select(const AtomID &atomid) return AtomStructureEditor(*this, atomIdx(atomid)); } +/** Return the alternate name for this residue */ +const ResName &ResStructureEditor::alternateName() const +{ + return StructureEditor::getAlternateResName(uid); +} + +/** Set the alternate residue name for this residue */ +ResStructureEditor &ResStructureEditor::setAlternateName(const ResName &altname) +{ + StructureEditor::setAlternateResName(uid, altname); + return *this; +} + +/** Set the alternate name for this residue */ +ResStructureEditor &ResStructureEditor::setAlternateName(const QString &altname) +{ + return this->setAlternateName(ResName(altname)); +} + /** Rename this residue to 'newname' */ ResStructureEditor &ResStructureEditor::rename(const ResName &newname) { @@ -454,6 +515,12 @@ ResStructureEditor &ResStructureEditor::rename(const ResName &newname) return *this; } +/** Rename this residue to 'newname' */ +ResStructureEditor &ResStructureEditor::rename(const QString &newname) +{ + return this->rename(ResName(newname)); +} + /** Renumber this residue to 'newnum' */ ResStructureEditor &ResStructureEditor::renumber(ResNum newnum) { @@ -461,6 +528,12 @@ ResStructureEditor &ResStructureEditor::renumber(ResNum newnum) return *this; } +/** Renumber this residue to 'newnum' */ +ResStructureEditor &ResStructureEditor::renumber(int newnum) +{ + return this->renumber(ResNum(newnum)); +} + /** Change the index of this residue to 'newidx'. If this is larger than the number of residues in the molecule then this residue is moved to the end */ @@ -470,6 +543,12 @@ ResStructureEditor &ResStructureEditor::reindex(ResIdx newidx) return *this; } +/** Reindex this residue to 'newidx' */ +ResStructureEditor &ResStructureEditor::reindex(int newidx) +{ + return this->reindex(ResIdx(newidx)); +} + /** Completely remove this residue from the molecule - this returns a MolStructureEditor that can be used to further edit the molecule */ MolStructureEditor ResStructureEditor::remove() diff --git a/corelib/src/libs/SireMol/reseditor.h b/corelib/src/libs/SireMol/reseditor.h index 59c4adc20..4a794ab3d 100644 --- a/corelib/src/libs/SireMol/reseditor.h +++ b/corelib/src/libs/SireMol/reseditor.h @@ -105,12 +105,12 @@ namespace SireMol ResEditor &renumber(int number); ResStructureEditor reindex(ResIdx index) const; - ResStructureEditor &reindex(int index) const; + ResStructureEditor reindex(int index) const; - ResEditor &setAlternatename(const ResName &name); - ResEditor &setAlternatename(const QString &name); + ResEditor &setAlternateName(const ResName &name); + ResEditor &setAlternateName(const QString &name); - const ResName &alternateName() const; + ResName alternateName() const; MolStructureEditor remove() const; @@ -189,8 +189,8 @@ namespace SireMol ResStructureEditor &renumber(int number); ResStructureEditor &reindex(int index); - ResStructureEditor &setAlternatename(const ResName &name); - ResStructureEditor &setAlternatename(const QString &name); + ResStructureEditor &setAlternateName(const ResName &name); + ResStructureEditor &setAlternateName(const QString &name); const ResName &alternateName() const; diff --git a/corelib/src/libs/SireMol/structureeditor.cpp b/corelib/src/libs/SireMol/structureeditor.cpp index 83f7e3b45..9cca38dee 100644 --- a/corelib/src/libs/SireMol/structureeditor.cpp +++ b/corelib/src/libs/SireMol/structureeditor.cpp @@ -3961,7 +3961,7 @@ void StructureEditor::renumberMolecule(MolNum newnum) } /** Set the alternate atom name */ -void StructureEditor::setAlternateName(quint32 uid, const AtomName &name) +void StructureEditor::setAlternateAtomName(quint32 uid, const AtomName &name) { this->assertSane(); @@ -3975,7 +3975,7 @@ void StructureEditor::setAlternateName(quint32 uid, const AtomName &name) } /** Set the alternate residue name */ -void StructureEditor::setAlternateName(quint32 uid, const ResName &name) +void StructureEditor::setAlternateResName(quint32 uid, const ResName &name) { this->assertSane(); @@ -3991,7 +3991,7 @@ void StructureEditor::setAlternateName(quint32 uid, const ResName &name) /** Return the alternate atom name - this will be the atom name if * this hasn't been set */ -const AtomName &StructureEditor::alternateAtomName(quint32 uid) const +const AtomName &StructureEditor::getAlternateAtomName(quint32 uid) const { this->assertSane(); @@ -4003,7 +4003,7 @@ const AtomName &StructureEditor::alternateAtomName(quint32 uid) const return atom.altname; } -const ResName &StructureEditor::alternateResName(quint32 uid) const +const ResName &StructureEditor::getAlternateResName(quint32 uid) const { this->assertSane(); diff --git a/corelib/src/libs/SireMol/structureeditor.h b/corelib/src/libs/SireMol/structureeditor.h index 097069bfb..1cd9396d7 100644 --- a/corelib/src/libs/SireMol/structureeditor.h +++ b/corelib/src/libs/SireMol/structureeditor.h @@ -276,11 +276,11 @@ namespace SireMol void renameSegment(quint32 uid, const SegName &name); void reindexSegment(quint32 uid, SegIdx index); - void setAlternateName(quint32 uid, const AtomName &name); - void setAlternateName(quint32 uid, const ResName &name); + void setAlternateAtomName(quint32 uid, const AtomName &name); + void setAlternateResName(quint32 uid, const ResName &name); - const AtomName &alternateAtomName(quint32 uid) const; - const ResName &alternateResName(quint32 uid) const; + const AtomName &getAlternateAtomName(quint32 uid) const; + const ResName &getAlternateResName(quint32 uid) const; void removeAtom(quint32 uid); void removeCutGroup(quint32 uid); diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index ba439748c..d06aa9c33 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -123,103 +123,71 @@ namespace SireSystem const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); - // first, check that the merge will not change any of the CutGroup assigments... - if (mol.nCutGroups() > 1) - { - bool merge_changes_cutgroups = false; - - QHash cg_map; - cg_map.reserve(mol.nCutGroups()); - - for (int i = 0; i < nmapped; ++i) - { - const auto cg0 = mapped_atoms0[i].cutGroup().index(); - const auto cg1 = mapped_atoms1[i].cutGroup().index(); - - if (cg_map.contains(cg0)) - { - if (cg_map[cg0] != cg1) - { - merge_changes_cutgroups = true; - break; - } - } - else - { - cg_map[cg0] = cg1; - } - } - - if (merge_changes_cutgroups) - { - // it is safest to move all atoms into a single cutgroup - mol.makeSingleCutGroup(); - } - } - // copy the properties from the reference state to both states QStringList merged_properties = {"charge", "LJ", "atomtype", "intrascale", "coordinates", "mass", "element", "bond", "angle", "dihedral", "improper"}; - for (int i = 0; i < mol.nAtoms(); ++i) - { - auto atom = mol.atom(AtomIdx(i)); - - for (const auto &prop : merged_properties) - { - if (mol0.hasProperty(map0[prop])) + /* + for (int i = 0; i < mol.nAtoms(); ++i) { - const auto &val = mol0.property(map0[prop]); + auto atom = mol.atom(AtomIdx(i)); - atom.setProperty(map[prop + "0"].source(), val); - atom.setProperty(map[prop + "1"].source(), val); + for (const auto &prop : merged_properties) + { + if (mol0.hasProperty(map0[prop])) + { + const auto &val = mol0.property(map0[prop]); + + atom.setProperty(map[prop + "0"].source(), val); + atom.setProperty(map[prop + "1"].source(), val); + } + } } - } - } - QVector matched_atoms; - matched_atoms.reserve(nmapped); + QVector matched_atoms; + matched_atoms.reserve(nmapped); - // now go through and update the values of properties for - // the atoms that mutate - ResStructureEditor last_res; - bool changed_res = false; + // now go through and update the values of properties for + // the atoms that mutate + ResStructureEditor last_res; + bool changed_res = false; - for (int i = 0; i < nmapped; ++i) - { - const auto atom0 = mapped_atoms0[i]; - const auto atom1 = mapped_atoms1[i]; + for (int i = 0; i < nmapped; ++i) + { + const auto atom0 = mapped_atoms0[i]; + const auto atom1 = mapped_atoms1[i]; - matched_atoms.append(mol.atom(atom0.index())); - auto &atom = matched_atoms.last(); + matched_atoms.append(mol.atom(atom0.index())); + auto &atom = matched_atoms.last(); - // save the perturbed state atom and residue names into new properties, so - // that we can use these when extracting the end states - atom.setAlternateName(atom1.name()); + // save the perturbed state atom and residue names into new properties, so + // that we can use these when extracting the end states + atom.setAlternateName(atom1.name()); - try - { - auto next_res = atom.residue(); + try + { + auto next_res = atom.residue(); - if (next_res != last_res) - { - changed_res = true; - last_res = next_res; - } - } - catch (...) - { - } + if (next_res != last_res) + { + changed_res = true; + last_res = next_res; + } + } + catch (...) + { + } - if (changed_res) - { - last_res.setAlternateName(atom1.residue().name()); - } + if (changed_res) + { + last_res.setAlternateName(atom1.residue().name()); + } - // check if we need to change residue - } + // check if we need to change residue + } + */ if (as_new_molecule) { diff --git a/wrapper/Mol/AtomEditor.pypp.cpp b/wrapper/Mol/AtomEditor.pypp.cpp index b7eb7d835..c5086d6dd 100644 --- a/wrapper/Mol/AtomEditor.pypp.cpp +++ b/wrapper/Mol/AtomEditor.pypp.cpp @@ -282,7 +282,7 @@ void register_AtomEditor_class(){ "setAlternateName" , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } @@ -295,7 +295,7 @@ void register_AtomEditor_class(){ "setAlternateName" , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } diff --git a/wrapper/Mol/AtomStructureEditor.pypp.cpp b/wrapper/Mol/AtomStructureEditor.pypp.cpp index 785a9616b..b45035909 100644 --- a/wrapper/Mol/AtomStructureEditor.pypp.cpp +++ b/wrapper/Mol/AtomStructureEditor.pypp.cpp @@ -395,27 +395,27 @@ void register_AtomStructureEditor_class(){ } { //::SireMol::AtomStructureEditor::setAlternateName - typedef void ( ::SireMol::AtomStructureEditor::*setAlternateName_function_type)( ::QString const & ) ; + typedef ::SireMol::AtomStructureEditor & ( ::SireMol::AtomStructureEditor::*setAlternateName_function_type)( ::QString const & ) ; setAlternateName_function_type setAlternateName_function_value( &::SireMol::AtomStructureEditor::setAlternateName ); AtomStructureEditor_exposer.def( "setAlternateName" , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } { //::SireMol::AtomStructureEditor::setAlternateName - typedef void ( ::SireMol::AtomStructureEditor::*setAlternateName_function_type)( ::SireMol::AtomName const & ) ; + typedef ::SireMol::AtomStructureEditor & ( ::SireMol::AtomStructureEditor::*setAlternateName_function_type)( ::SireMol::AtomName const & ) ; setAlternateName_function_type setAlternateName_function_value( &::SireMol::AtomStructureEditor::setAlternateName ); AtomStructureEditor_exposer.def( "setAlternateName" , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } diff --git a/wrapper/Mol/MolEditor.pypp.cpp b/wrapper/Mol/MolEditor.pypp.cpp index 105683b9c..ace848b6e 100644 --- a/wrapper/Mol/MolEditor.pypp.cpp +++ b/wrapper/Mol/MolEditor.pypp.cpp @@ -172,6 +172,18 @@ void register_MolEditor_class(){ , bp::release_gil_policy() , "Commit these changes and return a copy of the\nedited molecule" ); + } + { //::SireMol::MolEditor::makeSingleCutGroup + + typedef ::SireMol::MolStructureEditor ( ::SireMol::MolEditor::*makeSingleCutGroup_function_type)( ) const; + makeSingleCutGroup_function_type makeSingleCutGroup_function_value( &::SireMol::MolEditor::makeSingleCutGroup ); + + MolEditor_exposer.def( + "makeSingleCutGroup" + , makeSingleCutGroup_function_value + , bp::return_self< >() + , "" ); + } { //::SireMol::MolEditor::operator= diff --git a/wrapper/Mol/MolStructureEditor.pypp.cpp b/wrapper/Mol/MolStructureEditor.pypp.cpp index 5182545a8..23d99a8fa 100644 --- a/wrapper/Mol/MolStructureEditor.pypp.cpp +++ b/wrapper/Mol/MolStructureEditor.pypp.cpp @@ -207,7 +207,7 @@ void register_MolStructureEditor_class(){ MolStructureEditor_exposer.def( "makeSingleCutGroup" , makeSingleCutGroup_function_value - , bp::release_gil_policy() + , bp::return_self< >() , "Move all atoms into a single CutGroup" ); } diff --git a/wrapper/Mol/ResEditor.pypp.cpp b/wrapper/Mol/ResEditor.pypp.cpp index 99a65c8f2..07c210eab 100644 --- a/wrapper/Mol/ResEditor.pypp.cpp +++ b/wrapper/Mol/ResEditor.pypp.cpp @@ -3,7 +3,6 @@ // (C) Christopher Woods, GPL >= 3 License #include "boost/python.hpp" -#include "Helpers/clone_const_reference.hpp" #include "ResEditor.pypp.hpp" namespace bp = boost::python; @@ -88,13 +87,13 @@ void register_ResEditor_class(){ } { //::SireMol::ResEditor::alternateName - typedef ::SireMol::ResName const & ( ::SireMol::ResEditor::*alternateName_function_type)( ) const; + typedef ::SireMol::ResName ( ::SireMol::ResEditor::*alternateName_function_type)( ) const; alternateName_function_type alternateName_function_value( &::SireMol::ResEditor::alternateName ); ResEditor_exposer.def( "alternateName" , alternateName_function_value - , bp::return_value_policy() + , bp::release_gil_policy() , "" ); } @@ -151,7 +150,7 @@ void register_ResEditor_class(){ } { //::SireMol::ResEditor::reindex - typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResEditor::*reindex_function_type)( int ) const; + typedef ::SireMol::ResStructureEditor ( ::SireMol::ResEditor::*reindex_function_type)( int ) const; reindex_function_type reindex_function_value( &::SireMol::ResEditor::reindex ); ResEditor_exposer.def( @@ -265,29 +264,29 @@ void register_ResEditor_class(){ , "Move this residue into the chain with ID chainid\nThrow: SireMol::missing_chain\nThrow: SireMol::duplicate_chain\nThrow: SireError::invalid_index\n" ); } - { //::SireMol::ResEditor::setAlternatename + { //::SireMol::ResEditor::setAlternateName - typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*setAlternatename_function_type)( ::SireMol::ResName const & ) ; - setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResEditor::setAlternatename ); + typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*setAlternateName_function_type)( ::SireMol::ResName const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::ResEditor::setAlternateName ); ResEditor_exposer.def( - "setAlternatename" - , setAlternatename_function_value + "setAlternateName" + , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } - { //::SireMol::ResEditor::setAlternatename + { //::SireMol::ResEditor::setAlternateName - typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*setAlternatename_function_type)( ::QString const & ) ; - setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResEditor::setAlternatename ); + typedef ::SireMol::ResEditor & ( ::SireMol::ResEditor::*setAlternateName_function_type)( ::QString const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::ResEditor::setAlternateName ); ResEditor_exposer.def( - "setAlternatename" - , setAlternatename_function_value + "setAlternateName" + , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } diff --git a/wrapper/Mol/ResStructureEditor.pypp.cpp b/wrapper/Mol/ResStructureEditor.pypp.cpp index 2c0caef0a..c274f9e3f 100644 --- a/wrapper/Mol/ResStructureEditor.pypp.cpp +++ b/wrapper/Mol/ResStructureEditor.pypp.cpp @@ -400,29 +400,29 @@ void register_ResStructureEditor_class(){ , "Is this editor editing the entire molecule?" ); } - { //::SireMol::ResStructureEditor::setAlternatename + { //::SireMol::ResStructureEditor::setAlternateName - typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*setAlternatename_function_type)( ::SireMol::ResName const & ) ; - setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResStructureEditor::setAlternatename ); + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*setAlternateName_function_type)( ::SireMol::ResName const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::ResStructureEditor::setAlternateName ); ResStructureEditor_exposer.def( - "setAlternatename" - , setAlternatename_function_value + "setAlternateName" + , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } - { //::SireMol::ResStructureEditor::setAlternatename + { //::SireMol::ResStructureEditor::setAlternateName - typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*setAlternatename_function_type)( ::QString const & ) ; - setAlternatename_function_type setAlternatename_function_value( &::SireMol::ResStructureEditor::setAlternatename ); + typedef ::SireMol::ResStructureEditor & ( ::SireMol::ResStructureEditor::*setAlternateName_function_type)( ::QString const & ) ; + setAlternateName_function_type setAlternateName_function_value( &::SireMol::ResStructureEditor::setAlternateName ); ResStructureEditor_exposer.def( - "setAlternatename" - , setAlternatename_function_value + "setAlternateName" + , setAlternateName_function_value , ( bp::arg("name") ) - , bp::release_gil_policy() + , bp::return_self< >() , "" ); } diff --git a/wrapper/Mol/special_code.py b/wrapper/Mol/special_code.py index 87e6e390b..72c7a5eb5 100644 --- a/wrapper/Mol/special_code.py +++ b/wrapper/Mol/special_code.py @@ -205,6 +205,7 @@ def fix_BeadEditorBase(c): def fix_AtomEditor(c): + c.decls("setAlternateName").call_policies = call_policies.return_self() c.decls("rename").call_policies = call_policies.return_self() c.decls("renumber").call_policies = call_policies.return_self() @@ -251,6 +252,7 @@ def fix_CGStructureEditor(c): def fix_ResEditor(c): + c.decls("setAlternateName").call_policies = call_policies.return_self() c.decls("renumber").call_policies = call_policies.return_self() c.decls("rename").call_policies = call_policies.return_self() @@ -268,6 +270,7 @@ def fix_ResStructureEditor(c): def fix_MolEditor(c, include_links=True): c.decls("renumber").call_policies = call_policies.return_self() c.decls("rename").call_policies = call_policies.return_self() + c.decls("makeSingleCutGroup").call_policies = call_policies.return_self() if include_links: c.decls("addLink").call_policies = call_policies.return_self() From 85b2419bc5f66a8b8abce8a36ab666b9c85d1d50 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 22 Feb 2024 22:53:25 +0000 Subject: [PATCH 126/468] All functions implemented - can now compile and run code that has alternate atom and residue names. Needs testing, plus then integrating with the merge code --- corelib/src/libs/SireMol/atom.cpp | 6 ++++++ corelib/src/libs/SireMol/residue.cpp | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/corelib/src/libs/SireMol/atom.cpp b/corelib/src/libs/SireMol/atom.cpp index 4c50d97d3..6aa637805 100644 --- a/corelib/src/libs/SireMol/atom.cpp +++ b/corelib/src/libs/SireMol/atom.cpp @@ -213,6 +213,12 @@ AtomName Atom::name() const return d->info().name(atomidx); } +/** Return the alternate name of the atom */ +AtomName Atom::alternateName() const +{ + return d->getAlternateAtomName(atomidx); +} + /** Return the number of the atom */ AtomNum Atom::number() const { diff --git a/corelib/src/libs/SireMol/residue.cpp b/corelib/src/libs/SireMol/residue.cpp index cdf76ce34..a254f02cd 100644 --- a/corelib/src/libs/SireMol/residue.cpp +++ b/corelib/src/libs/SireMol/residue.cpp @@ -228,6 +228,12 @@ ResName Residue::name() const return d->info().name(residx); } +/** Return the alternate name of this residue */ +ResName Residue::alternateName() const +{ + return d->getAlternateResName(residx); +} + /** Return the number of this residue */ ResNum Residue::number() const { From 1d87e8fd2eb4427953b3b8c05c81ac766b3495bd Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 23 Feb 2024 19:03:59 +0000 Subject: [PATCH 127/468] Added functions to switch to or remove the alternate names. Added in code for fix_170 --- corelib/src/libs/SireMol/element.h | 16 ++ corelib/src/libs/SireMol/elementdb.cpp | 174 ++++++++++++---- corelib/src/libs/SireMol/moleculedata.cpp | 16 ++ corelib/src/libs/SireMol/moleculedata.h | 3 + corelib/src/libs/SireMol/moleculeinfo.cpp | 16 ++ corelib/src/libs/SireMol/moleculeinfo.h | 3 + corelib/src/libs/SireMol/moleculeinfodata.cpp | 82 ++++++++ corelib/src/libs/SireMol/moleculeinfodata.h | 3 + corelib/src/libs/SireMol/moleditor.cpp | 36 ++++ corelib/src/libs/SireMol/moleditor.h | 6 + corelib/src/libs/SireMol/structureeditor.cpp | 58 ++++++ corelib/src/libs/SireMol/structureeditor.h | 3 + src/sire/_pythonize.py | 2 +- src/sire/mm/__init__.py | 193 ++++++++++-------- src/sire/mol/__init__.py | 6 + src/sire/mol/_trajectory.py | 49 ++--- tests/mol/test_element.py | 51 +++++ wrapper/Mol/Atom.pypp.cpp | 2 +- wrapper/Mol/AtomEditor.pypp.cpp | 12 +- wrapper/Mol/AtomStructureEditor.pypp.cpp | 12 +- wrapper/Mol/Element.pypp.cpp | 60 ++++++ wrapper/Mol/MolEditor.pypp.cpp | 27 ++- wrapper/Mol/MolStructureEditor.pypp.cpp | 25 +++ wrapper/Mol/MoleculeInfo.pypp.cpp | 24 +++ wrapper/Mol/ResEditor.pypp.cpp | 8 +- wrapper/Mol/ResStructureEditor.pypp.cpp | 8 +- wrapper/Mol/Residue.pypp.cpp | 2 +- wrapper/Mol/SireMol_containers.cpp | 170 +++++++-------- wrapper/Mol/_Mol.main.cpp | 4 + wrapper/Mol/__init__.py | 6 + wrapper/Mol/special_code.py | 4 + 31 files changed, 810 insertions(+), 271 deletions(-) create mode 100644 tests/mol/test_element.py diff --git a/corelib/src/libs/SireMol/element.h b/corelib/src/libs/SireMol/element.h index e6dc6b209..66f95d1c1 100644 --- a/corelib/src/libs/SireMol/element.h +++ b/corelib/src/libs/SireMol/element.h @@ -79,11 +79,19 @@ namespace SireMol bool operator==(const Element &other) const; bool operator!=(const Element &other) const; + bool operator==(const QString &other) const; + bool operator!=(const QString &other) const; + bool operator>(const Element &other) const; bool operator<(const Element &other) const; bool operator>=(const Element &other) const; bool operator<=(const Element &other) const; + bool operator>(const QString &other) const; + bool operator<(const QString &other) const; + bool operator>=(const QString &other) const; + bool operator<=(const QString &other) const; + const Element &operator=(const Element &element); int nProtons() const; @@ -122,7 +130,15 @@ namespace SireMol static Element biologicalElement(const QString &name); + static void setElementIsBiological(const Element &element); + static void setElementIsNotBiological(const Element &element); + static void resetBiologicalElements(); + + static QList getBiologicalElements(); + private: + bool _locked_biological() const; + /** Pointer to the object containing the data for this element */ ElementData *eldata; }; diff --git a/corelib/src/libs/SireMol/elementdb.cpp b/corelib/src/libs/SireMol/elementdb.cpp index a02c103f9..c9f168176 100644 --- a/corelib/src/libs/SireMol/elementdb.cpp +++ b/corelib/src/libs/SireMol/elementdb.cpp @@ -27,6 +27,7 @@ #include #include +#include #include #include @@ -123,6 +124,111 @@ ElementDB *ElementDB::db = 0; /////////// Implementation of Element /////////// +Q_GLOBAL_STATIC(QReadWriteLock, globalLock); +Q_GLOBAL_STATIC(QSet, biological_elements); + +/** Set that the passed element should be considered to be biological */ +void Element::setElementIsBiological(const Element &element) +{ + QWriteLocker locker(globalLock()); + biological_elements->insert(element.nProtons()); +} + +/** Set that the passed element should considered to definitely + * not be biological + */ +void Element::setElementIsNotBiological(const Element &element) +{ + QWriteLocker locker(globalLock()); + biological_elements->remove(element.nProtons()); +} + +void Element::resetBiologicalElements() +{ + QWriteLocker locker(globalLock()); + biological_elements->clear(); + + for (int i = 0; i < 80; ++i) + { + Element el(i); + + if ((el.period() <= 3 and not el.nobleGas()) or el.halogen()) + biological_elements->insert(i); + } + + // also add Fe + biological_elements->insert(26); +} + +/** Return a biological element that has been guessed from the passed name. + Note that if no biological element was guessed, then the nearest + non-biological element match is used. A biological element is one that + is in the list of biological elements */ +Element Element::biologicalElement(const QString &name) +{ + QReadLocker locker(globalLock()); + + // guess an element with this name... + Element elmnt(name); + + // is this a biological element? - if so, return it! + if (elmnt._locked_biological()) + return elmnt; + + // try to guess the atom from just the first two letters... + Element elmnt2(name.left(2)); + + if (elmnt2._locked_biological()) + return elmnt2; + + // try to guess the atom from just the first letter... + Element elmnt3(name.left(1)); + + if (elmnt3._locked_biological()) + return elmnt3; + + // we couldn't find anything - return the original, non-biological guess + return elmnt; +} + +/** Return whether or not this is biological + (in first three periods and not a noble gas, or a halogen) + (this does preclude iron, potassium and calcium, which are + rather biological... :-) */ +bool Element::_locked_biological() const +{ + return biological_elements->contains(eldata->protnum); +} + +/** Return whether or not this is biological + (in first three periods and not a noble gas, or a halogen) + (this does preclude iron, potassium and calcium, which are + rather biological... :-) */ +bool Element::biological() const +{ + QReadLocker locker(globalLock()); + return this->_locked_biological(); +} + +/** Return a list of all of the elements that are considered + * to be biological + */ +QList Element::getBiologicalElements() +{ + QReadLocker locker(globalLock()); + QList prots = biological_elements->values(); + std::sort(prots.begin(), prots.end()); + + QList elements; + + for (int i = 0; i < prots.size(); ++i) + { + elements.append(Element(prots[i])); + } + + return elements; +} + /** Construct a dummy element */ Element::Element() { @@ -364,35 +470,6 @@ ElementData *ElementDB::element(const QString &s) const } } -/** Return a biological element that has been guessed from the passed name. - Note that if no biological element was guessed, then the nearest - non-biological element match is used. A biological element is one that - is in the first couple of rows (proton number < 18) and is not a noble gas. */ -Element Element::biologicalElement(const QString &name) -{ - // guess an element with this name... - Element elmnt(name); - - // is this a biological element? - if so, return it! - if (elmnt.biological()) - return elmnt; - - // try to guess the atom from just the first two letters... - Element elmnt2(name.left(2)); - - if (elmnt2.biological()) - return elmnt2; - - // try to guess the atom from just the first letter... - Element elmnt3(name.left(1)); - - if (elmnt3.biological()) - return elmnt3; - - // we couldn't find anything - return the original, non-biological guess - return elmnt; -} - /** Return whether or not this is a noble gas */ bool Element::nobleGas() const { @@ -405,15 +482,6 @@ bool Element::halogen() const return group() == 17; } -/** Return whether or not this is biological - (in first three periods and not a noble gas, or a halogen) - (this does preclude iron, potassium and calcium, which are - rather biological... :-) */ -bool Element::biological() const -{ - return (period() <= 3 and not nobleGas()) or halogen(); -} - /** Return whether or not this is an alkali metal (group 1 or 2) */ bool Element::alkaliMetal() const { @@ -450,6 +518,36 @@ bool Element::rareEarth() const return lanthanide() or actinide(); } +bool Element::operator==(const QString &other) const +{ + return this->operator==(Element(other)); +} + +bool Element::operator!=(const QString &other) const +{ + return not this->operator==(other); +} + +bool Element::operator>(const QString &other) const +{ + return this->operator>(Element(other)); +} + +bool Element::operator<(const QString &other) const +{ + return this->operator<(Element(other)); +} + +bool Element::operator>=(const QString &other) const +{ + return this->operator>=(Element(other)); +} + +bool Element::operator<=(const QString &other) const +{ + return this->operator<=(Element(other)); +} + /** Sorting operators. Elements are compared based on their proton numbers, with elements with greater numbers being higher. The functions are also very quick. */ diff --git a/corelib/src/libs/SireMol/moleculedata.cpp b/corelib/src/libs/SireMol/moleculedata.cpp index 08cf8bab7..0c35d73e4 100644 --- a/corelib/src/libs/SireMol/moleculedata.cpp +++ b/corelib/src/libs/SireMol/moleculedata.cpp @@ -714,6 +714,22 @@ ResName MoleculeData::getAlternateResName(ResIdx residx) const return molinfo->alternateName(residx); } +/** Switch to using the alternate names for all atoms and residues. + * If 'keep_originals' is true, then the original names will be + * stored in the alternate names. If 'keep_originals' is false, + * then the original names will be removed. + */ +void MoleculeData::switchToAlternateNames(bool keep_originals) +{ + molinfo = molinfo->switchToAlternateNames(keep_originals); +} + +/** Remove all alternate names from this molecule */ +void MoleculeData::removeAlternateNames() +{ + molinfo = molinfo->removeAlternateNames(); +} + /** Rename the atom at index 'atomidx' to 'newname' \throw SireError::invalid_index diff --git a/corelib/src/libs/SireMol/moleculedata.h b/corelib/src/libs/SireMol/moleculedata.h index 22293cbf1..191fb256f 100644 --- a/corelib/src/libs/SireMol/moleculedata.h +++ b/corelib/src/libs/SireMol/moleculedata.h @@ -253,6 +253,9 @@ namespace SireMol AtomName getAlternateAtomName(AtomIdx atomidx) const; ResName getAlternateResName(ResIdx residx) const; + void switchToAlternateNames(bool keep_originals = true); + void removeAlternateNames(); + void setProperty(const QString &key, const Property &value, bool clear_metadata = false); bool updateProperty(const QString &key, const Property &value, bool auto_add = true); diff --git a/corelib/src/libs/SireMol/moleculeinfo.cpp b/corelib/src/libs/SireMol/moleculeinfo.cpp index ec2c20442..648a3845f 100644 --- a/corelib/src/libs/SireMol/moleculeinfo.cpp +++ b/corelib/src/libs/SireMol/moleculeinfo.cpp @@ -1172,3 +1172,19 @@ MoleculeInfo MoleculeInfo::setAlternateName(ResIdx residx, const ResName &name) { return MoleculeInfo(d->setAlternateName(residx, name)); } + +/** Switch to using the alternate names for all atoms and residues. + * If 'keep_originals' is true, then the original names will be + * stored in the alternate names. If 'keep_originals' is false, + * then the original names will be removed. + */ +MoleculeInfo MoleculeInfo::switchToAlternateNames(bool keep_originals) const +{ + return MoleculeInfo(d->switchToAlternateNames(keep_originals)); +} + +/** Remove all alternate names from this molecule */ +MoleculeInfo MoleculeInfo::removeAlternateNames() const +{ + return MoleculeInfo(d->removeAlternateNames()); +} diff --git a/corelib/src/libs/SireMol/moleculeinfo.h b/corelib/src/libs/SireMol/moleculeinfo.h index cabb09332..38f8d3aea 100644 --- a/corelib/src/libs/SireMol/moleculeinfo.h +++ b/corelib/src/libs/SireMol/moleculeinfo.h @@ -132,6 +132,9 @@ namespace SireMol MoleculeInfo setAlternateName(AtomIdx atomidx, const AtomName &name) const; MoleculeInfo setAlternateName(ResIdx residx, const ResName &name) const; + MoleculeInfo switchToAlternateNames(bool keep_originals = true) const; + MoleculeInfo removeAlternateNames() const; + ResNum number(const ResID &resid) const; ResNum number(ResIdx residx) const; diff --git a/corelib/src/libs/SireMol/moleculeinfodata.cpp b/corelib/src/libs/SireMol/moleculeinfodata.cpp index 39ad2ee9b..bb5ee2c74 100644 --- a/corelib/src/libs/SireMol/moleculeinfodata.cpp +++ b/corelib/src/libs/SireMol/moleculeinfodata.cpp @@ -1457,6 +1457,88 @@ MoleculeInfoData MoleculeInfoData::setAlternateName(ResIdx residx, const ResName return newinfo; } +/** Switch to using the alternate names for all atoms and residues. + * If 'keep_originals' is true, then the original names will be + * stored in the alternate names. If 'keep_originals' is false, + * then the original names will be removed. + */ +MoleculeInfoData MoleculeInfoData::switchToAlternateNames(bool keep_originals) const +{ + MoleculeInfoData newinfo(*this); + + bool changed = false; + + for (int i = 0; i < newinfo.atoms_by_index.count(); ++i) + { + AtomInfo &atom = newinfo.atoms_by_index[i]; + + auto newname = atom.altname; + + if (newname.isNull()) + newname = atom.name; + + if (newname != atom.name) + { + if (keep_originals) + atom.altname = atom.name; + else + atom.altname = newname; + + atom.name = newname; + changed = true; + } + } + + for (int i = 0; i < newinfo.res_by_index.count(); ++i) + { + ResInfo &res = newinfo.res_by_index[i]; + + auto newname = res.altname; + + if (newname.isNull()) + newname = res.name; + + if (newname != res.name) + { + if (keep_originals) + res.altname = res.name; + else + res.altname = newname; + + res.name = newname; + changed = true; + } + } + + if (changed) + { + newinfo.rebuildNameAndNumberIndexes(); + newinfo.uid = QUuid::createUuid(); + } + + return newinfo; +} + +/** Remove all alternate names from this molecule */ +MoleculeInfoData MoleculeInfoData::removeAlternateNames() const +{ + MoleculeInfoData newinfo(*this); + + for (int i = 0; i < newinfo.atoms_by_index.count(); ++i) + { + AtomInfo &atom = newinfo.atoms_by_index[i]; + atom.altname = atom.name; + } + + for (int i = 0; i < newinfo.res_by_index.count(); ++i) + { + ResInfo &res = newinfo.res_by_index[i]; + res.altname = res.name; + } + + return newinfo; +} + /** Rename the atom at index 'atomidx' to have the new name 'newname'. \throw SireError::invalid_index diff --git a/corelib/src/libs/SireMol/moleculeinfodata.h b/corelib/src/libs/SireMol/moleculeinfodata.h index f12cb72a9..ffb30e52f 100644 --- a/corelib/src/libs/SireMol/moleculeinfodata.h +++ b/corelib/src/libs/SireMol/moleculeinfodata.h @@ -206,6 +206,9 @@ namespace SireMol MoleculeInfoData setAlternateName(AtomIdx atomidx, const AtomName &newname) const; MoleculeInfoData setAlternateName(ResIdx residx, const ResName &newname) const; + MoleculeInfoData switchToAlternateNames(bool keep_originals = true) const; + MoleculeInfoData removeAlternateNames() const; + MoleculeInfoData rename(AtomIdx atomidx, const AtomName &newname) const; MoleculeInfoData renumber(AtomIdx atomidx, const AtomNum &newnum) const; diff --git a/corelib/src/libs/SireMol/moleditor.cpp b/corelib/src/libs/SireMol/moleditor.cpp index 4876a08a5..ff7f3ef7e 100644 --- a/corelib/src/libs/SireMol/moleditor.cpp +++ b/corelib/src/libs/SireMol/moleditor.cpp @@ -137,6 +137,24 @@ MolEditor &MolEditor::rename(const QString &newname) return *this; } +/** Switch to using the alternate names for all atoms and residues. + * If 'keep_originals' is true, then the original names will be + * stored in the alternate names. If 'keep_originals' is false, + * then the original names will be removed. + */ +MolEditor &MolEditor::switchToAlternateNames(bool keep_originals) +{ + d->switchToAlternateNames(keep_originals); + return *this; +} + +/** Remove all alternate names from this molecule */ +MolEditor &MolEditor::removeAlternateNames() +{ + d->removeAlternateNames(); + return *this; +} + /** Give this molecule a new, unique ID number */ MolEditor &MolEditor::renumber() { @@ -642,6 +660,24 @@ MolStructureEditor &MolStructureEditor::rename(const MolName &newname) return *this; } +/** Switch to using the alternate names for all atoms and residues. + * If 'keep_originals' is true, then the original names will be + * stored in the alternate names. If 'keep_originals' is false, + * then the original names will be removed. + */ +MolStructureEditor MolStructureEditor::switchToAlternateNames(bool keep_originals) +{ + StructureEditor::switchToAlternates(keep_originals); + return *this; +} + +/** Remove all alternate names from this molecule */ +MolStructureEditor MolStructureEditor::removeAlternateNames() +{ + StructureEditor::removeAlternates(); + return *this; +} + /** Move all atoms into a single CutGroup */ MolStructureEditor &MolStructureEditor::makeSingleCutGroup() { diff --git a/corelib/src/libs/SireMol/moleditor.h b/corelib/src/libs/SireMol/moleditor.h index a2c8e759c..afd3f7190 100644 --- a/corelib/src/libs/SireMol/moleditor.h +++ b/corelib/src/libs/SireMol/moleditor.h @@ -111,6 +111,9 @@ namespace SireMol MolEditor &renumber(const QHash &resnums); MolEditor &renumber(const QHash &atomnums, const QHash &resnums); + MolEditor &switchToAlternateNames(bool keep_originals = true); + MolEditor &removeAlternateNames(); + bool updateProperty(const QString &key, const Property &value, bool auto_add = true); template @@ -211,6 +214,9 @@ namespace SireMol MolStructureEditor &renumber(MolNum newnum); MolStructureEditor &renumber(); + MolStructureEditor switchToAlternateNames(bool keep_originals = true); + MolStructureEditor removeAlternateNames(); + AtomStructureEditor add(const AtomName &atom); AtomStructureEditor add(const AtomNum &atom); diff --git a/corelib/src/libs/SireMol/structureeditor.cpp b/corelib/src/libs/SireMol/structureeditor.cpp index 9cca38dee..db5a93404 100644 --- a/corelib/src/libs/SireMol/structureeditor.cpp +++ b/corelib/src/libs/SireMol/structureeditor.cpp @@ -4015,6 +4015,64 @@ const ResName &StructureEditor::getAlternateResName(quint32 uid) const return res.altname; } +/** Switch to using the alternate names for all atoms and residues. + * If 'keep_originals' is true, then the original names will be + * stored in the alternate names. If 'keep_originals' is false, + * then the original names will be removed. + */ +void StructureEditor::switchToAlternates(bool keep_originals) +{ + this->assertSane(); + + for (auto it = d->atoms.begin(); it != d->atoms.end(); ++it) + { + if (not it.value().altname.isNull()) + { + auto newname = it.value().altname; + + if (keep_originals) + it.value().altname = it.value().name; + + it.value().name = newname; + } + } + + for (auto it = d->residues.begin(); it != d->residues.end(); ++it) + { + if (not it.value().altname.isNull()) + { + auto newname = it.value().altname; + + if (keep_originals) + it.value().altname = it.value().name; + + it.value().name = newname; + } + } +} + +/** Remove all alternate names from this molecule */ +void StructureEditor::removeAlternates() +{ + this->assertSane(); + + for (auto it = d->atoms.begin(); it != d->atoms.end(); ++it) + { + if (not it.value().altname.isNull()) + { + it.value().altname = AtomName(); + } + } + + for (auto it = d->residues.begin(); it != d->residues.end(); ++it) + { + if (not it.value().altname.isNull()) + { + it.value().altname = ResName(); + } + } +} + /** Rename the atom identified by 'uid' to 'newname' \throw SireMol::missing_atom diff --git a/corelib/src/libs/SireMol/structureeditor.h b/corelib/src/libs/SireMol/structureeditor.h index 1cd9396d7..209e04ce9 100644 --- a/corelib/src/libs/SireMol/structureeditor.h +++ b/corelib/src/libs/SireMol/structureeditor.h @@ -282,6 +282,9 @@ namespace SireMol const AtomName &getAlternateAtomName(quint32 uid) const; const ResName &getAlternateResName(quint32 uid) const; + void switchToAlternates(bool keep_originals = true); + void removeAlternates(); + void removeAtom(quint32 uid); void removeCutGroup(quint32 uid); void removeResidue(quint32 uid); diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index aa0ddc86d..ec6f4d3c7 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -193,13 +193,13 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): # call Pythonize on all of the new modules from .legacy import ( # noqa: F401 Base, + Mol, Move, IO, System, Squire, MM, FF, - Mol, Analysis, CAS, Cluster, diff --git a/src/sire/mm/__init__.py b/src/sire/mm/__init__.py index ff2af81a2..2255fd1ac 100644 --- a/src/sire/mm/__init__.py +++ b/src/sire/mm/__init__.py @@ -25,23 +25,6 @@ from ..legacy import MM as _MM -from ..mol import ( - __fix_getitem, - _add_evals, - _add_property_func, - _add_apply_func, - _cursor, - _cursors, - _cursorsm, - _dynamics, - _minimisation, - _selector_to_smiles, - _selector_to_smarts, - _selector_view2d, - _trajectory, - _viewfunc, -) - from .. import use_new_api as _use_new_api _use_new_api() @@ -101,74 +84,108 @@ except AttributeError: Improper.__len__ = Improper.num_atoms -for C in [ - Bond, - SelectorBond, - SelectorMBond, - Angle, - SelectorAngle, - SelectorMAngle, - Dihedral, - SelectorDihedral, - SelectorMDihedral, - Improper, - SelectorImproper, - SelectorMImproper, -]: - __fix_getitem(C) - _add_evals(C) - _add_property_func(C) - _add_apply_func(C) - -Bond.cursor = _cursor -SelectorBond.cursor = _cursors -Angle.cursor = _cursor -SelectorAngle.cursor = _cursors -Dihedral.cursor = _cursor -SelectorDihedral.cursor = _cursors -Improper.cursor = _cursor -SelectorImproper.cursor = _cursors - -SelectorMBond.cursor = _cursorsm -SelectorMAngle.cursor = _cursorsm -SelectorMDihedral.cursor = _cursorsm -SelectorMImproper.cursor = _cursorsm - -SelectorMBond.dynamics = _dynamics -SelectorMAngle.dynamics = _dynamics -SelectorMDihedral.dynamics = _dynamics -SelectorMImproper.dynamics = _dynamics - -SelectorMBond.minimisation = _minimisation -SelectorMAngle.minimisation = _minimisation -SelectorMDihedral.minimisation = _minimisation -SelectorMImproper.minimisation = _minimisation - -SelectorMBond.smiles = _selector_to_smiles -SelectorMAngle.smiles = _selector_to_smiles -SelectorMDihedral.smiles = _selector_to_smiles -SelectorMImproper.smiles = _selector_to_smiles -SelectorMBond.smarts = _selector_to_smarts -SelectorMAngle.smarts = _selector_to_smarts -SelectorMDihedral.smarts = _selector_to_smarts -SelectorMImproper.smarts = _selector_to_smarts - -SelectorMBond.trajectory = _trajectory -SelectorMAngle.trajectory = _trajectory -SelectorMDihedral.trajectory = _trajectory -SelectorMImproper.trajectory = _trajectory - -SelectorBond.view = _viewfunc -SelectorAngle.view = _viewfunc -SelectorDihedral.view = _viewfunc -SelectorImproper.view = _viewfunc - -SelectorMBond.view = _viewfunc -SelectorMAngle.view = _viewfunc -SelectorMDihedral.view = _viewfunc -SelectorMImproper.view = _viewfunc - -SelectorMBond.view2d = _selector_view2d -SelectorMAngle.view2d = _selector_view2d -SelectorMDihedral.view2d = _selector_view2d -SelectorMImproper.view2d = _selector_view2d + +_have_fixed_siremm = False + + +def _fix_siremm(): + global _have_fixed_siremm + if _have_fixed_siremm: + return + + from ..mol import ( + __fix_getitem, + _add_evals, + _add_property_func, + _add_apply_func, + _cursor, + _cursors, + _cursorsm, + _dynamics, + _minimisation, + _selector_to_smiles, + _selector_to_smarts, + _selector_view2d, + _trajectory, + _viewfunc, + ) + + _have_fixed_siremm = True + + for C in [ + Bond, + SelectorBond, + SelectorMBond, + Angle, + SelectorAngle, + SelectorMAngle, + Dihedral, + SelectorDihedral, + SelectorMDihedral, + Improper, + SelectorImproper, + SelectorMImproper, + ]: + __fix_getitem(C) + _add_evals(C) + _add_property_func(C) + _add_apply_func(C) + + Bond.cursor = _cursor + SelectorBond.cursor = _cursors + Angle.cursor = _cursor + SelectorAngle.cursor = _cursors + Dihedral.cursor = _cursor + SelectorDihedral.cursor = _cursors + Improper.cursor = _cursor + SelectorImproper.cursor = _cursors + + SelectorMBond.cursor = _cursorsm + SelectorMAngle.cursor = _cursorsm + SelectorMDihedral.cursor = _cursorsm + SelectorMImproper.cursor = _cursorsm + + SelectorMBond.dynamics = _dynamics + SelectorMAngle.dynamics = _dynamics + SelectorMDihedral.dynamics = _dynamics + SelectorMImproper.dynamics = _dynamics + + SelectorMBond.minimisation = _minimisation + SelectorMAngle.minimisation = _minimisation + SelectorMDihedral.minimisation = _minimisation + SelectorMImproper.minimisation = _minimisation + + SelectorMBond.smiles = _selector_to_smiles + SelectorMAngle.smiles = _selector_to_smiles + SelectorMDihedral.smiles = _selector_to_smiles + SelectorMImproper.smiles = _selector_to_smiles + SelectorMBond.smarts = _selector_to_smarts + SelectorMAngle.smarts = _selector_to_smarts + SelectorMDihedral.smarts = _selector_to_smarts + SelectorMImproper.smarts = _selector_to_smarts + + SelectorMBond.trajectory = _trajectory + SelectorMAngle.trajectory = _trajectory + SelectorMDihedral.trajectory = _trajectory + SelectorMImproper.trajectory = _trajectory + + SelectorBond.view = _viewfunc + SelectorAngle.view = _viewfunc + SelectorDihedral.view = _viewfunc + SelectorImproper.view = _viewfunc + + SelectorMBond.view = _viewfunc + SelectorMAngle.view = _viewfunc + SelectorMDihedral.view = _viewfunc + SelectorMImproper.view = _viewfunc + + SelectorMBond.view2d = _selector_view2d + SelectorMAngle.view2d = _selector_view2d + SelectorMDihedral.view2d = _selector_view2d + SelectorMImproper.view2d = _selector_view2d + + +try: + _fix_siremm() +except ImportError: + pass diff --git a/src/sire/mol/__init__.py b/src/sire/mol/__init__.py index 2511b5045..fba3e2f7c 100644 --- a/src/sire/mol/__init__.py +++ b/src/sire/mol/__init__.py @@ -2590,3 +2590,9 @@ def __molecule_is_perturbable(mol): # Remove some temporary variables del C + +# also initialise sire.mm (it can sometimes be uninitialised if +# sire.mol is loaded first) +from ..mm import _fix_siremm + +_fix_siremm() diff --git a/src/sire/mol/_trajectory.py b/src/sire/mol/_trajectory.py index b2dcdebc1..37ccac992 100644 --- a/src/sire/mol/_trajectory.py +++ b/src/sire/mol/_trajectory.py @@ -67,9 +67,7 @@ def __init__( self._map = create_map(map) self._view = view - self._values = list( - range(0, max(1, self._view.num_frames(self._map))) - ) + self._values = list(range(0, max(1, self._view.num_frames(self._map)))) self._times = None self._iter = None self._frame = None @@ -125,9 +123,7 @@ def __init__( find_all=False, ) - self._aligner = TrajectoryAligner( - align, reference, map=self._map - ) + self._aligner = TrajectoryAligner(align, reference, map=self._map) elif wrap or (smooth != 1): self._aligner = TrajectoryAligner( self._view.evaluate().center(), @@ -401,9 +397,7 @@ def energies(self, obj1=None, to_pandas=True, map=None): for v in self.first(): colnames.append(colname(v)) - forcefields.append( - create_forcefield(v, obj1_mols, map=map) - ) + forcefields.append(create_forcefield(v, obj1_mols, map=map)) else: for v in self.first(): colnames.append(colname(v)) @@ -427,9 +421,7 @@ def energies(self, obj1=None, to_pandas=True, map=None): components = {} - ff_nrgs = calculate_trajectory_energies( - forcefields, self._values, map=map - ) + ff_nrgs = calculate_trajectory_energies(forcefields, self._values, map=map) for ff_idx in range(0, len(forcefields)): nrg = ff_nrgs[ff_idx][0] @@ -449,9 +441,7 @@ def energies(self, obj1=None, to_pandas=True, map=None): for i in range(0, nframes): for ff_idx in range(0, len(forcefields)): nrg = ff_nrgs[ff_idx][i] - components[colname(colnames[ff_idx], "total")][ - i - ] = nrg.to_default() + components[colname(colnames[ff_idx], "total")][i] = nrg.to_default() for key in nrg.components().keys(): try: @@ -649,9 +639,7 @@ def _simple_measures(self, to_pandas): colnames.append(colname(view)) columns.append(np.zeros(nframes, dtype=float)) - with ProgressBar( - total=nframes, text="Looping through frames" - ) as progress: + with ProgressBar(total=nframes, text="Looping through frames") as progress: for idx, frame in enumerate(self.__iter__()): for i, measure in enumerate(frame.measures(map=self._map)): columns[i][idx] = measure.to_default() @@ -659,9 +647,7 @@ def _simple_measures(self, to_pandas): if measure_unit is None: if not measure.is_zero(): - measure_unit = ( - measure.get_default().unit_string() - ) + measure_unit = measure.get_default().unit_string() if time_unit is None: time = frame.frame_time() @@ -674,9 +660,7 @@ def _simple_measures(self, to_pandas): colnames.append(colname(self._view)) column = np.zeros(nframes, dtype=float) - with ProgressBar( - total=nframes, text="Looping through frames" - ) as progress: + with ProgressBar(total=nframes, text="Looping through frames") as progress: for idx, frame in enumerate(self.__iter__()): measure = frame.measure(map=self._map) column[idx] = measure.to_default() @@ -761,9 +745,7 @@ def _custom_measures(self, func, to_pandas): from ..base import ProgressBar - with ProgressBar( - total=nframes, text="Looping through frames" - ) as progress: + with ProgressBar(total=nframes, text="Looping through frames") as progress: for idx, frame in enumerate(self.__iter__()): for i, f in enumerate(func.values()): measure = f(frame) @@ -857,9 +839,7 @@ def apply(self, func, *args, **kwargs): if str(func) == func: # we calling a named function - with ProgressBar( - total=nframes, text="Looping through frames" - ) as progress: + with ProgressBar(total=nframes, text="Looping through frames") as progress: for i in range(0, nframes): obj = self.__getitem__(i).current() result.append(getattr(obj, func)(*args, **kwargs)) @@ -867,9 +847,7 @@ def apply(self, func, *args, **kwargs): else: # we have been passed the function to call - with ProgressBar( - total=nframes, text="Looping through frames" - ) as progress: + with ProgressBar(total=nframes, text="Looping through frames") as progress: for i in range(0, nframes): obj = self.__getitem__(i).current() result.append(func(obj, *args, **kwargs)) @@ -944,10 +922,7 @@ def rmsd( elif align is None: # auto-align only for smaller systems - if ( - hasattr(reference, "molecules") - and len(reference.molecules()) > 100 - ): + if hasattr(reference, "molecules") and len(reference.molecules()) > 100: align = False else: align = True diff --git a/tests/mol/test_element.py b/tests/mol/test_element.py new file mode 100644 index 000000000..42f245cb5 --- /dev/null +++ b/tests/mol/test_element.py @@ -0,0 +1,51 @@ +import pytest +import sire as sr + + +def test_element(): + # Create an element + el = sr.mol.Element("C") + assert el.symbol() == "C" + assert el.num_protons() == 6 + assert el.mass().to("g mol-1") == pytest.approx(12.01, abs=0.01) + + # Create an element from atomic number + el = sr.mol.Element(6) + assert el.symbol() == "C" + + # Create an element from name + el = sr.mol.Element("Carbon") + assert el.symbol() == "C" + + # Create an element from mass + el = sr.mol.Element.element_with_mass(sr.u("12 g mol-1")) + assert el.symbol() == "C" + + # Create a biological Iron + el = sr.mol.Element.biological_element("Fe") + + assert el.symbol() == "Fe" + assert el.num_protons() == 26 + assert el.mass().to("g mol-1") == pytest.approx(55.845) + assert el.name() == "Iron" + + # remove this as a biological element + sr.mol.Element.set_element_is_not_biological("Fe") + + el = sr.mol.Element.biological_element("Fe") + + assert el.symbol() != "Fe" + assert el.num_protons() != 26 + + # Add this back + sr.mol.Element.set_element_is_biological("Fe") + + el = sr.mol.Element.biological_element("Fe") + + assert el.symbol() == "Fe" + assert el.num_protons() == 26 + + # get the list of biological elements + elements = sr.mol.Element.get_biological_elements() + + assert sr.mol.Element("Fe") in elements diff --git a/wrapper/Mol/Atom.pypp.cpp b/wrapper/Mol/Atom.pypp.cpp index 0e22c4630..9ba282e34 100644 --- a/wrapper/Mol/Atom.pypp.cpp +++ b/wrapper/Mol/Atom.pypp.cpp @@ -301,7 +301,7 @@ void register_Atom_class(){ "alternateName" , alternateName_function_value , bp::release_gil_policy() - , "" ); + , "Return the alternate name of the atom" ); } { //::SireMol::Atom::assertContains diff --git a/wrapper/Mol/AtomEditor.pypp.cpp b/wrapper/Mol/AtomEditor.pypp.cpp index c5086d6dd..10539c4d4 100644 --- a/wrapper/Mol/AtomEditor.pypp.cpp +++ b/wrapper/Mol/AtomEditor.pypp.cpp @@ -76,7 +76,7 @@ void register_AtomEditor_class(){ "alternateName" , alternateName_function_value , bp::release_gil_policy() - , "" ); + , "Return the alternate name for this atom" ); } { //::SireMol::AtomEditor::operator= @@ -128,7 +128,7 @@ void register_AtomEditor_class(){ , reindex_function_value , ( bp::arg("atomidx") ) , bp::release_gil_policy() - , "Reindex this atom so that it lies at index newidx. Note\nthat if newidx is greater than the number of atoms, then\nthis will move this atom to be the last in the list" ); + , "Reindex this atom" ); } { //::SireMol::AtomEditor::remove @@ -166,7 +166,7 @@ void register_AtomEditor_class(){ , rename_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "Rename this atom so that it is called newname" ); + , "Rename this atom" ); } { //::SireMol::AtomEditor::renumber @@ -192,7 +192,7 @@ void register_AtomEditor_class(){ , renumber_function_value , ( bp::arg("number") ) , bp::return_self< >() - , "Renumber this atom so that it has number newnum" ); + , "Renumber this atom" ); } { //::SireMol::AtomEditor::reparent @@ -283,7 +283,7 @@ void register_AtomEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate name for this atom" ); } { //::SireMol::AtomEditor::setAlternateName @@ -296,7 +296,7 @@ void register_AtomEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate name for this atom" ); } { //::SireMol::AtomEditor::toString diff --git a/wrapper/Mol/AtomStructureEditor.pypp.cpp b/wrapper/Mol/AtomStructureEditor.pypp.cpp index b45035909..4cc96b5a0 100644 --- a/wrapper/Mol/AtomStructureEditor.pypp.cpp +++ b/wrapper/Mol/AtomStructureEditor.pypp.cpp @@ -76,7 +76,7 @@ void register_AtomStructureEditor_class(){ "alternateName" , alternateName_function_value , bp::return_value_policy() - , "" ); + , "Return the alternate name for this atom" ); } { //::SireMol::AtomStructureEditor::chain @@ -199,7 +199,7 @@ void register_AtomStructureEditor_class(){ , reindex_function_value , ( bp::arg("idx") ) , bp::return_self< >() - , "Reindex this atom to newidx - this will move the atom to\nthe end if newidx is greater than the number of atoms\nin the molecule" ); + , "Reindex this atom" ); } { //::SireMol::AtomStructureEditor::reindex @@ -237,7 +237,7 @@ void register_AtomStructureEditor_class(){ , rename_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "Rename this atom to newname" ); + , "Rename this atom" ); } { //::SireMol::AtomStructureEditor::rename @@ -263,7 +263,7 @@ void register_AtomStructureEditor_class(){ , renumber_function_value , ( bp::arg("number") ) , bp::return_self< >() - , "Renumber this atom to newnum" ); + , "Renumber this atom" ); } { //::SireMol::AtomStructureEditor::renumber @@ -403,7 +403,7 @@ void register_AtomStructureEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate name for this atom" ); } { //::SireMol::AtomStructureEditor::setAlternateName @@ -416,7 +416,7 @@ void register_AtomStructureEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate name for this atom" ); } { //::SireMol::AtomStructureEditor::toString diff --git a/wrapper/Mol/Element.pypp.cpp b/wrapper/Mol/Element.pypp.cpp index e8ab4d2b5..20e8fc4c7 100644 --- a/wrapper/Mol/Element.pypp.cpp +++ b/wrapper/Mol/Element.pypp.cpp @@ -139,6 +139,18 @@ void register_Element_class(){ , bp::release_gil_policy() , "Return an element which has the closest mass to mass (in atomic\nmass units, g mol-1)" ); + } + { //::SireMol::Element::getBiologicalElements + + typedef ::QList< SireMol::Element > ( *getBiologicalElements_function_type )( ); + getBiologicalElements_function_type getBiologicalElements_function_value( &::SireMol::Element::getBiologicalElements ); + + Element_exposer.def( + "getBiologicalElements" + , getBiologicalElements_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Element::green @@ -249,8 +261,11 @@ void register_Element_class(){ } Element_exposer.def( bp::self != bp::self ); + Element_exposer.def( bp::self != bp::other< QString >() ); Element_exposer.def( bp::self < bp::self ); + Element_exposer.def( bp::self < bp::other< QString >() ); Element_exposer.def( bp::self <= bp::self ); + Element_exposer.def( bp::self <= bp::other< QString >() ); { //::SireMol::Element::operator= typedef ::SireMol::Element const & ( ::SireMol::Element::*assign_function_type)( ::SireMol::Element const & ) ; @@ -265,8 +280,11 @@ void register_Element_class(){ } Element_exposer.def( bp::self == bp::self ); + Element_exposer.def( bp::self == bp::other< QString >() ); Element_exposer.def( bp::self > bp::self ); + Element_exposer.def( bp::self > bp::other< QString >() ); Element_exposer.def( bp::self >= bp::self ); + Element_exposer.def( bp::self >= bp::other< QString >() ); { //::SireMol::Element::period typedef int ( ::SireMol::Element::*period_function_type)( ) const; @@ -302,6 +320,44 @@ void register_Element_class(){ , bp::release_gil_policy() , "Return the red colour components (0.0->1.0) for\nthe colour of this element" ); + } + { //::SireMol::Element::resetBiologicalElements + + typedef void ( *resetBiologicalElements_function_type )( ); + resetBiologicalElements_function_type resetBiologicalElements_function_value( &::SireMol::Element::resetBiologicalElements ); + + Element_exposer.def( + "resetBiologicalElements" + , resetBiologicalElements_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::Element::setElementIsBiological + + typedef void ( *setElementIsBiological_function_type )( ::SireMol::Element const & ); + setElementIsBiological_function_type setElementIsBiological_function_value( &::SireMol::Element::setElementIsBiological ); + + Element_exposer.def( + "setElementIsBiological" + , setElementIsBiological_function_value + , ( bp::arg("element") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::Element::setElementIsNotBiological + + typedef void ( *setElementIsNotBiological_function_type )( ::SireMol::Element const & ); + setElementIsNotBiological_function_type setElementIsNotBiological_function_value( &::SireMol::Element::setElementIsNotBiological ); + + Element_exposer.def( + "setElementIsNotBiological" + , setElementIsNotBiological_function_value + , ( bp::arg("element") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::Element::symbol @@ -377,6 +433,10 @@ void register_Element_class(){ } Element_exposer.staticmethod( "biologicalElement" ); Element_exposer.staticmethod( "elementWithMass" ); + Element_exposer.staticmethod( "getBiologicalElements" ); + Element_exposer.staticmethod( "resetBiologicalElements" ); + Element_exposer.staticmethod( "setElementIsBiological" ); + Element_exposer.staticmethod( "setElementIsNotBiological" ); Element_exposer.staticmethod( "typeName" ); Element_exposer.def( "__copy__", &__copy__); Element_exposer.def( "__deepcopy__", &__copy__); diff --git a/wrapper/Mol/MolEditor.pypp.cpp b/wrapper/Mol/MolEditor.pypp.cpp index ace848b6e..4593e4838 100644 --- a/wrapper/Mol/MolEditor.pypp.cpp +++ b/wrapper/Mol/MolEditor.pypp.cpp @@ -182,7 +182,7 @@ void register_MolEditor_class(){ "makeSingleCutGroup" , makeSingleCutGroup_function_value , bp::return_self< >() - , "" ); + , "Return an editor where all atoms have been moved into a\n single cutgroup\n" ); } { //::SireMol::MolEditor::operator= @@ -347,6 +347,18 @@ void register_MolEditor_class(){ , bp::release_gil_policy() , "Remove all segments from this molecule. This returns an editor that\ncan be used to further edit the structure of this molecule" ); + } + { //::SireMol::MolEditor::removeAlternateNames + + typedef ::SireMol::MolEditor & ( ::SireMol::MolEditor::*removeAlternateNames_function_type)( ) ; + removeAlternateNames_function_type removeAlternateNames_function_value( &::SireMol::MolEditor::removeAlternateNames ); + + MolEditor_exposer.def( + "removeAlternateNames" + , removeAlternateNames_function_value + , bp::return_self< >() + , "Remove all alternate names from this molecule" ); + } { //::SireMol::MolEditor::removeLink @@ -437,6 +449,19 @@ void register_MolEditor_class(){ , bp::return_self< >() , "Renumber the atoms and residues in the molecule according to the passed maps" ); + } + { //::SireMol::MolEditor::switchToAlternateNames + + typedef ::SireMol::MolEditor & ( ::SireMol::MolEditor::*switchToAlternateNames_function_type)( bool ) ; + switchToAlternateNames_function_type switchToAlternateNames_function_value( &::SireMol::MolEditor::switchToAlternateNames ); + + MolEditor_exposer.def( + "switchToAlternateNames" + , switchToAlternateNames_function_value + , ( bp::arg("keep_originals")=(bool)(true) ) + , bp::return_self< >() + , "Switch to using the alternate names for all atoms and residues.\n If keep_originals is true, then the original names will be\n stored in the alternate names. If keep_originals is false,\n then the original names will be removed.\n" ); + } { //::SireMol::MolEditor::toString diff --git a/wrapper/Mol/MolStructureEditor.pypp.cpp b/wrapper/Mol/MolStructureEditor.pypp.cpp index 23d99a8fa..be0e4d589 100644 --- a/wrapper/Mol/MolStructureEditor.pypp.cpp +++ b/wrapper/Mol/MolStructureEditor.pypp.cpp @@ -458,6 +458,18 @@ void register_MolStructureEditor_class(){ , bp::return_self< >() , "Remove all segments from this molecule" ); + } + { //::SireMol::MolStructureEditor::removeAlternateNames + + typedef ::SireMol::MolStructureEditor ( ::SireMol::MolStructureEditor::*removeAlternateNames_function_type)( ) ; + removeAlternateNames_function_type removeAlternateNames_function_value( &::SireMol::MolStructureEditor::removeAlternateNames ); + + MolStructureEditor_exposer.def( + "removeAlternateNames" + , removeAlternateNames_function_value + , bp::return_self< >() + , "Remove all alternate names from this molecule" ); + } { //::SireMol::MolStructureEditor::rename @@ -599,6 +611,19 @@ void register_MolStructureEditor_class(){ , bp::release_gil_policy() , "Return whether or not this is a complete molecule" ); + } + { //::SireMol::MolStructureEditor::switchToAlternateNames + + typedef ::SireMol::MolStructureEditor ( ::SireMol::MolStructureEditor::*switchToAlternateNames_function_type)( bool ) ; + switchToAlternateNames_function_type switchToAlternateNames_function_value( &::SireMol::MolStructureEditor::switchToAlternateNames ); + + MolStructureEditor_exposer.def( + "switchToAlternateNames" + , switchToAlternateNames_function_value + , ( bp::arg("keep_originals")=(bool)(true) ) + , bp::return_self< >() + , "Switch to using the alternate names for all atoms and residues.\n If keep_originals is true, then the original names will be\n stored in the alternate names. If keep_originals is false,\n then the original names will be removed.\n" ); + } { //::SireMol::MolStructureEditor::toString diff --git a/wrapper/Mol/MoleculeInfo.pypp.cpp b/wrapper/Mol/MoleculeInfo.pypp.cpp index 2613fa2e6..3ed260992 100644 --- a/wrapper/Mol/MoleculeInfo.pypp.cpp +++ b/wrapper/Mol/MoleculeInfo.pypp.cpp @@ -2108,6 +2108,18 @@ void register_MoleculeInfo_class(){ , bp::release_gil_policy() , "Return the index of the parent segment of the identified atom" ); + } + { //::SireMol::MoleculeInfo::removeAlternateNames + + typedef ::SireMol::MoleculeInfo ( ::SireMol::MoleculeInfo::*removeAlternateNames_function_type)( ) const; + removeAlternateNames_function_type removeAlternateNames_function_value( &::SireMol::MoleculeInfo::removeAlternateNames ); + + MoleculeInfo_exposer.def( + "removeAlternateNames" + , removeAlternateNames_function_value + , bp::release_gil_policy() + , "Remove all alternate names from this molecule" ); + } { //::SireMol::MoleculeInfo::rename @@ -2264,6 +2276,18 @@ void register_MoleculeInfo_class(){ , bp::release_gil_policy() , "Use this function to minimise memory usage - this function\ncompares the shared data in this info with other, and where\nthey are equal it copies the data from other, thereby reducing\nwastage caused by duplicated storage\n" ); + } + { //::SireMol::MoleculeInfo::switchToAlternateNames + + typedef ::SireMol::MoleculeInfo ( ::SireMol::MoleculeInfo::*switchToAlternateNames_function_type)( bool ) const; + switchToAlternateNames_function_type switchToAlternateNames_function_value( &::SireMol::MoleculeInfo::switchToAlternateNames ); + + MoleculeInfo_exposer.def( + "switchToAlternateNames" + , switchToAlternateNames_function_value + , ( bp::arg("keep_originals")=(bool)(true) ) + , "Switch to using the alternate names for all atoms and residues.\n If keep_originals is true, then the original names will be\n stored in the alternate names. If keep_originals is false,\n then the original names will be removed.\n" ); + } { //::SireMol::MoleculeInfo::typeName diff --git a/wrapper/Mol/ResEditor.pypp.cpp b/wrapper/Mol/ResEditor.pypp.cpp index 07c210eab..6c961b701 100644 --- a/wrapper/Mol/ResEditor.pypp.cpp +++ b/wrapper/Mol/ResEditor.pypp.cpp @@ -94,7 +94,7 @@ void register_ResEditor_class(){ "alternateName" , alternateName_function_value , bp::release_gil_policy() - , "" ); + , "Return the alternate name for this residue" ); } { //::SireMol::ResEditor::commit @@ -158,7 +158,7 @@ void register_ResEditor_class(){ , reindex_function_value , ( bp::arg("index") ) , bp::release_gil_policy() - , "Change the index of this residue to newidx. If this\nis larger than the number of residues in the molecule\nthen this residue is moved to the end" ); + , "Reindex this residue to newidx" ); } { //::SireMol::ResEditor::remove @@ -274,7 +274,7 @@ void register_ResEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate residue name for this residue" ); } { //::SireMol::ResEditor::setAlternateName @@ -287,7 +287,7 @@ void register_ResEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate name for this residue" ); } { //::SireMol::ResEditor::toString diff --git a/wrapper/Mol/ResStructureEditor.pypp.cpp b/wrapper/Mol/ResStructureEditor.pypp.cpp index c274f9e3f..bb9f085b5 100644 --- a/wrapper/Mol/ResStructureEditor.pypp.cpp +++ b/wrapper/Mol/ResStructureEditor.pypp.cpp @@ -94,7 +94,7 @@ void register_ResStructureEditor_class(){ "alternateName" , alternateName_function_value , bp::return_value_policy() - , "" ); + , "Return the alternate name for this residue" ); } { //::SireMol::ResStructureEditor::atom @@ -256,7 +256,7 @@ void register_ResStructureEditor_class(){ , reindex_function_value , ( bp::arg("index") ) , bp::return_self< >() - , "Change the index of this residue to newidx. If this\nis larger than the number of residues in the molecule\nthen this residue is moved to the end" ); + , "Reindex this residue to newidx" ); } { //::SireMol::ResStructureEditor::remove @@ -410,7 +410,7 @@ void register_ResStructureEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate residue name for this residue" ); } { //::SireMol::ResStructureEditor::setAlternateName @@ -423,7 +423,7 @@ void register_ResStructureEditor_class(){ , setAlternateName_function_value , ( bp::arg("name") ) , bp::return_self< >() - , "" ); + , "Set the alternate name for this residue" ); } { //::SireMol::ResStructureEditor::toString diff --git a/wrapper/Mol/Residue.pypp.cpp b/wrapper/Mol/Residue.pypp.cpp index 0bd6713b9..e393c68ac 100644 --- a/wrapper/Mol/Residue.pypp.cpp +++ b/wrapper/Mol/Residue.pypp.cpp @@ -107,7 +107,7 @@ void register_Residue_class(){ "alternateName" , alternateName_function_value , bp::release_gil_policy() - , "" ); + , "Return the alternate name of this residue" ); } { //::SireMol::Residue::assertContainsMetadata diff --git a/wrapper/Mol/SireMol_containers.cpp b/wrapper/Mol/SireMol_containers.cpp index 07634129f..8b72cee54 100644 --- a/wrapper/Mol/SireMol_containers.cpp +++ b/wrapper/Mol/SireMol_containers.cpp @@ -46,6 +46,7 @@ #include "SireMol/cutgroup.h" #include "SireMol/residue.h" #include "SireMol/chain.h" +#include "SireMol/element.h" #include "SireMol/segment.h" #include "SireMol/molecule.h" #include "SireMol/atomselection.h" @@ -85,121 +86,122 @@ using boost::python::register_tuple; void register_SireMol_containers() { - register_viewsofmol_list(); + register_viewsofmol_list(); - register_list>(); - register_list>>(); - register_list>(); + register_list>(); + register_list>>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>>(); - register_list>>(); + register_list>>(); + register_list>>(); - register_list>>(); + register_list>>(); - register_list>>(); + register_list>>(); - register_list>(); - register_list>>(); + register_list>(); + register_list>>(); - register_list>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>>(); + register_list>>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>(); + register_list>(); - register_tuple>(); - register_tuple>(); - register_tuple>(); + register_tuple>(); + register_tuple>(); + register_tuple>(); - register_tuple>(); - register_tuple>(); + register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); - register_tuple>(); - register_tuple, SireBase::PropertyMap>>(); - register_tuple, SireBase::PropertyMap>>(); + register_tuple>(); + register_tuple>(); + register_tuple, SireBase::PropertyMap>>(); + register_tuple, SireBase::PropertyMap>>(); - register_PackedArray>(); - register_PackedArray>(); + register_PackedArray>(); + register_PackedArray>(); - register_dict>(); + register_dict>(); - register_dict>(); - register_dict>(); + register_dict>(); + register_dict>(); - register_dict>>(); + register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>(); - register_dict>(); - register_dict>(); + register_dict>>(); + register_dict>>(); + register_dict>>(); + register_dict>>(); + register_dict>>(); + register_dict>(); + register_dict>(); + register_dict>(); - register_set>(); - register_set>(); + register_set>(); + register_set>(); - register_set>(); - register_set>(); + register_set>(); + register_set>(); } diff --git a/wrapper/Mol/_Mol.main.cpp b/wrapper/Mol/_Mol.main.cpp index e2cb30d3c..346070212 100644 --- a/wrapper/Mol/_Mol.main.cpp +++ b/wrapper/Mol/_Mol.main.cpp @@ -585,6 +585,8 @@ namespace bp = boost::python; #include "SireMol/selectorm.hpp" +#include "SireMol/element.h" + BOOST_PYTHON_MODULE(_Mol){ register_SireMol_objects(); @@ -1144,6 +1146,8 @@ BOOST_PYTHON_MODULE(_Mol){ register_SireMol_properties(); + bp::implicitly_convertible< QString, SireMol::Element >(); + bp::implicitly_convertible< SireMol::AtomID, SireMol::AtomIdentifier >(); bp::implicitly_convertible< SireMol::CGID, SireMol::CGIdentifier >(); diff --git a/wrapper/Mol/__init__.py b/wrapper/Mol/__init__.py index dcfaee737..c93f6f5cf 100644 --- a/wrapper/Mol/__init__.py +++ b/wrapper/Mol/__init__.py @@ -16,6 +16,12 @@ _install_search_parser() +# initialise the list of biological elements +try: + _Mol.Element.resetBiologicalElements() +except AttributeError: + _Mol.Element.reset_biological_elements() + def __get_property__(molview, key): if hasattr(molview, "property_type"): diff --git a/wrapper/Mol/special_code.py b/wrapper/Mol/special_code.py index 72c7a5eb5..2c133d39d 100644 --- a/wrapper/Mol/special_code.py +++ b/wrapper/Mol/special_code.py @@ -271,6 +271,8 @@ def fix_MolEditor(c, include_links=True): c.decls("renumber").call_policies = call_policies.return_self() c.decls("rename").call_policies = call_policies.return_self() c.decls("makeSingleCutGroup").call_policies = call_policies.return_self() + c.decls("switchToAlternateNames").call_policies = call_policies.return_self() + c.decls("removeAlternateNames").call_policies = call_policies.return_self() if include_links: c.decls("addLink").call_policies = call_policies.return_self() @@ -541,6 +543,7 @@ def fix_SelectResultMover(c): } implicitly_convertible = [ + ("QString", "SireMol::Element"), ("SireMol::AtomID", "SireMol::AtomIdentifier"), ("SireMol::CGID", "SireMol::CGIdentifier"), ("SireMol::ChainID", "SireMol::ChainIdentifier"), @@ -581,3 +584,4 @@ def fixMB(mb): mb.add_declaration_code('#include "SireMol/moleculeinfo.h"') mb.add_declaration_code('#include "SireMol/selector.hpp"') mb.add_declaration_code('#include "SireMol/selectorm.hpp"') + mb.add_declaration_code('#include "SireMol/element.h"') From dc4347379e707fa6dcd64bda804fc9bac5bcae15 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 23 Feb 2024 19:32:40 +0000 Subject: [PATCH 128/468] Fixed new code - all compiles, links and tests pass. Out of the rabbit hole and ready to go back to the merge code ;-) --- corelib/src/libs/SireMol/moleculeinfodata.cpp | 4 ++-- corelib/src/libs/SireMol/structureeditor.cpp | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/corelib/src/libs/SireMol/moleculeinfodata.cpp b/corelib/src/libs/SireMol/moleculeinfodata.cpp index bb5ee2c74..24329965c 100644 --- a/corelib/src/libs/SireMol/moleculeinfodata.cpp +++ b/corelib/src/libs/SireMol/moleculeinfodata.cpp @@ -280,14 +280,14 @@ bool CGInfo::operator!=(const CGInfo &other) const QDataStream &operator<<(QDataStream &ds, const ResInfo &resinfo) { - ds << resinfo.name << resinfo.altname << resinfo.number << resinfo.chainidx << resinfo.atom_indicies; + ds << resinfo.name << resinfo.number << resinfo.chainidx << resinfo.atom_indicies; return ds; } QDataStream &operator>>(QDataStream &ds, ResInfo &resinfo) { - ds >> resinfo.name >> resinfo.altname >> resinfo.number >> resinfo.chainidx >> resinfo.atom_indicies; + ds >> resinfo.name >> resinfo.number >> resinfo.chainidx >> resinfo.atom_indicies; resinfo.altname = resinfo.name; diff --git a/corelib/src/libs/SireMol/structureeditor.cpp b/corelib/src/libs/SireMol/structureeditor.cpp index db5a93404..5c611afca 100644 --- a/corelib/src/libs/SireMol/structureeditor.cpp +++ b/corelib/src/libs/SireMol/structureeditor.cpp @@ -3201,7 +3201,7 @@ const MoleculeInfoData &StructureEditor::commitInfo() { const auto info = this->getAtomData(AtomIdx(i)); - if (info.get<2>().isNull()) + if (info.get<3>().isNull()) { // this atom isn't in a CutGroup // Reparent it into the first CutGroup From 2855d9fbb98757b8067f104b165f530bd5530e37 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 23 Feb 2024 23:30:30 +0000 Subject: [PATCH 129/468] Making good progress - realised that can use properties of the atoms to store the mappings - and then this could be passed to the properties so that they can update themselves internally --- corelib/src/libs/SireSystem/merge.cpp | 191 +++++++++++++++++--------- 1 file changed, 127 insertions(+), 64 deletions(-) diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index d06aa9c33..b1bc183bf 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -99,8 +99,8 @@ namespace SireSystem auto backwards_map = mols.swap(); // the list of mapped atoms - const auto mapped_atoms0 = mols.mappedAtoms0(); - const auto mapped_atoms1 = mols.mappedAtoms1(); + const auto mapped_atoms0 = mols.mappedAtoms0().toSingleMolecule(); + const auto mapped_atoms1 = mols.mappedAtoms1().toSingleMolecule(); if (mapped_atoms0.count() != mapped_atoms1.count()) { @@ -116,85 +116,148 @@ namespace SireSystem auto map0 = map.merge(mols.propertyMap0()); auto map1 = map.merge(mols.propertyMap1()); - // get an editable copy of the molecule to be changed - MolStructureEditor mol(mols.atoms0().toSingleMolecule().molecule()); + // get the MolEditor that can be used to set properties + MolEditor editmol = mols.atoms0().toSingleMolecule().molecule().edit(); // and a handle on the whole reference and perturbed molecule const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); - // copy the properties from the reference state to both states - QStringList merged_properties = {"charge", "LJ", "atomtype", "intrascale", - "coordinates", "mass", "element", - "bond", "angle", "dihedral", - "improper"}; + // get an editable copy of the molecule to be changed + MolStructureEditor mol(editmol); - /* - for (int i = 0; i < mol.nAtoms(); ++i) - { - auto atom = mol.atom(AtomIdx(i)); - - for (const auto &prop : merged_properties) - { - if (mol0.hasProperty(map0[prop])) - { - const auto &val = mol0.property(map0[prop]); - - atom.setProperty(map[prop + "0"].source(), val); - atom.setProperty(map[prop + "1"].source(), val); - } - } - } + // a map from the residue index in the mapped state back to the + // residue index in the merged molecule + QHash pert_to_merge_residx; + + // all of the residue indicies that we have seen + QHash residx_to_cgidx; + + // go through all of the common atoms and save their indicies + // and set the atom and residue names + for (int i = 0; i < nmapped; ++i) + { + const auto atom0 = mapped_atoms0(i); + const auto atom1 = mapped_atoms1(i); + + auto atom = mol.atom(atom0.index()); + + // save the index of this atom in both mol0 and mol1 + atom.setProperty("_mol0_index", atom0.index().value()); + atom.setProperty("_mol1_index", atom1.index().value()); + + // save the perturbed state atom and residue names into new properties, so + // that we can use these when extracting the end states + atom.setAlternateName(atom1.name()); + + ResIdx residx; + + try + { + residx = atom0.residue().index(); + } + catch (...) + { + } + + if (not(residx.isNull() or residx_to_cgidx.contains(residx))) + { + // we haven't seen this residue before - assume that + // all residues that are mapped from this residue + // exist in the same equivalent residue in the + // perturbed molecule (using the cutgroup of the + // first atom in this residue) + residx_to_cgidx.insert(residx, atom0.cutGroup().index()); + + // first, get an editor for this residue + // and save the alternate residue name for the mapped state + auto res = mol.residue(residx); + res.setAlternateName(atom1.residue().name()); + + // now save the mapping from perturbed residue index + // to merged residue index + pert_to_merge_residx[atom1.residue().index()] = residx; + } + } + + // now go through the unmapped atoms of the reference molecule and + // save their indicies + const auto unmapped_atoms0 = mols.unmappedAtoms0().toSingleMolecule(); - QVector matched_atoms; - matched_atoms.reserve(nmapped); + for (int i = 0; i < unmapped_atoms0.count(); ++i) + { + const auto atom0 = unmapped_atoms0(i); + + auto atom = mol.atom(atom0.index()); - // now go through and update the values of properties for - // the atoms that mutate - ResStructureEditor last_res; - bool changed_res = false; + // unmapped atoms are called "Xxx" + atom.setAlternateName("Xxx"); + atom.setProperty("_mol0_index", atom0.index().value()); + atom.setProperty("_mol1_index", -1); + } - for (int i = 0; i < nmapped; ++i) + // now go through the unmapped atoms of the perturbed molecule and + // add them to the merged molecule, saving their indicies + const auto unmapped_atoms1 = mols.unmappedAtoms1().toSingleMolecule(); + + for (int i = 0; i < unmapped_atoms1.count(); ++i) + { + const auto atom1 = unmapped_atoms1(i); + + // we should have seen this residue before... + auto residx = pert_to_merge_residx.value(atom1.residue().index()); + + if (residx.isNull()) + { + // we haven't seen this residue before, so we don't know + // really where to add the atoms. The best thing to do + // is add this to the last residue that we saw in the + // molecule (the one with the highest index) + if (residx_to_cgidx.isEmpty()) { - const auto atom0 = mapped_atoms0[i]; - const auto atom1 = mapped_atoms1[i]; - - matched_atoms.append(mol.atom(atom0.index())); - auto &atom = matched_atoms.last(); - - // save the perturbed state atom and residue names into new properties, so - // that we can use these when extracting the end states - atom.setAlternateName(atom1.name()); - - try - { - auto next_res = atom.residue(); - - if (next_res != last_res) - { - changed_res = true; - last_res = next_res; - } - } - catch (...) - { - } - - if (changed_res) - { - last_res.setAlternateName(atom1.residue().name()); - } - - // check if we need to change residue + throw SireError::program_bug(QObject::tr( + "We have not seen any residues before, so we don't know " + "where to add the atoms. This is a bug!"), + CODELOC); } - */ + + auto residxs = residx_to_cgidx.keys(); + std::sort(residxs.begin(), residxs.end()); + + residx = residxs.last(); + } + + auto cgidx = residx_to_cgidx.value(residx); + + if (cgidx.isNull()) + { + throw SireError::program_bug(QObject::tr( + "We don't know the CutGroup for the residue, so we don't know " + "where to add the atoms. This is a bug!"), + CODELOC); + } + + auto res = mol.residue(residx); + + // add the atom - it has the name "Xxx" as it doesn't exist + // in the reference state + auto atom = res.add(AtomName("Xxx")); + + // reparent this atom to the CutGroup for this residue + atom.reparent(cgidx); + + // save the name in the perturbed state + atom.setAlternateName(atom1.name()); + atom.setProperty("_mol0_index", -1); + atom.setProperty("_mol1_index", atom1.index().value()); + } if (as_new_molecule) { mol.renumber(); } - auto editmol = mol.commit().edit(); + editmol = mol.commit().edit(); // add the reference and perturbed molecules as 'molecule0' and 'molecule1' editmol.setProperty(map["molecule0"].source(), mol0); From 8d33ce3d06cd41cf7080f681b644eb00d8c5991c Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 25 Feb 2024 18:27:44 +0000 Subject: [PATCH 130/468] WIP (not compiling yet) Working on the code to move the merge into the properties themselves (where they know what they are doing) --- corelib/src/libs/SireMol/CMakeLists.txt | 4 +- corelib/src/libs/SireMol/atomidxmapping.cpp | 641 +++++++++++++++++++ corelib/src/libs/SireMol/atomidxmapping.h | 198 ++++++ corelib/src/libs/SireMol/atomproperty.hpp | 87 +++ corelib/src/libs/SireMol/atomselection.cpp | 21 + corelib/src/libs/SireMol/atomselection.h | 8 + corelib/src/libs/SireMol/molviewproperty.cpp | 5 + corelib/src/libs/SireMol/molviewproperty.h | 12 + corelib/src/libs/SireSystem/merge.cpp | 187 +++++- corelib/src/libs/SireSystem/merge.h | 1 + 10 files changed, 1161 insertions(+), 3 deletions(-) create mode 100644 corelib/src/libs/SireMol/atomidxmapping.cpp create mode 100644 corelib/src/libs/SireMol/atomidxmapping.h diff --git a/corelib/src/libs/SireMol/CMakeLists.txt b/corelib/src/libs/SireMol/CMakeLists.txt index 75decba70..d86b71459 100644 --- a/corelib/src/libs/SireMol/CMakeLists.txt +++ b/corelib/src/libs/SireMol/CMakeLists.txt @@ -29,6 +29,7 @@ set ( SIREMOL_HEADERS atomidcombos.h atomidentifier.h atomidx.h + atomidxmapping.h atommapping.h atommasses.h atommatch.h @@ -169,10 +170,11 @@ set ( SIREMOL_SOURCES angleid.cpp atom.cpp atomcoords.cpp + atomcutting.cpp atomeditor.cpp atomid.cpp atomidentifier.cpp - atomcutting.cpp + atomidxmapping.cpp atommapping.cpp atommatch.cpp atommatcher.cpp diff --git a/corelib/src/libs/SireMol/atomidxmapping.cpp b/corelib/src/libs/SireMol/atomidxmapping.cpp new file mode 100644 index 000000000..baad41a44 --- /dev/null +++ b/corelib/src/libs/SireMol/atomidxmapping.cpp @@ -0,0 +1,641 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "atomidxmapping.h" + +#include "moleculeinfodata.h" + +#include "SireID/index.h" + +#include "SireError/errors.h" +#include "SireMol/errors.h" + +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" + +using namespace SireMol; +using namespace SireBase; +using namespace SireStream; + +//////// +//////// Implementation of AtomIdxMappingEntry +//////// + +RegisterMetaType r_entry(NO_ROOT); + +QDataStream &operator<<(QDataStream &ds, const AtomIdxMappingEntry &entry) +{ + writeHeader(ds, r_entry, 1); + + SharedDataStream sds(ds); + + sds << entry.atomidx0 << entry.atomidx1 + << entry.cgatomidx0 << entry.cgatomidx1 + << entry.unmapped0; + + return ds; +} + +QDataStream &operator>>(QDataStream &ds, AtomIdxMappingEntry &entry) +{ + auto v = readHeader(ds, r_entry); + + if (v == 1) + { + SharedDataStream sds(ds); + + sds >> entry.atomidx0 >> entry.atomidx1 >> entry.cgatomidx0 >> entry.cgatomidx1 >> entry.unmapped0; + } + else + throw SireStream::version_error(v, "1", r_entry, CODELOC); + + return ds; +} + +/** Null constructor */ +AtomIdxMappingEntry::AtomIdxMappingEntry() + : atomidx0(), atomidx1(), cgatomidx0(), cgatomidx1(), unmapped0(false) +{ +} + +/** Construct to map from 'index0' in 'molinfo0' to 'index1' in 'molinfo1'. + * There is no mapping in the perturbed state if 'index1' is null. There + * is no mapping in the reference state if 'is_unmapped_in_reference' is true. + * It is an error to have 'index0' null, or if you cannot look up + * 'index0' in 'molinfo0' or 'index1' in 'molinfo1'. + */ +AtomIdxMappingEntry::AtomIdxMappingEntry(const AtomIdx &index0, const AtomIdx &index1, + const MoleculeInfoData &molinfo0, + const MoleculeInfoData &molinfo1, + bool is_unmapped_in_reference) + : atomidx0(index0), atomidx1(index1), unmapped0(is_unmapped_in_reference) +{ + if (atomidx0.isNull()) + { + throw SireError::incompatible_error(QObject::tr("The atom index in the reference state is null!"), CODELOC); + } + + cgatomidx0 = molinfo0.cgAtomIdx(atomidx0); + + if (not atomidx1.isNull()) + { + cgatomidx1 = molinfo1.cgAtomIdx(atomidx1); + } +} + +/** Copy constructor */ +AtomIdxMappingEntry::AtomIdxMappingEntry(const AtomIdxMappingEntry &other) + : atomidx0(other.atomidx0), atomidx1(other.atomidx1), + cgatomidx0(other.cgatomidx0), cgatomidx1(other.cgatomidx1), + unmapped0(other.unmapped0) +{ +} + +/** Destructor */ +AtomIdxMappingEntry::~AtomIdxMappingEntry() +{ +} + +/** Assignment operator */ +AtomIdxMappingEntry &AtomIdxMappingEntry::operator=(const AtomIdxMappingEntry &other) +{ + if (this != &other) + { + atomidx0 = other.atomidx0; + atomidx1 = other.atomidx1; + cgatomidx0 = other.cgatomidx0; + cgatomidx1 = other.cgatomidx1; + unmapped0 = other.unmapped0; + } + + return *this; +} + +/** Equality operator */ +bool AtomIdxMappingEntry::operator==(const AtomIdxMappingEntry &other) const +{ + return atomidx0 == other.atomidx0 and atomidx1 == other.atomidx1 and + cgatomidx0 == other.cgatomidx0 and cgatomidx1 == other.cgatomidx1 and + unmapped0 == other.unmapped0; +} + +/** Inequality operator */ +bool AtomIdxMappingEntry::operator!=(const AtomIdxMappingEntry &other) const +{ + return not this->operator==(other); +} + +/** Clone this object */ +AtomIdxMappingEntry *AtomIdxMappingEntry::clone() const +{ + return new AtomIdxMappingEntry(*this); +} + +/** Return whether or not this is a null entry */ +bool AtomIdxMappingEntry::isNull() const +{ + return atomidx0.isNull(); +} + +/** Convert this object to a string */ +QString AtomIdxMappingEntry::toString() const +{ + if (this->isNull()) + { + return QString("AtomIdxMappingEntry: null"); + } + else if (this->isUnmappedIn0()) + { + return QString("%1 unmapped -> %2").arg(this->atomIdx0().value()).arg(this->atomIdx1().value()); + } + else if (this->isUnmappedIn1()) + { + return QString("%1 -> unmapped").arg(this->atomIdx0().value()); + } + else + { + return QString("%1 -> %2").arg(this->atomIdx0().value()).arg(this->atomIdx1().value()); + } +} + +const char *AtomIdxMappingEntry::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *AtomIdxMappingEntry::what() const +{ + return AtomIdxMappingEntry::typeName(); +} + +/** Return whether or not this atom is unmapped in the reference state */ +bool AtomIdxMappingEntry::isUnmappedIn0() const +{ + return unmapped0; +} + +/** Return whether or not this atom is unmapped in the perturbed state */ +bool AtomIdxMappingEntry::isUnmappedIn1() const +{ + return atomidx1.isNull(); +} + +/** Return the atom index in the reference state. This will always have + * a value, even if the atom is unmapped in the reference state + * (this signals that any parameter with this index should be zero) + */ +AtomIdx AtomIdxMappingEntry::atomIdx0() const +{ + return atomidx0; +} + +/** Return the atom index in the perturbed state, or a null index if + * the atom is unmapped in the perturbed state */ +AtomIdx AtomIdxMappingEntry::atomIdx1() const +{ + return atomidx1; +} + +/** Return the atom index in the reference state. This will always have + * a value, even if the atom is unmapped in the reference state + * (this signals that any parameter with this index should be zero) + */ +CGAtomIdx AtomIdxMappingEntry::cgAtomIdx0() const +{ + return cgatomidx0; +} + +/** Return the atom index in the perturbed state, or a null index if + * the atom is unmapped in the perturbed state */ +CGAtomIdx AtomIdxMappingEntry::cgAtomIdx1() const +{ + return cgatomidx1; +} + +//////// +//////// Implementation of AtomIdxMapping +//////// + +RegisterMetaType r_mapping; + +QDataStream &operator<<(QDataStream &ds, const AtomIdxMapping &mapping) +{ + writeHeader(ds, r_mapping, 1); + + SharedDataStream sds(ds); + + sds << mapping.entries << static_cast(mapping); + + return ds; +} + +QDataStream &operator>>(QDataStream &ds, AtomIdxMapping &mapping) +{ + auto v = readHeader(ds, r_mapping); + + if (v == 1) + { + SharedDataStream sds(ds); + + sds >> mapping.entries >> static_cast(mapping); + } + else + throw SireStream::version_error(v, "1", r_mapping, CODELOC); + + return ds; +} + +/** Null constructor */ +AtomIdxMapping::AtomIdxMapping() + : ConcreteProperty() +{ +} + +/** Construct from a single entry */ +AtomIdxMapping::AtomIdxMapping(const AtomIdxMappingEntry &entry) + : ConcreteProperty() +{ + if (not entry.isNull()) + entries.append(entry); +} + +/** Assert that this object is sane */ +void AtomIdxMapping::assertSane() const +{ + QHash seen; + seen.reserve(entries.size()); + + for (const auto &entry : entries) + { + if (entry.isNull()) + { + throw SireError::incompatible_error(QObject::tr("The AtomIdxMapping contains a null entry!"), CODELOC); + } + else if (seen.contains(entry.atomIdx0().value())) + { + throw SireError::incompatible_error(QObject::tr("The AtomIdxMapping contains a duplicate entry (%1 vs %2)!") + .arg(entry.toString()) + .arg(seen[entry.atomIdx0().value()].toString()), + CODELOC); + } + else + { + seen.insert(entry.atomIdx0().value(), entry); + } + } +} + +/** Construct from a list of entries */ +AtomIdxMapping::AtomIdxMapping(const QList &e) + : ConcreteProperty() +{ + bool any_null = false; + + for (const auto &entry : e) + { + if (entry.isNull()) + { + any_null = true; + break; + } + } + + if (not any_null) + { + entries = e; + } + else + { + for (const auto &entry : e) + { + if (not entry.isNull()) + { + entries.append(entry); + } + } + } + + this->assertSane(); +} + +/** Copy constructor */ +AtomIdxMapping::AtomIdxMapping(const AtomIdxMapping &other) + : ConcreteProperty(other) +{ +} + +/** Destructor */ +AtomIdxMapping::~AtomIdxMapping() +{ +} + +/** Assignment operator */ +AtomIdxMapping &AtomIdxMapping::operator=(const AtomIdxMapping &other) +{ + if (this != &other) + { + entries = other.entries; + Property::operator=(other); + } + + return *this; +} + +/** Equality operator */ +bool AtomIdxMapping::operator==(const AtomIdxMapping &other) const +{ + return entries == other.entries and Property::operator==(other); +} + +/** Inequality operator */ +bool AtomIdxMapping::operator!=(const AtomIdxMapping &other) const +{ + return not this->operator==(other); +} + +/** Clone this object */ +AtomIdxMapping *AtomIdxMapping::clone() const +{ + return new AtomIdxMapping(*this); +} + +/** Convert this object to a string */ +QString AtomIdxMapping::toString() const +{ + if (this->isEmpty()) + { + return QObject::tr("AtomIdxMapping::empty"); + } + else + { + QStringList parts; + + const auto n = this->count(); + + if (n <= 10) + { + for (int i = 0; i < n; ++i) + { + parts.append(QObject::tr("%1: %2").arg(i).arg(this->operator[](i).toString())); + } + } + else + { + for (int i = 0; i < 5; ++i) + { + parts.append(QObject::tr("%1: %2").arg(i).arg(this->operator[](i).toString())); + } + + parts.append("..."); + + for (int i = n - 5; i < n; ++i) + { + parts.append(QObject::tr("%1: %2").arg(i).arg(this->operator[](i).toString())); + } + } + + return QObject::tr("AtomIdxMapping( size=%2\n%3\n)").arg(n).arg(parts.join("\n")); + } +} + +const char *AtomIdxMapping::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *AtomIdxMapping::what() const +{ + return AtomIdxMapping::typeName(); +} + +/** Add another mapping to this one */ +AtomIdxMapping &AtomIdxMapping::operator+=(const AtomIdxMapping &other) +{ + this->append(other); + return *this; +} + +/** Add another mapping to this one */ +AtomIdxMapping &AtomIdxMapping::operator+=(const AtomIdxMappingEntry &entry) +{ + this->append(entry); + return *this; +} + +/** Add another mapping to this one */ +AtomIdxMapping AtomIdxMapping::operator+(const AtomIdxMapping &other) const +{ + AtomIdxMapping result(*this); + result += other; + return result; +} + +/** Add another mapping to this one */ +AtomIdxMapping AtomIdxMapping::operator+(const AtomIdxMappingEntry &entry) const +{ + AtomIdxMapping result(*this); + result += entry; + return result; +} + +/** Return an iterator to the beginning of the list */ +QList::const_iterator AtomIdxMapping::begin() const +{ + return entries.begin(); +} + +/** Return an iterator to the beginning of the list */ +QList::const_iterator AtomIdxMapping::constBegin() const +{ + return entries.constBegin(); +} + +/** Return an iterator to the end of the list */ +QList::const_iterator AtomIdxMapping::end() const +{ + return entries.end(); +} + +/** Return an iterator to the end of the list */ +QList::const_iterator AtomIdxMapping::constEnd() const +{ + return entries.constEnd(); +} + +/** Find an entry in the list */ +QList::const_iterator AtomIdxMapping::find(AtomIdx atom) const +{ + return std::find_if(entries.constBegin(), entries.constEnd(), [atom](const AtomIdxMappingEntry &entry) + { return entry.atomIdx0() == atom; }); +} + +/** Find an entry in the list */ +QList::const_iterator AtomIdxMapping::find(CGAtomIdx atom) const +{ + return std::find_if(entries.constBegin(), entries.constEnd(), [atom](const AtomIdxMappingEntry &entry) + { return entry.cgAtomIdx0() == atom; }); +} + +/** Append an entry to the list */ +void AtomIdxMapping::append(const AtomIdxMappingEntry &new_entry) +{ + if (new_entry.isNull()) + return; + + for (const auto &entry : entries) + { + if (entry.atomIdx0() == new_entry.atomIdx0()) + { + throw SireError::incompatible_error(QObject::tr("The AtomIdxMapping already contains an entry for atom %1!") + .arg(new_entry.atomIdx0().value()), + CODELOC); + } + } + + entries.append(new_entry); +} + +/** Append all of the passed entries of other onto this list */ +void AtomIdxMapping::append(const AtomIdxMapping &other) +{ + AtomIdxMapping ret(*this); + + for (const auto &entry : other.entries) + { + ret.append(entry); + } + + *this = ret; +} + +/** Clear the list */ +void AtomIdxMapping::clear() +{ + entries.clear(); +} + +/** Return whether or not the list is empty */ +bool AtomIdxMapping::isEmpty() const +{ + return entries.isEmpty(); +} + +/** Return the size of the list */ +int AtomIdxMapping::size() const +{ + return entries.size(); +} + +/** Return the count of the list */ +int AtomIdxMapping::count() const +{ + return entries.count(); +} + +/** Return the entry at index 'i' */ +const AtomIdxMappingEntry &AtomIdxMapping::operator[](int i) const +{ + i = SireID::Index(i).map(entries.size()); + return entries[i]; +} + +/** Take the entry at index 'i' */ +AtomIdxMappingEntry AtomIdxMapping::take(int i) +{ + i = SireID::Index(i).map(entries.size()); + return entries.takeAt(i); +} + +/** Take the entry for atom 'atom' */ +AtomIdxMappingEntry AtomIdxMapping::take(const AtomIdx &atom) +{ + auto it = this->find(atom); + + if (it != this->constEnd()) + { + return this->take(std::distance(this->constBegin(), it)); + } + else + { + throw SireMol::missing_atom(QObject::tr( + "The AtomIdxMapping does not contain an entry for atom %1!") + .arg(atom.toString()), + CODELOC); + + return AtomIdxMappingEntry(); + } +} + +/** Take the entry for atom 'atom' */ +AtomIdxMappingEntry AtomIdxMapping::take(const CGAtomIdx &atom) +{ + auto it = this->find(atom); + + if (it != this->constEnd()) + { + return this->take(std::distance(this->constBegin(), it)); + } + else + { + throw SireMol::missing_atom(QObject::tr( + "The AtomIdxMapping does not contain an entry for atom %1!") + .arg(atom.toString()), + CODELOC); + + return AtomIdxMappingEntry(); + } +} + +/** Remove the entry at index 'i' */ +void AtomIdxMapping::remove(int i) +{ + i = SireID::Index(i).map(entries.size()); + entries.removeAt(i); +} + +/** Remove the entry for atom 'atom' */ +void AtomIdxMapping::remove(const AtomIdx &atom) +{ + auto it = this->find(atom); + + if (it != this->constEnd()) + { + this->remove(std::distance(this->constBegin(), it)); + } +} + +/** Remove the entry for atom 'atom' */ +void AtomIdxMapping::remove(const CGAtomIdx &atom) +{ + auto it = this->find(atom); + + if (it != this->constEnd()) + { + this->remove(std::distance(this->constBegin(), it)); + } +} diff --git a/corelib/src/libs/SireMol/atomidxmapping.h b/corelib/src/libs/SireMol/atomidxmapping.h new file mode 100644 index 000000000..cdd1d2354 --- /dev/null +++ b/corelib/src/libs/SireMol/atomidxmapping.h @@ -0,0 +1,198 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREMOL_ATOMIDXMAPPING_H +#define SIREMOL_ATOMIDXMAPPING_H + +#include "SireBase/property.h" + +#include "SireMol/atomidx.h" +#include "SireMol/cgatomidx.h" + +SIRE_BEGIN_HEADER + +namespace SireMol +{ + class AtomIdxMapping; + class AtomIdxMappingEntry; +} + +SIREMOL_EXPORT QDataStream &operator<<(QDataStream &, const SireMol::AtomIdxMapping &); +SIREMOL_EXPORT QDataStream &operator>>(QDataStream &, SireMol::AtomIdxMapping &); + +SIREMOL_EXPORT QDataStream &operator<<(QDataStream &, const SireMol::AtomIdxMappingEntry &); +SIREMOL_EXPORT QDataStream &operator>>(QDataStream &, SireMol::AtomIdxMappingEntry &); + +namespace SireMol +{ + /** This is an individual mapping for a single atom */ + class SIREMOL_EXPORT AtomIdxMappingEntry + { + friend QDataStream & ::operator<<(QDataStream &, const AtomIdxMappingEntry &); + friend QDataStream & ::operator>>(QDataStream &, AtomIdxMappingEntry &); + + public: + AtomIdxMappingEntry(); + AtomIdxMappingEntry(const AtomIdx &index0, const AtomIdx &index1, + const MoleculeInfoData &molinfo0, + const MoleculeInfoData &molinfo1, + bool is_unmapped_in_reference); + + AtomIdxMappingEntry(const AtomIdxMappingEntry &other); + ~AtomIdxMappingEntry(); + + AtomIdxMappingEntry &operator=(const AtomIdxMappingEntry &other); + + bool operator==(const AtomIdxMappingEntry &other) const; + bool operator!=(const AtomIdxMappingEntry &other) const; + + AtomIdxMappingEntry *clone() const; + + bool isNull() const; + + QString toString() const; + + static const char *typeName(); + const char *what() const; + + bool isUnmappedIn0() const; + bool isUnmappedIn1() const; + + AtomIdx atomIdx0() const; + AtomIdx atomIdx1() const; + + CGAtomIdx cgAtomIdx0() const; + CGAtomIdx cgAtomIdx1() const; + + private: + /** The atomidx in the reference state */ + AtomIdx atomidx0; + + /** The atomidx in the perturbed state */ + AtomIdx atomidx1; + + /** The CGAtomIdx in the reference state */ + CGAtomIdx cgatomidx0; + + /** The CGAtomIdx in the perturbed state */ + CGAtomIdx cgatomidx1; + + /** Whether or not this atom is unmapped in the reference state */ + bool unmapped0; + }; + + /** This class holds the mapping from one set of atom indices to another. + * This enables you to associate, atom by atom, atom indices in one set to + * atom indices in another set. This is useful, e.g. for building perturbations, + * or for specifying mappings for alignments or RMSD calculations etc. + * + * This is mainly designed to provide sufficient information to merge + * properties together. It lists not just the atoms that map, but + * also which atoms are the ghost atoms that map (i.e. were created + * as ghost equivalents) + */ + class SIREMOL_EXPORT AtomIdxMapping + : public SireBase::ConcreteProperty + { + friend QDataStream & ::operator<<(QDataStream &, const AtomIdxMapping &); + friend QDataStream & ::operator>>(QDataStream &, AtomIdxMapping &); + + public: + AtomIdxMapping(); + AtomIdxMapping(const AtomIdxMappingEntry &entry); + AtomIdxMapping(const QList &entries); + + AtomIdxMapping(const AtomIdxMapping &other); + + ~AtomIdxMapping(); + + AtomIdxMapping &operator=(const AtomIdxMapping &other); + + bool operator==(const AtomIdxMapping &other) const; + bool operator!=(const AtomIdxMapping &other) const; + + AtomIdxMapping *clone() const; + + QString toString() const; + + static const char *typeName(); + const char *what() const; + + AtomIdxMapping &operator+=(const AtomIdxMapping &other); + AtomIdxMapping &operator+=(const AtomIdxMappingEntry &entry); + + AtomIdxMapping operator+(const AtomIdxMapping &other) const; + AtomIdxMapping operator+(const AtomIdxMappingEntry &entry) const; + + QList::const_iterator begin() const; + QList::const_iterator constBegin() const; + + QList::const_iterator end() const; + QList::const_iterator constEnd() const; + + QList::const_iterator find(AtomIdx atom) const; + QList::const_iterator find(CGAtomIdx atom) const; + + void append(const AtomIdxMappingEntry &entry); + void append(const AtomIdxMapping &other); + + void clear(); + + bool isEmpty() const; + + int size() const; + int count() const; + + const AtomIdxMappingEntry &operator[](int i) const; + + AtomIdxMappingEntry take(int i); + AtomIdxMappingEntry take(const AtomIdx &atom); + AtomIdxMappingEntry take(const CGAtomIdx &atom); + + void remove(int i); + void remove(const AtomIdx &atom); + void remove(const CGAtomIdx &atom); + + private: + void assertSane() const; + + /** The list of atom entries */ + QList entries; + }; + +} // namespace SireMol + +Q_DECLARE_METATYPE(SireMol::AtomIdxMappingEntry) +Q_DECLARE_METATYPE(SireMol::AtomIdxMapping) + +SIRE_EXPOSE_CLASS(SireMol::AtomIdxMappingEntry) +SIRE_EXPOSE_CLASS(SireMol::AtomIdxMapping) + +SIRE_END_HEADER + +#endif diff --git a/corelib/src/libs/SireMol/atomproperty.hpp b/corelib/src/libs/SireMol/atomproperty.hpp index 7e241cdb2..b2596fcb9 100644 --- a/corelib/src/libs/SireMol/atomproperty.hpp +++ b/corelib/src/libs/SireMol/atomproperty.hpp @@ -34,6 +34,7 @@ #include "SireBase/qvariant_metatype.h" #include "atomselection.h" +#include "atomidxmapping.h" #include "moleculeinfo.h" #include "moleculeinfodata.h" #include "molviewproperty.h" @@ -110,6 +111,10 @@ namespace SireMol virtual PropertyPtr divide(const QVector &beads) const = 0; virtual PropertyPtr divideByResidue(const MoleculeInfoData &molinfo) const = 0; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const = 0; + protected: void throwIncorrectNumberOfAtoms(int nats, int ntotal) const; void throwIncorrectNumberOfSelectedAtoms(int nats, int nselected) const; @@ -162,6 +167,10 @@ namespace SireMol AtomProperty *clone() const; + AtomProperty *create() const; + AtomProperty *create(const MoleculeInfoData &molinfo, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + bool operator==(const AtomProperty &other) const; bool operator!=(const AtomProperty &other) const; @@ -234,6 +243,10 @@ namespace SireMol void assertCanConvert(const QVariant &value) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual atomic property values */ SireBase::PackedArray2D props; @@ -415,6 +428,19 @@ namespace SireMol return new AtomProperty(*this); } + template + SIRE_OUTOFLINE_TEMPLATE AtomProperty *AtomProperty::create() const + { + return new AtomProperty(); + } + + template + SIRE_OUTOFLINE_TEMPLATE AtomProperty *AtomProperty::create(const MoleculeInfoData &molinfo, + const SireBase::PropertyMap &map) const + { + return new AtomProperty(molinfo); + } + template SIRE_OUTOFLINE_TEMPLATE const char *AtomProperty::typeName() { @@ -1221,6 +1247,67 @@ namespace SireMol return AtomProperty(res_vals); } + template + SIRE_OUTOFLINE_TEMPLATE T _get_zero() + { + return T(); + } + + template <> + SIRE_OUTOFLINE_TEMPLATE qint64 _get_zero() + { + return 0; + } + + template <> + SIRE_OUTOFLINE_TEMPLATE double _get_zero() + { + return 0.0; + } + + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList AtomProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + const AtomProperty &ref = *this; + const AtomProperty &pert = other.asA>(); + + AtomProperty prop0 = ref; + AtomProperty prop1 = ref; + + for (const auto &index : mapping) + { + if (index.isUnmappedIn0()) + { + prop0.set(index.cgAtomIdx0(), _get_zero()); + } + + if (index.isUnmappedIn1()) + { + prop1.set(index.cgAtomIdx0(), _get_zero()); + } + else + { + prop1.set(index.cgAtomIdx0(), pert.get(index.cgAtomIdx1())); + } + } + + SireBase::PropertyList ret; + ret.append(prop0); + ret.append(prop1); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // namespace SireMol diff --git a/corelib/src/libs/SireMol/atomselection.cpp b/corelib/src/libs/SireMol/atomselection.cpp index 95dcb6713..ada16b845 100644 --- a/corelib/src/libs/SireMol/atomselection.cpp +++ b/corelib/src/libs/SireMol/atomselection.cpp @@ -160,6 +160,16 @@ AtomSelection::AtomSelection(const AtomSelection &other) { } +AtomSelection *AtomSelection::create() const +{ + return new AtomSelection(); +} + +AtomSelection *AtomSelection::create(const MoleculeInfoData &molinfo, const PropertyMap &) const +{ + return new AtomSelection(molinfo); +} + /** Destructor */ AtomSelection::~AtomSelection() { @@ -4224,3 +4234,14 @@ bool AtomSelection::isSegment() const return false; } + +PropertyList AtomSelection::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const SireBase::PropertyMap &map) const +{ + PropertyList ret; + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMol/atomselection.h b/corelib/src/libs/SireMol/atomselection.h index 81d631c8a..1d1813a08 100644 --- a/corelib/src/libs/SireMol/atomselection.h +++ b/corelib/src/libs/SireMol/atomselection.h @@ -117,6 +117,10 @@ namespace SireMol bool isEmpty() const; bool isNull() const; + AtomSelection *create() const; + AtomSelection *create(const MoleculeInfoData &molinfo, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + const MoleculeInfoData &info() const; int nSelected() const; @@ -454,6 +458,10 @@ namespace SireMol template void assertCompatibleWith(const AtomProperty &prop) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: bool _pvt_selected(const CGAtomIdx &cgatomidx) const; bool _pvt_selected(AtomIdx atomidx) const; diff --git a/corelib/src/libs/SireMol/molviewproperty.cpp b/corelib/src/libs/SireMol/molviewproperty.cpp index d6ddc7214..a11d76003 100644 --- a/corelib/src/libs/SireMol/molviewproperty.cpp +++ b/corelib/src/libs/SireMol/molviewproperty.cpp @@ -144,6 +144,11 @@ PropertyPtr MolViewProperty::makeCompatibleWith(const MoleculeView &molview, con return this->makeCompatibleWith(molview.data().info(), map); } +MolViewProperty *MolViewProperty::create() const +{ + return static_cast(Property::create()); +} + ///////// ///////// Implementation of MoleculeProperty ///////// diff --git a/corelib/src/libs/SireMol/molviewproperty.h b/corelib/src/libs/SireMol/molviewproperty.h index c2250e0f8..806afe4cd 100644 --- a/corelib/src/libs/SireMol/molviewproperty.h +++ b/corelib/src/libs/SireMol/molviewproperty.h @@ -31,6 +31,7 @@ #include #include "SireBase/property.h" +#include "SireBase/propertylist.h" #include "moleculeinfo.h" @@ -45,10 +46,12 @@ namespace SireMol { class MoleculeInfoData; + class MoleculeInfo; class MoleculeView; class AtomSelection; class AtomIdx; class AtomMatcher; + class AtomIdxMapping; /** This is the base class of all properties that are specifically attached to views of a molecule (e.g. AtomProperty, ResProperty, @@ -71,6 +74,11 @@ namespace SireMol return "SireMol::MolViewProperty"; } + virtual MolViewProperty *create() const; + + virtual MolViewProperty *create(const MoleculeInfoData &molinfo, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const = 0; + virtual bool isCompatibleWith(const MoleculeInfoData &molinfo) const = 0; virtual bool isCompatibleWith(const MoleculeInfo &molinfo) const; @@ -83,6 +91,10 @@ namespace SireMol SireBase::PropertyPtr makeCompatibleWith(const MoleculeView &mol, const AtomMatcher &atommatcher) const; SireBase::PropertyPtr makeCompatibleWith(const MoleculeView &mol, const QHash &map) const; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const = 0; + void assertCompatibleWith(const MoleculeInfoData &molinfo) const; void assertCompatibleWith(const MoleculeInfo &molinfo) const; diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index b1bc183bf..2c87fea72 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -30,6 +30,9 @@ #include "SireMol/core.h" #include "SireMol/moleditor.h" +#include "SireMol/atomidxmapping.h" + +#include "SireMM/mmdetail.h" using namespace SireMol; using namespace SireBase; @@ -40,6 +43,8 @@ namespace SireSystem * @brief Merge function that combines multiple molecules into a single molecule. * * @param mols The AtomMapping object that contains the molecules to be merged. + * @param properties The list of properties to be merged. If this is empty then + * a default set of properties will be merged. * @param as_new_molecule Flag indicating whether the merged molecule should be created as a new molecule. * @param allow_ring_breaking Whether to allow the opening/closing of rings during a merge. * @param allow_ring_size_change Whether to allow changes in ring size. @@ -51,9 +56,11 @@ namespace SireSystem * @param map The PropertyMap object that contains additional properties for the merged molecule. * @return The merged molecule. */ - Molecule merge(const AtomMapping &mols, bool as_new_molecule, + Molecule merge(const AtomMapping &mols, + const QStringList &properties, + bool as_new_molecule, bool allow_ring_breaking, bool allow_ring_size_change, - bool force, const PropertyMap &map) + bool force, const PropertyMap &input_map) { if (not mols.isSingleMolecule()) { @@ -63,6 +70,8 @@ namespace SireSystem .arg(mols.toString())); } + PropertyMap map = input_map; + if (map.specified("as_new_molecule")) { as_new_molecule = map["as_new_molecule"].value().asABoolean(); @@ -94,6 +103,31 @@ namespace SireSystem allow_ring_size_change = true; } + map.set("as_new_molecule", BooleanProperty(as_new_molecule)); + map.set("allow_ring_breaking", BooleanProperty(allow_ring_breaking)); + + // see which properties to merge + QStringList props = properties; + + if (props.isEmpty()) + { + props = QStringList({ + "angle", + "ambertype", + "atomtype", + "bond", + "charge", + "connectivity", + "coordinates", + "dihedral", + "element", + "improper", + "intrascale", + "LJ", + "mass", + }); + } + // get the forwards and backwards map auto forwards_map = mols; auto backwards_map = mols.swap(); @@ -119,10 +153,67 @@ namespace SireSystem // get the MolEditor that can be used to set properties MolEditor editmol = mols.atoms0().toSingleMolecule().molecule().edit(); + // check and set the forcefields + SireMM::MMDetail ffield0; + SireMM::MMDetail ffield1; + + bool have_ffield0 = false; + bool have_ffield1 = false; + + try + { + ffield0 = mapped_atoms0.data().property(map0["forcefield"]).asA(); + have_ffield0 = true; + } + catch (...) + { + } + + try + { + ffield1 = mapped_atoms1.data().property(map1["forcefield"]).asA(); + have_ffield1 = true; + } + catch (...) + { + } + + if (not(have_ffield0 and have_ffield1)) + { + throw SireError::incompatible_error(QObject::tr( + "You must specify a forcefield for both the reference and " + "perturbed states in order to merge the molecules."), + CODELOC); + } + else if (not have_ffield1) + { + ffield1 = ffield0; + } + else + { + ffield0 = ffield1; + } + + if (not ffield0.isCompatibleWith(ffield1)) + { + throw SireError::incompatible_error(QObject::tr( + "The forcefields for the reference and perturbed states are " + "incompatible. You cannot merge the molecules. The forcefields " + "are %1 and %2") + .arg(ffield0.toString()) + .arg(ffield1.toString()), + CODELOC); + } + // and a handle on the whole reference and perturbed molecule const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); + // use a property to track which atoms have been mapped - + // a value of -1 means that this atom is not mapped + editmol.setProperty("_mol0_index", AtomIntProperty(mol0.info(), -1)); + editmol.setProperty("_mol1_index", AtomIntProperty(mol1.info(), -1)); + // get an editable copy of the molecule to be changed MolStructureEditor mol(editmol); @@ -259,10 +350,102 @@ namespace SireSystem editmol = mol.commit().edit(); + // now we have the merged molecule, we need to work out the mapping + // of atoms from the reference to the perturbed state in this + // merged molecule + QList entries; + + const auto &molinfo0 = editmol.info(); + const auto &molinfo1 = mol1.info(); + + for (int i = 0; i < molinfo0.nAtoms(); ++i) + { + const auto atom = editmol.atom(AtomIdx(i)); + + const auto index0 = atom.property("_mol0_index"); + const auto index1 = atom.property("_mol1_index"); + + if (index0 == -1 and index1 == -1) + { + // this atom is not involved in the mapping + continue; + } + + const bool is_unmapped_in_reference = (index0 == -1); + + entries.append(AtomIdxMappingEntry(AtomIdx(i), AtomIdx(index1), + molinfo0, molinfo1, + is_unmapped_in_reference)); + } + + // now go through all of the properties that we want to merge + // and merge them using the AtomIdxMapping object - remove + // the common property of these + for (const auto &prop : props) + { + if (editmol.hasProperty(map0[prop]) and mol1.hasProperty(map1[prop])) + { + // we both have the property, so it should be mergeable + const auto &prop0 = editmol.property(map0[prop]); + const auto &prop1 = mol1.property(map1[prop]); + + if (prop0.what() != prop1.what()) + { + // the properties are not the same type + throw SireError::incompatible_error(QObject::tr( + "Cannot merge the molecule because the property %1 is not the " + "same type in both molecules. It is %2=%3 in the reference " + "and %4=%5 in the perturbed molecule.") + .arg(prop) + .arg(map0[prop].source()) + .arg(prop0.what()) + .arg(map1[prop].source()) + .arg(prop1.what()), + CODELOC); + } + + if (prop0.isA()) + { + // they can be properly merged + auto merged = prop0.asA().merge(prop1.asA(), + entries, map); + + if (merged.count() != 2) + throw SireError::program_bug(QObject::tr( + "The merge of the property %1 did not return two properties. " + "This is a bug!") + .arg(prop), + CODELOC); + + editmol.removeProperty(map0[prop]); + editmol.setProperty(map[prop + "0"].source(), merged[0]); + editmol.setProperty(map[prop + "1"].source() + "1", merged[1]); + } + else + { + // they are normal properties - they cannot be merged + // so just add them as the two end states + editmol.removeProperty(map0[prop]); + editmol.setProperty(map[prop + "0"].source(), prop0); + editmol.setProperty(map[prop + "1"].source(), prop1); + } + } + } + // add the reference and perturbed molecules as 'molecule0' and 'molecule1' editmol.setProperty(map["molecule0"].source(), mol0); editmol.setProperty(map["molecule1"].source(), mol1); + // add the forcefields for the two molecules + editmol.setProperty(map["forcefield0"].source(), ffield0); + editmol.setProperty(map["forcefield1"].source(), ffield1); + + // remove any property called "parameters" + if (editmol.hasProperty(map["parameters"].source())) + { + editmol.removeProperty(map["parameters"].source()); + } + // set the flag that this is a perturbable molecule editmol.setProperty(map["is_perturbable"].source(), BooleanProperty(true)); diff --git a/corelib/src/libs/SireSystem/merge.h b/corelib/src/libs/SireSystem/merge.h index 80592ba0c..e6f925b9f 100644 --- a/corelib/src/libs/SireSystem/merge.h +++ b/corelib/src/libs/SireSystem/merge.h @@ -39,6 +39,7 @@ SIRE_BEGIN_HEADER namespace SireSystem { SIRESYSTEM_EXPORT SireMol::Molecule merge(const SireMol::AtomMapping &mols, + const QStringList &properties = QStringList(), bool as_new_molecule = true, bool allow_ring_breaking = false, bool allow_ring_size_change = false, From 2338e9126ab1c32e3ea2d5577838a4e0dd32fa10 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 25 Feb 2024 23:19:28 +0000 Subject: [PATCH 131/468] WIP (still) - added ability to control the value of ghost atom parameters. Also beginning to fill in the various merge functions --- corelib/src/libs/SireMol/CMakeLists.txt | 1 + corelib/src/libs/SireMol/amberparameters.cpp | 13 ++ corelib/src/libs/SireMol/amberparameters.h | 5 + corelib/src/libs/SireMol/atomcoords.cpp | 50 ++++++ corelib/src/libs/SireMol/atomcoords.h | 5 + corelib/src/libs/SireMol/atomproperty.hpp | 45 +---- corelib/src/libs/SireMol/atomselection.cpp | 11 +- corelib/src/libs/SireMol/atomselection.h | 5 +- corelib/src/libs/SireMol/cgproperty.hpp | 39 ++++- corelib/src/libs/SireMol/getghostparam.hpp | 167 +++++++++++++++++++ corelib/src/libs/SireMol/molviewproperty.cpp | 5 - corelib/src/libs/SireMol/molviewproperty.h | 6 +- corelib/src/libs/SireSystem/merge.cpp | 15 +- 13 files changed, 303 insertions(+), 64 deletions(-) create mode 100644 corelib/src/libs/SireMol/getghostparam.hpp diff --git a/corelib/src/libs/SireMol/CMakeLists.txt b/corelib/src/libs/SireMol/CMakeLists.txt index d86b71459..9d725e90a 100644 --- a/corelib/src/libs/SireMol/CMakeLists.txt +++ b/corelib/src/libs/SireMol/CMakeLists.txt @@ -89,6 +89,7 @@ set ( SIREMOL_HEADERS improperid.h iswater.h geometryperturbation.h + getghostparam.hpp getrmsd.h groupatomids.h groupgroupids.h diff --git a/corelib/src/libs/SireMol/amberparameters.cpp b/corelib/src/libs/SireMol/amberparameters.cpp index 5c656b4c7..c10c52511 100644 --- a/corelib/src/libs/SireMol/amberparameters.cpp +++ b/corelib/src/libs/SireMol/amberparameters.cpp @@ -35,10 +35,13 @@ #include "SireMol/molecule.h" #include "SireMol/partialmolecule.h" +#include "SireError/errors.h" + #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" using namespace SireMol; +using namespace SireBase; using namespace SireStream; /////////// @@ -317,3 +320,13 @@ QList AmberParameters::getAll14Pairs() { return nb14pairs.keys(); } + +PropertyList AmberParameters::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + throw SireError::incomplete_code(QObject::tr( + "AmberParameters::merge() is not implemented yet!"), + CODELOC); +} diff --git a/corelib/src/libs/SireMol/amberparameters.h b/corelib/src/libs/SireMol/amberparameters.h index 7be7a9321..272b86fd0 100644 --- a/corelib/src/libs/SireMol/amberparameters.h +++ b/corelib/src/libs/SireMol/amberparameters.h @@ -125,6 +125,11 @@ namespace SireMol QList get14PairParams(const BondID &pair); QList getAll14Pairs(); + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The molecule that this flexibility operates on */ SireBase::SharedDataPointer molinfo; diff --git a/corelib/src/libs/SireMol/atomcoords.cpp b/corelib/src/libs/SireMol/atomcoords.cpp index 860e022bd..59b72c1f1 100644 --- a/corelib/src/libs/SireMol/atomcoords.cpp +++ b/corelib/src/libs/SireMol/atomcoords.cpp @@ -1031,3 +1031,53 @@ AtomProperty *AtomCoords::clone() const { return new AtomProperty(*this); } + +PropertyList AtomCoords::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + const AtomCoords &ref = *this; + const AtomCoords &pert = other.asA(); + + AtomCoords prop0 = ref; + AtomCoords prop1 = ref; + + Vector ghost_param(0); + + if (not ghost.isEmpty()) + { + ghost_param = Vector(ghost); + } + + for (const auto &index : mapping) + { + if (index.isUnmappedIn0()) + { + prop0.set(index.cgAtomIdx0(), ghost_param); + } + + if (index.isUnmappedIn1()) + { + prop1.set(index.cgAtomIdx0(), ghost_param); + } + else + { + prop1.set(index.cgAtomIdx0(), pert.get(index.cgAtomIdx1())); + } + } + + SireBase::PropertyList ret; + ret.append(prop0); + ret.append(prop1); + + return ret; +} diff --git a/corelib/src/libs/SireMol/atomcoords.h b/corelib/src/libs/SireMol/atomcoords.h index 06eb8aa7c..8c21da8a0 100644 --- a/corelib/src/libs/SireMol/atomcoords.h +++ b/corelib/src/libs/SireMol/atomcoords.h @@ -196,6 +196,11 @@ namespace SireMol void assertCanConvert(const QVariant &value) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual atomic coordinates, arranged into CoordGroups */ CoordGroupArray coords; diff --git a/corelib/src/libs/SireMol/atomproperty.hpp b/corelib/src/libs/SireMol/atomproperty.hpp index b2596fcb9..5c2c1d74a 100644 --- a/corelib/src/libs/SireMol/atomproperty.hpp +++ b/corelib/src/libs/SireMol/atomproperty.hpp @@ -38,6 +38,7 @@ #include "moleculeinfo.h" #include "moleculeinfodata.h" #include "molviewproperty.h" +#include "getghostparam.hpp" #include "SireBase/packedarray2d.hpp" #include "SireBase/quickcopy.hpp" @@ -113,6 +114,7 @@ namespace SireMol virtual SireBase::PropertyList merge(const MolViewProperty &other, const AtomIdxMapping &mapping, + const QString &ghost = QString(), const SireBase::PropertyMap &map = SireBase::PropertyMap()) const = 0; protected: @@ -167,10 +169,6 @@ namespace SireMol AtomProperty *clone() const; - AtomProperty *create() const; - AtomProperty *create(const MoleculeInfoData &molinfo, - const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; - bool operator==(const AtomProperty &other) const; bool operator!=(const AtomProperty &other) const; @@ -245,6 +243,7 @@ namespace SireMol SireBase::PropertyList merge(const MolViewProperty &other, const AtomIdxMapping &mapping, + const QString &ghost = QString(), const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; private: @@ -428,19 +427,6 @@ namespace SireMol return new AtomProperty(*this); } - template - SIRE_OUTOFLINE_TEMPLATE AtomProperty *AtomProperty::create() const - { - return new AtomProperty(); - } - - template - SIRE_OUTOFLINE_TEMPLATE AtomProperty *AtomProperty::create(const MoleculeInfoData &molinfo, - const SireBase::PropertyMap &map) const - { - return new AtomProperty(molinfo); - } - template SIRE_OUTOFLINE_TEMPLATE const char *AtomProperty::typeName() { @@ -1247,27 +1233,10 @@ namespace SireMol return AtomProperty(res_vals); } - template - SIRE_OUTOFLINE_TEMPLATE T _get_zero() - { - return T(); - } - - template <> - SIRE_OUTOFLINE_TEMPLATE qint64 _get_zero() - { - return 0; - } - - template <> - SIRE_OUTOFLINE_TEMPLATE double _get_zero() - { - return 0.0; - } - template SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList AtomProperty::merge(const MolViewProperty &other, const AtomIdxMapping &mapping, + const QString &ghost, const SireBase::PropertyMap &map) const { if (not other.isA>()) @@ -1284,16 +1253,18 @@ namespace SireMol AtomProperty prop0 = ref; AtomProperty prop1 = ref; + const T ghost_param = getGhostParam(ghost); + for (const auto &index : mapping) { if (index.isUnmappedIn0()) { - prop0.set(index.cgAtomIdx0(), _get_zero()); + prop0.set(index.cgAtomIdx0(), ghost_param); } if (index.isUnmappedIn1()) { - prop1.set(index.cgAtomIdx0(), _get_zero()); + prop1.set(index.cgAtomIdx0(), ghost_param); } else { diff --git a/corelib/src/libs/SireMol/atomselection.cpp b/corelib/src/libs/SireMol/atomselection.cpp index ada16b845..647f8f5ea 100644 --- a/corelib/src/libs/SireMol/atomselection.cpp +++ b/corelib/src/libs/SireMol/atomselection.cpp @@ -160,16 +160,6 @@ AtomSelection::AtomSelection(const AtomSelection &other) { } -AtomSelection *AtomSelection::create() const -{ - return new AtomSelection(); -} - -AtomSelection *AtomSelection::create(const MoleculeInfoData &molinfo, const PropertyMap &) const -{ - return new AtomSelection(molinfo); -} - /** Destructor */ AtomSelection::~AtomSelection() { @@ -4237,6 +4227,7 @@ bool AtomSelection::isSegment() const PropertyList AtomSelection::merge(const MolViewProperty &other, const AtomIdxMapping &mapping, + const QString &ghost, const SireBase::PropertyMap &map) const { PropertyList ret; diff --git a/corelib/src/libs/SireMol/atomselection.h b/corelib/src/libs/SireMol/atomselection.h index 1d1813a08..eecc66023 100644 --- a/corelib/src/libs/SireMol/atomselection.h +++ b/corelib/src/libs/SireMol/atomselection.h @@ -117,10 +117,6 @@ namespace SireMol bool isEmpty() const; bool isNull() const; - AtomSelection *create() const; - AtomSelection *create(const MoleculeInfoData &molinfo, - const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; - const MoleculeInfoData &info() const; int nSelected() const; @@ -460,6 +456,7 @@ namespace SireMol SireBase::PropertyList merge(const MolViewProperty &other, const AtomIdxMapping &mapping, + const QString &ghost = QString(), const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; private: diff --git a/corelib/src/libs/SireMol/cgproperty.hpp b/corelib/src/libs/SireMol/cgproperty.hpp index 215bc4ada..5e91963e4 100644 --- a/corelib/src/libs/SireMol/cgproperty.hpp +++ b/corelib/src/libs/SireMol/cgproperty.hpp @@ -36,6 +36,7 @@ #include "moleculeinfodata.h" #include "molviewproperty.h" +#include "getghostparam.hpp" #include "SireError/errors.h" @@ -105,7 +106,7 @@ namespace SireMol { friend SIREMOL_EXPORT QDataStream & ::operator<< <>(QDataStream &, const CGProperty &); - friend SIREMOL_EXPORT QDataStream & ::operator>><>(QDataStream &, CGProperty &); + friend SIREMOL_EXPORT QDataStream & ::operator>> <>(QDataStream &, CGProperty &); public: CGProperty(); @@ -169,6 +170,11 @@ namespace SireMol bool isCompatibleWith(const MoleculeInfoData &molinfo) const; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual CutGroup property values */ QVector props; @@ -548,6 +554,37 @@ namespace SireMol return molinfo.nCutGroups() == this->nCutGroups(); } + /** Merge this property with another property */ + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList CGProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + const CGProperty &ref = *this; + const CGProperty &pert = other.asA>(); + + CGProperty prop0 = ref; + CGProperty prop1 = ref; + + const T ghost_param = getGhostParam(ghost); + + SireBase::PropertyList ret; + + ret.append(prop0); + ret.append(prop1); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // namespace SireMol diff --git a/corelib/src/libs/SireMol/getghostparam.hpp b/corelib/src/libs/SireMol/getghostparam.hpp new file mode 100644 index 000000000..97fe064f0 --- /dev/null +++ b/corelib/src/libs/SireMol/getghostparam.hpp @@ -0,0 +1,167 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREMOL_GETGHOSTPARAM_HPP +#define SIREMOL_GETGHOSTPARAM_HPP + +#include "SireBase/booleanproperty.h" +#include "SireBase/stringproperty.h" + +#include "SireMol/element.h" + +#include "SireUnits/generalunit.h" + +SIRE_BEGIN_HEADER + +namespace SireMol +{ + template + inline T getGhostParam(const QString &ghost) + { + return T(); + } + + template <> + inline QString getGhostParam(const QString &ghost) + { + return ghost; + } + + template <> + inline qint64 getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return 0; + else + return ghost.toLongLong(); + } + + template <> + inline double getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return 0.0; + else + return ghost.toDouble(); + } + + template <> + inline bool getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return false; + else + return SireBase::BooleanProperty(ghost).value(); + } + + template <> + inline SireUnits::Dimension::GeneralUnit getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireUnits::Dimension::GeneralUnit(0); + else + return SireUnits::Dimension::GeneralUnit(ghost); + } + + template <> + inline QVariant getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return QVariant(); + else + return QVariant(ghost); + } + + template <> + inline SireUnits::Dimension::MolarMass getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireUnits::Dimension::MolarMass(0.0); + else + return SireUnits::Dimension::MolarMass(ghost); + } + + template <> + inline SireUnits::Dimension::MolarEnergy getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireUnits::Dimension::MolarEnergy(0.0); + else + return SireUnits::Dimension::MolarEnergy(ghost); + } + + template <> + inline SireUnits::Dimension::Charge getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireUnits::Dimension::Charge(0.0); + else + return SireUnits::Dimension::Charge(ghost); + } + + template <> + inline SireMol::Element getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireMol::Element(0); + else + return SireMol::Element(ghost); + } + + template <> + inline SireUnits::Dimension::Volume getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireUnits::Dimension::Volume(0.0); + else + return SireUnits::Dimension::Volume(ghost); + } + + template <> + SireUnits::Dimension::Length getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireUnits::Dimension::Length(0.0); + else + return SireUnits::Dimension::Length(ghost); + } + + template <> + SireBase::PropertyPtr getGhostParam(const QString &ghost) + { + if (ghost.isEmpty()) + return SireBase::PropertyPtr(); + else + return SireBase::PropertyPtr(SireBase::StringProperty(ghost)); + } + +} + +SIRE_END_HEADER + +#endif diff --git a/corelib/src/libs/SireMol/molviewproperty.cpp b/corelib/src/libs/SireMol/molviewproperty.cpp index a11d76003..d6ddc7214 100644 --- a/corelib/src/libs/SireMol/molviewproperty.cpp +++ b/corelib/src/libs/SireMol/molviewproperty.cpp @@ -144,11 +144,6 @@ PropertyPtr MolViewProperty::makeCompatibleWith(const MoleculeView &molview, con return this->makeCompatibleWith(molview.data().info(), map); } -MolViewProperty *MolViewProperty::create() const -{ - return static_cast(Property::create()); -} - ///////// ///////// Implementation of MoleculeProperty ///////// diff --git a/corelib/src/libs/SireMol/molviewproperty.h b/corelib/src/libs/SireMol/molviewproperty.h index 806afe4cd..a27770ec5 100644 --- a/corelib/src/libs/SireMol/molviewproperty.h +++ b/corelib/src/libs/SireMol/molviewproperty.h @@ -74,11 +74,6 @@ namespace SireMol return "SireMol::MolViewProperty"; } - virtual MolViewProperty *create() const; - - virtual MolViewProperty *create(const MoleculeInfoData &molinfo, - const SireBase::PropertyMap &map = SireBase::PropertyMap()) const = 0; - virtual bool isCompatibleWith(const MoleculeInfoData &molinfo) const = 0; virtual bool isCompatibleWith(const MoleculeInfo &molinfo) const; @@ -93,6 +88,7 @@ namespace SireMol virtual SireBase::PropertyList merge(const MolViewProperty &other, const AtomIdxMapping &mapping, + const QString &ghost = QString(), const SireBase::PropertyMap &map = SireBase::PropertyMap()) const = 0; void assertCompatibleWith(const MoleculeInfoData &molinfo) const; diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 2c87fea72..a95d01c4f 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -406,9 +406,20 @@ namespace SireSystem if (prop0.isA()) { - // they can be properly merged + // they can be properly merged - get the value of the ghost parameter for this property + QString ghost_param; + + if (map.specified("ghost_" + prop)) + { + ghost_param = map["ghost_" + prop].source(); + } + else if (prop == "atomtype" or prop == "ambertype") + { + ghost_param = "Xx"; + } + auto merged = prop0.asA().merge(prop1.asA(), - entries, map); + entries, ghost_param, map); if (merged.count() != 2) throw SireError::program_bug(QObject::tr( From 4588f208a0bd8125ab7da993596cd98ea098e12f Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 26 Feb 2024 23:11:45 +0000 Subject: [PATCH 132/468] Added a SireBase::Console that connects through the sire.utils.Console, so that we can emit debug, log, warning and error messages from C++ that correctly get printed up in the Python layer (and can be properly customised and controlled in the Python layer). This is the first step to consolidating all of the messaging into a single Python logging-compatible framework (i.e. also removing some of the rich.console layer) --- corelib/src/libs/SireBase/CMakeLists.txt | 2 + corelib/src/libs/SireBase/console.cpp | 88 ++++++++++++ corelib/src/libs/SireBase/console.h | 75 ++++++++++ wrapper/Base/releasegil_impl.cpp | 166 +++++++++++++++++++++++ 4 files changed, 331 insertions(+) create mode 100644 corelib/src/libs/SireBase/console.cpp create mode 100644 corelib/src/libs/SireBase/console.h diff --git a/corelib/src/libs/SireBase/CMakeLists.txt b/corelib/src/libs/SireBase/CMakeLists.txt index 92811520d..55f240aca 100644 --- a/corelib/src/libs/SireBase/CMakeLists.txt +++ b/corelib/src/libs/SireBase/CMakeLists.txt @@ -27,6 +27,7 @@ set ( SIREBASE_HEADERS combineproperties.h convert_property.hpp countflops.h + console.h cpuid.h errors.h findexe.h @@ -87,6 +88,7 @@ set ( SIREBASE_SOURCES chunkedhash.cpp chunkedvector.cpp combineproperties.cpp + console.cpp countflops.cpp cpuid.cpp errors.cpp diff --git a/corelib/src/libs/SireBase/console.cpp b/corelib/src/libs/SireBase/console.cpp new file mode 100644 index 000000000..8268df4db --- /dev/null +++ b/corelib/src/libs/SireBase/console.cpp @@ -0,0 +1,88 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "SireBase/console.h" + +using namespace SireBase; + +ConsoleBase::ConsoleBase() +{ +} + +ConsoleBase::~ConsoleBase() +{ +} + +ConsoleBase *Console::c(0); + +Console::Console() +{ +} + +Console::~Console() +{ +} + +/** Write the passed debug message to the console */ +void Console::debug(const QString &message) +{ + if (c) + c->debug(message); +} + +/** Write the passed warning message to the console */ +void Console::warning(const QString &message) +{ + if (c) + c->warning(message); +} + +/** Write the passed error message to the console */ +void Console::error(const QString &message) +{ + if (c) + c->error(message); +} + +/** Write the passed info message to the console */ +void Console::info(const QString &message) +{ + if (c) + c->info(message); +} + +/** Set the driver for the global console - this will delete + * any existing console - and will take ownership of the pointer! + */ +void Console::setConsole(ConsoleBase *console) +{ + if (c) + delete c; + + c = console; +} diff --git a/corelib/src/libs/SireBase/console.h b/corelib/src/libs/SireBase/console.h new file mode 100644 index 000000000..36a2525ad --- /dev/null +++ b/corelib/src/libs/SireBase/console.h @@ -0,0 +1,75 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREBASE_CONSOLE_H +#define SIREBASE_CONSOLE_H + +#include "sireglobal.h" + +SIRE_BEGIN_HEADER + +namespace SireBase +{ + /** Virtual base class of the actual console implementation */ + class SIREBASE_EXPORT ConsoleBase + { + public: + ConsoleBase(); + virtual ~ConsoleBase(); + + virtual void debug(const QString &message) const = 0; + virtual void warning(const QString &message) const = 0; + virtual void error(const QString &message) const = 0; + virtual void info(const QString &message) const = 0; + }; + + /** This class provides static functions that can be used + * to (sparingly) output messages to the console. This is + * controlled by the tools in sire.utils.console + */ + class SIREBASE_EXPORT Console + { + public: + static void debug(const QString &message); + static void warning(const QString &message); + static void error(const QString &message); + static void info(const QString &message); + + static void setConsole(ConsoleBase *console); + + private: + Console(); + ~Console(); + + static ConsoleBase *c; + }; +} + +SIRE_END_HEADER + +#endif // SIREBASE_CONSOLE_H diff --git a/wrapper/Base/releasegil_impl.cpp b/wrapper/Base/releasegil_impl.cpp index 99e2bc40b..35474cd0e 100644 --- a/wrapper/Base/releasegil_impl.cpp +++ b/wrapper/Base/releasegil_impl.cpp @@ -2,6 +2,7 @@ #include "boost/python.hpp" #include "SireBase/releasegil.h" +#include "SireBase/console.h" #include @@ -282,6 +283,169 @@ class ReleaseGIL : public SireBase::detail::ReleaseGILBase PyThreadState *thread_state; }; +class ConsoleImpl : public SireBase::ConsoleBase +{ +public: + ConsoleImpl() : SireBase::ConsoleBase(), pyconsole(0) + { + } + + ~ConsoleImpl() + { + if (pyconsole) + { + PyGILState_STATE gilstate = PyGILState_Ensure(); + Py_DECREF(pyconsole); + delete pyconsole; + pyconsole = 0; + PyGILState_Release(gilstate); + } + } + + void debug(const QString &message) const + { + const_cast(this)->get_pyconsole(); + + if (pyconsole) + { + PyGILState_STATE gilstate = PyGILState_Ensure(); + + PyObject *result = PyObject_CallMethod(pyconsole, "debug", "s", message.toUtf8().constData()); + + if (result == 0) + { + qDebug() << "UNABLE TO CALL DEBUG"; + qDebug() << message; + } + else + { + Py_DECREF(result); + } + + PyGILState_Release(gilstate); + } + else + { + qDebug() << "NO PYCONSOLE"; + qDebug() << message; + } + } + + void warning(const QString &message) const + { + const_cast(this)->get_pyconsole(); + + if (pyconsole) + { + PyGILState_STATE gilstate = PyGILState_Ensure(); + + PyObject *result = PyObject_CallMethod(pyconsole, "warning", "s", message.toUtf8().constData()); + + if (result == 0) + { + qWarning() << message; + } + else + { + Py_DECREF(result); + } + + PyGILState_Release(gilstate); + } + else + { + qWarning() << message; + } + } + + void error(const QString &message) const + { + const_cast(this)->get_pyconsole(); + + if (pyconsole) + { + PyGILState_STATE gilstate = PyGILState_Ensure(); + + PyObject *result = PyObject_CallMethod(pyconsole, "error", "s", message.toUtf8().constData()); + + if (result == 0) + { + qCritical() << message; + } + else + { + Py_DECREF(result); + } + + PyGILState_Release(gilstate); + } + else + { + qCritical() << message; + } + } + + void info(const QString &message) const + { + const_cast(this)->get_pyconsole(); + + if (pyconsole) + { + PyGILState_STATE gilstate = PyGILState_Ensure(); + + PyObject *result = PyObject_CallMethod(pyconsole, "info", "s", message.toUtf8().constData()); + + if (result == 0) + { + qInfo() << "UNABLE TO CALL INFO"; + qInfo() << message; + } + else + { + Py_DECREF(result); + } + + PyGILState_Release(gilstate); + } + else + { + qInfo() << "NO PYCONSOLE"; + qInfo() << message; + } + } + +private: + void get_pyconsole() + { + if (pyconsole) + return; + + PyGILState_STATE gilstate = PyGILState_Ensure(); + + PyObject *sire_utils = PyImport_ImportModule("sire.utils"); + + if (sire_utils == 0) + { + qWarning() << "COULD NOT IMPORT SIRE.UTILS"; + PyGILState_Release(gilstate); + return; + } + + pyconsole = PyObject_GetAttrString(sire_utils, "Console"); + + Py_DECREF(sire_utils); + + if (pyconsole == 0) + { + qWarning() << "Could not import Console from sire.utils"; + PyGILState_Release(gilstate); + return; + } + } + + PyObject *pyconsole; +}; + QMutex ReleaseGIL::release_mutex; std::weak_ptr ReleaseGIL::current_state; @@ -291,4 +455,6 @@ void register_releasegil() ReleaseGIL::register_releasegil(); boost::python::def("set_is_ipython", &set_is_ipython); + + SireBase::Console::setConsole(new ConsoleImpl()); } From ad7347221ed5a5c723685d3593c3000045d38137 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 26 Feb 2024 23:18:32 +0000 Subject: [PATCH 133/468] Added a warning that these higher-level properties aren't being merged yet. --- corelib/src/libs/SireMol/cgproperty.hpp | 14 ++++----- corelib/src/libs/SireMol/chainproperty.hpp | 34 +++++++++++++++++++++- corelib/src/libs/SireMol/resproperty.hpp | 34 +++++++++++++++++++++- corelib/src/libs/SireMol/segproperty.hpp | 34 +++++++++++++++++++++- 4 files changed, 104 insertions(+), 12 deletions(-) diff --git a/corelib/src/libs/SireMol/cgproperty.hpp b/corelib/src/libs/SireMol/cgproperty.hpp index 5e91963e4..ce0d564f6 100644 --- a/corelib/src/libs/SireMol/cgproperty.hpp +++ b/corelib/src/libs/SireMol/cgproperty.hpp @@ -33,6 +33,7 @@ #include "SireBase/convert_property.hpp" #include "SireBase/qvariant_metatype.h" #include "SireBase/slice.h" +#include "SireBase/console.h" #include "moleculeinfodata.h" #include "molviewproperty.h" @@ -569,18 +570,13 @@ namespace SireMol CODELOC); } - const CGProperty &ref = *this; - const CGProperty &pert = other.asA>(); - - CGProperty prop0 = ref; - CGProperty prop1 = ref; - - const T ghost_param = getGhostParam(ghost); + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); SireBase::PropertyList ret; - ret.append(prop0); - ret.append(prop1); + ret.append(*this); + ret.append(*this); return ret; } diff --git a/corelib/src/libs/SireMol/chainproperty.hpp b/corelib/src/libs/SireMol/chainproperty.hpp index 7df5f41b2..35c42c3ff 100644 --- a/corelib/src/libs/SireMol/chainproperty.hpp +++ b/corelib/src/libs/SireMol/chainproperty.hpp @@ -33,6 +33,7 @@ #include "SireBase/convert_property.hpp" #include "SireBase/qvariant_metatype.h" #include "SireBase/slice.h" +#include "SireBase/console.h" #include "moleculeinfodata.h" #include "molviewproperty.h" @@ -104,7 +105,7 @@ namespace SireMol { friend SIREMOL_EXPORT QDataStream & ::operator<< <>(QDataStream &, const ChainProperty &); - friend SIREMOL_EXPORT QDataStream & ::operator>><>(QDataStream &, ChainProperty &); + friend SIREMOL_EXPORT QDataStream & ::operator>> <>(QDataStream &, ChainProperty &); public: ChainProperty(); @@ -168,6 +169,11 @@ namespace SireMol void assertCanConvert(const QVariant &value) const; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual chain property values */ QVector props; @@ -547,6 +553,32 @@ namespace SireMol return molinfo.nChains() == this->nChains(); } + /** Merge this property with another property */ + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList ChainProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // namespace SireMol diff --git a/corelib/src/libs/SireMol/resproperty.hpp b/corelib/src/libs/SireMol/resproperty.hpp index 0ab9828b6..ca3448be2 100644 --- a/corelib/src/libs/SireMol/resproperty.hpp +++ b/corelib/src/libs/SireMol/resproperty.hpp @@ -33,6 +33,7 @@ #include "SireBase/convert_property.hpp" #include "SireBase/qvariant_metatype.h" #include "SireBase/slice.h" +#include "SireBase/console.h" #include "moleculeinfodata.h" #include "molviewproperty.h" @@ -104,7 +105,7 @@ namespace SireMol { friend SIREMOL_EXPORT QDataStream & ::operator<< <>(QDataStream &, const ResProperty &); - friend SIREMOL_EXPORT QDataStream & ::operator>><>(QDataStream &, ResProperty &); + friend SIREMOL_EXPORT QDataStream & ::operator>> <>(QDataStream &, ResProperty &); public: ResProperty(); @@ -168,6 +169,11 @@ namespace SireMol void assertCanConvert(const QVariant &value) const; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual residue property values */ QVector props; @@ -547,6 +553,32 @@ namespace SireMol return molinfo.nResidues() == this->nResidues(); } + /** Merge this property with another property */ + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList ResProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // namespace SireMol diff --git a/corelib/src/libs/SireMol/segproperty.hpp b/corelib/src/libs/SireMol/segproperty.hpp index de7518b93..e9eedc980 100644 --- a/corelib/src/libs/SireMol/segproperty.hpp +++ b/corelib/src/libs/SireMol/segproperty.hpp @@ -33,6 +33,7 @@ #include "SireBase/convert_property.hpp" #include "SireBase/qvariant_metatype.h" #include "SireBase/slice.h" +#include "SireBase/console.h" #include "moleculeinfodata.h" #include "molviewproperty.h" @@ -104,7 +105,7 @@ namespace SireMol { friend SIREMOL_EXPORT QDataStream & ::operator<< <>(QDataStream &, const SegProperty &); - friend SIREMOL_EXPORT QDataStream & ::operator>><>(QDataStream &, SegProperty &); + friend SIREMOL_EXPORT QDataStream & ::operator>> <>(QDataStream &, SegProperty &); public: SegProperty(); @@ -168,6 +169,11 @@ namespace SireMol void assertCanConvert(const QVariant &value) const; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual segment property values */ QVector props; @@ -547,6 +553,32 @@ namespace SireMol return molinfo.nSegments() == this->nSegments(); } + /** Merge this property with another property */ + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList SegProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // namespace SireMol From 60abd654e83fd477f764b487647e0c27b0f5f95f Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 27 Feb 2024 23:02:44 +0000 Subject: [PATCH 134/468] WIP - I've been filling in the merge function for most of the MolViewProperties, plus have generated the new wrappers. Mostly compiling now - just need to fill in missing atomidxmapping.h includes in the wrappers. --- corelib/src/libs/SireMM/amberparams.cpp | 26 ++ corelib/src/libs/SireMM/amberparams.h | 5 + corelib/src/libs/SireMM/atomfunctions.h | 1 + corelib/src/libs/SireMM/atomljs.cpp | 54 ++++ corelib/src/libs/SireMM/atomljs.h | 5 + corelib/src/libs/SireMM/atompairs.hpp | 37 ++- corelib/src/libs/SireMM/excludedpairs.cpp | 25 ++ corelib/src/libs/SireMM/excludedpairs.h | 5 + corelib/src/libs/SireMM/fouratomfunctions.cpp | 29 ++ corelib/src/libs/SireMM/fouratomfunctions.h | 5 + .../src/libs/SireMM/threeatomfunctions.cpp | 29 ++ corelib/src/libs/SireMM/threeatomfunctions.h | 5 + corelib/src/libs/SireMM/twoatomfunctions.cpp | 27 ++ corelib/src/libs/SireMM/twoatomfunctions.h | 5 + corelib/src/libs/SireMol/beading.cpp | 27 ++ corelib/src/libs/SireMol/beading.h | 5 + corelib/src/libs/SireMol/beadproperty.hpp | 34 ++- corelib/src/libs/SireMol/connectivity.cpp | 28 ++ corelib/src/libs/SireMol/connectivity.h | 5 + corelib/src/libs/SireMol/getghostparam.hpp | 4 +- corelib/src/libs/SireMol/trajectory.cpp | 51 ++++ corelib/src/libs/SireMol/trajectory.h | 10 + corelib/src/libs/SireMove/flexibility.cpp | 28 ++ corelib/src/libs/SireMove/flexibility.h | 5 + corelib/src/libs/SireMove/zmatrix.cpp | 52 ++++ corelib/src/libs/SireMove/zmatrix.h | 10 + corelib/src/libs/SireSystem/merge.cpp | 2 +- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 5 +- wrapper/MM/AmberAngle.pypp.cpp | 2 + wrapper/MM/AmberBond.pypp.cpp | 2 + wrapper/MM/AmberDihPart.pypp.cpp | 2 + wrapper/MM/AmberDihedral.pypp.cpp | 2 + wrapper/MM/AmberNB14.pypp.cpp | 2 + wrapper/MM/AmberParams.pypp.cpp | 14 + wrapper/MM/AtomLJs.pypp.cpp | 15 + wrapper/MM/AtomPairs_CLJScaleFactor_.pypp.cpp | 13 + .../MM/AtomPairs_CoulombScaleFactor_.pypp.cpp | 13 + wrapper/MM/AtomPairs_LJScaleFactor_.pypp.cpp | 13 + wrapper/MM/ExcludedPairs.pypp.cpp | 12 + wrapper/MM/FourAtomFunction.pypp.cpp | 4 + wrapper/MM/FourAtomFunctions.pypp.cpp | 16 + wrapper/MM/LJException.pypp.cpp | 2 + wrapper/MM/LJExceptionID.pypp.cpp | 2 + wrapper/MM/ThreeAtomFunction.pypp.cpp | 4 + wrapper/MM/ThreeAtomFunctions.pypp.cpp | 16 + wrapper/MM/TwoAtomFunction.pypp.cpp | 2 + wrapper/MM/TwoAtomFunctions.pypp.cpp | 14 + wrapper/Mol/AmberParameters.pypp.cpp | 14 + wrapper/Mol/AtomBeads.pypp.cpp | 13 + wrapper/Mol/AtomCharges.pypp.cpp | 13 + wrapper/Mol/AtomChiralities.pypp.cpp | 13 + wrapper/Mol/AtomCoords.pypp.cpp | 13 + wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp | 13 + wrapper/Mol/AtomElements.pypp.cpp | 13 + wrapper/Mol/AtomEnergies.pypp.cpp | 13 + wrapper/Mol/AtomFloatProperty.pypp.cpp | 13 + wrapper/Mol/AtomForces.pypp.cpp | 13 + wrapper/Mol/AtomHybridizations.pypp.cpp | 13 + wrapper/Mol/AtomIdxMapping.pypp.cpp | 278 ++++++++++++++++++ wrapper/Mol/AtomIdxMapping.pypp.hpp | 10 + wrapper/Mol/AtomIdxMappingEntry.pypp.cpp | 190 ++++++++++++ wrapper/Mol/AtomIdxMappingEntry.pypp.hpp | 10 + wrapper/Mol/AtomIntProperty.pypp.cpp | 13 + wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp | 13 + wrapper/Mol/AtomMasses.pypp.cpp | 13 + wrapper/Mol/AtomPolarisabilities.pypp.cpp | 13 + wrapper/Mol/AtomProp.pypp.cpp | 12 + wrapper/Mol/AtomPropertyList.pypp.cpp | 13 + wrapper/Mol/AtomPropertyProperty.pypp.cpp | 13 + wrapper/Mol/AtomRadicals.pypp.cpp | 13 + wrapper/Mol/AtomRadii.pypp.cpp | 13 + wrapper/Mol/AtomSelection.pypp.cpp | 12 + wrapper/Mol/AtomStringArrayProperty.pypp.cpp | 13 + wrapper/Mol/AtomStringProperty.pypp.cpp | 13 + wrapper/Mol/AtomVariantProperty.pypp.cpp | 13 + wrapper/Mol/AtomVelocities.pypp.cpp | 13 + wrapper/Mol/BeadFloatProperty.pypp.cpp | 13 + wrapper/Mol/BeadIntProperty.pypp.cpp | 13 + wrapper/Mol/BeadPropertyProperty.pypp.cpp | 13 + wrapper/Mol/BeadStringProperty.pypp.cpp | 13 + wrapper/Mol/BeadVariantProperty.pypp.cpp | 13 + wrapper/Mol/Beading.pypp.cpp | 14 + wrapper/Mol/CGFloatProperty.pypp.cpp | 13 + wrapper/Mol/CGIntProperty.pypp.cpp | 13 + wrapper/Mol/CGPropertyProperty.pypp.cpp | 13 + wrapper/Mol/CGStringProperty.pypp.cpp | 13 + wrapper/Mol/CGVariantProperty.pypp.cpp | 13 + wrapper/Mol/CMakeAutogenFile.txt | 2 + wrapper/Mol/ChainFloatProperty.pypp.cpp | 13 + wrapper/Mol/ChainIntProperty.pypp.cpp | 13 + wrapper/Mol/ChainPropertyProperty.pypp.cpp | 13 + wrapper/Mol/ChainStringProperty.pypp.cpp | 13 + wrapper/Mol/ChainVariantProperty.pypp.cpp | 13 + wrapper/Mol/Connectivity.pypp.cpp | 4 + wrapper/Mol/ConnectivityBase.pypp.cpp | 16 + wrapper/Mol/ConnectivityEditor.pypp.cpp | 4 + wrapper/Mol/Element.pypp.cpp | 8 +- wrapper/Mol/Frame.pypp.cpp | 14 + wrapper/Mol/MolViewProperty.pypp.cpp | 12 + wrapper/Mol/MoleculeBeading.pypp.cpp | 2 + wrapper/Mol/NullBeading.pypp.cpp | 2 + wrapper/Mol/ResFloatProperty.pypp.cpp | 13 + wrapper/Mol/ResIntProperty.pypp.cpp | 13 + wrapper/Mol/ResPropertyProperty.pypp.cpp | 13 + wrapper/Mol/ResStringProperty.pypp.cpp | 13 + wrapper/Mol/ResVariantProperty.pypp.cpp | 13 + wrapper/Mol/ResidueBeading.pypp.cpp | 2 + wrapper/Mol/SegFloatProperty.pypp.cpp | 13 + wrapper/Mol/SegIntProperty.pypp.cpp | 13 + wrapper/Mol/SegPropertyProperty.pypp.cpp | 13 + wrapper/Mol/SegStringProperty.pypp.cpp | 13 + wrapper/Mol/SegVariantProperty.pypp.cpp | 13 + wrapper/Mol/SireMol_properties.cpp | 1 + wrapper/Mol/SireMol_registrars.cpp | 3 + wrapper/Mol/Trajectory.pypp.cpp | 14 + wrapper/Mol/UserBeading.pypp.cpp | 2 + wrapper/Mol/_Mol.main.cpp | 8 + wrapper/Mol/active_headers.h | 1 + wrapper/Move/CMakeAutogenFile.txt | 130 ++++---- wrapper/Move/Flexibility.pypp.cpp | 12 + wrapper/Move/SireMove_properties.cpp | 178 +++++------ wrapper/Move/SireMove_registrars.cpp | 178 ++++++----- wrapper/Move/ZMatrix.pypp.cpp | 12 + wrapper/Move/ZMatrixCoords.pypp.cpp | 12 + 124 files changed, 2187 insertions(+), 255 deletions(-) create mode 100644 wrapper/Mol/AtomIdxMapping.pypp.cpp create mode 100644 wrapper/Mol/AtomIdxMapping.pypp.hpp create mode 100644 wrapper/Mol/AtomIdxMappingEntry.pypp.cpp create mode 100644 wrapper/Mol/AtomIdxMappingEntry.pypp.hpp diff --git a/corelib/src/libs/SireMM/amberparams.cpp b/corelib/src/libs/SireMM/amberparams.cpp index 275970234..bdb1dd249 100644 --- a/corelib/src/libs/SireMM/amberparams.cpp +++ b/corelib/src/libs/SireMM/amberparams.cpp @@ -52,6 +52,7 @@ #include "SireCAS/trigfuncs.h" #include "SireCAS/values.h" +#include "SireBase/console.h" #include "SireBase/parallel.h" #include "SireBase/stringproperty.h" @@ -2749,3 +2750,28 @@ PropertyPtr AmberParams::_pvt_makeCompatibleWith(const MoleculeInfoData &newinfo throw SireError::incomplete_code("Cannot make compatible if atom order has changed!", CODELOC); } + +/** Merge this property with another property */ +PropertyList AmberParams::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMM/amberparams.h b/corelib/src/libs/SireMM/amberparams.h index 635164b20..47fb2d1f4 100644 --- a/corelib/src/libs/SireMM/amberparams.h +++ b/corelib/src/libs/SireMM/amberparams.h @@ -513,6 +513,11 @@ namespace SireMM DihedralID convert(const DihedralID &dihedral) const; ImproperID convert(const ImproperID &improper) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, const AtomMatcher &atommatcher) const; diff --git a/corelib/src/libs/SireMM/atomfunctions.h b/corelib/src/libs/SireMM/atomfunctions.h index a81a28538..c2b249581 100644 --- a/corelib/src/libs/SireMM/atomfunctions.h +++ b/corelib/src/libs/SireMM/atomfunctions.h @@ -34,6 +34,7 @@ #include "SireMol/cgatomidx.h" #include "SireMol/molviewproperty.h" +#include "SireMol/atomidxmapping.h" #include "SireCAS/expression.h" #include "SireCAS/identities.h" diff --git a/corelib/src/libs/SireMM/atomljs.cpp b/corelib/src/libs/SireMM/atomljs.cpp index 90679ecae..fe3e445e6 100644 --- a/corelib/src/libs/SireMM/atomljs.cpp +++ b/corelib/src/libs/SireMM/atomljs.cpp @@ -29,6 +29,7 @@ #include "SireBase/quickcopy.hpp" #include "SireBase/incremint.h" +#include "SireBase/propertylist.h" #include "SireStream/magic_error.h" #include "SireStream/datastream.h" @@ -38,6 +39,7 @@ #include using namespace SireMM; +using namespace SireBase; using namespace SireMol; using namespace SireStream; @@ -1456,3 +1458,55 @@ QList AtomProperty::getExceptions(int i) const { return this->lj_exceptions.value(i); } + +/** Merge this property with another property */ +PropertyList AtomProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + const AtomProperty &ref = *this; + const AtomProperty &pert = other.asA>(); + + AtomProperty prop0 = ref; + AtomProperty prop1 = ref; + + for (const auto &index : mapping) + { + if (index.isUnmappedIn0() and index.isUnmappedIn1()) + { + prop0.set(index.cgAtomIdx0(), LJParameter::dummy()); + prop1.set(index.cgAtomIdx0(), LJParameter::dummy()); + } + else if (index.isUnmappedIn0()) + { + auto lj1 = pert.get(index.cgAtomIdx1()); + prop0.set(index.cgAtomIdx0(), LJParameter(lj1.sigma(), SireUnits::Dimension::MolarEnergy(0))); + } + else if (index.isUnmappedIn1()) + { + auto lj0 = ref.get(index.cgAtomIdx0()); + prop1.set(index.cgAtomIdx0(), LJParameter(lj0.sigma(), SireUnits::Dimension::MolarEnergy(0))); + } + else + { + prop1.set(index.cgAtomIdx0(), pert.get(index.cgAtomIdx1())); + } + } + + SireBase::PropertyList ret; + ret.append(prop0); + ret.append(prop1); + + return ret; + + return ret; +} diff --git a/corelib/src/libs/SireMM/atomljs.h b/corelib/src/libs/SireMM/atomljs.h index 83c01e071..eaad03761 100644 --- a/corelib/src/libs/SireMM/atomljs.h +++ b/corelib/src/libs/SireMM/atomljs.h @@ -274,6 +274,11 @@ namespace SireMol QList> getExceptions() const; QList> getExceptions(const AtomProperty &other) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual atomic property values */ SireBase::PackedArray2D props; diff --git a/corelib/src/libs/SireMM/atompairs.hpp b/corelib/src/libs/SireMM/atompairs.hpp index 6f8becc41..4cf92c2ab 100644 --- a/corelib/src/libs/SireMM/atompairs.hpp +++ b/corelib/src/libs/SireMM/atompairs.hpp @@ -30,12 +30,14 @@ #include "SireBase/property.h" #include "SireBase/sparsematrix.hpp" +#include "SireBase/console.h" #include "SireMol/atommatcher.h" #include "SireMol/cgatomidx.h" #include "SireMol/moleculeinfodata.h" #include "SireMol/moleculeview.h" #include "SireMol/molviewproperty.h" +#include "SireMol/atomidxmapping.h" #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -87,7 +89,7 @@ namespace SireMM { friend SIREMM_EXPORT QDataStream & ::operator<< <>(QDataStream &, const CGAtomPairs &); - friend SIREMM_EXPORT QDataStream & ::operator>><>(QDataStream &, CGAtomPairs &); + friend SIREMM_EXPORT QDataStream & ::operator>> <>(QDataStream &, CGAtomPairs &); template friend class CGAtomPairs; @@ -139,7 +141,7 @@ namespace SireMM { friend SIREMM_EXPORT QDataStream & ::operator<< <>(QDataStream &, const AtomPairs &); - friend SIREMM_EXPORT QDataStream & ::operator>><>(QDataStream &, AtomPairs &); + friend SIREMM_EXPORT QDataStream & ::operator>> <>(QDataStream &, AtomPairs &); template friend class AtomPairs; @@ -215,6 +217,11 @@ namespace SireMM bool isCompatibleWith(const MoleculeInfoData &molinfo) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, const AtomMatcher &atommatcher) const; @@ -874,6 +881,32 @@ namespace SireMM return ret; } + /** Merge this property with another property */ + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList AtomPairs::merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(SireBase::PropertyPtr(this->clone())); + ret.append(SireBase::PropertyPtr(this->clone())); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // end of namespace SireMM diff --git a/corelib/src/libs/SireMM/excludedpairs.cpp b/corelib/src/libs/SireMM/excludedpairs.cpp index 581de9912..a13438941 100644 --- a/corelib/src/libs/SireMM/excludedpairs.cpp +++ b/corelib/src/libs/SireMM/excludedpairs.cpp @@ -429,3 +429,28 @@ void ExcludedPairs::setExcluded(const AtomID &atom0, const AtomID &atom1, this->excl_pairs.removeAt(idx); } } + +/** Merge this property with another property */ +PropertyList ExcludedPairs::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMM/excludedpairs.h b/corelib/src/libs/SireMM/excludedpairs.h index e227bed1d..40ceccab6 100644 --- a/corelib/src/libs/SireMM/excludedpairs.h +++ b/corelib/src/libs/SireMM/excludedpairs.h @@ -92,6 +92,11 @@ namespace SireMM void setExcluded(const SireMol::AtomID &atom0, const SireMol::AtomID &atom1, bool are_excluded); + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: int getIndex(qint64 atom0, qint64 atom1) const; diff --git a/corelib/src/libs/SireMM/fouratomfunctions.cpp b/corelib/src/libs/SireMM/fouratomfunctions.cpp index 182f0c0fc..a86b4be1e 100644 --- a/corelib/src/libs/SireMM/fouratomfunctions.cpp +++ b/corelib/src/libs/SireMM/fouratomfunctions.cpp @@ -29,12 +29,16 @@ #include "fouratomfunctions.h" +#include "SireBase/console.h" + #include "SireCAS/symbols.h" #include "SireMol/atommatcher.h" #include "SireMol/atomselection.h" #include "SireMol/moleculeinfodata.h" +#include "SireError/errors.h" + #include "SireMol/errors.h" #include "SireStream/datastream.h" @@ -914,3 +918,28 @@ const char *FourAtomFunctions::typeName() { return QMetaType::typeName(qMetaTypeId()); } + +/** Merge this property with another property */ +PropertyList FourAtomFunctions::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMM/fouratomfunctions.h b/corelib/src/libs/SireMM/fouratomfunctions.h index 8f66d7175..f2021906a 100644 --- a/corelib/src/libs/SireMM/fouratomfunctions.h +++ b/corelib/src/libs/SireMM/fouratomfunctions.h @@ -227,6 +227,11 @@ namespace SireMM FourAtomFunctions includeOnly(const AtomSelection &selected_atoms, bool isstrict = true) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, const AtomMatcher &atommatcher) const; diff --git a/corelib/src/libs/SireMM/threeatomfunctions.cpp b/corelib/src/libs/SireMM/threeatomfunctions.cpp index 2d573e911..42a18c1a4 100644 --- a/corelib/src/libs/SireMM/threeatomfunctions.cpp +++ b/corelib/src/libs/SireMM/threeatomfunctions.cpp @@ -29,12 +29,16 @@ #include "threeatomfunctions.h" +#include "SireBase/console.h" + #include "SireCAS/symbols.h" #include "SireMol/atommatcher.h" #include "SireMol/atomselection.h" #include "SireMol/moleculeinfodata.h" +#include "SireError/errors.h" + #include "SireMol/errors.h" #include "SireStream/datastream.h" @@ -792,3 +796,28 @@ const char *ThreeAtomFunctions::typeName() { return QMetaType::typeName(qMetaTypeId()); } + +/** Merge this property with another property */ +PropertyList ThreeAtomFunctions::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMM/threeatomfunctions.h b/corelib/src/libs/SireMM/threeatomfunctions.h index a6781b622..8cb27fa5c 100644 --- a/corelib/src/libs/SireMM/threeatomfunctions.h +++ b/corelib/src/libs/SireMM/threeatomfunctions.h @@ -210,6 +210,11 @@ namespace SireMM ThreeAtomFunctions includeOnly(const AtomSelection &selected_atoms, bool isstrict = true) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, const AtomMatcher &atommatcher) const; diff --git a/corelib/src/libs/SireMM/twoatomfunctions.cpp b/corelib/src/libs/SireMM/twoatomfunctions.cpp index a1ddbc452..dc0c48167 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.cpp +++ b/corelib/src/libs/SireMM/twoatomfunctions.cpp @@ -29,6 +29,8 @@ #include "twoatomfunctions.h" +#include "SireBase/console.h" + #include "SireCAS/symbols.h" #include "SireMol/atommatcher.h" @@ -758,3 +760,28 @@ const char *TwoAtomFunctions::typeName() { return QMetaType::typeName(qMetaTypeId()); } + +/** Merge this property with another property */ +PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMM/twoatomfunctions.h b/corelib/src/libs/SireMM/twoatomfunctions.h index 2eeaf9ea3..b70b42fba 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.h +++ b/corelib/src/libs/SireMM/twoatomfunctions.h @@ -202,6 +202,11 @@ namespace SireMM TwoAtomFunctions includeOnly(const AtomSelection &selection, bool isstrict = true) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, const AtomMatcher &atommatcher) const; diff --git a/corelib/src/libs/SireMol/beading.cpp b/corelib/src/libs/SireMol/beading.cpp index 78d8e84d0..fcca1ad82 100644 --- a/corelib/src/libs/SireMol/beading.cpp +++ b/corelib/src/libs/SireMol/beading.cpp @@ -35,6 +35,8 @@ #include +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireError/errors.h" @@ -135,6 +137,31 @@ NullBeading Beading::null() return NullBeading(); } +/** Merge this property with another property */ +SireBase::PropertyList Beading::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} + ////////// ////////// Implementation of MoleculeBeading ////////// diff --git a/corelib/src/libs/SireMol/beading.h b/corelib/src/libs/SireMol/beading.h index 1f76b2712..124f9ee97 100644 --- a/corelib/src/libs/SireMol/beading.h +++ b/corelib/src/libs/SireMol/beading.h @@ -109,6 +109,11 @@ namespace SireMol bool isCompatibleWith(const MoleculeInfoData &molinfo) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: Beading &operator=(const Beading &other); bool operator==(const Beading &other) const; diff --git a/corelib/src/libs/SireMol/beadproperty.hpp b/corelib/src/libs/SireMol/beadproperty.hpp index fe2ea9b86..82876c94d 100644 --- a/corelib/src/libs/SireMol/beadproperty.hpp +++ b/corelib/src/libs/SireMol/beadproperty.hpp @@ -32,6 +32,7 @@ #include "SireBase/qvariant_metatype.h" #include "SireBase/slice.h" +#include "SireBase/console.h" #include "beadidx.h" #include "beading.h" @@ -124,7 +125,7 @@ namespace SireMol { friend SIREMOL_EXPORT QDataStream & ::operator<< <>(QDataStream &, const BeadProperty &); - friend SIREMOL_EXPORT QDataStream & ::operator>><>(QDataStream &, BeadProperty &); + friend SIREMOL_EXPORT QDataStream & ::operator>> <>(QDataStream &, BeadProperty &); public: BeadProperty(); @@ -185,6 +186,11 @@ namespace SireMol void assertCanConvert(const QVariant &value) const; + virtual SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The actual bead property values */ QVector props; @@ -545,6 +551,32 @@ namespace SireMol return this->getNBeads(molinfo) == this->nBeads(); } + /** Merge this property with another property */ + template + SIRE_OUTOFLINE_TEMPLATE SireBase::PropertyList BeadProperty::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const + { + if (not other.isA>()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; + } + #endif // SIRE_SKIP_INLINE_FUNCTIONS } // namespace SireMol diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 3f2e562e2..2a9ea2416 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -46,8 +46,11 @@ #include "SireMol/errors.h" #include "SireBase/errors.h" +#include "SireBase/console.h" #include "SireBase/parallel.h" +#include "SireError/errors.h" + #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -3373,6 +3376,31 @@ void ConnectivityBase::assertHasProperty(const ImproperID &improper, const Prope CODELOC); } +/** Merge this property with another property */ +PropertyList ConnectivityBase::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} + ///////// ///////// Implementation of Connectivity ///////// diff --git a/corelib/src/libs/SireMol/connectivity.h b/corelib/src/libs/SireMol/connectivity.h index 5a9f7f5ca..b4b0be2e5 100644 --- a/corelib/src/libs/SireMol/connectivity.h +++ b/corelib/src/libs/SireMol/connectivity.h @@ -329,6 +329,11 @@ namespace SireMol void assertHasProperty(const ImproperID &imp, const SireBase::PropertyName &key) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: ConnectivityBase(); ConnectivityBase(const MoleculeInfo &molinfo); diff --git a/corelib/src/libs/SireMol/getghostparam.hpp b/corelib/src/libs/SireMol/getghostparam.hpp index 97fe064f0..35426f68d 100644 --- a/corelib/src/libs/SireMol/getghostparam.hpp +++ b/corelib/src/libs/SireMol/getghostparam.hpp @@ -143,7 +143,7 @@ namespace SireMol } template <> - SireUnits::Dimension::Length getGhostParam(const QString &ghost) + inline SireUnits::Dimension::Length getGhostParam(const QString &ghost) { if (ghost.isEmpty()) return SireUnits::Dimension::Length(0.0); @@ -152,7 +152,7 @@ namespace SireMol } template <> - SireBase::PropertyPtr getGhostParam(const QString &ghost) + inline SireBase::PropertyPtr getGhostParam(const QString &ghost) { if (ghost.isEmpty()) return SireBase::PropertyPtr(); diff --git a/corelib/src/libs/SireMol/trajectory.cpp b/corelib/src/libs/SireMol/trajectory.cpp index 3f13c6766..ab760a768 100644 --- a/corelib/src/libs/SireMol/trajectory.cpp +++ b/corelib/src/libs/SireMol/trajectory.cpp @@ -41,6 +41,7 @@ #include "SireBase/generalunitproperty.h" #include "SireBase/lazyevaluator.h" +#include "SireBase/console.h" #include "SireBase/slice.h" @@ -1010,6 +1011,31 @@ bool Trajectory::isCompatibleWith(const MoleculeInfoData &molinfo) const return this->nAtoms() == molinfo.nAtoms(); } +/** Merge this property with another property */ +PropertyList Trajectory::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} + /////// /////// Implementation of Frame /////// @@ -1839,3 +1865,28 @@ Frame Frame::join(const QVector &frames, return ret; } + +/** Merge this property with another property */ +PropertyList Frame::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMol/trajectory.h b/corelib/src/libs/SireMol/trajectory.h index 1a44040d3..bd22823b1 100644 --- a/corelib/src/libs/SireMol/trajectory.h +++ b/corelib/src/libs/SireMol/trajectory.h @@ -165,6 +165,11 @@ namespace SireMol bool isCompatibleWith(const MoleculeInfoData &molinfo) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + static Frame join(const QVector &frames, bool use_parallel = true); @@ -367,6 +372,11 @@ namespace SireMol bool isCompatibleWith(const MoleculeInfoData &molinfo) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: int _getIndexForFrame(int &frame) const; diff --git a/corelib/src/libs/SireMove/flexibility.cpp b/corelib/src/libs/SireMove/flexibility.cpp index 24d9c0c14..ae4301822 100644 --- a/corelib/src/libs/SireMove/flexibility.cpp +++ b/corelib/src/libs/SireMove/flexibility.cpp @@ -40,6 +40,8 @@ #include "SireUnits/convert.h" #include "SireUnits/units.h" +#include "SireBase/console.h" + #include "SireError/errors.h" #include "SireMol/errors.h" #include "SireMove/errors.h" @@ -49,6 +51,7 @@ using namespace SireMove; using namespace SireMol; +using namespace SireBase; using namespace SireUnits; using namespace SireUnits::Dimension; using namespace SireStream; @@ -586,3 +589,28 @@ const char *Flexibility::typeName() { return QMetaType::typeName(qMetaTypeId()); } + +/** Merge this property with another property */ +PropertyList Flexibility::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMove/flexibility.h b/corelib/src/libs/SireMove/flexibility.h index 9ae1a0289..abe6a9d4e 100644 --- a/corelib/src/libs/SireMove/flexibility.h +++ b/corelib/src/libs/SireMove/flexibility.h @@ -195,6 +195,11 @@ namespace SireMove QList flexibleAngles() const; QList flexibleDihedrals() const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: /** The molecule that this flexibility operates on */ SireBase::SharedDataPointer molinfo; diff --git a/corelib/src/libs/SireMove/zmatrix.cpp b/corelib/src/libs/SireMove/zmatrix.cpp index 80dd88901..5792a1e01 100644 --- a/corelib/src/libs/SireMove/zmatrix.cpp +++ b/corelib/src/libs/SireMove/zmatrix.cpp @@ -42,6 +42,8 @@ #include "SireUnits/convert.h" #include "SireUnits/units.h" +#include "SireBase/console.h" + #include "SireError/errors.h" #include "SireMol/errors.h" #include "SireMove/errors.h" @@ -1511,6 +1513,31 @@ const char *ZMatrix::typeName() return QMetaType::typeName(qMetaTypeId()); } +/** Merge this property with another property */ +PropertyList ZMatrix::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} + ////////// ////////// Implementation of ZMatrixCoords ////////// @@ -2856,3 +2883,28 @@ const char *ZMatrixCoords::typeName() { return QMetaType::typeName(qMetaTypeId()); } + +/** Merge this property with another property */ +PropertyList ZMatrixCoords::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") + .arg(this->what())); + + SireBase::PropertyList ret; + + ret.append(*this); + ret.append(*this); + + return ret; +} diff --git a/corelib/src/libs/SireMove/zmatrix.h b/corelib/src/libs/SireMove/zmatrix.h index 5cee724df..867becacc 100644 --- a/corelib/src/libs/SireMove/zmatrix.h +++ b/corelib/src/libs/SireMove/zmatrix.h @@ -298,6 +298,11 @@ namespace SireMove bool isCompatibleWith(const SireMol::MoleculeInfoData &molinfo) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + protected: SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, const AtomMatcher &atommatcher) const; @@ -480,6 +485,11 @@ namespace SireMove ZMatrixCoords matchToSelection(const AtomSelection &selection) const; + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + private: void rebuildInternals(); void rebuildCartesian() const; diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index a95d01c4f..96a6be5cb 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -171,7 +171,7 @@ namespace SireSystem try { - ffield1 = mapped_atoms1.data().property(map1["forcefield"]).asA(); + ffield1 = mapped_atoms1.data().property(map1["forcefield"]).asA(); have_ffield1 = true; } catch (...) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 694e7fb99..c3309afb4 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -561,6 +561,9 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, double mass = std::max(mass0, mass1); + const bool mass0_is_light = (mass0 >= 1 and mass0 < 2.5); + const bool mass1_is_light = (mass1 >= 1 and mass1 < 2.5); + if (mass < 0.05) { mass = 0.0; @@ -571,7 +574,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, // this must be a ghost in both end states? light_atoms.insert(i); } - else if (check_for_h_by_mass and (mass < 2.5 or mass1 < 2.5)) + else if (check_for_h_by_mass and (mass0_is_light or mass1_is_light)) { // one of the atoms is H or He light_atoms.insert(i); diff --git a/wrapper/MM/AmberAngle.pypp.cpp b/wrapper/MM/AmberAngle.pypp.cpp index e350ce314..3a0c92514 100644 --- a/wrapper/MM/AmberAngle.pypp.cpp +++ b/wrapper/MM/AmberAngle.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" diff --git a/wrapper/MM/AmberBond.pypp.cpp b/wrapper/MM/AmberBond.pypp.cpp index 6defbb1a8..cd1d926e2 100644 --- a/wrapper/MM/AmberBond.pypp.cpp +++ b/wrapper/MM/AmberBond.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" diff --git a/wrapper/MM/AmberDihPart.pypp.cpp b/wrapper/MM/AmberDihPart.pypp.cpp index 145eb49c5..901450127 100644 --- a/wrapper/MM/AmberDihPart.pypp.cpp +++ b/wrapper/MM/AmberDihPart.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" diff --git a/wrapper/MM/AmberDihedral.pypp.cpp b/wrapper/MM/AmberDihedral.pypp.cpp index 572d00d3d..de9fce62c 100644 --- a/wrapper/MM/AmberDihedral.pypp.cpp +++ b/wrapper/MM/AmberDihedral.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" diff --git a/wrapper/MM/AmberNB14.pypp.cpp b/wrapper/MM/AmberNB14.pypp.cpp index 2e7423dab..de9f3bd99 100644 --- a/wrapper/MM/AmberNB14.pypp.cpp +++ b/wrapper/MM/AmberNB14.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" diff --git a/wrapper/MM/AmberParams.pypp.cpp b/wrapper/MM/AmberParams.pypp.cpp index 10db71762..a1306fe96 100644 --- a/wrapper/MM/AmberParams.pypp.cpp +++ b/wrapper/MM/AmberParams.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" @@ -574,6 +576,18 @@ void register_AmberParams_class(){ , bp::release_gil_policy() , "Return the atom masses" ); + } + { //::SireMM::AmberParams::merge + + typedef ::SireBase::PropertyList ( ::SireMM::AmberParams::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::AmberParams::merge ); + + AmberParams_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMM::AmberParams::nb14s diff --git a/wrapper/MM/AtomLJs.pypp.cpp b/wrapper/MM/AtomLJs.pypp.cpp index 80ffcfe98..5664f9e4c 100644 --- a/wrapper/MM/AtomLJs.pypp.cpp +++ b/wrapper/MM/AtomLJs.pypp.cpp @@ -9,6 +9,8 @@ namespace bp = boost::python; #include "SireBase/incremint.h" +#include "SireBase/propertylist.h" + #include "SireBase/quickcopy.hpp" #include "SireStream/datastream.h" @@ -493,6 +495,19 @@ void register_AtomLJs_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMM::LJParameter >::merge + + typedef SireMol::AtomProperty< SireMM::LJParameter > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMM::LJParameter >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMM::LJParameter >::merge ); + + AtomLJs_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMM::LJParameter >::nAtoms diff --git a/wrapper/MM/AtomPairs_CLJScaleFactor_.pypp.cpp b/wrapper/MM/AtomPairs_CLJScaleFactor_.pypp.cpp index 7c2035a26..690194983 100644 --- a/wrapper/MM/AtomPairs_CLJScaleFactor_.pypp.cpp +++ b/wrapper/MM/AtomPairs_CLJScaleFactor_.pypp.cpp @@ -180,6 +180,19 @@ void register_AtomPairs_CLJScaleFactor__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMM::AtomPairs< SireMM::CLJScaleFactor >::merge + + typedef SireMM::AtomPairs< SireMM::CLJScaleFactor > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMM::AtomPairs< SireMM::CLJScaleFactor >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::AtomPairs< SireMM::CLJScaleFactor >::merge ); + + AtomPairs_CLJScaleFactor__exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMM::AtomPairs< SireMM::CLJScaleFactor >::nAtoms diff --git a/wrapper/MM/AtomPairs_CoulombScaleFactor_.pypp.cpp b/wrapper/MM/AtomPairs_CoulombScaleFactor_.pypp.cpp index 78a736ccb..1f29b1983 100644 --- a/wrapper/MM/AtomPairs_CoulombScaleFactor_.pypp.cpp +++ b/wrapper/MM/AtomPairs_CoulombScaleFactor_.pypp.cpp @@ -180,6 +180,19 @@ void register_AtomPairs_CoulombScaleFactor__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMM::AtomPairs< SireMM::CoulombScaleFactor >::merge + + typedef SireMM::AtomPairs< SireMM::CoulombScaleFactor > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMM::AtomPairs< SireMM::CoulombScaleFactor >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::AtomPairs< SireMM::CoulombScaleFactor >::merge ); + + AtomPairs_CoulombScaleFactor__exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMM::AtomPairs< SireMM::CoulombScaleFactor >::nAtoms diff --git a/wrapper/MM/AtomPairs_LJScaleFactor_.pypp.cpp b/wrapper/MM/AtomPairs_LJScaleFactor_.pypp.cpp index 5a0a55eda..5f8f516a4 100644 --- a/wrapper/MM/AtomPairs_LJScaleFactor_.pypp.cpp +++ b/wrapper/MM/AtomPairs_LJScaleFactor_.pypp.cpp @@ -180,6 +180,19 @@ void register_AtomPairs_LJScaleFactor__class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMM::AtomPairs< SireMM::LJScaleFactor >::merge + + typedef SireMM::AtomPairs< SireMM::LJScaleFactor > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMM::AtomPairs< SireMM::LJScaleFactor >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::AtomPairs< SireMM::LJScaleFactor >::merge ); + + AtomPairs_LJScaleFactor__exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMM::AtomPairs< SireMM::LJScaleFactor >::nAtoms diff --git a/wrapper/MM/ExcludedPairs.pypp.cpp b/wrapper/MM/ExcludedPairs.pypp.cpp index 8d990c987..3b4c4d621 100644 --- a/wrapper/MM/ExcludedPairs.pypp.cpp +++ b/wrapper/MM/ExcludedPairs.pypp.cpp @@ -84,6 +84,18 @@ void register_ExcludedPairs_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMM::ExcludedPairs::merge + + typedef ::SireBase::PropertyList ( ::SireMM::ExcludedPairs::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::ExcludedPairs::merge ); + + ExcludedPairs_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMM::ExcludedPairs::nExcludedPairs diff --git a/wrapper/MM/FourAtomFunction.pypp.cpp b/wrapper/MM/FourAtomFunction.pypp.cpp index 6b20f2d18..2456677e9 100644 --- a/wrapper/MM/FourAtomFunction.pypp.cpp +++ b/wrapper/MM/FourAtomFunction.pypp.cpp @@ -8,8 +8,12 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/symbols.h" +#include "SireError/errors.h" + #include "SireMol/atommatcher.h" #include "SireMol/atomselection.h" diff --git a/wrapper/MM/FourAtomFunctions.pypp.cpp b/wrapper/MM/FourAtomFunctions.pypp.cpp index 8263ceda2..e4e66995c 100644 --- a/wrapper/MM/FourAtomFunctions.pypp.cpp +++ b/wrapper/MM/FourAtomFunctions.pypp.cpp @@ -7,8 +7,12 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/symbols.h" +#include "SireError/errors.h" + #include "SireMol/atommatcher.h" #include "SireMol/atomselection.h" @@ -224,6 +228,18 @@ void register_FourAtomFunctions_class(){ , bp::release_gil_policy() , "Return whether or not this is empty (has no potentials for any internals)" ); + } + { //::SireMM::FourAtomFunctions::merge + + typedef ::SireBase::PropertyList ( ::SireMM::FourAtomFunctions::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::FourAtomFunctions::merge ); + + FourAtomFunctions_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMM::FourAtomFunctions::nFunctions diff --git a/wrapper/MM/LJException.pypp.cpp b/wrapper/MM/LJException.pypp.cpp index 2af1c90c1..489b6c53a 100644 --- a/wrapper/MM/LJException.pypp.cpp +++ b/wrapper/MM/LJException.pypp.cpp @@ -9,6 +9,8 @@ namespace bp = boost::python; #include "SireBase/incremint.h" +#include "SireBase/propertylist.h" + #include "SireBase/quickcopy.hpp" #include "SireStream/datastream.h" diff --git a/wrapper/MM/LJExceptionID.pypp.cpp b/wrapper/MM/LJExceptionID.pypp.cpp index c1fe158ed..ea5b47dbe 100644 --- a/wrapper/MM/LJExceptionID.pypp.cpp +++ b/wrapper/MM/LJExceptionID.pypp.cpp @@ -9,6 +9,8 @@ namespace bp = boost::python; #include "SireBase/incremint.h" +#include "SireBase/propertylist.h" + #include "SireBase/quickcopy.hpp" #include "SireStream/datastream.h" diff --git a/wrapper/MM/ThreeAtomFunction.pypp.cpp b/wrapper/MM/ThreeAtomFunction.pypp.cpp index fb446f073..96a5d3b2c 100644 --- a/wrapper/MM/ThreeAtomFunction.pypp.cpp +++ b/wrapper/MM/ThreeAtomFunction.pypp.cpp @@ -8,8 +8,12 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/symbols.h" +#include "SireError/errors.h" + #include "SireMol/atommatcher.h" #include "SireMol/atomselection.h" diff --git a/wrapper/MM/ThreeAtomFunctions.pypp.cpp b/wrapper/MM/ThreeAtomFunctions.pypp.cpp index 6338a305a..21e3686fc 100644 --- a/wrapper/MM/ThreeAtomFunctions.pypp.cpp +++ b/wrapper/MM/ThreeAtomFunctions.pypp.cpp @@ -7,8 +7,12 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/symbols.h" +#include "SireError/errors.h" + #include "SireMol/atommatcher.h" #include "SireMol/atomselection.h" @@ -198,6 +202,18 @@ void register_ThreeAtomFunctions_class(){ , bp::release_gil_policy() , "Return whether or not this is empty (has no potentials for any internals)" ); + } + { //::SireMM::ThreeAtomFunctions::merge + + typedef ::SireBase::PropertyList ( ::SireMM::ThreeAtomFunctions::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::ThreeAtomFunctions::merge ); + + ThreeAtomFunctions_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMM::ThreeAtomFunctions::nFunctions diff --git a/wrapper/MM/TwoAtomFunction.pypp.cpp b/wrapper/MM/TwoAtomFunction.pypp.cpp index faaeffea5..a21e15e4d 100644 --- a/wrapper/MM/TwoAtomFunction.pypp.cpp +++ b/wrapper/MM/TwoAtomFunction.pypp.cpp @@ -8,6 +8,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/symbols.h" #include "SireError/errors.h" diff --git a/wrapper/MM/TwoAtomFunctions.pypp.cpp b/wrapper/MM/TwoAtomFunctions.pypp.cpp index a3dd07cce..f30b3c89f 100644 --- a/wrapper/MM/TwoAtomFunctions.pypp.cpp +++ b/wrapper/MM/TwoAtomFunctions.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/symbols.h" #include "SireError/errors.h" @@ -200,6 +202,18 @@ void register_TwoAtomFunctions_class(){ , bp::release_gil_policy() , "Return whether or not this is empty (has no potentials for any internals)" ); + } + { //::SireMM::TwoAtomFunctions::merge + + typedef ::SireBase::PropertyList ( ::SireMM::TwoAtomFunctions::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::TwoAtomFunctions::merge ); + + TwoAtomFunctions_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMM::TwoAtomFunctions::nFunctions diff --git a/wrapper/Mol/AmberParameters.pypp.cpp b/wrapper/Mol/AmberParameters.pypp.cpp index 5781e5329..23ccac952 100644 --- a/wrapper/Mol/AmberParameters.pypp.cpp +++ b/wrapper/Mol/AmberParameters.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireError/errors.h" + #include "SireMol/angleid.h" #include "SireMol/atomidx.h" @@ -259,6 +261,18 @@ void register_AmberParameters_class(){ , bp::release_gil_policy() , "Return whether or not this flexibility is compatible with the molecule\nwhose info is in molinfo" ); + } + { //::SireMol::AmberParameters::merge + + typedef ::SireBase::PropertyList ( ::SireMol::AmberParameters::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AmberParameters::merge ); + + AmberParameters_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } AmberParameters_exposer.def( bp::self != bp::self ); { //::SireMol::AmberParameters::operator= diff --git a/wrapper/Mol/AtomBeads.pypp.cpp b/wrapper/Mol/AtomBeads.pypp.cpp index 54d1a9c62..7c26a2da4 100644 --- a/wrapper/Mol/AtomBeads.pypp.cpp +++ b/wrapper/Mol/AtomBeads.pypp.cpp @@ -359,6 +359,19 @@ void register_AtomBeads_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMol::BeadNum >::merge + + typedef SireMol::AtomProperty< SireMol::BeadNum > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMol::BeadNum >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMol::BeadNum >::merge ); + + AtomBeads_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMol::BeadNum >::nAtoms diff --git a/wrapper/Mol/AtomCharges.pypp.cpp b/wrapper/Mol/AtomCharges.pypp.cpp index d7540a710..40068d67c 100644 --- a/wrapper/Mol/AtomCharges.pypp.cpp +++ b/wrapper/Mol/AtomCharges.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomCharges_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 0, 0, 1, 0, 0, 0 > >::merge + + typedef SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 0, 0, 1, 0, 0, 0 > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 0, 0, 1, 0, 0, 0 > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 0, 0, 1, 0, 0, 0 > >::merge ); + + AtomCharges_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 0, 0, 1, 0, 0, 0 > >::nAtoms diff --git a/wrapper/Mol/AtomChiralities.pypp.cpp b/wrapper/Mol/AtomChiralities.pypp.cpp index d2d9ecc82..5d5062c43 100644 --- a/wrapper/Mol/AtomChiralities.pypp.cpp +++ b/wrapper/Mol/AtomChiralities.pypp.cpp @@ -366,6 +366,19 @@ void register_AtomChiralities_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMol::Chirality >::merge + + typedef SireMol::AtomProperty< SireMol::Chirality > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMol::Chirality >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMol::Chirality >::merge ); + + AtomChiralities_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMol::Chirality >::nAtoms diff --git a/wrapper/Mol/AtomCoords.pypp.cpp b/wrapper/Mol/AtomCoords.pypp.cpp index e724577d2..48958719e 100644 --- a/wrapper/Mol/AtomCoords.pypp.cpp +++ b/wrapper/Mol/AtomCoords.pypp.cpp @@ -403,6 +403,19 @@ void register_AtomCoords_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMaths::Vector >::merge + + typedef SireMol::AtomProperty< SireMaths::Vector > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMaths::Vector >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMaths::Vector >::merge ); + + AtomCoords_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMaths::Vector >::nAtoms diff --git a/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp b/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp index f721db282..0ec36be59 100644 --- a/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp +++ b/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomDoubleArrayProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireBase::DoubleArrayProperty >::merge + + typedef SireMol::AtomProperty< SireBase::DoubleArrayProperty > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireBase::DoubleArrayProperty >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireBase::DoubleArrayProperty >::merge ); + + AtomDoubleArrayProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireBase::DoubleArrayProperty >::nAtoms diff --git a/wrapper/Mol/AtomElements.pypp.cpp b/wrapper/Mol/AtomElements.pypp.cpp index 989c14cdd..5757d158b 100644 --- a/wrapper/Mol/AtomElements.pypp.cpp +++ b/wrapper/Mol/AtomElements.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomElements_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMol::Element >::merge + + typedef SireMol::AtomProperty< SireMol::Element > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMol::Element >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMol::Element >::merge ); + + AtomElements_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMol::Element >::nAtoms diff --git a/wrapper/Mol/AtomEnergies.pypp.cpp b/wrapper/Mol/AtomEnergies.pypp.cpp index cbe0b661c..c20e5154e 100644 --- a/wrapper/Mol/AtomEnergies.pypp.cpp +++ b/wrapper/Mol/AtomEnergies.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomEnergies_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 2, -2, 0, 0, -1, 0 > >::merge + + typedef SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 2, -2, 0, 0, -1, 0 > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 2, -2, 0, 0, -1, 0 > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 2, -2, 0, 0, -1, 0 > >::merge ); + + AtomEnergies_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 2, -2, 0, 0, -1, 0 > >::nAtoms diff --git a/wrapper/Mol/AtomFloatProperty.pypp.cpp b/wrapper/Mol/AtomFloatProperty.pypp.cpp index 76ad8c6d7..c0f8a1d5c 100644 --- a/wrapper/Mol/AtomFloatProperty.pypp.cpp +++ b/wrapper/Mol/AtomFloatProperty.pypp.cpp @@ -386,6 +386,19 @@ void register_AtomFloatProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< double >::merge + + typedef SireMol::AtomProperty< double > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< double >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< double >::merge ); + + AtomFloatProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< double >::nAtoms diff --git a/wrapper/Mol/AtomForces.pypp.cpp b/wrapper/Mol/AtomForces.pypp.cpp index 0daa08c2b..eca661d83 100644 --- a/wrapper/Mol/AtomForces.pypp.cpp +++ b/wrapper/Mol/AtomForces.pypp.cpp @@ -359,6 +359,19 @@ void register_AtomForces_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Force > >::merge + + typedef SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Force > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Force > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Force > >::merge ); + + AtomForces_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Force > >::nAtoms diff --git a/wrapper/Mol/AtomHybridizations.pypp.cpp b/wrapper/Mol/AtomHybridizations.pypp.cpp index 3149a8e56..27b248c36 100644 --- a/wrapper/Mol/AtomHybridizations.pypp.cpp +++ b/wrapper/Mol/AtomHybridizations.pypp.cpp @@ -366,6 +366,19 @@ void register_AtomHybridizations_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMol::Hybridization >::merge + + typedef SireMol::AtomProperty< SireMol::Hybridization > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMol::Hybridization >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMol::Hybridization >::merge ); + + AtomHybridizations_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMol::Hybridization >::nAtoms diff --git a/wrapper/Mol/AtomIdxMapping.pypp.cpp b/wrapper/Mol/AtomIdxMapping.pypp.cpp new file mode 100644 index 000000000..81dc4a45f --- /dev/null +++ b/wrapper/Mol/AtomIdxMapping.pypp.cpp @@ -0,0 +1,278 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "Helpers/clone_const_reference.hpp" +#include "AtomIdxMapping.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireID/index.h" + +#include "SireMol/errors.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "atomidxmapping.h" + +#include "moleculeinfodata.h" + +#include "atomidxmapping.h" + +SireMol::AtomIdxMapping __copy__(const SireMol::AtomIdxMapping &other){ return SireMol::AtomIdxMapping(other); } + +#include "Qt/qdatastream.hpp" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +#include "Helpers/len.hpp" + +void register_AtomIdxMapping_class(){ + + { //::SireMol::AtomIdxMapping + typedef bp::class_< SireMol::AtomIdxMapping, bp::bases< SireBase::Property > > AtomIdxMapping_exposer_t; + AtomIdxMapping_exposer_t AtomIdxMapping_exposer = AtomIdxMapping_exposer_t( "AtomIdxMapping", "This class holds the mapping from one set of atom indices to another.\nThis enables you to associate, atom by atom, atom indices in one set to\natom indices in another set. This is useful, e.g. for building perturbations,\nor for specifying mappings for alignments or RMSD calculations etc.\n\nThis is mainly designed to provide sufficient information to merge\nproperties together. It lists not just the atoms that map, but\nalso which atoms are the ghost atoms that map (i.e. were created\nas ghost equivalents)\n", bp::init< >("Null constructor") ); + bp::scope AtomIdxMapping_scope( AtomIdxMapping_exposer ); + AtomIdxMapping_exposer.def( bp::init< SireMol::AtomIdxMappingEntry const & >(( bp::arg("entry") ), "Construct from a single entry") ); + AtomIdxMapping_exposer.def( bp::init< QList< SireMol::AtomIdxMappingEntry > const & >(( bp::arg("entries") ), "Construct from a list of entries") ); + AtomIdxMapping_exposer.def( bp::init< SireMol::AtomIdxMapping const & >(( bp::arg("other") ), "Copy constructor") ); + { //::SireMol::AtomIdxMapping::append + + typedef void ( ::SireMol::AtomIdxMapping::*append_function_type)( ::SireMol::AtomIdxMappingEntry const & ) ; + append_function_type append_function_value( &::SireMol::AtomIdxMapping::append ); + + AtomIdxMapping_exposer.def( + "append" + , append_function_value + , ( bp::arg("entry") ) + , bp::release_gil_policy() + , "Append an entry to the list" ); + + } + { //::SireMol::AtomIdxMapping::append + + typedef void ( ::SireMol::AtomIdxMapping::*append_function_type)( ::SireMol::AtomIdxMapping const & ) ; + append_function_type append_function_value( &::SireMol::AtomIdxMapping::append ); + + AtomIdxMapping_exposer.def( + "append" + , append_function_value + , ( bp::arg("other") ) + , bp::release_gil_policy() + , "Append all of the passed entries of other onto this list" ); + + } + { //::SireMol::AtomIdxMapping::clear + + typedef void ( ::SireMol::AtomIdxMapping::*clear_function_type)( ) ; + clear_function_type clear_function_value( &::SireMol::AtomIdxMapping::clear ); + + AtomIdxMapping_exposer.def( + "clear" + , clear_function_value + , bp::release_gil_policy() + , "Clear the list" ); + + } + { //::SireMol::AtomIdxMapping::count + + typedef int ( ::SireMol::AtomIdxMapping::*count_function_type)( ) const; + count_function_type count_function_value( &::SireMol::AtomIdxMapping::count ); + + AtomIdxMapping_exposer.def( + "count" + , count_function_value + , bp::release_gil_policy() + , "Return the count of the list" ); + + } + { //::SireMol::AtomIdxMapping::isEmpty + + typedef bool ( ::SireMol::AtomIdxMapping::*isEmpty_function_type)( ) const; + isEmpty_function_type isEmpty_function_value( &::SireMol::AtomIdxMapping::isEmpty ); + + AtomIdxMapping_exposer.def( + "isEmpty" + , isEmpty_function_value + , bp::release_gil_policy() + , "Return whether or not the list is empty" ); + + } + AtomIdxMapping_exposer.def( bp::self != bp::self ); + AtomIdxMapping_exposer.def( bp::self + bp::self ); + AtomIdxMapping_exposer.def( bp::self + bp::other< SireMol::AtomIdxMappingEntry >() ); + { //::SireMol::AtomIdxMapping::operator= + + typedef ::SireMol::AtomIdxMapping & ( ::SireMol::AtomIdxMapping::*assign_function_type)( ::SireMol::AtomIdxMapping const & ) ; + assign_function_type assign_function_value( &::SireMol::AtomIdxMapping::operator= ); + + AtomIdxMapping_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + + } + AtomIdxMapping_exposer.def( bp::self == bp::self ); + { //::SireMol::AtomIdxMapping::operator[] + + typedef ::SireMol::AtomIdxMappingEntry const & ( ::SireMol::AtomIdxMapping::*__getitem___function_type)( int ) const; + __getitem___function_type __getitem___function_value( &::SireMol::AtomIdxMapping::operator[] ); + + AtomIdxMapping_exposer.def( + "__getitem__" + , __getitem___function_value + , ( bp::arg("i") ) + , bp::return_value_policy() + , "" ); + + } + { //::SireMol::AtomIdxMapping::remove + + typedef void ( ::SireMol::AtomIdxMapping::*remove_function_type)( int ) ; + remove_function_type remove_function_value( &::SireMol::AtomIdxMapping::remove ); + + AtomIdxMapping_exposer.def( + "remove" + , remove_function_value + , ( bp::arg("i") ) + , bp::release_gil_policy() + , "Remove the entry at index i" ); + + } + { //::SireMol::AtomIdxMapping::remove + + typedef void ( ::SireMol::AtomIdxMapping::*remove_function_type)( ::SireMol::AtomIdx const & ) ; + remove_function_type remove_function_value( &::SireMol::AtomIdxMapping::remove ); + + AtomIdxMapping_exposer.def( + "remove" + , remove_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Remove the entry for atom atom" ); + + } + { //::SireMol::AtomIdxMapping::remove + + typedef void ( ::SireMol::AtomIdxMapping::*remove_function_type)( ::SireMol::CGAtomIdx const & ) ; + remove_function_type remove_function_value( &::SireMol::AtomIdxMapping::remove ); + + AtomIdxMapping_exposer.def( + "remove" + , remove_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Remove the entry for atom atom" ); + + } + { //::SireMol::AtomIdxMapping::size + + typedef int ( ::SireMol::AtomIdxMapping::*size_function_type)( ) const; + size_function_type size_function_value( &::SireMol::AtomIdxMapping::size ); + + AtomIdxMapping_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "Return the size of the list" ); + + } + { //::SireMol::AtomIdxMapping::take + + typedef ::SireMol::AtomIdxMappingEntry ( ::SireMol::AtomIdxMapping::*take_function_type)( int ) ; + take_function_type take_function_value( &::SireMol::AtomIdxMapping::take ); + + AtomIdxMapping_exposer.def( + "take" + , take_function_value + , ( bp::arg("i") ) + , bp::release_gil_policy() + , "Take the entry at index i" ); + + } + { //::SireMol::AtomIdxMapping::take + + typedef ::SireMol::AtomIdxMappingEntry ( ::SireMol::AtomIdxMapping::*take_function_type)( ::SireMol::AtomIdx const & ) ; + take_function_type take_function_value( &::SireMol::AtomIdxMapping::take ); + + AtomIdxMapping_exposer.def( + "take" + , take_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Take the entry for atom atom" ); + + } + { //::SireMol::AtomIdxMapping::take + + typedef ::SireMol::AtomIdxMappingEntry ( ::SireMol::AtomIdxMapping::*take_function_type)( ::SireMol::CGAtomIdx const & ) ; + take_function_type take_function_value( &::SireMol::AtomIdxMapping::take ); + + AtomIdxMapping_exposer.def( + "take" + , take_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Take the entry for atom atom" ); + + } + { //::SireMol::AtomIdxMapping::toString + + typedef ::QString ( ::SireMol::AtomIdxMapping::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireMol::AtomIdxMapping::toString ); + + AtomIdxMapping_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "Convert this object to a string" ); + + } + { //::SireMol::AtomIdxMapping::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMol::AtomIdxMapping::typeName ); + + AtomIdxMapping_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomIdxMapping::what + + typedef char const * ( ::SireMol::AtomIdxMapping::*what_function_type)( ) const; + what_function_type what_function_value( &::SireMol::AtomIdxMapping::what ); + + AtomIdxMapping_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + + } + AtomIdxMapping_exposer.staticmethod( "typeName" ); + AtomIdxMapping_exposer.def( "__copy__", &__copy__); + AtomIdxMapping_exposer.def( "__deepcopy__", &__copy__); + AtomIdxMapping_exposer.def( "clone", &__copy__); + AtomIdxMapping_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::AtomIdxMapping >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + AtomIdxMapping_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::AtomIdxMapping >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + AtomIdxMapping_exposer.def_pickle(sire_pickle_suite< ::SireMol::AtomIdxMapping >()); + AtomIdxMapping_exposer.def( "__str__", &__str__< ::SireMol::AtomIdxMapping > ); + AtomIdxMapping_exposer.def( "__repr__", &__str__< ::SireMol::AtomIdxMapping > ); + AtomIdxMapping_exposer.def( "__len__", &__len_size< ::SireMol::AtomIdxMapping > ); + } + +} diff --git a/wrapper/Mol/AtomIdxMapping.pypp.hpp b/wrapper/Mol/AtomIdxMapping.pypp.hpp new file mode 100644 index 000000000..43f33b75f --- /dev/null +++ b/wrapper/Mol/AtomIdxMapping.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef AtomIdxMapping_hpp__pyplusplus_wrapper +#define AtomIdxMapping_hpp__pyplusplus_wrapper + +void register_AtomIdxMapping_class(); + +#endif//AtomIdxMapping_hpp__pyplusplus_wrapper diff --git a/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp b/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp new file mode 100644 index 000000000..46da0cad8 --- /dev/null +++ b/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp @@ -0,0 +1,190 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "AtomIdxMappingEntry.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireID/index.h" + +#include "SireMol/errors.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "atomidxmapping.h" + +#include "moleculeinfodata.h" + +#include "atomidxmapping.h" + +SireMol::AtomIdxMappingEntry __copy__(const SireMol::AtomIdxMappingEntry &other){ return SireMol::AtomIdxMappingEntry(other); } + +#include "Qt/qdatastream.hpp" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +void register_AtomIdxMappingEntry_class(){ + + { //::SireMol::AtomIdxMappingEntry + typedef bp::class_< SireMol::AtomIdxMappingEntry > AtomIdxMappingEntry_exposer_t; + AtomIdxMappingEntry_exposer_t AtomIdxMappingEntry_exposer = AtomIdxMappingEntry_exposer_t( "AtomIdxMappingEntry", "This is an individual mapping for a single atom", bp::init< >("Null constructor") ); + bp::scope AtomIdxMappingEntry_scope( AtomIdxMappingEntry_exposer ); + AtomIdxMappingEntry_exposer.def( bp::init< SireMol::AtomIdx const &, SireMol::AtomIdx const &, SireMol::MoleculeInfoData const &, SireMol::MoleculeInfoData const &, bool >(( bp::arg("index0"), bp::arg("index1"), bp::arg("molinfo0"), bp::arg("molinfo1"), bp::arg("is_unmapped_in_reference") ), "Construct to map from index0 in molinfo0 to index1 in molinfo1.\n There is no mapping in the perturbed state if index1 is null. There\n is no mapping in the reference state if is_unmapped_in_reference is true.\n It is an error to have index0 null, or if you cannot look up\n index0 in molinfo0 or index1 in molinfo1.\n") ); + AtomIdxMappingEntry_exposer.def( bp::init< SireMol::AtomIdxMappingEntry const & >(( bp::arg("other") ), "Copy constructor") ); + { //::SireMol::AtomIdxMappingEntry::atomIdx0 + + typedef ::SireMol::AtomIdx ( ::SireMol::AtomIdxMappingEntry::*atomIdx0_function_type)( ) const; + atomIdx0_function_type atomIdx0_function_value( &::SireMol::AtomIdxMappingEntry::atomIdx0 ); + + AtomIdxMappingEntry_exposer.def( + "atomIdx0" + , atomIdx0_function_value + , bp::release_gil_policy() + , "Return the atom index in the reference state. This will always have\n a value, even if the atom is unmapped in the reference state\n (this signals that any parameter with this index should be zero)\n" ); + + } + { //::SireMol::AtomIdxMappingEntry::atomIdx1 + + typedef ::SireMol::AtomIdx ( ::SireMol::AtomIdxMappingEntry::*atomIdx1_function_type)( ) const; + atomIdx1_function_type atomIdx1_function_value( &::SireMol::AtomIdxMappingEntry::atomIdx1 ); + + AtomIdxMappingEntry_exposer.def( + "atomIdx1" + , atomIdx1_function_value + , bp::release_gil_policy() + , "Return the atom index in the perturbed state, or a null index if\n the atom is unmapped in the perturbed state" ); + + } + { //::SireMol::AtomIdxMappingEntry::cgAtomIdx0 + + typedef ::SireMol::CGAtomIdx ( ::SireMol::AtomIdxMappingEntry::*cgAtomIdx0_function_type)( ) const; + cgAtomIdx0_function_type cgAtomIdx0_function_value( &::SireMol::AtomIdxMappingEntry::cgAtomIdx0 ); + + AtomIdxMappingEntry_exposer.def( + "cgAtomIdx0" + , cgAtomIdx0_function_value + , bp::release_gil_policy() + , "Return the atom index in the reference state. This will always have\n a value, even if the atom is unmapped in the reference state\n (this signals that any parameter with this index should be zero)\n" ); + + } + { //::SireMol::AtomIdxMappingEntry::cgAtomIdx1 + + typedef ::SireMol::CGAtomIdx ( ::SireMol::AtomIdxMappingEntry::*cgAtomIdx1_function_type)( ) const; + cgAtomIdx1_function_type cgAtomIdx1_function_value( &::SireMol::AtomIdxMappingEntry::cgAtomIdx1 ); + + AtomIdxMappingEntry_exposer.def( + "cgAtomIdx1" + , cgAtomIdx1_function_value + , bp::release_gil_policy() + , "Return the atom index in the perturbed state, or a null index if\n the atom is unmapped in the perturbed state" ); + + } + { //::SireMol::AtomIdxMappingEntry::isNull + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireMol::AtomIdxMappingEntry::isNull ); + + AtomIdxMappingEntry_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "Return whether or not this is a null entry" ); + + } + { //::SireMol::AtomIdxMappingEntry::isUnmappedIn0 + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isUnmappedIn0_function_type)( ) const; + isUnmappedIn0_function_type isUnmappedIn0_function_value( &::SireMol::AtomIdxMappingEntry::isUnmappedIn0 ); + + AtomIdxMappingEntry_exposer.def( + "isUnmappedIn0" + , isUnmappedIn0_function_value + , bp::release_gil_policy() + , "Return whether or not this atom is unmapped in the reference state" ); + + } + { //::SireMol::AtomIdxMappingEntry::isUnmappedIn1 + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isUnmappedIn1_function_type)( ) const; + isUnmappedIn1_function_type isUnmappedIn1_function_value( &::SireMol::AtomIdxMappingEntry::isUnmappedIn1 ); + + AtomIdxMappingEntry_exposer.def( + "isUnmappedIn1" + , isUnmappedIn1_function_value + , bp::release_gil_policy() + , "Return whether or not this atom is unmapped in the perturbed state" ); + + } + AtomIdxMappingEntry_exposer.def( bp::self != bp::self ); + { //::SireMol::AtomIdxMappingEntry::operator= + + typedef ::SireMol::AtomIdxMappingEntry & ( ::SireMol::AtomIdxMappingEntry::*assign_function_type)( ::SireMol::AtomIdxMappingEntry const & ) ; + assign_function_type assign_function_value( &::SireMol::AtomIdxMappingEntry::operator= ); + + AtomIdxMappingEntry_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + + } + AtomIdxMappingEntry_exposer.def( bp::self == bp::self ); + { //::SireMol::AtomIdxMappingEntry::toString + + typedef ::QString ( ::SireMol::AtomIdxMappingEntry::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireMol::AtomIdxMappingEntry::toString ); + + AtomIdxMappingEntry_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "Convert this object to a string" ); + + } + { //::SireMol::AtomIdxMappingEntry::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMol::AtomIdxMappingEntry::typeName ); + + AtomIdxMappingEntry_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomIdxMappingEntry::what + + typedef char const * ( ::SireMol::AtomIdxMappingEntry::*what_function_type)( ) const; + what_function_type what_function_value( &::SireMol::AtomIdxMappingEntry::what ); + + AtomIdxMappingEntry_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + + } + AtomIdxMappingEntry_exposer.staticmethod( "typeName" ); + AtomIdxMappingEntry_exposer.def( "__copy__", &__copy__); + AtomIdxMappingEntry_exposer.def( "__deepcopy__", &__copy__); + AtomIdxMappingEntry_exposer.def( "clone", &__copy__); + AtomIdxMappingEntry_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::AtomIdxMappingEntry >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + AtomIdxMappingEntry_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::AtomIdxMappingEntry >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + AtomIdxMappingEntry_exposer.def_pickle(sire_pickle_suite< ::SireMol::AtomIdxMappingEntry >()); + AtomIdxMappingEntry_exposer.def( "__str__", &__str__< ::SireMol::AtomIdxMappingEntry > ); + AtomIdxMappingEntry_exposer.def( "__repr__", &__str__< ::SireMol::AtomIdxMappingEntry > ); + } + +} diff --git a/wrapper/Mol/AtomIdxMappingEntry.pypp.hpp b/wrapper/Mol/AtomIdxMappingEntry.pypp.hpp new file mode 100644 index 000000000..aa5d36d01 --- /dev/null +++ b/wrapper/Mol/AtomIdxMappingEntry.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef AtomIdxMappingEntry_hpp__pyplusplus_wrapper +#define AtomIdxMappingEntry_hpp__pyplusplus_wrapper + +void register_AtomIdxMappingEntry_class(); + +#endif//AtomIdxMappingEntry_hpp__pyplusplus_wrapper diff --git a/wrapper/Mol/AtomIntProperty.pypp.cpp b/wrapper/Mol/AtomIntProperty.pypp.cpp index 3aefcbdeb..7062a1960 100644 --- a/wrapper/Mol/AtomIntProperty.pypp.cpp +++ b/wrapper/Mol/AtomIntProperty.pypp.cpp @@ -386,6 +386,19 @@ void register_AtomIntProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< long long >::merge + + typedef SireMol::AtomProperty< long long > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< long long >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< long long >::merge ); + + AtomIntProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< long long >::nAtoms diff --git a/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp b/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp index 4c3e0f0c0..a3d033372 100644 --- a/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp +++ b/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomIntegerArrayProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireBase::IntegerArrayProperty >::merge + + typedef SireMol::AtomProperty< SireBase::IntegerArrayProperty > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireBase::IntegerArrayProperty >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireBase::IntegerArrayProperty >::merge ); + + AtomIntegerArrayProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireBase::IntegerArrayProperty >::nAtoms diff --git a/wrapper/Mol/AtomMasses.pypp.cpp b/wrapper/Mol/AtomMasses.pypp.cpp index a80c8e4d6..98d183dc1 100644 --- a/wrapper/Mol/AtomMasses.pypp.cpp +++ b/wrapper/Mol/AtomMasses.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomMasses_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 0, 0, 0, 0, -1, 0 > >::merge + + typedef SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 0, 0, 0, 0, -1, 0 > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 0, 0, 0, 0, -1, 0 > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 0, 0, 0, 0, -1, 0 > >::merge ); + + AtomMasses_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 1, 0, 0, 0, 0, -1, 0 > >::nAtoms diff --git a/wrapper/Mol/AtomPolarisabilities.pypp.cpp b/wrapper/Mol/AtomPolarisabilities.pypp.cpp index 3c5fd5c98..14cb5559d 100644 --- a/wrapper/Mol/AtomPolarisabilities.pypp.cpp +++ b/wrapper/Mol/AtomPolarisabilities.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomPolarisabilities_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 3, 0, 0, 0, 0, 0 > >::merge + + typedef SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 3, 0, 0, 0, 0, 0 > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 3, 0, 0, 0, 0, 0 > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 3, 0, 0, 0, 0, 0 > >::merge ); + + AtomPolarisabilities_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 3, 0, 0, 0, 0, 0 > >::nAtoms diff --git a/wrapper/Mol/AtomProp.pypp.cpp b/wrapper/Mol/AtomProp.pypp.cpp index d69175be0..e8d2a4f88 100644 --- a/wrapper/Mol/AtomProp.pypp.cpp +++ b/wrapper/Mol/AtomProp.pypp.cpp @@ -154,6 +154,18 @@ void register_AtomProp_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProp::merge + + typedef ::SireBase::PropertyList ( ::SireMol::AtomProp::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProp::merge ); + + AtomProp_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProp::operator= diff --git a/wrapper/Mol/AtomPropertyList.pypp.cpp b/wrapper/Mol/AtomPropertyList.pypp.cpp index c50f6c871..8834a9a53 100644 --- a/wrapper/Mol/AtomPropertyList.pypp.cpp +++ b/wrapper/Mol/AtomPropertyList.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomPropertyList_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireBase::PropertyList >::merge + + typedef SireMol::AtomProperty< SireBase::PropertyList > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireBase::PropertyList >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireBase::PropertyList >::merge ); + + AtomPropertyList_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireBase::PropertyList >::nAtoms diff --git a/wrapper/Mol/AtomPropertyProperty.pypp.cpp b/wrapper/Mol/AtomPropertyProperty.pypp.cpp index ec593be7b..cd0a88f8f 100644 --- a/wrapper/Mol/AtomPropertyProperty.pypp.cpp +++ b/wrapper/Mol/AtomPropertyProperty.pypp.cpp @@ -386,6 +386,19 @@ void register_AtomPropertyProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireBase::PropPtr< SireBase::Property > >::merge + + typedef SireMol::AtomProperty< SireBase::PropPtr< SireBase::Property > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireBase::PropPtr< SireBase::Property > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireBase::PropPtr< SireBase::Property > >::merge ); + + AtomPropertyProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireBase::PropPtr< SireBase::Property > >::nAtoms diff --git a/wrapper/Mol/AtomRadicals.pypp.cpp b/wrapper/Mol/AtomRadicals.pypp.cpp index 6161d13da..33d262cf5 100644 --- a/wrapper/Mol/AtomRadicals.pypp.cpp +++ b/wrapper/Mol/AtomRadicals.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomRadicals_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMol::Radical >::merge + + typedef SireMol::AtomProperty< SireMol::Radical > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMol::Radical >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMol::Radical >::merge ); + + AtomRadicals_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMol::Radical >::nAtoms diff --git a/wrapper/Mol/AtomRadii.pypp.cpp b/wrapper/Mol/AtomRadii.pypp.cpp index f7464a4bb..d41f4a9c5 100644 --- a/wrapper/Mol/AtomRadii.pypp.cpp +++ b/wrapper/Mol/AtomRadii.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomRadii_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 1, 0, 0, 0, 0, 0 > >::merge + + typedef SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 1, 0, 0, 0, 0, 0 > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 1, 0, 0, 0, 0, 0 > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 1, 0, 0, 0, 0, 0 > >::merge ); + + AtomRadii_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireUnits::Dimension::PhysUnit< 0, 1, 0, 0, 0, 0, 0 > >::nAtoms diff --git a/wrapper/Mol/AtomSelection.pypp.cpp b/wrapper/Mol/AtomSelection.pypp.cpp index 965a79995..9bac30abe 100644 --- a/wrapper/Mol/AtomSelection.pypp.cpp +++ b/wrapper/Mol/AtomSelection.pypp.cpp @@ -1372,6 +1372,18 @@ void register_AtomSelection_class(){ , bp::return_self< >() , "Mask this selection by other\nThrow: SireError::incompatible_error\n" ); + } + { //::SireMol::AtomSelection::merge + + typedef ::SireBase::PropertyList ( ::SireMol::AtomSelection::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomSelection::merge ); + + AtomSelection_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomSelection::nAtoms diff --git a/wrapper/Mol/AtomStringArrayProperty.pypp.cpp b/wrapper/Mol/AtomStringArrayProperty.pypp.cpp index 578b25820..6825c389e 100644 --- a/wrapper/Mol/AtomStringArrayProperty.pypp.cpp +++ b/wrapper/Mol/AtomStringArrayProperty.pypp.cpp @@ -358,6 +358,19 @@ void register_AtomStringArrayProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireBase::StringArrayProperty >::merge + + typedef SireMol::AtomProperty< SireBase::StringArrayProperty > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireBase::StringArrayProperty >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireBase::StringArrayProperty >::merge ); + + AtomStringArrayProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireBase::StringArrayProperty >::nAtoms diff --git a/wrapper/Mol/AtomStringProperty.pypp.cpp b/wrapper/Mol/AtomStringProperty.pypp.cpp index 005a54d58..0a46109bd 100644 --- a/wrapper/Mol/AtomStringProperty.pypp.cpp +++ b/wrapper/Mol/AtomStringProperty.pypp.cpp @@ -386,6 +386,19 @@ void register_AtomStringProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< QString >::merge + + typedef SireMol::AtomProperty< QString > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< QString >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< QString >::merge ); + + AtomStringProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< QString >::nAtoms diff --git a/wrapper/Mol/AtomVariantProperty.pypp.cpp b/wrapper/Mol/AtomVariantProperty.pypp.cpp index 03d350f0c..8958024a5 100644 --- a/wrapper/Mol/AtomVariantProperty.pypp.cpp +++ b/wrapper/Mol/AtomVariantProperty.pypp.cpp @@ -386,6 +386,19 @@ void register_AtomVariantProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< QVariant >::merge + + typedef SireMol::AtomProperty< QVariant > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< QVariant >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< QVariant >::merge ); + + AtomVariantProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< QVariant >::nAtoms diff --git a/wrapper/Mol/AtomVelocities.pypp.cpp b/wrapper/Mol/AtomVelocities.pypp.cpp index 6e8957222..ff7f9bbab 100644 --- a/wrapper/Mol/AtomVelocities.pypp.cpp +++ b/wrapper/Mol/AtomVelocities.pypp.cpp @@ -359,6 +359,19 @@ void register_AtomVelocities_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Velocity > >::merge + + typedef SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Velocity > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Velocity > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Velocity > >::merge ); + + AtomVelocities_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::AtomProperty< SireMaths::Vector3D< SireUnits::Dimension::Velocity > >::nAtoms diff --git a/wrapper/Mol/BeadFloatProperty.pypp.cpp b/wrapper/Mol/BeadFloatProperty.pypp.cpp index d605af684..85d74c1ed 100644 --- a/wrapper/Mol/BeadFloatProperty.pypp.cpp +++ b/wrapper/Mol/BeadFloatProperty.pypp.cpp @@ -198,6 +198,19 @@ void register_BeadFloatProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::BeadProperty< double >::merge + + typedef SireMol::BeadProperty< double > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::BeadProperty< double >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::BeadProperty< double >::merge ); + + BeadFloatProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::BeadProperty< double >::nBeads diff --git a/wrapper/Mol/BeadIntProperty.pypp.cpp b/wrapper/Mol/BeadIntProperty.pypp.cpp index 2fe26469a..ea0910bac 100644 --- a/wrapper/Mol/BeadIntProperty.pypp.cpp +++ b/wrapper/Mol/BeadIntProperty.pypp.cpp @@ -198,6 +198,19 @@ void register_BeadIntProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::BeadProperty< long long >::merge + + typedef SireMol::BeadProperty< long long > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::BeadProperty< long long >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::BeadProperty< long long >::merge ); + + BeadIntProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::BeadProperty< long long >::nBeads diff --git a/wrapper/Mol/BeadPropertyProperty.pypp.cpp b/wrapper/Mol/BeadPropertyProperty.pypp.cpp index 2cccc3f0c..baf24dddb 100644 --- a/wrapper/Mol/BeadPropertyProperty.pypp.cpp +++ b/wrapper/Mol/BeadPropertyProperty.pypp.cpp @@ -198,6 +198,19 @@ void register_BeadPropertyProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::BeadProperty< SireBase::PropPtr< SireBase::Property > >::merge + + typedef SireMol::BeadProperty< SireBase::PropPtr< SireBase::Property > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::BeadProperty< SireBase::PropPtr< SireBase::Property > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::BeadProperty< SireBase::PropPtr< SireBase::Property > >::merge ); + + BeadPropertyProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::BeadProperty< SireBase::PropPtr< SireBase::Property > >::nBeads diff --git a/wrapper/Mol/BeadStringProperty.pypp.cpp b/wrapper/Mol/BeadStringProperty.pypp.cpp index 5afeab2cc..276484d39 100644 --- a/wrapper/Mol/BeadStringProperty.pypp.cpp +++ b/wrapper/Mol/BeadStringProperty.pypp.cpp @@ -198,6 +198,19 @@ void register_BeadStringProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::BeadProperty< QString >::merge + + typedef SireMol::BeadProperty< QString > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::BeadProperty< QString >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::BeadProperty< QString >::merge ); + + BeadStringProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::BeadProperty< QString >::nBeads diff --git a/wrapper/Mol/BeadVariantProperty.pypp.cpp b/wrapper/Mol/BeadVariantProperty.pypp.cpp index 555f895a6..a7b3526cf 100644 --- a/wrapper/Mol/BeadVariantProperty.pypp.cpp +++ b/wrapper/Mol/BeadVariantProperty.pypp.cpp @@ -198,6 +198,19 @@ void register_BeadVariantProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::BeadProperty< QVariant >::merge + + typedef SireMol::BeadProperty< QVariant > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::BeadProperty< QVariant >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::BeadProperty< QVariant >::merge ); + + BeadVariantProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::BeadProperty< QVariant >::nBeads diff --git a/wrapper/Mol/Beading.pypp.cpp b/wrapper/Mol/Beading.pypp.cpp index ac8b3efa7..1ee8e55e8 100644 --- a/wrapper/Mol/Beading.pypp.cpp +++ b/wrapper/Mol/Beading.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireError/errors.h" @@ -57,6 +59,18 @@ void register_Beading_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Beading::merge + + typedef ::SireBase::PropertyList ( ::SireMol::Beading::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::Beading::merge ); + + Beading_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMol::Beading::null diff --git a/wrapper/Mol/CGFloatProperty.pypp.cpp b/wrapper/Mol/CGFloatProperty.pypp.cpp index 35ff46ef6..8ba3c9728 100644 --- a/wrapper/Mol/CGFloatProperty.pypp.cpp +++ b/wrapper/Mol/CGFloatProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_CGFloatProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::CGProperty< double >::merge + + typedef SireMol::CGProperty< double > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::CGProperty< double >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::CGProperty< double >::merge ); + + CGFloatProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::CGProperty< double >::nCutGroups diff --git a/wrapper/Mol/CGIntProperty.pypp.cpp b/wrapper/Mol/CGIntProperty.pypp.cpp index 9df74a473..f8e268c11 100644 --- a/wrapper/Mol/CGIntProperty.pypp.cpp +++ b/wrapper/Mol/CGIntProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_CGIntProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::CGProperty< long long >::merge + + typedef SireMol::CGProperty< long long > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::CGProperty< long long >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::CGProperty< long long >::merge ); + + CGIntProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::CGProperty< long long >::nCutGroups diff --git a/wrapper/Mol/CGPropertyProperty.pypp.cpp b/wrapper/Mol/CGPropertyProperty.pypp.cpp index f976cc2aa..959d9022d 100644 --- a/wrapper/Mol/CGPropertyProperty.pypp.cpp +++ b/wrapper/Mol/CGPropertyProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_CGPropertyProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::CGProperty< SireBase::PropPtr< SireBase::Property > >::merge + + typedef SireMol::CGProperty< SireBase::PropPtr< SireBase::Property > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::CGProperty< SireBase::PropPtr< SireBase::Property > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::CGProperty< SireBase::PropPtr< SireBase::Property > >::merge ); + + CGPropertyProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::CGProperty< SireBase::PropPtr< SireBase::Property > >::nCutGroups diff --git a/wrapper/Mol/CGStringProperty.pypp.cpp b/wrapper/Mol/CGStringProperty.pypp.cpp index 527b9e4d0..92263e6c5 100644 --- a/wrapper/Mol/CGStringProperty.pypp.cpp +++ b/wrapper/Mol/CGStringProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_CGStringProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::CGProperty< QString >::merge + + typedef SireMol::CGProperty< QString > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::CGProperty< QString >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::CGProperty< QString >::merge ); + + CGStringProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::CGProperty< QString >::nCutGroups diff --git a/wrapper/Mol/CGVariantProperty.pypp.cpp b/wrapper/Mol/CGVariantProperty.pypp.cpp index e225fa039..dbb8f9b08 100644 --- a/wrapper/Mol/CGVariantProperty.pypp.cpp +++ b/wrapper/Mol/CGVariantProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_CGVariantProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::CGProperty< QVariant >::merge + + typedef SireMol::CGProperty< QVariant > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::CGProperty< QVariant >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::CGProperty< QVariant >::merge ); + + CGVariantProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::CGProperty< QVariant >::nCutGroups diff --git a/wrapper/Mol/CMakeAutogenFile.txt b/wrapper/Mol/CMakeAutogenFile.txt index 2a199e84c..027bd4d77 100644 --- a/wrapper/Mol/CMakeAutogenFile.txt +++ b/wrapper/Mol/CMakeAutogenFile.txt @@ -37,6 +37,7 @@ set ( PYPP_SOURCES ResNum.pypp.cpp Atom.pypp.cpp ResIntProperty.pypp.cpp + AtomIdxMappingEntry.pypp.cpp Frame.pypp.cpp Hybridization.pypp.cpp BondID.pypp.cpp @@ -145,6 +146,7 @@ set ( PYPP_SOURCES GeometryPerturbation.pypp.cpp VolumeMap.pypp.cpp Mover_Beads_.pypp.cpp + AtomIdxMapping.pypp.cpp MoverBase.pypp.cpp AtomPropertyList.pypp.cpp IDOrSet_CGID_.pypp.cpp diff --git a/wrapper/Mol/ChainFloatProperty.pypp.cpp b/wrapper/Mol/ChainFloatProperty.pypp.cpp index 3c305f7f9..85f06f465 100644 --- a/wrapper/Mol/ChainFloatProperty.pypp.cpp +++ b/wrapper/Mol/ChainFloatProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ChainFloatProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ChainProperty< double >::merge + + typedef SireMol::ChainProperty< double > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ChainProperty< double >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ChainProperty< double >::merge ); + + ChainFloatProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ChainProperty< double >::nChains diff --git a/wrapper/Mol/ChainIntProperty.pypp.cpp b/wrapper/Mol/ChainIntProperty.pypp.cpp index 2f46c9c30..9463b40c5 100644 --- a/wrapper/Mol/ChainIntProperty.pypp.cpp +++ b/wrapper/Mol/ChainIntProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ChainIntProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ChainProperty< long long >::merge + + typedef SireMol::ChainProperty< long long > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ChainProperty< long long >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ChainProperty< long long >::merge ); + + ChainIntProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ChainProperty< long long >::nChains diff --git a/wrapper/Mol/ChainPropertyProperty.pypp.cpp b/wrapper/Mol/ChainPropertyProperty.pypp.cpp index 87f1e9a26..0a724e60a 100644 --- a/wrapper/Mol/ChainPropertyProperty.pypp.cpp +++ b/wrapper/Mol/ChainPropertyProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ChainPropertyProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ChainProperty< SireBase::PropPtr< SireBase::Property > >::merge + + typedef SireMol::ChainProperty< SireBase::PropPtr< SireBase::Property > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ChainProperty< SireBase::PropPtr< SireBase::Property > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ChainProperty< SireBase::PropPtr< SireBase::Property > >::merge ); + + ChainPropertyProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ChainProperty< SireBase::PropPtr< SireBase::Property > >::nChains diff --git a/wrapper/Mol/ChainStringProperty.pypp.cpp b/wrapper/Mol/ChainStringProperty.pypp.cpp index a1d1e6651..cf7496375 100644 --- a/wrapper/Mol/ChainStringProperty.pypp.cpp +++ b/wrapper/Mol/ChainStringProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ChainStringProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ChainProperty< QString >::merge + + typedef SireMol::ChainProperty< QString > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ChainProperty< QString >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ChainProperty< QString >::merge ); + + ChainStringProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ChainProperty< QString >::nChains diff --git a/wrapper/Mol/ChainVariantProperty.pypp.cpp b/wrapper/Mol/ChainVariantProperty.pypp.cpp index 80408e949..5707cb2f4 100644 --- a/wrapper/Mol/ChainVariantProperty.pypp.cpp +++ b/wrapper/Mol/ChainVariantProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ChainVariantProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ChainProperty< QVariant >::merge + + typedef SireMol::ChainProperty< QVariant > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ChainProperty< QVariant >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ChainProperty< QVariant >::merge ); + + ChainVariantProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ChainProperty< QVariant >::nChains diff --git a/wrapper/Mol/Connectivity.pypp.cpp b/wrapper/Mol/Connectivity.pypp.cpp index 21fdd8d1f..d9fb565c9 100644 --- a/wrapper/Mol/Connectivity.pypp.cpp +++ b/wrapper/Mol/Connectivity.pypp.cpp @@ -7,10 +7,14 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" +#include "SireError/errors.h" + #include "SireMol/errors.h" #include "SireStream/datastream.h" diff --git a/wrapper/Mol/ConnectivityBase.pypp.cpp b/wrapper/Mol/ConnectivityBase.pypp.cpp index 9aecbab9e..9592d8783 100644 --- a/wrapper/Mol/ConnectivityBase.pypp.cpp +++ b/wrapper/Mol/ConnectivityBase.pypp.cpp @@ -8,10 +8,14 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" +#include "SireError/errors.h" + #include "SireMol/errors.h" #include "SireStream/datastream.h" @@ -813,6 +817,18 @@ void register_ConnectivityBase_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ConnectivityBase::merge + + typedef ::SireBase::PropertyList ( ::SireMol::ConnectivityBase::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ConnectivityBase::merge ); + + ConnectivityBase_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMol::ConnectivityBase::nConnections diff --git a/wrapper/Mol/ConnectivityEditor.pypp.cpp b/wrapper/Mol/ConnectivityEditor.pypp.cpp index c494b0c57..3e83b10f5 100644 --- a/wrapper/Mol/ConnectivityEditor.pypp.cpp +++ b/wrapper/Mol/ConnectivityEditor.pypp.cpp @@ -7,10 +7,14 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireBase/parallel.h" +#include "SireError/errors.h" + #include "SireMol/errors.h" #include "SireStream/datastream.h" diff --git a/wrapper/Mol/Element.pypp.cpp b/wrapper/Mol/Element.pypp.cpp index 20e8fc4c7..f4f6db97c 100644 --- a/wrapper/Mol/Element.pypp.cpp +++ b/wrapper/Mol/Element.pypp.cpp @@ -88,7 +88,7 @@ void register_Element_class(){ , biologicalElement_function_value , ( bp::arg("name") ) , bp::release_gil_policy() - , "Return a biological element that has been guessed from the passed name.\nNote that if no biological element was guessed, then the nearest\nnon-biological element match is used. A biological element is one that\nis in the first couple of rows (proton number < 18) and is not a noble gas." ); + , "Return a biological element that has been guessed from the passed name.\nNote that if no biological element was guessed, then the nearest\nnon-biological element match is used. A biological element is one that\nis in the list of biological elements" ); } { //::SireMol::Element::blue @@ -149,7 +149,7 @@ void register_Element_class(){ "getBiologicalElements" , getBiologicalElements_function_value , bp::release_gil_policy() - , "" ); + , "Return a list of all of the elements that are considered\n to be biological\n" ); } { //::SireMol::Element::green @@ -343,7 +343,7 @@ void register_Element_class(){ , setElementIsBiological_function_value , ( bp::arg("element") ) , bp::release_gil_policy() - , "" ); + , "Set that the passed element should be considered to be biological" ); } { //::SireMol::Element::setElementIsNotBiological @@ -356,7 +356,7 @@ void register_Element_class(){ , setElementIsNotBiological_function_value , ( bp::arg("element") ) , bp::release_gil_policy() - , "" ); + , "Set that the passed element should considered to definitely\n not be biological\n" ); } { //::SireMol::Element::symbol diff --git a/wrapper/Mol/Frame.pypp.cpp b/wrapper/Mol/Frame.pypp.cpp index 1c01beb1f..4445fd2e9 100644 --- a/wrapper/Mol/Frame.pypp.cpp +++ b/wrapper/Mol/Frame.pypp.cpp @@ -8,6 +8,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/generalunitproperty.h" #include "SireBase/lazyevaluator.h" @@ -180,6 +182,18 @@ void register_Frame_class(){ , ( bp::arg("frames"), bp::arg("use_parallel")=(bool)(true) ) , "Join the vector of passed frames into a single frame. The\n frames are joined in order, e.g. from the first atom in\n the first frame to the last atom in the last frame\n" ); + } + { //::SireMol::Frame::merge + + typedef ::SireBase::PropertyList ( ::SireMol::Frame::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::Frame::merge ); + + Frame_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMol::Frame::nAtoms diff --git a/wrapper/Mol/MolViewProperty.pypp.cpp b/wrapper/Mol/MolViewProperty.pypp.cpp index dcfa4909f..66333b89a 100644 --- a/wrapper/Mol/MolViewProperty.pypp.cpp +++ b/wrapper/Mol/MolViewProperty.pypp.cpp @@ -160,6 +160,18 @@ void register_MolViewProperty_class(){ , bp::release_gil_policy() , "Do everything possible to make this property compatible with the\nMoleculeInfoData layout in info - otherwise raise an error\nThrow: SireError::incompatible_error\n" ); + } + { //::SireMol::MolViewProperty::merge + + typedef ::SireBase::PropertyList ( ::SireMol::MolViewProperty::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::MolViewProperty::merge ); + + MolViewProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::MolViewProperty::typeName diff --git a/wrapper/Mol/MoleculeBeading.pypp.cpp b/wrapper/Mol/MoleculeBeading.pypp.cpp index 7482cd847..4e48be71b 100644 --- a/wrapper/Mol/MoleculeBeading.pypp.cpp +++ b/wrapper/Mol/MoleculeBeading.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireError/errors.h" diff --git a/wrapper/Mol/NullBeading.pypp.cpp b/wrapper/Mol/NullBeading.pypp.cpp index 71e678af2..3b6ffb4ea 100644 --- a/wrapper/Mol/NullBeading.pypp.cpp +++ b/wrapper/Mol/NullBeading.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireError/errors.h" diff --git a/wrapper/Mol/ResFloatProperty.pypp.cpp b/wrapper/Mol/ResFloatProperty.pypp.cpp index 53fd22615..c950b2540 100644 --- a/wrapper/Mol/ResFloatProperty.pypp.cpp +++ b/wrapper/Mol/ResFloatProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ResFloatProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ResProperty< double >::merge + + typedef SireMol::ResProperty< double > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ResProperty< double >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ResProperty< double >::merge ); + + ResFloatProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ResProperty< double >::nResidues diff --git a/wrapper/Mol/ResIntProperty.pypp.cpp b/wrapper/Mol/ResIntProperty.pypp.cpp index 0514e645d..a7d82b290 100644 --- a/wrapper/Mol/ResIntProperty.pypp.cpp +++ b/wrapper/Mol/ResIntProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ResIntProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ResProperty< long long >::merge + + typedef SireMol::ResProperty< long long > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ResProperty< long long >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ResProperty< long long >::merge ); + + ResIntProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ResProperty< long long >::nResidues diff --git a/wrapper/Mol/ResPropertyProperty.pypp.cpp b/wrapper/Mol/ResPropertyProperty.pypp.cpp index 926bc3611..fe9bb60ce 100644 --- a/wrapper/Mol/ResPropertyProperty.pypp.cpp +++ b/wrapper/Mol/ResPropertyProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ResPropertyProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ResProperty< SireBase::PropPtr< SireBase::Property > >::merge + + typedef SireMol::ResProperty< SireBase::PropPtr< SireBase::Property > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ResProperty< SireBase::PropPtr< SireBase::Property > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ResProperty< SireBase::PropPtr< SireBase::Property > >::merge ); + + ResPropertyProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ResProperty< SireBase::PropPtr< SireBase::Property > >::nResidues diff --git a/wrapper/Mol/ResStringProperty.pypp.cpp b/wrapper/Mol/ResStringProperty.pypp.cpp index 8a0ec0ec5..5f39f59e2 100644 --- a/wrapper/Mol/ResStringProperty.pypp.cpp +++ b/wrapper/Mol/ResStringProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ResStringProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ResProperty< QString >::merge + + typedef SireMol::ResProperty< QString > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ResProperty< QString >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ResProperty< QString >::merge ); + + ResStringProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ResProperty< QString >::nResidues diff --git a/wrapper/Mol/ResVariantProperty.pypp.cpp b/wrapper/Mol/ResVariantProperty.pypp.cpp index bdc098bb3..734748fe9 100644 --- a/wrapper/Mol/ResVariantProperty.pypp.cpp +++ b/wrapper/Mol/ResVariantProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_ResVariantProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::ResProperty< QVariant >::merge + + typedef SireMol::ResProperty< QVariant > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::ResProperty< QVariant >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ResProperty< QVariant >::merge ); + + ResVariantProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::ResProperty< QVariant >::nResidues diff --git a/wrapper/Mol/ResidueBeading.pypp.cpp b/wrapper/Mol/ResidueBeading.pypp.cpp index 484f79e51..f467b357c 100644 --- a/wrapper/Mol/ResidueBeading.pypp.cpp +++ b/wrapper/Mol/ResidueBeading.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireError/errors.h" diff --git a/wrapper/Mol/SegFloatProperty.pypp.cpp b/wrapper/Mol/SegFloatProperty.pypp.cpp index 354e83ff9..e7ef9404d 100644 --- a/wrapper/Mol/SegFloatProperty.pypp.cpp +++ b/wrapper/Mol/SegFloatProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_SegFloatProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SegProperty< double >::merge + + typedef SireMol::SegProperty< double > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::SegProperty< double >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::SegProperty< double >::merge ); + + SegFloatProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::SegProperty< double >::nSegments diff --git a/wrapper/Mol/SegIntProperty.pypp.cpp b/wrapper/Mol/SegIntProperty.pypp.cpp index c32f054a9..227bb720e 100644 --- a/wrapper/Mol/SegIntProperty.pypp.cpp +++ b/wrapper/Mol/SegIntProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_SegIntProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SegProperty< long long >::merge + + typedef SireMol::SegProperty< long long > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::SegProperty< long long >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::SegProperty< long long >::merge ); + + SegIntProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::SegProperty< long long >::nSegments diff --git a/wrapper/Mol/SegPropertyProperty.pypp.cpp b/wrapper/Mol/SegPropertyProperty.pypp.cpp index 3f5e6d649..97ccac33a 100644 --- a/wrapper/Mol/SegPropertyProperty.pypp.cpp +++ b/wrapper/Mol/SegPropertyProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_SegPropertyProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SegProperty< SireBase::PropPtr< SireBase::Property > >::merge + + typedef SireMol::SegProperty< SireBase::PropPtr< SireBase::Property > > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::SegProperty< SireBase::PropPtr< SireBase::Property > >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::SegProperty< SireBase::PropPtr< SireBase::Property > >::merge ); + + SegPropertyProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::SegProperty< SireBase::PropPtr< SireBase::Property > >::nSegments diff --git a/wrapper/Mol/SegStringProperty.pypp.cpp b/wrapper/Mol/SegStringProperty.pypp.cpp index 0aa1fecec..a35b2152d 100644 --- a/wrapper/Mol/SegStringProperty.pypp.cpp +++ b/wrapper/Mol/SegStringProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_SegStringProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SegProperty< QString >::merge + + typedef SireMol::SegProperty< QString > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::SegProperty< QString >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::SegProperty< QString >::merge ); + + SegStringProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::SegProperty< QString >::nSegments diff --git a/wrapper/Mol/SegVariantProperty.pypp.cpp b/wrapper/Mol/SegVariantProperty.pypp.cpp index 7aad41a51..c710206af 100644 --- a/wrapper/Mol/SegVariantProperty.pypp.cpp +++ b/wrapper/Mol/SegVariantProperty.pypp.cpp @@ -226,6 +226,19 @@ void register_SegVariantProperty_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::SegProperty< QVariant >::merge + + typedef SireMol::SegProperty< QVariant > exported_class_t; + typedef ::SireBase::PropertyList ( ::SireMol::SegProperty< QVariant >::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::SegProperty< QVariant >::merge ); + + SegVariantProperty_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMol::SegProperty< QVariant >::nSegments diff --git a/wrapper/Mol/SireMol_properties.cpp b/wrapper/Mol/SireMol_properties.cpp index 55a7f93a7..1481c317f 100644 --- a/wrapper/Mol/SireMol_properties.cpp +++ b/wrapper/Mol/SireMol_properties.cpp @@ -77,6 +77,7 @@ #include "trajectoryaligner.h" #include #include "moleculeview.h" +#include "SireBase/console.h" #include "SireBase/errors.h" #include "SireError/errors.h" #include "SireStream/datastream.h" diff --git a/wrapper/Mol/SireMol_registrars.cpp b/wrapper/Mol/SireMol_registrars.cpp index 0792a37aa..77899909b 100644 --- a/wrapper/Mol/SireMol_registrars.cpp +++ b/wrapper/Mol/SireMol_registrars.cpp @@ -98,6 +98,7 @@ #include "hybridization.h" #include "atomeditor.h" #include "volumemap.h" +#include "atomidxmapping.h" #include "resname.h" #include "atompropertylist.h" #include "chaineditor.h" @@ -316,6 +317,8 @@ void register_SireMol_objects() ObjectRegistry::registerConverterFor< SireMol::AtomEditor >(); ObjectRegistry::registerConverterFor< SireMol::AtomStructureEditor >(); ObjectRegistry::registerConverterFor< SireMol::VolumeMap >(); + ObjectRegistry::registerConverterFor< SireMol::AtomIdxMappingEntry >(); + ObjectRegistry::registerConverterFor< SireMol::AtomIdxMapping >(); ObjectRegistry::registerConverterFor< SireMol::ResName >(); ObjectRegistry::registerConverterFor< SireMol::AtomPropertyList >(); ObjectRegistry::registerConverterFor< SireMol::AtomDoubleArrayProperty >(); diff --git a/wrapper/Mol/Trajectory.pypp.cpp b/wrapper/Mol/Trajectory.pypp.cpp index b34717614..3cfae3d2a 100644 --- a/wrapper/Mol/Trajectory.pypp.cpp +++ b/wrapper/Mol/Trajectory.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/generalunitproperty.h" #include "SireBase/lazyevaluator.h" @@ -185,6 +187,18 @@ void register_Trajectory_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::Trajectory::merge + + typedef ::SireBase::PropertyList ( ::SireMol::Trajectory::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::Trajectory::merge ); + + Trajectory_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMol::Trajectory::nAtoms diff --git a/wrapper/Mol/UserBeading.pypp.cpp b/wrapper/Mol/UserBeading.pypp.cpp index eb2c6f025..373e91219 100644 --- a/wrapper/Mol/UserBeading.pypp.cpp +++ b/wrapper/Mol/UserBeading.pypp.cpp @@ -8,6 +8,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/errors.h" #include "SireError/errors.h" diff --git a/wrapper/Mol/_Mol.main.cpp b/wrapper/Mol/_Mol.main.cpp index 346070212..9be6f2b36 100644 --- a/wrapper/Mol/_Mol.main.cpp +++ b/wrapper/Mol/_Mol.main.cpp @@ -53,6 +53,10 @@ #include "AtomIdx.pypp.hpp" +#include "AtomIdxMapping.pypp.hpp" + +#include "AtomIdxMappingEntry.pypp.hpp" + #include "AtomIdxMatcher.pypp.hpp" #include "AtomIntProperty.pypp.hpp" @@ -710,6 +714,10 @@ BOOST_PYTHON_MODULE(_Mol){ register_AtomIdx_class(); + register_AtomIdxMapping_class(); + + register_AtomIdxMappingEntry_class(); + register_AtomIdxMatcher_class(); register_AtomMCSMatcher_class(); diff --git a/wrapper/Mol/active_headers.h b/wrapper/Mol/active_headers.h index ff3789391..79a12c77f 100644 --- a/wrapper/Mol/active_headers.h +++ b/wrapper/Mol/active_headers.h @@ -17,6 +17,7 @@ #include "atomid.h" #include "atomidentifier.h" #include "atomidx.h" +#include "atomidxmapping.h" #include "atommapping.h" #include "atommasses.h" #include "atommatch.h" diff --git a/wrapper/Move/CMakeAutogenFile.txt b/wrapper/Move/CMakeAutogenFile.txt index 8f4afa1af..41147f875 100644 --- a/wrapper/Move/CMakeAutogenFile.txt +++ b/wrapper/Move/CMakeAutogenFile.txt @@ -1,84 +1,84 @@ # WARNING - AUTOGENERATED FILE - CONTENTS WILL BE OVERWRITTEN! set ( PYPP_SOURCES + SupraSubMoves.pypp.cpp + OpenMMFrEnergyST.pypp.cpp + SameMoves.pypp.cpp DLMRigidBody.pypp.cpp - DofID.pypp.cpp - Dynamics.pypp.cpp - Ensemble.pypp.cpp - Flexibility.pypp.cpp - GetCOGPoint.pypp.cpp + WeightedMoves.pypp.cpp + SameSupraSubMoves.pypp.cpp + ScaleVolumeFromCenter.pypp.cpp + Sampler.pypp.cpp + ZMatrix.pypp.cpp + VelocityGenerator.pypp.cpp + SimStore.pypp.cpp + MolDeleter.pypp.cpp + SupraSim.pypp.cpp + ZMatrixLine.pypp.cpp + NullDeleter.pypp.cpp + ZMatrixCoordsLine.pypp.cpp GetCOMPoint.pypp.cpp - GetCentroidPoint.pypp.cpp + TitrationMove.pypp.cpp + SupraMove.pypp.cpp + MolecularDynamics.pypp.cpp + Flexibility.pypp.cpp + Replicas.pypp.cpp + NullVolumeChanger.pypp.cpp GetPoint.pypp.cpp - HMCGenerator.pypp.cpp HMCVelGen.pypp.cpp - HybridMC.pypp.cpp - Integrator.pypp.cpp - InternalMove.pypp.cpp - InternalMoveSingle.pypp.cpp - MTSMC.pypp.cpp - MaxwellBoltzmann.pypp.cpp - MolDeleter.pypp.cpp - MolInserter.pypp.cpp - MolecularDynamics.pypp.cpp - MonteCarlo.pypp.cpp - Move.pypp.cpp + GetCOGPoint.pypp.cpp + ZMatMove.pypp.cpp + UniformInserter.pypp.cpp + VelocityVerlet.pypp.cpp + OpenMMPMEFEP.pypp.cpp Moves.pypp.cpp - NullDeleter.pypp.cpp - NullGetPoint.pypp.cpp - NullInserter.pypp.cpp + MaxwellBoltzmann.pypp.cpp + HybridMC.pypp.cpp + RBWorkspaceJM.pypp.cpp NullIntegrator.pypp.cpp - NullMove.pypp.cpp - NullSupraMove.pypp.cpp - NullSupraSubMove.pypp.cpp + SystemWideDeleter.pypp.cpp + SupraSimPacket.pypp.cpp NullVelocityGenerator.pypp.cpp - NullVolumeChanger.pypp.cpp - OpenMMFrEnergyDT.pypp.cpp - OpenMMFrEnergyST.pypp.cpp - OpenMMMDIntegrator.pypp.cpp - OpenMMPMEFEP.pypp.cpp - PrefSampler.pypp.cpp - RBWorkspaceJM.pypp.cpp + VolumeChanger.pypp.cpp RepExMove.pypp.cpp - RepExMove2.pypp.cpp + SupraSubMove.pypp.cpp + SupraSubSim.pypp.cpp + Titrator.pypp.cpp RepExSubMove.pypp.cpp - Replica.pypp.cpp - Replicas.pypp.cpp - RigidBodyMC.pypp.cpp - SameMoves.pypp.cpp + SupraMoves.pypp.cpp + OpenMMFrEnergyDT.pypp.cpp + NullSupraMove.pypp.cpp + Dynamics.pypp.cpp + MolInserter.pypp.cpp SameSupraMoves.pypp.cpp - SameSupraSubMoves.pypp.cpp - Sampler.pypp.cpp - ScaleVolumeFromCenter.pypp.cpp - SimPacket.pypp.cpp - SimStore.pypp.cpp - Simulation.pypp.cpp + PrefSampler.pypp.cpp + OpenMMMDIntegrator.pypp.cpp + HMCGenerator.pypp.cpp + VolumeMove.pypp.cpp + SupraSubSystem.pypp.cpp SpecifiedGroupsDeleter.pypp.cpp - SupraMove.pypp.cpp - SupraMoves.pypp.cpp - SupraSim.pypp.cpp - SupraSimPacket.pypp.cpp - SupraSubMove.pypp.cpp - SupraSubMoves.pypp.cpp - SupraSubSim.pypp.cpp + NullInserter.pypp.cpp + Integrator.pypp.cpp SupraSubSimPacket.pypp.cpp - SupraSubSystem.pypp.cpp - SupraSystem.pypp.cpp - SystemWideDeleter.pypp.cpp - TitrationMove.pypp.cpp - Titrator.pypp.cpp - UniformInserter.pypp.cpp - UniformSampler.pypp.cpp + RepExMove2.pypp.cpp + MonteCarlo.pypp.cpp + Simulation.pypp.cpp + NullGetPoint.pypp.cpp + RigidBodyMC.pypp.cpp + SimPacket.pypp.cpp + NullMove.pypp.cpp VelocitiesFromProperty.pypp.cpp - VelocityGenerator.pypp.cpp - VelocityVerlet.pypp.cpp - VolumeChanger.pypp.cpp - VolumeMove.pypp.cpp - WeightedMoves.pypp.cpp - ZMatMove.pypp.cpp - ZMatrix.pypp.cpp + DofID.pypp.cpp + UniformSampler.pypp.cpp + NullSupraSubMove.pypp.cpp + Ensemble.pypp.cpp + MTSMC.pypp.cpp + InternalMove.pypp.cpp + InternalMoveSingle.pypp.cpp + SupraSystem.pypp.cpp + Replica.pypp.cpp + GetCentroidPoint.pypp.cpp + Move.pypp.cpp ZMatrixCoords.pypp.cpp - ZMatrixCoordsLine.pypp.cpp - ZMatrixLine.pypp.cpp SireMove_containers.cpp SireMove_properties.cpp SireMove_registrars.cpp diff --git a/wrapper/Move/Flexibility.pypp.cpp b/wrapper/Move/Flexibility.pypp.cpp index 0bef087ac..89f4827c9 100644 --- a/wrapper/Move/Flexibility.pypp.cpp +++ b/wrapper/Move/Flexibility.pypp.cpp @@ -270,6 +270,18 @@ void register_Flexibility_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMove::Flexibility::merge + + typedef ::SireBase::PropertyList ( ::SireMove::Flexibility::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMove::Flexibility::merge ); + + Flexibility_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } Flexibility_exposer.def( bp::self != bp::self ); { //::SireMove::Flexibility::operator= diff --git a/wrapper/Move/SireMove_properties.cpp b/wrapper/Move/SireMove_properties.cpp index 69d3787c4..76008f006 100644 --- a/wrapper/Move/SireMove_properties.cpp +++ b/wrapper/Move/SireMove_properties.cpp @@ -4,31 +4,46 @@ #include "Base/convertproperty.hpp" #include "SireMove_properties.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "suprasubsystem.h" +#include "suprasubsystem.h" +#include "SireMol/molecule.h" +#include "SireMol/partialmolecule.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "SireSystem/system.h" +#include "sampler.h" +#include "uniformsampler.h" +#include "sampler.h" #include "SireError/errors.h" -#include "SireMaths/vector.h" -#include "SireMol/atom.h" -#include "SireMol/atomcoords.h" -#include "SireMol/evaluator.h" -#include "SireMol/moleculeview.h" -#include "SireMol/mover.hpp" -#include "SireMol/selector.hpp" #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" -#include "getpoint.h" -#include -#include "getpoint.h" -#include "SireCAS/symbol.h" -#include "SireFF/forcefields.h" -#include "SireFF/forcetable.h" -#include "SireMaths/rangenerator.h" -#include "SireMol/moleculegroup.h" -#include "SireMol/moleculeview.h" +#include "suprasubmoves.h" +#include "suprasubsystem.h" +#include "suprasubmoves.h" +#include "SireError/errors.h" +#include "SireID/index.h" #include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" #include "SireSystem/system.h" -#include "ensemble.h" -#include "integrator.h" -#include "integratorworkspace.h" -#include "integrator.h" +#include "SireSystem/systemmonitor.h" +#include "moves.h" +#include "simstore.h" +#include "suprasystem.h" +#include "suprasystem.h" +#include "SireError/errors.h" +#include "SireID/index.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "supramoves.h" +#include "suprasystem.h" +#include "supramoves.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "supramove.h" +#include "suprasystem.h" +#include "supramove.h" #include "SireMol/molecule.h" #include "SireMol/moleculegroup.h" #include "SireStream/datastream.h" @@ -50,6 +65,45 @@ #include "molinserter.h" #include "molinserter.h" #include "SireError/errors.h" +#include "SireMaths/vector.h" +#include "SireMol/atom.h" +#include "SireMol/atomcoords.h" +#include "SireMol/evaluator.h" +#include "SireMol/moleculeview.h" +#include "SireMol/mover.hpp" +#include "SireMol/selector.hpp" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "getpoint.h" +#include +#include "getpoint.h" +#include "SireCAS/symbol.h" +#include "SireMol/atomelements.h" +#include "SireMol/atommasses.h" +#include "SireMol/atomvelocities.h" +#include "SireMol/moleculedata.h" +#include "SireMol/moleculeinfodata.h" +#include "SireMol/moleculeview.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "SireUnits/dimensions.h" +#include "SireUnits/temperature.h" +#include "SireUnits/units.h" +#include "velocitygenerator.h" +#include "velocitygenerator.h" +#include "SireCAS/symbol.h" +#include "SireFF/forcefields.h" +#include "SireFF/forcetable.h" +#include "SireMaths/rangenerator.h" +#include "SireMol/moleculegroup.h" +#include "SireMol/moleculeview.h" +#include "SireStream/datastream.h" +#include "SireSystem/system.h" +#include "ensemble.h" +#include "integrator.h" +#include "integratorworkspace.h" +#include "integrator.h" +#include "SireError/errors.h" #include "SireMaths/rangenerator.h" #include "SireMol/core.h" #include "SireStream/datastream.h" @@ -61,6 +115,11 @@ #include "move.h" #include #include "move.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "suprasubmove.h" +#include "suprasubsystem.h" +#include "suprasubmove.h" #include "SireError/errors.h" #include "SireMaths/rangenerator.h" #include "SireStream/datastream.h" @@ -78,79 +137,20 @@ #include #include #include "moves.h" -#include "SireMol/molecule.h" -#include "SireMol/partialmolecule.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "SireSystem/system.h" -#include "sampler.h" -#include "uniformsampler.h" -#include "sampler.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "supramove.h" -#include "suprasystem.h" -#include "supramove.h" -#include "SireError/errors.h" -#include "SireID/index.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "supramoves.h" -#include "suprasystem.h" -#include "supramoves.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "suprasubmove.h" -#include "suprasubsystem.h" -#include "suprasubmove.h" -#include "SireError/errors.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "suprasubmoves.h" -#include "suprasubsystem.h" -#include "suprasubmoves.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "suprasubsystem.h" -#include "suprasubsystem.h" -#include "SireError/errors.h" -#include "SireID/index.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "SireSystem/system.h" -#include "SireSystem/systemmonitor.h" -#include "moves.h" -#include "simstore.h" -#include "suprasystem.h" -#include "suprasystem.h" -#include "SireCAS/symbol.h" -#include "SireMol/atomelements.h" -#include "SireMol/atommasses.h" -#include "SireMol/atomvelocities.h" -#include "SireMol/moleculedata.h" -#include "SireMol/moleculeinfodata.h" -#include "SireMol/moleculeview.h" -#include "SireStream/datastream.h" -#include "SireStream/shareddatastream.h" -#include "SireUnits/dimensions.h" -#include "SireUnits/temperature.h" -#include "SireUnits/units.h" -#include "velocitygenerator.h" -#include "velocitygenerator.h" void register_SireMove_properties() { - register_property_container< SireMove::GetPointPtr, SireMove::GetPoint >(); - register_property_container< SireMove::IntegratorPtr, SireMove::Integrator >(); - register_property_container< SireMove::MolDeleterPtr, SireMove::MolDeleter >(); - register_property_container< SireMove::MolInserterPtr, SireMove::MolInserter >(); - register_property_container< SireMove::MovePtr, SireMove::Move >(); - register_property_container< SireMove::MovesPtr, SireMove::Moves >(); + register_property_container< SireMove::SupraSubSystemPtr, SireMove::SupraSubSystem >(); register_property_container< SireMove::SamplerPtr, SireMove::Sampler >(); - register_property_container< SireMove::SupraMovePtr, SireMove::SupraMove >(); - register_property_container< SireMove::SupraMovesPtr, SireMove::SupraMoves >(); - register_property_container< SireMove::SupraSubMovePtr, SireMove::SupraSubMove >(); register_property_container< SireMove::SupraSubMovesPtr, SireMove::SupraSubMoves >(); - register_property_container< SireMove::SupraSubSystemPtr, SireMove::SupraSubSystem >(); register_property_container< SireMove::SupraSystemPtr, SireMove::SupraSystem >(); + register_property_container< SireMove::SupraMovesPtr, SireMove::SupraMoves >(); + register_property_container< SireMove::SupraMovePtr, SireMove::SupraMove >(); + register_property_container< SireMove::MolDeleterPtr, SireMove::MolDeleter >(); + register_property_container< SireMove::MolInserterPtr, SireMove::MolInserter >(); + register_property_container< SireMove::GetPointPtr, SireMove::GetPoint >(); register_property_container< SireMove::VelGenPtr, SireMove::VelocityGenerator >(); + register_property_container< SireMove::IntegratorPtr, SireMove::Integrator >(); + register_property_container< SireMove::MovePtr, SireMove::Move >(); + register_property_container< SireMove::SupraSubMovePtr, SireMove::SupraSubMove >(); + register_property_container< SireMove::MovesPtr, SireMove::Moves >(); } diff --git a/wrapper/Move/SireMove_registrars.cpp b/wrapper/Move/SireMove_registrars.cpp index 1734f7429..a1fcf7391 100644 --- a/wrapper/Move/SireMove_registrars.cpp +++ b/wrapper/Move/SireMove_registrars.cpp @@ -3,131 +3,129 @@ #include "SireMove_registrars.h" - - -#include "dlmrigidbody.h" -#include "ensemble.h" -#include "flexibility.h" -#include "getpoint.h" -#include "hybridmc.h" -#include "integrator.h" -#include "integratorworkspace.h" +#include "zmatrix.h" #include "integratorworkspacejm.h" #include "internalmove.h" +#include "simpacket.h" +#include "weightedmoves.h" +#include "openmmmdintegrator.h" +#include "zmatmove.h" +#include "replicas.h" +#include "mtsmc.h" +#include "uniformsampler.h" +#include "suprasubsystem.h" +#include "simstore.h" +#include "suprasubsimpacket.h" +#include "suprasubmoves.h" +#include "prefsampler.h" +#include "velocityverlet.h" +#include "openmmpmefep.h" +#include "suprasystem.h" +#include "rbworkspace.h" +#include "suprasimpacket.h" +#include "supramoves.h" +#include "volumemove.h" +#include "repexmove.h" +#include "supramove.h" #include "internalmovesingle.h" #include "moldeleter.h" +#include "repexmove2.h" #include "moleculardynamics.h" #include "molinserter.h" -#include "move.h" -#include "moves.h" -#include "mtsmc.h" -#include "openmmfrenergydt.h" +#include "dlmrigidbody.h" #include "openmmfrenergyst.h" -#include "openmmmdintegrator.h" -#include "openmmpmefep.h" -#include "prefsampler.h" -#include "rbworkspace.h" +#include "integratorworkspace.h" #include "rbworkspacejm.h" -#include "repexmove.h" -#include "repexmove2.h" +#include "getpoint.h" +#include "velocitygenerator.h" +#include "volumechanger.h" +#include "flexibility.h" +#include "integrator.h" +#include "titrator.h" +#include "move.h" #include "replica.h" -#include "replicas.h" +#include "hybridmc.h" #include "rigidbodymc.h" -#include "simpacket.h" -#include "simstore.h" -#include "supramove.h" -#include "supramoves.h" -#include "suprasimpacket.h" -#include "suprasubmove.h" -#include "suprasubmoves.h" -#include "suprasubsimpacket.h" -#include "suprasubsystem.h" -#include "suprasystem.h" +#include "ensemble.h" #include "titrationmove.h" -#include "titrator.h" -#include "uniformsampler.h" -#include "velocitygenerator.h" -#include "velocityverlet.h" -#include "volumechanger.h" -#include "volumemove.h" -#include "weightedmoves.h" -#include "zmatmove.h" -#include "zmatrix.h" +#include "openmmfrenergydt.h" +#include "suprasubmove.h" +#include "moves.h" #include "Helpers/objectregistry.hpp" void register_SireMove_objects() { - ObjectRegistry::registerConverterFor< SireMove::DLMRigidBody >(); - ObjectRegistry::registerConverterFor< SireMove::Ensemble >(); - ObjectRegistry::registerConverterFor< SireMove::DofID >(); - ObjectRegistry::registerConverterFor< SireMove::Flexibility >(); - ObjectRegistry::registerConverterFor< SireMove::NullGetPoint >(); - ObjectRegistry::registerConverterFor< SireMove::GetCOMPoint >(); - ObjectRegistry::registerConverterFor< SireMove::GetCOGPoint >(); - ObjectRegistry::registerConverterFor< SireMove::GetCentroidPoint >(); - ObjectRegistry::registerConverterFor< SireMove::HybridMC >(); - ObjectRegistry::registerConverterFor< SireMove::HMCGenerator >(); - ObjectRegistry::registerConverterFor< SireMove::NullIntegrator >(); - ObjectRegistry::registerConverterFor< SireMove::NullIntegratorWorkspace >(); - ObjectRegistry::registerConverterFor< SireMove::AtomicVelocityWorkspace >(); + ObjectRegistry::registerConverterFor< SireMove::ZMatrix >(); + ObjectRegistry::registerConverterFor< SireMove::ZMatrixLine >(); + ObjectRegistry::registerConverterFor< SireMove::ZMatrixCoords >(); + ObjectRegistry::registerConverterFor< SireMove::ZMatrixCoordsLine >(); ObjectRegistry::registerConverterFor< SireMove::NullIntegratorWorkspaceJM >(); ObjectRegistry::registerConverterFor< SireMove::AtomicVelocityWorkspaceJM >(); ObjectRegistry::registerConverterFor< SireMove::InternalMove >(); + ObjectRegistry::registerConverterFor< SireMove::SimPacket >(); + ObjectRegistry::registerConverterFor< SireMove::WeightedMoves >(); + ObjectRegistry::registerConverterFor< SireMove::OpenMMMDIntegrator >(); + ObjectRegistry::registerConverterFor< SireMove::OpenMMMDIntegrator >(); + ObjectRegistry::registerConverterFor< SireMove::ZMatMove >(); + ObjectRegistry::registerConverterFor< SireMove::Replicas >(); + ObjectRegistry::registerConverterFor< SireMove::MTSMC >(); + ObjectRegistry::registerConverterFor< SireMove::UniformSampler >(); + ObjectRegistry::registerConverterFor< SireMove::SupraSubSystem >(); + ObjectRegistry::registerConverterFor< SireMove::SimStore >(); + ObjectRegistry::registerConverterFor< SireMove::SupraSubSimPacket >(); + ObjectRegistry::registerConverterFor< SireMove::SameSupraSubMoves >(); + ObjectRegistry::registerConverterFor< SireMove::PrefSampler >(); + ObjectRegistry::registerConverterFor< SireMove::VelocityVerlet >(); + ObjectRegistry::registerConverterFor< SireMove::OpenMMPMEFEP >(); + ObjectRegistry::registerConverterFor< SireMove::OpenMMPMEFEP >(); + ObjectRegistry::registerConverterFor< SireMove::SupraSystem >(); + ObjectRegistry::registerConverterFor< SireMove::RBWorkspace >(); + ObjectRegistry::registerConverterFor< SireMove::SupraSimPacket >(); + ObjectRegistry::registerConverterFor< SireMove::SameSupraMoves >(); + ObjectRegistry::registerConverterFor< SireMove::VolumeMove >(); + ObjectRegistry::registerConverterFor< SireMove::RepExMove >(); + ObjectRegistry::registerConverterFor< SireMove::RepExSubMove >(); + ObjectRegistry::registerConverterFor< SireMove::NullSupraMove >(); ObjectRegistry::registerConverterFor< SireMove::InternalMoveSingle >(); ObjectRegistry::registerConverterFor< SireMove::NullDeleter >(); ObjectRegistry::registerConverterFor< SireMove::SpecifiedGroupsDeleter >(); ObjectRegistry::registerConverterFor< SireMove::SystemWideDeleter >(); + ObjectRegistry::registerConverterFor< SireMove::RepExMove2 >(); ObjectRegistry::registerConverterFor< SireMove::MolecularDynamics >(); ObjectRegistry::registerConverterFor< SireMove::NullInserter >(); ObjectRegistry::registerConverterFor< SireMove::UniformInserter >(); - ObjectRegistry::registerConverterFor< SireMove::NullMove >(); - ObjectRegistry::registerConverterFor< SireMove::SameMoves >(); - ObjectRegistry::registerConverterFor< SireMove::MTSMC >(); - ObjectRegistry::registerConverterFor< SireMove::OpenMMFrEnergyDT >(); - ObjectRegistry::registerConverterFor< SireMove::OpenMMFrEnergyDT >(); + ObjectRegistry::registerConverterFor< SireMove::DLMRigidBody >(); ObjectRegistry::registerConverterFor< SireMove::OpenMMFrEnergyST >(); ObjectRegistry::registerConverterFor< SireMove::OpenMMFrEnergyST >(); - ObjectRegistry::registerConverterFor< SireMove::OpenMMMDIntegrator >(); - ObjectRegistry::registerConverterFor< SireMove::OpenMMMDIntegrator >(); - ObjectRegistry::registerConverterFor< SireMove::OpenMMPMEFEP >(); - ObjectRegistry::registerConverterFor< SireMove::OpenMMPMEFEP >(); - ObjectRegistry::registerConverterFor< SireMove::PrefSampler >(); - ObjectRegistry::registerConverterFor< SireMove::RBWorkspace >(); + ObjectRegistry::registerConverterFor< SireMove::NullIntegratorWorkspace >(); + ObjectRegistry::registerConverterFor< SireMove::AtomicVelocityWorkspace >(); ObjectRegistry::registerConverterFor< SireMove::RBWorkspaceJM >(); - ObjectRegistry::registerConverterFor< SireMove::RepExMove >(); - ObjectRegistry::registerConverterFor< SireMove::RepExSubMove >(); - ObjectRegistry::registerConverterFor< SireMove::RepExMove2 >(); - ObjectRegistry::registerConverterFor< SireMove::Replica >(); - ObjectRegistry::registerConverterFor< SireMove::Replicas >(); - ObjectRegistry::registerConverterFor< SireMove::RigidBodyMC >(); - ObjectRegistry::registerConverterFor< SireMove::SimPacket >(); - ObjectRegistry::registerConverterFor< SireMove::SimStore >(); - ObjectRegistry::registerConverterFor< SireMove::NullSupraMove >(); - ObjectRegistry::registerConverterFor< SireMove::SameSupraMoves >(); - ObjectRegistry::registerConverterFor< SireMove::SupraSimPacket >(); - ObjectRegistry::registerConverterFor< SireMove::NullSupraSubMove >(); - ObjectRegistry::registerConverterFor< SireMove::SameSupraSubMoves >(); - ObjectRegistry::registerConverterFor< SireMove::SupraSubSimPacket >(); - ObjectRegistry::registerConverterFor< SireMove::SupraSubSystem >(); - ObjectRegistry::registerConverterFor< SireMove::SupraSystem >(); - ObjectRegistry::registerConverterFor< SireMove::TitrationMove >(); - ObjectRegistry::registerConverterFor< SireMove::Titrator >(); - ObjectRegistry::registerConverterFor< SireMove::UniformSampler >(); + ObjectRegistry::registerConverterFor< SireMove::NullGetPoint >(); + ObjectRegistry::registerConverterFor< SireMove::GetCOMPoint >(); + ObjectRegistry::registerConverterFor< SireMove::GetCOGPoint >(); + ObjectRegistry::registerConverterFor< SireMove::GetCentroidPoint >(); ObjectRegistry::registerConverterFor< SireMove::NullVelocityGenerator >(); ObjectRegistry::registerConverterFor< SireMove::VelocitiesFromProperty >(); ObjectRegistry::registerConverterFor< SireMove::MaxwellBoltzmann >(); - ObjectRegistry::registerConverterFor< SireMove::VelocityVerlet >(); ObjectRegistry::registerConverterFor< SireMove::NullVolumeChanger >(); ObjectRegistry::registerConverterFor< SireMove::ScaleVolumeFromCenter >(); - ObjectRegistry::registerConverterFor< SireMove::VolumeMove >(); - ObjectRegistry::registerConverterFor< SireMove::WeightedMoves >(); - ObjectRegistry::registerConverterFor< SireMove::ZMatMove >(); - ObjectRegistry::registerConverterFor< SireMove::ZMatrix >(); - ObjectRegistry::registerConverterFor< SireMove::ZMatrixLine >(); - ObjectRegistry::registerConverterFor< SireMove::ZMatrixCoords >(); - ObjectRegistry::registerConverterFor< SireMove::ZMatrixCoordsLine >(); + ObjectRegistry::registerConverterFor< SireMove::DofID >(); + ObjectRegistry::registerConverterFor< SireMove::Flexibility >(); + ObjectRegistry::registerConverterFor< SireMove::NullIntegrator >(); + ObjectRegistry::registerConverterFor< SireMove::Titrator >(); + ObjectRegistry::registerConverterFor< SireMove::NullMove >(); + ObjectRegistry::registerConverterFor< SireMove::Replica >(); + ObjectRegistry::registerConverterFor< SireMove::HybridMC >(); + ObjectRegistry::registerConverterFor< SireMove::HMCGenerator >(); + ObjectRegistry::registerConverterFor< SireMove::RigidBodyMC >(); + ObjectRegistry::registerConverterFor< SireMove::Ensemble >(); + ObjectRegistry::registerConverterFor< SireMove::TitrationMove >(); + ObjectRegistry::registerConverterFor< SireMove::OpenMMFrEnergyDT >(); + ObjectRegistry::registerConverterFor< SireMove::OpenMMFrEnergyDT >(); + ObjectRegistry::registerConverterFor< SireMove::NullSupraSubMove >(); + ObjectRegistry::registerConverterFor< SireMove::SameMoves >(); } diff --git a/wrapper/Move/ZMatrix.pypp.cpp b/wrapper/Move/ZMatrix.pypp.cpp index b9dc4d77b..30c44ca72 100644 --- a/wrapper/Move/ZMatrix.pypp.cpp +++ b/wrapper/Move/ZMatrix.pypp.cpp @@ -488,6 +488,18 @@ void register_ZMatrix_class(){ , bp::release_gil_policy() , "Return a z-matrix that only contains lines that involve the atoms\nthat are in selection" ); + } + { //::SireMove::ZMatrix::merge + + typedef ::SireBase::PropertyList ( ::SireMove::ZMatrix::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMove::ZMatrix::merge ); + + ZMatrix_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMove::ZMatrix::nLines diff --git a/wrapper/Move/ZMatrixCoords.pypp.cpp b/wrapper/Move/ZMatrixCoords.pypp.cpp index 0ea9229a7..1478e4b07 100644 --- a/wrapper/Move/ZMatrixCoords.pypp.cpp +++ b/wrapper/Move/ZMatrixCoords.pypp.cpp @@ -607,6 +607,18 @@ void register_ZMatrixCoords_class(){ , bp::release_gil_policy() , "Return a z-matrix that only contains lines that involve the atoms\nthat are in selection" ); + } + { //::SireMove::ZMatrixCoords::merge + + typedef ::SireBase::PropertyList ( ::SireMove::ZMatrixCoords::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMove::ZMatrixCoords::merge ); + + ZMatrixCoords_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMove::ZMatrixCoords::move From e6a322317787a330a843e699e654e81919c83650 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 28 Feb 2024 17:56:36 +0000 Subject: [PATCH 135/468] Finished filling in null merge functions for the MolViewProperty classes, and have now added all of the python wrappers. This all compiles, links and passes unit tests. Next step is to actually write the underlying merge code... --- corelib/src/libs/SireMol/amberparameters.cpp | 1 + corelib/src/libs/SireMol/amberparameters.h | 1 + corelib/src/libs/SireMol/atomselection.cpp | 2 +- corelib/src/libs/SireMol/connectivity.cpp | 1 + corelib/src/libs/SireMol/molviewproperty.cpp | 1 + corelib/src/libs/SireMol/trajectory.cpp | 1 + corelib/src/libs/SireMol/trajectory.h | 1 + corelib/src/libs/SireMove/flexibility.cpp | 1 + corelib/src/libs/SireMove/flexibility.h | 1 + wrapper/Mol/AmberParameters.pypp.cpp | 2 + wrapper/Mol/Atom.pypp.cpp | 4 +- wrapper/Mol/AtomBeads.pypp.cpp | 2 + wrapper/Mol/AtomCharges.pypp.cpp | 2 + wrapper/Mol/AtomChiralities.pypp.cpp | 2 + wrapper/Mol/AtomCoords.pypp.cpp | 2 + wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp | 2 + wrapper/Mol/AtomEditorBase.pypp.cpp | 4 +- wrapper/Mol/AtomElements.pypp.cpp | 2 + wrapper/Mol/AtomEnergies.pypp.cpp | 2 + wrapper/Mol/AtomFloatProperty.pypp.cpp | 2 + wrapper/Mol/AtomForces.pypp.cpp | 2 + wrapper/Mol/AtomHybridizations.pypp.cpp | 2 + wrapper/Mol/AtomIntProperty.pypp.cpp | 2 + wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp | 2 + wrapper/Mol/AtomMasses.pypp.cpp | 2 + wrapper/Mol/AtomPolarisabilities.pypp.cpp | 2 + wrapper/Mol/AtomPropertyList.pypp.cpp | 2 + wrapper/Mol/AtomPropertyProperty.pypp.cpp | 2 + wrapper/Mol/AtomRadicals.pypp.cpp | 2 + wrapper/Mol/AtomRadii.pypp.cpp | 2 + wrapper/Mol/AtomSelection.pypp.cpp | 2 + wrapper/Mol/AtomStringArrayProperty.pypp.cpp | 2 + wrapper/Mol/AtomStringProperty.pypp.cpp | 2 + wrapper/Mol/AtomVariantProperty.pypp.cpp | 2 + wrapper/Mol/AtomVelocities.pypp.cpp | 2 + wrapper/Mol/BeadFloatProperty.pypp.cpp | 2 + wrapper/Mol/BeadIntProperty.pypp.cpp | 2 + wrapper/Mol/BeadPropertyProperty.pypp.cpp | 2 + wrapper/Mol/BeadStringProperty.pypp.cpp | 2 + wrapper/Mol/BeadVariantProperty.pypp.cpp | 2 + wrapper/Mol/CGFloatProperty.pypp.cpp | 2 + wrapper/Mol/CGIntProperty.pypp.cpp | 2 + wrapper/Mol/CGPropertyProperty.pypp.cpp | 2 + wrapper/Mol/CGStringProperty.pypp.cpp | 2 + wrapper/Mol/CGVariantProperty.pypp.cpp | 2 + wrapper/Mol/ChainFloatProperty.pypp.cpp | 2 + wrapper/Mol/ChainIntProperty.pypp.cpp | 2 + wrapper/Mol/ChainPropertyProperty.pypp.cpp | 2 + wrapper/Mol/ChainStringProperty.pypp.cpp | 2 + wrapper/Mol/ChainVariantProperty.pypp.cpp | 2 + wrapper/Mol/Connectivity.pypp.cpp | 116 +- wrapper/Mol/ConnectivityBase.pypp.cpp | 1890 ++++++----------- wrapper/Mol/ConnectivityEditor.pypp.cpp | 466 ++-- wrapper/Mol/Frame.pypp.cpp | 2 + wrapper/Mol/MolViewProperty.pypp.cpp | 2 + wrapper/Mol/MoleculeProperty.pypp.cpp | 2 + wrapper/Mol/ResFloatProperty.pypp.cpp | 2 + wrapper/Mol/ResIntProperty.pypp.cpp | 2 + wrapper/Mol/ResPropertyProperty.pypp.cpp | 2 + wrapper/Mol/ResStringProperty.pypp.cpp | 2 + wrapper/Mol/ResVariantProperty.pypp.cpp | 2 + wrapper/Mol/SegFloatProperty.pypp.cpp | 2 + wrapper/Mol/SegIntProperty.pypp.cpp | 2 + wrapper/Mol/SegPropertyProperty.pypp.cpp | 2 + wrapper/Mol/SegStringProperty.pypp.cpp | 2 + wrapper/Mol/SegVariantProperty.pypp.cpp | 2 + wrapper/Mol/Trajectory.pypp.cpp | 2 + wrapper/Mol/special_code.py | 1 + .../System/_System_free_functions.pypp.cpp | 12 +- 69 files changed, 1029 insertions(+), 1580 deletions(-) diff --git a/corelib/src/libs/SireMol/amberparameters.cpp b/corelib/src/libs/SireMol/amberparameters.cpp index c10c52511..6e112227d 100644 --- a/corelib/src/libs/SireMol/amberparameters.cpp +++ b/corelib/src/libs/SireMol/amberparameters.cpp @@ -34,6 +34,7 @@ #include "SireMol/improperid.h" #include "SireMol/molecule.h" #include "SireMol/partialmolecule.h" +#include "SireMol/atomidxmapping.h" #include "SireError/errors.h" diff --git a/corelib/src/libs/SireMol/amberparameters.h b/corelib/src/libs/SireMol/amberparameters.h index 272b86fd0..89fe20c53 100644 --- a/corelib/src/libs/SireMol/amberparameters.h +++ b/corelib/src/libs/SireMol/amberparameters.h @@ -39,6 +39,7 @@ #include "SireMol/molviewproperty.h" #include "SireMol/mover.hpp" #include "SireMol/partialmolecule.h" +#include "SireMol/atomidxmapping.h" SIRE_BEGIN_HEADER diff --git a/corelib/src/libs/SireMol/atomselection.cpp b/corelib/src/libs/SireMol/atomselection.cpp index 647f8f5ea..c0c81ecc1 100644 --- a/corelib/src/libs/SireMol/atomselection.cpp +++ b/corelib/src/libs/SireMol/atomselection.cpp @@ -28,7 +28,7 @@ #include "atomselection.h" #include "moleculedata.h" #include "moleculeview.h" - +#include "atomidxmapping.h" #include "moleculeinfodata.h" #include "SireError/errors.h" diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 2a9ea2416..9fbc04a06 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -37,6 +37,7 @@ #include "moleculeinfo.h" #include "moleculeinfodata.h" #include "moleculeview.h" +#include "atomidxmapping.h" #include "angleid.h" #include "bondid.h" diff --git a/corelib/src/libs/SireMol/molviewproperty.cpp b/corelib/src/libs/SireMol/molviewproperty.cpp index d6ddc7214..6be688a0d 100644 --- a/corelib/src/libs/SireMol/molviewproperty.cpp +++ b/corelib/src/libs/SireMol/molviewproperty.cpp @@ -29,6 +29,7 @@ #include "atommatcher.h" #include "atommatchers.h" #include "moleculeinfodata.h" +#include "atomidxmapping.h" #include "mover.hpp" diff --git a/corelib/src/libs/SireMol/trajectory.cpp b/corelib/src/libs/SireMol/trajectory.cpp index ab760a768..c2728c59f 100644 --- a/corelib/src/libs/SireMol/trajectory.cpp +++ b/corelib/src/libs/SireMol/trajectory.cpp @@ -27,6 +27,7 @@ #include "trajectory.h" #include "trajectoryaligner.h" +#include "atomidxmapping.h" #include "SireID/index.h" diff --git a/corelib/src/libs/SireMol/trajectory.h b/corelib/src/libs/SireMol/trajectory.h index bd22823b1..c5172d2a9 100644 --- a/corelib/src/libs/SireMol/trajectory.h +++ b/corelib/src/libs/SireMol/trajectory.h @@ -32,6 +32,7 @@ #include "SireMol/atomforces.h" #include "SireMol/atomvelocities.h" #include "SireMol/molviewproperty.h" +#include "SireMol/atomidxmapping.h" #include "SireVol/space.h" diff --git a/corelib/src/libs/SireMove/flexibility.cpp b/corelib/src/libs/SireMove/flexibility.cpp index ae4301822..67a109abe 100644 --- a/corelib/src/libs/SireMove/flexibility.cpp +++ b/corelib/src/libs/SireMove/flexibility.cpp @@ -36,6 +36,7 @@ #include "SireMol/molecule.h" #include "SireMol/mover.hpp" #include "SireMol/partialmolecule.h" +#include "SireMol/atomidxmapping.h" #include "SireUnits/convert.h" #include "SireUnits/units.h" diff --git a/corelib/src/libs/SireMove/flexibility.h b/corelib/src/libs/SireMove/flexibility.h index abe6a9d4e..06f617a01 100644 --- a/corelib/src/libs/SireMove/flexibility.h +++ b/corelib/src/libs/SireMove/flexibility.h @@ -34,6 +34,7 @@ #include "SireMol/atomidx.h" #include "SireMol/molviewproperty.h" #include "SireMol/mover.hpp" +#include "SireMol/atomidxmapping.h" #include "SireUnits/units.h" diff --git a/wrapper/Mol/AmberParameters.pypp.cpp b/wrapper/Mol/AmberParameters.pypp.cpp index 23ccac952..f3c859120 100644 --- a/wrapper/Mol/AmberParameters.pypp.cpp +++ b/wrapper/Mol/AmberParameters.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; #include "SireMol/atomidx.h" +#include "SireMol/atomidxmapping.h" + #include "SireMol/bondid.h" #include "SireMol/dihedralid.h" diff --git a/wrapper/Mol/Atom.pypp.cpp b/wrapper/Mol/Atom.pypp.cpp index 9ba282e34..8e8487bde 100644 --- a/wrapper/Mol/Atom.pypp.cpp +++ b/wrapper/Mol/Atom.pypp.cpp @@ -50,6 +50,8 @@ namespace bp = boost::python; #include "SireBase/incremint.h" +#include "SireBase/propertylist.h" + #include "SireBase/quickcopy.hpp" #include "SireStream/datastream.h" @@ -104,8 +106,6 @@ namespace bp = boost::python; #include "atomradii.h" -#include "SireBase/propertylist.h" - #include "SireMaths/vector.h" #include "atomproperty.hpp" diff --git a/wrapper/Mol/AtomBeads.pypp.cpp b/wrapper/Mol/AtomBeads.pypp.cpp index 7c26a2da4..dbf52bdbd 100644 --- a/wrapper/Mol/AtomBeads.pypp.cpp +++ b/wrapper/Mol/AtomBeads.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomCharges.pypp.cpp b/wrapper/Mol/AtomCharges.pypp.cpp index 40068d67c..cbf972a50 100644 --- a/wrapper/Mol/AtomCharges.pypp.cpp +++ b/wrapper/Mol/AtomCharges.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomChiralities.pypp.cpp b/wrapper/Mol/AtomChiralities.pypp.cpp index 5d5062c43..40993f820 100644 --- a/wrapper/Mol/AtomChiralities.pypp.cpp +++ b/wrapper/Mol/AtomChiralities.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomCoords.pypp.cpp b/wrapper/Mol/AtomCoords.pypp.cpp index 48958719e..b06a0f95b 100644 --- a/wrapper/Mol/AtomCoords.pypp.cpp +++ b/wrapper/Mol/AtomCoords.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + #include "SireMaths/quaternion.h" #include "SireMaths/matrix.h" diff --git a/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp b/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp index 0ec36be59..7c896d51a 100644 --- a/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp +++ b/wrapper/Mol/AtomDoubleArrayProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomEditorBase.pypp.cpp b/wrapper/Mol/AtomEditorBase.pypp.cpp index a62d338c5..368ad6063 100644 --- a/wrapper/Mol/AtomEditorBase.pypp.cpp +++ b/wrapper/Mol/AtomEditorBase.pypp.cpp @@ -51,6 +51,8 @@ namespace bp = boost::python; #include "SireBase/incremint.h" +#include "SireBase/propertylist.h" + #include "SireBase/quickcopy.hpp" #include "SireStream/datastream.h" @@ -105,8 +107,6 @@ namespace bp = boost::python; #include "atomradii.h" -#include "SireBase/propertylist.h" - #include "SireMaths/vector.h" #include "atomproperty.hpp" diff --git a/wrapper/Mol/AtomElements.pypp.cpp b/wrapper/Mol/AtomElements.pypp.cpp index 5757d158b..cc4258d9b 100644 --- a/wrapper/Mol/AtomElements.pypp.cpp +++ b/wrapper/Mol/AtomElements.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomEnergies.pypp.cpp b/wrapper/Mol/AtomEnergies.pypp.cpp index c20e5154e..08738545f 100644 --- a/wrapper/Mol/AtomEnergies.pypp.cpp +++ b/wrapper/Mol/AtomEnergies.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomFloatProperty.pypp.cpp b/wrapper/Mol/AtomFloatProperty.pypp.cpp index c0f8a1d5c..1c223ce55 100644 --- a/wrapper/Mol/AtomFloatProperty.pypp.cpp +++ b/wrapper/Mol/AtomFloatProperty.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomForces.pypp.cpp b/wrapper/Mol/AtomForces.pypp.cpp index eca661d83..24f517c86 100644 --- a/wrapper/Mol/AtomForces.pypp.cpp +++ b/wrapper/Mol/AtomForces.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomHybridizations.pypp.cpp b/wrapper/Mol/AtomHybridizations.pypp.cpp index 27b248c36..d4b5b7710 100644 --- a/wrapper/Mol/AtomHybridizations.pypp.cpp +++ b/wrapper/Mol/AtomHybridizations.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomIntProperty.pypp.cpp b/wrapper/Mol/AtomIntProperty.pypp.cpp index 7062a1960..ad28a47cd 100644 --- a/wrapper/Mol/AtomIntProperty.pypp.cpp +++ b/wrapper/Mol/AtomIntProperty.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp b/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp index a3d033372..25149c5e2 100644 --- a/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp +++ b/wrapper/Mol/AtomIntegerArrayProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomMasses.pypp.cpp b/wrapper/Mol/AtomMasses.pypp.cpp index 98d183dc1..72765da79 100644 --- a/wrapper/Mol/AtomMasses.pypp.cpp +++ b/wrapper/Mol/AtomMasses.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomPolarisabilities.pypp.cpp b/wrapper/Mol/AtomPolarisabilities.pypp.cpp index 14cb5559d..d635fc133 100644 --- a/wrapper/Mol/AtomPolarisabilities.pypp.cpp +++ b/wrapper/Mol/AtomPolarisabilities.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomPropertyList.pypp.cpp b/wrapper/Mol/AtomPropertyList.pypp.cpp index 8834a9a53..5327e311b 100644 --- a/wrapper/Mol/AtomPropertyList.pypp.cpp +++ b/wrapper/Mol/AtomPropertyList.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomPropertyProperty.pypp.cpp b/wrapper/Mol/AtomPropertyProperty.pypp.cpp index cd0a88f8f..b4620dac4 100644 --- a/wrapper/Mol/AtomPropertyProperty.pypp.cpp +++ b/wrapper/Mol/AtomPropertyProperty.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomRadicals.pypp.cpp b/wrapper/Mol/AtomRadicals.pypp.cpp index 33d262cf5..afce09e6b 100644 --- a/wrapper/Mol/AtomRadicals.pypp.cpp +++ b/wrapper/Mol/AtomRadicals.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomRadii.pypp.cpp b/wrapper/Mol/AtomRadii.pypp.cpp index d41f4a9c5..0e4519b79 100644 --- a/wrapper/Mol/AtomRadii.pypp.cpp +++ b/wrapper/Mol/AtomRadii.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomSelection.pypp.cpp b/wrapper/Mol/AtomSelection.pypp.cpp index 9bac30abe..f726b517c 100644 --- a/wrapper/Mol/AtomSelection.pypp.cpp +++ b/wrapper/Mol/AtomSelection.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireStream/shareddatastream.h" +#include "atomidxmapping.h" + #include "atomselection.h" #include "moleculedata.h" diff --git a/wrapper/Mol/AtomStringArrayProperty.pypp.cpp b/wrapper/Mol/AtomStringArrayProperty.pypp.cpp index 6825c389e..fa0f142d0 100644 --- a/wrapper/Mol/AtomStringArrayProperty.pypp.cpp +++ b/wrapper/Mol/AtomStringArrayProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomStringProperty.pypp.cpp b/wrapper/Mol/AtomStringProperty.pypp.cpp index 0a46109bd..a14191a9a 100644 --- a/wrapper/Mol/AtomStringProperty.pypp.cpp +++ b/wrapper/Mol/AtomStringProperty.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomVariantProperty.pypp.cpp b/wrapper/Mol/AtomVariantProperty.pypp.cpp index 8958024a5..d7bb721c3 100644 --- a/wrapper/Mol/AtomVariantProperty.pypp.cpp +++ b/wrapper/Mol/AtomVariantProperty.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/AtomVelocities.pypp.cpp b/wrapper/Mol/AtomVelocities.pypp.cpp index ff7f9bbab..d367098bf 100644 --- a/wrapper/Mol/AtomVelocities.pypp.cpp +++ b/wrapper/Mol/AtomVelocities.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::AtomProperty > __copy__(const SireMol::AtomProperty > &other){ return SireMol::AtomProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/BeadFloatProperty.pypp.cpp b/wrapper/Mol/BeadFloatProperty.pypp.cpp index 85d74c1ed..4d643353e 100644 --- a/wrapper/Mol/BeadFloatProperty.pypp.cpp +++ b/wrapper/Mol/BeadFloatProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::BeadProperty __copy__(const SireMol::BeadProperty &other){ return SireMol::BeadProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/BeadIntProperty.pypp.cpp b/wrapper/Mol/BeadIntProperty.pypp.cpp index ea0910bac..be6a0d3c8 100644 --- a/wrapper/Mol/BeadIntProperty.pypp.cpp +++ b/wrapper/Mol/BeadIntProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::BeadProperty __copy__(const SireMol::BeadProperty &other){ return SireMol::BeadProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/BeadPropertyProperty.pypp.cpp b/wrapper/Mol/BeadPropertyProperty.pypp.cpp index baf24dddb..17b02ae8b 100644 --- a/wrapper/Mol/BeadPropertyProperty.pypp.cpp +++ b/wrapper/Mol/BeadPropertyProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::BeadProperty > __copy__(const SireMol::BeadProperty > &other){ return SireMol::BeadProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/BeadStringProperty.pypp.cpp b/wrapper/Mol/BeadStringProperty.pypp.cpp index 276484d39..1cce2d11c 100644 --- a/wrapper/Mol/BeadStringProperty.pypp.cpp +++ b/wrapper/Mol/BeadStringProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::BeadProperty __copy__(const SireMol::BeadProperty &other){ return SireMol::BeadProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/BeadVariantProperty.pypp.cpp b/wrapper/Mol/BeadVariantProperty.pypp.cpp index a7b3526cf..fc66d9610 100644 --- a/wrapper/Mol/BeadVariantProperty.pypp.cpp +++ b/wrapper/Mol/BeadVariantProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::BeadProperty __copy__(const SireMol::BeadProperty &other){ return SireMol::BeadProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/CGFloatProperty.pypp.cpp b/wrapper/Mol/CGFloatProperty.pypp.cpp index 8ba3c9728..d711bc735 100644 --- a/wrapper/Mol/CGFloatProperty.pypp.cpp +++ b/wrapper/Mol/CGFloatProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::CGProperty __copy__(const SireMol::CGProperty &other){ return SireMol::CGProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/CGIntProperty.pypp.cpp b/wrapper/Mol/CGIntProperty.pypp.cpp index f8e268c11..b668c6da6 100644 --- a/wrapper/Mol/CGIntProperty.pypp.cpp +++ b/wrapper/Mol/CGIntProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::CGProperty __copy__(const SireMol::CGProperty &other){ return SireMol::CGProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/CGPropertyProperty.pypp.cpp b/wrapper/Mol/CGPropertyProperty.pypp.cpp index 959d9022d..0df839d3f 100644 --- a/wrapper/Mol/CGPropertyProperty.pypp.cpp +++ b/wrapper/Mol/CGPropertyProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::CGProperty > __copy__(const SireMol::CGProperty > &other){ return SireMol::CGProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/CGStringProperty.pypp.cpp b/wrapper/Mol/CGStringProperty.pypp.cpp index 92263e6c5..e635add52 100644 --- a/wrapper/Mol/CGStringProperty.pypp.cpp +++ b/wrapper/Mol/CGStringProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::CGProperty __copy__(const SireMol::CGProperty &other){ return SireMol::CGProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/CGVariantProperty.pypp.cpp b/wrapper/Mol/CGVariantProperty.pypp.cpp index dbb8f9b08..fa9585b4b 100644 --- a/wrapper/Mol/CGVariantProperty.pypp.cpp +++ b/wrapper/Mol/CGVariantProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::CGProperty __copy__(const SireMol::CGProperty &other){ return SireMol::CGProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ChainFloatProperty.pypp.cpp b/wrapper/Mol/ChainFloatProperty.pypp.cpp index 85f06f465..28d406758 100644 --- a/wrapper/Mol/ChainFloatProperty.pypp.cpp +++ b/wrapper/Mol/ChainFloatProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ChainProperty __copy__(const SireMol::ChainProperty &other){ return SireMol::ChainProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ChainIntProperty.pypp.cpp b/wrapper/Mol/ChainIntProperty.pypp.cpp index 9463b40c5..e46b0649b 100644 --- a/wrapper/Mol/ChainIntProperty.pypp.cpp +++ b/wrapper/Mol/ChainIntProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ChainProperty __copy__(const SireMol::ChainProperty &other){ return SireMol::ChainProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ChainPropertyProperty.pypp.cpp b/wrapper/Mol/ChainPropertyProperty.pypp.cpp index 0a724e60a..41d1c5ae1 100644 --- a/wrapper/Mol/ChainPropertyProperty.pypp.cpp +++ b/wrapper/Mol/ChainPropertyProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ChainProperty > __copy__(const SireMol::ChainProperty > &other){ return SireMol::ChainProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ChainStringProperty.pypp.cpp b/wrapper/Mol/ChainStringProperty.pypp.cpp index cf7496375..a5a716994 100644 --- a/wrapper/Mol/ChainStringProperty.pypp.cpp +++ b/wrapper/Mol/ChainStringProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ChainProperty __copy__(const SireMol::ChainProperty &other){ return SireMol::ChainProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ChainVariantProperty.pypp.cpp b/wrapper/Mol/ChainVariantProperty.pypp.cpp index 5707cb2f4..2269dbe1c 100644 --- a/wrapper/Mol/ChainVariantProperty.pypp.cpp +++ b/wrapper/Mol/ChainVariantProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ChainProperty __copy__(const SireMol::ChainProperty &other){ return SireMol::ChainProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/Connectivity.pypp.cpp b/wrapper/Mol/Connectivity.pypp.cpp index d9fb565c9..a776a84ac 100644 --- a/wrapper/Mol/Connectivity.pypp.cpp +++ b/wrapper/Mol/Connectivity.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; #include "angleid.h" +#include "atomidxmapping.h" + #include "atommatcher.h" #include "atomselection.h" @@ -55,7 +57,7 @@ namespace bp = boost::python; #include "connectivity.h" -SireMol::Connectivity __copy__(const SireMol::Connectivity &other){ return SireMol::Connectivity(other); } +SireMol::Connectivity __copy__(const SireMol::Connectivity &other) { return SireMol::Connectivity(other); } #include "Qt/qdatastream.hpp" @@ -63,80 +65,62 @@ SireMol::Connectivity __copy__(const SireMol::Connectivity &other){ return SireM #include "Helpers/release_gil_policy.hpp" -void register_Connectivity_class(){ +void register_Connectivity_class() +{ { //::SireMol::Connectivity - typedef bp::class_< SireMol::Connectivity, bp::bases< SireMol::ConnectivityBase, SireMol::MolViewProperty, SireBase::Property > > Connectivity_exposer_t; - Connectivity_exposer_t Connectivity_exposer = Connectivity_exposer_t( "Connectivity", "This class contains the connectivity of the molecule, namely which\natoms are connected to which other atoms. The connectivity is used\nto move parts of the molecule (e.g. moving an atom also moves all\nof the atoms that it is connected to), and to automatically generate\nthe internal geometry of the molecule (e.g. to auto-generate\nall of the bonds, angles and dihedrals). Note that the connectivity\nis not the same as the bonding - the connectivity is used to move\nparts of the molecule (e.g. moving an atom should move all of the\natoms it is connected to) and also to auto-generate internal angles\n(e.g. auto-generation of bonds, angles and dihedrals)\n\nAuthor: Christopher Woods\n\n", bp::init< >("Null constructor") ); - bp::scope Connectivity_scope( Connectivity_exposer ); - Connectivity_exposer.def( bp::init< SireMol::MoleculeInfo const & >(( bp::arg("molinfo") ), "Construct the connectivity for the passed molecule info") ); - Connectivity_exposer.def( bp::init< SireMol::MoleculeData const & >(( bp::arg("moldata") ), "Construct the connectivity for the molecule whose data\nis in moldata") ); - Connectivity_exposer.def( bp::init< SireMol::MoleculeView const &, bp::optional< SireMol::BondHunter const &, SireBase::PropertyMap const & > >(( bp::arg("molview"), bp::arg("bondhunter")=SireMol::CovalentBondHunter(), bp::arg("map")=SireBase::PropertyMap() ), "Construct the connectivity for the molecule viewed in the\npassed view. This automatically uses the bond hunting\nfunction to add all of the bonds for the atoms in this view") ); - Connectivity_exposer.def( bp::init< SireMol::ConnectivityEditor const & >(( bp::arg("editor") ), "Construct the connectivity from the passed editor") ); - Connectivity_exposer.def( bp::init< SireMol::Connectivity const & >(( bp::arg("other") ), "Copy constructor") ); + typedef bp::class_> Connectivity_exposer_t; + Connectivity_exposer_t Connectivity_exposer = Connectivity_exposer_t("Connectivity", "This class contains the connectivity of the molecule, namely which\natoms are connected to which other atoms. The connectivity is used\nto move parts of the molecule (e.g. moving an atom also moves all\nof the atoms that it is connected to), and to automatically generate\nthe internal geometry of the molecule (e.g. to auto-generate\nall of the bonds, angles and dihedrals). Note that the connectivity\nis not the same as the bonding - the connectivity is used to move\nparts of the molecule (e.g. moving an atom should move all of the\natoms it is connected to) and also to auto-generate internal angles\n(e.g. auto-generation of bonds, angles and dihedrals)\n\nAuthor: Christopher Woods\n\n", bp::init<>("Null constructor")); + bp::scope Connectivity_scope(Connectivity_exposer); + Connectivity_exposer.def(bp::init((bp::arg("molinfo")), "Construct the connectivity for the passed molecule info")); + Connectivity_exposer.def(bp::init((bp::arg("moldata")), "Construct the connectivity for the molecule whose data\nis in moldata")); + Connectivity_exposer.def(bp::init>((bp::arg("molview"), bp::arg("bondhunter") = SireMol::CovalentBondHunter(), bp::arg("map") = SireBase::PropertyMap()), "Construct the connectivity for the molecule viewed in the\npassed view. This automatically uses the bond hunting\nfunction to add all of the bonds for the atoms in this view")); + Connectivity_exposer.def(bp::init((bp::arg("editor")), "Construct the connectivity from the passed editor")); + Connectivity_exposer.def(bp::init((bp::arg("other")), "Copy constructor")); { //::SireMol::Connectivity::edit - - typedef ::SireMol::ConnectivityEditor ( ::SireMol::Connectivity::*edit_function_type)( ) const; - edit_function_type edit_function_value( &::SireMol::Connectivity::edit ); - - Connectivity_exposer.def( - "edit" - , edit_function_value - , bp::release_gil_policy() - , "Return an editor that can edit a copy of this connectivity" ); - + + typedef ::SireMol::ConnectivityEditor (::SireMol::Connectivity::*edit_function_type)() const; + edit_function_type edit_function_value(&::SireMol::Connectivity::edit); + + Connectivity_exposer.def( + "edit", edit_function_value, bp::release_gil_policy(), "Return an editor that can edit a copy of this connectivity"); } - Connectivity_exposer.def( bp::self != bp::self ); + Connectivity_exposer.def(bp::self != bp::self); { //::SireMol::Connectivity::operator= - - typedef ::SireMol::Connectivity & ( ::SireMol::Connectivity::*assign_function_type)( ::SireMol::Connectivity const & ) ; - assign_function_type assign_function_value( &::SireMol::Connectivity::operator= ); - - Connectivity_exposer.def( - "assign" - , assign_function_value - , ( bp::arg("other") ) - , bp::return_self< >() - , "" ); - + + typedef ::SireMol::Connectivity &(::SireMol::Connectivity::*assign_function_type)(::SireMol::Connectivity const &); + assign_function_type assign_function_value(&::SireMol::Connectivity::operator=); + + Connectivity_exposer.def( + "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); } { //::SireMol::Connectivity::operator= - - typedef ::SireMol::Connectivity & ( ::SireMol::Connectivity::*assign_function_type)( ::SireMol::ConnectivityEditor const & ) ; - assign_function_type assign_function_value( &::SireMol::Connectivity::operator= ); - - Connectivity_exposer.def( - "assign" - , assign_function_value - , ( bp::arg("editor") ) - , bp::return_self< >() - , "" ); - + + typedef ::SireMol::Connectivity &(::SireMol::Connectivity::*assign_function_type)(::SireMol::ConnectivityEditor const &); + assign_function_type assign_function_value(&::SireMol::Connectivity::operator=); + + Connectivity_exposer.def( + "assign", assign_function_value, (bp::arg("editor")), bp::return_self<>(), ""); } - Connectivity_exposer.def( bp::self == bp::self ); + Connectivity_exposer.def(bp::self == bp::self); { //::SireMol::Connectivity::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireMol::Connectivity::typeName ); - - Connectivity_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(*typeName_function_type)(); + typeName_function_type typeName_function_value(&::SireMol::Connectivity::typeName); + + Connectivity_exposer.def( + "typeName", typeName_function_value, bp::release_gil_policy(), ""); } - Connectivity_exposer.staticmethod( "typeName" ); - Connectivity_exposer.def( "__copy__", &__copy__); - Connectivity_exposer.def( "__deepcopy__", &__copy__); - Connectivity_exposer.def( "clone", &__copy__); - Connectivity_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::Connectivity >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - Connectivity_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::Connectivity >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - Connectivity_exposer.def_pickle(sire_pickle_suite< ::SireMol::Connectivity >()); - Connectivity_exposer.def( "__str__", &__str__< ::SireMol::Connectivity > ); - Connectivity_exposer.def( "__repr__", &__str__< ::SireMol::Connectivity > ); + Connectivity_exposer.staticmethod("typeName"); + Connectivity_exposer.def("__copy__", &__copy__); + Connectivity_exposer.def("__deepcopy__", &__copy__); + Connectivity_exposer.def("clone", &__copy__); + Connectivity_exposer.def("__rlshift__", &__rlshift__QDataStream<::SireMol::Connectivity>, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); + Connectivity_exposer.def("__rrshift__", &__rrshift__QDataStream<::SireMol::Connectivity>, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); + Connectivity_exposer.def_pickle(sire_pickle_suite<::SireMol::Connectivity>()); + Connectivity_exposer.def("__str__", &__str__<::SireMol::Connectivity>); + Connectivity_exposer.def("__repr__", &__str__<::SireMol::Connectivity>); } - } diff --git a/wrapper/Mol/ConnectivityBase.pypp.cpp b/wrapper/Mol/ConnectivityBase.pypp.cpp index 9592d8783..0e0c9d21c 100644 --- a/wrapper/Mol/ConnectivityBase.pypp.cpp +++ b/wrapper/Mol/ConnectivityBase.pypp.cpp @@ -24,6 +24,8 @@ namespace bp = boost::python; #include "angleid.h" +#include "atomidxmapping.h" + #include "atommatcher.h" #include "atomselection.h" @@ -62,1440 +64,900 @@ namespace bp = boost::python; #include "Helpers/release_gil_policy.hpp" -void register_ConnectivityBase_class(){ +void register_ConnectivityBase_class() +{ { //::SireMol::ConnectivityBase - typedef bp::class_< SireMol::ConnectivityBase, bp::bases< SireMol::MolViewProperty, SireBase::Property >, boost::noncopyable > ConnectivityBase_exposer_t; - ConnectivityBase_exposer_t ConnectivityBase_exposer = ConnectivityBase_exposer_t( "ConnectivityBase", "The base class of Connectivity and ConnectivityEditor\n\nAuthor: Christopher Woods\n", bp::no_init ); - bp::scope ConnectivityBase_scope( ConnectivityBase_exposer ); + typedef bp::class_, boost::noncopyable> ConnectivityBase_exposer_t; + ConnectivityBase_exposer_t ConnectivityBase_exposer = ConnectivityBase_exposer_t("ConnectivityBase", "The base class of Connectivity and ConnectivityEditor\n\nAuthor: Christopher Woods\n", bp::no_init); + bp::scope ConnectivityBase_scope(ConnectivityBase_exposer); { //::SireMol::ConnectivityBase::areAngled - - typedef bool ( ::SireMol::ConnectivityBase::*areAngled_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - areAngled_function_type areAngled_function_value( &::SireMol::ConnectivityBase::areAngled ); - - ConnectivityBase_exposer.def( - "areAngled" - , areAngled_function_value - , ( bp::arg("atom0"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "Return whether or not the two atoms are angled together" ); - + + typedef bool (::SireMol::ConnectivityBase::*areAngled_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + areAngled_function_type areAngled_function_value(&::SireMol::ConnectivityBase::areAngled); + + ConnectivityBase_exposer.def( + "areAngled", areAngled_function_value, (bp::arg("atom0"), bp::arg("atom2")), bp::release_gil_policy(), "Return whether or not the two atoms are angled together"); } { //::SireMol::ConnectivityBase::areAngled - - typedef bool ( ::SireMol::ConnectivityBase::*areAngled_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - areAngled_function_type areAngled_function_value( &::SireMol::ConnectivityBase::areAngled ); - - ConnectivityBase_exposer.def( - "areAngled" - , areAngled_function_value - , ( bp::arg("atom0"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "Return whether or not the two atoms are angled together" ); - + + typedef bool (::SireMol::ConnectivityBase::*areAngled_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + areAngled_function_type areAngled_function_value(&::SireMol::ConnectivityBase::areAngled); + + ConnectivityBase_exposer.def( + "areAngled", areAngled_function_value, (bp::arg("atom0"), bp::arg("atom2")), bp::release_gil_policy(), "Return whether or not the two atoms are angled together"); } { //::SireMol::ConnectivityBase::areBonded - - typedef bool ( ::SireMol::ConnectivityBase::*areBonded_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - areBonded_function_type areBonded_function_value( &::SireMol::ConnectivityBase::areBonded ); - - ConnectivityBase_exposer.def( - "areBonded" - , areBonded_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return whether or not the two atoms are bonded together" ); - + + typedef bool (::SireMol::ConnectivityBase::*areBonded_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + areBonded_function_type areBonded_function_value(&::SireMol::ConnectivityBase::areBonded); + + ConnectivityBase_exposer.def( + "areBonded", areBonded_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the two atoms are bonded together"); } { //::SireMol::ConnectivityBase::areBonded - - typedef bool ( ::SireMol::ConnectivityBase::*areBonded_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - areBonded_function_type areBonded_function_value( &::SireMol::ConnectivityBase::areBonded ); - - ConnectivityBase_exposer.def( - "areBonded" - , areBonded_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return whether or not the two atoms are bonded together" ); - + + typedef bool (::SireMol::ConnectivityBase::*areBonded_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + areBonded_function_type areBonded_function_value(&::SireMol::ConnectivityBase::areBonded); + + ConnectivityBase_exposer.def( + "areBonded", areBonded_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the two atoms are bonded together"); } { //::SireMol::ConnectivityBase::areConnected - - typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); - - ConnectivityBase_exposer.def( - "areConnected" - , areConnected_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return whether or not the atoms at indicies atom0 and atom1\nare connected\nThrow: SireError::invalid_index\n" ); - + + typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); + + ConnectivityBase_exposer.def( + "areConnected", areConnected_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the atoms at indicies atom0 and atom1\nare connected\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::areConnected - - typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); - - ConnectivityBase_exposer.def( - "areConnected" - , areConnected_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return whether or not the atoms identified by atom0 and atom1\nare connected\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); - + + typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); + + ConnectivityBase_exposer.def( + "areConnected", areConnected_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the atoms identified by atom0 and atom1\nare connected\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::areConnected - - typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::ResIdx,::SireMol::ResIdx ) const; - areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); - - ConnectivityBase_exposer.def( - "areConnected" - , areConnected_function_value - , ( bp::arg("res0"), bp::arg("res1") ) - , bp::release_gil_policy() - , "Return whether or not the residues at indicies res0 and res1\nare connected\nThrow: SireError::invalid_index\n" ); - + + typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::ResIdx, ::SireMol::ResIdx) const; + areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); + + ConnectivityBase_exposer.def( + "areConnected", areConnected_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return whether or not the residues at indicies res0 and res1\nare connected\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::areConnected - - typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::ResID const &,::SireMol::ResID const & ) const; - areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); - - ConnectivityBase_exposer.def( - "areConnected" - , areConnected_function_value - , ( bp::arg("res0"), bp::arg("res1") ) - , bp::release_gil_policy() - , "Return whether the residues identified by res0 and res1 are connected" ); - + + typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::ResID const &, ::SireMol::ResID const &) const; + areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); + + ConnectivityBase_exposer.def( + "areConnected", areConnected_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return whether the residues identified by res0 and res1 are connected"); } { //::SireMol::ConnectivityBase::areConnected - - typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::CGIdx,::SireMol::CGIdx ) const; - areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); - - ConnectivityBase_exposer.def( - "areConnected" - , areConnected_function_value - , ( bp::arg("cg0"), bp::arg("cg1") ) - , bp::release_gil_policy() - , "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected" ); - + + typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::CGIdx, ::SireMol::CGIdx) const; + areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); + + ConnectivityBase_exposer.def( + "areConnected", areConnected_function_value, (bp::arg("cg0"), bp::arg("cg1")), bp::release_gil_policy(), "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected"); } { //::SireMol::ConnectivityBase::areConnected - - typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::CGID const &,::SireMol::CGID const & ) const; - areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); - - ConnectivityBase_exposer.def( - "areConnected" - , areConnected_function_value - , ( bp::arg("cg0"), bp::arg("cg1") ) - , bp::release_gil_policy() - , "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected" ); - + + typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::CGID const &, ::SireMol::CGID const &) const; + areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); + + ConnectivityBase_exposer.def( + "areConnected", areConnected_function_value, (bp::arg("cg0"), bp::arg("cg1")), bp::release_gil_policy(), "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected"); } { //::SireMol::ConnectivityBase::areDihedraled - - typedef bool ( ::SireMol::ConnectivityBase::*areDihedraled_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - areDihedraled_function_type areDihedraled_function_value( &::SireMol::ConnectivityBase::areDihedraled ); - - ConnectivityBase_exposer.def( - "areDihedraled" - , areDihedraled_function_value - , ( bp::arg("atom0"), bp::arg("atom3") ) - , bp::release_gil_policy() - , "Return whether or not the two atoms are dihedraled together" ); - + + typedef bool (::SireMol::ConnectivityBase::*areDihedraled_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + areDihedraled_function_type areDihedraled_function_value(&::SireMol::ConnectivityBase::areDihedraled); + + ConnectivityBase_exposer.def( + "areDihedraled", areDihedraled_function_value, (bp::arg("atom0"), bp::arg("atom3")), bp::release_gil_policy(), "Return whether or not the two atoms are dihedraled together"); } { //::SireMol::ConnectivityBase::areDihedraled - - typedef bool ( ::SireMol::ConnectivityBase::*areDihedraled_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - areDihedraled_function_type areDihedraled_function_value( &::SireMol::ConnectivityBase::areDihedraled ); - - ConnectivityBase_exposer.def( - "areDihedraled" - , areDihedraled_function_value - , ( bp::arg("atom0"), bp::arg("atom3") ) - , bp::release_gil_policy() - , "Return whether or not the two atoms are bonded together" ); - + + typedef bool (::SireMol::ConnectivityBase::*areDihedraled_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + areDihedraled_function_type areDihedraled_function_value(&::SireMol::ConnectivityBase::areDihedraled); + + ConnectivityBase_exposer.def( + "areDihedraled", areDihedraled_function_value, (bp::arg("atom0"), bp::arg("atom3")), bp::release_gil_policy(), "Return whether or not the two atoms are bonded together"); } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; - assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); - - ConnectivityBase_exposer.def( - "assertHasProperty" - , assertHasProperty_function_value - , ( bp::arg("bond"), bp::arg("key") ) - , bp::release_gil_policy() - , "Assert that the specified bond has the specified property" ); - + + typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; + assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); + + ConnectivityBase_exposer.def( + "assertHasProperty", assertHasProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified bond has the specified property"); } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; - assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); - - ConnectivityBase_exposer.def( - "assertHasProperty" - , assertHasProperty_function_value - , ( bp::arg("ang"), bp::arg("key") ) - , bp::release_gil_policy() - , "Assert that the specified angle has the specified property" ); - + + typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; + assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); + + ConnectivityBase_exposer.def( + "assertHasProperty", assertHasProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified angle has the specified property"); } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; - assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); - - ConnectivityBase_exposer.def( - "assertHasProperty" - , assertHasProperty_function_value - , ( bp::arg("dih"), bp::arg("key") ) - , bp::release_gil_policy() - , "Assert that the specified angle has the specified property" ); - + + typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; + assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); + + ConnectivityBase_exposer.def( + "assertHasProperty", assertHasProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified angle has the specified property"); } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; - assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); - - ConnectivityBase_exposer.def( - "assertHasProperty" - , assertHasProperty_function_value - , ( bp::arg("imp"), bp::arg("key") ) - , bp::release_gil_policy() - , "Assert that the specified angle has the specified property" ); - + + typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; + assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); + + ConnectivityBase_exposer.def( + "assertHasProperty", assertHasProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified angle has the specified property"); } { //::SireMol::ConnectivityBase::connectionType - - typedef int ( ::SireMol::ConnectivityBase::*connectionType_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - connectionType_function_type connectionType_function_value( &::SireMol::ConnectivityBase::connectionType ); - - ConnectivityBase_exposer.def( - "connectionType" - , connectionType_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return the connection type of the passed two atoms. This returns;\n" ); - + + typedef int (::SireMol::ConnectivityBase::*connectionType_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + connectionType_function_type connectionType_function_value(&::SireMol::ConnectivityBase::connectionType); + + ConnectivityBase_exposer.def( + "connectionType", connectionType_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return the connection type of the passed two atoms. This returns;\n"); } { //::SireMol::ConnectivityBase::connectionType - - typedef int ( ::SireMol::ConnectivityBase::*connectionType_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - connectionType_function_type connectionType_function_value( &::SireMol::ConnectivityBase::connectionType ); - - ConnectivityBase_exposer.def( - "connectionType" - , connectionType_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return the connection type of the passed two atoms. This returns;\n" ); - + + typedef int (::SireMol::ConnectivityBase::*connectionType_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + connectionType_function_type connectionType_function_value(&::SireMol::ConnectivityBase::connectionType); + + ConnectivityBase_exposer.def( + "connectionType", connectionType_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return the connection type of the passed two atoms. This returns;\n"); } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet< SireMol::AtomIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::AtomIdx ) const; - connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); - - ConnectivityBase_exposer.def( - "connectionsTo" - , connectionsTo_function_value - , ( bp::arg("atomidx") ) - , bp::return_value_policy< bp::copy_const_reference >() - , "Return the indicies of atoms connected to the atom at index atomidx.\nThis returns an empty set if there are no atoms connected to\nthis atom\nThrow: SireError::invalid_index\n" ); - + + typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::AtomIdx) const; + connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); + + ConnectivityBase_exposer.def( + "connectionsTo", connectionsTo_function_value, (bp::arg("atomidx")), bp::return_value_policy(), "Return the indicies of atoms connected to the atom at index atomidx.\nThis returns an empty set if there are no atoms connected to\nthis atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet< SireMol::AtomIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::AtomID const & ) const; - connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); - - ConnectivityBase_exposer.def( - "connectionsTo" - , connectionsTo_function_value - , ( bp::arg("atomid") ) - , bp::return_value_policy< bp::copy_const_reference >() - , "Return the indicies of atoms connected to the atom identified\nby resid - this returns an empty set if there are no connections\nto this atom\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); - + + typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::AtomID const &) const; + connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); + + ConnectivityBase_exposer.def( + "connectionsTo", connectionsTo_function_value, (bp::arg("atomid")), bp::return_value_policy(), "Return the indicies of atoms connected to the atom identified\nby resid - this returns an empty set if there are no connections\nto this atom\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet< SireMol::ResIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::ResIdx ) const; - connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); - - ConnectivityBase_exposer.def( - "connectionsTo" - , connectionsTo_function_value - , ( bp::arg("residx") ) - , bp::return_value_policy< bp::copy_const_reference >() - , "Return the indicies of the residues connected to the residue at\nindex residx. This returns an empty set if there are no residues\nconnected to this residue\nThrow: SireError::invalid_index\n" ); - + + typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::ResIdx) const; + connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); + + ConnectivityBase_exposer.def( + "connectionsTo", connectionsTo_function_value, (bp::arg("residx")), bp::return_value_policy(), "Return the indicies of the residues connected to the residue at\nindex residx. This returns an empty set if there are no residues\nconnected to this residue\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet< SireMol::ResIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::ResID const & ) const; - connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); - - ConnectivityBase_exposer.def( - "connectionsTo" - , connectionsTo_function_value - , ( bp::arg("resid") ) - , bp::return_value_policy< bp::copy_const_reference >() - , "Return the indicies of the residues connectd to the residue\nidentified by resid. This returns an empty set if there are\nno residues connected to this residue.\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); - + + typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::ResID const &) const; + connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); + + ConnectivityBase_exposer.def( + "connectionsTo", connectionsTo_function_value, (bp::arg("resid")), bp::return_value_policy(), "Return the indicies of the residues connectd to the residue\nidentified by resid. This returns an empty set if there are\nno residues connected to this residue.\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); - - ConnectivityBase_exposer.def( - "findPath" - , findPath_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); + + ConnectivityBase_exposer.def( + "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms"); } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,int ) const; - findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); - - ConnectivityBase_exposer.def( - "findPath" - , findPath_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) - , bp::release_gil_policy() - , "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, int) const; + findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); + + ConnectivityBase_exposer.def( + "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms"); } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); - - ConnectivityBase_exposer.def( - "findPath" - , findPath_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); + + ConnectivityBase_exposer.def( + "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms"); } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,int ) const; - findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); - - ConnectivityBase_exposer.def( - "findPath" - , findPath_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) - , bp::release_gil_policy() - , "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms where the path has\na maximum length." ); - + + typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, int) const; + findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); + + ConnectivityBase_exposer.def( + "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms where the path has\na maximum length."); } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); - - ConnectivityBase_exposer.def( - "findPaths" - , findPaths_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms" ); - + + typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); + + ConnectivityBase_exposer.def( + "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms"); } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,int ) const; - findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); - - ConnectivityBase_exposer.def( - "findPaths" - , findPaths_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) - , bp::release_gil_policy() - , "Return all possible bonded paths between two atoms where the path has\na maximum length. This returns an empty list if there are no bonded\npaths between the two atoms" ); - + + typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, int) const; + findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); + + ConnectivityBase_exposer.def( + "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms where the path has\na maximum length. This returns an empty list if there are no bonded\npaths between the two atoms"); } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); - - ConnectivityBase_exposer.def( - "findPaths" - , findPaths_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms" ); - + + typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); + + ConnectivityBase_exposer.def( + "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms"); } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,int ) const; - findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); - - ConnectivityBase_exposer.def( - "findPaths" - , findPaths_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) - , bp::release_gil_policy() - , "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms" ); - + + typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, int) const; + findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); + + ConnectivityBase_exposer.def( + "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms"); } { //::SireMol::ConnectivityBase::getAngles - - typedef ::QList< SireMol::AngleID > ( ::SireMol::ConnectivityBase::*getAngles_function_type)( ) const; - getAngles_function_type getAngles_function_value( &::SireMol::ConnectivityBase::getAngles ); - - ConnectivityBase_exposer.def( - "getAngles" - , getAngles_function_value - , bp::release_gil_policy() - , "Return a list of angles defined by the connectivity" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getAngles_function_type)() const; + getAngles_function_type getAngles_function_value(&::SireMol::ConnectivityBase::getAngles); + + ConnectivityBase_exposer.def( + "getAngles", getAngles_function_value, bp::release_gil_policy(), "Return a list of angles defined by the connectivity"); } { //::SireMol::ConnectivityBase::getAngles - - typedef ::QList< SireMol::AngleID > ( ::SireMol::ConnectivityBase::*getAngles_function_type)( ::SireMol::AtomID const & ) const; - getAngles_function_type getAngles_function_value( &::SireMol::ConnectivityBase::getAngles ); - - ConnectivityBase_exposer.def( - "getAngles" - , getAngles_function_value - , ( bp::arg("atom0") ) - , bp::release_gil_policy() - , "Return a list of angles defined by the connectivity that involve atom0" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getAngles_function_type)(::SireMol::AtomID const &) const; + getAngles_function_type getAngles_function_value(&::SireMol::ConnectivityBase::getAngles); + + ConnectivityBase_exposer.def( + "getAngles", getAngles_function_value, (bp::arg("atom0")), bp::release_gil_policy(), "Return a list of angles defined by the connectivity that involve atom0"); } { //::SireMol::ConnectivityBase::getAngles - - typedef ::QList< SireMol::AngleID > ( ::SireMol::ConnectivityBase::*getAngles_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - getAngles_function_type getAngles_function_value( &::SireMol::ConnectivityBase::getAngles ); - - ConnectivityBase_exposer.def( - "getAngles" - , getAngles_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return a list of angles defined by the connectivity that involve atom0 and atom1" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getAngles_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + getAngles_function_type getAngles_function_value(&::SireMol::ConnectivityBase::getAngles); + + ConnectivityBase_exposer.def( + "getAngles", getAngles_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return a list of angles defined by the connectivity that involve atom0 and atom1"); } { //::SireMol::ConnectivityBase::getBondMatrix - - typedef ::QVector< QVector< bool > > ( ::SireMol::ConnectivityBase::*getBondMatrix_function_type)( int ) const; - getBondMatrix_function_type getBondMatrix_function_value( &::SireMol::ConnectivityBase::getBondMatrix ); - - ConnectivityBase_exposer.def( - "getBondMatrix" - , getBondMatrix_function_value - , ( bp::arg("order") ) - , bp::release_gil_policy() - , "Return a matrix (organised by AtomIdx) that says which atoms are bonded up to\norder order (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)" ); - + + typedef ::QVector> (::SireMol::ConnectivityBase::*getBondMatrix_function_type)(int) const; + getBondMatrix_function_type getBondMatrix_function_value(&::SireMol::ConnectivityBase::getBondMatrix); + + ConnectivityBase_exposer.def( + "getBondMatrix", getBondMatrix_function_value, (bp::arg("order")), bp::release_gil_policy(), "Return a matrix (organised by AtomIdx) that says which atoms are bonded up to\norder order (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)"); } { //::SireMol::ConnectivityBase::getBondMatrix - - typedef ::QVector< QVector< bool > > ( ::SireMol::ConnectivityBase::*getBondMatrix_function_type)( int,int ) const; - getBondMatrix_function_type getBondMatrix_function_value( &::SireMol::ConnectivityBase::getBondMatrix ); - - ConnectivityBase_exposer.def( - "getBondMatrix" - , getBondMatrix_function_value - , ( bp::arg("start"), bp::arg("end") ) - , bp::release_gil_policy() - , "Return a matrix (organised by AtomIdx) that says which atoms are bonded between\norder start and order end (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)" ); - + + typedef ::QVector> (::SireMol::ConnectivityBase::*getBondMatrix_function_type)(int, int) const; + getBondMatrix_function_type getBondMatrix_function_value(&::SireMol::ConnectivityBase::getBondMatrix); + + ConnectivityBase_exposer.def( + "getBondMatrix", getBondMatrix_function_value, (bp::arg("start"), bp::arg("end")), bp::release_gil_policy(), "Return a matrix (organised by AtomIdx) that says which atoms are bonded between\norder start and order end (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)"); } { //::SireMol::ConnectivityBase::getBonds - - typedef ::QList< SireMol::BondID > ( ::SireMol::ConnectivityBase::*getBonds_function_type)( ) const; - getBonds_function_type getBonds_function_value( &::SireMol::ConnectivityBase::getBonds ); - - ConnectivityBase_exposer.def( - "getBonds" - , getBonds_function_value - , bp::release_gil_policy() - , "Return the list of bonds present in this connectivity" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getBonds_function_type)() const; + getBonds_function_type getBonds_function_value(&::SireMol::ConnectivityBase::getBonds); + + ConnectivityBase_exposer.def( + "getBonds", getBonds_function_value, bp::release_gil_policy(), "Return the list of bonds present in this connectivity"); } { //::SireMol::ConnectivityBase::getBonds - - typedef ::QList< SireMol::BondID > ( ::SireMol::ConnectivityBase::*getBonds_function_type)( ::SireMol::AtomID const & ) const; - getBonds_function_type getBonds_function_value( &::SireMol::ConnectivityBase::getBonds ); - - ConnectivityBase_exposer.def( - "getBonds" - , getBonds_function_value - , ( bp::arg("atom") ) - , bp::release_gil_policy() - , "Return the list of bonds in the connectivity containing atom" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getBonds_function_type)(::SireMol::AtomID const &) const; + getBonds_function_type getBonds_function_value(&::SireMol::ConnectivityBase::getBonds); + + ConnectivityBase_exposer.def( + "getBonds", getBonds_function_value, (bp::arg("atom")), bp::release_gil_policy(), "Return the list of bonds in the connectivity containing atom"); } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ) const; - getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); - - ConnectivityBase_exposer.def( - "getDihedrals" - , getDihedrals_function_value - , bp::release_gil_policy() - , "Return a list of dihedrals defined by the connectivity" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)() const; + getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); + + ConnectivityBase_exposer.def( + "getDihedrals", getDihedrals_function_value, bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity"); } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ::SireMol::AtomID const & ) const; - getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); - - ConnectivityBase_exposer.def( - "getDihedrals" - , getDihedrals_function_value - , ( bp::arg("atom0") ) - , bp::release_gil_policy() - , "Return a list of dihedrals defined by the connectivity that involve atom0" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)(::SireMol::AtomID const &) const; + getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); + + ConnectivityBase_exposer.def( + "getDihedrals", getDihedrals_function_value, (bp::arg("atom0")), bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity that involve atom0"); } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); - - ConnectivityBase_exposer.def( - "getDihedrals" - , getDihedrals_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Return a list of dihedrals defined by the connectivity that involve atom0 and atom1" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); + + ConnectivityBase_exposer.def( + "getDihedrals", getDihedrals_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity that involve atom0 and atom1"); } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); - - ConnectivityBase_exposer.def( - "getDihedrals" - , getDihedrals_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "Return a list of dihedrals defined by the connectivity that involve atom0, atom1 and atom2" ); - + + typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); + + ConnectivityBase_exposer.def( + "getDihedrals", getDihedrals_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity that involve atom0, atom1 and atom2"); } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; - hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); - - ConnectivityBase_exposer.def( - "hasProperty" - , hasProperty_function_value - , ( bp::arg("bond"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return whether the specified bond has a property at key key" ); - + + typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; + hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); + + ConnectivityBase_exposer.def( + "hasProperty", hasProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified bond has a property at key key"); } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; - hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); - - ConnectivityBase_exposer.def( - "hasProperty" - , hasProperty_function_value - , ( bp::arg("ang"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return whether the specified angle has a property at key key" ); - + + typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; + hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); + + ConnectivityBase_exposer.def( + "hasProperty", hasProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified angle has a property at key key"); } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; - hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); - - ConnectivityBase_exposer.def( - "hasProperty" - , hasProperty_function_value - , ( bp::arg("dih"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return whether the specified dihedral has a property at key key" ); - + + typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; + hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); + + ConnectivityBase_exposer.def( + "hasProperty", hasProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified dihedral has a property at key key"); } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; - hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); - - ConnectivityBase_exposer.def( - "hasProperty" - , hasProperty_function_value - , ( bp::arg("imp"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return whether the specified improper has a property at key key" ); - + + typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; + hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); + + ConnectivityBase_exposer.def( + "hasProperty", hasProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified improper has a property at key key"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom") ) - , bp::release_gil_policy() - , "This function returns whether or not the atom is in a ring." ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom")), bp::release_gil_policy(), "This function returns whether or not the atom is in a ring."); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "This function returns whether or not the two passed atoms are connected" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "This function returns whether or not the two passed atoms are connected"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "This function returns whether or not the three passed atoms are connected\nvia a ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "This function returns whether or not the three passed atoms are connected\nvia a ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) - , bp::release_gil_policy() - , "This function returns whether or not the four passed atoms are connected\nvia a same ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "This function returns whether or not the four passed atoms are connected\nvia a same ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom") ) - , bp::release_gil_policy() - , "This function returns whether or not the atom is in a ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom")), bp::release_gil_policy(), "This function returns whether or not the atom is in a ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "This function returns whether or not the two passed atoms are connected\nvia a ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "This function returns whether or not the two passed atoms are connected\nvia a ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "This function returns whether or not the three passed atoms are connected\nvia a ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "This function returns whether or not the three passed atoms are connected\nvia a ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) - , bp::release_gil_policy() - , "This function returns whether or not the two passed atoms are connected\nvia a ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "This function returns whether or not the two passed atoms are connected\nvia a ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::BondID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("bond") ) - , bp::release_gil_policy() - , "This function returns whether or not the two atoms in the passed bond\nare both part of the same ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::BondID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("bond")), bp::release_gil_policy(), "This function returns whether or not the two atoms in the passed bond\nare both part of the same ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AngleID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("angle") ) - , bp::release_gil_policy() - , "This function returns whether or not the three atoms in the passed angle\nare all part of the same ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AngleID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("angle")), bp::release_gil_policy(), "This function returns whether or not the three atoms in the passed angle\nare all part of the same ring"); } { //::SireMol::ConnectivityBase::inRing - - typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::DihedralID const & ) const; - inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); - - ConnectivityBase_exposer.def( - "inRing" - , inRing_function_value - , ( bp::arg("dihedral") ) - , bp::release_gil_policy() - , "This function returns whether or not the four atoms in the passed dihedral\nare all part of the same ring" ); - + + typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::DihedralID const &) const; + inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); + + ConnectivityBase_exposer.def( + "inRing", inRing_function_value, (bp::arg("dihedral")), bp::release_gil_policy(), "This function returns whether or not the four atoms in the passed dihedral\nare all part of the same ring"); } { //::SireMol::ConnectivityBase::info - - typedef ::SireMol::MoleculeInfo ( ::SireMol::ConnectivityBase::*info_function_type)( ) const; - info_function_type info_function_value( &::SireMol::ConnectivityBase::info ); - - ConnectivityBase_exposer.def( - "info" - , info_function_value - , bp::release_gil_policy() - , "Return the info object that describes the molecule for which this connectivity applies" ); - + + typedef ::SireMol::MoleculeInfo (::SireMol::ConnectivityBase::*info_function_type)() const; + info_function_type info_function_value(&::SireMol::ConnectivityBase::info); + + ConnectivityBase_exposer.def( + "info", info_function_value, bp::release_gil_policy(), "Return the info object that describes the molecule for which this connectivity applies"); } { //::SireMol::ConnectivityBase::isCompatibleWith - - typedef bool ( ::SireMol::ConnectivityBase::*isCompatibleWith_function_type)( ::SireMol::MoleculeInfoData const & ) const; - isCompatibleWith_function_type isCompatibleWith_function_value( &::SireMol::ConnectivityBase::isCompatibleWith ); - - ConnectivityBase_exposer.def( - "isCompatibleWith" - , isCompatibleWith_function_value - , ( bp::arg("molinfo") ) - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireMol::ConnectivityBase::*isCompatibleWith_function_type)(::SireMol::MoleculeInfoData const &) const; + isCompatibleWith_function_type isCompatibleWith_function_value(&::SireMol::ConnectivityBase::isCompatibleWith); + + ConnectivityBase_exposer.def( + "isCompatibleWith", isCompatibleWith_function_value, (bp::arg("molinfo")), bp::release_gil_policy(), ""); } { //::SireMol::ConnectivityBase::merge - - typedef ::SireBase::PropertyList ( ::SireMol::ConnectivityBase::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; - merge_function_type merge_function_value( &::SireMol::ConnectivityBase::merge ); - - ConnectivityBase_exposer.def( - "merge" - , merge_function_value - , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) - , "Merge this property with another property" ); - + + typedef ::SireBase::PropertyList (::SireMol::ConnectivityBase::*merge_function_type)(::SireMol::MolViewProperty const &, ::SireMol::AtomIdxMapping const &, ::QString const &, ::SireBase::PropertyMap const &) const; + merge_function_type merge_function_value(&::SireMol::ConnectivityBase::merge); + + ConnectivityBase_exposer.def( + "merge", merge_function_value, (bp::arg("other"), bp::arg("mapping"), bp::arg("ghost") = ::QString(), bp::arg("map") = SireBase::PropertyMap()), "Merge this property with another property"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , bp::release_gil_policy() - , "Return the total number of connections between atoms\nin this connectivity object" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)() const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, bp::release_gil_policy(), "Return the total number of connections between atoms\nin this connectivity object"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::AtomIdx ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , ( bp::arg("atomidx") ) - , bp::release_gil_policy() - , "Return the number of connections to the atom at index atomidx\nThrow: SireError::index_error\n" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::AtomIdx) const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, (bp::arg("atomidx")), bp::release_gil_policy(), "Return the number of connections to the atom at index atomidx\nThrow: SireError::index_error\n"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::AtomID const & ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , ( bp::arg("atomid") ) - , bp::release_gil_policy() - , "Return the number of connections to the atom with ID atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::AtomID const &) const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, (bp::arg("atomid")), bp::release_gil_policy(), "Return the number of connections to the atom with ID atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResIdx ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , ( bp::arg("residx") ) - , bp::release_gil_policy() - , "Return the number of connections to the residue at index residx\nThrow: SireError::invalid_index\n" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResIdx) const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, (bp::arg("residx")), bp::release_gil_policy(), "Return the number of connections to the residue at index residx\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResID const & ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , ( bp::arg("resid") ) - , bp::release_gil_policy() - , "Return the number of connections to the residue identified\nby resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResID const &) const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, (bp::arg("resid")), bp::release_gil_policy(), "Return the number of connections to the residue identified\nby resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResIdx,::SireMol::ResIdx ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , ( bp::arg("res0"), bp::arg("res1") ) - , bp::release_gil_policy() - , "Return the number of atom connections between the residues at\nindicies res0 and res1\nThrow: SireError::invalid_index\n" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResIdx, ::SireMol::ResIdx) const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return the number of atom connections between the residues at\nindicies res0 and res1\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::nConnections - - typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResID const &,::SireMol::ResID const & ) const; - nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); - - ConnectivityBase_exposer.def( - "nConnections" - , nConnections_function_value - , ( bp::arg("res0"), bp::arg("res1") ) - , bp::release_gil_policy() - , "Return the number of atom connections between the residues\nidentified by res0 and res1\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); - + + typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResID const &, ::SireMol::ResID const &) const; + nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); + + ConnectivityBase_exposer.def( + "nConnections", nConnections_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return the number of atom connections between the residues\nidentified by res0 and res1\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::BondID const & ) const; - properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); - - ConnectivityBase_exposer.def( - "properties" - , properties_function_value - , ( bp::arg("bond") ) - , bp::release_gil_policy() - , "Return the properties of the passed bond" ); - + + typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::BondID const &) const; + properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); + + ConnectivityBase_exposer.def( + "properties", properties_function_value, (bp::arg("bond")), bp::release_gil_policy(), "Return the properties of the passed bond"); } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::AngleID const & ) const; - properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); - - ConnectivityBase_exposer.def( - "properties" - , properties_function_value - , ( bp::arg("ang") ) - , bp::release_gil_policy() - , "Return the properties of the passed angle" ); - + + typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::AngleID const &) const; + properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); + + ConnectivityBase_exposer.def( + "properties", properties_function_value, (bp::arg("ang")), bp::release_gil_policy(), "Return the properties of the passed angle"); } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::DihedralID const & ) const; - properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); - - ConnectivityBase_exposer.def( - "properties" - , properties_function_value - , ( bp::arg("dih") ) - , bp::release_gil_policy() - , "Return the properties of the passed dihedral" ); - + + typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::DihedralID const &) const; + properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); + + ConnectivityBase_exposer.def( + "properties", properties_function_value, (bp::arg("dih")), bp::release_gil_policy(), "Return the properties of the passed dihedral"); } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::ImproperID const & ) const; - properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); - - ConnectivityBase_exposer.def( - "properties" - , properties_function_value - , ( bp::arg("imp") ) - , bp::release_gil_policy() - , "Return the properties of the passed improper" ); - + + typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::ImproperID const &) const; + properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); + + ConnectivityBase_exposer.def( + "properties", properties_function_value, (bp::arg("imp")), bp::release_gil_policy(), "Return the properties of the passed improper"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("bond"), bp::arg("key") ) - , bp::return_value_policy() - , "Return the specified property of the specified bond" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("bond"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified bond"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("bond"), bp::arg("key"), bp::arg("default_value") ) - , bp::return_value_policy() - , "Return the specified property of the specified bond, or\ndefault_value if such a property is not defined\n" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("bond"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified bond, or\ndefault_value if such a property is not defined\n"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("ang"), bp::arg("key") ) - , bp::return_value_policy() - , "Return the specified property of the specified angle" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("ang"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified angle"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("ang"), bp::arg("key"), bp::arg("default_value") ) - , bp::return_value_policy() - , "Return the specified property of the specified angle, or\ndefault_value if such a property is not defined\n" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("ang"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified angle, or\ndefault_value if such a property is not defined\n"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("dih"), bp::arg("key") ) - , bp::return_value_policy() - , "Return the specified property of the specified dihedral" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("dih"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified dihedral"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("dih"), bp::arg("key"), bp::arg("default_value") ) - , bp::return_value_policy() - , "Return the specified property of the specified dihedral, or\ndefault_value if such a property is not defined\n" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("dih"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified dihedral, or\ndefault_value if such a property is not defined\n"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("imp"), bp::arg("key") ) - , bp::return_value_policy() - , "Return the specified property of the specified improper" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("imp"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified improper"); } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; - property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); - - ConnectivityBase_exposer.def( - "property" - , property_function_value - , ( bp::arg("imp"), bp::arg("key"), bp::arg("default_value") ) - , bp::return_value_policy() - , "Return the specified property of the specified improper, or\ndefault_value if such a property is not defined\n" ); - + + typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; + property_function_type property_function_value(&::SireMol::ConnectivityBase::property); + + ConnectivityBase_exposer.def( + "property", property_function_value, (bp::arg("imp"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified improper, or\ndefault_value if such a property is not defined\n"); } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ) const; - propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); - - ConnectivityBase_exposer.def( - "propertyKeys" - , propertyKeys_function_value - , bp::release_gil_policy() - , "Return all of the property keys for all of the bonds" ); - + + typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)() const; + propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); + + ConnectivityBase_exposer.def( + "propertyKeys", propertyKeys_function_value, bp::release_gil_policy(), "Return all of the property keys for all of the bonds"); } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::BondID const & ) const; - propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); - - ConnectivityBase_exposer.def( - "propertyKeys" - , propertyKeys_function_value - , ( bp::arg("bond") ) - , bp::release_gil_policy() - , "Return the property keys for the specified bond" ); - + + typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::BondID const &) const; + propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); + + ConnectivityBase_exposer.def( + "propertyKeys", propertyKeys_function_value, (bp::arg("bond")), bp::release_gil_policy(), "Return the property keys for the specified bond"); } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::AngleID const & ) const; - propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); - - ConnectivityBase_exposer.def( - "propertyKeys" - , propertyKeys_function_value - , ( bp::arg("ang") ) - , bp::release_gil_policy() - , "Return the property keys for the specified angle" ); - + + typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::AngleID const &) const; + propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); + + ConnectivityBase_exposer.def( + "propertyKeys", propertyKeys_function_value, (bp::arg("ang")), bp::release_gil_policy(), "Return the property keys for the specified angle"); } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::DihedralID const & ) const; - propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); - - ConnectivityBase_exposer.def( - "propertyKeys" - , propertyKeys_function_value - , ( bp::arg("dih") ) - , bp::release_gil_policy() - , "Return the property keys for the specified dihedral" ); - + + typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::DihedralID const &) const; + propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); + + ConnectivityBase_exposer.def( + "propertyKeys", propertyKeys_function_value, (bp::arg("dih")), bp::release_gil_policy(), "Return the property keys for the specified dihedral"); } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::ImproperID const & ) const; - propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); - - ConnectivityBase_exposer.def( - "propertyKeys" - , propertyKeys_function_value - , ( bp::arg("imp") ) - , bp::release_gil_policy() - , "Return the property keys for the specified improper" ); - + + typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::ImproperID const &) const; + propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); + + ConnectivityBase_exposer.def( + "propertyKeys", propertyKeys_function_value, (bp::arg("imp")), bp::release_gil_policy(), "Return the property keys for the specified improper"); } { //::SireMol::ConnectivityBase::propertyType - - typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; - propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); - - ConnectivityBase_exposer.def( - "propertyType" - , propertyType_function_value - , ( bp::arg("bond"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return the type of the property for the specified bond at key key" ); - + + typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; + propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); + + ConnectivityBase_exposer.def( + "propertyType", propertyType_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified bond at key key"); } { //::SireMol::ConnectivityBase::propertyType - - typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; - propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); - - ConnectivityBase_exposer.def( - "propertyType" - , propertyType_function_value - , ( bp::arg("ang"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return the type of the property for the specified angle at key key" ); - + + typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; + propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); + + ConnectivityBase_exposer.def( + "propertyType", propertyType_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified angle at key key"); } { //::SireMol::ConnectivityBase::propertyType - - typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; - propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); - - ConnectivityBase_exposer.def( - "propertyType" - , propertyType_function_value - , ( bp::arg("dih"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return the type of the property for the specified dihedral at key key" ); - + + typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; + propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); + + ConnectivityBase_exposer.def( + "propertyType", propertyType_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified dihedral at key key"); } { //::SireMol::ConnectivityBase::propertyType - - typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; - propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); - - ConnectivityBase_exposer.def( - "propertyType" - , propertyType_function_value - , ( bp::arg("imp"), bp::arg("key") ) - , bp::release_gil_policy() - , "Return the type of the property for the specified improper at key key" ); - + + typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; + propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); + + ConnectivityBase_exposer.def( + "propertyType", propertyType_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified improper at key key"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Split this molecule into two parts about the atoms\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Split this molecule into two parts about the atoms\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::release_gil_policy() - , "Split the molecule into two parts about the bond between atom0 and atom1.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Split the molecule into two parts about the bond between atom0 and atom1.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::BondID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("bond") ) - , bp::release_gil_policy() - , "Split the molecule into two parts about the bond bond\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::BondID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("bond")), bp::release_gil_policy(), "Split the molecule into two parts about the bond bond\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms of this molecule into two parts about the atoms\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into two parts about the atoms\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms of this molecule about the atoms\natom0 and atom1\nThrow: SireMol::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule about the atoms\natom0 and atom1\nThrow: SireMol::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::BondID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("bond"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms of this molecule into two parts\nabout the bond bond\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::BondID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("bond"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into two parts\nabout the bond bond\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "Split this molecule into three parts about the atoms\natom0, atom1 and atom2.\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "Split this molecule into three parts about the atoms\natom0, atom1 and atom2.\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) - , bp::release_gil_policy() - , "Split the molecule into two parts based on the three supplied atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "Split the molecule into two parts based on the three supplied atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AngleID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("angle") ) - , bp::release_gil_policy() - , "Split the molecule into two parts based on the supplied angle\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AngleID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("angle")), bp::release_gil_policy(), "Split the molecule into two parts based on the supplied angle\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms of this molecule into three parts about the atoms\natom0, atom1 and atom2.\nNote that all three atoms must be contained in the selection or else\na missing_atom exception will be thrown\nAn exception will be thrown if it is not possible to split the molecule\nunambiguously in two, as the angle is part of a ring.\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into three parts about the atoms\natom0, atom1 and atom2.\nNote that all three atoms must be contained in the selection or else\na missing_atom exception will be thrown\nAn exception will be thrown if it is not possible to split the molecule\nunambiguously in two, as the angle is part of a ring.\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms of the molecule into two groups around the\nthree supplied atoms\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of the molecule into two groups around the\nthree supplied atoms\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AngleID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("angle"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the angle identified in\nangle. This splits the molecule about atom0() and atom2()\nof the angle, ignoring atom atom1().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AngleID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("angle"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the angle identified in\nangle. This splits the molecule about atom0() and atom2()\nof the angle, ignoring atom atom1().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) - , bp::release_gil_policy() - , "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) - , bp::release_gil_policy() - , "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::DihedralID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("dihedral") ) - , bp::release_gil_policy() - , "Split this molecule into two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::DihedralID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("dihedral")), bp::release_gil_policy(), "Split this molecule into two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms of this molecule into two parts\nbased on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nAll four atoms must be selected in selected_atoms or else\na missing_atom exception will be thrown\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into two parts\nbased on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nAll four atoms must be selected in selected_atoms or else\na missing_atom exception will be thrown\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the passed atoms. This splits\nthe molecule between atom0 and atom3, ignoring atom1 and\natom2.\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the passed atoms. This splits\nthe molecule between atom0 and atom3, ignoring atom1 and\natom2.\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::DihedralID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("dihedral"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::DihedralID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("dihedral"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::ImproperID const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("improper") ) - , bp::release_gil_policy() - , "Split this molecule into two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::ImproperID const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("improper")), bp::release_gil_policy(), "Split this molecule into two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::ImproperID const &,::SireMol::AtomSelection const & ) const; - split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); - - ConnectivityBase_exposer.def( - "split" - , split_function_value - , ( bp::arg("improper"), bp::arg("selected_atoms") ) - , bp::release_gil_policy() - , "Split the selected atoms in selected_atoms in this molecule\ninto two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); - + + typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::ImproperID const &, ::SireMol::AtomSelection const &) const; + split_function_type split_function_value(&::SireMol::ConnectivityBase::split); + + ConnectivityBase_exposer.def( + "split", split_function_value, (bp::arg("improper"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms in selected_atoms in this molecule\ninto two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); } { //::SireMol::ConnectivityBase::toCONECT - - typedef ::QString ( ::SireMol::ConnectivityBase::*toCONECT_function_type)( int ) const; - toCONECT_function_type toCONECT_function_value( &::SireMol::ConnectivityBase::toCONECT ); - - ConnectivityBase_exposer.def( - "toCONECT" - , toCONECT_function_value - , ( bp::arg("offset")=(int)(0) ) - , "Return a PDB format CONECT record for this connectivity object." ); - + + typedef ::QString (::SireMol::ConnectivityBase::*toCONECT_function_type)(int) const; + toCONECT_function_type toCONECT_function_value(&::SireMol::ConnectivityBase::toCONECT); + + ConnectivityBase_exposer.def( + "toCONECT", toCONECT_function_value, (bp::arg("offset") = (int)(0)), "Return a PDB format CONECT record for this connectivity object."); } { //::SireMol::ConnectivityBase::toString - - typedef ::QString ( ::SireMol::ConnectivityBase::*toString_function_type)( ) const; - toString_function_type toString_function_value( &::SireMol::ConnectivityBase::toString ); - - ConnectivityBase_exposer.def( - "toString" - , toString_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::QString (::SireMol::ConnectivityBase::*toString_function_type)() const; + toString_function_type toString_function_value(&::SireMol::ConnectivityBase::toString); + + ConnectivityBase_exposer.def( + "toString", toString_function_value, bp::release_gil_policy(), ""); } { //::SireMol::ConnectivityBase::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireMol::ConnectivityBase::typeName ); - - ConnectivityBase_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "" ); - - } - ConnectivityBase_exposer.staticmethod( "typeName" ); - ConnectivityBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::ConnectivityBase >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - ConnectivityBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::ConnectivityBase >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - ConnectivityBase_exposer.def_pickle(sire_pickle_suite< ::SireMol::ConnectivityBase >()); - ConnectivityBase_exposer.def( "__str__", &__str__< ::SireMol::ConnectivityBase > ); - ConnectivityBase_exposer.def( "__repr__", &__str__< ::SireMol::ConnectivityBase > ); - } + typedef char const *(*typeName_function_type)(); + typeName_function_type typeName_function_value(&::SireMol::ConnectivityBase::typeName); + + ConnectivityBase_exposer.def( + "typeName", typeName_function_value, bp::release_gil_policy(), ""); + } + ConnectivityBase_exposer.staticmethod("typeName"); + ConnectivityBase_exposer.def("__rlshift__", &__rlshift__QDataStream<::SireMol::ConnectivityBase>, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); + ConnectivityBase_exposer.def("__rrshift__", &__rrshift__QDataStream<::SireMol::ConnectivityBase>, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); + ConnectivityBase_exposer.def_pickle(sire_pickle_suite<::SireMol::ConnectivityBase>()); + ConnectivityBase_exposer.def("__str__", &__str__<::SireMol::ConnectivityBase>); + ConnectivityBase_exposer.def("__repr__", &__str__<::SireMol::ConnectivityBase>); + } } diff --git a/wrapper/Mol/ConnectivityEditor.pypp.cpp b/wrapper/Mol/ConnectivityEditor.pypp.cpp index 3e83b10f5..0b60550e0 100644 --- a/wrapper/Mol/ConnectivityEditor.pypp.cpp +++ b/wrapper/Mol/ConnectivityEditor.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; #include "angleid.h" +#include "atomidxmapping.h" + #include "atommatcher.h" #include "atomselection.h" @@ -55,7 +57,7 @@ namespace bp = boost::python; #include "connectivity.h" -SireMol::ConnectivityEditor __copy__(const SireMol::ConnectivityEditor &other){ return SireMol::ConnectivityEditor(other); } +SireMol::ConnectivityEditor __copy__(const SireMol::ConnectivityEditor &other) { return SireMol::ConnectivityEditor(other); } #include "Qt/qdatastream.hpp" @@ -63,349 +65,227 @@ SireMol::ConnectivityEditor __copy__(const SireMol::ConnectivityEditor &other){ #include "Helpers/release_gil_policy.hpp" -void register_ConnectivityEditor_class(){ +void register_ConnectivityEditor_class() +{ { //::SireMol::ConnectivityEditor - typedef bp::class_< SireMol::ConnectivityEditor, bp::bases< SireMol::ConnectivityBase, SireMol::MolViewProperty, SireBase::Property > > ConnectivityEditor_exposer_t; - ConnectivityEditor_exposer_t ConnectivityEditor_exposer = ConnectivityEditor_exposer_t( "ConnectivityEditor", "An editor that can be used to edit a Connectivity object\n\nAuthor: Christopher Woods\n", bp::init< >("Null constructor") ); - bp::scope ConnectivityEditor_scope( ConnectivityEditor_exposer ); - ConnectivityEditor_exposer.def( bp::init< SireMol::Connectivity const & >(( bp::arg("connectivity") ), "Construct an editor to edit a copy of the passed\nConnectivity object") ); - ConnectivityEditor_exposer.def( bp::init< SireMol::ConnectivityEditor const & >(( bp::arg("other") ), "Copy constructor") ); + typedef bp::class_> ConnectivityEditor_exposer_t; + ConnectivityEditor_exposer_t ConnectivityEditor_exposer = ConnectivityEditor_exposer_t("ConnectivityEditor", "An editor that can be used to edit a Connectivity object\n\nAuthor: Christopher Woods\n", bp::init<>("Null constructor")); + bp::scope ConnectivityEditor_scope(ConnectivityEditor_exposer); + ConnectivityEditor_exposer.def(bp::init((bp::arg("connectivity")), "Construct an editor to edit a copy of the passed\nConnectivity object")); + ConnectivityEditor_exposer.def(bp::init((bp::arg("other")), "Copy constructor")); { //::SireMol::ConnectivityEditor::commit - - typedef ::SireMol::Connectivity ( ::SireMol::ConnectivityEditor::*commit_function_type)( ) const; - commit_function_type commit_function_value( &::SireMol::ConnectivityEditor::commit ); - - ConnectivityEditor_exposer.def( - "commit" - , commit_function_value - , bp::release_gil_policy() - , "Return the editied connectivity" ); - + + typedef ::SireMol::Connectivity (::SireMol::ConnectivityEditor::*commit_function_type)() const; + commit_function_type commit_function_value(&::SireMol::ConnectivityEditor::commit); + + ConnectivityEditor_exposer.def( + "commit", commit_function_value, bp::release_gil_policy(), "Return the editied connectivity"); } { //::SireMol::ConnectivityEditor::connect - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*connect_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) ; - connect_function_type connect_function_value( &::SireMol::ConnectivityEditor::connect ); - - ConnectivityEditor_exposer.def( - "connect" - , connect_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::return_self< >() - , "Record the connection between the atoms at indicies atom0\nand atom1\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*connect_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx); + connect_function_type connect_function_value(&::SireMol::ConnectivityEditor::connect); + + ConnectivityEditor_exposer.def( + "connect", connect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Record the connection between the atoms at indicies atom0\nand atom1\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::connect - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*connect_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) ; - connect_function_type connect_function_value( &::SireMol::ConnectivityEditor::connect ); - - ConnectivityEditor_exposer.def( - "connect" - , connect_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::return_self< >() - , "Record a connection between the atom identified by atom0 and\nthe atom identified by atom1\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*connect_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &); + connect_function_type connect_function_value(&::SireMol::ConnectivityEditor::connect); + + ConnectivityEditor_exposer.def( + "connect", connect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Record a connection between the atom identified by atom0 and\nthe atom identified by atom1\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnect - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) ; - disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); - - ConnectivityEditor_exposer.def( - "disconnect" - , disconnect_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::return_self< >() - , "Remove the connection between the atoms at indicies atom0\nand atom1 - this does nothing if there isnt already a connection\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnect_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx); + disconnect_function_type disconnect_function_value(&::SireMol::ConnectivityEditor::disconnect); + + ConnectivityEditor_exposer.def( + "disconnect", disconnect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Remove the connection between the atoms at indicies atom0\nand atom1 - this does nothing if there isnt already a connection\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnect - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) ; - disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); - - ConnectivityEditor_exposer.def( - "disconnect" - , disconnect_function_value - , ( bp::arg("atom0"), bp::arg("atom1") ) - , bp::return_self< >() - , "Disconnect the atoms that are identified by atom0 and atom1 -\nthis does nothing if there isnt a connection between these atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnect_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &); + disconnect_function_type disconnect_function_value(&::SireMol::ConnectivityEditor::disconnect); + + ConnectivityEditor_exposer.def( + "disconnect", disconnect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Disconnect the atoms that are identified by atom0 and atom1 -\nthis does nothing if there isnt a connection between these atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::AtomIdx ) ; - disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); - - ConnectivityEditor_exposer.def( - "disconnectAll" - , disconnectAll_function_value - , ( bp::arg("atomidx") ) - , bp::return_self< >() - , "Remove all of the connections to the atom at index atomidx\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::AtomIdx); + disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); + + ConnectivityEditor_exposer.def( + "disconnectAll", disconnectAll_function_value, (bp::arg("atomidx")), bp::return_self<>(), "Remove all of the connections to the atom at index atomidx\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::ResIdx ) ; - disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); - - ConnectivityEditor_exposer.def( - "disconnectAll" - , disconnectAll_function_value - , ( bp::arg("residx") ) - , bp::return_self< >() - , "Remove all of the connections that involve any of the atoms\nin the residue at index residx\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::ResIdx); + disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); + + ConnectivityEditor_exposer.def( + "disconnectAll", disconnectAll_function_value, (bp::arg("residx")), bp::return_self<>(), "Remove all of the connections that involve any of the atoms\nin the residue at index residx\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::AtomID const & ) ; - disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); - - ConnectivityEditor_exposer.def( - "disconnectAll" - , disconnectAll_function_value - , ( bp::arg("atomid") ) - , bp::return_self< >() - , "Remove all of the connections to the atom identified by atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::AtomID const &); + disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); + + ConnectivityEditor_exposer.def( + "disconnectAll", disconnectAll_function_value, (bp::arg("atomid")), bp::return_self<>(), "Remove all of the connections to the atom identified by atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::ResID const & ) ; - disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); - - ConnectivityEditor_exposer.def( - "disconnectAll" - , disconnectAll_function_value - , ( bp::arg("resid") ) - , bp::return_self< >() - , "Remove all of the connections that involve any of the atoms\nin the residue identified by resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::ResID const &); + disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); + + ConnectivityEditor_exposer.def( + "disconnectAll", disconnectAll_function_value, (bp::arg("resid")), bp::return_self<>(), "Remove all of the connections that involve any of the atoms\nin the residue identified by resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ) ; - disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); - - ConnectivityEditor_exposer.def( - "disconnectAll" - , disconnectAll_function_value - , bp::return_self< >() - , "Remove all bonds from this molecule" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(); + disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); + + ConnectivityEditor_exposer.def( + "disconnectAll", disconnectAll_function_value, bp::return_self<>(), "Remove all bonds from this molecule"); } - ConnectivityEditor_exposer.def( bp::self != bp::self ); + ConnectivityEditor_exposer.def(bp::self != bp::self); { //::SireMol::ConnectivityEditor::operator= - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*assign_function_type)( ::SireMol::ConnectivityBase const & ) ; - assign_function_type assign_function_value( &::SireMol::ConnectivityEditor::operator= ); - - ConnectivityEditor_exposer.def( - "assign" - , assign_function_value - , ( bp::arg("other") ) - , bp::return_self< >() - , "" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*assign_function_type)(::SireMol::ConnectivityBase const &); + assign_function_type assign_function_value(&::SireMol::ConnectivityEditor::operator=); + + ConnectivityEditor_exposer.def( + "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); } - ConnectivityEditor_exposer.def( bp::self == bp::self ); + ConnectivityEditor_exposer.def(bp::self == bp::self); { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::QString const & ) ; - removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); - - ConnectivityEditor_exposer.def( - "removeProperty" - , removeProperty_function_value - , ( bp::arg("key") ) - , bp::return_self< >() - , "Remove the specified property from all bonds" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::QString const &); + removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); + + ConnectivityEditor_exposer.def( + "removeProperty", removeProperty_function_value, (bp::arg("key")), bp::return_self<>(), "Remove the specified property from all bonds"); } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::BondID const &,::QString const & ) ; - removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); - - ConnectivityEditor_exposer.def( - "removeProperty" - , removeProperty_function_value - , ( bp::arg("bond"), bp::arg("key") ) - , bp::return_self< >() - , "Remove the specified property from the specified bond" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::BondID const &, ::QString const &); + removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); + + ConnectivityEditor_exposer.def( + "removeProperty", removeProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified bond"); } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::AngleID const &,::QString const & ) ; - removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); - - ConnectivityEditor_exposer.def( - "removeProperty" - , removeProperty_function_value - , ( bp::arg("ang"), bp::arg("key") ) - , bp::return_self< >() - , "Remove the specified property from the specified angle" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::AngleID const &, ::QString const &); + removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); + + ConnectivityEditor_exposer.def( + "removeProperty", removeProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified angle"); } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::DihedralID const &,::QString const & ) ; - removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); - - ConnectivityEditor_exposer.def( - "removeProperty" - , removeProperty_function_value - , ( bp::arg("dih"), bp::arg("key") ) - , bp::return_self< >() - , "Remove the specified property from the specified dihedral" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::DihedralID const &, ::QString const &); + removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); + + ConnectivityEditor_exposer.def( + "removeProperty", removeProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified dihedral"); } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::ImproperID const &,::QString const & ) ; - removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); - - ConnectivityEditor_exposer.def( - "removeProperty" - , removeProperty_function_value - , ( bp::arg("imp"), bp::arg("key") ) - , bp::return_self< >() - , "Remove the specified property from the specified improper" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::ImproperID const &, ::QString const &); + removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); + + ConnectivityEditor_exposer.def( + "removeProperty", removeProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified improper"); } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::BondID const &,::QString const &,::SireBase::Property const & ) ; - setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); - - ConnectivityEditor_exposer.def( - "setProperty" - , setProperty_function_value - , ( bp::arg("bond"), bp::arg("key"), bp::arg("value") ) - , bp::return_self< >() - , "Set the property for the specified bond, at the specified key, to value" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::BondID const &, ::QString const &, ::SireBase::Property const &); + setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); + + ConnectivityEditor_exposer.def( + "setProperty", setProperty_function_value, (bp::arg("bond"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified bond, at the specified key, to value"); } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::AngleID const &,::QString const &,::SireBase::Property const & ) ; - setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); - - ConnectivityEditor_exposer.def( - "setProperty" - , setProperty_function_value - , ( bp::arg("ang"), bp::arg("key"), bp::arg("value") ) - , bp::return_self< >() - , "Set the property for the specified angle, at the specified key, to value" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::AngleID const &, ::QString const &, ::SireBase::Property const &); + setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); + + ConnectivityEditor_exposer.def( + "setProperty", setProperty_function_value, (bp::arg("ang"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified angle, at the specified key, to value"); } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::DihedralID const &,::QString const &,::SireBase::Property const & ) ; - setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); - - ConnectivityEditor_exposer.def( - "setProperty" - , setProperty_function_value - , ( bp::arg("dih"), bp::arg("key"), bp::arg("value") ) - , bp::return_self< >() - , "Set the property for the specified dihedral, at the specified key, to value" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::DihedralID const &, ::QString const &, ::SireBase::Property const &); + setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); + + ConnectivityEditor_exposer.def( + "setProperty", setProperty_function_value, (bp::arg("dih"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified dihedral, at the specified key, to value"); } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::ImproperID const &,::QString const &,::SireBase::Property const & ) ; - setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); - - ConnectivityEditor_exposer.def( - "setProperty" - , setProperty_function_value - , ( bp::arg("imp"), bp::arg("key"), bp::arg("value") ) - , bp::return_self< >() - , "Set the property for the specified improper, at the specified key, to value" ); - + + typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::ImproperID const &, ::QString const &, ::SireBase::Property const &); + setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); + + ConnectivityEditor_exposer.def( + "setProperty", setProperty_function_value, (bp::arg("imp"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified improper, at the specified key, to value"); } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::BondID const &,::QString const & ) ; - takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); - - ConnectivityEditor_exposer.def( - "takeProperty" - , takeProperty_function_value - , ( bp::arg("bond"), bp::arg("key") ) - , bp::release_gil_policy() - , "Take the specified property from the specified bond - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); - + + typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::BondID const &, ::QString const &); + takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); + + ConnectivityEditor_exposer.def( + "takeProperty", takeProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified bond - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::AngleID const &,::QString const & ) ; - takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); - - ConnectivityEditor_exposer.def( - "takeProperty" - , takeProperty_function_value - , ( bp::arg("ang"), bp::arg("key") ) - , bp::release_gil_policy() - , "Take the specified property from the specified angle - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); - + + typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::AngleID const &, ::QString const &); + takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); + + ConnectivityEditor_exposer.def( + "takeProperty", takeProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified angle - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::DihedralID const &,::QString const & ) ; - takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); - - ConnectivityEditor_exposer.def( - "takeProperty" - , takeProperty_function_value - , ( bp::arg("dih"), bp::arg("key") ) - , bp::release_gil_policy() - , "Take the specified property from the specified dihedral - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); - + + typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::DihedralID const &, ::QString const &); + takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); + + ConnectivityEditor_exposer.def( + "takeProperty", takeProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified dihedral - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::ImproperID const &,::QString const & ) ; - takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); - - ConnectivityEditor_exposer.def( - "takeProperty" - , takeProperty_function_value - , ( bp::arg("imp"), bp::arg("key") ) - , bp::release_gil_policy() - , "Take the specified property from the specified improper - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); - + + typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::ImproperID const &, ::QString const &); + takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); + + ConnectivityEditor_exposer.def( + "takeProperty", takeProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified improper - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); } { //::SireMol::ConnectivityEditor::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireMol::ConnectivityEditor::typeName ); - - ConnectivityEditor_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(*typeName_function_type)(); + typeName_function_type typeName_function_value(&::SireMol::ConnectivityEditor::typeName); + + ConnectivityEditor_exposer.def( + "typeName", typeName_function_value, bp::release_gil_policy(), ""); } - ConnectivityEditor_exposer.staticmethod( "typeName" ); - ConnectivityEditor_exposer.def( "__copy__", &__copy__); - ConnectivityEditor_exposer.def( "__deepcopy__", &__copy__); - ConnectivityEditor_exposer.def( "clone", &__copy__); - ConnectivityEditor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::ConnectivityEditor >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - ConnectivityEditor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::ConnectivityEditor >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - ConnectivityEditor_exposer.def_pickle(sire_pickle_suite< ::SireMol::ConnectivityEditor >()); - ConnectivityEditor_exposer.def( "__str__", &__str__< ::SireMol::ConnectivityEditor > ); - ConnectivityEditor_exposer.def( "__repr__", &__str__< ::SireMol::ConnectivityEditor > ); + ConnectivityEditor_exposer.staticmethod("typeName"); + ConnectivityEditor_exposer.def("__copy__", &__copy__); + ConnectivityEditor_exposer.def("__deepcopy__", &__copy__); + ConnectivityEditor_exposer.def("clone", &__copy__); + ConnectivityEditor_exposer.def("__rlshift__", &__rlshift__QDataStream<::SireMol::ConnectivityEditor>, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); + ConnectivityEditor_exposer.def("__rrshift__", &__rrshift__QDataStream<::SireMol::ConnectivityEditor>, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); + ConnectivityEditor_exposer.def_pickle(sire_pickle_suite<::SireMol::ConnectivityEditor>()); + ConnectivityEditor_exposer.def("__str__", &__str__<::SireMol::ConnectivityEditor>); + ConnectivityEditor_exposer.def("__repr__", &__str__<::SireMol::ConnectivityEditor>); } - } diff --git a/wrapper/Mol/Frame.pypp.cpp b/wrapper/Mol/Frame.pypp.cpp index 4445fd2e9..eb5b6dc84 100644 --- a/wrapper/Mol/Frame.pypp.cpp +++ b/wrapper/Mol/Frame.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; #include "SireVol/space.h" +#include "atomidxmapping.h" + #include "trajectory.h" #include "trajectoryaligner.h" diff --git a/wrapper/Mol/MolViewProperty.pypp.cpp b/wrapper/Mol/MolViewProperty.pypp.cpp index 66333b89a..541d5fd96 100644 --- a/wrapper/Mol/MolViewProperty.pypp.cpp +++ b/wrapper/Mol/MolViewProperty.pypp.cpp @@ -9,6 +9,8 @@ namespace bp = boost::python; #include "SireError/errors.h" +#include "atomidxmapping.h" + #include "atommatcher.h" #include "atommatchers.h" diff --git a/wrapper/Mol/MoleculeProperty.pypp.cpp b/wrapper/Mol/MoleculeProperty.pypp.cpp index fda91a530..90b44777d 100644 --- a/wrapper/Mol/MoleculeProperty.pypp.cpp +++ b/wrapper/Mol/MoleculeProperty.pypp.cpp @@ -9,6 +9,8 @@ namespace bp = boost::python; #include "SireError/errors.h" +#include "atomidxmapping.h" + #include "atommatcher.h" #include "atommatchers.h" diff --git a/wrapper/Mol/ResFloatProperty.pypp.cpp b/wrapper/Mol/ResFloatProperty.pypp.cpp index c950b2540..5d8652d4d 100644 --- a/wrapper/Mol/ResFloatProperty.pypp.cpp +++ b/wrapper/Mol/ResFloatProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ResProperty __copy__(const SireMol::ResProperty &other){ return SireMol::ResProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ResIntProperty.pypp.cpp b/wrapper/Mol/ResIntProperty.pypp.cpp index a7d82b290..b51ac84bf 100644 --- a/wrapper/Mol/ResIntProperty.pypp.cpp +++ b/wrapper/Mol/ResIntProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ResProperty __copy__(const SireMol::ResProperty &other){ return SireMol::ResProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ResPropertyProperty.pypp.cpp b/wrapper/Mol/ResPropertyProperty.pypp.cpp index fe9bb60ce..0f07c299a 100644 --- a/wrapper/Mol/ResPropertyProperty.pypp.cpp +++ b/wrapper/Mol/ResPropertyProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ResProperty > __copy__(const SireMol::ResProperty > &other){ return SireMol::ResProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ResStringProperty.pypp.cpp b/wrapper/Mol/ResStringProperty.pypp.cpp index 5f39f59e2..688925b05 100644 --- a/wrapper/Mol/ResStringProperty.pypp.cpp +++ b/wrapper/Mol/ResStringProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ResProperty __copy__(const SireMol::ResProperty &other){ return SireMol::ResProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/ResVariantProperty.pypp.cpp b/wrapper/Mol/ResVariantProperty.pypp.cpp index 734748fe9..48e50158c 100644 --- a/wrapper/Mol/ResVariantProperty.pypp.cpp +++ b/wrapper/Mol/ResVariantProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::ResProperty __copy__(const SireMol::ResProperty &other){ return SireMol::ResProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/SegFloatProperty.pypp.cpp b/wrapper/Mol/SegFloatProperty.pypp.cpp index e7ef9404d..9800ae7d7 100644 --- a/wrapper/Mol/SegFloatProperty.pypp.cpp +++ b/wrapper/Mol/SegFloatProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::SegProperty __copy__(const SireMol::SegProperty &other){ return SireMol::SegProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/SegIntProperty.pypp.cpp b/wrapper/Mol/SegIntProperty.pypp.cpp index 227bb720e..aca4cdd1e 100644 --- a/wrapper/Mol/SegIntProperty.pypp.cpp +++ b/wrapper/Mol/SegIntProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::SegProperty __copy__(const SireMol::SegProperty &other){ return SireMol::SegProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/SegPropertyProperty.pypp.cpp b/wrapper/Mol/SegPropertyProperty.pypp.cpp index 97ccac33a..f39176194 100644 --- a/wrapper/Mol/SegPropertyProperty.pypp.cpp +++ b/wrapper/Mol/SegPropertyProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::SegProperty > __copy__(const SireMol::SegProperty > &other){ return SireMol::SegProperty >(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/SegStringProperty.pypp.cpp b/wrapper/Mol/SegStringProperty.pypp.cpp index a35b2152d..ea018af56 100644 --- a/wrapper/Mol/SegStringProperty.pypp.cpp +++ b/wrapper/Mol/SegStringProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::SegProperty __copy__(const SireMol::SegProperty &other){ return SireMol::SegProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/SegVariantProperty.pypp.cpp b/wrapper/Mol/SegVariantProperty.pypp.cpp index c710206af..aa156b22e 100644 --- a/wrapper/Mol/SegVariantProperty.pypp.cpp +++ b/wrapper/Mol/SegVariantProperty.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; #include "SireMol/moleculeview.h" +#include "SireMol/atomidxmapping.h" + SireMol::SegProperty __copy__(const SireMol::SegProperty &other){ return SireMol::SegProperty(other); } #include "Qt/qdatastream.hpp" diff --git a/wrapper/Mol/Trajectory.pypp.cpp b/wrapper/Mol/Trajectory.pypp.cpp index 3cfae3d2a..0921e0e02 100644 --- a/wrapper/Mol/Trajectory.pypp.cpp +++ b/wrapper/Mol/Trajectory.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; #include "SireVol/space.h" +#include "atomidxmapping.h" + #include "trajectory.h" #include "trajectoryaligner.h" diff --git a/wrapper/Mol/special_code.py b/wrapper/Mol/special_code.py index 2c133d39d..810ccd1c3 100644 --- a/wrapper/Mol/special_code.py +++ b/wrapper/Mol/special_code.py @@ -351,6 +351,7 @@ def fix_Mover(c): def fix_MolViewProperty(c): c.add_declaration_code('#include "SireMaths/vector.h"') c.add_declaration_code('#include "SireMol/moleculeview.h"') + c.add_declaration_code('#include "SireMol/atomidxmapping.h"') c.decls("set").call_policies = call_policies.return_self() diff --git a/wrapper/System/_System_free_functions.pypp.cpp b/wrapper/System/_System_free_functions.pypp.cpp index 3992360c6..19a7794de 100644 --- a/wrapper/System/_System_free_functions.pypp.cpp +++ b/wrapper/System/_System_free_functions.pypp.cpp @@ -721,6 +721,14 @@ namespace bp = boost::python; #include "create_test_molecule.h" +#include "SireMM/mmdetail.h" + +#include "SireMol/atomidxmapping.h" + +#include "SireMol/core.h" + +#include "SireMol/moleditor.h" + #include "SireSystem/merge.h" #include "merge.h" @@ -977,13 +985,13 @@ void register_free_functions(){ { //::SireSystem::merge - typedef ::SireMol::Molecule ( *merge_function_type )( ::SireMol::AtomMapping const &,bool,bool,bool,bool,::SireBase::PropertyMap const & ); + typedef ::SireMol::Molecule ( *merge_function_type )( ::SireMol::AtomMapping const &,::QStringList const &,bool,bool,bool,bool,::SireBase::PropertyMap const & ); merge_function_type merge_function_value( &::SireSystem::merge ); bp::def( "merge" , merge_function_value - , ( bp::arg("mols"), bp::arg("as_new_molecule")=(bool)(true), bp::arg("allow_ring_breaking")=(bool)(false), bp::arg("allow_ring_size_change")=(bool)(false), bp::arg("force")=(bool)(false), bp::arg("map")=SireBase::PropertyMap() ) + , ( bp::arg("mols"), bp::arg("properties")=::QStringList( ), bp::arg("as_new_molecule")=(bool)(true), bp::arg("allow_ring_breaking")=(bool)(false), bp::arg("allow_ring_size_change")=(bool)(false), bp::arg("force")=(bool)(false), bp::arg("map")=SireBase::PropertyMap() ) , "" ); } From 04f103e83f510bec6b5cb2d3c02f9d4261e5902e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 28 Feb 2024 22:36:22 +0000 Subject: [PATCH 136/468] AtomProperty merging is working quite well :-) Next onto internal merging --- corelib/src/libs/SireMM/atomljs.cpp | 7 ++++ corelib/src/libs/SireMol/atomproperty.hpp | 12 ++++-- corelib/src/libs/SireSystem/merge.cpp | 47 ++++++++++++++++++++--- 3 files changed, 58 insertions(+), 8 deletions(-) diff --git a/corelib/src/libs/SireMM/atomljs.cpp b/corelib/src/libs/SireMM/atomljs.cpp index fe3e445e6..8bc272b25 100644 --- a/corelib/src/libs/SireMM/atomljs.cpp +++ b/corelib/src/libs/SireMM/atomljs.cpp @@ -30,6 +30,7 @@ #include "SireBase/quickcopy.hpp" #include "SireBase/incremint.h" #include "SireBase/propertylist.h" +#include "SireBase/console.h" #include "SireStream/magic_error.h" #include "SireStream/datastream.h" @@ -1479,6 +1480,11 @@ PropertyList AtomProperty::merge(const MolViewProperty &other, AtomProperty prop0 = ref; AtomProperty prop1 = ref; + if (not ghost.isEmpty()) + { + Console::warning(QObject::tr("The ghost parameter '%1' for LJ parameters is ignored").arg(ghost)); + } + for (const auto &index : mapping) { if (index.isUnmappedIn0() and index.isUnmappedIn1()) @@ -1490,6 +1496,7 @@ PropertyList AtomProperty::merge(const MolViewProperty &other, { auto lj1 = pert.get(index.cgAtomIdx1()); prop0.set(index.cgAtomIdx0(), LJParameter(lj1.sigma(), SireUnits::Dimension::MolarEnergy(0))); + prop1.set(index.cgAtomIdx0(), lj1); } else if (index.isUnmappedIn1()) { diff --git a/corelib/src/libs/SireMol/atomproperty.hpp b/corelib/src/libs/SireMol/atomproperty.hpp index 5c2c1d74a..2e6604995 100644 --- a/corelib/src/libs/SireMol/atomproperty.hpp +++ b/corelib/src/libs/SireMol/atomproperty.hpp @@ -1257,12 +1257,18 @@ namespace SireMol for (const auto &index : mapping) { - if (index.isUnmappedIn0()) + if (index.isUnmappedIn0() and index.isUnmappedIn1()) { prop0.set(index.cgAtomIdx0(), ghost_param); + prop1.set(index.cgAtomIdx0(), ghost_param); } - - if (index.isUnmappedIn1()) + else if (index.isUnmappedIn0()) + { + auto lj1 = pert.get(index.cgAtomIdx1()); + prop0.set(index.cgAtomIdx0(), ghost_param); + prop1.set(index.cgAtomIdx0(), lj1); + } + else if (index.isUnmappedIn1()) { prop1.set(index.cgAtomIdx0(), ghost_param); } diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 96a6be5cb..29da7b69d 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -209,6 +209,29 @@ namespace SireSystem const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); + if (mol0.isEmpty()) + return mol0; + + // find the largest AtomNum in mol0 + AtomNum largest_atomnum; + + const auto &molinfo = mol0.info(); + + for (int i = 0; i < molinfo.nAtoms(); ++i) + { + const auto num = molinfo.number(AtomIdx(i)); + + if (largest_atomnum.isNull()) + { + largest_atomnum = num; + } + else if (not num.isNull()) + { + if (num.value() > largest_atomnum.value()) + largest_atomnum = num; + } + } + // use a property to track which atoms have been mapped - // a value of -1 means that this atom is not mapped editmol.setProperty("_mol0_index", AtomIntProperty(mol0.info(), -1)); @@ -333,6 +356,8 @@ namespace SireSystem // add the atom - it has the name "Xxx" as it doesn't exist // in the reference state auto atom = res.add(AtomName("Xxx")); + largest_atomnum = AtomNum(largest_atomnum.value() + 1); + atom.renumber(largest_atomnum); // reparent this atom to the CutGroup for this residue atom.reparent(cgidx); @@ -353,7 +378,7 @@ namespace SireSystem // now we have the merged molecule, we need to work out the mapping // of atoms from the reference to the perturbed state in this // merged molecule - QList entries; + QList idx_entries; const auto &molinfo0 = editmol.info(); const auto &molinfo1 = mol1.info(); @@ -373,11 +398,23 @@ namespace SireSystem const bool is_unmapped_in_reference = (index0 == -1); - entries.append(AtomIdxMappingEntry(AtomIdx(i), AtomIdx(index1), - molinfo0, molinfo1, - is_unmapped_in_reference)); + AtomIdx atomidx1(index1); + + if (index1 == -1) + { + // this atom is not in the perturbed state, so this + // index should be set to null + atomidx1 = AtomIdx(); + } + + idx_entries.append(AtomIdxMappingEntry(AtomIdx(i), atomidx1, + molinfo0, molinfo1, + is_unmapped_in_reference)); } + AtomIdxMapping entries(idx_entries); + idx_entries.clear(); + // now go through all of the properties that we want to merge // and merge them using the AtomIdxMapping object - remove // the common property of these @@ -430,7 +467,7 @@ namespace SireSystem editmol.removeProperty(map0[prop]); editmol.setProperty(map[prop + "0"].source(), merged[0]); - editmol.setProperty(map[prop + "1"].source() + "1", merged[1]); + editmol.setProperty(map[prop + "1"].source(), merged[1]); } else { From 44a4eaaafbaa8a08092211a322b3104014405f77 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 28 Feb 2024 22:57:35 +0000 Subject: [PATCH 137/468] WIP - working out how to merge bonds... --- corelib/src/libs/SireMM/twoatomfunctions.cpp | 69 ++++++++++++++++++-- corelib/src/libs/SireMM/twoatomfunctions.h | 4 ++ corelib/src/libs/SireMol/atomidxmapping.h | 9 +++ 3 files changed, 78 insertions(+), 4 deletions(-) diff --git a/corelib/src/libs/SireMM/twoatomfunctions.cpp b/corelib/src/libs/SireMM/twoatomfunctions.cpp index dc0c48167..ee35b1608 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.cpp +++ b/corelib/src/libs/SireMM/twoatomfunctions.cpp @@ -429,6 +429,45 @@ void TwoAtomFunctions::clear(AtomIdx atom) } } +/** Clear all functions that invole any of the atoms in 'atoms' + * - if 'exclusive' is true, then this only removes functions + * that exclusively involve these atoms - if false, then + * if removes functions that involve any of these atoms + */ +void TwoAtomFunctions::clear(const QList &atoms, bool exclusive) +{ + QSet atms; + atms.reserve(atoms.count()); + + for (const auto &atom : atoms) + { + atms.insert(atom.map(info().nAtoms())); + } + + QList keys = potentials_by_atoms.keys(); + + if (exclusive) + { + for (const auto &key : keys) + { + if (atms.contains(key.atom0) and atms.contains(key.atom1)) + { + TwoAtomFunctions::removeSymbols(potentials_by_atoms.take(key).symbols()); + } + } + } + else + { + for (const auto &key : keys) + { + if (atms.contains(key.atom0) or atms.contains(key.atom1)) + { + TwoAtomFunctions::removeSymbols(potentials_by_atoms.take(key).symbols()); + } + } + } +} + /** Clear any function that acts on the atoms identified by 'atom' \throw SireMol::missing_atom @@ -775,13 +814,35 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, CODELOC); } - SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") - .arg(this->what())); + const TwoAtomFunctions &ref = *this; + const TwoAtomFunctions &pert = other.asA(); + + TwoAtomFunctions prop0 = ref; + TwoAtomFunctions prop1 = ref; + + // the prop0 properties are already correct + + // the prop1 properties are made by finding all of the atoms that + // are involved in bonds in 'pert' and removing any bonds involving + // only those atoms from 'prop1', and then adding back the matching + // bonds from 'pert' + prop1.clear(mapping.mappedIn1(), true); + + auto map1to0 = mapping.map1to0(); + + const auto pert_bonds = pert.potentials(map1to0.keys(), true); + + for (const auto &pert_bond : pert_bonds) + { + prop1.set(map1to0.value(info().atomIdx(pert_bond.atom0())), + map1to0.value(info().atomIdx(pert_bond.atom1())), + pert_bond.function()); + } SireBase::PropertyList ret; - ret.append(*this); - ret.append(*this); + ret.append(prop0); + ret.append(prop1); return ret; } diff --git a/corelib/src/libs/SireMM/twoatomfunctions.h b/corelib/src/libs/SireMM/twoatomfunctions.h index b70b42fba..cc6d1cfee 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.h +++ b/corelib/src/libs/SireMM/twoatomfunctions.h @@ -181,6 +181,8 @@ namespace SireMM void clear(const AtomID &atom0, const AtomID &atom1); void clear(const BondID &bondid); + void clear(const QList &atoms, bool exclusive = true); + void clear(); void substitute(const Identities &identities); @@ -200,6 +202,8 @@ namespace SireMM QVector potentials() const; QVector forces(const Symbol &symbol) const; + QVector potentials(const QList &atoms, bool exclusive = true) const; + TwoAtomFunctions includeOnly(const AtomSelection &selection, bool isstrict = true) const; SireBase::PropertyList merge(const MolViewProperty &other, diff --git a/corelib/src/libs/SireMol/atomidxmapping.h b/corelib/src/libs/SireMol/atomidxmapping.h index cdd1d2354..af701484d 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.h +++ b/corelib/src/libs/SireMol/atomidxmapping.h @@ -178,6 +178,15 @@ namespace SireMol void remove(const AtomIdx &atom); void remove(const CGAtomIdx &atom); + QList unmappedIn0() const; + QList unmappedIn1() const; + + QList mappedIn0() const; + QList mappedIn1() const; + + QHash map0to1() const; + QHash map1to0() const; + private: void assertSane() const; From 6bdf012290c5d97f5eeebd3c977c6008c7faf2c9 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 1 Mar 2024 19:53:02 +0000 Subject: [PATCH 138/468] Making progress - am merging the bonds. To test this, I need to next merge the connectivities together, as well as create a single merged connectivity. --- corelib/src/libs/SireMM/twoatomfunctions.cpp | 51 +- corelib/src/libs/SireMol/atomidxmapping.cpp | 170 ++ corelib/src/libs/SireMol/atomidxmapping.h | 7 +- corelib/src/libs/SireSystem/merge.cpp | 3 + wrapper/Mol/Atom.pypp.cpp | 2 + wrapper/Mol/AtomEditorBase.pypp.cpp | 2 + wrapper/Mol/AtomIdxMapping.pypp.cpp | 72 + wrapper/Mol/AtomIdxMappingEntry.pypp.cpp | 24 + wrapper/Mol/Connectivity.pypp.cpp | 114 +- wrapper/Mol/ConnectivityBase.pypp.cpp | 1888 +++++++++++------- wrapper/Mol/ConnectivityEditor.pypp.cpp | 464 +++-- wrapper/Mol/SireMol_containers.cpp | 172 +- 12 files changed, 1987 insertions(+), 982 deletions(-) diff --git a/corelib/src/libs/SireMM/twoatomfunctions.cpp b/corelib/src/libs/SireMM/twoatomfunctions.cpp index ee35b1608..5ab22c92f 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.cpp +++ b/corelib/src/libs/SireMM/twoatomfunctions.cpp @@ -639,6 +639,41 @@ Expression TwoAtomFunctions::force(const BondID &bondid, const Symbol &symbol) c return -(this->potential(bondid).differentiate(symbol)); } +/** Return the potential energy functions acting between the identified + pairs of atoms - if exclusive is true then only return potentials where + both atoms are in the bond +*/ +QVector TwoAtomFunctions::potentials(const QList &atms, bool exclusive) const +{ + QVector funcs; + funcs.reserve(potentials_by_atoms.count()); + + QSet atoms(atms.begin(), atms.end()); + + for (QHash::const_iterator it = potentials_by_atoms.constBegin(); + it != potentials_by_atoms.constEnd(); ++it) + { + if (exclusive) + { + if (atoms.contains(AtomIdx(it.key().atom0)) and atoms.contains(AtomIdx(it.key().atom1))) + { + funcs.append(TwoAtomFunction(info().cgAtomIdx(AtomIdx(it.key().atom0)), + info().cgAtomIdx(AtomIdx(it.key().atom1)), it.value())); + } + } + else + { + if (atoms.contains(AtomIdx(it.key().atom0)) or atoms.contains(AtomIdx(it.key().atom1))) + { + funcs.append(TwoAtomFunction(info().cgAtomIdx(AtomIdx(it.key().atom0)), + info().cgAtomIdx(AtomIdx(it.key().atom1)), it.value())); + } + } + } + + return funcs; +} + /** Return the potential energy functions acting between the identified pairs of atoms */ QVector TwoAtomFunctions::potentials() const @@ -814,6 +849,11 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, CODELOC); } + if (not ghost.isEmpty()) + { + Console::warning(QObject::tr("The ghost parameter '%1' for bond parameters is ignored").arg(ghost)); + } + const TwoAtomFunctions &ref = *this; const TwoAtomFunctions &pert = other.asA(); @@ -825,11 +865,18 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, // the prop1 properties are made by finding all of the atoms that // are involved in bonds in 'pert' and removing any bonds involving // only those atoms from 'prop1', and then adding back the matching - // bonds from 'pert' + // bonds from 'pert'. Use 'true' to only remove bonds where both + // atoms are in the mapping prop1.clear(mapping.mappedIn1(), true); - auto map1to0 = mapping.map1to0(); + // get the mapping from the perturbed to reference states, including + // atoms that don't exist in the reference state. In all cases, + // the values are the indexes in the merged molecule + auto map1to0 = mapping.map1to0(true); + // now find all of the bonds in 'pert' where both atoms in the + // bond are in map1to0.keys() - i.e. exist and are mapped from + // the perturbed state const auto pert_bonds = pert.potentials(map1to0.keys(), true); for (const auto &pert_bond : pert_bonds) diff --git a/corelib/src/libs/SireMol/atomidxmapping.cpp b/corelib/src/libs/SireMol/atomidxmapping.cpp index baad41a44..6ab83b583 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.cpp +++ b/corelib/src/libs/SireMol/atomidxmapping.cpp @@ -205,6 +205,18 @@ bool AtomIdxMappingEntry::isUnmappedIn1() const return atomidx1.isNull(); } +/** Return whether or not this atom is mapped in the reference state */ +bool AtomIdxMappingEntry::isMappedIn0() const +{ + return not unmapped0; +} + +/** Return whether or not this atom is mapped in the perturbed state */ +bool AtomIdxMappingEntry::isMappedIn1() const +{ + return not atomidx1.isNull(); +} + /** Return the atom index in the reference state. This will always have * a value, even if the atom is unmapped in the reference state * (this signals that any parameter with this index should be zero) @@ -639,3 +651,161 @@ void AtomIdxMapping::remove(const CGAtomIdx &atom) this->remove(std::distance(this->constBegin(), it)); } } + +/** Return the indexes, in the merged molecule, of atoms that + * are not mapped in the reference state (i.e. they only exist + * in the perturbed state). Note - these are the indicies of these + * atoms in the merged molecule, not the perturbed molecule. + */ +QList AtomIdxMapping::unmappedIn0() const +{ + QList ret; + + for (const auto &entry : entries) + { + if (entry.isUnmappedIn0()) + { + ret.append(entry.atomIdx0()); + } + } + + return ret; +} + +/** Return the indexes, in the merged molecule, of atoms that + * are not mapped in the perturbed state (i.e. they only exist + * in the reference state). Note - these are the indicies of these + * atoms in the merged molecule, not the reference molecule. + */ +QList AtomIdxMapping::unmappedIn1() const +{ + QList ret; + + for (const auto &entry : entries) + { + if (entry.isUnmappedIn1()) + { + ret.append(entry.atomIdx0()); + } + } + + return ret; +} + +/** Return the indexes, in the merged molecule, of atoms that + * are mapped in the reference state (i.e. they exist in the + * reference state, regardless of whether or not they exist + * in the perturbed state). Note - these are the indicies of + * these atoms in the merged molecule, not the reference molecule. + */ +QList AtomIdxMapping::mappedIn0() const +{ + QList ret; + + for (const auto &entry : entries) + { + if (entry.isMappedIn0()) + { + ret.append(entry.atomIdx0()); + } + } + + return ret; +} + +/** Return the indexes, in the merged molecule, of atoms that + * are mapped in the perturbed state (i.e. they exist in the + * perturbed state, regardless of whether or not they exist + * in the reference state). Note - these are the indicies of + * these atoms in the merged molecule, not the perturbed molecule. + */ +QList AtomIdxMapping::mappedIn1() const +{ + QList ret; + + for (const auto &entry : entries) + { + if (entry.isMappedIn1()) + { + ret.append(entry.atomIdx0()); + } + } + + return ret; +} + +/** Return the mapping for the atoms that exist in both the reference + * and perturbed states, from the index of the atom in the merged + * molecule to the index of the atom in the perturbed molecule. + * Note - the reference index is the index in the merged molecule. + * + * If 'include_unmapped' is true, then also include atoms that are + * unmapped in either end state. In these cases, the reference index + * will be the index in the merged molecule (so will always be valid) + * but the perturbed index will be null for atoms that are unmapped + * in the perturbed state. + */ +QHash AtomIdxMapping::map0to1(bool include_unmapped) const +{ + QHash ret; + ret.reserve(entries.size()); + + if (include_unmapped) + { + for (const auto &entry : entries) + { + if (not entry.atomIdx0().isNull()) + ret.insert(entry.atomIdx0(), entry.atomIdx1()); + } + } + else + { + for (const auto &entry : entries) + { + if (entry.isMappedIn0() and entry.isMappedIn1()) + { + ret.insert(entry.atomIdx0(), entry.atomIdx1()); + } + } + } + + return ret; +} + +/** Return the mapping for the atoms that exist in both the reference + * and perturbed states, from the index of the atom in the perturbed + * molecule to the index of the atom in the merged molecule. + * Note - the reference index is the index in the merged molecule. + * + * If 'include_unmapped' is true, then also include atoms that are + * unmapped in either end state. In these cases, the reference index + * will be the index in the merged molecule (so will always be valid) + * and atoms that are unmapped in the perturbed state are not + * included in the returned dictionary. + */ +QHash AtomIdxMapping::map1to0(bool include_unmapped) const +{ + QHash ret; + ret.reserve(entries.size()); + + if (include_unmapped) + { + for (const auto &entry : entries) + { + if (not entry.atomIdx1().isNull()) + ret.insert(entry.atomIdx1(), entry.atomIdx0()); + } + } + else + { + for (const auto &entry : entries) + { + if (entry.isMappedIn0() and entry.isMappedIn1()) + { + ret.insert(entry.atomIdx1(), entry.atomIdx0()); + } + } + } + + return ret; +} diff --git a/corelib/src/libs/SireMol/atomidxmapping.h b/corelib/src/libs/SireMol/atomidxmapping.h index af701484d..78576af82 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.h +++ b/corelib/src/libs/SireMol/atomidxmapping.h @@ -83,6 +83,9 @@ namespace SireMol bool isUnmappedIn0() const; bool isUnmappedIn1() const; + bool isMappedIn0() const; + bool isMappedIn1() const; + AtomIdx atomIdx0() const; AtomIdx atomIdx1() const; @@ -184,8 +187,8 @@ namespace SireMol QList mappedIn0() const; QList mappedIn1() const; - QHash map0to1() const; - QHash map1to0() const; + QHash map0to1(bool include_unmapped = false) const; + QHash map1to0(bool include_unmapped = false) const; private: void assertSane() const; diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 29da7b69d..5883db3a3 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -494,6 +494,9 @@ namespace SireSystem editmol.removeProperty(map["parameters"].source()); } + // set the connectivity to the merged connectivity (BELOW CODE IS WRONG!!!) + editmol.setProperty(map["connectivity"].source(), editmol.property("connectivity0")); + // set the flag that this is a perturbable molecule editmol.setProperty(map["is_perturbable"].source(), BooleanProperty(true)); diff --git a/wrapper/Mol/Atom.pypp.cpp b/wrapper/Mol/Atom.pypp.cpp index 8e8487bde..c9d207273 100644 --- a/wrapper/Mol/Atom.pypp.cpp +++ b/wrapper/Mol/Atom.pypp.cpp @@ -48,6 +48,8 @@ namespace bp = boost::python; #include "atom.h" +#include "SireBase/console.h" + #include "SireBase/incremint.h" #include "SireBase/propertylist.h" diff --git a/wrapper/Mol/AtomEditorBase.pypp.cpp b/wrapper/Mol/AtomEditorBase.pypp.cpp index 368ad6063..e2daa4272 100644 --- a/wrapper/Mol/AtomEditorBase.pypp.cpp +++ b/wrapper/Mol/AtomEditorBase.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; #include "atomeditor.h" +#include "SireBase/console.h" + #include "SireBase/incremint.h" #include "SireBase/propertylist.h" diff --git a/wrapper/Mol/AtomIdxMapping.pypp.cpp b/wrapper/Mol/AtomIdxMapping.pypp.cpp index 81dc4a45f..f4a31bf64 100644 --- a/wrapper/Mol/AtomIdxMapping.pypp.cpp +++ b/wrapper/Mol/AtomIdxMapping.pypp.cpp @@ -104,6 +104,54 @@ void register_AtomIdxMapping_class(){ , bp::release_gil_policy() , "Return whether or not the list is empty" ); + } + { //::SireMol::AtomIdxMapping::map0to1 + + typedef ::QHash< SireMol::AtomIdx, SireMol::AtomIdx > ( ::SireMol::AtomIdxMapping::*map0to1_function_type)( bool ) const; + map0to1_function_type map0to1_function_value( &::SireMol::AtomIdxMapping::map0to1 ); + + AtomIdxMapping_exposer.def( + "map0to1" + , map0to1_function_value + , ( bp::arg("include_unmapped")=(bool)(false) ) + , "Return the mapping for the atoms that exist in both the reference\n and perturbed states, from the index of the atom in the merged\n molecule to the index of the atom in the perturbed molecule.\n Note - the reference index is the index in the merged molecule.\n\n If include_unmapped is true, then also include atoms that are\n unmapped in either end state. In these cases, the reference index\n will be the index in the merged molecule (so will always be valid)\n but the perturbed index will be null for atoms that are unmapped\n in the perturbed state.\n" ); + + } + { //::SireMol::AtomIdxMapping::map1to0 + + typedef ::QHash< SireMol::AtomIdx, SireMol::AtomIdx > ( ::SireMol::AtomIdxMapping::*map1to0_function_type)( bool ) const; + map1to0_function_type map1to0_function_value( &::SireMol::AtomIdxMapping::map1to0 ); + + AtomIdxMapping_exposer.def( + "map1to0" + , map1to0_function_value + , ( bp::arg("include_unmapped")=(bool)(false) ) + , "Return the mapping for the atoms that exist in both the reference\n and perturbed states, from the index of the atom in the perturbed\n molecule to the index of the atom in the merged molecule.\n Note - the reference index is the index in the merged molecule.\n\n If include_unmapped is true, then also include atoms that are\n unmapped in either end state. In these cases, the reference index\n will be the index in the merged molecule (so will always be valid)\n and atoms that are unmapped in the perturbed state are not\n included in the returned dictionary.\n" ); + + } + { //::SireMol::AtomIdxMapping::mappedIn0 + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::AtomIdxMapping::*mappedIn0_function_type)( ) const; + mappedIn0_function_type mappedIn0_function_value( &::SireMol::AtomIdxMapping::mappedIn0 ); + + AtomIdxMapping_exposer.def( + "mappedIn0" + , mappedIn0_function_value + , bp::release_gil_policy() + , "Return the indexes, in the merged molecule, of atoms that\n are mapped in the reference state (i.e. they exist in the\n reference state, regardless of whether or not they exist\n in the perturbed state). Note - these are the indicies of\n these atoms in the merged molecule, not the reference molecule.\n" ); + + } + { //::SireMol::AtomIdxMapping::mappedIn1 + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::AtomIdxMapping::*mappedIn1_function_type)( ) const; + mappedIn1_function_type mappedIn1_function_value( &::SireMol::AtomIdxMapping::mappedIn1 ); + + AtomIdxMapping_exposer.def( + "mappedIn1" + , mappedIn1_function_value + , bp::release_gil_policy() + , "Return the indexes, in the merged molecule, of atoms that\n are mapped in the perturbed state (i.e. they exist in the\n perturbed state, regardless of whether or not they exist\n in the reference state). Note - these are the indicies of\n these atoms in the merged molecule, not the perturbed molecule.\n" ); + } AtomIdxMapping_exposer.def( bp::self != bp::self ); AtomIdxMapping_exposer.def( bp::self + bp::self ); @@ -248,6 +296,30 @@ void register_AtomIdxMapping_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomIdxMapping::unmappedIn0 + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::AtomIdxMapping::*unmappedIn0_function_type)( ) const; + unmappedIn0_function_type unmappedIn0_function_value( &::SireMol::AtomIdxMapping::unmappedIn0 ); + + AtomIdxMapping_exposer.def( + "unmappedIn0" + , unmappedIn0_function_value + , bp::release_gil_policy() + , "Return the indexes, in the merged molecule, of atoms that\n are not mapped in the reference state (i.e. they only exist\n in the perturbed state). Note - these are the indicies of these\n atoms in the merged molecule, not the perturbed molecule.\n" ); + + } + { //::SireMol::AtomIdxMapping::unmappedIn1 + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::AtomIdxMapping::*unmappedIn1_function_type)( ) const; + unmappedIn1_function_type unmappedIn1_function_value( &::SireMol::AtomIdxMapping::unmappedIn1 ); + + AtomIdxMapping_exposer.def( + "unmappedIn1" + , unmappedIn1_function_value + , bp::release_gil_policy() + , "Return the indexes, in the merged molecule, of atoms that\n are not mapped in the perturbed state (i.e. they only exist\n in the reference state). Note - these are the indicies of these\n atoms in the merged molecule, not the reference molecule.\n" ); + } { //::SireMol::AtomIdxMapping::what diff --git a/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp b/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp index 46da0cad8..d71c5b96a 100644 --- a/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp +++ b/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp @@ -86,6 +86,30 @@ void register_AtomIdxMappingEntry_class(){ , bp::release_gil_policy() , "Return the atom index in the perturbed state, or a null index if\n the atom is unmapped in the perturbed state" ); + } + { //::SireMol::AtomIdxMappingEntry::isMappedIn0 + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isMappedIn0_function_type)( ) const; + isMappedIn0_function_type isMappedIn0_function_value( &::SireMol::AtomIdxMappingEntry::isMappedIn0 ); + + AtomIdxMappingEntry_exposer.def( + "isMappedIn0" + , isMappedIn0_function_value + , bp::release_gil_policy() + , "Return whether or not this atom is mapped in the reference state" ); + + } + { //::SireMol::AtomIdxMappingEntry::isMappedIn1 + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isMappedIn1_function_type)( ) const; + isMappedIn1_function_type isMappedIn1_function_value( &::SireMol::AtomIdxMappingEntry::isMappedIn1 ); + + AtomIdxMappingEntry_exposer.def( + "isMappedIn1" + , isMappedIn1_function_value + , bp::release_gil_policy() + , "Return whether or not this atom is mapped in the perturbed state" ); + } { //::SireMol::AtomIdxMappingEntry::isNull diff --git a/wrapper/Mol/Connectivity.pypp.cpp b/wrapper/Mol/Connectivity.pypp.cpp index a776a84ac..da6ffb1aa 100644 --- a/wrapper/Mol/Connectivity.pypp.cpp +++ b/wrapper/Mol/Connectivity.pypp.cpp @@ -57,7 +57,7 @@ namespace bp = boost::python; #include "connectivity.h" -SireMol::Connectivity __copy__(const SireMol::Connectivity &other) { return SireMol::Connectivity(other); } +SireMol::Connectivity __copy__(const SireMol::Connectivity &other){ return SireMol::Connectivity(other); } #include "Qt/qdatastream.hpp" @@ -65,62 +65,80 @@ SireMol::Connectivity __copy__(const SireMol::Connectivity &other) { return Sire #include "Helpers/release_gil_policy.hpp" -void register_Connectivity_class() -{ +void register_Connectivity_class(){ { //::SireMol::Connectivity - typedef bp::class_> Connectivity_exposer_t; - Connectivity_exposer_t Connectivity_exposer = Connectivity_exposer_t("Connectivity", "This class contains the connectivity of the molecule, namely which\natoms are connected to which other atoms. The connectivity is used\nto move parts of the molecule (e.g. moving an atom also moves all\nof the atoms that it is connected to), and to automatically generate\nthe internal geometry of the molecule (e.g. to auto-generate\nall of the bonds, angles and dihedrals). Note that the connectivity\nis not the same as the bonding - the connectivity is used to move\nparts of the molecule (e.g. moving an atom should move all of the\natoms it is connected to) and also to auto-generate internal angles\n(e.g. auto-generation of bonds, angles and dihedrals)\n\nAuthor: Christopher Woods\n\n", bp::init<>("Null constructor")); - bp::scope Connectivity_scope(Connectivity_exposer); - Connectivity_exposer.def(bp::init((bp::arg("molinfo")), "Construct the connectivity for the passed molecule info")); - Connectivity_exposer.def(bp::init((bp::arg("moldata")), "Construct the connectivity for the molecule whose data\nis in moldata")); - Connectivity_exposer.def(bp::init>((bp::arg("molview"), bp::arg("bondhunter") = SireMol::CovalentBondHunter(), bp::arg("map") = SireBase::PropertyMap()), "Construct the connectivity for the molecule viewed in the\npassed view. This automatically uses the bond hunting\nfunction to add all of the bonds for the atoms in this view")); - Connectivity_exposer.def(bp::init((bp::arg("editor")), "Construct the connectivity from the passed editor")); - Connectivity_exposer.def(bp::init((bp::arg("other")), "Copy constructor")); + typedef bp::class_< SireMol::Connectivity, bp::bases< SireMol::ConnectivityBase, SireMol::MolViewProperty, SireBase::Property > > Connectivity_exposer_t; + Connectivity_exposer_t Connectivity_exposer = Connectivity_exposer_t( "Connectivity", "This class contains the connectivity of the molecule, namely which\natoms are connected to which other atoms. The connectivity is used\nto move parts of the molecule (e.g. moving an atom also moves all\nof the atoms that it is connected to), and to automatically generate\nthe internal geometry of the molecule (e.g. to auto-generate\nall of the bonds, angles and dihedrals). Note that the connectivity\nis not the same as the bonding - the connectivity is used to move\nparts of the molecule (e.g. moving an atom should move all of the\natoms it is connected to) and also to auto-generate internal angles\n(e.g. auto-generation of bonds, angles and dihedrals)\n\nAuthor: Christopher Woods\n\n", bp::init< >("Null constructor") ); + bp::scope Connectivity_scope( Connectivity_exposer ); + Connectivity_exposer.def( bp::init< SireMol::MoleculeInfo const & >(( bp::arg("molinfo") ), "Construct the connectivity for the passed molecule info") ); + Connectivity_exposer.def( bp::init< SireMol::MoleculeData const & >(( bp::arg("moldata") ), "Construct the connectivity for the molecule whose data\nis in moldata") ); + Connectivity_exposer.def( bp::init< SireMol::MoleculeView const &, bp::optional< SireMol::BondHunter const &, SireBase::PropertyMap const & > >(( bp::arg("molview"), bp::arg("bondhunter")=SireMol::CovalentBondHunter(), bp::arg("map")=SireBase::PropertyMap() ), "Construct the connectivity for the molecule viewed in the\npassed view. This automatically uses the bond hunting\nfunction to add all of the bonds for the atoms in this view") ); + Connectivity_exposer.def( bp::init< SireMol::ConnectivityEditor const & >(( bp::arg("editor") ), "Construct the connectivity from the passed editor") ); + Connectivity_exposer.def( bp::init< SireMol::Connectivity const & >(( bp::arg("other") ), "Copy constructor") ); { //::SireMol::Connectivity::edit - - typedef ::SireMol::ConnectivityEditor (::SireMol::Connectivity::*edit_function_type)() const; - edit_function_type edit_function_value(&::SireMol::Connectivity::edit); - - Connectivity_exposer.def( - "edit", edit_function_value, bp::release_gil_policy(), "Return an editor that can edit a copy of this connectivity"); + + typedef ::SireMol::ConnectivityEditor ( ::SireMol::Connectivity::*edit_function_type)( ) const; + edit_function_type edit_function_value( &::SireMol::Connectivity::edit ); + + Connectivity_exposer.def( + "edit" + , edit_function_value + , bp::release_gil_policy() + , "Return an editor that can edit a copy of this connectivity" ); + } - Connectivity_exposer.def(bp::self != bp::self); + Connectivity_exposer.def( bp::self != bp::self ); { //::SireMol::Connectivity::operator= - - typedef ::SireMol::Connectivity &(::SireMol::Connectivity::*assign_function_type)(::SireMol::Connectivity const &); - assign_function_type assign_function_value(&::SireMol::Connectivity::operator=); - - Connectivity_exposer.def( - "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); + + typedef ::SireMol::Connectivity & ( ::SireMol::Connectivity::*assign_function_type)( ::SireMol::Connectivity const & ) ; + assign_function_type assign_function_value( &::SireMol::Connectivity::operator= ); + + Connectivity_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + } { //::SireMol::Connectivity::operator= - - typedef ::SireMol::Connectivity &(::SireMol::Connectivity::*assign_function_type)(::SireMol::ConnectivityEditor const &); - assign_function_type assign_function_value(&::SireMol::Connectivity::operator=); - - Connectivity_exposer.def( - "assign", assign_function_value, (bp::arg("editor")), bp::return_self<>(), ""); + + typedef ::SireMol::Connectivity & ( ::SireMol::Connectivity::*assign_function_type)( ::SireMol::ConnectivityEditor const & ) ; + assign_function_type assign_function_value( &::SireMol::Connectivity::operator= ); + + Connectivity_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("editor") ) + , bp::return_self< >() + , "" ); + } - Connectivity_exposer.def(bp::self == bp::self); + Connectivity_exposer.def( bp::self == bp::self ); { //::SireMol::Connectivity::typeName - - typedef char const *(*typeName_function_type)(); - typeName_function_type typeName_function_value(&::SireMol::Connectivity::typeName); - - Connectivity_exposer.def( - "typeName", typeName_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMol::Connectivity::typeName ); + + Connectivity_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + } - Connectivity_exposer.staticmethod("typeName"); - Connectivity_exposer.def("__copy__", &__copy__); - Connectivity_exposer.def("__deepcopy__", &__copy__); - Connectivity_exposer.def("clone", &__copy__); - Connectivity_exposer.def("__rlshift__", &__rlshift__QDataStream<::SireMol::Connectivity>, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); - Connectivity_exposer.def("__rrshift__", &__rrshift__QDataStream<::SireMol::Connectivity>, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); - Connectivity_exposer.def_pickle(sire_pickle_suite<::SireMol::Connectivity>()); - Connectivity_exposer.def("__str__", &__str__<::SireMol::Connectivity>); - Connectivity_exposer.def("__repr__", &__str__<::SireMol::Connectivity>); + Connectivity_exposer.staticmethod( "typeName" ); + Connectivity_exposer.def( "__copy__", &__copy__); + Connectivity_exposer.def( "__deepcopy__", &__copy__); + Connectivity_exposer.def( "clone", &__copy__); + Connectivity_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::Connectivity >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + Connectivity_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::Connectivity >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + Connectivity_exposer.def_pickle(sire_pickle_suite< ::SireMol::Connectivity >()); + Connectivity_exposer.def( "__str__", &__str__< ::SireMol::Connectivity > ); + Connectivity_exposer.def( "__repr__", &__str__< ::SireMol::Connectivity > ); } + } diff --git a/wrapper/Mol/ConnectivityBase.pypp.cpp b/wrapper/Mol/ConnectivityBase.pypp.cpp index 0e0c9d21c..0ae5f2820 100644 --- a/wrapper/Mol/ConnectivityBase.pypp.cpp +++ b/wrapper/Mol/ConnectivityBase.pypp.cpp @@ -64,900 +64,1440 @@ namespace bp = boost::python; #include "Helpers/release_gil_policy.hpp" -void register_ConnectivityBase_class() -{ +void register_ConnectivityBase_class(){ { //::SireMol::ConnectivityBase - typedef bp::class_, boost::noncopyable> ConnectivityBase_exposer_t; - ConnectivityBase_exposer_t ConnectivityBase_exposer = ConnectivityBase_exposer_t("ConnectivityBase", "The base class of Connectivity and ConnectivityEditor\n\nAuthor: Christopher Woods\n", bp::no_init); - bp::scope ConnectivityBase_scope(ConnectivityBase_exposer); + typedef bp::class_< SireMol::ConnectivityBase, bp::bases< SireMol::MolViewProperty, SireBase::Property >, boost::noncopyable > ConnectivityBase_exposer_t; + ConnectivityBase_exposer_t ConnectivityBase_exposer = ConnectivityBase_exposer_t( "ConnectivityBase", "The base class of Connectivity and ConnectivityEditor\n\nAuthor: Christopher Woods\n", bp::no_init ); + bp::scope ConnectivityBase_scope( ConnectivityBase_exposer ); { //::SireMol::ConnectivityBase::areAngled - - typedef bool (::SireMol::ConnectivityBase::*areAngled_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - areAngled_function_type areAngled_function_value(&::SireMol::ConnectivityBase::areAngled); - - ConnectivityBase_exposer.def( - "areAngled", areAngled_function_value, (bp::arg("atom0"), bp::arg("atom2")), bp::release_gil_policy(), "Return whether or not the two atoms are angled together"); + + typedef bool ( ::SireMol::ConnectivityBase::*areAngled_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + areAngled_function_type areAngled_function_value( &::SireMol::ConnectivityBase::areAngled ); + + ConnectivityBase_exposer.def( + "areAngled" + , areAngled_function_value + , ( bp::arg("atom0"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "Return whether or not the two atoms are angled together" ); + } { //::SireMol::ConnectivityBase::areAngled - - typedef bool (::SireMol::ConnectivityBase::*areAngled_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - areAngled_function_type areAngled_function_value(&::SireMol::ConnectivityBase::areAngled); - - ConnectivityBase_exposer.def( - "areAngled", areAngled_function_value, (bp::arg("atom0"), bp::arg("atom2")), bp::release_gil_policy(), "Return whether or not the two atoms are angled together"); + + typedef bool ( ::SireMol::ConnectivityBase::*areAngled_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + areAngled_function_type areAngled_function_value( &::SireMol::ConnectivityBase::areAngled ); + + ConnectivityBase_exposer.def( + "areAngled" + , areAngled_function_value + , ( bp::arg("atom0"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "Return whether or not the two atoms are angled together" ); + } { //::SireMol::ConnectivityBase::areBonded - - typedef bool (::SireMol::ConnectivityBase::*areBonded_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - areBonded_function_type areBonded_function_value(&::SireMol::ConnectivityBase::areBonded); - - ConnectivityBase_exposer.def( - "areBonded", areBonded_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the two atoms are bonded together"); + + typedef bool ( ::SireMol::ConnectivityBase::*areBonded_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + areBonded_function_type areBonded_function_value( &::SireMol::ConnectivityBase::areBonded ); + + ConnectivityBase_exposer.def( + "areBonded" + , areBonded_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return whether or not the two atoms are bonded together" ); + } { //::SireMol::ConnectivityBase::areBonded - - typedef bool (::SireMol::ConnectivityBase::*areBonded_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - areBonded_function_type areBonded_function_value(&::SireMol::ConnectivityBase::areBonded); - - ConnectivityBase_exposer.def( - "areBonded", areBonded_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the two atoms are bonded together"); + + typedef bool ( ::SireMol::ConnectivityBase::*areBonded_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + areBonded_function_type areBonded_function_value( &::SireMol::ConnectivityBase::areBonded ); + + ConnectivityBase_exposer.def( + "areBonded" + , areBonded_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return whether or not the two atoms are bonded together" ); + } { //::SireMol::ConnectivityBase::areConnected - - typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); - - ConnectivityBase_exposer.def( - "areConnected", areConnected_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the atoms at indicies atom0 and atom1\nare connected\nThrow: SireError::invalid_index\n"); + + typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); + + ConnectivityBase_exposer.def( + "areConnected" + , areConnected_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return whether or not the atoms at indicies atom0 and atom1\nare connected\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::areConnected - - typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); - - ConnectivityBase_exposer.def( - "areConnected", areConnected_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return whether or not the atoms identified by atom0 and atom1\nare connected\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); + + typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); + + ConnectivityBase_exposer.def( + "areConnected" + , areConnected_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return whether or not the atoms identified by atom0 and atom1\nare connected\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::areConnected - - typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::ResIdx, ::SireMol::ResIdx) const; - areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); - - ConnectivityBase_exposer.def( - "areConnected", areConnected_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return whether or not the residues at indicies res0 and res1\nare connected\nThrow: SireError::invalid_index\n"); + + typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::ResIdx,::SireMol::ResIdx ) const; + areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); + + ConnectivityBase_exposer.def( + "areConnected" + , areConnected_function_value + , ( bp::arg("res0"), bp::arg("res1") ) + , bp::release_gil_policy() + , "Return whether or not the residues at indicies res0 and res1\nare connected\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::areConnected - - typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::ResID const &, ::SireMol::ResID const &) const; - areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); - - ConnectivityBase_exposer.def( - "areConnected", areConnected_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return whether the residues identified by res0 and res1 are connected"); + + typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::ResID const &,::SireMol::ResID const & ) const; + areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); + + ConnectivityBase_exposer.def( + "areConnected" + , areConnected_function_value + , ( bp::arg("res0"), bp::arg("res1") ) + , bp::release_gil_policy() + , "Return whether the residues identified by res0 and res1 are connected" ); + } { //::SireMol::ConnectivityBase::areConnected - - typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::CGIdx, ::SireMol::CGIdx) const; - areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); - - ConnectivityBase_exposer.def( - "areConnected", areConnected_function_value, (bp::arg("cg0"), bp::arg("cg1")), bp::release_gil_policy(), "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected"); + + typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::CGIdx,::SireMol::CGIdx ) const; + areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); + + ConnectivityBase_exposer.def( + "areConnected" + , areConnected_function_value + , ( bp::arg("cg0"), bp::arg("cg1") ) + , bp::release_gil_policy() + , "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected" ); + } { //::SireMol::ConnectivityBase::areConnected - - typedef bool (::SireMol::ConnectivityBase::*areConnected_function_type)(::SireMol::CGID const &, ::SireMol::CGID const &) const; - areConnected_function_type areConnected_function_value(&::SireMol::ConnectivityBase::areConnected); - - ConnectivityBase_exposer.def( - "areConnected", areConnected_function_value, (bp::arg("cg0"), bp::arg("cg1")), bp::release_gil_policy(), "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected"); + + typedef bool ( ::SireMol::ConnectivityBase::*areConnected_function_type)( ::SireMol::CGID const &,::SireMol::CGID const & ) const; + areConnected_function_type areConnected_function_value( &::SireMol::ConnectivityBase::areConnected ); + + ConnectivityBase_exposer.def( + "areConnected" + , areConnected_function_value + , ( bp::arg("cg0"), bp::arg("cg1") ) + , bp::release_gil_policy() + , "Return whether or not the CutGroups at indicies cg0 and cg1 are\nconnected" ); + } { //::SireMol::ConnectivityBase::areDihedraled - - typedef bool (::SireMol::ConnectivityBase::*areDihedraled_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - areDihedraled_function_type areDihedraled_function_value(&::SireMol::ConnectivityBase::areDihedraled); - - ConnectivityBase_exposer.def( - "areDihedraled", areDihedraled_function_value, (bp::arg("atom0"), bp::arg("atom3")), bp::release_gil_policy(), "Return whether or not the two atoms are dihedraled together"); + + typedef bool ( ::SireMol::ConnectivityBase::*areDihedraled_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + areDihedraled_function_type areDihedraled_function_value( &::SireMol::ConnectivityBase::areDihedraled ); + + ConnectivityBase_exposer.def( + "areDihedraled" + , areDihedraled_function_value + , ( bp::arg("atom0"), bp::arg("atom3") ) + , bp::release_gil_policy() + , "Return whether or not the two atoms are dihedraled together" ); + } { //::SireMol::ConnectivityBase::areDihedraled - - typedef bool (::SireMol::ConnectivityBase::*areDihedraled_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - areDihedraled_function_type areDihedraled_function_value(&::SireMol::ConnectivityBase::areDihedraled); - - ConnectivityBase_exposer.def( - "areDihedraled", areDihedraled_function_value, (bp::arg("atom0"), bp::arg("atom3")), bp::release_gil_policy(), "Return whether or not the two atoms are bonded together"); + + typedef bool ( ::SireMol::ConnectivityBase::*areDihedraled_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + areDihedraled_function_type areDihedraled_function_value( &::SireMol::ConnectivityBase::areDihedraled ); + + ConnectivityBase_exposer.def( + "areDihedraled" + , areDihedraled_function_value + , ( bp::arg("atom0"), bp::arg("atom3") ) + , bp::release_gil_policy() + , "Return whether or not the two atoms are bonded together" ); + } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; - assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); - - ConnectivityBase_exposer.def( - "assertHasProperty", assertHasProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified bond has the specified property"); + + typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; + assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); + + ConnectivityBase_exposer.def( + "assertHasProperty" + , assertHasProperty_function_value + , ( bp::arg("bond"), bp::arg("key") ) + , bp::release_gil_policy() + , "Assert that the specified bond has the specified property" ); + } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; - assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); - - ConnectivityBase_exposer.def( - "assertHasProperty", assertHasProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified angle has the specified property"); + + typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; + assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); + + ConnectivityBase_exposer.def( + "assertHasProperty" + , assertHasProperty_function_value + , ( bp::arg("ang"), bp::arg("key") ) + , bp::release_gil_policy() + , "Assert that the specified angle has the specified property" ); + } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; - assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); - - ConnectivityBase_exposer.def( - "assertHasProperty", assertHasProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified angle has the specified property"); + + typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; + assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); + + ConnectivityBase_exposer.def( + "assertHasProperty" + , assertHasProperty_function_value + , ( bp::arg("dih"), bp::arg("key") ) + , bp::release_gil_policy() + , "Assert that the specified angle has the specified property" ); + } { //::SireMol::ConnectivityBase::assertHasProperty - - typedef void (::SireMol::ConnectivityBase::*assertHasProperty_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; - assertHasProperty_function_type assertHasProperty_function_value(&::SireMol::ConnectivityBase::assertHasProperty); - - ConnectivityBase_exposer.def( - "assertHasProperty", assertHasProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Assert that the specified angle has the specified property"); + + typedef void ( ::SireMol::ConnectivityBase::*assertHasProperty_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; + assertHasProperty_function_type assertHasProperty_function_value( &::SireMol::ConnectivityBase::assertHasProperty ); + + ConnectivityBase_exposer.def( + "assertHasProperty" + , assertHasProperty_function_value + , ( bp::arg("imp"), bp::arg("key") ) + , bp::release_gil_policy() + , "Assert that the specified angle has the specified property" ); + } { //::SireMol::ConnectivityBase::connectionType - - typedef int (::SireMol::ConnectivityBase::*connectionType_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - connectionType_function_type connectionType_function_value(&::SireMol::ConnectivityBase::connectionType); - - ConnectivityBase_exposer.def( - "connectionType", connectionType_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return the connection type of the passed two atoms. This returns;\n"); + + typedef int ( ::SireMol::ConnectivityBase::*connectionType_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + connectionType_function_type connectionType_function_value( &::SireMol::ConnectivityBase::connectionType ); + + ConnectivityBase_exposer.def( + "connectionType" + , connectionType_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return the connection type of the passed two atoms. This returns;\n" ); + } { //::SireMol::ConnectivityBase::connectionType - - typedef int (::SireMol::ConnectivityBase::*connectionType_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - connectionType_function_type connectionType_function_value(&::SireMol::ConnectivityBase::connectionType); - - ConnectivityBase_exposer.def( - "connectionType", connectionType_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return the connection type of the passed two atoms. This returns;\n"); + + typedef int ( ::SireMol::ConnectivityBase::*connectionType_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + connectionType_function_type connectionType_function_value( &::SireMol::ConnectivityBase::connectionType ); + + ConnectivityBase_exposer.def( + "connectionType" + , connectionType_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return the connection type of the passed two atoms. This returns;\n" ); + } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::AtomIdx) const; - connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); - - ConnectivityBase_exposer.def( - "connectionsTo", connectionsTo_function_value, (bp::arg("atomidx")), bp::return_value_policy(), "Return the indicies of atoms connected to the atom at index atomidx.\nThis returns an empty set if there are no atoms connected to\nthis atom\nThrow: SireError::invalid_index\n"); + + typedef ::QSet< SireMol::AtomIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::AtomIdx ) const; + connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); + + ConnectivityBase_exposer.def( + "connectionsTo" + , connectionsTo_function_value + , ( bp::arg("atomidx") ) + , bp::return_value_policy< bp::copy_const_reference >() + , "Return the indicies of atoms connected to the atom at index atomidx.\nThis returns an empty set if there are no atoms connected to\nthis atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::AtomID const &) const; - connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); - - ConnectivityBase_exposer.def( - "connectionsTo", connectionsTo_function_value, (bp::arg("atomid")), bp::return_value_policy(), "Return the indicies of atoms connected to the atom identified\nby resid - this returns an empty set if there are no connections\nto this atom\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); + + typedef ::QSet< SireMol::AtomIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::AtomID const & ) const; + connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); + + ConnectivityBase_exposer.def( + "connectionsTo" + , connectionsTo_function_value + , ( bp::arg("atomid") ) + , bp::return_value_policy< bp::copy_const_reference >() + , "Return the indicies of atoms connected to the atom identified\nby resid - this returns an empty set if there are no connections\nto this atom\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::ResIdx) const; - connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); - - ConnectivityBase_exposer.def( - "connectionsTo", connectionsTo_function_value, (bp::arg("residx")), bp::return_value_policy(), "Return the indicies of the residues connected to the residue at\nindex residx. This returns an empty set if there are no residues\nconnected to this residue\nThrow: SireError::invalid_index\n"); + + typedef ::QSet< SireMol::ResIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::ResIdx ) const; + connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); + + ConnectivityBase_exposer.def( + "connectionsTo" + , connectionsTo_function_value + , ( bp::arg("residx") ) + , bp::return_value_policy< bp::copy_const_reference >() + , "Return the indicies of the residues connected to the residue at\nindex residx. This returns an empty set if there are no residues\nconnected to this residue\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::connectionsTo - - typedef ::QSet const &(::SireMol::ConnectivityBase::*connectionsTo_function_type)(::SireMol::ResID const &) const; - connectionsTo_function_type connectionsTo_function_value(&::SireMol::ConnectivityBase::connectionsTo); - - ConnectivityBase_exposer.def( - "connectionsTo", connectionsTo_function_value, (bp::arg("resid")), bp::return_value_policy(), "Return the indicies of the residues connectd to the residue\nidentified by resid. This returns an empty set if there are\nno residues connected to this residue.\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); + + typedef ::QSet< SireMol::ResIdx > const & ( ::SireMol::ConnectivityBase::*connectionsTo_function_type)( ::SireMol::ResID const & ) const; + connectionsTo_function_type connectionsTo_function_value( &::SireMol::ConnectivityBase::connectionsTo ); + + ConnectivityBase_exposer.def( + "connectionsTo" + , connectionsTo_function_value + , ( bp::arg("resid") ) + , bp::return_value_policy< bp::copy_const_reference >() + , "Return the indicies of the residues connectd to the residue\nidentified by resid. This returns an empty set if there are\nno residues connected to this residue.\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); - - ConnectivityBase_exposer.def( - "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms"); + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); + + ConnectivityBase_exposer.def( + "findPath" + , findPath_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms" ); + } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, int) const; - findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); - - ConnectivityBase_exposer.def( - "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms"); + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,int ) const; + findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); + + ConnectivityBase_exposer.def( + "findPath" + , findPath_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) + , bp::release_gil_policy() + , "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms" ); + } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); - - ConnectivityBase_exposer.def( - "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms"); + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); + + ConnectivityBase_exposer.def( + "findPath" + , findPath_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms" ); + } { //::SireMol::ConnectivityBase::findPath - - typedef ::QList (::SireMol::ConnectivityBase::*findPath_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, int) const; - findPath_function_type findPath_function_value(&::SireMol::ConnectivityBase::findPath); - - ConnectivityBase_exposer.def( - "findPath", findPath_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms where the path has\na maximum length."); + + typedef ::QList< SireMol::AtomIdx > ( ::SireMol::ConnectivityBase::*findPath_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,int ) const; + findPath_function_type findPath_function_value( &::SireMol::ConnectivityBase::findPath ); + + ConnectivityBase_exposer.def( + "findPath" + , findPath_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) + , bp::release_gil_policy() + , "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms where the path has\na maximum length." ); + } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); - - ConnectivityBase_exposer.def( - "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms"); + + typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); + + ConnectivityBase_exposer.def( + "findPaths" + , findPaths_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return all possible bonded paths between two atoms. This returns an empty\nlist if there are no bonded paths between the two atoms" ); + } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, int) const; - findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); - - ConnectivityBase_exposer.def( - "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Return all possible bonded paths between two atoms where the path has\na maximum length. This returns an empty list if there are no bonded\npaths between the two atoms"); + + typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,int ) const; + findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); + + ConnectivityBase_exposer.def( + "findPaths" + , findPaths_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) + , bp::release_gil_policy() + , "Return all possible bonded paths between two atoms where the path has\na maximum length. This returns an empty list if there are no bonded\npaths between the two atoms" ); + } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); - - ConnectivityBase_exposer.def( - "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms"); + + typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); + + ConnectivityBase_exposer.def( + "findPaths" + , findPaths_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Find the shortest bonded path between two atoms. This returns an empty\nlist if there is no bonded path between these two atoms" ); + } { //::SireMol::ConnectivityBase::findPaths - - typedef ::QList> (::SireMol::ConnectivityBase::*findPaths_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, int) const; - findPaths_function_type findPaths_function_value(&::SireMol::ConnectivityBase::findPaths); - - ConnectivityBase_exposer.def( - "findPaths", findPaths_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length")), bp::release_gil_policy(), "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms"); + + typedef ::QList< QList< SireMol::AtomIdx > > ( ::SireMol::ConnectivityBase::*findPaths_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,int ) const; + findPaths_function_type findPaths_function_value( &::SireMol::ConnectivityBase::findPaths ); + + ConnectivityBase_exposer.def( + "findPaths" + , findPaths_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("max_length") ) + , bp::release_gil_policy() + , "Find the shortest bonded path between two atoms where the path has\na maximum length. This returns an empty list if there is no bonded\npath between these two atoms" ); + } { //::SireMol::ConnectivityBase::getAngles - - typedef ::QList (::SireMol::ConnectivityBase::*getAngles_function_type)() const; - getAngles_function_type getAngles_function_value(&::SireMol::ConnectivityBase::getAngles); - - ConnectivityBase_exposer.def( - "getAngles", getAngles_function_value, bp::release_gil_policy(), "Return a list of angles defined by the connectivity"); + + typedef ::QList< SireMol::AngleID > ( ::SireMol::ConnectivityBase::*getAngles_function_type)( ) const; + getAngles_function_type getAngles_function_value( &::SireMol::ConnectivityBase::getAngles ); + + ConnectivityBase_exposer.def( + "getAngles" + , getAngles_function_value + , bp::release_gil_policy() + , "Return a list of angles defined by the connectivity" ); + } { //::SireMol::ConnectivityBase::getAngles - - typedef ::QList (::SireMol::ConnectivityBase::*getAngles_function_type)(::SireMol::AtomID const &) const; - getAngles_function_type getAngles_function_value(&::SireMol::ConnectivityBase::getAngles); - - ConnectivityBase_exposer.def( - "getAngles", getAngles_function_value, (bp::arg("atom0")), bp::release_gil_policy(), "Return a list of angles defined by the connectivity that involve atom0"); + + typedef ::QList< SireMol::AngleID > ( ::SireMol::ConnectivityBase::*getAngles_function_type)( ::SireMol::AtomID const & ) const; + getAngles_function_type getAngles_function_value( &::SireMol::ConnectivityBase::getAngles ); + + ConnectivityBase_exposer.def( + "getAngles" + , getAngles_function_value + , ( bp::arg("atom0") ) + , bp::release_gil_policy() + , "Return a list of angles defined by the connectivity that involve atom0" ); + } { //::SireMol::ConnectivityBase::getAngles - - typedef ::QList (::SireMol::ConnectivityBase::*getAngles_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - getAngles_function_type getAngles_function_value(&::SireMol::ConnectivityBase::getAngles); - - ConnectivityBase_exposer.def( - "getAngles", getAngles_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return a list of angles defined by the connectivity that involve atom0 and atom1"); + + typedef ::QList< SireMol::AngleID > ( ::SireMol::ConnectivityBase::*getAngles_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + getAngles_function_type getAngles_function_value( &::SireMol::ConnectivityBase::getAngles ); + + ConnectivityBase_exposer.def( + "getAngles" + , getAngles_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return a list of angles defined by the connectivity that involve atom0 and atom1" ); + } { //::SireMol::ConnectivityBase::getBondMatrix - - typedef ::QVector> (::SireMol::ConnectivityBase::*getBondMatrix_function_type)(int) const; - getBondMatrix_function_type getBondMatrix_function_value(&::SireMol::ConnectivityBase::getBondMatrix); - - ConnectivityBase_exposer.def( - "getBondMatrix", getBondMatrix_function_value, (bp::arg("order")), bp::release_gil_policy(), "Return a matrix (organised by AtomIdx) that says which atoms are bonded up to\norder order (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)"); + + typedef ::QVector< QVector< bool > > ( ::SireMol::ConnectivityBase::*getBondMatrix_function_type)( int ) const; + getBondMatrix_function_type getBondMatrix_function_value( &::SireMol::ConnectivityBase::getBondMatrix ); + + ConnectivityBase_exposer.def( + "getBondMatrix" + , getBondMatrix_function_value + , ( bp::arg("order") ) + , bp::release_gil_policy() + , "Return a matrix (organised by AtomIdx) that says which atoms are bonded up to\norder order (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)" ); + } { //::SireMol::ConnectivityBase::getBondMatrix - - typedef ::QVector> (::SireMol::ConnectivityBase::*getBondMatrix_function_type)(int, int) const; - getBondMatrix_function_type getBondMatrix_function_value(&::SireMol::ConnectivityBase::getBondMatrix); - - ConnectivityBase_exposer.def( - "getBondMatrix", getBondMatrix_function_value, (bp::arg("start"), bp::arg("end")), bp::release_gil_policy(), "Return a matrix (organised by AtomIdx) that says which atoms are bonded between\norder start and order end (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)"); + + typedef ::QVector< QVector< bool > > ( ::SireMol::ConnectivityBase::*getBondMatrix_function_type)( int,int ) const; + getBondMatrix_function_type getBondMatrix_function_value( &::SireMol::ConnectivityBase::getBondMatrix ); + + ConnectivityBase_exposer.def( + "getBondMatrix" + , getBondMatrix_function_value + , ( bp::arg("start"), bp::arg("end") ) + , bp::release_gil_policy() + , "Return a matrix (organised by AtomIdx) that says which atoms are bonded between\norder start and order end (e.g. if order is two, it returns true for each atom pair that\nare bonded together, if order is three, then true for each atom pair that are\nbonded or angled together, if order is four, then true for each atom pair\nthat are bonded, angled or dihedraled)" ); + } { //::SireMol::ConnectivityBase::getBonds - - typedef ::QList (::SireMol::ConnectivityBase::*getBonds_function_type)() const; - getBonds_function_type getBonds_function_value(&::SireMol::ConnectivityBase::getBonds); - - ConnectivityBase_exposer.def( - "getBonds", getBonds_function_value, bp::release_gil_policy(), "Return the list of bonds present in this connectivity"); + + typedef ::QList< SireMol::BondID > ( ::SireMol::ConnectivityBase::*getBonds_function_type)( ) const; + getBonds_function_type getBonds_function_value( &::SireMol::ConnectivityBase::getBonds ); + + ConnectivityBase_exposer.def( + "getBonds" + , getBonds_function_value + , bp::release_gil_policy() + , "Return the list of bonds present in this connectivity" ); + } { //::SireMol::ConnectivityBase::getBonds - - typedef ::QList (::SireMol::ConnectivityBase::*getBonds_function_type)(::SireMol::AtomID const &) const; - getBonds_function_type getBonds_function_value(&::SireMol::ConnectivityBase::getBonds); - - ConnectivityBase_exposer.def( - "getBonds", getBonds_function_value, (bp::arg("atom")), bp::release_gil_policy(), "Return the list of bonds in the connectivity containing atom"); + + typedef ::QList< SireMol::BondID > ( ::SireMol::ConnectivityBase::*getBonds_function_type)( ::SireMol::AtomID const & ) const; + getBonds_function_type getBonds_function_value( &::SireMol::ConnectivityBase::getBonds ); + + ConnectivityBase_exposer.def( + "getBonds" + , getBonds_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return the list of bonds in the connectivity containing atom" ); + } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)() const; - getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); - - ConnectivityBase_exposer.def( - "getDihedrals", getDihedrals_function_value, bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity"); + + typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ) const; + getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); + + ConnectivityBase_exposer.def( + "getDihedrals" + , getDihedrals_function_value + , bp::release_gil_policy() + , "Return a list of dihedrals defined by the connectivity" ); + } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)(::SireMol::AtomID const &) const; - getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); - - ConnectivityBase_exposer.def( - "getDihedrals", getDihedrals_function_value, (bp::arg("atom0")), bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity that involve atom0"); + + typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ::SireMol::AtomID const & ) const; + getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); + + ConnectivityBase_exposer.def( + "getDihedrals" + , getDihedrals_function_value + , ( bp::arg("atom0") ) + , bp::release_gil_policy() + , "Return a list of dihedrals defined by the connectivity that involve atom0" ); + } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); - - ConnectivityBase_exposer.def( - "getDihedrals", getDihedrals_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity that involve atom0 and atom1"); + + typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); + + ConnectivityBase_exposer.def( + "getDihedrals" + , getDihedrals_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Return a list of dihedrals defined by the connectivity that involve atom0 and atom1" ); + } { //::SireMol::ConnectivityBase::getDihedrals - - typedef ::QList (::SireMol::ConnectivityBase::*getDihedrals_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - getDihedrals_function_type getDihedrals_function_value(&::SireMol::ConnectivityBase::getDihedrals); - - ConnectivityBase_exposer.def( - "getDihedrals", getDihedrals_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "Return a list of dihedrals defined by the connectivity that involve atom0, atom1 and atom2"); + + typedef ::QList< SireMol::DihedralID > ( ::SireMol::ConnectivityBase::*getDihedrals_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + getDihedrals_function_type getDihedrals_function_value( &::SireMol::ConnectivityBase::getDihedrals ); + + ConnectivityBase_exposer.def( + "getDihedrals" + , getDihedrals_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "Return a list of dihedrals defined by the connectivity that involve atom0, atom1 and atom2" ); + } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; - hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); - - ConnectivityBase_exposer.def( - "hasProperty", hasProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified bond has a property at key key"); + + typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; + hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); + + ConnectivityBase_exposer.def( + "hasProperty" + , hasProperty_function_value + , ( bp::arg("bond"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return whether the specified bond has a property at key key" ); + } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; - hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); - - ConnectivityBase_exposer.def( - "hasProperty", hasProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified angle has a property at key key"); + + typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; + hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); + + ConnectivityBase_exposer.def( + "hasProperty" + , hasProperty_function_value + , ( bp::arg("ang"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return whether the specified angle has a property at key key" ); + } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; - hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); - - ConnectivityBase_exposer.def( - "hasProperty", hasProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified dihedral has a property at key key"); + + typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; + hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); + + ConnectivityBase_exposer.def( + "hasProperty" + , hasProperty_function_value + , ( bp::arg("dih"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return whether the specified dihedral has a property at key key" ); + } { //::SireMol::ConnectivityBase::hasProperty - - typedef bool (::SireMol::ConnectivityBase::*hasProperty_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; - hasProperty_function_type hasProperty_function_value(&::SireMol::ConnectivityBase::hasProperty); - - ConnectivityBase_exposer.def( - "hasProperty", hasProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Return whether the specified improper has a property at key key"); + + typedef bool ( ::SireMol::ConnectivityBase::*hasProperty_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; + hasProperty_function_type hasProperty_function_value( &::SireMol::ConnectivityBase::hasProperty ); + + ConnectivityBase_exposer.def( + "hasProperty" + , hasProperty_function_value + , ( bp::arg("imp"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return whether the specified improper has a property at key key" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom")), bp::release_gil_policy(), "This function returns whether or not the atom is in a ring."); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "This function returns whether or not the atom is in a ring." ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "This function returns whether or not the two passed atoms are connected"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "This function returns whether or not the two passed atoms are connected" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "This function returns whether or not the three passed atoms are connected\nvia a ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "This function returns whether or not the three passed atoms are connected\nvia a ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "This function returns whether or not the four passed atoms are connected\nvia a same ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) + , bp::release_gil_policy() + , "This function returns whether or not the four passed atoms are connected\nvia a same ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom")), bp::release_gil_policy(), "This function returns whether or not the atom is in a ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "This function returns whether or not the atom is in a ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "This function returns whether or not the two passed atoms are connected\nvia a ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "This function returns whether or not the two passed atoms are connected\nvia a ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "This function returns whether or not the three passed atoms are connected\nvia a ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "This function returns whether or not the three passed atoms are connected\nvia a ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "This function returns whether or not the two passed atoms are connected\nvia a ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) + , bp::release_gil_policy() + , "This function returns whether or not the two passed atoms are connected\nvia a ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::BondID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("bond")), bp::release_gil_policy(), "This function returns whether or not the two atoms in the passed bond\nare both part of the same ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::BondID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("bond") ) + , bp::release_gil_policy() + , "This function returns whether or not the two atoms in the passed bond\nare both part of the same ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::AngleID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("angle")), bp::release_gil_policy(), "This function returns whether or not the three atoms in the passed angle\nare all part of the same ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::AngleID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("angle") ) + , bp::release_gil_policy() + , "This function returns whether or not the three atoms in the passed angle\nare all part of the same ring" ); + } { //::SireMol::ConnectivityBase::inRing - - typedef bool (::SireMol::ConnectivityBase::*inRing_function_type)(::SireMol::DihedralID const &) const; - inRing_function_type inRing_function_value(&::SireMol::ConnectivityBase::inRing); - - ConnectivityBase_exposer.def( - "inRing", inRing_function_value, (bp::arg("dihedral")), bp::release_gil_policy(), "This function returns whether or not the four atoms in the passed dihedral\nare all part of the same ring"); + + typedef bool ( ::SireMol::ConnectivityBase::*inRing_function_type)( ::SireMol::DihedralID const & ) const; + inRing_function_type inRing_function_value( &::SireMol::ConnectivityBase::inRing ); + + ConnectivityBase_exposer.def( + "inRing" + , inRing_function_value + , ( bp::arg("dihedral") ) + , bp::release_gil_policy() + , "This function returns whether or not the four atoms in the passed dihedral\nare all part of the same ring" ); + } { //::SireMol::ConnectivityBase::info - - typedef ::SireMol::MoleculeInfo (::SireMol::ConnectivityBase::*info_function_type)() const; - info_function_type info_function_value(&::SireMol::ConnectivityBase::info); - - ConnectivityBase_exposer.def( - "info", info_function_value, bp::release_gil_policy(), "Return the info object that describes the molecule for which this connectivity applies"); + + typedef ::SireMol::MoleculeInfo ( ::SireMol::ConnectivityBase::*info_function_type)( ) const; + info_function_type info_function_value( &::SireMol::ConnectivityBase::info ); + + ConnectivityBase_exposer.def( + "info" + , info_function_value + , bp::release_gil_policy() + , "Return the info object that describes the molecule for which this connectivity applies" ); + } { //::SireMol::ConnectivityBase::isCompatibleWith - - typedef bool (::SireMol::ConnectivityBase::*isCompatibleWith_function_type)(::SireMol::MoleculeInfoData const &) const; - isCompatibleWith_function_type isCompatibleWith_function_value(&::SireMol::ConnectivityBase::isCompatibleWith); - - ConnectivityBase_exposer.def( - "isCompatibleWith", isCompatibleWith_function_value, (bp::arg("molinfo")), bp::release_gil_policy(), ""); + + typedef bool ( ::SireMol::ConnectivityBase::*isCompatibleWith_function_type)( ::SireMol::MoleculeInfoData const & ) const; + isCompatibleWith_function_type isCompatibleWith_function_value( &::SireMol::ConnectivityBase::isCompatibleWith ); + + ConnectivityBase_exposer.def( + "isCompatibleWith" + , isCompatibleWith_function_value + , ( bp::arg("molinfo") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::ConnectivityBase::merge - - typedef ::SireBase::PropertyList (::SireMol::ConnectivityBase::*merge_function_type)(::SireMol::MolViewProperty const &, ::SireMol::AtomIdxMapping const &, ::QString const &, ::SireBase::PropertyMap const &) const; - merge_function_type merge_function_value(&::SireMol::ConnectivityBase::merge); - - ConnectivityBase_exposer.def( - "merge", merge_function_value, (bp::arg("other"), bp::arg("mapping"), bp::arg("ghost") = ::QString(), bp::arg("map") = SireBase::PropertyMap()), "Merge this property with another property"); + + typedef ::SireBase::PropertyList ( ::SireMol::ConnectivityBase::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMol::ConnectivityBase::merge ); + + ConnectivityBase_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "Merge this property with another property" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)() const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, bp::release_gil_policy(), "Return the total number of connections between atoms\nin this connectivity object"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , bp::release_gil_policy() + , "Return the total number of connections between atoms\nin this connectivity object" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::AtomIdx) const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, (bp::arg("atomidx")), bp::release_gil_policy(), "Return the number of connections to the atom at index atomidx\nThrow: SireError::index_error\n"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::AtomIdx ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , ( bp::arg("atomidx") ) + , bp::release_gil_policy() + , "Return the number of connections to the atom at index atomidx\nThrow: SireError::index_error\n" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::AtomID const &) const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, (bp::arg("atomid")), bp::release_gil_policy(), "Return the number of connections to the atom with ID atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::AtomID const & ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , ( bp::arg("atomid") ) + , bp::release_gil_policy() + , "Return the number of connections to the atom with ID atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResIdx) const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, (bp::arg("residx")), bp::release_gil_policy(), "Return the number of connections to the residue at index residx\nThrow: SireError::invalid_index\n"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResIdx ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , ( bp::arg("residx") ) + , bp::release_gil_policy() + , "Return the number of connections to the residue at index residx\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResID const &) const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, (bp::arg("resid")), bp::release_gil_policy(), "Return the number of connections to the residue identified\nby resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResID const & ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , ( bp::arg("resid") ) + , bp::release_gil_policy() + , "Return the number of connections to the residue identified\nby resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResIdx, ::SireMol::ResIdx) const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return the number of atom connections between the residues at\nindicies res0 and res1\nThrow: SireError::invalid_index\n"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResIdx,::SireMol::ResIdx ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , ( bp::arg("res0"), bp::arg("res1") ) + , bp::release_gil_policy() + , "Return the number of atom connections between the residues at\nindicies res0 and res1\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::nConnections - - typedef int (::SireMol::ConnectivityBase::*nConnections_function_type)(::SireMol::ResID const &, ::SireMol::ResID const &) const; - nConnections_function_type nConnections_function_value(&::SireMol::ConnectivityBase::nConnections); - - ConnectivityBase_exposer.def( - "nConnections", nConnections_function_value, (bp::arg("res0"), bp::arg("res1")), bp::release_gil_policy(), "Return the number of atom connections between the residues\nidentified by res0 and res1\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); + + typedef int ( ::SireMol::ConnectivityBase::*nConnections_function_type)( ::SireMol::ResID const &,::SireMol::ResID const & ) const; + nConnections_function_type nConnections_function_value( &::SireMol::ConnectivityBase::nConnections ); + + ConnectivityBase_exposer.def( + "nConnections" + , nConnections_function_value + , ( bp::arg("res0"), bp::arg("res1") ) + , bp::release_gil_policy() + , "Return the number of atom connections between the residues\nidentified by res0 and res1\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::BondID const &) const; - properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); - - ConnectivityBase_exposer.def( - "properties", properties_function_value, (bp::arg("bond")), bp::release_gil_policy(), "Return the properties of the passed bond"); + + typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::BondID const & ) const; + properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); + + ConnectivityBase_exposer.def( + "properties" + , properties_function_value + , ( bp::arg("bond") ) + , bp::release_gil_policy() + , "Return the properties of the passed bond" ); + } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::AngleID const &) const; - properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); - - ConnectivityBase_exposer.def( - "properties", properties_function_value, (bp::arg("ang")), bp::release_gil_policy(), "Return the properties of the passed angle"); + + typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::AngleID const & ) const; + properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); + + ConnectivityBase_exposer.def( + "properties" + , properties_function_value + , ( bp::arg("ang") ) + , bp::release_gil_policy() + , "Return the properties of the passed angle" ); + } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::DihedralID const &) const; - properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); - - ConnectivityBase_exposer.def( - "properties", properties_function_value, (bp::arg("dih")), bp::release_gil_policy(), "Return the properties of the passed dihedral"); + + typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::DihedralID const & ) const; + properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); + + ConnectivityBase_exposer.def( + "properties" + , properties_function_value + , ( bp::arg("dih") ) + , bp::release_gil_policy() + , "Return the properties of the passed dihedral" ); + } { //::SireMol::ConnectivityBase::properties - - typedef ::SireBase::Properties (::SireMol::ConnectivityBase::*properties_function_type)(::SireMol::ImproperID const &) const; - properties_function_type properties_function_value(&::SireMol::ConnectivityBase::properties); - - ConnectivityBase_exposer.def( - "properties", properties_function_value, (bp::arg("imp")), bp::release_gil_policy(), "Return the properties of the passed improper"); + + typedef ::SireBase::Properties ( ::SireMol::ConnectivityBase::*properties_function_type)( ::SireMol::ImproperID const & ) const; + properties_function_type properties_function_value( &::SireMol::ConnectivityBase::properties ); + + ConnectivityBase_exposer.def( + "properties" + , properties_function_value + , ( bp::arg("imp") ) + , bp::release_gil_policy() + , "Return the properties of the passed improper" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("bond"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified bond"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("bond"), bp::arg("key") ) + , bp::return_value_policy() + , "Return the specified property of the specified bond" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("bond"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified bond, or\ndefault_value if such a property is not defined\n"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("bond"), bp::arg("key"), bp::arg("default_value") ) + , bp::return_value_policy() + , "Return the specified property of the specified bond, or\ndefault_value if such a property is not defined\n" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("ang"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified angle"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("ang"), bp::arg("key") ) + , bp::return_value_policy() + , "Return the specified property of the specified angle" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("ang"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified angle, or\ndefault_value if such a property is not defined\n"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("ang"), bp::arg("key"), bp::arg("default_value") ) + , bp::return_value_policy() + , "Return the specified property of the specified angle, or\ndefault_value if such a property is not defined\n" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("dih"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified dihedral"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("dih"), bp::arg("key") ) + , bp::return_value_policy() + , "Return the specified property of the specified dihedral" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("dih"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified dihedral, or\ndefault_value if such a property is not defined\n"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("dih"), bp::arg("key"), bp::arg("default_value") ) + , bp::return_value_policy() + , "Return the specified property of the specified dihedral, or\ndefault_value if such a property is not defined\n" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("imp"), bp::arg("key")), bp::return_value_policy(), "Return the specified property of the specified improper"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("imp"), bp::arg("key") ) + , bp::return_value_policy() + , "Return the specified property of the specified improper" ); + } { //::SireMol::ConnectivityBase::property - - typedef ::SireBase::Property const &(::SireMol::ConnectivityBase::*property_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &, ::SireBase::Property const &) const; - property_function_type property_function_value(&::SireMol::ConnectivityBase::property); - - ConnectivityBase_exposer.def( - "property", property_function_value, (bp::arg("imp"), bp::arg("key"), bp::arg("default_value")), bp::return_value_policy(), "Return the specified property of the specified improper, or\ndefault_value if such a property is not defined\n"); + + typedef ::SireBase::Property const & ( ::SireMol::ConnectivityBase::*property_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const &,::SireBase::Property const & ) const; + property_function_type property_function_value( &::SireMol::ConnectivityBase::property ); + + ConnectivityBase_exposer.def( + "property" + , property_function_value + , ( bp::arg("imp"), bp::arg("key"), bp::arg("default_value") ) + , bp::return_value_policy() + , "Return the specified property of the specified improper, or\ndefault_value if such a property is not defined\n" ); + } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)() const; - propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); - - ConnectivityBase_exposer.def( - "propertyKeys", propertyKeys_function_value, bp::release_gil_policy(), "Return all of the property keys for all of the bonds"); + + typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ) const; + propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); + + ConnectivityBase_exposer.def( + "propertyKeys" + , propertyKeys_function_value + , bp::release_gil_policy() + , "Return all of the property keys for all of the bonds" ); + } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::BondID const &) const; - propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); - - ConnectivityBase_exposer.def( - "propertyKeys", propertyKeys_function_value, (bp::arg("bond")), bp::release_gil_policy(), "Return the property keys for the specified bond"); + + typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::BondID const & ) const; + propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); + + ConnectivityBase_exposer.def( + "propertyKeys" + , propertyKeys_function_value + , ( bp::arg("bond") ) + , bp::release_gil_policy() + , "Return the property keys for the specified bond" ); + } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::AngleID const &) const; - propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); - - ConnectivityBase_exposer.def( - "propertyKeys", propertyKeys_function_value, (bp::arg("ang")), bp::release_gil_policy(), "Return the property keys for the specified angle"); + + typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::AngleID const & ) const; + propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); + + ConnectivityBase_exposer.def( + "propertyKeys" + , propertyKeys_function_value + , ( bp::arg("ang") ) + , bp::release_gil_policy() + , "Return the property keys for the specified angle" ); + } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::DihedralID const &) const; - propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); - - ConnectivityBase_exposer.def( - "propertyKeys", propertyKeys_function_value, (bp::arg("dih")), bp::release_gil_policy(), "Return the property keys for the specified dihedral"); + + typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::DihedralID const & ) const; + propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); + + ConnectivityBase_exposer.def( + "propertyKeys" + , propertyKeys_function_value + , ( bp::arg("dih") ) + , bp::release_gil_policy() + , "Return the property keys for the specified dihedral" ); + } { //::SireMol::ConnectivityBase::propertyKeys - - typedef ::QStringList (::SireMol::ConnectivityBase::*propertyKeys_function_type)(::SireMol::ImproperID const &) const; - propertyKeys_function_type propertyKeys_function_value(&::SireMol::ConnectivityBase::propertyKeys); - - ConnectivityBase_exposer.def( - "propertyKeys", propertyKeys_function_value, (bp::arg("imp")), bp::release_gil_policy(), "Return the property keys for the specified improper"); + + typedef ::QStringList ( ::SireMol::ConnectivityBase::*propertyKeys_function_type)( ::SireMol::ImproperID const & ) const; + propertyKeys_function_type propertyKeys_function_value( &::SireMol::ConnectivityBase::propertyKeys ); + + ConnectivityBase_exposer.def( + "propertyKeys" + , propertyKeys_function_value + , ( bp::arg("imp") ) + , bp::release_gil_policy() + , "Return the property keys for the specified improper" ); + } { //::SireMol::ConnectivityBase::propertyType - - typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::BondID const &, ::SireBase::PropertyName const &) const; - propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); - - ConnectivityBase_exposer.def( - "propertyType", propertyType_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified bond at key key"); + + typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::BondID const &,::SireBase::PropertyName const & ) const; + propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); + + ConnectivityBase_exposer.def( + "propertyType" + , propertyType_function_value + , ( bp::arg("bond"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return the type of the property for the specified bond at key key" ); + } { //::SireMol::ConnectivityBase::propertyType - - typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::AngleID const &, ::SireBase::PropertyName const &) const; - propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); - - ConnectivityBase_exposer.def( - "propertyType", propertyType_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified angle at key key"); + + typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::AngleID const &,::SireBase::PropertyName const & ) const; + propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); + + ConnectivityBase_exposer.def( + "propertyType" + , propertyType_function_value + , ( bp::arg("ang"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return the type of the property for the specified angle at key key" ); + } { //::SireMol::ConnectivityBase::propertyType - - typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::DihedralID const &, ::SireBase::PropertyName const &) const; - propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); - - ConnectivityBase_exposer.def( - "propertyType", propertyType_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified dihedral at key key"); + + typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::DihedralID const &,::SireBase::PropertyName const & ) const; + propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); + + ConnectivityBase_exposer.def( + "propertyType" + , propertyType_function_value + , ( bp::arg("dih"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return the type of the property for the specified dihedral at key key" ); + } { //::SireMol::ConnectivityBase::propertyType - - typedef char const *(::SireMol::ConnectivityBase::*propertyType_function_type)(::SireMol::ImproperID const &, ::SireBase::PropertyName const &) const; - propertyType_function_type propertyType_function_value(&::SireMol::ConnectivityBase::propertyType); - - ConnectivityBase_exposer.def( - "propertyType", propertyType_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Return the type of the property for the specified improper at key key"); + + typedef char const * ( ::SireMol::ConnectivityBase::*propertyType_function_type)( ::SireMol::ImproperID const &,::SireBase::PropertyName const & ) const; + propertyType_function_type propertyType_function_value( &::SireMol::ConnectivityBase::propertyType ); + + ConnectivityBase_exposer.def( + "propertyType" + , propertyType_function_value + , ( bp::arg("imp"), bp::arg("key") ) + , bp::release_gil_policy() + , "Return the type of the property for the specified improper at key key" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Split this molecule into two parts about the atoms\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Split this molecule into two parts about the atoms\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::release_gil_policy(), "Split the molecule into two parts about the bond between atom0 and atom1.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::release_gil_policy() + , "Split the molecule into two parts about the bond between atom0 and atom1.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::BondID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("bond")), bp::release_gil_policy(), "Split the molecule into two parts about the bond bond\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::BondID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("bond") ) + , bp::release_gil_policy() + , "Split the molecule into two parts about the bond bond\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into two parts about the atoms\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms of this molecule into two parts about the atoms\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule about the atoms\natom0 and atom1\nThrow: SireMol::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms of this molecule about the atoms\natom0 and atom1\nThrow: SireMol::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::BondID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("bond"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into two parts\nabout the bond bond\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::BondID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("bond"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms of this molecule into two parts\nabout the bond bond\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "Split this molecule into three parts about the atoms\natom0, atom1 and atom2.\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "Split this molecule into three parts about the atoms\natom0, atom1 and atom2.\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2")), bp::release_gil_policy(), "Split the molecule into two parts based on the three supplied atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2") ) + , bp::release_gil_policy() + , "Split the molecule into two parts based on the three supplied atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AngleID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("angle")), bp::release_gil_policy(), "Split the molecule into two parts based on the supplied angle\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AngleID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("angle") ) + , bp::release_gil_policy() + , "Split the molecule into two parts based on the supplied angle\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into three parts about the atoms\natom0, atom1 and atom2.\nNote that all three atoms must be contained in the selection or else\na missing_atom exception will be thrown\nAn exception will be thrown if it is not possible to split the molecule\nunambiguously in two, as the angle is part of a ring.\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms of this molecule into three parts about the atoms\natom0, atom1 and atom2.\nNote that all three atoms must be contained in the selection or else\na missing_atom exception will be thrown\nAn exception will be thrown if it is not possible to split the molecule\nunambiguously in two, as the angle is part of a ring.\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of the molecule into two groups around the\nthree supplied atoms\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms of the molecule into two groups around the\nthree supplied atoms\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AngleID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("angle"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the angle identified in\nangle. This splits the molecule about atom0() and atom2()\nof the angle, ignoring atom atom1().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AngleID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("angle"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the angle identified in\nangle. This splits the molecule about atom0() and atom2()\nof the angle, ignoring atom atom1().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) + , bp::release_gil_policy() + , "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3")), bp::release_gil_policy(), "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3") ) + , bp::release_gil_policy() + , "Split this molecule into two parts based on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::DihedralID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("dihedral")), bp::release_gil_policy(), "Split this molecule into two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::DihedralID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("dihedral") ) + , bp::release_gil_policy() + , "Split this molecule into two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomIdx, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms of this molecule into two parts\nbased on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nAll four atoms must be selected in selected_atoms or else\na missing_atom exception will be thrown\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomIdx,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms of this molecule into two parts\nbased on the passed atoms.\nThis splits the molecule between atom0 and atom3, ignoring\natom1 and atom2.\nAll four atoms must be selected in selected_atoms or else\na missing_atom exception will be thrown\nC1 C4--C5--C6\n\ \nC2 C8--C9\n \ \nC3 C7\n\\nC10--C11\nSplitting C4,C2,C7,C10 will return\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the passed atoms. This splits\nthe molecule between atom0 and atom3, ignoring atom1 and\natom2.\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("atom0"), bp::arg("atom1"), bp::arg("atom2"), bp::arg("atom3"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the passed atoms. This splits\nthe molecule between atom0 and atom3, ignoring atom1 and\natom2.\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::DihedralID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("dihedral"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::DihedralID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("dihedral"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms selected_atoms of this molecule\ninto two parts based on the dihedral identified in\ndihedral. This splits the molecule about atom0() and atom3()\nof the dihedral, ignoring atoms atom1() and atom2().\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::ImproperID const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("improper")), bp::release_gil_policy(), "Split this molecule into two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::ImproperID const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("improper") ) + , bp::release_gil_policy() + , "Split this molecule into two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::split - - typedef ::boost::tuples::tuple (::SireMol::ConnectivityBase::*split_function_type)(::SireMol::ImproperID const &, ::SireMol::AtomSelection const &) const; - split_function_type split_function_value(&::SireMol::ConnectivityBase::split); - - ConnectivityBase_exposer.def( - "split", split_function_value, (bp::arg("improper"), bp::arg("selected_atoms")), bp::release_gil_policy(), "Split the selected atoms in selected_atoms in this molecule\ninto two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n"); + + typedef ::boost::tuples::tuple< SireMol::AtomSelection, SireMol::AtomSelection, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireMol::ConnectivityBase::*split_function_type)( ::SireMol::ImproperID const &,::SireMol::AtomSelection const & ) const; + split_function_type split_function_value( &::SireMol::ConnectivityBase::split ); + + ConnectivityBase_exposer.def( + "split" + , split_function_value + , ( bp::arg("improper"), bp::arg("selected_atoms") ) + , bp::release_gil_policy() + , "Split the selected atoms in selected_atoms in this molecule\ninto two parts based on the improper angle\nidentified by improper. This splits the molecule about\nbond between atom0() and atom1() of the improper\nThrow: SireError::incompatible_error\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\nThrow: SireMol::ring_error\n" ); + } { //::SireMol::ConnectivityBase::toCONECT - - typedef ::QString (::SireMol::ConnectivityBase::*toCONECT_function_type)(int) const; - toCONECT_function_type toCONECT_function_value(&::SireMol::ConnectivityBase::toCONECT); - - ConnectivityBase_exposer.def( - "toCONECT", toCONECT_function_value, (bp::arg("offset") = (int)(0)), "Return a PDB format CONECT record for this connectivity object."); + + typedef ::QString ( ::SireMol::ConnectivityBase::*toCONECT_function_type)( int ) const; + toCONECT_function_type toCONECT_function_value( &::SireMol::ConnectivityBase::toCONECT ); + + ConnectivityBase_exposer.def( + "toCONECT" + , toCONECT_function_value + , ( bp::arg("offset")=(int)(0) ) + , "Return a PDB format CONECT record for this connectivity object." ); + } { //::SireMol::ConnectivityBase::toString - - typedef ::QString (::SireMol::ConnectivityBase::*toString_function_type)() const; - toString_function_type toString_function_value(&::SireMol::ConnectivityBase::toString); - - ConnectivityBase_exposer.def( - "toString", toString_function_value, bp::release_gil_policy(), ""); + + typedef ::QString ( ::SireMol::ConnectivityBase::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireMol::ConnectivityBase::toString ); + + ConnectivityBase_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireMol::ConnectivityBase::typeName - - typedef char const *(*typeName_function_type)(); - typeName_function_type typeName_function_value(&::SireMol::ConnectivityBase::typeName); - - ConnectivityBase_exposer.def( - "typeName", typeName_function_value, bp::release_gil_policy(), ""); - } - ConnectivityBase_exposer.staticmethod("typeName"); - ConnectivityBase_exposer.def("__rlshift__", &__rlshift__QDataStream<::SireMol::ConnectivityBase>, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); - ConnectivityBase_exposer.def("__rrshift__", &__rrshift__QDataStream<::SireMol::ConnectivityBase>, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); - ConnectivityBase_exposer.def_pickle(sire_pickle_suite<::SireMol::ConnectivityBase>()); - ConnectivityBase_exposer.def("__str__", &__str__<::SireMol::ConnectivityBase>); - ConnectivityBase_exposer.def("__repr__", &__str__<::SireMol::ConnectivityBase>); + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMol::ConnectivityBase::typeName ); + + ConnectivityBase_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + ConnectivityBase_exposer.staticmethod( "typeName" ); + ConnectivityBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::ConnectivityBase >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + ConnectivityBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::ConnectivityBase >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + ConnectivityBase_exposer.def_pickle(sire_pickle_suite< ::SireMol::ConnectivityBase >()); + ConnectivityBase_exposer.def( "__str__", &__str__< ::SireMol::ConnectivityBase > ); + ConnectivityBase_exposer.def( "__repr__", &__str__< ::SireMol::ConnectivityBase > ); } + } diff --git a/wrapper/Mol/ConnectivityEditor.pypp.cpp b/wrapper/Mol/ConnectivityEditor.pypp.cpp index 0b60550e0..e70627651 100644 --- a/wrapper/Mol/ConnectivityEditor.pypp.cpp +++ b/wrapper/Mol/ConnectivityEditor.pypp.cpp @@ -57,7 +57,7 @@ namespace bp = boost::python; #include "connectivity.h" -SireMol::ConnectivityEditor __copy__(const SireMol::ConnectivityEditor &other) { return SireMol::ConnectivityEditor(other); } +SireMol::ConnectivityEditor __copy__(const SireMol::ConnectivityEditor &other){ return SireMol::ConnectivityEditor(other); } #include "Qt/qdatastream.hpp" @@ -65,227 +65,349 @@ SireMol::ConnectivityEditor __copy__(const SireMol::ConnectivityEditor &other) { #include "Helpers/release_gil_policy.hpp" -void register_ConnectivityEditor_class() -{ +void register_ConnectivityEditor_class(){ { //::SireMol::ConnectivityEditor - typedef bp::class_> ConnectivityEditor_exposer_t; - ConnectivityEditor_exposer_t ConnectivityEditor_exposer = ConnectivityEditor_exposer_t("ConnectivityEditor", "An editor that can be used to edit a Connectivity object\n\nAuthor: Christopher Woods\n", bp::init<>("Null constructor")); - bp::scope ConnectivityEditor_scope(ConnectivityEditor_exposer); - ConnectivityEditor_exposer.def(bp::init((bp::arg("connectivity")), "Construct an editor to edit a copy of the passed\nConnectivity object")); - ConnectivityEditor_exposer.def(bp::init((bp::arg("other")), "Copy constructor")); + typedef bp::class_< SireMol::ConnectivityEditor, bp::bases< SireMol::ConnectivityBase, SireMol::MolViewProperty, SireBase::Property > > ConnectivityEditor_exposer_t; + ConnectivityEditor_exposer_t ConnectivityEditor_exposer = ConnectivityEditor_exposer_t( "ConnectivityEditor", "An editor that can be used to edit a Connectivity object\n\nAuthor: Christopher Woods\n", bp::init< >("Null constructor") ); + bp::scope ConnectivityEditor_scope( ConnectivityEditor_exposer ); + ConnectivityEditor_exposer.def( bp::init< SireMol::Connectivity const & >(( bp::arg("connectivity") ), "Construct an editor to edit a copy of the passed\nConnectivity object") ); + ConnectivityEditor_exposer.def( bp::init< SireMol::ConnectivityEditor const & >(( bp::arg("other") ), "Copy constructor") ); { //::SireMol::ConnectivityEditor::commit - - typedef ::SireMol::Connectivity (::SireMol::ConnectivityEditor::*commit_function_type)() const; - commit_function_type commit_function_value(&::SireMol::ConnectivityEditor::commit); - - ConnectivityEditor_exposer.def( - "commit", commit_function_value, bp::release_gil_policy(), "Return the editied connectivity"); + + typedef ::SireMol::Connectivity ( ::SireMol::ConnectivityEditor::*commit_function_type)( ) const; + commit_function_type commit_function_value( &::SireMol::ConnectivityEditor::commit ); + + ConnectivityEditor_exposer.def( + "commit" + , commit_function_value + , bp::release_gil_policy() + , "Return the editied connectivity" ); + } { //::SireMol::ConnectivityEditor::connect - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*connect_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx); - connect_function_type connect_function_value(&::SireMol::ConnectivityEditor::connect); - - ConnectivityEditor_exposer.def( - "connect", connect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Record the connection between the atoms at indicies atom0\nand atom1\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*connect_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) ; + connect_function_type connect_function_value( &::SireMol::ConnectivityEditor::connect ); + + ConnectivityEditor_exposer.def( + "connect" + , connect_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::return_self< >() + , "Record the connection between the atoms at indicies atom0\nand atom1\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::connect - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*connect_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &); - connect_function_type connect_function_value(&::SireMol::ConnectivityEditor::connect); - - ConnectivityEditor_exposer.def( - "connect", connect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Record a connection between the atom identified by atom0 and\nthe atom identified by atom1\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*connect_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) ; + connect_function_type connect_function_value( &::SireMol::ConnectivityEditor::connect ); + + ConnectivityEditor_exposer.def( + "connect" + , connect_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::return_self< >() + , "Record a connection between the atom identified by atom0 and\nthe atom identified by atom1\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnect - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnect_function_type)(::SireMol::AtomIdx, ::SireMol::AtomIdx); - disconnect_function_type disconnect_function_value(&::SireMol::ConnectivityEditor::disconnect); - - ConnectivityEditor_exposer.def( - "disconnect", disconnect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Remove the connection between the atoms at indicies atom0\nand atom1 - this does nothing if there isnt already a connection\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::SireMol::AtomIdx,::SireMol::AtomIdx ) ; + disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); + + ConnectivityEditor_exposer.def( + "disconnect" + , disconnect_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::return_self< >() + , "Remove the connection between the atoms at indicies atom0\nand atom1 - this does nothing if there isnt already a connection\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnect - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnect_function_type)(::SireMol::AtomID const &, ::SireMol::AtomID const &); - disconnect_function_type disconnect_function_value(&::SireMol::ConnectivityEditor::disconnect); - - ConnectivityEditor_exposer.def( - "disconnect", disconnect_function_value, (bp::arg("atom0"), bp::arg("atom1")), bp::return_self<>(), "Disconnect the atoms that are identified by atom0 and atom1 -\nthis does nothing if there isnt a connection between these atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::SireMol::AtomID const &,::SireMol::AtomID const & ) ; + disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); + + ConnectivityEditor_exposer.def( + "disconnect" + , disconnect_function_value + , ( bp::arg("atom0"), bp::arg("atom1") ) + , bp::return_self< >() + , "Disconnect the atoms that are identified by atom0 and atom1 -\nthis does nothing if there isnt a connection between these atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::AtomIdx); - disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); - - ConnectivityEditor_exposer.def( - "disconnectAll", disconnectAll_function_value, (bp::arg("atomidx")), bp::return_self<>(), "Remove all of the connections to the atom at index atomidx\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::AtomIdx ) ; + disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); + + ConnectivityEditor_exposer.def( + "disconnectAll" + , disconnectAll_function_value + , ( bp::arg("atomidx") ) + , bp::return_self< >() + , "Remove all of the connections to the atom at index atomidx\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::ResIdx); - disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); - - ConnectivityEditor_exposer.def( - "disconnectAll", disconnectAll_function_value, (bp::arg("residx")), bp::return_self<>(), "Remove all of the connections that involve any of the atoms\nin the residue at index residx\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::ResIdx ) ; + disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); + + ConnectivityEditor_exposer.def( + "disconnectAll" + , disconnectAll_function_value + , ( bp::arg("residx") ) + , bp::return_self< >() + , "Remove all of the connections that involve any of the atoms\nin the residue at index residx\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::AtomID const &); - disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); - - ConnectivityEditor_exposer.def( - "disconnectAll", disconnectAll_function_value, (bp::arg("atomid")), bp::return_self<>(), "Remove all of the connections to the atom identified by atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::AtomID const & ) ; + disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); + + ConnectivityEditor_exposer.def( + "disconnectAll" + , disconnectAll_function_value + , ( bp::arg("atomid") ) + , bp::return_self< >() + , "Remove all of the connections to the atom identified by atomid\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(::SireMol::ResID const &); - disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); - - ConnectivityEditor_exposer.def( - "disconnectAll", disconnectAll_function_value, (bp::arg("resid")), bp::return_self<>(), "Remove all of the connections that involve any of the atoms\nin the residue identified by resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ::SireMol::ResID const & ) ; + disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); + + ConnectivityEditor_exposer.def( + "disconnectAll" + , disconnectAll_function_value + , ( bp::arg("resid") ) + , bp::return_self< >() + , "Remove all of the connections that involve any of the atoms\nin the residue identified by resid\nThrow: SireMol::missing_residue\nThrow: SireMol::duplicate_residue\nThrow: SireError::invalid_index\n" ); + } { //::SireMol::ConnectivityEditor::disconnectAll - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*disconnectAll_function_type)(); - disconnectAll_function_type disconnectAll_function_value(&::SireMol::ConnectivityEditor::disconnectAll); - - ConnectivityEditor_exposer.def( - "disconnectAll", disconnectAll_function_value, bp::return_self<>(), "Remove all bonds from this molecule"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnectAll_function_type)( ) ; + disconnectAll_function_type disconnectAll_function_value( &::SireMol::ConnectivityEditor::disconnectAll ); + + ConnectivityEditor_exposer.def( + "disconnectAll" + , disconnectAll_function_value + , bp::return_self< >() + , "Remove all bonds from this molecule" ); + } - ConnectivityEditor_exposer.def(bp::self != bp::self); + ConnectivityEditor_exposer.def( bp::self != bp::self ); { //::SireMol::ConnectivityEditor::operator= - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*assign_function_type)(::SireMol::ConnectivityBase const &); - assign_function_type assign_function_value(&::SireMol::ConnectivityEditor::operator=); - - ConnectivityEditor_exposer.def( - "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*assign_function_type)( ::SireMol::ConnectivityBase const & ) ; + assign_function_type assign_function_value( &::SireMol::ConnectivityEditor::operator= ); + + ConnectivityEditor_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + } - ConnectivityEditor_exposer.def(bp::self == bp::self); + ConnectivityEditor_exposer.def( bp::self == bp::self ); { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::QString const &); - removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); - - ConnectivityEditor_exposer.def( - "removeProperty", removeProperty_function_value, (bp::arg("key")), bp::return_self<>(), "Remove the specified property from all bonds"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::QString const & ) ; + removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); + + ConnectivityEditor_exposer.def( + "removeProperty" + , removeProperty_function_value + , ( bp::arg("key") ) + , bp::return_self< >() + , "Remove the specified property from all bonds" ); + } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::BondID const &, ::QString const &); - removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); - - ConnectivityEditor_exposer.def( - "removeProperty", removeProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified bond"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::BondID const &,::QString const & ) ; + removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); + + ConnectivityEditor_exposer.def( + "removeProperty" + , removeProperty_function_value + , ( bp::arg("bond"), bp::arg("key") ) + , bp::return_self< >() + , "Remove the specified property from the specified bond" ); + } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::AngleID const &, ::QString const &); - removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); - - ConnectivityEditor_exposer.def( - "removeProperty", removeProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified angle"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::AngleID const &,::QString const & ) ; + removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); + + ConnectivityEditor_exposer.def( + "removeProperty" + , removeProperty_function_value + , ( bp::arg("ang"), bp::arg("key") ) + , bp::return_self< >() + , "Remove the specified property from the specified angle" ); + } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::DihedralID const &, ::QString const &); - removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); - - ConnectivityEditor_exposer.def( - "removeProperty", removeProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified dihedral"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::DihedralID const &,::QString const & ) ; + removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); + + ConnectivityEditor_exposer.def( + "removeProperty" + , removeProperty_function_value + , ( bp::arg("dih"), bp::arg("key") ) + , bp::return_self< >() + , "Remove the specified property from the specified dihedral" ); + } { //::SireMol::ConnectivityEditor::removeProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*removeProperty_function_type)(::SireMol::ImproperID const &, ::QString const &); - removeProperty_function_type removeProperty_function_value(&::SireMol::ConnectivityEditor::removeProperty); - - ConnectivityEditor_exposer.def( - "removeProperty", removeProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::return_self<>(), "Remove the specified property from the specified improper"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*removeProperty_function_type)( ::SireMol::ImproperID const &,::QString const & ) ; + removeProperty_function_type removeProperty_function_value( &::SireMol::ConnectivityEditor::removeProperty ); + + ConnectivityEditor_exposer.def( + "removeProperty" + , removeProperty_function_value + , ( bp::arg("imp"), bp::arg("key") ) + , bp::return_self< >() + , "Remove the specified property from the specified improper" ); + } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::BondID const &, ::QString const &, ::SireBase::Property const &); - setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); - - ConnectivityEditor_exposer.def( - "setProperty", setProperty_function_value, (bp::arg("bond"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified bond, at the specified key, to value"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::BondID const &,::QString const &,::SireBase::Property const & ) ; + setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); + + ConnectivityEditor_exposer.def( + "setProperty" + , setProperty_function_value + , ( bp::arg("bond"), bp::arg("key"), bp::arg("value") ) + , bp::return_self< >() + , "Set the property for the specified bond, at the specified key, to value" ); + } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::AngleID const &, ::QString const &, ::SireBase::Property const &); - setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); - - ConnectivityEditor_exposer.def( - "setProperty", setProperty_function_value, (bp::arg("ang"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified angle, at the specified key, to value"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::AngleID const &,::QString const &,::SireBase::Property const & ) ; + setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); + + ConnectivityEditor_exposer.def( + "setProperty" + , setProperty_function_value + , ( bp::arg("ang"), bp::arg("key"), bp::arg("value") ) + , bp::return_self< >() + , "Set the property for the specified angle, at the specified key, to value" ); + } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::DihedralID const &, ::QString const &, ::SireBase::Property const &); - setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); - - ConnectivityEditor_exposer.def( - "setProperty", setProperty_function_value, (bp::arg("dih"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified dihedral, at the specified key, to value"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::DihedralID const &,::QString const &,::SireBase::Property const & ) ; + setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); + + ConnectivityEditor_exposer.def( + "setProperty" + , setProperty_function_value + , ( bp::arg("dih"), bp::arg("key"), bp::arg("value") ) + , bp::return_self< >() + , "Set the property for the specified dihedral, at the specified key, to value" ); + } { //::SireMol::ConnectivityEditor::setProperty - - typedef ::SireMol::ConnectivityEditor &(::SireMol::ConnectivityEditor::*setProperty_function_type)(::SireMol::ImproperID const &, ::QString const &, ::SireBase::Property const &); - setProperty_function_type setProperty_function_value(&::SireMol::ConnectivityEditor::setProperty); - - ConnectivityEditor_exposer.def( - "setProperty", setProperty_function_value, (bp::arg("imp"), bp::arg("key"), bp::arg("value")), bp::return_self<>(), "Set the property for the specified improper, at the specified key, to value"); + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*setProperty_function_type)( ::SireMol::ImproperID const &,::QString const &,::SireBase::Property const & ) ; + setProperty_function_type setProperty_function_value( &::SireMol::ConnectivityEditor::setProperty ); + + ConnectivityEditor_exposer.def( + "setProperty" + , setProperty_function_value + , ( bp::arg("imp"), bp::arg("key"), bp::arg("value") ) + , bp::return_self< >() + , "Set the property for the specified improper, at the specified key, to value" ); + } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::BondID const &, ::QString const &); - takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); - - ConnectivityEditor_exposer.def( - "takeProperty", takeProperty_function_value, (bp::arg("bond"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified bond - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); + + typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::BondID const &,::QString const & ) ; + takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); + + ConnectivityEditor_exposer.def( + "takeProperty" + , takeProperty_function_value + , ( bp::arg("bond"), bp::arg("key") ) + , bp::release_gil_policy() + , "Take the specified property from the specified bond - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); + } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::AngleID const &, ::QString const &); - takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); - - ConnectivityEditor_exposer.def( - "takeProperty", takeProperty_function_value, (bp::arg("ang"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified angle - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); + + typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::AngleID const &,::QString const & ) ; + takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); + + ConnectivityEditor_exposer.def( + "takeProperty" + , takeProperty_function_value + , ( bp::arg("ang"), bp::arg("key") ) + , bp::release_gil_policy() + , "Take the specified property from the specified angle - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); + } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::DihedralID const &, ::QString const &); - takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); - - ConnectivityEditor_exposer.def( - "takeProperty", takeProperty_function_value, (bp::arg("dih"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified dihedral - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); + + typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::DihedralID const &,::QString const & ) ; + takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); + + ConnectivityEditor_exposer.def( + "takeProperty" + , takeProperty_function_value + , ( bp::arg("dih"), bp::arg("key") ) + , bp::release_gil_policy() + , "Take the specified property from the specified dihedral - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); + } { //::SireMol::ConnectivityEditor::takeProperty - - typedef ::SireBase::PropertyPtr (::SireMol::ConnectivityEditor::*takeProperty_function_type)(::SireMol::ImproperID const &, ::QString const &); - takeProperty_function_type takeProperty_function_value(&::SireMol::ConnectivityEditor::takeProperty); - - ConnectivityEditor_exposer.def( - "takeProperty", takeProperty_function_value, (bp::arg("imp"), bp::arg("key")), bp::release_gil_policy(), "Take the specified property from the specified improper - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n"); + + typedef ::SireBase::PropertyPtr ( ::SireMol::ConnectivityEditor::*takeProperty_function_type)( ::SireMol::ImproperID const &,::QString const & ) ; + takeProperty_function_type takeProperty_function_value( &::SireMol::ConnectivityEditor::takeProperty ); + + ConnectivityEditor_exposer.def( + "takeProperty" + , takeProperty_function_value + , ( bp::arg("imp"), bp::arg("key") ) + , bp::release_gil_policy() + , "Take the specified property from the specified improper - this removes\nand returns the property if it exists. If it doesnt, then\na NullProperty is returned\n" ); + } { //::SireMol::ConnectivityEditor::typeName - - typedef char const *(*typeName_function_type)(); - typeName_function_type typeName_function_value(&::SireMol::ConnectivityEditor::typeName); - - ConnectivityEditor_exposer.def( - "typeName", typeName_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMol::ConnectivityEditor::typeName ); + + ConnectivityEditor_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + } - ConnectivityEditor_exposer.staticmethod("typeName"); - ConnectivityEditor_exposer.def("__copy__", &__copy__); - ConnectivityEditor_exposer.def("__deepcopy__", &__copy__); - ConnectivityEditor_exposer.def("clone", &__copy__); - ConnectivityEditor_exposer.def("__rlshift__", &__rlshift__QDataStream<::SireMol::ConnectivityEditor>, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); - ConnectivityEditor_exposer.def("__rrshift__", &__rrshift__QDataStream<::SireMol::ConnectivityEditor>, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1, 2>>()); - ConnectivityEditor_exposer.def_pickle(sire_pickle_suite<::SireMol::ConnectivityEditor>()); - ConnectivityEditor_exposer.def("__str__", &__str__<::SireMol::ConnectivityEditor>); - ConnectivityEditor_exposer.def("__repr__", &__str__<::SireMol::ConnectivityEditor>); + ConnectivityEditor_exposer.staticmethod( "typeName" ); + ConnectivityEditor_exposer.def( "__copy__", &__copy__); + ConnectivityEditor_exposer.def( "__deepcopy__", &__copy__); + ConnectivityEditor_exposer.def( "clone", &__copy__); + ConnectivityEditor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::ConnectivityEditor >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + ConnectivityEditor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::ConnectivityEditor >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + ConnectivityEditor_exposer.def_pickle(sire_pickle_suite< ::SireMol::ConnectivityEditor >()); + ConnectivityEditor_exposer.def( "__str__", &__str__< ::SireMol::ConnectivityEditor > ); + ConnectivityEditor_exposer.def( "__repr__", &__str__< ::SireMol::ConnectivityEditor > ); } + } diff --git a/wrapper/Mol/SireMol_containers.cpp b/wrapper/Mol/SireMol_containers.cpp index 8b72cee54..6f3c55649 100644 --- a/wrapper/Mol/SireMol_containers.cpp +++ b/wrapper/Mol/SireMol_containers.cpp @@ -40,6 +40,7 @@ #include "Base/convertpackedarray.hpp" #include "SireMol/atom.h" +#include "SireMol/atomidxmapping.h" #include "SireMol/beadnum.h" #include "SireMol/element.h" #include "SireMol/atomidentifier.h" @@ -86,122 +87,123 @@ using boost::python::register_tuple; void register_SireMol_containers() { - register_viewsofmol_list(); + register_viewsofmol_list(); - register_list>(); - register_list>>(); - register_list>(); + register_list>(); + register_list>>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); + register_list>(); - register_list>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>>(); - register_list>>(); + register_list>>(); + register_list>>(); - register_list>>(); + register_list>>(); - register_list>>(); + register_list>>(); - register_list>(); - register_list>>(); + register_list>(); + register_list>>(); - register_list>(); + register_list>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>>(); + register_list>>(); - register_list>(); - register_list>(); + register_list>(); + register_list>(); - register_list>(); + register_list>(); - register_tuple>(); - register_tuple>(); - register_tuple>(); + register_tuple>(); + register_tuple>(); + register_tuple>(); - register_tuple>(); - register_tuple>(); + register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); + register_tuple>(); - register_tuple>(); - register_tuple>(); - register_tuple, SireBase::PropertyMap>>(); - register_tuple, SireBase::PropertyMap>>(); + register_tuple>(); + register_tuple>(); + register_tuple, SireBase::PropertyMap>>(); + register_tuple, SireBase::PropertyMap>>(); - register_PackedArray>(); - register_PackedArray>(); + register_PackedArray>(); + register_PackedArray>(); - register_dict>(); + register_dict>(); - register_dict>(); - register_dict>(); + register_dict>(); + register_dict>(); - register_dict>>(); + register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>>(); - register_dict>(); - register_dict>(); - register_dict>(); + register_dict>>(); + register_dict>>(); + register_dict>>(); + register_dict>>(); + register_dict>>(); + register_dict>(); + register_dict>(); + register_dict>(); + register_dict>(); - register_set>(); - register_set>(); + register_set>(); + register_set>(); - register_set>(); - register_set>(); + register_set>(); + register_set>(); } From ce465947033a55a2a2c2f255edec9a15a3b74ebb Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 2 Mar 2024 18:36:03 +0000 Subject: [PATCH 139/468] Added code to merge the connectivities, plus build a shared connectivity object. Testing it... --- corelib/src/libs/SireIO/amber.cpp | 2 - corelib/src/libs/SireMol/connectivity.cpp | 159 +++++++++++++++++++++- corelib/src/libs/SireMol/connectivity.h | 11 ++ corelib/src/libs/SireSystem/merge.cpp | 15 +- wrapper/Mol/ConnectivityBase.pypp.cpp | 12 ++ wrapper/Mol/ConnectivityEditor.pypp.cpp | 65 +++++++++ 6 files changed, 257 insertions(+), 7 deletions(-) diff --git a/corelib/src/libs/SireIO/amber.cpp b/corelib/src/libs/SireIO/amber.cpp index 29cfa63a8..4f6c824e4 100644 --- a/corelib/src/libs/SireIO/amber.cpp +++ b/corelib/src/libs/SireIO/amber.cpp @@ -1966,7 +1966,6 @@ tuple Amber::readCrdTop(const QString &crdfile, const Q MoleculeGroup molecules(QString("%1:%2").arg(crdfile, topfile)); - int molnum = 1; int resnum = 1; int total_molecules; @@ -2147,7 +2146,6 @@ tuple Amber::readCrdTop(const QString &crdfile, const Q molecule = editmol.commit(); molecules.add(molecule); - ++molnum; } // Now the box information diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 9fbc04a06..f35e8d7f8 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -2413,6 +2413,45 @@ QList ConnectivityBase::getBonds(const AtomID &atom) const return ret; } +/** Return all of the connections that involve the passed atoms - if exclusive is true, + * then return only connections where both atoms are present in the list. + */ +QList ConnectivityBase::getBonds(const QList &atoms, bool exclusive) const +{ + QList ret; + + const QSet atoms_set(atoms.begin(), atoms.end()); + + if (exclusive) + { + for (const auto &bond : this->getBonds()) + { + const auto atom0 = this->minfo.atomIdx(bond.atom0()); + const auto atom1 = this->minfo.atomIdx(bond.atom1()); + + if (atoms_set.contains(atom0) and atoms_set.contains(atom1)) + { + ret.append(bond); + } + } + } + else + { + for (const auto &bond : this->getBonds()) + { + const auto atom0 = this->minfo.atomIdx(bond.atom0()); + const auto atom1 = this->minfo.atomIdx(bond.atom1()); + + if (atoms_set.contains(atom0) or atoms_set.contains(atom1)) + { + ret.append(bond); + } + } + } + + return ret; +} + namespace SireMol { namespace detail @@ -3391,13 +3430,47 @@ PropertyList ConnectivityBase::merge(const MolViewProperty &other, CODELOC); } - SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") - .arg(this->what())); + if (not ghost.isEmpty()) + { + Console::warning(QObject::tr("The ghost parameter '%1' for bond parameters is ignored").arg(ghost)); + } + + const ConnectivityBase &ref = *this; + const ConnectivityBase &pert = other.asA(); + + auto prop0 = Connectivity(ref); + auto prop1 = Connectivity(ref).edit(); + + // the prop0 properties are already correct + + // the prop1 properties are made by finding all of the atoms that + // are involved in bonds in 'pert' and removing any bonds involving + // only those atoms from 'prop1', and then adding back the matching + // bonds from 'pert'. Use 'true' to only remove bonds where both + // atoms are in the mapping + prop1.disconnect(mapping.mappedIn1(), true); + + // get the mapping from the perturbed to reference states, including + // atoms that don't exist in the reference state. In all cases, + // the values are the indexes in the merged molecule + auto map1to0 = mapping.map1to0(true); + + // now find all of the bonds in 'pert' where both atoms in the + // bond are in map1to0.keys() - i.e. exist and are mapped from + // the perturbed state + const auto pert_bonds = pert.getBonds(map1to0.keys(), true); + + // connect those bonds together + for (const auto &pert_bond : pert_bonds) + { + prop1.connect(map1to0.value(info().atomIdx(pert_bond.atom0())), + map1to0.value(info().atomIdx(pert_bond.atom1()))); + } SireBase::PropertyList ret; - ret.append(*this); - ret.append(*this); + ret.append(prop0); + ret.append(prop1.commit()); return ret; } @@ -3658,6 +3731,23 @@ ConnectivityEditor &ConnectivityEditor::connect(const AtomID &atom0, const AtomI return this->connect(info().atomIdx(atom0), info().atomIdx(atom1)); } +/** Create a connection for the passed bond */ +ConnectivityEditor &ConnectivityEditor::connect(const BondID &bond) +{ + return this->connect(bond.atom0(), bond.atom1()); +} + +/** Create a connection for the passed bonds */ +ConnectivityEditor &ConnectivityEditor::connect(const QList &bonds) +{ + for (const auto &bond : bonds) + { + this->connect(bond); + } + + return *this; +} + /** Remove the connection between the atoms at indicies 'atom0' and 'atom1' - this does nothing if there isn't already a connection @@ -3702,6 +3792,67 @@ ConnectivityEditor &ConnectivityEditor::disconnect(const AtomID &atom0, const At return this->disconnect(info().atomIdx(atom0), info().atomIdx(atom1)); } +/** Disconnect the atoms in the passed bond - this does nothing if the + * atoms aren't connected */ +ConnectivityEditor &ConnectivityEditor::disconnect(const BondID &bond) +{ + return this->disconnect(bond.atom0(), bond.atom1()); +} + +/** Disconnect the atoms in the passed bonds - this does nothing for any + * of the atoms that aren't connected */ +ConnectivityEditor &ConnectivityEditor::disconnect(const QList &bonds) +{ + for (const auto &bond : bonds) + { + this->disconnect(bond); + } + + return *this; +} + +/** Disconnect any and all bonds involving the passed atoms. If exclusive is true, + * then this only removes connection where both atoms are in 'atoms', otherwise + * it removes connections which have one of more atoms in 'atoms' + */ +ConnectivityEditor &ConnectivityEditor::disconnect(const QList &atoms, bool exclusive) +{ + const QSet atoms_set(atoms.begin(), atoms.end()); + + if (exclusive) + { + const auto bonds = this->getBonds(); + + for (const auto &bond : bonds) + { + const auto atom0 = info().atomIdx(bond.atom0()); + const auto atom1 = info().atomIdx(bond.atom1()); + + if (atoms_set.contains(atom0) and atoms_set.contains(atom1)) + { + this->disconnect(atom0, atom1); + } + } + } + else + { + const auto bonds = this->getBonds(); + + for (const auto &bond : bonds) + { + const auto atom0 = info().atomIdx(bond.atom0()); + const auto atom1 = info().atomIdx(bond.atom1()); + + if (atoms_set.contains(atom0) or atoms_set.contains(atom1)) + { + this->disconnect(atom0, atom1); + } + } + } + + return *this; +} + /** Remove all of the connections to the atom at index 'atomidx' \throw SireError::invalid_index diff --git a/corelib/src/libs/SireMol/connectivity.h b/corelib/src/libs/SireMol/connectivity.h index b4b0be2e5..f75472737 100644 --- a/corelib/src/libs/SireMol/connectivity.h +++ b/corelib/src/libs/SireMol/connectivity.h @@ -248,6 +248,9 @@ namespace SireMol QList getBonds() const; QList getBonds(const AtomID &atom) const; + + QList getBonds(const QList &atoms, bool exclusive = true) const; + QList getAngles() const; QList getAngles(const AtomID &atom0) const; QList getAngles(const AtomID &atom0, const AtomID &atom1) const; @@ -471,6 +474,14 @@ namespace SireMol ConnectivityEditor &connect(const AtomID &atom0, const AtomID &atom1); ConnectivityEditor &disconnect(const AtomID &atom0, const AtomID &atom1); + ConnectivityEditor &connect(const BondID &bond); + ConnectivityEditor &disconnect(const BondID &bond); + + ConnectivityEditor &connect(const QList &bonds); + ConnectivityEditor &disconnect(const QList &bonds); + + ConnectivityEditor &disconnect(const QList &atoms, bool exclusive = true); + ConnectivityEditor &disconnectAll(AtomIdx atomidx); ConnectivityEditor &disconnectAll(ResIdx residx); diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 5883db3a3..53cee9610 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -31,6 +31,8 @@ #include "SireMol/core.h" #include "SireMol/moleditor.h" #include "SireMol/atomidxmapping.h" +#include "SireMol/connectivity.h" +#include "SireMol/bondid.h" #include "SireMM/mmdetail.h" @@ -468,6 +470,18 @@ namespace SireSystem editmol.removeProperty(map0[prop]); editmol.setProperty(map[prop + "0"].source(), merged[0]); editmol.setProperty(map[prop + "1"].source(), merged[1]); + + if (prop == "connectivity") + { + // we need to set the connectivity of the merged molecule + auto merged_connectivity = merged[0].asA().edit(); + + // the merged connectivity has the connections of both the + // reference and perturbed states + merged_connectivity.connect(merged[1].asA().getBonds()); + + editmol.setProperty(map["connectivity"].source(), merged_connectivity.commit()); + } } else { @@ -494,7 +508,6 @@ namespace SireSystem editmol.removeProperty(map["parameters"].source()); } - // set the connectivity to the merged connectivity (BELOW CODE IS WRONG!!!) editmol.setProperty(map["connectivity"].source(), editmol.property("connectivity0")); // set the flag that this is a perturbable molecule diff --git a/wrapper/Mol/ConnectivityBase.pypp.cpp b/wrapper/Mol/ConnectivityBase.pypp.cpp index 0ae5f2820..693b180a4 100644 --- a/wrapper/Mol/ConnectivityBase.pypp.cpp +++ b/wrapper/Mol/ConnectivityBase.pypp.cpp @@ -548,6 +548,18 @@ void register_ConnectivityBase_class(){ , bp::release_gil_policy() , "Return the list of bonds in the connectivity containing atom" ); + } + { //::SireMol::ConnectivityBase::getBonds + + typedef ::QList< SireMol::BondID > ( ::SireMol::ConnectivityBase::*getBonds_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) const; + getBonds_function_type getBonds_function_value( &::SireMol::ConnectivityBase::getBonds ); + + ConnectivityBase_exposer.def( + "getBonds" + , getBonds_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Return all of the connections that involve the passed atoms - if exclusive is true,\n then return only connections where both atoms are present in the list.\n" ); + } { //::SireMol::ConnectivityBase::getDihedrals diff --git a/wrapper/Mol/ConnectivityEditor.pypp.cpp b/wrapper/Mol/ConnectivityEditor.pypp.cpp index e70627651..f3128db33 100644 --- a/wrapper/Mol/ConnectivityEditor.pypp.cpp +++ b/wrapper/Mol/ConnectivityEditor.pypp.cpp @@ -110,6 +110,32 @@ void register_ConnectivityEditor_class(){ , bp::return_self< >() , "Record a connection between the atom identified by atom0 and\nthe atom identified by atom1\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } + { //::SireMol::ConnectivityEditor::connect + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*connect_function_type)( ::SireMol::BondID const & ) ; + connect_function_type connect_function_value( &::SireMol::ConnectivityEditor::connect ); + + ConnectivityEditor_exposer.def( + "connect" + , connect_function_value + , ( bp::arg("bond") ) + , bp::return_self< >() + , "Create a connection for the passed bond" ); + + } + { //::SireMol::ConnectivityEditor::connect + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*connect_function_type)( ::QList< SireMol::BondID > const & ) ; + connect_function_type connect_function_value( &::SireMol::ConnectivityEditor::connect ); + + ConnectivityEditor_exposer.def( + "connect" + , connect_function_value + , ( bp::arg("bonds") ) + , bp::return_self< >() + , "Create a connection for the passed bonds" ); + } { //::SireMol::ConnectivityEditor::disconnect @@ -136,6 +162,45 @@ void register_ConnectivityEditor_class(){ , bp::return_self< >() , "Disconnect the atoms that are identified by atom0 and atom1 -\nthis does nothing if there isnt a connection between these atoms\nThrow: SireMol::missing_atom\nThrow: SireMol::duplicate_atom\nThrow: SireError::invalid_index\n" ); + } + { //::SireMol::ConnectivityEditor::disconnect + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::SireMol::BondID const & ) ; + disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); + + ConnectivityEditor_exposer.def( + "disconnect" + , disconnect_function_value + , ( bp::arg("bond") ) + , bp::return_self< >() + , "Disconnect the atoms in the passed bond - this does nothing if the\n atoms arent connected" ); + + } + { //::SireMol::ConnectivityEditor::disconnect + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::QList< SireMol::BondID > const & ) ; + disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); + + ConnectivityEditor_exposer.def( + "disconnect" + , disconnect_function_value + , ( bp::arg("bonds") ) + , bp::return_self< >() + , "Disconnect the atoms in the passed bonds - this does nothing for any\n of the atoms that arent connected" ); + + } + { //::SireMol::ConnectivityEditor::disconnect + + typedef ::SireMol::ConnectivityEditor & ( ::SireMol::ConnectivityEditor::*disconnect_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) ; + disconnect_function_type disconnect_function_value( &::SireMol::ConnectivityEditor::disconnect ); + + ConnectivityEditor_exposer.def( + "disconnect" + , disconnect_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , bp::return_self< >() + , "Disconnect any and all bonds involving the passed atoms. If exclusive is true,\n then this only removes connection where both atoms are in atoms, otherwise\n it removes connections which have one of more atoms in atoms\n" ); + } { //::SireMol::ConnectivityEditor::disconnectAll From 4f27171845dec87ac24b6281cc7525e4e74c71f3 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 2 Mar 2024 23:25:15 +0000 Subject: [PATCH 140/468] Connectivity, atomtype, charge, LJ, mass, name and bond properties look like they are merging properly :-) --- corelib/src/libs/SireMol/selector.hpp | 6 +- corelib/src/libs/SireMol/selectorm.hpp | 8 +- corelib/src/libs/SireSystem/merge.cpp | 243 +++++++++++++------------ 3 files changed, 139 insertions(+), 118 deletions(-) diff --git a/corelib/src/libs/SireMol/selector.hpp b/corelib/src/libs/SireMol/selector.hpp index c9ee1256b..58d24d2cb 100644 --- a/corelib/src/libs/SireMol/selector.hpp +++ b/corelib/src/libs/SireMol/selector.hpp @@ -1860,9 +1860,9 @@ namespace SireMol { if (not this->isSingleMolecule()) { - throw SireMol::duplicate_molecule(QObject::tr( - "There are no molecules represented in this object."), - CODELOC); + throw SireMol::missing_molecule(QObject::tr( + "There are no molecules represented in this object."), + CODELOC); } } diff --git a/corelib/src/libs/SireMol/selectorm.hpp b/corelib/src/libs/SireMol/selectorm.hpp index ebf13f37d..7852e66ed 100644 --- a/corelib/src/libs/SireMol/selectorm.hpp +++ b/corelib/src/libs/SireMol/selectorm.hpp @@ -2890,7 +2890,13 @@ namespace SireMol template SIRE_OUTOFLINE_TEMPLATE void SelectorM::assertSingleMolecule() const { - if (not this->isSingleMolecule()) + if (this->isEmpty()) + { + throw SireMol::missing_molecule(QObject::tr( + "There are no molecules represented in this object - it is empty."), + CODELOC); + } + else if (not this->isSingleMolecule()) { throw SireMol::duplicate_molecule(QObject::tr( "There is more than one molecule represented in this object. The molecules are: %1") diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 53cee9610..8bca1bb37 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -64,7 +64,18 @@ namespace SireSystem bool allow_ring_breaking, bool allow_ring_size_change, bool force, const PropertyMap &input_map) { - if (not mols.isSingleMolecule()) + // and a handle on the whole reference and perturbed molecule + if (mols.atoms0().isEmpty()) + { + // notiing to map + return Molecule(); + } + else if (mols.atoms1().isEmpty()) + { + // nothing to map to + return mols.atoms0().toSingleMolecule().molecule(); + } + else if (not mols.isSingleMolecule()) { throw SireError::incompatible_error(QObject::tr( "You can only create a merged molecule from a mapping that " @@ -134,26 +145,15 @@ namespace SireSystem auto forwards_map = mols; auto backwards_map = mols.swap(); - // the list of mapped atoms - const auto mapped_atoms0 = mols.mappedAtoms0().toSingleMolecule(); - const auto mapped_atoms1 = mols.mappedAtoms1().toSingleMolecule(); - - if (mapped_atoms0.count() != mapped_atoms1.count()) - { - throw SireError::program_bug(QObject::tr( - "The number of atoms in the forward and backward mappings " - "are not the same. This is a bug!."), - CODELOC); - } - - const int nmapped = mapped_atoms0.count(); - // get the merged maps for the reference and perturbed states auto map0 = map.merge(mols.propertyMap0()); auto map1 = map.merge(mols.propertyMap1()); + const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); + const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); + // get the MolEditor that can be used to set properties - MolEditor editmol = mols.atoms0().toSingleMolecule().molecule().edit(); + MolEditor editmol = mol0.edit(); // check and set the forcefields SireMM::MMDetail ffield0; @@ -164,7 +164,7 @@ namespace SireSystem try { - ffield0 = mapped_atoms0.data().property(map0["forcefield"]).asA(); + ffield0 = mol0.data().property(map0["forcefield"]).asA(); have_ffield0 = true; } catch (...) @@ -173,7 +173,7 @@ namespace SireSystem try { - ffield1 = mapped_atoms1.data().property(map1["forcefield"]).asA(); + ffield1 = mol1.data().property(map1["forcefield"]).asA(); have_ffield1 = true; } catch (...) @@ -207,13 +207,6 @@ namespace SireSystem CODELOC); } - // and a handle on the whole reference and perturbed molecule - const auto mol0 = mols.atoms0().toSingleMolecule().molecule(); - const auto mol1 = mols.atoms1().toSingleMolecule().molecule(); - - if (mol0.isEmpty()) - return mol0; - // find the largest AtomNum in mol0 AtomNum largest_atomnum; @@ -237,7 +230,7 @@ namespace SireSystem // use a property to track which atoms have been mapped - // a value of -1 means that this atom is not mapped editmol.setProperty("_mol0_index", AtomIntProperty(mol0.info(), -1)); - editmol.setProperty("_mol1_index", AtomIntProperty(mol1.info(), -1)); + editmol.setProperty("_mol1_index", AtomIntProperty(mol0.info(), -1)); // get an editable copy of the molecule to be changed MolStructureEditor mol(editmol); @@ -249,125 +242,146 @@ namespace SireSystem // all of the residue indicies that we have seen QHash residx_to_cgidx; - // go through all of the common atoms and save their indicies - // and set the atom and residue names - for (int i = 0; i < nmapped; ++i) + if (not mols.mappedAtoms0().isEmpty()) { - const auto atom0 = mapped_atoms0(i); - const auto atom1 = mapped_atoms1(i); + // the list of mapped atoms + const auto mapped_atoms0 = mols.mappedAtoms0().toSingleMolecule(); + const auto mapped_atoms1 = mols.mappedAtoms1().toSingleMolecule(); - auto atom = mol.atom(atom0.index()); + if (mapped_atoms0.count() != mapped_atoms1.count()) + { + throw SireError::program_bug(QObject::tr( + "The number of atoms in the forward and backward mappings " + "are not the same. This is a bug!."), + CODELOC); + } - // save the index of this atom in both mol0 and mol1 - atom.setProperty("_mol0_index", atom0.index().value()); - atom.setProperty("_mol1_index", atom1.index().value()); + // go through all of the common atoms and save their indicies + // and set the atom and residue names + for (int i = 0; i < mapped_atoms0.count(); ++i) + { + const auto atom0 = mapped_atoms0(i); + const auto atom1 = mapped_atoms1(i); - // save the perturbed state atom and residue names into new properties, so - // that we can use these when extracting the end states - atom.setAlternateName(atom1.name()); + auto atom = mol.atom(atom0.index()); - ResIdx residx; + // save the index of this atom in both mol0 and mol1 + atom.setProperty("_mol0_index", atom0.index().value()); + atom.setProperty("_mol1_index", atom1.index().value()); - try - { - residx = atom0.residue().index(); - } - catch (...) - { - } + // save the perturbed state atom and residue names into new properties, so + // that we can use these when extracting the end states + atom.setAlternateName(atom1.name()); - if (not(residx.isNull() or residx_to_cgidx.contains(residx))) - { - // we haven't seen this residue before - assume that - // all residues that are mapped from this residue - // exist in the same equivalent residue in the - // perturbed molecule (using the cutgroup of the - // first atom in this residue) - residx_to_cgidx.insert(residx, atom0.cutGroup().index()); - - // first, get an editor for this residue - // and save the alternate residue name for the mapped state - auto res = mol.residue(residx); - res.setAlternateName(atom1.residue().name()); + ResIdx residx; - // now save the mapping from perturbed residue index - // to merged residue index - pert_to_merge_residx[atom1.residue().index()] = residx; + try + { + residx = atom0.residue().index(); + } + catch (...) + { + } + + if (not(residx.isNull() or residx_to_cgidx.contains(residx))) + { + // we haven't seen this residue before - assume that + // all residues that are mapped from this residue + // exist in the same equivalent residue in the + // perturbed molecule (using the cutgroup of the + // first atom in this residue) + residx_to_cgidx.insert(residx, atom0.cutGroup().index()); + + // first, get an editor for this residue + // and save the alternate residue name for the mapped state + auto res = mol.residue(residx); + res.setAlternateName(atom1.residue().name()); + + // now save the mapping from perturbed residue index + // to merged residue index + pert_to_merge_residx[atom1.residue().index()] = residx; + } } } // now go through the unmapped atoms of the reference molecule and // save their indicies - const auto unmapped_atoms0 = mols.unmappedAtoms0().toSingleMolecule(); - - for (int i = 0; i < unmapped_atoms0.count(); ++i) + if (not mols.unmappedAtoms0().isEmpty()) { - const auto atom0 = unmapped_atoms0(i); + const auto unmapped_atoms0 = mols.unmappedAtoms0().toSingleMolecule(); + + for (int i = 0; i < unmapped_atoms0.count(); ++i) + { + const auto atom0 = unmapped_atoms0(i); - auto atom = mol.atom(atom0.index()); + auto atom = mol.atom(atom0.index()); - // unmapped atoms are called "Xxx" - atom.setAlternateName("Xxx"); - atom.setProperty("_mol0_index", atom0.index().value()); - atom.setProperty("_mol1_index", -1); + // unmapped atoms are called "Xxx" + atom.setAlternateName("Xxx"); + atom.setProperty("_mol0_index", atom0.index().value()); + atom.setProperty("_mol1_index", -1); + } } // now go through the unmapped atoms of the perturbed molecule and // add them to the merged molecule, saving their indicies - const auto unmapped_atoms1 = mols.unmappedAtoms1().toSingleMolecule(); - - for (int i = 0; i < unmapped_atoms1.count(); ++i) + if (not mols.unmappedAtoms1().isEmpty()) { - const auto atom1 = unmapped_atoms1(i); - - // we should have seen this residue before... - auto residx = pert_to_merge_residx.value(atom1.residue().index()); + const auto unmapped_atoms1 = mols.unmappedAtoms1().toSingleMolecule(); - if (residx.isNull()) + for (int i = 0; i < unmapped_atoms1.count(); ++i) { - // we haven't seen this residue before, so we don't know - // really where to add the atoms. The best thing to do - // is add this to the last residue that we saw in the - // molecule (the one with the highest index) - if (residx_to_cgidx.isEmpty()) + const auto atom1 = unmapped_atoms1(i); + + // we should have seen this residue before... + auto residx = pert_to_merge_residx.value(atom1.residue().index()); + + if (residx.isNull()) + { + // we haven't seen this residue before, so we don't know + // really where to add the atoms. The best thing to do + // is add this to the last residue that we saw in the + // molecule (the one with the highest index) + if (residx_to_cgidx.isEmpty()) + { + throw SireError::program_bug(QObject::tr( + "We have not seen any residues before, so we don't know " + "where to add the atoms. This is a bug!"), + CODELOC); + } + + auto residxs = residx_to_cgidx.keys(); + std::sort(residxs.begin(), residxs.end()); + + residx = residxs.last(); + } + + auto cgidx = residx_to_cgidx.value(residx); + + if (cgidx.isNull()) { throw SireError::program_bug(QObject::tr( - "We have not seen any residues before, so we don't know " + "We don't know the CutGroup for the residue, so we don't know " "where to add the atoms. This is a bug!"), CODELOC); } - auto residxs = residx_to_cgidx.keys(); - std::sort(residxs.begin(), residxs.end()); + auto res = mol.residue(residx); - residx = residxs.last(); - } + // add the atom - it has the name "Xxx" as it doesn't exist + // in the reference state + auto atom = res.add(AtomName("Xxx")); + largest_atomnum = AtomNum(largest_atomnum.value() + 1); + atom.renumber(largest_atomnum); - auto cgidx = residx_to_cgidx.value(residx); + // reparent this atom to the CutGroup for this residue + atom.reparent(cgidx); - if (cgidx.isNull()) - { - throw SireError::program_bug(QObject::tr( - "We don't know the CutGroup for the residue, so we don't know " - "where to add the atoms. This is a bug!"), - CODELOC); + // save the name in the perturbed state + atom.setAlternateName(atom1.name()); + atom.setProperty("_mol0_index", -1); + atom.setProperty("_mol1_index", atom1.index().value()); } - - auto res = mol.residue(residx); - - // add the atom - it has the name "Xxx" as it doesn't exist - // in the reference state - auto atom = res.add(AtomName("Xxx")); - largest_atomnum = AtomNum(largest_atomnum.value() + 1); - atom.renumber(largest_atomnum); - - // reparent this atom to the CutGroup for this residue - atom.reparent(cgidx); - - // save the name in the perturbed state - atom.setAlternateName(atom1.name()); - atom.setProperty("_mol0_index", -1); - atom.setProperty("_mol1_index", atom1.index().value()); } if (as_new_molecule) @@ -498,9 +512,10 @@ namespace SireSystem editmol.setProperty(map["molecule0"].source(), mol0); editmol.setProperty(map["molecule1"].source(), mol1); - // add the forcefields for the two molecules + // add the forcefields for the two molecules - need the same, + // so choosing ffield0 editmol.setProperty(map["forcefield0"].source(), ffield0); - editmol.setProperty(map["forcefield1"].source(), ffield1); + editmol.setProperty(map["forcefield1"].source(), ffield0); // remove any property called "parameters" if (editmol.hasProperty(map["parameters"].source())) From 9b1005c1bb0d581d3db23ebb4ce400d01e7bba8b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 3 Mar 2024 18:56:46 +0000 Subject: [PATCH 141/468] Some optimisation, plus made sure that bonds involving atoms that exist only in the perturbed state are copied into the reference state --- corelib/src/libs/SireMM/twoatomfunctions.cpp | 36 +++- corelib/src/libs/SireMol/atomidxmapping.cpp | 193 +++++++++++-------- corelib/src/libs/SireMol/atomidxmapping.h | 64 ++++++ wrapper/Mol/AtomIdxMapping.pypp.cpp | 26 +++ 4 files changed, 230 insertions(+), 89 deletions(-) diff --git a/corelib/src/libs/SireMM/twoatomfunctions.cpp b/corelib/src/libs/SireMM/twoatomfunctions.cpp index 5ab22c92f..8d1c4b799 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.cpp +++ b/corelib/src/libs/SireMM/twoatomfunctions.cpp @@ -835,6 +835,20 @@ const char *TwoAtomFunctions::typeName() return QMetaType::typeName(qMetaTypeId()); } +template +QSet _to_set(const QList &vals) +{ + QSet ret; + ret.reserve(vals.count()); + + for (const auto &val : vals) + { + ret.insert(val); + } + + return ret; +} + /** Merge this property with another property */ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, const AtomIdxMapping &mapping, @@ -860,8 +874,6 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, TwoAtomFunctions prop0 = ref; TwoAtomFunctions prop1 = ref; - // the prop0 properties are already correct - // the prop1 properties are made by finding all of the atoms that // are involved in bonds in 'pert' and removing any bonds involving // only those atoms from 'prop1', and then adding back the matching @@ -881,11 +893,25 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, for (const auto &pert_bond : pert_bonds) { - prop1.set(map1to0.value(info().atomIdx(pert_bond.atom0())), - map1to0.value(info().atomIdx(pert_bond.atom1())), - pert_bond.function()); + const auto atom0 = map1to0.value(info().atomIdx(pert_bond.atom0())); + const auto atom1 = map1to0.value(info().atomIdx(pert_bond.atom1())); + + prop1.set(atom0, atom1, pert_bond.function()); + + if (mapping.isUnmappedIn0(atom0) or mapping.isUnmappedIn0(atom1)) + { + // the prop0 properties are nearly correct - we just need to add + // in bonds from 'pert' that involve the atoms that are not mapped + // in the reference state - this way, those added atoms are held + // by a constant bond potential, so won't fly away in the + // simulation of the reference state + prop0.set(atom0, atom1, pert_bond.function()); + } } + // the bonds for atoms that are unmapped in the perturbed state are + // already in prop1, as this was copied from prop0 + SireBase::PropertyList ret; ret.append(prop0); diff --git a/corelib/src/libs/SireMol/atomidxmapping.cpp b/corelib/src/libs/SireMol/atomidxmapping.cpp index 6ab83b583..f75824734 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.cpp +++ b/corelib/src/libs/SireMol/atomidxmapping.cpp @@ -275,6 +275,8 @@ QDataStream &operator>>(QDataStream &ds, AtomIdxMapping &mapping) SharedDataStream sds(ds); sds >> mapping.entries >> static_cast(mapping); + + mapping.rebuild(); } else throw SireStream::version_error(v, "1", r_mapping, CODELOC); @@ -294,13 +296,16 @@ AtomIdxMapping::AtomIdxMapping(const AtomIdxMappingEntry &entry) { if (not entry.isNull()) entries.append(entry); + + this->rebuild(); } /** Assert that this object is sane */ void AtomIdxMapping::assertSane() const { - QHash seen; - seen.reserve(entries.size()); + QHash seen_0, seen_1; + seen_0.reserve(entries.size()); + seen_1.reserve(entries.size()); for (const auto &entry : entries) { @@ -308,16 +313,20 @@ void AtomIdxMapping::assertSane() const { throw SireError::incompatible_error(QObject::tr("The AtomIdxMapping contains a null entry!"), CODELOC); } - else if (seen.contains(entry.atomIdx0().value())) + else if (seen_0.contains(entry.atomIdx0().value()) or + (entry.isMappedIn1() and seen_1.contains(entry.atomIdx1().value()))) { throw SireError::incompatible_error(QObject::tr("The AtomIdxMapping contains a duplicate entry (%1 vs %2)!") .arg(entry.toString()) - .arg(seen[entry.atomIdx0().value()].toString()), + .arg(seen_0[entry.atomIdx0().value()].toString()), CODELOC); } else { - seen.insert(entry.atomIdx0().value(), entry); + seen_0.insert(entry.atomIdx0().value(), entry); + + if (entry.isMappedIn1()) + seen_1.insert(entry.atomIdx1().value(), entry); } } } @@ -353,11 +362,18 @@ AtomIdxMapping::AtomIdxMapping(const QList &e) } this->assertSane(); + this->rebuild(); } /** Copy constructor */ AtomIdxMapping::AtomIdxMapping(const AtomIdxMapping &other) - : ConcreteProperty(other) + : ConcreteProperty(other), + entries(other.entries), + unmapped0_set(other.unmapped0_set), unmapped1_set(other.unmapped1_set), + unmapped0_list(other.unmapped0_list), unmapped1_list(other.unmapped1_list), + mapped0_list(other.mapped0_list), mapped1_list(other.mapped1_list), + map0_to_1_inc(other.map0_to_1_inc), map1_to_0_inc(other.map1_to_0_inc), + map0_to_1_exc(other.map0_to_1_exc), map1_to_0_exc(other.map1_to_0_exc) { } @@ -372,6 +388,17 @@ AtomIdxMapping &AtomIdxMapping::operator=(const AtomIdxMapping &other) if (this != &other) { entries = other.entries; + unmapped0_set = other.unmapped0_set; + unmapped1_set = other.unmapped1_set; + unmapped0_list = other.unmapped0_list; + unmapped1_list = other.unmapped1_list; + mapped0_list = other.mapped0_list; + mapped1_list = other.mapped1_list; + map0_to_1_inc = other.map0_to_1_inc; + map1_to_0_inc = other.map1_to_0_inc; + map0_to_1_exc = other.map0_to_1_exc; + map1_to_0_exc = other.map1_to_0_exc; + Property::operator=(other); } @@ -530,6 +557,7 @@ void AtomIdxMapping::append(const AtomIdxMappingEntry &new_entry) } entries.append(new_entry); + this->rebuild(); } /** Append all of the passed entries of other onto this list */ @@ -542,6 +570,8 @@ void AtomIdxMapping::append(const AtomIdxMapping &other) ret.append(entry); } + ret.rebuild(); + *this = ret; } @@ -549,6 +579,7 @@ void AtomIdxMapping::append(const AtomIdxMapping &other) void AtomIdxMapping::clear() { entries.clear(); + this->rebuild(); } /** Return whether or not the list is empty */ @@ -580,7 +611,9 @@ const AtomIdxMappingEntry &AtomIdxMapping::operator[](int i) const AtomIdxMappingEntry AtomIdxMapping::take(int i) { i = SireID::Index(i).map(entries.size()); - return entries.takeAt(i); + auto entry = entries.takeAt(i); + this->rebuild(); + return entry; } /** Take the entry for atom 'atom' */ @@ -628,6 +661,7 @@ void AtomIdxMapping::remove(int i) { i = SireID::Index(i).map(entries.size()); entries.removeAt(i); + this->rebuild(); } /** Remove the entry for atom 'atom' */ @@ -652,24 +686,75 @@ void AtomIdxMapping::remove(const CGAtomIdx &atom) } } -/** Return the indexes, in the merged molecule, of atoms that - * are not mapped in the reference state (i.e. they only exist - * in the perturbed state). Note - these are the indicies of these - * atoms in the merged molecule, not the perturbed molecule. - */ -QList AtomIdxMapping::unmappedIn0() const +void AtomIdxMapping::rebuild() { - QList ret; + unmapped0_set.clear(); + unmapped1_set.clear(); + unmapped0_list.clear(); + unmapped1_list.clear(); + mapped0_list.clear(); + mapped1_list.clear(); + map0_to_1_inc.clear(); + map1_to_0_inc.clear(); + map0_to_1_exc.clear(); + map1_to_0_exc.clear(); for (const auto &entry : entries) { - if (entry.isUnmappedIn0()) + if (entry.isMappedIn0()) + { + mapped0_list.append(entry.atomIdx0()); + } + else + { + unmapped0_set.insert(entry.atomIdx0()); + unmapped0_list.append(entry.atomIdx0()); + } + + if (entry.isMappedIn1()) + { + mapped1_list.append(entry.atomIdx1()); + } + else + { + unmapped1_set.insert(entry.atomIdx1()); + unmapped1_list.append(entry.atomIdx1()); + } + + if (entry.isMappedIn0() and entry.isMappedIn1()) { - ret.append(entry.atomIdx0()); + map0_to_1_inc.insert(entry.atomIdx0(), entry.atomIdx1()); + map1_to_0_inc.insert(entry.atomIdx1(), entry.atomIdx0()); + map0_to_1_exc.insert(entry.atomIdx0(), entry.atomIdx1()); + map1_to_0_exc.insert(entry.atomIdx1(), entry.atomIdx0()); + } + else if (entry.isMappedIn0()) + { + if (not entry.atomIdx0().isNull()) + { + map0_to_1_inc.insert(entry.atomIdx0(), entry.atomIdx1()); + map0_to_1_exc.insert(entry.atomIdx0(), entry.atomIdx1()); + } + } + else if (entry.isMappedIn1()) + { + if (not entry.atomIdx1().isNull()) + { + map1_to_0_inc.insert(entry.atomIdx1(), entry.atomIdx0()); + map1_to_0_exc.insert(entry.atomIdx1(), entry.atomIdx0()); + } } } +} - return ret; +/** Return the indexes, in the merged molecule, of atoms that + * are not mapped in the reference state (i.e. they only exist + * in the perturbed state). Note - these are the indicies of these + * atoms in the merged molecule, not the perturbed molecule. + */ +QList AtomIdxMapping::unmappedIn0() const +{ + return unmapped0_list; } /** Return the indexes, in the merged molecule, of atoms that @@ -679,17 +764,7 @@ QList AtomIdxMapping::unmappedIn0() const */ QList AtomIdxMapping::unmappedIn1() const { - QList ret; - - for (const auto &entry : entries) - { - if (entry.isUnmappedIn1()) - { - ret.append(entry.atomIdx0()); - } - } - - return ret; + return unmapped1_list; } /** Return the indexes, in the merged molecule, of atoms that @@ -700,17 +775,7 @@ QList AtomIdxMapping::unmappedIn1() const */ QList AtomIdxMapping::mappedIn0() const { - QList ret; - - for (const auto &entry : entries) - { - if (entry.isMappedIn0()) - { - ret.append(entry.atomIdx0()); - } - } - - return ret; + return mapped0_list; } /** Return the indexes, in the merged molecule, of atoms that @@ -721,17 +786,7 @@ QList AtomIdxMapping::mappedIn0() const */ QList AtomIdxMapping::mappedIn1() const { - QList ret; - - for (const auto &entry : entries) - { - if (entry.isMappedIn1()) - { - ret.append(entry.atomIdx0()); - } - } - - return ret; + return mapped1_list; } /** Return the mapping for the atoms that exist in both the reference @@ -747,29 +802,14 @@ QList AtomIdxMapping::mappedIn1() const */ QHash AtomIdxMapping::map0to1(bool include_unmapped) const { - QHash ret; - ret.reserve(entries.size()); - if (include_unmapped) { - for (const auto &entry : entries) - { - if (not entry.atomIdx0().isNull()) - ret.insert(entry.atomIdx0(), entry.atomIdx1()); - } + return map0_to_1_inc; } else { - for (const auto &entry : entries) - { - if (entry.isMappedIn0() and entry.isMappedIn1()) - { - ret.insert(entry.atomIdx0(), entry.atomIdx1()); - } - } + return map0_to_1_exc; } - - return ret; } /** Return the mapping for the atoms that exist in both the reference @@ -785,27 +825,12 @@ QHash AtomIdxMapping::map0to1(bool include_unmapped) const */ QHash AtomIdxMapping::map1to0(bool include_unmapped) const { - QHash ret; - ret.reserve(entries.size()); - if (include_unmapped) { - for (const auto &entry : entries) - { - if (not entry.atomIdx1().isNull()) - ret.insert(entry.atomIdx1(), entry.atomIdx0()); - } + return map1_to_0_inc; } else { - for (const auto &entry : entries) - { - if (entry.isMappedIn0() and entry.isMappedIn1()) - { - ret.insert(entry.atomIdx1(), entry.atomIdx0()); - } - } + return map1_to_0_exc; } - - return ret; } diff --git a/corelib/src/libs/SireMol/atomidxmapping.h b/corelib/src/libs/SireMol/atomidxmapping.h index 78576af82..1e10caa16 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.h +++ b/corelib/src/libs/SireMol/atomidxmapping.h @@ -187,16 +187,80 @@ namespace SireMol QList mappedIn0() const; QList mappedIn1() const; + bool isUnmappedIn0(const AtomIdx &atom) const; + bool isUnmappedIn1(const AtomIdx &atom) const; + QHash map0to1(bool include_unmapped = false) const; QHash map1to0(bool include_unmapped = false) const; private: void assertSane() const; + void rebuild(); /** The list of atom entries */ QList entries; + + /** The set of atoms that are unmapped in the reference state */ + QSet unmapped0_set; + + /** The set of atoms that are unmapped in the perturbed state */ + QSet unmapped1_set; + + /** The list of atoms that are unmapped in the reference state */ + QList unmapped0_list; + + /** The list of atoms that are unmapped in the perturbed state */ + QList unmapped1_list; + + /** The list of atoms that are mapped in the reference state */ + QList mapped0_list; + + /** The list of atoms that are mapped in the perturbed state */ + QList mapped1_list; + + /** The mapping from reference to perturbed atoms, + * which includes the unmapped atoms + */ + QHash map0_to_1_inc; + + /** The mapping from perturbed to reference atoms, + * which includes the unmapped atoms + */ + QHash map1_to_0_inc; + + /** The mapping from reference to perturbed atoms, + * which excludes the unmapped atoms + */ + QHash map0_to_1_exc; + + /** The mapping from perturbed to reference atoms, + * which excludes the unmapped atoms + */ + QHash map1_to_0_exc; }; +#ifndef SIRE_SKIP_INLINE_FUNCTIONS + + /** Return whether or not the passed atom is unmapped in the + * reference state - the atom index should be for the + * merged molecule + */ + inline bool AtomIdxMapping::isUnmappedIn0(const AtomIdx &atom) const + { + return unmapped0_set.contains(atom); + } + + /** Return whether or not the passed atom is unmapped in the + * perturbed state - the atom index should be for the + * merged molecule + */ + inline bool AtomIdxMapping::isUnmappedIn1(const AtomIdx &atom) const + { + return unmapped1_set.contains(atom); + } + +#endif // SIRE_SKIP_INLINE_FUNCTIONS + } // namespace SireMol Q_DECLARE_METATYPE(SireMol::AtomIdxMappingEntry) diff --git a/wrapper/Mol/AtomIdxMapping.pypp.cpp b/wrapper/Mol/AtomIdxMapping.pypp.cpp index f4a31bf64..bf7af65c7 100644 --- a/wrapper/Mol/AtomIdxMapping.pypp.cpp +++ b/wrapper/Mol/AtomIdxMapping.pypp.cpp @@ -104,6 +104,32 @@ void register_AtomIdxMapping_class(){ , bp::release_gil_policy() , "Return whether or not the list is empty" ); + } + { //::SireMol::AtomIdxMapping::isUnmappedIn0 + + typedef bool ( ::SireMol::AtomIdxMapping::*isUnmappedIn0_function_type)( ::SireMol::AtomIdx const & ) const; + isUnmappedIn0_function_type isUnmappedIn0_function_value( &::SireMol::AtomIdxMapping::isUnmappedIn0 ); + + AtomIdxMapping_exposer.def( + "isUnmappedIn0" + , isUnmappedIn0_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomIdxMapping::isUnmappedIn1 + + typedef bool ( ::SireMol::AtomIdxMapping::*isUnmappedIn1_function_type)( ::SireMol::AtomIdx const & ) const; + isUnmappedIn1_function_type isUnmappedIn1_function_value( &::SireMol::AtomIdxMapping::isUnmappedIn1 ); + + AtomIdxMapping_exposer.def( + "isUnmappedIn1" + , isUnmappedIn1_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "" ); + } { //::SireMol::AtomIdxMapping::map0to1 From e0f36745e5d3fce6591c59c05abb2acd925f6618 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 3 Mar 2024 19:27:02 +0000 Subject: [PATCH 142/468] Added the same code to ThreeAtomFunctions and FourAtomFunctions and are now merging angles, dihedrals and impropers. But this all needs testing. Will do that after I have added in the code to merge the CLJNBPairs --- corelib/src/libs/SireMM/fouratomfunctions.cpp | 136 +++++++++++++++++- corelib/src/libs/SireMM/fouratomfunctions.h | 8 +- .../src/libs/SireMM/threeatomfunctions.cpp | 133 ++++++++++++++++- corelib/src/libs/SireMM/threeatomfunctions.h | 8 +- wrapper/MM/AtomLJs.pypp.cpp | 2 + wrapper/MM/FourAtomFunctions.pypp.cpp | 24 ++++ wrapper/MM/LJException.pypp.cpp | 2 + wrapper/MM/LJExceptionID.pypp.cpp | 2 + wrapper/MM/ThreeAtomFunctions.pypp.cpp | 24 ++++ wrapper/MM/TwoAtomFunctions.pypp.cpp | 24 ++++ 10 files changed, 351 insertions(+), 12 deletions(-) diff --git a/corelib/src/libs/SireMM/fouratomfunctions.cpp b/corelib/src/libs/SireMM/fouratomfunctions.cpp index a86b4be1e..69c47faa3 100644 --- a/corelib/src/libs/SireMM/fouratomfunctions.cpp +++ b/corelib/src/libs/SireMM/fouratomfunctions.cpp @@ -496,6 +496,45 @@ void FourAtomFunctions::clear(AtomIdx atom) } } +/** Clear all functions that involve any of the atoms in 'atoms' + * - if 'exclusive' is true, then this only removes functions + * that exclusively involve these atoms - if false, then + * if removes functions that involve any of these atoms + */ +void FourAtomFunctions::clear(const QList &atoms, bool exclusive) +{ + QSet atms; + atms.reserve(atoms.count()); + + for (const auto &atom : atoms) + { + atms.insert(atom.map(info().nAtoms())); + } + + QList keys = potentials_by_atoms.keys(); + + if (exclusive) + { + for (const auto &key : keys) + { + if (atms.contains(key.atom0) and atms.contains(key.atom1) and atms.contains(key.atom2) and atms.contains(key.atom3)) + { + FourAtomFunctions::removeSymbols(potentials_by_atoms.take(key).symbols()); + } + } + } + else + { + for (const auto &key : keys) + { + if (atms.contains(key.atom0) or atms.contains(key.atom1) or atms.contains(key.atom2) or atms.contains(key.atom3)) + { + FourAtomFunctions::removeSymbols(potentials_by_atoms.take(key).symbols()); + } + } + } +} + /** Clear any function that acts on the atoms identified by 'atom' \throw SireMol::missing_atom @@ -750,6 +789,47 @@ Expression FourAtomFunctions::force(const ImproperID &improperid, const Symbol & return -(this->potential(improperid).differentiate(symbol)); } +/** Return the potential energy functions acting between the identified + atoms - if exclusive is true then only return potentials where + all atoms are in the dihedral or improper +*/ +QVector FourAtomFunctions::potentials(const QList &atms, bool exclusive) const +{ + QVector funcs; + funcs.reserve(potentials_by_atoms.count()); + + QSet atoms(atms.begin(), atms.end()); + + for (QHash::const_iterator it = potentials_by_atoms.constBegin(); + it != potentials_by_atoms.constEnd(); ++it) + { + if (exclusive) + { + if (atoms.contains(AtomIdx(it.key().atom0)) and atoms.contains(AtomIdx(it.key().atom1)) and atoms.contains(AtomIdx(it.key().atom2)) and atoms.contains(AtomIdx(it.key().atom3))) + { + funcs.append(FourAtomFunction(info().cgAtomIdx(AtomIdx(it.key().atom0)), + info().cgAtomIdx(AtomIdx(it.key().atom1)), + info().cgAtomIdx(AtomIdx(it.key().atom2)), + info().cgAtomIdx(AtomIdx(it.key().atom3)), + it.value())); + } + } + else + { + if (atoms.contains(AtomIdx(it.key().atom0)) or atoms.contains(AtomIdx(it.key().atom1)) or atoms.contains(AtomIdx(it.key().atom2)) or atoms.contains(AtomIdx(it.key().atom3))) + { + funcs.append(FourAtomFunction(info().cgAtomIdx(AtomIdx(it.key().atom0)), + info().cgAtomIdx(AtomIdx(it.key().atom1)), + info().cgAtomIdx(AtomIdx(it.key().atom2)), + info().cgAtomIdx(AtomIdx(it.key().atom3)), + it.value())); + } + } + } + + return funcs; +} + /** Return the potential energy functions acting between the identified quads of atoms */ QVector FourAtomFunctions::potentials() const @@ -933,13 +1013,61 @@ PropertyList FourAtomFunctions::merge(const MolViewProperty &other, CODELOC); } - SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") - .arg(this->what())); + if (not ghost.isEmpty()) + { + Console::warning(QObject::tr("The ghost parameter '%1' for dihedral/improper parameters is ignored").arg(ghost)); + } + + const FourAtomFunctions &ref = *this; + const FourAtomFunctions &pert = other.asA(); + + FourAtomFunctions prop0 = ref; + FourAtomFunctions prop1 = ref; + + // the prop1 properties are made by finding all of the atoms that + // are involved in dihedrals in 'pert' and removing any involving + // only those atoms from 'prop1', and then adding back the matching + // dihedral from 'pert'. Use 'true' to only remove angles where all + // atoms are in the mapping + prop1.clear(mapping.mappedIn1(), true); + + // get the mapping from the perturbed to reference states, including + // atoms that don't exist in the reference state. In all cases, + // the values are the indexes in the merged molecule + auto map1to0 = mapping.map1to0(true); + + // now find all of the dihedrals in 'pert' where all atoms in the + // dihedral are in map1to0.keys() - i.e. exist and are mapped from + // the perturbed state + const auto pert_dihs = pert.potentials(map1to0.keys(), true); + + for (const auto &pert_dih : pert_dihs) + { + const auto atom0 = map1to0.value(info().atomIdx(pert_dih.atom0())); + const auto atom1 = map1to0.value(info().atomIdx(pert_dih.atom1())); + const auto atom2 = map1to0.value(info().atomIdx(pert_dih.atom2())); + const auto atom3 = map1to0.value(info().atomIdx(pert_dih.atom3())); + + prop1.set(atom0, atom1, atom2, atom3, pert_dih.function()); + + if (mapping.isUnmappedIn0(atom0) or mapping.isUnmappedIn0(atom1) or mapping.isUnmappedIn0(atom2) or mapping.isUnmappedIn0(atom3)) + { + // the prop0 properties are nearly correct - we just need to add + // in dihedrals from 'pert' that involve the atoms that are not mapped + // in the reference state - this way, those added atoms are held + // by a constant dihedral potential, so won't fly away in the + // simulation of the reference state + prop0.set(atom0, atom1, atom2, atom3, pert_dih.function()); + } + } + + // the dihedrals for atoms that are unmapped in the perturbed state are + // already in prop1, as this was copied from prop0 SireBase::PropertyList ret; - ret.append(*this); - ret.append(*this); + ret.append(prop0); + ret.append(prop1); return ret; } diff --git a/corelib/src/libs/SireMM/fouratomfunctions.h b/corelib/src/libs/SireMM/fouratomfunctions.h index f2021906a..ea83aa9dd 100644 --- a/corelib/src/libs/SireMM/fouratomfunctions.h +++ b/corelib/src/libs/SireMM/fouratomfunctions.h @@ -184,8 +184,6 @@ namespace SireMM QString toString() const; - int nFunctions() const; - void set(AtomIdx atom0, AtomIdx atom1, AtomIdx atom2, AtomIdx atom3, const Expression &expression); void set(const AtomID &atom0, const AtomID &atom1, const AtomID &atom2, const AtomID &atom3, @@ -203,12 +201,16 @@ namespace SireMM void clear(const DihedralID &dihedralid); void clear(const ImproperID &improperid); + void clear(const QList &atoms, bool exclusive = true); + void clear(); void substitute(const Identities &identities); bool isEmpty() const; + int nFunctions() const; + Expression potential(AtomIdx atom0, AtomIdx atom1, AtomIdx atom2, AtomIdx atom3) const; Expression potential(const AtomID &atom0, const AtomID &atom1, const AtomID &atom2, const AtomID &atom3) const; @@ -225,6 +227,8 @@ namespace SireMM QVector potentials() const; QVector forces(const Symbol &symbol) const; + QVector potentials(const QList &atoms, bool exclusive = true) const; + FourAtomFunctions includeOnly(const AtomSelection &selected_atoms, bool isstrict = true) const; SireBase::PropertyList merge(const MolViewProperty &other, diff --git a/corelib/src/libs/SireMM/threeatomfunctions.cpp b/corelib/src/libs/SireMM/threeatomfunctions.cpp index 42a18c1a4..2544eadf8 100644 --- a/corelib/src/libs/SireMM/threeatomfunctions.cpp +++ b/corelib/src/libs/SireMM/threeatomfunctions.cpp @@ -450,6 +450,45 @@ void ThreeAtomFunctions::clear(AtomIdx atom) } } +/** Clear all functions that involve any of the atoms in 'atoms' + * - if 'exclusive' is true, then this only removes functions + * that exclusively involve these atoms - if false, then + * if removes functions that involve any of these atoms + */ +void ThreeAtomFunctions::clear(const QList &atoms, bool exclusive) +{ + QSet atms; + atms.reserve(atoms.count()); + + for (const auto &atom : atoms) + { + atms.insert(atom.map(info().nAtoms())); + } + + QList keys = potentials_by_atoms.keys(); + + if (exclusive) + { + for (const auto &key : keys) + { + if (atms.contains(key.atom0) and atms.contains(key.atom1) and atms.contains(key.atom2)) + { + ThreeAtomFunctions::removeSymbols(potentials_by_atoms.take(key).symbols()); + } + } + } + else + { + for (const auto &key : keys) + { + if (atms.contains(key.atom0) or atms.contains(key.atom1) or atms.contains(key.atom2)) + { + ThreeAtomFunctions::removeSymbols(potentials_by_atoms.take(key).symbols()); + } + } + } +} + /** Clear any function that acts on the atoms identified by 'atom' \throw SireMol::missing_atom @@ -631,6 +670,45 @@ Expression ThreeAtomFunctions::force(const AngleID &angleid, const Symbol &symbo return -(this->potential(angleid).differentiate(symbol)); } +/** Return the potential energy functions acting between the identified + atoms - if exclusive is true then only return potentials where + all atoms are in the angle +*/ +QVector ThreeAtomFunctions::potentials(const QList &atms, bool exclusive) const +{ + QVector funcs; + funcs.reserve(potentials_by_atoms.count()); + + QSet atoms(atms.begin(), atms.end()); + + for (QHash::const_iterator it = potentials_by_atoms.constBegin(); + it != potentials_by_atoms.constEnd(); ++it) + { + if (exclusive) + { + if (atoms.contains(AtomIdx(it.key().atom0)) and atoms.contains(AtomIdx(it.key().atom1)) and atoms.contains(AtomIdx(it.key().atom2))) + { + funcs.append(ThreeAtomFunction(info().cgAtomIdx(AtomIdx(it.key().atom0)), + info().cgAtomIdx(AtomIdx(it.key().atom1)), + info().cgAtomIdx(AtomIdx(it.key().atom2)), + it.value())); + } + } + else + { + if (atoms.contains(AtomIdx(it.key().atom0)) or atoms.contains(AtomIdx(it.key().atom1)) or atoms.contains(AtomIdx(it.key().atom2))) + { + funcs.append(ThreeAtomFunction(info().cgAtomIdx(AtomIdx(it.key().atom0)), + info().cgAtomIdx(AtomIdx(it.key().atom1)), + info().cgAtomIdx(AtomIdx(it.key().atom2)), + it.value())); + } + } + } + + return funcs; +} + /** Return the potential energy functions acting between the identified triples of atoms */ QVector ThreeAtomFunctions::potentials() const @@ -811,13 +889,60 @@ PropertyList ThreeAtomFunctions::merge(const MolViewProperty &other, CODELOC); } - SireBase::Console::warning(QObject::tr("Merging %1 properties is not yet implemented. Returning two copies of the original property.") - .arg(this->what())); + if (not ghost.isEmpty()) + { + Console::warning(QObject::tr("The ghost parameter '%1' for angle parameters is ignored").arg(ghost)); + } + + const ThreeAtomFunctions &ref = *this; + const ThreeAtomFunctions &pert = other.asA(); + + ThreeAtomFunctions prop0 = ref; + ThreeAtomFunctions prop1 = ref; + + // the prop1 properties are made by finding all of the atoms that + // are involved in angles in 'pert' and removing any angles involving + // only those atoms from 'prop1', and then adding back the matching + // angle from 'pert'. Use 'true' to only remove angles where all + // atoms are in the mapping + prop1.clear(mapping.mappedIn1(), true); + + // get the mapping from the perturbed to reference states, including + // atoms that don't exist in the reference state. In all cases, + // the values are the indexes in the merged molecule + auto map1to0 = mapping.map1to0(true); + + // now find all of the angles in 'pert' where all atoms in the + // angle are in map1to0.keys() - i.e. exist and are mapped from + // the perturbed state + const auto pert_angs = pert.potentials(map1to0.keys(), true); + + for (const auto &pert_ang : pert_angs) + { + const auto atom0 = map1to0.value(info().atomIdx(pert_ang.atom0())); + const auto atom1 = map1to0.value(info().atomIdx(pert_ang.atom1())); + const auto atom2 = map1to0.value(info().atomIdx(pert_ang.atom2())); + + prop1.set(atom0, atom1, atom2, pert_ang.function()); + + if (mapping.isUnmappedIn0(atom0) or mapping.isUnmappedIn0(atom1) or mapping.isUnmappedIn0(atom2)) + { + // the prop0 properties are nearly correct - we just need to add + // in angles from 'pert' that involve the atoms that are not mapped + // in the reference state - this way, those added atoms are held + // by a constant angle potential, so won't fly away in the + // simulation of the reference state + prop0.set(atom0, atom1, atom2, pert_ang.function()); + } + } + + // the angles for atoms that are unmapped in the perturbed state are + // already in prop1, as this was copied from prop0 SireBase::PropertyList ret; - ret.append(*this); - ret.append(*this); + ret.append(prop0); + ret.append(prop1); return ret; } diff --git a/corelib/src/libs/SireMM/threeatomfunctions.h b/corelib/src/libs/SireMM/threeatomfunctions.h index 8cb27fa5c..e4415b323 100644 --- a/corelib/src/libs/SireMM/threeatomfunctions.h +++ b/corelib/src/libs/SireMM/threeatomfunctions.h @@ -189,14 +189,16 @@ namespace SireMM void clear(const AtomID &atom0, const AtomID &atom1, const AtomID &atom2); void clear(const AngleID &angleid); + void clear(const QList &atoms, bool exclusive = true); + void clear(); void substitute(const Identities &identities); - int nFunctions() const; - bool isEmpty() const; + int nFunctions() const; + Expression potential(AtomIdx atom0, AtomIdx atom1, AtomIdx atom2) const; Expression potential(const AtomID &atom0, const AtomID &atom1, const AtomID &atom2) const; Expression potential(const AngleID &angleid) const; @@ -208,6 +210,8 @@ namespace SireMM QVector potentials() const; QVector forces(const Symbol &symbol) const; + QVector potentials(const QList &atoms, bool exclusive = true) const; + ThreeAtomFunctions includeOnly(const AtomSelection &selected_atoms, bool isstrict = true) const; SireBase::PropertyList merge(const MolViewProperty &other, diff --git a/wrapper/MM/AtomLJs.pypp.cpp b/wrapper/MM/AtomLJs.pypp.cpp index 5664f9e4c..44b00dc65 100644 --- a/wrapper/MM/AtomLJs.pypp.cpp +++ b/wrapper/MM/AtomLJs.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/incremint.h" #include "SireBase/propertylist.h" diff --git a/wrapper/MM/FourAtomFunctions.pypp.cpp b/wrapper/MM/FourAtomFunctions.pypp.cpp index e4e66995c..ff40dfe7d 100644 --- a/wrapper/MM/FourAtomFunctions.pypp.cpp +++ b/wrapper/MM/FourAtomFunctions.pypp.cpp @@ -127,6 +127,18 @@ void register_FourAtomFunctions_class(){ , bp::release_gil_policy() , "Clear the potential that acts over the improper identified by improperid\nThis clears all matching impropers, so 1-2-3-4 and 1-2-4-3\nThrow: SireMol::missing_atom\nThrow: SireError::invalid_index\n" ); + } + { //::SireMM::FourAtomFunctions::clear + + typedef void ( ::SireMM::FourAtomFunctions::*clear_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) ; + clear_function_type clear_function_value( &::SireMM::FourAtomFunctions::clear ); + + FourAtomFunctions_exposer.def( + "clear" + , clear_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Clear all functions that involve any of the atoms in atoms\n - if exclusive is true, then this only removes functions\n that exclusively involve these atoms - if false, then\n if removes functions that involve any of these atoms\n" ); + } { //::SireMM::FourAtomFunctions::clear @@ -331,6 +343,18 @@ void register_FourAtomFunctions_class(){ , bp::release_gil_policy() , "Return the potential energy functions acting between the identified\nquads of atoms" ); + } + { //::SireMM::FourAtomFunctions::potentials + + typedef ::QVector< SireMM::FourAtomFunction > ( ::SireMM::FourAtomFunctions::*potentials_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) const; + potentials_function_type potentials_function_value( &::SireMM::FourAtomFunctions::potentials ); + + FourAtomFunctions_exposer.def( + "potentials" + , potentials_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Return the potential energy functions acting between the identified\natoms - if exclusive is true then only return potentials where\nall atoms are in the dihedral or improper\n" ); + } { //::SireMM::FourAtomFunctions::set diff --git a/wrapper/MM/LJException.pypp.cpp b/wrapper/MM/LJException.pypp.cpp index 489b6c53a..cf1805cc4 100644 --- a/wrapper/MM/LJException.pypp.cpp +++ b/wrapper/MM/LJException.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/incremint.h" #include "SireBase/propertylist.h" diff --git a/wrapper/MM/LJExceptionID.pypp.cpp b/wrapper/MM/LJExceptionID.pypp.cpp index ea5b47dbe..cc5842269 100644 --- a/wrapper/MM/LJExceptionID.pypp.cpp +++ b/wrapper/MM/LJExceptionID.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/incremint.h" #include "SireBase/propertylist.h" diff --git a/wrapper/MM/ThreeAtomFunctions.pypp.cpp b/wrapper/MM/ThreeAtomFunctions.pypp.cpp index 21e3686fc..5dfeb3e2c 100644 --- a/wrapper/MM/ThreeAtomFunctions.pypp.cpp +++ b/wrapper/MM/ThreeAtomFunctions.pypp.cpp @@ -114,6 +114,18 @@ void register_ThreeAtomFunctions_class(){ , bp::release_gil_policy() , "Clear the potential that acts over the angle identified by angleid\nThis clears both 1-2-3 and 3-2-1\nThrow: SireMol::missing_atom\nThrow: SireError::invalid_index\n" ); + } + { //::SireMM::ThreeAtomFunctions::clear + + typedef void ( ::SireMM::ThreeAtomFunctions::*clear_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) ; + clear_function_type clear_function_value( &::SireMM::ThreeAtomFunctions::clear ); + + ThreeAtomFunctions_exposer.def( + "clear" + , clear_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Clear all functions that involve any of the atoms in atoms\n - if exclusive is true, then this only removes functions\n that exclusively involve these atoms - if false, then\n if removes functions that involve any of these atoms\n" ); + } { //::SireMM::ThreeAtomFunctions::clear @@ -292,6 +304,18 @@ void register_ThreeAtomFunctions_class(){ , bp::release_gil_policy() , "Return the potential energy functions acting between the identified\ntriples of atoms" ); + } + { //::SireMM::ThreeAtomFunctions::potentials + + typedef ::QVector< SireMM::ThreeAtomFunction > ( ::SireMM::ThreeAtomFunctions::*potentials_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) const; + potentials_function_type potentials_function_value( &::SireMM::ThreeAtomFunctions::potentials ); + + ThreeAtomFunctions_exposer.def( + "potentials" + , potentials_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Return the potential energy functions acting between the identified\natoms - if exclusive is true then only return potentials where\nall atoms are in the angle\n" ); + } { //::SireMM::ThreeAtomFunctions::set diff --git a/wrapper/MM/TwoAtomFunctions.pypp.cpp b/wrapper/MM/TwoAtomFunctions.pypp.cpp index f30b3c89f..45c42139c 100644 --- a/wrapper/MM/TwoAtomFunctions.pypp.cpp +++ b/wrapper/MM/TwoAtomFunctions.pypp.cpp @@ -114,6 +114,18 @@ void register_TwoAtomFunctions_class(){ , bp::release_gil_policy() , "Clear the potential that acts over the bond identified by bondid\nNote that this removes both 1-2 and 2-1\nThrow: SireMol::missing_atom\nThrow: SireError::invalid_index\n" ); + } + { //::SireMM::TwoAtomFunctions::clear + + typedef void ( ::SireMM::TwoAtomFunctions::*clear_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) ; + clear_function_type clear_function_value( &::SireMM::TwoAtomFunctions::clear ); + + TwoAtomFunctions_exposer.def( + "clear" + , clear_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Clear all functions that invole any of the atoms in atoms\n - if exclusive is true, then this only removes functions\n that exclusively involve these atoms - if false, then\n if removes functions that involve any of these atoms\n" ); + } { //::SireMM::TwoAtomFunctions::clear @@ -292,6 +304,18 @@ void register_TwoAtomFunctions_class(){ , bp::release_gil_policy() , "Return the potential energy functions acting between the identified\npairs of atoms" ); + } + { //::SireMM::TwoAtomFunctions::potentials + + typedef ::QVector< SireMM::TwoAtomFunction > ( ::SireMM::TwoAtomFunctions::*potentials_function_type)( ::QList< SireMol::AtomIdx > const &,bool ) const; + potentials_function_type potentials_function_value( &::SireMM::TwoAtomFunctions::potentials ); + + TwoAtomFunctions_exposer.def( + "potentials" + , potentials_function_value + , ( bp::arg("atoms"), bp::arg("exclusive")=(bool)(true) ) + , "Return the potential energy functions acting between the identified\npairs of atoms - if exclusive is true then only return potentials where\nboth atoms are in the bond\n" ); + } { //::SireMM::TwoAtomFunctions::set From 026cb1546413e65ff48db8a43a7386fbb0a73025 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 3 Mar 2024 19:44:48 +0000 Subject: [PATCH 143/468] Make sure to add connections from ghosts to reference atoms in the reference state --- corelib/src/libs/SireMol/connectivity.cpp | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index f35e8d7f8..88a0f971c 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -3438,7 +3438,7 @@ PropertyList ConnectivityBase::merge(const MolViewProperty &other, const ConnectivityBase &ref = *this; const ConnectivityBase &pert = other.asA(); - auto prop0 = Connectivity(ref); + auto prop0 = Connectivity(ref).edit(); auto prop1 = Connectivity(ref).edit(); // the prop0 properties are already correct @@ -3463,13 +3463,24 @@ PropertyList ConnectivityBase::merge(const MolViewProperty &other, // connect those bonds together for (const auto &pert_bond : pert_bonds) { - prop1.connect(map1to0.value(info().atomIdx(pert_bond.atom0())), - map1to0.value(info().atomIdx(pert_bond.atom1()))); + const auto atom0 = map1to0.value(info().atomIdx(pert_bond.atom0())); + const auto atom1 = map1to0.value(info().atomIdx(pert_bond.atom1())); + + prop1.connect(atom0, atom1); + + if (mapping.isUnmappedIn0(atom0) or mapping.isUnmappedIn0(atom1)) + { + // the prop0 properties are nearly correct - we just need to add + // in a connection from 'pert' that involve the atoms that are not mapped + // in the reference state - this way, those added atoms are + // connected to the reference atoms + prop0.connect(atom0, atom1); + } } SireBase::PropertyList ret; - ret.append(prop0); + ret.append(prop0.commit()); ret.append(prop1.commit()); return ret; From 42ff6bd8a41116be99f65815f89bea678c067ffd Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 3 Mar 2024 22:53:33 +0000 Subject: [PATCH 144/468] Fixed a bug in AtomIdxMapping, and remembered to add the connections/bonds/angles/dihedrals for atoms unmapped in the perturbed state copied from the match in the reference state --- corelib/src/libs/SireMM/fouratomfunctions.cpp | 22 +++++++++++++++++-- .../src/libs/SireMM/threeatomfunctions.cpp | 21 ++++++++++++++++-- corelib/src/libs/SireMM/twoatomfunctions.cpp | 20 +++++++++++++++-- corelib/src/libs/SireMol/atomidxmapping.cpp | 6 ++--- corelib/src/libs/SireMol/connectivity.cpp | 18 +++++++++++++++ 5 files changed, 78 insertions(+), 9 deletions(-) diff --git a/corelib/src/libs/SireMM/fouratomfunctions.cpp b/corelib/src/libs/SireMM/fouratomfunctions.cpp index 69c47faa3..220c712f7 100644 --- a/corelib/src/libs/SireMM/fouratomfunctions.cpp +++ b/corelib/src/libs/SireMM/fouratomfunctions.cpp @@ -1061,8 +1061,26 @@ PropertyList FourAtomFunctions::merge(const MolViewProperty &other, } } - // the dihedrals for atoms that are unmapped in the perturbed state are - // already in prop1, as this was copied from prop0 + // now add in the dihedrals to the perturbed state from the reference + // state for any atoms that aren't mapped to the perturbed state. + // This way, the removed atoms are held by a constant potential, + // so won't fly away in the simulation of the perturbed state + auto map0to1 = mapping.map0to1(true); + + const auto ref_dihs = prop0.potentials(map0to1.keys(), true); + + for (const auto &ref_dih : ref_dihs) + { + const auto atom0 = info().atomIdx(ref_dih.atom0()); + const auto atom1 = info().atomIdx(ref_dih.atom1()); + const auto atom2 = info().atomIdx(ref_dih.atom2()); + const auto atom3 = info().atomIdx(ref_dih.atom3()); + + if (mapping.isUnmappedIn1(atom0) or mapping.isUnmappedIn1(atom1) or mapping.isUnmappedIn1(atom2) or mapping.isUnmappedIn1(atom3)) + { + prop1.set(atom0, atom1, atom2, atom3, ref_dih.function()); + } + } SireBase::PropertyList ret; diff --git a/corelib/src/libs/SireMM/threeatomfunctions.cpp b/corelib/src/libs/SireMM/threeatomfunctions.cpp index 2544eadf8..0b9f90886 100644 --- a/corelib/src/libs/SireMM/threeatomfunctions.cpp +++ b/corelib/src/libs/SireMM/threeatomfunctions.cpp @@ -936,8 +936,25 @@ PropertyList ThreeAtomFunctions::merge(const MolViewProperty &other, } } - // the angles for atoms that are unmapped in the perturbed state are - // already in prop1, as this was copied from prop0 + // now add in the angles to the perturbed state from the reference + // state for any atoms that aren't mapped to the perturbed state. + // This way, the removed atoms are held by a constant angle potential, + // so won't fly away in the simulation of the perturbed state + auto map0to1 = mapping.map0to1(true); + + const auto ref_angs = prop0.potentials(map0to1.keys(), true); + + for (const auto &ref_ang : ref_angs) + { + const auto atom0 = info().atomIdx(ref_ang.atom0()); + const auto atom1 = info().atomIdx(ref_ang.atom1()); + const auto atom2 = info().atomIdx(ref_ang.atom2()); + + if (mapping.isUnmappedIn1(atom0) or mapping.isUnmappedIn1(atom1) or mapping.isUnmappedIn1(atom2)) + { + prop1.set(atom0, atom1, atom2, ref_ang.function()); + } + } SireBase::PropertyList ret; diff --git a/corelib/src/libs/SireMM/twoatomfunctions.cpp b/corelib/src/libs/SireMM/twoatomfunctions.cpp index 8d1c4b799..32e41dc1e 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.cpp +++ b/corelib/src/libs/SireMM/twoatomfunctions.cpp @@ -909,8 +909,24 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, } } - // the bonds for atoms that are unmapped in the perturbed state are - // already in prop1, as this was copied from prop0 + // now add in the bonds to the perturbed state from the reference + // state for any atoms that aren't mapped to the perturbed state. + // This way, the removed atoms are held by a constant bond potential, + // so won't fly away in the simulation of the perturbed state + auto map0to1 = mapping.map0to1(true); + + const auto ref_bonds = prop0.potentials(map0to1.keys(), true); + + for (const auto &ref_bond : ref_bonds) + { + const auto atom0 = info().atomIdx(ref_bond.atom0()); + const auto atom1 = info().atomIdx(ref_bond.atom1()); + + if (mapping.isUnmappedIn1(atom0) or mapping.isUnmappedIn1(atom1)) + { + prop1.set(atom0, atom1, ref_bond.function()); + } + } SireBase::PropertyList ret; diff --git a/corelib/src/libs/SireMol/atomidxmapping.cpp b/corelib/src/libs/SireMol/atomidxmapping.cpp index f75824734..f2046adca 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.cpp +++ b/corelib/src/libs/SireMol/atomidxmapping.cpp @@ -713,12 +713,12 @@ void AtomIdxMapping::rebuild() if (entry.isMappedIn1()) { - mapped1_list.append(entry.atomIdx1()); + mapped1_list.append(entry.atomIdx0()); } else { - unmapped1_set.insert(entry.atomIdx1()); - unmapped1_list.append(entry.atomIdx1()); + unmapped1_set.insert(entry.atomIdx0()); + unmapped1_list.append(entry.atomIdx0()); } if (entry.isMappedIn0() and entry.isMappedIn1()) diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 88a0f971c..a5ebc6639 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -3478,6 +3478,24 @@ PropertyList ConnectivityBase::merge(const MolViewProperty &other, } } + // now add in the connections to the perturbed state from the reference + // state for any atoms that aren't mapped to the perturbed state. + // This way, the removed atoms are connected to the perturbed atoms + auto map0to1 = mapping.map0to1(true); + + const auto ref_bonds = ref.getBonds(map0to1.keys(), true); + + for (const auto &ref_bond : ref_bonds) + { + const auto atom0 = info().atomIdx(ref_bond.atom0()); + const auto atom1 = info().atomIdx(ref_bond.atom1()); + + if (mapping.isUnmappedIn1(atom0) or mapping.isUnmappedIn1(atom1)) + { + prop1.connect(atom0, atom1); + } + } + SireBase::PropertyList ret; ret.append(prop0.commit()); From 1dab9f39dfa489574b28dcf82cc368894b592e05 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 4 Mar 2024 18:38:23 +0000 Subject: [PATCH 145/468] Added the code to merge the CLJNBPairs. Initial tests show quite good agreement in energies. Need to debug though... --- corelib/src/libs/SireMM/cljnbpairs.cpp | 92 ++++++++++++++++++++++++++ corelib/src/libs/SireMM/cljnbpairs.h | 5 ++ wrapper/MM/CLJNBPairs.pypp.cpp | 12 ++++ 3 files changed, 109 insertions(+) diff --git a/corelib/src/libs/SireMM/cljnbpairs.cpp b/corelib/src/libs/SireMM/cljnbpairs.cpp index 641d3f075..bef315cba 100644 --- a/corelib/src/libs/SireMM/cljnbpairs.cpp +++ b/corelib/src/libs/SireMM/cljnbpairs.cpp @@ -969,3 +969,95 @@ const char *LJNBPairs::typeName() { return QMetaType::typeName(qMetaTypeId()); } + +/** Merge this property with another property */ +PropertyList CLJNBPairs::merge(const MolViewProperty &other, + const AtomIdxMapping &mapping, + const QString &ghost, + const SireBase::PropertyMap &map) const +{ + if (not other.isA()) + { + throw SireError::incompatible_error(QObject::tr("Cannot merge %1 with %2 as they are different types.") + .arg(this->what()) + .arg(other.what()), + CODELOC); + } + + if (not ghost.isEmpty()) + { + Console::warning(QObject::tr("The ghost parameter '%1' for CLJNBPairs parameters is ignored").arg(ghost)); + } + + const CLJNBPairs &ref = *this; + const CLJNBPairs &pert = other.asA(); + + CLJNBPairs prop0 = ref; + CLJNBPairs prop1 = ref; + + // we now go through all of the atoms that are mapped and set the + // CLJ NB pair to the right value for each end state. We copy the + // values from the alternate end state for ghost atoms, as we can + // assume that the ghost atoms will have the same bonding + // arrangement as in their end state + for (auto it1 = mapping.begin(); it1 != mapping.end(); ++it1) + { + const auto &atom_a = *it1; + + for (auto it2 = it1 + 1; it2 != mapping.end(); ++it2) + { + const auto &atom_b = *it2; + + if (atom_a.isUnmappedIn0() or atom_b.isUnmappedIn0()) + { + // this pair does not exist in the reference state + if (atom_a.isUnmappedIn1() or atom_b.isUnmappedIn1()) + { + // this pair does not exist in the perturbed state either. + // This pair should not interact with each other + prop0.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), CLJScaleFactor(0, 0)); + prop1.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), CLJScaleFactor(0, 0)); + } + else + { + // set both end states to the value in the perturbed state + const auto &scl = pert.get(atom_a.cgAtomIdx1(), atom_b.cgAtomIdx1()); + + prop0.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), scl); + prop1.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), scl); + } + } + else if (atom_a.isUnmappedIn1() or atom_b.isUnmappedIn1()) + { + if (atom_a.isUnmappedIn0() or atom_b.isUnmappedIn0()) + { + // this pair does not exist in the reference state + // This pair should not interact with each other + prop0.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), CLJScaleFactor(0, 0)); + prop1.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), CLJScaleFactor(0, 0)); + } + else + { + // set both end states to the value in the reference state + const auto &scl = ref.get(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0()); + // already set in the reference state + prop1.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), scl); + } + } + else + { + // we only need to update the pertubed state to equal the + // value from the perturbed parameters + prop1.set(atom_a.cgAtomIdx0(), atom_b.cgAtomIdx0(), + pert.get(atom_a.cgAtomIdx1(), atom_b.cgAtomIdx1())); + } + } + } + + SireBase::PropertyList ret; + + ret.append(prop0); + ret.append(prop1); + + return ret; +} diff --git a/corelib/src/libs/SireMM/cljnbpairs.h b/corelib/src/libs/SireMM/cljnbpairs.h index ee6e46b5b..d683d1fdc 100644 --- a/corelib/src/libs/SireMM/cljnbpairs.h +++ b/corelib/src/libs/SireMM/cljnbpairs.h @@ -294,6 +294,11 @@ namespace SireMM QVector excludedAtoms(const AtomID &atomid) const; QHash> excludedAtoms(CGIdx cgidx) const; + + SireBase::PropertyList merge(const MolViewProperty &other, + const SireMol::AtomIdxMapping &mapping, + const QString &ghost = QString(), + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; }; } // namespace SireMM diff --git a/wrapper/MM/CLJNBPairs.pypp.cpp b/wrapper/MM/CLJNBPairs.pypp.cpp index 0a164e5c8..c918920de 100644 --- a/wrapper/MM/CLJNBPairs.pypp.cpp +++ b/wrapper/MM/CLJNBPairs.pypp.cpp @@ -73,6 +73,18 @@ void register_CLJNBPairs_class(){ , bp::release_gil_policy() , "Return all of the excluded atoms for the atoms in the specified\n CutGroup, returned in a hash indexed by the AtomIdx of those\n atoms. This is equivalent to calling excludedAtoms individually,\n but is far more efficient if trying to get all of the\n excluded atoms in the whole molecule\n" ); + } + { //::SireMM::CLJNBPairs::merge + + typedef ::SireBase::PropertyList ( ::SireMM::CLJNBPairs::*merge_function_type)( ::SireMol::MolViewProperty const &,::SireMol::AtomIdxMapping const &,::QString const &,::SireBase::PropertyMap const & ) const; + merge_function_type merge_function_value( &::SireMM::CLJNBPairs::merge ); + + CLJNBPairs_exposer.def( + "merge" + , merge_function_value + , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) + , "" ); + } { //::SireMM::CLJNBPairs::nExcludedAtoms From f53bae380038e394510b3863d5840194b18473af Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 4 Mar 2024 19:42:16 +0000 Subject: [PATCH 146/468] Added a "to_xml" function so that it is easier to convert sire OpenMM objects to XML for debugging. Just do a ``mols.dynamics().to_xml()`` to get the XML dump. Or call ``to_xml`` directly on the ``SOMMContext``. --- src/sire/mol/_dynamics.py | 18 ++++++++++++++++++ wrapper/Convert/SireOpenMM/_sommcontext.py | 17 +++++++++++++++++ 2 files changed, 35 insertions(+) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 824d06458..71c98b52c 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -969,6 +969,15 @@ class NeedsMinimiseError(Exception): self.run(**orig_args) return + def to_xml(self, f=None): + """ + Save the current state of the dynamics to XML. + This is mostly used for debugging. This will return the + XML string if 'f' is None. Otherwise it will write the + XML to 'f' (either a filename, or a FILE object) + """ + return self._omm_mols.to_xml(f=f) + def commit(self, return_as_system: bool = False): if self.is_null(): return @@ -1528,6 +1537,15 @@ def energy_trajectory(self, to_pandas: bool = False, to_alchemlyb: bool = False) else: return t + def to_xml(self, f=None): + """ + Save the current state of the dynamics to XML. + This is mostly used for debugging. This will return the + XML string if 'f' is None. Otherwise it will write the + XML to 'f' (either a filename, or a FILE object) + """ + return self._d.to_xml(f=f) + def commit(self, return_as_system: bool = False): """ Commit the dynamics and return the molecules after the simulation. diff --git a/wrapper/Convert/SireOpenMM/_sommcontext.py b/wrapper/Convert/SireOpenMM/_sommcontext.py index 8f3c23d79..3757b0078 100644 --- a/wrapper/Convert/SireOpenMM/_sommcontext.py +++ b/wrapper/Convert/SireOpenMM/_sommcontext.py @@ -294,3 +294,20 @@ def get_constraints(self): ) return constraints + + def to_xml(self, f=None): + """ + Save the current state of the dynamics to XML. + This is mostly used for debugging. This will return the + XML string if 'f' is None. Otherwise it will write the + XML to 'f' (either a filename, or a FILE object) + """ + from openmm.openmm import XmlSerializer as _XmlSerializer + + if f is None: + return _XmlSerializer.serialize(self.getSystem()) + elif isinstance(f, str): + with open(f, "w") as handle: + handle.write(_XmlSerializer.serialize(self.getSystem())) + else: + f.write(_XmlSerializer.serialize(self.getSystem())) From 5348fcdf3d35ace3f422f2da1a7d1526ff89ca8b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 4 Mar 2024 23:02:42 +0000 Subject: [PATCH 147/468] Added an AtomNumMatcher as this perfectly re-matches the separated existing merged molecules, so that I can remerge them and verify that the energy is correct. It is - which gives me a lot of confidence that this new merging code is working. Also added the ability to specify the match and prematch to the sr.morph.match and sr.morph.merge functions. --- corelib/src/libs/SireMol/atommatchers.cpp | 255 +++++++++++++++++++--- corelib/src/libs/SireMol/atommatchers.h | 43 ++++ src/sire/_match.py | 26 ++- src/sire/morph/_merge.py | 16 +- wrapper/Mol/AtomNumMatcher.pypp.cpp | 127 +++++++++++ wrapper/Mol/AtomNumMatcher.pypp.hpp | 10 + wrapper/Mol/CMakeAutogenFile.txt | 1 + wrapper/Mol/SireMol_registrars.cpp | 1 + wrapper/Mol/_Mol.main.cpp | 4 + 9 files changed, 449 insertions(+), 34 deletions(-) create mode 100644 wrapper/Mol/AtomNumMatcher.pypp.cpp create mode 100644 wrapper/Mol/AtomNumMatcher.pypp.hpp diff --git a/corelib/src/libs/SireMol/atommatchers.cpp b/corelib/src/libs/SireMol/atommatchers.cpp index 3bbe343e3..29ce1593e 100644 --- a/corelib/src/libs/SireMol/atommatchers.cpp +++ b/corelib/src/libs/SireMol/atommatchers.cpp @@ -86,14 +86,12 @@ QDataStream &operator>>(QDataStream &ds, AtomCoordMatcher &coordmatcher) } /** Constructor */ -AtomCoordMatcher::AtomCoordMatcher() : - ConcreteProperty(), zero_com(false) +AtomCoordMatcher::AtomCoordMatcher() : ConcreteProperty(), zero_com(false) { } /** Constructor */ -AtomCoordMatcher::AtomCoordMatcher(bool zero_com) : - ConcreteProperty(), zero_com(zero_com) +AtomCoordMatcher::AtomCoordMatcher(bool zero_com) : ConcreteProperty(), zero_com(zero_com) { } @@ -500,6 +498,7 @@ QHash AtomNameMatcher::pvt_match(const MoleculeView &mol0, con const MoleculeView &mol1, const PropertyMap &map1) const { QHash map; + QHash reverse_map; const AtomSelection sel0 = mol0.selection(); const AtomSelection sel1 = mol1.selection(); @@ -512,37 +511,48 @@ QHash AtomNameMatcher::pvt_match(const MoleculeView &mol0, con const AtomName name = mol0.data().info().name(idx0); - try - { - AtomIdx idx1 = mol1.data().info().atomIdx(name); - map.insert(idx0, idx1); - } - catch (...) + auto matches = mol1.data().info().mapNoThrow(name); + + // can only match unique matches + if (matches.count() == 1) { + if (reverse_map.contains(matches[0])) + { + // remove the duplicate match + map.remove(reverse_map[matches[0]]); + } + else + { + reverse_map.insert(matches[0], idx0); + map.insert(idx0, matches[0]); + } } } } else { - foreach (const AtomIdx idx0, sel0.selectedAtoms()) + for (const AtomIdx &idx0 : sel0.selectedAtoms()) { const AtomName name0 = mol0.data().info().name(idx0); - // A list of matches. - QList matches; - - foreach (const AtomIdx idx1, sel1.selectedAtoms()) + for (const AtomIdx &idx1 : sel1.selectedAtoms()) { const AtomName name1 = mol1.data().info().name(idx1); - // Add the match. if (name0 == name1) - matches.append(idx1); + { + if (reverse_map.contains(idx1)) + { + // remove the duplicate match + map.remove(reverse_map[idx1]); + } + else + { + reverse_map.insert(idx1, idx0); + map.insert(idx0, idx1); + } + } } - - // Only insert unique matche into the map. - if (matches.count() == 1) - map.insert(idx0, matches[0]); } } @@ -558,6 +568,7 @@ QHash AtomNameMatcher::pvt_match(const MoleculeView &mol0, con QHash AtomNameMatcher::pvt_match(const MoleculeInfoData &mol0, const MoleculeInfoData &mol1) const { QHash map; + QHash reverse_map; for (int i = 0; i < mol0.nAtoms(); ++i) { @@ -565,13 +576,21 @@ QHash AtomNameMatcher::pvt_match(const MoleculeInfoData &mol0, const AtomName name = mol0.name(idx0); - try - { - AtomIdx idx1 = mol1.atomIdx(name); - map.insert(idx0, idx1); - } - catch (...) + auto matches = mol1.mapNoThrow(name); + + // can only match unique matches + if (matches.count() == 1) { + if (reverse_map.contains(matches[0])) + { + // remove the duplicate match + map.remove(reverse_map[matches[0]]); + } + else + { + reverse_map.insert(matches[0], idx0); + map.insert(idx0, matches[0]); + } } } @@ -583,6 +602,188 @@ const char *AtomNameMatcher::typeName() return QMetaType::typeName(qMetaTypeId()); } +///////// +///////// Implementation of AtomNumMatcher +///////// + +static const RegisterMetaType r_nummatcher; + +/** Serialise to a binary datastream */ +QDataStream &operator<<(QDataStream &ds, const AtomNumMatcher &nummatcher) +{ + writeHeader(ds, r_nummatcher, 1); + ds << static_cast(nummatcher); + + return ds; +} + +/** Extract from a binary datastream */ +QDataStream &operator>>(QDataStream &ds, AtomNumMatcher &nummatcher) +{ + VersionID v = readHeader(ds, r_nummatcher); + + if (v == 1) + { + ds >> static_cast(nummatcher); + } + else + throw version_error(v, "1", r_nummatcher, CODELOC); + + return ds; +} + +/** Constructor */ +AtomNumMatcher::AtomNumMatcher() : ConcreteProperty() +{ +} + +/** Copy constructor */ +AtomNumMatcher::AtomNumMatcher(const AtomNumMatcher &other) : ConcreteProperty(other) +{ +} + +/** Destructor */ +AtomNumMatcher::~AtomNumMatcher() +{ +} + +/** Copy assignment operator */ +AtomNumMatcher &AtomNumMatcher::operator=(const AtomNumMatcher &other) +{ + return *this; +} + +/** Comparison operator */ +bool AtomNumMatcher::operator==(const AtomNumMatcher &other) const +{ + return true; +} + +/** Comparison operator */ +bool AtomNumMatcher::operator!=(const AtomNumMatcher &other) const +{ + return false; +} + +QString AtomNumMatcher::toString() const +{ + return QObject::tr("AtomNumMatcher()"); +} + +/** Match the atoms in 'mol1' to the atoms in 'mol0' - this + returns the AtomIdxs of the atoms in 'mol1' that are in + 'mol0', indexed by the AtomIdx of the atom in 'mol0'. + + This skips atoms in 'mol1' that are not in 'mol0' +*/ +QHash AtomNumMatcher::pvt_match(const MoleculeView &mol0, const PropertyMap &map0, + const MoleculeView &mol1, const PropertyMap &map1) const +{ + QHash map; + QHash reverse_map; + + const AtomSelection sel0 = mol0.selection(); + const AtomSelection sel1 = mol1.selection(); + + if (sel0.selectedAll() and sel1.selectedAll()) + { + for (int i = 0; i < mol0.data().info().nAtoms(); ++i) + { + const AtomIdx idx0(i); + + const AtomNum num = mol0.data().info().number(idx0); + + auto matches = mol1.data().info().mapNoThrow(num); + + // can only match unique matches + if (matches.count() == 1) + { + if (reverse_map.contains(matches[0])) + { + // remove the duplicate match + map.remove(reverse_map[matches[0]]); + } + else + { + reverse_map.insert(matches[0], idx0); + map.insert(idx0, matches[0]); + } + } + } + } + else + { + for (const AtomIdx &idx0 : sel0.selectedAtoms()) + { + const AtomNum num0 = mol0.data().info().number(idx0); + + for (const AtomIdx &idx1 : sel1.selectedAtoms()) + { + const AtomNum num1 = mol1.data().info().number(idx1); + + if (num0 == num1) + { + if (reverse_map.contains(idx1)) + { + // remove the duplicate match + map.remove(reverse_map[idx1]); + } + else + { + reverse_map.insert(idx1, idx0); + map.insert(idx0, idx1); + } + } + } + } + } + + return map; +} + +/** Match the atoms in 'mol1' to the atoms in 'mol0' - this + returns the AtomIdxs of the atoms in 'mol1' that are in + 'mol0', indexed by the AtomIdx of the atom in 'mol0'. + + This skips atoms in 'mol1' that are not in 'mol0' +*/ +QHash AtomNumMatcher::pvt_match(const MoleculeInfoData &mol0, const MoleculeInfoData &mol1) const +{ + QHash map; + QHash reverse_match; + + for (int i = 0; i < mol0.nAtoms(); ++i) + { + const AtomIdx idx0(i); + + const AtomNum num = mol0.number(idx0); + + auto matches = mol1.mapNoThrow(num); + + // can only match unique matches + if (matches.count() == 1) + { + if (reverse_match.contains(matches[0])) + { + // remove the duplicate match + map.remove(reverse_match[matches[0]]); + } + else + { + reverse_match.insert(matches[0], idx0); + map.insert(idx0, matches[0]); + } + } + } + + return map; +} + +const char *AtomNumMatcher::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + ///////// ///////// Implementation of AtomMCSMatcher ///////// diff --git a/corelib/src/libs/SireMol/atommatchers.h b/corelib/src/libs/SireMol/atommatchers.h index 136b015e3..b806d99b3 100644 --- a/corelib/src/libs/SireMol/atommatchers.h +++ b/corelib/src/libs/SireMol/atommatchers.h @@ -38,6 +38,7 @@ namespace SireMol class AtomCoordMatcher; class AtomIdxMatcher; class AtomNameMatcher; + class AtomNumMatcher; class AtomIDMatcher; class AtomMultiMatcher; class AtomMCSMatcher; @@ -56,6 +57,9 @@ SIREMOL_EXPORT QDataStream &operator>>(QDataStream &, SireMol::AtomIdxMatcher &) SIREMOL_EXPORT QDataStream &operator<<(QDataStream &, const SireMol::AtomNameMatcher &); SIREMOL_EXPORT QDataStream &operator>>(QDataStream &, SireMol::AtomNameMatcher &); +SIREMOL_EXPORT QDataStream &operator<<(QDataStream &, const SireMol::AtomNumMatcher &); +SIREMOL_EXPORT QDataStream &operator>>(QDataStream &, SireMol::AtomNumMatcher &); + SIREMOL_EXPORT QDataStream &operator<<(QDataStream &, const SireMol::AtomIDMatcher &); SIREMOL_EXPORT QDataStream &operator>>(QDataStream &, SireMol::AtomIDMatcher &); @@ -212,6 +216,43 @@ namespace SireMol const MoleculeView &molview1, const PropertyMap &map1) const; }; + /** This is a simple atom matcher that matches the atoms based + on their numbers, so the atom with number '1' in molinfo0 will + be matched to the atom with number '1' in molinfo1 + */ + class SIREMOL_EXPORT AtomNumMatcher : public SireBase::ConcreteProperty + { + + friend SIREMOL_EXPORT QDataStream & ::operator<<(QDataStream &, const AtomNumMatcher &); + friend SIREMOL_EXPORT QDataStream & ::operator>>(QDataStream &, AtomNumMatcher &); + + public: + AtomNumMatcher(); + AtomNumMatcher(const AtomNumMatcher &); + + ~AtomNumMatcher(); + + static const char *typeName(); + + const char *what() const + { + return AtomNumMatcher::typeName(); + } + + AtomNumMatcher &operator=(const AtomNumMatcher &other); + + bool operator==(const AtomNumMatcher &other) const; + bool operator!=(const AtomNumMatcher &other) const; + + QString toString() const; + + protected: + QHash pvt_match(const MoleculeInfoData &molinfo0, const MoleculeInfoData &molinfo1) const; + + QHash pvt_match(const MoleculeView &molview0, const PropertyMap &map0, + const MoleculeView &molview1, const PropertyMap &map1) const; + }; + /** This is an atom matcher that allows the user to specify exactly how one atom matches another in the molecule by mapping one AtomIdentifier to another @@ -568,6 +609,7 @@ namespace SireMol Q_DECLARE_METATYPE(SireMol::AtomCoordMatcher) Q_DECLARE_METATYPE(SireMol::AtomIdxMatcher) Q_DECLARE_METATYPE(SireMol::AtomNameMatcher) +Q_DECLARE_METATYPE(SireMol::AtomNumMatcher) Q_DECLARE_METATYPE(SireMol::AtomIDMatcher) Q_DECLARE_METATYPE(SireMol::AtomMultiMatcher) Q_DECLARE_METATYPE(SireMol::AtomMCSMatcher) @@ -579,6 +621,7 @@ Q_DECLARE_METATYPE(SireMol::ResIdxAtomCoordMatcher) SIRE_EXPOSE_CLASS(SireMol::AtomCoordMatcher) SIRE_EXPOSE_CLASS(SireMol::AtomIdxMatcher) SIRE_EXPOSE_CLASS(SireMol::AtomNameMatcher) +SIRE_EXPOSE_CLASS(SireMol::AtomNumMatcher) SIRE_EXPOSE_CLASS(SireMol::AtomIDMatcher) SIRE_EXPOSE_CLASS(SireMol::AtomMultiMatcher) SIRE_EXPOSE_CLASS(SireMol::AtomMCSMatcher) diff --git a/src/sire/_match.py b/src/sire/_match.py index 34d197af9..0e35fc36c 100644 --- a/src/sire/_match.py +++ b/src/sire/_match.py @@ -1,19 +1,39 @@ __all__ = ["match_atoms"] -def match_atoms(mol0, mol1, match_light_atoms=False, map0=None, map1=None): +def match_atoms( + mol0, mol1, match=None, prematch=None, match_light_atoms=False, map0=None, map1=None +): """ Perform a simple match that tries to identify the mapping from atoms in 'mol0' to the atoms in 'mol1'. """ from .mol import AtomMapping - from .legacy.Mol import AtomMCSMatcher + from .legacy.Mol import AtomMCSMatcher, AtomMatcher from .base import create_map map0 = create_map(map0) map1 = create_map(map1) - matcher = AtomMCSMatcher(match_light_atoms=match_light_atoms, verbose=False) + if match is not None: + if not isinstance(match, AtomMatcher): + from .legacy.Mol import AtomIDMatcher + + matcher = AtomIDMatcher(match) + else: + matcher = match + + elif prematch is not None: + if not isinstance(prematch, AtomMatcher): + from .legacy.Mol import AtomIDMatcher + + prematch = AtomIDMatcher(prematch) + + matcher = AtomMCSMatcher( + prematcher=prematch, match_light_atoms=match_light_atoms, verbose=False + ) + else: + matcher = AtomMCSMatcher(match_light_atoms=match_light_atoms, verbose=False) m = matcher.match(mol0, map0, mol1, map1) diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py index 09eac236d..8c2f996f8 100644 --- a/src/sire/morph/_merge.py +++ b/src/sire/morph/_merge.py @@ -13,7 +13,7 @@ def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): return _merge(mapping, as_new_molecule=as_new_molecule, map=map) -def merge(mol0, mol1, map=None, map0=None, map1=None): +def merge(mol0, mol1, match=None, prematch=None, map=None, map0=None, map1=None): from ..base import create_map map = create_map(map) @@ -28,9 +28,17 @@ def merge(mol0, mol1, map=None, map0=None, map1=None): else: map1 = create_map(map, map1) - from . import match - - mapping = match(mol0=mol0, mol1=mol1, match_light_atoms=True, map0=map0, map1=map1) + from . import match as _match + + mapping = _match( + mol0=mol0, + mol1=mol1, + match=match, + prematch=prematch, + match_light_atoms=True, + map0=map0, + map1=map1, + ) return mapping.merge(as_new_molecule=True, map=map) diff --git a/wrapper/Mol/AtomNumMatcher.pypp.cpp b/wrapper/Mol/AtomNumMatcher.pypp.cpp new file mode 100644 index 000000000..380d72d54 --- /dev/null +++ b/wrapper/Mol/AtomNumMatcher.pypp.cpp @@ -0,0 +1,127 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "AtomNumMatcher.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireUnits/units.h" + +#include "atom.h" + +#include "atomidentifier.h" + +#include "atomidx.h" + +#include "atommatcher.h" + +#include "atommatchers.h" + +#include "atomname.h" + +#include "atomselection.h" + +#include "evaluator.h" + +#include "moleculeinfodata.h" + +#include "moleculeview.h" + +#include "mover.h" + +#include "mover.hpp" + +#include "selector.hpp" + +#include "tostring.h" + +#include "atommatchers.h" + +SireMol::AtomNumMatcher __copy__(const SireMol::AtomNumMatcher &other){ return SireMol::AtomNumMatcher(other); } + +#include "Qt/qdatastream.hpp" + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +void register_AtomNumMatcher_class(){ + + { //::SireMol::AtomNumMatcher + typedef bp::class_< SireMol::AtomNumMatcher, bp::bases< SireMol::AtomMatcher, SireBase::Property > > AtomNumMatcher_exposer_t; + AtomNumMatcher_exposer_t AtomNumMatcher_exposer = AtomNumMatcher_exposer_t( "AtomNumMatcher", "This is a simple atom matcher that matches the atoms based\non their numbers, so the atom with number 1 in molinfo0 will\nbe matched to the atom with number 1 in molinfo1\n", bp::init< >("") ); + bp::scope AtomNumMatcher_scope( AtomNumMatcher_exposer ); + AtomNumMatcher_exposer.def( bp::init< SireMol::AtomNumMatcher const & >(( bp::arg("arg0") ), "") ); + AtomNumMatcher_exposer.def( bp::self != bp::self ); + { //::SireMol::AtomNumMatcher::operator= + + typedef ::SireMol::AtomNumMatcher & ( ::SireMol::AtomNumMatcher::*assign_function_type)( ::SireMol::AtomNumMatcher const & ) ; + assign_function_type assign_function_value( &::SireMol::AtomNumMatcher::operator= ); + + AtomNumMatcher_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + + } + AtomNumMatcher_exposer.def( bp::self == bp::self ); + { //::SireMol::AtomNumMatcher::toString + + typedef ::QString ( ::SireMol::AtomNumMatcher::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireMol::AtomNumMatcher::toString ); + + AtomNumMatcher_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomNumMatcher::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMol::AtomNumMatcher::typeName ); + + AtomNumMatcher_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::AtomNumMatcher::what + + typedef char const * ( ::SireMol::AtomNumMatcher::*what_function_type)( ) const; + what_function_type what_function_value( &::SireMol::AtomNumMatcher::what ); + + AtomNumMatcher_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + + } + AtomNumMatcher_exposer.staticmethod( "typeName" ); + AtomNumMatcher_exposer.def( "__copy__", &__copy__); + AtomNumMatcher_exposer.def( "__deepcopy__", &__copy__); + AtomNumMatcher_exposer.def( "clone", &__copy__); + AtomNumMatcher_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::AtomNumMatcher >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + AtomNumMatcher_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::AtomNumMatcher >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + AtomNumMatcher_exposer.def_pickle(sire_pickle_suite< ::SireMol::AtomNumMatcher >()); + AtomNumMatcher_exposer.def( "__str__", &__str__< ::SireMol::AtomNumMatcher > ); + AtomNumMatcher_exposer.def( "__repr__", &__str__< ::SireMol::AtomNumMatcher > ); + } + +} diff --git a/wrapper/Mol/AtomNumMatcher.pypp.hpp b/wrapper/Mol/AtomNumMatcher.pypp.hpp new file mode 100644 index 000000000..25a905346 --- /dev/null +++ b/wrapper/Mol/AtomNumMatcher.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef AtomNumMatcher_hpp__pyplusplus_wrapper +#define AtomNumMatcher_hpp__pyplusplus_wrapper + +void register_AtomNumMatcher_class(); + +#endif//AtomNumMatcher_hpp__pyplusplus_wrapper diff --git a/wrapper/Mol/CMakeAutogenFile.txt b/wrapper/Mol/CMakeAutogenFile.txt index 027bd4d77..67aa7f594 100644 --- a/wrapper/Mol/CMakeAutogenFile.txt +++ b/wrapper/Mol/CMakeAutogenFile.txt @@ -259,6 +259,7 @@ set ( PYPP_SOURCES ChainIntProperty.pypp.cpp IDAndSet_CGID_.pypp.cpp Specify_SegID_.pypp.cpp + AtomNumMatcher.pypp.cpp Molecule.pypp.cpp Mover_Chain_.pypp.cpp ChainStructureEditor.pypp.cpp diff --git a/wrapper/Mol/SireMol_registrars.cpp b/wrapper/Mol/SireMol_registrars.cpp index 77899909b..c0072a575 100644 --- a/wrapper/Mol/SireMol_registrars.cpp +++ b/wrapper/Mol/SireMol_registrars.cpp @@ -244,6 +244,7 @@ void register_SireMol_objects() ObjectRegistry::registerConverterFor< SireMol::AtomCoordMatcher >(); ObjectRegistry::registerConverterFor< SireMol::AtomIdxMatcher >(); ObjectRegistry::registerConverterFor< SireMol::AtomNameMatcher >(); + ObjectRegistry::registerConverterFor< SireMol::AtomNumMatcher >(); ObjectRegistry::registerConverterFor< SireMol::AtomIDMatcher >(); ObjectRegistry::registerConverterFor< SireMol::AtomMultiMatcher >(); ObjectRegistry::registerConverterFor< SireMol::AtomMCSMatcher >(); diff --git a/wrapper/Mol/_Mol.main.cpp b/wrapper/Mol/_Mol.main.cpp index 9be6f2b36..c0973b1e0 100644 --- a/wrapper/Mol/_Mol.main.cpp +++ b/wrapper/Mol/_Mol.main.cpp @@ -85,6 +85,8 @@ #include "AtomNum.pypp.hpp" +#include "AtomNumMatcher.pypp.hpp" + #include "AtomPolarisabilities.pypp.hpp" #include "AtomProp.pypp.hpp" @@ -740,6 +742,8 @@ BOOST_PYTHON_MODULE(_Mol){ register_AtomNum_class(); + register_AtomNumMatcher_class(); + register_AtomProp_class(); register_AtomStringProperty_class(); From b4d06d8f6f9a025cf4191f56b0b3e33562aff7e2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 5 Mar 2024 14:18:33 +0000 Subject: [PATCH 148/468] Need to zero intramolecular non-bonded interactions between QM atoms. --- src/sire/qm/_utils.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 5279a6e0a..2331dd6ee 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -436,6 +436,7 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): improper_prop = map["improper"] charge_prop = map["charge"] connectivity_prop = map["connectivity"] + intrascale_prop = map["intrascale"] # Get the molecular info object. info = qm_mol.info() @@ -589,6 +590,27 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): elif prop == connectivity_prop: pass + # Intrascale. + elif prop == intrascale_prop: + # We need to remove intramolecular non-bonded exceptions between QM atoms. + + # Get the existing property. + intrascale = qm_mol.property(prop) + + # Set as the lambda = 0 (MM) end state. + edit_mol = edit_mol.set_property(prop + "0", intrascale).molecule() + + # Zero the scale factors for all QM-QM interactions. + for idx in qm_idxs: + for idx2 in qm_idxs: + intrascale.set(idx, idx2, _MM.CLJScaleFactor(0, 0)) + + # Set as the lambda = 1 (QM) end state. + edit_mol = edit_mol.set_property(prop + "1", intrascale).molecule() + + # Remove the existing property. + edit_mol = edit_mol.remove_property(prop).molecule() + # All other properties remain the same in both end states. else: edit_mol = edit_mol.set_property( From 0a6c0aeaa20e49c186818cf75387f4494ff16f2d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 5 Mar 2024 19:51:17 +0000 Subject: [PATCH 149/468] I've added alignment and also got the mutation working. A quick look in Jupyter shows that mutation of a protein residue has worked really well. Next step is adding some documentation and unit tests. --- corelib/src/libs/SireMol/atommapping.cpp | 74 ++++++++++++++++++++++++ corelib/src/libs/SireMol/atommapping.h | 5 ++ src/sire/morph/_merge.py | 8 ++- src/sire/morph/_mutate.py | 2 +- wrapper/Mol/AtomMapping.pypp.cpp | 36 ++++++++++++ wrapper/Mol/AtomNumMatcher.pypp.cpp | 4 +- 6 files changed, 124 insertions(+), 5 deletions(-) diff --git a/corelib/src/libs/SireMol/atommapping.cpp b/corelib/src/libs/SireMol/atommapping.cpp index 8e683d487..c38616017 100644 --- a/corelib/src/libs/SireMol/atommapping.cpp +++ b/corelib/src/libs/SireMol/atommapping.cpp @@ -28,6 +28,10 @@ #include "atommapping.h" +#include "SireMaths/align.h" + +#include "SireMol/core.h" + #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -697,3 +701,73 @@ const PropertyMap &AtomMapping::propertyMap1() const { return this->map1; } + +/** Return the mapping where the perturbed state (1) has been + * aligned against the reference state (0). + */ +AtomMapping AtomMapping::align() const +{ + return this->alignTo0(); +} + +/** Return the mapping where the perturbed state (1) has been + * aligned against the reference state (0). + */ +AtomMapping AtomMapping::alignTo0() const +{ + if (this->isEmpty()) + return *this; + else if (this->atms0.isEmpty()) + return *this; + + QVector coords0 = this->atms0.property(map0["coordinates"]).toVector(); + QVector coords1 = this->atms1.property(map1["coordinates"]).toVector(); + + // calculate the transform to do a RMSD aligment of the two sets of coordinates + auto transform = SireMaths::getAlignment(coords0, coords1, true); + + auto mols1 = this->orig_atms1.molecules(); + + AtomMapping ret(*this); + + for (int i = 0; i < mols1.count(); ++i) + { + auto mol = mols1[i].move().transform(transform, map1).commit(); + + ret.atms1.update(mol); + ret.orig_atms1.update(mol); + } + + return ret; +} + +/** Return the mapping where the perturbed state (1) has been + * aligned against the reference state (0). + */ +AtomMapping AtomMapping::alignTo1() const +{ + if (this->isEmpty()) + return *this; + else if (this->atms0.isEmpty()) + return *this; + + QVector coords0 = this->atms0.property(map0["coordinates"]).toVector(); + QVector coords1 = this->atms1.property(map1["coordinates"]).toVector(); + + // calculate the transform to do a RMSD aligment of the two sets of coordinates + auto transform = SireMaths::getAlignment(coords1, coords0, true); + + auto mols0 = this->orig_atms0.molecules(); + + AtomMapping ret(*this); + + for (int i = 0; i < mols0.count(); ++i) + { + auto mol = mols0[i].move().transform(transform, map0).commit(); + + ret.atms0.update(mol); + ret.orig_atms0.update(mol); + } + + return ret; +} diff --git a/corelib/src/libs/SireMol/atommapping.h b/corelib/src/libs/SireMol/atommapping.h index dc224d2f9..579d9d4d0 100644 --- a/corelib/src/libs/SireMol/atommapping.h +++ b/corelib/src/libs/SireMol/atommapping.h @@ -151,6 +151,11 @@ namespace SireMol AtomMapping swap() const; + AtomMapping align() const; + + AtomMapping alignTo0() const; + AtomMapping alignTo1() const; + Atom map(const Atom &atom, bool find_all = true) const; SelectorM map(const MoleculeView &atoms, diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py index 8c2f996f8..48257bb57 100644 --- a/src/sire/morph/_merge.py +++ b/src/sire/morph/_merge.py @@ -5,12 +5,16 @@ def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): - from ..legacy.System import merge as _merge + from ..legacy.System import merge as _merge_mols from ..base import create_map map = create_map(map) - return _merge(mapping, as_new_molecule=as_new_molecule, map=map) + # now align the perturbed state onto the reference state, + # so that any added atoms have roughly the right coordinates + aligned_mapping = mapping.align() + + return _merge_mols(aligned_mapping, as_new_molecule=as_new_molecule, map=map) def merge(mol0, mol1, match=None, prematch=None, map=None, map0=None, map1=None): diff --git a/src/sire/morph/_mutate.py b/src/sire/morph/_mutate.py index 859c1a1e3..dbe6d40de 100644 --- a/src/sire/morph/_mutate.py +++ b/src/sire/morph/_mutate.py @@ -7,7 +7,7 @@ def _mutate(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): return ( mapping.merge(as_new_molecule=as_new_molecule, map=map) - .morph(map=map) + .perturbation() .extract_perturbed(remove_ghosts=True) ) diff --git a/wrapper/Mol/AtomMapping.pypp.cpp b/wrapper/Mol/AtomMapping.pypp.cpp index 243bb1624..357fb22f8 100644 --- a/wrapper/Mol/AtomMapping.pypp.cpp +++ b/wrapper/Mol/AtomMapping.pypp.cpp @@ -43,6 +43,42 @@ void register_AtomMapping_class(){ AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("atoms0"), bp::arg("atoms1"), bp::arg("matched_atoms0"), bp::arg("matched_atoms1"), bp::arg("map")=SireBase::PropertyMap() ), "") ); AtomMapping_exposer.def( bp::init< SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireMol::SelectorM< SireMol::Atom > const &, SireBase::PropertyMap const &, SireBase::PropertyMap const & >(( bp::arg("atoms0"), bp::arg("atoms1"), bp::arg("matched_atoms0"), bp::arg("matched_atoms1"), bp::arg("map0"), bp::arg("map1") ), "") ); AtomMapping_exposer.def( bp::init< SireMol::AtomMapping const & >(( bp::arg("other") ), "") ); + { //::SireMol::AtomMapping::align + + typedef ::SireMol::AtomMapping ( ::SireMol::AtomMapping::*align_function_type)( ) const; + align_function_type align_function_value( &::SireMol::AtomMapping::align ); + + AtomMapping_exposer.def( + "align" + , align_function_value + , bp::release_gil_policy() + , "Return the mapping where the perturbed state (1) has been\n aligned against the reference state (0).\n" ); + + } + { //::SireMol::AtomMapping::alignTo0 + + typedef ::SireMol::AtomMapping ( ::SireMol::AtomMapping::*alignTo0_function_type)( ) const; + alignTo0_function_type alignTo0_function_value( &::SireMol::AtomMapping::alignTo0 ); + + AtomMapping_exposer.def( + "alignTo0" + , alignTo0_function_value + , bp::release_gil_policy() + , "Return the mapping where the perturbed state (1) has been\n aligned against the reference state (0).\n" ); + + } + { //::SireMol::AtomMapping::alignTo1 + + typedef ::SireMol::AtomMapping ( ::SireMol::AtomMapping::*alignTo1_function_type)( ) const; + alignTo1_function_type alignTo1_function_value( &::SireMol::AtomMapping::alignTo1 ); + + AtomMapping_exposer.def( + "alignTo1" + , alignTo1_function_value + , bp::release_gil_policy() + , "Return the mapping where the perturbed state (1) has been\n aligned against the reference state (0).\n" ); + + } { //::SireMol::AtomMapping::assertSingleMolecule typedef void ( ::SireMol::AtomMapping::*assertSingleMolecule_function_type)( ) const; diff --git a/wrapper/Mol/AtomNumMatcher.pypp.cpp b/wrapper/Mol/AtomNumMatcher.pypp.cpp index 380d72d54..be2480507 100644 --- a/wrapper/Mol/AtomNumMatcher.pypp.cpp +++ b/wrapper/Mol/AtomNumMatcher.pypp.cpp @@ -57,9 +57,9 @@ void register_AtomNumMatcher_class(){ { //::SireMol::AtomNumMatcher typedef bp::class_< SireMol::AtomNumMatcher, bp::bases< SireMol::AtomMatcher, SireBase::Property > > AtomNumMatcher_exposer_t; - AtomNumMatcher_exposer_t AtomNumMatcher_exposer = AtomNumMatcher_exposer_t( "AtomNumMatcher", "This is a simple atom matcher that matches the atoms based\non their numbers, so the atom with number 1 in molinfo0 will\nbe matched to the atom with number 1 in molinfo1\n", bp::init< >("") ); + AtomNumMatcher_exposer_t AtomNumMatcher_exposer = AtomNumMatcher_exposer_t( "AtomNumMatcher", "This is a simple atom matcher that matches the atoms based\non their numbers, so the atom with number 1 in molinfo0 will\nbe matched to the atom with number 1 in molinfo1\n", bp::init< >("Constructor") ); bp::scope AtomNumMatcher_scope( AtomNumMatcher_exposer ); - AtomNumMatcher_exposer.def( bp::init< SireMol::AtomNumMatcher const & >(( bp::arg("arg0") ), "") ); + AtomNumMatcher_exposer.def( bp::init< SireMol::AtomNumMatcher const & >(( bp::arg("arg0") ), "Copy constructor") ); AtomNumMatcher_exposer.def( bp::self != bp::self ); { //::SireMol::AtomNumMatcher::operator= From 51a68eb850facd33c4ed01b94bd02460ac4cb608 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 5 Mar 2024 23:25:03 +0000 Subject: [PATCH 150/468] Working on adding in the checks for ring size breaking and changing, ported from Python to C++ WIP --- corelib/src/libs/SireMM/twoatomfunctions.cpp | 31 +++ corelib/src/libs/SireMol/connectivity.cpp | 203 +++++++++++++++++++ 2 files changed, 234 insertions(+) diff --git a/corelib/src/libs/SireMM/twoatomfunctions.cpp b/corelib/src/libs/SireMM/twoatomfunctions.cpp index 32e41dc1e..9c4f91b8f 100644 --- a/corelib/src/libs/SireMM/twoatomfunctions.cpp +++ b/corelib/src/libs/SireMM/twoatomfunctions.cpp @@ -928,6 +928,37 @@ PropertyList TwoAtomFunctions::merge(const MolViewProperty &other, } } + // check if we are allowed to change the size of a ring or break rings + bool allow_ring_breaking = true; + bool allow_ring_size_change = true; + + if (map.specified("allow_ring_breaking")) + { + allow_ring_breaking = map["allow_ring_breaking"].value().asABoolean(); + } + + if (map.specified("allow_ring_size_change")) + { + allow_ring_size_change = map["allow_ring_size_change"].value().asABoolean(); + } + + if (not(allow_ring_breaking or allow_ring_size_change)) + { + if (prop0.nFunctions() != prop1.nFunctions()) + { + // number of bond functions has changed - this indicates + // (but not necessarily proves) that a ring has been broken + // or a ring size has changed + throw SireError::incompatible_error( + QObject::tr("The number of bonds in the reference (%1) and " + "perturbed (%2) states is different, indicating that a ring has been broken or a ring size has changed. " + "If you want to allow this perturbation, set 'allow_ring_breaking' or 'allow_ring_size_change' to true.") + .arg(prop0.nFunctions()) + .arg(prop1.nFunctions()), + CODELOC); + } + } + SireBase::PropertyList ret; ret.append(prop0); diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index a5ebc6639..90e5bd196 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -3416,6 +3416,149 @@ void ConnectivityBase::assertHasProperty(const ImproperID &improper, const Prope CODELOC); } +/** Return whether or not this atom is in a ring */ +static bool is_on_ring(const Connectivity &conn, const AtomIdx &atom) +{ + if (conn.inRing(atom)) + { + // loop over all atoms connected to this atom + for (const auto &neighbour : conn.connectionsTo(atom)) + { + // if the neighbour is in the ring, then this atom is in the ring + if (not(conn.inRing(neighbour, atom))) + return true; + } + } + + return false; +} + +/** Return whether or not there is a change in ring between the passed + * two atoms in the passed two connectivities */ +static bool is_ring_size_changed(const Connectivity &conn0, + const Connectivity &conn1, + const AtomIdxMappingEntry &atom0, + const AtomIdxMappingEntry &atom1, + int max_ring_size = 12) +{ + // Have a ring changed size? If so, then the minimum path size between + // two atoms will have changed. + + // Work out the paths connecting the atoms in the two end states. + auto paths0 = conn0.findPaths(atom0.atomIdx0(), atom1.atomIdx0(), max_ring_size); + auto paths1 = conn1.findPaths(atom0.atomIdx1(), atom1.atomIdx1(), max_ring_size); + + // Initialise the ring size in each end state. + auto ring0 = -1; + auto ring1 = -1; + + // Determine the minimum path in the lambda = 0 state. + if (paths0.count() > 1) + { + QVector path_lengths0; + + for (const auto &path : paths0) + { + path_lengths0.append(path.count()); + } + + ring0 = *(std::min_element(path_lengths0.begin(), path_lengths0.end())); + } + + if (ring0 == -1) + return false; + + // Determine the minimum path in the lambda = 1 state. + if (paths1.count() > 1) + { + QVector path_lengths1; + + for (const auto &path : paths1) + { + path_lengths1.append(path.count()); + } + + ring1 = *(std::min_element(path_lengths1.begin(), path_lengths1.end())); + } + + // Return whether the ring has changed size. + return ring0 != ring1; +} + +/** Return whether any ring that both the atoms are on is broken/formed + * during the merge */ +static bool is_ring_broken(const Connectivity &conn0, + const Connectivity &conn1, + const AtomIdxMappingEntry &atom0, + const AtomIdxMappingEntry &atom1) +{ + // Have we opened/closed a ring? This means that both atoms are part of a + // ring in one end state (either in it, or on it), whereas at least one + // isn't in the other state. + + // Whether each atom is in a ring in both end states. + auto in_ring_idx0 = conn0.inRing(atom0.atomIdx0()); + auto in_ring_idy0 = conn0.inRing(atom1.atomIdx0()); + auto in_ring_idx1 = conn1.inRing(atom0.atomIdx1()); + auto in_ring_idy1 = conn1.inRing(atom1.atomIdx1()); + + // Whether each atom is on a ring in both end states. + auto on_ring_idx0 = is_on_ring(conn0, atom0.atomIdx0()); + auto on_ring_idy0 = is_on_ring(conn0, atom1.atomIdx0()); + auto on_ring_idx1 = is_on_ring(conn1, atom0.atomIdx1()); + auto on_ring_idy1 = is_on_ring(conn1, atom1.atomIdx1()); + + # Both atoms are in a ring in one end state and at least one isn't in the other. + if (in_ring_idx0 & in_ring_idy0) ^ (in_ring_idx1 & in_ring_idy1): + return True + + # Both atoms are on a ring in one end state and at least one isn't in the other. + if (on_ring_idx0 & on_ring_idy0 & (conn0.connectionType(idx0, idy0) == 4)) ^ ( + on_ring_idx1 & on_ring_idy1 & (conn1.connectionType(idx1, idy1) == 4) + ): + # Make sure that the change isn't a result of ring growth, i.e. one of + # the atoms isn't in a ring in one end state, while its "on" ring status + # has changed between states. + if not ( + (in_ring_idx0 | in_ring_idx1) & (on_ring_idx0 ^ on_ring_idx1) + or (in_ring_idy0 | in_ring_idy1) & (on_ring_idy0 ^ on_ring_idy1) + ): + return True + + # Both atoms are in or on a ring in one state and at least one isn't in the other. + if ( + (in_ring_idx0 | on_ring_idx0) + & (in_ring_idy0 | on_ring_idy0) + & (conn0.connectionType(idx0, idy0) == 3) + ) ^ ( + (in_ring_idx1 | on_ring_idx1) + & (in_ring_idy1 | on_ring_idy1) + & (conn1.connectionType(idx1, idy1) == 3) + ): + iscn0 = set(conn0.connectionsTo(idx0)).intersection( + set(conn0.connectionsTo(idy0)) + ) + if len(iscn0) != 1: + return True + common_idx = iscn0.pop() + in_ring_bond0 = conn0.inRing(idx0, common_idx) | conn0.inRing(idy0, common_idx) + iscn1 = set(conn1.connectionsTo(idx1)).intersection( + set(conn1.connectionsTo(idy1)) + ) + if len(iscn1) != 1: + return True + common_idx = iscn1.pop() + in_ring_bond1 = conn1.inRing(idx1, common_idx) | conn1.inRing(idy1, common_idx) + if in_ring_bond0 ^ in_ring_bond1: + return True + + # If we get this far, then a ring wasn't broken. + return False + */ + + return false; +} + /** Merge this property with another property */ PropertyList ConnectivityBase::merge(const MolViewProperty &other, const AtomIdxMapping &mapping, @@ -3496,11 +3639,71 @@ PropertyList ConnectivityBase::merge(const MolViewProperty &other, } } + // check if we are allowed to change the size of a ring or break rings + bool allow_ring_breaking = true; + bool allow_ring_size_change = true; + + if (map.specified("allow_ring_breaking")) + { + allow_ring_breaking = map["allow_ring_breaking"].value().asABoolean(); + } + + if (map.specified("allow_ring_size_change")) + { + allow_ring_size_change = map["allow_ring_size_change"].value().asABoolean(); + } + SireBase::PropertyList ret; ret.append(prop0.commit()); ret.append(prop1.commit()); + if (allow_ring_breaking and allow_ring_size_change) + { + // nothing more to do + return ret; + } + + // we need to check that the merge doesn't break or change rings - do this + // by looping over pairs of atoms mapped in both states and checking, + // if they are in a ring, if that ring has changed size or been broken or + // formed by the merge + for (auto it0 = mapping.constBegin(); it0 != mapping.constEnd(); ++it0) + { + const auto &atom0 = *it0; + + for (auto it1 = it0 + 1; it1 != mapping.constEnd(); ++it1) + { + const auto &atom1 = *it1; + + if (not allow_ring_size_change) + { + if (is_ring_size_changed(ref, pert, atom0, atom1)) + { + throw SireError::incompatible_error(QObject::tr("The merge has changed the size of a ring. To allow this " + "perturbation, set the 'allow_ring_size_change' option " + "to 'True'. Be aware that this perturbation may not work " + "and a transition through an intermediate state may be " + "preferable."), + CODELOC); + } + } + + if (not allow_ring_breaking) + { + if (is_ring_broken(ref, pert, atom0, atom1)) + { + throw SireError::incompatible_error(QObject::tr("The merge has changed the molecular connectivity " + "but a ring didn't open/close or change size. " + "If you want to proceed with this mapping pass " + "'force=True'. You are warned that the resulting " + "perturbation will likely be unstable."), + CODELOC); + } + } + } + } + return ret; } From e344caa03335a48fcd4ca3c79febc66af97117fe Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 6 Mar 2024 18:43:03 +0000 Subject: [PATCH 151/468] Added in the ring growing and breaking checks, ported from Python to C++ Still need to add in tests and docs... --- corelib/src/libs/SireMol/atomidxmapping.cpp | 36 ++++++ corelib/src/libs/SireMol/atomidxmapping.h | 9 ++ corelib/src/libs/SireMol/connectivity.cpp | 132 +++++++++++--------- wrapper/Mol/AtomIdxMapping.pypp.cpp | 52 ++++++++ wrapper/Mol/AtomIdxMappingEntry.pypp.cpp | 24 ++++ wrapper/Mol/AtomMapping.pypp.cpp | 4 + 6 files changed, 200 insertions(+), 57 deletions(-) diff --git a/corelib/src/libs/SireMol/atomidxmapping.cpp b/corelib/src/libs/SireMol/atomidxmapping.cpp index f2046adca..eab4cb321 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.cpp +++ b/corelib/src/libs/SireMol/atomidxmapping.cpp @@ -217,6 +217,18 @@ bool AtomIdxMappingEntry::isMappedIn1() const return not atomidx1.isNull(); } +/** Return whether or not this atom is unmapped in both end states */ +bool AtomIdxMappingEntry::isUnmappedInBoth() const +{ + return this->isUnmappedIn0() and this->isUnmappedIn1(); +} + +/** Return whether or not this atom is mapped in both end states */ +bool AtomIdxMappingEntry::isMappedInBoth() const +{ + return this->isMappedIn0() and this->isMappedIn1(); +} + /** Return the atom index in the reference state. This will always have * a value, even if the atom is unmapped in the reference state * (this signals that any parameter with this index should be zero) @@ -834,3 +846,27 @@ QHash AtomIdxMapping::map1to0(bool include_unmapped) const return map1_to_0_exc; } } + +/** Return whether or not this atom is mapped in the reference state */ +bool AtomIdxMapping::isMappedIn0(const AtomIdx &atom) const +{ + return not this->isUnmappedIn0(atom); +} + +/** Return whether or not this atom is mapped in the perturbed state */ +bool AtomIdxMapping::isMappedIn1(const AtomIdx &atom) const +{ + return not this->isUnmappedIn1(atom); +} + +/** Return whether or not this atom is unmapped in both end states */ +bool AtomIdxMapping::isUnmappedInBoth(const AtomIdx &atom) const +{ + return this->isUnmappedIn0(atom) and this->isUnmappedIn1(atom); +} + +/** Return whether or not this atom is mapped in both end states */ +bool AtomIdxMapping::isMappedInBoth(const AtomIdx &atom) const +{ + return this->isMappedIn0(atom) and this->isMappedIn1(atom); +} diff --git a/corelib/src/libs/SireMol/atomidxmapping.h b/corelib/src/libs/SireMol/atomidxmapping.h index 1e10caa16..7acebb4d1 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.h +++ b/corelib/src/libs/SireMol/atomidxmapping.h @@ -86,6 +86,9 @@ namespace SireMol bool isMappedIn0() const; bool isMappedIn1() const; + bool isMappedInBoth() const; + bool isUnmappedInBoth() const; + AtomIdx atomIdx0() const; AtomIdx atomIdx1() const; @@ -190,6 +193,12 @@ namespace SireMol bool isUnmappedIn0(const AtomIdx &atom) const; bool isUnmappedIn1(const AtomIdx &atom) const; + bool isMappedIn0(const AtomIdx &atom) const; + bool isMappedIn1(const AtomIdx &atom) const; + + bool isMappedInBoth(const AtomIdx &atom) const; + bool isUnmappedInBoth(const AtomIdx &atom) const; + QHash map0to1(bool include_unmapped = false) const; QHash map1to0(bool include_unmapped = false) const; diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 90e5bd196..514d20376 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -3417,7 +3417,7 @@ void ConnectivityBase::assertHasProperty(const ImproperID &improper, const Prope } /** Return whether or not this atom is in a ring */ -static bool is_on_ring(const Connectivity &conn, const AtomIdx &atom) +static bool is_on_ring(const AtomIdx &atom, const Connectivity &conn) { if (conn.inRing(atom)) { @@ -3496,66 +3496,76 @@ static bool is_ring_broken(const Connectivity &conn0, // ring in one end state (either in it, or on it), whereas at least one // isn't in the other state. + if (not(atom0.isMappedInBoth() and atom1.isMappedInBoth())) + // either atom isn't in both end states, so cannot be part + // of a ring that is in both end states... + return false; + + const auto idx0 = atom0.atomIdx0(); + const auto idy0 = atom1.atomIdx0(); + + const auto idx1 = atom0.atomIdx1(); + const auto idy1 = atom1.atomIdx1(); + // Whether each atom is in a ring in both end states. - auto in_ring_idx0 = conn0.inRing(atom0.atomIdx0()); - auto in_ring_idy0 = conn0.inRing(atom1.atomIdx0()); - auto in_ring_idx1 = conn1.inRing(atom0.atomIdx1()); - auto in_ring_idy1 = conn1.inRing(atom1.atomIdx1()); + const auto in_ring_idx0 = conn0.inRing(idx0); + const auto in_ring_idy0 = conn0.inRing(idy0); + const auto in_ring_idx1 = conn1.inRing(idx1); + const auto in_ring_idy1 = conn1.inRing(idy1); // Whether each atom is on a ring in both end states. - auto on_ring_idx0 = is_on_ring(conn0, atom0.atomIdx0()); - auto on_ring_idy0 = is_on_ring(conn0, atom1.atomIdx0()); - auto on_ring_idx1 = is_on_ring(conn1, atom0.atomIdx1()); - auto on_ring_idy1 = is_on_ring(conn1, atom1.atomIdx1()); - - # Both atoms are in a ring in one end state and at least one isn't in the other. - if (in_ring_idx0 & in_ring_idy0) ^ (in_ring_idx1 & in_ring_idy1): - return True - - # Both atoms are on a ring in one end state and at least one isn't in the other. - if (on_ring_idx0 & on_ring_idy0 & (conn0.connectionType(idx0, idy0) == 4)) ^ ( - on_ring_idx1 & on_ring_idy1 & (conn1.connectionType(idx1, idy1) == 4) - ): - # Make sure that the change isn't a result of ring growth, i.e. one of - # the atoms isn't in a ring in one end state, while its "on" ring status - # has changed between states. - if not ( - (in_ring_idx0 | in_ring_idx1) & (on_ring_idx0 ^ on_ring_idx1) - or (in_ring_idy0 | in_ring_idy1) & (on_ring_idy0 ^ on_ring_idy1) - ): - return True - - # Both atoms are in or on a ring in one state and at least one isn't in the other. - if ( - (in_ring_idx0 | on_ring_idx0) - & (in_ring_idy0 | on_ring_idy0) - & (conn0.connectionType(idx0, idy0) == 3) - ) ^ ( - (in_ring_idx1 | on_ring_idx1) - & (in_ring_idy1 | on_ring_idy1) - & (conn1.connectionType(idx1, idy1) == 3) - ): - iscn0 = set(conn0.connectionsTo(idx0)).intersection( - set(conn0.connectionsTo(idy0)) - ) - if len(iscn0) != 1: - return True - common_idx = iscn0.pop() - in_ring_bond0 = conn0.inRing(idx0, common_idx) | conn0.inRing(idy0, common_idx) - iscn1 = set(conn1.connectionsTo(idx1)).intersection( - set(conn1.connectionsTo(idy1)) - ) - if len(iscn1) != 1: - return True - common_idx = iscn1.pop() - in_ring_bond1 = conn1.inRing(idx1, common_idx) | conn1.inRing(idy1, common_idx) - if in_ring_bond0 ^ in_ring_bond1: - return True - - # If we get this far, then a ring wasn't broken. - return False - */ + const auto on_ring_idx0 = is_on_ring(idx0, conn0); + const auto on_ring_idy0 = is_on_ring(idy0, conn0); + const auto on_ring_idx1 = is_on_ring(idx1, conn1); + const auto on_ring_idy1 = is_on_ring(idy1, conn1); + // Both atoms are in a ring in one end state and at least one isn't in the other. + if ((in_ring_idx0 & in_ring_idy0) ^ (in_ring_idx1 & in_ring_idy1)) + return true; + + // Both atoms are on a ring in one end state and at least one isn't in the other. + if ((on_ring_idx0 & on_ring_idy0 & (conn0.connectionType(idx0, idy0) == 4)) ^ (on_ring_idx1 & on_ring_idy1 & (conn1.connectionType(idx1, idy1) == 4))) + { + // Make sure that the change isn't a result of ring growth, i.e. one of + // the atoms isn't in a ring in one end state, while its "on" ring status + // has changed between states. + if (not((in_ring_idx0 | in_ring_idx1) & (on_ring_idx0 ^ on_ring_idx1) or (in_ring_idy0 | in_ring_idy1) & (on_ring_idy0 ^ on_ring_idy1))) + { + return true; + } + } + + // Both atoms are in or on a ring in one state and at least one isn't in the other. + if (((in_ring_idx0 | on_ring_idx0) & (in_ring_idy0 | on_ring_idy0) & (conn0.connectionType(idx0, idy0) == 3)) ^ + ((in_ring_idx1 | on_ring_idx1) & (in_ring_idy1 | on_ring_idy1) & (conn1.connectionType(idx1, idy1) == 3))) + { + auto iscn0 = conn0.connectionsTo(idx0); + iscn0.intersect(conn0.connectionsTo(idy0)); + + if (iscn0.count() != 1) + return true; + + auto common_idx = *(iscn0.constBegin()); + iscn0.remove(common_idx); + + const auto in_ring_bond0 = conn0.inRing(idx0, common_idx) or conn0.inRing(idy0, common_idx); + + auto iscn1 = conn1.connectionsTo(idx1); + iscn1.intersect(conn1.connectionsTo(idy1)); + + if (iscn1.count() != 1) + return true; + + common_idx = *(iscn1.constBegin()); + iscn1.remove(common_idx); + + const auto in_ring_bond1 = conn1.inRing(idx1, common_idx) or conn1.inRing(idy1, common_idx); + + if (in_ring_bond0 ^ in_ring_bond1) + return true; + } + + // If we get this far, then a ring wasn't broken. return false; } @@ -3672,10 +3682,18 @@ PropertyList ConnectivityBase::merge(const MolViewProperty &other, { const auto &atom0 = *it0; + if (not atom0.isMappedInBoth()) + // this cannot be part of a ring, as it is not in both states + continue; + for (auto it1 = it0 + 1; it1 != mapping.constEnd(); ++it1) { const auto &atom1 = *it1; + if (not atom1.isMappedInBoth()) + // this cannot be part of a ring, as it is not in both states + continue; + if (not allow_ring_size_change) { if (is_ring_size_changed(ref, pert, atom0, atom1)) diff --git a/wrapper/Mol/AtomIdxMapping.pypp.cpp b/wrapper/Mol/AtomIdxMapping.pypp.cpp index bf7af65c7..4a4118ace 100644 --- a/wrapper/Mol/AtomIdxMapping.pypp.cpp +++ b/wrapper/Mol/AtomIdxMapping.pypp.cpp @@ -104,6 +104,45 @@ void register_AtomIdxMapping_class(){ , bp::release_gil_policy() , "Return whether or not the list is empty" ); + } + { //::SireMol::AtomIdxMapping::isMappedIn0 + + typedef bool ( ::SireMol::AtomIdxMapping::*isMappedIn0_function_type)( ::SireMol::AtomIdx const & ) const; + isMappedIn0_function_type isMappedIn0_function_value( &::SireMol::AtomIdxMapping::isMappedIn0 ); + + AtomIdxMapping_exposer.def( + "isMappedIn0" + , isMappedIn0_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return whether or not this atom is mapped in the reference state" ); + + } + { //::SireMol::AtomIdxMapping::isMappedIn1 + + typedef bool ( ::SireMol::AtomIdxMapping::*isMappedIn1_function_type)( ::SireMol::AtomIdx const & ) const; + isMappedIn1_function_type isMappedIn1_function_value( &::SireMol::AtomIdxMapping::isMappedIn1 ); + + AtomIdxMapping_exposer.def( + "isMappedIn1" + , isMappedIn1_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return whether or not this atom is mapped in the perturbed state" ); + + } + { //::SireMol::AtomIdxMapping::isMappedInBoth + + typedef bool ( ::SireMol::AtomIdxMapping::*isMappedInBoth_function_type)( ::SireMol::AtomIdx const & ) const; + isMappedInBoth_function_type isMappedInBoth_function_value( &::SireMol::AtomIdxMapping::isMappedInBoth ); + + AtomIdxMapping_exposer.def( + "isMappedInBoth" + , isMappedInBoth_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return whether or not this atom is mapped in both end states" ); + } { //::SireMol::AtomIdxMapping::isUnmappedIn0 @@ -130,6 +169,19 @@ void register_AtomIdxMapping_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomIdxMapping::isUnmappedInBoth + + typedef bool ( ::SireMol::AtomIdxMapping::*isUnmappedInBoth_function_type)( ::SireMol::AtomIdx const & ) const; + isUnmappedInBoth_function_type isUnmappedInBoth_function_value( &::SireMol::AtomIdxMapping::isUnmappedInBoth ); + + AtomIdxMapping_exposer.def( + "isUnmappedInBoth" + , isUnmappedInBoth_function_value + , ( bp::arg("atom") ) + , bp::release_gil_policy() + , "Return whether or not this atom is unmapped in both end states" ); + } { //::SireMol::AtomIdxMapping::map0to1 diff --git a/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp b/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp index d71c5b96a..91fed776b 100644 --- a/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp +++ b/wrapper/Mol/AtomIdxMappingEntry.pypp.cpp @@ -110,6 +110,18 @@ void register_AtomIdxMappingEntry_class(){ , bp::release_gil_policy() , "Return whether or not this atom is mapped in the perturbed state" ); + } + { //::SireMol::AtomIdxMappingEntry::isMappedInBoth + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isMappedInBoth_function_type)( ) const; + isMappedInBoth_function_type isMappedInBoth_function_value( &::SireMol::AtomIdxMappingEntry::isMappedInBoth ); + + AtomIdxMappingEntry_exposer.def( + "isMappedInBoth" + , isMappedInBoth_function_value + , bp::release_gil_policy() + , "Return whether or not this atom is mapped in both end states" ); + } { //::SireMol::AtomIdxMappingEntry::isNull @@ -146,6 +158,18 @@ void register_AtomIdxMappingEntry_class(){ , bp::release_gil_policy() , "Return whether or not this atom is unmapped in the perturbed state" ); + } + { //::SireMol::AtomIdxMappingEntry::isUnmappedInBoth + + typedef bool ( ::SireMol::AtomIdxMappingEntry::*isUnmappedInBoth_function_type)( ) const; + isUnmappedInBoth_function_type isUnmappedInBoth_function_value( &::SireMol::AtomIdxMappingEntry::isUnmappedInBoth ); + + AtomIdxMappingEntry_exposer.def( + "isUnmappedInBoth" + , isUnmappedInBoth_function_value + , bp::release_gil_policy() + , "Return whether or not this atom is unmapped in both end states" ); + } AtomIdxMappingEntry_exposer.def( bp::self != bp::self ); { //::SireMol::AtomIdxMappingEntry::operator= diff --git a/wrapper/Mol/AtomMapping.pypp.cpp b/wrapper/Mol/AtomMapping.pypp.cpp index 357fb22f8..56684b55f 100644 --- a/wrapper/Mol/AtomMapping.pypp.cpp +++ b/wrapper/Mol/AtomMapping.pypp.cpp @@ -8,6 +8,10 @@ namespace bp = boost::python; +#include "SireMaths/align.h" + +#include "SireMol/core.h" + #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" From ec46c5c47990d32b2c20c5d04788e853c715087c Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 6 Mar 2024 23:24:09 +0000 Subject: [PATCH 152/468] Added function-level documentation, plus also the sr.morph.decouple function to generate merged molecules that can be used for double-decoupling --- src/sire/_match.py | 36 ++++++++++- src/sire/morph/__init__.py | 4 ++ src/sire/morph/_decouple.py | 115 ++++++++++++++++++++++++++++++++++++ src/sire/morph/_merge.py | 59 ++++++++++++++++++ src/sire/morph/_mutate.py | 67 ++++++++++++++++++++- 5 files changed, 279 insertions(+), 2 deletions(-) create mode 100644 src/sire/morph/_decouple.py diff --git a/src/sire/_match.py b/src/sire/_match.py index 0e35fc36c..cd653deca 100644 --- a/src/sire/_match.py +++ b/src/sire/_match.py @@ -6,7 +6,41 @@ def match_atoms( ): """ Perform a simple match that tries to identify the mapping from - atoms in 'mol0' to the atoms in 'mol1'. + atoms in 'mol0' to the atoms in 'mol1'. This uses the `AtomMCSMatcher` + to match the atoms, using the passed `prematch` argument. + + However, if the `match` argument is provided, this will be used + as the atom mapping directly (it can either be a dictionary mapping + atom identifiers, or an `AtomMatcher` object). + + Parameters + ---------- + mol0 : Molecule view + The reference state molecule (or part of molecule) + mol1 : Molecule view + The perturbed state molecule (or part of molecule) + match : dict, AtomMatcher, optional + The atom matcher to use to match atoms. If this is a dictionary + of atom identifiers, then this will be passed to a + `AtomIDMatcher` object. If this is an `AtomMatcher` object, then + this will be used directly. + prematch : dict, AtomMatcher, optional + The atom matcher to use to prematch atoms. If `match` is not + supplied, then this will be used as the `prematch` argument + to the `AtomMCSMatcher` used to find the maximum common subgraph + match. + match_light_atoms : bool, optional + Whether to match light atoms (i.e. hydrogen atoms) if using the + default `AtomMCSMatcher`. Default is False. + map0 : dict, optional + Property map to find properties in `mol0` + map1 : dict, optional + Property map to find properties in `mol1` + + Returns + ------- + AtomMapping + The atom mapping between the two molecules (or parts of molecules) """ from .mol import AtomMapping from .legacy.Mol import AtomMCSMatcher, AtomMatcher diff --git a/src/sire/morph/__init__.py b/src/sire/morph/__init__.py index 0cc8be327..e5931ee5e 100644 --- a/src/sire/morph/__init__.py +++ b/src/sire/morph/__init__.py @@ -8,6 +8,8 @@ "extract_perturbed", "link_to_reference", "link_to_perturbed", + "annihilate", + "decouple", "match", "merge", "mutate", @@ -44,3 +46,5 @@ from ._merge import merge from ._mutate import mutate + +from ._decouple import annihilate, decouple diff --git a/src/sire/morph/_decouple.py b/src/sire/morph/_decouple.py new file mode 100644 index 000000000..cd7f811d8 --- /dev/null +++ b/src/sire/morph/_decouple.py @@ -0,0 +1,115 @@ +__all__ = ["annihilate", "decouple"] + + +def annihilate(mol, as_new_molecule: bool = True, map=None): + """ + Return a merged molecule that represents the perturbation that + completely annihilates the molecule. The returned merged molecule + will be suitable for using in a double-annihilation free energy + simulation, e.g. to calculate absolute binding free energies. + + Parameters + ---------- + mol : Molecule view + The molecule (or part of molecule) to annihilate. + This will only annihilate the atoms in this molecule view. + Normally, you would want to pass in the entire molecule. + as_new_molecule : bool, optional + Whether to return the merged molecule as a new molecule, + or to assign a new molecule number to the result. Default is True. + map : dict, optional + Property map to assign properties in the returned, + merged molecule, plus to find the properties that will be + annihilated. + + Returns + ------- + Molecule + The merged molecule representing the annihilation perturbation + """ + pass + + +def decouple(mol, as_new_molecule: bool = True, map=None): + """ + Return a merged molecule that represents the perturbation that + completely decouples the molecule. The returned merged molecule + will be suitable for using in a double-decoupling free energy + simulation, e.g. to calculate absolute binding free energies. + + Parameters + ---------- + mol : Molecule view + The molecule (or part of molecule) to decouple. + This will only decouple the atoms in this molecule view. + Normally, you would want to pass in the entire molecule. + as_new_molecule : bool, optional + Whether to return the merged molecule as a new molecule, + or to assign a new molecule number to the result. Default is True. + map : dict, optional + Property map to assign properties in the returned, + merged molecule, plus to find the properties that will be + decoupled. + + Returns + ------- + Molecule + The merged molecule representing the decoupling perturbation + """ + try: + # make sure we have only the reference state + mol = mol.perturbation().extract_reference(remove_ghosts=True) + except Exception: + pass + + from ..base import create_map + from ..mm import LJParameter + from ..units import kcal_per_mol, mod_electron + + map = create_map(map) + + c = mol.cursor() + + c_mol = c.molecule() + c_mol["is_perturbable"] = True + + for key in [ + "charge", + "LJ", + "bond", + "angle", + "dihedral", + "improper", + "forcefield", + "intrascale", + "mass", + "element", + "atomtype", + "ambertype", + "connectivity", + ]: + key = map[key].source() + + if key in c: + c_mol[f"{key}0"] = c_mol[key] + c_mol[f"{key}1"] = c_mol[key] + del c_mol[key] + + lj_prop = map["LJ"].source() + chg_prop = map["charge"].source() + + for atom in c.atoms(): + lj = atom[f"{lj_prop}0"] + + atom[f"{lj_prop}1"] = LJParameter(lj.sigma(), 0.0 * kcal_per_mol) + atom[f"{chg_prop}1"] = 0 * mod_electron + + mol = c_mol.commit() + + c_mol["molecule0"] = mol.perturbation().extract_reference(remove_ghosts=True) + c_mol["molecule1"] = mol.perturbation().extract_perturbed(remove_ghosts=True) + + if as_new_molecule: + c_mol.renumber() + + return c.commit() diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py index 48257bb57..c7e1feeb4 100644 --- a/src/sire/morph/_merge.py +++ b/src/sire/morph/_merge.py @@ -5,6 +5,29 @@ def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): + """ + Merge the atoms in this mapping and return as a single merged + (perturbable) molecule. This function will conduct a merge and + return a perturbable molecule such that it is equivalent to + `mol0` at the reference state (lambda=0) and equivalent to `mol1` + at the perturbed state (lambda=1). + + Parameters + ---------- + + as_new_molecule : bool, optional + If True, the merged molecule will be assigned a new molecule + number and treated as a new molecule. If False, the merged + molecule will use the molecule number of the reference molecule. + map : dict, optional + Property map to assign properties in the returned, + merged molecule. + + Returns + ------- + Molecule + The merged molecule + """ from ..legacy.System import merge as _merge_mols from ..base import create_map @@ -18,6 +41,42 @@ def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): def merge(mol0, mol1, match=None, prematch=None, map=None, map0=None, map1=None): + """ + Merge together the atoms in 'mol0' and 'mol1' and return as a single + merged (perturbable) molecule. This function will conduct a merge + and return a perturbable molecule such that it is equivalent to + `mol0` at the reference state (lambda=0) and equivalent to `mol1` at + the perturbed state (lambda=1). + + The `sr.morph.match_atoms` function will be called with the passed + `match` and `prematch` arguments to determine the atom mapping between + the two molecules. + + Parameters + ---------- + mol0 : Molecule view + The reference state molecule (or part of molecule) + mol1 : Molecule view + The perturbed state molecule (or part of molecule) + match : dict, AtomMapping, optional + If provided, this will be passed as the `match` argument + to `sr.morph.match_atoms`, to aid in the atom mapping. + prematch : dict, AtomMapping, optional + If provided, this will be passed as the `prematch` argument + to `sr.morph.match_atoms`, to aid in the atom mapping. + map : dict, optional + Property map to assign properties in the returned, + merged molecule. + map0 : dict, optional + Property map to find properties in `mol0` + map1 : dict, optional + Property map to find properties in `mol1` + + Returns + ------- + Molecule + The merged molecule + """ from ..base import create_map map = create_map(map) diff --git a/src/sire/morph/_mutate.py b/src/sire/morph/_mutate.py index dbe6d40de..5613b1bed 100644 --- a/src/sire/morph/_mutate.py +++ b/src/sire/morph/_mutate.py @@ -5,6 +5,34 @@ def _mutate(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): + """ + Mutate the reference atoms in this mapping to the perturbed atoms, + returning the mutated (new) molecule. + + This is equivalent to calling `merge` and then extracting the + perturbed state from the returned merged molecule. + + This function is most useful for mutating parts of molecules, + e.g. calling this on a mapping of two residues would mutate + one residue into another within the larger molecule containing + the reference mapping. This can be used for mutating residues + in proteins, or for copying and pasting parts of one molecule + into another. + + Parameters + ---------- + as_new_molecule : bool, optional + Whether to return the mutated molecule as a new molecule, + or to mutate the original molecule in place. Default is True. + map : dict, optional + Property map to assign properties in the returned, + mutated molecule. + + Returns + ------- + Molecule + The mutated molecule + """ return ( mapping.merge(as_new_molecule=as_new_molecule, map=map) .perturbation() @@ -12,7 +40,44 @@ def _mutate(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): ) -def mutate(mol0, mol1, map=None, map0=None, map1=None): +def mutate(mol0, mol1, match=None, prematch=None, map=None, map0=None, map1=None): + """ + Mutate `mol0` to `mol1`, returning the mutated (new) molecule. + This is equivalent to calling `merge` on the two molecules (or + parts of molecules) and then extracting the perturbed state. + + This function is most useful for mutating parts of molecules, + e.g. passing in two residues as `mol0` and `mol1` would mutate + that residue to the other within the larger molecule containing + `mol0`. This can be used for mutating residues in proteins, or + for copying and pasting parts of one molecule into another. + + Parameters + ---------- + mol0 : Molecule view + The molecule (or part of molecule) that will be mutated. + mol1 : Molecule view + The molecule (or part of molecule) that will be mutated to. + This will replace the atoms in `mol0`. + match : dict, AtomMatcher, optional + If provided, this will be passed as the `match` argument + to `sr.morph.match_atoms`, to aid in the atom mapping. + prematch : dict, AtomMatcher, optional + If provided, this will be passed as the `prematch` argument + to `sr.morph.match_atoms`, to aid in the atom mapping. + map : dict, optional + Property map to assign properties in the returned, + mutated molecule. + map0 : dict, optional + Property map to find properties in `mol0` + map1 : dict, optional + Property map to find properties in `mol1` + + Returns + ------- + Molecule + The mutated molecule + """ from ..base import create_map map = create_map(map) From 8bde2df346718bf3399204cb0431601bb9aef501 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 7 Mar 2024 23:22:15 +0000 Subject: [PATCH 153/468] Fixes to make the merge, mutate and decouple work for the demo --- corelib/src/libs/SireMol/atomcoords.cpp | 12 +++++++----- src/sire/morph/CMakeLists.txt | 1 + src/sire/morph/_decouple.py | 22 +++++++++++++++++++--- src/sire/morph/_merge.py | 6 +++++- src/sire/morph/_perturbation.py | 2 ++ 5 files changed, 34 insertions(+), 9 deletions(-) diff --git a/corelib/src/libs/SireMol/atomcoords.cpp b/corelib/src/libs/SireMol/atomcoords.cpp index 59b72c1f1..0f527a9b8 100644 --- a/corelib/src/libs/SireMol/atomcoords.cpp +++ b/corelib/src/libs/SireMol/atomcoords.cpp @@ -33,6 +33,7 @@ #include "SireVol/space.h" +#include "SireBase/console.h" #include "SireBase/quickcopy.hpp" #include "SireMaths/vectorproperty.h" @@ -1051,26 +1052,27 @@ PropertyList AtomCoords::merge(const MolViewProperty &other, AtomCoords prop0 = ref; AtomCoords prop1 = ref; - Vector ghost_param(0); - if (not ghost.isEmpty()) { - ghost_param = Vector(ghost); + Console::warning(QObject::tr("The ghost parameter '%1' for LJ parameters is ignored").arg(ghost)); } for (const auto &index : mapping) { if (index.isUnmappedIn0()) { - prop0.set(index.cgAtomIdx0(), ghost_param); + // use the coordinates of the perturbed state + prop0.set(index.cgAtomIdx0(), pert.get(index.cgAtomIdx1())); } if (index.isUnmappedIn1()) { - prop1.set(index.cgAtomIdx0(), ghost_param); + // use the coordinates of the reference state + prop1.set(index.cgAtomIdx0(), prop0.get(index.cgAtomIdx0())); } else { + // we can use the coordinates of the perturbed state prop1.set(index.cgAtomIdx0(), pert.get(index.cgAtomIdx1())); } } diff --git a/src/sire/morph/CMakeLists.txt b/src/sire/morph/CMakeLists.txt index b4e0428f5..11ea25882 100644 --- a/src/sire/morph/CMakeLists.txt +++ b/src/sire/morph/CMakeLists.txt @@ -8,6 +8,7 @@ set ( SCRIPTS __init__.py _alchemy.py + _decouple.py _ghost_atoms.py _hmr.py _merge.py diff --git a/src/sire/morph/_decouple.py b/src/sire/morph/_decouple.py index cd7f811d8..5384e7d9d 100644 --- a/src/sire/morph/_decouple.py +++ b/src/sire/morph/_decouple.py @@ -27,7 +27,7 @@ def annihilate(mol, as_new_molecule: bool = True, map=None): Molecule The merged molecule representing the annihilation perturbation """ - pass + return mol def decouple(mol, as_new_molecule: bool = True, map=None): @@ -93,7 +93,9 @@ def decouple(mol, as_new_molecule: bool = True, map=None): if key in c: c_mol[f"{key}0"] = c_mol[key] c_mol[f"{key}1"] = c_mol[key] - del c_mol[key] + + if key != "connectivity": + del c_mol[key] lj_prop = map["LJ"].source() chg_prop = map["charge"].source() @@ -109,7 +111,21 @@ def decouple(mol, as_new_molecule: bool = True, map=None): c_mol["molecule0"] = mol.perturbation().extract_reference(remove_ghosts=True) c_mol["molecule1"] = mol.perturbation().extract_perturbed(remove_ghosts=True) + if "parameters" in c_mol: + del c_mol["parameters"] + + if "amberparams" in c_mol: + del c_mol["amberparams"] + if as_new_molecule: c_mol.renumber() - return c.commit() + # need to add a LambdaSchedule that could be used to decouple + # the molecule + from ..cas import LambdaSchedule + + c_mol["schedule"] = LambdaSchedule() + + mol = c_mol.commit().perturbation().link_to_reference() + + return mol diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py index c7e1feeb4..ef0119377 100644 --- a/src/sire/morph/_merge.py +++ b/src/sire/morph/_merge.py @@ -37,7 +37,11 @@ def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): # so that any added atoms have roughly the right coordinates aligned_mapping = mapping.align() - return _merge_mols(aligned_mapping, as_new_molecule=as_new_molecule, map=map) + mol = _merge_mols(aligned_mapping, as_new_molecule=as_new_molecule, map=map) + + mol = mol.perturbation().link_to_reference() + + return mol def merge(mol0, mol1, match=None, prematch=None, map=None, map0=None, map1=None): diff --git a/src/sire/morph/_perturbation.py b/src/sire/morph/_perturbation.py index 3cb36a9ba..7b7b06ca2 100644 --- a/src/sire/morph/_perturbation.py +++ b/src/sire/morph/_perturbation.py @@ -351,6 +351,8 @@ def extract_perturbed( if mol.has_property("is_perturbable"): mol.remove_property("is_perturbable") + mol.switch_to_alternate_names() + mol = mol.commit().molecule() if remove_ghosts: From 5cf821cf4f389647af6552f8ee0fc372b6a11929 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 8 Mar 2024 22:53:43 +0000 Subject: [PATCH 154/468] Added kartograf support to the match function. Can now pass in a KartografAtomMapper as the `match` argument of the function. --- src/sire/_match.py | 62 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) diff --git a/src/sire/_match.py b/src/sire/_match.py index cd653deca..a393b2040 100644 --- a/src/sire/_match.py +++ b/src/sire/_match.py @@ -46,13 +46,75 @@ def match_atoms( from .legacy.Mol import AtomMCSMatcher, AtomMatcher from .base import create_map + if mol0.num_molecules() > 1 or mol1.num_molecules() > 1: + raise ValueError("You cannot match multiple molecules at once") + + from .system import System + + if System.is_system(mol0): + mol0 = mol0[0] + + if System.is_system(mol1): + mol1 = mol1[0] + map0 = create_map(map0) map1 = create_map(map1) if match is not None: + if prematch is not None: + raise ValueError("You cannot provide both a `match` and a `prematch`") + if not isinstance(match, AtomMatcher): from .legacy.Mol import AtomIDMatcher + # create a dictionary of atom identifiers + if isinstance(match, dict): + from . import atomid + + matches = {} + + for atom0, atom1 in match.items(): + if isinstance(atom0, int): + atom0 = atomid(idx=atom0) + elif isinstance(atom0, str): + atom0 = atomid(name=atom0) + + if isinstance(atom1, int): + atom1 = atomid(idx=atom1) + elif isinstance(atom1, str): + atom1 = atomid(name=atom1) + + matches[atom0] = atom1 + + match = matches + + elif "KartografAtomMapper" in str(match.__class__): + # use Kartograf to get the mapping - convert to RDKit then Kartograf + from kartograf.atom_aligner import align_mol_shape + from kartograf import KartografAtomMapper, SmallMoleculeComponent + + if not isinstance(match, KartografAtomMapper): + raise TypeError("match must be a KartografAtomMapper") + + from .convert import to + from . import atomid + + rd_mol0 = to(mol0, "rdkit") + rd_mol1 = to(mol1, "rdkit") + + k_mol0, k_mol1 = [ + SmallMoleculeComponent.from_rdkit(m) for m in [rd_mol0, rd_mol1] + ] + + k_0mol1 = align_mol_shape(k_mol1, ref_mol=k_mol0) + + mapping = next(match.suggest_mappings(k_mol0, k_0mol1)) + + match = {} + + for k, v in mapping.componentA_to_componentB.items(): + match[atomid(idx=k)] = atomid(idx=v) + matcher = AtomIDMatcher(match) else: matcher = match From ce1baa6a31aca3f7671f0cf0e5dba7b4b3ed3000 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 9 Mar 2024 23:02:07 +0000 Subject: [PATCH 155/468] Optimised the code that edits proteins, so that the merge is not O(N2) but is instead closer to O(N) (and is now a couple of seconds for neuraminidase) I am sure there is scope for further speedup --- corelib/src/libs/SireMM/cljnbpairs.cpp | 124 ++++++++++++++++++++++ corelib/src/libs/SireMM/cljnbpairs.h | 6 ++ corelib/src/libs/SireMol/connectivity.cpp | 28 ++++- src/sire/_match.py | 2 +- 4 files changed, 158 insertions(+), 2 deletions(-) diff --git a/corelib/src/libs/SireMM/cljnbpairs.cpp b/corelib/src/libs/SireMM/cljnbpairs.cpp index bef315cba..62bdca023 100644 --- a/corelib/src/libs/SireMM/cljnbpairs.cpp +++ b/corelib/src/libs/SireMM/cljnbpairs.cpp @@ -1061,3 +1061,127 @@ PropertyList CLJNBPairs::merge(const MolViewProperty &other, return ret; } + +/** Return a copy of this property that has been made to be compatible + with the molecule layout in 'molinfo' - this uses the atom matching + functions in 'atommatcher' to match atoms from the current molecule + to the atoms in the molecule whose layout is in 'molinfo' + + This will only copy the values of pairs of atoms that are + successfully matched - all other pairs will have the default + value of this AtomPairs object. + + \throw SireError::incompatible_error +*/ +SireBase::PropertyPtr CLJNBPairs::_pvt_makeCompatibleWith( + const MoleculeInfoData &other_info, const AtomMatcher &atommatcher) const +{ + // if the atommatcher doesn't change order and the new molecule info + // has the same number of atoms in the same number of cutgroups, then + // there is nothing that we need to do + if (not atommatcher.changesOrder(this->info(), other_info)) + { + bool same_arrangement = true; + + // ensure that the number of atoms and number of cutgroups are the same + if (this->info().nAtoms() == other_info.nAtoms() and this->info().nCutGroups() == other_info.nCutGroups()) + { + for (int i = 0; i < other_info.nCutGroups(); ++i) + { + if (this->info().nAtoms(CGIdx(i)) != other_info.nAtoms(CGIdx(i))) + { + same_arrangement = false; + break; + } + } + } + + if (same_arrangement) + { + // there is no change in the atom order - this AtomPairs object is still valid, + // create a copy of the object and update the molinfo + CLJNBPairs ret(*this); + ret.molinfo = other_info; + return ret; + } + } + + QHash matched_atoms = atommatcher.match(this->info(), other_info); + + // check to see if the AtomIdx to AtomIdx map changes - if not, then + // we can return a copy of this object with the new molinfo + bool same_mapping = true; + + for (auto it = matched_atoms.begin(); it != matched_atoms.end(); ++it) + { + if (it.key() != it.value()) + { + same_mapping = false; + break; + } + } + + if (same_mapping) + { + CLJNBPairs ret(*this); + ret.molinfo = other_info; + return ret; + } + else + return this->_pvt_makeCompatibleWith(other_info, matched_atoms); +} + +/** Return a copy of this property that has been made to be compatible + with the molecule layout in 'molinfo' - this uses the atom map in + 'map' to match atoms from the current molecule to the atoms in the + molecule whose layout is in 'molinfo' + + This will only copy the values of pairs of atoms that are + successfully matched - all other pairs will have the default + value of this AtomPairs object. + + \throw SireError::incompatible_error +*/ +SireBase::PropertyPtr CLJNBPairs::_pvt_makeCompatibleWith( + const MoleculeInfoData &other_info, const QHash &map) const +{ + const auto &this_info = this->info(); + + // create a map from CGAtomIdx to CGAtomIdx for both states + QHash cg_map; + cg_map.reserve(map.count()); + QVector changed_atoms; + + for (auto it = map.begin(); it != map.end(); ++it) + { + const auto &atom0 = this_info.cgAtomIdx(it.key()); + const auto &atom1 = other_info.cgAtomIdx(it.value()); + + if (atom0 != atom1) + { + // this has changed + cg_map.insert(atom0, atom1); + changed_atoms.append(atom0); + } + } + + // create a copy of this object + CLJNBPairs ret(*this); + ret.molinfo = other_info; + + // now update all the pairs that have changed index + for (int i = 0; i < changed_atoms.count(); ++i) + { + for (int j = i; j < changed_atoms.count(); ++j) + { + const auto &atom0 = changed_atoms[i]; + const auto &atom1 = changed_atoms[j]; + + const auto &scl = this->get(atom0, atom1); + + ret.set(cg_map.value(atom0), cg_map.value(atom1), scl); + } + } + + return ret; +} diff --git a/corelib/src/libs/SireMM/cljnbpairs.h b/corelib/src/libs/SireMM/cljnbpairs.h index d683d1fdc..0a119c1b2 100644 --- a/corelib/src/libs/SireMM/cljnbpairs.h +++ b/corelib/src/libs/SireMM/cljnbpairs.h @@ -299,6 +299,12 @@ namespace SireMM const SireMol::AtomIdxMapping &mapping, const QString &ghost = QString(), const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + + protected: + SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, + const AtomMatcher &atommatcher) const; + SireBase::PropertyPtr _pvt_makeCompatibleWith(const MoleculeInfoData &molinfo, + const QHash &map) const; }; } // namespace SireMM diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 514d20376..2da6ce92d 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -324,7 +324,9 @@ PropertyPtr ConnectivityBase::_pvt_makeCompatibleWith(const MoleculeInfoData &mo // AtomIdx indicies are still valid Connectivity ret; ret.connected_atoms = connected_atoms; + ret.connected_atoms.resize(molinfo.nAtoms()); ret.connected_res = connected_res; + ret.connected_res.resize(molinfo.nResidues()); ret.bond_props = bond_props; ret.minfo = MoleculeInfo(molinfo); return ret; @@ -332,7 +334,31 @@ PropertyPtr ConnectivityBase::_pvt_makeCompatibleWith(const MoleculeInfoData &mo QHash matched_atoms = atommatcher.match(this->info(), molinfo); - return this->_pvt_makeCompatibleWith(molinfo, matched_atoms); + // see if there is any actual change - if not, then we can just return + bool same_mapping = true; + + for (auto it = matched_atoms.begin(); it != matched_atoms.end(); ++it) + { + if (it.key() != it.value()) + { + same_mapping = false; + break; + } + } + + if (same_mapping) + { + Connectivity ret; + ret.connected_atoms = connected_atoms; + ret.connected_atoms.resize(molinfo.nAtoms()); + ret.connected_res = connected_res; + ret.connected_res.resize(molinfo.nResidues()); + ret.bond_props = bond_props; + ret.minfo = MoleculeInfo(molinfo); + return ret; + } + else + return this->_pvt_makeCompatibleWith(molinfo, matched_atoms); } catch (const SireError::exception &e) { diff --git a/src/sire/_match.py b/src/sire/_match.py index a393b2040..de83f9003 100644 --- a/src/sire/_match.py +++ b/src/sire/_match.py @@ -46,7 +46,7 @@ def match_atoms( from .legacy.Mol import AtomMCSMatcher, AtomMatcher from .base import create_map - if mol0.num_molecules() > 1 or mol1.num_molecules() > 1: + if len(mol0.molecules()) != 1 or len(mol1.molecules()) != 1: raise ValueError("You cannot match multiple molecules at once") from .system import System From 0fbd040d48e5aaade3bdc85902dfa8cfecd13642 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 17:52:12 +0000 Subject: [PATCH 156/468] Optimised the CLJNBPairs makeCompatible function, so that it works and is not O(n2) --- corelib/src/libs/SireMM/cljnbpairs.cpp | 132 +++++++++++++++++-- corelib/src/libs/SireMol/structureeditor.cpp | 9 +- corelib/src/libs/SireSystem/merge.cpp | 37 ++++-- 3 files changed, 155 insertions(+), 23 deletions(-) diff --git a/corelib/src/libs/SireMM/cljnbpairs.cpp b/corelib/src/libs/SireMM/cljnbpairs.cpp index 62bdca023..848ca2316 100644 --- a/corelib/src/libs/SireMM/cljnbpairs.cpp +++ b/corelib/src/libs/SireMM/cljnbpairs.cpp @@ -1148,38 +1148,142 @@ SireBase::PropertyPtr CLJNBPairs::_pvt_makeCompatibleWith( const auto &this_info = this->info(); // create a map from CGAtomIdx to CGAtomIdx for both states + // Only insert values where they have changed - use a null + // value to indicate that the atom does not exist in the new map QHash cg_map; cg_map.reserve(map.count()); - QVector changed_atoms; + + QSet changed_cgroups, deleted_cgroups, mapped_cgroups; + const int ncg = this_info.nCutGroups(); + mapped_cgroups.reserve(ncg); + changed_cgroups.reserve(ncg); + deleted_cgroups.reserve(ncg); + + for (CGIdx i(0); i < ncg; ++i) + { + deleted_cgroups.insert(i); + } for (auto it = map.begin(); it != map.end(); ++it) { - const auto &atom0 = this_info.cgAtomIdx(it.key()); - const auto &atom1 = other_info.cgAtomIdx(it.value()); + CGAtomIdx atom0 = this_info.cgAtomIdx(it.key()); + CGAtomIdx atom1; + + if (not it.value().isNull()) + atom1 = other_info.cgAtomIdx(it.value()); + + if (not atom1.isNull()) + { + deleted_cgroups.remove(atom1.cutGroup()); + mapped_cgroups.insert(atom0.cutGroup()); + } if (atom0 != atom1) { // this has changed cg_map.insert(atom0, atom1); - changed_atoms.append(atom0); + changed_cgroups.insert(atom0.cutGroup()); + + if (not atom1.isNull()) + changed_cgroups.insert(atom1.cutGroup()); } } - // create a copy of this object - CLJNBPairs ret(*this); - ret.molinfo = other_info; + if (cg_map.isEmpty()) + { + // nothing has changed - we don't need to do any work + CLJNBPairs ret(*this); + ret.molinfo = other_info; + return ret; + } + + // there are some changes - start by creating a completely + // empty set of pairs, using a default value of 1,1 + CLJNBPairs ret(other_info, CLJScaleFactor(1, 1)); - // now update all the pairs that have changed index - for (int i = 0; i < changed_atoms.count(); ++i) + // now go through all of the atom pairs, in CGIdx order, and + // copy where we can from this object to the new object, and + // if not possible, then copy individual values + for (CGIdx i(0); i < ncg; ++i) { - for (int j = i; j < changed_atoms.count(); ++j) + bool changed_i = changed_cgroups.contains(i); + const int nats_i = this_info.nAtoms(i); + + if (not mapped_cgroups.contains(i)) + { + // this CutGroup has been deleted + continue; + } + + for (CGIdx j(i); j < ncg; ++j) { - const auto &atom0 = changed_atoms[i]; - const auto &atom1 = changed_atoms[j]; + if (not mapped_cgroups.contains(j)) + { + // this CutGroup has been deleted + continue; + } + + bool changed_j = changed_cgroups.contains(j); - const auto &scl = this->get(atom0, atom1); + const auto &cgpairs = this->get(i, j); - ret.set(cg_map.value(atom0), cg_map.value(atom1), scl); + if (not(changed_i or changed_j)) + { + // nothing has changed, so copy in the original values (only if the CutGroup + // pair hasn't been deleted) + if (not(deleted_cgroups.contains(i) or deleted_cgroups.contains(j))) + ret.cgpairs.set(i, j, cgpairs); + + continue; + } + + // there's change, so just copy the values for all atom pairs + const int nats_j = this_info.nAtoms(j); + + auto new_cgpairs = CGPairs(CLJScaleFactor(1, 1)); + bool changed_atom_pair = false; + + for (int atom_i = 0; atom_i < nats_i; ++atom_i) + { + auto new_cgidx_i = cg_map.value(CGAtomIdx(i, Index(atom_i)), CGAtomIdx(i, Index(atom_i))); + + if (new_cgidx_i.isNull()) + // this atom isn't mapped, so don't copy any values + continue; + + for (int atom_j = 0; atom_j < nats_j; ++atom_j) + { + auto new_cgidx_j = cg_map.value(CGAtomIdx(j, Index(atom_j)), CGAtomIdx(j, Index(atom_j))); + + if (new_cgidx_j.isNull()) + { + // this atom isn't mapped, so don't copy any values + continue; + } + + // get the current value at the current index + const auto &scl0 = cgpairs.get(atom_i, atom_j); + + // set the new value at the new index + if (new_cgidx_i.cutGroup() == i and new_cgidx_j.cutGroup() == j) + { + // this is in the current CutGroup pair, so can set directly + new_cgpairs.set(new_cgidx_i.atom().value(), new_cgidx_j.atom().value(), scl0); + changed_atom_pair = true; + } + else + { + // this is in a completely different CutGroup pair! + ret.set(new_cgidx_i, new_cgidx_j, scl0); + } + } + } + + // save the cgpairs + if (changed_atom_pair) + { + ret.cgpairs.set(i, j, new_cgpairs); + } } } diff --git a/corelib/src/libs/SireMol/structureeditor.cpp b/corelib/src/libs/SireMol/structureeditor.cpp index 5c611afca..df276c401 100644 --- a/corelib/src/libs/SireMol/structureeditor.cpp +++ b/corelib/src/libs/SireMol/structureeditor.cpp @@ -75,6 +75,7 @@ #include "segproperty.hpp" #include "SireBase/properties.h" +#include "SireBase/console.h" #include "tostring.h" @@ -5045,8 +5046,14 @@ Properties StructureEditor::properties() const { updated_property = updated_property->asA().makeCompatibleWith(this->info(), mapping); } - catch (...) + catch (const SireError::exception &e) { + SireBase::Console::warning(QObject::tr("Could not convert the old property at key %1 with type %2 to match " + "the new, edited molecule. This property has been deleted.\nError was %3: %4") + .arg(key) + .arg(updated_property->what()) + .arg(e.what()) + .arg(e.error())); updated_property = NullProperty(); } } diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 8bca1bb37..2bc2dceb9 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -207,6 +207,27 @@ namespace SireSystem CODELOC); } + // remove the parameters properties + if (editmol.hasProperty(map["parameters"])) + { + editmol.removeProperty(map["parameters"]); + } + + if (editmol.hasProperty(map0["parameters"])) + { + editmol.removeProperty(map0["parameters"]); + } + + if (editmol.hasProperty(map["amberparams"])) + { + editmol.removeProperty(map["amberparams"]); + } + + if (editmol.hasProperty(map0["amberparams"])) + { + editmol.removeProperty(map0["amberparams"]); + } + // find the largest AtomNum in mol0 AtomNum largest_atomnum; @@ -482,8 +503,6 @@ namespace SireSystem CODELOC); editmol.removeProperty(map0[prop]); - editmol.setProperty(map[prop + "0"].source(), merged[0]); - editmol.setProperty(map[prop + "1"].source(), merged[1]); if (prop == "connectivity") { @@ -496,6 +515,14 @@ namespace SireSystem editmol.setProperty(map["connectivity"].source(), merged_connectivity.commit()); } + else if (prop == "intrascale") + { + // we need to copy the intrascale parameters involving ghost atoms + // from the state where they are not ghosts + } + + editmol.setProperty(map[prop + "0"].source(), merged[0]); + editmol.setProperty(map[prop + "1"].source(), merged[1]); } else { @@ -517,12 +544,6 @@ namespace SireSystem editmol.setProperty(map["forcefield0"].source(), ffield0); editmol.setProperty(map["forcefield1"].source(), ffield0); - // remove any property called "parameters" - if (editmol.hasProperty(map["parameters"].source())) - { - editmol.removeProperty(map["parameters"].source()); - } - editmol.setProperty(map["connectivity"].source(), editmol.property("connectivity0")); // set the flag that this is a perturbable molecule From 79ac2b69cd209d400af0a784ff26bacd9adb34b7 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 17:53:26 +0000 Subject: [PATCH 157/468] Bringing in the fix for Mol2 atom types --- corelib/src/libs/SireIO/mol2.cpp | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/corelib/src/libs/SireIO/mol2.cpp b/corelib/src/libs/SireIO/mol2.cpp index db3b0531c..d608b4145 100644 --- a/corelib/src/libs/SireIO/mol2.cpp +++ b/corelib/src/libs/SireIO/mol2.cpp @@ -2624,7 +2624,15 @@ MolEditor Mol2::getMolecule(int imol, const PropertyMap &map) const status_bits.set(cgatomidx, atom.getStatusBits()); // Infer the element from the SYBYL atom type. - elements.set(cgatomidx, Element::biologicalElement(atom.getType())); + if (atom.getType() != "Du") + { + elements.set(cgatomidx, Element::biologicalElement(atom.getType())); + } + else + { + // try to infer the element from the atom name + elements.set(cgatomidx, Element::biologicalElement(atom.getName())); + } } // Instantiate the residue property objects that we need. From 05969bbc8dd651c64949457d5689456ee830c047 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 19:03:51 +0000 Subject: [PATCH 158/468] Copying ghost NBSCL parameters from the alternate end state. Added some unit tests for extracting and merging --- corelib/src/libs/SireMol/atomidxmapping.cpp | 64 ++++++++++++ corelib/src/libs/SireMol/atomidxmapping.h | 6 ++ corelib/src/libs/SireSystem/merge.cpp | 37 +++++++ tests/conftest.py | 5 + tests/mol/test_extract.py | 34 +++++++ tests/morph/test_merge.py | 106 ++++++++++++++++++++ 6 files changed, 252 insertions(+) create mode 100644 tests/mol/test_extract.py create mode 100644 tests/morph/test_merge.py diff --git a/corelib/src/libs/SireMol/atomidxmapping.cpp b/corelib/src/libs/SireMol/atomidxmapping.cpp index eab4cb321..f8b1cd9f7 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.cpp +++ b/corelib/src/libs/SireMol/atomidxmapping.cpp @@ -801,6 +801,70 @@ QList AtomIdxMapping::mappedIn1() const return mapped1_list; } +/** Equivalent of unmappedIn0, but return as a CGAtomIdx */ +QList AtomIdxMapping::unmappedCGAtomIdxIn0() const +{ + QList result; + + for (const auto &entry : entries) + { + if (entry.isUnmappedIn0()) + { + result.append(entry.cgAtomIdx0()); + } + } + + return result; +} + +/** Equivalent of unmappedIn1, but return as a CGAtomIdx */ +QList AtomIdxMapping::unmappedCGAtomIdxIn1() const +{ + QList result; + + for (const auto &entry : entries) + { + if (entry.isUnmappedIn1()) + { + result.append(entry.cgAtomIdx0()); + } + } + + return result; +} + +/** Equivalent of mappedIn0, but return as a CGAtomIdx */ +QList AtomIdxMapping::mappedCGAtomIdxIn0() const +{ + QList result; + + for (const auto &entry : entries) + { + if (entry.isMappedIn0()) + { + result.append(entry.cgAtomIdx0()); + } + } + + return result; +} + +/** Equivalent of mappedIn1, but return as a CGAtomIdx */ +QList AtomIdxMapping::mappedCGAtomIdxIn1() const +{ + QList result; + + for (const auto &entry : entries) + { + if (entry.isMappedIn1()) + { + result.append(entry.cgAtomIdx0()); + } + } + + return result; +} + /** Return the mapping for the atoms that exist in both the reference * and perturbed states, from the index of the atom in the merged * molecule to the index of the atom in the perturbed molecule. diff --git a/corelib/src/libs/SireMol/atomidxmapping.h b/corelib/src/libs/SireMol/atomidxmapping.h index 7acebb4d1..393ad7599 100644 --- a/corelib/src/libs/SireMol/atomidxmapping.h +++ b/corelib/src/libs/SireMol/atomidxmapping.h @@ -190,6 +190,12 @@ namespace SireMol QList mappedIn0() const; QList mappedIn1() const; + QList unmappedCGAtomIdxIn0() const; + QList unmappedCGAtomIdxIn1() const; + + QList mappedCGAtomIdxIn0() const; + QList mappedCGAtomIdxIn1() const; + bool isUnmappedIn0(const AtomIdx &atom) const; bool isUnmappedIn1(const AtomIdx &atom) const; diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 2bc2dceb9..a18657ab1 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -35,6 +35,7 @@ #include "SireMol/bondid.h" #include "SireMM/mmdetail.h" +#include "SireMM/cljnbpairs.h" using namespace SireMol; using namespace SireBase; @@ -519,6 +520,42 @@ namespace SireSystem { // we need to copy the intrascale parameters involving ghost atoms // from the state where they are not ghosts + const auto unmapped_in0 = entries.unmappedCGAtomIdxIn0(); + const auto unmapped_in1 = entries.unmappedCGAtomIdxIn1(); + + if (not(unmapped_in0.isEmpty() and unmapped_in1.isEmpty())) + { + auto scl0 = merged[0].asA(); + auto scl1 = merged[1].asA(); + + merged.clear(); + + const int nats = editmol.nAtoms(); + + for (AtomIdx idx(0); idx < nats; ++idx) + { + const auto i = editmol.info().cgAtomIdx(idx); + + // set all of the CLJ scale factors for atoms unmapped + // in the reference state to equal the scale factor + // for this pair in the perturbed state + for (const auto &j : unmapped_in0) + { + scl0.set(i, j, scl1.get(i, j)); + } + + // set all of the CLJ scale factors for atoms unmapped + // in the perturbed state to equal the scale factor + // for this pair in the reference state + for (const auto &j : unmapped_in1) + { + scl0.set(j, i, scl1.get(j, i)); + } + } + + merged.append(scl0); + merged.append(scl1); + } } editmol.setProperty(map[prop + "0"].source(), merged[0]); diff --git a/tests/conftest.py b/tests/conftest.py index 6d114a972..61ed9db30 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -60,6 +60,11 @@ def ose_mols(): return sr.load_test_files("ose.top", "ose.crd") +@pytest.fixture(scope="session") +def zan_mols(): + return sr.load_test_files("zan.top", "zan.rst") + + @pytest.fixture(scope="session") def h7n9_mols(): return sr.load_test_files("h7n9.pdb", "h7n9.dcd") diff --git a/tests/mol/test_extract.py b/tests/mol/test_extract.py new file mode 100644 index 000000000..ea2d2d1fe --- /dev/null +++ b/tests/mol/test_extract.py @@ -0,0 +1,34 @@ +import sire as sr + +import pytest + + +def test_extract(neura_mols): + protein = neura_mols["protein"] + + # Extract the middle 10 residues + middle_residues = protein.residues()[10:20] + + extracted_middle_residues = middle_residues.extract().molecule() + + assert middle_residues.num_atoms() == extracted_middle_residues.num_atoms() + + assert middle_residues.num_residues() == extracted_middle_residues.num_residues() + + # Extract the third of these residues + res_0 = middle_residues[2].extract().molecule() + res_1 = extracted_middle_residues.residues()[2].extract().molecule() + + assert res_0.num_atoms() == middle_residues[2].num_atoms() + assert res_0.num_residues() == 1 + + assert res_0.num_atoms() == res_1.num_atoms() + assert res_0.num_residues() == res_1.num_residues() + + # this validates that most of the properties have been extracted + # properly + assert res_0.energy().value() == pytest.approx(res_1.energy().value()) + assert res_0.energy().value() == pytest.approx(middle_residues[2].energy().value()) + assert extracted_middle_residues.energy().value() == pytest.approx( + middle_residues.energy().value() + ) diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py new file mode 100644 index 000000000..3a2087e8b --- /dev/null +++ b/tests/morph/test_merge.py @@ -0,0 +1,106 @@ +import sire as sr + +import pytest + +try: + from kartograf import KartografAtomMapper +except ImportError: + KartografAtomMapper = None + + +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats(), + reason="openmm support is not available", +) +def test_extract_remerge(merged_zan_ose, openmm_platform): + merged = merged_zan_ose[0].perturbation().link_to_reference() + + extracted_ose = merged.perturbation().extract_reference() + extracted_zan = merged.perturbation().extract_perturbed() + + remerged = sr.morph.merge( + extracted_ose, extracted_zan, match=sr.legacy.Mol.AtomNumMatcher() + ) + + nrg_merged_0 = merged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_merged_1 = merged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + + nrg_remerged_0 = remerged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_remerged_1 = remerged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + + assert nrg_merged_0.value() == pytest.approx(nrg_remerged_0.value()) + assert nrg_merged_1.value() == pytest.approx(nrg_remerged_1.value()) + + +@pytest.mark.slow +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats() or KartografAtomMapper is None, + reason="openmm support is not available", +) +def test_merge(ose_mols, zan_mols, openmm_platform): + ose = ose_mols[0] + zan = zan_mols[0] + + merged = sr.morph.merge( + ose, zan, match=KartografAtomMapper(atom_map_hydrogens=True) + ) + + ose_nrg = ose.dynamics(platform=openmm_platform).current_potential_energy() + zan_nrg = zan.dynamics(platform=openmm_platform).current_potential_energy() + + extracted_ose = merged.perturbation().extract_reference() + extracted_zan = merged.perturbation().extract_perturbed() + + extracted_ose_nrg = extracted_ose.dynamics( + platform=openmm_platform + ).current_potential_energy() + + extracted_zan_nrg = extracted_zan.dynamics( + platform=openmm_platform + ).current_potential_energy() + + assert extracted_ose_nrg.value() == pytest.approx(ose_nrg.value()) + assert extracted_zan_nrg.value() == pytest.approx(zan_nrg.value()) + + merged = merged.perturbation().link_to_reference() + + nrg_merged_0 = merged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_merged_1 = merged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + + print(ose_nrg, zan_nrg) + print(extracted_ose_nrg, extracted_zan_nrg) + print(nrg_merged_0, nrg_merged_1) + + assert ose_nrg.value() == pytest.approx(nrg_merged_0.value()) + assert zan_nrg.value() == pytest.approx(nrg_merged_1.value()) + + +@pytest.mark.veryslow +def test_merge_protein(neura_mols): + protein = neura_mols["protein"] + + ala = protein.residues("ALA")[1] + lys = protein.residues("LYS")[1] + + merged = sr.morph.merge(ala, lys) + + merged_ala = merged.perturbation().extract_reference()[ala.number()] + merged_lys = merged.perturbation().extract_perturbed()[lys.number()] + + assert ala.energy().value() == pytest.approx(merged_ala.energy().value()) + assert lys.energy().value() == pytest.approx(merged_lys.energy().value()) From ae47981269d9c74e6460305b02bc9b4e48703b1a Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 19:11:58 +0000 Subject: [PATCH 159/468] Added more to the merge test This is failing as the energy of the merged molecule isn't right, despite this being right for a re-merge and also for the extracted end states... Debugging needed --- tests/morph/test_merge.py | 56 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index 3a2087e8b..be4ed53a7 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -86,6 +86,62 @@ def test_merge(ose_mols, zan_mols, openmm_platform): print(extracted_ose_nrg, extracted_zan_nrg) print(nrg_merged_0, nrg_merged_1) + merged = merged.perturbation().link_to_reference() + + nrg_merged_0 = merged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_merged_1 = merged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + + print(nrg_merged_0, nrg_merged_1) + + merged = sr.morph.merge( + zan, ose, match=KartografAtomMapper(atom_map_hydrogens=True) + ) + + extracted_zan = merged.perturbation().extract_reference() + extracted_ose = merged.perturbation().extract_perturbed() + + extracted_ose_nrg = extracted_ose.dynamics( + platform=openmm_platform + ).current_potential_energy() + + extracted_zan_nrg = extracted_zan.dynamics( + platform=openmm_platform + ).current_potential_energy() + + assert extracted_ose_nrg.value() == pytest.approx(ose_nrg.value()) + assert extracted_zan_nrg.value() == pytest.approx(zan_nrg.value()) + + merged = merged.perturbation().link_to_reference() + + nrg_merged_0 = merged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_merged_1 = merged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + + print(zan_nrg, ose_nrg) + print(extracted_zan_nrg, extracted_ose_nrg) + print(nrg_merged_0, nrg_merged_1) + + merged = merged.perturbation().link_to_reference() + + nrg_merged_0 = merged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_merged_1 = merged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + + print(nrg_merged_0, nrg_merged_1) + assert ose_nrg.value() == pytest.approx(nrg_merged_0.value()) assert zan_nrg.value() == pytest.approx(nrg_merged_1.value()) From f724cf89e9941e94c54dee00d7eeedf4fe2185d1 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 20:10:59 +0000 Subject: [PATCH 160/468] Optimised the perturbation object, fixed a small bug in the merge code, added kartograf to the host/BSS requirements, and added more unit tests for merge. --- corelib/src/libs/SireSystem/merge.cpp | 2 - requirements_bss.txt | 1 + requirements_host.txt | 2 +- src/sire/morph/_merge.py | 4 +- src/sire/morph/_perturbation.py | 53 ++++++++------ tests/morph/test_merge.py | 101 ++++++++++++-------------- 6 files changed, 80 insertions(+), 83 deletions(-) diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index a18657ab1..5031f81d8 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -581,8 +581,6 @@ namespace SireSystem editmol.setProperty(map["forcefield0"].source(), ffield0); editmol.setProperty(map["forcefield1"].source(), ffield0); - editmol.setProperty(map["connectivity"].source(), editmol.property("connectivity0")); - // set the flag that this is a perturbable molecule editmol.setProperty(map["is_perturbable"].source(), BooleanProperty(true)); diff --git a/requirements_bss.txt b/requirements_bss.txt index aa5d60ec7..72507c7bb 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -30,6 +30,7 @@ pygtail pyyaml rdkit >=2023.0.0 gemmi >=0.6.4 +kartograf >= 1.0.0 # The below are packages that aren't available on all # platforms/OSs and so need to be conditionally included diff --git a/requirements_host.txt b/requirements_host.txt index 13cd912df..8925b6a31 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -14,4 +14,4 @@ tbb tbb-devel gemmi >=0.6.4 rdkit >=2023.0.0 - +kartograf >= 1.0.0 diff --git a/src/sire/morph/_merge.py b/src/sire/morph/_merge.py index ef0119377..b31383b29 100644 --- a/src/sire/morph/_merge.py +++ b/src/sire/morph/_merge.py @@ -39,9 +39,7 @@ def _merge(mapping: _AtomMapping, as_new_molecule: bool = True, map=None): mol = _merge_mols(aligned_mapping, as_new_molecule=as_new_molecule, map=map) - mol = mol.perturbation().link_to_reference() - - return mol + return mol.perturbation().link_to_reference() def merge(mol0, mol1, match=None, prematch=None, map=None, map0=None, map1=None): diff --git a/src/sire/morph/_perturbation.py b/src/sire/morph/_perturbation.py index 7b7b06ca2..99d05c586 100644 --- a/src/sire/morph/_perturbation.py +++ b/src/sire/morph/_perturbation.py @@ -134,17 +134,7 @@ def __init__(self, mol, map=None): # construct the perturbation objects that can move the # coordinates between the end states - from ..legacy.Mol import ( - BondPerturbation, - AnglePerturbation, - GeometryPerturbations, - ) - - from ..legacy.MM import AmberBond, AmberAngle - from ..cas import Symbol - from ..units import angstrom, radian - - self._perturbations = GeometryPerturbations() + self._perturbations = None props = [ "LJ", @@ -171,6 +161,33 @@ def __init__(self, mol, map=None): self._map0 = map.add_suffix("0", props) self._map1 = map.add_suffix("1", props) + self._mol = mol.clone() + + def __str__(self): + return f"Perturbation( {self._mol} )" + + def __repr__(self): + return self.__str__() + + def _get_perturbations(self): + """ + Find all of the perturbations in the molecule + """ + from ..legacy.MM import AmberBond, AmberAngle + from ..cas import Symbol + from ..units import angstrom, radian + from ..legacy.System import ( + GeometryPerturbations, + BondPerturbation, + AnglePerturbation, + ) + + if self._perturbations is not None: + return self._perturbations + + mol = self._mol + self._perturbations = GeometryPerturbations() + # identify all of the ghost atoms from_ghosts = [] to_ghosts = [] @@ -236,14 +253,6 @@ def __init__(self, mol, map=None): ) ) - self._mol = mol.clone() - - def __str__(self): - return f"Perturbation( {self._mol} )" - - def __repr__(self): - return self.__str__() - def extract_reference( self, properties: list[str] = None, @@ -473,7 +482,7 @@ def set_lambda(self, lam_val: float): ) vals = Values({Symbol("lambda"): lam_val}) - self._mol.update(self._perturbations.perturb(mol, vals)) + self._mol.update(self._get_perturbations().perturb(mol, vals)) return self def commit(self): @@ -520,12 +529,12 @@ def view(self, *args, state="perturbed", **kwargs): for lam in range(0, 11): vals = Values({Symbol("lambda"): 0.1 * lam}) - mol = self._perturbations.perturb(mol, vals) + mol = self._get_perturbations().perturb(mol, vals) mol.save_frame() for lam in range(9, 0, -1): vals = Values({Symbol("lambda"): 0.1 * lam}) - mol = self._perturbations.perturb(mol, vals) + mol = self._get_perturbations().perturb(mol, vals) mol.save_frame() return mol["not element Xx"].view(*args, **kwargs) diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index be4ed53a7..91f6a61ea 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -10,7 +10,7 @@ @pytest.mark.skipif( "openmm" not in sr.convert.supported_formats(), - reason="openmm support is not available", + reason="openmm or kartograf support is not available", ) def test_extract_remerge(merged_zan_ose, openmm_platform): merged = merged_zan_ose[0].perturbation().link_to_reference() @@ -45,7 +45,7 @@ def test_extract_remerge(merged_zan_ose, openmm_platform): @pytest.mark.slow @pytest.mark.skipif( "openmm" not in sr.convert.supported_formats() or KartografAtomMapper is None, - reason="openmm support is not available", + reason="openmm or kartograf support is not available", ) def test_merge(ose_mols, zan_mols, openmm_platform): ose = ose_mols[0] @@ -72,32 +72,6 @@ def test_merge(ose_mols, zan_mols, openmm_platform): assert extracted_ose_nrg.value() == pytest.approx(ose_nrg.value()) assert extracted_zan_nrg.value() == pytest.approx(zan_nrg.value()) - merged = merged.perturbation().link_to_reference() - - nrg_merged_0 = merged.dynamics( - lambda_value=0, platform=openmm_platform - ).current_potential_energy() - - nrg_merged_1 = merged.dynamics( - lambda_value=1, platform=openmm_platform - ).current_potential_energy() - - print(ose_nrg, zan_nrg) - print(extracted_ose_nrg, extracted_zan_nrg) - print(nrg_merged_0, nrg_merged_1) - - merged = merged.perturbation().link_to_reference() - - nrg_merged_0 = merged.dynamics( - lambda_value=0, platform=openmm_platform - ).current_potential_energy() - - nrg_merged_1 = merged.dynamics( - lambda_value=1, platform=openmm_platform - ).current_potential_energy() - - print(nrg_merged_0, nrg_merged_1) - merged = sr.morph.merge( zan, ose, match=KartografAtomMapper(atom_map_hydrogens=True) ) @@ -116,21 +90,41 @@ def test_merge(ose_mols, zan_mols, openmm_platform): assert extracted_ose_nrg.value() == pytest.approx(ose_nrg.value()) assert extracted_zan_nrg.value() == pytest.approx(zan_nrg.value()) - merged = merged.perturbation().link_to_reference() + # we don't test merged molecule energies are these + # energies are not equal because there are additional bonds, + # angle and dihedrals to ghost atoms in the merged molecule - nrg_merged_0 = merged.dynamics( - lambda_value=0, platform=openmm_platform - ).current_potential_energy() - nrg_merged_1 = merged.dynamics( - lambda_value=1, platform=openmm_platform - ).current_potential_energy() +@pytest.mark.veryslow +def test_merge_protein(neura_mols): + protein = neura_mols["protein"] + + ala = protein.residues("ALA")[1] + lys = protein.residues("LYS")[1] + + merged = sr.morph.merge(ala, lys) + + merged_ala = merged.perturbation().extract_reference()[ala.number()] + merged_lys = merged.perturbation().extract_perturbed()[lys.number()] + + assert ala.energy().value() == pytest.approx(merged_ala.energy().value()) + assert lys.energy().value() == pytest.approx(merged_lys.energy().value()) - print(zan_nrg, ose_nrg) - print(extracted_zan_nrg, extracted_ose_nrg) - print(nrg_merged_0, nrg_merged_1) - merged = merged.perturbation().link_to_reference() +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats() or KartografAtomMapper is None, + reason="openmm or kartograf support is not available", +) +def test_merge_neopentane_methane(neopentane_methane, openmm_platform): + neopentane = neopentane_methane[0].perturbation().extract_reference() + methane = neopentane_methane[0].perturbation().extract_perturbed() + + nrg_neo = neopentane.dynamics(platform=openmm_platform).current_potential_energy() + nrg_met = methane.dynamics(platform=openmm_platform).current_potential_energy() + + merged = sr.morph.merge( + neopentane, methane, match=KartografAtomMapper(atom_map_hydrogens=True) + ) nrg_merged_0 = merged.dynamics( lambda_value=0, platform=openmm_platform @@ -140,23 +134,20 @@ def test_merge(ose_mols, zan_mols, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() - print(nrg_merged_0, nrg_merged_1) - - assert ose_nrg.value() == pytest.approx(nrg_merged_0.value()) - assert zan_nrg.value() == pytest.approx(nrg_merged_1.value()) + extracted_neo = merged.perturbation().extract_reference() + extracted_met = merged.perturbation().extract_perturbed() + nrg_extracted_neo = extracted_neo.dynamics( + platform=openmm_platform + ).current_potential_energy() -@pytest.mark.veryslow -def test_merge_protein(neura_mols): - protein = neura_mols["protein"] - - ala = protein.residues("ALA")[1] - lys = protein.residues("LYS")[1] - - merged = sr.morph.merge(ala, lys) + nrg_extracted_met = extracted_met.dynamics( + platform=openmm_platform + ).current_potential_energy() - merged_ala = merged.perturbation().extract_reference()[ala.number()] - merged_lys = merged.perturbation().extract_perturbed()[lys.number()] + assert nrg_neo.value() == pytest.approx(nrg_extracted_neo.value(), abs=1e-3) + assert nrg_met.value() == pytest.approx(nrg_extracted_met.value(), abs=1e-3) - assert ala.energy().value() == pytest.approx(merged_ala.energy().value()) - assert lys.energy().value() == pytest.approx(merged_lys.energy().value()) + # These energies aren't correct - extra ghost atom internals? + assert nrg_neo.value() == pytest.approx(nrg_merged_0.value(), abs=1e-3) + # assert nrg_met.value() == pytest.approx(nrg_merged_1.value(), abs=1e-3) From c639827309a8eb1b828e0358016d9f3efd5da54c Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 22:22:59 +0000 Subject: [PATCH 161/468] Remerged does give the same energy as original merge --- tests/morph/test_merge.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index 91f6a61ea..65c0faa42 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -119,6 +119,8 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform): neopentane = neopentane_methane[0].perturbation().extract_reference() methane = neopentane_methane[0].perturbation().extract_perturbed() + orig_merged = sr.morph.link_to_reference(neopentane_methane[0]) + nrg_neo = neopentane.dynamics(platform=openmm_platform).current_potential_energy() nrg_met = methane.dynamics(platform=openmm_platform).current_potential_energy() @@ -145,9 +147,20 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform): platform=openmm_platform ).current_potential_energy() + nrg_orig_merged_0 = orig_merged.dynamics( + lambda_value=0, platform=openmm_platform + ).current_potential_energy() + + nrg_orig_merged_1 = orig_merged.dynamics( + lambda_value=1, platform=openmm_platform + ).current_potential_energy() + assert nrg_neo.value() == pytest.approx(nrg_extracted_neo.value(), abs=1e-3) assert nrg_met.value() == pytest.approx(nrg_extracted_met.value(), abs=1e-3) + assert nrg_merged_0.value() == pytest.approx(nrg_orig_merged_0.value(), abs=1e-3) + assert nrg_merged_1.value() == pytest.approx(nrg_orig_merged_1.value(), abs=1e-3) + # These energies aren't correct - extra ghost atom internals? assert nrg_neo.value() == pytest.approx(nrg_merged_0.value(), abs=1e-3) # assert nrg_met.value() == pytest.approx(nrg_merged_1.value(), abs=1e-3) From 08141be0c7d75095fd41f3e40616413f2706f711 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 10 Mar 2024 22:26:11 +0000 Subject: [PATCH 162/468] Added in lambda=0.5 check - it is different - worth checking why --- tests/morph/test_merge.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index 65c0faa42..f42f6d227 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -30,6 +30,10 @@ def test_extract_remerge(merged_zan_ose, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() + nrg_merged_05 = merged.dynamics( + lambda_value=0.5, platform=openmm_platform + ).current_potential_energy() + nrg_remerged_0 = remerged.dynamics( lambda_value=0, platform=openmm_platform ).current_potential_energy() @@ -38,9 +42,16 @@ def test_extract_remerge(merged_zan_ose, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() + nrg_remerged_05 = remerged.dynamics( + lambda_value=0.5, platform=openmm_platform + ).current_potential_energy() + assert nrg_merged_0.value() == pytest.approx(nrg_remerged_0.value()) assert nrg_merged_1.value() == pytest.approx(nrg_remerged_1.value()) + # this is different - worth checking why! + # assert nrg_merged_05.value() == pytest.approx(nrg_remerged_05.value()) + @pytest.mark.slow @pytest.mark.skipif( @@ -136,6 +147,10 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() + nrg_merged_05 = merged.dynamics( + lambda_value=0.5, platform=openmm_platform + ).current_potential_energy() + extracted_neo = merged.perturbation().extract_reference() extracted_met = merged.perturbation().extract_perturbed() @@ -155,12 +170,19 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() + nrg_orig_merged_05 = orig_merged.dynamics( + lambda_value=0.5, platform=openmm_platform + ).current_potential_energy() + assert nrg_neo.value() == pytest.approx(nrg_extracted_neo.value(), abs=1e-3) assert nrg_met.value() == pytest.approx(nrg_extracted_met.value(), abs=1e-3) assert nrg_merged_0.value() == pytest.approx(nrg_orig_merged_0.value(), abs=1e-3) assert nrg_merged_1.value() == pytest.approx(nrg_orig_merged_1.value(), abs=1e-3) + # this is different - worth checking why! + # assert nrg_merged_05.value() == pytest.approx(nrg_orig_merged_05.value(), abs=1e-3) + # These energies aren't correct - extra ghost atom internals? assert nrg_neo.value() == pytest.approx(nrg_merged_0.value(), abs=1e-3) # assert nrg_met.value() == pytest.approx(nrg_merged_1.value(), abs=1e-3) From 86b3ca04f86616efa4745f6836049cc403d7d921 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 17 Mar 2024 12:02:20 +0000 Subject: [PATCH 163/468] Fixed the crash (I think) caused by not removing atoms from the connectivity --- corelib/src/libs/SireMol/connectivity.cpp | 62 +++++++++++++++++++++++ tests/morph/test_merge.py | 22 ++++++++ 2 files changed, 84 insertions(+) diff --git a/corelib/src/libs/SireMol/connectivity.cpp b/corelib/src/libs/SireMol/connectivity.cpp index 2da6ce92d..e884e9caf 100644 --- a/corelib/src/libs/SireMol/connectivity.cpp +++ b/corelib/src/libs/SireMol/connectivity.cpp @@ -355,6 +355,68 @@ PropertyPtr ConnectivityBase::_pvt_makeCompatibleWith(const MoleculeInfoData &mo ret.connected_res.resize(molinfo.nResidues()); ret.bond_props = bond_props; ret.minfo = MoleculeInfo(molinfo); + + if (ret.minfo.nAtoms() < this->minfo.nAtoms()) + { + const int nats = ret.minfo.nAtoms(); + const int nres = ret.minfo.nResidues(); + + // atoms have been removed, so need to remove any references + // to atoms that no longer exist + for (int i = 0; i < ret.connected_atoms.count(); ++i) + { + QSet &connected = ret.connected_atoms[i]; + + for (auto it = connected.begin(); it != connected.end();) + { + if (it->value() >= nats) + { + it = connected.erase(it); + } + else + { + ++it; + } + } + } + + for (int i = 0; i < ret.connected_res.count(); ++i) + { + QSet &connected = ret.connected_res[i]; + + for (auto it = connected.begin(); it != connected.end();) + { + if (it->value() >= nres) + { + it = connected.erase(it); + } + else + { + ++it; + } + } + } + + // remove any bond properties that refer to atoms that no longer exist + for (auto it = ret.bond_props.begin(); it != ret.bond_props.end();) + { + if (it.key().atom0 >= nats or it.key().atom1 >= nats) + { + it = ret.bond_props.erase(it); + } + else + { + ++it; + } + } + + // clear the angle, dihedral and improper properties as + // these are too complex to make compatible + ret.ang_props.clear(); + ret.dih_props.clear(); + ret.imp_props.clear(); + } + return ret; } else diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index f42f6d227..42b0f0ea3 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -118,6 +118,28 @@ def test_merge_protein(neura_mols): merged_ala = merged.perturbation().extract_reference()[ala.number()] merged_lys = merged.perturbation().extract_perturbed()[lys.number()] + scl_ala = ala.property("intrascale") + scl_merged_ala = merged_ala.property("intrascale") + + for i in range(ala.num_atoms()): + for j in range(ala.num_atoms()): + atom0 = sr.atomid(idx=i) + atom1 = sr.atomid(idx=j) + s_ala = scl_ala.get(atom0, atom1) + s_merged_ala = scl_merged_ala.get(atom0, atom1) + assert s_ala == s_merged_ala + + scl_lys = lys.property("intrascale") + scl_merged_lys = merged_lys.property("intrascale") + + for i in range(lys.num_atoms()): + for j in range(lys.num_atoms()): + atom0 = sr.atomid(idx=i) + atom1 = sr.atomid(idx=j) + s_lys = scl_lys.get(atom0, atom1) + s_merged_lys = scl_merged_lys.get(atom0, atom1) + assert s_lys == s_merged_lys + assert ala.energy().value() == pytest.approx(merged_ala.energy().value()) assert lys.energy().value() == pytest.approx(merged_lys.energy().value()) From dc78ac237ca51cddf828838b8b3415e906c3765a Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 17 Mar 2024 12:07:25 +0000 Subject: [PATCH 164/468] Updated requirements to not pull in kartograf on Windows --- requirements_bss.txt | 5 ++++- requirements_host.txt | 5 ++++- requirements_test.txt | 4 ++++ 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index 72507c7bb..b99ad4384 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -14,6 +14,10 @@ openmmtools >= 0.21.5 ambertools >= 22 ; sys_platform != "win32" gromacs ; sys_platform != "win32" +# kartograf on Windows pulls in an openfe that has an old / incompatble +# ambertools +kartograf >= 1.0.0 ; sys_platform != "win32" + # The following are actual BioSimSpace run-time requirements. Please update # this list as new requirements are added. configargparse @@ -30,7 +34,6 @@ pygtail pyyaml rdkit >=2023.0.0 gemmi >=0.6.4 -kartograf >= 1.0.0 # The below are packages that aren't available on all # platforms/OSs and so need to be conditionally included diff --git a/requirements_host.txt b/requirements_host.txt index 8925b6a31..533413597 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -14,4 +14,7 @@ tbb tbb-devel gemmi >=0.6.4 rdkit >=2023.0.0 -kartograf >= 1.0.0 + +# kartograf on Windows pulls in an openfe that has an old / incompatble +# ambertools +kartograf >= 1.0.0 ; sys_platform != "win32" diff --git a/requirements_test.txt b/requirements_test.txt index dbd4a6cdd..b8800e418 100644 --- a/requirements_test.txt +++ b/requirements_test.txt @@ -3,3 +3,7 @@ rdkit >=2023.0.0 gemmi >=0.6.4 + +# kartograf on Windows pulls in an openfe that has an old / incompatble +# ambertools +kartograf >= 1.0.0 ; sys_platform != "win32" From 50fab9af9ee5fd9f2725b9054f26931438c56521 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 17 Mar 2024 18:15:56 +0000 Subject: [PATCH 165/468] Added decorators to skip tests for functionality not supported on windows [ci skip] --- tests/morph/test_match.py | 6 ++++++ tests/morph/test_merge.py | 18 ++++++------------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/morph/test_match.py b/tests/morph/test_match.py index 17921d644..b1d6a872d 100644 --- a/tests/morph/test_match.py +++ b/tests/morph/test_match.py @@ -1,8 +1,14 @@ import sire as sr import pytest +import sys +# skip if we run on windows +@pytest.mark.skipif( + sys.platform == "win32", + reason="Does not run on Windows because there is no match support", +) def test_match(kigaki_mols): mols = kigaki_mols diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index 42b0f0ea3..8d5311569 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -1,6 +1,7 @@ import sire as sr import pytest +import sys try: from kartograf import KartografAtomMapper @@ -10,7 +11,7 @@ @pytest.mark.skipif( "openmm" not in sr.convert.supported_formats(), - reason="openmm or kartograf support is not available", + reason="openmm support is not available", ) def test_extract_remerge(merged_zan_ose, openmm_platform): merged = merged_zan_ose[0].perturbation().link_to_reference() @@ -30,10 +31,6 @@ def test_extract_remerge(merged_zan_ose, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() - nrg_merged_05 = merged.dynamics( - lambda_value=0.5, platform=openmm_platform - ).current_potential_energy() - nrg_remerged_0 = remerged.dynamics( lambda_value=0, platform=openmm_platform ).current_potential_energy() @@ -42,16 +39,9 @@ def test_extract_remerge(merged_zan_ose, openmm_platform): lambda_value=1, platform=openmm_platform ).current_potential_energy() - nrg_remerged_05 = remerged.dynamics( - lambda_value=0.5, platform=openmm_platform - ).current_potential_energy() - assert nrg_merged_0.value() == pytest.approx(nrg_remerged_0.value()) assert nrg_merged_1.value() == pytest.approx(nrg_remerged_1.value()) - # this is different - worth checking why! - # assert nrg_merged_05.value() == pytest.approx(nrg_remerged_05.value()) - @pytest.mark.slow @pytest.mark.skipif( @@ -107,6 +97,10 @@ def test_merge(ose_mols, zan_mols, openmm_platform): @pytest.mark.veryslow +@pytest.mark.skipif( + sys.platform == "win32", + reason="Does not run on Windows because there is no match support", +) def test_merge_protein(neura_mols): protein = neura_mols["protein"] From ec5f357a7906f294be5af6d5c8a8e094c04d1a22 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 17 Mar 2024 19:33:14 +0000 Subject: [PATCH 166/468] Added the annihilate function, and cleaned up the LambdaSchedule functions for creating defaults for decoupling and annihilation perturbations. Note that the actual schedules aren't created yet. Also note that the annihilated CLJScl value is not yet correct - it needs to be null for an AmberParams to be created correctly... --- corelib/src/libs/SireCAS/lambdaschedule.cpp | 73 +++++++++++- corelib/src/libs/SireCAS/lambdaschedule.h | 6 + src/sire/morph/_decouple.py | 116 +++++++++++++++++++- src/sire/morph/_perturbation.py | 22 +++- wrapper/CAS/LambdaSchedule.pypp.cpp | 106 +++++++++++++----- 5 files changed, 290 insertions(+), 33 deletions(-) diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp index 71f6b3ae6..68b1af7fc 100644 --- a/corelib/src/libs/SireCAS/lambdaschedule.cpp +++ b/corelib/src/libs/SireCAS/lambdaschedule.cpp @@ -30,6 +30,8 @@ #include "SireCAS/values.h" +#include "SireBase/console.h" + #include "SireError/errors.h" #include "SireStream/datastream.h" @@ -300,6 +302,11 @@ LambdaSchedule LambdaSchedule::charge_scaled_morph(double scale) return l; } +/** Return a schedule that can be used for a standard double-decoupling + * free energy perturbation. If `perturbed_is_decoupled` is true, then + * the perturbed state is decoupled, otherwise the reference state is + * decoupled. + */ LambdaSchedule LambdaSchedule::standard_decouple(bool perturbed_is_decoupled) { LambdaSchedule l; @@ -308,6 +315,13 @@ LambdaSchedule LambdaSchedule::standard_decouple(bool perturbed_is_decoupled) return l; } +/** Return a schedule that can be used for a standard double-decoupling + * free energy perturbation. If `perturbed_is_decoupled` is true, then + * the perturbed state is decoupled, otherwise the reference state is + * decoupled. In this case also add states to decharge and recharge + * the molecule either side of the decoupling stage, where the charges + * are scaled to 'scale' times their original value. + */ LambdaSchedule LambdaSchedule::charge_scaled_decouple(double scale, bool perturbed_is_decoupled) { LambdaSchedule l; @@ -317,6 +331,35 @@ LambdaSchedule LambdaSchedule::charge_scaled_decouple(double scale, bool perturb return l; } +/** Return a schedule that can be used for a standard double-annihilation + * free energy perturbation. If `perturbed_is_annihilated` is true, then + * the perturbed state is annihilated, otherwise the reference state is + * annihilated. + */ +LambdaSchedule LambdaSchedule::standard_annihilate(bool perturbed_is_annihilated) +{ + LambdaSchedule l; + l.addAnnihilateStage(perturbed_is_annihilated); + + return l; +} + +/** Return a schedule that can be used for a standard double-annihilation + * free energy perturbation. If `perturbed_is_annihilated` is true, then + * the perturbed state is annihilated, otherwise the reference state is + * annihilated. In this case also add states to decharge and recharge + * the molecule either side of the annihilation stage, where the charges + * are scaled to 'scale' times their original value. + */ +LambdaSchedule LambdaSchedule::charge_scaled_annihilate(double scale, bool perturbed_is_annihilated) +{ + LambdaSchedule l; + l.addAnnihilateStage(perturbed_is_annihilated); + l.addChargeScaleStages(scale); + + return l; +} + /** Return the symbol used to represent the :lambda: coordinate. * This symbol is used to represent the per-stage :lambda: * variable that goes from 0.0-1.0 within that stage. @@ -633,16 +676,40 @@ void LambdaSchedule::addMorphStage() this->addMorphStage("morph"); } +/** Add a stage to the schedule that will decouple the perturbed + * state if `perturbed_is_decoupled` is true, otherwise the + * reference state is decoupled. The stage will be called 'decouple'. + */ void LambdaSchedule::addDecoupleStage(bool perturbed_is_decoupled) { this->addDecoupleStage("decouple", perturbed_is_decoupled); } +/** Add a named stage to the schedule that will decouple the perturbed + * state if `perturbed_is_decoupled` is true, otherwise the + * reference state is decoupled. + */ void LambdaSchedule::addDecoupleStage(const QString &name, bool perturbed_is_decoupled) { - throw SireError::incomplete_code(QObject::tr( - "Decouple stages are not yet implemented."), - CODELOC); + Console::warning(QObject::tr("Decouple stages are not yet implemented.")); +} + +/** Add a stage to the schedule that will annihilate the perturbed + * state if `perturbed_is_annihilated` is true, otherwise the + * reference state is annihilated. The stage will be called 'annihilate'. + */ +void LambdaSchedule::addAnnihilateStage(bool perturbed_is_annihilated) +{ + this->addAnnihilateStage("annihilate", perturbed_is_annihilated); +} + +/** Add a named stage to the schedule that will annihilate the perturbed + * state if `perturbed_is_annihilated` is true, otherwise the + * reference state is annihilated. + */ +void LambdaSchedule::addAnnihilateStage(const QString &name, bool perturbed_is_annihilated) +{ + Console::warning(QObject::tr("Annihilate stages are not yet implemented.")); } /** Sandwich the current set of stages with a charge-descaling and diff --git a/corelib/src/libs/SireCAS/lambdaschedule.h b/corelib/src/libs/SireCAS/lambdaschedule.h index 7e48e8e01..1ac9fa9f6 100644 --- a/corelib/src/libs/SireCAS/lambdaschedule.h +++ b/corelib/src/libs/SireCAS/lambdaschedule.h @@ -82,6 +82,9 @@ namespace SireCAS static LambdaSchedule standard_decouple(bool perturbed_is_decoupled = true); static LambdaSchedule charge_scaled_decouple(double scale = 0.2, bool perturbed_is_decoupled = true); + static LambdaSchedule standard_annihilate(bool perturbed_is_annihilated = true); + static LambdaSchedule charge_scaled_annihilate(double scale = 0.2, bool perturbed_is_annihilated = true); + static SireCAS::Symbol lam(); static SireCAS::Symbol initial(); static SireCAS::Symbol final(); @@ -142,6 +145,9 @@ namespace SireCAS void addDecoupleStage(bool perturbed_is_decoupled = true); void addDecoupleStage(const QString &name, bool perturbed_is_decoupled = true); + void addAnnihilateStage(bool perturbed_is_annihilated = true); + void addAnnihilateStage(const QString &name, bool perturbed_is_annihilated = true); + void setDefaultStageEquation(const QString &stage, const SireCAS::Expression &equation); diff --git a/src/sire/morph/_decouple.py b/src/sire/morph/_decouple.py index 5384e7d9d..f5770d930 100644 --- a/src/sire/morph/_decouple.py +++ b/src/sire/morph/_decouple.py @@ -27,6 +27,118 @@ def annihilate(mol, as_new_molecule: bool = True, map=None): Molecule The merged molecule representing the annihilation perturbation """ + try: + # make sure we have only the reference state + mol = mol.perturbation().extract_reference(remove_ghosts=True) + except Exception: + pass + + from ..base import create_map + from ..mm import LJParameter + from ..mol import Element + from ..units import kcal_per_mol, mod_electron, g_per_mol + + map = create_map(map) + + c = mol.cursor() + c_mol = c.molecule() + + c["is_perturbable"] = True + + has_key = {} + + for key in [ + "charge", + "LJ", + "bond", + "angle", + "dihedral", + "improper", + "forcefield", + "intrascale", + "mass", + "element", + "atomtype", + "ambertype", + "connectivity", + ]: + key = map[key].source() + + if key in c: + c_mol[f"{key}0"] = c_mol[key] + c_mol[f"{key}1"] = c_mol[key] + + has_key[key] = True + + if key != "connectivity": + del c_mol[key] + else: + has_key[key] = False + + lj_prop = map["LJ"].source() + chg_prop = map["charge"].source() + elem_prop = map["element"].source() + ambtype_prop = map["ambertype"].source() + atomtype_prop = map["atomtype"].source() + mass_prop = map["mass"].source() + + # destroy all of the atoms + for atom in c.atoms(): + lj = atom[f"{lj_prop}0"] + + atom[f"{lj_prop}1"] = LJParameter(lj.sigma(), 0.0 * kcal_per_mol) + atom[f"{chg_prop}1"] = 0 * mod_electron + + if has_key[elem_prop]: + atom[f"{elem_prop}1"] = Element(0) + + if has_key[ambtype_prop]: + atom[f"{ambtype_prop}1"] = "Xx" + + if has_key[atomtype_prop]: + atom[f"{atomtype_prop}1"] = "Xx" + + if has_key[mass_prop]: + atom[f"{mass_prop}1"] = 0.0 * g_per_mol + + # now remove all of the bonds, angles, dihedrals, impropers + for key in ["bond", "angle", "dihedral", "improper"]: + if has_key[key]: + p = c[f"{key}1"] + p.clear() + c[f"{key}1"] = p + + # we will leave the intrascale property as is, as this accounts + # for the connectivity of this molecule, and would likely break + # things if we scaled it with lambda (the charge and LJ are already + # being scaled down) + + mol = c_mol.commit() + + c_mol["molecule0"] = mol.perturbation().extract_reference(remove_ghosts=True) + c_mol["molecule1"] = mol.perturbation().extract_perturbed(remove_ghosts=True) + + if "parameters" in c_mol: + del c_mol["parameters"] + + if "amberparams" in c_mol: + del c_mol["amberparams"] + + if as_new_molecule: + c_mol.renumber() + + # need to add a LambdaSchedule that could be used to decouple + # the molecule + from ..cas import LambdaSchedule + + # we decouple via a standard morph which does not scale the + # intramolecular terms + c_mol["schedule"] = LambdaSchedule.standard_annihilate( + perturbed_is_annihilated=True + ) + + mol = c_mol.commit().perturbation().link_to_reference() + return mol @@ -124,7 +236,9 @@ def decouple(mol, as_new_molecule: bool = True, map=None): # the molecule from ..cas import LambdaSchedule - c_mol["schedule"] = LambdaSchedule() + # we decouple via a standard morph which does not scale the + # intramolecular terms + c_mol["schedule"] = LambdaSchedule.standard_decouple(perturbed_is_decoupled=True) mol = c_mol.commit().perturbation().link_to_reference() diff --git a/src/sire/morph/_perturbation.py b/src/sire/morph/_perturbation.py index 99d05c586..5f85750c6 100644 --- a/src/sire/morph/_perturbation.py +++ b/src/sire/morph/_perturbation.py @@ -306,7 +306,15 @@ def extract_reference( mol = mol.commit().molecule() if remove_ghosts: - mol = mol["not element Xx"].extract(to_same_molecule=True) + try: + mol = mol["not element Xx"] + except Exception: + # there are no non-ghost atoms! + from ..mol import Molecule + + return Molecule() + + mol = mol.extract(to_same_molecule=True) return mol @@ -365,7 +373,17 @@ def extract_perturbed( mol = mol.commit().molecule() if remove_ghosts: - mol = mol["not element Xx"].extract(to_same_molecule=True) + try: + mol = mol["not element Xx"] + except Exception: + # there are no non-ghost atoms! + from ..mol import Molecule + + return Molecule() + + mol = mol.extract(to_same_molecule=True) + + return mol return mol diff --git a/wrapper/CAS/LambdaSchedule.pypp.cpp b/wrapper/CAS/LambdaSchedule.pypp.cpp index f2709cd9e..34f75ae16 100644 --- a/wrapper/CAS/LambdaSchedule.pypp.cpp +++ b/wrapper/CAS/LambdaSchedule.pypp.cpp @@ -8,6 +8,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireCAS/values.h" #include "SireError/errors.h" @@ -35,6 +37,30 @@ void register_LambdaSchedule_class(){ LambdaSchedule_exposer_t LambdaSchedule_exposer = LambdaSchedule_exposer_t( "LambdaSchedule", "This is a schedule that specifies how parameters are changed according\nto a global lambda value. The change can be broken up by sub lever,\nand by stage.\n", bp::init< >("") ); bp::scope LambdaSchedule_scope( LambdaSchedule_exposer ); LambdaSchedule_exposer.def( bp::init< SireCAS::LambdaSchedule const & >(( bp::arg("other") ), "") ); + { //::SireCAS::LambdaSchedule::addAnnihilateStage + + typedef void ( ::SireCAS::LambdaSchedule::*addAnnihilateStage_function_type)( bool ) ; + addAnnihilateStage_function_type addAnnihilateStage_function_value( &::SireCAS::LambdaSchedule::addAnnihilateStage ); + + LambdaSchedule_exposer.def( + "addAnnihilateStage" + , addAnnihilateStage_function_value + , ( bp::arg("perturbed_is_annihilated")=(bool)(true) ) + , "Add a stage to the schedule that will annihilate the perturbed\n state if `perturbed_is_annihilated` is true, otherwise the\n reference state is annihilated. The stage will be called annihilate.\n" ); + + } + { //::SireCAS::LambdaSchedule::addAnnihilateStage + + typedef void ( ::SireCAS::LambdaSchedule::*addAnnihilateStage_function_type)( ::QString const &,bool ) ; + addAnnihilateStage_function_type addAnnihilateStage_function_value( &::SireCAS::LambdaSchedule::addAnnihilateStage ); + + LambdaSchedule_exposer.def( + "addAnnihilateStage" + , addAnnihilateStage_function_value + , ( bp::arg("name"), bp::arg("perturbed_is_annihilated")=(bool)(true) ) + , "Add a named stage to the schedule that will annihilate the perturbed\n state if `perturbed_is_annihilated` is true, otherwise the\n reference state is annihilated.\n" ); + + } { //::SireCAS::LambdaSchedule::addChargeScaleStages typedef void ( ::SireCAS::LambdaSchedule::*addChargeScaleStages_function_type)( double ) ; @@ -68,7 +94,7 @@ void register_LambdaSchedule_class(){ "addDecoupleStage" , addDecoupleStage_function_value , ( bp::arg("perturbed_is_decoupled")=(bool)(true) ) - , "" ); + , "Add a stage to the schedule that will decouple the perturbed\n state if `perturbed_is_decoupled` is true, otherwise the\n reference state is decoupled. The stage will be called decouple.\n" ); } { //::SireCAS::LambdaSchedule::addDecoupleStage @@ -80,7 +106,7 @@ void register_LambdaSchedule_class(){ "addDecoupleStage" , addDecoupleStage_function_value , ( bp::arg("name"), bp::arg("perturbed_is_decoupled")=(bool)(true) ) - , "" ); + , "Add a named stage to the schedule that will decouple the perturbed\n state if `perturbed_is_decoupled` is true, otherwise the\n reference state is decoupled.\n" ); } { //::SireCAS::LambdaSchedule::addForce @@ -93,7 +119,7 @@ void register_LambdaSchedule_class(){ , addForce_function_value , ( bp::arg("force") ) , bp::release_gil_policy() - , "" ); + , "Add a force to a schedule. This is only useful if you want to\n plot how the equations would affect the lever. Forces will be\n automatically added by any perturbation run that needs them,\n so you dont need to add them manually yourself.\n" ); } { //::SireCAS::LambdaSchedule::addForces @@ -106,7 +132,7 @@ void register_LambdaSchedule_class(){ , addForces_function_value , ( bp::arg("forces") ) , bp::release_gil_policy() - , "" ); + , "Add some forces to a schedule. This is only useful if you want to\n plot how the equations would affect the lever. Forces will be\n automatically added by any perturbation run that needs them,\n so you dont need to add them manually yourself.\n" ); } { //::SireCAS::LambdaSchedule::addLever @@ -185,6 +211,18 @@ void register_LambdaSchedule_class(){ , bp::release_gil_policy() , "Append a stage called name which uses the passed equation\n to the end of this schedule. The equation will be the default\n equation that scales all parameters (levers) that dont have\n a custom lever for this stage.\n" ); + } + { //::SireCAS::LambdaSchedule::charge_scaled_annihilate + + typedef ::SireCAS::LambdaSchedule ( *charge_scaled_annihilate_function_type )( double,bool ); + charge_scaled_annihilate_function_type charge_scaled_annihilate_function_value( &::SireCAS::LambdaSchedule::charge_scaled_annihilate ); + + LambdaSchedule_exposer.def( + "charge_scaled_annihilate" + , charge_scaled_annihilate_function_value + , ( bp::arg("scale")=0.20000000000000001, bp::arg("perturbed_is_annihilated")=(bool)(true) ) + , "Return a schedule that can be used for a standard double-annihilation\n free energy perturbation. If `perturbed_is_annihilated` is true, then\n the perturbed state is annihilated, otherwise the reference state is\n annihilated. In this case also add states to decharge and recharge\n the molecule either side of the annihilation stage, where the charges\n are scaled to scale times their original value.\n" ); + } { //::SireCAS::LambdaSchedule::charge_scaled_decouple @@ -195,7 +233,7 @@ void register_LambdaSchedule_class(){ "charge_scaled_decouple" , charge_scaled_decouple_function_value , ( bp::arg("scale")=0.20000000000000001, bp::arg("perturbed_is_decoupled")=(bool)(true) ) - , "" ); + , "Return a schedule that can be used for a standard double-decoupling\n free energy perturbation. If `perturbed_is_decoupled` is true, then\n the perturbed state is decoupled, otherwise the reference state is\n decoupled. In this case also add states to decharge and recharge\n the molecule either side of the decoupling stage, where the charges\n are scaled to scale times their original value.\n" ); } { //::SireCAS::LambdaSchedule::charge_scaled_morph @@ -295,7 +333,7 @@ void register_LambdaSchedule_class(){ "getEquation" , getEquation_function_value , ( bp::arg("stage")="*", bp::arg("force")="*", bp::arg("lever")="*" ) - , "" ); + , "Return the equation used to control the specified lever\n in the specified force at the specified stage. This will\n be a custom equation if that has been set for this lever in this\n force, or else it will be a custom equation set for this lever,\n else it will be the default equation for this stage\n" ); } { //::SireCAS::LambdaSchedule::getForces @@ -307,7 +345,7 @@ void register_LambdaSchedule_class(){ "getForces" , getForces_function_value , bp::release_gil_policy() - , "" ); + , "Return all of the forces that have been explicitly added\n to the schedule. Note that forces will be automatically added\n by any perturbation run that needs them, so you dont normally\n need to manage them manually yourself.\n" ); } { //::SireCAS::LambdaSchedule::getLambdaInStage @@ -333,7 +371,7 @@ void register_LambdaSchedule_class(){ , getLeverStages_function_value , ( bp::arg("lambda_values") ) , bp::release_gil_policy() - , "Return the list of lever stages that are used for the passed list\n of lambda values. The lever names will be returned in the matching\n order of the lambda values.\n" ); + , "Return the list of stages that are used for the passed list\n of lambda values. The stage names will be returned in the matching\n order of the lambda values.\n" ); } { //::SireCAS::LambdaSchedule::getLeverStages @@ -345,7 +383,7 @@ void register_LambdaSchedule_class(){ "getLeverStages" , getLeverStages_function_value , ( bp::arg("num_lambda")=(int)(101) ) - , "Return the lever stages used for the list of `nvalue` lambda values\n generated for the global lambda value between 0 and 1 inclusive.\n" ); + , "Return the stages used for the list of `nvalue` lambda values\n generated for the global lambda value between 0 and 1 inclusive.\n" ); } { //::SireCAS::LambdaSchedule::getLeverValues @@ -357,7 +395,7 @@ void register_LambdaSchedule_class(){ "getLeverValues" , getLeverValues_function_value , ( bp::arg("lambda_values"), bp::arg("initial")=1., bp::arg("final")=2. ) - , "Return the lever name and parameter values for that lever\n for the specified list of lambda values, assuming that a\n parameter for that lever has an initial value of\n `initial_value` and a final value of `final_value`. This\n is mostly useful for testing and graphing how this\n schedule would change some hyperthetical forcefield\n parameters for the specified lambda values.\n" ); + , "Return the stage name and parameter values for that lever\n for the specified list of lambda values, assuming that a\n parameter for that stage has an initial value of\n `initial_value` and a final value of `final_value`. This\n is mostly useful for testing and graphing how this\n schedule would change some hyperthetical forcefield\n parameters for the specified lambda values.\n" ); } { //::SireCAS::LambdaSchedule::getLeverValues @@ -394,7 +432,7 @@ void register_LambdaSchedule_class(){ , getMoleculeSchedule_function_value , ( bp::arg("pert_mol_id") ) , bp::return_value_policy() - , "" ); + , "Return the schedule used to control perturbations for the\n perturbable molecule (or part of molecule) that is identified by the\n passed pert_mol_id. This schedule will be used to control\n all of the levers for this molecule (or part of molecule).\n\n This returns this schedule if there is no specified schedule\n for this molecule\n" ); } { //::SireCAS::LambdaSchedule::getStage @@ -431,7 +469,7 @@ void register_LambdaSchedule_class(){ "hasForceSpecificEquation" , hasForceSpecificEquation_function_value , ( bp::arg("stage")="*", bp::arg("force")="*", bp::arg("lever")="*" ) - , "" ); + , "Return whether or not the specified lever in the specified force\n at the specified stage has a custom equation set for it\n" ); } { //::SireCAS::LambdaSchedule::hasMoleculeSchedule @@ -444,7 +482,7 @@ void register_LambdaSchedule_class(){ , hasMoleculeSchedule_function_value , ( bp::arg("pert_mol_id") ) , bp::release_gil_policy() - , "" ); + , "Return whether or not the perturbable molecule (or part of molecule)\n that is identified by passed pert_mol_id has its own schedule" ); } { //::SireCAS::LambdaSchedule::initial @@ -505,7 +543,7 @@ void register_LambdaSchedule_class(){ "morph" , morph_function_value , ( bp::arg("force")="*", bp::arg("lever")="*", bp::arg("initial")=0, bp::arg("final")=1, bp::arg("lambda_value")=0 ) - , "" ); + , "Return the parameters for the specified lever called `lever_name`\n in the force force\n that have been morphed from the passed list of initial values\n (in `initial`) to the passed list of final values (in `final`)\n for the specified global value of :lambda: (in `lambda_value`).\n\n The morphed parameters will be returned in the matching\n order to `initial` and `final`.\n\n This morphs a single floating point parameters.\n" ); } { //::SireCAS::LambdaSchedule::morph @@ -517,7 +555,7 @@ void register_LambdaSchedule_class(){ "morph" , morph_function_value , ( bp::arg("force")="*", bp::arg("lever")="*", bp::arg("initial")=::QVector( ), bp::arg("final")=::QVector( ), bp::arg("lambda_value")=0. ) - , "" ); + , "Return the parameters for the specified lever called `lever_name`\n in the specified force,\n that have been morphed from the passed list of initial values\n (in `initial`) to the passed list of final values (in `final`)\n for the specified global value of :lambda: (in `lambda_value`).\n\n The morphed parameters will be returned in the matching\n order to `initial` and `final`.\n\n This morphs floating point parameters. There is an overload\n of this function that morphs integer parameters, in which\n case the result would be rounded to the nearest integer.\n" ); } { //::SireCAS::LambdaSchedule::morph @@ -529,7 +567,7 @@ void register_LambdaSchedule_class(){ "morph" , morph_function_value , ( bp::arg("force")="*", bp::arg("lever")="*", bp::arg("initial")=::QVector( ), bp::arg("final")=::QVector( ), bp::arg("lambda_value")=0. ) - , "" ); + , "Return the parameters for the specified lever called `lever_name`\n for the specified force\n that have been morphed from the passed list of initial values\n (in `initial`) to the passed list of final values (in `final`)\n for the specified global value of :lambda: (in `lambda_value`).\n\n The morphed parameters will be returned in the matching\n order to `initial` and `final`.\n\n This function morphs integer parameters. In this case,\n the result will be the rounded to the nearest integer.\n" ); } { //::SireCAS::LambdaSchedule::nForces @@ -541,7 +579,7 @@ void register_LambdaSchedule_class(){ "nForces" , nForces_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of forces that have been explicitly added\n to the schedule. Note that forces will be automatically added\n by any perturbation run that needs them, so you dont normally\n need to manage them manually yourself.\n" ); } { //::SireCAS::LambdaSchedule::nLevers @@ -605,7 +643,7 @@ void register_LambdaSchedule_class(){ "removeEquation" , removeEquation_function_value , ( bp::arg("stage")="*", bp::arg("force")="*", bp::arg("lever")="*" ) - , "" ); + , "Remove the custom equation for the specified `lever` in the\n specified force at the specified `stage`.\n The lever will now use the equation specified for this\n lever for this stage, or the default lever for the stage\n if this isnt set\n" ); } { //::SireCAS::LambdaSchedule::removeForce @@ -618,7 +656,7 @@ void register_LambdaSchedule_class(){ , removeForce_function_value , ( bp::arg("force") ) , bp::release_gil_policy() - , "" ); + , "Remove a force from a schedule. This will not impact any\n perturbation runs that use this schedule, as any missing\n forces will be re-added.\n" ); } { //::SireCAS::LambdaSchedule::removeForces @@ -631,7 +669,7 @@ void register_LambdaSchedule_class(){ , removeForces_function_value , ( bp::arg("forces") ) , bp::release_gil_policy() - , "" ); + , "Remove some forces from a schedule. This will not impact any\n perturbation runs that use this schedule, as any missing\n forces will be re-added.\n" ); } { //::SireCAS::LambdaSchedule::removeLever @@ -670,7 +708,7 @@ void register_LambdaSchedule_class(){ , removeMoleculeSchedule_function_value , ( bp::arg("pert_mol_id") ) , bp::release_gil_policy() - , "" ); + , "Remove the perturbable molecule-specific schedule associated\n with the perturbable molecule (or part of molecule) that is\n identified by the passed pert_mol_id.\n" ); } { //::SireCAS::LambdaSchedule::removeStage @@ -683,7 +721,7 @@ void register_LambdaSchedule_class(){ , removeStage_function_value , ( bp::arg("stage") ) , bp::release_gil_policy() - , "" ); + , "Remove the stage stage" ); } { //::SireCAS::LambdaSchedule::setConstant @@ -722,7 +760,7 @@ void register_LambdaSchedule_class(){ , setDefaultStageEquation_function_value , ( bp::arg("stage"), bp::arg("equation") ) , bp::release_gil_policy() - , "" ); + , "Set the default equation used to control levers for the\n stage stage to equation. This equation will be used\n to control any levers in this stage that dont have\n their own custom equation.\n" ); } { //::SireCAS::LambdaSchedule::setEquation @@ -734,7 +772,7 @@ void register_LambdaSchedule_class(){ "setEquation" , setEquation_function_value , ( bp::arg("stage")="*", bp::arg("force")="*", bp::arg("lever")="*", bp::arg("equation")=SireCAS::Expression() ) - , "" ); + , "Set the custom equation used to control the specified lever\n for the specified force at the stage stage to equation.\n This equation will only be used to control the parameters for the\n specified lever in the specified force at the specified stage\n" ); } { //::SireCAS::LambdaSchedule::setMoleculeSchedule @@ -747,7 +785,19 @@ void register_LambdaSchedule_class(){ , setMoleculeSchedule_function_value , ( bp::arg("pert_mol_id"), bp::arg("schedule") ) , bp::release_gil_policy() - , "" ); + , "Set schedule as the molecule-specific schedule for the\n perturbable molecule (or part of molecule) that is identified by the\n passed pert_mol_id. This schedule will be used to control\n all of the levers for this molecule (or part of molecule),\n and replaces any levers provided by this schedule\n" ); + + } + { //::SireCAS::LambdaSchedule::standard_annihilate + + typedef ::SireCAS::LambdaSchedule ( *standard_annihilate_function_type )( bool ); + standard_annihilate_function_type standard_annihilate_function_value( &::SireCAS::LambdaSchedule::standard_annihilate ); + + LambdaSchedule_exposer.def( + "standard_annihilate" + , standard_annihilate_function_value + , ( bp::arg("perturbed_is_annihilated")=(bool)(true) ) + , "Return a schedule that can be used for a standard double-annihilation\n free energy perturbation. If `perturbed_is_annihilated` is true, then\n the perturbed state is annihilated, otherwise the reference state is\n annihilated.\n" ); } { //::SireCAS::LambdaSchedule::standard_decouple @@ -759,7 +809,7 @@ void register_LambdaSchedule_class(){ "standard_decouple" , standard_decouple_function_value , ( bp::arg("perturbed_is_decoupled")=(bool)(true) ) - , "" ); + , "Return a schedule that can be used for a standard double-decoupling\n free energy perturbation. If `perturbed_is_decoupled` is true, then\n the perturbed state is decoupled, otherwise the reference state is\n decoupled.\n" ); } { //::SireCAS::LambdaSchedule::standard_morph @@ -784,7 +834,7 @@ void register_LambdaSchedule_class(){ , takeMoleculeSchedule_function_value , ( bp::arg("pert_mol_id") ) , bp::release_gil_policy() - , "" ); + , "Remove the perturbable molecule-specific schedule associated\n with the perturbable molecule (or part of molecule) that is\n identified by the passed pert_mol_id. This returns the\n schedule that was removed. If no such schedule exists, then\n a copy of this schedule is returned.\n" ); } { //::SireCAS::LambdaSchedule::toString @@ -823,11 +873,13 @@ void register_LambdaSchedule_class(){ , "" ); } + LambdaSchedule_exposer.staticmethod( "charge_scaled_annihilate" ); LambdaSchedule_exposer.staticmethod( "charge_scaled_decouple" ); LambdaSchedule_exposer.staticmethod( "charge_scaled_morph" ); LambdaSchedule_exposer.staticmethod( "final" ); LambdaSchedule_exposer.staticmethod( "initial" ); LambdaSchedule_exposer.staticmethod( "lam" ); + LambdaSchedule_exposer.staticmethod( "standard_annihilate" ); LambdaSchedule_exposer.staticmethod( "standard_decouple" ); LambdaSchedule_exposer.staticmethod( "standard_morph" ); LambdaSchedule_exposer.staticmethod( "typeName" ); From d211da6d6077b4fec657b3e94934d9f2cc3b2afe Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 18 Mar 2024 21:00:00 +0000 Subject: [PATCH 167/468] Added in the code to create the schedules for decoupling and annihilation --- corelib/src/libs/SireCAS/lambdaschedule.cpp | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp index 68b1af7fc..62f48ad29 100644 --- a/corelib/src/libs/SireCAS/lambdaschedule.cpp +++ b/corelib/src/libs/SireCAS/lambdaschedule.cpp @@ -691,7 +691,15 @@ void LambdaSchedule::addDecoupleStage(bool perturbed_is_decoupled) */ void LambdaSchedule::addDecoupleStage(const QString &name, bool perturbed_is_decoupled) { - Console::warning(QObject::tr("Decouple stages are not yet implemented.")); + auto state = LambdaSchedule::initial(); + + if (not perturbed_is_decoupled) + state = LambdaSchedule::final(); + + this->addStage(name, state); + + // the only thing we scale with lambda is the ghost/non-ghost force + this->setEquation(name, "ghost/non-ghost", "*", default_morph_equation); } /** Add a stage to the schedule that will annihilate the perturbed @@ -703,13 +711,13 @@ void LambdaSchedule::addAnnihilateStage(bool perturbed_is_annihilated) this->addAnnihilateStage("annihilate", perturbed_is_annihilated); } -/** Add a named stage to the schedule that will annihilate the perturbed +/** Add a named stage to the schedule that will annihilate the perturbed * state if `perturbed_is_annihilated` is true, otherwise the * reference state is annihilated. */ void LambdaSchedule::addAnnihilateStage(const QString &name, bool perturbed_is_annihilated) { - Console::warning(QObject::tr("Annihilate stages are not yet implemented.")); + this->addStage(name, default_morph_equation); } /** Sandwich the current set of stages with a charge-descaling and From ec1fc468d84e3c626a0cb2dee5f80ea5ee14d18d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 18 Mar 2024 22:17:25 +0000 Subject: [PATCH 168/468] Added ability to print out changed constraints Also realised that the way constraints are found is not correct, if the bonds or angles are perturbing. It only does the param0 bonds search, missing out bonds only in params1 --- src/sire/morph/_decouple.py | 15 ++++-- wrapper/Convert/SireOpenMM/_perturbablemol.py | 47 +++++++++++++++++++ wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 8 ++++ wrapper/Convert/__init__.py | 2 + 4 files changed, 68 insertions(+), 4 deletions(-) diff --git a/src/sire/morph/_decouple.py b/src/sire/morph/_decouple.py index f5770d930..d7ca2e98c 100644 --- a/src/sire/morph/_decouple.py +++ b/src/sire/morph/_decouple.py @@ -103,15 +103,22 @@ def annihilate(mol, as_new_molecule: bool = True, map=None): # now remove all of the bonds, angles, dihedrals, impropers for key in ["bond", "angle", "dihedral", "improper"]: + key = map[key].source() + if has_key[key]: p = c[f"{key}1"] p.clear() c[f"{key}1"] = p - # we will leave the intrascale property as is, as this accounts - # for the connectivity of this molecule, and would likely break - # things if we scaled it with lambda (the charge and LJ are already - # being scaled down) + # now scale the nbpairs to zero, as we can't have any + # 1-4 interactions when there are no dihedrals... + sclkey = map["intrascale"].source() + if has_key[sclkey]: + from ..legacy.MM import CLJScaleFactor + + nbscl = c[f"{sclkey}1"] + nbscl.set_all(CLJScaleFactor(0, 0)) + c[f"{sclkey}1"] = nbscl mol = c_mol.commit() diff --git a/wrapper/Convert/SireOpenMM/_perturbablemol.py b/wrapper/Convert/SireOpenMM/_perturbablemol.py index b6b4da935..ecfdb6f84 100644 --- a/wrapper/Convert/SireOpenMM/_perturbablemol.py +++ b/wrapper/Convert/SireOpenMM/_perturbablemol.py @@ -5,6 +5,7 @@ "_changed_torsions", "_changed_exceptions", "_changed_constraints", + "_changed_nbscls", ] @@ -212,6 +213,52 @@ def _changed_torsions(obj, to_pandas: bool = True): return changed_torsions +def _changed_nbscls(obj, to_pandas: bool = True): + """ + Return a list of the non-bonded scaling factors that change + parameters in this perturbation + + Parameters + ---------- + + to_pandas: bool, optional, default=True + If True then the list of non-bonded scaling factors will be + returned as a pandas DataFrame + """ + changed_nbscls = [] + + atoms = obj.atoms() + + for atompair, chg_scl0, chg_scl1, lj_scl0, lj_scl1 in zip( + obj.get_exception_atoms(), + obj.get_charge_scales0(), + obj.get_charge_scales1(), + obj.get_lj_scales0(), + obj.get_lj_scales1(), + ): + if chg_scl0 != chg_scl1 or lj_scl0 != lj_scl1: + if to_pandas: + atompair = f"{_name(atoms[atompair[0]])}-{_name(atoms[atompair[1]])}" + + changed_nbscls.append((atompair, chg_scl0, chg_scl1, lj_scl0, lj_scl1)) + + if to_pandas: + import pandas as pd + + changed_nbscls = pd.DataFrame( + changed_nbscls, + columns=[ + "atompair", + "charge_scale0", + "charge_scale1", + "lj_scale0", + "lj_scale1", + ], + ) + + return changed_nbscls + + def _changed_exceptions(obj, to_pandas: bool = True): """ Return a list of the exceptions that change parameters in this diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 2922a2a55..e650a8651 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -761,6 +761,14 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, double k_1 = bondparam1.k() * bond_k_to_openmm; r0_1 = bondparam1.r0() * bond_r0_to_openmm; + if (r0_1 == 0) + { + // we cannot shrink the bond to 0 - this must be + // a bond that is disappearing - we should simply + // keep it the same length + r0_1 = r0; + } + if (std::abs(k_1 - k) > 1e-3 or std::abs(r0_1 - r0) > 1e-3) { // we need to check against the "NOT_PERTURBED"-style constraints diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 266d6dd68..40df0f2c9 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -87,6 +87,7 @@ def smarts_to_rdkit(*args, **kwargs): _changed_bonds, _changed_angles, _changed_torsions, + _changed_nbscls, _changed_exceptions, _changed_constraints, ) @@ -103,6 +104,7 @@ def smarts_to_rdkit(*args, **kwargs): PerturbableOpenMMMolecule.changed_bonds = _changed_bonds PerturbableOpenMMMolecule.changed_angles = _changed_angles PerturbableOpenMMMolecule.changed_torsions = _changed_torsions + PerturbableOpenMMMolecule.changed_nbscls = _changed_nbscls PerturbableOpenMMMolecule.changed_exceptions = _changed_exceptions PerturbableOpenMMMolecule.changed_constraints = _changed_constraints From 2cdf38cbcc69c68025ccd96c84415b57b5340295 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 18 Mar 2024 22:41:54 +0000 Subject: [PATCH 169/468] Worked it out - just need to add in the missing bonds and angles to each state, so a mini-pre-align Added the stub of a unit test to test all this. Will write properly later. --- tests/morph/test_decouple.py | 25 ++++++++++ wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 48 ++++++++++++++++++- 2 files changed, 71 insertions(+), 2 deletions(-) create mode 100644 tests/morph/test_decouple.py diff --git a/tests/morph/test_decouple.py b/tests/morph/test_decouple.py new file mode 100644 index 000000000..7102053a2 --- /dev/null +++ b/tests/morph/test_decouple.py @@ -0,0 +1,25 @@ +import sire as sr + +import pytest + + +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats(), + reason="openmm support is not available", +def test_decouple(ala_mols): + mol = ala_mols[0] + + amol = sr.morph.annihilate(mol) + + omm_fwds = amol.perturbation().to_openmm(constraint="h-bonds") + + omm_bwds = amol.perturbation().to_openmm(constraint="h-bonds", + swap_end_states=True) + + # use .changed_bonds() etc to validate that the forwards + # and backwards perturbations are the same + + # also check that parameters are being set equal to zero correctly + + # raise an error until I have written this! + assert False \ No newline at end of file diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index e650a8651..6d883d78b 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -713,8 +713,26 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, dynamic_constraints = map["dynamic_constraints"].value().asABoolean(); } - for (auto it = params.bonds().constBegin(); - it != params.bonds().constEnd(); + auto bonds = params.bonds(); + + if (is_perturbable) + { + // add in any bonds that exist only in the other state + // - use the same r0 but set k to 0 + for (auto it = params1.bonds().constBegin(); + it != params1.bonds().constEnd(); + ++it) + { + if (not bonds.contains(it.key())) + { + bonds.insert(it.key(), QPair(AmberBond(0.0, it.value().first.r0()), + it.value().second)); + } + } + } + + for (auto it = bonds.constBegin(); + it != bonds.constEnd(); ++it) { const auto bondid = it.key().map(molinfo); @@ -820,6 +838,24 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, ang_params.clear(); + auto angles = params.angles(); + + if (is_perturbable) + { + // add in any angles that exist only in the other state + // - use the same theta0 but set k to 0 + for (auto it = params1.angles().constBegin(); + it != params1.angles().constEnd(); + ++it) + { + if (not angles.contains(it.key())) + { + angles.insert(it.key(), QPair(AmberAngle(0.0, it.value().first.theta0()), + it.value().second)); + } + } + } + for (auto it = params.angles().constBegin(); it != params.angles().constEnd(); ++it) @@ -867,6 +903,14 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, double k_1 = angparam.k() * angle_k_to_openmm; theta0_1 = angparam.theta0(); + if (theta0_1 == 0) + { + // we cannot shrink the angle to 0 - this must be + // an angle that is disappearing - we should simply + // keep it the same angle + theta0_1 = theta0; + } + if (std::abs(k_1 - k) > 1e-3 or std::abs(theta0_1 - theta0) > 1e-3) { // this angle perturbs From d3b2dd48b07b56024a7ef48096e885b593ddcf9d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 20 Mar 2024 00:41:53 +0000 Subject: [PATCH 170/468] Added good tests of the annihilate and decouple functions. Also found that OpenMM optimistically removes charge support from NonbondedForce if all charges are zero, meaning that you can't then update the charges with updateParametersInContext. Set these charges to near zero for perturbable molecules, so that this doesn't happen Also removed duplicate `changed_nbscls` function, as I had already written `changed_exceptions` --- tests/morph/test_decouple.py | 193 +++++++++++++++++- wrapper/Convert/SireOpenMM/_perturbablemol.py | 47 ----- .../SireOpenMM/sire_to_openmm_system.cpp | 15 +- wrapper/Convert/__init__.py | 2 - 4 files changed, 199 insertions(+), 58 deletions(-) diff --git a/tests/morph/test_decouple.py b/tests/morph/test_decouple.py index 7102053a2..f6a3b44d3 100644 --- a/tests/morph/test_decouple.py +++ b/tests/morph/test_decouple.py @@ -6,20 +6,201 @@ @pytest.mark.skipif( "openmm" not in sr.convert.supported_formats(), reason="openmm support is not available", -def test_decouple(ala_mols): +) +def test_decouple(ala_mols, openmm_platform): + mol = ala_mols[0] + + dmol = sr.morph.decouple(mol) + + # check the energies are the same forwards and backwards + d_fwds = dmol.dynamics(platform=openmm_platform, constraint="h-bonds") + d_bwds = dmol.dynamics( + platform=openmm_platform, constraint="h-bonds", swap_end_states=True + ) + + d_fwds.set_lambda(0.0) + d_bwds.set_lambda(1.0) + + assert d_fwds.current_potential_energy().value() == pytest.approx( + d_bwds.current_potential_energy().value(), abs=1e-4 + ) + + d_fwds.set_lambda(1.0) + d_bwds.set_lambda(0.0) + + assert d_fwds.current_potential_energy().value() == pytest.approx( + d_bwds.current_potential_energy().value(), abs=1e-4 + ) + + # use .changed_bonds() etc to validate that the forwards + # and backwards perturbations are the same + omm_fwds = dmol.perturbation().to_openmm(constraint="h-bonds") + + omm_bwds = dmol.perturbation().to_openmm(constraint="h-bonds", swap_end_states=True) + + fwds = omm_fwds.changed_atoms() + bwds = omm_bwds.changed_atoms() + + assert fwds["charge0"].equals(bwds["charge1"]) + assert fwds["charge1"].equals(bwds["charge0"]) + assert fwds["sigma0"].equals(bwds["sigma1"]) + assert fwds["sigma1"].equals(bwds["sigma0"]) + assert fwds["epsilon0"].equals(bwds["epsilon1"]) + assert fwds["epsilon1"].equals(bwds["epsilon0"]) + + # also check that parameters are being set equal to zero correctly + assert (fwds["charge1"] == 0.0).all() + assert (fwds["sigma1"] != 0.0).all() + assert (fwds["epsilon1"] == 0.0).all() + assert (bwds["charge0"] == 0.0).all() + assert (bwds["sigma0"] != 0.0).all() + assert (bwds["epsilon0"] == 0.0).all() + + fwds = omm_fwds.changed_bonds() + bwds = omm_bwds.changed_bonds() + + assert fwds.empty + assert bwds.empty + + fwds = omm_fwds.changed_angles() + bwds = omm_bwds.changed_angles() + + assert fwds.empty + assert bwds.empty + + fwds = omm_fwds.changed_torsions() + bwds = omm_bwds.changed_torsions() + + assert fwds.empty + assert bwds.empty + + fwds = omm_fwds.changed_exceptions() + bwds = omm_bwds.changed_exceptions() + + assert fwds.empty + assert bwds.empty + + fwds = omm_fwds.changed_constraints() + bwds = omm_bwds.changed_constraints() + + assert fwds.empty + assert bwds.empty + + +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats(), + reason="openmm support is not available", +) +def test_annihilate(ala_mols, openmm_platform): mol = ala_mols[0] amol = sr.morph.annihilate(mol) - omm_fwds = amol.perturbation().to_openmm(constraint="h-bonds") + # check the energies are the same forwards and backwards + d_fwds = amol.dynamics(platform=openmm_platform, constraint="h-bonds") + d_bwds = amol.dynamics( + platform=openmm_platform, constraint="h-bonds", swap_end_states=True + ) + + d_fwds.set_lambda(0.0) + d_bwds.set_lambda(1.0) - omm_bwds = amol.perturbation().to_openmm(constraint="h-bonds", - swap_end_states=True) + assert d_fwds.current_potential_energy().value() == pytest.approx( + d_bwds.current_potential_energy().value(), abs=1e-4 + ) + + d_fwds.set_lambda(1.0) + d_bwds.set_lambda(0.0) + + assert d_fwds.current_potential_energy().value() == pytest.approx( + d_bwds.current_potential_energy().value(), abs=1e-4 + ) # use .changed_bonds() etc to validate that the forwards # and backwards perturbations are the same + omm_fwds = amol.perturbation().to_openmm(constraint="h-bonds") + + omm_bwds = amol.perturbation().to_openmm(constraint="h-bonds", swap_end_states=True) + + fwds = omm_fwds.changed_atoms() + bwds = omm_bwds.changed_atoms() + + assert fwds["charge0"].equals(bwds["charge1"]) + assert fwds["charge1"].equals(bwds["charge0"]) + assert fwds["sigma0"].equals(bwds["sigma1"]) + assert fwds["sigma1"].equals(bwds["sigma0"]) + assert fwds["epsilon0"].equals(bwds["epsilon1"]) + assert fwds["epsilon1"].equals(bwds["epsilon0"]) + + # also check that parameters are being set equal to zero correctly + assert (fwds["charge1"] == 0.0).all() + assert (fwds["sigma1"] != 0.0).all() + assert (fwds["epsilon1"] == 0.0).all() + assert (bwds["charge0"] == 0.0).all() + assert (bwds["sigma0"] != 0.0).all() + assert (bwds["epsilon0"] == 0.0).all() + + fwds = omm_fwds.changed_bonds() + bwds = omm_bwds.changed_bonds() + + assert fwds["length0"].equals(bwds["length1"]) + assert fwds["length1"].equals(bwds["length0"]) + assert fwds["k0"].equals(bwds["k1"]) + assert fwds["k1"].equals(bwds["k0"]) # also check that parameters are being set equal to zero correctly + assert (fwds["length1"] != 0.0).all() + assert (fwds["k1"] == 0.0).all() + assert (bwds["length0"] != 0.0).all() + assert (bwds["k0"] == 0.0).all() + + fwds = omm_fwds.changed_angles() + bwds = omm_bwds.changed_angles() + + assert fwds["size0"].equals(bwds["size1"]) + assert fwds["size1"].equals(bwds["size0"]) + assert fwds["k0"].equals(bwds["k1"]) + assert fwds["k1"].equals(bwds["k0"]) + + # also check that parameters are being set equal to zero correctly + assert (fwds["size1"] != 0.0).all() + assert (fwds["k1"] == 0.0).all() + assert (bwds["size0"] != 0.0).all() + assert (bwds["k0"] == 0.0).all() + + fwds = omm_fwds.changed_torsions() + bwds = omm_bwds.changed_torsions() + + assert fwds["periodicity0"].equals(bwds["periodicity1"]) + assert fwds["periodicity1"].equals(bwds["periodicity0"]) + assert fwds["phase0"].equals(bwds["phase1"]) + assert fwds["phase1"].equals(bwds["phase0"]) + assert fwds["k0"].equals(bwds["k1"]) + assert fwds["k1"].equals(bwds["k0"]) + + # also check that parameters are being set equal to zero correctly + assert (fwds["k1"] == 0.0).all() + assert (bwds["k0"] == 0.0).all() + + fwds = omm_fwds.changed_exceptions() + bwds = omm_bwds.changed_exceptions() + + joined = fwds.merge(bwds, on="atompair", suffixes=("_fwds", "_bwds")) + + assert joined["charge_scale0_fwds"].equals(joined["charge_scale1_bwds"]) + assert joined["charge_scale1_fwds"].equals(joined["charge_scale0_bwds"]) + assert joined["lj_scale0_fwds"].equals(joined["lj_scale1_bwds"]) + assert joined["lj_scale1_fwds"].equals(joined["lj_scale0_bwds"]) + + # also check that parameters are being set equal to zero correctly + assert (joined["charge_scale1_fwds"] == 0.0).all() + assert (joined["lj_scale1_fwds"] == 0.0).all() + assert (joined["charge_scale0_bwds"] == 0.0).all() + assert (joined["lj_scale0_bwds"] == 0.0).all() + + fwds = omm_fwds.changed_constraints() + bwds = omm_bwds.changed_constraints() - # raise an error until I have written this! - assert False \ No newline at end of file + # there should be no changed constraints + assert fwds.empty + assert bwds.empty diff --git a/wrapper/Convert/SireOpenMM/_perturbablemol.py b/wrapper/Convert/SireOpenMM/_perturbablemol.py index ecfdb6f84..b6b4da935 100644 --- a/wrapper/Convert/SireOpenMM/_perturbablemol.py +++ b/wrapper/Convert/SireOpenMM/_perturbablemol.py @@ -5,7 +5,6 @@ "_changed_torsions", "_changed_exceptions", "_changed_constraints", - "_changed_nbscls", ] @@ -213,52 +212,6 @@ def _changed_torsions(obj, to_pandas: bool = True): return changed_torsions -def _changed_nbscls(obj, to_pandas: bool = True): - """ - Return a list of the non-bonded scaling factors that change - parameters in this perturbation - - Parameters - ---------- - - to_pandas: bool, optional, default=True - If True then the list of non-bonded scaling factors will be - returned as a pandas DataFrame - """ - changed_nbscls = [] - - atoms = obj.atoms() - - for atompair, chg_scl0, chg_scl1, lj_scl0, lj_scl1 in zip( - obj.get_exception_atoms(), - obj.get_charge_scales0(), - obj.get_charge_scales1(), - obj.get_lj_scales0(), - obj.get_lj_scales1(), - ): - if chg_scl0 != chg_scl1 or lj_scl0 != lj_scl1: - if to_pandas: - atompair = f"{_name(atoms[atompair[0]])}-{_name(atoms[atompair[1]])}" - - changed_nbscls.append((atompair, chg_scl0, chg_scl1, lj_scl0, lj_scl1)) - - if to_pandas: - import pandas as pd - - changed_nbscls = pd.DataFrame( - changed_nbscls, - columns=[ - "atompair", - "charge_scale0", - "charge_scale1", - "lj_scale0", - "lj_scale1", - ], - ) - - return changed_nbscls - - def _changed_exceptions(obj, to_pandas: bool = True): """ Return a list of the exceptions that change parameters in this diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 8c399b5e7..d2a7bf490 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1184,8 +1184,17 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // now the reference CLJ parameters const auto &clj = cljs_data[j]; + // make sure that charges are added here - if all are zero, + // the NonbondedForce will not include support for charge! + double charge = boost::get<0>(clj); + + if (charge == 0.0) + { + charge = 1.0e-6; + } + // reduced_q - custom_params[0] = boost::get<0>(clj); + custom_params[0] = charge; // half_sigma custom_params[1] = 0.5 * boost::get<1>(clj); // two_sqrt_epsilon @@ -1211,13 +1220,13 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // calculated using the ghost forcefields // (the ghost forcefields include a coulomb term // that subtracts from whatever was calculated here) - cljff->addParticle(boost::get<0>(clj), 0.0, 0.0); + cljff->addParticle(charge, 0.0, 0.0); } else { // this isn't a ghost atom. Record this fact and // just add it to the standard cljff as normal - cljff->addParticle(boost::get<0>(clj), boost::get<1>(clj), + cljff->addParticle(charge, boost::get<1>(clj), boost::get<2>(clj)); non_ghost_atoms.insert(atom_index); } diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 40df0f2c9..266d6dd68 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -87,7 +87,6 @@ def smarts_to_rdkit(*args, **kwargs): _changed_bonds, _changed_angles, _changed_torsions, - _changed_nbscls, _changed_exceptions, _changed_constraints, ) @@ -104,7 +103,6 @@ def smarts_to_rdkit(*args, **kwargs): PerturbableOpenMMMolecule.changed_bonds = _changed_bonds PerturbableOpenMMMolecule.changed_angles = _changed_angles PerturbableOpenMMMolecule.changed_torsions = _changed_torsions - PerturbableOpenMMMolecule.changed_nbscls = _changed_nbscls PerturbableOpenMMMolecule.changed_exceptions = _changed_exceptions PerturbableOpenMMMolecule.changed_constraints = _changed_constraints From 4a0dea05a9afe890eef9d6e79bfb36edfabdbf2d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 20 Mar 2024 00:50:38 +0000 Subject: [PATCH 171/468] Small fix to iterate over the right object... --- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 6d883d78b..357ddcfc6 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -856,8 +856,8 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } } - for (auto it = params.angles().constBegin(); - it != params.angles().constEnd(); + for (auto it = angles.constBegin(); + it != angles.constEnd(); ++it) { const auto angid = it.key().map(molinfo); From 79f4f110d2c82e422e79858b9256b47ff5814b13 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 22 Mar 2024 08:49:03 +0000 Subject: [PATCH 172/468] Committing test changes --- tests/morph/test_decouple.py | 54 ++++++++++++++++++++---------------- 1 file changed, 30 insertions(+), 24 deletions(-) diff --git a/tests/morph/test_decouple.py b/tests/morph/test_decouple.py index f6a3b44d3..5c0a817c4 100644 --- a/tests/morph/test_decouple.py +++ b/tests/morph/test_decouple.py @@ -143,44 +143,50 @@ def test_annihilate(ala_mols, openmm_platform): fwds = omm_fwds.changed_bonds() bwds = omm_bwds.changed_bonds() - assert fwds["length0"].equals(bwds["length1"]) - assert fwds["length1"].equals(bwds["length0"]) - assert fwds["k0"].equals(bwds["k1"]) - assert fwds["k1"].equals(bwds["k0"]) + joined = fwds.merge(bwds, on="bond", suffixes=("_fwds", "_bwds")) + + assert joined["length0_fwds"].equals(joined["length1_bwds"]) + assert joined["length1_fwds"].equals(joined["length0_bwds"]) + assert joined["k0_fwds"].equals(joined["k1_bwds"]) + assert joined["k1_fwds"].equals(joined["k0_bwds"]) # also check that parameters are being set equal to zero correctly - assert (fwds["length1"] != 0.0).all() - assert (fwds["k1"] == 0.0).all() - assert (bwds["length0"] != 0.0).all() - assert (bwds["k0"] == 0.0).all() + assert (joined["length1_fwds"] != 0.0).all() + assert (joined["k1_fwds"] == 0.0).all() + assert (joined["length0_bwds"] != 0.0).all() + assert (joined["k0_bwds"] == 0.0).all() fwds = omm_fwds.changed_angles() bwds = omm_bwds.changed_angles() - assert fwds["size0"].equals(bwds["size1"]) - assert fwds["size1"].equals(bwds["size0"]) - assert fwds["k0"].equals(bwds["k1"]) - assert fwds["k1"].equals(bwds["k0"]) + joined = fwds.merge(bwds, on="angle", suffixes=("_fwds", "_bwds")) + + assert joined["size0_fwds"].equals(joined["size1_bwds"]) + assert joined["size1_fwds"].equals(joined["size0_bwds"]) + assert joined["k0_fwds"].equals(joined["k1_bwds"]) + assert joined["k1_fwds"].equals(joined["k0_bwds"]) # also check that parameters are being set equal to zero correctly - assert (fwds["size1"] != 0.0).all() - assert (fwds["k1"] == 0.0).all() - assert (bwds["size0"] != 0.0).all() - assert (bwds["k0"] == 0.0).all() + assert (joined["size1_fwds"] != 0.0).all() + assert (joined["k1_fwds"] == 0.0).all() + assert (joined["size0_bwds"] != 0.0).all() + assert (joined["k0_bwds"] == 0.0).all() fwds = omm_fwds.changed_torsions() bwds = omm_bwds.changed_torsions() - assert fwds["periodicity0"].equals(bwds["periodicity1"]) - assert fwds["periodicity1"].equals(bwds["periodicity0"]) - assert fwds["phase0"].equals(bwds["phase1"]) - assert fwds["phase1"].equals(bwds["phase0"]) - assert fwds["k0"].equals(bwds["k1"]) - assert fwds["k1"].equals(bwds["k0"]) + joined = fwds.merge(bwds, on="torsion", suffixes=("_fwds", "_bwds")) + + assert joined["periodicity0_fwds"].equals(joined["periodicity1_bwds"]) + assert joined["periodicity1_fwds"].equals(joined["periodicity0_bwds"]) + assert joined["phase0_fwds"].equals(joined["phase1_bwds"]) + assert joined["phase1_fwds"].equals(joined["phase0_bwds"]) + assert joined["k0_fwds"].equals(joined["k1_bwds"]) + assert joined["k1_fwds"].equals(joined["k0_bwds"]) # also check that parameters are being set equal to zero correctly - assert (fwds["k1"] == 0.0).all() - assert (bwds["k0"] == 0.0).all() + assert (joined["k1_fwds"] == 0.0).all() + assert (joined["k0_bwds"] == 0.0).all() fwds = omm_fwds.changed_exceptions() bwds = omm_bwds.changed_exceptions() From 269b6cc2afb76cf1f1fd6c93a3af4124c8e9736e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 25 Mar 2024 18:34:09 +0000 Subject: [PATCH 173/468] Writing the tutorial section that documents the softening potential --- doc/source/tutorial/index_part07.rst | 2 + doc/source/tutorial/part07/02_levers.rst | 17 ++- doc/source/tutorial/part07/03_ghosts.rst | 130 +++++++++++++++++++++++ src/sire/cas/__init__.py | 6 +- 4 files changed, 151 insertions(+), 4 deletions(-) create mode 100644 doc/source/tutorial/part07/03_ghosts.rst diff --git a/doc/source/tutorial/index_part07.rst b/doc/source/tutorial/index_part07.rst index 35766ff77..863aa7c08 100644 --- a/doc/source/tutorial/index_part07.rst +++ b/doc/source/tutorial/index_part07.rst @@ -22,3 +22,5 @@ calculating free energies that involve breaking rings in ligands. part07/01_perturbation part07/02_levers + part07/03_ghosts + diff --git a/doc/source/tutorial/part07/02_levers.rst b/doc/source/tutorial/part07/02_levers.rst index 24d3ac3e2..3dac267b4 100644 --- a/doc/source/tutorial/part07/02_levers.rst +++ b/doc/source/tutorial/part07/02_levers.rst @@ -28,7 +28,7 @@ system will be morphed in a single stage (called "morph"), using a linear interpolation between the initial and final values of the parameters. As we saw in the :doc:`last section <01_perturbation>`, we can find the exact -values of all of the perturbable parameters of a perturbable molecle via +values of all of the perturbable parameters of a perturbable molecule via the perturbation object. >>> p = mols[0].perturbation() @@ -51,6 +51,11 @@ and the above schedule will morph the bond length from 0.15375 nm to 0.10969 nm, and the force constant from 251793.12 kJ mol-1 nm-2 to 276646.08 kJ mol-1 nm-2, linearly with respect to λ. +.. note:: + + The parameters are directly as would be used in an OpenMM force, + i.e. in OpenMM default units of nanometers and kilojoules per mole. + Controlling individual levers ----------------------------- @@ -96,6 +101,16 @@ interpolated from the initial to final value by λ^2, rather than λ. All of the other levers continue to use the default equation for this stage, which is the linear interpolation between the initial and final values. +You can change the default equation used for a stage using the +:meth:`~sire.cas.LambdaSchedule.set_default_equation` function, e.g. + +>>> s.set_default_equation(stage="morph", equation=(1-l)*init + l*fin) +>>> print(s) +LambdaSchedule( + morph: initial * (-λ + 1) + final * λ + bond_length: initial * (-λ^2 + 1) + final * λ^2 +) + Controlling individual levers in individual forces -------------------------------------------------- diff --git a/doc/source/tutorial/part07/03_ghosts.rst b/doc/source/tutorial/part07/03_ghosts.rst new file mode 100644 index 000000000..930b0dfc6 --- /dev/null +++ b/doc/source/tutorial/part07/03_ghosts.rst @@ -0,0 +1,130 @@ +======================================== +Ghost Atoms, Anniliations and Decoupling +======================================== + +Ghost atoms are used by the sire/OpenMM interface +to represent atoms that either appear or disappear during a +perturbation. They are used as part of the implementation of a +soft-core potential in OpenMM, to avoid singularities / crashes +when atoms are annihilated or created. + +A ghost atom is one which has zero charge **and** zero LJ parameters in +either the reference or perturbed end states. + +.. note:: + + In this case, "zero LJ parameters" means either the sigma or epsilon + parameter is zero (or both). + + +Only atoms that have a zero charge **and** zero LJ parameters at either +end state are ghost atoms. These atoms are treated differently to the +rest of the atoms in the system. + +All normal atoms (called "non-ghost atoms") are treated as standard atoms +in the sire to OpenMM conversion, and added to standard OpenMM Force objects +(e.g. NonBondedForce, HarmonicBondForce, etc). + +Ghost atoms are treated differently. They are added to the OpenMM Force objects +as other atoms, but with the following key difference: + +* Ghost atoms are added to the NonBondedForce with their standard charge, + but with zero LJ parameters. This means that only the electrostatic + energy and force from ghost atoms is evaluated here. + +Ghost atoms are then added to three custom OpenMM Forces: + +1. A CustomNonbondedForce called the "ghost/ghost" force. This uses a + custom energy function to calculate the soft-core electrostatic and + LJ interactions between all ghost atoms. It also calculates the + "hard" electrostatic interaction and subtracts this from the + total (to remove the real-space contribution that was calculated + in the standard OpenMM NonBondedForce). + +2. A CustomNonbondedForce called the "ghost/non-ghost" force. This uses a + custom energy function to calculate the soft-core electrostatic and + LJ interactions between all ghost atoms and all non-ghost atoms. + It also calculates the "hard" electrostatic interaction and subtracts + this from the total (to remove the real-space contribution that was + calculated in the standard OpenMM NonBondedForce). + +3. A CustomBondForce called the "ghost-14" force. This uses a custom + energy function to calculate the soft-core electrostatic and LJ + interactions between all 1-4 non-bonded interactions involving + ghost atoms. It also calculates the "hard" electrostatic + interaction and subtracts this from the total (to remove the real-space + contribution that was calculated in the standard OpenMM NonBondedForce). + +There are two different soft-core potentials available. The default is +the Zacharias potential, while the second is the Taylor potential. + +Zacharias softening +------------------- + +This is the default soft-core potential. You can also use it by +setting the map option ``use_zacharias_softening`` to True. + +It is based on the following electrostatic and Lennard-Jones potentials: + +.. math:: + + V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}^2}} - \frac{\kappa}{r} \right] + + V_{\text{LJ}}(r) = 4\epsilon \left[ \frac{\sigma^{12}}{(\delta_\text{LJ} \sigma + r^2)^6} - \frac{\sigma^6}{(\delta_\text{LJ} \sigma + r^2)^3} \right] + +where + +.. math:: + + \delta_\text{coulomb} = \alpha \times \text{shift_coulomb} + + \delta_\text{LJ} = \alpha \times \text{shift_LJ} + +and + +.. math:: + + \alpha = \max(\alpha_i, \alpha_j) + + \kappa = \max(\kappa_i, \kappa_j) + +The parameters ``r``, ``q_i``, ``q_j``, ``\epsilon``, and ``\sigma`` +are the standard parameters for the electrostatic and Lennard-Jones +potentials. + +The soft-core parameters are: + +* ``α_i`` and ``α_j`` control the amount of "softening" of the + electrostatic and LJ interactions. A value of 0 means no softening + (fully hard), while a value of 1 means fully soft. Ghost atoms which + disappear as a function of λ have a value of α of 0 in the + reference state, and 1 in the perturbed state. Ghost atoms which appear + as a function of λ have a value of α of 1 in the reference + state, and 0 in the perturbed state. These values can be perturbed + via the ``alpha`` lever in the λ-schedule. + +* ``n`` is the "coulomb power", and is set to 0 by default. It can be + any integer between 0 and 4. It is set via ``coulomb_power`` map + parameter. + +* ``shift_coulomb`` and ``shift_LJ`` are the so-called "shift delta" + parameters, which are specified individually for the coulomb and LJ\ + potentials. They are set via the ``shift_coulomb`` and ``shift_delta`` + map parameters. They default to 1 Å and 2.5 Å respectively. + +* ``κ_i`` and ``κ_j`` are the "hard" electrostatic parameters, + which control whether or not to calculate the "hard" electrostatic + interaction to subtract from the total energy and force (thus cancelling + out the double-counting of this interaction from the NonbondedForce). + By default, these are always equal to 1. You can perturb these via the + ``kappa`` lever in the λ-schedule, e.g. if you want to decouple the + intramolecular electrostatic interactions, when the "hard" interaction + would not be calculated in the NonbondedForce. + + +Taylor softening +---------------- + +This is the second soft-core potential. You can use it by setting the +map option ``use_taylor_softening`` to True. + diff --git a/src/sire/cas/__init__.py b/src/sire/cas/__init__.py index 8de0212a0..59ebd8f14 100644 --- a/src/sire/cas/__init__.py +++ b/src/sire/cas/__init__.py @@ -22,10 +22,10 @@ def _fix_lambdaschedule(): try: LambdaSchedule.__orig__get_lever_values = LambdaSchedule.getLeverValues + LambdaSchedule.set_default_equation = LambdaSchedule.setDefaultStageEquation except AttributeError: - LambdaSchedule.__orig__get_lever_values = ( - LambdaSchedule.get_lever_values - ) + LambdaSchedule.__orig__get_lever_values = LambdaSchedule.get_lever_values + LambdaSchedule.set_default_equation = LambdaSchedule.set_default_stage_equation def get_lever_values( obj, From d8cce6be1a87d37d35eb07c48512b65fafa51c82 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 27 Mar 2024 19:10:55 +0000 Subject: [PATCH 174/468] Changed 1/r to 1/r_safe for custom forces, where r_safe is max(r, 0.001) This should prevent crashes when r < 0.001 --- .../SireOpenMM/sire_to_openmm_system.cpp | 20 +++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index d2a7bf490..bb4733f93 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -891,9 +891,10 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { nb14_expression = QString( "coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r^2))-(kappa/r));" + "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));" "lj_nrg=four_epsilon*sig6*(sig6-1);" - "sig6=(sigma^6)/(%3*sigma^6 + r^6);") + "sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);" + "r_safe=max(r, 0.001);") .arg(coulomb_power_expression("alpha", coulomb_power)) .arg(shift_coulomb) .arg(taylor_power_expression("alpha", taylor_power)) @@ -903,9 +904,10 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { nb14_expression = QString( "coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r^2))-(kappa/r));" + "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));" "lj_nrg=four_epsilon*sig6*(sig6-1);" - "sig6=(sigma^6)/(((sigma*delta) + r^2)^3);" + "sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);" + "r_safe=max(r, 0.001);" "delta=%3*alpha;") .arg(coulomb_power_expression("alpha", coulomb_power)) .arg(shift_coulomb) @@ -949,9 +951,10 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // kJ mol-1 given the units of charge (|e|) and distance (nm) // clj_expression = QString("coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r^2))-(max_kappa/r));" + "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));" "lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);" - "sig6=(sigma^6)/(%3*sigma^6 + r^6);" + "sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);" + "r_safe=max(r, 0.001);" "max_kappa=max(kappa1, kappa2);" "max_alpha=max(alpha1, alpha2);" "sigma=half_sigma1+half_sigma2;") @@ -986,10 +989,11 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // kJ mol-1 given the units of charge (|e|) and distance (nm) // clj_expression = QString("coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r^2))-(max_kappa/r));" + "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));" "lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);" - "sig6=(sigma^6)/(((sigma*delta) + r^2)^3);" + "sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);" "delta=%3*max_alpha;" + "r_safe=max(r, 0.001);" "max_kappa=max(kappa1, kappa2);" "max_alpha=max(alpha1, alpha2);" "sigma=half_sigma1+half_sigma2;") From 9d7f058c7f30a2cbac5669cef79ca62ab7294eb3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 28 Mar 2024 10:35:24 +0000 Subject: [PATCH 175/468] Warn the user if there is a constraint on the QM region. --- src/sire/mol/_dynamics.py | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index bc4f5485a..b10014288 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -40,12 +40,41 @@ def __init__(self, mols=None, map=None, **kwargs): qm_engine = map["qm_engine"].value() from ..legacy.Convert import QMEngine + from warnings import warn if qm_engine and not isinstance(qm_engine, QMEngine): raise ValueError( "'qm_engine' must be an instance of 'sire.legacy.Convert.QMEngine'" ) + # Check the constraints and raise a warning if the perturbable_constraint + # is not "none". + + if map.specified("perturbable_constraint"): + perturbable_constraint = map["perturbable_constraint"].source() + if perturbable_constraint.lower() != "none": + warn( + "Running a QM/MM simulation with constraints on the QM " + "region is not recommended." + ) + else: + # The perturbable constraint is unset, so will follow the constraint. + # Make sure this is "none". + if map.specified("constraint"): + constraint = map["constraint"].source() + if constraint.lower() != "none": + warn( + "Running a QM/MM simulation with constraints on the QM " + "region is not recommended." + ) + # Constraints will be automatically applied, so we can't guarantee that + # the constraint is "none". + else: + warn( + "Running a QM/MM simulation with constraints on the QM " + "region is not recommended." + ) + # see if this is an interpolation simulation if map.specified("lambda_interpolate"): if map["lambda_interpolate"].has_value(): From c825e7b3c29b16b78746abd6148a3ca2843871c7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 28 Mar 2024 10:40:55 +0000 Subject: [PATCH 176/468] Pin to boa version 0.16 and upgrade setup-miniconda. --- .github/workflows/choose_branch.yaml | 4 ++-- .github/workflows/devel.yaml | 4 ++-- .github/workflows/emle.yaml | 4 ++-- .github/workflows/main.yaml | 4 ++-- .github/workflows/pr.yaml | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 611368a6f..df2a4bffb 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -49,7 +49,7 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -62,7 +62,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa=0.16 anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 07d54eb54..e2318f03c 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -44,7 +44,7 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -57,7 +57,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa=0.16 anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 987f676c2..849aaefbd 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -40,7 +40,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -53,7 +53,7 @@ jobs: run: git clone -b feature_emle https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa=0.16 anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 3934946d3..8e89303d1 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -40,7 +40,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -53,7 +53,7 @@ jobs: run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa=0.16 anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index c1badfa4e..617d02e7c 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -46,7 +46,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -59,7 +59,7 @@ jobs: run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa=0.16 anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py From 942abd26b3610726330b6b49516078a50c213162 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 28 Mar 2024 22:56:52 +0000 Subject: [PATCH 177/468] Working on docs - updated miniconda recipe to v3 --- .github/workflows/choose_branch.yaml | 2 +- .github/workflows/devel.yaml | 2 +- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 2 +- doc/source/tutorial/part07/03_ghosts.rst | 56 ++++++++++++++++++++++++ 5 files changed, 60 insertions(+), 4 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 611368a6f..415067fe4 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -49,7 +49,7 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 07d54eb54..653162474 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -44,7 +44,7 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 3934946d3..701684211 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -40,7 +40,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index c1badfa4e..353601602 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -46,7 +46,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} diff --git a/doc/source/tutorial/part07/03_ghosts.rst b/doc/source/tutorial/part07/03_ghosts.rst index 930b0dfc6..d8df4a3ea 100644 --- a/doc/source/tutorial/part07/03_ghosts.rst +++ b/doc/source/tutorial/part07/03_ghosts.rst @@ -128,3 +128,59 @@ Taylor softening This is the second soft-core potential. You can use it by setting the map option ``use_taylor_softening`` to True. +It is based on the following electrostatic and Lennard-Jones potentials: + +.. math:: + + V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}^2}} - \frac{\kappa}{r} \right] + + V_{\text{LJ}}(r) = 4\epsilon \left[ \frac{\sigma^{12}}{(\delta_\text{LJ} \sigma + r^2)^6} - \frac{\sigma^6}{(\delta_\text{LJ} \sigma + r^2)^3} \right] + +where + +.. math:: + + \delta_\text{coulomb} = \alpha \times \text{shift_coulomb} + + \delta_\text{LJ} = \alpha \times \text{shift_LJ} + +and + +.. math:: + + \alpha = \max(\alpha_i, \alpha_j) + + \kappa = \max(\kappa_i, \kappa_j) + +The parameters ``r``, ``q_i``, ``q_j``, ``\epsilon``, and ``\sigma`` +are the standard parameters for the electrostatic and Lennard-Jones +potentials. + +The soft-core parameters are: + +* ``α_i`` and ``α_j`` control the amount of "softening" of the + electrostatic and LJ interactions. A value of 0 means no softening + (fully hard), while a value of 1 means fully soft. Ghost atoms which + disappear as a function of λ have a value of α of 0 in the + reference state, and 1 in the perturbed state. Ghost atoms which appear + as a function of λ have a value of α of 1 in the reference + state, and 0 in the perturbed state. These values can be perturbed + via the ``alpha`` lever in the λ-schedule. + +* ``n`` is the "coulomb power", and is set to 0 by default. It can be + any integer between 0 and 4. It is set via ``coulomb_power`` map + parameter. + +* ``shift_coulomb`` and ``shift_LJ`` are the so-called "shift delta" + parameters, which are specified individually for the coulomb and LJ\ + potentials. They are set via the ``shift_coulomb`` and ``shift_delta`` + map parameters. They default to 1 Å and 2.5 Å respectively. + +* ``κ_i`` and ``κ_j`` are the "hard" electrostatic parameters, + which control whether or not to calculate the "hard" electrostatic + interaction to subtract from the total energy and force (thus cancelling + out the double-counting of this interaction from the NonbondedForce). + By default, these are always equal to 1. You can perturb these via the + ``kappa`` lever in the λ-schedule, e.g. if you want to decouple the + intramolecular electrostatic interactions, when the "hard" interaction + would not be calculated in the NonbondedForce. From 93bc4fd8bbd54417ce5f728cd3e604be4a7e8d58 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 28 Mar 2024 23:12:35 +0000 Subject: [PATCH 178/468] Laying out the structure of the rest of the tutorial --- doc/source/tutorial/index_part07.rst | 2 ++ doc/source/tutorial/part07/03_ghosts.rst | 26 ++++++++++++---------- doc/source/tutorial/part07/04_merge.rst | 5 +++++ doc/source/tutorial/part07/05_decouple.rst | 5 +++++ doc/source/tutorial/part07/06_residue.rst | 6 +++++ 5 files changed, 32 insertions(+), 12 deletions(-) create mode 100644 doc/source/tutorial/part07/04_merge.rst create mode 100644 doc/source/tutorial/part07/05_decouple.rst create mode 100644 doc/source/tutorial/part07/06_residue.rst diff --git a/doc/source/tutorial/index_part07.rst b/doc/source/tutorial/index_part07.rst index 863aa7c08..4ce6e4a82 100644 --- a/doc/source/tutorial/index_part07.rst +++ b/doc/source/tutorial/index_part07.rst @@ -23,4 +23,6 @@ calculating free energies that involve breaking rings in ligands. part07/01_perturbation part07/02_levers part07/03_ghosts + part07/04_merge + part07/05_decouple diff --git a/doc/source/tutorial/part07/03_ghosts.rst b/doc/source/tutorial/part07/03_ghosts.rst index d8df4a3ea..6ca0e65be 100644 --- a/doc/source/tutorial/part07/03_ghosts.rst +++ b/doc/source/tutorial/part07/03_ghosts.rst @@ -1,6 +1,6 @@ -======================================== -Ghost Atoms, Anniliations and Decoupling -======================================== +=========== +Ghost Atoms +=========== Ghost atoms are used by the sire/OpenMM interface to represent atoms that either appear or disappear during a @@ -132,17 +132,15 @@ It is based on the following electrostatic and Lennard-Jones potentials: .. math:: - V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta_\text{coulomb}^2}} - \frac{\kappa}{r} \right] + V_{\text{elec}}(r) = q_i q_j \left[ \frac{(1 - \alpha)^n}{\sqrt{r^2 + \delta^2}} - \frac{\kappa}{r} \right] - V_{\text{LJ}}(r) = 4\epsilon \left[ \frac{\sigma^{12}}{(\delta_\text{LJ} \sigma + r^2)^6} - \frac{\sigma^6}{(\delta_\text{LJ} \sigma + r^2)^3} \right] + V_{\text{LJ}}(r) = 4\epsilon \left[ \frac{\sigma^{12}}{(\alpha^m \sigma^6 + r^6)^2} - \frac{\sigma^6}{\alpha^m \sigma^6 + r^6} \right] where .. math:: - \delta_\text{coulomb} = \alpha \times \text{shift_coulomb} - - \delta_\text{LJ} = \alpha \times \text{shift_LJ} + \delta = \alpha \times \text{shift_coulomb} and @@ -167,14 +165,18 @@ The soft-core parameters are: state, and 0 in the perturbed state. These values can be perturbed via the ``alpha`` lever in the λ-schedule. +* ``m`` is the "taylor power", and is set to 1 by default. It can be + any integer between 0 and 4. It is set via ``taylor_power`` map + parameter. + * ``n`` is the "coulomb power", and is set to 0 by default. It can be any integer between 0 and 4. It is set via ``coulomb_power`` map parameter. -* ``shift_coulomb`` and ``shift_LJ`` are the so-called "shift delta" - parameters, which are specified individually for the coulomb and LJ\ - potentials. They are set via the ``shift_coulomb`` and ``shift_delta`` - map parameters. They default to 1 Å and 2.5 Å respectively. +* ``shift_coulomb`` is the so-called "shift delta" + parameters, which are specified only for the coulomb + potential. This is set via the ``shift_coulomb`` + map parameters. This defaults to 1 Å. * ``κ_i`` and ``κ_j`` are the "hard" electrostatic parameters, which control whether or not to calculate the "hard" electrostatic diff --git a/doc/source/tutorial/part07/04_merge.rst b/doc/source/tutorial/part07/04_merge.rst new file mode 100644 index 000000000..4d3731ce3 --- /dev/null +++ b/doc/source/tutorial/part07/04_merge.rst @@ -0,0 +1,5 @@ +======================== +Creating merge molecules +======================== + +Describe :func:`sire.morph.merge`. diff --git a/doc/source/tutorial/part07/05_decouple.rst b/doc/source/tutorial/part07/05_decouple.rst new file mode 100644 index 000000000..01ec76ba1 --- /dev/null +++ b/doc/source/tutorial/part07/05_decouple.rst @@ -0,0 +1,5 @@ +=========================== +Annihilation and Decoupling +=========================== + +Describe :func:`sire.morph.decouple` and :func:`sire.morph.annihilate`. diff --git a/doc/source/tutorial/part07/06_residue.rst b/doc/source/tutorial/part07/06_residue.rst new file mode 100644 index 000000000..4d9f05fc8 --- /dev/null +++ b/doc/source/tutorial/part07/06_residue.rst @@ -0,0 +1,6 @@ +================= +Residue mutations +================= + +Describe residue mutations and calculating free energies of mutating +residues. From 50dce6c20decebe442329355bb579127a54d0617 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 29 Mar 2024 12:19:42 +0000 Subject: [PATCH 179/468] Working on the tutorial... --- doc/source/tutorial/index_part07.rst | 5 +- doc/source/tutorial/part07/03_ghosts.rst | 36 +++++- doc/source/tutorial/part07/04_merge.rst | 58 +++++++++- doc/source/tutorial/part07/05_pertfile.rst | 108 ++++++++++++++++++ .../{05_decouple.rst => 06_decouple.rst} | 0 .../part07/{06_residue.rst => 07_residue.rst} | 0 .../tutorial/part07/images/07_03_01.jpg | Bin 0 -> 22488 bytes .../tutorial/part07/images/07_04_01.jpg | Bin 0 -> 16567 bytes .../tutorial/part07/images/07_04_02.jpg | Bin 0 -> 11054 bytes src/sire/morph/_perturbation.py | 2 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 1 - 11 files changed, 202 insertions(+), 8 deletions(-) create mode 100644 doc/source/tutorial/part07/05_pertfile.rst rename doc/source/tutorial/part07/{05_decouple.rst => 06_decouple.rst} (100%) rename doc/source/tutorial/part07/{06_residue.rst => 07_residue.rst} (100%) create mode 100644 doc/source/tutorial/part07/images/07_03_01.jpg create mode 100644 doc/source/tutorial/part07/images/07_04_01.jpg create mode 100644 doc/source/tutorial/part07/images/07_04_02.jpg diff --git a/doc/source/tutorial/index_part07.rst b/doc/source/tutorial/index_part07.rst index 4ce6e4a82..174ff8e6b 100644 --- a/doc/source/tutorial/index_part07.rst +++ b/doc/source/tutorial/index_part07.rst @@ -24,5 +24,6 @@ calculating free energies that involve breaking rings in ligands. part07/02_levers part07/03_ghosts part07/04_merge - part07/05_decouple - + part07/05_pertfile + part07/06_decouple + part07/07_residue diff --git a/doc/source/tutorial/part07/03_ghosts.rst b/doc/source/tutorial/part07/03_ghosts.rst index 6ca0e65be..c044b1057 100644 --- a/doc/source/tutorial/part07/03_ghosts.rst +++ b/doc/source/tutorial/part07/03_ghosts.rst @@ -1,6 +1,6 @@ -=========== -Ghost Atoms -=========== +==================================== +Ghost Atoms and Softening Potentials +==================================== Ghost atoms are used by the sire/OpenMM interface to represent atoms that either appear or disappear during a @@ -186,3 +186,33 @@ The soft-core parameters are: ``kappa`` lever in the λ-schedule, e.g. if you want to decouple the intramolecular electrostatic interactions, when the "hard" interaction would not be calculated in the NonbondedForce. + +Good practice +------------- + +Softening potentials can help to avoid singularities and crashes +when atoms are annihilated or created. However, you still need to be +careful when using them. For example, it is best when creating or +destroying an atom to keep the sigma LJ parameter the same for both +end states. This way, only the epsilon parameter is scaled to zero, +while the atom keeps its same "size". This avoids the atom shrinking +as a function of λ, which could result in atoms (and thus charges) +getting too close to one another. + +For complex or large molecules, it may be better to separate out the +decharging from the decoupling or annihilation, e.g. first set up +a λ-schedule to have two stages; the first stage decouples the charges, +while the second stage annihilates or decouples the atoms. + +This could be achieved using the following λ-schedule: + +>>> import sire as sr +>>> s = sr.cas.LambdaSchedule.standard_morph() +>>> s.set_equation(stage="morph", lever="charge", equation=s.final()) +>>> s.prepend_stage("decharge", s.initial()) +>>> s.set_equation(stage="decharge", lever="charge", +... equation=l.lam() * s.final() + s.initial() * (1 - s.lam())) +>>> s.get_lever_values(initial=2.0, final=3.0).plot() + +.. image:: images/07_03_01.jpg + :alt: How parameters would be changed by the above λ-schedule. diff --git a/doc/source/tutorial/part07/04_merge.rst b/doc/source/tutorial/part07/04_merge.rst index 4d3731ce3..5e5f5c74c 100644 --- a/doc/source/tutorial/part07/04_merge.rst +++ b/doc/source/tutorial/part07/04_merge.rst @@ -2,4 +2,60 @@ Creating merge molecules ======================== -Describe :func:`sire.morph.merge`. + +Merged molecules are used in free energy calculations to represent the +perturbation between two molecules; the reference molecule (at λ=0) +and the perturbed molecule (at λ=1). + +To start, let's load up two molecules, neopentane and methane, which we +will use to create a merged molecule to calculate the relative hydration +free energy. + +>>> neopentane = sr.load_test_files("neopentane.prm7", "neopentane.rst")[0] +>>> neopentane.view() + +.. image:: images/07_04_01.jpg + :alt: A picture of neopentane + +>>> methane = sr.load_test_files("methane.prm7", "methane.rst")[0] +>>> methane.view() + +.. image:: images/07_04_02.jpg + :alt: A picture of methane + +Matching atoms +-------------- + +The first step to creating a merged molecule is to decide how atoms +should relate between the two end states. This is done by matching atoms +from the reference molecule (in this case neopentane) to the perturbed +molecule (in this case methane). + +For example, let's say that we want the central carbon of neopentane to +perturb into the central carbon of methane. We could specify this by +creating a dictionary that says that the name of this atom in neopentane +should map to the name of the equivalent atom in methane. + +We can get the name of these atoms using the 3D viewer, as shown above. +The central carbon of neopentane is called ``C1``, while the central +carbon of methane is also called ``C1``. + +>>> matching = {"C1": "C1"} + +Next, we would match each of the other carbon atoms in neopentane to +the hydrogen atoms in methane. + +>>> matching["C2"] = "H2" +>>> matching["C3"] = "H3" +>>> matching["C4"] = "H4" +>>> matching["C5"] = "H5" +>>> print(matching) +{'C1': 'C1', 'C2': 'H2', 'C3': 'H3', 'C4': 'H4', 'C5': 'H5'} + +Merging molecules +----------------- + +We use the :func:`sire.morph.merge` + + + diff --git a/doc/source/tutorial/part07/05_pertfile.rst b/doc/source/tutorial/part07/05_pertfile.rst new file mode 100644 index 000000000..60584e84f --- /dev/null +++ b/doc/source/tutorial/part07/05_pertfile.rst @@ -0,0 +1,108 @@ +============================== +Perturbation Files (pertfiles) +============================== + +Perturbation files (or pertfiles) are an older mechanism that was used +in ``somd`` to create a merged molecule from a passed input molecule. +They are a simple text file that describes the perturbation in terms +of changing forcefield parameters. You can create a merged molecule +from a single molecule plus pertfile using the +:func:`sire.morph.create_from_pertfile` function. + +>>> merged_mol = sr.morph.create_from_pertfile(mol, "neopentane_methane.pert") +>>> print(merged_mol.property("charge0")) + +>>> print(merged_mol.property("charge1")) + +.. note:: + + This is an older mechanism that has many limitations due to the + inherent limits of the pertfile format. It is provided to aid + compatibility with older ``somd`` workflows, but is not + recommended for new use cases. + +Updating internals involving ghost atoms +---------------------------------------- + +Sometimes you want to update the internals (bonds, angles, torsions) when +one or more of the atoms involved are ghosts in either the reference or +perturbed states. + +The function :func:`sire.morph.zero_ghost_torsions` will automatically add +torsion perturbations that zero the force constant of any torsions that +involve ghost atoms in that state. This is useful when you want to +fade in or out torsion forces as ghost atoms appear or disappear. + +>>> mols = sr.morph.zero_ghost_torsions(mols) +>>> print(mols[0].perturbation().to_openmm().changed_torsions()) + torsion k0 k1 periodicity0 periodicity1 phase0 phase1 +0 C5:5-C2:2-C3:3-H11:11 0.66944 0.0 3 3 -0.0 -0.0 +1 C1:1-C2:2-C3:3-H11:11 0.66944 0.0 3 3 -0.0 -0.0 +2 C5:5-C2:2-C3:3-H10:10 0.66944 0.0 3 3 -0.0 -0.0 +3 C3:3-C2:2-C4:4-H12:12 0.66944 0.0 3 3 -0.0 -0.0 +4 C1:1-C2:2-C3:3-H10:10 0.66944 0.0 3 3 -0.0 -0.0 +5 C1:1-C2:2-C5:5-H16:16 0.66944 0.0 3 3 -0.0 -0.0 +6 C5:5-C2:2-C3:3-H9:9 0.66944 0.0 3 3 -0.0 -0.0 +7 C1:1-C2:2-C3:3-H9:9 0.66944 0.0 3 3 -0.0 -0.0 +8 C3:3-C2:2-C1:1-H7:7 0.66944 0.0 3 3 -0.0 -0.0 +9 C3:3-C2:2-C1:1-H8:8 0.66944 0.0 3 3 -0.0 -0.0 +10 C3:3-C2:2-C1:1-H6:6 0.66944 0.0 3 3 -0.0 -0.0 +11 C1:1-C2:2-C5:5-H15:15 0.66944 0.0 3 3 -0.0 -0.0 +12 C4:4-C2:2-C5:5-H17:17 0.66944 0.0 3 3 -0.0 -0.0 +13 C4:4-C2:2-C3:3-H11:11 0.66944 0.0 3 3 -0.0 -0.0 +14 C4:4-C2:2-C3:3-H10:10 0.66944 0.0 3 3 -0.0 -0.0 +15 C4:4-C2:2-C5:5-H16:16 0.66944 0.0 3 3 -0.0 -0.0 +16 C4:4-C2:2-C3:3-H9:9 0.66944 0.0 3 3 -0.0 -0.0 +17 C5:5-C2:2-C4:4-H14:14 0.66944 0.0 3 3 -0.0 -0.0 +18 C5:5-C2:2-C4:4-H13:13 0.66944 0.0 3 3 -0.0 -0.0 +19 C1:1-C2:2-C4:4-H14:14 0.66944 0.0 3 3 -0.0 -0.0 +20 C4:4-C2:2-C5:5-H15:15 0.66944 0.0 3 3 -0.0 -0.0 +21 C3:3-C2:2-C5:5-H17:17 0.66944 0.0 3 3 -0.0 -0.0 +22 C1:1-C2:2-C4:4-H13:13 0.66944 0.0 3 3 -0.0 -0.0 +23 C5:5-C2:2-C4:4-H12:12 0.66944 0.0 3 3 -0.0 -0.0 +24 C1:1-C2:2-C4:4-H12:12 0.66944 0.0 3 3 -0.0 -0.0 +25 C3:3-C2:2-C5:5-H16:16 0.66944 0.0 3 3 -0.0 -0.0 +26 C5:5-C2:2-C1:1-H7:7 0.66944 0.0 3 3 -0.0 -0.0 +27 C5:5-C2:2-C1:1-H8:8 0.66944 0.0 3 3 -0.0 -0.0 +28 C5:5-C2:2-C1:1-H6:6 0.66944 0.0 3 3 -0.0 -0.0 +29 C3:3-C2:2-C5:5-H15:15 0.66944 0.0 3 3 -0.0 -0.0 +30 C3:3-C2:2-C4:4-H14:14 0.66944 0.0 3 3 -0.0 -0.0 +31 C3:3-C2:2-C4:4-H13:13 0.66944 0.0 3 3 -0.0 -0.0 +32 C4:4-C2:2-C1:1-H7:7 0.66944 0.0 3 3 -0.0 -0.0 +33 C4:4-C2:2-C1:1-H8:8 0.66944 0.0 3 3 -0.0 -0.0 +34 C4:4-C2:2-C1:1-H6:6 0.66944 0.0 3 3 -0.0 -0.0 +35 C1:1-C2:2-C5:5-H17:17 0.66944 0.0 3 3 -0.0 -0.0 + +Similarly, the :func:`sire.morph.shrink_ghost_atoms` function will automatically +adjust the bond lengths of bonds that involve ghost atoms, so that they will +either be pulled into, or emerge from their connected atoms. + +>>> mols = sr.morph.shrink_ghost_atoms(mols) +>>> print(mols[0].perturbation().to_openmm(constraint="bonds").changed_constraints()) + atompair length0 length1 +0 C2:2-C3:3 0.15375 0.06000 +1 C5:5-H17:17 0.10969 0.06000 +2 C2:2-C4:4 0.15375 0.10969 +3 C1:1-C2:2 0.15375 0.06000 +4 C1:1-H7:7 0.10969 0.06000 +5 C2:2-C5:5 0.15375 0.06000 +6 C1:1-H8:8 0.10969 0.06000 +7 C1:1-H6:6 0.10969 0.06000 +8 C3:3-H11:11 0.10969 0.06000 +9 C5:5-H15:15 0.10969 0.06000 +10 C3:3-H9:9 0.10969 0.06000 +11 C5:5-H16:16 0.10969 0.06000 +12 C3:3-H10:10 0.10969 0.06000 + +.. note:: + + You can control the length of the ghost bond using the ``length`` + argument, e.g. ``shrink_ghost_atoms(mols, length="0.2A")`` would + shrink the bond to 0.2 Å. The default length is 0.6 Å. + +.. note:: + + In general, you don't often need to pull ghost atoms into or out + from their connected atoms. This is because a soft-core potential + is used to soften interactions involving ghost atoms, such that + they fade away smoothly as they disappear. diff --git a/doc/source/tutorial/part07/05_decouple.rst b/doc/source/tutorial/part07/06_decouple.rst similarity index 100% rename from doc/source/tutorial/part07/05_decouple.rst rename to doc/source/tutorial/part07/06_decouple.rst diff --git a/doc/source/tutorial/part07/06_residue.rst b/doc/source/tutorial/part07/07_residue.rst similarity index 100% rename from doc/source/tutorial/part07/06_residue.rst rename to doc/source/tutorial/part07/07_residue.rst diff --git a/doc/source/tutorial/part07/images/07_03_01.jpg b/doc/source/tutorial/part07/images/07_03_01.jpg new file mode 100644 index 0000000000000000000000000000000000000000..4bcf7f6eccab7b137ba0f28b8f55b553ec63d85b GIT binary patch literal 22488 zcmeHu2|Sfs+xLwODMaS6P(*|ZnKnhHBxQ$=vuuIqpO*SfJo*ajHAgD08ml_ zxBvhk0tj#@06g#t2mAwY=mGq1*8rf7!|>a+E)M6fb#MUy_w+yN`jMicEOH< 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+ from ..legacy.Mol import ( GeometryPerturbations, BondPerturbation, AnglePerturbation, diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 59ccd848a..06038ef28 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -1042,7 +1042,6 @@ double LambdaLever::setLambda(OpenMM::Context &context, // follow whatever is set by lambda, e.g. 'initial*lambda' // to switch them on, or `final*lambda` to switch them off) const double rho = lambda_schedule.morph("*", - restraint, 1.0, 1.0, lambda_value); From c326adca40d5dc707a4781c9207e42ce5c3ae205 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 29 Mar 2024 13:01:36 +0000 Subject: [PATCH 180/468] Continuing the tutorial... --- doc/source/tutorial/part07/04_merge.rst | 16 +++++++++++++++- doc/source/tutorial/part07/images/07_04_03.jpg | Bin 0 -> 20080 bytes src/sire/morph/_perturbation.py | 6 ++++-- 3 files changed, 19 insertions(+), 3 deletions(-) create mode 100644 doc/source/tutorial/part07/images/07_04_03.jpg diff --git a/doc/source/tutorial/part07/04_merge.rst b/doc/source/tutorial/part07/04_merge.rst index 5e5f5c74c..f98a8640d 100644 --- a/doc/source/tutorial/part07/04_merge.rst +++ b/doc/source/tutorial/part07/04_merge.rst @@ -55,7 +55,21 @@ the hydrogen atoms in methane. Merging molecules ----------------- -We use the :func:`sire.morph.merge` +We use the :func:`sire.morph.merge` function to create merged molecules. +This takes in the two molecules you want to merge, and the matching +dictionary you have created. + +>>> merged = sr.morph.merge(mol0=neopentane, mol1=methane, match=matching) +>>> merged.perturbation().view_reference() + +.. image:: images/07_04_03.jpg + :alt: A picture of the merged neopentance to methane + +.. note:: + + The reference state is numbered ``0`` (i.e. ``mol0``) while the + perturbed state is numbered ``1`` (i.e. ``mol1``). 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This is used to remind us what λ-value each state corresponds to. - - +We can see how the underlying OpenMM parameters will be perturbed by +checking the :class:`~sire.legacy.Convert.PerturbableOpenMMMolecule` +that would be created from the merged molecule. + +>>> p = merged.perturbation().to_openmm() +>>> print(p.changed_atoms()) + atom charge0 charge1 sigma0 sigma1 epsilon0 epsilon1 alpha0 alpha1 kappa0 kappa1 +0 C2:1 -0.085335 0.0271 0.339967 0.264953 0.457730 0.065689 0.0 0.0 0.0 0.0 +1 C1:2 -0.060235 -0.1084 0.339967 0.339967 0.457730 0.457730 0.0 0.0 0.0 0.0 +2 C3:3 -0.085335 0.0271 0.339967 0.264953 0.457730 0.065689 0.0 0.0 0.0 0.0 +3 C4:4 -0.085335 0.0271 0.339967 0.264953 0.457730 0.065689 0.0 0.0 0.0 0.0 +4 C5:5 -0.085335 0.0271 0.339967 0.264953 0.457730 0.065689 0.0 0.0 0.0 0.0 +5 H6:6 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +6 H7:7 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +7 H8:8 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +8 H9:9 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +9 H10:10 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +10 H11:11 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +11 H12:12 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +12 H13:13 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +13 H14:14 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +14 H15:15 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +15 H16:16 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +16 H17:17 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 + +We can see here that the five carbons in neopentane have their charge +and LJ parameters perturbed from the neopentane values to the methane +values. + +We can also see that the hydrogens in neopentane are converted to ghost +atoms, as they have no match in methane. The conversion to ghost atoms +involves setting their charge to zero, and setting the LJ epsilon parameter +of the atoms to zero (keeping the sigma parameter the same, as suggested +as best practice in the :doc:`last tutorial <03_ghosts>`). + +Note also how the alpha parameters of the hydrogens changes from 0 to 1 +as those atoms become ghosts. + +We can also look at the changes in internal parameters. + +>>> print(p.changed_bonds()) + bond length0 length1 k0 k1 +0 C2:1-C1:2 0.15375 0.10969 251793.12 276646.08 +1 C1:2-C3:3 0.15375 0.10969 251793.12 276646.08 +2 C1:2-C4:4 0.15375 0.10969 251793.12 276646.08 +3 C1:2-C5:5 0.15375 0.10969 251793.12 276646.08 +>>> print(p.changed_angles()) + angle size0 size1 k0 k1 +0 C4:4-C1:2-C5:5 1.946217 1.877626 526.3472 329.6992 +1 C3:3-C1:2-C4:4 1.946217 1.877626 526.3472 329.6992 +2 C3:3-C1:2-C5:5 1.946217 1.877626 526.3472 329.6992 +3 C2:1-C1:2-C3:3 1.946217 1.877626 526.3472 329.6992 +4 C2:1-C1:2-C4:4 1.946217 1.877626 526.3472 329.6992 +5 C2:1-C1:2-C5:5 1.946217 1.877626 526.3472 329.6992 +>>> print(p.changed_torsions()) +Empty DataFrame +Columns: [torsion, k0, k1, periodicity0, periodicity1, phase0, phase1] +Index: [] + +We can see that the bond lengths and angles are perturbed from their values +in neopentane (representing C-C bonds and C-C-C angles) to their values +in methane (representing C-H bonds and H-C-H angles). Note that the +bonds, angles and torsions for the hydrogens in neopentane are not +perturbed. This is because all of these atoms are converted to ghost atoms, +and the default is that internals involving ghost atoms keep the parameters +from the end state where they are not ghosts (i.e. the reference state +values in this case). + +Implementation - AtomMapping +---------------------------- + +Under the hood, the above merge was implemented via the +:class:`sire.mol.AtomMapping` class. This class holds all of the information +about how atoms are mapped between end states, and an object of this +class was created automatically by the :func:`~sire.morph.merge` function. + +We can create the mapping object directly using the +:func:`sire.morph.match` function. + +>>> m = sr.morph.match(mol0=neopentane, mol1=methane, match=matching) +>>> print(m) +AtomMapping( size=5, unmapped0=12, unmapped1=0 +0: MolNum(3) Atom( C1:2 ) <=> MolNum(2) Atom( C1:2 ) +1: MolNum(3) Atom( C2:1 ) <=> MolNum(2) Atom( H2:1 ) +2: MolNum(3) Atom( C4:4 ) <=> MolNum(2) Atom( H4:4 ) +3: MolNum(3) Atom( C3:3 ) <=> MolNum(2) Atom( H3:3 ) +4: MolNum(3) Atom( C5:5 ) <=> MolNum(2) Atom( H5:5 ) +) + +This shows how the five carbon atoms in neopentane are mapped to the +carbon and four hydrogens of methane. It also shows how 12 atoms in the +reference state are unmapped (``unmapped0=12``) and how no atoms in the +perturbed state are unmapped (``unmapped1=0``). + +This class has some useful functions. One is +:func:`~sire.mol.AtomMapping.align`, which aligns the perturbed state +against the reference state, using an algorithm that minimises the +RMSD of the mapped atoms. + +>>> m = m.align() + +Another useful function is :func:`~sire.mol.AtomMapping.merge`, which +actually performs the merge, returning the merged molecule, with +perturbable properties linked to the reference state. + +>>> merged = m.merge() +>>> print(merged) +Molecule( NEO:7 num_atoms=17 num_residues=1 ) + +The :func:`~sire.morph.merge` function is really a wrapper that create +this :class:`~sire.mol.AtomMapping` object, calls align, and then +calls the :func:`~sire.mol.AtomMapping.merge` function. + +Automatic matching +------------------ + +Creating the matching dictionary by hand can be a bit tedious! Fortunately, +there are lots of tools that can help automate this process. + +One such tool is the above :func:`~sire.morph.match` function. If you don't +pass in a ``match`` argument, then an internal maximum common substructure +algorithm will be used to try to infer the matching. + +>>> m = sr.morph.match(mol0=neopentane, mol1=methane) +>>> print(m) +AtomMapping( size=1, unmapped0=16, unmapped1=4 +0: MolNum(3) Atom( C2:1 ) <=> MolNum(2) Atom( C1:2 ) +) + +.. warning:: + + The maximum common substructure algorithm is not supported on Windows. + This will only work on MacOS and Linux. + +By default, this algorithm ignores hydrogens. This is why only a single +atom was matched above. You can change this by passing in the +``ignore_light_atoms=True`` argument. + +>>> m = sr.morph.match(mol0=neopentane, mol1=methane, match_light_atoms=True) +>>> print(m) +AtomMapping( size=4, unmapped0=13, unmapped1=1 +0: MolNum(3) Atom( C2:1 ) <=> MolNum(2) Atom( C1:2 ) +1: MolNum(3) Atom( H6:6 ) <=> MolNum(2) Atom( H2:1 ) +2: MolNum(3) Atom( H8:8 ) <=> MolNum(2) Atom( H4:4 ) +3: MolNum(3) Atom( H7:7 ) <=> MolNum(2) Atom( H3:3 ) +) + +Note how this has come up with a different mapping than the one we created +manually. + +The internal algorithm is quite slow, especially for large molecules. +It is also not aware of stereochemistry, and generally not recommended +if other tools are available. + +Fortunately, because the funtion accepts a python dictionary, it is very +easy to use other tools to generate the mapping and pass to this function. From 204cd90740876b5865f927a6332d04ccc303525e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 29 Mar 2024 18:03:23 +0000 Subject: [PATCH 182/468] Finished the merge section of the tutorial. Included a description on how to use Kartograf mappings --- doc/source/tutorial/part07/04_merge.rst | 219 +++++++++++++++++++++++- 1 file changed, 218 insertions(+), 1 deletion(-) diff --git a/doc/source/tutorial/part07/04_merge.rst b/doc/source/tutorial/part07/04_merge.rst index 8d98dbd8f..625c6e558 100644 --- a/doc/source/tutorial/part07/04_merge.rst +++ b/doc/source/tutorial/part07/04_merge.rst @@ -2,7 +2,6 @@ Creating merge molecules ======================== - Merged molecules are used in free energy calculations to represent the perturbation between two molecules; the reference molecule (at λ=0) and the perturbed molecule (at λ=1). @@ -227,3 +226,221 @@ if other tools are available. Fortunately, because the funtion accepts a python dictionary, it is very easy to use other tools to generate the mapping and pass to this function. + +Using Kartograf mappings +------------------------ + +`Kartograf `__ is a package +for generating atom mappings which takes into account 3D geometries. +This means that mappings can account for stereochemistry. It is also +extremely fast and robust, with lots of active development. It is a very +good choice for generating atom mappings. + +To use Kartograf, you may need to install it. You can do this with conda. + +.. code-block:: bash + + conda install -c conda-forge kartograf + +Next, we will import the components of Kartograf that we need. + +>>> from kartograf.atom_aligner import align_mol_shape +>>> from kartograf import KartografAtomMapper, SmallMoleculeComponent + +Kartograf can work from RDKit molecules, so we'll now convert our sire +molecules to RDKit. + +>>> rd_neopentane = sr.convert.to(neopentane, "rdkit") +>>> rd_methane = sr.convert.to(methane, "rdkit") + +Next, we will create two Kartograf molecules from these RDKit molecules. + +>>> k_neopentane, k_methane = [ +... SmallMoleculeComponent.from_rdkit(m) for m in [rd_neopentane, rd_methane] +... ] + +Now, we align the molecules based on their shape, aligning methane on top +of neopentane. + +>>> k_aligned_methane = align_mol_shape(k_methane, ref_mol=k_neopentane) + +To generate the mappings, we will create a KartografAtomMapper object +which is allowed to match light atoms. + +>>> mapper = KartografAtomMapper(atom_map_hydrogens=True) + +This can be used to generate the mappings. + +>>> mappings = mapper.suggest_mappings(k_neopentane, k_aligned_methane) + +We will now get the first mapping... + +>>> mapping = next(mappings) +>>> print(mapping) +LigandAtomMapping(componentA=SmallMoleculeComponent(name=NEO), + componentB=SmallMoleculeComponent(name=CH4), + componentA_to_componentB={1: 0, 11: 2, 12: 3, 13: 4, 3: 1}, + annotations={}) + +The mappings are atom indexes. We can collect these and create a +dictionary that maps from atom index to atom index using this code. + +>>> matching = {} +>>> for atom0, atom1 in mapping.componentA_to_componentB.items(): +... matching[sr.atomid(idx=atom0)] = sr.atomid(idx=atom1) +>>> print(matching) +{AtomIdx(1): AtomIdx(0), AtomIdx(11): AtomIdx(2), AtomIdx(12): AtomIdx(3), + AtomIdx(13): AtomIdx(4), AtomIdx(3): AtomIdx(1)} + +Finally, we can pass this into the :func:`~sire.morph.match` function +to create the :class:`~sire.mol.AtomMapping` object. + +>>> mapping = sr.morph.match(mol0=neopentane, mol1=methane, match=matching) +>>> print(mapping) +AtomMapping( size=5, unmapped0=12, unmapped1=0 +0: MolNum(3) Atom( H12:12 ) <=> MolNum(2) Atom( H3:3 ) +1: MolNum(3) Atom( H14:14 ) <=> MolNum(2) Atom( H5:5 ) +2: MolNum(3) Atom( H13:13 ) <=> MolNum(2) Atom( H4:4 ) +3: MolNum(3) Atom( C1:2 ) <=> MolNum(2) Atom( H2:1 ) +4: MolNum(3) Atom( C4:4 ) <=> MolNum(2) Atom( C1:2 ) +) + +Automatic Kartograf mapping +--------------------------- + +The above code can be quite tedious to write, so we have created the +ability to pass in a ``KartografAtomMapper`` object as the ``match`` +argument to the :func:`~sire.morph.match` and :func:`~sire.morph.merge` +functions, which then does all of the above automatically. + +>>> mapper = KartografAtomMapper(atom_map_hydrogens=True) +>>> mapping = sr.morph.match(mol0=neopentane, mol1=methane, match=mapper) +>>> print(mapping) +AtomMapping( size=5, unmapped0=12, unmapped1=0 +0: MolNum(3) Atom( H12:12 ) <=> MolNum(2) Atom( H3:3 ) +1: MolNum(3) Atom( H14:14 ) <=> MolNum(2) Atom( H5:5 ) +2: MolNum(3) Atom( H13:13 ) <=> MolNum(2) Atom( H4:4 ) +3: MolNum(3) Atom( C1:2 ) <=> MolNum(2) Atom( H2:1 ) +4: MolNum(3) Atom( C4:4 ) <=> MolNum(2) Atom( C1:2 ) +) +>>> merged = sr.morph.merge(mol0=neopentane, mol1=methane, match=mapper) +>>> print(merged) +Molecule( NEO:8 num_atoms=17 num_residues=1 ) +>>> m = merged.perturbation().to_openmm() +>>> print(m.changed_atoms()) + atom charge0 charge1 sigma0 sigma1 epsilon0 epsilon1 alpha0 alpha1 kappa0 kappa1 +0 C2:1 -0.085335 0.0000 0.339967 0.339967 0.457730 0.000000 0.0 1.0 1.0 1.0 +1 C1:2 -0.060235 0.0271 0.339967 0.264953 0.457730 0.065689 0.0 0.0 0.0 0.0 +2 C3:3 -0.085335 0.0000 0.339967 0.339967 0.457730 0.000000 0.0 1.0 1.0 1.0 +3 C4:4 -0.085335 -0.1084 0.339967 0.339967 0.457730 0.457730 0.0 0.0 0.0 0.0 +4 C5:5 -0.085335 0.0000 0.339967 0.339967 0.457730 0.000000 0.0 1.0 1.0 1.0 +5 H6:6 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +6 H7:7 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +7 H8:8 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +8 H9:9 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +9 H10:10 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +10 H11:11 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +11 H12:12 0.033465 0.0271 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +12 H13:13 0.033465 0.0271 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +13 H14:14 0.033465 0.0271 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +14 H15:15 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +15 H16:16 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +16 H17:17 0.033465 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 + +This is a much easier way to create merged molecules! + +Extracting the end states +------------------------- + +As with all merged molecules, we can extract the end states via the +:func:`sire.morph.extract_reference` and :func:`sire.morph.extract_perturbed` +functions. + +>>> neopentane = sr.morph.extract_reference(merged) +>>> print(neopentane.atoms()) +Selector( size=17 +0: Atom( C2:1 [ 2.24, 1.01, 0.00] ) +1: Atom( C1:2 [ 1.26, 0.09, -0.75] ) +2: Atom( C3:3 [ 0.99, 0.66, -2.15] ) +3: Atom( C4:4 [ -0.06, -0.00, 0.04] ) +4: Atom( C5:5 [ 1.88, -1.32, -0.88] ) +... +12: Atom( H13:13 [ -0.78, -0.67, -0.49] ) +13: Atom( H14:14 [ 0.11, -0.42, 1.05] ) +14: Atom( H15:15 [ 2.83, -1.27, -1.44] ) +15: Atom( H16:16 [ 2.08, -1.75, 0.13] ) +16: Atom( H17:17 [ 1.19, -2.00, -1.42] ) +) +>>> methane = sr.morph.extract_perturbed(merged) +>>> print(methane.atoms()) +Selector( size=5 +0: Atom( H2:2 [ -0.45, 1.01, 0.10] ) +1: Atom( C1:4 [ -0.00, 0.00, 0.00] ) +2: Atom( H3:12 [ -0.71, -0.67, -0.53] ) +3: Atom( H4:13 [ 0.95, 0.07, -0.57] ) +4: Atom( H5:14 [ 0.21, -0.41, 1.01] ) +) + +The names of the atoms and residues are preserved in the merged molecule, +meaning that they are correctly output for each end state. In the merged +molecule, the atom and residue names default to the reference state names. +The perturbed state names are held in the "alternate" names. + +>>> print(merged.residues()[0].name(), merged.residues()[0].alternate_name()) +ResName('NEO') ResName('CH4') +>>> print(merged[1].name(), merged[1].alternate_name()) +AtomName('C1') AtomName('H2') + +Atoms that are unmapped in an end state are called ``Xxx``, e.g. + +>>> print(merged[0].name(), merged[0].alternate_name()) +AtomName('C2') AtomName('Xxx') + +You can switch between the standard and alternate names of a molecule +by calling the :func:`~sire.legacy.Mol.MolEditor.switch_to_alternate_names` +function. + +>>> print(merged.atoms()) +Selector( size=17 +0: Atom( C2:1 [ 2.24, 1.01, 0.00] ) +1: Atom( C1:2 [ 1.26, 0.09, -0.75] ) +2: Atom( C3:3 [ 0.99, 0.66, -2.15] ) +3: Atom( C4:4 [ -0.06, -0.00, 0.04] ) +4: Atom( C5:5 [ 1.88, -1.32, -0.88] ) +... +12: Atom( H13:13 [ -0.78, -0.67, -0.49] ) +13: Atom( H14:14 [ 0.11, -0.42, 1.05] ) +14: Atom( H15:15 [ 2.83, -1.27, -1.44] ) +15: Atom( H16:16 [ 2.08, -1.75, 0.13] ) +16: Atom( H17:17 [ 1.19, -2.00, -1.42] ) +) +>>> merged = merged.edit().switch_to_alternate_names().commit() +>>> print(merged.atoms()) +Selector( size=17 +0: Atom( Xxx:1 [ 2.24, 1.01, 0.00] ) +1: Atom( H2:2 [ 1.26, 0.09, -0.75] ) +2: Atom( Xxx:3 [ 0.99, 0.66, -2.15] ) +3: Atom( C1:4 [ -0.06, -0.00, 0.04] ) +4: Atom( Xxx:5 [ 1.88, -1.32, -0.88] ) +... +12: Atom( H4:13 [ -0.78, -0.67, -0.49] ) +13: Atom( H5:14 [ 0.11, -0.42, 1.05] ) +14: Atom( Xxx:15 [ 2.83, -1.27, -1.44] ) +15: Atom( Xxx:16 [ 2.08, -1.75, 0.13] ) +16: Atom( Xxx:17 [ 1.19, -2.00, -1.42] ) +) +>>> merged = merged.edit().switch_to_alternate_names().commit() +>>> print(merged.atoms()) +Selector( size=17 +0: Atom( C2:1 [ 2.24, 1.01, 0.00] ) +1: Atom( C1:2 [ 1.26, 0.09, -0.75] ) +2: Atom( C3:3 [ 0.99, 0.66, -2.15] ) +3: Atom( C4:4 [ -0.06, -0.00, 0.04] ) +4: Atom( C5:5 [ 1.88, -1.32, -0.88] ) +... +12: Atom( H13:13 [ -0.78, -0.67, -0.49] ) +13: Atom( H14:14 [ 0.11, -0.42, 1.05] ) +14: Atom( H15:15 [ 2.83, -1.27, -1.44] ) +15: Atom( H16:16 [ 2.08, -1.75, 0.13] ) +16: Atom( H17:17 [ 1.19, -2.00, -1.42] ) +) From 0e92aaae6ff0556c0fd5ebf0a1493a7314d549f0 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 29 Mar 2024 18:47:43 +0000 Subject: [PATCH 183/468] Working on the decoupling chapter. Working on how to handle kappa for decoupling --- corelib/src/libs/SireCAS/lambdaschedule.cpp | 23 ++- doc/source/tutorial/part07/06_decouple.rst | 154 +++++++++++++++++++- 2 files changed, 170 insertions(+), 7 deletions(-) diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp index 62f48ad29..582240015 100644 --- a/corelib/src/libs/SireCAS/lambdaschedule.cpp +++ b/corelib/src/libs/SireCAS/lambdaschedule.cpp @@ -691,15 +691,26 @@ void LambdaSchedule::addDecoupleStage(bool perturbed_is_decoupled) */ void LambdaSchedule::addDecoupleStage(const QString &name, bool perturbed_is_decoupled) { - auto state = LambdaSchedule::initial(); + this->addStage(name, default_morph_equation); - if (not perturbed_is_decoupled) - state = LambdaSchedule::final(); + // we now need to ensure that the ghost/ghost parameters are not + // perturbed + if (perturbed_is_decoupled) + { + this->setEquation(name, "ghost/ghost", "*", this->initial()); - this->addStage(name, state); + // we also need to scale down kappa as the decoupled state is + // not evaluated in the NonbondedForce, so must not be cancelled + this->setEquation(name, "ghost/ghost", "kappa", 1.0 - this->lam()); + } + else + { + this->setEquation(name, "ghost/ghost", "*", this->final()); - // the only thing we scale with lambda is the ghost/non-ghost force - this->setEquation(name, "ghost/non-ghost", "*", default_morph_equation); + // we also need to scale up kappa as the decoupled state is + // not evaluated in the NonbondedForce, so must not be cancelled + this->setEquation(name, "ghost/ghost", "kappa", this->lam()); + } } /** Add a stage to the schedule that will annihilate the perturbed diff --git a/doc/source/tutorial/part07/06_decouple.rst b/doc/source/tutorial/part07/06_decouple.rst index 01ec76ba1..26e1f2ebe 100644 --- a/doc/source/tutorial/part07/06_decouple.rst +++ b/doc/source/tutorial/part07/06_decouple.rst @@ -2,4 +2,156 @@ Annihilation and Decoupling =========================== -Describe :func:`sire.morph.decouple` and :func:`sire.morph.annihilate`. +So far, we have discussed how to construct merge molecules that represent +perturbations from one molecule to another. These are useful for +relative free energy calculations. + +Absolute free energy calculations require perturbations that decouple +or annihilate molecules. The :func:`sire.morph.decouple` and +:func:`sire.morph.annihilate` create merged molecules that represent +these perturbations. + +Decoupling +---------- + +Decoupling is the process of turning off the interactions between the +molecule of interest, and all other molecules in the system. + +For example, let's load up a system comprising benzene in a box of +water (with some ions). + +>>> import sire as sr +>>> mols = sr.load_test_files("benzene.prm7", "benzene.rst") +>>> benzene = mols[0] +>>> print(benzene) +Molecule( BEN:2 num_atoms=12 num_residues=1 ) + +We can create a merged molecule that represents the decoupling of the +benzene via the :func:`sire.morph.decouple` function. + +>>> benzene = sr.morph.decouple(benzene, as_new_molecule=False) +>>> print(benzene) +Molecule( BEN:2 num_atoms=12 num_residues=1 ) + +.. note:: + + We pass in ``as_new_molecule=False`` so that the resulting merged + molecule keeps the same molecule number as the original benzene. + If we had passed in ``as_new_molecule=True`` (which is the default) + then the returned molecule would be a "new" molecule, with its + own, unique molecule number. + +The decoupled benzene molecule is a merged molecule where all of the +atoms are converted to ghost atoms. + +>>> p = benzene.perturbation().to_openmm() +>>> print(p.changed_atoms()) + atom charge0 charge1 sigma0 sigma1 epsilon0 epsilon1 alpha0 alpha1 kappa0 kappa1 +0 C:1 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +1 C2:2 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +2 C3:3 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +3 C4:4 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +4 C5:5 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +5 C6:6 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +6 H1:7 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +7 H2:8 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +8 H3:9 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +9 H4:10 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +10 H5:11 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +11 H6:12 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 + +.. note:: + + Note how the atoms are converted to ghosts by setting the charge and epsilon + parameters to zero, and setting the alpha value to 1.0 in the end state, + and the kappa values to 1.0 in both end states. + +All of the internals (bonds, angles, torsions) are kept the same at both +end states. + +>>> print(p.changed_bonds()) +Empty DataFrame +Columns: [bond, length0, length1, k0, k1] +Index: [] +>>> print(p.changed_angles()) +Empty DataFrame +Columns: [angle, size0, size1, k0, k1 +Index: [] +>>> print(p.changed_torsions()) +Empty DataFrame +Columns: [torsion, k0, k1, periodicity0, periodicity1, phase0, phase1] +Index: [] + +To decouple the benzene molecule correctly, a custom :class:`sire.cas.LambdaSchedule` +is needed. This schedule turns off intermolecular interactions involving the +benzene, while keeping the intramolecular interactions the same. + +The :func:`sire.morph.decouple` function creates a suitable schedule by +default, and attaches it to the merged molecule via its ``schedule`` +property. + +>>> schedule = benzene.property("schedule") +>>> print(schedule) +LambdaSchedule( + decouple: (-λ + 1) * initial + λ * final + ghost/ghost::*: initial + ghost/ghost::kappa: -λ + 1 +) + +This schedule has a single stage called ``decouple``. The default is that +all levers use the standard morphing equation to linearly interpolate +from the initial to final states. This has the effect of turning off +all charge and LJ interactions involving benzene. + +However, we want to preserve the intramolecular charge and LJ interactions +of benzene. Since all atoms are ghost atoms, these are +all evaluated in the ghost/ghost force. We therefore set all levers +in the ghost/ghost force to use the parameters in the initial state +(i.e. the full charges and epsilon LJ parameters for benzene). + +But, because the ghost/ghost force includes a correction to subtract +a double-counted electrostatic interaction from the NonbondedForce, +we also need to have a lever that scales kappa with 1-λ. In this way, +the kappa parameter will ensure that the correction is applied at +λ=0, when the electrostatic interactions of benzene are evaluated in both +the NonbondedForce and the ghost/ghost force, while it will scale kappa +to 0 at λ=1, when the electrostatic interactions of benzene are only +evaluated in the ghost/ghost force. + +We can view exactly how a schedule will perturb the real parameters of +a merged molecule using the.... + +FUNCTION THAT DOES THIS! + +Running a decoupling simulation +------------------------------- + +We can run a decoupling simulation in the same way as any other +free energy simulation. + +First, we will update the system to use the decoupled benzene molecule. + +>>> mols.update(benzene) + +This works because we used ``as_new_molecule=False`` when creating +the merged molecule, so it kept its original molecule number. + +Next, we will create a simulation object. + +>>> d = mols.dynamics(timestep="2fs", temperature="25oC", +... schedule=schedule, lambda_value=1.0) +>>> d.run("100ps", lambda_windows=[0.0, 0.5, 1.0]) +>>> print(d.energy_trajectory()) +EnergyTrajectory( size=4 +time lambda 0.0 0.5 1.0 kinetic potential +25 1.0 8.04862e+06 -8780.12 -8940.64 1583.16 -8940.64 +50 1.0 7.02803e+10 -8675.02 -8922.59 1637.65 -8922.59 +75 1.0 1.65099e+06 -8568.8 -8812.94 1607.64 -8812.94 +100 1.0 2.34737e+09 -8340.83 -8894.35 1599.82 -8894.35 +) + +.. note:: + + We expect the energies at λ=0 to be high in this case, as the simulation + was run at λ=1, where the benzene is not interacting with the the rest + of the system, and thus free to overlap with other atoms. From 27d84533d1380b9cb8b2acf2169ae6a5db3fa3b1 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 12:16:29 +0000 Subject: [PATCH 184/468] Working on a function to print out all of the parameters as a function of lambda for a given LambdaSchedule for a given PerturbableOpenMMMolecule. This should make debugging easier :-) --- .../Convert/SireOpenMM/LambdaLever.pypp.cpp | 21 + .../_SireOpenMM_free_functions.pypp.cpp | 40 ++ wrapper/Convert/SireOpenMM/_perturbablemol.py | 52 ++ wrapper/Convert/SireOpenMM/lambdalever.cpp | 487 ++++++++++++++++++ wrapper/Convert/SireOpenMM/lambdalever.h | 3 + wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 8 + wrapper/Convert/SireOpenMM/openmmmolecule.h | 2 + wrapper/Convert/__init__.py | 2 + 8 files changed, 615 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp index 4602fc721..ac45c54ee 100644 --- a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp @@ -7,12 +7,20 @@ namespace bp = boost::python; +#include "SireBase/arrayproperty.hpp" + +#include "SireBase/propertymap.h" + #include "SireCAS/values.h" #include "lambdalever.h" #include "tostring.h" +#include "SireBase/arrayproperty.hpp" + +#include "SireBase/propertymap.h" + #include "SireCAS/values.h" #include "lambdalever.h" @@ -96,6 +104,19 @@ void register_LambdaLever_class(){ , bp::release_gil_policy() , "Get the C++ type of the force called name. Returns an\n empty string if there is no such force\n" ); + } + { //::SireOpenMM::LambdaLever::getLeverValues + + typedef ::SireBase::PropertyList ( ::SireOpenMM::LambdaLever::*getLeverValues_function_type)( ::QVector< double > const &,::SireOpenMM::PerturbableOpenMMMolecule const & ) const; + getLeverValues_function_type getLeverValues_function_value( &::SireOpenMM::LambdaLever::getLeverValues ); + + LambdaLever_exposer.def( + "getLeverValues" + , getLeverValues_function_value + , ( bp::arg("lambda_values"), bp::arg("mol") ) + , bp::release_gil_policy() + , "" ); + } { //::SireOpenMM::LambdaLever::getPerturbableMoleculeMaps diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp index 172713bbb..e75947576 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp @@ -991,8 +991,18 @@ namespace bp = boost::python; #include +#include + +#include + +#include + +#include + #include +#include + #include #include @@ -1021,8 +1031,18 @@ namespace bp = boost::python; #include +#include + +#include + +#include + +#include + #include +#include + #include #include @@ -1051,8 +1071,18 @@ namespace bp = boost::python; #include +#include + +#include + +#include + +#include + #include +#include + #include #include @@ -1081,8 +1111,18 @@ namespace bp = boost::python; #include +#include + +#include + +#include + +#include + #include +#include + #include #include diff --git a/wrapper/Convert/SireOpenMM/_perturbablemol.py b/wrapper/Convert/SireOpenMM/_perturbablemol.py index b6b4da935..fa5158b13 100644 --- a/wrapper/Convert/SireOpenMM/_perturbablemol.py +++ b/wrapper/Convert/SireOpenMM/_perturbablemol.py @@ -5,9 +5,61 @@ "_changed_torsions", "_changed_exceptions", "_changed_constraints", + "_get_lever_values", ] +def _get_lever_values( + obj, + schedule=None, + lambda_values=None, + num_lambda: int = 101, + to_pandas: bool = True, +): + """ + Return the value of all of the parameters for this perturbable molecule + at all of the specified values of lambda, given the passed + lambda schedule. If no schedule is passed then a default morph + will be used. + """ + if lambda_values is None: + import numpy as np + + lambda_values = np.linspace(0.0, 1.0, num_lambda) + + lambda_values = [float(x) for x in lambda_values] + + if schedule is None: + from ...cas import LambdaSchedule + + schedule = LambdaSchedule.standard_morph() + + from . import LambdaLever + + lever = LambdaLever() + lever.set_schedule(schedule) + + results = lever.get_lever_values(lambda_values=lambda_values, mol=obj) + + if to_pandas: + import pandas as pd + + colnames = results[0] + columns = results + columns.pop_front() + + results = {} + + results["index"] = list(range(len(columns[0]))) + + for i in range(len(colnames)): + results[colnames[i]] = [x for x in columns[i]] + + results = pd.DataFrame(results) + + return results + + def _name(atom): return f"{atom.name().value()}:{atom.number().value()}" diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 06038ef28..cb0d58edc 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -28,12 +28,16 @@ #include "lambdalever.h" +#include "SireBase/propertymap.h" +#include "SireBase/arrayproperty.hpp" + #include "SireCAS/values.h" #include "tostring.h" using namespace SireOpenMM; using namespace SireCAS; +using namespace SireBase; ////// ////// Implementation of MolLambdaCache @@ -402,6 +406,489 @@ get_exception(int atom0, int atom1, int start_index, alpha, kappa); } +/** Get all of the lever values that would be set for the passed + * lambda values using the current context. This returns a PropertyList + * of columns, where each column is a PropertyMap with the column name + * and either double or QString array property of values. + * + * This is designed to be used by a higher-level python function that + * will convert this output into, e.g. a pandas DataFrame + */ +PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, + const PerturbableOpenMMMolecule &mol) const +{ + if (lambda_values.isEmpty() or this->lambda_schedule.isNull() or mol.isNull()) + return PropertyList(); + + PropertyList ret; + + const auto &schedule = this->lambda_schedule.getMoleculeSchedule(0); + + QVector force; + QVector lever; + QVector column_names; + + bool is_first = true; + + for (auto lambda_value : lambda_values) + { + lambda_value = this->lambda_schedule.clamp(lambda_value); + + const auto &cache = this->lambda_cache.get(0, lambda_value); + + QVector vals; + + const auto morphed_charges = cache.morph( + schedule, + "clj", "charge", + mol.getCharges0(), + mol.getCharges1()); + + vals += morphed_charges; + + if (is_first) + { + force += QVector(morphed_charges.count(), "clj"); + lever += QVector(morphed_charges.count(), "charge"); + } + + const auto morphed_sigmas = cache.morph( + schedule, + "clj", "sigma", + mol.getSigmas0(), + mol.getSigmas1()); + + vals += morphed_sigmas; + + if (is_first) + { + force += QVector(morphed_sigmas.count(), "clj"); + lever += QVector(morphed_sigmas.count(), "sigma"); + } + + const auto morphed_epsilons = cache.morph( + schedule, + "clj", "epsilon", + mol.getEpsilons0(), + mol.getEpsilons1()); + + vals += morphed_epsilons; + + if (is_first) + { + + force += QVector(morphed_epsilons.count(), "clj"); + lever += QVector(morphed_epsilons.count(), "epsilon"); + } + + const auto morphed_alphas = cache.morph( + schedule, + "clj", "alpha", + mol.getAlphas0(), + mol.getAlphas1()); + + vals += morphed_alphas; + + if (is_first) + { + force += QVector(morphed_alphas.count(), "clj"); + lever += QVector(morphed_alphas.count(), "alpha"); + } + + const auto morphed_kappas = cache.morph( + schedule, + "clj", "kappa", + mol.getKappas0(), + mol.getKappas1()); + + vals += morphed_kappas; + + if (is_first) + { + force += QVector(morphed_kappas.count(), "clj"); + lever += QVector(morphed_kappas.count(), "kappa"); + } + + const auto morphed_charge_scale = cache.morph( + schedule, + "clj", "charge_scale", + mol.getChargeScales0(), + mol.getChargeScales1()); + + vals += morphed_charge_scale; + + if (is_first) + { + force += QVector(morphed_charge_scale.count(), "clj"); + lever += QVector(morphed_charge_scale.count(), "charge_scale"); + } + + const auto morphed_lj_scale = cache.morph( + schedule, + "clj", "lj_scale", + mol.getLJScales0(), + mol.getLJScales1()); + + vals += morphed_lj_scale; + + if (is_first) + { + force += QVector(morphed_lj_scale.count(), "clj"); + lever += QVector(morphed_lj_scale.count(), "lj_scale"); + } + + const auto morphed_ghost_charges = cache.morph( + schedule, + "ghost/ghost", "charge", + mol.getCharges0(), + mol.getCharges1()); + + vals += morphed_ghost_charges; + + if (is_first) + { + force += QVector(morphed_ghost_charges.count(), "ghost/ghost"); + lever += QVector(morphed_ghost_charges.count(), "charge"); + } + + const auto morphed_ghost_sigmas = cache.morph( + schedule, + "ghost/ghost", "sigma", + mol.getSigmas0(), + mol.getSigmas1()); + + vals += morphed_ghost_sigmas; + + if (is_first) + { + force += QVector(morphed_ghost_sigmas.count(), "ghost/ghost"); + lever += QVector(morphed_ghost_sigmas.count(), "sigma"); + } + + const auto morphed_ghost_epsilons = cache.morph( + schedule, + "ghost/ghost", "epsilon", + mol.getEpsilons0(), + mol.getEpsilons1()); + + vals += morphed_ghost_epsilons; + + if (is_first) + { + force += QVector(morphed_ghost_epsilons.count(), "ghost/ghost"); + lever += QVector(morphed_ghost_epsilons.count(), "epsilon"); + } + + const auto morphed_ghost_alphas = cache.morph( + schedule, + "ghost/ghost", "alpha", + mol.getAlphas0(), + mol.getAlphas1()); + + vals += morphed_ghost_alphas; + + if (is_first) + { + force += QVector(morphed_ghost_alphas.count(), "ghost/ghost"); + lever += QVector(morphed_ghost_alphas.count(), "alpha"); + } + + const auto morphed_ghost_kappas = cache.morph( + schedule, + "ghost/ghost", "kappa", + mol.getKappas0(), + mol.getKappas1()); + + vals += morphed_ghost_kappas; + + if (is_first) + { + force += QVector(morphed_ghost_kappas.count(), "ghost/ghost"); + lever += QVector(morphed_ghost_kappas.count(), "kappa"); + } + + const auto morphed_nonghost_charges = cache.morph( + schedule, + "ghost/non-ghost", "charge", + mol.getCharges0(), + mol.getCharges1()); + + vals += morphed_nonghost_charges; + + if (is_first) + { + force += QVector(morphed_nonghost_charges.count(), "ghost/non-ghost"); + lever += QVector(morphed_nonghost_charges.count(), "charge"); + } + + const auto morphed_nonghost_sigmas = cache.morph( + schedule, + "ghost/non-ghost", "sigma", + mol.getSigmas0(), + mol.getSigmas1()); + + vals += morphed_nonghost_sigmas; + + if (is_first) + { + force += QVector(morphed_nonghost_sigmas.count(), "ghost/non-ghost"); + lever += QVector(morphed_nonghost_sigmas.count(), "sigma"); + } + + const auto morphed_nonghost_epsilons = cache.morph( + schedule, + "ghost/non-ghost", "epsilon", + mol.getEpsilons0(), + mol.getEpsilons1()); + + vals += morphed_nonghost_epsilons; + + if (is_first) + { + force += QVector(morphed_nonghost_epsilons.count(), "ghost/non-ghost"); + lever += QVector(morphed_nonghost_epsilons.count(), "epsilon"); + } + + const auto morphed_nonghost_alphas = cache.morph( + schedule, + "ghost/non-ghost", "alpha", + mol.getAlphas0(), + mol.getAlphas1()); + + vals += morphed_nonghost_alphas; + + if (is_first) + { + force += QVector(morphed_nonghost_alphas.count(), "ghost/non-ghost"); + lever += QVector(morphed_nonghost_alphas.count(), "alpha"); + } + + const auto morphed_nonghost_kappas = cache.morph( + schedule, + "ghost/non-ghost", "kappa", + mol.getKappas0(), + mol.getKappas1()); + + vals += morphed_nonghost_kappas; + + if (is_first) + { + force += QVector(morphed_nonghost_kappas.count(), "ghost/non-ghost"); + lever += QVector(morphed_nonghost_kappas.count(), "kappa"); + } + + const auto morphed_ghost14_charges = cache.morph( + schedule, + "ghost-14", "charge", + mol.getCharges0(), + mol.getCharges1()); + + vals += morphed_ghost14_charges; + + if (is_first) + { + force += QVector(morphed_ghost14_charges.count(), "ghost-14"); + lever += QVector(morphed_ghost14_charges.count(), "charge"); + } + + const auto morphed_ghost14_sigmas = cache.morph( + schedule, + "ghost-14", "sigma", + mol.getSigmas0(), + mol.getSigmas1()); + + vals += morphed_ghost14_sigmas; + + if (is_first) + { + force += QVector(morphed_ghost14_sigmas.count(), "ghost-14"); + lever += QVector(morphed_ghost14_sigmas.count(), "sigma"); + } + + const auto morphed_ghost14_epsilons = cache.morph( + schedule, + "ghost-14", "epsilon", + mol.getEpsilons0(), + mol.getEpsilons1()); + + vals += morphed_ghost14_epsilons; + + if (is_first) + { + force += QVector(morphed_ghost14_epsilons.count(), "ghost-14"); + lever += QVector(morphed_ghost14_epsilons.count(), "epsilon"); + } + + const auto morphed_ghost14_alphas = cache.morph( + schedule, + "ghost-14", "alpha", + mol.getAlphas0(), + mol.getAlphas1()); + + vals += morphed_ghost14_alphas; + + if (is_first) + { + force += QVector(morphed_ghost14_alphas.count(), "ghost-14"); + lever += QVector(morphed_ghost14_alphas.count(), "alpha"); + } + + const auto morphed_ghost14_kappas = cache.morph( + schedule, + "ghost-14", "kappa", + mol.getKappas0(), + mol.getKappas1()); + + vals += morphed_ghost14_kappas; + + if (is_first) + { + force += QVector(morphed_ghost14_kappas.count(), "ghost-14"); + lever += QVector(morphed_ghost14_kappas.count(), "kappa"); + } + + const auto morphed_ghost14_charge_scale = cache.morph( + schedule, + "ghost-14", "charge_scale", + mol.getChargeScales0(), + mol.getChargeScales1()); + + vals += morphed_ghost14_charge_scale; + + if (is_first) + { + force += QVector(morphed_ghost14_charge_scale.count(), "ghost-14"); + lever += QVector(morphed_ghost14_charge_scale.count(), "charge_scale"); + } + + const auto morphed_ghost14_lj_scale = cache.morph( + schedule, + "ghost-14", "lj_scale", + mol.getLJScales0(), + mol.getLJScales1()); + + vals += morphed_ghost14_lj_scale; + + if (is_first) + { + force += QVector(morphed_ghost14_lj_scale.count(), "ghost-14"); + lever += QVector(morphed_ghost14_lj_scale.count(), "lj_scale"); + } + + auto perturbable_constraints = mol.getPerturbableConstraints(); + + const auto &idxs = boost::get<0>(perturbable_constraints); + const auto &r0_0 = boost::get<1>(perturbable_constraints); + const auto &r0_1 = boost::get<2>(perturbable_constraints); + + if (not idxs.isEmpty()) + { + const auto morphed_constraint_length = cache.morph( + schedule, + "bond", "bond_length", "constraint", + r0_0, r0_1); + + if (is_first) + { + force += QVector(morphed_constraint_length.count(), "constraint"); + lever += QVector(morphed_constraint_length.count(), "bond_length"); + } + + vals += morphed_constraint_length; + } + + const auto morphed_bond_k = cache.morph( + schedule, + "bond", "bond_k", + mol.getBondKs0(), + mol.getBondKs1()); + + const auto morphed_bond_length = cache.morph( + schedule, + "bond", "bond_length", + mol.getBondLengths0(), + mol.getBondLengths1()); + + if (is_first) + { + force += QVector(morphed_bond_k.count(), "bond"); + lever += QVector(morphed_bond_k.count(), "bond_k"); + + force += QVector(morphed_bond_length.count(), "bond"); + lever += QVector(morphed_bond_length.count(), "bond_length"); + } + + vals += morphed_bond_k; + vals += morphed_bond_length; + + const auto morphed_angle_k = cache.morph( + schedule, + "angle", "angle_k", + mol.getAngleKs0(), + mol.getAngleKs1()); + + const auto morphed_angle_size = cache.morph( + schedule, + "angle", "angle_size", + mol.getAngleSizes0(), + mol.getAngleSizes1()); + + if (is_first) + { + force += QVector(morphed_angle_k.count(), "angle"); + lever += QVector(morphed_angle_k.count(), "angle_k"); + + force += QVector(morphed_angle_size.count(), "angle"); + lever += QVector(morphed_angle_size.count(), "angle_size"); + } + + vals += morphed_angle_k; + vals += morphed_angle_size; + + const auto morphed_torsion_phase = cache.morph( + schedule, + "torsion", "torsion_phase", + mol.getTorsionPhases0(), + mol.getTorsionPhases1()); + + const auto morphed_torsion_k = cache.morph( + schedule, + "torsion", "torsion_k", + mol.getTorsionKs0(), + mol.getTorsionKs1()); + + if (is_first) + { + force += QVector(morphed_torsion_phase.count(), "torsion"); + lever += QVector(morphed_torsion_phase.count(), "torsion_phase"); + + force += QVector(morphed_torsion_k.count(), "torsion"); + lever += QVector(morphed_torsion_k.count(), "torsion_k"); + } + + vals += morphed_torsion_phase; + vals += morphed_torsion_k; + + if (is_first) + { + column_names.append("force"); + column_names.append("lever"); + + ret.append(StringArrayProperty(force)); + ret.append(StringArrayProperty(lever)); + + is_first = false; + } + + column_names.append(QString::number(lambda_value)); + ret.append(DoubleArrayProperty(vals)); + } + + ret.prepend(StringArrayProperty(column_names)); + + return ret; +} + /** Set the value of lambda in the passed context. Returns the * actual value of lambda set. */ diff --git a/wrapper/Convert/SireOpenMM/lambdalever.h b/wrapper/Convert/SireOpenMM/lambdalever.h index 13b8e3d0c..9bf0b60d7 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.h +++ b/wrapper/Convert/SireOpenMM/lambdalever.h @@ -112,6 +112,9 @@ namespace SireOpenMM const char *what() const; static const char *typeName(); + SireBase::PropertyList getLeverValues(const QVector &lambda_values, + const PerturbableOpenMMMolecule &mol) const; + double setLambda(OpenMM::Context &system, double lambda_value, bool update_constraints = true) const; diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index a69909e0a..a56c6102d 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -2016,6 +2016,14 @@ PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const Molecule &mol, this->operator=(PerturbableOpenMMMolecule(OpenMMMolecule(mol, map))); } +/** Return whether or not this is null */ +bool PerturbableOpenMMMolecule::isNull() const +{ + return perturbed_atoms.isEmpty() and perturbed_bonds.isEmpty() and + perturbed_angs.isEmpty() and perturbed_dihs.isEmpty() and + perturbable_constraints.isEmpty(); +} + /** Construct from the passed OpenMMMolecule */ PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const OpenMMMolecule &mol) : ConcreteProperty() diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 8215ed7d9..7a4222851 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -224,6 +224,8 @@ namespace SireOpenMM PerturbableOpenMMMolecule *clone() const; + bool isNull() const; + QVector getAlphas0() const; QVector getAlphas1() const; diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 266d6dd68..31d13503e 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -89,6 +89,7 @@ def smarts_to_rdkit(*args, **kwargs): _changed_torsions, _changed_exceptions, _changed_constraints, + _get_lever_values, ) from ._SireOpenMM import LambdaLever, PerturbableOpenMMMolecule, OpenMMMetaData @@ -105,6 +106,7 @@ def smarts_to_rdkit(*args, **kwargs): PerturbableOpenMMMolecule.changed_torsions = _changed_torsions PerturbableOpenMMMolecule.changed_exceptions = _changed_exceptions PerturbableOpenMMMolecule.changed_constraints = _changed_constraints + PerturbableOpenMMMolecule.get_lever_values = _get_lever_values _has_openmm = True From b851341768437b7449c5e2ef7c286a662665533b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 15:04:18 +0000 Subject: [PATCH 185/468] Fixed a bug in the LambdaSchedule that meant that standard morphs in additional stages were not evaluated correctly. Also cleaned up the code to show how parameters morph with lambda. This was extremely helpful for debugging! --- corelib/src/libs/SireCAS/lambdaschedule.cpp | 12 +- wrapper/Convert/SireOpenMM/_perturbablemol.py | 84 ++- wrapper/Convert/SireOpenMM/lambdalever.cpp | 495 +++++++++++++----- 3 files changed, 452 insertions(+), 139 deletions(-) diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp index 582240015..8d0a5970a 100644 --- a/corelib/src/libs/SireCAS/lambdaschedule.cpp +++ b/corelib/src/libs/SireCAS/lambdaschedule.cpp @@ -1406,10 +1406,12 @@ QVector LambdaSchedule::morph(const QString &force, if (equation == default_morph_equation) { + double stage_lam = std::get<1>(resolved); + for (int i = 0; i < nparams; ++i) { - morphed_data[i] = (1.0 - lambda_value) * initial_data[i] + - lambda_value * final_data[i]; + morphed_data[i] = (1.0 - stage_lam) * initial_data[i] + + stage_lam * final_data[i]; } } else @@ -1475,10 +1477,12 @@ QVector LambdaSchedule::morph(const QString &force, if (equation == default_morph_equation) { + double stage_lam = std::get<1>(resolved); + for (int i = 0; i < nparams; ++i) { - morphed_data[i] = int((1.0 - lambda_value) * initial_data[i] + - lambda_value * final_data[i]); + morphed_data[i] = int((1.0 - stage_lam) * initial_data[i] + + stage_lam * final_data[i]); } } else diff --git a/wrapper/Convert/SireOpenMM/_perturbablemol.py b/wrapper/Convert/SireOpenMM/_perturbablemol.py index fa5158b13..8697ba817 100644 --- a/wrapper/Convert/SireOpenMM/_perturbablemol.py +++ b/wrapper/Convert/SireOpenMM/_perturbablemol.py @@ -20,7 +20,48 @@ def _get_lever_values( Return the value of all of the parameters for this perturbable molecule at all of the specified values of lambda, given the passed lambda schedule. If no schedule is passed then a default morph - will be used. + will be used. Return this as a pandas DataFrame if 'to_pandas' is True + + If a pandas DataFrame is returned then note the following two points: + + 1. Note that this function will only return the values of parameters + that change during the morph. If a parameter does not change then + it is not included. + + 2. Also note that columns are merged together if they have identical + values. You can see which columns have been merged by looking at the + "merged" attribute of the returned DataFrame (e.g. 'df.attrs["merged"]') + + Otherwise, the raw data is returned as a set of dictionaries with + no additional processing. + + Parameters + ---------- + + schedule: LambdaSchedule, optional, default=None + The lambda schedule to use for the morph. If this is not + passed then a default morph will be used + + lambda_values: list[float], optional, default=None + A list of lambda values to evaluate. If this is not passed + then the lambda values will be auto-generated based on an + even spacing between 0 and 1 of 'num_lambda' points + + num_lambda: int, optional, default=101 + The number of lambda values to evaluate if 'lambda_values' + is not passed + + to_pandas: bool, optional, default=True + Whether or not to return the result as a pandas DataFrame + (defaults to True) + + Returns + ------- + + pandas.DataFrame or dict + A pandas DataFrame containing the values of the parameters + at each of the lambda values, or a dictionary containing + the values of the parameters at each of the lambda values """ if lambda_values is None: import numpy as np @@ -45,17 +86,54 @@ def _get_lever_values( import pandas as pd colnames = results[0] + + if len(colnames) < 2: + return None + columns = results columns.pop_front() results = {} - results["index"] = list(range(len(columns[0]))) + merged = {} + # only add in columns that change values for i in range(len(colnames)): - results[colnames[i]] = [x for x in columns[i]] + column = columns[i] + + if len(column) > 1: + changed = False + + for j in range(1, len(column)): + if column[j] != column[j - 1]: + changed = True + break + + if not changed: + continue + + colname = colnames[i].replace("lambda", "λ") + + column = [x for x in column] + + # see if this is a duplicate of existing columns + is_duplicate = None + for key, value in results.items(): + if key != "λ" and value == column: + is_duplicate = key + + if is_duplicate is None: + if colname != "λ": + merged[colname] = [] + + results[colname] = [x for x in column] + else: + merged[is_duplicate].append(colname) results = pd.DataFrame(results) + results = results.set_index("λ") + + results.attrs["merged"] = merged return results diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index cb0d58edc..f44b38f90 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -424,16 +424,23 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, const auto &schedule = this->lambda_schedule.getMoleculeSchedule(0); - QVector force; - QVector lever; QVector column_names; + column_names.append("lambda"); + + QVector lamvals; + QVector> lever_values; + bool is_first = true; for (auto lambda_value : lambda_values) { + int idx = 0; + lambda_value = this->lambda_schedule.clamp(lambda_value); + lamvals.append(lambda_value); + const auto &cache = this->lambda_cache.get(0, lambda_value); QVector vals; @@ -448,8 +455,17 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, if (is_first) { - force += QVector(morphed_charges.count(), "clj"); - lever += QVector(morphed_charges.count(), "charge"); + for (int i = 0; i < morphed_charges.count(); ++i) + { + column_names.append(QString("clj-charge-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : vals) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_sigmas = cache.morph( @@ -458,12 +474,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getSigmas0(), mol.getSigmas1()); - vals += morphed_sigmas; - if (is_first) { - force += QVector(morphed_sigmas.count(), "clj"); - lever += QVector(morphed_sigmas.count(), "sigma"); + for (int i = 0; i < morphed_sigmas.count(); ++i) + { + column_names.append(QString("clj-sigma-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_sigmas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_epsilons = cache.morph( @@ -472,13 +495,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getEpsilons0(), mol.getEpsilons1()); - vals += morphed_epsilons; - if (is_first) { + for (int i = 0; i < morphed_epsilons.count(); ++i) + { + column_names.append(QString("clj-epsilon-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } - force += QVector(morphed_epsilons.count(), "clj"); - lever += QVector(morphed_epsilons.count(), "epsilon"); + for (const auto &val : morphed_epsilons) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_alphas = cache.morph( @@ -487,12 +516,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getAlphas0(), mol.getAlphas1()); - vals += morphed_alphas; - if (is_first) { - force += QVector(morphed_alphas.count(), "clj"); - lever += QVector(morphed_alphas.count(), "alpha"); + for (int i = 0; i < morphed_alphas.count(); ++i) + { + column_names.append(QString("clj-alpha-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_alphas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_kappas = cache.morph( @@ -501,12 +537,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getKappas0(), mol.getKappas1()); - vals += morphed_kappas; - if (is_first) { - force += QVector(morphed_kappas.count(), "clj"); - lever += QVector(morphed_kappas.count(), "kappa"); + for (int i = 0; i < morphed_kappas.count(); ++i) + { + column_names.append(QString("clj-kappa-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_kappas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_charge_scale = cache.morph( @@ -515,12 +558,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getChargeScales0(), mol.getChargeScales1()); - vals += morphed_charge_scale; - if (is_first) { - force += QVector(morphed_charge_scale.count(), "clj"); - lever += QVector(morphed_charge_scale.count(), "charge_scale"); + for (int i = 0; i < morphed_charge_scale.count(); ++i) + { + column_names.append(QString("clj-charge_scale-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_charge_scale) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_lj_scale = cache.morph( @@ -529,12 +579,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getLJScales0(), mol.getLJScales1()); - vals += morphed_lj_scale; - if (is_first) { - force += QVector(morphed_lj_scale.count(), "clj"); - lever += QVector(morphed_lj_scale.count(), "lj_scale"); + for (int i = 0; i < morphed_lj_scale.count(); ++i) + { + column_names.append(QString("clj-lj_scale-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_lj_scale) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost_charges = cache.morph( @@ -543,12 +600,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getCharges0(), mol.getCharges1()); - vals += morphed_ghost_charges; - if (is_first) { - force += QVector(morphed_ghost_charges.count(), "ghost/ghost"); - lever += QVector(morphed_ghost_charges.count(), "charge"); + for (int i = 0; i < morphed_ghost_charges.count(); ++i) + { + column_names.append(QString("ghost/ghost-charge-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost_charges) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost_sigmas = cache.morph( @@ -557,12 +621,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getSigmas0(), mol.getSigmas1()); - vals += morphed_ghost_sigmas; - if (is_first) { - force += QVector(morphed_ghost_sigmas.count(), "ghost/ghost"); - lever += QVector(morphed_ghost_sigmas.count(), "sigma"); + for (int i = 0; i < morphed_ghost_sigmas.count(); ++i) + { + column_names.append(QString("ghost/ghost-sigma-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost_sigmas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost_epsilons = cache.morph( @@ -571,12 +642,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getEpsilons0(), mol.getEpsilons1()); - vals += morphed_ghost_epsilons; - if (is_first) { - force += QVector(morphed_ghost_epsilons.count(), "ghost/ghost"); - lever += QVector(morphed_ghost_epsilons.count(), "epsilon"); + for (int i = 0; i < morphed_ghost_epsilons.count(); ++i) + { + column_names.append(QString("ghost/ghost-epsilon-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost_epsilons) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost_alphas = cache.morph( @@ -585,12 +663,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getAlphas0(), mol.getAlphas1()); - vals += morphed_ghost_alphas; - if (is_first) { - force += QVector(morphed_ghost_alphas.count(), "ghost/ghost"); - lever += QVector(morphed_ghost_alphas.count(), "alpha"); + for (int i = 0; i < morphed_ghost_alphas.count(); ++i) + { + column_names.append(QString("ghost/ghost-alpha-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost_alphas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost_kappas = cache.morph( @@ -599,12 +684,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getKappas0(), mol.getKappas1()); - vals += morphed_ghost_kappas; - if (is_first) { - force += QVector(morphed_ghost_kappas.count(), "ghost/ghost"); - lever += QVector(morphed_ghost_kappas.count(), "kappa"); + for (int i = 0; i < morphed_ghost_kappas.count(); ++i) + { + column_names.append(QString("ghost/ghost-kappa-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost_kappas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_nonghost_charges = cache.morph( @@ -613,12 +705,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getCharges0(), mol.getCharges1()); - vals += morphed_nonghost_charges; - if (is_first) { - force += QVector(morphed_nonghost_charges.count(), "ghost/non-ghost"); - lever += QVector(morphed_nonghost_charges.count(), "charge"); + for (int i = 0; i < morphed_nonghost_charges.count(); ++i) + { + column_names.append(QString("ghost/non-ghost-charge-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_nonghost_charges) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_nonghost_sigmas = cache.morph( @@ -627,12 +726,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getSigmas0(), mol.getSigmas1()); - vals += morphed_nonghost_sigmas; - if (is_first) { - force += QVector(morphed_nonghost_sigmas.count(), "ghost/non-ghost"); - lever += QVector(morphed_nonghost_sigmas.count(), "sigma"); + for (int i = 0; i < morphed_nonghost_sigmas.count(); ++i) + { + column_names.append(QString("ghost/non-ghost-sigma-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_nonghost_sigmas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_nonghost_epsilons = cache.morph( @@ -641,12 +747,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getEpsilons0(), mol.getEpsilons1()); - vals += morphed_nonghost_epsilons; - if (is_first) { - force += QVector(morphed_nonghost_epsilons.count(), "ghost/non-ghost"); - lever += QVector(morphed_nonghost_epsilons.count(), "epsilon"); + for (int i = 0; i < morphed_nonghost_epsilons.count(); ++i) + { + column_names.append(QString("ghost/non-ghost-epsilon-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_nonghost_epsilons) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_nonghost_alphas = cache.morph( @@ -655,12 +768,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getAlphas0(), mol.getAlphas1()); - vals += morphed_nonghost_alphas; - if (is_first) { - force += QVector(morphed_nonghost_alphas.count(), "ghost/non-ghost"); - lever += QVector(morphed_nonghost_alphas.count(), "alpha"); + for (int i = 0; i < morphed_nonghost_alphas.count(); ++i) + { + column_names.append(QString("ghost/non-ghost-alpha-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_nonghost_alphas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_nonghost_kappas = cache.morph( @@ -669,12 +789,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getKappas0(), mol.getKappas1()); - vals += morphed_nonghost_kappas; - if (is_first) { - force += QVector(morphed_nonghost_kappas.count(), "ghost/non-ghost"); - lever += QVector(morphed_nonghost_kappas.count(), "kappa"); + for (int i = 0; i < morphed_nonghost_kappas.count(); ++i) + { + column_names.append(QString("ghost/non-ghost-kappa-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_nonghost_kappas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_charges = cache.morph( @@ -683,12 +810,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getCharges0(), mol.getCharges1()); - vals += morphed_ghost14_charges; - if (is_first) { - force += QVector(morphed_ghost14_charges.count(), "ghost-14"); - lever += QVector(morphed_ghost14_charges.count(), "charge"); + for (int i = 0; i < morphed_ghost14_charges.count(); ++i) + { + column_names.append(QString("ghost-14-charge-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_charges) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_sigmas = cache.morph( @@ -697,12 +831,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getSigmas0(), mol.getSigmas1()); - vals += morphed_ghost14_sigmas; - if (is_first) { - force += QVector(morphed_ghost14_sigmas.count(), "ghost-14"); - lever += QVector(morphed_ghost14_sigmas.count(), "sigma"); + for (int i = 0; i < morphed_ghost14_sigmas.count(); ++i) + { + column_names.append(QString("ghost-14-sigma-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_sigmas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_epsilons = cache.morph( @@ -711,12 +852,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getEpsilons0(), mol.getEpsilons1()); - vals += morphed_ghost14_epsilons; - if (is_first) { - force += QVector(morphed_ghost14_epsilons.count(), "ghost-14"); - lever += QVector(morphed_ghost14_epsilons.count(), "epsilon"); + for (int i = 0; i < morphed_ghost14_epsilons.count(); ++i) + { + column_names.append(QString("ghost-14-epsilon-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_epsilons) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_alphas = cache.morph( @@ -725,12 +873,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getAlphas0(), mol.getAlphas1()); - vals += morphed_ghost14_alphas; - if (is_first) { - force += QVector(morphed_ghost14_alphas.count(), "ghost-14"); - lever += QVector(morphed_ghost14_alphas.count(), "alpha"); + for (int i = 0; i < morphed_ghost14_alphas.count(); ++i) + { + column_names.append(QString("ghost-14-alpha-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_alphas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_kappas = cache.morph( @@ -739,12 +894,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getKappas0(), mol.getKappas1()); - vals += morphed_ghost14_kappas; - if (is_first) { - force += QVector(morphed_ghost14_kappas.count(), "ghost-14"); - lever += QVector(morphed_ghost14_kappas.count(), "kappa"); + for (int i = 0; i < morphed_ghost14_kappas.count(); ++i) + { + column_names.append(QString("ghost-14-kappa-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_kappas) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_charge_scale = cache.morph( @@ -753,12 +915,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getChargeScales0(), mol.getChargeScales1()); - vals += morphed_ghost14_charge_scale; - if (is_first) { - force += QVector(morphed_ghost14_charge_scale.count(), "ghost-14"); - lever += QVector(morphed_ghost14_charge_scale.count(), "charge_scale"); + for (int i = 0; i < morphed_ghost14_charge_scale.count(); ++i) + { + column_names.append(QString("ghost-14-charge_scale-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_charge_scale) + { + lever_values[idx].append(val); + idx += 1; } const auto morphed_ghost14_lj_scale = cache.morph( @@ -767,12 +936,19 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getLJScales0(), mol.getLJScales1()); - vals += morphed_ghost14_lj_scale; - if (is_first) { - force += QVector(morphed_ghost14_lj_scale.count(), "ghost-14"); - lever += QVector(morphed_ghost14_lj_scale.count(), "lj_scale"); + for (int i = 0; i < morphed_ghost14_lj_scale.count(); ++i) + { + column_names.append(QString("ghost-14-lj_scale-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_ghost14_lj_scale) + { + lever_values[idx].append(val); + idx += 1; } auto perturbable_constraints = mol.getPerturbableConstraints(); @@ -790,11 +966,18 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, if (is_first) { - force += QVector(morphed_constraint_length.count(), "constraint"); - lever += QVector(morphed_constraint_length.count(), "bond_length"); + for (int i = 0; i < morphed_constraint_length.count(); ++i) + { + column_names.append(QString("bond-constraint-%1").arg(i + 1)); + lever_values.append(QVector()); + } } - vals += morphed_constraint_length; + for (const auto &val : morphed_constraint_length) + { + lever_values[idx].append(val); + idx += 1; + } } const auto morphed_bond_k = cache.morph( @@ -803,6 +986,21 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getBondKs0(), mol.getBondKs1()); + if (is_first) + { + for (int i = 0; i < morphed_bond_k.count(); ++i) + { + column_names.append(QString("bond-bond_k-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_bond_k) + { + lever_values[idx].append(val); + idx += 1; + } + const auto morphed_bond_length = cache.morph( schedule, "bond", "bond_length", @@ -811,15 +1009,18 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, if (is_first) { - force += QVector(morphed_bond_k.count(), "bond"); - lever += QVector(morphed_bond_k.count(), "bond_k"); - - force += QVector(morphed_bond_length.count(), "bond"); - lever += QVector(morphed_bond_length.count(), "bond_length"); + for (int i = 0; i < morphed_bond_length.count(); ++i) + { + column_names.append(QString("bond-bond_length-%1").arg(i + 1)); + lever_values.append(QVector()); + } } - vals += morphed_bond_k; - vals += morphed_bond_length; + for (const auto &val : morphed_bond_length) + { + lever_values[idx].append(val); + idx += 1; + } const auto morphed_angle_k = cache.morph( schedule, @@ -827,6 +1028,21 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getAngleKs0(), mol.getAngleKs1()); + if (is_first) + { + for (int i = 0; i < morphed_angle_k.count(); ++i) + { + column_names.append(QString("angle-angle_k-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_angle_k) + { + lever_values[idx].append(val); + idx += 1; + } + const auto morphed_angle_size = cache.morph( schedule, "angle", "angle_size", @@ -835,15 +1051,18 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, if (is_first) { - force += QVector(morphed_angle_k.count(), "angle"); - lever += QVector(morphed_angle_k.count(), "angle_k"); - - force += QVector(morphed_angle_size.count(), "angle"); - lever += QVector(morphed_angle_size.count(), "angle_size"); + for (int i = 0; i < morphed_angle_size.count(); ++i) + { + column_names.append(QString("angle-angle_size-%1").arg(i + 1)); + lever_values.append(QVector()); + } } - vals += morphed_angle_k; - vals += morphed_angle_size; + for (const auto &val : morphed_angle_size) + { + lever_values[idx].append(val); + idx += 1; + } const auto morphed_torsion_phase = cache.morph( schedule, @@ -851,6 +1070,21 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, mol.getTorsionPhases0(), mol.getTorsionPhases1()); + if (is_first) + { + for (int i = 0; i < morphed_torsion_phase.count(); ++i) + { + column_names.append(QString("torsion-torsion_phase-%1").arg(i + 1)); + lever_values.append(QVector()); + } + } + + for (const auto &val : morphed_torsion_phase) + { + lever_values[idx].append(val); + idx += 1; + } + const auto morphed_torsion_k = cache.morph( schedule, "torsion", "torsion_k", @@ -859,32 +1093,29 @@ PropertyList LambdaLever::getLeverValues(const QVector &lambda_values, if (is_first) { - force += QVector(morphed_torsion_phase.count(), "torsion"); - lever += QVector(morphed_torsion_phase.count(), "torsion_phase"); - - force += QVector(morphed_torsion_k.count(), "torsion"); - lever += QVector(morphed_torsion_k.count(), "torsion_k"); + for (int i = 0; i < morphed_torsion_k.count(); ++i) + { + column_names.append(QString("torsion-torsion_k-%1").arg(i + 1)); + lever_values.append(QVector()); + } } - vals += morphed_torsion_phase; - vals += morphed_torsion_k; - - if (is_first) + for (const auto &val : morphed_torsion_k) { - column_names.append("force"); - column_names.append("lever"); - - ret.append(StringArrayProperty(force)); - ret.append(StringArrayProperty(lever)); - - is_first = false; + lever_values[idx].append(val); + idx += 1; } - column_names.append(QString::number(lambda_value)); - ret.append(DoubleArrayProperty(vals)); + is_first = false; } - ret.prepend(StringArrayProperty(column_names)); + ret.append(StringArrayProperty(column_names)); + ret.append(DoubleArrayProperty(lamvals)); + + for (const auto &column : lever_values) + { + ret.append(DoubleArrayProperty(column)); + } return ret; } From fa45c8fe4d464aa334c92b05fa811743517be9a2 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 17:02:20 +0000 Subject: [PATCH 186/468] Added a section to show how to use the new functionality to print out the impact of a schedule on a molecule. --- doc/source/tutorial/part07/02_levers.rst | 51 ++++++++++++++++++ .../tutorial/part07/images/07_02_01.jpg | Bin 0 -> 70156 bytes .../tutorial/part07/images/07_02_02.jpg | Bin 0 -> 80715 bytes 3 files changed, 51 insertions(+) create mode 100644 doc/source/tutorial/part07/images/07_02_01.jpg create mode 100644 doc/source/tutorial/part07/images/07_02_02.jpg diff --git a/doc/source/tutorial/part07/02_levers.rst b/doc/source/tutorial/part07/02_levers.rst index 3dac267b4..5d240fe34 100644 --- a/doc/source/tutorial/part07/02_levers.rst +++ b/doc/source/tutorial/part07/02_levers.rst @@ -244,3 +244,54 @@ LambdaSchedule( ghost/ghost::alpha: 0.5 * (initial * (-λ + 1) + final * λ) ) ) + +Viewing the effect of levers on a merged molecule +------------------------------------------------- + +You can view the effect of the :class:`~sire.cas.LambdaSchedule` on a +the :class:`~sire.legacy.Convert.PerturbableOpenMMMolecule` using +the :meth:`~sire.legacy.Convert.PerturbableOpenMMMolecule.get_lever_values` +function. + +>>> df = p_omm.get_lever_values(schedule=orig_s) +>>> print(df) + clj-charge-1 clj-charge-2 clj-charge-4 ... bond-bond_length-3 angle-angle_k-19 angle-angle_size-19 +λ ... +0.00 -0.085335 -0.060235 -0.085335 ... 0.10969 387.438400 1.916372 +0.01 -0.084482 -0.059362 -0.085566 ... 0.10969 386.861008 1.915985 +0.02 -0.083629 -0.058489 -0.085797 ... 0.10969 386.283616 1.915597 +0.03 -0.082775 -0.057615 -0.086027 ... 0.10969 385.706224 1.915210 +0.04 -0.081922 -0.056742 -0.086258 ... 0.10969 385.128832 1.914822 +... ... ... ... ... ... ... ... +0.96 -0.003413 0.023607 -0.107477 ... 0.10969 332.008768 1.879176 +0.97 -0.002560 0.024480 -0.107708 ... 0.10969 331.431376 1.878788 +0.98 -0.001707 0.025353 -0.107939 ... 0.10969 330.853984 1.878401 +0.99 -0.000853 0.026227 -0.108169 ... 0.10969 330.276592 1.878013 +1.00 0.000000 0.027100 -0.108400 ... 0.10969 329.699200 1.877626 +[101 rows x 19 columns] + +It can be useful to plot these, to check that the morphing is as expected. + +>>> ax = df.plot() +>>> ax.legend(bbox_to_anchor=(1.0, 1.0)) + +.. image:: images/07_02_01.jpg + :alt: Graph of the effect of all levers on the perturbable molecule. + +.. note:: + + The line ``ax.legend(bbox_to_anchor=(1.0, 1.0))`` is used to move the + legend outside of the plot area, so that it doesn't obscure the data. + +Unfortunately, the large values of the bond force constant make it very +difficult to see the effect of the :class:`~sire.cas.LambdaSchedule` on the +other parameters. To fix this, lets filter out any columns that contain +values that have an absolute value greater than 5. + +>>> skip_columns = df.abs().gt(5).apply(lambda x: x.index[x].tolist(), axis=1)[0] +>>> ax = df.loc[:, ~df.columns.isin(skip_columns)].plot() +>>> ax.legend(bbox_to_anchor=(1.0, 1.0)) + +.. image:: images/07_02_02.jpg + :alt: Graph of the effect of all levers on the perturbable molecule for + levers with parameters with values less than 5. diff --git a/doc/source/tutorial/part07/images/07_02_01.jpg b/doc/source/tutorial/part07/images/07_02_01.jpg new file mode 100644 index 0000000000000000000000000000000000000000..e7da5743030b812e13de25dc88b1b88727c7671a GIT binary patch literal 70156 zcmeFa1zc3yyEndRK|+vDC8Pud38hg10VydZm5>H0X@(GKP!JH5PD$wwNd@VYX6RcF@FL8ii!XS008Fz zY%~%818kvzKL8pvfc32n0GentKezSK*nadu2LSYozw{3<2QYv12gm$Y?*91w`}?_< z0DuEt!Mw)D$NLKHdm9ZM1BiU_txW>n`;z=qAKq)%lF@z{JsJI{(XpwLF@9=e*rsFu z=mS1{R;1K!%gKT7YDV@ZCN>UcwvGURf})ek-M($0a$i|S?w&M&2F?y0^YPQCR%ajB 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682051e00655ef9da1ce54f9576ab9dcc4fa4500 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 18:28:16 +0000 Subject: [PATCH 187/468] Finished the decoupling section --- corelib/src/libs/SireCAS/lambdaschedule.cpp | 8 ++- doc/source/tutorial/part07/06_decouple.rst | 52 +++++++++++++----- .../tutorial/part07/images/07_06_01.jpg | Bin 0 -> 61697 bytes 3 files changed, 44 insertions(+), 16 deletions(-) create mode 100644 doc/source/tutorial/part07/images/07_06_01.jpg diff --git a/corelib/src/libs/SireCAS/lambdaschedule.cpp b/corelib/src/libs/SireCAS/lambdaschedule.cpp index 8d0a5970a..11eae8e35 100644 --- a/corelib/src/libs/SireCAS/lambdaschedule.cpp +++ b/corelib/src/libs/SireCAS/lambdaschedule.cpp @@ -693,23 +693,27 @@ void LambdaSchedule::addDecoupleStage(const QString &name, bool perturbed_is_dec { this->addStage(name, default_morph_equation); - // we now need to ensure that the ghost/ghost parameters are not - // perturbed + // we now need to ensure that the ghost/ghost and ghost-14 parameters are + // not perturbed if (perturbed_is_decoupled) { this->setEquation(name, "ghost/ghost", "*", this->initial()); + this->setEquation(name, "ghost-14", "*", this->initial()); // we also need to scale down kappa as the decoupled state is // not evaluated in the NonbondedForce, so must not be cancelled this->setEquation(name, "ghost/ghost", "kappa", 1.0 - this->lam()); + this->setEquation(name, "ghost-14", "kappa", 1.0 - this->lam()); } else { this->setEquation(name, "ghost/ghost", "*", this->final()); + this->setEquation(name, "ghost-14", "*", this->final()); // we also need to scale up kappa as the decoupled state is // not evaluated in the NonbondedForce, so must not be cancelled this->setEquation(name, "ghost/ghost", "kappa", this->lam()); + this->setEquation(name, "ghost-14", "kappa", this->lam()); } } diff --git a/doc/source/tutorial/part07/06_decouple.rst b/doc/source/tutorial/part07/06_decouple.rst index 26e1f2ebe..e8d373837 100644 --- a/doc/source/tutorial/part07/06_decouple.rst +++ b/doc/source/tutorial/part07/06_decouple.rst @@ -94,6 +94,8 @@ property. >>> print(schedule) LambdaSchedule( decouple: (-λ + 1) * initial + λ * final + ghost-14::*: initial + ghost-14::kappa: -λ + 1 ghost/ghost::*: initial ghost/ghost::kappa: -λ + 1 ) @@ -105,23 +107,45 @@ all charge and LJ interactions involving benzene. However, we want to preserve the intramolecular charge and LJ interactions of benzene. Since all atoms are ghost atoms, these are -all evaluated in the ghost/ghost force. We therefore set all levers -in the ghost/ghost force to use the parameters in the initial state -(i.e. the full charges and epsilon LJ parameters for benzene). +all evaluated in the ghost/ghost and ghost-14 forces. We therefore set all +levers in the ghost/ghost and ghost-14 forces to use the parameters in the +initial state (i.e. the full charges and epsilon LJ parameters for benzene). But, because the ghost/ghost force includes a correction to subtract a double-counted electrostatic interaction from the NonbondedForce, we also need to have a lever that scales kappa with 1-λ. In this way, the kappa parameter will ensure that the correction is applied at λ=0, when the electrostatic interactions of benzene are evaluated in both -the NonbondedForce and the ghost/ghost force, while it will scale kappa -to 0 at λ=1, when the electrostatic interactions of benzene are only -evaluated in the ghost/ghost force. +the NonbondedForce and the ghost/ghost and ghost-14 forces, while it will +scale kappa to 0 at λ=1, when the electrostatic interactions of benzene are +only evaluated in the ghost/ghost and ghost-14 forces. We can view exactly how a schedule will perturb the real parameters of -a merged molecule using the.... - -FUNCTION THAT DOES THIS! +a merged molecule using the +:meth:`~sire.legacy.Convert.PerturbableOpenMMMolecule.get_lever_values` +function. + +>>> df = p.get_lever_values(schedule=schedule) +>>> print(df) + clj-charge-1 clj-charge-7 clj-epsilon-1 clj-epsilon-7 clj-alpha-1 ghost/ghost-kappa-1 +λ +0.00 -0.1300 0.1300 0.363503 0.065318 0.00 1.00 +0.01 -0.1287 0.1287 0.359868 0.064665 0.01 0.99 +0.02 -0.1274 0.1274 0.356233 0.064012 0.02 0.98 +0.03 -0.1261 0.1261 0.352598 0.063358 0.03 0.97 +0.04 -0.1248 0.1248 0.348963 0.062705 0.04 0.96 +... ... ... ... ... ... ... +0.96 -0.0052 0.0052 0.014540 0.002613 0.96 0.04 +0.97 -0.0039 0.0039 0.010905 0.001960 0.97 0.03 +0.98 -0.0026 0.0026 0.007270 0.001306 0.98 0.02 +0.99 -0.0013 0.0013 0.003635 0.000653 0.99 0.01 +1.00 0.0000 0.0000 0.000000 0.000000 1.00 0.00 +[101 rows x 6 columns] + +>>> ax = df.plot() + +.. image:: images/07_06_01.jpg + :alt: Graph of the effect of all levers on the decoupled molecule. Running a decoupling simulation ------------------------------- @@ -143,11 +167,11 @@ Next, we will create a simulation object. >>> d.run("100ps", lambda_windows=[0.0, 0.5, 1.0]) >>> print(d.energy_trajectory()) EnergyTrajectory( size=4 -time lambda 0.0 0.5 1.0 kinetic potential -25 1.0 8.04862e+06 -8780.12 -8940.64 1583.16 -8940.64 -50 1.0 7.02803e+10 -8675.02 -8922.59 1637.65 -8922.59 -75 1.0 1.65099e+06 -8568.8 -8812.94 1607.64 -8812.94 -100 1.0 2.34737e+09 -8340.83 -8894.35 1599.82 -8894.35 +time lambda 0.0 0.5 1.0 kinetic potential +25 1.0 2.49529e+06 -8686.04 -8895.63 1583.95 -8895.63 +50 1.0 1.54343e+06 -8750.01 -8914.34 1527.78 -8914.34 +75 1.0 2.20708e+08 -8465.13 -8872.06 1624.18 -8872.06 +100 1.0 1.02181e+11 -8534.06 -8949.38 1537.6 -8949.38 ) .. note:: diff --git a/doc/source/tutorial/part07/images/07_06_01.jpg b/doc/source/tutorial/part07/images/07_06_01.jpg new file mode 100644 index 0000000000000000000000000000000000000000..43fdd5fc3a5c35ffb980de739eeec078edcc1414 GIT 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zg|>*x8?m;}-)Vyhnx_hObC5$;e#E>i}Fb_?U;droFyhEl0Rn zdGi3>-4s6%3kDEnvNv_jXKH<>bfTW0GowX$L-PNMRsOvUOb)|wYYh*7H9NL)8I2wG z319-ZHbJiCID($V@Of>$tkFaF<-F3B2G)UEaG+Axxnu9RL>i~BaP^M^bIC7PB@-TR zH3-i~Gx3kv({e{F8_7PIL(nxWS@uz>ZWPFklVlB z$3p3kM?JE@u|pQA*YYM$WxH^?<=OafOvT^+Oof-mKNlDj$x+DUDp?ZMpk~anjvcMc zO{uh~hbX!|R-JyZY#hnF4t5<3m^y+zU)JqvR159=R? zU*(dnrN`fV?M~^D;PIYiiA|Tg4}(}JQDZWU(J78meGaoZ+V$?`U775%r2AKdPI$r{4Zlt=N? zsXfQ4Pl~r&`0f z!>$Ykbpjuz%o6slt^1dH=eW*Yhx3WCPl<1rQhP+69os!dNC}BhLZiC;CcmAF*IvI7 z^~%uPcP8+rzO0Y;J7@XLPt26t&meHeRU!9qQ{k-!;009&J{()NYg>DE1z+T2>3v)G z4_Ki|t!6PP=E!5ab$%eDZIAo0ZuRaxuKaDfx4#E6Do=cSQ1q>F<-FiZi~If4ZMEA! z%x}%x(tUcbcW`QT=Mz=0Z^6Ju-2Jxgx{1Zr4|neSVzjaU@4=&0e=FafZ_R)Fv8bZi yFU6xLQ6>2PwY^+)@1o-By3#}39@}*)0~xm?&~B_pK8(O{pnCC6LKyP@zX<^UxU7l* literal 0 HcmV?d00001 From 2c39aefe18d54d0a2b444985153db76c8ecc0a21 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 19:13:58 +0000 Subject: [PATCH 188/468] Finished the annihilation section of the tutorial --- doc/source/tutorial/part07/06_decouple.rst | 137 +++++++++++++++++++++ 1 file changed, 137 insertions(+) diff --git a/doc/source/tutorial/part07/06_decouple.rst b/doc/source/tutorial/part07/06_decouple.rst index e8d373837..eca57afaf 100644 --- a/doc/source/tutorial/part07/06_decouple.rst +++ b/doc/source/tutorial/part07/06_decouple.rst @@ -179,3 +179,140 @@ time lambda 0.0 0.5 1.0 kinetic potentia We expect the energies at λ=0 to be high in this case, as the simulation was run at λ=1, where the benzene is not interacting with the the rest of the system, and thus free to overlap with other atoms. + +Annihilation +------------ + +Annihilation is the process of turning off all interactions involving +all of the atoms of the molecule being annihilated. Note that this will +also turn off all intramolecular interactions, so care must be taken +to use restraints to prevent the simulation exploding. + +You can create an annihilated molecule using the :func:`sire.morph.annihilate`. + +>>> benzene = sr.morph.annihilate(benzene, as_new_molecule=False) +>>> print(benzene) +Molecule( BEN:2 num_atoms=12 num_residues=1 ) + +.. note:: + + As before, we pass in ``as_new_molecule=False`` so that the resulting merged + molecule keeps the same molecule number as the original benzene. + +The annihilated benzene molecule is a merged molecule where all of the +atoms are converted to ghost atoms, and all of the intramolecular interactions +are turned off. + +>>> p = benzene.perturbation().to_openmm() +>>> print(p.changed_atoms()) + atom charge0 charge1 sigma0 sigma1 epsilon0 epsilon1 alpha0 alpha1 kappa0 kappa1 +0 C:1 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +1 C2:2 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +2 C3:3 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +3 C4:4 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +4 C5:5 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +5 C6:6 -0.13 0.0 0.348065 0.348065 0.363503 0.0 0.0 1.0 1.0 1.0 +6 H1:7 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +7 H2:8 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +8 H3:9 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +9 H4:10 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +10 H5:11 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +11 H6:12 0.13 0.0 0.257258 0.257258 0.065318 0.0 0.0 1.0 1.0 1.0 +>>> print(p.changed_bonds()) + bond length0 length1 k0 k1 +0 C2:2-C3:3 0.138719 0.138719 301905.092179 0.0 +1 C:1-C2:2 0.138719 0.138719 301905.092179 0.0 +2 C6:6-H6:12 0.108536 0.108536 332422.631707 0.0 +3 C5:5-H5:11 0.108536 0.108536 332422.631707 0.0 +4 C4:4-H4:10 0.108536 0.108536 332422.631707 0.0 +5 C3:3-H3:9 0.108536 0.108536 332422.631707 0.0 +6 C5:5-C6:6 0.138719 0.138719 301905.092179 0.0 +7 C2:2-H2:8 0.108536 0.108536 332422.631707 0.0 +8 C4:4-C5:5 0.138719 0.138719 301905.092179 0.0 +9 C:1-H1:7 0.108536 0.108536 332422.631707 0.0 +10 C:1-C6:6 0.138719 0.138719 301905.092179 0.0 +11 C3:3-C4:4 0.138719 0.138719 301905.092179 0.0 + +To annihilate the benzene molecule correctly, a custom :class:`sire.cas.LambdaSchedule` +is needed. + +The :func:`sire.morph.annihilate` function creates a suitable schedule by +default, and attaches it to the merged molecule via its ``schedule`` +property. + +>>> schedule = benzene.property("schedule") +>>> print(schedule) +LambdaSchedule( + annihilate: initial * (-λ + 1) + final * λ +) + +As before, we can view exactly how a schedule will perturb the real parameters +of a merged molecule using the +:meth:`~sire.legacy.Convert.PerturbableOpenMMMolecule.get_lever_values` +function. + +>>> df = p.get_lever_values(schedule=schedule) +>>> print(df) + clj-charge-1 clj-charge-7 clj-epsilon-1 ... angle-angle_k-5 torsion-torsion_k-1 torsion-torsion_k-3 +λ ... +0.00 -0.1300 0.1300 0.363503 ... 484.492886 1.534133 15.321516 +0.01 -0.1287 0.1287 0.359868 ... 479.647957 1.518792 15.168300 +0.02 -0.1274 0.1274 0.356233 ... 474.803028 1.503451 15.015085 +0.03 -0.1261 0.1261 0.352598 ... 469.958099 1.488109 14.861870 +0.04 -0.1248 0.1248 0.348963 ... 465.113170 1.472768 14.708655 +... ... ... ... ... ... ... ... +0.96 -0.0052 0.0052 0.014540 ... 19.379715 0.061365 0.612861 +0.97 -0.0039 0.0039 0.010905 ... 14.534787 0.046024 0.459645 +0.98 -0.0026 0.0026 0.007270 ... 9.689858 0.030683 0.306430 +0.99 -0.0013 0.0013 0.003635 ... 4.844929 0.015341 0.153215 +1.00 0.0000 0.0000 0.000000 ... 0.000000 0.000000 0.000000 +[101 rows x 14 columns] + +The key difference between the annihilation schedule and the decoupling +schedule is that the annihilation schedule linearly scales down all interactions +involving the atoms of the molecule being annihilated, rather than +only turning off the intermolecular interactions. + +Running an annihilation simulation +---------------------------------- + +We can run an annihilation simulation in the same way as any other +free energy simulation. + +First, we will update the system to use the annihilated benzene molecule. + +>>> mols.update(benzene) + +This works because we used ``as_new_molecule=False`` when creating +the merged molecule, so it kept its original molecule number. + +Next, we will create a simulation object. + +>>> d = mols.dynamics(timestep="2fs", temperature="25oC", +... schedule=schedule, lambda_value=1.0) +>>> d.run("100ps", lambda_windows=[0.0, 0.5, 1.0]) +>>> print(d.energy_trajectory()) +EnergyTrajectory( size=4 +time lambda 0.0 0.5 1.0 kinetic potential +25 1.0 2.20919e+08 3.70208e+06 -8898.02 1561.3 -8898.02 +50 1.0 2.73685e+07 1.26643e+07 -8863.57 1591.31 -8863.57 +75 1.0 2.49653e+07 1.24605e+07 -8894.69 1611.1 -8894.69 +100 1.0 1.20317e+09 1.90568e+07 -8908.07 1516.37 -8908.07 +) + +.. note:: + + We expect the energies at all values except λ=1 to be very high in this case, + as the simulation was run at λ=1, where the atoms of the benzene + are not interacting with the the rest of the system, and thus free + to overlap with other atoms, and also be too far from each other to give + sensible energies for their intramolecular interactions. + +Ideally, in the above simulation you should add positional restraints to +all atoms in benzene which gradually switch on to hold the atoms in +position as their interactions are annihilated. The end state would +represent non-interacting particles in harmonic wells, for which an +analytical solution exists to calculate the free energy of annihilation. + +While this is not covered in this tutorial, future versions of +:mod:`sire` will include tools to help with this. From 6c34007dcaf6b0c8166cee1df35ccbc8828801a7 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 19:49:00 +0000 Subject: [PATCH 189/468] Finished up part 7 of the tutorial now. Just some more cleaning, plus some extra gems --- doc/source/features.rst | 7 + doc/source/tutorial/index_part05.rst | 3 +- doc/source/tutorial/part07/07_residue.rst | 226 +++++++++++++++++++++- 3 files changed, 233 insertions(+), 3 deletions(-) diff --git a/doc/source/features.rst b/doc/source/features.rst index 5fa08b231..b08bc9f12 100644 --- a/doc/source/features.rst +++ b/doc/source/features.rst @@ -44,6 +44,13 @@ molecular (predominantly biomolecular) systems. including across :doc:`frames of trajectories ` (or subsets of trajectories). +* Create merged molecules that represent perturbations for + :doc:`relative ` and + :doc:`absolute ` free energy calculations. +* Create merged molecules that represnet perturbations of + :doc:`residues in proteins `. +* Mutate residues or parts of molecules via + :doc:`copy-and-pasting ` bits of molecules. * A powerful :doc:`property system ` that lets you associate nearly any data with nearly any molecular view or sub-view. For example, you can assign multiple different coordinate properties diff --git a/doc/source/tutorial/index_part05.rst b/doc/source/tutorial/index_part05.rst index 412f984a1..30aeb051f 100644 --- a/doc/source/tutorial/index_part05.rst +++ b/doc/source/tutorial/index_part05.rst @@ -7,7 +7,8 @@ and work with other molecular modelling python packages. You can also convert molecules between the :mod:`sire` format and the format of other popular molecular packages, e.g. -`rdkit `__, `openmm `_ and +`rdkit `__, `openmm `_, +`Gemmi `__ and `BioSimSpace `__. This chapter will teach you how to do the conversion, and also how diff --git a/doc/source/tutorial/part07/07_residue.rst b/doc/source/tutorial/part07/07_residue.rst index 4d9f05fc8..969be7526 100644 --- a/doc/source/tutorial/part07/07_residue.rst +++ b/doc/source/tutorial/part07/07_residue.rst @@ -2,5 +2,227 @@ Residue mutations ================= -Describe residue mutations and calculating free energies of mutating -residues. +So far, perturbations have involved changing an entire molecule. +However, we can also change individual residues in a molecule. This +can be useful to, e.g. study the effect of residue mutation on a protein, +and how this could impact ligand binding or protein folding. + +Sub-structure matching +---------------------- + +To start, we need to define the sub-structure that we want to change. + +Let's first load the kigaki protein system. + +>>> import sire as sr +>>> mols = sr.load_test_files("kigaki.gro", "kigaki.top") +>>> protein = mols[0] +>>> print(protein) +Molecule( Protein:6 num_atoms=302 num_residues=19 ) +>>> print(protein.residues().names()) +[ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('ALA'), + ResName('LYS'), ResName('ILE'), ResName('LYS'), ResName('ILE'), + ResName('GLY'), ResName('ALA'), ResName('LYS'), ResName('ILE'), + ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('ALA'), + ResName('LYS'), ResName('ILE'), ResName('NH2')] + +To start with, let's mutate the first alanine residue that we find in the +protein into a lysine. First, let's select the first alanine... + +>>> ala = protein["resname ALA"][0] +>>> print(ala) +Residue( ALA:4 num_atoms=10 ) + +To mutate this into a lysine, we need to tell :mod:`sire` what a +lysine looks like. Fortunately, our protein already contains lysine +residues, so let's select on of those... + +>>> lys = protein["resname LYS"][1] +>>> print(lys) +Residue( LYS:5 num_atoms=22 ) + +.. note:: + + We have selected the second lysine residue in the protein, + as the first lysine residue is the N-terminal residue. Since + our alanine is a mid-chain residue, it makes more sense to + use a mid-chain lysine. + +Next, we need to match the alanine residue to the lysine residue, +just as we did when perturbing entire molecules. Calling +:func:`sire.morph.match` on sub-views of molecules will only match +the atoms in those views. + +>>> mapping = sr.morph.match(ala, lys, match_light_atoms=True) +>>> print(mapping) +AtomMapping( size=9, unmapped0=1, unmapped1=13 +0: MolNum(6) Atom( HA:54 ) <=> MolNum(6) Atom( HA:64 ) +1: MolNum(6) Atom( CA:53 ) <=> MolNum(6) Atom( CA:63 ) +2: MolNum(6) Atom( O:60 ) <=> MolNum(6) Atom( O:82 ) +3: MolNum(6) Atom( C:59 ) <=> MolNum(6) Atom( C:81 ) +4: MolNum(6) Atom( HB2:57 ) <=> MolNum(6) Atom( HB2:67 ) +5: MolNum(6) Atom( H:52 ) <=> MolNum(6) Atom( H:62 ) +6: MolNum(6) Atom( N:51 ) <=> MolNum(6) Atom( N:61 ) +7: MolNum(6) Atom( HB1:56 ) <=> MolNum(6) Atom( HB1:66 ) +8: MolNum(6) Atom( CB:55 ) <=> MolNum(6) Atom( CB:65 ) +) + +.. warning:: + + This used the default MCS matching algorithm built into :mod:`sire`. + This is not supported on Windows. You may want to use a different + matching algorithm, e.g. using + `Kartograf `__ + +We can see that this mapping has nicely matched the atoms in alanine +to the corresponding atoms in lysine. + +Next, we will align the lysine in the mapping onto the alanine. + +>>> mapping = mapping.align() + +And finally, we will create the merged molecule. + +>>> merged = mapping.merge(as_new_molecule=False) +>>> print(merged) +Molecule( Protein:6 num_atoms=315 num_residues=19 ) + +This has created the merged molecule as before. To see what has changed, +we can check the perturbation... + +>>> p_omm = merged.perturbation().to_openmm() +>>> print(p_omm.changed_atoms()) + atom charge0 charge1 sigma0 sigma1 epsilon0 epsilon1 alpha0 alpha1 kappa0 kappa1 +0 N:51 -0.4157 -0.3479 0.325000 0.325000 0.711280 0.711280 0.0 0.0 0.0 0.0 +1 H:52 0.2719 0.2747 0.106908 0.106908 0.065689 0.065689 0.0 0.0 0.0 0.0 +2 CA:53 0.0337 -0.2400 0.339967 0.339967 0.457730 0.457730 0.0 0.0 0.0 0.0 +3 HA:54 0.0823 0.1426 0.247135 0.247135 0.065689 0.065689 0.0 0.0 0.0 0.0 +4 CB:55 -0.1825 -0.0094 0.339967 0.339967 0.457730 0.457730 0.0 0.0 0.0 0.0 +5 HB1:56 0.0603 0.0362 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +6 HB2:57 0.0603 0.0362 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +7 HB3:58 0.0603 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +8 C:59 0.5973 0.7341 0.339967 0.339967 0.359824 0.359824 0.0 0.0 0.0 0.0 +9 O:60 -0.5679 -0.5894 0.295992 0.295992 0.878640 0.878640 0.0 0.0 0.0 0.0 +10 Xxx:303 0.0000 0.0187 0.339967 0.339967 0.000000 0.457730 1.0 0.0 1.0 1.0 +11 Xxx:304 0.0000 0.0103 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +12 Xxx:305 0.0000 0.0103 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +13 Xxx:306 0.0000 -0.0479 0.339967 0.339967 0.000000 0.457730 1.0 0.0 1.0 1.0 +14 Xxx:307 0.0000 0.0621 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +15 Xxx:308 0.0000 0.0621 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +16 Xxx:309 0.0000 -0.0143 0.339967 0.339967 0.000000 0.457730 1.0 0.0 1.0 1.0 +17 Xxx:310 0.0000 0.1135 0.195998 0.195998 0.000000 0.065689 1.0 0.0 1.0 1.0 +18 Xxx:311 0.0000 0.1135 0.195998 0.195998 0.000000 0.065689 1.0 0.0 1.0 1.0 +19 Xxx:312 0.0000 -0.3854 0.325000 0.325000 0.000000 0.711280 1.0 0.0 1.0 1.0 +20 Xxx:313 0.0000 0.3400 0.106908 0.106908 0.000000 0.065689 1.0 0.0 1.0 1.0 +21 Xxx:314 0.0000 0.3400 0.106908 0.106908 0.000000 0.065689 1.0 0.0 1.0 1.0 +22 Xxx:315 0.0000 0.3400 0.106908 0.106908 0.000000 0.065689 1.0 0.0 1.0 1.0 + +This shows how the atoms in alanine have been perturbed into the equivalent +atoms in lysine, plus how a number of ghost atoms have been added that +correspond to the additional atoms in lysine. In addition, the HB3 atom +of alanine is turned into a ghost. + +One-stop function +----------------- + +Just as before, the entire set of steps above can be performed in one +step via the :func:`sire.morph.merge` function. + +>>> merged = sr.morph.merge(ala, lys) +>>> print(merged) +Molecule( Protein:3627 num_atoms=315 num_residues=19 ) +>>> p_omm = merged.perturbation().to_openmm() +>>> print(p_omm.changed_atoms()) + atom charge0 charge1 sigma0 sigma1 epsilon0 epsilon1 alpha0 alpha1 kappa0 kappa1 +0 N:51 -0.4157 -0.3479 0.325000 0.325000 0.711280 0.711280 0.0 0.0 0.0 0.0 +1 H:52 0.2719 0.2747 0.106908 0.106908 0.065689 0.065689 0.0 0.0 0.0 0.0 +2 CA:53 0.0337 -0.2400 0.339967 0.339967 0.457730 0.457730 0.0 0.0 0.0 0.0 +3 HA:54 0.0823 0.1426 0.247135 0.247135 0.065689 0.065689 0.0 0.0 0.0 0.0 +4 CB:55 -0.1825 -0.0094 0.339967 0.339967 0.457730 0.457730 0.0 0.0 0.0 0.0 +5 HB1:56 0.0603 0.0362 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +6 HB2:57 0.0603 0.0362 0.264953 0.264953 0.065689 0.065689 0.0 0.0 0.0 0.0 +7 HB3:58 0.0603 0.0000 0.264953 0.264953 0.065689 0.000000 0.0 1.0 1.0 1.0 +8 C:59 0.5973 0.7341 0.339967 0.339967 0.359824 0.359824 0.0 0.0 0.0 0.0 +9 O:60 -0.5679 -0.5894 0.295992 0.295992 0.878640 0.878640 0.0 0.0 0.0 0.0 +10 Xxx:303 0.0000 0.0187 0.339967 0.339967 0.000000 0.457730 1.0 0.0 1.0 1.0 +11 Xxx:304 0.0000 0.0103 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +12 Xxx:305 0.0000 0.0103 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +13 Xxx:306 0.0000 -0.0479 0.339967 0.339967 0.000000 0.457730 1.0 0.0 1.0 1.0 +14 Xxx:307 0.0000 0.0621 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +15 Xxx:308 0.0000 0.0621 0.264953 0.264953 0.000000 0.065689 1.0 0.0 1.0 1.0 +16 Xxx:309 0.0000 -0.0143 0.339967 0.339967 0.000000 0.457730 1.0 0.0 1.0 1.0 +17 Xxx:310 0.0000 0.1135 0.195998 0.195998 0.000000 0.065689 1.0 0.0 1.0 1.0 +18 Xxx:311 0.0000 0.1135 0.195998 0.195998 0.000000 0.065689 1.0 0.0 1.0 1.0 +19 Xxx:312 0.0000 -0.3854 0.325000 0.325000 0.000000 0.711280 1.0 0.0 1.0 1.0 +20 Xxx:313 0.0000 0.3400 0.106908 0.106908 0.000000 0.065689 1.0 0.0 1.0 1.0 +21 Xxx:314 0.0000 0.3400 0.106908 0.106908 0.000000 0.065689 1.0 0.0 1.0 1.0 +22 Xxx:315 0.0000 0.3400 0.106908 0.106908 0.000000 0.065689 1.0 0.0 1.0 1.0 + +This merged molecule can be used in a free energy simulation in the same +way as any other merged molecule. + +Protein Mutation +---------------- + +Just as for other merged molecules, we can extract the end states using +the :func:`sire.morph.extract_reference` and +:func:`sire.morph.extract_perturbed` functions. + +>>> ref_prot = sr.morph.extract_reference(merged) +>>> pert_prot = sr.morph.extract_perturbed(merged) +>>> print(ref_prot.residues().names()) +[ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('ALA'), + ResName('LYS'), ResName('ILE'), ResName('LYS'), ResName('ILE'), + ResName('GLY'), ResName('ALA'), ResName('LYS'), ResName('ILE'), + ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('ALA'), + ResName('LYS'), ResName('ILE'), ResName('NH2')] +>>> print(pert_prot.residues().names()) +[ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('LYS'), + ResName('LYS'), ResName('ILE'), ResName('LYS'), ResName('ILE'), + ResName('GLY'), ResName('ALA'), ResName('LYS'), ResName('ILE'), + ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('ALA'), + ResName('LYS'), ResName('ILE'), ResName('NH2')] + +This shows that the first alanine residue has been mutated into a +lysine residue. + +Interestingly, if you are only interested in mutation, and are not +interested in the merged molecule, then mutation is just the process +of performing a merge, and then extracting the perturbed end state. + +To make this easier, there is a one-stop function for this, +:func:`sire.morph.mutate`. + +>>> mutated_protein = sr.morph.mutate(ala, lys) +>>> print(mutated_protein.residues().names()) +[ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('LYS'), + ResName('LYS'), ResName('ILE'), ResName('LYS'), ResName('ILE'), + ResName('GLY'), ResName('ALA'), ResName('LYS'), ResName('ILE'), + ResName('LYS'), ResName('ILE'), ResName('GLY'), ResName('ALA'), + ResName('LYS'), ResName('ILE'), ResName('NH2')] + +.. warning:: + + By default this uses the (potentially slow) internal MCS matching + algorithm (which also is not supported on Windows). You may want to + use a different matching algorithm, either by passing in the + dictionary of the mapping you want to use via the ``match`` + argument, or by using `Kartograf `__. + The ``match`` argument works identically in this function as it + does in the ``merge`` and ``match`` functions. + +In this case, we copied and pasted the lysine residue from one part of the +protein over the alanine. But, you can copy and paste in this way between +different molecules. For example, you could have a template library of +different residues that you could use for mutation. + +Assuming ``template["lys"]`` contained your template for a lysine residue, +then you could have run the following; + +>>> mutated_protein = sr.morph.mutate(ala, template["lys"]) + +This works for any kind of molecules - not just proteins. In future +versions of :mod:`sire` we will add functionality to make it easier to +manage libraries of templates, and to perform molecular editing by +copying and pasting between molecules, and between fragments constructed +via, e.g. smiles strings. From 3c2d46e3bfccaba1fec5dc6eff0d9a6951ab9d52 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 22:37:36 +0000 Subject: [PATCH 190/468] Fixed the logic of the randomly failing test --- tests/morph/test_decouple.py | 32 ++++++++++++++++++++++---------- 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/tests/morph/test_decouple.py b/tests/morph/test_decouple.py index 5c0a817c4..8c0dc68c3 100644 --- a/tests/morph/test_decouple.py +++ b/tests/morph/test_decouple.py @@ -175,18 +175,30 @@ def test_annihilate(ala_mols, openmm_platform): fwds = omm_fwds.changed_torsions() bwds = omm_bwds.changed_torsions() - joined = fwds.merge(bwds, on="torsion", suffixes=("_fwds", "_bwds")) - - assert joined["periodicity0_fwds"].equals(joined["periodicity1_bwds"]) - assert joined["periodicity1_fwds"].equals(joined["periodicity0_bwds"]) - assert joined["phase0_fwds"].equals(joined["phase1_bwds"]) - assert joined["phase1_fwds"].equals(joined["phase0_bwds"]) - assert joined["k0_fwds"].equals(joined["k1_bwds"]) - assert joined["k1_fwds"].equals(joined["k0_bwds"]) + # there are multiple torsions, so these need searching for + # and matching directly + for _, row_fwds in fwds.iterrows(): + torsion = row_fwds["torsion"] + + found = False + + for _, row_bwds in bwds[bwds["torsion"] == torsion].iterrows(): + if ( + row_fwds["k0"] == row_bwds["k1"] + and row_fwds["k1"] == row_bwds["k0"] + and row_fwds["periodicity0"] == row_bwds["periodicity1"] + and row_fwds["periodicity1"] == row_bwds["periodicity0"] + and row_fwds["phase0"] == row_bwds["phase1"] + and row_fwds["phase1"] == row_bwds["phase0"] + ): + found = True + break + + assert found # also check that parameters are being set equal to zero correctly - assert (joined["k1_fwds"] == 0.0).all() - assert (joined["k0_bwds"] == 0.0).all() + assert (fwds["k1"] == 0.0).all() + assert (bwds["k0"] == 0.0).all() fwds = omm_fwds.changed_exceptions() bwds = omm_bwds.changed_exceptions() From cdf360ad975fe478c2d4fc477682e2ff0bd1e988 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 22:49:14 +0000 Subject: [PATCH 191/468] Updated the changelog :-) --- doc/source/changelog.rst | 85 ++++++++++++++++++++++++++++------------ 1 file changed, 60 insertions(+), 25 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index e0c665db9..78c61e3d0 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -12,7 +12,7 @@ Development was migrated into the `OpenBioSim `__ organisation on `GitHub `__. -`2024.1.0 `__ - March 2024 +`2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ * BREAKING CHANGE: Updated the API of :class:`sire.cas.LambdaSchedule` so that @@ -28,6 +28,21 @@ organisation on `GitHub `__. to add support for calculating absolute binding free energies. This is described in the new :doc:`tutorial chapter `. +* Exposed the underlying :class:`~sire.legacy.Convert.PerturbableOpenMMMolecule` + class, which can be created from a merged molecule via + ``mol.perturbation().to_openmm()``. This lets you easily see which parameters + are changing between the reference and perturbed states. This is described + in the :doc:`tutorial `. + +* Added the ability for the lambda schedule to show how it will actually + act to perturb the parameters of the + :class:`~sire.legacy.Convert.PerturbableOpenMMMolecule` molecule. + This is described in the :doc:`tutorial `. + +* Added support for reading older somd-style pertfiles, and creating + merged molecules from these. This is described in + the :doc:`tutorial `. + * Added "not-perturbable" constraints so that bonds and angles that change with lambda are not perturbed. As part of this, have also added a ``dynamic_constraints`` option that lets constrained bonds update with @@ -90,6 +105,19 @@ organisation on `GitHub `__. It was a little-used part of the code, with the main use case being the replacement with the easier ``sire.morph.link_to_XXX`` functions. +* Added ability to create merge molecules for relative free energy calculations + via :func:`sire.morph.merge` and :func:`sire.morph.match`. This is + described in the :doc:`tutorial `. + +* Added ability to create merge molecules for absolute free energy + calculations via :func:`sire.morph.decouple` and + :func:`sire.morph.annihilate`. This is described in the + :doc:`tutorial `. + +* Added support for residue perturbations and also for mutating residues + and parts of molecules using a new "copy and paste" algorithm. This is + described in the :doc:`tutorial `. + * Exposed the ``SOMMContext``, ``PerturbableOpenMMMolecule``, ``OpenMMMetaData`` and ``LambdaLever`` classes to Python, as part of the new ``sire.convert.openmm`` module. These are useful if you want more @@ -99,13 +127,6 @@ organisation on `GitHub `__. be used to get changing parameters as dataframes, which is really useful for debugging. These are described in the :doc:`new tutorial `. -* Added an ``AtomCoordMatcher`` to match atoms by coordinates in two selections. - -* Fix bug that disabled the ``DEBUG`` log level from the global logger. - -* Fixed bug in :class`sire.legacy.Mol.ResIdxAtomCoordMatcher` by ensuring - that we only compare residues with the same number of atoms. - * Preserve user atom names when writing to PDB format. * Updated the :class:`~sire.mol.Cursor` so that it is easier to get and @@ -128,17 +149,6 @@ organisation on `GitHub `__. iterations reset. If it fails again, then this structure, with constraints re-applied, is returned. -* Code can now detect when an Amber PRMTOP file has discontiguous molecules, - and thus when atoms are reordered after load. This information is passed - to subsequent frame file parsers that are loaded at the same time, so - that they are able to reorder the frames before being added to the atoms. - This happens transparently, so that the user doesn't have to worry about - the reordering. This fixes issue #164. - -* Added ``map`` support to writing perturbable Gromacs topology files. This - enables the user to specify which perturbable properties to use, - e.g. ``map={"dihedral0": "dihedral_a", "dihedral1": "dihedral_b"}``. - * Added more support for Boresch restraints. Specifically, :func:`sire.restraints.boresch` now supports the specification of equilibrium values, uses different default force constants, and warns the user if the restraints are likely to be unstable. @@ -146,6 +156,36 @@ organisation on `GitHub `__. restraints. Tests were added for restraint creation and for the standard state correction. Boresch restraints were added to :doc:`tutorial `. +* Fixed a bug in the algorithm used to infer bond order when converting to + RDKit format. This fixes issue #177. + +* Fixed a bug in the :class:`~sire.legacy.Convert.LambdaLever` class where + it was not using the stage-specific value of lambda when using multiple + stages where one or more stages contained a standard morph equation. + +* Please add an item to this changelog when you create your PR + +`2023.5.2 `__ - March 2024 +------------------------------------------------------------------------------------------ + +* Fix bug that disabled the ``DEBUG`` log level from the global logger. + +* Fixed bug in :class`sire.legacy.Mol.ResIdxAtomCoordMatcher` by ensuring + that we only compare residues with the same number of atoms. + +* Added an ``AtomCoordMatcher`` to match atoms by coordinates in two selections. + +* Added ``map`` support to writing perturbable Gromacs topology files. This + enables the user to specify which perturbable properties to use, + e.g. ``map={"dihedral0": "dihedral_a", "dihedral1": "dihedral_b"}``. + +* Code can now detect when an Amber PRMTOP file has discontiguous molecules, + and thus when atoms are reordered after load. This information is passed + to subsequent frame file parsers that are loaded at the same time, so + that they are able to reorder the frames before being added to the atoms. + This happens transparently, so that the user doesn't have to worry about + the reordering. This fixes issue #164. + * Fixed a bug where the SDF parser would wrongly try to parse Amber RST7 files that weren't immediately recognised as such. The fix adds ``.inpcrd`` as a recognised extension for Amber RST7 files, and changes the scoring logic of the SDF parser @@ -155,15 +195,10 @@ organisation on `GitHub `__. when reading Mol2 files. This is more robust than using the atom name. Fixes issue #166. -* Made it easier to convert from strings to elements. Added the ability to +* Made it easier to convert from strings to elements. Added the ability to customise the list of elements that are considered biological. This fixes issue #170. -* Fixed a bug in the algorithm used to infer bond order when converting to - RDKit format. This fixes issue #177. - -* Please add an item to this changelog when you create your PR - `2023.5.1 `__ - January 2024 -------------------------------------------------------------------------------------------- From 670875808ed30634834548d57911d875fb634438 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 23:07:54 +0000 Subject: [PATCH 192/468] Added power and square root support to GeneralUnit --- doc/source/changelog.rst | 6 ++++++ src/sire/__init__.py | 11 ++++++++++ src/sire/units/__init__.py | 41 ++++++++++++++++++++++++++++++++++++++ 3 files changed, 58 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 78c61e3d0..efb21c7c8 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -156,6 +156,12 @@ organisation on `GitHub `__. restraints. Tests were added for restraint creation and for the standard state correction. Boresch restraints were added to :doc:`tutorial `. +* Added power support to GeneralUnit in python. You can now raise a unit value + to a valid power, e.g. ``sr.u("5A")**2``. You can also square root via a new + ``.sqrt()`` function on the unit. There is also a new ``sire.sqrt`` function + that will automatically called ``obj.sqrt()`` if that exists, or will fall + back to ``math.sqrt`` if not. + * Fixed a bug in the algorithm used to infer bond order when converting to RDKit format. This fixes issue #177. diff --git a/src/sire/__init__.py b/src/sire/__init__.py index 631ae5930..7422391a6 100644 --- a/src/sire/__init__.py +++ b/src/sire/__init__.py @@ -45,6 +45,7 @@ "set_max_num_threads", "smiles", "smarts", + "sqrt", "supported_formats", "tutorial_url", "u", @@ -121,6 +122,16 @@ def _fix_openmm_path(): _fix_openmm_path() +def sqrt(x): + """Return the square root of the passed value""" + if hasattr(x, "sqrt"): + return x.sqrt() + else: + import math + + return math.sqrt(x) + + def u(unit): """ Return a sire unit created from the passed expression. If this is a diff --git a/src/sire/units/__init__.py b/src/sire/units/__init__.py index 041988a6e..7db6573c2 100644 --- a/src/sire/units/__init__.py +++ b/src/sire/units/__init__.py @@ -382,10 +382,51 @@ def __generalunit__abs__(obj): else: return obj + def __generalunit__pow__(obj, power): + try: + power = float(power) + except Exception: + raise TypeError( + "unsupported operand type(s) for ^: '%s' and '%s'" + % (obj.__class__.__qualname__, power.__class__.__qualname__) + ) + + if obj.is_zero(): + return obj + + elif power == 0: + return obj / obj + + value = obj.value() ** power + + dims = obj.dimensions() + + # Compute the new dimensions, rounding floats to 16 decimal places. + new_dims = [round(dim * power, 16) for dim in dims] + + # Make sure the new dimensions are integers. + def is_integer(dim): + return dim == int(dim) + + if not all(is_integer(dim) for dim in new_dims): + raise ValueError( + "The exponent must be a factor of all the unit dimensions." + ) + + # Convert to integers. + new_dims = [int(dim) for dim in new_dims] + + return GeneralUnit(value, new_dims) + + def __generalunit__sqrt__(obj): + return obj**0.5 + GeneralUnit.__bool__ = __generalunit__bool__ GeneralUnit.__float__ = __generalunit__float__ GeneralUnit.__int__ = __generalunit__int__ GeneralUnit.__abs__ = __generalunit__abs__ + GeneralUnit.__pow__ = __generalunit__pow__ + GeneralUnit.sqrt = __generalunit__sqrt__ if not hasattr(GeneralUnit, "to_default"): From 85751b70574e7a06b1f70988a8824f91f8aacc5b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 23:23:37 +0000 Subject: [PATCH 193/468] Fully switch over to conda build --- .github/workflows/choose_branch.yaml | 6 ++---- .github/workflows/devel.yaml | 6 ++---- .github/workflows/main.yaml | 6 ++---- .github/workflows/pr.yaml | 6 ++---- 4 files changed, 8 insertions(+), 16 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 415067fe4..d36fc8dfe 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -55,14 +55,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the desired branch run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -71,7 +69,7 @@ jobs: run: mkdir ${{ github.workspace }}/build # - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 653162474..dcc9f31b2 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -50,14 +50,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the devel branch (push to devel) run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -66,7 +64,7 @@ jobs: run: mkdir ${{ github.workspace }}/build # - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 701684211..dd29f053c 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -46,14 +46,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the main branch (push to main) run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -62,7 +60,7 @@ jobs: run: mkdir ${{ github.workspace }}/build # - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # upload to the 'test' channel diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 353601602..684beaefb 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -52,14 +52,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the feature branch (pull request to devel) run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging=21 pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -68,4 +66,4 @@ jobs: run: mkdir ${{ github.workspace }}/build # - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire From 3ea0e3f377172ae14a33cb7b0480b0623c305448 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 30 Mar 2024 23:31:55 +0000 Subject: [PATCH 194/468] Switched back to older miniconda setup, plus removed even more mamba --- .github/workflows/choose_branch.yaml | 4 ++-- .github/workflows/devel.yaml | 4 ++-- .github/workflows/main.yaml | 4 ++-- .github/workflows/pr.yaml | 4 ++-- actions/update_recipe.py | 2 +- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index d36fc8dfe..50e59a932 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -49,7 +49,7 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v3 + - uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -68,7 +68,7 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build + - name: Build Conda package using conda build run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index dcc9f31b2..6fc3252ce 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -44,7 +44,7 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v3 + - uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -63,7 +63,7 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build + - name: Build Conda package using conda build run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index dd29f053c..bb0a73592 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -40,7 +40,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v3 + - uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -59,7 +59,7 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build + - name: Build Conda package using conda build run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 684beaefb..dd5653c97 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -46,7 +46,7 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v3 + - uses: conda-incubator/setup-miniconda@v2 with: auto-update-conda: true python-version: ${{ matrix.python-version }} @@ -65,5 +65,5 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build + - name: Build Conda package using conda build run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire diff --git a/actions/update_recipe.py b/actions/update_recipe.py index 41e93d5cf..b21922146 100644 --- a/actions/update_recipe.py +++ b/actions/update_recipe.py @@ -254,4 +254,4 @@ def check_reqs(reqs0, reqs1): channels = " ".join([f"-c {x}" for x in channels]) print("\nBuild this package using the command") -print(f"conda mambabuild {channels} {condadir}") +print(f"conda build {channels} {condadir}") From eeb2ccdef7186dd803d84a06d426244881f3ff5b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 31 Mar 2024 11:41:03 +0100 Subject: [PATCH 195/468] Pinned gemmi to 0.6.4 on Windows to see if that resolves the symbol problem. Pinned boa to 0.16 for now, as suggested by Lester to fix the conda build problems --- .github/workflows/choose_branch.yaml | 10 ++++++---- .github/workflows/devel.yaml | 10 ++++++---- .github/workflows/main.yaml | 10 ++++++---- .github/workflows/pr.yaml | 10 ++++++---- requirements_build.txt | 7 +++++-- requirements_host.txt | 7 ++++++- requirements_test.txt | 6 +++++- 7 files changed, 40 insertions(+), 20 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 50e59a932..499f69ce9 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -49,18 +49,20 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest + miniforge-variant: Mambaforge + use-mamba: true # - name: Clone the desired branch run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -68,8 +70,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using conda build - run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using mamba build + run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 6fc3252ce..47e223981 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -44,18 +44,20 @@ jobs: REPO: "${{ github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest + miniforge-variant: Mambaforge + use-mamba: true # - name: Clone the devel branch (push to devel) run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -63,8 +65,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using conda build - run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using mamba build + run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index bb0a73592..018a984f7 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -40,18 +40,20 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest + miniforge-variant: Mambaforge + use-mamba: true # - name: Clone the main branch (push to main) run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -59,8 +61,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using conda build - run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using mamba build + run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # upload to the 'test' channel diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index dd5653c97..a2c37da7a 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -46,18 +46,20 @@ jobs: REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # - - uses: conda-incubator/setup-miniconda@v2 + - uses: conda-incubator/setup-miniconda@v3 with: auto-update-conda: true python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest + miniforge-variant: Mambaforge + use-mamba: true # - name: Clone the feature branch (pull request to devel) run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -65,5 +67,5 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using conda build - run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using mamba build + run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire diff --git a/requirements_build.txt b/requirements_build.txt index c2b7173ea..6fa115ba2 100644 --- a/requirements_build.txt +++ b/requirements_build.txt @@ -17,6 +17,9 @@ rdkit >=2023.0.0 rdkit-dev >=2023.0.0 # These packages are needed to compile -# the SireGemmi plugin -gemmi >=0.6.4 +# the SireGemmi plugin. gemmi::Structure objects +# can't be resolved on Windows with 0.6.5 +gemmi ==0.6.4 ; sys_platform == "win32" +gemmi >=0.6.4 ; sys_platform != "win32" + pybind11 diff --git a/requirements_host.txt b/requirements_host.txt index 533413597..bc7614c9b 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -12,9 +12,14 @@ qt-main rich tbb tbb-devel -gemmi >=0.6.4 rdkit >=2023.0.0 +# gemmi::Structure objects +# can't be resolved on Windows with 0.6.5 +gemmi ==0.6.4 ; sys_platform == "win32" +gemmi >=0.6.4 ; sys_platform != "win32" + + # kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools kartograf >= 1.0.0 ; sys_platform != "win32" diff --git a/requirements_test.txt b/requirements_test.txt index b8800e418..ac3b6deec 100644 --- a/requirements_test.txt +++ b/requirements_test.txt @@ -2,7 +2,11 @@ # enable test to run to validate advanced functionality rdkit >=2023.0.0 -gemmi >=0.6.4 + +# gemmi::Structure objects +# can't be resolved on Windows with 0.6.5 +gemmi ==0.6.4 ; sys_platform == "win32" +gemmi >=0.6.4 ; sys_platform != "win32" # kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools From a3cd27b8471c0bc672391b42980ea87f11ccbff5 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 31 Mar 2024 11:45:17 +0100 Subject: [PATCH 196/468] Removed the boa pin and experimenting with removing the pin for packaging (as suggested) --- .github/workflows/choose_branch.yaml | 2 +- .github/workflows/devel.yaml | 2 +- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 499f69ce9..76630293e 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -62,7 +62,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 47e223981..9fcb69ed4 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -57,7 +57,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 018a984f7..e430a8bf7 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -53,7 +53,7 @@ jobs: run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index a2c37da7a..a8a93cc84 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -59,7 +59,7 @@ jobs: run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge "boa==0.16" anaconda-client packaging=21 pip-requirements-parser + run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py From 096eff60d9019709f029150e2405b8a4992bf799 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 31 Mar 2024 11:59:16 +0100 Subject: [PATCH 197/468] Missed this gemmi pin [ci skip] --- requirements_bss.txt | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index b99ad4384..5dc0898d8 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -14,7 +14,7 @@ openmmtools >= 0.21.5 ambertools >= 22 ; sys_platform != "win32" gromacs ; sys_platform != "win32" -# kartograf on Windows pulls in an openfe that has an old / incompatble +# kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools kartograf >= 1.0.0 ; sys_platform != "win32" @@ -33,7 +33,11 @@ pydot pygtail pyyaml rdkit >=2023.0.0 -gemmi >=0.6.4 + +# gemmi::Structure objects +# can't be resolved on Windows with 0.6.5 +gemmi ==0.6.4 ; sys_platform == "win32" +gemmi >=0.6.4 ; sys_platform != "win32" # The below are packages that aren't available on all # platforms/OSs and so need to be conditionally included From 7e36a4a1d037c7635c5893a3f8605bf8b709d362 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 1 Apr 2024 18:07:14 +0100 Subject: [PATCH 198/468] Removed the pin on gemmi and moved it to windows for pybind11 Updated supported Python versions to 3.10, 3.11 and 3.12 --- .github/workflows/choose_branch.yaml | 10 +++++----- .github/workflows/devel.yaml | 8 ++++---- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 10 +++++----- requirements_bss.txt | 6 +----- requirements_build.txt | 9 ++++----- requirements_host.txt | 7 +------ requirements_test.txt | 6 +----- 8 files changed, 22 insertions(+), 36 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 76630293e..f771b62fb 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -20,7 +20,7 @@ jobs: max-parallel: 5 fail-fast: false matrix: - python-version: ["3.8", "3.9", "3.10"] + python-version: ["3.10", "3.11", "3.12"] platform: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } @@ -30,14 +30,14 @@ jobs: # but Linux - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.8" + python-version: "3.10" - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.8" + python-version: "3.10" - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.9" + python-version: "3.11" - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.9" + python-version: "3.11" environment: name: sire-build defaults: diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 9fcb69ed4..85d9e3b8a 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -18,7 +18,7 @@ jobs: max-parallel: 5 fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12"] platform: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } @@ -28,11 +28,11 @@ jobs: # but Linux - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.9" - - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.9" + python-version: "3.11" - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } python-version: "3.10" + - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } + python-version: "3.11" environment: name: sire-build defaults: diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index e430a8bf7..182e9a679 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -24,7 +24,7 @@ jobs: max-parallel: 9 fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12"] platform: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index a8a93cc84..0419d3263 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -17,7 +17,7 @@ jobs: max-parallel: 5 fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12"] platform: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } @@ -27,14 +27,14 @@ jobs: # but Linux - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.9" + python-version: "3.10" - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.9" + python-version: "3.10" - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.10" + python-version: "3.11" - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.10" + python-version: "3.11" environment: name: sire-build defaults: diff --git a/requirements_bss.txt b/requirements_bss.txt index 5dc0898d8..98a166778 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -33,11 +33,7 @@ pydot pygtail pyyaml rdkit >=2023.0.0 - -# gemmi::Structure objects -# can't be resolved on Windows with 0.6.5 -gemmi ==0.6.4 ; sys_platform == "win32" -gemmi >=0.6.4 ; sys_platform != "win32" +gemmi >=0.6.4 # The below are packages that aren't available on all # platforms/OSs and so need to be conditionally included diff --git a/requirements_build.txt b/requirements_build.txt index 6fa115ba2..a9ea6f100 100644 --- a/requirements_build.txt +++ b/requirements_build.txt @@ -17,9 +17,8 @@ rdkit >=2023.0.0 rdkit-dev >=2023.0.0 # These packages are needed to compile -# the SireGemmi plugin. gemmi::Structure objects -# can't be resolved on Windows with 0.6.5 -gemmi ==0.6.4 ; sys_platform == "win32" -gemmi >=0.6.4 ; sys_platform != "win32" +# the SireGemmi plugin +gemmi >=0.6.4 -pybind11 +pybind11 ==2.11.1 ; sys_platform == "win32" +pybind11 sys_platform != "win32" diff --git a/requirements_host.txt b/requirements_host.txt index bc7614c9b..9b0e2a797 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -13,12 +13,7 @@ rich tbb tbb-devel rdkit >=2023.0.0 - -# gemmi::Structure objects -# can't be resolved on Windows with 0.6.5 -gemmi ==0.6.4 ; sys_platform == "win32" -gemmi >=0.6.4 ; sys_platform != "win32" - +gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools diff --git a/requirements_test.txt b/requirements_test.txt index ac3b6deec..b8800e418 100644 --- a/requirements_test.txt +++ b/requirements_test.txt @@ -2,11 +2,7 @@ # enable test to run to validate advanced functionality rdkit >=2023.0.0 - -# gemmi::Structure objects -# can't be resolved on Windows with 0.6.5 -gemmi ==0.6.4 ; sys_platform == "win32" -gemmi >=0.6.4 ; sys_platform != "win32" +gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools From e4f72b3b9a2bfd0c4a1c2cd765ca6df98b63b4fc Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 1 Apr 2024 18:38:35 +0100 Subject: [PATCH 199/468] MacOS x86 3.12 didn't work, so using 3.11 for MacOS for now. Updated the changelog with details about support Python versions. --- .github/workflows/choose_branch.yaml | 2 +- .github/workflows/devel.yaml | 4 ++-- .github/workflows/main.yaml | 4 ++++ .github/workflows/pr.yaml | 2 +- doc/source/changelog.rst | 5 +++++ 5 files changed, 13 insertions(+), 4 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index f771b62fb..534742c71 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -35,7 +35,7 @@ jobs: python-version: "3.10" - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.11" + python-version: "3.12" # MacOS can't run 3.12 yet... - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } python-version: "3.11" environment: diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 85d9e3b8a..e63e5072a 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -15,7 +15,7 @@ jobs: name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) runs-on: ${{ matrix.platform.os }} strategy: - max-parallel: 5 + max-parallel: 6 fail-fast: false matrix: python-version: ["3.10", "3.11", "3.12"] @@ -28,7 +28,7 @@ jobs: # but Linux - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.11" + python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11 - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } python-version: "3.10" - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 182e9a679..76732f2ec 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -29,6 +29,10 @@ jobs: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + exclude: + - platform: + { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + python-version: "3.12" # MacOS can't run 3.12 yet... environment: name: sire-build defaults: diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 0419d3263..e1a45542b 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -32,7 +32,7 @@ jobs: python-version: "3.10" - platform: { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.11" + python-version: "3.12" # MacOS can't run 3.12 yet... - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } python-version: "3.11" environment: diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index efb21c7c8..6cba6d3dd 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -15,6 +15,11 @@ organisation on `GitHub `__. `2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ +* Dropped official builds and support for Python 3.9, and added official + builds and support for Python 3.12. Note that MacOS builds are currently + 3.10 and 3.11 only, due to missing dependencies. This will be fixed + in upcoming point releases. + * BREAKING CHANGE: Updated the API of :class:`sire.cas.LambdaSchedule` so that you have to use named arguments for many of the functions (e.g. :meth:`~sire.cas.LambdaSchedule.set_equation`). This is because the addition From 73fe3849dae58934397dfd26e2ca496185c3905a Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 1 Apr 2024 19:35:37 +0100 Subject: [PATCH 200/468] Update documentation about support Python versions, plus added instructions on how to install packages from our archive channel. This is a doc-only commit, so no need for CI [ci skip] --- README.rst | 39 +++++++++++++++++++++++++++++++++++++-- doc/source/install.rst | 37 +++++++++++++++++++++++++++++++++---- 2 files changed, 70 insertions(+), 6 deletions(-) diff --git a/README.rst b/README.rst index 564b5296c..4689732d8 100644 --- a/README.rst +++ b/README.rst @@ -43,7 +43,7 @@ To create a new environment: .. code-block:: bash - conda create -n openbiosim "python<3.12" + conda create -n openbiosim "python<3.13" conda activate openbiosim conda install -c conda-forge -c openbiosim sire @@ -51,10 +51,45 @@ To install the latest development version you can use: .. code-block:: bash - conda create -n openbiosim-dev "python<3.12" + conda create -n openbiosim-dev "python<3.13" conda activate openbiosim-dev conda install -c conda-forge -c openbiosim/label/dev sire +Installing older versions +------------------------- + +You can install a specific version of sire by specifying the version number +in the conda install command, e.g. + +.. code-block:: bash + + conda install -c conda-forge -c openbiosim sire==2024.1.0 + +Note that limited space means that we can only keep a small number of +versions of sire on the official openbiosim conda channel. Generally +these are all point releases of the latest major version, plus the latest +point release of the last major version. + +We do provide an +`archive channel `__ +of all previous releases. You can search this archive channel for the +release you are interested in using the following command: + +.. code-block:: bash + + conda search -c https://openbiosim.blob.core.windows.net/archive sire + +This will return a list of all versions of sire available in the archive. + +You can install a specific version from the archive using a command like: + +.. code-block:: bash + + conda install -c https://openbiosim.blob.core.windows.net/archive sire==2023.2.3 + +Installation from source +------------------------ + However, as you are here, it is likely you want to download the latest, greatest version of the code, which you will need to compile. To compile sire, diff --git a/doc/source/install.rst b/doc/source/install.rst index 97db15d3f..72e745f9b 100644 --- a/doc/source/install.rst +++ b/doc/source/install.rst @@ -92,16 +92,16 @@ And then... Install sire into a new environment We recommend that :mod:`sire` is installed into a new (clean) environment. This minimises the risk of failures caused by incompatible dependencies. -Sire is currently packaged for Python 3.9, 3.10 and Python 3.11. We will start -by creating a Python 3.11 environment that we will call ``openbiosim``. +Sire is currently packaged for Python 3.10, 3.11 and Python 3.12. We will start +by creating a Python 3.12 environment that we will call ``openbiosim``. .. code-block:: bash - $ conda create -n openbiosim "python<3.12" + $ conda create -n openbiosim "python<3.13" .. note:: - We use ``python<3.12`` as this will install the most recent 3.11 + We use ``python<3.13`` as this will install the most recent 3.12 release of python. We can now install :mod:`sire` into that environment by typing @@ -125,6 +125,35 @@ If you want the latest development release, then install by typing $ conda install -n openbiosim -c conda-forge -c "openbiosim/label/dev" sire +You can install a specific version of sire by specifying the version number +in the conda install command, e.g. + +.. code-block:: bash + + conda install -n openbiosim -c conda-forge -c openbiosim sire==2024.1.0 + +Note that limited space means that we can only keep a small number of +versions of sire on the official openbiosim conda channel. Generally +these are all point releases of the latest major version, plus the latest +point release of the last major version. + +We do provide an +`archive channel `__ +of all previous releases. You can search this archive channel for the +release you are interested in using the following command: + +.. code-block:: bash + + conda search -c https://openbiosim.blob.core.windows.net/archive sire + +This will return a list of all versions of sire available in the archive. + +You can install a specific version from the archive using a command like: + +.. code-block:: bash + + conda install -n openbiosim -c https://openbiosim.blob.core.windows.net/archive sire==2023.2.3 + You may (optionally) want to install additional tools such as ``ipython`` and ``jupyterlab``. To do this, type From ae2f9d3e1cfe3c7d0cdc16ee8f465a286863fdcc Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 1 Apr 2024 22:40:28 +0100 Subject: [PATCH 201/468] Atom/residue name information is now saved to the RDKit molecule :-) Next up is to read it back so that it can be preserved as when we convert to/from RDKit --- wrapper/Convert/SireRDKit/sire_rdkit.cpp | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/wrapper/Convert/SireRDKit/sire_rdkit.cpp b/wrapper/Convert/SireRDKit/sire_rdkit.cpp index 7eecc3fdc..75d5ecd82 100644 --- a/wrapper/Convert/SireRDKit/sire_rdkit.cpp +++ b/wrapper/Convert/SireRDKit/sire_rdkit.cpp @@ -9,6 +9,7 @@ #include #include #include +#include #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -612,6 +613,29 @@ namespace SireRDKit molecule.addAtom(true); auto a = molecule.getActiveAtom(); + // create a AtomPDBResidueInfo object for the atom, and + // populate it with the name and residue information + auto info = new RDKit::AtomPDBResidueInfo(); + + info->setSerialNumber(atom.number().value()); + info->setName(atom.name().value().toStdString()); + + if (atom.isWithinResidue()) + { + auto residue = atom.residue(); + info->setResidueName(residue.name().value().toStdString()); + info->setResidueNumber(residue.number().value()); + } + + if (atom.isWithinChain()) + { + auto chain = atom.chain(); + info->setChainId(chain.name().value().toStdString()); + } + + a->setMonomerInfo(info); + a->setProp("molFileAlias", info->getName()); + const auto element = atom.property(map["element"]); a->setAtomicNum(element.nProtons()); From 8e4981e0ee013398f91ee784a64b8e8153a4eba2 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 2 Apr 2024 18:53:31 +0100 Subject: [PATCH 202/468] I've added in support for preserving metadata when converting to and from RDKit :-) --- doc/source/changelog.rst | 11 ++- tests/convert/test_rdkit.py | 30 +++++++ wrapper/Convert/SireRDKit/sire_rdkit.cpp | 101 +++++++++++++++++++++-- 3 files changed, 134 insertions(+), 8 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 6cba6d3dd..34be4b086 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -165,7 +165,16 @@ organisation on `GitHub `__. to a valid power, e.g. ``sr.u("5A")**2``. You can also square root via a new ``.sqrt()`` function on the unit. There is also a new ``sire.sqrt`` function that will automatically called ``obj.sqrt()`` if that exists, or will fall - back to ``math.sqrt`` if not. + back to ``math.sqrt`` if not. This implements wishlist item #176. + +* Conversion to and from RDKit now preserves atoms and residue names and + numbers. This makes used of AtomPDBResidueInfo in RDKit to populate metadata + when the RDKit molecule is created. On conversion to sire, the atom monomer + info will be checked. If it is simple, then only the atom name will be + obtained. If it is a AtomPDBResidueInfo, then the atom name and number, + and residue name and number (plus any chain information) will be extracted. + If no atom name is set, then the value of the property + "molFileAlias" will be checked. This implements wishlist item #168. * Fixed a bug in the algorithm used to infer bond order when converting to RDKit format. This fixes issue #177. diff --git a/tests/convert/test_rdkit.py b/tests/convert/test_rdkit.py index 363aca631..780f4e3a8 100644 --- a/tests/convert/test_rdkit.py +++ b/tests/convert/test_rdkit.py @@ -135,3 +135,33 @@ def test_rdkit_infer_bonds(ejm55_sdf, ejm55_gro): for s, g in zip(match_sdf, match_gro): assert s.number() == g.number() + + +@pytest.mark.skipif( + "rdkit" not in sr.convert.supported_formats(), + reason="rdkit support is not available", +) +def test_rdkit_preserve_info(ala_mols, ejm55_gro): + mol0 = ala_mols[0] + mol1 = ejm55_gro["not (protein or water)"].molecule() + + r0 = sr.convert.to(mol0, "rdkit") + r1 = sr.convert.to(mol1, "rdkit") + + m0 = sr.convert.to(r0, "sire") + m1 = sr.convert.to(r1, "sire") + + for mol, m in [(mol0, m0), (mol1, m1)]: + for res0, res1 in zip(mol.residues(), m.residues()): + assert res0.name() == res1.name() + assert res0.number() == res1.number() + + for atom0, atom1 in zip(mol.atoms(), m.atoms()): + assert atom0.name() == atom1.name() + assert atom0.number() == atom1.number() + + res0 = atom0.residue() + res1 = atom1.residue() + + assert res0.name() == res1.name() + assert res0.number() == res1.number() diff --git a/wrapper/Convert/SireRDKit/sire_rdkit.cpp b/wrapper/Convert/SireRDKit/sire_rdkit.cpp index 75d5ecd82..f5574cdc4 100644 --- a/wrapper/Convert/SireRDKit/sire_rdkit.cpp +++ b/wrapper/Convert/SireRDKit/sire_rdkit.cpp @@ -871,8 +871,6 @@ namespace SireRDKit } auto cg = Molecule().edit().rename(molname).add(SireMol::CGName("0")); - auto res = cg.molecule().add(SireMol::ResNum(1)); - res.rename(SireMol::ResName("LIG")); int n = 0; @@ -884,12 +882,101 @@ namespace SireRDKit { atom_to_idx[atom] = n; n += 1; - auto a = cg.add(SireMol::AtomNum(n)); + + // see if there is a PDBResidueInfo object for this atom + const auto *info = atom->getMonomerInfo(); + + SireMol::AtomName atomname; + SireMol::AtomNum atomnum; + SireMol::ResName resname; + SireMol::ResNum resnum; + SireMol::ChainName chainname; + + if (info != 0) + { + atomname = SireMol::AtomName(QString::fromStdString(info->getName())); + + if (info->getMonomerType() == RDKit::AtomMonomerInfo::PDBRESIDUE) + { + auto resinfo = static_cast(info); + + atomname = SireMol::AtomName(QString::fromStdString(resinfo->getName())); + atomnum = SireMol::AtomNum(resinfo->getSerialNumber()); + resname = SireMol::ResName(QString::fromStdString(resinfo->getResidueName())); + resnum = SireMol::ResNum(resinfo->getResidueNumber()); + chainname = SireMol::ChainName(QString::fromStdString(resinfo->getChainId())); + } + else + { + atomnum = SireMol::AtomNum(n); + } + } + else + { + atomnum = SireMol::AtomNum(n); + } + + // check the molFileAlias property if the atom name hasn't been set + if (atomname.value().isEmpty()) + { + std::string alias; + + if (atom->getPropIfPresent("molFileAlias", alias)) + { + atomname = SireMol::AtomName(QString::fromStdString(alias)); + } + } + + if (atomname.value().isEmpty()) + { + atomname = SireMol::AtomName(QString("%1%2").arg(QString::fromStdString(atom->getSymbol())).arg(n)); + } + + // place all atoms into the same cutgroup + auto a = cg.add(atomnum); + + // now find a residue + if (resname.value().isEmpty()) + { + resname = SireMol::ResName("LIG"); + } + + if (resnum.isNull()) + { + resnum = SireMol::ResNum(1); + } + + // find this residue - if it doesn't exist, then create it + SireMol::ResStructureEditor res; + + try + { + res = cg.molecule().select(resnum); + } + catch (...) + { + res = cg.molecule().add(resnum); + res.rename(resname); + } + + if (not chainname.value().isEmpty()) + { + SireMol::ChainStructureEditor chain; + + try + { + chain = cg.molecule().select(chainname); + } + catch (...) + { + chain = cg.molecule().add(chainname); + } + + res.reparent(chain.name()); + } + a.reparent(res.number()); - a.rename(SireMol::AtomName( - QString("%1%2") - .arg(QString::fromStdString(atom->getSymbol())) - .arg(n))); + a.rename(atomname); set_prop(a, "element", SireMol::Element(atom->getAtomicNum()), map); set_prop(a, "formal_charge", atom->getFormalCharge() * SireUnits::mod_electron, map); From 2549c3ecf097e79161cddd5fa78720f73db1899d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 3 Apr 2024 18:42:41 +0100 Subject: [PATCH 203/468] Added a "auto-bonds" constraint option that constrains bonds based on comparing their vibrational period to the timestep --- src/sire/options/_dynamics_options.py | 6 ++ wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 100 ++++++++++++++---- wrapper/Convert/SireOpenMM/openmmmolecule.h | 2 + wrapper/Convert/__init__.py | 1 + 4 files changed, 89 insertions(+), 20 deletions(-) diff --git a/src/sire/options/_dynamics_options.py b/src/sire/options/_dynamics_options.py index 4da2dcb25..1f0fd35f8 100644 --- a/src/sire/options/_dynamics_options.py +++ b/src/sire/options/_dynamics_options.py @@ -95,6 +95,12 @@ class Constraint(_Option): "excluding those that are perturbed " "but do not involve a hydrogen in any end state.", ) + AUTO_BONDS = ( + "auto_bonds", + "Choose the constraints automatically, constraining bonds based " + "on whether their predicted vibrational periods are less than a " + "tenth of the simulaton timestep.", + ) @staticmethod def create(option: str): diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index a56c6102d..7062c1451 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -141,11 +141,15 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, { constraint_type = CONSTRAIN_BONDS | CONSTRAIN_HANGLES | CONSTRAIN_NOT_HEAVY_PERTURBED; } + else if (c == "auto-bonds") + { + constraint_type = CONSTRAIN_AUTO_BONDS; + } else { throw SireError::invalid_key(QObject::tr( "Unrecognised constraint type '%1'. Valid values are " - "'none', 'h-bonds', " + "'none', 'auto-bonds', 'h-bonds', " "'h-bonds-not-perturbed', 'h-bonds-not-heavy-perturbed', " "'h-bonds-h-angles-not-perturbed', 'h-bonds-h-angles-not-heavy-perturbed' " "'bonds', 'bonds-not-perturbed', 'bonds-not-heavy-perturbed', " @@ -216,11 +220,15 @@ OpenMMMolecule::OpenMMMolecule(const Molecule &mol, { perturbable_constraint_type = CONSTRAIN_BONDS | CONSTRAIN_HANGLES | CONSTRAIN_NOT_HEAVY_PERTURBED; } + else if (c == "auto-bonds") + { + perturbable_constraint_type = CONSTRAIN_AUTO_BONDS; + } else { throw SireError::invalid_key(QObject::tr( "Unrecognised perturbable constraint type '%1'. Valid values are " - "'none', 'h-bonds', " + "'none', 'auto-bonds', 'h-bonds', " "'h-bonds-not-perturbed', 'h-bonds-not-heavy-perturbed', " "'h-bonds-h-angles-not-perturbed', 'h-bonds-h-angles-not-heavy-perturbed' " "'bonds', 'bonds-not-perturbed', 'bonds-not-heavy-perturbed', " @@ -736,6 +744,38 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, dynamic_constraints = map["dynamic_constraints"].value().asABoolean(); } + double auto_constraints_factor = 10.0; + + if (map.specified("auto_constraints_factor")) + { + auto_constraints_factor = map["auto_constraints_factor"].value().asADouble(); + + if (auto_constraints_factor < 1) + { + auto_constraints_factor = 1; + } + else if (auto_constraints_factor > 1e6) + { + auto_constraints_factor = 1e6; + } + } + + double timestep_in_fs = 2.0; + + if (map.specified("timestep_in_fs")) + { + timestep_in_fs = map["timestep_in_fs"].value().asADouble(); + + if (timestep_in_fs < 1.0) + { + timestep_in_fs = 1.0; + } + else if (timestep_in_fs > 100) + { + timestep_in_fs = 100; + } + } + auto bonds = params.bonds(); if (is_perturbable) @@ -769,6 +809,7 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, const double k = bondparam.k() * bond_k_to_openmm; const double r0 = bondparam.r0() * bond_r0_to_openmm; + double r0_1 = r0; if (k != 0) { @@ -787,13 +828,32 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } bool bond_is_not_constrained = true; + bool should_constrain_bond = false; - if ((not has_massless_atom) and ((this_constraint_type & CONSTRAIN_BONDS) or - (has_light_atom and (this_constraint_type & CONSTRAIN_HBONDS)))) + if (this_constraint_type == CONSTRAIN_AUTO_BONDS) { - bool should_constrain_bond = true; + // constrain the bond if its predicted vibrational frequency is less than + // 10 times the simulation timestep + const double mass0 = masses_data[atom0]; + const double mass1 = masses_data[atom1]; + + // masses in g mol-1 - this converts the reduced mass to kg + const static double mass_to_reduced_mass = 0.001 / SireUnits::mole.value(); + const double reduced_mass_in_kg = ((mass0 * mass1) / (mass0 + mass1)) * mass_to_reduced_mass; + + // k in kJ mol-1 nm-2 - this converts to J m-2 + const static double k_to_J_m2 = 4184 * 1e20 / SireUnits::mole.value(); + const double k_in_J_m2 = bondparam.k() * k_to_J_m2; + + // vibrational period in femtoseconds + const double vibrational_period = 2e15 * SireMaths::pi * std::sqrt(reduced_mass_in_kg / k_in_J_m2); - double r0_1 = r0; + should_constrain_bond = vibrational_period < auto_constraints_factor * timestep_in_fs; + } + else if ((not has_massless_atom) and ((this_constraint_type & CONSTRAIN_BONDS) or + (has_light_atom and (this_constraint_type & CONSTRAIN_HBONDS)))) + { + should_constrain_bond = true; if (is_perturbable) { @@ -832,23 +892,23 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, } } } + } - if (should_constrain_bond) + if (should_constrain_bond) + { + if (dynamic_constraints and (std::abs(r0 - r0_1) > 1e-4)) // match to somd1 { - if (dynamic_constraints and (std::abs(r0 - r0_1) > 1e-4)) // match to somd1 - { - // this is a dynamic constraint that should change with lambda - this->perturbable_constraints.append(boost::make_tuple(atom0, atom1, r0, r0_1)); - } - else - { - // use the r0 for the bond - this->constraints.append(boost::make_tuple(atom0, atom1, r0)); - } - - constrained_pairs.insert(to_pair(atom0, atom1)); - bond_is_not_constrained = false; + // this is a dynamic constraint that should change with lambda + this->perturbable_constraints.append(boost::make_tuple(atom0, atom1, r0, r0_1)); } + else + { + // use the r0 for the bond + this->constraints.append(boost::make_tuple(atom0, atom1, r0)); + } + + constrained_pairs.insert(to_pair(atom0, atom1)); + bond_is_not_constrained = false; } if (include_constrained_energies or bond_is_not_constrained) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 7a4222851..30420f0be 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -38,6 +38,8 @@ namespace SireOpenMM CONSTRAIN_HANGLES = 0x00001000, CONSTRAIN_NOT_PERTURBED = 0x00010000, CONSTRAIN_NOT_HEAVY_PERTURBED = 0x00100000, + CONSTRAIN_AUTO = 0x01000000, + CONSTRAIN_AUTO_BONDS = CONSTRAIN_BONDS | CONSTRAIN_AUTO, }; OpenMMMolecule(); diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 31d13503e..31f915362 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -164,6 +164,7 @@ def sire_to_openmm(mols, map): timestep_in_fs = timestep.to(femtosecond) timestep = timestep.to(picosecond) * openmm.unit.picosecond + map.set("timestep_in_fs", timestep_in_fs) ensemble = Ensemble(map=map) From b613f48d69638e89faf87210b6012d2aa75e894f Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 3 Apr 2024 19:52:22 +0100 Subject: [PATCH 204/468] Added the unit test, changelog entry and documentation. Accidentally put this in feature_merge2, so am going to add this to the 2024.1.0 release. --- doc/source/changelog.rst | 7 +++ doc/source/cheatsheet/openmm.rst | 10 +++- doc/source/tutorial/part05/05_dynamics.rst | 28 +++++------ tests/convert/test_openmm_constraints.py | 55 ++++++++++++++++++++++ 4 files changed, 85 insertions(+), 15 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 34be4b086..92e3f27f7 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -176,6 +176,13 @@ organisation on `GitHub `__. If no atom name is set, then the value of the property "molFileAlias" will be checked. This implements wishlist item #168. +* Implemented the ``auto-bonds`` constraint, which automatically chooses + bonds to constrain by comparing the estimated vibrational frequency + against the simulation timestep multiplied by the factor + ``auto_bonds_factor`` (defaults to 10). + This is described in the :doc:`OpenMM detailed guide `. + This implements wishlist item #185. + * Fixed a bug in the algorithm used to infer bond order when converting to RDKit format. This fixes issue #177. diff --git a/doc/source/cheatsheet/openmm.rst b/doc/source/cheatsheet/openmm.rst index 72e14b64e..d53daa436 100644 --- a/doc/source/cheatsheet/openmm.rst +++ b/doc/source/cheatsheet/openmm.rst @@ -76,6 +76,13 @@ Available keys and allowable values are listed below. +------------------------------+----------------------------------------------------------+ | Key | Valid values | +==============================+==========================================================+ +| auto_constraints_factor | The factor by which to multiply the timestep when | +| | deciding whether or not an auto-constrained bond should | +| | be constrained. The calculated period of a bond | +| | vibration is compared to the simulation timestep | +| | multiplied by this factor. If the period is less than | +| | this, the bond is constrained. This defaults to 10. | ++------------------------------+----------------------------------------------------------+ | barostat_frequency | The frequency at which the barostat acts to perform | | | the MC moves to change the box volume when performing | | | constant pressure simulations (default 25). | @@ -102,7 +109,8 @@ Available keys and allowable values are listed below. | | removed. | +------------------------------+----------------------------------------------------------+ | constraint | Type of constraint to use for bonds and/or angles. | -| | Valid strings are ``none``, ``h-bonds``, | +| | Valid strings are ``none``, | +| | ``auto-bonds``, ``h-bonds``, | | | ``h-bonds-not-perturbed``, | | | ``h-bonds-not-heavy-perturbed``, | | | ``bonds``, ``bonds-not-perturbed``, | diff --git a/doc/source/tutorial/part05/05_dynamics.rst b/doc/source/tutorial/part05/05_dynamics.rst index 02600b635..f1f064939 100644 --- a/doc/source/tutorial/part05/05_dynamics.rst +++ b/doc/source/tutorial/part05/05_dynamics.rst @@ -72,7 +72,7 @@ the amount of time between saved coordinate/velocity snapshots. For example, here we will run 10 picoseconds of dynamics, saving a frame every 0.5 picoseconds ->>> d.run(10*sr.units.picosecond, 0.5*sr.units.picosecond) +>>> d.run("10ps", "0.5ps") Dynamics(completed=10 ps, energy=-8.82722 kcal mol-1, speed=119.2 ns day-1) .. note:: @@ -95,7 +95,7 @@ of the loaded system. We can perform dynamics on all the molecules by calling :func:`~sire.mol.SelectorMol.dynamics` on the complete collection. >>> d = mols.dynamics() ->>> d.run(10*sr.units.picosecond, 0.5*sr.units.picosecond) +>>> d.run("10ps", "0.5ps") Dynamics(completed=6010 ps, energy=-5974.09 kcal mol-1, speed=80.5 ns day-1) >>> mols = d.commit() >>> mols.trajectory().energy().pretty_plot() @@ -121,14 +121,14 @@ intervals to save frames for each run. For example, you could have a long "equilibration" run that doesn't save frames at all by setting ``save_frequency`` to ``0``. ->>> d.run(10*sr.units.picosecond, save_frequency=0) +>>> d.run("10ps", save_frequency=0) Dynamics(completed=6020 ps, energy=-5974.9 kcal mol-1, speed=89.2 ns day-1) You can run as many blocks as you like, e.g. ->>> d.run(1*sr.units.picosecond, save_frequency=0.01*sr.units.picosecond) +>>> d.run("1ps", save_frequency="0.01ps") Dynamics(completed=6021 ps, energy=-5974.61 kcal mol-1, speed=84.4 ns day-1) ->>> d.run(50*sr.units.picosecond, save_frequency=1*sr.units.picosecond) +>>> d.run("50ps", save_frequency="1ps") Dynamics(completed=6071 ps, energy=-5976.05 kcal mol-1, speed=58.3 ns day-1) >>> mols = d.commit() >>> mols.view() @@ -164,17 +164,17 @@ the :class:`~sire.mol.Dynamics` object. Available options are; 25 picoseconds (ps). * ``constraint`` - the level of constraints to apply to the molecules, e.g. constraining bonds, angles etc. By default this is inferred from - the value of ``timestep``. It defaults to no constraints. But timesteps - greater than 1 femtoseconds will constrain all bonds involving hydrogen - and all angles involving hydrogen. Timesteps greater than 2 femtoseconds will - constrain all bonds, and all angles involving hydrogen. + the value of ``timestep``. It defaults to no constraints. A good choice + for this parameter is ``auto-bonds``, which will automatically constrain + bonds based on a comparison between the bonds vibrational frequency + and the simulation timestep. For example >>> d = mols.dynamics(cutoff_type="reaction_field", -... timestep=4*sr.units.femtosecond, -... save_frequency=1*sr.units.picosecond) ->>> d.run(10*sr.units.picosecond) +... timestep="4fs", +... save_frequency="1ps") +>>> d.run("10ps") Dynamics(completed=6081 ps, energy=-6601.59 kcal mol-1, speed=432.2 ns day-1) will perform 10 picoseconds of dynamics saving a frame every 1 picosecond. @@ -196,10 +196,10 @@ that can be re-used between multiple dynamics runs. ... "timestep": 4*sr.units.femtosecond, ... "save_frequency": 1*sr.units.picosecond} >>> d = mols.dynamics(map=m) ->>> d.run(10*sr.units.picosecond) +>>> d.run("10ps") Dynamics(completed=6081 ps, energy=-6601.01 kcal mol-1, speed=439.8 ns day-1) >>> d2 = mols.dynamics(map=m) ->>> d2.run(10*sr.units.picosecond) +>>> d2.run("10ps") Dynamics(completed=6081 ps, energy=-6601.01 kcal mol-1, speed=440.6 ns day-1) The parameter map approach can be used to set other properties of the diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index a3c38e795..a8cf77371 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -396,3 +396,58 @@ def test_dynamic_constraints(merged_ethane_methanol, openmm_platform): nrg = d.current_potential_energy() assert nrg.value() == pytest.approx(13.8969, abs=0.001) + + +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats(), + reason="openmm support is not available", +) +def test_auto_constraints(ala_mols, openmm_platform): + mols = ala_mols + mol = mols[0] + + NA = 6.02214076e23 + CONV = 0.695039 + + periods = {} + + for bond in mol.bonds(): + mass0 = bond.atom0().mass().value() / (1000.0 * NA) + mass1 = bond.atom1().mass().value() / (1000.0 * NA) + k = sr.mm.AmberBond(bond.potential(), sr.cas.Symbol("r")).k() * CONV + + mu = (mass0 * mass1) / (mass0 + mass1) + + # period in fs + period = 1e15 * 2.0 * 3.14159 * (mu / k) ** 0.5 + periods[bond.id()] = period + + for factor in [5.0, 10.0, 15.0]: + for timestep in [sr.u("1fs"), sr.u("2fs"), sr.u("4fs")]: + fs = timestep.to("fs") + + constrained = [] + + for bond in mol.bonds(): + period = periods[bond.id()] + + if period < factor * fs: + constrained.append(bond.id()) + + d = mol.dynamics( + constraint="auto-bonds", + platform=openmm_platform, + timestep=timestep, + temperature="25oC", + map={"auto_constraints_factor": factor}, + ) + + constraints = d.get_constraints() + + assert len(constraints) == len(constrained) + + for constraint in constraints: + bond = sr.bondid( + constraint[0].atom(0).index(), constraint[0].atom(1).index() + ) + assert bond in constrained From 3ca7989b94181bb3eec6f35a6d6081e0b1dc4adc Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 6 Apr 2024 19:55:47 +0100 Subject: [PATCH 205/468] WIP - working on a new SystemTrajectory object that will make it (1) quicker to save and load trajectory frames when the trajectory is generated as part of a dynamics simulation, and (2) will cache frames to disk so that running dynamics won't use up all of RAM --- corelib/src/libs/SireIO/moleculeparser.cpp | 4 +- corelib/src/libs/SireMol/moleculegroups.cpp | 5 + corelib/src/libs/SireMol/trajectory.cpp | 65 +++++- corelib/src/libs/SireMol/trajectory.h | 5 + corelib/src/libs/SireSystem/CMakeLists.txt | 2 + corelib/src/libs/SireSystem/system.cpp | 71 +++++- corelib/src/libs/SireSystem/system.h | 6 + .../src/libs/SireSystem/systemtrajectory.cpp | 204 ++++++++++++++++++ .../src/libs/SireSystem/systemtrajectory.h | 178 +++++++++++++++ wrapper/Mol/AtomCoords.pypp.cpp | 2 + wrapper/Mol/AtomIdxMapping.pypp.cpp | 48 +++++ wrapper/Mol/Trajectory.pypp.cpp | 28 +++ wrapper/System/System.pypp.cpp | 2 + .../System/_System_free_functions.pypp.cpp | 6 + 14 files changed, 614 insertions(+), 12 deletions(-) create mode 100644 corelib/src/libs/SireSystem/systemtrajectory.cpp create mode 100644 corelib/src/libs/SireSystem/systemtrajectory.h diff --git a/corelib/src/libs/SireIO/moleculeparser.cpp b/corelib/src/libs/SireIO/moleculeparser.cpp index e08275f6a..305be0f87 100644 --- a/corelib/src/libs/SireIO/moleculeparser.cpp +++ b/corelib/src/libs/SireIO/moleculeparser.cpp @@ -2856,7 +2856,9 @@ System MoleculeParser::toSystem(const QList &others, const Pr } } - system.setProperty("trajectory", SireMol::Trajectory(trajectories)); + // comment out as we don't use the System trajectory property, + // and it is confusing if it isn't updated... + // system.setProperty("trajectory", SireMol::Trajectory(trajectories)); // we now have to assume that the trajectories all had the atomic // data in the same order and that this matches the atomidx order diff --git a/corelib/src/libs/SireMol/moleculegroups.cpp b/corelib/src/libs/SireMol/moleculegroups.cpp index 1dc2481ff..c54e028ea 100644 --- a/corelib/src/libs/SireMol/moleculegroups.cpp +++ b/corelib/src/libs/SireMol/moleculegroups.cpp @@ -1664,6 +1664,11 @@ bool MolGroupsBase::isEmpty() const Note that this is a potentially very slow operation! */ Molecules MolGroupsBase::molecules() const { + if (this->nGroups() == 1) + { + return this->getGroup(this->mgNums()[0]).molecules(); + } + Molecules all_mols; const QHash groups = this->getGroups(); diff --git a/corelib/src/libs/SireMol/trajectory.cpp b/corelib/src/libs/SireMol/trajectory.cpp index c2728c59f..43f2ac6c8 100644 --- a/corelib/src/libs/SireMol/trajectory.cpp +++ b/corelib/src/libs/SireMol/trajectory.cpp @@ -539,14 +539,23 @@ Trajectory::Trajectory() : ConcreteProperty(), sta { } -Trajectory::Trajectory(const TrajectoryData &data) +Trajectory::Trajectory(const TrajectoryDataPtr &data) : ConcreteProperty(), start_atom(0), natoms(0) { - start_atom = 0; - natoms = data.nAtoms(); + if (data.constData() != 0) + { + start_atom = 0; + natoms = data->nAtoms(); - if (data.nFrames() > 0) - d.append(TrajectoryDataPtr(data)); + if (data->nFrames() > 0) + d.append(data); + } +} + +Trajectory::Trajectory(const TrajectoryData &data) + : ConcreteProperty(), start_atom(0), natoms(0) +{ + this->operator=(Trajectory(TrajectoryDataPtr(data))); } Trajectory::Trajectory(const QList &data) @@ -580,21 +589,31 @@ Trajectory::Trajectory(const QList &data) } } -Trajectory::Trajectory(const TrajectoryData &data, int s, int n) +Trajectory::Trajectory(const TrajectoryDataPtr &data, int s, int n) : ConcreteProperty(), start_atom(s), natoms(n) { - if (natoms <= 0 or data.nFrames() <= 0) + if (natoms <= 0 or data.constData() == 0) + { + start_atom = 0; + natoms = 0; return; + } - if (start_atom < 0 or (start_atom + natoms) > data.nAtoms()) + if (start_atom < 0 or (start_atom + natoms) > data->nAtoms()) throw SireError::incompatible_error( QObject::tr("Cannot use start_atom %1 and natoms %2 for a trajectory with %3 atoms.") .arg(start_atom) .arg(natoms) - .arg(data.nAtoms()), + .arg(data->nAtoms()), CODELOC); - d.append(TrajectoryDataPtr(data)); + d.append(data); +} + +Trajectory::Trajectory(const TrajectoryData &data, int s, int n) + : ConcreteProperty(), start_atom(0), natoms(0) +{ + this->operator=(Trajectory(TrajectoryDataPtr(data), s, n)); } Trajectory::Trajectory(const QList &data, int s, int n) @@ -953,6 +972,32 @@ void Trajectory::setFrame(int i, const Frame &frame) } } +void Trajectory::append(const TrajectoryDataPtr &data) +{ + if (data.constData() == 0) + return; + + // check that the start and number of atoms would be compatible + // with this trajectory + if (start_atom + natoms > data->nAtoms()) + { + throw SireError::incompatible_error( + QObject::tr("Cannot append a trajectory with %1 atoms to a trajectory with %2 atoms " + "and start_atom %3.") + .arg(data->nAtoms()) + .arg(natoms) + .arg(start_atom), + CODELOC); + } + + d.append(data); +} + +void Trajectory::append(const TrajectoryData &data) +{ + this->append(TrajectoryDataPtr(data)); +} + void Trajectory::appendFrame(const Frame &frame) { if (frame.isEmpty()) diff --git a/corelib/src/libs/SireMol/trajectory.h b/corelib/src/libs/SireMol/trajectory.h index c5172d2a9..670b2a5f7 100644 --- a/corelib/src/libs/SireMol/trajectory.h +++ b/corelib/src/libs/SireMol/trajectory.h @@ -323,9 +323,11 @@ namespace SireMol Trajectory(); Trajectory(const TrajectoryData &trajectory); + Trajectory(const TrajectoryDataPtr &trajectory); Trajectory(const QList &trajectories); Trajectory(const TrajectoryData &trajectory, int start_atom, int natoms); + Trajectory(const TrajectoryDataPtr &trajectory, int start_atom, int natoms); Trajectory(const QList &trajectories, int start_atom, int natoms); @@ -371,6 +373,9 @@ namespace SireMol void insertFrame(int i, const Frame &frame); void deleteFrame(int i); + void append(const TrajectoryData &data); + void append(const TrajectoryDataPtr &data); + bool isCompatibleWith(const MoleculeInfoData &molinfo) const; SireBase::PropertyList merge(const MolViewProperty &other, diff --git a/corelib/src/libs/SireSystem/CMakeLists.txt b/corelib/src/libs/SireSystem/CMakeLists.txt index 6bdea44f9..bfae5f3ad 100644 --- a/corelib/src/libs/SireSystem/CMakeLists.txt +++ b/corelib/src/libs/SireSystem/CMakeLists.txt @@ -52,6 +52,7 @@ set ( SIRESYSTEM_HEADERS system.h systemmonitor.h systemmonitors.h + systemtrajectory.h volmapmonitor.h ) @@ -94,6 +95,7 @@ set ( SIRESYSTEM_SOURCES system.cpp systemmonitor.cpp systemmonitors.cpp + systemtrajectory.cpp volmapmonitor.cpp ${SIRESYSTEM_HEADERS} diff --git a/corelib/src/libs/SireSystem/system.cpp b/corelib/src/libs/SireSystem/system.cpp index a0ca6a9d1..6586d02d7 100644 --- a/corelib/src/libs/SireSystem/system.cpp +++ b/corelib/src/libs/SireSystem/system.cpp @@ -31,6 +31,7 @@ #include "delta.h" #include "monitorname.h" #include "system.h" +#include "systemtrajectory.h" #include "SireFF/energytable.h" #include "SireFF/ff.h" @@ -279,6 +280,7 @@ System::System(const System &other) sysversion(other.sysversion), sysmonitors(other.sysmonitors), cons(other.cons), mgroups_by_num(other.mgroups_by_num), shared_properties(other.shared_properties), + system_trajectory(other.system_trajectory), subversion(other.subversion) { molgroups[0] = other.molgroups[0]; @@ -304,6 +306,7 @@ System &System::operator=(const System &other) cons = other.cons; mgroups_by_num = other.mgroups_by_num; shared_properties = other.shared_properties; + system_trajectory = other.system_trajectory; subversion = other.subversion; MolGroupsBase::operator=(other); @@ -3883,6 +3886,12 @@ void System::loadFrame(int frame, const LazyEvaluator &evaluator, void System::saveFrame(int frame, const SireBase::PropertyMap &map) { + if (frame == this->nFrames(map)) + { + this->saveFrame(map); + return; + } + this->accept(); this->mustNowRecalculateFromScratch(); MolGroupsBase::saveFrame(frame, map); @@ -3890,9 +3899,69 @@ void System::saveFrame(int frame, const SireBase::PropertyMap &map) void System::saveFrame(const SireBase::PropertyMap &map) { + auto traj_prop = map["trajectory"]; + + if (not traj_prop.hasSource()) + return; + this->accept(); this->mustNowRecalculateFromScratch(); - MolGroupsBase::saveFrame(map); + + // do we have an active SystemTrajectory? + bool must_create = false; + + if (system_trajectory.constData() == 0) + { + must_create = true; + } + + auto mols = this->molecules(); + + SystemTrajectory *traj = dynamic_cast(system_trajectory.data()); + + if (traj == 0) + { + must_create = true; + } + else + { + must_create = not traj->isCompatibleWith(mols, map); + } + + if (must_create) + { + system_trajectory = new SystemTrajectory(mols, map); + + // add this trajectory onto all of the molecules... + auto mols2 = mols; + + for (auto it = mols.constBegin(); it != mols.constEnd(); ++it) + { + auto mol = it->molecule().data(); + + Trajectory moltraj; + + if (mol.hasProperty(traj_prop)) + { + moltraj = mol.property(traj_prop).asA(); + moltraj.append(traj->getTrajectory(mol.number())); + } + else + { + moltraj = Trajectory(traj->getTrajectory(mol.number())); + } + + mol.setProperty(traj_prop.source(), moltraj); + mols2.update(mol); + } + + mols = mols2; + this->update(mols); + } + + // save the frame into the system_trajectory - this will automatically + // update all molecules containing this trajectory + traj->saveFrame(mols, map); } void System::deleteFrame(int frame, const SireBase::PropertyMap &map) diff --git a/corelib/src/libs/SireSystem/system.h b/corelib/src/libs/SireSystem/system.h index d13cf1d69..195e5c934 100644 --- a/corelib/src/libs/SireSystem/system.h +++ b/corelib/src/libs/SireSystem/system.h @@ -39,6 +39,7 @@ #include "SireMol/mgnum.h" #include "SireMol/moleculegroup.h" #include "SireMol/moleculegroups.h" +#include "SireMol/trajectory.h" #include "SireFF/forcefields.h" @@ -528,6 +529,11 @@ namespace SireSystem By default, these are the "space" and "time" properties */ QStringList shared_properties; + /** Shared pointer to the current active SystemTrajectory. + * This will either be null or a valid pointer to a + * SystemTrajectory object */ + SireMol::TrajectoryDataPtr system_trajectory; + /** The subversion of this system - this is incremented when delta updates are being applied. A system with non-zero subversion is not guaranteed to be in a valid state */ diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp new file mode 100644 index 000000000..4337de198 --- /dev/null +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -0,0 +1,204 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "systemtrajectory.h" + +#include "SireMol/errors.h" + +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" + +using namespace SireSystem; +using namespace SireMol; +using namespace SireBase; +using namespace SireStream; + +//////// +//////// Implementation of MolSystemTrajectory +//////// + +static const RegisterMetaType r_moltraj; + +SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &ds, const MolSystemTrajectory &traj) +{ + writeHeader(ds, r_moltraj, 1); + + // we don't stream the trajectory as it would be too big + ds << static_cast(traj); + + return ds; +} + +SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &ds, MolSystemTrajectory &traj) +{ + auto v = readHeader(ds, r_moltraj); + + if (v == 1) + { + // we don't stream the trajectory as it would be too big + traj.clear(); + ds >> static_cast(traj); + } + else + throw version_error(v, "1", r_moltraj, CODELOC); + + return ds; +} + +MolSystemTrajectory::MolSystemTrajectory() + : TrajectoryData(), start_atom(0), natoms(0) +{ +} + +MolSystemTrajectory::MolSystemTrajectory(const SystemTrajectory &trajectory, + SireMol::MolNum molnum) + : TrajectoryData(trajectory), start_atom(0), natoms(0) +{ + d = trajectory.d; + + auto it = trajectory.mol_atoms.constFind(molnum); + + if (it == trajectory.mol_atoms.constEnd()) + { + throw SireMol::missing_molecule(QObject::tr( + "There is no molecule with number %1 in the system") + .arg(molnum.value()), + CODELOC); + } + + start_atom = it.value().first; + natoms = it.value().second; +} + +MolSystemTrajectory::MolSystemTrajectory(const MolSystemTrajectory &other) + : TrajectoryData(other), d(other.d), start_atom(other.start_atom), natoms(other.natoms) +{ +} + +MolSystemTrajectory::~MolSystemTrajectory() +{ +} + +MolSystemTrajectory &MolSystemTrajectory::operator=(const MolSystemTrajectory &other) +{ + if (this != &other) + { + TrajectoryData::operator=(other); + d = other.d; + start_atom = other.start_atom; + natoms = other.natoms; + } + + return *this; +} + +bool MolSystemTrajectory::operator==(const MolSystemTrajectory &other) const +{ + return TrajectoryData::operator==(other) && + d.get() == other.d.get() && + start_atom == other.start_atom && + natoms == other.natoms; +} + +bool MolSystemTrajectory::operator!=(const MolSystemTrajectory &other) const +{ + return not this->operator==(other); +} + +const char *MolSystemTrajectory::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *MolSystemTrajectory::what() const +{ + return MolSystemTrajectory::typeName(); +} + +MolSystemTrajectory *MolSystemTrajectory::clone() const +{ + return new MolSystemTrajectory(*this); +} + +void MolSystemTrajectory::clear() +{ + d.reset(); + start_atom = 0; + natoms = 0; +} + +int MolSystemTrajectory::nFrames() const +{ + if (d.get() == 0) + return 0; + else + return d->nFrames(); +} + +int MolSystemTrajectory::nAtoms() const +{ + return natoms; +} + +QStringList MolSystemTrajectory::filenames() const +{ + return QStringList(); +} + +Frame MolSystemTrajectory::getFrame(int i) const +{ + i = SireID::Index(i).map(this->nFrames()); + + return d->getFrame(i, start_atom, natoms); +} + +Frame MolSystemTrajectory::getFrame(int i, const SireBase::LazyEvaluator &evaluator) const +{ + i = SireID::Index(i).map(this->nFrames()); + + return d->getFrame(i, start_atom, natoms, evaluator); +} + +bool MolSystemTrajectory::isEditable() const +{ + return false; +} + +bool MolSystemTrajectory::_equals(const TrajectoryData &other) const +{ + const MolSystemTrajectory *p = dynamic_cast(&other); + + if (p) + return this->operator==(*p); + else + return false; +} + +//////// +//////// Implementation of SystemTrajectory +//////// diff --git a/corelib/src/libs/SireSystem/systemtrajectory.h b/corelib/src/libs/SireSystem/systemtrajectory.h new file mode 100644 index 000000000..be0897c2e --- /dev/null +++ b/corelib/src/libs/SireSystem/systemtrajectory.h @@ -0,0 +1,178 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIRESYSTEM_SYSTEMTRAJECTORY_H +#define SIRESYSTEM_SYSTEMTRAJECTORY_H + +#include "SireMol/trajectory.h" +#include "SireMol/molecules.h" + +#include + +SIRE_BEGIN_HEADER + +namespace SireSystem +{ + class SystemTrajectory; + class MolSystemTrajectory; +} + +SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &stream, const SireSystem::SystemTrajectory &trajectory); +SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &stream, SireSystem::SystemTrajectory &trajectory); + +SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &stream, const SireSystem::MolSystemTrajectory &trajectory); +SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &stream, SireSystem::MolSystemTrajectory &trajectory); + +namespace SireSystem +{ + class SystemFrames; + + /** This is a TrajectoryData object that is used to hold the trajectory + * data for all molecules in a system. This is used to both speed + * up the reading and writing of trajectory data for entire + * systems (e.g. during a dynamics simulation), plus also to + * support offloading of trajectory data from memory to disk + * as the simulation progresses + */ + class SIRESYSTEM_EXPORT SystemTrajectory : public SireMol::TrajectoryData + { + friend QDataStream &operator<<(QDataStream &stream, const SystemTrajectory &trajectory); + friend QDataStream &operator>>(QDataStream &stream, SystemTrajectory &trajectory); + + friend class MolSystemTrajectory; + + public: + SystemTrajectory(); + SystemTrajectory(const SireMol::Molecules &mols, const SireBase::PropertyMap &map = SireBase::PropertyMap()); + + SystemTrajectory(const SystemTrajectory &other); + + ~SystemTrajectory(); + + SystemTrajectory &operator=(const SystemTrajectory &other); + + bool operator==(const SystemTrajectory &other) const; + bool operator!=(const SystemTrajectory &other) const; + + static const char *typeName(); + + const char *what() const; + + SystemTrajectory *clone() const; + + void clear(); + + bool isCompatibleWith(const SireMol::Molecules &mols, + const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; + + void saveFrame(const SireMol::Molecules &mols, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); + + SireMol::TrajectoryDataPtr getTrajectory(SireMol::MolNum molnum) const; + + int nFrames() const; + int nAtoms() const; + + QStringList filenames() const; + + SireMol::Frame getFrame(int i) const; + SireMol::Frame getFrame(int i, const SireBase::LazyEvaluator &evaluator) const; + + bool isEditable() const; + + protected: + bool _equals(const TrajectoryData &other) const; + + private: + /** Shared pointer to the underlying trajectory frames */ + std::shared_ptr d; + + /** The start index and number of atoms for each molecule + * in the system + */ + QHash> mol_atoms; + }; + + /** This is the view of a SystemTrajectory that is used to + * access the trajectory data for a single molecule in the system + */ + class SIRESYSTEM_EXPORT MolSystemTrajectory : public SireMol::TrajectoryData + { + public: + MolSystemTrajectory(); + + MolSystemTrajectory(const SystemTrajectory &trajectory, SireMol::MolNum molnum); + + MolSystemTrajectory(const MolSystemTrajectory &other); + + ~MolSystemTrajectory(); + + MolSystemTrajectory &operator=(const MolSystemTrajectory &other); + + bool operator==(const MolSystemTrajectory &other) const; + bool operator!=(const MolSystemTrajectory &other) const; + + static const char *typeName(); + + const char *what() const; + + MolSystemTrajectory *clone() const; + + void clear(); + + int nFrames() const; + int nAtoms() const; + + QStringList filenames() const; + + SireMol::Frame getFrame(int i) const; + SireMol::Frame getFrame(int i, const SireBase::LazyEvaluator &evaluator) const; + + bool isEditable() const; + + protected: + bool _equals(const TrajectoryData &other) const; + + private: + /** Shared pointer to the underlying trajectory frames */ + std::shared_ptr d; + + /** The start index of the atoms in this molecule */ + qint64 start_atom; + + /** The number of atoms in this molecule */ + qint64 natoms; + }; +} + +Q_DECLARE_METATYPE(SireSystem::SystemTrajectory) +Q_DECLARE_METATYPE(SireSystem::MolSystemTrajectory) + +SIRE_END_HEADER + +#endif diff --git a/wrapper/Mol/AtomCoords.pypp.cpp b/wrapper/Mol/AtomCoords.pypp.cpp index b06a0f95b..27140df22 100644 --- a/wrapper/Mol/AtomCoords.pypp.cpp +++ b/wrapper/Mol/AtomCoords.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/console.h" + #include "SireBase/quickcopy.hpp" #include "SireBase/slice.h" diff --git a/wrapper/Mol/AtomIdxMapping.pypp.cpp b/wrapper/Mol/AtomIdxMapping.pypp.cpp index 4a4118ace..67f98649a 100644 --- a/wrapper/Mol/AtomIdxMapping.pypp.cpp +++ b/wrapper/Mol/AtomIdxMapping.pypp.cpp @@ -206,6 +206,30 @@ void register_AtomIdxMapping_class(){ , ( bp::arg("include_unmapped")=(bool)(false) ) , "Return the mapping for the atoms that exist in both the reference\n and perturbed states, from the index of the atom in the perturbed\n molecule to the index of the atom in the merged molecule.\n Note - the reference index is the index in the merged molecule.\n\n If include_unmapped is true, then also include atoms that are\n unmapped in either end state. In these cases, the reference index\n will be the index in the merged molecule (so will always be valid)\n and atoms that are unmapped in the perturbed state are not\n included in the returned dictionary.\n" ); + } + { //::SireMol::AtomIdxMapping::mappedCGAtomIdxIn0 + + typedef ::QList< SireMol::CGAtomIdx > ( ::SireMol::AtomIdxMapping::*mappedCGAtomIdxIn0_function_type)( ) const; + mappedCGAtomIdxIn0_function_type mappedCGAtomIdxIn0_function_value( &::SireMol::AtomIdxMapping::mappedCGAtomIdxIn0 ); + + AtomIdxMapping_exposer.def( + "mappedCGAtomIdxIn0" + , mappedCGAtomIdxIn0_function_value + , bp::release_gil_policy() + , "Equivalent of mappedIn0, but return as a CGAtomIdx" ); + + } + { //::SireMol::AtomIdxMapping::mappedCGAtomIdxIn1 + + typedef ::QList< SireMol::CGAtomIdx > ( ::SireMol::AtomIdxMapping::*mappedCGAtomIdxIn1_function_type)( ) const; + mappedCGAtomIdxIn1_function_type mappedCGAtomIdxIn1_function_value( &::SireMol::AtomIdxMapping::mappedCGAtomIdxIn1 ); + + AtomIdxMapping_exposer.def( + "mappedCGAtomIdxIn1" + , mappedCGAtomIdxIn1_function_value + , bp::release_gil_policy() + , "Equivalent of mappedIn1, but return as a CGAtomIdx" ); + } { //::SireMol::AtomIdxMapping::mappedIn0 @@ -374,6 +398,30 @@ void register_AtomIdxMapping_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireMol::AtomIdxMapping::unmappedCGAtomIdxIn0 + + typedef ::QList< SireMol::CGAtomIdx > ( ::SireMol::AtomIdxMapping::*unmappedCGAtomIdxIn0_function_type)( ) const; + unmappedCGAtomIdxIn0_function_type unmappedCGAtomIdxIn0_function_value( &::SireMol::AtomIdxMapping::unmappedCGAtomIdxIn0 ); + + AtomIdxMapping_exposer.def( + "unmappedCGAtomIdxIn0" + , unmappedCGAtomIdxIn0_function_value + , bp::release_gil_policy() + , "Equivalent of unmappedIn0, but return as a CGAtomIdx" ); + + } + { //::SireMol::AtomIdxMapping::unmappedCGAtomIdxIn1 + + typedef ::QList< SireMol::CGAtomIdx > ( ::SireMol::AtomIdxMapping::*unmappedCGAtomIdxIn1_function_type)( ) const; + unmappedCGAtomIdxIn1_function_type unmappedCGAtomIdxIn1_function_value( &::SireMol::AtomIdxMapping::unmappedCGAtomIdxIn1 ); + + AtomIdxMapping_exposer.def( + "unmappedCGAtomIdxIn1" + , unmappedCGAtomIdxIn1_function_value + , bp::release_gil_policy() + , "Equivalent of unmappedIn1, but return as a CGAtomIdx" ); + } { //::SireMol::AtomIdxMapping::unmappedIn0 diff --git a/wrapper/Mol/Trajectory.pypp.cpp b/wrapper/Mol/Trajectory.pypp.cpp index 0921e0e02..13c956fff 100644 --- a/wrapper/Mol/Trajectory.pypp.cpp +++ b/wrapper/Mol/Trajectory.pypp.cpp @@ -58,10 +58,38 @@ void register_Trajectory_class(){ Trajectory_exposer_t Trajectory_exposer = Trajectory_exposer_t( "Trajectory", "This is a molecular property that holds the handle to the\ntrajectory data for that molecule. In addition to the\nhandle, this also holds the index of the first atom\nin the underlying trajectory data (trajectory data is a\nvector of coordinates in atom index order for each molecule)\n", bp::init< >("") ); bp::scope Trajectory_scope( Trajectory_exposer ); Trajectory_exposer.def( bp::init< SireMol::TrajectoryData const & >(( bp::arg("trajectory") ), "") ); + Trajectory_exposer.def( bp::init< SireMol::TrajectoryDataPtr const & >(( bp::arg("trajectory") ), "") ); Trajectory_exposer.def( bp::init< QList< SireBase::SharedPolyPointer< SireMol::TrajectoryData > > const & >(( bp::arg("trajectories") ), "") ); Trajectory_exposer.def( bp::init< SireMol::TrajectoryData const &, int, int >(( bp::arg("trajectory"), bp::arg("start_atom"), bp::arg("natoms") ), "") ); + Trajectory_exposer.def( bp::init< SireMol::TrajectoryDataPtr const &, int, int >(( bp::arg("trajectory"), bp::arg("start_atom"), bp::arg("natoms") ), "") ); Trajectory_exposer.def( bp::init< QList< SireBase::SharedPolyPointer< SireMol::TrajectoryData > > const &, int, int >(( bp::arg("trajectories"), bp::arg("start_atom"), bp::arg("natoms") ), "") ); Trajectory_exposer.def( bp::init< SireMol::Trajectory const & >(( bp::arg("other") ), "") ); + { //::SireMol::Trajectory::append + + typedef void ( ::SireMol::Trajectory::*append_function_type)( ::SireMol::TrajectoryData const & ) ; + append_function_type append_function_value( &::SireMol::Trajectory::append ); + + Trajectory_exposer.def( + "append" + , append_function_value + , ( bp::arg("data") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireMol::Trajectory::append + + typedef void ( ::SireMol::Trajectory::*append_function_type)( ::SireMol::TrajectoryDataPtr const & ) ; + append_function_type append_function_value( &::SireMol::Trajectory::append ); + + Trajectory_exposer.def( + "append" + , append_function_value + , ( bp::arg("data") ) + , bp::release_gil_policy() + , "" ); + + } { //::SireMol::Trajectory::appendFrame typedef void ( ::SireMol::Trajectory::*appendFrame_function_type)( ::SireMol::Frame const & ) ; diff --git a/wrapper/System/System.pypp.cpp b/wrapper/System/System.pypp.cpp index 56389b2b7..99f71009f 100644 --- a/wrapper/System/System.pypp.cpp +++ b/wrapper/System/System.pypp.cpp @@ -60,6 +60,8 @@ namespace bp = boost::python; #include "system.h" +#include "systemtrajectory.h" + #include #include diff --git a/wrapper/System/_System_free_functions.pypp.cpp b/wrapper/System/_System_free_functions.pypp.cpp index 19a7794de..e2c15b143 100644 --- a/wrapper/System/_System_free_functions.pypp.cpp +++ b/wrapper/System/_System_free_functions.pypp.cpp @@ -721,10 +721,16 @@ namespace bp = boost::python; #include "create_test_molecule.h" +#include "SireMM/cljnbpairs.h" + #include "SireMM/mmdetail.h" #include "SireMol/atomidxmapping.h" +#include "SireMol/bondid.h" + +#include "SireMol/connectivity.h" + #include "SireMol/core.h" #include "SireMol/moleditor.h" From 37084bc3735b0f78ba8d07199b9fc41df45251ee Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 6 Apr 2024 22:58:32 +0100 Subject: [PATCH 206/468] WIP - implemented function stubs. Code compiles, runs, but crashes --- .../src/libs/SireSystem/systemtrajectory.cpp | 262 +++++++++++++++++- .../src/libs/SireSystem/systemtrajectory.h | 15 +- 2 files changed, 269 insertions(+), 8 deletions(-) diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index 4337de198..3e7e1f943 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -30,6 +30,8 @@ #include "SireMol/errors.h" +#include "SireBase/lazyevaluator.h" + #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -38,6 +40,56 @@ using namespace SireMol; using namespace SireBase; using namespace SireStream; +namespace SireSystem +{ + class SystemFrames + { + public: + SystemFrames(); + ~SystemFrames(); + + int nFrames() const; + int nAtoms() const; + + Frame getFrame(int i); + Frame getFrame(int i, const LazyEvaluator &evaluator); + + void saveFrame(const Molecules &mols, const PropertyMap &map); + }; +} + +SystemFrames::SystemFrames() +{ +} + +SystemFrames::~SystemFrames() +{ +} + +int SystemFrames::nAtoms() const +{ + return 0; +} + +int SystemFrames::nFrames() const +{ + return 0; +} + +Frame SystemFrames::getFrame(int i) +{ + return Frame(); +} + +Frame SystemFrames::getFrame(int i, const LazyEvaluator &evaluator) +{ + return Frame(); +} + +void SystemFrames::saveFrame(const Molecules &mols, const PropertyMap &map) +{ +} + //////// //////// Implementation of MolSystemTrajectory //////// @@ -174,14 +226,19 @@ Frame MolSystemTrajectory::getFrame(int i) const { i = SireID::Index(i).map(this->nFrames()); - return d->getFrame(i, start_atom, natoms); + return d->getFrame(i).subset(start_atom, natoms); } Frame MolSystemTrajectory::getFrame(int i, const SireBase::LazyEvaluator &evaluator) const { i = SireID::Index(i).map(this->nFrames()); - return d->getFrame(i, start_atom, natoms, evaluator); + auto key = QString("%1-%2").arg(qintptr(d.get())).arg(i); + + auto frame = evaluator.evaluate(key, [&]() + { return d->getFrame(i); }); + + return frame.read().asA().subset(start_atom, natoms); } bool MolSystemTrajectory::isEditable() const @@ -202,3 +259,204 @@ bool MolSystemTrajectory::_equals(const TrajectoryData &other) const //////// //////// Implementation of SystemTrajectory //////// + +static const RegisterMetaType r_traj; + +SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &ds, const SystemTrajectory &traj) +{ + writeHeader(ds, r_traj, 1); + + // we don't stream the trajectory as it would be too big + ds << static_cast(traj); + + return ds; +} + +SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &ds, SystemTrajectory &traj) +{ + auto v = readHeader(ds, r_traj); + + if (v == 1) + { + // we don't stream the trajectory as it would be too big + traj.clear(); + ds >> static_cast(traj); + } + else + throw version_error(v, "1", r_traj, CODELOC); + + return ds; +} + +SystemTrajectory::SystemTrajectory() : TrajectoryData() +{ +} + +SystemTrajectory::SystemTrajectory(const Molecules &mols, const PropertyMap &map) + : TrajectoryData() +{ +} + +SystemTrajectory::SystemTrajectory(const SystemTrajectory &other) + : TrajectoryData(other), d(other.d), mol_atoms(other.mol_atoms) +{ +} + +SystemTrajectory::~SystemTrajectory() +{ +} + +SystemTrajectory &SystemTrajectory::operator=(const SystemTrajectory &other) +{ + if (this != &other) + { + TrajectoryData::operator=(other); + d = other.d; + mol_atoms = other.mol_atoms; + } + + return *this; +} + +bool SystemTrajectory::operator==(const SystemTrajectory &other) const +{ + return TrajectoryData::operator==(other) && + d.get() == other.d.get() && + mol_atoms == other.mol_atoms; +} + +bool SystemTrajectory::operator!=(const SystemTrajectory &other) const +{ + return not this->operator==(other); +} + +const char *SystemTrajectory::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *SystemTrajectory::what() const +{ + return SystemTrajectory::typeName(); +} + +SystemTrajectory *SystemTrajectory::clone() const +{ + return new SystemTrajectory(*this); +} + +void SystemTrajectory::clear() +{ + d.reset(); + mol_atoms.clear(); +} + +bool SystemTrajectory::isCompatibleWith(const Molecules &mols, + const PropertyMap &map) const +{ + if (d.get() == 0) + return false; + + // make sure that all of the molecules exist in the hash + // and the number of atoms match + for (const auto &mol : mols) + { + const auto &moldata = mol.data(); + + auto it = mol_atoms.constFind(moldata.number()); + + if (it == mol_atoms.constEnd()) + return false; + + if (it.value().second != moldata.info().nAtoms()) + return false; + } + + return true; +} + +void SystemTrajectory::saveFrame(const Molecules &mols, + const PropertyMap &map) +{ + if (d.get() == 0) + { + // create the data + int natoms = 0; + + for (const auto &mol : mols) + { + const auto &moldata = mol.data(); + + mol_atoms.insert(moldata.number(), qMakePair(natoms, moldata.info().nAtoms())); + + natoms += moldata.info().nAtoms(); + } + + d.reset(new SystemFrames()); + } + + // save the frame + d->saveFrame(mols, map); +} + +TrajectoryDataPtr SystemTrajectory::getTrajectory(MolNum molnum) const +{ + return TrajectoryDataPtr(new MolSystemTrajectory(*this, molnum)); +} + +int SystemTrajectory::nFrames() const +{ + if (d.get() == 0) + return 0; + else + return d->nFrames(); +} + +int SystemTrajectory::nAtoms() const +{ + if (d.get() == 0) + { + int natoms = 0; + + for (const auto &mol : mol_atoms) + natoms += mol.second; + + return natoms; + } + else + { + return d->nAtoms(); + } +} + +QStringList SystemTrajectory::filenames() const +{ + return QStringList(); +} + +Frame SystemTrajectory::getFrame(int i) const +{ + i = SireID::Index(i).map(this->nFrames()); + return d->getFrame(i); +} + +Frame SystemTrajectory::getFrame(int i, const LazyEvaluator &evaluator) const +{ + i = SireID::Index(i).map(this->nFrames()); + return d->getFrame(i, evaluator); +} + +bool SystemTrajectory::isEditable() const +{ + return false; +} + +bool SystemTrajectory::_equals(const TrajectoryData &other) const +{ + const SystemTrajectory *p = dynamic_cast(&other); + + if (p) + return this->operator==(*p); + else + return false; +} diff --git a/corelib/src/libs/SireSystem/systemtrajectory.h b/corelib/src/libs/SireSystem/systemtrajectory.h index be0897c2e..5ca931d83 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.h +++ b/corelib/src/libs/SireSystem/systemtrajectory.h @@ -42,11 +42,11 @@ namespace SireSystem class MolSystemTrajectory; } -SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &stream, const SireSystem::SystemTrajectory &trajectory); -SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &stream, SireSystem::SystemTrajectory &trajectory); +SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &, const SireSystem::SystemTrajectory &); +SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &, SireSystem::SystemTrajectory &); -SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &stream, const SireSystem::MolSystemTrajectory &trajectory); -SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &stream, SireSystem::MolSystemTrajectory &trajectory); +SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &, const SireSystem::MolSystemTrajectory &); +SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &, SireSystem::MolSystemTrajectory &); namespace SireSystem { @@ -61,8 +61,8 @@ namespace SireSystem */ class SIRESYSTEM_EXPORT SystemTrajectory : public SireMol::TrajectoryData { - friend QDataStream &operator<<(QDataStream &stream, const SystemTrajectory &trajectory); - friend QDataStream &operator>>(QDataStream &stream, SystemTrajectory &trajectory); + friend QDataStream & ::operator<<(QDataStream &, const SystemTrajectory &); + friend QDataStream & ::operator>>(QDataStream &, SystemTrajectory &); friend class MolSystemTrajectory; @@ -123,6 +123,9 @@ namespace SireSystem */ class SIRESYSTEM_EXPORT MolSystemTrajectory : public SireMol::TrajectoryData { + friend QDataStream & ::operator<<(QDataStream &, const MolSystemTrajectory &); + friend QDataStream & ::operator>>(QDataStream &, MolSystemTrajectory &); + public: MolSystemTrajectory(); From 2e6e6e2d218e19b748e64059e7369ba2dd04ae68 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 7 Apr 2024 18:15:07 +0100 Subject: [PATCH 207/468] Making progress - tests all pass, although have completely broken trajectory saving ;-) --- corelib/src/libs/SireSystem/system.cpp | 120 +++++- corelib/src/libs/SireSystem/system.h | 4 + .../src/libs/SireSystem/systemtrajectory.cpp | 386 +++++++++++++----- .../src/libs/SireSystem/systemtrajectory.h | 18 +- 4 files changed, 410 insertions(+), 118 deletions(-) diff --git a/corelib/src/libs/SireSystem/system.cpp b/corelib/src/libs/SireSystem/system.cpp index 6586d02d7..d56467684 100644 --- a/corelib/src/libs/SireSystem/system.cpp +++ b/corelib/src/libs/SireSystem/system.cpp @@ -3895,6 +3895,7 @@ void System::saveFrame(int frame, const SireBase::PropertyMap &map) this->accept(); this->mustNowRecalculateFromScratch(); MolGroupsBase::saveFrame(frame, map); + system_trajectory = 0; } void System::saveFrame(const SireBase::PropertyMap &map) @@ -3907,6 +3908,118 @@ void System::saveFrame(const SireBase::PropertyMap &map) this->accept(); this->mustNowRecalculateFromScratch(); + // get all of the molecules in the system + auto mols = this->molecules(); + + // get the space and time values + const auto space_property = map["space"]; + const auto time_property = map["time"]; + + QString time_property_source("time"); + QString space_property_source("space"); + + if (time_property.hasSource()) + time_property_source = QString(time_property.source()); + + if (space_property.hasSource()) + space_property_source = QString(space_property.source()); + + // we must get the space property and a time property + SpacePtr space; + SireUnits::Dimension::Time time; + bool found_space = false; + bool found_time = false; + + try + { + space = this->property(space_property_source).asA(); + found_space = true; + } + catch (...) + { + } + + try + { + time = get_time_from_property(this->property(time_property_source)); + found_time = true; + } + catch (...) + { + } + + if (not found_space) + { + if (space_property.hasValue()) + { + try + { + space = space_property.value().asA(); + found_space = true; + } + catch (...) + { + } + } + + if (not found_space) + { + for (const auto &mol : mols) + { + try + { + space = mol.data().property(space_property_source).asA(); + found_space = true; + break; + } + catch (...) + { + } + } + } + } + + if (not found_time) + { + if (time_property.hasValue()) + { + try + { + time = get_time_from_property(time_property.value()); + found_time = true; + } + catch (...) + { + } + } + + if (not found_time) + { + for (const auto &mol : mols) + { + try + { + time = get_time_from_property(mol.data().property(time_property_source)); + found_time = true; + break; + } + catch (...) + { + } + } + } + } + + if (not found_space) + { + space = Cartesian(); + } + + if (not found_time) + { + time = SireUnits::Dimension::Time(0); + } + // do we have an active SystemTrajectory? bool must_create = false; @@ -3915,8 +4028,6 @@ void System::saveFrame(const SireBase::PropertyMap &map) must_create = true; } - auto mols = this->molecules(); - SystemTrajectory *traj = dynamic_cast(system_trajectory.data()); if (traj == 0) @@ -3930,7 +4041,8 @@ void System::saveFrame(const SireBase::PropertyMap &map) if (must_create) { - system_trajectory = new SystemTrajectory(mols, map); + traj = new SystemTrajectory(mols, map); + system_trajectory = traj; // add this trajectory onto all of the molecules... auto mols2 = mols; @@ -3961,7 +4073,7 @@ void System::saveFrame(const SireBase::PropertyMap &map) // save the frame into the system_trajectory - this will automatically // update all molecules containing this trajectory - traj->saveFrame(mols, map); + traj->saveFrame(mols, space, time, Properties(), map); } void System::deleteFrame(int frame, const SireBase::PropertyMap &map) diff --git a/corelib/src/libs/SireSystem/system.h b/corelib/src/libs/SireSystem/system.h index 195e5c934..83d5f3698 100644 --- a/corelib/src/libs/SireSystem/system.h +++ b/corelib/src/libs/SireSystem/system.h @@ -423,16 +423,20 @@ namespace SireSystem void loadFrame(int frame); void loadFrame(int frame, const SireBase::LazyEvaluator &evaluator); + void saveFrame(int frame); void saveFrame(); + void deleteFrame(int frame); void deleteAllFrames(); void loadFrame(int frame, const SireBase::PropertyMap &map); void loadFrame(int frame, const SireBase::LazyEvaluator &evaluator, const SireBase::PropertyMap &map); + void saveFrame(int frame, const SireBase::PropertyMap &map); void saveFrame(const SireBase::PropertyMap &map); + void deleteFrame(int frame, const SireBase::PropertyMap &map); void deleteAllFrames(const SireBase::PropertyMap &map); diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index 3e7e1f943..85a74201c 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -45,48 +45,248 @@ namespace SireSystem class SystemFrames { public: + enum FrameType + { + EMPTY = 0x0000, + COORDINATES = 0x0001, + VELOCITIES = 0x0010, + FORCES = 0x0100 + }; + SystemFrames(); + SystemFrames(const Molecules &mols, const PropertyMap &map); ~SystemFrames(); int nFrames() const; + int nAtoms() const; + int nAtoms(MolNum molnum) const; + + bool saveCoordinates() const; + bool saveVelocities() const; + bool saveForces() const; + + Frame getFrame(int i) const; + Frame getFrame(int i, const LazyEvaluator &evaluator) const; + + Frame getFrame(MolNum molnum, int i) const; + Frame getFrame(MolNum molnum, int i, + const LazyEvaluator &evaluator) const; - Frame getFrame(int i); - Frame getFrame(int i, const LazyEvaluator &evaluator); + void saveFrame(const Molecules &mols, + const Space &space, + SireUnits::Dimension::Time time, + const Properties &props, + const PropertyMap &map); - void saveFrame(const Molecules &mols, const PropertyMap &map); + bool isCompatibleWith(const Molecules &mols, + const PropertyMap &map) const; + + private: + /** The start index and number of atoms for each molecule + * in the system. This is the same for all frames + */ + QHash> mol_atoms; + + /** The data for the trajectory */ + QVector frames; + + /** The total number of atoms */ + int natoms; + + /** What type of frame data - coordinates, velocities, forces */ + int frame_type; }; } -SystemFrames::SystemFrames() +SystemFrames::SystemFrames() : natoms(0), frame_type(EMPTY) { } +SystemFrames::SystemFrames(const Molecules &mols, const PropertyMap &map) + : natoms(0), frame_type(EMPTY) +{ + for (const auto &mol : mols) + { + const auto &moldata = mol.data(); + + mol_atoms.insert(moldata.number(), qMakePair(natoms, moldata.info().nAtoms())); + + natoms += moldata.info().nAtoms(); + } + + // should work out if coords, vels and/or forces should be saved + // based on the properties in the map + frame_type = COORDINATES; + + bool save_coordinates = true; + bool save_velocities = false; + bool save_forces = false; + + if (map.specified("save_coordinates")) + { + save_coordinates = map["save_coordinates"].value().asABoolean(); + } + + if (map.specified("save_velocities")) + { + save_velocities = map["save_velocities"].value().asABoolean(); + } + + if (map.specified("save_forces")) + { + save_forces = map["save_forces"].value().asABoolean(); + } + + if (save_coordinates) + frame_type |= COORDINATES; + + if (save_velocities) + frame_type |= VELOCITIES; + + if (save_forces) + frame_type |= FORCES; +} + SystemFrames::~SystemFrames() { } +bool SystemFrames::saveCoordinates() const +{ + return frame_type & COORDINATES; +} + +bool SystemFrames::saveVelocities() const +{ + return frame_type & VELOCITIES; +} + +bool SystemFrames::saveForces() const +{ + return frame_type & FORCES; +} + int SystemFrames::nAtoms() const { - return 0; + return natoms; +} + +int SystemFrames::nAtoms(MolNum molnum) const +{ + auto it = mol_atoms.constFind(molnum); + + if (it == mol_atoms.constEnd()) + { + throw SireMol::missing_molecule(QObject::tr( + "There is no molecule with number %1 in the system") + .arg(molnum.value()), + CODELOC); + } + + return it.value().second; } int SystemFrames::nFrames() const { - return 0; + return frames.count(); +} + +/** It is only compatible if we have the same molecules with + * the same number of atoms. This is because we cannot cope + * with molecules being added or removed from the system, + * or with the number of atoms changing. These events will + * trigger the creation of a new SystemFrames higher in the + * stack + */ +bool SystemFrames::isCompatibleWith(const Molecules &mols, + const PropertyMap &map) const +{ + if (mols.nMolecules() != mol_atoms.size()) + return false; + + // make sure that all of the molecules exist in the hash + // and the number of atoms match + for (const auto &mol : mols) + { + const auto &moldata = mol.data(); + + auto it = mol_atoms.constFind(moldata.number()); + + if (it == mol_atoms.constEnd()) + return false; + + if (it.value().second != moldata.info().nAtoms()) + return false; + } + + return true; +} + +Frame SystemFrames::getFrame(int i) const +{ + try + { + i = Index(i).map(this->nFrames()); + } + catch (...) + { + throw SireError::invalid_index( + QObject::tr("Invalid frame index %1. Number of frames is %2.") + .arg(i) + .arg(this->nFrames()), + CODELOC); + } + + return this->frames.at(i); +} + +Frame SystemFrames::getFrame(int i, const LazyEvaluator &evaluator) const +{ + auto key = QString("%1-%2").arg(qintptr(this)).arg(i); + + auto frame = evaluator.evaluate(key, [&]() + { return this->getFrame(i); }); + + return frame.read().asA(); } -Frame SystemFrames::getFrame(int i) +Frame SystemFrames::getFrame(MolNum molnum, int i) const { - return Frame(); + auto it = mol_atoms.constFind(molnum); + + if (it == mol_atoms.constEnd()) + { + throw SireMol::missing_molecule(QObject::tr( + "There is no molecule with number %1 in the system") + .arg(molnum.value()), + CODELOC); + } + + return this->getFrame(i).subset(it.value().first, it.value().second); } -Frame SystemFrames::getFrame(int i, const LazyEvaluator &evaluator) +Frame SystemFrames::getFrame(MolNum molnum, int i, + const LazyEvaluator &evaluator) const { - return Frame(); + auto it = mol_atoms.constFind(molnum); + + if (it == mol_atoms.constEnd()) + { + throw SireMol::missing_molecule(QObject::tr( + "There is no molecule with number %1 in the system") + .arg(molnum.value()), + CODELOC); + } + + return this->getFrame(i, evaluator).subset(it.value().first, it.value().second); } -void SystemFrames::saveFrame(const Molecules &mols, const PropertyMap &map) +void SystemFrames::saveFrame(const Molecules &mols, + const Space &space, + SireUnits::Dimension::Time time, + const Properties &props, + const PropertyMap &map) { } @@ -101,7 +301,8 @@ SIRESYSTEM_EXPORT QDataStream &operator<<(QDataStream &ds, const MolSystemTrajec writeHeader(ds, r_moltraj, 1); // we don't stream the trajectory as it would be too big - ds << static_cast(traj); + ds << traj.molnum + << static_cast(traj); return ds; } @@ -114,7 +315,7 @@ SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &ds, MolSystemTrajectory & { // we don't stream the trajectory as it would be too big traj.clear(); - ds >> static_cast(traj); + ds >> traj.molnum >> static_cast(traj); } else throw version_error(v, "1", r_moltraj, CODELOC); @@ -122,33 +323,18 @@ SIRESYSTEM_EXPORT QDataStream &operator>>(QDataStream &ds, MolSystemTrajectory & return ds; } -MolSystemTrajectory::MolSystemTrajectory() - : TrajectoryData(), start_atom(0), natoms(0) +MolSystemTrajectory::MolSystemTrajectory() : TrajectoryData() { } MolSystemTrajectory::MolSystemTrajectory(const SystemTrajectory &trajectory, - SireMol::MolNum molnum) - : TrajectoryData(trajectory), start_atom(0), natoms(0) + SireMol::MolNum mnum) + : TrajectoryData(trajectory), d(trajectory.d), molnum(mnum) { - d = trajectory.d; - - auto it = trajectory.mol_atoms.constFind(molnum); - - if (it == trajectory.mol_atoms.constEnd()) - { - throw SireMol::missing_molecule(QObject::tr( - "There is no molecule with number %1 in the system") - .arg(molnum.value()), - CODELOC); - } - - start_atom = it.value().first; - natoms = it.value().second; } MolSystemTrajectory::MolSystemTrajectory(const MolSystemTrajectory &other) - : TrajectoryData(other), d(other.d), start_atom(other.start_atom), natoms(other.natoms) + : TrajectoryData(other), d(other.d), molnum(other.molnum) { } @@ -162,8 +348,7 @@ MolSystemTrajectory &MolSystemTrajectory::operator=(const MolSystemTrajectory &o { TrajectoryData::operator=(other); d = other.d; - start_atom = other.start_atom; - natoms = other.natoms; + molnum = other.molnum; } return *this; @@ -173,8 +358,7 @@ bool MolSystemTrajectory::operator==(const MolSystemTrajectory &other) const { return TrajectoryData::operator==(other) && d.get() == other.d.get() && - start_atom == other.start_atom && - natoms == other.natoms; + molnum == other.molnum; } bool MolSystemTrajectory::operator!=(const MolSystemTrajectory &other) const @@ -200,13 +384,12 @@ MolSystemTrajectory *MolSystemTrajectory::clone() const void MolSystemTrajectory::clear() { d.reset(); - start_atom = 0; - natoms = 0; + molnum = MolNum(); } int MolSystemTrajectory::nFrames() const { - if (d.get() == 0) + if (not d) return 0; else return d->nFrames(); @@ -214,7 +397,14 @@ int MolSystemTrajectory::nFrames() const int MolSystemTrajectory::nAtoms() const { - return natoms; + if (d) + { + return d->nAtoms(molnum); + } + else + { + return 0; + } } QStringList MolSystemTrajectory::filenames() const @@ -224,21 +414,24 @@ QStringList MolSystemTrajectory::filenames() const Frame MolSystemTrajectory::getFrame(int i) const { - i = SireID::Index(i).map(this->nFrames()); - - return d->getFrame(i).subset(start_atom, natoms); + if (d) + return d->getFrame(molnum, i); + else + throw SireError::invalid_index( + QObject::tr("Invalid frame index %1. Number of frames is 0.") + .arg(i), + CODELOC); } Frame MolSystemTrajectory::getFrame(int i, const SireBase::LazyEvaluator &evaluator) const { - i = SireID::Index(i).map(this->nFrames()); - - auto key = QString("%1-%2").arg(qintptr(d.get())).arg(i); - - auto frame = evaluator.evaluate(key, [&]() - { return d->getFrame(i); }); - - return frame.read().asA().subset(start_atom, natoms); + if (d) + return d->getFrame(molnum, i, evaluator); + else + throw SireError::invalid_index( + QObject::tr("Invalid frame index %1. Number of frames is 0.") + .arg(i), + CODELOC); } bool MolSystemTrajectory::isEditable() const @@ -293,12 +486,12 @@ SystemTrajectory::SystemTrajectory() : TrajectoryData() } SystemTrajectory::SystemTrajectory(const Molecules &mols, const PropertyMap &map) - : TrajectoryData() + : TrajectoryData(), d(new SystemFrames(mols, map)) { } SystemTrajectory::SystemTrajectory(const SystemTrajectory &other) - : TrajectoryData(other), d(other.d), mol_atoms(other.mol_atoms) + : TrajectoryData(other), d(other.d) { } @@ -312,7 +505,6 @@ SystemTrajectory &SystemTrajectory::operator=(const SystemTrajectory &other) { TrajectoryData::operator=(other); d = other.d; - mol_atoms = other.mol_atoms; } return *this; @@ -321,8 +513,7 @@ SystemTrajectory &SystemTrajectory::operator=(const SystemTrajectory &other) bool SystemTrajectory::operator==(const SystemTrajectory &other) const { return TrajectoryData::operator==(other) && - d.get() == other.d.get() && - mol_atoms == other.mol_atoms; + d.get() == other.d.get(); } bool SystemTrajectory::operator!=(const SystemTrajectory &other) const @@ -348,65 +539,47 @@ SystemTrajectory *SystemTrajectory::clone() const void SystemTrajectory::clear() { d.reset(); - mol_atoms.clear(); } bool SystemTrajectory::isCompatibleWith(const Molecules &mols, const PropertyMap &map) const { - if (d.get() == 0) + if (d) + return d->isCompatibleWith(mols, map); + else return false; - - // make sure that all of the molecules exist in the hash - // and the number of atoms match - for (const auto &mol : mols) - { - const auto &moldata = mol.data(); - - auto it = mol_atoms.constFind(moldata.number()); - - if (it == mol_atoms.constEnd()) - return false; - - if (it.value().second != moldata.info().nAtoms()) - return false; - } - - return true; } void SystemTrajectory::saveFrame(const Molecules &mols, + const Space &space, + SireUnits::Dimension::Time time, + const Properties &props, const PropertyMap &map) { - if (d.get() == 0) + if (not d) { - // create the data - int natoms = 0; - - for (const auto &mol : mols) - { - const auto &moldata = mol.data(); - - mol_atoms.insert(moldata.number(), qMakePair(natoms, moldata.info().nAtoms())); - - natoms += moldata.info().nAtoms(); - } - - d.reset(new SystemFrames()); + d.reset(new SystemFrames(mols, map)); } - // save the frame - d->saveFrame(mols, map); + d->saveFrame(mols, space, time, props, map); } TrajectoryDataPtr SystemTrajectory::getTrajectory(MolNum molnum) const { + if (not d) + { + throw SireMol::missing_molecule(QObject::tr( + "There is no molecule with number %1 in the system") + .arg(molnum.value()), + CODELOC); + } + return TrajectoryDataPtr(new MolSystemTrajectory(*this, molnum)); } int SystemTrajectory::nFrames() const { - if (d.get() == 0) + if (not d) return 0; else return d->nFrames(); @@ -414,18 +587,13 @@ int SystemTrajectory::nFrames() const int SystemTrajectory::nAtoms() const { - if (d.get() == 0) + if (d) { - int natoms = 0; - - for (const auto &mol : mol_atoms) - natoms += mol.second; - - return natoms; + return d->nAtoms(); } else { - return d->nAtoms(); + return 0; } } @@ -436,14 +604,24 @@ QStringList SystemTrajectory::filenames() const Frame SystemTrajectory::getFrame(int i) const { - i = SireID::Index(i).map(this->nFrames()); - return d->getFrame(i); + if (d) + return d->getFrame(i); + else + throw SireError::invalid_index( + QObject::tr("Invalid frame index %1. Number of frames is 0.") + .arg(i), + CODELOC); } Frame SystemTrajectory::getFrame(int i, const LazyEvaluator &evaluator) const { - i = SireID::Index(i).map(this->nFrames()); - return d->getFrame(i, evaluator); + if (d) + return d->getFrame(i, evaluator); + else + throw SireError::invalid_index( + QObject::tr("Invalid frame index %1. Number of frames is 0.") + .arg(i), + CODELOC); } bool SystemTrajectory::isEditable() const diff --git a/corelib/src/libs/SireSystem/systemtrajectory.h b/corelib/src/libs/SireSystem/systemtrajectory.h index 5ca931d83..ad414eaed 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.h +++ b/corelib/src/libs/SireSystem/systemtrajectory.h @@ -32,6 +32,9 @@ #include "SireMol/trajectory.h" #include "SireMol/molecules.h" +#include "SireVol/space.h" +#include "SireUnits/dimensions.h" + #include SIRE_BEGIN_HEADER @@ -91,6 +94,9 @@ namespace SireSystem const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; void saveFrame(const SireMol::Molecules &mols, + const SireVol::Space &space, + SireUnits::Dimension::Time time, + const SireBase::Properties &props, const SireBase::PropertyMap &map = SireBase::PropertyMap()); SireMol::TrajectoryDataPtr getTrajectory(SireMol::MolNum molnum) const; @@ -111,11 +117,6 @@ namespace SireSystem private: /** Shared pointer to the underlying trajectory frames */ std::shared_ptr d; - - /** The start index and number of atoms for each molecule - * in the system - */ - QHash> mol_atoms; }; /** This is the view of a SystemTrajectory that is used to @@ -165,11 +166,8 @@ namespace SireSystem /** Shared pointer to the underlying trajectory frames */ std::shared_ptr d; - /** The start index of the atoms in this molecule */ - qint64 start_atom; - - /** The number of atoms in this molecule */ - qint64 natoms; + /** The Molecule number for the molecule that owns this trajectory */ + SireMol::MolNum molnum; }; } From ae43ce258e9d1d247f53742d3ff03d2ad76da0bf Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 7 Apr 2024 19:36:15 +0100 Subject: [PATCH 208/468] Frames are being saved, but this isn't updating to the molecule. Most of the code for in-memory trajectories is now done - just needs debugging. --- corelib/src/libs/SireMol/trajectory.cpp | 17 +- corelib/src/libs/SireMol/trajectory.h | 2 + corelib/src/libs/SireSystem/system.cpp | 5 +- .../src/libs/SireSystem/systemtrajectory.cpp | 191 ++++++++++++++++-- .../src/libs/SireSystem/systemtrajectory.h | 9 +- 5 files changed, 202 insertions(+), 22 deletions(-) diff --git a/corelib/src/libs/SireMol/trajectory.cpp b/corelib/src/libs/SireMol/trajectory.cpp index 43f2ac6c8..b905ff047 100644 --- a/corelib/src/libs/SireMol/trajectory.cpp +++ b/corelib/src/libs/SireMol/trajectory.cpp @@ -122,6 +122,15 @@ bool TrajectoryData::isEmpty() const return this->nFrames() == 0; } +/** Return whether or not this trajectory is live - live trajectories + * are capable of being actively updated during new frame data, + * e.g. during a dynamics simulation. + */ +bool TrajectoryData::isLive() const +{ + return false; +} + QList TrajectoryData::getFrames() const { QList frames; @@ -547,7 +556,7 @@ Trajectory::Trajectory(const TrajectoryDataPtr &data) start_atom = 0; natoms = data->nAtoms(); - if (data->nFrames() > 0) + if (data->isLive() or data->nFrames() > 0) d.append(data); } } @@ -568,7 +577,7 @@ Trajectory::Trajectory(const QList &data) { if (ptr.constData() != 0) { - if (ptr->nFrames() > 0) + if (ptr->isLive() or ptr->nFrames() > 0) { if (natoms == 0) { @@ -628,7 +637,7 @@ Trajectory::Trajectory(const QList &data, int s, int n) { if (ptr.constData() != 0) { - if (ptr->nFrames() > 0) + if (ptr->isLive() or ptr->nFrames() > 0) { if (n == 0) { @@ -979,7 +988,7 @@ void Trajectory::append(const TrajectoryDataPtr &data) // check that the start and number of atoms would be compatible // with this trajectory - if (start_atom + natoms > data->nAtoms()) + if (natoms != data->nAtoms() and (start_atom + natoms > data->nAtoms())) { throw SireError::incompatible_error( QObject::tr("Cannot append a trajectory with %1 atoms to a trajectory with %2 atoms " diff --git a/corelib/src/libs/SireMol/trajectory.h b/corelib/src/libs/SireMol/trajectory.h index 670b2a5f7..22ff7823a 100644 --- a/corelib/src/libs/SireMol/trajectory.h +++ b/corelib/src/libs/SireMol/trajectory.h @@ -226,6 +226,8 @@ namespace SireMol virtual QStringList filenames() const = 0; + virtual bool isLive() const; + virtual Frame getFrame(int i) const = 0; virtual Frame getFrame(int i, const LazyEvaluator &evaluator) const = 0; diff --git a/corelib/src/libs/SireSystem/system.cpp b/corelib/src/libs/SireSystem/system.cpp index d56467684..9e43e37b8 100644 --- a/corelib/src/libs/SireSystem/system.cpp +++ b/corelib/src/libs/SireSystem/system.cpp @@ -3909,6 +3909,7 @@ void System::saveFrame(const SireBase::PropertyMap &map) this->mustNowRecalculateFromScratch(); // get all of the molecules in the system + auto molnums = this->molNums(); auto mols = this->molecules(); // get the space and time values @@ -4036,12 +4037,12 @@ void System::saveFrame(const SireBase::PropertyMap &map) } else { - must_create = not traj->isCompatibleWith(mols, map); + must_create = not traj->isCompatibleWith(molnums, mols, map); } if (must_create) { - traj = new SystemTrajectory(mols, map); + traj = new SystemTrajectory(molnums, mols, map); system_trajectory = traj; // add this trajectory onto all of the molecules... diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index 85a74201c..dc8996443 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -31,6 +31,7 @@ #include "SireMol/errors.h" #include "SireBase/lazyevaluator.h" +#include "SireBase/parallel.h" #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -54,7 +55,8 @@ namespace SireSystem }; SystemFrames(); - SystemFrames(const Molecules &mols, const PropertyMap &map); + SystemFrames(const QList &molnums, + const Molecules &mols, const PropertyMap &map); ~SystemFrames(); int nFrames() const; @@ -79,10 +81,14 @@ namespace SireSystem const Properties &props, const PropertyMap &map); - bool isCompatibleWith(const Molecules &mols, + bool isCompatibleWith(const QList &molnums, + const Molecules &mols, const PropertyMap &map) const; private: + /** The order the molecules should appear in the trajectory */ + QList molnums; + /** The start index and number of atoms for each molecule * in the system. This is the same for all frames */ @@ -103,14 +109,23 @@ SystemFrames::SystemFrames() : natoms(0), frame_type(EMPTY) { } -SystemFrames::SystemFrames(const Molecules &mols, const PropertyMap &map) - : natoms(0), frame_type(EMPTY) +SystemFrames::SystemFrames(const QList &nums, + const Molecules &mols, const PropertyMap &map) + : molnums(nums), natoms(0), frame_type(EMPTY) { - for (const auto &mol : mols) + for (const auto &molnum : molnums) { - const auto &moldata = mol.data(); + auto it = mols.constFind(molnum); + + if (it == mols.constEnd()) + throw SireMol::missing_molecule(QObject::tr( + "There is no molecule with number %1 in the system") + .arg(molnum.value()), + CODELOC); - mol_atoms.insert(moldata.number(), qMakePair(natoms, moldata.info().nAtoms())); + const auto &moldata = it.value().data(); + + mol_atoms.insert(molnum, qMakePair(natoms, moldata.info().nAtoms())); natoms += moldata.info().nAtoms(); } @@ -199,10 +214,11 @@ int SystemFrames::nFrames() const * trigger the creation of a new SystemFrames higher in the * stack */ -bool SystemFrames::isCompatibleWith(const Molecules &mols, +bool SystemFrames::isCompatibleWith(const QList &nums, + const Molecules &mols, const PropertyMap &map) const { - if (mols.nMolecules() != mol_atoms.size()) + if (molnums != nums or mols.nMolecules() != mol_atoms.size()) return false; // make sure that all of the molecules exist in the hash @@ -288,6 +304,143 @@ void SystemFrames::saveFrame(const Molecules &mols, const Properties &props, const PropertyMap &map) { + const bool save_coords = this->saveCoordinates(); + const bool save_vels = this->saveVelocities(); + const bool save_forces = this->saveForces(); + + if (not save_coords and not save_vels and not save_forces) + { + return; + } + + QVector coordinates; + QVector velocities; + QVector forces; + + Vector *coordinates_data = 0; + Velocity3D *velocities_data = 0; + Force3D *forces_data = 0; + + if (save_coords) + { + coordinates.resize(natoms); + coordinates_data = coordinates.data(); + } + + if (save_vels) + { + velocities.resize(natoms); + velocities_data = velocities.data(); + } + + if (save_forces) + { + forces.resize(natoms); + forces_data = forces.data(); + } + + auto save_frame = [&](MolNum molnum) + { + auto it = mol_atoms.constFind(molnum); + + if (it == mol_atoms.constEnd()) + { + return; + } + + auto it2 = mols.constFind(molnum); + + if (it2 == mols.constEnd()) + { + return; + } + + int start_atom = it.value().first; + int nats = it.value().second; + + if (start_atom < 0 or nats == 0 or start_atom + nats > natoms) + { + return; + } + + const auto &moldata = it2.value().data(); + + if (save_coords) + { + try + { + const auto &coords = moldata.property(map["coordinates"]).asA(); + + if (coords.nAtoms() != nats) + { + return; + } + + std::memcpy(coordinates_data + start_atom, coords.constData(CGIdx(0)), + nats * sizeof(Vector)); + } + catch (...) + { + } + } + + if (save_vels) + { + try + { + const auto &vels = moldata.property(map["velocities"]).asA(); + + if (vels.nAtoms() != nats) + { + return; + } + + std::memcpy(velocities_data + start_atom, vels.constData(CGIdx(0)), + nats * sizeof(Velocity3D)); + } + catch (...) + { + } + } + + if (save_forces) + { + try + { + const auto &frcs = moldata.property(map["forces"]).asA(); + + if (frcs.nAtoms() != nats) + { + return; + } + + std::memcpy(forces_data + start_atom, frcs.constData(CGIdx(0)), + nats * sizeof(Force3D)); + } + catch (...) + { + } + } + }; + + if (should_run_in_parallel(molnums.count(), map)) + { + tbb::parallel_for(tbb::blocked_range(0, molnums.count()), [&](const tbb::blocked_range &r) + { + for (int i = r.begin(); i < r.end(); ++i) + { + save_frame(molnums[i]); + } }); + } + else + { + for (const auto &molnum : molnums) + { + save_frame(molnum); + } + } + + frames.append(Frame(coordinates, velocities, forces, space, time, props)); } //////// @@ -485,8 +638,10 @@ SystemTrajectory::SystemTrajectory() : TrajectoryData() { } -SystemTrajectory::SystemTrajectory(const Molecules &mols, const PropertyMap &map) - : TrajectoryData(), d(new SystemFrames(mols, map)) +SystemTrajectory::SystemTrajectory(const QList &molnums, + const Molecules &mols, + const PropertyMap &map) + : TrajectoryData(), d(new SystemFrames(molnums, mols, map)) { } @@ -536,16 +691,22 @@ SystemTrajectory *SystemTrajectory::clone() const return new SystemTrajectory(*this); } +bool SystemTrajectory::isLive() const +{ + return true; +} + void SystemTrajectory::clear() { d.reset(); } -bool SystemTrajectory::isCompatibleWith(const Molecules &mols, +bool SystemTrajectory::isCompatibleWith(const QList &molnums, + const Molecules &mols, const PropertyMap &map) const { if (d) - return d->isCompatibleWith(mols, map); + return d->isCompatibleWith(molnums, mols, map); else return false; } @@ -558,7 +719,9 @@ void SystemTrajectory::saveFrame(const Molecules &mols, { if (not d) { - d.reset(new SystemFrames(mols, map)); + throw SireError::invalid_state( + QObject::tr("The trajectory is not initialized"), + CODELOC); } d->saveFrame(mols, space, time, props, map); diff --git a/corelib/src/libs/SireSystem/systemtrajectory.h b/corelib/src/libs/SireSystem/systemtrajectory.h index ad414eaed..673666a34 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.h +++ b/corelib/src/libs/SireSystem/systemtrajectory.h @@ -71,7 +71,9 @@ namespace SireSystem public: SystemTrajectory(); - SystemTrajectory(const SireMol::Molecules &mols, const SireBase::PropertyMap &map = SireBase::PropertyMap()); + SystemTrajectory(const QList &molnums, + const SireMol::Molecules &mols, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); SystemTrajectory(const SystemTrajectory &other); @@ -88,9 +90,12 @@ namespace SireSystem SystemTrajectory *clone() const; + bool isLive() const; + void clear(); - bool isCompatibleWith(const SireMol::Molecules &mols, + bool isCompatibleWith(const QList &molnums, + const SireMol::Molecules &mols, const SireBase::PropertyMap &map = SireBase::PropertyMap()) const; void saveFrame(const SireMol::Molecules &mols, From 74841ef8c2b9487888001d8b10c44a351e9c18f7 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 8 Apr 2024 19:12:27 +0100 Subject: [PATCH 209/468] Saving and loading system frames is now working - I've tested by running a dynamics simulation and viewing in a notebook --- corelib/src/libs/SireSystem/system.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/corelib/src/libs/SireSystem/system.cpp b/corelib/src/libs/SireSystem/system.cpp index 9e43e37b8..d64c3996b 100644 --- a/corelib/src/libs/SireSystem/system.cpp +++ b/corelib/src/libs/SireSystem/system.cpp @@ -4044,7 +4044,14 @@ void System::saveFrame(const SireBase::PropertyMap &map) { traj = new SystemTrajectory(molnums, mols, map); system_trajectory = traj; + } + + // save the frame into the system_trajectory - this will automatically + // update all molecules containing this trajectory + traj->saveFrame(mols, space, time, Properties(), map); + if (must_create) + { // add this trajectory onto all of the molecules... auto mols2 = mols; @@ -4068,13 +4075,8 @@ void System::saveFrame(const SireBase::PropertyMap &map) mols2.update(mol); } - mols = mols2; - this->update(mols); + this->update(mols2); } - - // save the frame into the system_trajectory - this will automatically - // update all molecules containing this trajectory - traj->saveFrame(mols, space, time, Properties(), map); } void System::deleteFrame(int frame, const SireBase::PropertyMap &map) From 8e40db01a29f85a15ee16d2e6e8829f3fa93b190 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 8 Apr 2024 20:06:10 +0100 Subject: [PATCH 210/468] Working on parallelising and optimising the trajectory loading / saving. Also moved to keeping the trajectory as byte arrays so that they are easier to cache back to disk Need to deal with segfaults... --- corelib/src/libs/SireMol/molecules.cpp | 21 +++- .../src/libs/SireSystem/systemtrajectory.cpp | 100 ++++++++++++++++-- 2 files changed, 110 insertions(+), 11 deletions(-) diff --git a/corelib/src/libs/SireMol/molecules.cpp b/corelib/src/libs/SireMol/molecules.cpp index d5d55b7e9..1613782d4 100644 --- a/corelib/src/libs/SireMol/molecules.cpp +++ b/corelib/src/libs/SireMol/molecules.cpp @@ -45,6 +45,7 @@ #include "select.h" #include "SireBase/lazyevaluator.h" +#include "SireBase/parallel.h" #include "SireMol/errors.h" @@ -1150,9 +1151,25 @@ void Molecules::loadFrame(int frame, const LazyEvaluator &evaluator, frame = Index(frame).map(n); - for (auto it = this->mols.begin(); it != this->mols.end(); ++it) + if (should_run_in_parallel(mols.count(), map)) + { + const auto molnums = this->molNums().values(); + + tbb::parallel_for(tbb::blocked_range(0, molnums.count()), + [&](const tbb::blocked_range &r) + { + for (int i = r.begin(); i < r.end(); ++i) + { + mols.find(molnums[i])->loadFrame(frame, evaluator, map); + } + }); + } + else { - it->loadFrame(frame, evaluator, map); + for (auto it = this->mols.begin(); it != this->mols.end(); ++it) + { + it->loadFrame(frame, evaluator, map); + } } } diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index dc8996443..d87684ff2 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -36,6 +36,8 @@ #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" +#include + using namespace SireSystem; using namespace SireMol; using namespace SireBase; @@ -86,6 +88,9 @@ namespace SireSystem const PropertyMap &map) const; private: + tbb::spin_mutex &getMutex() const; + Frame _lkr_getFrame(int i) const; + /** The order the molecules should appear in the trajectory */ QList molnums; @@ -95,7 +100,16 @@ namespace SireSystem QHash> mol_atoms; /** The data for the trajectory */ - QVector frames; + QVector frames; + + /** Mutex to serialize access to the data of this class */ + tbb::spin_mutex mutex; + + /** The current (unpacked) frame */ + Frame current_frame; + + /** The index of the current frame */ + int current_frame_index; /** The total number of atoms */ int natoms; @@ -105,14 +119,22 @@ namespace SireSystem }; } -SystemFrames::SystemFrames() : natoms(0), frame_type(EMPTY) +tbb::spin_mutex &SystemFrames::getMutex() const +{ + return *(const_cast(&mutex)); +} + +SystemFrames::SystemFrames() + : current_frame_index(-1), natoms(0), frame_type(EMPTY) { } SystemFrames::SystemFrames(const QList &nums, const Molecules &mols, const PropertyMap &map) - : molnums(nums), natoms(0), frame_type(EMPTY) + : molnums(nums), current_frame_index(-1), natoms(0), frame_type(EMPTY) { + tbb::spin_mutex::scoped_lock lock(getMutex()); + for (const auto &molnum : molnums) { auto it = mols.constFind(molnum); @@ -189,6 +211,8 @@ int SystemFrames::nAtoms() const int SystemFrames::nAtoms(MolNum molnum) const { + tbb::spin_mutex::scoped_lock lock(getMutex()); + auto it = mol_atoms.constFind(molnum); if (it == mol_atoms.constEnd()) @@ -204,6 +228,7 @@ int SystemFrames::nAtoms(MolNum molnum) const int SystemFrames::nFrames() const { + tbb::spin_mutex::scoped_lock lock(getMutex()); return frames.count(); } @@ -218,6 +243,8 @@ bool SystemFrames::isCompatibleWith(const QList &nums, const Molecules &mols, const PropertyMap &map) const { + tbb::spin_mutex::scoped_lock lock(getMutex()); + if (molnums != nums or mols.nMolecules() != mol_atoms.size()) return false; @@ -239,22 +266,47 @@ bool SystemFrames::isCompatibleWith(const QList &nums, return true; } -Frame SystemFrames::getFrame(int i) const +Frame SystemFrames::_lkr_getFrame(int i) const { try { - i = Index(i).map(this->nFrames()); + i = Index(i).map(frames.count()); } catch (...) { throw SireError::invalid_index( QObject::tr("Invalid frame index %1. Number of frames is %2.") .arg(i) - .arg(this->nFrames()), + .arg(frames.count()), CODELOC); } - return this->frames.at(i); + if (i == current_frame_index) + { + return current_frame; + } + + QDataStream ds(frames.at(i)); + + Frame frame; + + auto start_time = std::chrono::high_resolution_clock::now(); + ds >> frame; + auto end_time = std::chrono::high_resolution_clock::now(); + + qDebug() << "Loading frame" << i << "with" << frames.at(i).size() << "bytes" << frame.numBytes(); + qDebug() << "Deserialization time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + + const_cast(this)->current_frame = frame; + const_cast(this)->current_frame_index = i; + + return current_frame; +} + +Frame SystemFrames::getFrame(int i) const +{ + tbb::spin_mutex::scoped_lock lock(getMutex()); + return this->_lkr_getFrame(i); } Frame SystemFrames::getFrame(int i, const LazyEvaluator &evaluator) const @@ -269,6 +321,8 @@ Frame SystemFrames::getFrame(int i, const LazyEvaluator &evaluator) const Frame SystemFrames::getFrame(MolNum molnum, int i) const { + tbb::spin_mutex::scoped_lock lock(getMutex()); + auto it = mol_atoms.constFind(molnum); if (it == mol_atoms.constEnd()) @@ -279,12 +333,13 @@ Frame SystemFrames::getFrame(MolNum molnum, int i) const CODELOC); } - return this->getFrame(i).subset(it.value().first, it.value().second); + return this->_lkr_getFrame(i).subset(it.value().first, it.value().second); } Frame SystemFrames::getFrame(MolNum molnum, int i, const LazyEvaluator &evaluator) const { + tbb::spin_mutex::scoped_lock lock(getMutex()); auto it = mol_atoms.constFind(molnum); if (it == mol_atoms.constEnd()) @@ -295,6 +350,9 @@ Frame SystemFrames::getFrame(MolNum molnum, int i, CODELOC); } + // below function call gets the lock, so unlock now + lock.release(); + return this->getFrame(i, evaluator).subset(it.value().first, it.value().second); } @@ -440,7 +498,31 @@ void SystemFrames::saveFrame(const Molecules &mols, } } - frames.append(Frame(coordinates, velocities, forces, space, time, props)); + Frame frame(coordinates, velocities, forces, space, time, props); + + auto start_time = std::chrono::high_resolution_clock::now(); + + QByteArray data; + data.reserve(2 * frame.numBytes()); + + auto mem_time = std::chrono::high_resolution_clock::now(); + + QDataStream ds(&data, QIODevice::WriteOnly); + ds << frame; + + auto end_time = std::chrono::high_resolution_clock::now(); + + qDebug() << "Saving frame" << frames.count() << "with" << data.size() << "bytes" << frame.numBytes(); + qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - start_time).count() << "microseconds"; + qDebug() << "Serialization time" << std::chrono::duration_cast(end_time - mem_time).count() << "microseconds"; + qDebug() << "Total time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + + // need to hold the write lock, as we are updating global state + // for everyone who holds this live trajectory data + tbb::spin_mutex::scoped_lock lock(getMutex()); + frames.append(data); + current_frame = frame; + current_frame_index = frames.count() - 1; } //////// From 0df149948ad3b53bbf9801187f00841f24fbb72c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 9 Apr 2024 16:20:01 +0100 Subject: [PATCH 211/468] Move tutorial to avoid clash with other development work. --- .../tutorial/{index_part08.rst => index_partXX.rst} | 8 ++++---- doc/source/tutorial/{part08 => partXX}/01_emle.rst | 0 2 files changed, 4 insertions(+), 4 deletions(-) rename doc/source/tutorial/{index_part08.rst => index_partXX.rst} (91%) rename doc/source/tutorial/{part08 => partXX}/01_emle.rst (100%) diff --git a/doc/source/tutorial/index_part08.rst b/doc/source/tutorial/index_partXX.rst similarity index 91% rename from doc/source/tutorial/index_part08.rst rename to doc/source/tutorial/index_partXX.rst index 6f9cb84c3..413e59783 100644 --- a/doc/source/tutorial/index_part08.rst +++ b/doc/source/tutorial/index_partXX.rst @@ -1,6 +1,6 @@ -============== -Part 8 - QM/MM -============== +=============== +Part XX - QM/MM +=============== QM/MM is a method that combines the accuracy of quantum mechanics with the speed of molecular mechanics. In QM/MM, a small region of the system is treated @@ -15,4 +15,4 @@ QM/MM simulations using ``sire``. .. toctree:: :maxdepth: 1 - part08/01_emle + partXX/01_emle diff --git a/doc/source/tutorial/part08/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst similarity index 100% rename from doc/source/tutorial/part08/01_emle.rst rename to doc/source/tutorial/partXX/01_emle.rst From 1428ac05ad4be103cc52c6424ef0115a640e29c9 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 9 Apr 2024 18:32:56 +0100 Subject: [PATCH 212/468] Updating version and changelog for 2024.2.0 development [ci skip] --- doc/source/changelog.rst | 7 +++++-- version.txt | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 92e3f27f7..3645708a8 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -12,6 +12,11 @@ Development was migrated into the `OpenBioSim `__ organisation on `GitHub `__. +`2024.2.0 `__ - June 2024 +----------------------------------------------------------------------------------------- + +* Please add an item to this changelog when you create your PR + `2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ @@ -190,8 +195,6 @@ organisation on `GitHub `__. it was not using the stage-specific value of lambda when using multiple stages where one or more stages contained a standard morph equation. -* Please add an item to this changelog when you create your PR - `2023.5.2 `__ - March 2024 ------------------------------------------------------------------------------------------ diff --git a/version.txt b/version.txt index d2abdbbd1..5dc9f0c61 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -2024.1.0.dev +2024.2.0.dev From f90cf85374b1191a6960a8a1f06c8fcf7f674644 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 9 Apr 2024 23:10:27 +0100 Subject: [PATCH 213/468] Bringing the typo fix across to devel --- doc/source/tutorial/part07/04_merge.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/part07/04_merge.rst b/doc/source/tutorial/part07/04_merge.rst index 625c6e558..2855675cc 100644 --- a/doc/source/tutorial/part07/04_merge.rst +++ b/doc/source/tutorial/part07/04_merge.rst @@ -206,7 +206,7 @@ AtomMapping( size=1, unmapped0=16, unmapped1=4 By default, this algorithm ignores hydrogens. This is why only a single atom was matched above. You can change this by passing in the -``ignore_light_atoms=True`` argument. +``match_light_atoms=True`` argument. >>> m = sr.morph.match(mol0=neopentane, mol1=methane, match_light_atoms=True) >>> print(m) From 06ea8e3a1065faf4c40e976ce31bc051b5854456 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 11 Apr 2024 18:12:17 +0100 Subject: [PATCH 214/468] Improved setup.py that gives more control over dependencies --- setup.py | 118 +++++++++++++++++++++++++++++++------------------------ 1 file changed, 66 insertions(+), 52 deletions(-) diff --git a/setup.py b/setup.py index 03cd5bc46..48239a2ff 100644 --- a/setup.py +++ b/setup.py @@ -91,7 +91,7 @@ conda_base = os.path.abspath(os.environ["PREFIX"]) print(f"Setting conda-base to {conda_base}") else: - # Find the path to the conda or mamba executable + # Find the path to the conda executable conda_base = os.path.abspath(os.path.dirname(sys.executable)) if os.path.basename(conda_base) == "bin": @@ -133,21 +133,6 @@ sys.exit(-1) -def find_mamba(): - """Find mamba""" - if conda.endswith(".exe"): - m = os.path.join(os.path.dirname(conda), "mamba.exe") - else: - m = os.path.join(os.path.dirname(conda), "mamba") - - if os.path.exists(m): - return m - else: - return None - - -mamba = find_mamba() - # Get the build operating system and processor is_linux = False is_windows = False @@ -277,6 +262,13 @@ def parse_args(): help="Skip the installation of the dependencies (only use if you know " "that they are already installed)", ) + parser.add_argument( + "--skip-dep", + action="append", + help="List of dependencies to skip when installing. This is useful when " + "you know that a particular dependency is already installed or " + "it is uninstallable on your system.", + ) parser.add_argument( "--skip-build", action="store_true", @@ -331,8 +323,10 @@ def _add_to_dependencies(dependencies, lines): _is_conda_prepped = False +dependencies_to_skip = [] + -def conda_install(dependencies, install_bss_reqs=False): +def conda_install(dependencies, install_bss_reqs=False, yes=True): """Install the passed list of dependencies using conda""" conda_exe = conda @@ -365,35 +359,60 @@ def conda_install(dependencies, install_bss_reqs=False): _is_conda_prepped = True - if mamba is None: - conda_install = [conda, "install", "--yes"] - else: - conda_install = [mamba, "install", "--yes"] + conda_install = [conda, "install"] + + if yes: + conda_install.append("--yes") + + deps = [] + + global dependencies_to_skip + + try: + if len(dependencies_to_skip) > 0: + print(f"Skipping the following dependencies: {dependencies_to_skip}") + except Exception: + dependencies_to_skip = [] + + for dependency in dependencies: + if dependency == "python" or is_installed(dependency, conda_exe): + # no need to install again + continue + + skip_dep = False + + for skip in dependencies_to_skip: + if dependency.find(skip) != -1: + skip_dep = True + break + + if skip_dep: + print(f"Skipping {dependency}") + continue + + # remove duplicates + dep = f'"{dependency}"' + + if dep not in deps: + deps.append(dep) - dependencies = [f'"{dep}"' for dep in dependencies] + dependencies = deps cmd = [*conda_install, *dependencies] - print("\nInstalling packages using: '%s'" % " ".join(cmd)) + print("\nInstalling packages using:\n\n%s\n\n" % " ".join(cmd)) status = subprocess.run(cmd) if status.returncode != 0: - if mamba is not None: - # try with conda, as mamba was broken? - conda_install = [conda, "install", "--yes"] - cmd = [*conda_install, *dependencies] - print("\nTrying again using: '%s'" % " ".join(cmd)) - status = subprocess.run(cmd) - - if status.returncode != 0: - print("Something went wrong installing dependencies!") - print("If the python or conda/mamba executables were updated") - print("in the last install, then this can prevent them") - print("from running again. Please re-execute this script.") - sys.exit(-1) + print("Something went wrong installing dependencies!") + print("If the python or conda executables were updated") + print("in the last install, then this can prevent them") + print("from running again. Please re-execute this script.") + sys.exit(-1) -def install_requires(install_bss_reqs=False): - """Installs all of the dependencies. This can safely be called +def install_requires(install_bss_reqs=False, yes=True): + """ + Installs all of the dependencies. This can safely be called multiple times, as it will cache the result to prevent future installs taking too long """ @@ -408,21 +427,13 @@ def install_requires(install_bss_reqs=False): ) sys.exit(-1) - # install mamba if it doesn't exist already - global mamba - - if mamba is None: - # install mamba first! - conda_install(["mamba"], install_bss_reqs) - mamba = find_mamba() - try: import pip_requirements_parser as _pip_requirements_parser from parse_requirements import parse_requirements except Exception: # this didn't import - maybe we are missing pip-requirements-parser print("Installing pip-requirements-parser") - conda_install(["pip-requirements-parser"], install_bss_reqs) + conda_install(["pip-requirements-parser"], install_bss_reqs, yes=yes) try: from parse_requirements import parse_requirements except ImportError as e: @@ -438,7 +449,7 @@ def install_requires(install_bss_reqs=False): reqs = reqs + bss_reqs dependencies = build_reqs + reqs - conda_install(dependencies, install_bss_reqs) + conda_install(dependencies, install_bss_reqs, yes=yes) def add_default_cmake_defs(cmake_defs, ncores): @@ -546,7 +557,7 @@ def build(ncores: int = 1, npycores: int = 1, coredefs=[], pydefs=[]): CXX = glob.glob(os.path.join(bindir, "clang++"))[0] CC = glob.glob(os.path.join(bindir, "clang"))[0] except Exception: - conda_install(["clang", "clangxx"], False) + conda_install(["clang", "clangxx"], False, yes=True) try: CXX = glob.glob(os.path.join(bindir, "clang++"))[0] CC = glob.glob(os.path.join(bindir, "clang"))[0] @@ -561,9 +572,9 @@ def build(ncores: int = 1, npycores: int = 1, coredefs=[], pydefs=[]): CXX = glob.glob(os.path.join(bindir, "*-g++"))[0] CC = glob.glob(os.path.join(bindir, "*-gcc"))[0] except Exception: - # Need this version of gcc to stay compatible with conda-forge + # Need this version of gcc to stay compatible with conda-forge # (i.e. gemmi needs the exact same compiler version) - conda_install(["gcc==12.3.0", "gxx==12.3.0"], False) + conda_install(["gcc==12.3.0", "gxx==12.3.0"], False, yes=True) try: CXX = glob.glob(os.path.join(bindir, "*-g++"))[0] CC = glob.glob(os.path.join(bindir, "*-gcc"))[0] @@ -869,6 +880,9 @@ def install(ncores: int = 1, npycores: int = 1): install_bss = args.install_bss_deps + if args.skip_dep is not None: + dependencies_to_skip = args.skip_dep + action = args.action[0] if is_windows and (args.generator is None or len(args.generator) == 0): @@ -905,7 +919,7 @@ def install(ncores: int = 1, npycores: int = 1): ) elif action == "install_requires": - install_requires(install_bss_reqs=install_bss) + install_requires(install_bss_reqs=install_bss, yes=False) elif action == "install_module": install_module(ncores=args.ncores[0]) From 3f25354db16e6cde5b55b879eaf65fbebcbddbed Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 12 Apr 2024 23:22:00 +0100 Subject: [PATCH 215/468] Fixed crash on trajectory write caused by the code that parallelised molecule frame updates --- corelib/src/libs/SireMol/molecules.cpp | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/corelib/src/libs/SireMol/molecules.cpp b/corelib/src/libs/SireMol/molecules.cpp index 1613782d4..e654d4f23 100644 --- a/corelib/src/libs/SireMol/molecules.cpp +++ b/corelib/src/libs/SireMol/molecules.cpp @@ -1153,16 +1153,27 @@ void Molecules::loadFrame(int frame, const LazyEvaluator &evaluator, if (should_run_in_parallel(mols.count(), map)) { - const auto molnums = this->molNums().values(); + QVector mols2; + const int nmols = mols.count(); + mols2.reserve(nmols); - tbb::parallel_for(tbb::blocked_range(0, molnums.count()), + for (auto it = this->mols.constBegin(); it != this->mols.constEnd(); ++it) + { + mols2.append(it.value().molecule()); + } + + auto mols2_array = mols2.data(); + + tbb::parallel_for(tbb::blocked_range(0, nmols), [&](const tbb::blocked_range &r) { for (int i = r.begin(); i < r.end(); ++i) { - mols.find(molnums[i])->loadFrame(frame, evaluator, map); + mols2_array[i].loadFrame(frame, evaluator, map); } }); + + this->update(Molecules(mols2)); } else { From 18697592f1c0203579d231047bbc120ece247654 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 13 Apr 2024 23:18:21 +0100 Subject: [PATCH 216/468] Adding in the PageCache class, which will handle moving of data between memory and disk --- corelib/src/libs/SireBase/CMakeLists.txt | 2 + corelib/src/libs/SireBase/pagecache.cpp | 570 +++++++++++++++++ corelib/src/libs/SireBase/pagecache.h | 193 ++++++ .../src/libs/SireSystem/systemtrajectory.cpp | 22 +- wrapper/Base/CMakeAutogenFile.txt | 1 + wrapper/Base/PageCache.pypp.cpp | 579 ++++++++++++++++++ wrapper/Base/PageCache.pypp.hpp | 10 + wrapper/Base/_Base.main.cpp | 4 + wrapper/Base/active_headers.h | 1 + wrapper/System/active_headers.h | 1 + 10 files changed, 1372 insertions(+), 11 deletions(-) create mode 100644 corelib/src/libs/SireBase/pagecache.cpp create mode 100644 corelib/src/libs/SireBase/pagecache.h create mode 100644 wrapper/Base/PageCache.pypp.cpp create mode 100644 wrapper/Base/PageCache.pypp.hpp diff --git a/corelib/src/libs/SireBase/CMakeLists.txt b/corelib/src/libs/SireBase/CMakeLists.txt index 55f240aca..0217a3463 100644 --- a/corelib/src/libs/SireBase/CMakeLists.txt +++ b/corelib/src/libs/SireBase/CMakeLists.txt @@ -46,6 +46,7 @@ set ( SIREBASE_HEADERS packedarray2d.h packedarray2d.hpp packedarrays.h + pagecache.h pairmatrix.hpp range.h ranges.h @@ -103,6 +104,7 @@ set ( SIREBASE_SOURCES meminfo.cpp numberproperty.cpp packedarray2d.cpp + pagecache.cpp parallel.cpp process.cpp progressbar.cpp diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp new file mode 100644 index 000000000..df5f227e8 --- /dev/null +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -0,0 +1,570 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "pagecache.h" + +#include "SireError/errors.h" + +#include + +#include + +namespace SireBase +{ + namespace detail + { + class CacheData : public boost::noncopyable + { + public: + CacheData(QString cachedir, int page_size); + ~CacheData(); + + QString cacheDir() const; + + PageCache::Handle cache(const QByteArray &data); + + int pageSize() const; + + int nPages() const; + int nBytes() const; + + private: + QString cache_dir; + int page_size; + }; + + class PageData : public boost::noncopyable + { + public: + PageData(int max_size); + ~PageData(); + + int maxBytes() const; + int nBytes() const; + int bytesRemaining() const; + + bool isResident() const; + bool isCached() const; + + PageCache::Handle cache(const QByteArray &data); + + QByteArray fetch(int offset, int n_bytes) const; + + PageCache parent() const; + + private: + std::weak_ptr c; + int max_bytes; + int nbytes; + }; + + class HandleData : public boost::noncopyable + { + public: + HandleData(); + ~HandleData(); + + QByteArray fetch() const; + + PageCache::Page page() const; + + int nBytes() const; + + bool isValid() const; + bool isNull() const; + + PageCache parent() const; + + private: + /** The page containing this data */ + PageCache::Page p; + + /** The offset of this data within the page */ + int offset; + + /** The number of bytes of data */ + int nbytes; + }; + } +} + +using namespace SireBase; +using namespace SireBase::detail; + +/////// +/////// Implementation of detail::CacheData +/////// + +CacheData::CacheData(QString c, int p) + : cache_dir(c), page_size(p) +{ + if (c.simplified().isEmpty()) + { + // by default, go into the current directory + cache_dir = "."; + } + + if (page_size < 1024) + { + throw SireError::invalid_arg( + QObject::tr("Page size must be greater than 1024!"), CODELOC); + } +} + +CacheData::~CacheData() +{ +} + +PageCache::Handle CacheData::cache(const QByteArray &data) +{ + return PageCache::Handle(); +} + +QString CacheData::cacheDir() const +{ + return cache_dir; +} + +int CacheData::pageSize() const +{ + return page_size; +} + +int CacheData::nPages() const +{ + return 0; +} + +int CacheData::nBytes() const +{ + return 0; +} + +/////// +/////// Implementation of detail::PageData +/////// + +PageData::PageData(int max_size) + : max_bytes(max_size), nbytes(0) +{ + if (max_bytes < 1024) + { + throw SireError::invalid_arg( + QObject::tr("Page size must be greater than 1024!"), CODELOC); + } +} + +PageData::~PageData() +{ +} + +int PageData::maxBytes() const +{ + return max_bytes; +} + +int PageData::nBytes() const +{ + return nbytes; +} + +int PageData::bytesRemaining() const +{ + return max_bytes - nbytes; +} + +bool PageData::isResident() const +{ + return true; +} + +bool PageData::isCached() const +{ + return false; +} + +PageCache::Handle PageData::cache(const QByteArray &data) +{ + return PageCache::Handle(); +} + +QByteArray PageData::fetch(int offset, int n_bytes) const +{ + return QByteArray(); +} + +PageCache PageData::parent() const +{ + return PageCache(c.lock()); +} + +/////// +/////// Implementation of detail::HandleData +/////// + +HandleData::HandleData() + : offset(0), nbytes(0) +{ +} + +HandleData::~HandleData() +{ +} + +QByteArray HandleData::fetch() const +{ + return p.fetch(offset, nbytes); +} + +PageCache::Page HandleData::page() const +{ + return p; +} + +int HandleData::nBytes() const +{ + return nbytes; +} + +bool HandleData::isValid() const +{ + return nbytes > 0; +} + +bool HandleData::isNull() const +{ + return nbytes == 0; +} + +PageCache HandleData::parent() const +{ + return p.parent(); +} + +/////// +/////// Implementation of PageCache::Page +/////// + +PageCache::Page::Page() + : p(nullptr) +{ +} + +PageCache::Page::Page(std::shared_ptr data) + : p(data) +{ +} + +PageCache::Page::Page(const PageCache::Page &other) + : p(other.p) +{ +} + +PageCache::Page::~Page() +{ +} + +PageCache::Page &PageCache::Page::operator=(const PageCache::Page &other) +{ + p = other.p; + return *this; +} + +const char *PageCache::Page::typeName() +{ + return "SireBase::PageCache::Page"; +} + +const char *PageCache::Page::what() const +{ + return PageCache::Page::typeName(); +} + +QString PageCache::Page::toString() const +{ + return QString("PageCache::Page"); +} + +void PageCache::Page::assertValid() const +{ + if (p == nullptr) + { + throw SireError::invalid_state( + QObject::tr("Page object is null"), CODELOC); + } +} + +bool PageCache::Page::isValid() const +{ + return p != nullptr; +} + +bool PageCache::Page::isNull() const +{ + return p == nullptr; +} + +bool PageCache::Page::isResident() const +{ + assertValid(); + return p->isResident(); +} + +bool PageCache::Page::isCached() const +{ + assertValid(); + return p->isCached(); +} + +int PageCache::Page::nBytes() const +{ + assertValid(); + return p->nBytes(); +} + +int PageCache::Page::size() const +{ + return this->nBytes(); +} + +PageCache PageCache::Page::parent() const +{ + assertValid(); + return p->parent(); +} + +QByteArray PageCache::Page::fetch(int offset, int n_bytes) const +{ + assertValid(); + return p->fetch(offset, n_bytes); +} + +/////// +/////// Implementation of PageCache::Handle +/////// + +PageCache::Handle::Handle() + : h(nullptr) +{ +} + +PageCache::Handle::Handle(std::shared_ptr data) + : h(data) +{ +} + +PageCache::Handle::Handle(const PageCache::Handle &other) + : h(other.h) +{ +} + +PageCache::Handle::~Handle() +{ +} + +PageCache::Handle &PageCache::Handle::operator=(const PageCache::Handle &other) +{ + h = other.h; + return *this; +} + +const char *PageCache::Handle::typeName() +{ + return "SireBase::PageCache::Handle"; +} + +const char *PageCache::Handle::what() const +{ + return PageCache::Handle::typeName(); +} + +QString PageCache::Handle::toString() const +{ + return QString("PageCache::Handle"); +} + +void PageCache::Handle::assertValid() const +{ + if (h == nullptr) + { + throw SireError::invalid_state( + QObject::tr("Handle object is null"), CODELOC); + } +} + +PageCache::Page PageCache::Handle::page() const +{ + assertValid(); + return Page(h->page()); +} + +QByteArray PageCache::Handle::fetch() const +{ + assertValid(); + return h->fetch(); +} + +PageCache PageCache::Handle::parent() const +{ + assertValid(); + return h->parent(); +} + +bool PageCache::Handle::isValid() const +{ + return h != nullptr; +} + +bool PageCache::Handle::isNull() const +{ + return h == nullptr; +} + +int PageCache::Handle::size() const +{ + return this->nBytes(); +} + +int PageCache::Handle::nBytes() const +{ + assertValid(); + return h->nBytes(); +} + +void PageCache::Handle::clear() +{ + h.reset(); +} + +void PageCache::Handle::reset() +{ + h.reset(); +} + +/////// +/////// Implementation of PageCache +/////// + +PageCache::PageCache(int page_size) + : d(new CacheData(QString("."), page_size)) +{ +} + +PageCache::PageCache(const QString &cachedir, int page_size) + : d(new CacheData(cachedir, page_size)) +{ +} + +PageCache::PageCache(std::shared_ptr data) + : d(data) +{ +} + +PageCache::PageCache(const PageCache &other) + : d(other.d) +{ +} + +PageCache::~PageCache() +{ +} + +PageCache &PageCache::operator=(const PageCache &other) +{ + d = other.d; + return *this; +} + +const char *PageCache::typeName() +{ + return "SireBase::PageCache"; +} + +const char *PageCache::what() const +{ + return PageCache::typeName(); +} + +QString PageCache::toString() const +{ + return QString("PageCache"); +} + +void PageCache::assertValid() const +{ + if (d == nullptr) + { + throw SireError::invalid_state( + QObject::tr("PageCache object is null"), CODELOC); + } +} + +QString PageCache::cacheDir() const +{ + assertValid(); + return d->cacheDir(); +} + +int PageCache::pageSize() const +{ + assertValid(); + return d->pageSize(); +} + +int PageCache::nPages() const +{ + assertValid(); + return d->nPages(); +} + +int PageCache::nBytes() const +{ + assertValid(); + return d->nBytes(); +} + +int PageCache::size() const +{ + return this->nBytes(); +} + +bool PageCache::isValid() const +{ + return d != nullptr; +} + +bool PageCache::isNull() const +{ + return d == nullptr; +} + +PageCache::Handle PageCache::cache(const QByteArray &data) +{ + assertValid(); + return Handle(d->cache(data)); +} diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h new file mode 100644 index 000000000..b8d433e0f --- /dev/null +++ b/corelib/src/libs/SireBase/pagecache.h @@ -0,0 +1,193 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREBASE_PAGECACHE_H +#define SIREBASE_PAGECACHE_H + +#include "sireglobal.h" + +#include + +#include + +SIRE_BEGIN_HEADER + +namespace SireBase +{ + namespace detail + { + class CacheData; + class PageData; + class HandleData; + } + + /** This class manages a swap cache of binary data that can be + * paged to and from disk. The cache can receive binary data + * of any size, and will automatically manage the paging of + * that data to and from disk as it is accessed. + * + * You can create different caches, and have control over the maximum + * size of each cache page. + * + * Note that deleting the cache will delete all data contained + * therein - including data paged to disk + */ + class SIREBASE_EXPORT PageCache + { + public: + PageCache(int page_size = 32 * 1024 * 1024); + PageCache(const QString &cache_dir, + int page_size = 32 * 1024 * 1024); + PageCache(std::shared_ptr data); + PageCache(const PageCache &other); + ~PageCache(); + + PageCache &operator=(const PageCache &other); + + const char *what() const; + static const char *typeName(); + + PageCache *clone() const; + + QString toString() const; + + QString cacheDir() const; + + int pageSize() const; + int nPages() const; + int nBytes() const; + + int size() const; + + bool isValid() const; + bool isNull() const; + + void assertValid() const; + + /** This is a page in the cache. This can hold multiple + * objects - the whole page is either resident in memory + * or cached to disk. + */ + class SIREBASE_EXPORT Page + { + friend class detail::HandleData; + + public: + Page(); + Page(std::shared_ptr data); + Page(const Page &other); + ~Page(); + + Page &operator=(const Page &other); + + const char *what() const; + static const char *typeName(); + + Page *clone() const; + + QString toString() const; + + bool isValid() const; + bool isNull() const; + + void assertValid() const; + + bool isResident() const; + bool isCached() const; + + int nBytes() const; + int size() const; + + PageCache parent() const; + + protected: + QByteArray fetch(int offset, int n_bytes) const; + + private: + std::shared_ptr p; + }; + + /** This is a handle to a piece of data that has + * been added to the cache. This will either contain + * the actual data, or will hold the information + * necessary to retrieve that data from disk. + * + * Data is removed from the cache when all handles + * to it are deleted + */ + class SIREBASE_EXPORT Handle + { + public: + Handle(); + Handle(std::shared_ptr data); + Handle(const Handle &other); + ~Handle(); + + Handle &operator=(const Handle &other); + + const char *what() const; + static const char *typeName(); + + Handle *clone() const; + + QString toString() const; + + Page page() const; + QByteArray fetch() const; + + PageCache parent() const; + + bool isValid() const; + bool isNull() const; + + void assertValid() const; + + int size() const; + int nBytes() const; + + void clear(); + void reset(); + + private: + std::shared_ptr h; + }; + + Handle cache(const QByteArray &data); + + private: + std::shared_ptr d; + }; +} + +SIRE_EXPOSE_CLASS(SireBase::PageCache) +SIRE_EXPOSE_CLASS(SireBase::PageCache::Page) +SIRE_EXPOSE_CLASS(SireBase::PageCache::Handle) + +SIRE_END_HEADER + +#endif diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index d87684ff2..a2e93057c 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -290,12 +290,12 @@ Frame SystemFrames::_lkr_getFrame(int i) const Frame frame; - auto start_time = std::chrono::high_resolution_clock::now(); + // auto start_time = std::chrono::high_resolution_clock::now(); ds >> frame; - auto end_time = std::chrono::high_resolution_clock::now(); + // auto end_time = std::chrono::high_resolution_clock::now(); - qDebug() << "Loading frame" << i << "with" << frames.at(i).size() << "bytes" << frame.numBytes(); - qDebug() << "Deserialization time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + // qDebug() << "Loading frame" << i << "with" << frames.at(i).size() << "bytes" << frame.numBytes(); + // qDebug() << "Deserialization time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; const_cast(this)->current_frame = frame; const_cast(this)->current_frame_index = i; @@ -500,22 +500,22 @@ void SystemFrames::saveFrame(const Molecules &mols, Frame frame(coordinates, velocities, forces, space, time, props); - auto start_time = std::chrono::high_resolution_clock::now(); + // auto start_time = std::chrono::high_resolution_clock::now(); QByteArray data; data.reserve(2 * frame.numBytes()); - auto mem_time = std::chrono::high_resolution_clock::now(); + // auto mem_time = std::chrono::high_resolution_clock::now(); QDataStream ds(&data, QIODevice::WriteOnly); ds << frame; - auto end_time = std::chrono::high_resolution_clock::now(); + // auto end_time = std::chrono::high_resolution_clock::now(); - qDebug() << "Saving frame" << frames.count() << "with" << data.size() << "bytes" << frame.numBytes(); - qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - start_time).count() << "microseconds"; - qDebug() << "Serialization time" << std::chrono::duration_cast(end_time - mem_time).count() << "microseconds"; - qDebug() << "Total time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + // qDebug() << "Saving frame" << frames.count() << "with" << data.size() << "bytes" << frame.numBytes(); + // qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - start_time).count() << "microseconds"; + // qDebug() << "Serialization time" << std::chrono::duration_cast(end_time - mem_time).count() << "microseconds"; + // qDebug() << "Total time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; // need to hold the write lock, as we are updating global state // for everyone who holds this live trajectory data diff --git a/wrapper/Base/CMakeAutogenFile.txt b/wrapper/Base/CMakeAutogenFile.txt index 5995b1747..b5db1bb86 100644 --- a/wrapper/Base/CMakeAutogenFile.txt +++ b/wrapper/Base/CMakeAutogenFile.txt @@ -43,6 +43,7 @@ set ( PYPP_SOURCES Properties.pypp.cpp PropertyList.pypp.cpp TrigArray2D_double_.pypp.cpp + PageCache.pypp.cpp PackedArray2D_StringArrayProperty.pypp.cpp VariantProperty.pypp.cpp ArrayProperty_QString_.pypp.cpp diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp new file mode 100644 index 000000000..0eb9850aa --- /dev/null +++ b/wrapper/Base/PageCache.pypp.cpp @@ -0,0 +1,579 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "PageCache.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "pagecache.h" + +#include + +#include + +#include "pagecache.h" + +SireBase::PageCache __copy__(const SireBase::PageCache &other){ return SireBase::PageCache(other); } + +const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCache";} + +#include "Helpers/release_gil_policy.hpp" + +#include "SireError/errors.h" + +#include "pagecache.h" + +#include + +#include + +#include "pagecache.h" + +SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ return SireBase::PageCache::Handle(other); } + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +#include "Helpers/len.hpp" + +#include "SireError/errors.h" + +#include "pagecache.h" + +#include + +#include + +#include "pagecache.h" + +SireBase::PageCache::Page __copy__(const SireBase::PageCache::Page &other){ return SireBase::PageCache::Page(other); } + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +#include "Helpers/len.hpp" + +void register_PageCache_class(){ + + { //::SireBase::PageCache + typedef bp::class_< SireBase::PageCache > PageCache_exposer_t; + PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< bp::optional< int > >(( bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); + bp::scope PageCache_scope( PageCache_exposer ); + { //::SireBase::PageCache::Handle + typedef bp::class_< SireBase::PageCache::Handle > Handle_exposer_t; + Handle_exposer_t Handle_exposer = Handle_exposer_t( "Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init< >("") ); + bp::scope Handle_scope( Handle_exposer ); + Handle_exposer.def( bp::init< std::shared_ptr< SireBase::detail::HandleData > >(( bp::arg("data") ), "") ); + Handle_exposer.def( bp::init< SireBase::PageCache::Handle const & >(( bp::arg("other") ), "") ); + { //::SireBase::PageCache::Handle::assertValid + + typedef void ( ::SireBase::PageCache::Handle::*assertValid_function_type)( ) const; + assertValid_function_type assertValid_function_value( &::SireBase::PageCache::Handle::assertValid ); + + Handle_exposer.def( + "assertValid" + , assertValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::clear + + typedef void ( ::SireBase::PageCache::Handle::*clear_function_type)( ) ; + clear_function_type clear_function_value( &::SireBase::PageCache::Handle::clear ); + + Handle_exposer.def( + "clear" + , clear_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::fetch + + typedef ::QByteArray ( ::SireBase::PageCache::Handle::*fetch_function_type)( ) const; + fetch_function_type fetch_function_value( &::SireBase::PageCache::Handle::fetch ); + + Handle_exposer.def( + "fetch" + , fetch_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::isNull + + typedef bool ( ::SireBase::PageCache::Handle::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireBase::PageCache::Handle::isNull ); + + Handle_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::isValid + + typedef bool ( ::SireBase::PageCache::Handle::*isValid_function_type)( ) const; + isValid_function_type isValid_function_value( &::SireBase::PageCache::Handle::isValid ); + + Handle_exposer.def( + "isValid" + , isValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::nBytes + + typedef int ( ::SireBase::PageCache::Handle::*nBytes_function_type)( ) const; + nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Handle::nBytes ); + + Handle_exposer.def( + "nBytes" + , nBytes_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::operator= + + typedef ::SireBase::PageCache::Handle & ( ::SireBase::PageCache::Handle::*assign_function_type)( ::SireBase::PageCache::Handle const & ) ; + assign_function_type assign_function_value( &::SireBase::PageCache::Handle::operator= ); + + Handle_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + + } + { //::SireBase::PageCache::Handle::page + + typedef ::SireBase::PageCache::Page ( ::SireBase::PageCache::Handle::*page_function_type)( ) const; + page_function_type page_function_value( &::SireBase::PageCache::Handle::page ); + + Handle_exposer.def( + "page" + , page_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::parent + + typedef ::SireBase::PageCache ( ::SireBase::PageCache::Handle::*parent_function_type)( ) const; + parent_function_type parent_function_value( &::SireBase::PageCache::Handle::parent ); + + Handle_exposer.def( + "parent" + , parent_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::reset + + typedef void ( ::SireBase::PageCache::Handle::*reset_function_type)( ) ; + reset_function_type reset_function_value( &::SireBase::PageCache::Handle::reset ); + + Handle_exposer.def( + "reset" + , reset_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::size + + typedef int ( ::SireBase::PageCache::Handle::*size_function_type)( ) const; + size_function_type size_function_value( &::SireBase::PageCache::Handle::size ); + + Handle_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::toString + + typedef ::QString ( ::SireBase::PageCache::Handle::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireBase::PageCache::Handle::toString ); + + Handle_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireBase::PageCache::Handle::typeName ); + + Handle_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Handle::what + + typedef char const * ( ::SireBase::PageCache::Handle::*what_function_type)( ) const; + what_function_type what_function_value( &::SireBase::PageCache::Handle::what ); + + Handle_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + + } + Handle_exposer.staticmethod( "typeName" ); + Handle_exposer.def( "__copy__", &__copy__); + Handle_exposer.def( "__deepcopy__", &__copy__); + Handle_exposer.def( "clone", &__copy__); + Handle_exposer.def( "__str__", &__str__< ::SireBase::PageCache::Handle > ); + Handle_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Handle > ); + Handle_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Handle > ); + } + { //::SireBase::PageCache::Page + typedef bp::class_< SireBase::PageCache::Page > Page_exposer_t; + Page_exposer_t Page_exposer = Page_exposer_t( "Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init< >("") ); + bp::scope Page_scope( Page_exposer ); + Page_exposer.def( bp::init< std::shared_ptr< SireBase::detail::PageData > >(( bp::arg("data") ), "") ); + Page_exposer.def( bp::init< SireBase::PageCache::Page const & >(( bp::arg("other") ), "") ); + { //::SireBase::PageCache::Page::assertValid + + typedef void ( ::SireBase::PageCache::Page::*assertValid_function_type)( ) const; + assertValid_function_type assertValid_function_value( &::SireBase::PageCache::Page::assertValid ); + + Page_exposer.def( + "assertValid" + , assertValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::isCached + + typedef bool ( ::SireBase::PageCache::Page::*isCached_function_type)( ) const; + isCached_function_type isCached_function_value( &::SireBase::PageCache::Page::isCached ); + + Page_exposer.def( + "isCached" + , isCached_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::isNull + + typedef bool ( ::SireBase::PageCache::Page::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireBase::PageCache::Page::isNull ); + + Page_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::isResident + + typedef bool ( ::SireBase::PageCache::Page::*isResident_function_type)( ) const; + isResident_function_type isResident_function_value( &::SireBase::PageCache::Page::isResident ); + + Page_exposer.def( + "isResident" + , isResident_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::isValid + + typedef bool ( ::SireBase::PageCache::Page::*isValid_function_type)( ) const; + isValid_function_type isValid_function_value( &::SireBase::PageCache::Page::isValid ); + + Page_exposer.def( + "isValid" + , isValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::nBytes + + typedef int ( ::SireBase::PageCache::Page::*nBytes_function_type)( ) const; + nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Page::nBytes ); + + Page_exposer.def( + "nBytes" + , nBytes_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::operator= + + typedef ::SireBase::PageCache::Page & ( ::SireBase::PageCache::Page::*assign_function_type)( ::SireBase::PageCache::Page const & ) ; + assign_function_type assign_function_value( &::SireBase::PageCache::Page::operator= ); + + Page_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + + } + { //::SireBase::PageCache::Page::parent + + typedef ::SireBase::PageCache ( ::SireBase::PageCache::Page::*parent_function_type)( ) const; + parent_function_type parent_function_value( &::SireBase::PageCache::Page::parent ); + + Page_exposer.def( + "parent" + , parent_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::size + + typedef int ( ::SireBase::PageCache::Page::*size_function_type)( ) const; + size_function_type size_function_value( &::SireBase::PageCache::Page::size ); + + Page_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::toString + + typedef ::QString ( ::SireBase::PageCache::Page::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireBase::PageCache::Page::toString ); + + Page_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireBase::PageCache::Page::typeName ); + + Page_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::what + + typedef char const * ( ::SireBase::PageCache::Page::*what_function_type)( ) const; + what_function_type what_function_value( &::SireBase::PageCache::Page::what ); + + Page_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + + } + Page_exposer.staticmethod( "typeName" ); + Page_exposer.def( "__copy__", &__copy__); + Page_exposer.def( "__deepcopy__", &__copy__); + Page_exposer.def( "clone", &__copy__); + Page_exposer.def( "__str__", &__str__< ::SireBase::PageCache::Page > ); + Page_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Page > ); + Page_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Page > ); + } + PageCache_exposer.def( bp::init< QString const &, bp::optional< int > >(( bp::arg("cache_dir"), bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); + PageCache_exposer.def( bp::init< std::shared_ptr< SireBase::detail::CacheData > >(( bp::arg("data") ), "") ); + PageCache_exposer.def( bp::init< SireBase::PageCache const & >(( bp::arg("other") ), "") ); + { //::SireBase::PageCache::assertValid + + typedef void ( ::SireBase::PageCache::*assertValid_function_type)( ) const; + assertValid_function_type assertValid_function_value( &::SireBase::PageCache::assertValid ); + + PageCache_exposer.def( + "assertValid" + , assertValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::cache + + typedef ::SireBase::PageCache::Handle ( ::SireBase::PageCache::*cache_function_type)( ::QByteArray const & ) ; + cache_function_type cache_function_value( &::SireBase::PageCache::cache ); + + PageCache_exposer.def( + "cache" + , cache_function_value + , ( bp::arg("data") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::cacheDir + + typedef ::QString ( ::SireBase::PageCache::*cacheDir_function_type)( ) const; + cacheDir_function_type cacheDir_function_value( &::SireBase::PageCache::cacheDir ); + + PageCache_exposer.def( + "cacheDir" + , cacheDir_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::isNull + + typedef bool ( ::SireBase::PageCache::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireBase::PageCache::isNull ); + + PageCache_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::isValid + + typedef bool ( ::SireBase::PageCache::*isValid_function_type)( ) const; + isValid_function_type isValid_function_value( &::SireBase::PageCache::isValid ); + + PageCache_exposer.def( + "isValid" + , isValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::nBytes + + typedef int ( ::SireBase::PageCache::*nBytes_function_type)( ) const; + nBytes_function_type nBytes_function_value( &::SireBase::PageCache::nBytes ); + + PageCache_exposer.def( + "nBytes" + , nBytes_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::nPages + + typedef int ( ::SireBase::PageCache::*nPages_function_type)( ) const; + nPages_function_type nPages_function_value( &::SireBase::PageCache::nPages ); + + PageCache_exposer.def( + "nPages" + , nPages_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::operator= + + typedef ::SireBase::PageCache & ( ::SireBase::PageCache::*assign_function_type)( ::SireBase::PageCache const & ) ; + assign_function_type assign_function_value( &::SireBase::PageCache::operator= ); + + PageCache_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + + } + { //::SireBase::PageCache::pageSize + + typedef int ( ::SireBase::PageCache::*pageSize_function_type)( ) const; + pageSize_function_type pageSize_function_value( &::SireBase::PageCache::pageSize ); + + PageCache_exposer.def( + "pageSize" + , pageSize_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::size + + typedef int ( ::SireBase::PageCache::*size_function_type)( ) const; + size_function_type size_function_value( &::SireBase::PageCache::size ); + + PageCache_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::toString + + typedef ::QString ( ::SireBase::PageCache::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireBase::PageCache::toString ); + + PageCache_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireBase::PageCache::typeName ); + + PageCache_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::what + + typedef char const * ( ::SireBase::PageCache::*what_function_type)( ) const; + what_function_type what_function_value( &::SireBase::PageCache::what ); + + PageCache_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + + } + PageCache_exposer.staticmethod( "typeName" ); + PageCache_exposer.def( "__copy__", &__copy__); + PageCache_exposer.def( "__deepcopy__", &__copy__); + PageCache_exposer.def( "clone", &__copy__); + PageCache_exposer.def( "__str__", &pvt_get_name); + PageCache_exposer.def( "__repr__", &pvt_get_name); + } + +} diff --git a/wrapper/Base/PageCache.pypp.hpp b/wrapper/Base/PageCache.pypp.hpp new file mode 100644 index 000000000..7c407910d --- /dev/null +++ b/wrapper/Base/PageCache.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef PageCache_hpp__pyplusplus_wrapper +#define PageCache_hpp__pyplusplus_wrapper + +void register_PageCache_class(); + +#endif//PageCache_hpp__pyplusplus_wrapper diff --git a/wrapper/Base/_Base.main.cpp b/wrapper/Base/_Base.main.cpp index e22cf2b89..da80e35c3 100644 --- a/wrapper/Base/_Base.main.cpp +++ b/wrapper/Base/_Base.main.cpp @@ -89,6 +89,8 @@ #include "PackedArray2D_int_Array.pypp.hpp" +#include "PageCache.pypp.hpp" + #include "Process.pypp.hpp" #include "ProgressBar.pypp.hpp" @@ -236,6 +238,8 @@ BOOST_PYTHON_MODULE(_Base){ register_PackedArray2D_int__class(); + register_PageCache_class(); + register_Process_class(); register_ProgressBar_class(); diff --git a/wrapper/Base/active_headers.h b/wrapper/Base/active_headers.h index 21915c18a..87689fc7e 100644 --- a/wrapper/Base/active_headers.h +++ b/wrapper/Base/active_headers.h @@ -23,6 +23,7 @@ #include "meminfo.h" #include "numberproperty.h" #include "packedarrays.h" +#include "pagecache.h" #include "parallel.h" #include "progressbar.h" #include "properties.h" diff --git a/wrapper/System/active_headers.h b/wrapper/System/active_headers.h index a532f983f..d40b0bbc7 100644 --- a/wrapper/System/active_headers.h +++ b/wrapper/System/active_headers.h @@ -39,6 +39,7 @@ #include "system.h" #include "systemmonitor.h" #include "systemmonitors.h" +#include "systemtrajectory.h" #include "volmapmonitor.h" #endif From da858a3be0cc64d15ee45c38d2565a29c76c42d6 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 14 Apr 2024 17:46:44 +0100 Subject: [PATCH 217/468] Can now compile the cache and access it from Python --- corelib/src/libs/SireBase/pagecache.cpp | 15 + wrapper/Base/PageCache.pypp.cpp | 713 +++++++++--------------- wrapper/Helpers/copy.hpp | 46 ++ 3 files changed, 334 insertions(+), 440 deletions(-) create mode 100644 wrapper/Helpers/copy.hpp diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index df5f227e8..3a6b103c3 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -310,6 +310,11 @@ QString PageCache::Page::toString() const return QString("PageCache::Page"); } +PageCache::Page *PageCache::Page::clone() const +{ + return new PageCache::Page(*this); +} + void PageCache::Page::assertValid() const { if (p == nullptr) @@ -408,6 +413,11 @@ QString PageCache::Handle::toString() const return QString("PageCache::Handle"); } +PageCache::Handle *PageCache::Handle::clone() const +{ + return new PageCache::Handle(*this); +} + void PageCache::Handle::assertValid() const { if (h == nullptr) @@ -515,6 +525,11 @@ QString PageCache::toString() const return QString("PageCache"); } +PageCache *PageCache::clone() const +{ + return new PageCache(*this); +} + void PageCache::assertValid() const { if (d == nullptr) diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index 0eb9850aa..c88ffc1fa 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -17,10 +17,6 @@ namespace bp = boost::python; #include "pagecache.h" -SireBase::PageCache __copy__(const SireBase::PageCache &other){ return SireBase::PageCache(other); } - -const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCache";} - #include "Helpers/release_gil_policy.hpp" #include "SireError/errors.h" @@ -33,8 +29,6 @@ const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCach #include "pagecache.h" -SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ return SireBase::PageCache::Handle(other); } - #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -51,529 +45,368 @@ SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ #include "pagecache.h" -SireBase::PageCache::Page __copy__(const SireBase::PageCache::Page &other){ return SireBase::PageCache::Page(other); } - #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" #include "Helpers/len.hpp" +#include "Helpers/copy.hpp" -void register_PageCache_class(){ +void register_PageCache_class() +{ { //::SireBase::PageCache - typedef bp::class_< SireBase::PageCache > PageCache_exposer_t; - PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< bp::optional< int > >(( bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); - bp::scope PageCache_scope( PageCache_exposer ); + typedef bp::class_ PageCache_exposer_t; + PageCache_exposer_t PageCache_exposer = PageCache_exposer_t("PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init>((bp::arg("page_size") = (int)(32 * 1024 * 1024)), "")); + bp::scope PageCache_scope(PageCache_exposer); { //::SireBase::PageCache::Handle - typedef bp::class_< SireBase::PageCache::Handle > Handle_exposer_t; - Handle_exposer_t Handle_exposer = Handle_exposer_t( "Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init< >("") ); - bp::scope Handle_scope( Handle_exposer ); - Handle_exposer.def( bp::init< std::shared_ptr< SireBase::detail::HandleData > >(( bp::arg("data") ), "") ); - Handle_exposer.def( bp::init< SireBase::PageCache::Handle const & >(( bp::arg("other") ), "") ); + typedef bp::class_ Handle_exposer_t; + Handle_exposer_t Handle_exposer = Handle_exposer_t("Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init<>("")); + bp::scope Handle_scope(Handle_exposer); + Handle_exposer.def(bp::init>((bp::arg("data")), "")); + Handle_exposer.def(bp::init((bp::arg("other")), "")); { //::SireBase::PageCache::Handle::assertValid - - typedef void ( ::SireBase::PageCache::Handle::*assertValid_function_type)( ) const; - assertValid_function_type assertValid_function_value( &::SireBase::PageCache::Handle::assertValid ); - - Handle_exposer.def( - "assertValid" - , assertValid_function_value - , bp::release_gil_policy() - , "" ); - + + typedef void (::SireBase::PageCache::Handle::*assertValid_function_type)() const; + assertValid_function_type assertValid_function_value(&::SireBase::PageCache::Handle::assertValid); + + Handle_exposer.def( + "assertValid", assertValid_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::clear - - typedef void ( ::SireBase::PageCache::Handle::*clear_function_type)( ) ; - clear_function_type clear_function_value( &::SireBase::PageCache::Handle::clear ); - - Handle_exposer.def( - "clear" - , clear_function_value - , bp::release_gil_policy() - , "" ); - + + typedef void (::SireBase::PageCache::Handle::*clear_function_type)(); + clear_function_type clear_function_value(&::SireBase::PageCache::Handle::clear); + + Handle_exposer.def( + "clear", clear_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::fetch - - typedef ::QByteArray ( ::SireBase::PageCache::Handle::*fetch_function_type)( ) const; - fetch_function_type fetch_function_value( &::SireBase::PageCache::Handle::fetch ); - - Handle_exposer.def( - "fetch" - , fetch_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::QByteArray (::SireBase::PageCache::Handle::*fetch_function_type)() const; + fetch_function_type fetch_function_value(&::SireBase::PageCache::Handle::fetch); + + Handle_exposer.def( + "fetch", fetch_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::isNull - - typedef bool ( ::SireBase::PageCache::Handle::*isNull_function_type)( ) const; - isNull_function_type isNull_function_value( &::SireBase::PageCache::Handle::isNull ); - - Handle_exposer.def( - "isNull" - , isNull_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::Handle::*isNull_function_type)() const; + isNull_function_type isNull_function_value(&::SireBase::PageCache::Handle::isNull); + + Handle_exposer.def( + "isNull", isNull_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::isValid - - typedef bool ( ::SireBase::PageCache::Handle::*isValid_function_type)( ) const; - isValid_function_type isValid_function_value( &::SireBase::PageCache::Handle::isValid ); - - Handle_exposer.def( - "isValid" - , isValid_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::Handle::*isValid_function_type)() const; + isValid_function_type isValid_function_value(&::SireBase::PageCache::Handle::isValid); + + Handle_exposer.def( + "isValid", isValid_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::nBytes - - typedef int ( ::SireBase::PageCache::Handle::*nBytes_function_type)( ) const; - nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Handle::nBytes ); - - Handle_exposer.def( - "nBytes" - , nBytes_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::Handle::*nBytes_function_type)() const; + nBytes_function_type nBytes_function_value(&::SireBase::PageCache::Handle::nBytes); + + Handle_exposer.def( + "nBytes", nBytes_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::operator= - - typedef ::SireBase::PageCache::Handle & ( ::SireBase::PageCache::Handle::*assign_function_type)( ::SireBase::PageCache::Handle const & ) ; - assign_function_type assign_function_value( &::SireBase::PageCache::Handle::operator= ); - - Handle_exposer.def( - "assign" - , assign_function_value - , ( bp::arg("other") ) - , bp::return_self< >() - , "" ); - + + typedef ::SireBase::PageCache::Handle &(::SireBase::PageCache::Handle::*assign_function_type)(::SireBase::PageCache::Handle const &); + assign_function_type assign_function_value(&::SireBase::PageCache::Handle::operator=); + + Handle_exposer.def( + "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); } { //::SireBase::PageCache::Handle::page - - typedef ::SireBase::PageCache::Page ( ::SireBase::PageCache::Handle::*page_function_type)( ) const; - page_function_type page_function_value( &::SireBase::PageCache::Handle::page ); - - Handle_exposer.def( - "page" - , page_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::SireBase::PageCache::Page (::SireBase::PageCache::Handle::*page_function_type)() const; + page_function_type page_function_value(&::SireBase::PageCache::Handle::page); + + Handle_exposer.def( + "page", page_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::parent - - typedef ::SireBase::PageCache ( ::SireBase::PageCache::Handle::*parent_function_type)( ) const; - parent_function_type parent_function_value( &::SireBase::PageCache::Handle::parent ); - - Handle_exposer.def( - "parent" - , parent_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::SireBase::PageCache (::SireBase::PageCache::Handle::*parent_function_type)() const; + parent_function_type parent_function_value(&::SireBase::PageCache::Handle::parent); + + Handle_exposer.def( + "parent", parent_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::reset - - typedef void ( ::SireBase::PageCache::Handle::*reset_function_type)( ) ; - reset_function_type reset_function_value( &::SireBase::PageCache::Handle::reset ); - - Handle_exposer.def( - "reset" - , reset_function_value - , bp::release_gil_policy() - , "" ); - + + typedef void (::SireBase::PageCache::Handle::*reset_function_type)(); + reset_function_type reset_function_value(&::SireBase::PageCache::Handle::reset); + + Handle_exposer.def( + "reset", reset_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::size - - typedef int ( ::SireBase::PageCache::Handle::*size_function_type)( ) const; - size_function_type size_function_value( &::SireBase::PageCache::Handle::size ); - - Handle_exposer.def( - "size" - , size_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::Handle::*size_function_type)() const; + size_function_type size_function_value(&::SireBase::PageCache::Handle::size); + + Handle_exposer.def( + "size", size_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::toString - - typedef ::QString ( ::SireBase::PageCache::Handle::*toString_function_type)( ) const; - toString_function_type toString_function_value( &::SireBase::PageCache::Handle::toString ); - - Handle_exposer.def( - "toString" - , toString_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::QString (::SireBase::PageCache::Handle::*toString_function_type)() const; + toString_function_type toString_function_value(&::SireBase::PageCache::Handle::toString); + + Handle_exposer.def( + "toString", toString_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireBase::PageCache::Handle::typeName ); - - Handle_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(*typeName_function_type)(); + typeName_function_type typeName_function_value(&::SireBase::PageCache::Handle::typeName); + + Handle_exposer.def( + "typeName", typeName_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Handle::what - - typedef char const * ( ::SireBase::PageCache::Handle::*what_function_type)( ) const; - what_function_type what_function_value( &::SireBase::PageCache::Handle::what ); - - Handle_exposer.def( - "what" - , what_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(::SireBase::PageCache::Handle::*what_function_type)() const; + what_function_type what_function_value(&::SireBase::PageCache::Handle::what); + + Handle_exposer.def( + "what", what_function_value, bp::release_gil_policy(), ""); } - Handle_exposer.staticmethod( "typeName" ); - Handle_exposer.def( "__copy__", &__copy__); - Handle_exposer.def( "__deepcopy__", &__copy__); - Handle_exposer.def( "clone", &__copy__); - Handle_exposer.def( "__str__", &__str__< ::SireBase::PageCache::Handle > ); - Handle_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Handle > ); - Handle_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Handle > ); + Handle_exposer.staticmethod("typeName"); + Handle_exposer.def("__copy__", &__copy__); + Handle_exposer.def("__deepcopy__", &__copy__); + Handle_exposer.def("clone", &__copy__); + Handle_exposer.def("__str__", &__str__<::SireBase::PageCache::Handle>); + Handle_exposer.def("__repr__", &__str__<::SireBase::PageCache::Handle>); + Handle_exposer.def("__len__", &__len_size<::SireBase::PageCache::Handle>); } { //::SireBase::PageCache::Page - typedef bp::class_< SireBase::PageCache::Page > Page_exposer_t; - Page_exposer_t Page_exposer = Page_exposer_t( "Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init< >("") ); - bp::scope Page_scope( Page_exposer ); - Page_exposer.def( bp::init< std::shared_ptr< SireBase::detail::PageData > >(( bp::arg("data") ), "") ); - Page_exposer.def( bp::init< SireBase::PageCache::Page const & >(( bp::arg("other") ), "") ); + typedef bp::class_ Page_exposer_t; + Page_exposer_t Page_exposer = Page_exposer_t("Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init<>("")); + bp::scope Page_scope(Page_exposer); + Page_exposer.def(bp::init>((bp::arg("data")), "")); + Page_exposer.def(bp::init((bp::arg("other")), "")); { //::SireBase::PageCache::Page::assertValid - - typedef void ( ::SireBase::PageCache::Page::*assertValid_function_type)( ) const; - assertValid_function_type assertValid_function_value( &::SireBase::PageCache::Page::assertValid ); - - Page_exposer.def( - "assertValid" - , assertValid_function_value - , bp::release_gil_policy() - , "" ); - + + typedef void (::SireBase::PageCache::Page::*assertValid_function_type)() const; + assertValid_function_type assertValid_function_value(&::SireBase::PageCache::Page::assertValid); + + Page_exposer.def( + "assertValid", assertValid_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::isCached - - typedef bool ( ::SireBase::PageCache::Page::*isCached_function_type)( ) const; - isCached_function_type isCached_function_value( &::SireBase::PageCache::Page::isCached ); - - Page_exposer.def( - "isCached" - , isCached_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::Page::*isCached_function_type)() const; + isCached_function_type isCached_function_value(&::SireBase::PageCache::Page::isCached); + + Page_exposer.def( + "isCached", isCached_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::isNull - - typedef bool ( ::SireBase::PageCache::Page::*isNull_function_type)( ) const; - isNull_function_type isNull_function_value( &::SireBase::PageCache::Page::isNull ); - - Page_exposer.def( - "isNull" - , isNull_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::Page::*isNull_function_type)() const; + isNull_function_type isNull_function_value(&::SireBase::PageCache::Page::isNull); + + Page_exposer.def( + "isNull", isNull_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::isResident - - typedef bool ( ::SireBase::PageCache::Page::*isResident_function_type)( ) const; - isResident_function_type isResident_function_value( &::SireBase::PageCache::Page::isResident ); - - Page_exposer.def( - "isResident" - , isResident_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::Page::*isResident_function_type)() const; + isResident_function_type isResident_function_value(&::SireBase::PageCache::Page::isResident); + + Page_exposer.def( + "isResident", isResident_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::isValid - - typedef bool ( ::SireBase::PageCache::Page::*isValid_function_type)( ) const; - isValid_function_type isValid_function_value( &::SireBase::PageCache::Page::isValid ); - - Page_exposer.def( - "isValid" - , isValid_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::Page::*isValid_function_type)() const; + isValid_function_type isValid_function_value(&::SireBase::PageCache::Page::isValid); + + Page_exposer.def( + "isValid", isValid_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::nBytes - - typedef int ( ::SireBase::PageCache::Page::*nBytes_function_type)( ) const; - nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Page::nBytes ); - - Page_exposer.def( - "nBytes" - , nBytes_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::Page::*nBytes_function_type)() const; + nBytes_function_type nBytes_function_value(&::SireBase::PageCache::Page::nBytes); + + Page_exposer.def( + "nBytes", nBytes_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::operator= - - typedef ::SireBase::PageCache::Page & ( ::SireBase::PageCache::Page::*assign_function_type)( ::SireBase::PageCache::Page const & ) ; - assign_function_type assign_function_value( &::SireBase::PageCache::Page::operator= ); - - Page_exposer.def( - "assign" - , assign_function_value - , ( bp::arg("other") ) - , bp::return_self< >() - , "" ); - + + typedef ::SireBase::PageCache::Page &(::SireBase::PageCache::Page::*assign_function_type)(::SireBase::PageCache::Page const &); + assign_function_type assign_function_value(&::SireBase::PageCache::Page::operator=); + + Page_exposer.def( + "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); } { //::SireBase::PageCache::Page::parent - - typedef ::SireBase::PageCache ( ::SireBase::PageCache::Page::*parent_function_type)( ) const; - parent_function_type parent_function_value( &::SireBase::PageCache::Page::parent ); - - Page_exposer.def( - "parent" - , parent_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::SireBase::PageCache (::SireBase::PageCache::Page::*parent_function_type)() const; + parent_function_type parent_function_value(&::SireBase::PageCache::Page::parent); + + Page_exposer.def( + "parent", parent_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::size - - typedef int ( ::SireBase::PageCache::Page::*size_function_type)( ) const; - size_function_type size_function_value( &::SireBase::PageCache::Page::size ); - - Page_exposer.def( - "size" - , size_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::Page::*size_function_type)() const; + size_function_type size_function_value(&::SireBase::PageCache::Page::size); + + Page_exposer.def( + "size", size_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::toString - - typedef ::QString ( ::SireBase::PageCache::Page::*toString_function_type)( ) const; - toString_function_type toString_function_value( &::SireBase::PageCache::Page::toString ); - - Page_exposer.def( - "toString" - , toString_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::QString (::SireBase::PageCache::Page::*toString_function_type)() const; + toString_function_type toString_function_value(&::SireBase::PageCache::Page::toString); + + Page_exposer.def( + "toString", toString_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireBase::PageCache::Page::typeName ); - - Page_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(*typeName_function_type)(); + typeName_function_type typeName_function_value(&::SireBase::PageCache::Page::typeName); + + Page_exposer.def( + "typeName", typeName_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::Page::what - - typedef char const * ( ::SireBase::PageCache::Page::*what_function_type)( ) const; - what_function_type what_function_value( &::SireBase::PageCache::Page::what ); - - Page_exposer.def( - "what" - , what_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(::SireBase::PageCache::Page::*what_function_type)() const; + what_function_type what_function_value(&::SireBase::PageCache::Page::what); + + Page_exposer.def( + "what", what_function_value, bp::release_gil_policy(), ""); } - Page_exposer.staticmethod( "typeName" ); - Page_exposer.def( "__copy__", &__copy__); - Page_exposer.def( "__deepcopy__", &__copy__); - Page_exposer.def( "clone", &__copy__); - Page_exposer.def( "__str__", &__str__< ::SireBase::PageCache::Page > ); - Page_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Page > ); - Page_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Page > ); + Page_exposer.staticmethod("typeName"); + Page_exposer.def("__copy__", &__copy__); + Page_exposer.def("__deepcopy__", &__copy__); + Page_exposer.def("clone", &__copy__); + Page_exposer.def("__str__", &__str__<::SireBase::PageCache::Page>); + Page_exposer.def("__repr__", &__str__<::SireBase::PageCache::Page>); + Page_exposer.def("__len__", &__len_size<::SireBase::PageCache::Page>); } - PageCache_exposer.def( bp::init< QString const &, bp::optional< int > >(( bp::arg("cache_dir"), bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); - PageCache_exposer.def( bp::init< std::shared_ptr< SireBase::detail::CacheData > >(( bp::arg("data") ), "") ); - PageCache_exposer.def( bp::init< SireBase::PageCache const & >(( bp::arg("other") ), "") ); + PageCache_exposer.def(bp::init>((bp::arg("cache_dir"), bp::arg("page_size") = (int)(32 * 1024 * 1024)), "")); + PageCache_exposer.def(bp::init>((bp::arg("data")), "")); + PageCache_exposer.def(bp::init((bp::arg("other")), "")); { //::SireBase::PageCache::assertValid - - typedef void ( ::SireBase::PageCache::*assertValid_function_type)( ) const; - assertValid_function_type assertValid_function_value( &::SireBase::PageCache::assertValid ); - - PageCache_exposer.def( - "assertValid" - , assertValid_function_value - , bp::release_gil_policy() - , "" ); - + + typedef void (::SireBase::PageCache::*assertValid_function_type)() const; + assertValid_function_type assertValid_function_value(&::SireBase::PageCache::assertValid); + + PageCache_exposer.def( + "assertValid", assertValid_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::cache - - typedef ::SireBase::PageCache::Handle ( ::SireBase::PageCache::*cache_function_type)( ::QByteArray const & ) ; - cache_function_type cache_function_value( &::SireBase::PageCache::cache ); - - PageCache_exposer.def( - "cache" - , cache_function_value - , ( bp::arg("data") ) - , bp::release_gil_policy() - , "" ); - + + typedef ::SireBase::PageCache::Handle (::SireBase::PageCache::*cache_function_type)(::QByteArray const &); + cache_function_type cache_function_value(&::SireBase::PageCache::cache); + + PageCache_exposer.def( + "cache", cache_function_value, (bp::arg("data")), bp::release_gil_policy(), ""); } { //::SireBase::PageCache::cacheDir - - typedef ::QString ( ::SireBase::PageCache::*cacheDir_function_type)( ) const; - cacheDir_function_type cacheDir_function_value( &::SireBase::PageCache::cacheDir ); - - PageCache_exposer.def( - "cacheDir" - , cacheDir_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::QString (::SireBase::PageCache::*cacheDir_function_type)() const; + cacheDir_function_type cacheDir_function_value(&::SireBase::PageCache::cacheDir); + + PageCache_exposer.def( + "cacheDir", cacheDir_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::isNull - - typedef bool ( ::SireBase::PageCache::*isNull_function_type)( ) const; - isNull_function_type isNull_function_value( &::SireBase::PageCache::isNull ); - - PageCache_exposer.def( - "isNull" - , isNull_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::*isNull_function_type)() const; + isNull_function_type isNull_function_value(&::SireBase::PageCache::isNull); + + PageCache_exposer.def( + "isNull", isNull_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::isValid - - typedef bool ( ::SireBase::PageCache::*isValid_function_type)( ) const; - isValid_function_type isValid_function_value( &::SireBase::PageCache::isValid ); - - PageCache_exposer.def( - "isValid" - , isValid_function_value - , bp::release_gil_policy() - , "" ); - + + typedef bool (::SireBase::PageCache::*isValid_function_type)() const; + isValid_function_type isValid_function_value(&::SireBase::PageCache::isValid); + + PageCache_exposer.def( + "isValid", isValid_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::nBytes - - typedef int ( ::SireBase::PageCache::*nBytes_function_type)( ) const; - nBytes_function_type nBytes_function_value( &::SireBase::PageCache::nBytes ); - - PageCache_exposer.def( - "nBytes" - , nBytes_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::*nBytes_function_type)() const; + nBytes_function_type nBytes_function_value(&::SireBase::PageCache::nBytes); + + PageCache_exposer.def( + "nBytes", nBytes_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::nPages - - typedef int ( ::SireBase::PageCache::*nPages_function_type)( ) const; - nPages_function_type nPages_function_value( &::SireBase::PageCache::nPages ); - - PageCache_exposer.def( - "nPages" - , nPages_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::*nPages_function_type)() const; + nPages_function_type nPages_function_value(&::SireBase::PageCache::nPages); + + PageCache_exposer.def( + "nPages", nPages_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::operator= - - typedef ::SireBase::PageCache & ( ::SireBase::PageCache::*assign_function_type)( ::SireBase::PageCache const & ) ; - assign_function_type assign_function_value( &::SireBase::PageCache::operator= ); - - PageCache_exposer.def( - "assign" - , assign_function_value - , ( bp::arg("other") ) - , bp::return_self< >() - , "" ); - + + typedef ::SireBase::PageCache &(::SireBase::PageCache::*assign_function_type)(::SireBase::PageCache const &); + assign_function_type assign_function_value(&::SireBase::PageCache::operator=); + + PageCache_exposer.def( + "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); } { //::SireBase::PageCache::pageSize - - typedef int ( ::SireBase::PageCache::*pageSize_function_type)( ) const; - pageSize_function_type pageSize_function_value( &::SireBase::PageCache::pageSize ); - - PageCache_exposer.def( - "pageSize" - , pageSize_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::*pageSize_function_type)() const; + pageSize_function_type pageSize_function_value(&::SireBase::PageCache::pageSize); + + PageCache_exposer.def( + "pageSize", pageSize_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::size - - typedef int ( ::SireBase::PageCache::*size_function_type)( ) const; - size_function_type size_function_value( &::SireBase::PageCache::size ); - - PageCache_exposer.def( - "size" - , size_function_value - , bp::release_gil_policy() - , "" ); - + + typedef int (::SireBase::PageCache::*size_function_type)() const; + size_function_type size_function_value(&::SireBase::PageCache::size); + + PageCache_exposer.def( + "size", size_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::toString - - typedef ::QString ( ::SireBase::PageCache::*toString_function_type)( ) const; - toString_function_type toString_function_value( &::SireBase::PageCache::toString ); - - PageCache_exposer.def( - "toString" - , toString_function_value - , bp::release_gil_policy() - , "" ); - + + typedef ::QString (::SireBase::PageCache::*toString_function_type)() const; + toString_function_type toString_function_value(&::SireBase::PageCache::toString); + + PageCache_exposer.def( + "toString", toString_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireBase::PageCache::typeName ); - - PageCache_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(*typeName_function_type)(); + typeName_function_type typeName_function_value(&::SireBase::PageCache::typeName); + + PageCache_exposer.def( + "typeName", typeName_function_value, bp::release_gil_policy(), ""); } { //::SireBase::PageCache::what - - typedef char const * ( ::SireBase::PageCache::*what_function_type)( ) const; - what_function_type what_function_value( &::SireBase::PageCache::what ); - - PageCache_exposer.def( - "what" - , what_function_value - , bp::release_gil_policy() - , "" ); - + + typedef char const *(::SireBase::PageCache::*what_function_type)() const; + what_function_type what_function_value(&::SireBase::PageCache::what); + + PageCache_exposer.def( + "what", what_function_value, bp::release_gil_policy(), ""); } - PageCache_exposer.staticmethod( "typeName" ); - PageCache_exposer.def( "__copy__", &__copy__); - PageCache_exposer.def( "__deepcopy__", &__copy__); - PageCache_exposer.def( "clone", &__copy__); - PageCache_exposer.def( "__str__", &pvt_get_name); - PageCache_exposer.def( "__repr__", &pvt_get_name); + PageCache_exposer.staticmethod("typeName"); + PageCache_exposer.def("__copy__", &__copy__); + PageCache_exposer.def("__deepcopy__", &__copy__); + PageCache_exposer.def("clone", &__copy__); + PageCache_exposer.def("__str__", &__str__<::SireBase::PageCache>); + PageCache_exposer.def("__repr__", &__str__<::SireBase::PageCache>); } - } diff --git a/wrapper/Helpers/copy.hpp b/wrapper/Helpers/copy.hpp new file mode 100644 index 000000000..88d967815 --- /dev/null +++ b/wrapper/Helpers/copy.hpp @@ -0,0 +1,46 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef PYWRAP_SIREPY_COPY_HPP +#define PYWRAP_SIREPY_COPY_HPP + +#include +#include + +#include "sireglobal.h" + +SIRE_BEGIN_HEADER + +template +T __copy__(const T &obj) +{ + return T(obj); +} + +SIRE_END_HEADER + +#endif From c7f7b9ebe496d005d6b79a1d96f861f8b44fb7dc Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 14 Apr 2024 18:26:36 +0100 Subject: [PATCH 218/468] Got the machinery in place to cache and fetch from Python --- src/sire/base/CMakeLists.txt | 1 + src/sire/base/__init__.py | 11 +++++++- src/sire/base/_pagecache.py | 49 ++++++++++++++++++++++++++++++++++++ 3 files changed, 60 insertions(+), 1 deletion(-) create mode 100644 src/sire/base/_pagecache.py diff --git a/src/sire/base/CMakeLists.txt b/src/sire/base/CMakeLists.txt index ba207178b..1a59adf5b 100644 --- a/src/sire/base/CMakeLists.txt +++ b/src/sire/base/CMakeLists.txt @@ -7,6 +7,7 @@ # Add your script to this list set ( SCRIPTS __init__.py + _pagecache.py _progressbar.py ) diff --git a/src/sire/base/__init__.py b/src/sire/base/__init__.py index 07cf795e5..ccc91ab86 100644 --- a/src/sire/base/__init__.py +++ b/src/sire/base/__init__.py @@ -1,4 +1,11 @@ -__all__ = ["create_map", "wrap", "PropertyMap", "ProgressBar", "Properties"] +__all__ = [ + "create_map", + "wrap", + "PageCache", + "PropertyMap", + "ProgressBar", + "Properties", +] from ..legacy import Base as _Base @@ -8,6 +15,8 @@ from ._progressbar import ProgressBar +from ._pagecache import PageCache + _use_new_api(is_base=True) wrap = _Base.wrap diff --git a/src/sire/base/_pagecache.py b/src/sire/base/_pagecache.py new file mode 100644 index 000000000..a4337bfc8 --- /dev/null +++ b/src/sire/base/_pagecache.py @@ -0,0 +1,49 @@ +__all__ = ["PageCache"] + +from ..legacy.Base import PageCache + + +def __cache__(obj, data): + """ + Add the passed object onto the cache. This will convert the object + into a binary form (pickled, then hex-encoded) and it will store + it in the cache. This returns a handle to the object in the cache, + which can be used to restore it. + """ + from ..legacy.Qt import QByteArray + from pickle import dumps + + data = dumps(data) + + # now convert this to a QByteArray + b = QByteArray(data.hex()) + return obj.__orig__cache__(b) + + +def __fetch__(obj): + """ + Fetch the object from the cache and return it + """ + from ..legacy.Qt import QByteArray + from pickle import loads + + data = obj.__orig__fetch__() + + data = QByteArray.fromHex(obj) + return loads(data) + + +if not hasattr(PageCache, "__orig__cache__"): + PageCache.__orig__cache__ = PageCache.cache + PageCache.cache = __cache__ + + if hasattr(PageCache, "handle"): + PageCache.Handle = PageCache.handle + delattr(PageCache, "handle") + + if hasattr(PageCache, "page"): + PageCache.Page = PageCache.page + delattr(PageCache, "page") + + PageCache.Handle.__orig__fetch__ = PageCache.Handle.fetch + PageCache.Handle.fetch = __fetch__ From 7759a6eb9f1f812ee97b6c28a4e0a1e2ebc23071 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 14 Apr 2024 19:32:21 +0100 Subject: [PATCH 219/468] Have a background thread that provides a workqueue so that items can be quickly put into the cache, without waiting for any processing --- corelib/src/libs/SireBase/pagecache.cpp | 160 ++++++++++++++++++++++-- corelib/src/libs/SireBase/pagecache.h | 2 + src/sire/base/_pagecache.py | 6 +- 3 files changed, 159 insertions(+), 9 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 3a6b103c3..2cba43776 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -30,7 +30,12 @@ #include "SireError/errors.h" +#include "SireBase/parallel.h" + #include +#include +#include +#include #include @@ -38,7 +43,7 @@ namespace SireBase { namespace detail { - class CacheData : public boost::noncopyable + class CacheData : public QThread { public: CacheData(QString cachedir, int page_size); @@ -53,7 +58,15 @@ namespace SireBase int nPages() const; int nBytes() const; + protected: + void run(); + private: + void enqueue(const PageCache::Handle &handle); + + QMutex mutex; + QQueue queue; + QString cache_dir; int page_size; }; @@ -86,7 +99,14 @@ namespace SireBase class HandleData : public boost::noncopyable { public: - HandleData(); + enum State + { + EMPTY = 0, + PRE_CACHE = 1, + POST_CACHE = 2 + }; + + HandleData(const QByteArray &data); ~HandleData(); QByteArray fetch() const; @@ -104,6 +124,16 @@ namespace SireBase /** The page containing this data */ PageCache::Page p; + /** Mutex to lock access to this data */ + QMutex mutex; + + /** The data being cached - this is stored here until it is + property added to the cache */ + QByteArray d; + + /** The current state of the handle */ + State state; + /** The offset of this data within the page */ int offset; @@ -138,11 +168,15 @@ CacheData::CacheData(QString c, int p) CacheData::~CacheData() { + this->requestInterruption(); + this->wait(); } PageCache::Handle CacheData::cache(const QByteArray &data) { - return PageCache::Handle(); + auto handle = PageCache::Handle(std::make_shared(data)); + this->enqueue(handle); + return handle; } QString CacheData::cacheDir() const @@ -165,6 +199,82 @@ int CacheData::nBytes() const return 0; } +void CacheData::enqueue(const PageCache::Handle &handle) +{ + QMutexLocker lkr(&mutex); + queue.enqueue(handle); + + if (not this->isRunning()) + { + this->start(); + } +} + +void CacheData::run() +{ + while (true) + { + if (this->isInterruptionRequested()) + { + // stop what we are doing + return; + } + + PageCache::Handle handle; + bool have_item = false; + + // pull an item off the queue + { + QMutexLocker lkr(&mutex); + + if (this->isInterruptionRequested()) + { + // stop what we are doing + return; + } + + if (not queue.isEmpty()) + { + handle = queue.dequeue(); + have_item = true; + } + } + + if (have_item) + { + qDebug() << "CACHE THE ITEM"; + } + + if (this->isInterruptionRequested()) + { + // stop what we are doing + return; + } + + bool is_empty = true; + + if (have_item) + { + // check to see if there is anything else to process + QMutexLocker lkr(&mutex); + is_empty = queue.isEmpty(); + lkr.unlock(); + } + + if (is_empty) + { + if (this->isInterruptionRequested()) + { + // stop what we are doing + return; + } + + // sleep for a bit + this->msleep(100); + } + } +} + /////// /////// Implementation of detail::PageData /////// @@ -227,9 +337,17 @@ PageCache PageData::parent() const /////// Implementation of detail::HandleData /////// -HandleData::HandleData() - : offset(0), nbytes(0) +HandleData::HandleData(const QByteArray &data) + : d(data), offset(0), nbytes(data.size()) { + if (nbytes == 0) + { + state = EMPTY; + } + else + { + state = PRE_CACHE; + } } HandleData::~HandleData() @@ -238,6 +356,15 @@ HandleData::~HandleData() QByteArray HandleData::fetch() const { + QMutexLocker lkr(const_cast(&mutex)); + + if (state == EMPTY or state == PRE_CACHE) + { + return d; + } + + lkr.unlock(); + return p.fetch(offset, nbytes); } @@ -307,7 +434,9 @@ const char *PageCache::Page::what() const QString PageCache::Page::toString() const { - return QString("PageCache::Page"); + return QString("PageCache::Page(%1 KB used from %2 KB)") + .arg(this->nBytes() / 1024.0) + .arg(this->maxBytes() / 1024.0); } PageCache::Page *PageCache::Page::clone() const @@ -357,6 +486,12 @@ int PageCache::Page::size() const return this->nBytes(); } +int PageCache::Page::maxBytes() const +{ + assertValid(); + return p->maxBytes(); +} + PageCache PageCache::Page::parent() const { assertValid(); @@ -410,7 +545,16 @@ const char *PageCache::Handle::what() const QString PageCache::Handle::toString() const { - return QString("PageCache::Handle"); + const int nbytes = this->nBytes(); + + if (nbytes == 0) + { + return QString("PageCache::Handle::empty"); + } + else + { + return QString("PageCache::Handle(size = %1 KB)").arg(nbytes / 1024.0); + } } PageCache::Handle *PageCache::Handle::clone() const @@ -522,7 +666,7 @@ const char *PageCache::what() const QString PageCache::toString() const { - return QString("PageCache"); + return QString("PageCache(size = %1 KB)").arg(this->nBytes() / 1024.0); } PageCache *PageCache::clone() const diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index b8d433e0f..f57b30dbd 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -123,6 +123,8 @@ namespace SireBase int nBytes() const; int size() const; + int maxBytes() const; + PageCache parent() const; protected: diff --git a/src/sire/base/_pagecache.py b/src/sire/base/_pagecache.py index a4337bfc8..0f8212abb 100644 --- a/src/sire/base/_pagecache.py +++ b/src/sire/base/_pagecache.py @@ -29,7 +29,11 @@ def __fetch__(obj): data = obj.__orig__fetch__() - data = QByteArray.fromHex(obj) + if hasattr(data, "constData"): + data = bytes.fromhex(data.constData()) + else: + data = bytes.fromhex(data.const_data()) + return loads(data) From 3f141c69e4cf2d1463312dfd74b5e7ca2ec1074c Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 14 Apr 2024 19:42:23 +0100 Subject: [PATCH 220/468] Removed race condition when the thread exits. Added code that stops the cache thread if there is nothing to cache --- corelib/src/libs/SireBase/pagecache.cpp | 26 ++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 2cba43776..6d65c6d81 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -69,6 +69,8 @@ namespace SireBase QString cache_dir; int page_size; + + bool exiting; }; class PageData : public boost::noncopyable @@ -151,7 +153,7 @@ using namespace SireBase::detail; /////// CacheData::CacheData(QString c, int p) - : cache_dir(c), page_size(p) + : cache_dir(c), page_size(p), exiting(false) { if (c.simplified().isEmpty()) { @@ -202,6 +204,16 @@ int CacheData::nBytes() const void CacheData::enqueue(const PageCache::Handle &handle) { QMutexLocker lkr(&mutex); + + if (this->exiting) + { + // this is the race condition where the current thread loop + // is in the process of exiting, but we need to wait for that + // to complete + this->wait(); + this->exiting = false; + } + queue.enqueue(handle); if (not this->isRunning()) @@ -212,6 +224,8 @@ void CacheData::enqueue(const PageCache::Handle &handle) void CacheData::run() { + int empty_count = 0; + while (true) { if (this->isInterruptionRequested()) @@ -243,6 +257,7 @@ void CacheData::run() if (have_item) { qDebug() << "CACHE THE ITEM"; + empty_count = 0; } if (this->isInterruptionRequested()) @@ -258,6 +273,15 @@ void CacheData::run() // check to see if there is anything else to process QMutexLocker lkr(&mutex); is_empty = queue.isEmpty(); + empty_count += 1; + + if (empty_count > 10) + { + // we have been idle for a while, so we can stop + this->exiting = true; + return; + } + lkr.unlock(); } From 0e80da046e01175e8322c3b09b1eb39c93dc7c25 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 14 Apr 2024 22:37:20 +0100 Subject: [PATCH 221/468] Data now moves from the handle to the page --- corelib/src/libs/SireBase/pagecache.cpp | 156 ++++++++++++++++++++---- 1 file changed, 134 insertions(+), 22 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 6d65c6d81..e41a58b6f 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -58,14 +58,20 @@ namespace SireBase int nPages() const; int nBytes() const; + std::weak_ptr self; + protected: void run(); private: - void enqueue(const PageCache::Handle &handle); + void enqueue(const std::shared_ptr &handle); QMutex mutex; - QQueue queue; + QQueue> queue; + + std::weak_ptr current_page; + + QList> pages; QString cache_dir; int page_size; @@ -76,7 +82,7 @@ namespace SireBase class PageData : public boost::noncopyable { public: - PageData(int max_size); + PageData(int max_size, const std::shared_ptr &cache); ~PageData(); int maxBytes() const; @@ -86,16 +92,19 @@ namespace SireBase bool isResident() const; bool isCached() const; - PageCache::Handle cache(const QByteArray &data); + int cache(const QByteArray &data); QByteArray fetch(int offset, int n_bytes) const; PageCache parent() const; private: - std::weak_ptr c; + std::shared_ptr c; + int max_bytes; int nbytes; + + char *d; }; class HandleData : public boost::noncopyable @@ -104,8 +113,8 @@ namespace SireBase enum State { EMPTY = 0, - PRE_CACHE = 1, - POST_CACHE = 2 + DATA_IN_HANDLE = 1, + DATA_ON_PAGE = 2 }; HandleData(const QByteArray &data); @@ -122,6 +131,8 @@ namespace SireBase PageCache parent() const; + void setPage(const PageCache::Page &page, int offset); + private: /** The page containing this data */ PageCache::Page p; @@ -176,9 +187,9 @@ CacheData::~CacheData() PageCache::Handle CacheData::cache(const QByteArray &data) { - auto handle = PageCache::Handle(std::make_shared(data)); + auto handle = std::make_shared(data); this->enqueue(handle); - return handle; + return PageCache::Handle(handle); } QString CacheData::cacheDir() const @@ -201,8 +212,13 @@ int CacheData::nBytes() const return 0; } -void CacheData::enqueue(const PageCache::Handle &handle) +void CacheData::enqueue(const std::shared_ptr &handle) { + if (handle.get() == nullptr) + { + return; + } + QMutexLocker lkr(&mutex); if (this->exiting) @@ -234,7 +250,7 @@ void CacheData::run() return; } - PageCache::Handle handle; + std::shared_ptr handle; bool have_item = false; // pull an item off the queue @@ -247,16 +263,64 @@ void CacheData::run() return; } - if (not queue.isEmpty()) + while (not queue.isEmpty()) { handle = queue.dequeue(); - have_item = true; + + if (handle.get() != nullptr) + { + have_item = true; + break; + } } } if (have_item) { - qDebug() << "CACHE THE ITEM"; + // get the data + QByteArray data = handle->fetch(); + + const int n_bytes = data.size(); + + if (n_bytes >= page_size) + { + // this is bigger than a page, so needs to have its + // own page! + auto page = std::make_shared(n_bytes, this->self.lock()); + this->pages.append(page); + auto offset = page->cache(data); + handle->setPage(PageCache::Page(page), offset); + } + else if (n_bytes != 0) + { + // make sure we have a current page... + auto current = current_page.lock(); + + if (current.get() == nullptr) + { + current = std::make_shared(page_size, this->self.lock()); + current_page = current; + } + + // is there space left on the current page + if (current->bytesRemaining() >= n_bytes) + { + auto offset = current->cache(data); + handle->setPage(PageCache::Page(current), offset); + } + else + { + // add the current page to the list of old pages + this->pages.append(current_page); + + // we need to create a new page + current = std::make_shared(page_size, this->self.lock()); + current_page = current; + auto offset = current->cache(data); + handle->setPage(PageCache::Page(current), offset); + } + } + empty_count = 0; } @@ -303,18 +367,26 @@ void CacheData::run() /////// Implementation of detail::PageData /////// -PageData::PageData(int max_size) - : max_bytes(max_size), nbytes(0) +PageData::PageData(int max_size, const std::shared_ptr &cache) + : c(cache), max_bytes(max_size), nbytes(0), d(0) { if (max_bytes < 1024) { throw SireError::invalid_arg( QObject::tr("Page size must be greater than 1024!"), CODELOC); } + else if (max_bytes > 128 * 1024 * 1024) + { + throw SireError::invalid_arg( + QObject::tr("Page size must be less than 128 MB!"), CODELOC); + } + + d = new char[max_bytes]; } PageData::~PageData() { + delete[] d; } int PageData::maxBytes() const @@ -342,19 +414,36 @@ bool PageData::isCached() const return false; } -PageCache::Handle PageData::cache(const QByteArray &data) +int PageData::cache(const QByteArray &data) { - return PageCache::Handle(); + if (data.size() > this->bytesRemaining()) + { + throw SireError::invalid_arg( + QObject::tr("Data is too large to fit on this page!"), CODELOC); + } + + std::memcpy(d + nbytes, data.constData(), data.size()); + + int offset = nbytes; + nbytes += data.size(); + + return offset; } QByteArray PageData::fetch(int offset, int n_bytes) const { - return QByteArray(); + if (offset + n_bytes > nbytes) + { + throw SireError::invalid_arg( + QObject::tr("Data is too large to fit on this page!"), CODELOC); + } + + return QByteArray(d + offset, n_bytes); } PageCache PageData::parent() const { - return PageCache(c.lock()); + return PageCache(c); } /////// @@ -370,7 +459,7 @@ HandleData::HandleData(const QByteArray &data) } else { - state = PRE_CACHE; + state = DATA_IN_HANDLE; } } @@ -382,7 +471,7 @@ QByteArray HandleData::fetch() const { QMutexLocker lkr(const_cast(&mutex)); - if (state == EMPTY or state == PRE_CACHE) + if (state == EMPTY or state == DATA_IN_HANDLE) { return d; } @@ -392,6 +481,27 @@ QByteArray HandleData::fetch() const return p.fetch(offset, nbytes); } +void HandleData::setPage(const PageCache::Page &page, int off) +{ + QMutexLocker lkr(&mutex); + + if (state == EMPTY) + { + throw SireError::invalid_state( + QObject::tr("Handle is empty"), CODELOC); + } + else if (state == DATA_ON_PAGE) + { + throw SireError::invalid_state( + QObject::tr("Handle is already on the page!"), CODELOC); + } + + p = page; + offset = off; + state = DATA_ON_PAGE; + d = QByteArray(); +} + PageCache::Page HandleData::page() const { return p; @@ -651,11 +761,13 @@ void PageCache::Handle::reset() PageCache::PageCache(int page_size) : d(new CacheData(QString("."), page_size)) { + d->self = d; } PageCache::PageCache(const QString &cachedir, int page_size) : d(new CacheData(cachedir, page_size)) { + d->self = d; } PageCache::PageCache(std::shared_ptr data) From d9eb744c7baf5e4da050b61b027202831dbe0cd6 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 15 Apr 2024 20:10:50 +0100 Subject: [PATCH 222/468] WIP - continuing to work on saving the frame. Significant speed up when directly copying the frame to a memory buffer, rather than using serialisation. Also now push the frame data directly to the cache, which is shared between all instances of a SystemTrajectory Looks stable - just a rare crash at exit during cleanup when a thread waits for itself... --- corelib/src/libs/SireBase/pagecache.cpp | 10 + corelib/src/libs/SireBase/pagecache.h | 1 + corelib/src/libs/SireMol/trajectory.cpp | 99 +++ corelib/src/libs/SireMol/trajectory.h | 3 + .../src/libs/SireSystem/systemtrajectory.cpp | 69 +- wrapper/AutoGenerate/create_wrappers.py | 14 +- wrapper/Base/Array2D_double_.pypp.cpp | 8 +- wrapper/Base/BooleanProperty.pypp.cpp | 8 +- wrapper/Base/CPUID.pypp.cpp | 8 +- wrapper/Base/ChunkedVector_double_.pypp.cpp | 8 +- wrapper/Base/DoubleArrayProperty.pypp.cpp | 8 +- wrapper/Base/FlopsMark.pypp.cpp | 8 +- .../Base/GeneralUnitArrayProperty.pypp.cpp | 8 +- wrapper/Base/GeneralUnitProperty.pypp.cpp | 8 +- wrapper/Base/Incremint.pypp.cpp | 8 +- wrapper/Base/IntegerArrayProperty.pypp.cpp | 8 +- wrapper/Base/LazyEvaluator.pypp.cpp | 8 +- wrapper/Base/LengthProperty.pypp.cpp | 8 +- wrapper/Base/LinkToProperty.pypp.cpp | 8 +- wrapper/Base/LowerCaseString.pypp.cpp | 8 +- wrapper/Base/MajorMinorVersion.pypp.cpp | 8 +- wrapper/Base/MemInfo.pypp.cpp | 8 +- wrapper/Base/NoMangling.pypp.cpp | 8 +- wrapper/Base/NullProperty.pypp.cpp | 8 +- wrapper/Base/NumberProperty.pypp.cpp | 8 +- ...PackedArray2D_DoubleArrayProperty.pypp.cpp | 8 +- ...Array2D_DoubleArrayProperty_Array.pypp.cpp | 8 +- ...ackedArray2D_IntegerArrayProperty.pypp.cpp | 8 +- ...rray2D_IntegerArrayProperty_Array.pypp.cpp | 8 +- .../Base/PackedArray2D_PropertyList.pypp.cpp | 8 +- .../PackedArray2D_PropertyList_Array.pypp.cpp | 8 +- wrapper/Base/PackedArray2D_QString_.pypp.cpp | 8 +- .../Base/PackedArray2D_QString_Array.pypp.cpp | 8 +- wrapper/Base/PackedArray2D_QVariant_.pypp.cpp | 8 +- .../PackedArray2D_QVariant_Array.pypp.cpp | 8 +- ...PackedArray2D_StringArrayProperty.pypp.cpp | 8 +- ...Array2D_StringArrayProperty_Array.pypp.cpp | 8 +- wrapper/Base/PackedArray2D_double_.pypp.cpp | 8 +- .../Base/PackedArray2D_double_Array.pypp.cpp | 8 +- wrapper/Base/PackedArray2D_int_.pypp.cpp | 8 +- wrapper/Base/PackedArray2D_int_Array.pypp.cpp | 8 +- wrapper/Base/PageCache.pypp.cpp | 744 +++++++++++------- wrapper/Base/Process.pypp.cpp | 8 +- wrapper/Base/ProgressBar.pypp.cpp | 8 +- wrapper/Base/Properties.pypp.cpp | 8 +- wrapper/Base/PropertyList.pypp.cpp | 8 +- wrapper/Base/PropertyMap.pypp.cpp | 8 +- wrapper/Base/PropertyName.pypp.cpp | 8 +- wrapper/Base/SimpleRange.pypp.cpp | 8 +- wrapper/Base/StringArrayProperty.pypp.cpp | 8 +- wrapper/Base/StringProperty.pypp.cpp | 8 +- wrapper/Base/TimeProperty.pypp.cpp | 8 +- wrapper/Base/TrigArray2D_double_.pypp.cpp | 8 +- wrapper/Base/TrimString.pypp.cpp | 8 +- wrapper/Base/UnitTest.pypp.cpp | 8 +- wrapper/Base/UpperCaseString.pypp.cpp | 8 +- wrapper/Base/VariantProperty.pypp.cpp | 8 +- wrapper/Base/Version.pypp.cpp | 8 +- 58 files changed, 909 insertions(+), 439 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index e41a58b6f..c5a5a6c04 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -500,6 +500,11 @@ void HandleData::setPage(const PageCache::Page &page, int off) offset = off; state = DATA_ON_PAGE; d = QByteArray(); + + lkr.unlock(); + qDebug() << "DATA MOVED TO PAGE"; + + qDebug() << p.toString(); } PageCache::Page HandleData::page() const @@ -863,3 +868,8 @@ PageCache::Handle PageCache::cache(const QByteArray &data) assertValid(); return Handle(d->cache(data)); } + +PageCache::Handle PageCache::store(const QByteArray &data) +{ + return this->cache(data); +} diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index f57b30dbd..13058f52d 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -180,6 +180,7 @@ namespace SireBase }; Handle cache(const QByteArray &data); + Handle store(const QByteArray &data); private: std::shared_ptr d; diff --git a/corelib/src/libs/SireMol/trajectory.cpp b/corelib/src/libs/SireMol/trajectory.cpp index b905ff047..3755fc280 100644 --- a/corelib/src/libs/SireMol/trajectory.cpp +++ b/corelib/src/libs/SireMol/trajectory.cpp @@ -1352,6 +1352,105 @@ bool Frame::operator!=(const Frame &other) const return not operator==(other); } +QByteArray Frame::toByteArray() const +{ + // calculate the size we need... + int nbytes = 0; + + // magic and version + nbytes += 2 * sizeof(quint32); + + // coordinates + nbytes += sizeof(quint32); + nbytes += coords.count() * sizeof(Vector); + + // velocities + nbytes += sizeof(quint32); + nbytes += vels.count() * sizeof(Velocity3D); + + // forces + nbytes += sizeof(quint32); + nbytes += frcs.count() * sizeof(Force3D); + + // append the space, time and properties + QByteArray extra; + QDataStream ds(&extra, QIODevice::WriteOnly); + + ds << spc << t.to(picosecond) << props; + + nbytes += sizeof(quint32); + nbytes += extra.count(); + + QByteArray data("\0", nbytes); + + auto data_ptr = data.data(); + + // magic and version + quint32 val = r_frame.magicID(); + std::memcpy(data_ptr, &val, sizeof(quint32)); + data_ptr += sizeof(quint32); + + val = 1; + std::memcpy(data_ptr, &val, sizeof(quint32)); + data_ptr += sizeof(quint32); + + val = coords.count(); + std::memcpy(data_ptr, &val, sizeof(quint32)); + data_ptr += sizeof(quint32); + + if (val != 0) + { + std::memcpy(data_ptr, coords.constData(), val * sizeof(Vector)); + data_ptr += val * sizeof(Vector); + } + + val = vels.count(); + std::memcpy(data_ptr, &val, sizeof(quint32)); + data_ptr += sizeof(quint32); + + if (val != 0) + { + std::memcpy(data_ptr, vels.constData(), val * sizeof(Velocity3D)); + data_ptr += val * sizeof(Velocity3D); + } + + val = frcs.count(); + std::memcpy(data_ptr, &val, sizeof(quint32)); + data_ptr += sizeof(quint32); + + if (val != 0) + { + std::memcpy(data_ptr, frcs.constData(), val * sizeof(Force3D)); + data_ptr += val * sizeof(Force3D); + } + + val = extra.count(); + std::memcpy(data_ptr, &val, sizeof(quint32)); + data_ptr += sizeof(quint32); + + if (val != 0) + { + std::memcpy(data_ptr, extra.constData(), val); + data_ptr += val; + } + + if (data_ptr - data.constData() != data.count()) + { + throw SireError::program_bug(QObject::tr( + "Memory corruption? %1 versus %2") + .arg(data_ptr - data.constData()) + .arg(data.count()), + CODELOC); + } + + return data; +} + +Frame Frame::fromByteArray(const QByteArray &data) +{ + return Frame(); +} + const char *Frame::typeName() { return QMetaType::typeName(qMetaTypeId()); diff --git a/corelib/src/libs/SireMol/trajectory.h b/corelib/src/libs/SireMol/trajectory.h index 22ff7823a..848fc761e 100644 --- a/corelib/src/libs/SireMol/trajectory.h +++ b/corelib/src/libs/SireMol/trajectory.h @@ -124,6 +124,9 @@ namespace SireMol QString toString() const; + QByteArray toByteArray() const; + static Frame fromByteArray(const QByteArray &data); + bool isEmpty() const; bool hasCoordinates() const; diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index a2e93057c..0621dac70 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -32,12 +32,15 @@ #include "SireBase/lazyevaluator.h" #include "SireBase/parallel.h" +#include "SireBase/pagecache.h" #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" #include +#include + using namespace SireSystem; using namespace SireMol; using namespace SireBase; @@ -45,6 +48,34 @@ using namespace SireStream; namespace SireSystem { + std::weak_ptr shared_cache; + + /** Return a pointer to the PageCache that is shared by + * all SystemFrames objects + */ + std::shared_ptr getSharedCache() + { + auto cache = shared_cache.lock(); + + static QMutex mutex; + + if (not cache) + { + QMutexLocker locker(&mutex); + cache = shared_cache.lock(); + + if (not cache) + { + QString cache_dir = QDir::current().absoluteFilePath("trajectory_cache_XXXXXX"); + // use 32 MB pages + cache = std::make_shared(cache_dir, 32 * 1024 * 1024); + shared_cache = cache; + } + } + + return cache; + } + class SystemFrames { public: @@ -100,7 +131,10 @@ namespace SireSystem QHash> mol_atoms; /** The data for the trajectory */ - QVector frames; + QVector frames; + + /** Pointer to the shared pagecache */ + std::shared_ptr cache; /** Mutex to serialize access to the data of this class */ tbb::spin_mutex mutex; @@ -127,12 +161,15 @@ tbb::spin_mutex &SystemFrames::getMutex() const SystemFrames::SystemFrames() : current_frame_index(-1), natoms(0), frame_type(EMPTY) { + cache = getSharedCache(); } SystemFrames::SystemFrames(const QList &nums, const Molecules &mols, const PropertyMap &map) : molnums(nums), current_frame_index(-1), natoms(0), frame_type(EMPTY) { + cache = getSharedCache(); + tbb::spin_mutex::scoped_lock lock(getMutex()); for (const auto &molnum : molnums) @@ -286,7 +323,9 @@ Frame SystemFrames::_lkr_getFrame(int i) const return current_frame; } - QDataStream ds(frames.at(i)); + auto data = frames.at(i).fetch(); + + QDataStream ds(data); Frame frame; @@ -500,27 +539,37 @@ void SystemFrames::saveFrame(const Molecules &mols, Frame frame(coordinates, velocities, forces, space, time, props); - // auto start_time = std::chrono::high_resolution_clock::now(); + auto start_time = std::chrono::high_resolution_clock::now(); + + QByteArray data1 = frame.toByteArray(); + + auto mem_time1 = std::chrono::high_resolution_clock::now(); QByteArray data; data.reserve(2 * frame.numBytes()); - // auto mem_time = std::chrono::high_resolution_clock::now(); + auto mem_time = std::chrono::high_resolution_clock::now(); QDataStream ds(&data, QIODevice::WriteOnly); ds << frame; - // auto end_time = std::chrono::high_resolution_clock::now(); + auto cache_time = std::chrono::high_resolution_clock::now(); + + auto handle = cache->store(data); + + auto end_time = std::chrono::high_resolution_clock::now(); - // qDebug() << "Saving frame" << frames.count() << "with" << data.size() << "bytes" << frame.numBytes(); - // qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - start_time).count() << "microseconds"; - // qDebug() << "Serialization time" << std::chrono::duration_cast(end_time - mem_time).count() << "microseconds"; - // qDebug() << "Total time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + qDebug() << "Saving frame" << frames.count() << "with" << data.size() << "bytes" << frame.numBytes(); + qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - start_time).count() << "microseconds"; + qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - mem_time1).count() << "microseconds"; + qDebug() << "Serialization time" << std::chrono::duration_cast(cache_time - mem_time).count() << "microseconds"; + qDebug() << "Cache time" << std::chrono::duration_cast(end_time - cache_time).count() << "microseconds"; + qDebug() << "Total time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; // need to hold the write lock, as we are updating global state // for everyone who holds this live trajectory data tbb::spin_mutex::scoped_lock lock(getMutex()); - frames.append(data); + frames.append(handle); current_frame = frame; current_frame_index = frames.count() - 1; } diff --git a/wrapper/AutoGenerate/create_wrappers.py b/wrapper/AutoGenerate/create_wrappers.py index 5665cfc72..9f719bfdc 100644 --- a/wrapper/AutoGenerate/create_wrappers.py +++ b/wrapper/AutoGenerate/create_wrappers.py @@ -375,6 +375,7 @@ def call_with_released_gil(c, func_name): all_exported_classes = {} + def export_class( mb, classname, aliases, includes, special_code, auto_str_function=True ): @@ -508,10 +509,17 @@ def export_class( % (class_name, class_name, class_name) ) - c.add_registration_code('def( "__copy__", &__copy__)') + c.add_declaration_code('#include "Helpers/copy.hpp"') + c.add_registration_code( + 'def( "__copy__", &__copy__<%s>)' % class_name + ) - c.add_registration_code('def( "__deepcopy__", &__copy__)') - c.add_registration_code('def( "clone", &__copy__)') + c.add_registration_code( + 'def( "__deepcopy__", &__copy__<%s>)' % class_name + ) + c.add_registration_code( + 'def( "clone", &__copy__<%s>)' % class_name + ) # only do this once for the class break diff --git a/wrapper/Base/Array2D_double_.pypp.cpp b/wrapper/Base/Array2D_double_.pypp.cpp index e10715505..815c3e81f 100644 --- a/wrapper/Base/Array2D_double_.pypp.cpp +++ b/wrapper/Base/Array2D_double_.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::Array2D __copy__(const SireBase::Array2D &other){ return SireBase::Array2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -160,9 +162,9 @@ void register_Array2D_double__class(){ , "" ); } - Array2D_double__exposer.def( "__copy__", &__copy__); - Array2D_double__exposer.def( "__deepcopy__", &__copy__); - Array2D_double__exposer.def( "clone", &__copy__); + Array2D_double__exposer.def( "__copy__", &__copy__>); + Array2D_double__exposer.def( "__deepcopy__", &__copy__>); + Array2D_double__exposer.def( "clone", &__copy__>); Array2D_double__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::Array2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Array2D_double__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::Array2D >, diff --git a/wrapper/Base/BooleanProperty.pypp.cpp b/wrapper/Base/BooleanProperty.pypp.cpp index dae7b661e..5be45fac7 100644 --- a/wrapper/Base/BooleanProperty.pypp.cpp +++ b/wrapper/Base/BooleanProperty.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireBase::BooleanProperty __copy__(const SireBase::BooleanProperty &other){ return SireBase::BooleanProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -185,9 +187,9 @@ void register_BooleanProperty_class(){ } BooleanProperty_exposer.staticmethod( "typeName" ); - BooleanProperty_exposer.def( "__copy__", &__copy__); - BooleanProperty_exposer.def( "__deepcopy__", &__copy__); - BooleanProperty_exposer.def( "clone", &__copy__); + BooleanProperty_exposer.def( "__copy__", &__copy__); + BooleanProperty_exposer.def( "__deepcopy__", &__copy__); + BooleanProperty_exposer.def( "clone", &__copy__); BooleanProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::BooleanProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BooleanProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::BooleanProperty >, diff --git a/wrapper/Base/CPUID.pypp.cpp b/wrapper/Base/CPUID.pypp.cpp index ae7305af4..cf9c2394f 100644 --- a/wrapper/Base/CPUID.pypp.cpp +++ b/wrapper/Base/CPUID.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::CPUID __copy__(const SireBase::CPUID &other){ return SireBase::CPUID(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -193,9 +195,9 @@ void register_CPUID_class(){ } CPUID_exposer.staticmethod( "typeName" ); - CPUID_exposer.def( "__copy__", &__copy__); - CPUID_exposer.def( "__deepcopy__", &__copy__); - CPUID_exposer.def( "clone", &__copy__); + CPUID_exposer.def( "__copy__", &__copy__); + CPUID_exposer.def( "__deepcopy__", &__copy__); + CPUID_exposer.def( "clone", &__copy__); CPUID_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::CPUID >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CPUID_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::CPUID >, diff --git a/wrapper/Base/ChunkedVector_double_.pypp.cpp b/wrapper/Base/ChunkedVector_double_.pypp.cpp index 8d2c3b455..49d2d4a19 100644 --- a/wrapper/Base/ChunkedVector_double_.pypp.cpp +++ b/wrapper/Base/ChunkedVector_double_.pypp.cpp @@ -15,6 +15,8 @@ namespace bp = boost::python; SireBase::ChunkedVector __copy__(const SireBase::ChunkedVector &other){ return SireBase::ChunkedVector(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireBase::ChunkedVector&){ return "SireBase::ChunkedVector";} @@ -406,9 +408,9 @@ void register_ChunkedVector_double__class(){ ChunkedVector_double__exposer.staticmethod( "fromList" ); ChunkedVector_double__exposer.staticmethod( "fromStdVector" ); ChunkedVector_double__exposer.staticmethod( "fromVector" ); - ChunkedVector_double__exposer.def( "__copy__", &__copy__); - ChunkedVector_double__exposer.def( "__deepcopy__", &__copy__); - ChunkedVector_double__exposer.def( "clone", &__copy__); + ChunkedVector_double__exposer.def( "__copy__", &__copy__>); + ChunkedVector_double__exposer.def( "__deepcopy__", &__copy__>); + ChunkedVector_double__exposer.def( "clone", &__copy__>); ChunkedVector_double__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::ChunkedVector >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ChunkedVector_double__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::ChunkedVector >, diff --git a/wrapper/Base/DoubleArrayProperty.pypp.cpp b/wrapper/Base/DoubleArrayProperty.pypp.cpp index ceeb4e49c..657d3e012 100644 --- a/wrapper/Base/DoubleArrayProperty.pypp.cpp +++ b/wrapper/Base/DoubleArrayProperty.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireBase::DoubleArrayProperty __copy__(const SireBase::DoubleArrayProperty &other){ return SireBase::DoubleArrayProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -188,9 +190,9 @@ void register_DoubleArrayProperty_class(){ } DoubleArrayProperty_exposer.staticmethod( "typeName" ); - DoubleArrayProperty_exposer.def( "__copy__", &__copy__); - DoubleArrayProperty_exposer.def( "__deepcopy__", &__copy__); - DoubleArrayProperty_exposer.def( "clone", &__copy__); + DoubleArrayProperty_exposer.def( "__copy__", &__copy__); + DoubleArrayProperty_exposer.def( "__deepcopy__", &__copy__); + DoubleArrayProperty_exposer.def( "clone", &__copy__); DoubleArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::DoubleArrayProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DoubleArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::DoubleArrayProperty >, diff --git a/wrapper/Base/FlopsMark.pypp.cpp b/wrapper/Base/FlopsMark.pypp.cpp index b1f0f7f49..77cf4223a 100644 --- a/wrapper/Base/FlopsMark.pypp.cpp +++ b/wrapper/Base/FlopsMark.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::FlopsMark __copy__(const SireBase::FlopsMark &other){ return SireBase::FlopsMark(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireBase::FlopsMark&){ return "SireBase::FlopsMark";} #include "Helpers/release_gil_policy.hpp" @@ -145,9 +147,9 @@ void register_FlopsMark_class(){ FlopsMark_exposer.staticmethod( "benchmarkProduct" ); FlopsMark_exposer.staticmethod( "benchmarkQuotient" ); FlopsMark_exposer.staticmethod( "benchmarkSum" ); - FlopsMark_exposer.def( "__copy__", &__copy__); - FlopsMark_exposer.def( "__deepcopy__", &__copy__); - FlopsMark_exposer.def( "clone", &__copy__); + FlopsMark_exposer.def( "__copy__", &__copy__); + FlopsMark_exposer.def( "__deepcopy__", &__copy__); + FlopsMark_exposer.def( "clone", &__copy__); FlopsMark_exposer.def( "__str__", &pvt_get_name); FlopsMark_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Base/GeneralUnitArrayProperty.pypp.cpp b/wrapper/Base/GeneralUnitArrayProperty.pypp.cpp index d6f4612d5..7700949fc 100644 --- a/wrapper/Base/GeneralUnitArrayProperty.pypp.cpp +++ b/wrapper/Base/GeneralUnitArrayProperty.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireBase::GeneralUnitArrayProperty __copy__(const SireBase::GeneralUnitArrayProperty &other){ return SireBase::GeneralUnitArrayProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -90,9 +92,9 @@ void register_GeneralUnitArrayProperty_class(){ } GeneralUnitArrayProperty_exposer.staticmethod( "typeName" ); - GeneralUnitArrayProperty_exposer.def( "__copy__", &__copy__); - GeneralUnitArrayProperty_exposer.def( "__deepcopy__", &__copy__); - GeneralUnitArrayProperty_exposer.def( "clone", &__copy__); + GeneralUnitArrayProperty_exposer.def( "__copy__", &__copy__); + GeneralUnitArrayProperty_exposer.def( "__deepcopy__", &__copy__); + GeneralUnitArrayProperty_exposer.def( "clone", &__copy__); GeneralUnitArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::GeneralUnitArrayProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GeneralUnitArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::GeneralUnitArrayProperty >, diff --git a/wrapper/Base/GeneralUnitProperty.pypp.cpp b/wrapper/Base/GeneralUnitProperty.pypp.cpp index 7e3ea428c..a206d6475 100644 --- a/wrapper/Base/GeneralUnitProperty.pypp.cpp +++ b/wrapper/Base/GeneralUnitProperty.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireBase::GeneralUnitProperty __copy__(const SireBase::GeneralUnitProperty &other){ return SireBase::GeneralUnitProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -207,9 +209,9 @@ void register_GeneralUnitProperty_class(){ } GeneralUnitProperty_exposer.staticmethod( "typeName" ); - GeneralUnitProperty_exposer.def( "__copy__", &__copy__); - GeneralUnitProperty_exposer.def( "__deepcopy__", &__copy__); - GeneralUnitProperty_exposer.def( "clone", &__copy__); + GeneralUnitProperty_exposer.def( "__copy__", &__copy__); + GeneralUnitProperty_exposer.def( "__deepcopy__", &__copy__); + GeneralUnitProperty_exposer.def( "clone", &__copy__); GeneralUnitProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::GeneralUnitProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GeneralUnitProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::GeneralUnitProperty >, diff --git a/wrapper/Base/Incremint.pypp.cpp b/wrapper/Base/Incremint.pypp.cpp index 3a41f5b18..44cb1c1f6 100644 --- a/wrapper/Base/Incremint.pypp.cpp +++ b/wrapper/Base/Incremint.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::Incremint __copy__(const SireBase::Incremint &other){ return SireBase::Incremint(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireBase::Incremint&){ return "SireBase::Incremint";} #include "Helpers/release_gil_policy.hpp" @@ -36,9 +38,9 @@ void register_Incremint_class(){ , "" ); } - Incremint_exposer.def( "__copy__", &__copy__); - Incremint_exposer.def( "__deepcopy__", &__copy__); - Incremint_exposer.def( "clone", &__copy__); + Incremint_exposer.def( "__copy__", &__copy__); + Incremint_exposer.def( "__deepcopy__", &__copy__); + Incremint_exposer.def( "clone", &__copy__); Incremint_exposer.def( "__str__", &pvt_get_name); Incremint_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Base/IntegerArrayProperty.pypp.cpp b/wrapper/Base/IntegerArrayProperty.pypp.cpp index 08ede1ee4..d9498df27 100644 --- a/wrapper/Base/IntegerArrayProperty.pypp.cpp +++ b/wrapper/Base/IntegerArrayProperty.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireBase::IntegerArrayProperty __copy__(const SireBase::IntegerArrayProperty &other){ return SireBase::IntegerArrayProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -188,9 +190,9 @@ void register_IntegerArrayProperty_class(){ } IntegerArrayProperty_exposer.staticmethod( "typeName" ); - IntegerArrayProperty_exposer.def( "__copy__", &__copy__); - IntegerArrayProperty_exposer.def( "__deepcopy__", &__copy__); - IntegerArrayProperty_exposer.def( "clone", &__copy__); + IntegerArrayProperty_exposer.def( "__copy__", &__copy__); + IntegerArrayProperty_exposer.def( "__deepcopy__", &__copy__); + IntegerArrayProperty_exposer.def( "clone", &__copy__); IntegerArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::IntegerArrayProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntegerArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::IntegerArrayProperty >, diff --git a/wrapper/Base/LazyEvaluator.pypp.cpp b/wrapper/Base/LazyEvaluator.pypp.cpp index c996070fc..f403f897b 100644 --- a/wrapper/Base/LazyEvaluator.pypp.cpp +++ b/wrapper/Base/LazyEvaluator.pypp.cpp @@ -25,6 +25,8 @@ namespace bp = boost::python; SireBase::LazyEvaluator __copy__(const SireBase::LazyEvaluator &other){ return SireBase::LazyEvaluator(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireBase::LazyEvaluator&){ return "SireBase::LazyEvaluator";} #include "Helpers/release_gil_policy.hpp" @@ -49,9 +51,9 @@ void register_LazyEvaluator_class(){ , "" ); } - LazyEvaluator_exposer.def( "__copy__", &__copy__); - LazyEvaluator_exposer.def( "__deepcopy__", &__copy__); - LazyEvaluator_exposer.def( "clone", &__copy__); + LazyEvaluator_exposer.def( "__copy__", &__copy__); + LazyEvaluator_exposer.def( "__deepcopy__", &__copy__); + LazyEvaluator_exposer.def( "clone", &__copy__); LazyEvaluator_exposer.def( "__str__", &pvt_get_name); LazyEvaluator_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Base/LengthProperty.pypp.cpp b/wrapper/Base/LengthProperty.pypp.cpp index c44348ecc..824413b30 100644 --- a/wrapper/Base/LengthProperty.pypp.cpp +++ b/wrapper/Base/LengthProperty.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireBase::LengthProperty __copy__(const SireBase::LengthProperty &other){ return SireBase::LengthProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -90,9 +92,9 @@ void register_LengthProperty_class(){ } LengthProperty_exposer.staticmethod( "typeName" ); - LengthProperty_exposer.def( "__copy__", &__copy__); - LengthProperty_exposer.def( "__deepcopy__", &__copy__); - LengthProperty_exposer.def( "clone", &__copy__); + LengthProperty_exposer.def( "__copy__", &__copy__); + LengthProperty_exposer.def( "__deepcopy__", &__copy__); + LengthProperty_exposer.def( "clone", &__copy__); LengthProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::LengthProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LengthProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::LengthProperty >, diff --git a/wrapper/Base/LinkToProperty.pypp.cpp b/wrapper/Base/LinkToProperty.pypp.cpp index 829ab2f33..ff9411ac2 100644 --- a/wrapper/Base/LinkToProperty.pypp.cpp +++ b/wrapper/Base/LinkToProperty.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireBase::LinkToProperty __copy__(const SireBase::LinkToProperty &other){ return SireBase::LinkToProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -109,9 +111,9 @@ void register_LinkToProperty_class(){ } LinkToProperty_exposer.staticmethod( "typeName" ); - LinkToProperty_exposer.def( "__copy__", &__copy__); - LinkToProperty_exposer.def( "__deepcopy__", &__copy__); - LinkToProperty_exposer.def( "clone", &__copy__); + LinkToProperty_exposer.def( "__copy__", &__copy__); + LinkToProperty_exposer.def( "__deepcopy__", &__copy__); + LinkToProperty_exposer.def( "clone", &__copy__); LinkToProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::LinkToProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LinkToProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::LinkToProperty >, diff --git a/wrapper/Base/LowerCaseString.pypp.cpp b/wrapper/Base/LowerCaseString.pypp.cpp index 71774b421..e238109ac 100644 --- a/wrapper/Base/LowerCaseString.pypp.cpp +++ b/wrapper/Base/LowerCaseString.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::LowerCaseString __copy__(const SireBase::LowerCaseString &other){ return SireBase::LowerCaseString(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -73,9 +75,9 @@ void register_LowerCaseString_class(){ } LowerCaseString_exposer.staticmethod( "typeName" ); - LowerCaseString_exposer.def( "__copy__", &__copy__); - LowerCaseString_exposer.def( "__deepcopy__", &__copy__); - LowerCaseString_exposer.def( "clone", &__copy__); + LowerCaseString_exposer.def( "__copy__", &__copy__); + LowerCaseString_exposer.def( "__deepcopy__", &__copy__); + LowerCaseString_exposer.def( "clone", &__copy__); LowerCaseString_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::LowerCaseString >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LowerCaseString_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::LowerCaseString >, diff --git a/wrapper/Base/MajorMinorVersion.pypp.cpp b/wrapper/Base/MajorMinorVersion.pypp.cpp index f96f2dbbe..71181afa5 100644 --- a/wrapper/Base/MajorMinorVersion.pypp.cpp +++ b/wrapper/Base/MajorMinorVersion.pypp.cpp @@ -20,6 +20,8 @@ namespace bp = boost::python; SireBase::MajorMinorVersion __copy__(const SireBase::MajorMinorVersion &other){ return SireBase::MajorMinorVersion(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireBase::MajorMinorVersion&){ return "SireBase::MajorMinorVersion";} #include "Helpers/release_gil_policy.hpp" @@ -133,9 +135,9 @@ void register_MajorMinorVersion_class(){ } MajorMinorVersion_exposer.staticmethod( "typeName" ); - MajorMinorVersion_exposer.def( "__copy__", &__copy__); - MajorMinorVersion_exposer.def( "__deepcopy__", &__copy__); - MajorMinorVersion_exposer.def( "clone", &__copy__); + MajorMinorVersion_exposer.def( "__copy__", &__copy__); + MajorMinorVersion_exposer.def( "__deepcopy__", &__copy__); + MajorMinorVersion_exposer.def( "clone", &__copy__); MajorMinorVersion_exposer.def( "__str__", &pvt_get_name); MajorMinorVersion_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Base/MemInfo.pypp.cpp b/wrapper/Base/MemInfo.pypp.cpp index 39e9e157b..cf2367d9c 100644 --- a/wrapper/Base/MemInfo.pypp.cpp +++ b/wrapper/Base/MemInfo.pypp.cpp @@ -27,6 +27,8 @@ namespace bp = boost::python; SireBase::MemInfo __copy__(const SireBase::MemInfo &other){ return SireBase::MemInfo(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -198,9 +200,9 @@ void register_MemInfo_class(){ MemInfo_exposer.staticmethod( "startMonitoring" ); MemInfo_exposer.staticmethod( "stopMonitoring" ); MemInfo_exposer.staticmethod( "takeMeasurement" ); - MemInfo_exposer.def( "__copy__", &__copy__); - MemInfo_exposer.def( "__deepcopy__", &__copy__); - MemInfo_exposer.def( "clone", &__copy__); + MemInfo_exposer.def( "__copy__", &__copy__); + MemInfo_exposer.def( "__deepcopy__", &__copy__); + MemInfo_exposer.def( "clone", &__copy__); MemInfo_exposer.def( "__str__", &__str__< ::SireBase::MemInfo > ); MemInfo_exposer.def( "__repr__", &__str__< ::SireBase::MemInfo > ); } diff --git a/wrapper/Base/NoMangling.pypp.cpp b/wrapper/Base/NoMangling.pypp.cpp index c11436412..484051fc0 100644 --- a/wrapper/Base/NoMangling.pypp.cpp +++ b/wrapper/Base/NoMangling.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::NoMangling __copy__(const SireBase::NoMangling &other){ return SireBase::NoMangling(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -73,9 +75,9 @@ void register_NoMangling_class(){ } NoMangling_exposer.staticmethod( "typeName" ); - NoMangling_exposer.def( "__copy__", &__copy__); - NoMangling_exposer.def( "__deepcopy__", &__copy__); - NoMangling_exposer.def( "clone", &__copy__); + NoMangling_exposer.def( "__copy__", &__copy__); + NoMangling_exposer.def( "__deepcopy__", &__copy__); + NoMangling_exposer.def( "clone", &__copy__); NoMangling_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::NoMangling >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NoMangling_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::NoMangling >, diff --git a/wrapper/Base/NullProperty.pypp.cpp b/wrapper/Base/NullProperty.pypp.cpp index fac5fba3f..ec8be9085 100644 --- a/wrapper/Base/NullProperty.pypp.cpp +++ b/wrapper/Base/NullProperty.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireBase::NullProperty __copy__(const SireBase::NullProperty &other){ return SireBase::NullProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -67,9 +69,9 @@ void register_NullProperty_class(){ } NullProperty_exposer.staticmethod( "typeName" ); - NullProperty_exposer.def( "__copy__", &__copy__); - NullProperty_exposer.def( "__deepcopy__", &__copy__); - NullProperty_exposer.def( "clone", &__copy__); + NullProperty_exposer.def( "__copy__", &__copy__); + NullProperty_exposer.def( "__deepcopy__", &__copy__); + NullProperty_exposer.def( "clone", &__copy__); NullProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::NullProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NullProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::NullProperty >, diff --git a/wrapper/Base/NumberProperty.pypp.cpp b/wrapper/Base/NumberProperty.pypp.cpp index 9751807fd..f5bfbcbaa 100644 --- a/wrapper/Base/NumberProperty.pypp.cpp +++ b/wrapper/Base/NumberProperty.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireBase::NumberProperty __copy__(const SireBase::NumberProperty &other){ return SireBase::NumberProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -212,9 +214,9 @@ void register_NumberProperty_class(){ } NumberProperty_exposer.staticmethod( "typeName" ); - NumberProperty_exposer.def( "__copy__", &__copy__); - NumberProperty_exposer.def( "__deepcopy__", &__copy__); - NumberProperty_exposer.def( "clone", &__copy__); + NumberProperty_exposer.def( "__copy__", &__copy__); + NumberProperty_exposer.def( "__deepcopy__", &__copy__); + NumberProperty_exposer.def( "clone", &__copy__); NumberProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::NumberProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NumberProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::NumberProperty >, diff --git a/wrapper/Base/PackedArray2D_DoubleArrayProperty.pypp.cpp b/wrapper/Base/PackedArray2D_DoubleArrayProperty.pypp.cpp index 00d1a7088..250aa3c27 100644 --- a/wrapper/Base/PackedArray2D_DoubleArrayProperty.pypp.cpp +++ b/wrapper/Base/PackedArray2D_DoubleArrayProperty.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_DoubleArrayProperty_class(){ } PackedArray2D_DoubleArrayProperty_exposer.staticmethod( "fromVariant" ); - PackedArray2D_DoubleArrayProperty_exposer.def( "__copy__", &__copy__); - PackedArray2D_DoubleArrayProperty_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_DoubleArrayProperty_exposer.def( "clone", &__copy__); + PackedArray2D_DoubleArrayProperty_exposer.def( "__copy__", &__copy__>); + PackedArray2D_DoubleArrayProperty_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_DoubleArrayProperty_exposer.def( "clone", &__copy__>); PackedArray2D_DoubleArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_DoubleArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_DoubleArrayProperty_Array.pypp.cpp b/wrapper/Base/PackedArray2D_DoubleArrayProperty_Array.pypp.cpp index 870fa1bd9..405edef2a 100644 --- a/wrapper/Base/PackedArray2D_DoubleArrayProperty_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_DoubleArrayProperty_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_DoubleArrayProperty_Array_class(){ , "" ); } - PackedArray2D_DoubleArrayProperty_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_DoubleArrayProperty_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_DoubleArrayProperty_Array_exposer.def( "clone", &__copy__); + PackedArray2D_DoubleArrayProperty_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_DoubleArrayProperty_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_DoubleArrayProperty_Array_exposer.def( "clone", &__copy__>); PackedArray2D_DoubleArrayProperty_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_DoubleArrayProperty_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_IntegerArrayProperty.pypp.cpp b/wrapper/Base/PackedArray2D_IntegerArrayProperty.pypp.cpp index d6e32d410..17f7bfc76 100644 --- a/wrapper/Base/PackedArray2D_IntegerArrayProperty.pypp.cpp +++ b/wrapper/Base/PackedArray2D_IntegerArrayProperty.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_IntegerArrayProperty_class(){ } PackedArray2D_IntegerArrayProperty_exposer.staticmethod( "fromVariant" ); - PackedArray2D_IntegerArrayProperty_exposer.def( "__copy__", &__copy__); - PackedArray2D_IntegerArrayProperty_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_IntegerArrayProperty_exposer.def( "clone", &__copy__); + PackedArray2D_IntegerArrayProperty_exposer.def( "__copy__", &__copy__>); + PackedArray2D_IntegerArrayProperty_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_IntegerArrayProperty_exposer.def( "clone", &__copy__>); PackedArray2D_IntegerArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_IntegerArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_IntegerArrayProperty_Array.pypp.cpp b/wrapper/Base/PackedArray2D_IntegerArrayProperty_Array.pypp.cpp index d753b9392..b43e39efc 100644 --- a/wrapper/Base/PackedArray2D_IntegerArrayProperty_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_IntegerArrayProperty_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_IntegerArrayProperty_Array_class(){ , "" ); } - PackedArray2D_IntegerArrayProperty_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_IntegerArrayProperty_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_IntegerArrayProperty_Array_exposer.def( "clone", &__copy__); + PackedArray2D_IntegerArrayProperty_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_IntegerArrayProperty_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_IntegerArrayProperty_Array_exposer.def( "clone", &__copy__>); PackedArray2D_IntegerArrayProperty_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_IntegerArrayProperty_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_PropertyList.pypp.cpp b/wrapper/Base/PackedArray2D_PropertyList.pypp.cpp index 808c7f9ad..69c71830e 100644 --- a/wrapper/Base/PackedArray2D_PropertyList.pypp.cpp +++ b/wrapper/Base/PackedArray2D_PropertyList.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_PropertyList_class(){ } PackedArray2D_PropertyList_exposer.staticmethod( "fromVariant" ); - PackedArray2D_PropertyList_exposer.def( "__copy__", &__copy__); - PackedArray2D_PropertyList_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_PropertyList_exposer.def( "clone", &__copy__); + PackedArray2D_PropertyList_exposer.def( "__copy__", &__copy__>); + PackedArray2D_PropertyList_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_PropertyList_exposer.def( "clone", &__copy__>); PackedArray2D_PropertyList_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_PropertyList_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_PropertyList_Array.pypp.cpp b/wrapper/Base/PackedArray2D_PropertyList_Array.pypp.cpp index c6452d940..deca13123 100644 --- a/wrapper/Base/PackedArray2D_PropertyList_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_PropertyList_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_PropertyList_Array_class(){ , "" ); } - PackedArray2D_PropertyList_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_PropertyList_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_PropertyList_Array_exposer.def( "clone", &__copy__); + PackedArray2D_PropertyList_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_PropertyList_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_PropertyList_Array_exposer.def( "clone", &__copy__>); PackedArray2D_PropertyList_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_PropertyList_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_QString_.pypp.cpp b/wrapper/Base/PackedArray2D_QString_.pypp.cpp index 4db442d00..4eac81d99 100644 --- a/wrapper/Base/PackedArray2D_QString_.pypp.cpp +++ b/wrapper/Base/PackedArray2D_QString_.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_QString__class(){ } PackedArray2D_QString__exposer.staticmethod( "fromVariant" ); - PackedArray2D_QString__exposer.def( "__copy__", &__copy__); - PackedArray2D_QString__exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_QString__exposer.def( "clone", &__copy__); + PackedArray2D_QString__exposer.def( "__copy__", &__copy__>); + PackedArray2D_QString__exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_QString__exposer.def( "clone", &__copy__>); PackedArray2D_QString__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_QString__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_QString_Array.pypp.cpp b/wrapper/Base/PackedArray2D_QString_Array.pypp.cpp index de4e13e51..10954b208 100644 --- a/wrapper/Base/PackedArray2D_QString_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_QString_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_QString_Array_class(){ , "" ); } - PackedArray2D_QString_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_QString_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_QString_Array_exposer.def( "clone", &__copy__); + PackedArray2D_QString_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_QString_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_QString_Array_exposer.def( "clone", &__copy__>); PackedArray2D_QString_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_QString_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_QVariant_.pypp.cpp b/wrapper/Base/PackedArray2D_QVariant_.pypp.cpp index cfec2202f..379cc8682 100644 --- a/wrapper/Base/PackedArray2D_QVariant_.pypp.cpp +++ b/wrapper/Base/PackedArray2D_QVariant_.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_QVariant__class(){ } PackedArray2D_QVariant__exposer.staticmethod( "fromVariant" ); - PackedArray2D_QVariant__exposer.def( "__copy__", &__copy__); - PackedArray2D_QVariant__exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_QVariant__exposer.def( "clone", &__copy__); + PackedArray2D_QVariant__exposer.def( "__copy__", &__copy__>); + PackedArray2D_QVariant__exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_QVariant__exposer.def( "clone", &__copy__>); PackedArray2D_QVariant__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_QVariant__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_QVariant_Array.pypp.cpp b/wrapper/Base/PackedArray2D_QVariant_Array.pypp.cpp index de93160a3..5733a667b 100644 --- a/wrapper/Base/PackedArray2D_QVariant_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_QVariant_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_QVariant_Array_class(){ , "" ); } - PackedArray2D_QVariant_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_QVariant_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_QVariant_Array_exposer.def( "clone", &__copy__); + PackedArray2D_QVariant_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_QVariant_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_QVariant_Array_exposer.def( "clone", &__copy__>); PackedArray2D_QVariant_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_QVariant_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_StringArrayProperty.pypp.cpp b/wrapper/Base/PackedArray2D_StringArrayProperty.pypp.cpp index ae1938e64..2f98adc73 100644 --- a/wrapper/Base/PackedArray2D_StringArrayProperty.pypp.cpp +++ b/wrapper/Base/PackedArray2D_StringArrayProperty.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_StringArrayProperty_class(){ } PackedArray2D_StringArrayProperty_exposer.staticmethod( "fromVariant" ); - PackedArray2D_StringArrayProperty_exposer.def( "__copy__", &__copy__); - PackedArray2D_StringArrayProperty_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_StringArrayProperty_exposer.def( "clone", &__copy__); + PackedArray2D_StringArrayProperty_exposer.def( "__copy__", &__copy__>); + PackedArray2D_StringArrayProperty_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_StringArrayProperty_exposer.def( "clone", &__copy__>); PackedArray2D_StringArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_StringArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_StringArrayProperty_Array.pypp.cpp b/wrapper/Base/PackedArray2D_StringArrayProperty_Array.pypp.cpp index 44279eb36..97a91e95a 100644 --- a/wrapper/Base/PackedArray2D_StringArrayProperty_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_StringArrayProperty_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_StringArrayProperty_Array_class(){ , "" ); } - PackedArray2D_StringArrayProperty_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_StringArrayProperty_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_StringArrayProperty_Array_exposer.def( "clone", &__copy__); + PackedArray2D_StringArrayProperty_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_StringArrayProperty_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_StringArrayProperty_Array_exposer.def( "clone", &__copy__>); PackedArray2D_StringArrayProperty_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_StringArrayProperty_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_double_.pypp.cpp b/wrapper/Base/PackedArray2D_double_.pypp.cpp index 6f397c986..01013b220 100644 --- a/wrapper/Base/PackedArray2D_double_.pypp.cpp +++ b/wrapper/Base/PackedArray2D_double_.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_double__class(){ } PackedArray2D_double__exposer.staticmethod( "fromVariant" ); - PackedArray2D_double__exposer.def( "__copy__", &__copy__); - PackedArray2D_double__exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_double__exposer.def( "clone", &__copy__); + PackedArray2D_double__exposer.def( "__copy__", &__copy__>); + PackedArray2D_double__exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_double__exposer.def( "clone", &__copy__>); PackedArray2D_double__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_double__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_double_Array.pypp.cpp b/wrapper/Base/PackedArray2D_double_Array.pypp.cpp index 3046beafc..b2e3655fe 100644 --- a/wrapper/Base/PackedArray2D_double_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_double_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_double_Array_class(){ , "" ); } - PackedArray2D_double_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_double_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_double_Array_exposer.def( "clone", &__copy__); + PackedArray2D_double_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_double_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_double_Array_exposer.def( "clone", &__copy__>); PackedArray2D_double_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_double_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PackedArray2D_int_.pypp.cpp b/wrapper/Base/PackedArray2D_int_.pypp.cpp index 68d277be8..1a697ebbc 100644 --- a/wrapper/Base/PackedArray2D_int_.pypp.cpp +++ b/wrapper/Base/PackedArray2D_int_.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::PackedArray2D __copy__(const SireBase::PackedArray2D &other){ return SireBase::PackedArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -404,9 +406,9 @@ void register_PackedArray2D_int__class(){ } PackedArray2D_int__exposer.staticmethod( "fromVariant" ); - PackedArray2D_int__exposer.def( "__copy__", &__copy__); - PackedArray2D_int__exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_int__exposer.def( "clone", &__copy__); + PackedArray2D_int__exposer.def( "__copy__", &__copy__>); + PackedArray2D_int__exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_int__exposer.def( "clone", &__copy__>); PackedArray2D_int__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PackedArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_int__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PackedArray2D >, diff --git a/wrapper/Base/PackedArray2D_int_Array.pypp.cpp b/wrapper/Base/PackedArray2D_int_Array.pypp.cpp index 43a432bb2..5f2f3d26b 100644 --- a/wrapper/Base/PackedArray2D_int_Array.pypp.cpp +++ b/wrapper/Base/PackedArray2D_int_Array.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::detail::PackedArray2D_Array __copy__(const SireBase::detail::PackedArray2D_Array &other){ return SireBase::detail::PackedArray2D_Array(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -195,9 +197,9 @@ void register_PackedArray2D_int_Array_class(){ , "" ); } - PackedArray2D_int_Array_exposer.def( "__copy__", &__copy__); - PackedArray2D_int_Array_exposer.def( "__deepcopy__", &__copy__); - PackedArray2D_int_Array_exposer.def( "clone", &__copy__); + PackedArray2D_int_Array_exposer.def( "__copy__", &__copy__>); + PackedArray2D_int_Array_exposer.def( "__deepcopy__", &__copy__>); + PackedArray2D_int_Array_exposer.def( "clone", &__copy__>); PackedArray2D_int_Array_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PackedArray2D_int_Array_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::detail::PackedArray2D_Array >, diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index c88ffc1fa..8db09555d 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -17,6 +17,12 @@ namespace bp = boost::python; #include "pagecache.h" +SireBase::PageCache __copy__(const SireBase::PageCache &other){ return SireBase::PageCache(other); } + +#include "Helpers/copy.hpp" + +const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCache";} + #include "Helpers/release_gil_policy.hpp" #include "SireError/errors.h" @@ -29,6 +35,10 @@ namespace bp = boost::python; #include "pagecache.h" +SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ return SireBase::PageCache::Handle(other); } + +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -45,368 +55,556 @@ namespace bp = boost::python; #include "pagecache.h" +SireBase::PageCache::Page __copy__(const SireBase::PageCache::Page &other){ return SireBase::PageCache::Page(other); } + +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" #include "Helpers/len.hpp" -#include "Helpers/copy.hpp" -void register_PageCache_class() -{ +void register_PageCache_class(){ { //::SireBase::PageCache - typedef bp::class_ PageCache_exposer_t; - PageCache_exposer_t PageCache_exposer = PageCache_exposer_t("PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init>((bp::arg("page_size") = (int)(32 * 1024 * 1024)), "")); - bp::scope PageCache_scope(PageCache_exposer); + typedef bp::class_< SireBase::PageCache > PageCache_exposer_t; + PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< bp::optional< int > >(( bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); + bp::scope PageCache_scope( PageCache_exposer ); { //::SireBase::PageCache::Handle - typedef bp::class_ Handle_exposer_t; - Handle_exposer_t Handle_exposer = Handle_exposer_t("Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init<>("")); - bp::scope Handle_scope(Handle_exposer); - Handle_exposer.def(bp::init>((bp::arg("data")), "")); - Handle_exposer.def(bp::init((bp::arg("other")), "")); + typedef bp::class_< SireBase::PageCache::Handle > Handle_exposer_t; + Handle_exposer_t Handle_exposer = Handle_exposer_t( "Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init< >("") ); + bp::scope Handle_scope( Handle_exposer ); + Handle_exposer.def( bp::init< std::shared_ptr< SireBase::detail::HandleData > >(( bp::arg("data") ), "") ); + Handle_exposer.def( bp::init< SireBase::PageCache::Handle const & >(( bp::arg("other") ), "") ); { //::SireBase::PageCache::Handle::assertValid - - typedef void (::SireBase::PageCache::Handle::*assertValid_function_type)() const; - assertValid_function_type assertValid_function_value(&::SireBase::PageCache::Handle::assertValid); - - Handle_exposer.def( - "assertValid", assertValid_function_value, bp::release_gil_policy(), ""); + + typedef void ( ::SireBase::PageCache::Handle::*assertValid_function_type)( ) const; + assertValid_function_type assertValid_function_value( &::SireBase::PageCache::Handle::assertValid ); + + Handle_exposer.def( + "assertValid" + , assertValid_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::clear - - typedef void (::SireBase::PageCache::Handle::*clear_function_type)(); - clear_function_type clear_function_value(&::SireBase::PageCache::Handle::clear); - - Handle_exposer.def( - "clear", clear_function_value, bp::release_gil_policy(), ""); + + typedef void ( ::SireBase::PageCache::Handle::*clear_function_type)( ) ; + clear_function_type clear_function_value( &::SireBase::PageCache::Handle::clear ); + + Handle_exposer.def( + "clear" + , clear_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::fetch - - typedef ::QByteArray (::SireBase::PageCache::Handle::*fetch_function_type)() const; - fetch_function_type fetch_function_value(&::SireBase::PageCache::Handle::fetch); - - Handle_exposer.def( - "fetch", fetch_function_value, bp::release_gil_policy(), ""); + + typedef ::QByteArray ( ::SireBase::PageCache::Handle::*fetch_function_type)( ) const; + fetch_function_type fetch_function_value( &::SireBase::PageCache::Handle::fetch ); + + Handle_exposer.def( + "fetch" + , fetch_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::isNull - - typedef bool (::SireBase::PageCache::Handle::*isNull_function_type)() const; - isNull_function_type isNull_function_value(&::SireBase::PageCache::Handle::isNull); - - Handle_exposer.def( - "isNull", isNull_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::Handle::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireBase::PageCache::Handle::isNull ); + + Handle_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::isValid - - typedef bool (::SireBase::PageCache::Handle::*isValid_function_type)() const; - isValid_function_type isValid_function_value(&::SireBase::PageCache::Handle::isValid); - - Handle_exposer.def( - "isValid", isValid_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::Handle::*isValid_function_type)( ) const; + isValid_function_type isValid_function_value( &::SireBase::PageCache::Handle::isValid ); + + Handle_exposer.def( + "isValid" + , isValid_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::nBytes - - typedef int (::SireBase::PageCache::Handle::*nBytes_function_type)() const; - nBytes_function_type nBytes_function_value(&::SireBase::PageCache::Handle::nBytes); - - Handle_exposer.def( - "nBytes", nBytes_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::Handle::*nBytes_function_type)( ) const; + nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Handle::nBytes ); + + Handle_exposer.def( + "nBytes" + , nBytes_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::operator= - - typedef ::SireBase::PageCache::Handle &(::SireBase::PageCache::Handle::*assign_function_type)(::SireBase::PageCache::Handle const &); - assign_function_type assign_function_value(&::SireBase::PageCache::Handle::operator=); - - Handle_exposer.def( - "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); + + typedef ::SireBase::PageCache::Handle & ( ::SireBase::PageCache::Handle::*assign_function_type)( ::SireBase::PageCache::Handle const & ) ; + assign_function_type assign_function_value( &::SireBase::PageCache::Handle::operator= ); + + Handle_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + } { //::SireBase::PageCache::Handle::page - - typedef ::SireBase::PageCache::Page (::SireBase::PageCache::Handle::*page_function_type)() const; - page_function_type page_function_value(&::SireBase::PageCache::Handle::page); - - Handle_exposer.def( - "page", page_function_value, bp::release_gil_policy(), ""); + + typedef ::SireBase::PageCache::Page ( ::SireBase::PageCache::Handle::*page_function_type)( ) const; + page_function_type page_function_value( &::SireBase::PageCache::Handle::page ); + + Handle_exposer.def( + "page" + , page_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::parent - - typedef ::SireBase::PageCache (::SireBase::PageCache::Handle::*parent_function_type)() const; - parent_function_type parent_function_value(&::SireBase::PageCache::Handle::parent); - - Handle_exposer.def( - "parent", parent_function_value, bp::release_gil_policy(), ""); + + typedef ::SireBase::PageCache ( ::SireBase::PageCache::Handle::*parent_function_type)( ) const; + parent_function_type parent_function_value( &::SireBase::PageCache::Handle::parent ); + + Handle_exposer.def( + "parent" + , parent_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::reset - - typedef void (::SireBase::PageCache::Handle::*reset_function_type)(); - reset_function_type reset_function_value(&::SireBase::PageCache::Handle::reset); - - Handle_exposer.def( - "reset", reset_function_value, bp::release_gil_policy(), ""); + + typedef void ( ::SireBase::PageCache::Handle::*reset_function_type)( ) ; + reset_function_type reset_function_value( &::SireBase::PageCache::Handle::reset ); + + Handle_exposer.def( + "reset" + , reset_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::size - - typedef int (::SireBase::PageCache::Handle::*size_function_type)() const; - size_function_type size_function_value(&::SireBase::PageCache::Handle::size); - - Handle_exposer.def( - "size", size_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::Handle::*size_function_type)( ) const; + size_function_type size_function_value( &::SireBase::PageCache::Handle::size ); + + Handle_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::toString - - typedef ::QString (::SireBase::PageCache::Handle::*toString_function_type)() const; - toString_function_type toString_function_value(&::SireBase::PageCache::Handle::toString); - - Handle_exposer.def( - "toString", toString_function_value, bp::release_gil_policy(), ""); + + typedef ::QString ( ::SireBase::PageCache::Handle::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireBase::PageCache::Handle::toString ); + + Handle_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::typeName - - typedef char const *(*typeName_function_type)(); - typeName_function_type typeName_function_value(&::SireBase::PageCache::Handle::typeName); - - Handle_exposer.def( - "typeName", typeName_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireBase::PageCache::Handle::typeName ); + + Handle_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Handle::what - - typedef char const *(::SireBase::PageCache::Handle::*what_function_type)() const; - what_function_type what_function_value(&::SireBase::PageCache::Handle::what); - - Handle_exposer.def( - "what", what_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( ::SireBase::PageCache::Handle::*what_function_type)( ) const; + what_function_type what_function_value( &::SireBase::PageCache::Handle::what ); + + Handle_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + } - Handle_exposer.staticmethod("typeName"); - Handle_exposer.def("__copy__", &__copy__); - Handle_exposer.def("__deepcopy__", &__copy__); - Handle_exposer.def("clone", &__copy__); - Handle_exposer.def("__str__", &__str__<::SireBase::PageCache::Handle>); - Handle_exposer.def("__repr__", &__str__<::SireBase::PageCache::Handle>); - Handle_exposer.def("__len__", &__len_size<::SireBase::PageCache::Handle>); + Handle_exposer.staticmethod( "typeName" ); + Handle_exposer.def( "__copy__", &__copy__); + Handle_exposer.def( "__deepcopy__", &__copy__); + Handle_exposer.def( "clone", &__copy__); + Handle_exposer.def( "__str__", &__str__< ::SireBase::PageCache::Handle > ); + Handle_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Handle > ); + Handle_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Handle > ); } { //::SireBase::PageCache::Page - typedef bp::class_ Page_exposer_t; - Page_exposer_t Page_exposer = Page_exposer_t("Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init<>("")); - bp::scope Page_scope(Page_exposer); - Page_exposer.def(bp::init>((bp::arg("data")), "")); - Page_exposer.def(bp::init((bp::arg("other")), "")); + typedef bp::class_< SireBase::PageCache::Page > Page_exposer_t; + Page_exposer_t Page_exposer = Page_exposer_t( "Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init< >("") ); + bp::scope Page_scope( Page_exposer ); + Page_exposer.def( bp::init< std::shared_ptr< SireBase::detail::PageData > >(( bp::arg("data") ), "") ); + Page_exposer.def( bp::init< SireBase::PageCache::Page const & >(( bp::arg("other") ), "") ); { //::SireBase::PageCache::Page::assertValid - - typedef void (::SireBase::PageCache::Page::*assertValid_function_type)() const; - assertValid_function_type assertValid_function_value(&::SireBase::PageCache::Page::assertValid); - - Page_exposer.def( - "assertValid", assertValid_function_value, bp::release_gil_policy(), ""); + + typedef void ( ::SireBase::PageCache::Page::*assertValid_function_type)( ) const; + assertValid_function_type assertValid_function_value( &::SireBase::PageCache::Page::assertValid ); + + Page_exposer.def( + "assertValid" + , assertValid_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::isCached - - typedef bool (::SireBase::PageCache::Page::*isCached_function_type)() const; - isCached_function_type isCached_function_value(&::SireBase::PageCache::Page::isCached); - - Page_exposer.def( - "isCached", isCached_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::Page::*isCached_function_type)( ) const; + isCached_function_type isCached_function_value( &::SireBase::PageCache::Page::isCached ); + + Page_exposer.def( + "isCached" + , isCached_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::isNull - - typedef bool (::SireBase::PageCache::Page::*isNull_function_type)() const; - isNull_function_type isNull_function_value(&::SireBase::PageCache::Page::isNull); - - Page_exposer.def( - "isNull", isNull_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::Page::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireBase::PageCache::Page::isNull ); + + Page_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::isResident - - typedef bool (::SireBase::PageCache::Page::*isResident_function_type)() const; - isResident_function_type isResident_function_value(&::SireBase::PageCache::Page::isResident); - - Page_exposer.def( - "isResident", isResident_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::Page::*isResident_function_type)( ) const; + isResident_function_type isResident_function_value( &::SireBase::PageCache::Page::isResident ); + + Page_exposer.def( + "isResident" + , isResident_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::isValid - - typedef bool (::SireBase::PageCache::Page::*isValid_function_type)() const; - isValid_function_type isValid_function_value(&::SireBase::PageCache::Page::isValid); - - Page_exposer.def( - "isValid", isValid_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::Page::*isValid_function_type)( ) const; + isValid_function_type isValid_function_value( &::SireBase::PageCache::Page::isValid ); + + Page_exposer.def( + "isValid" + , isValid_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::Page::maxBytes + + typedef int ( ::SireBase::PageCache::Page::*maxBytes_function_type)( ) const; + maxBytes_function_type maxBytes_function_value( &::SireBase::PageCache::Page::maxBytes ); + + Page_exposer.def( + "maxBytes" + , maxBytes_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::nBytes - - typedef int (::SireBase::PageCache::Page::*nBytes_function_type)() const; - nBytes_function_type nBytes_function_value(&::SireBase::PageCache::Page::nBytes); - - Page_exposer.def( - "nBytes", nBytes_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::Page::*nBytes_function_type)( ) const; + nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Page::nBytes ); + + Page_exposer.def( + "nBytes" + , nBytes_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::operator= - - typedef ::SireBase::PageCache::Page &(::SireBase::PageCache::Page::*assign_function_type)(::SireBase::PageCache::Page const &); - assign_function_type assign_function_value(&::SireBase::PageCache::Page::operator=); - - Page_exposer.def( - "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); + + typedef ::SireBase::PageCache::Page & ( ::SireBase::PageCache::Page::*assign_function_type)( ::SireBase::PageCache::Page const & ) ; + assign_function_type assign_function_value( &::SireBase::PageCache::Page::operator= ); + + Page_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + } { //::SireBase::PageCache::Page::parent - - typedef ::SireBase::PageCache (::SireBase::PageCache::Page::*parent_function_type)() const; - parent_function_type parent_function_value(&::SireBase::PageCache::Page::parent); - - Page_exposer.def( - "parent", parent_function_value, bp::release_gil_policy(), ""); + + typedef ::SireBase::PageCache ( ::SireBase::PageCache::Page::*parent_function_type)( ) const; + parent_function_type parent_function_value( &::SireBase::PageCache::Page::parent ); + + Page_exposer.def( + "parent" + , parent_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::size - - typedef int (::SireBase::PageCache::Page::*size_function_type)() const; - size_function_type size_function_value(&::SireBase::PageCache::Page::size); - - Page_exposer.def( - "size", size_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::Page::*size_function_type)( ) const; + size_function_type size_function_value( &::SireBase::PageCache::Page::size ); + + Page_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::toString - - typedef ::QString (::SireBase::PageCache::Page::*toString_function_type)() const; - toString_function_type toString_function_value(&::SireBase::PageCache::Page::toString); - - Page_exposer.def( - "toString", toString_function_value, bp::release_gil_policy(), ""); + + typedef ::QString ( ::SireBase::PageCache::Page::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireBase::PageCache::Page::toString ); + + Page_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::typeName - - typedef char const *(*typeName_function_type)(); - typeName_function_type typeName_function_value(&::SireBase::PageCache::Page::typeName); - - Page_exposer.def( - "typeName", typeName_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireBase::PageCache::Page::typeName ); + + Page_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::Page::what - - typedef char const *(::SireBase::PageCache::Page::*what_function_type)() const; - what_function_type what_function_value(&::SireBase::PageCache::Page::what); - - Page_exposer.def( - "what", what_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( ::SireBase::PageCache::Page::*what_function_type)( ) const; + what_function_type what_function_value( &::SireBase::PageCache::Page::what ); + + Page_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + } - Page_exposer.staticmethod("typeName"); - Page_exposer.def("__copy__", &__copy__); - Page_exposer.def("__deepcopy__", &__copy__); - Page_exposer.def("clone", &__copy__); - Page_exposer.def("__str__", &__str__<::SireBase::PageCache::Page>); - Page_exposer.def("__repr__", &__str__<::SireBase::PageCache::Page>); - Page_exposer.def("__len__", &__len_size<::SireBase::PageCache::Page>); + Page_exposer.staticmethod( "typeName" ); + Page_exposer.def( "__copy__", &__copy__); + Page_exposer.def( "__deepcopy__", &__copy__); + Page_exposer.def( "clone", &__copy__); + Page_exposer.def( "__str__", &__str__< ::SireBase::PageCache::Page > ); + Page_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Page > ); + Page_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Page > ); } - PageCache_exposer.def(bp::init>((bp::arg("cache_dir"), bp::arg("page_size") = (int)(32 * 1024 * 1024)), "")); - PageCache_exposer.def(bp::init>((bp::arg("data")), "")); - PageCache_exposer.def(bp::init((bp::arg("other")), "")); + PageCache_exposer.def( bp::init< QString const &, bp::optional< int > >(( bp::arg("cache_dir"), bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); + PageCache_exposer.def( bp::init< std::shared_ptr< SireBase::detail::CacheData > >(( bp::arg("data") ), "") ); + PageCache_exposer.def( bp::init< SireBase::PageCache const & >(( bp::arg("other") ), "") ); { //::SireBase::PageCache::assertValid - - typedef void (::SireBase::PageCache::*assertValid_function_type)() const; - assertValid_function_type assertValid_function_value(&::SireBase::PageCache::assertValid); - - PageCache_exposer.def( - "assertValid", assertValid_function_value, bp::release_gil_policy(), ""); + + typedef void ( ::SireBase::PageCache::*assertValid_function_type)( ) const; + assertValid_function_type assertValid_function_value( &::SireBase::PageCache::assertValid ); + + PageCache_exposer.def( + "assertValid" + , assertValid_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::cache - - typedef ::SireBase::PageCache::Handle (::SireBase::PageCache::*cache_function_type)(::QByteArray const &); - cache_function_type cache_function_value(&::SireBase::PageCache::cache); - - PageCache_exposer.def( - "cache", cache_function_value, (bp::arg("data")), bp::release_gil_policy(), ""); + + typedef ::SireBase::PageCache::Handle ( ::SireBase::PageCache::*cache_function_type)( ::QByteArray const & ) ; + cache_function_type cache_function_value( &::SireBase::PageCache::cache ); + + PageCache_exposer.def( + "cache" + , cache_function_value + , ( bp::arg("data") ) + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::cacheDir - - typedef ::QString (::SireBase::PageCache::*cacheDir_function_type)() const; - cacheDir_function_type cacheDir_function_value(&::SireBase::PageCache::cacheDir); - - PageCache_exposer.def( - "cacheDir", cacheDir_function_value, bp::release_gil_policy(), ""); + + typedef ::QString ( ::SireBase::PageCache::*cacheDir_function_type)( ) const; + cacheDir_function_type cacheDir_function_value( &::SireBase::PageCache::cacheDir ); + + PageCache_exposer.def( + "cacheDir" + , cacheDir_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::isNull - - typedef bool (::SireBase::PageCache::*isNull_function_type)() const; - isNull_function_type isNull_function_value(&::SireBase::PageCache::isNull); - - PageCache_exposer.def( - "isNull", isNull_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireBase::PageCache::isNull ); + + PageCache_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::isValid - - typedef bool (::SireBase::PageCache::*isValid_function_type)() const; - isValid_function_type isValid_function_value(&::SireBase::PageCache::isValid); - - PageCache_exposer.def( - "isValid", isValid_function_value, bp::release_gil_policy(), ""); + + typedef bool ( ::SireBase::PageCache::*isValid_function_type)( ) const; + isValid_function_type isValid_function_value( &::SireBase::PageCache::isValid ); + + PageCache_exposer.def( + "isValid" + , isValid_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::nBytes - - typedef int (::SireBase::PageCache::*nBytes_function_type)() const; - nBytes_function_type nBytes_function_value(&::SireBase::PageCache::nBytes); - - PageCache_exposer.def( - "nBytes", nBytes_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::*nBytes_function_type)( ) const; + nBytes_function_type nBytes_function_value( &::SireBase::PageCache::nBytes ); + + PageCache_exposer.def( + "nBytes" + , nBytes_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::nPages - - typedef int (::SireBase::PageCache::*nPages_function_type)() const; - nPages_function_type nPages_function_value(&::SireBase::PageCache::nPages); - - PageCache_exposer.def( - "nPages", nPages_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::*nPages_function_type)( ) const; + nPages_function_type nPages_function_value( &::SireBase::PageCache::nPages ); + + PageCache_exposer.def( + "nPages" + , nPages_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::operator= - - typedef ::SireBase::PageCache &(::SireBase::PageCache::*assign_function_type)(::SireBase::PageCache const &); - assign_function_type assign_function_value(&::SireBase::PageCache::operator=); - - PageCache_exposer.def( - "assign", assign_function_value, (bp::arg("other")), bp::return_self<>(), ""); + + typedef ::SireBase::PageCache & ( ::SireBase::PageCache::*assign_function_type)( ::SireBase::PageCache const & ) ; + assign_function_type assign_function_value( &::SireBase::PageCache::operator= ); + + PageCache_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "" ); + } { //::SireBase::PageCache::pageSize - - typedef int (::SireBase::PageCache::*pageSize_function_type)() const; - pageSize_function_type pageSize_function_value(&::SireBase::PageCache::pageSize); - - PageCache_exposer.def( - "pageSize", pageSize_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::*pageSize_function_type)( ) const; + pageSize_function_type pageSize_function_value( &::SireBase::PageCache::pageSize ); + + PageCache_exposer.def( + "pageSize" + , pageSize_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::size - - typedef int (::SireBase::PageCache::*size_function_type)() const; - size_function_type size_function_value(&::SireBase::PageCache::size); - - PageCache_exposer.def( - "size", size_function_value, bp::release_gil_policy(), ""); + + typedef int ( ::SireBase::PageCache::*size_function_type)( ) const; + size_function_type size_function_value( &::SireBase::PageCache::size ); + + PageCache_exposer.def( + "size" + , size_function_value + , bp::release_gil_policy() + , "" ); + + } + { //::SireBase::PageCache::store + + typedef ::SireBase::PageCache::Handle ( ::SireBase::PageCache::*store_function_type)( ::QByteArray const & ) ; + store_function_type store_function_value( &::SireBase::PageCache::store ); + + PageCache_exposer.def( + "store" + , store_function_value + , ( bp::arg("data") ) + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::toString - - typedef ::QString (::SireBase::PageCache::*toString_function_type)() const; - toString_function_type toString_function_value(&::SireBase::PageCache::toString); - - PageCache_exposer.def( - "toString", toString_function_value, bp::release_gil_policy(), ""); + + typedef ::QString ( ::SireBase::PageCache::*toString_function_type)( ) const; + toString_function_type toString_function_value( &::SireBase::PageCache::toString ); + + PageCache_exposer.def( + "toString" + , toString_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::typeName - - typedef char const *(*typeName_function_type)(); - typeName_function_type typeName_function_value(&::SireBase::PageCache::typeName); - - PageCache_exposer.def( - "typeName", typeName_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireBase::PageCache::typeName ); + + PageCache_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::what - - typedef char const *(::SireBase::PageCache::*what_function_type)() const; - what_function_type what_function_value(&::SireBase::PageCache::what); - - PageCache_exposer.def( - "what", what_function_value, bp::release_gil_policy(), ""); + + typedef char const * ( ::SireBase::PageCache::*what_function_type)( ) const; + what_function_type what_function_value( &::SireBase::PageCache::what ); + + PageCache_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "" ); + } - PageCache_exposer.staticmethod("typeName"); - PageCache_exposer.def("__copy__", &__copy__); - PageCache_exposer.def("__deepcopy__", &__copy__); - PageCache_exposer.def("clone", &__copy__); - PageCache_exposer.def("__str__", &__str__<::SireBase::PageCache>); - PageCache_exposer.def("__repr__", &__str__<::SireBase::PageCache>); + PageCache_exposer.staticmethod( "typeName" ); + PageCache_exposer.def( "__copy__", &__copy__); + PageCache_exposer.def( "__deepcopy__", &__copy__); + PageCache_exposer.def( "clone", &__copy__); + PageCache_exposer.def( "__str__", &pvt_get_name); + PageCache_exposer.def( "__repr__", &pvt_get_name); } + } diff --git a/wrapper/Base/Process.pypp.cpp b/wrapper/Base/Process.pypp.cpp index 921f1c9da..fe4a80e50 100644 --- a/wrapper/Base/Process.pypp.cpp +++ b/wrapper/Base/Process.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireBase::Process __copy__(const SireBase::Process &other){ return SireBase::Process(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireBase::Process&){ return "SireBase::Process";} #include "Helpers/release_gil_policy.hpp" @@ -241,9 +243,9 @@ void register_Process_class(){ Process_exposer.staticmethod( "killAll" ); Process_exposer.staticmethod( "run" ); Process_exposer.staticmethod( "typeName" ); - Process_exposer.def( "__copy__", &__copy__); - Process_exposer.def( "__deepcopy__", &__copy__); - Process_exposer.def( "clone", &__copy__); + Process_exposer.def( "__copy__", &__copy__); + Process_exposer.def( "__deepcopy__", &__copy__); + Process_exposer.def( "clone", &__copy__); Process_exposer.def( "__str__", &pvt_get_name); Process_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Base/ProgressBar.pypp.cpp b/wrapper/Base/ProgressBar.pypp.cpp index e702d0fec..cf15bacb0 100644 --- a/wrapper/Base/ProgressBar.pypp.cpp +++ b/wrapper/Base/ProgressBar.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireBase::ProgressBar __copy__(const SireBase::ProgressBar &other){ return SireBase::ProgressBar(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -328,9 +330,9 @@ void register_ProgressBar_class(){ ProgressBar_exposer.staticmethod( "setSilent" ); ProgressBar_exposer.staticmethod( "setTheme" ); ProgressBar_exposer.staticmethod( "typeName" ); - ProgressBar_exposer.def( "__copy__", &__copy__); - ProgressBar_exposer.def( "__deepcopy__", &__copy__); - ProgressBar_exposer.def( "clone", &__copy__); + ProgressBar_exposer.def( "__copy__", &__copy__); + ProgressBar_exposer.def( "__deepcopy__", &__copy__); + ProgressBar_exposer.def( "clone", &__copy__); ProgressBar_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::ProgressBar >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ProgressBar_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::ProgressBar >, diff --git a/wrapper/Base/Properties.pypp.cpp b/wrapper/Base/Properties.pypp.cpp index ae40b6f4d..73316a656 100644 --- a/wrapper/Base/Properties.pypp.cpp +++ b/wrapper/Base/Properties.pypp.cpp @@ -30,6 +30,8 @@ namespace bp = boost::python; SireBase::Properties __copy__(const SireBase::Properties &other){ return SireBase::Properties(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -605,9 +607,9 @@ void register_Properties_class(){ } Properties_exposer.staticmethod( "typeName" ); - Properties_exposer.def( "__copy__", &__copy__); - Properties_exposer.def( "__deepcopy__", &__copy__); - Properties_exposer.def( "clone", &__copy__); + Properties_exposer.def( "__copy__", &__copy__); + Properties_exposer.def( "__deepcopy__", &__copy__); + Properties_exposer.def( "clone", &__copy__); Properties_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::Properties >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Properties_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::Properties >, diff --git a/wrapper/Base/PropertyList.pypp.cpp b/wrapper/Base/PropertyList.pypp.cpp index 664246bc8..66ea4c6b3 100644 --- a/wrapper/Base/PropertyList.pypp.cpp +++ b/wrapper/Base/PropertyList.pypp.cpp @@ -32,6 +32,8 @@ namespace bp = boost::python; SireBase::PropertyList __copy__(const SireBase::PropertyList &other){ return SireBase::PropertyList(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -579,9 +581,9 @@ void register_PropertyList_class(){ } PropertyList_exposer.staticmethod( "typeName" ); - PropertyList_exposer.def( "__copy__", &__copy__); - PropertyList_exposer.def( "__deepcopy__", &__copy__); - PropertyList_exposer.def( "clone", &__copy__); + PropertyList_exposer.def( "__copy__", &__copy__); + PropertyList_exposer.def( "__deepcopy__", &__copy__); + PropertyList_exposer.def( "clone", &__copy__); PropertyList_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PropertyList >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PropertyList_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PropertyList >, diff --git a/wrapper/Base/PropertyMap.pypp.cpp b/wrapper/Base/PropertyMap.pypp.cpp index b16f7f7ab..b8fa8c5ea 100644 --- a/wrapper/Base/PropertyMap.pypp.cpp +++ b/wrapper/Base/PropertyMap.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireBase::PropertyMap __copy__(const SireBase::PropertyMap &other){ return SireBase::PropertyMap(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -253,9 +255,9 @@ void register_PropertyMap_class(){ } PropertyMap_exposer.staticmethod( "typeName" ); - PropertyMap_exposer.def( "__copy__", &__copy__); - PropertyMap_exposer.def( "__deepcopy__", &__copy__); - PropertyMap_exposer.def( "clone", &__copy__); + PropertyMap_exposer.def( "__copy__", &__copy__); + PropertyMap_exposer.def( "__deepcopy__", &__copy__); + PropertyMap_exposer.def( "clone", &__copy__); PropertyMap_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PropertyMap >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PropertyMap_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PropertyMap >, diff --git a/wrapper/Base/PropertyName.pypp.cpp b/wrapper/Base/PropertyName.pypp.cpp index cba50c8c0..328db19b8 100644 --- a/wrapper/Base/PropertyName.pypp.cpp +++ b/wrapper/Base/PropertyName.pypp.cpp @@ -22,6 +22,8 @@ namespace bp = boost::python; SireBase::PropertyName __copy__(const SireBase::PropertyName &other){ return SireBase::PropertyName(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -176,9 +178,9 @@ void register_PropertyName_class(){ } PropertyName_exposer.staticmethod( "none" ); PropertyName_exposer.staticmethod( "typeName" ); - PropertyName_exposer.def( "__copy__", &__copy__); - PropertyName_exposer.def( "__deepcopy__", &__copy__); - PropertyName_exposer.def( "clone", &__copy__); + PropertyName_exposer.def( "__copy__", &__copy__); + PropertyName_exposer.def( "__deepcopy__", &__copy__); + PropertyName_exposer.def( "clone", &__copy__); PropertyName_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::PropertyName >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PropertyName_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::PropertyName >, diff --git a/wrapper/Base/SimpleRange.pypp.cpp b/wrapper/Base/SimpleRange.pypp.cpp index 62c3f7b79..55e8b1de6 100644 --- a/wrapper/Base/SimpleRange.pypp.cpp +++ b/wrapper/Base/SimpleRange.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireBase::SimpleRange __copy__(const SireBase::SimpleRange &other){ return SireBase::SimpleRange(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -125,9 +127,9 @@ void register_SimpleRange_class(){ } SimpleRange_exposer.staticmethod( "typeName" ); - SimpleRange_exposer.def( "__copy__", &__copy__); - SimpleRange_exposer.def( "__deepcopy__", &__copy__); - SimpleRange_exposer.def( "clone", &__copy__); + SimpleRange_exposer.def( "__copy__", &__copy__); + SimpleRange_exposer.def( "__deepcopy__", &__copy__); + SimpleRange_exposer.def( "clone", &__copy__); SimpleRange_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::SimpleRange >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SimpleRange_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::SimpleRange >, diff --git a/wrapper/Base/StringArrayProperty.pypp.cpp b/wrapper/Base/StringArrayProperty.pypp.cpp index 9e33b4fcd..94e16b7bf 100644 --- a/wrapper/Base/StringArrayProperty.pypp.cpp +++ b/wrapper/Base/StringArrayProperty.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireBase::StringArrayProperty __copy__(const SireBase::StringArrayProperty &other){ return SireBase::StringArrayProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -188,9 +190,9 @@ void register_StringArrayProperty_class(){ } StringArrayProperty_exposer.staticmethod( "typeName" ); - StringArrayProperty_exposer.def( "__copy__", &__copy__); - StringArrayProperty_exposer.def( "__deepcopy__", &__copy__); - StringArrayProperty_exposer.def( "clone", &__copy__); + StringArrayProperty_exposer.def( "__copy__", &__copy__); + StringArrayProperty_exposer.def( "__deepcopy__", &__copy__); + StringArrayProperty_exposer.def( "clone", &__copy__); StringArrayProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::StringArrayProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); StringArrayProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::StringArrayProperty >, diff --git a/wrapper/Base/StringProperty.pypp.cpp b/wrapper/Base/StringProperty.pypp.cpp index 8e42c55f4..b6d031edc 100644 --- a/wrapper/Base/StringProperty.pypp.cpp +++ b/wrapper/Base/StringProperty.pypp.cpp @@ -27,6 +27,8 @@ namespace bp = boost::python; SireBase::StringProperty __copy__(const SireBase::StringProperty &other){ return SireBase::StringProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -191,9 +193,9 @@ void register_StringProperty_class(){ } StringProperty_exposer.staticmethod( "typeName" ); - StringProperty_exposer.def( "__copy__", &__copy__); - StringProperty_exposer.def( "__deepcopy__", &__copy__); - StringProperty_exposer.def( "clone", &__copy__); + StringProperty_exposer.def( "__copy__", &__copy__); + StringProperty_exposer.def( "__deepcopy__", &__copy__); + StringProperty_exposer.def( "clone", &__copy__); StringProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::StringProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); StringProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::StringProperty >, diff --git a/wrapper/Base/TimeProperty.pypp.cpp b/wrapper/Base/TimeProperty.pypp.cpp index e569eab93..0e91a3b1c 100644 --- a/wrapper/Base/TimeProperty.pypp.cpp +++ b/wrapper/Base/TimeProperty.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireBase::TimeProperty __copy__(const SireBase::TimeProperty &other){ return SireBase::TimeProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -90,9 +92,9 @@ void register_TimeProperty_class(){ } TimeProperty_exposer.staticmethod( "typeName" ); - TimeProperty_exposer.def( "__copy__", &__copy__); - TimeProperty_exposer.def( "__deepcopy__", &__copy__); - TimeProperty_exposer.def( "clone", &__copy__); + TimeProperty_exposer.def( "__copy__", &__copy__); + TimeProperty_exposer.def( "__deepcopy__", &__copy__); + TimeProperty_exposer.def( "clone", &__copy__); TimeProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::TimeProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TimeProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::TimeProperty >, diff --git a/wrapper/Base/TrigArray2D_double_.pypp.cpp b/wrapper/Base/TrigArray2D_double_.pypp.cpp index 60de5deee..6a896bbe9 100644 --- a/wrapper/Base/TrigArray2D_double_.pypp.cpp +++ b/wrapper/Base/TrigArray2D_double_.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::TrigArray2D __copy__(const SireBase::TrigArray2D &other){ return SireBase::TrigArray2D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -162,9 +164,9 @@ void register_TrigArray2D_double__class(){ , "" ); } - TrigArray2D_double__exposer.def( "__copy__", &__copy__); - TrigArray2D_double__exposer.def( "__deepcopy__", &__copy__); - TrigArray2D_double__exposer.def( "clone", &__copy__); + TrigArray2D_double__exposer.def( "__copy__", &__copy__>); + TrigArray2D_double__exposer.def( "__deepcopy__", &__copy__>); + TrigArray2D_double__exposer.def( "clone", &__copy__>); TrigArray2D_double__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::TrigArray2D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TrigArray2D_double__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::TrigArray2D >, diff --git a/wrapper/Base/TrimString.pypp.cpp b/wrapper/Base/TrimString.pypp.cpp index 58b09e0fd..03411434d 100644 --- a/wrapper/Base/TrimString.pypp.cpp +++ b/wrapper/Base/TrimString.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::TrimString __copy__(const SireBase::TrimString &other){ return SireBase::TrimString(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -73,9 +75,9 @@ void register_TrimString_class(){ } TrimString_exposer.staticmethod( "typeName" ); - TrimString_exposer.def( "__copy__", &__copy__); - TrimString_exposer.def( "__deepcopy__", &__copy__); - TrimString_exposer.def( "clone", &__copy__); + TrimString_exposer.def( "__copy__", &__copy__); + TrimString_exposer.def( "__deepcopy__", &__copy__); + TrimString_exposer.def( "clone", &__copy__); TrimString_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::TrimString >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TrimString_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::TrimString >, diff --git a/wrapper/Base/UnitTest.pypp.cpp b/wrapper/Base/UnitTest.pypp.cpp index aceb0ad11..b9d2230b1 100644 --- a/wrapper/Base/UnitTest.pypp.cpp +++ b/wrapper/Base/UnitTest.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::UnitTest __copy__(const SireBase::UnitTest &other){ return SireBase::UnitTest(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireBase::UnitTest&){ return "SireBase::UnitTest";} #include "Helpers/release_gil_policy.hpp" @@ -129,9 +131,9 @@ void register_UnitTest_class(){ UnitTest_exposer.staticmethod( "runAll" ); UnitTest_exposer.staticmethod( "tests" ); bp::register_ptr_to_python< std::shared_ptr< SireBase::UnitTest > >(); - UnitTest_exposer.def( "__copy__", &__copy__); - UnitTest_exposer.def( "__deepcopy__", &__copy__); - UnitTest_exposer.def( "clone", &__copy__); + UnitTest_exposer.def( "__copy__", &__copy__); + UnitTest_exposer.def( "__deepcopy__", &__copy__); + UnitTest_exposer.def( "clone", &__copy__); UnitTest_exposer.def( "__str__", &pvt_get_name); UnitTest_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Base/UpperCaseString.pypp.cpp b/wrapper/Base/UpperCaseString.pypp.cpp index 68e280a95..ee90bfcf9 100644 --- a/wrapper/Base/UpperCaseString.pypp.cpp +++ b/wrapper/Base/UpperCaseString.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::UpperCaseString __copy__(const SireBase::UpperCaseString &other){ return SireBase::UpperCaseString(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -73,9 +75,9 @@ void register_UpperCaseString_class(){ } UpperCaseString_exposer.staticmethod( "typeName" ); - UpperCaseString_exposer.def( "__copy__", &__copy__); - UpperCaseString_exposer.def( "__deepcopy__", &__copy__); - UpperCaseString_exposer.def( "clone", &__copy__); + UpperCaseString_exposer.def( "__copy__", &__copy__); + UpperCaseString_exposer.def( "__deepcopy__", &__copy__); + UpperCaseString_exposer.def( "clone", &__copy__); UpperCaseString_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::UpperCaseString >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); UpperCaseString_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::UpperCaseString >, diff --git a/wrapper/Base/VariantProperty.pypp.cpp b/wrapper/Base/VariantProperty.pypp.cpp index f653c2b54..ee642e3d4 100644 --- a/wrapper/Base/VariantProperty.pypp.cpp +++ b/wrapper/Base/VariantProperty.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::VariantProperty __copy__(const SireBase::VariantProperty &other){ return SireBase::VariantProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -233,9 +235,9 @@ void register_VariantProperty_class(){ } VariantProperty_exposer.staticmethod( "typeName" ); - VariantProperty_exposer.def( "__copy__", &__copy__); - VariantProperty_exposer.def( "__deepcopy__", &__copy__); - VariantProperty_exposer.def( "clone", &__copy__); + VariantProperty_exposer.def( "__copy__", &__copy__); + VariantProperty_exposer.def( "__deepcopy__", &__copy__); + VariantProperty_exposer.def( "clone", &__copy__); VariantProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::VariantProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); VariantProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::VariantProperty >, diff --git a/wrapper/Base/Version.pypp.cpp b/wrapper/Base/Version.pypp.cpp index d414d2d12..e08dc2e42 100644 --- a/wrapper/Base/Version.pypp.cpp +++ b/wrapper/Base/Version.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireBase::Version __copy__(const SireBase::Version &other){ return SireBase::Version(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -108,9 +110,9 @@ void register_Version_class(){ } Version_exposer.staticmethod( "typeName" ); - Version_exposer.def( "__copy__", &__copy__); - Version_exposer.def( "__deepcopy__", &__copy__); - Version_exposer.def( "clone", &__copy__); + Version_exposer.def( "__copy__", &__copy__); + Version_exposer.def( "__deepcopy__", &__copy__); + Version_exposer.def( "clone", &__copy__); Version_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireBase::Version >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Version_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireBase::Version >, From c401394fa2ec137969e1bf60fa6ae20bc193bb90 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 16 Apr 2024 14:24:14 +0100 Subject: [PATCH 223/468] Infer element1 property from ambertype1. [closes #186] --- src/sire/morph/_pertfile.py | 13 +++++++++++-- tests/morph/test_pert.py | 18 ++++++++++++++++++ 2 files changed, 29 insertions(+), 2 deletions(-) diff --git a/src/sire/morph/_pertfile.py b/src/sire/morph/_pertfile.py index d85c37f57..7506d6c65 100644 --- a/src/sire/morph/_pertfile.py +++ b/src/sire/morph/_pertfile.py @@ -26,6 +26,7 @@ def create_from_pertfile(mol, pertfile, map=None): from ..legacy.IO import PerturbationsLibrary from ..base import create_map + from ..mol import Element map = create_map(map) @@ -65,6 +66,7 @@ def create_from_pertfile(mol, pertfile, map=None): chg_prop = map["charge"].source() lj_prop = map["LJ"].source() typ_prop = map["ambertype"].source() + elem_prop = map["element"].source() c["charge0"] = c[chg_prop] c["charge1"] = c[chg_prop] @@ -75,9 +77,13 @@ def create_from_pertfile(mol, pertfile, map=None): c["ambertype0"] = c[typ_prop] c["ambertype1"] = c[typ_prop] + c["element0"] = c[elem_prop] + for atom in c.atoms(): atomname = atom.name + atom["element1"] = atom["element"] + try: q0 = template.get_init_charge(atomname) q1 = template.get_final_charge(atomname) @@ -97,6 +103,8 @@ def create_from_pertfile(mol, pertfile, map=None): atom["ambertype0"] = typ0 atom["ambertype1"] = typ1 + atom["element1"] = Element.biological_element(typ1) + # now update all of the internals bond_prop = map["bond"].source() ang_prop = map["angle"].source() @@ -251,8 +259,8 @@ def create_from_pertfile(mol, pertfile, map=None): c["improper0"] = impropers0 c["improper1"] = impropers1 - # duplicate the coordinates, mass, and element properties - for prop in ["coordinates", "mass", "element", "forcefield", "intrascale"]: + # duplicate unperturbed properties + for prop in ["coordinates", "mass", "forcefield", "intrascale"]: orig_prop = map[prop].source() c[prop + "0"] = c[orig_prop] c[prop + "1"] = c[orig_prop] @@ -262,6 +270,7 @@ def create_from_pertfile(mol, pertfile, map=None): del c[chg_prop] del c[lj_prop] del c[typ_prop] + del c[elem_prop] del c[bond_prop] del c[ang_prop] del c[dih_prop] diff --git a/tests/morph/test_pert.py b/tests/morph/test_pert.py index 535830194..36e76b240 100644 --- a/tests/morph/test_pert.py +++ b/tests/morph/test_pert.py @@ -320,3 +320,21 @@ def test_extract_and_link_solv(solvated_neopentane_methane, openmm_platform): nrg_pert = pert_mols.dynamics(map=map).current_potential_energy().value() assert nrg_1_1 == pytest.approx(nrg_pert, 1e-3) + + +def test_ambertype_to_element(neopentane_methane): + from sire.mol import Element + + mols = neopentane_methane.clone() + + mols = sr.morph.link_to_reference(mols) + + mols2 = sr.morph.extract_reference(mols) + + mol = sr.morph.create_from_pertfile(mols2[0], neopentane_methane_pert) + + element1 = mol.property("element1") + ambertype1 = mol.property("ambertype1") + + for a, e in zip(ambertype1, element1): + assert e == Element.biological_element(a) From 7da7ce622400b0ac77ae069f5db9f142460dcc29 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 16 Apr 2024 14:28:18 +0100 Subject: [PATCH 224/468] Added CHANGELOG entry. --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 3645708a8..5e528c5d1 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -16,6 +16,7 @@ organisation on `GitHub `__. ----------------------------------------------------------------------------------------- * Please add an item to this changelog when you create your PR +* Correctly set the ``element1`` property in ``sire.morph.create_from_pertfile``. `2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ From 8858c28cf1779ec84765406b8baa16bdeb2d3a3e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 16 Apr 2024 15:35:38 +0100 Subject: [PATCH 225/468] Simplify. [ci skip] --- src/sire/morph/_pertfile.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/sire/morph/_pertfile.py b/src/sire/morph/_pertfile.py index 7506d6c65..ccd594cc6 100644 --- a/src/sire/morph/_pertfile.py +++ b/src/sire/morph/_pertfile.py @@ -78,12 +78,11 @@ def create_from_pertfile(mol, pertfile, map=None): c["ambertype1"] = c[typ_prop] c["element0"] = c[elem_prop] + c["element1"] = c[elem_prop] for atom in c.atoms(): atomname = atom.name - atom["element1"] = atom["element"] - try: q0 = template.get_init_charge(atomname) q1 = template.get_final_charge(atomname) From d4f653d7ec99d133184af639762b88bb66b3f8e0 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 16 Apr 2024 18:55:24 +0100 Subject: [PATCH 226/468] Frame data is correctly block saved and loaded from a binary array. This is being correctly cached back to a page, and restored from that page. --- corelib/src/libs/SireBase/pagecache.cpp | 11 +- corelib/src/libs/SireMol/trajectory.cpp | 131 +++++++++++++++++- .../src/libs/SireSystem/systemtrajectory.cpp | 44 +----- 3 files changed, 142 insertions(+), 44 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index c5a5a6c04..507dc4ced 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -182,7 +182,9 @@ CacheData::CacheData(QString c, int p) CacheData::~CacheData() { this->requestInterruption(); - this->wait(); + + if (QThread::currentThread() != this) + this->wait(); } PageCache::Handle CacheData::cache(const QByteArray &data) @@ -226,7 +228,9 @@ void CacheData::enqueue(const std::shared_ptr &handle) // this is the race condition where the current thread loop // is in the process of exiting, but we need to wait for that // to complete - this->wait(); + if (QThread::currentThread() != this) + this->wait(); + this->exiting = false; } @@ -502,9 +506,6 @@ void HandleData::setPage(const PageCache::Page &page, int off) d = QByteArray(); lkr.unlock(); - qDebug() << "DATA MOVED TO PAGE"; - - qDebug() << p.toString(); } PageCache::Page HandleData::page() const diff --git a/corelib/src/libs/SireMol/trajectory.cpp b/corelib/src/libs/SireMol/trajectory.cpp index 3755fc280..4e4414d73 100644 --- a/corelib/src/libs/SireMol/trajectory.cpp +++ b/corelib/src/libs/SireMol/trajectory.cpp @@ -50,6 +50,7 @@ #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" +#include "SireStream/magic_error.h" using namespace SireMol; using namespace SireVol; @@ -1448,7 +1449,135 @@ QByteArray Frame::toByteArray() const Frame Frame::fromByteArray(const QByteArray &data) { - return Frame(); + if (data.count() < 4) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + auto data_ptr = data.constData(); + + quint32 val; + std::memcpy(&val, data_ptr, sizeof(quint32)); + data_ptr += sizeof(quint32); + + if (val != r_frame.magicID()) + { + throw SireStream::magic_error(QObject::tr("The data is not a frame! %1").arg(val), CODELOC); + } + + std::memcpy(&val, data_ptr, sizeof(quint32)); + data_ptr += sizeof(quint32); + + if (val != 1) + { + throw SireStream::version_error(val, "1", r_frame, CODELOC); + } + + if (data_ptr + sizeof(quint32) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + std::memcpy(&val, data_ptr, sizeof(quint32)); + data_ptr += sizeof(quint32); + + QVector coords; + + if (val != 0) + { + if (data_ptr + val * sizeof(Vector) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + coords.resize(val); + std::memcpy(coords.data(), data_ptr, val * sizeof(Vector)); + data_ptr += val * sizeof(Vector); + } + + if (data_ptr + sizeof(quint32) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + std::memcpy(&val, data_ptr, sizeof(quint32)); + data_ptr += sizeof(quint32); + + QVector vels; + + if (val != 0) + { + if (data_ptr + val * sizeof(Velocity3D) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + vels.resize(val); + std::memcpy(vels.data(), data_ptr, val * sizeof(Velocity3D)); + data_ptr += val * sizeof(Velocity3D); + } + + if (data_ptr + sizeof(quint32) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + std::memcpy(&val, data_ptr, sizeof(quint32)); + data_ptr += sizeof(quint32); + + QVector frcs; + + if (val != 0) + { + if (data_ptr + val * sizeof(Force3D) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + frcs.resize(val); + std::memcpy(frcs.data(), data_ptr, val * sizeof(Force3D)); + data_ptr += val * sizeof(Force3D); + } + + if (data_ptr + sizeof(quint32) > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + std::memcpy(&val, data_ptr, sizeof(quint32)); + data_ptr += sizeof(quint32); + + SpacePtr spc; + Time t; + Properties props; + + if (val != 0) + { + if (data_ptr + val > data.constData() + data.count()) + { + throw SireError::incompatible_error(QObject::tr("The data is too short to be a frame! %1").arg(data.count()), + CODELOC); + } + + QByteArray extra(data_ptr, val); + QDataStream ds(extra); + + double time; + + ds >> spc >> time >> props; + + t = time * picosecond; + } + + return Frame(coords, vels, frcs, spc, t, props); } const char *Frame::typeName() diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index 0621dac70..146e0af40 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -323,18 +323,10 @@ Frame SystemFrames::_lkr_getFrame(int i) const return current_frame; } + // fetch the data from the cache and load it into a frame auto data = frames.at(i).fetch(); - - QDataStream ds(data); - - Frame frame; - - // auto start_time = std::chrono::high_resolution_clock::now(); - ds >> frame; - // auto end_time = std::chrono::high_resolution_clock::now(); - - // qDebug() << "Loading frame" << i << "with" << frames.at(i).size() << "bytes" << frame.numBytes(); - // qDebug() << "Deserialization time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + Frame frame = Frame::fromByteArray(data); + data.clear(); const_cast(this)->current_frame = frame; const_cast(this)->current_frame_index = i; @@ -537,34 +529,10 @@ void SystemFrames::saveFrame(const Molecules &mols, } } + // create the frame, convert it to a data array, then cache + // that array to get the handle Frame frame(coordinates, velocities, forces, space, time, props); - - auto start_time = std::chrono::high_resolution_clock::now(); - - QByteArray data1 = frame.toByteArray(); - - auto mem_time1 = std::chrono::high_resolution_clock::now(); - - QByteArray data; - data.reserve(2 * frame.numBytes()); - - auto mem_time = std::chrono::high_resolution_clock::now(); - - QDataStream ds(&data, QIODevice::WriteOnly); - ds << frame; - - auto cache_time = std::chrono::high_resolution_clock::now(); - - auto handle = cache->store(data); - - auto end_time = std::chrono::high_resolution_clock::now(); - - qDebug() << "Saving frame" << frames.count() << "with" << data.size() << "bytes" << frame.numBytes(); - qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - start_time).count() << "microseconds"; - qDebug() << "Memory time" << std::chrono::duration_cast(mem_time - mem_time1).count() << "microseconds"; - qDebug() << "Serialization time" << std::chrono::duration_cast(cache_time - mem_time).count() << "microseconds"; - qDebug() << "Cache time" << std::chrono::duration_cast(end_time - cache_time).count() << "microseconds"; - qDebug() << "Total time" << std::chrono::duration_cast(end_time - start_time).count() << "microseconds"; + auto handle = cache->store(frame.toByteArray()); // need to hold the write lock, as we are updating global state // for everyone who holds this live trajectory data From 2436e81c24e022f2940a28d51f3e1eb55e812ab8 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Tue, 16 Apr 2024 19:31:22 +0100 Subject: [PATCH 227/468] Can now easily print out the stats about the caches via a single static function --- corelib/src/libs/SireBase/pagecache.cpp | 154 ++++++++++++++++++++++-- corelib/src/libs/SireBase/pagecache.h | 2 + wrapper/Base/PageCache.pypp.cpp | 13 ++ 3 files changed, 159 insertions(+), 10 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 507dc4ced..e8f9e73b7 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -49,6 +49,8 @@ namespace SireBase CacheData(QString cachedir, int page_size); ~CacheData(); + static QString getStatistics(); + QString cacheDir() const; PageCache::Handle cache(const QByteArray &data); @@ -58,7 +60,7 @@ namespace SireBase int nPages() const; int nBytes() const; - std::weak_ptr self; + void registerCache(const std::shared_ptr &cache); protected: void run(); @@ -66,13 +68,18 @@ namespace SireBase private: void enqueue(const std::shared_ptr &handle); - QMutex mutex; + static QMutex caches_mutex; + static QList> caches; + + QMutex queue_mutex; QQueue> queue; + QMutex page_mutex; std::weak_ptr current_page; - QList> pages; + std::weak_ptr self; + QString cache_dir; int page_size; @@ -163,6 +170,75 @@ using namespace SireBase::detail; /////// Implementation of detail::CacheData /////// +QMutex CacheData::caches_mutex; +QList> CacheData::caches; + +void CacheData::registerCache(const std::shared_ptr &cache) +{ + QMutexLocker lkr(&caches_mutex); + caches.append(cache); + self = cache; +} + +QString CacheData::getStatistics() +{ + QMutexLocker lkr(&caches_mutex); + QList> local_caches = caches; + lkr.unlock(); + + QString stats; + + for (auto &cache : local_caches) + { + auto c = cache.lock(); + + if (c.get() != nullptr) + { + stats += QString("Cache: %1\n") + .arg(c->cacheDir()); + + QMutexLocker lkr2(&(c->page_mutex)); + + auto current = c->current_page.lock(); + + int total_bytes = 0; + + if (current.get() != nullptr) + { + stats += QString(" Current Page: %1 KB : is_resident %2\n") + .arg(current->nBytes() / 1024.0) + .arg(current->isResident()); + + total_bytes += current->nBytes(); + } + + int page_count = 0; + + for (auto &page : c->pages) + { + auto p = page.lock(); + + if (p.get() != nullptr) + { + page_count += 1; + + stats += QString(" Page %1: %2 KB : is_resident %3\n") + .arg(page_count) + .arg(p->nBytes() / 1024.0) + .arg(p->isResident()); + + total_bytes += p->nBytes(); + } + } + + stats += QString(" Total size: %1 KB\n") + .arg(total_bytes / 1024.0); + } + } + + return stats; +} + CacheData::CacheData(QString c, int p) : cache_dir(c), page_size(p), exiting(false) { @@ -184,7 +260,13 @@ CacheData::~CacheData() this->requestInterruption(); if (QThread::currentThread() != this) + { this->wait(); + } + else + { + qWarning() << "CacheData is deleting itself!" << this->cacheDir(); + } } PageCache::Handle CacheData::cache(const QByteArray &data) @@ -206,12 +288,49 @@ int CacheData::pageSize() const int CacheData::nPages() const { - return 0; + QMutexLocker lkr(const_cast(&page_mutex)); + int npages = 0; + + if (current_page.lock().get() != nullptr) + { + npages += 1; + } + + for (auto &page : pages) + { + if (page.lock().get() != nullptr) + { + npages += 1; + } + } + + return npages; } int CacheData::nBytes() const { - return 0; + QMutexLocker lkr(const_cast(&page_mutex)); + + int nbytes = 0; + + auto current = current_page.lock(); + + if (current.get() != nullptr) + { + nbytes += current->nBytes(); + } + + for (auto &page : pages) + { + auto p = page.lock(); + + if (p.get() != nullptr) + { + nbytes += p->nBytes(); + } + } + + return nbytes; } void CacheData::enqueue(const std::shared_ptr &handle) @@ -221,7 +340,7 @@ void CacheData::enqueue(const std::shared_ptr &handle) return; } - QMutexLocker lkr(&mutex); + QMutexLocker lkr(&queue_mutex); if (this->exiting) { @@ -244,6 +363,10 @@ void CacheData::enqueue(const std::shared_ptr &handle) void CacheData::run() { + // get hold of a pointer to self, so that we aren't + // deleted while we are running + auto locked_self = self.lock(); + int empty_count = 0; while (true) @@ -259,7 +382,7 @@ void CacheData::run() // pull an item off the queue { - QMutexLocker lkr(&mutex); + QMutexLocker lkr(&queue_mutex); if (this->isInterruptionRequested()) { @@ -291,7 +414,9 @@ void CacheData::run() // this is bigger than a page, so needs to have its // own page! auto page = std::make_shared(n_bytes, this->self.lock()); + QMutexLocker lkr(&page_mutex); this->pages.append(page); + lkr.unlock(); auto offset = page->cache(data); handle->setPage(PageCache::Page(page), offset); } @@ -303,6 +428,7 @@ void CacheData::run() if (current.get() == nullptr) { current = std::make_shared(page_size, this->self.lock()); + QMutexLocker lkr(&page_mutex); current_page = current; } @@ -315,11 +441,14 @@ void CacheData::run() else { // add the current page to the list of old pages + QMutexLocker lkr(&page_mutex); this->pages.append(current_page); // we need to create a new page current = std::make_shared(page_size, this->self.lock()); current_page = current; + lkr.unlock(); + auto offset = current->cache(data); handle->setPage(PageCache::Page(current), offset); } @@ -339,7 +468,7 @@ void CacheData::run() if (have_item) { // check to see if there is anything else to process - QMutexLocker lkr(&mutex); + QMutexLocker lkr(&queue_mutex); is_empty = queue.isEmpty(); empty_count += 1; @@ -767,13 +896,13 @@ void PageCache::Handle::reset() PageCache::PageCache(int page_size) : d(new CacheData(QString("."), page_size)) { - d->self = d; + d->registerCache(d); } PageCache::PageCache(const QString &cachedir, int page_size) : d(new CacheData(cachedir, page_size)) { - d->self = d; + d->registerCache(d); } PageCache::PageCache(std::shared_ptr data) @@ -825,6 +954,11 @@ void PageCache::assertValid() const } } +QString PageCache::getStatistics() +{ + return CacheData::getStatistics(); +} + QString PageCache::cacheDir() const { assertValid(); diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index 13058f52d..9c90fcea9 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -89,6 +89,8 @@ namespace SireBase void assertValid() const; + static QString getStatistics(); + /** This is a page in the cache. This can hold multiple * objects - the whole page is either resident in memory * or cached to disk. diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index 8db09555d..27cb4faeb 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -464,6 +464,18 @@ void register_PageCache_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireBase::PageCache::getStatistics + + typedef ::QString ( *getStatistics_function_type )( ); + getStatistics_function_type getStatistics_function_value( &::SireBase::PageCache::getStatistics ); + + PageCache_exposer.def( + "getStatistics" + , getStatistics_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::isNull @@ -599,6 +611,7 @@ void register_PageCache_class(){ , "" ); } + PageCache_exposer.staticmethod( "getStatistics" ); PageCache_exposer.staticmethod( "typeName" ); PageCache_exposer.def( "__copy__", &__copy__); PageCache_exposer.def( "__deepcopy__", &__copy__); From d13df39da9692ed93d60011725e4742e9cef5900 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 17 Apr 2024 19:42:23 +0100 Subject: [PATCH 228/468] Can page back to disk. Temp files and dirs work well. Have a problem if the cache thread is still running at shutdown, as it doesn't correctly empty everything as the cache thread holds a pointer to itself... --- corelib/src/libs/SireBase/pagecache.cpp | 184 +++++++++++++++--- .../src/libs/SireSystem/systemtrajectory.cpp | 4 +- 2 files changed, 162 insertions(+), 26 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index e8f9e73b7..36f683641 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -36,6 +36,9 @@ #include #include #include +#include +#include +#include #include @@ -67,6 +70,7 @@ namespace SireBase private: void enqueue(const std::shared_ptr &handle); + std::shared_ptr getCacheDir(); static QMutex caches_mutex; static QList> caches; @@ -80,7 +84,9 @@ namespace SireBase std::weak_ptr self; - QString cache_dir; + std::weak_ptr cache_dir; + QString cache_dir_template; + int page_size; bool exiting; @@ -101,6 +107,8 @@ namespace SireBase int cache(const QByteArray &data); + void freeze(std::shared_ptr cache_dir); + QByteArray fetch(int offset, int n_bytes) const; PageCache parent() const; @@ -108,10 +116,19 @@ namespace SireBase private: std::shared_ptr c; + QMutex mutex; + QAtomicInt nreaders; + std::shared_ptr cache_dir; + std::shared_ptr cache_file; + int max_bytes; int nbytes; + quint16 checksum; + char *d; + + bool is_frozen; }; class HandleData : public boost::noncopyable @@ -240,12 +257,12 @@ QString CacheData::getStatistics() } CacheData::CacheData(QString c, int p) - : cache_dir(c), page_size(p), exiting(false) + : page_size(p), exiting(false) { if (c.simplified().isEmpty()) { // by default, go into the current directory - cache_dir = "."; + c = ".cache_XXXXXX"; } if (page_size < 1024) @@ -253,6 +270,8 @@ CacheData::CacheData(QString c, int p) throw SireError::invalid_arg( QObject::tr("Page size must be greater than 1024!"), CODELOC); } + + cache_dir_template = c; } CacheData::~CacheData() @@ -269,6 +288,28 @@ CacheData::~CacheData() } } +std::shared_ptr CacheData::getCacheDir() +{ + auto c = cache_dir.lock(); + + if (c.get() == nullptr) + { + c = std::make_shared(cache_dir_template); + + if (not c->isValid()) + { + throw SireError::io_error(QObject::tr("Failed to create cache directory %1. %2") + .arg(cache_dir_template) + .arg(c->errorString()), + CODELOC); + } + + cache_dir = c; + } + + return c; +} + PageCache::Handle CacheData::cache(const QByteArray &data) { auto handle = std::make_shared(data); @@ -278,7 +319,16 @@ PageCache::Handle CacheData::cache(const QByteArray &data) QString CacheData::cacheDir() const { - return cache_dir; + auto c = cache_dir.lock(); + + if (c == nullptr) + { + return cache_dir_template; + } + else + { + return c->path(); + } } int CacheData::pageSize() const @@ -363,6 +413,8 @@ void CacheData::enqueue(const std::shared_ptr &handle) void CacheData::run() { + qDebug() << "THREAD RUNNING"; + // get hold of a pointer to self, so that we aren't // deleted while we are running auto locked_self = self.lock(); @@ -371,10 +423,12 @@ void CacheData::run() while (true) { + qDebug() << "LOOP"; + if (this->isInterruptionRequested()) { // stop what we are doing - return; + break; } std::shared_ptr handle; @@ -387,7 +441,7 @@ void CacheData::run() if (this->isInterruptionRequested()) { // stop what we are doing - return; + break; } while (not queue.isEmpty()) @@ -418,6 +472,11 @@ void CacheData::run() this->pages.append(page); lkr.unlock(); auto offset = page->cache(data); + + // straight write this to disk and prevent any changes + page->freeze(this->getCacheDir()); + + // return a handle to the new page handle->setPage(PageCache::Page(page), offset); } else if (n_bytes != 0) @@ -440,6 +499,9 @@ void CacheData::run() } else { + // freeze this page to prevent any further changes + current->freeze(this->getCacheDir()); + // add the current page to the list of old pages QMutexLocker lkr(&page_mutex); this->pages.append(current_page); @@ -460,7 +522,7 @@ void CacheData::run() if (this->isInterruptionRequested()) { // stop what we are doing - return; + break; } bool is_empty = true; @@ -470,16 +532,6 @@ void CacheData::run() // check to see if there is anything else to process QMutexLocker lkr(&queue_mutex); is_empty = queue.isEmpty(); - empty_count += 1; - - if (empty_count > 10) - { - // we have been idle for a while, so we can stop - this->exiting = true; - return; - } - - lkr.unlock(); } if (is_empty) @@ -487,13 +539,40 @@ void CacheData::run() if (this->isInterruptionRequested()) { // stop what we are doing - return; + break; + } + + if (locked_self.unique()) + { + // we are the last reference to this object, so we can + // stop processing + qDebug() << "UNIQUE"; + break; + } + + empty_count += 1; + + if (empty_count > 10) + { + // we have been idle for a while, so we can stop + this->exiting = true; + break; } // sleep for a bit + qDebug() << "SLEEP"; this->msleep(100); } + + if (locked_self.unique()) + { + // we are the last reference to this object, so we can + // stop processing + break; + } } + + qDebug() << "THREAD EXITING" << this->cacheDir(); } /////// @@ -501,7 +580,7 @@ void CacheData::run() /////// PageData::PageData(int max_size, const std::shared_ptr &cache) - : c(cache), max_bytes(max_size), nbytes(0), d(0) + : c(cache), max_bytes(max_size), nbytes(0), checksum(0), d(0), is_frozen(false) { if (max_bytes < 1024) { @@ -524,7 +603,14 @@ PageData::~PageData() int PageData::maxBytes() const { - return max_bytes; + if (is_frozen) + { + return nbytes; + } + else + { + return max_bytes; + } } int PageData::nBytes() const @@ -534,17 +620,24 @@ int PageData::nBytes() const int PageData::bytesRemaining() const { - return max_bytes - nbytes; + if (is_frozen) + { + return 0; + } + else + { + return max_bytes - nbytes; + } } bool PageData::isResident() const { - return true; + return d != 0; } bool PageData::isCached() const { - return false; + return is_frozen; } int PageData::cache(const QByteArray &data) @@ -574,6 +667,49 @@ QByteArray PageData::fetch(int offset, int n_bytes) const return QByteArray(d + offset, n_bytes); } +void PageData::freeze(std::shared_ptr c) +{ + if (d == 0 or nbytes == 0 or is_frozen) + { + return; + } + + QMutexLocker lkr(&mutex); + + if (cache_file.get() != nullptr) + { + qWarning() << "Page is already frozen!"; + return; + } + + if (c.get() == nullptr) + { + throw SireError::invalid_state( + QObject::tr("Cache directory is null!"), CODELOC); + } + + cache_dir = c; + + cache_file = std::make_shared(cache_dir->filePath("page_XXXXXX")); + + if (not cache_file->open()) + { + throw SireError::file_error(*cache_file, CODELOC); + } + + // compress the data and write it to a temporary file + QByteArray compressed_data = qCompress(QByteArray::fromRawData(d, nbytes), 9); + + checksum = qChecksum(compressed_data.constData(), compressed_data.size()); + + if (compressed_data.size() != cache_file->write(compressed_data)) + { + throw SireError::file_error(*cache_file, CODELOC); + } + + is_frozen = true; +} + PageCache PageData::parent() const { return PageCache(c); @@ -894,7 +1030,7 @@ void PageCache::Handle::reset() /////// PageCache::PageCache(int page_size) - : d(new CacheData(QString("."), page_size)) + : d(new CacheData(QString(), page_size)) { d->registerCache(d); } diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index 146e0af40..b5b3b55d3 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -67,8 +67,8 @@ namespace SireSystem if (not cache) { QString cache_dir = QDir::current().absoluteFilePath("trajectory_cache_XXXXXX"); - // use 32 MB pages - cache = std::make_shared(cache_dir, 32 * 1024 * 1024); + // use 32 MB pages (using 32 KB now for debugging) + cache = std::make_shared(cache_dir, 32 * 1024); shared_cache = cache; } } From 42e374a07cfd5ff88b225610c98de55ecae96085 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 17 Apr 2024 22:50:11 +0100 Subject: [PATCH 229/468] Fixed a lot of the cache logic. Paged cache now properly cleans up at exit. Only remaining issue is an unpaged cache exits on a waited thread... --- corelib/src/libs/SireBase/pagecache.cpp | 35 ++++++++++++++++--------- 1 file changed, 22 insertions(+), 13 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 36f683641..92329e181 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -76,7 +76,7 @@ namespace SireBase static QList> caches; QMutex queue_mutex; - QQueue> queue; + QQueue> queue; QMutex page_mutex; std::weak_ptr current_page; @@ -114,7 +114,7 @@ namespace SireBase PageCache parent() const; private: - std::shared_ptr c; + std::weak_ptr c; QMutex mutex; QAtomicInt nreaders; @@ -446,7 +446,7 @@ void CacheData::run() while (not queue.isEmpty()) { - handle = queue.dequeue(); + handle = queue.dequeue().lock(); if (handle.get() != nullptr) { @@ -517,6 +517,10 @@ void CacheData::run() } empty_count = 0; + + // we've finished with 'handle' - release the shared + // pointer so we aren't holding onto it for longer than we need + handle.reset(); } if (this->isInterruptionRequested()) @@ -598,6 +602,15 @@ PageData::PageData(int max_size, const std::shared_ptr &cache) PageData::~PageData() { + if (cache_file.get() != nullptr) + { + qDebug() << "DELETE PAGE" << cache_file->fileName(); + } + else + { + qDebug() << "DELETE PAGE"; + } + delete[] d; } @@ -667,9 +680,9 @@ QByteArray PageData::fetch(int offset, int n_bytes) const return QByteArray(d + offset, n_bytes); } -void PageData::freeze(std::shared_ptr c) +void PageData::freeze(std::shared_ptr dir) { - if (d == 0 or nbytes == 0 or is_frozen) + if (d == 0 or nbytes == 0 or is_frozen or dir.get() == nullptr) { return; } @@ -682,13 +695,7 @@ void PageData::freeze(std::shared_ptr c) return; } - if (c.get() == nullptr) - { - throw SireError::invalid_state( - QObject::tr("Cache directory is null!"), CODELOC); - } - - cache_dir = c; + cache_dir = dir; cache_file = std::make_shared(cache_dir->filePath("page_XXXXXX")); @@ -708,11 +715,13 @@ void PageData::freeze(std::shared_ptr c) } is_frozen = true; + + qDebug() << "FROZEN PAGE" << cache_file->fileName(); } PageCache PageData::parent() const { - return PageCache(c); + return PageCache(c.lock()); } /////// From a9c3a022d2905f49f73c0a2b48e1383de98c9a76 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Wed, 17 Apr 2024 23:00:15 +0100 Subject: [PATCH 230/468] Fixed that last issue - clean up of the cache now works, no errors on shutdown. Only issue now is jupyter seems to kill the process rather than let it clean up properly when you do a restart kernel and clear cells... --- corelib/src/libs/SireBase/pagecache.cpp | 35 +------------------------ 1 file changed, 1 insertion(+), 34 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 92329e181..2698fbb78 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -413,18 +413,14 @@ void CacheData::enqueue(const std::shared_ptr &handle) void CacheData::run() { - qDebug() << "THREAD RUNNING"; - // get hold of a pointer to self, so that we aren't // deleted while we are running - auto locked_self = self.lock(); + // auto locked_self = self.lock(); int empty_count = 0; while (true) { - qDebug() << "LOOP"; - if (this->isInterruptionRequested()) { // stop what we are doing @@ -546,14 +542,6 @@ void CacheData::run() break; } - if (locked_self.unique()) - { - // we are the last reference to this object, so we can - // stop processing - qDebug() << "UNIQUE"; - break; - } - empty_count += 1; if (empty_count > 10) @@ -564,19 +552,9 @@ void CacheData::run() } // sleep for a bit - qDebug() << "SLEEP"; this->msleep(100); } - - if (locked_self.unique()) - { - // we are the last reference to this object, so we can - // stop processing - break; - } } - - qDebug() << "THREAD EXITING" << this->cacheDir(); } /////// @@ -602,15 +580,6 @@ PageData::PageData(int max_size, const std::shared_ptr &cache) PageData::~PageData() { - if (cache_file.get() != nullptr) - { - qDebug() << "DELETE PAGE" << cache_file->fileName(); - } - else - { - qDebug() << "DELETE PAGE"; - } - delete[] d; } @@ -715,8 +684,6 @@ void PageData::freeze(std::shared_ptr dir) } is_frozen = true; - - qDebug() << "FROZEN PAGE" << cache_file->fileName(); } PageCache PageData::parent() const From 6ae1694dbffa31fe094e2f5cf398561ec4740ee4 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 18 Apr 2024 22:15:34 +0100 Subject: [PATCH 231/468] Data is now deleted from memory, and then restored from the file cache when read (complete with compression to save space and checksum for validation) --- corelib/src/libs/SireBase/pagecache.cpp | 43 +++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 2698fbb78..fa4cff947 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -646,6 +646,44 @@ QByteArray PageData::fetch(int offset, int n_bytes) const QObject::tr("Data is too large to fit on this page!"), CODELOC); } + QMutexLocker lkr(const_cast(&mutex)); + + if (d == 0) + { + // we need to read the data from disk + if (cache_file.get() == nullptr) + { + throw SireError::invalid_state( + QObject::tr("Page has not been frozen to disk?"), CODELOC); + } + + if (not cache_file->open()) + { + throw SireError::file_error(*cache_file, CODELOC); + } + + QByteArray compressed_data = cache_file->readAll(); + + cache_file->close(); + + if (qChecksum(compressed_data.constData(), compressed_data.size()) != checksum) + { + throw SireError::invalid_state( + QObject::tr("Checksum failed on page data!"), CODELOC); + } + + QByteArray decompressed_data = qUncompress(compressed_data); + + if (decompressed_data.size() != nbytes) + { + throw SireError::invalid_state( + QObject::tr("Decompressed data size does not match expected size!"), CODELOC); + } + + const_cast(this)->d = new char[nbytes]; + std::memcpy(d, decompressed_data.constData(), nbytes); + } + return QByteArray(d + offset, n_bytes); } @@ -683,6 +721,11 @@ void PageData::freeze(std::shared_ptr dir) throw SireError::file_error(*cache_file, CODELOC); } + cache_file->close(); + + delete[] d; + d = 0; + is_frozen = true; } From 220e538055216bac02f2d85e66866a89c86afd29 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Thu, 18 Apr 2024 22:35:56 +0100 Subject: [PATCH 232/468] Added automatic clearing of restored pages from memory using a TTL cache and some clever use of shared pointers and atomic integers :-) --- corelib/src/libs/SireBase/pagecache.cpp | 118 +++++++++++++++++++++++- 1 file changed, 113 insertions(+), 5 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index fa4cff947..b3951d5bc 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -92,6 +92,24 @@ namespace SireBase bool exiting; }; + class RestoredPage : public boost::noncopyable + { + public: + RestoredPage(const QByteArray &data); + ~RestoredPage(); + + QByteArray fetch(int offset, int n_bytes) const; + + static std::shared_ptr store(const QByteArray &data); + + private: + static QMutex mutex; + static QList> restored_pages; + + QByteArray d; + QAtomicInt ttl; + }; + class PageData : public boost::noncopyable { public: @@ -121,6 +139,8 @@ namespace SireBase std::shared_ptr cache_dir; std::shared_ptr cache_file; + std::weak_ptr restored_page; + int max_bytes; int nbytes; @@ -557,6 +577,75 @@ void CacheData::run() } } +/////// +/////// Implementation of detail::RestoredPage +/////// + +RestoredPage::RestoredPage(const QByteArray &data) + : d(data), ttl(100) +{ +} + +RestoredPage::~RestoredPage() +{ +} + +QByteArray RestoredPage::fetch(int offset, int n_bytes) const +{ + if (offset + n_bytes > d.size()) + { + throw SireError::invalid_arg( + QObject::tr("Data is too large to fit on this page!"), CODELOC); + } + + const_cast(this)->ttl.storeRelaxed(100); + + return QByteArray(d.constData() + offset, n_bytes); +} + +QMutex RestoredPage::mutex; + +QList> RestoredPage::restored_pages; + +std::shared_ptr RestoredPage::store(const QByteArray &data) +{ + auto page = std::make_shared(data); + + QMutexLocker lkr(&mutex); + + int smallest_index = -1; + int smallest_value = -1; + + for (int i = 0; i < restored_pages.size(); i++) + { + if (restored_pages[i].get() == nullptr) + { + smallest_index = i; + } + else + { + int val = restored_pages[i]->ttl.fetchAndAddRelaxed(-1); + + if (smallest_index == -1 or smallest_value > val) + { + smallest_index = i; + smallest_value = val; + } + } + } + + if (restored_pages.count() < 5) + { + restored_pages.append(page); + } + else + { + restored_pages[smallest_index] = page; + } + + return page; +} + /////// /////// Implementation of detail::PageData /////// @@ -614,7 +703,7 @@ int PageData::bytesRemaining() const bool PageData::isResident() const { - return d != 0; + return d != 0 or restored_page.lock().get() != nullptr; } bool PageData::isCached() const @@ -646,10 +735,24 @@ QByteArray PageData::fetch(int offset, int n_bytes) const QObject::tr("Data is too large to fit on this page!"), CODELOC); } + auto fetched_page = restored_page.lock(); + + if (fetched_page.get() != nullptr) + { + return fetched_page->fetch(offset, n_bytes); + } + QMutexLocker lkr(const_cast(&mutex)); if (d == 0) { + auto fetched_page = restored_page.lock(); + + if (fetched_page.get() != nullptr) + { + return fetched_page->fetch(offset, n_bytes); + } + // we need to read the data from disk if (cache_file.get() == nullptr) { @@ -680,11 +783,16 @@ QByteArray PageData::fetch(int offset, int n_bytes) const QObject::tr("Decompressed data size does not match expected size!"), CODELOC); } - const_cast(this)->d = new char[nbytes]; - std::memcpy(d, decompressed_data.constData(), nbytes); - } + fetched_page = RestoredPage::store(decompressed_data); + + const_cast(this)->restored_page = fetched_page; - return QByteArray(d + offset, n_bytes); + return fetched_page->fetch(offset, n_bytes); + } + else + { + return QByteArray(d + offset, n_bytes); + } } void PageData::freeze(std::shared_ptr dir) From f65916479962a869de66d8ed9943795cb92bff16 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Apr 2024 11:36:57 +0100 Subject: [PATCH 233/468] Fix link atom information container. --- wrapper/Convert/SireOpenMM/register_extras.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/register_extras.cpp b/wrapper/Convert/SireOpenMM/register_extras.cpp index a77bea907..422a7e5f0 100644 --- a/wrapper/Convert/SireOpenMM/register_extras.cpp +++ b/wrapper/Convert/SireOpenMM/register_extras.cpp @@ -59,7 +59,7 @@ namespace SireOpenMM register_dict>(); register_dict>>(); - // A tuple for passing link atom information to EMLEEngine. - bp::register_tuple, QMap>>>(); + // A tuple for returning link atom information from EMLEEngine. + bp::register_tuple, QMap>, QMap>>(); } } From 41f0bca803641821f6fbf99c47b5dd60ccb8d5ee Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Fri, 19 Apr 2024 20:21:34 +0100 Subject: [PATCH 234/468] Cleaned up the code, added code level docs, error handling and more logic to freezing and restoring (now via a PageHandler class) It works really well :-) --- corelib/src/libs/SireBase/pagecache.cpp | 1163 +++++++++++------ corelib/src/libs/SireBase/pagecache.h | 23 +- .../src/libs/SireSystem/systemtrajectory.cpp | 6 +- src/sire/base/_pagecache.py | 12 +- wrapper/Base/PageCache.pypp.cpp | 145 +- 5 files changed, 909 insertions(+), 440 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index b3951d5bc..1eaac4054 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -31,10 +31,12 @@ #include "SireError/errors.h" #include "SireBase/parallel.h" +#include "SireBase/console.h" #include #include #include +#include #include #include #include @@ -46,109 +48,210 @@ namespace SireBase { namespace detail { + /** This class holds a page of data that has been restored from disk */ + class RestoredPage : public boost::noncopyable + { + public: + RestoredPage(const QByteArray &data); + ~RestoredPage(); + + QByteArray fetch(unsigned int offset, unsigned int n_bytes) const; + + int timeToLive() const; + + private: + /** The restored data */ + QByteArray d; + + /** The time to live - this is reset every time the + * data is accessed via the fetch method */ + QAtomicInt ttl; + }; + + /** This class handles the movement of pages between disk + * and memory + */ + class PageHandler : boost::noncopyable + { + public: + PageHandler(QString cache_dir_template); + ~PageHandler(); + + QTemporaryFile *store(const QByteArray &data); + std::shared_ptr restore(QTemporaryFile &pagefile); + + QString path() const; + + private: + /** Mutex to protect access to the data of this class */ + QMutex mutex; + + /** List of all pages restored by this handler */ + QList> restored_pages; + + /** Checksum of the data in all temporary page files */ + QHash checksums; + + /** Pointer to the temporary directory for all pagefiles */ + QTemporaryDir *cache_dir; + }; + + /** This class holds all of the data for a PageCache, providing + * a cache where data is stored, returning a handle to the + * stored data, through which it can be fetched. The data + * is internally divided into pages, which are pushed to disk + * so that memory usage is kept to a minimum. + */ class CacheData : public QThread { public: - CacheData(QString cachedir, int page_size); + CacheData(QString cachedir, unsigned int page_size); ~CacheData(); static QString getStatistics(); QString cacheDir() const; - PageCache::Handle cache(const QByteArray &data); + PageCache::Handle store(const QByteArray &data); - int pageSize() const; + unsigned int pageSize() const; - int nPages() const; - int nBytes() const; + unsigned int nPages() const; + unsigned int nBytes() const; - void registerCache(const std::shared_ptr &cache); + void setSelf(const std::shared_ptr &cache); protected: void run(); private: void enqueue(const std::shared_ptr &handle); - std::shared_ptr getCacheDir(); + std::shared_ptr getPageHandler(); + /** Mutex protecting the list of all caches */ static QMutex caches_mutex; + + /** The list of all caches - weak pointers so that they + * can be deleted when the last reference is removed + */ static QList> caches; + /** Mutex protected the queue of Handles containing data + * that should be pushed to the cache + */ QMutex queue_mutex; + + /** Queue of handles that are yet to be cached */ QQueue> queue; + /** Mutex to protect access to the list of pages + * associated with this cache + */ QMutex page_mutex; + + /** The current page of data being filled - weak pointer + * so that it is deleted if no longer needed + */ std::weak_ptr current_page; + + /** The list of filled pages of data, which have been frozen + * to disk. Weak pointers so that they are deleted if no longer + * needed + */ QList> pages; + /** Weak point to self */ std::weak_ptr self; - std::weak_ptr cache_dir; + /** Weak pointer to the page handler for this cache. + * This is passed to pages when they are frozen so that + * the handler can be used to restore the data. + * Weak pointer to that is is automatically deleted when + * all pages are deleted + */ + std::weak_ptr page_handler; + + /** Template used for the cache directory - this is in a format + * that is recognised by QTemporaryDir + */ QString cache_dir_template; + /** The default maximum page size for pages. This is a guide, + * i.e. items larger than this size will be cached into their + * own page. Also, a new page will be automatically created + * if there is insufficient space on the current page + */ int page_size; + /** Flag set when the underlying thread is exiting. This is used + * to prevent race conditions + */ bool exiting; }; - class RestoredPage : public boost::noncopyable - { - public: - RestoredPage(const QByteArray &data); - ~RestoredPage(); - - QByteArray fetch(int offset, int n_bytes) const; - - static std::shared_ptr store(const QByteArray &data); - - private: - static QMutex mutex; - static QList> restored_pages; - - QByteArray d; - QAtomicInt ttl; - }; - + /** This class holds the implementation of a single page of data */ class PageData : public boost::noncopyable { public: - PageData(int max_size, const std::shared_ptr &cache); + PageData(unsigned int max_size, const std::shared_ptr &cache); ~PageData(); - int maxBytes() const; - int nBytes() const; - int bytesRemaining() const; + unsigned int maxBytes() const; + unsigned int nBytes() const; + unsigned int bytesRemaining() const; bool isResident() const; bool isCached() const; - int cache(const QByteArray &data); + unsigned int store(const QByteArray &data); - void freeze(std::shared_ptr cache_dir); + void freeze(std::shared_ptr handler); - QByteArray fetch(int offset, int n_bytes) const; + QByteArray fetch(unsigned int offset, unsigned int n_bytes) const; PageCache parent() const; private: + /** Weak pointer to the parent cache - weak so that the + * cache is automatically deleted if the user releases + * all references to it + */ std::weak_ptr c; + /** Mutex to protect access to the data of this page */ QMutex mutex; - QAtomicInt nreaders; - std::shared_ptr cache_dir; - std::shared_ptr cache_file; + /** The handler used to restore this page from disk. + * This is null if the page has not yet been frozen + */ + std::shared_ptr page_handler; + + /** Weak pointer to the restored page. This is weak so + * that, if the page handler decides to remove the page + * from memory, then this pointer will be automatically + * set to null in a thread-safe way + */ std::weak_ptr restored_page; - int max_bytes; - int nbytes; + /** The maximum number of bytes allowed in the page. + * This is set equal to the current number of bytes + * when the page is frozen + */ + unsigned int max_bytes; - quint16 checksum; + /** The current number of bytes in the page */ + unsigned int nbytes; - char *d; + /** Pointer to the temporary file used to hold the frozen + * page + */ + QTemporaryFile *cache_file; - bool is_frozen; + /** Pointer to the page of data - this is only used when the + * page is being filled. It is set to null when the page + * is frozen to disk + */ + char *d; }; class HandleData : public boost::noncopyable @@ -168,7 +271,7 @@ namespace SireBase PageCache::Page page() const; - int nBytes() const; + unsigned int nBytes() const; bool isValid() const; bool isNull() const; @@ -192,10 +295,10 @@ namespace SireBase State state; /** The offset of this data within the page */ - int offset; + unsigned int offset; /** The number of bytes of data */ - int nbytes; + unsigned int nbytes; }; } } @@ -203,6 +306,211 @@ namespace SireBase using namespace SireBase; using namespace SireBase::detail; +/////// +/////// Implementation of detail::RestoredPage +/////// + +/** Construct to hold the restored data in 'data'. By default, + * the ttl starts at 100 + */ +RestoredPage::RestoredPage(const QByteArray &data) + : d(data), ttl(100) +{ +} + +/** Destructor */ +RestoredPage::~RestoredPage() +{ +} + +/** Return the time to live for this page, and decrement it by 1 */ +int RestoredPage::timeToLive() const +{ + // this uses an atomic integer, so is thread-safe + return const_cast(this)->ttl.fetchAndAddRelaxed(-1); +} + +/** Fetch 'n_bytes' bytes of data starting at 'offset' */ +QByteArray RestoredPage::fetch(unsigned int offset, unsigned int n_bytes) const +{ + if (offset + n_bytes > d.size()) + { + throw SireError::invalid_arg( + QObject::tr("Impossible to fetch %1 bytes starting at " + "offset %2 from a page of only %3 bytes") + .arg(n_bytes) + .arg(offset) + .arg(d.size()), + CODELOC); + } + + // reset the TTL to 100 - this uses an atomic integer, so is thread-safe + const_cast(this)->ttl.storeRelaxed(100); + + // return the requested data + return QByteArray(d.constData() + offset, n_bytes); +} + +/////// +/////// Implementation of detail::PageHandler +/////// + +/** Construct a PageHandler that will handle freezing and restoring + * pages from a temporary directory following the passed template + */ +PageHandler::PageHandler(QString cache_dir_template) + : cache_dir(new QTemporaryDir(cache_dir_template)) +{ + if (not cache_dir->isValid()) + { + auto message = QObject::tr("Failed to create cache directory %1. %2") + .arg(cache_dir_template) + .arg(cache_dir->errorString()); + + Console::error(message); + throw SireError::io_error(message, CODELOC); + } +} + +/** Destructor */ +PageHandler::~PageHandler() +{ + delete cache_dir; +} + +/** Return the path to the cache directory */ +QString PageHandler::path() const +{ + return cache_dir->path(); +} + +/** Store the passed page of data to a temporary page cache file. + * This returns a pointer to the created temporary file, + * which is owned by the caller (in this case, the PageData) + */ +QTemporaryFile *PageHandler::store(const QByteArray &data) +{ + QTemporaryFile *cache_file = new QTemporaryFile(cache_dir->filePath("page_XXXXXX.bin")); + + try + { + if (not cache_file->open()) + { + Console::error(QObject::tr("Failed to open temporary file %1. %2") + .arg(cache_file->fileName()) + .arg(cache_file->errorString())); + throw SireError::file_error(*cache_file, CODELOC); + } + + // compress the data and write it to a temporary file + QByteArray compressed_data = qCompress(data, 9); + + auto checksum = qChecksum(compressed_data.constData(), + compressed_data.size()); + + if (compressed_data.size() != cache_file->write(compressed_data)) + { + throw SireError::file_error(*cache_file, CODELOC); + } + + cache_file->close(); + + checksums.insert(cache_file, checksum); + + return cache_file; + } + catch (...) + { + delete cache_file; + throw; + } +} + +/** Restore the QByteArray held in the passed pagefile, and + * add it to the list of restored pages. If there are more than + * 5 restored pages, then the oldest page is replaced with the + * new page (oldest based on looking at the TTL values of each page) + */ +std::shared_ptr PageHandler::restore(QTemporaryFile &pagefile) +{ + if (not pagefile.open()) + { + Console::error(QObject::tr("Failed to open temporary file %1. %2") + .arg(pagefile.fileName()) + .arg(pagefile.errorString())); + throw SireError::file_error(pagefile, CODELOC); + } + + // read the raw data + QByteArray compressed_data = pagefile.readAll(); + pagefile.close(); + + // make sure that the checksum matches what we calculated when we + // stored the data to disk + auto checksum = checksums.value(&pagefile, 0); + auto readsum = qChecksum(compressed_data.constData(), compressed_data.size()); + + if (checksum != readsum) + { + QString message = QObject::tr("Checksum failed on page data for %1: %2 versus %3") + .arg(pagefile.fileName()) + .arg(checksum) + .arg(readsum); + + Console::error(message); + + throw SireError::invalid_state(message, CODELOC); + } + + // uncompress the data + QByteArray decompressed_data = qUncompress(compressed_data); + compressed_data = QByteArray(); + + // create a new RestoredPage object for this data + auto restored = std::make_shared(decompressed_data); + decompressed_data = QByteArray(); + + // now check to see if we need to replace an old page + QMutexLocker lkr(&mutex); + + if (restored_pages.count() < 5) + { + restored_pages.append(restored); + return restored; + } + + // we need to replace a page... + int smallest_index = -1; + int smallest_value = -1; + + for (int i = 0; i < restored_pages.size(); i++) + { + if (restored_pages[i].get() == nullptr) + { + // this page has already been deleted, so should + // be removed first + smallest_index = i; + } + else + { + // find the oldest page to restore - do this by reducing + // the TTL for each page each time we go through this loop, + // and then find the first page with the smallest TTL + int val = restored_pages[i]->timeToLive(); + + if (smallest_index == -1 or smallest_value > val) + { + smallest_index = i; + smallest_value = val; + } + } + } + + restored_pages[smallest_index] = restored; + + return restored; +} + /////// /////// Implementation of detail::CacheData /////// @@ -210,13 +518,42 @@ using namespace SireBase::detail; QMutex CacheData::caches_mutex; QList> CacheData::caches; -void CacheData::registerCache(const std::shared_ptr &cache) +/** Set the self pointer for this cache */ +void CacheData::setSelf(const std::shared_ptr &cache) { + if (cache.get() == nullptr) + { + return; + } + + if (self.lock().get() != nullptr) + { + QString message = QObject::tr("Cache already has a self pointer!"); + Console::error(message); + throw SireError::invalid_state(message, CODELOC); + } + + if (cache.get() != this) + { + QString message = QObject::tr("Cache self pointer does not match this cache!"); + Console::error(message); + throw SireError::invalid_state(message, CODELOC); + } + QMutexLocker lkr(&caches_mutex); + + if (self.lock().get() != nullptr) + { + QString message = QObject::tr("Cache already has a self pointer!"); + Console::error(message); + throw SireError::invalid_state(message, CODELOC); + } + caches.append(cache); self = cache; } +/** Return a string giving all of the statistics for all caches */ QString CacheData::getStatistics() { QMutexLocker lkr(&caches_mutex); @@ -276,90 +613,106 @@ QString CacheData::getStatistics() return stats; } -CacheData::CacheData(QString c, int p) +/** Construct the data for a single cache, using the passed + * template for the cache directory and the passed suggested + * maximum page size + */ +CacheData::CacheData(QString c, unsigned int p) : page_size(p), exiting(false) { if (c.simplified().isEmpty()) { // by default, go into the current directory - c = ".cache_XXXXXX"; + c = "temp_XXXXXX"; } if (page_size < 1024) { - throw SireError::invalid_arg( - QObject::tr("Page size must be greater than 1024!"), CODELOC); + Console::warning(QObject::tr("Setting page size to the minimum of 1024 bytes.")); + page_size = 1024; + } + else if (page_size > 128 * 1024 * 1024) + { + Console::warning(QObject::tr("Setting page size to the maximum of 128 MB.")); + page_size = 128 * 1024 * 1024; } cache_dir_template = c; } +/** Destructor */ CacheData::~CacheData() { + // tell the thread to stop this->requestInterruption(); if (QThread::currentThread() != this) { + // wait for the thread to stop this->wait(); } else { + // we are in the thread, so we can't wait for it to stop + // (use qWarning, as at this point the Console may be gone...) qWarning() << "CacheData is deleting itself!" << this->cacheDir(); } } -std::shared_ptr CacheData::getCacheDir() +/** Return the PageHandler for this cache - this automatically creates + * a new one if it doesn't exist, or if the old one was lost + * (happens if all pages are deleted) + * + * Note that this function is ONLY called from the background running + * thread, so does not need to be (and isn't) thread-safe + */ +std::shared_ptr CacheData::getPageHandler() { - auto c = cache_dir.lock(); + auto handler = page_handler.lock(); - if (c.get() == nullptr) + if (handler.get() == nullptr) { - c = std::make_shared(cache_dir_template); - - if (not c->isValid()) - { - throw SireError::io_error(QObject::tr("Failed to create cache directory %1. %2") - .arg(cache_dir_template) - .arg(c->errorString()), - CODELOC); - } - - cache_dir = c; + handler = std::make_shared(cache_dir_template); + page_handler = handler; } - return c; + return handler; } -PageCache::Handle CacheData::cache(const QByteArray &data) +/** Store the data in the cache, returning a handle to the data */ +PageCache::Handle CacheData::store(const QByteArray &data) { auto handle = std::make_shared(data); this->enqueue(handle); return PageCache::Handle(handle); } +/** Return the cache directory for this cache */ QString CacheData::cacheDir() const { - auto c = cache_dir.lock(); + auto handler = page_handler.lock(); - if (c == nullptr) + if (handler.get() == nullptr) { return cache_dir_template; } else { - return c->path(); + return handler->path(); } } -int CacheData::pageSize() const +/** Return the suggested maximum page size for this cache */ +unsigned int CacheData::pageSize() const { return page_size; } -int CacheData::nPages() const +/** Return the number of pages in this cache */ +unsigned int CacheData::nPages() const { QMutexLocker lkr(const_cast(&page_mutex)); - int npages = 0; + unsigned int npages = 0; if (current_page.lock().get() != nullptr) { @@ -377,11 +730,12 @@ int CacheData::nPages() const return npages; } -int CacheData::nBytes() const +/** Return the number of bytes in this cache */ +unsigned int CacheData::nBytes() const { QMutexLocker lkr(const_cast(&page_mutex)); - int nbytes = 0; + unsigned int nbytes = 0; auto current = current_page.lock(); @@ -403,6 +757,9 @@ int CacheData::nBytes() const return nbytes; } +/** Internal function that is used to add a handler to the queue + * to be processed by the background thread and copied to a page + */ void CacheData::enqueue(const std::shared_ptr &handle) { if (handle.get() == nullptr) @@ -425,256 +782,209 @@ void CacheData::enqueue(const std::shared_ptr &handle) queue.enqueue(handle); + // Start the background thread if it is not running + // (it automatically stops if there is nothing to do) if (not this->isRunning()) { this->start(); } } +/** The background thread that processes the queue of data to be + * added to the cache + */ void CacheData::run() { - // get hold of a pointer to self, so that we aren't - // deleted while we are running - // auto locked_self = self.lock(); - - int empty_count = 0; - - while (true) + try { - if (this->isInterruptionRequested()) - { - // stop what we are doing - break; - } - - std::shared_ptr handle; - bool have_item = false; + int empty_count = 0; - // pull an item off the queue + while (true) { - QMutexLocker lkr(&queue_mutex); - if (this->isInterruptionRequested()) { // stop what we are doing break; } - while (not queue.isEmpty()) + std::shared_ptr handle; + bool have_item = false; + + // pull an item off the queue { - handle = queue.dequeue().lock(); + QMutexLocker lkr(&queue_mutex); - if (handle.get() != nullptr) + if (this->isInterruptionRequested()) { - have_item = true; + // stop what we are doing break; } - } - } - - if (have_item) - { - // get the data - QByteArray data = handle->fetch(); - const int n_bytes = data.size(); + while (not queue.isEmpty()) + { + handle = queue.dequeue().lock(); - if (n_bytes >= page_size) - { - // this is bigger than a page, so needs to have its - // own page! - auto page = std::make_shared(n_bytes, this->self.lock()); - QMutexLocker lkr(&page_mutex); - this->pages.append(page); - lkr.unlock(); - auto offset = page->cache(data); - - // straight write this to disk and prevent any changes - page->freeze(this->getCacheDir()); - - // return a handle to the new page - handle->setPage(PageCache::Page(page), offset); + if (handle.get() != nullptr) + { + have_item = true; + break; + } + } } - else if (n_bytes != 0) + + if (have_item) { - // make sure we have a current page... - auto current = current_page.lock(); + // get the data + QByteArray data = handle->fetch(); - if (current.get() == nullptr) - { - current = std::make_shared(page_size, this->self.lock()); - QMutexLocker lkr(&page_mutex); - current_page = current; - } + const int n_bytes = data.size(); - // is there space left on the current page - if (current->bytesRemaining() >= n_bytes) - { - auto offset = current->cache(data); - handle->setPage(PageCache::Page(current), offset); - } - else + if (n_bytes >= page_size) { - // freeze this page to prevent any further changes - current->freeze(this->getCacheDir()); - - // add the current page to the list of old pages + // this is bigger than a page, so needs to have its + // own page! + auto page = std::make_shared(n_bytes, this->self.lock()); QMutexLocker lkr(&page_mutex); - this->pages.append(current_page); - - // we need to create a new page - current = std::make_shared(page_size, this->self.lock()); - current_page = current; + this->pages.append(page); lkr.unlock(); + auto offset = page->store(data); - auto offset = current->cache(data); - handle->setPage(PageCache::Page(current), offset); - } - } - - empty_count = 0; + // straight write this to disk and prevent any changes + page->freeze(this->getPageHandler()); - // we've finished with 'handle' - release the shared - // pointer so we aren't holding onto it for longer than we need - handle.reset(); - } - - if (this->isInterruptionRequested()) - { - // stop what we are doing - break; - } + // return a handle to the new page + handle->setPage(PageCache::Page(page), offset); + } + else if (n_bytes != 0) + { + // make sure we have a current page... + auto current = current_page.lock(); + + if (current.get() == nullptr) + { + current = std::make_shared(page_size, this->self.lock()); + QMutexLocker lkr(&page_mutex); + current_page = current; + } + + // is there space left on the current page + if (current->bytesRemaining() >= n_bytes) + { + auto offset = current->store(data); + handle->setPage(PageCache::Page(current), offset); + } + else + { + // freeze this page to prevent any further changes + current->freeze(this->getPageHandler()); + + // add the current page to the list of old pages + QMutexLocker lkr(&page_mutex); + this->pages.append(current_page); + + // we need to create a new page + current = std::make_shared(page_size, this->self.lock()); + current_page = current; + lkr.unlock(); + + auto offset = current->store(data); + handle->setPage(PageCache::Page(current), offset); + } + } - bool is_empty = true; + empty_count = 0; - if (have_item) - { - // check to see if there is anything else to process - QMutexLocker lkr(&queue_mutex); - is_empty = queue.isEmpty(); - } + // we've finished with 'handle' - release the shared + // pointer so we aren't holding onto it for longer than we need + handle.reset(); + } - if (is_empty) - { if (this->isInterruptionRequested()) { // stop what we are doing break; } - empty_count += 1; + bool is_empty = true; - if (empty_count > 10) + if (have_item) { - // we have been idle for a while, so we can stop - this->exiting = true; - break; + // check to see if there is anything else to process + QMutexLocker lkr(&queue_mutex); + is_empty = queue.isEmpty(); } - // sleep for a bit - this->msleep(100); - } - } -} - -/////// -/////// Implementation of detail::RestoredPage -/////// - -RestoredPage::RestoredPage(const QByteArray &data) - : d(data), ttl(100) -{ -} - -RestoredPage::~RestoredPage() -{ -} - -QByteArray RestoredPage::fetch(int offset, int n_bytes) const -{ - if (offset + n_bytes > d.size()) - { - throw SireError::invalid_arg( - QObject::tr("Data is too large to fit on this page!"), CODELOC); - } - - const_cast(this)->ttl.storeRelaxed(100); - - return QByteArray(d.constData() + offset, n_bytes); -} - -QMutex RestoredPage::mutex; - -QList> RestoredPage::restored_pages; - -std::shared_ptr RestoredPage::store(const QByteArray &data) -{ - auto page = std::make_shared(data); - - QMutexLocker lkr(&mutex); + if (is_empty) + { + if (this->isInterruptionRequested()) + { + // stop what we are doing + break; + } - int smallest_index = -1; - int smallest_value = -1; + empty_count += 1; - for (int i = 0; i < restored_pages.size(); i++) - { - if (restored_pages[i].get() == nullptr) - { - smallest_index = i; - } - else - { - int val = restored_pages[i]->ttl.fetchAndAddRelaxed(-1); + if (empty_count > 10) + { + // we have been idle for a while, so we can stop + this->exiting = true; + break; + } - if (smallest_index == -1 or smallest_value > val) - { - smallest_index = i; - smallest_value = val; + // sleep for a bit + this->msleep(100); } } } - - if (restored_pages.count() < 5) + catch (const SireError::exception &e) { - restored_pages.append(page); + Console::error(e.error()); } - else + catch (const std::exception &e) { - restored_pages[smallest_index] = page; + Console::error(e.what()); + } + catch (...) + { + Console::error("Unknown error in CacheData::run()"); } - - return page; } /////// /////// Implementation of detail::PageData /////// -PageData::PageData(int max_size, const std::shared_ptr &cache) - : c(cache), max_bytes(max_size), nbytes(0), checksum(0), d(0), is_frozen(false) +/** Construct an empty new page of data of specified maximum size, + * associated with the specified cache + */ +PageData::PageData(unsigned int max_size, const std::shared_ptr &cache) + : c(cache), max_bytes(max_size), nbytes(0), cache_file(0), d(0) { if (max_bytes < 1024) { - throw SireError::invalid_arg( - QObject::tr("Page size must be greater than 1024!"), CODELOC); + Console::warning(QObject::tr("Setting page size to the minimum of 1024 bytes.")); + max_bytes = 1024; } else if (max_bytes > 128 * 1024 * 1024) { - throw SireError::invalid_arg( - QObject::tr("Page size must be less than 128 MB!"), CODELOC); + Console::warning(QObject::tr("Setting page size to the maximum of 128 MB.")); + max_bytes = 128 * 1024 * 1024; } d = new char[max_bytes]; } +/** Destructor */ PageData::~PageData() { + delete cache_file; delete[] d; } -int PageData::maxBytes() const +/** Return the maximum number of bytes that can be stored in this page */ +unsigned int PageData::maxBytes() const { - if (is_frozen) + if (d == 0) { return nbytes; } @@ -684,14 +994,16 @@ int PageData::maxBytes() const } } -int PageData::nBytes() const +/** Return the number of bytes currently stored in this page */ +unsigned int PageData::nBytes() const { return nbytes; } -int PageData::bytesRemaining() const +/** Return the number of bytes remaining in this page */ +unsigned int PageData::bytesRemaining() const { - if (is_frozen) + if (d == 0) { return 0; } @@ -701,93 +1013,95 @@ int PageData::bytesRemaining() const } } +/** Return true if the page is resident in memory */ bool PageData::isResident() const { return d != 0 or restored_page.lock().get() != nullptr; } +/** Return true if the page is cached to disk */ bool PageData::isCached() const { - return is_frozen; + return cache_file != 0; } -int PageData::cache(const QByteArray &data) +/** Store the data in the page, returning the offset at which + * the data is stored. This function is only ever called by + * the background thread of a CacheData, so does not need to + * be (and isn't) thread-safe + */ +unsigned int PageData::store(const QByteArray &data) { + // this test will fail if the page is frozen if (data.size() > this->bytesRemaining()) { + QString message = QObject::tr("Data is too large to fit on this page!"); + Console::error(message); throw SireError::invalid_arg( QObject::tr("Data is too large to fit on this page!"), CODELOC); } + // only the thread calling this function will change d, so it is + // save to assume that d will not change during this function + + if (d == 0) + { + QString message = QObject::tr("Page is already frozen!"); + Console::error(message); + throw SireError::invalid_state( + QObject::tr("Page is already frozen!"), CODELOC); + } + + // copy the data into the page std::memcpy(d + nbytes, data.constData(), data.size()); - int offset = nbytes; + // update the number of bytes in the page and get the offset + unsigned int offset = nbytes; nbytes += data.size(); return offset; } -QByteArray PageData::fetch(int offset, int n_bytes) const +/** Fetch 'n_bytes' bytes of data starting at 'offset' from this page */ +QByteArray PageData::fetch(unsigned int offset, unsigned int n_bytes) const { if (offset + n_bytes > nbytes) { throw SireError::invalid_arg( - QObject::tr("Data is too large to fit on this page!"), CODELOC); + QObject::tr("Impossible to fetch %1 bytes starting at " + "offset %2 from a page of only %3 bytes") + .arg(n_bytes) + .arg(offset) + .arg(nbytes), + CODELOC); } - auto fetched_page = restored_page.lock(); + auto restored = restored_page.lock(); - if (fetched_page.get() != nullptr) + if (restored.get() != nullptr) { - return fetched_page->fetch(offset, n_bytes); + return restored->fetch(offset, n_bytes); } - QMutexLocker lkr(const_cast(&mutex)); + // need to lock because the background thread may be changing + // the data (moving d to the page) + QMutexLocker lkr(&(const_cast(this)->mutex)); if (d == 0) { - auto fetched_page = restored_page.lock(); - - if (fetched_page.get() != nullptr) + if (page_handler.get() == nullptr or cache_file == 0) { - return fetched_page->fetch(offset, n_bytes); + QString message = QObject::tr("Page has not been frozen to disk?"); + Console::error(message); + return QByteArray(); } - // we need to read the data from disk - if (cache_file.get() == nullptr) - { - throw SireError::invalid_state( - QObject::tr("Page has not been frozen to disk?"), CODELOC); - } - - if (not cache_file->open()) - { - throw SireError::file_error(*cache_file, CODELOC); - } - - QByteArray compressed_data = cache_file->readAll(); - - cache_file->close(); - - if (qChecksum(compressed_data.constData(), compressed_data.size()) != checksum) - { - throw SireError::invalid_state( - QObject::tr("Checksum failed on page data!"), CODELOC); - } - - QByteArray decompressed_data = qUncompress(compressed_data); - - if (decompressed_data.size() != nbytes) - { - throw SireError::invalid_state( - QObject::tr("Decompressed data size does not match expected size!"), CODELOC); - } - - fetched_page = RestoredPage::store(decompressed_data); + auto restored = page_handler->restore(*cache_file); - const_cast(this)->restored_page = fetched_page; + const_cast(this)->restored_page = restored; + lkr.unlock(); - return fetched_page->fetch(offset, n_bytes); + return restored->fetch(offset, n_bytes); } else { @@ -795,46 +1109,27 @@ QByteArray PageData::fetch(int offset, int n_bytes) const } } -void PageData::freeze(std::shared_ptr dir) +/** Freeze the page to disk, using the passed handler. This function + * will only ever be called by the background thread of a CacheData, + * so does not need to be (and isn't) thread-safe + */ +void PageData::freeze(std::shared_ptr handler) { - if (d == 0 or nbytes == 0 or is_frozen or dir.get() == nullptr) - { - return; - } - - QMutexLocker lkr(&mutex); - - if (cache_file.get() != nullptr) + // page is already frozen, or something else weird + if (d == 0 or nbytes == 0 or handler.get() == nullptr or + page_handler.get() != nullptr or cache_file != 0) { - qWarning() << "Page is already frozen!"; + Console::error(QObject::tr("Page is already frozen?")); return; } - cache_dir = dir; - - cache_file = std::make_shared(cache_dir->filePath("page_XXXXXX")); - - if (not cache_file->open()) - { - throw SireError::file_error(*cache_file, CODELOC); - } - - // compress the data and write it to a temporary file - QByteArray compressed_data = qCompress(QByteArray::fromRawData(d, nbytes), 9); - - checksum = qChecksum(compressed_data.constData(), compressed_data.size()); - - if (compressed_data.size() != cache_file->write(compressed_data)) - { - throw SireError::file_error(*cache_file, CODELOC); - } - - cache_file->close(); + cache_file = handler->store(QByteArray::fromRawData(d, nbytes)); + QMutexLocker lkr(&mutex); + // need to lock before deleting d because fetch() may be called delete[] d; d = 0; - - is_frozen = true; + page_handler = handler; } PageCache PageData::parent() const @@ -846,6 +1141,7 @@ PageCache PageData::parent() const /////// Implementation of detail::HandleData /////// +/** Construct a HandleData object containing the passed data */ HandleData::HandleData(const QByteArray &data) : d(data), offset(0), nbytes(data.size()) { @@ -859,12 +1155,16 @@ HandleData::HandleData(const QByteArray &data) } } +/** Destructor */ HandleData::~HandleData() { } +/** Fetch the data from this handle */ QByteArray HandleData::fetch() const { + // need to lock because the background thread may be + // changing the data (moving d to the page) QMutexLocker lkr(const_cast(&mutex)); if (state == EMPTY or state == DATA_IN_HANDLE) @@ -874,22 +1174,28 @@ QByteArray HandleData::fetch() const lkr.unlock(); + // this is a page, so fetch it from here (this call is thread-safe) return p.fetch(offset, nbytes); } +/** Internal function used to set the page containing this data */ void HandleData::setPage(const PageCache::Page &page, int off) { + // Need to lock because the background thread will call this, + // while we may be accessing the data via the thread-safe fetch() QMutexLocker lkr(&mutex); if (state == EMPTY) { - throw SireError::invalid_state( - QObject::tr("Handle is empty"), CODELOC); + QString message = QObject::tr("Handle is empty"); + Console::error(message); + throw SireError::invalid_state(message, CODELOC); } else if (state == DATA_ON_PAGE) { - throw SireError::invalid_state( - QObject::tr("Handle is already on the page!"), CODELOC); + QString message = QObject::tr("Handle is already on the page!"); + Console::error(message); + throw SireError::invalid_state(message, CODELOC); } p = page; @@ -900,28 +1206,37 @@ void HandleData::setPage(const PageCache::Page &page, int off) lkr.unlock(); } +/** Return the page containing this data. This will be a null + * page if the data is not yet on a page + */ PageCache::Page HandleData::page() const { + QMutexLocker lkr(const_cast(&mutex)); return p; } -int HandleData::nBytes() const +/** Return the number of bytes of the data held in this handle */ +unsigned int HandleData::nBytes() const { return nbytes; } +/** Return whether or not this handle is valid (actually holds anything) */ bool HandleData::isValid() const { return nbytes > 0; } +/** Return whether or not this handle is null (does not hold anything) */ bool HandleData::isNull() const { return nbytes == 0; } +/** Return the cache that this handle is associated with */ PageCache HandleData::parent() const { + QMutexLocker lkr(const_cast(&mutex)); return p.parent(); } @@ -929,41 +1244,49 @@ PageCache HandleData::parent() const /////// Implementation of PageCache::Page /////// +/** Construct an empty page */ PageCache::Page::Page() : p(nullptr) { } +/** Construct a page from the passed data */ PageCache::Page::Page(std::shared_ptr data) : p(data) { } +/** Copy constructor */ PageCache::Page::Page(const PageCache::Page &other) : p(other.p) { } +/** Destructor */ PageCache::Page::~Page() { } +/** Assignment operator */ PageCache::Page &PageCache::Page::operator=(const PageCache::Page &other) { p = other.p; return *this; } +/** Return the type name for this object */ const char *PageCache::Page::typeName() { return "SireBase::PageCache::Page"; } +/** Return the type name for this object */ const char *PageCache::Page::what() const { return PageCache::Page::typeName(); } +/** Return a string representation of this object */ QString PageCache::Page::toString() const { return QString("PageCache::Page(%1 KB used from %2 KB)") @@ -971,11 +1294,13 @@ QString PageCache::Page::toString() const .arg(this->maxBytes() / 1024.0); } +/** Clone this object */ PageCache::Page *PageCache::Page::clone() const { return new PageCache::Page(*this); } +/** Assert that this object is valid */ void PageCache::Page::assertValid() const { if (p == nullptr) @@ -985,54 +1310,88 @@ void PageCache::Page::assertValid() const } } +/** Return whether this page is valid (has some size) */ bool PageCache::Page::isValid() const { return p != nullptr; } +/** Return whether this page is null (has no size) */ bool PageCache::Page::isNull() const { return p == nullptr; } +/** Return whether this page is resident in memory */ bool PageCache::Page::isResident() const { - assertValid(); + if (this->isNull()) + { + return false; + } + return p->isResident(); } +/** Return whether this page is cached to disk */ bool PageCache::Page::isCached() const { - assertValid(); + if (this->isNull()) + { + return false; + } + return p->isCached(); } -int PageCache::Page::nBytes() const +/** Return the number of bytes in this page */ +unsigned int PageCache::Page::nBytes() const { - assertValid(); + if (this->isNull()) + { + return 0; + } + return p->nBytes(); } -int PageCache::Page::size() const +/** Return the number of bytes in this page */ +unsigned int PageCache::Page::size() const { return this->nBytes(); } -int PageCache::Page::maxBytes() const +/** Return the maximum number of bytes that can be stored in this page */ +unsigned int PageCache::Page::maxBytes() const { - assertValid(); + if (this->isNull()) + { + return 0; + } + return p->maxBytes(); } +/** Return the parent cache for this page */ PageCache PageCache::Page::parent() const { - assertValid(); + if (this->isNull()) + { + return PageCache(); + } + return p->parent(); } QByteArray PageCache::Page::fetch(int offset, int n_bytes) const { - assertValid(); + if (this->isNull()) + { + throw SireError::invalid_state( + QObject::tr("Page object is null - you cannot fetch any bytes!"), + CODELOC); + } + return p->fetch(offset, n_bytes); } @@ -1040,41 +1399,49 @@ QByteArray PageCache::Page::fetch(int offset, int n_bytes) const /////// Implementation of PageCache::Handle /////// +/** Construct an empty handle */ PageCache::Handle::Handle() : h(nullptr) { } +/** Construct a handle from the passed data */ PageCache::Handle::Handle(std::shared_ptr data) : h(data) { } +/** Copy constructor */ PageCache::Handle::Handle(const PageCache::Handle &other) : h(other.h) { } +/** Destructor */ PageCache::Handle::~Handle() { } +/** Assignment operator */ PageCache::Handle &PageCache::Handle::operator=(const PageCache::Handle &other) { h = other.h; return *this; } +/** Return the type name for this object */ const char *PageCache::Handle::typeName() { return "SireBase::PageCache::Handle"; } +/** Return the type name for this object */ const char *PageCache::Handle::what() const { return PageCache::Handle::typeName(); } +/** Return a string representation of this object */ QString PageCache::Handle::toString() const { const int nbytes = this->nBytes(); @@ -1089,11 +1456,13 @@ QString PageCache::Handle::toString() const } } +/** Clone this object */ PageCache::Handle *PageCache::Handle::clone() const { return new PageCache::Handle(*this); } +/** Assert that this object is valid */ void PageCache::Handle::assertValid() const { if (h == nullptr) @@ -1103,50 +1472,77 @@ void PageCache::Handle::assertValid() const } } +/** Return the page on which the data for this handle is placed. + * This will be null if the data has not yet been put on a page + */ PageCache::Page PageCache::Handle::page() const { - assertValid(); + if (this->isNull()) + { + return PageCache::Page(); + } + return Page(h->page()); } +/** Return the data held in this handle */ QByteArray PageCache::Handle::fetch() const { - assertValid(); + if (this->isNull()) + { + return QByteArray(); + } + return h->fetch(); } +/** Return the parent cache for this handle */ PageCache PageCache::Handle::parent() const { - assertValid(); + if (this->isNull()) + { + return PageCache(); + } + return h->parent(); } +/** Return whether this handle is valid (holds data) */ bool PageCache::Handle::isValid() const { return h != nullptr; } +/** Return whether this handle is null (does not hold data) */ bool PageCache::Handle::isNull() const { return h == nullptr; } -int PageCache::Handle::size() const +/** Return the number of bytes in this handle */ +unsigned int PageCache::Handle::size() const { return this->nBytes(); } -int PageCache::Handle::nBytes() const +/** Return the number of bytes in this handle */ +unsigned int PageCache::Handle::nBytes() const { - assertValid(); + if (this->isNull()) + { + return 0; + } + return h->nBytes(); } +/** Clear the data from this handle */ void PageCache::Handle::clear() { h.reset(); } +/** Clear the data in this handle */ void PageCache::Handle::reset() { h.reset(); @@ -1156,58 +1552,72 @@ void PageCache::Handle::reset() /////// Implementation of PageCache /////// -PageCache::PageCache(int page_size) +/** Construct a new page cache with the specified + recomended maximum page size */ +PageCache::PageCache(unsigned int page_size) : d(new CacheData(QString(), page_size)) { - d->registerCache(d); + d->setSelf(d); } -PageCache::PageCache(const QString &cachedir, int page_size) +/** Construct a new page cache with the specified + recomended maximum page size and cache directory + template (using QTemporaryDir format) */ +PageCache::PageCache(const QString &cachedir, unsigned int page_size) : d(new CacheData(cachedir, page_size)) { - d->registerCache(d); + d->setSelf(d); } +/** Internal constructor used to construct from a CacheData */ PageCache::PageCache(std::shared_ptr data) : d(data) { } +/** Copy constructor */ PageCache::PageCache(const PageCache &other) : d(other.d) { } +/** Destructor */ PageCache::~PageCache() { } +/** Assignment operator */ PageCache &PageCache::operator=(const PageCache &other) { d = other.d; return *this; } +/** Return the type name for this object */ const char *PageCache::typeName() { return "SireBase::PageCache"; } +/** Return the type name for this object */ const char *PageCache::what() const { return PageCache::typeName(); } +/** Return a string representation of this object */ QString PageCache::toString() const { return QString("PageCache(size = %1 KB)").arg(this->nBytes() / 1024.0); } +/** Clone this object */ PageCache *PageCache::clone() const { return new PageCache(*this); } +/** Assert that this object is valid */ void PageCache::assertValid() const { if (d == nullptr) @@ -1217,57 +1627,82 @@ void PageCache::assertValid() const } } +/** Return the statistics for all caches */ QString PageCache::getStatistics() { return CacheData::getStatistics(); } +/** Return the cache directory for this cache */ QString PageCache::cacheDir() const { - assertValid(); + if (this->isNull()) + { + return QString(); + } + return d->cacheDir(); } -int PageCache::pageSize() const +/** Return the suggested maximum page size for this cache */ +unsigned int PageCache::pageSize() const { - assertValid(); + if (this->isNull()) + { + return 0; + } + return d->pageSize(); } -int PageCache::nPages() const +/** Return the number of pages in this cache */ +unsigned int PageCache::nPages() const { - assertValid(); + if (this->isNull()) + { + return 0; + } + return d->nPages(); } -int PageCache::nBytes() const +/** Return the number of bytes saved in this cache */ +unsigned int PageCache::nBytes() const { - assertValid(); + if (this->isNull()) + { + return 0; + } + return d->nBytes(); } -int PageCache::size() const +/** Return the number of bytes saved in this cache */ +unsigned int PageCache::size() const { return this->nBytes(); } +/** Return whether or not this cache is valid */ bool PageCache::isValid() const { return d != nullptr; } +/** Return whether or not this cache is null */ bool PageCache::isNull() const { return d == nullptr; } -PageCache::Handle PageCache::cache(const QByteArray &data) -{ - assertValid(); - return Handle(d->cache(data)); -} - +/** Store the data in the cache, returning a handle to the data */ PageCache::Handle PageCache::store(const QByteArray &data) { - return this->cache(data); + if (this->isNull()) + { + // create a cache now + d = std::make_shared(QString(), 32 * 1024 * 1024); + } + + return Handle(d->store(data)); } diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index 9c90fcea9..c02167434 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -60,9 +60,9 @@ namespace SireBase class SIREBASE_EXPORT PageCache { public: - PageCache(int page_size = 32 * 1024 * 1024); + PageCache(unsigned int page_size = 32 * 1024 * 1024); PageCache(const QString &cache_dir, - int page_size = 32 * 1024 * 1024); + unsigned int page_size = 32 * 1024 * 1024); PageCache(std::shared_ptr data); PageCache(const PageCache &other); ~PageCache(); @@ -78,11 +78,11 @@ namespace SireBase QString cacheDir() const; - int pageSize() const; - int nPages() const; - int nBytes() const; + unsigned int pageSize() const; + unsigned int nPages() const; + unsigned int nBytes() const; - int size() const; + unsigned int size() const; bool isValid() const; bool isNull() const; @@ -122,10 +122,10 @@ namespace SireBase bool isResident() const; bool isCached() const; - int nBytes() const; - int size() const; + unsigned int nBytes() const; + unsigned int size() const; - int maxBytes() const; + unsigned int maxBytes() const; PageCache parent() const; @@ -171,8 +171,8 @@ namespace SireBase void assertValid() const; - int size() const; - int nBytes() const; + unsigned int size() const; + unsigned int nBytes() const; void clear(); void reset(); @@ -181,7 +181,6 @@ namespace SireBase std::shared_ptr h; }; - Handle cache(const QByteArray &data); Handle store(const QByteArray &data); private: diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index b5b3b55d3..44ea55bf4 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -66,9 +66,9 @@ namespace SireSystem if (not cache) { - QString cache_dir = QDir::current().absoluteFilePath("trajectory_cache_XXXXXX"); - // use 32 MB pages (using 32 KB now for debugging) - cache = std::make_shared(cache_dir, 32 * 1024); + QString cache_dir = QDir::current().absoluteFilePath("temp_traj_XXXXXX"); + // use 32 MB pages + cache = std::make_shared(cache_dir, 32 * 1024 * 1024); shared_cache = cache; } } diff --git a/src/sire/base/_pagecache.py b/src/sire/base/_pagecache.py index 0f8212abb..09523c299 100644 --- a/src/sire/base/_pagecache.py +++ b/src/sire/base/_pagecache.py @@ -3,9 +3,9 @@ from ..legacy.Base import PageCache -def __cache__(obj, data): +def __store__(obj, data): """ - Add the passed object onto the cache. This will convert the object + Store the passed object into the cache. This will convert the object into a binary form (pickled, then hex-encoded) and it will store it in the cache. This returns a handle to the object in the cache, which can be used to restore it. @@ -17,7 +17,7 @@ def __cache__(obj, data): # now convert this to a QByteArray b = QByteArray(data.hex()) - return obj.__orig__cache__(b) + return obj.__orig__store__(b) def __fetch__(obj): @@ -37,9 +37,9 @@ def __fetch__(obj): return loads(data) -if not hasattr(PageCache, "__orig__cache__"): - PageCache.__orig__cache__ = PageCache.cache - PageCache.cache = __cache__ +if not hasattr(PageCache, "__orig__store__"): + PageCache.__orig__store__ = PageCache.store + PageCache.store = __store__ if hasattr(PageCache, "handle"): PageCache.Handle = PageCache.handle diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index 27cb4faeb..f6d96d462 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -7,12 +7,28 @@ namespace bp = boost::python; +#include "SireBase/console.h" + +#include "SireBase/parallel.h" + #include "SireError/errors.h" #include "pagecache.h" +#include + #include +#include + +#include + +#include + +#include + +#include + #include #include "pagecache.h" @@ -25,12 +41,28 @@ const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCach #include "Helpers/release_gil_policy.hpp" +#include "SireBase/console.h" + +#include "SireBase/parallel.h" + #include "SireError/errors.h" #include "pagecache.h" +#include + #include +#include + +#include + +#include + +#include + +#include + #include #include "pagecache.h" @@ -45,12 +77,28 @@ SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ #include "Helpers/len.hpp" +#include "SireBase/console.h" + +#include "SireBase/parallel.h" + #include "SireError/errors.h" #include "pagecache.h" +#include + #include +#include + +#include + +#include + +#include + +#include + #include #include "pagecache.h" @@ -69,14 +117,14 @@ void register_PageCache_class(){ { //::SireBase::PageCache typedef bp::class_< SireBase::PageCache > PageCache_exposer_t; - PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< bp::optional< int > >(( bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); + PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< bp::optional< unsigned int > >(( bp::arg("page_size")=(unsigned int)(32 * 1024 * 1024) ), "") ); bp::scope PageCache_scope( PageCache_exposer ); { //::SireBase::PageCache::Handle typedef bp::class_< SireBase::PageCache::Handle > Handle_exposer_t; - Handle_exposer_t Handle_exposer = Handle_exposer_t( "Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init< >("") ); + Handle_exposer_t Handle_exposer = Handle_exposer_t( "Handle", "This is a handle to a piece of data that has\nbeen added to the cache. This will either contain\nthe actual data, or will hold the information\nnecessary to retrieve that data from disk.\n\nData is removed from the cache when all handles\nto it are deleted\n", bp::init< >("Construct an empty handle") ); bp::scope Handle_scope( Handle_exposer ); - Handle_exposer.def( bp::init< std::shared_ptr< SireBase::detail::HandleData > >(( bp::arg("data") ), "") ); - Handle_exposer.def( bp::init< SireBase::PageCache::Handle const & >(( bp::arg("other") ), "") ); + Handle_exposer.def( bp::init< std::shared_ptr< SireBase::detail::HandleData > >(( bp::arg("data") ), "Construct a handle from the passed data") ); + Handle_exposer.def( bp::init< SireBase::PageCache::Handle const & >(( bp::arg("other") ), "Copy constructor") ); { //::SireBase::PageCache::Handle::assertValid typedef void ( ::SireBase::PageCache::Handle::*assertValid_function_type)( ) const; @@ -86,7 +134,7 @@ void register_PageCache_class(){ "assertValid" , assertValid_function_value , bp::release_gil_policy() - , "" ); + , "Assert that this object is valid" ); } { //::SireBase::PageCache::Handle::clear @@ -98,7 +146,7 @@ void register_PageCache_class(){ "clear" , clear_function_value , bp::release_gil_policy() - , "" ); + , "Clear the data from this handle" ); } { //::SireBase::PageCache::Handle::fetch @@ -110,7 +158,7 @@ void register_PageCache_class(){ "fetch" , fetch_function_value , bp::release_gil_policy() - , "" ); + , "Return the data held in this handle" ); } { //::SireBase::PageCache::Handle::isNull @@ -122,7 +170,7 @@ void register_PageCache_class(){ "isNull" , isNull_function_value , bp::release_gil_policy() - , "" ); + , "Return whether this handle is null (does not hold data)" ); } { //::SireBase::PageCache::Handle::isValid @@ -134,19 +182,19 @@ void register_PageCache_class(){ "isValid" , isValid_function_value , bp::release_gil_policy() - , "" ); + , "Return whether this handle is valid (holds data)" ); } { //::SireBase::PageCache::Handle::nBytes - typedef int ( ::SireBase::PageCache::Handle::*nBytes_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::Handle::*nBytes_function_type)( ) const; nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Handle::nBytes ); Handle_exposer.def( "nBytes" , nBytes_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of bytes in this handle" ); } { //::SireBase::PageCache::Handle::operator= @@ -171,7 +219,7 @@ void register_PageCache_class(){ "page" , page_function_value , bp::release_gil_policy() - , "" ); + , "Return the page on which the data for this handle is placed.\n This will be null if the data has not yet been put on a page\n" ); } { //::SireBase::PageCache::Handle::parent @@ -183,7 +231,7 @@ void register_PageCache_class(){ "parent" , parent_function_value , bp::release_gil_policy() - , "" ); + , "Return the parent cache for this handle" ); } { //::SireBase::PageCache::Handle::reset @@ -195,19 +243,19 @@ void register_PageCache_class(){ "reset" , reset_function_value , bp::release_gil_policy() - , "" ); + , "Clear the data in this handle" ); } { //::SireBase::PageCache::Handle::size - typedef int ( ::SireBase::PageCache::Handle::*size_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::Handle::*size_function_type)( ) const; size_function_type size_function_value( &::SireBase::PageCache::Handle::size ); Handle_exposer.def( "size" , size_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of bytes in this handle" ); } { //::SireBase::PageCache::Handle::toString @@ -219,7 +267,7 @@ void register_PageCache_class(){ "toString" , toString_function_value , bp::release_gil_policy() - , "" ); + , "Return a string representation of this object" ); } { //::SireBase::PageCache::Handle::typeName @@ -231,7 +279,7 @@ void register_PageCache_class(){ "typeName" , typeName_function_value , bp::release_gil_policy() - , "" ); + , "Return the type name for this object" ); } { //::SireBase::PageCache::Handle::what @@ -243,7 +291,7 @@ void register_PageCache_class(){ "what" , what_function_value , bp::release_gil_policy() - , "" ); + , "Return the type name for this object" ); } Handle_exposer.staticmethod( "typeName" ); @@ -256,10 +304,10 @@ void register_PageCache_class(){ } { //::SireBase::PageCache::Page typedef bp::class_< SireBase::PageCache::Page > Page_exposer_t; - Page_exposer_t Page_exposer = Page_exposer_t( "Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init< >("") ); + Page_exposer_t Page_exposer = Page_exposer_t( "Page", "This is a page in the cache. This can hold multiple\nobjects - the whole page is either resident in memory\nor cached to disk.\n", bp::init< >("Construct an empty page") ); bp::scope Page_scope( Page_exposer ); - Page_exposer.def( bp::init< std::shared_ptr< SireBase::detail::PageData > >(( bp::arg("data") ), "") ); - Page_exposer.def( bp::init< SireBase::PageCache::Page const & >(( bp::arg("other") ), "") ); + Page_exposer.def( bp::init< std::shared_ptr< SireBase::detail::PageData > >(( bp::arg("data") ), "Construct a page from the passed data") ); + Page_exposer.def( bp::init< SireBase::PageCache::Page const & >(( bp::arg("other") ), "Copy constructor") ); { //::SireBase::PageCache::Page::assertValid typedef void ( ::SireBase::PageCache::Page::*assertValid_function_type)( ) const; @@ -269,7 +317,7 @@ void register_PageCache_class(){ "assertValid" , assertValid_function_value , bp::release_gil_policy() - , "" ); + , "Assert that this object is valid" ); } { //::SireBase::PageCache::Page::isCached @@ -281,7 +329,7 @@ void register_PageCache_class(){ "isCached" , isCached_function_value , bp::release_gil_policy() - , "" ); + , "Return whether this page is cached to disk" ); } { //::SireBase::PageCache::Page::isNull @@ -293,7 +341,7 @@ void register_PageCache_class(){ "isNull" , isNull_function_value , bp::release_gil_policy() - , "" ); + , "Return whether this page is null (has no size)" ); } { //::SireBase::PageCache::Page::isResident @@ -305,7 +353,7 @@ void register_PageCache_class(){ "isResident" , isResident_function_value , bp::release_gil_policy() - , "" ); + , "Return whether this page is resident in memory" ); } { //::SireBase::PageCache::Page::isValid @@ -317,31 +365,31 @@ void register_PageCache_class(){ "isValid" , isValid_function_value , bp::release_gil_policy() - , "" ); + , "Return whether this page is valid (has some size)" ); } { //::SireBase::PageCache::Page::maxBytes - typedef int ( ::SireBase::PageCache::Page::*maxBytes_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::Page::*maxBytes_function_type)( ) const; maxBytes_function_type maxBytes_function_value( &::SireBase::PageCache::Page::maxBytes ); Page_exposer.def( "maxBytes" , maxBytes_function_value , bp::release_gil_policy() - , "" ); + , "Return the maximum number of bytes that can be stored in this page" ); } { //::SireBase::PageCache::Page::nBytes - typedef int ( ::SireBase::PageCache::Page::*nBytes_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::Page::*nBytes_function_type)( ) const; nBytes_function_type nBytes_function_value( &::SireBase::PageCache::Page::nBytes ); Page_exposer.def( "nBytes" , nBytes_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of bytes in this page" ); } { //::SireBase::PageCache::Page::operator= @@ -366,19 +414,19 @@ void register_PageCache_class(){ "parent" , parent_function_value , bp::release_gil_policy() - , "" ); + , "Return the parent cache for this page" ); } { //::SireBase::PageCache::Page::size - typedef int ( ::SireBase::PageCache::Page::*size_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::Page::*size_function_type)( ) const; size_function_type size_function_value( &::SireBase::PageCache::Page::size ); Page_exposer.def( "size" , size_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of bytes in this page" ); } { //::SireBase::PageCache::Page::toString @@ -390,7 +438,7 @@ void register_PageCache_class(){ "toString" , toString_function_value , bp::release_gil_policy() - , "" ); + , "Return a string representation of this object" ); } { //::SireBase::PageCache::Page::typeName @@ -402,7 +450,7 @@ void register_PageCache_class(){ "typeName" , typeName_function_value , bp::release_gil_policy() - , "" ); + , "Return the type name for this object" ); } { //::SireBase::PageCache::Page::what @@ -414,7 +462,7 @@ void register_PageCache_class(){ "what" , what_function_value , bp::release_gil_policy() - , "" ); + , "Return the type name for this object" ); } Page_exposer.staticmethod( "typeName" ); @@ -425,7 +473,7 @@ void register_PageCache_class(){ Page_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Page > ); Page_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Page > ); } - PageCache_exposer.def( bp::init< QString const &, bp::optional< int > >(( bp::arg("cache_dir"), bp::arg("page_size")=(int)(32 * 1024 * 1024) ), "") ); + PageCache_exposer.def( bp::init< QString const &, bp::optional< unsigned int > >(( bp::arg("cache_dir"), bp::arg("page_size")=(unsigned int)(32 * 1024 * 1024) ), "") ); PageCache_exposer.def( bp::init< std::shared_ptr< SireBase::detail::CacheData > >(( bp::arg("data") ), "") ); PageCache_exposer.def( bp::init< SireBase::PageCache const & >(( bp::arg("other") ), "") ); { //::SireBase::PageCache::assertValid @@ -439,19 +487,6 @@ void register_PageCache_class(){ , bp::release_gil_policy() , "" ); - } - { //::SireBase::PageCache::cache - - typedef ::SireBase::PageCache::Handle ( ::SireBase::PageCache::*cache_function_type)( ::QByteArray const & ) ; - cache_function_type cache_function_value( &::SireBase::PageCache::cache ); - - PageCache_exposer.def( - "cache" - , cache_function_value - , ( bp::arg("data") ) - , bp::release_gil_policy() - , "" ); - } { //::SireBase::PageCache::cacheDir @@ -503,7 +538,7 @@ void register_PageCache_class(){ } { //::SireBase::PageCache::nBytes - typedef int ( ::SireBase::PageCache::*nBytes_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::*nBytes_function_type)( ) const; nBytes_function_type nBytes_function_value( &::SireBase::PageCache::nBytes ); PageCache_exposer.def( @@ -515,7 +550,7 @@ void register_PageCache_class(){ } { //::SireBase::PageCache::nPages - typedef int ( ::SireBase::PageCache::*nPages_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::*nPages_function_type)( ) const; nPages_function_type nPages_function_value( &::SireBase::PageCache::nPages ); PageCache_exposer.def( @@ -540,7 +575,7 @@ void register_PageCache_class(){ } { //::SireBase::PageCache::pageSize - typedef int ( ::SireBase::PageCache::*pageSize_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::*pageSize_function_type)( ) const; pageSize_function_type pageSize_function_value( &::SireBase::PageCache::pageSize ); PageCache_exposer.def( @@ -552,7 +587,7 @@ void register_PageCache_class(){ } { //::SireBase::PageCache::size - typedef int ( ::SireBase::PageCache::*size_function_type)( ) const; + typedef unsigned int ( ::SireBase::PageCache::*size_function_type)( ) const; size_function_type size_function_value( &::SireBase::PageCache::size ); PageCache_exposer.def( From 68c68e6335190befeec6c9420cd34a370e56d144 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Apr 2024 21:25:21 +0100 Subject: [PATCH 235/468] Clone the system so the original remains unmodified. --- src/sire/qm/_emle.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 6096527a1..bfcf82b3a 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -64,6 +64,9 @@ def emle( if not isinstance(mols, _System): raise TypeError("mols must be a of type 'sire.System'") + # Clone the system. + mols = mols.clone() + try: qm_atoms = _selection_to_atoms(mols, qm_atoms) except: From 54bc28fdd2111e52e05f5fd5879dedbf58c9005b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Apr 2024 21:30:01 +0100 Subject: [PATCH 236/468] Pythonize all exposed EMLE classes. --- src/sire/_pythonize.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index 6cd9f2968..c624b4be9 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -238,8 +238,10 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): delete_old=delete_old, ) - # Pythonize the EMLEEngine class. + # Pythonize the EMLE classes. + _pythonize(Convert._SireOpenMM.EMLECallback, delete_old=delete_old) _pythonize(Convert._SireOpenMM.EMLEEngine, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.EMLEForce, delete_old=delete_old) try: import lazy_import From 453e0d9e1ef471ae76c1baa126780398e4bfd5a3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Apr 2024 21:30:40 +0100 Subject: [PATCH 237/468] Fix formatting. --- wrapper/Convert/SireOpenMM/register_extras.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/register_extras.cpp b/wrapper/Convert/SireOpenMM/register_extras.cpp index 422a7e5f0..998fc1301 100644 --- a/wrapper/Convert/SireOpenMM/register_extras.cpp +++ b/wrapper/Convert/SireOpenMM/register_extras.cpp @@ -59,7 +59,7 @@ namespace SireOpenMM register_dict>(); register_dict>>(); - // A tuple for returning link atom information from EMLEEngine. - bp::register_tuple, QMap>, QMap>>(); + // A tuple for passing link atom information to EMLEEngine. + bp::register_tuple, QMap>>>(); } } From 60f425967df4e712165192afc2bc025d39b16c97 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Apr 2024 21:31:22 +0100 Subject: [PATCH 238/468] Add support for serialization in Sire and OpenMM. --- .../Convert/SireOpenMM/EMLECallback.pypp.cpp | 15 ++ .../Convert/SireOpenMM/EMLEEngine.pypp.cpp | 20 ++ wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp | 28 +++ .../Convert/SireOpenMM/LambdaLever.pypp.cpp | 2 +- .../PerturbableOpenMMMolecule.pypp.cpp | 12 ++ wrapper/Convert/SireOpenMM/emle.cpp | 186 ++++++++++++++++++ wrapper/Convert/SireOpenMM/emle.h | 27 +++ 7 files changed, 289 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp index c464d95e3..c0863c5db 100644 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp @@ -11,6 +11,10 @@ namespace bp = boost::python; #include "SireMaths/vector.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + #include "SireVol/triclinicbox.h" #include "emle.h" @@ -19,12 +23,18 @@ namespace bp = boost::python; #include "SireMaths/vector.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + #include "SireVol/triclinicbox.h" #include "emle.h" SireOpenMM::EMLECallback __copy__(const SireOpenMM::EMLECallback &other){ return SireOpenMM::EMLECallback(other); } +#include "Qt/qdatastream.hpp" + const char* pvt_get_name(const SireOpenMM::EMLECallback&){ return "SireOpenMM::EMLECallback";} #include "Helpers/release_gil_policy.hpp" @@ -77,6 +87,11 @@ void register_EMLECallback_class(){ EMLECallback_exposer.def( "__copy__", &__copy__); EMLECallback_exposer.def( "__deepcopy__", &__copy__); EMLECallback_exposer.def( "clone", &__copy__); + EMLECallback_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::EMLECallback >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + EMLECallback_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::EMLECallback >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + EMLECallback_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::EMLECallback >()); EMLECallback_exposer.def( "__str__", &pvt_get_name); EMLECallback_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp index 5c19ad65a..e6016d97c 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp @@ -11,6 +11,10 @@ namespace bp = boost::python; #include "SireMaths/vector.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + #include "SireVol/triclinicbox.h" #include "emle.h" @@ -19,6 +23,10 @@ namespace bp = boost::python; #include "SireMaths/vector.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + #include "SireVol/triclinicbox.h" #include "emle.h" @@ -97,6 +105,18 @@ void register_EMLEEngine_class(){ , bp::release_gil_policy() , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); + } + { //::SireOpenMM::EMLEEngine::getForce + + typedef ::SireOpenMM::EMLEForce ( ::SireOpenMM::EMLEEngine::*getForce_function_type)( ) const; + getForce_function_type getForce_function_value( &::SireOpenMM::EMLEEngine::getForce ); + + EMLEEngine_exposer.def( + "getForce" + , getForce_function_value + , bp::release_gil_policy() + , "Get the EMLE force object." ); + } { //::SireOpenMM::EMLEEngine::getLambda diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp index ac3d6bd27..4e9f2c3b2 100644 --- a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp @@ -11,6 +11,10 @@ namespace bp = boost::python; #include "SireMaths/vector.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + #include "SireVol/triclinicbox.h" #include "emle.h" @@ -19,12 +23,18 @@ namespace bp = boost::python; #include "SireMaths/vector.h" +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + #include "SireVol/triclinicbox.h" #include "emle.h" SireOpenMM::EMLEForce __copy__(const SireOpenMM::EMLEForce &other){ return SireOpenMM::EMLEForce(other); } +#include "Qt/qdatastream.hpp" + const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLEForce";} #include "Helpers/release_gil_policy.hpp" @@ -61,6 +71,19 @@ void register_EMLEForce_class(){ , bp::release_gil_policy() , "Get the indices of the atoms in the QM region.\nReturn:s\nA vector of atom indices for the QM region.\n" ); + } + { //::SireOpenMM::EMLEForce::setCallback + + typedef void ( ::SireOpenMM::EMLEForce::*setCallback_function_type)( ::SireOpenMM::EMLECallback ) ; + setCallback_function_type setCallback_function_value( &::SireOpenMM::EMLEForce::setCallback ); + + EMLEForce_exposer.def( + "setCallback" + , setCallback_function_value + , ( bp::arg("callback") ) + , bp::release_gil_policy() + , "Set the callback object.\nPar:am callback\nA Python object that contains the callback function.\n" ); + } { //::SireOpenMM::EMLEForce::getCallback @@ -212,6 +235,11 @@ void register_EMLEForce_class(){ EMLEForce_exposer.def( "__copy__", &__copy__); EMLEForce_exposer.def( "__deepcopy__", &__copy__); EMLEForce_exposer.def( "clone", &__copy__); + EMLEForce_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::EMLEForce >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + EMLEForce_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::EMLEForce >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + EMLEForce_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::EMLEForce >()); EMLEForce_exposer.def( "__str__", &pvt_get_name); EMLEForce_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp index 723877af0..5be152634 100644 --- a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp @@ -119,7 +119,7 @@ void register_LambdaLever_class(){ , getLeverValues_function_value , ( bp::arg("lambda_values"), bp::arg("mol") ) , bp::release_gil_policy() - , "" ); + , "Get all of the lever values that would be set for the passed\n lambda values using the current context. This returns a PropertyList\n of columns, where each column is a PropertyMap with the column name\n and either double or QString array property of values.\n\n This is designed to be used by a higher-level python function that\n will convert this output into, e.g. a pandas DataFrame\n" ); } { //::SireOpenMM::LambdaLever::getPerturbableMoleculeMaps diff --git a/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp b/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp index b24f08114..37a03ccf9 100644 --- a/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp @@ -595,6 +595,18 @@ void register_PerturbableOpenMMMolecule_class(){ , bp::release_gil_policy() , "Return true if the atom is a ghost atom in the\n referenece or perturbed states" ); + } + { //::SireOpenMM::PerturbableOpenMMMolecule::isNull + + typedef bool ( ::SireOpenMM::PerturbableOpenMMMolecule::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::isNull ); + + PerturbableOpenMMMolecule_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "Return whether or not this is null" ); + } PerturbableOpenMMMolecule_exposer.def( bp::self != bp::self ); { //::SireOpenMM::PerturbableOpenMMMolecule::operator= diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 00f498547..76f360097 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -26,14 +26,22 @@ * \*********************************************/ +#include + +#include "openmm/serialization/SerializationNode.h" +#include "openmm/serialization/SerializationProxy.h" + #include "SireError/errors.h" #include "SireMaths/vector.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" #include "SireVol/triclinicbox.h" #include "emle.h" using namespace SireMaths; using namespace SireOpenMM; +using namespace SireStream; using namespace SireVol; // The delta used to place virtual point charges either side of the MM2 @@ -53,6 +61,35 @@ class GILLock ///////// Implementation of EMLECallback ///////// +static const RegisterMetaType r_emlecallback(NO_ROOT); + +QDataStream &operator<<(QDataStream &ds, const EMLECallback &emlecallback) +{ + writeHeader(ds, r_emlecallback, 1); + + SharedDataStream sds(ds); + + sds << emlecallback.callback; + + return ds; +} + +QDataStream &operator>>(QDataStream &ds, EMLECallback &emlecallback) +{ + VersionID v = readHeader(ds, r_emlecallback); + + if (v == 1) + { + SharedDataStream sds(ds); + + sds >> emlecallback.callback; + } + else + throw version_error(v, "1", r_emlecallback, CODELOC); + + return ds; +} + EMLECallback::EMLECallback() { } @@ -97,6 +134,41 @@ const char *EMLECallback::what() const ///////// Implementation of EMLEForce ///////// +static const RegisterMetaType r_emleforce(NO_ROOT); + +QDataStream &operator<<(QDataStream &ds, const EMLEForce &emleforce) +{ + writeHeader(ds, r_emleforce, 1); + + SharedDataStream sds(ds); + + sds << emleforce.callback << emleforce.cutoff << emleforce.neighbour_list_frequency + << emleforce.lambda << emleforce.atoms << emleforce.mm1_to_qm + << emleforce.mm1_to_mm2 << emleforce.bond_scale_factors << emleforce.mm2_atoms + << emleforce.numbers << emleforce.charges; + + return ds; +} + +QDataStream &operator>>(QDataStream &ds, EMLEForce &emleforce) +{ + VersionID v = readHeader(ds, r_emleforce); + + if (v == 1) + { + SharedDataStream sds(ds); + + sds >> emleforce.callback >> emleforce.cutoff >> emleforce.neighbour_list_frequency + >> emleforce.lambda >> emleforce.atoms >> emleforce.mm1_to_qm + >> emleforce.mm1_to_mm2 >> emleforce.bond_scale_factors >> emleforce.mm2_atoms + >> emleforce.numbers >> emleforce.charges; + } + else + throw version_error(v, "1", r_emleforce, CODELOC); + + return ds; +} + EMLEForce::EMLEForce() { } @@ -158,6 +230,11 @@ EMLEForce &EMLEForce::operator=(const EMLEForce &other) return *this; } +void EMLEForce::setCallback(EMLECallback callback) +{ + this->callback = callback; +} + EMLECallback EMLEForce::getCallback() const { return this->callback; @@ -237,6 +314,93 @@ EMLEForce::call( return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); } +///////// +///////// OpenMM Serialization +///////// + +namespace OpenMM +{ + // A callback object to store the callback function. + EMLECallback callback; + + // A mutex to protect the callback. + std::mutex callback_mutex; + + // Set the callback using a mutex. + void setCallback(EMLECallback cb) + { + std::lock_guard lock(callback_mutex); + callback = cb; + } + + // Get the callback using a mutex. + EMLECallback getCallback() + { + std::lock_guard lock(callback_mutex); + return callback; + } + + class EMLEForceProxy : public SerializationProxy { + public: + EMLEForceProxy() : SerializationProxy("EMLEForce") + { + }; + + void serialize(const void* object, SerializationNode& node) const + { + // Serialize the object. + QByteArray data; + QDataStream ds(&data, QIODevice::WriteOnly); + EMLEForce emleforce = *static_cast(object); + ds << emleforce; + + // Set the version. + node.setIntProperty("version", 0); + + // Set the data by converting the QByteArray to a hexidecimal string. + node.setStringProperty("data", data.toHex().data()); + + // Set the callback. + setCallback(emleforce.getCallback()); + }; + + void* deserialize(const SerializationNode& node) const + { + // Check the version. + int version = node.getIntProperty("version"); + if (version != 0) + throw OpenMM::OpenMMException("Unsupported version number"); + + // Get the data as a std::string. + auto string = node.getStringProperty("data"); + + // Convert to hexidecimal. + auto hex = QByteArray::fromRawData(string.data(), string.size()); + + // Convert to a QByteArray. + auto data = QByteArray::fromHex(hex); + + // Deserialize the object. + QDataStream ds(data); + EMLEForce emleforce; + ds >> emleforce; + + // Create a new EMLEForce object. + auto emleforce_ptr = new EMLEForce(emleforce); + + // Set the callback. + emleforce_ptr->setCallback(getCallback()); + + return emleforce_ptr; + }; + }; + + // Register the EMLEForce serialization proxy. + extern "C" void registerEmleSerializationProxies() { + SerializationProxy::registerProxy(typeid(EMLEForce), new EMLEForceProxy()); + } +}; + ///////// ///////// Implementation of EMLEForceImpl ///////// @@ -602,6 +766,8 @@ double EMLEForceImpl::computeForce( EMLEEngine::EMLEEngine() : ConcreteProperty() { + // Register the serialization proxies. + OpenMM::registerEmleSerializationProxies(); } EMLEEngine::EMLEEngine( @@ -615,6 +781,9 @@ EMLEEngine::EMLEEngine( neighbour_list_frequency(neighbour_list_frequency), lambda(lambda) { + // Register the serialization proxies. + OpenMM::registerEmleSerializationProxies(); + if (this->neighbour_list_frequency < 0) { neighbour_list_frequency = 0; @@ -807,3 +976,20 @@ QMForce* EMLEEngine::createForce() const this->charges ); } + +EMLEForce EMLEEngine::getForce() const +{ + return EMLEForce( + this->callback, + this->cutoff, + this->neighbour_list_frequency, + this->lambda, + this->atoms, + this->mm1_to_qm, + this->mm1_to_mm2, + this->bond_scale_factors, + this->mm2_atoms, + this->numbers, + this->charges + ); +} diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index ded7f971d..963b7c64e 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -53,12 +53,27 @@ namespace bp = boost::python; SIRE_BEGIN_HEADER +namespace SireOpenMM +{ + class EMLECallback; + class EMLEForce; +} + +QDataStream &operator<<(QDataStream &, const SireOpenMM::EMLECallback &); +QDataStream &operator>>(QDataStream &, SireOpenMM::EMLECallback &); + +QDataStream &operator<<(QDataStream &, const SireOpenMM::EMLEForce &); +QDataStream &operator>>(QDataStream &, SireOpenMM::EMLEForce &); + namespace SireOpenMM { // A callback wrapper class to allow use of electrostatic embedding of // machine learning potentials via emle-engine. class EMLECallback { + friend QDataStream & ::operator<<(QDataStream &, const EMLECallback &); + friend QDataStream & ::operator>>(QDataStream &, EMLECallback &); + public: //! Default constructor. EMLECallback(); @@ -115,6 +130,9 @@ namespace SireOpenMM class EMLEForce : public QMForce { + friend QDataStream & ::operator<<(QDataStream &, const EMLEForce &); + friend QDataStream & ::operator>>(QDataStream &, EMLEForce &); + public: //! Default constructor. EMLEForce(); @@ -181,6 +199,12 @@ namespace SireOpenMM //! Assignment operator. EMLEForce &operator=(const EMLEForce &other); + //! Set the callback object. + /*! \param callback + A Python object that contains the callback function. + */ + void setCallback(EMLECallback callback); + //! Get the callback object. /*! \returns A Python object that contains the callback function. @@ -531,6 +555,9 @@ namespace SireOpenMM //! Create an EMLE force object. QMForce* createForce() const; + //! Get the EMLE force object. + EMLEForce getForce() const; + private: EMLECallback callback; SireUnits::Dimension::Length cutoff; From 444cd59b3f991a2eb9a58ab45ddc0787558ff556 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 19 Apr 2024 22:16:19 +0100 Subject: [PATCH 239/468] Implement a simple registry for the EMLECallback. --- wrapper/Convert/SireOpenMM/emle.cpp | 48 ++++++++++++++++++++--------- 1 file changed, 34 insertions(+), 14 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 76f360097..16a993f8a 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -28,6 +28,9 @@ #include +#include +#include + #include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationProxy.h" @@ -320,24 +323,30 @@ EMLEForce::call( namespace OpenMM { - // A callback object to store the callback function. - EMLECallback callback; + // A callback registry; + QHash callback_registry; - // A mutex to protect the callback. + // A mutex to protect the registry. std::mutex callback_mutex; - // Set the callback using a mutex. - void setCallback(EMLECallback cb) + // Set a callback in the registry using a mutex. + void setCallback(EMLECallback cb, QString uuid) { std::lock_guard lock(callback_mutex); - callback = cb; - } + callback_registry[uuid] = cb; + }; - // Get the callback using a mutex. - EMLECallback getCallback() + // Get a callback from the registry using a mutex. + EMLECallback getCallback(QString uuid) { std::lock_guard lock(callback_mutex); - return callback; + + if (not callback_registry.contains(uuid)) + { + throw OpenMM::OpenMMException("Unable to find UUID in the EMLEForce callback registry."); + } + + return callback_registry[uuid]; } class EMLEForceProxy : public SerializationProxy { @@ -354,22 +363,30 @@ namespace OpenMM EMLEForce emleforce = *static_cast(object); ds << emleforce; + // Generate a unique identifier for the callback. + auto uuid = QUuid::createUuid().toString(); + // Set the version. node.setIntProperty("version", 0); // Set the data by converting the QByteArray to a hexidecimal string. node.setStringProperty("data", data.toHex().data()); + // Set the UID. + node.setStringProperty("uuid", uuid.toStdString()); + // Set the callback. - setCallback(emleforce.getCallback()); + setCallback(emleforce.getCallback(), uuid); }; void* deserialize(const SerializationNode& node) const { // Check the version. int version = node.getIntProperty("version"); - if (version != 0) - throw OpenMM::OpenMMException("Unsupported version number"); + if (version != 0) + { + throw OpenMM::OpenMMException("Unsupported version number"); + } // Get the data as a std::string. auto string = node.getStringProperty("data"); @@ -385,11 +402,14 @@ namespace OpenMM EMLEForce emleforce; ds >> emleforce; + // Get the UID string. + auto uuid = QString::fromStdString(node.getStringProperty("uuid")); + // Create a new EMLEForce object. auto emleforce_ptr = new EMLEForce(emleforce); // Set the callback. - emleforce_ptr->setCallback(getCallback()); + emleforce_ptr->setCallback(getCallback(uuid)); return emleforce_ptr; }; From a2034509737de9aeca5f0a4ffe0f2be5a1efc73a Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 20 Apr 2024 12:50:42 +0100 Subject: [PATCH 240/468] Changed the default page size to 8 MB and made it easier to change the page size from Python --- corelib/src/libs/SireBase/pagecache.cpp | 80 +++++++++++++++++++ corelib/src/libs/SireBase/pagecache.h | 14 +++- .../src/libs/SireSystem/systemtrajectory.cpp | 3 +- wrapper/Base/PageCache.pypp.cpp | 66 +++++++++++---- 4 files changed, 142 insertions(+), 21 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 1eaac4054..da12c368e 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -110,6 +110,9 @@ namespace SireBase static QString getStatistics(); + static void setMaxPageSize(unsigned int size, bool update_existing); + static unsigned int maxPageSize(); + QString cacheDir() const; PageCache::Handle store(const QByteArray &data); @@ -136,6 +139,9 @@ namespace SireBase */ static QList> caches; + /** The current default maximum page size */ + static unsigned int max_page_size; + /** Mutex protected the queue of Handles containing data * that should be pushed to the cache */ @@ -518,6 +524,50 @@ std::shared_ptr PageHandler::restore(QTemporaryFile &pagefile) QMutex CacheData::caches_mutex; QList> CacheData::caches; +/** Default to 8 MB pages - this seems to be a good balance for + * not having pages so large that they take a noticeable time to + * load from disk + */ +unsigned int CacheData::max_page_size = 8 * 1024 * 1024; + +/** Set the maximum page size to the passed value */ +void CacheData::setMaxPageSize(unsigned int size, bool update_existing) +{ + if (size < 1024) + { + Console::warning(QObject::tr("Setting page size to the minimum of 1024 bytes.")); + size = 1024; + } + else if (size > 128 * 1024 * 1024) + { + Console::warning(QObject::tr("Setting page size to the maximum of 128 MB.")); + size = 128 * 1024 * 1024; + } + + QMutexLocker lkr(&caches_mutex); + max_page_size = size; + + if (update_existing) + { + for (auto &cache : caches) + { + auto c = cache.lock(); + + if (c.get() != nullptr) + { + c->page_size = size; + } + } + } +} + +/** Return the current maximum page size */ +unsigned int CacheData::maxPageSize() +{ + QMutexLocker lkr(&caches_mutex); + return max_page_size; +} + /** Set the self pointer for this cache */ void CacheData::setSelf(const std::shared_ptr &cache) { @@ -1552,6 +1602,14 @@ void PageCache::Handle::reset() /////// Implementation of PageCache /////// +/** Construct a new page cache with the default + * recomended maximum page size */ +PageCache::PageCache() + : d(new CacheData(QString(), CacheData::maxPageSize())) +{ + d->setSelf(d); +} + /** Construct a new page cache with the specified recomended maximum page size */ PageCache::PageCache(unsigned int page_size) @@ -1560,6 +1618,14 @@ PageCache::PageCache(unsigned int page_size) d->setSelf(d); } +/** Construct a new page cache with specified cache directory + and recomended maximum page size */ +PageCache::PageCache(const QString &cachedir) + : d(new CacheData(cachedir, CacheData::maxPageSize())) +{ + d->setSelf(d); +} + /** Construct a new page cache with the specified recomended maximum page size and cache directory template (using QTemporaryDir format) */ @@ -1617,6 +1683,20 @@ PageCache *PageCache::clone() const return new PageCache(*this); } +/** Set the default maximum page cache size for all new created + * caches that don't specify it themselves */ +void PageCache::setMaxPageSize(unsigned int page_size, + bool update_existing) +{ + CacheData::setMaxPageSize(page_size, update_existing); +} + +/** Return the current recommend maximum page size */ +unsigned int PageCache::maxPageSize() +{ + return CacheData::maxPageSize(); +} + /** Assert that this object is valid */ void PageCache::assertValid() const { diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index c02167434..1560e24f7 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -60,11 +60,15 @@ namespace SireBase class SIREBASE_EXPORT PageCache { public: - PageCache(unsigned int page_size = 32 * 1024 * 1024); - PageCache(const QString &cache_dir, - unsigned int page_size = 32 * 1024 * 1024); + PageCache(); + PageCache(const QString &cache_dir); + + PageCache(unsigned int max_page_size); + PageCache(const QString &cache_dir, unsigned int max_page_size); + PageCache(std::shared_ptr data); PageCache(const PageCache &other); + ~PageCache(); PageCache &operator=(const PageCache &other); @@ -72,6 +76,10 @@ namespace SireBase const char *what() const; static const char *typeName(); + static unsigned int maxPageSize(); + static void setMaxPageSize(unsigned int max_page_size, + bool update_existing = false); + PageCache *clone() const; QString toString() const; diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index 44ea55bf4..f880c554e 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -67,8 +67,7 @@ namespace SireSystem if (not cache) { QString cache_dir = QDir::current().absoluteFilePath("temp_traj_XXXXXX"); - // use 32 MB pages - cache = std::make_shared(cache_dir, 32 * 1024 * 1024); + cache = std::make_shared(cache_dir); shared_cache = cache; } } diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index f6d96d462..91773b763 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; #include +#include + #include #include @@ -53,6 +55,8 @@ const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCach #include +#include + #include #include @@ -89,6 +93,8 @@ SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ #include +#include + #include #include @@ -117,7 +123,7 @@ void register_PageCache_class(){ { //::SireBase::PageCache typedef bp::class_< SireBase::PageCache > PageCache_exposer_t; - PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< bp::optional< unsigned int > >(( bp::arg("page_size")=(unsigned int)(32 * 1024 * 1024) ), "") ); + PageCache_exposer_t PageCache_exposer = PageCache_exposer_t( "PageCache", "This class manages a swap cache of binary data that can be\npaged to and from disk. The cache can receive binary data\nof any size, and will automatically manage the paging of\nthat data to and from disk as it is accessed.\n\nYou can create different caches, and have control over the maximum\nsize of each cache page.\n\nNote that deleting the cache will delete all data contained\ntherein - including data paged to disk\n", bp::init< >("Construct a new page cache with the default\n recomended maximum page size") ); bp::scope PageCache_scope( PageCache_exposer ); { //::SireBase::PageCache::Handle typedef bp::class_< SireBase::PageCache::Handle > Handle_exposer_t; @@ -473,9 +479,11 @@ void register_PageCache_class(){ Page_exposer.def( "__repr__", &__str__< ::SireBase::PageCache::Page > ); Page_exposer.def( "__len__", &__len_size< ::SireBase::PageCache::Page > ); } - PageCache_exposer.def( bp::init< QString const &, bp::optional< unsigned int > >(( bp::arg("cache_dir"), bp::arg("page_size")=(unsigned int)(32 * 1024 * 1024) ), "") ); - PageCache_exposer.def( bp::init< std::shared_ptr< SireBase::detail::CacheData > >(( bp::arg("data") ), "") ); - PageCache_exposer.def( bp::init< SireBase::PageCache const & >(( bp::arg("other") ), "") ); + PageCache_exposer.def( bp::init< QString const & >(( bp::arg("cache_dir") ), "Construct a new page cache with specified cache directory\nand recomended maximum page size") ); + PageCache_exposer.def( bp::init< unsigned int >(( bp::arg("max_page_size") ), "Construct a new page cache with the specified\nrecomended maximum page size") ); + PageCache_exposer.def( bp::init< QString const &, unsigned int >(( bp::arg("cache_dir"), bp::arg("max_page_size") ), "Construct a new page cache with the specified\nrecomended maximum page size and cache directory\ntemplate (using QTemporaryDir format)") ); + PageCache_exposer.def( bp::init< std::shared_ptr< SireBase::detail::CacheData > >(( bp::arg("data") ), "Internal constructor used to construct from a CacheData") ); + PageCache_exposer.def( bp::init< SireBase::PageCache const & >(( bp::arg("other") ), "Copy constructor") ); { //::SireBase::PageCache::assertValid typedef void ( ::SireBase::PageCache::*assertValid_function_type)( ) const; @@ -485,7 +493,7 @@ void register_PageCache_class(){ "assertValid" , assertValid_function_value , bp::release_gil_policy() - , "" ); + , "Assert that this object is valid" ); } { //::SireBase::PageCache::cacheDir @@ -497,7 +505,7 @@ void register_PageCache_class(){ "cacheDir" , cacheDir_function_value , bp::release_gil_policy() - , "" ); + , "Return the cache directory for this cache" ); } { //::SireBase::PageCache::getStatistics @@ -509,7 +517,7 @@ void register_PageCache_class(){ "getStatistics" , getStatistics_function_value , bp::release_gil_policy() - , "" ); + , "Return the statistics for all caches" ); } { //::SireBase::PageCache::isNull @@ -521,7 +529,7 @@ void register_PageCache_class(){ "isNull" , isNull_function_value , bp::release_gil_policy() - , "" ); + , "Return whether or not this cache is null" ); } { //::SireBase::PageCache::isValid @@ -533,7 +541,19 @@ void register_PageCache_class(){ "isValid" , isValid_function_value , bp::release_gil_policy() - , "" ); + , "Return whether or not this cache is valid" ); + + } + { //::SireBase::PageCache::maxPageSize + + typedef unsigned int ( *maxPageSize_function_type )( ); + maxPageSize_function_type maxPageSize_function_value( &::SireBase::PageCache::maxPageSize ); + + PageCache_exposer.def( + "maxPageSize" + , maxPageSize_function_value + , bp::release_gil_policy() + , "Return the current recommend maximum page size" ); } { //::SireBase::PageCache::nBytes @@ -545,7 +565,7 @@ void register_PageCache_class(){ "nBytes" , nBytes_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of bytes saved in this cache" ); } { //::SireBase::PageCache::nPages @@ -557,7 +577,7 @@ void register_PageCache_class(){ "nPages" , nPages_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of pages in this cache" ); } { //::SireBase::PageCache::operator= @@ -582,6 +602,18 @@ void register_PageCache_class(){ "pageSize" , pageSize_function_value , bp::release_gil_policy() + , "Return the suggested maximum page size for this cache" ); + + } + { //::SireBase::PageCache::setMaxPageSize + + typedef void ( *setMaxPageSize_function_type )( unsigned int,bool ); + setMaxPageSize_function_type setMaxPageSize_function_value( &::SireBase::PageCache::setMaxPageSize ); + + PageCache_exposer.def( + "setMaxPageSize" + , setMaxPageSize_function_value + , ( bp::arg("max_page_size"), bp::arg("update_existing")=(bool)(false) ) , "" ); } @@ -594,7 +626,7 @@ void register_PageCache_class(){ "size" , size_function_value , bp::release_gil_policy() - , "" ); + , "Return the number of bytes saved in this cache" ); } { //::SireBase::PageCache::store @@ -607,7 +639,7 @@ void register_PageCache_class(){ , store_function_value , ( bp::arg("data") ) , bp::release_gil_policy() - , "" ); + , "Store the data in the cache, returning a handle to the data" ); } { //::SireBase::PageCache::toString @@ -619,7 +651,7 @@ void register_PageCache_class(){ "toString" , toString_function_value , bp::release_gil_policy() - , "" ); + , "Return a string representation of this object" ); } { //::SireBase::PageCache::typeName @@ -631,7 +663,7 @@ void register_PageCache_class(){ "typeName" , typeName_function_value , bp::release_gil_policy() - , "" ); + , "Return the type name for this object" ); } { //::SireBase::PageCache::what @@ -643,10 +675,12 @@ void register_PageCache_class(){ "what" , what_function_value , bp::release_gil_policy() - , "" ); + , "Return the type name for this object" ); } PageCache_exposer.staticmethod( "getStatistics" ); + PageCache_exposer.staticmethod( "maxPageSize" ); + PageCache_exposer.staticmethod( "setMaxPageSize" ); PageCache_exposer.staticmethod( "typeName" ); PageCache_exposer.def( "__copy__", &__copy__); PageCache_exposer.def( "__deepcopy__", &__copy__); From 48743cc30a43ea26991d2c7040faa10a46599eca Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 20 Apr 2024 18:25:23 +0100 Subject: [PATCH 241/468] Added control over the maximum number of resident pages per cache, and also made sure that pages frozen are not removed from memory straight away - they only get removed as they become old --- corelib/src/libs/SireBase/pagecache.cpp | 151 +++++++++++++++++------- corelib/src/libs/SireBase/pagecache.h | 3 + wrapper/Base/PageCache.pypp.cpp | 27 +++++ 3 files changed, 140 insertions(+), 41 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index da12c368e..b70fb1cb0 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -77,12 +77,22 @@ namespace SireBase PageHandler(QString cache_dir_template); ~PageHandler(); - QTemporaryFile *store(const QByteArray &data); + QPair> store(const QByteArray &data); std::shared_ptr restore(QTemporaryFile &pagefile); QString path() const; + static void setMaxResidentPages(unsigned int n_pages); + static unsigned int maxResidentPages(); + private: + void addToRestored(std::shared_ptr page); + + /** The maximum number of pages left resident in memory + * per cache + */ + static unsigned int max_resident_pages; + /** Mutex to protect access to the data of this class */ QMutex mutex; @@ -390,11 +400,85 @@ QString PageHandler::path() const return cache_dir->path(); } +// this would be a maximum of 256 MB resident per cache +unsigned int PageHandler::max_resident_pages = 32; + +/** Set the maximum number of pages that can be resident in memory + * at any one time + */ +void PageHandler::setMaxResidentPages(unsigned int n_pages) +{ + if (n_pages < 1) + { + Console::warning(QObject::tr("Setting maximum resident pages to the minimum of 1.")); + n_pages = 1; + } + else if (n_pages > 256) + { + Console::warning(QObject::tr("Setting maximum resident pages to the maximum of 256.")); + n_pages = 256; + } + + max_resident_pages = n_pages; +} + +/** Return the current maximum number of pages that can be resident + * in memory at any one time + */ +unsigned int PageHandler::maxResidentPages() +{ + return max_resident_pages; +} + +/** Add the passed restored page to the cache */ +void PageHandler::addToRestored(std::shared_ptr restored) +{ + // check to see if we need to replace an old page + QMutexLocker lkr(&mutex); + + auto max_resident = max_resident_pages; + + if (restored_pages.count() < max_resident) + { + restored_pages.append(restored); + return; + } + + // we need to replace a page... + int smallest_index = -1; + int smallest_value = -1; + + for (int i = 0; i < restored_pages.size(); i++) + { + if (restored_pages[i].get() == nullptr) + { + // this page has already been deleted, so should + // be removed first + smallest_index = i; + } + else + { + // find the oldest page to restore - do this by reducing + // the TTL for each page each time we go through this loop, + // and then find the first page with the smallest TTL + int val = restored_pages[i]->timeToLive(); + + if (smallest_index == -1 or smallest_value > val) + { + smallest_index = i; + smallest_value = val; + } + } + } + + restored_pages[smallest_index] = restored; +} + /** Store the passed page of data to a temporary page cache file. * This returns a pointer to the created temporary file, * which is owned by the caller (in this case, the PageData) */ -QTemporaryFile *PageHandler::store(const QByteArray &data) +QPair> PageHandler::store(const QByteArray &data) { QTemporaryFile *cache_file = new QTemporaryFile(cache_dir->filePath("page_XXXXXX.bin")); @@ -408,6 +492,9 @@ QTemporaryFile *PageHandler::store(const QByteArray &data) throw SireError::file_error(*cache_file, CODELOC); } + // create a handle to the restored page + auto restored_page = std::make_shared(data); + // compress the data and write it to a temporary file QByteArray compressed_data = qCompress(data, 9); @@ -423,7 +510,10 @@ QTemporaryFile *PageHandler::store(const QByteArray &data) checksums.insert(cache_file, checksum); - return cache_file; + // save this restored page so that it is not immediately deleted + this->addToRestored(restored_page); + + return QPair>(cache_file, restored_page); } catch (...) { @@ -476,43 +566,7 @@ std::shared_ptr PageHandler::restore(QTemporaryFile &pagefile) auto restored = std::make_shared(decompressed_data); decompressed_data = QByteArray(); - // now check to see if we need to replace an old page - QMutexLocker lkr(&mutex); - - if (restored_pages.count() < 5) - { - restored_pages.append(restored); - return restored; - } - - // we need to replace a page... - int smallest_index = -1; - int smallest_value = -1; - - for (int i = 0; i < restored_pages.size(); i++) - { - if (restored_pages[i].get() == nullptr) - { - // this page has already been deleted, so should - // be removed first - smallest_index = i; - } - else - { - // find the oldest page to restore - do this by reducing - // the TTL for each page each time we go through this loop, - // and then find the first page with the smallest TTL - int val = restored_pages[i]->timeToLive(); - - if (smallest_index == -1 or smallest_value > val) - { - smallest_index = i; - smallest_value = val; - } - } - } - - restored_pages[smallest_index] = restored; + this->addToRestored(restored); return restored; } @@ -1173,13 +1227,16 @@ void PageData::freeze(std::shared_ptr handler) return; } - cache_file = handler->store(QByteArray::fromRawData(d, nbytes)); + auto cached = handler->store(QByteArray::fromRawData(d, nbytes)); + + cache_file = cached.first; QMutexLocker lkr(&mutex); // need to lock before deleting d because fetch() may be called delete[] d; d = 0; page_handler = handler; + restored_page = cached.second; } PageCache PageData::parent() const @@ -1691,6 +1748,18 @@ void PageCache::setMaxPageSize(unsigned int page_size, CacheData::setMaxPageSize(page_size, update_existing); } +/** Set the maximum number of resident pages per cache */ +void PageCache::setMaxResidentPages(unsigned int n_pages) +{ + PageHandler::setMaxResidentPages(n_pages); +} + +/** Return the maximum number of resident pages per cache */ +unsigned int PageCache::maxResidentPages() +{ + return PageHandler::maxResidentPages(); +} + /** Return the current recommend maximum page size */ unsigned int PageCache::maxPageSize() { diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index 1560e24f7..93e61a891 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -80,6 +80,9 @@ namespace SireBase static void setMaxPageSize(unsigned int max_page_size, bool update_existing = false); + static void setMaxResidentPages(unsigned int n_pages); + static unsigned int maxResidentPages(); + PageCache *clone() const; QString toString() const; diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index 91773b763..dc0ceffbb 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -555,6 +555,18 @@ void register_PageCache_class(){ , bp::release_gil_policy() , "Return the current recommend maximum page size" ); + } + { //::SireBase::PageCache::maxResidentPages + + typedef unsigned int ( *maxResidentPages_function_type )( ); + maxResidentPages_function_type maxResidentPages_function_value( &::SireBase::PageCache::maxResidentPages ); + + PageCache_exposer.def( + "maxResidentPages" + , maxResidentPages_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::nBytes @@ -616,6 +628,19 @@ void register_PageCache_class(){ , ( bp::arg("max_page_size"), bp::arg("update_existing")=(bool)(false) ) , "" ); + } + { //::SireBase::PageCache::setMaxResidentPages + + typedef void ( *setMaxResidentPages_function_type )( unsigned int ); + setMaxResidentPages_function_type setMaxResidentPages_function_value( &::SireBase::PageCache::setMaxResidentPages ); + + PageCache_exposer.def( + "setMaxResidentPages" + , setMaxResidentPages_function_value + , ( bp::arg("n_pages") ) + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::size @@ -680,7 +705,9 @@ void register_PageCache_class(){ } PageCache_exposer.staticmethod( "getStatistics" ); PageCache_exposer.staticmethod( "maxPageSize" ); + PageCache_exposer.staticmethod( "maxResidentPages" ); PageCache_exposer.staticmethod( "setMaxPageSize" ); + PageCache_exposer.staticmethod( "setMaxResidentPages" ); PageCache_exposer.staticmethod( "typeName" ); PageCache_exposer.def( "__copy__", &__copy__); PageCache_exposer.def( "__deepcopy__", &__copy__); From e58ee84e1a1a81ad4152face4eb4ef42e1520f6d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 20 Apr 2024 22:54:45 +0100 Subject: [PATCH 242/468] Fixed bug when I didn't delete the frozen data from memory. Starting work on an atexit handler to make sure to remove cache files in Jupyter --- corelib/src/libs/SireBase/pagecache.cpp | 18 +++++++++++------- wrapper/Base/__init__.py | 13 +++++++++++++ 2 files changed, 24 insertions(+), 7 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index b70fb1cb0..e295b167f 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -86,7 +86,7 @@ namespace SireBase static unsigned int maxResidentPages(); private: - void addToRestored(std::shared_ptr page); + void _lkr_addToRestored(const std::shared_ptr &page); /** The maximum number of pages left resident in memory * per cache @@ -431,11 +431,9 @@ unsigned int PageHandler::maxResidentPages() } /** Add the passed restored page to the cache */ -void PageHandler::addToRestored(std::shared_ptr restored) +void PageHandler::_lkr_addToRestored(const std::shared_ptr &restored) { // check to see if we need to replace an old page - QMutexLocker lkr(&mutex); - auto max_resident = max_resident_pages; if (restored_pages.count() < max_resident) @@ -508,10 +506,12 @@ QPair> PageHandler::store(const cache_file->close(); + QMutexLocker lkr(&mutex); + checksums.insert(cache_file, checksum); // save this restored page so that it is not immediately deleted - this->addToRestored(restored_page); + this->_lkr_addToRestored(restored_page); return QPair>(cache_file, restored_page); } @@ -543,6 +543,8 @@ std::shared_ptr PageHandler::restore(QTemporaryFile &pagefile) // make sure that the checksum matches what we calculated when we // stored the data to disk + QMutexLocker lkr(&mutex); + auto checksum = checksums.value(&pagefile, 0); auto readsum = qChecksum(compressed_data.constData(), compressed_data.size()); @@ -566,7 +568,7 @@ std::shared_ptr PageHandler::restore(QTemporaryFile &pagefile) auto restored = std::make_shared(decompressed_data); decompressed_data = QByteArray(); - this->addToRestored(restored); + this->_lkr_addToRestored(restored); return restored; } @@ -1227,7 +1229,9 @@ void PageData::freeze(std::shared_ptr handler) return; } - auto cached = handler->store(QByteArray::fromRawData(d, nbytes)); + // make sure that the QByteArray takes a copy of the data in d + // so that we don't get any memory corruption + auto cached = handler->store(QByteArray(d, nbytes)); cache_file = cached.first; diff --git a/wrapper/Base/__init__.py b/wrapper/Base/__init__.py index 2061027f6..ee385641f 100644 --- a/wrapper/Base/__init__.py +++ b/wrapper/Base/__init__.py @@ -1,11 +1,24 @@ from ..Units import _Units # Need to import so that we have GeneralUnit from ._Base import * +import atexit as _atexit + _wrap_functions = [] _base_wrap = wrap +@_atexit.register +def _cleanup(): + """ + This function is called when Python exits - this will call the + cleanup function in the C++ code to ensure that all memory is + freed up and all temporary files deleted, threads stopped, + network connections closed etc + """ + print("Cleaning up!") + + def wrap(value): """Wrap the passed value into a :class:`~sire.base.Property` object. This works recursively, wrapping all items in From ea3d049442eb44b5b01c43a65d1ff35216bf94f7 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 20 Apr 2024 23:06:37 +0100 Subject: [PATCH 243/468] Added in the C++ clean_up() function, which is called from an atexit python function. This is called correctly when Jupyter exits. Now just need to write a function that can clear the caches and register a callback --- corelib/src/libs/SireBase/CMakeLists.txt | 2 + corelib/src/libs/SireBase/atexit.cpp | 56 ++++++++++++++++++++++ corelib/src/libs/SireBase/atexit.h | 51 ++++++++++++++++++++ wrapper/Base/PageCache.pypp.cpp | 6 +-- wrapper/Base/_Base_free_functions.pypp.cpp | 16 +++++++ wrapper/Base/__init__.py | 4 +- wrapper/Base/active_headers.h | 1 + 7 files changed, 131 insertions(+), 5 deletions(-) create mode 100644 corelib/src/libs/SireBase/atexit.cpp create mode 100644 corelib/src/libs/SireBase/atexit.h diff --git a/corelib/src/libs/SireBase/CMakeLists.txt b/corelib/src/libs/SireBase/CMakeLists.txt index 0217a3463..099e81b99 100644 --- a/corelib/src/libs/SireBase/CMakeLists.txt +++ b/corelib/src/libs/SireBase/CMakeLists.txt @@ -21,6 +21,7 @@ set ( SIREBASE_HEADERS array2d.hpp array2d.h arrayproperty.hpp + atexit.h booleanproperty.h chunkedhash.hpp chunkedvector.hpp @@ -85,6 +86,7 @@ set ( SIREBASE_SOURCES array2d.cpp arrayproperty.cpp + atexit.cpp booleanproperty.cpp chunkedhash.cpp chunkedvector.cpp diff --git a/corelib/src/libs/SireBase/atexit.cpp b/corelib/src/libs/SireBase/atexit.cpp new file mode 100644 index 000000000..cf1db375f --- /dev/null +++ b/corelib/src/libs/SireBase/atexit.cpp @@ -0,0 +1,56 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "SireBase/atexit.h" + +#include + +#include + +namespace SireBase +{ + std::vector> clean_up_functions; + + void clean_up() + { + qDebug() << "Cleaning up..."; + + for (auto &func : clean_up_functions) + { + func(); + } + + qDebug() << "...goodbye!"; + } + + void register_clean_up_function(std::function func) + { + clean_up_functions.push_back(func); + } + +} // namespace SireBase diff --git a/corelib/src/libs/SireBase/atexit.h b/corelib/src/libs/SireBase/atexit.h new file mode 100644 index 000000000..73d8937e4 --- /dev/null +++ b/corelib/src/libs/SireBase/atexit.h @@ -0,0 +1,51 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2024 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREBASE_ATEXIT_H +#define SIREBASE_ATEXIT_H + +#include "sireglobal.h" + +#include + +SIRE_BEGIN_HEADER + +namespace SireBase +{ + + SIREBASE_EXPORT void clean_up(); + + SIREBASE_EXPORT void register_clean_up_function(std::function func); + +} // namespace SireBase + +SIRE_EXPOSE_FUNCTION(SireBase::clean_up); + +SIRE_END_HEADER + +#endif \ No newline at end of file diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index dc0ceffbb..1c296e45d 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -565,7 +565,7 @@ void register_PageCache_class(){ "maxResidentPages" , maxResidentPages_function_value , bp::release_gil_policy() - , "" ); + , "Return the maximum number of resident pages per cache" ); } { //::SireBase::PageCache::nBytes @@ -626,7 +626,7 @@ void register_PageCache_class(){ "setMaxPageSize" , setMaxPageSize_function_value , ( bp::arg("max_page_size"), bp::arg("update_existing")=(bool)(false) ) - , "" ); + , "Set the default maximum page cache size for all new created\n caches that dont specify it themselves" ); } { //::SireBase::PageCache::setMaxResidentPages @@ -639,7 +639,7 @@ void register_PageCache_class(){ , setMaxResidentPages_function_value , ( bp::arg("n_pages") ) , bp::release_gil_policy() - , "" ); + , "Set the maximum number of resident pages per cache" ); } { //::SireBase::PageCache::size diff --git a/wrapper/Base/_Base_free_functions.pypp.cpp b/wrapper/Base/_Base_free_functions.pypp.cpp index daade0ac5..7a1d1d9aa 100644 --- a/wrapper/Base/_Base_free_functions.pypp.cpp +++ b/wrapper/Base/_Base_free_functions.pypp.cpp @@ -7,6 +7,10 @@ namespace bp = boost::python; +#include "atexit.h" + +#include "atexit.h" + #include "SireError/errors.h" #include "findexe.h" @@ -1033,6 +1037,18 @@ namespace bp = boost::python; void register_free_functions(){ + { //::SireBase::clean_up + + typedef void ( *clean_up_function_type )( ); + clean_up_function_type clean_up_function_value( &::SireBase::clean_up ); + + bp::def( + "clean_up" + , clean_up_function_value + , "" ); + + } + { //::SireBase::findExe typedef ::QFileInfo ( *findExe_function_type )( ::QString const & ); diff --git a/wrapper/Base/__init__.py b/wrapper/Base/__init__.py index ee385641f..3bd4d04fc 100644 --- a/wrapper/Base/__init__.py +++ b/wrapper/Base/__init__.py @@ -12,11 +12,11 @@ def _cleanup(): """ This function is called when Python exits - this will call the - cleanup function in the C++ code to ensure that all memory is + clean_up() function in the C++ code to ensure that all memory is freed up and all temporary files deleted, threads stopped, network connections closed etc """ - print("Cleaning up!") + clean_up() def wrap(value): diff --git a/wrapper/Base/active_headers.h b/wrapper/Base/active_headers.h index 87689fc7e..224b1a269 100644 --- a/wrapper/Base/active_headers.h +++ b/wrapper/Base/active_headers.h @@ -6,6 +6,7 @@ #include "array2d.h" #include "array2d.hpp" #include "arrayproperty.hpp" +#include "atexit.h" #include "booleanproperty.h" #include "chunkedvector.hpp" #include "combineproperties.h" From 9e641398afde37841d5ca4900d2ca8e2fda752c4 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 21 Apr 2024 18:13:42 +0100 Subject: [PATCH 244/468] Wrote the code to properly clean up the cache at exit. Also wrote the class to register clean up functions easily. Tested and it works well, even from a Jupyter notebook :-) --- corelib/src/libs/SireBase/atexit.cpp | 14 ++- corelib/src/libs/SireBase/atexit.h | 32 ++++++- corelib/src/libs/SireBase/pagecache.cpp | 116 ++++++++++++++++++++++++ 3 files changed, 156 insertions(+), 6 deletions(-) diff --git a/corelib/src/libs/SireBase/atexit.cpp b/corelib/src/libs/SireBase/atexit.cpp index cf1db375f..d0eca61ea 100644 --- a/corelib/src/libs/SireBase/atexit.cpp +++ b/corelib/src/libs/SireBase/atexit.cpp @@ -38,14 +38,18 @@ namespace SireBase void clean_up() { - qDebug() << "Cleaning up..."; - for (auto &func : clean_up_functions) { - func(); + try + { + func(); + } + catch (...) + { + // we can't raise exceptions now, and shouldn't + // print anything, so just fail silently + } } - - qDebug() << "...goodbye!"; } void register_clean_up_function(std::function func) diff --git a/corelib/src/libs/SireBase/atexit.h b/corelib/src/libs/SireBase/atexit.h index 73d8937e4..b4022947a 100644 --- a/corelib/src/libs/SireBase/atexit.h +++ b/corelib/src/libs/SireBase/atexit.h @@ -37,11 +37,41 @@ SIRE_BEGIN_HEADER namespace SireBase { - SIREBASE_EXPORT void clean_up(); SIREBASE_EXPORT void register_clean_up_function(std::function func); + /** This class makes it easier to register a function to be called + * when the program exits. This is useful for cleaning up resources + * that are allocated during the program's execution. + * + * Simply define your function (should be void func() { ... }) and + * then create a static instance of this class with the function as the + * argument. The constructor will be called at library load + * (static initialisation) and the function will be registered to be + * called at exit. + * + * e.g. + * + * void my_exit_function() + * { + * // clean up code here + * } + * + * static RegisterExitFunction my_exit_function_instance(my_exit_function); + * + */ + class SIREBASE_EXPORT RegisterExitFunction + { + public: + RegisterExitFunction(std::function func) + { + SireBase::register_clean_up_function(func); + } + + ~RegisterExitFunction() {} + }; + } // namespace SireBase SIRE_EXPOSE_FUNCTION(SireBase::clean_up); diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index e295b167f..4eabdc8fb 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -32,6 +32,7 @@ #include "SireBase/parallel.h" #include "SireBase/console.h" +#include "SireBase/atexit.h" #include #include @@ -82,6 +83,8 @@ namespace SireBase QString path() const; + void cleanUpOnExit(); + static void setMaxResidentPages(unsigned int n_pages); static unsigned int maxResidentPages(); @@ -134,6 +137,8 @@ namespace SireBase void setSelf(const std::shared_ptr &cache); + static void cleanUpOnExit(); + protected: void run(); @@ -227,6 +232,8 @@ namespace SireBase PageCache parent() const; + void cleanUpOnExit(); + private: /** Weak pointer to the parent cache - weak so that the * cache is automatically deleted if the user releases @@ -394,6 +401,16 @@ PageHandler::~PageHandler() delete cache_dir; } +/** Clean up the PageHandler (called on exit) */ +void PageHandler::cleanUpOnExit() +{ + QMutexLocker lkr(&mutex); + delete cache_dir; + cache_dir = 0; + checksums.clear(); + restored_pages.clear(); +} + /** Return the path to the cache directory */ QString PageHandler::path() const { @@ -478,6 +495,12 @@ void PageHandler::_lkr_addToRestored(const std::shared_ptr &restor */ QPair> PageHandler::store(const QByteArray &data) { + if (cache_dir == 0) + { + // we are likely being shut down, so return a null pointer + return QPair>(0, 0); + } + QTemporaryFile *cache_file = new QTemporaryFile(cache_dir->filePath("page_XXXXXX.bin")); try @@ -586,6 +609,78 @@ QList> CacheData::caches; */ unsigned int CacheData::max_page_size = 8 * 1024 * 1024; +/** Clean-up function that will remove all temporary files etc when + * the program exits, and will interupt all of the background threads + * so that they will (hopefully) exit + */ +void CacheData::cleanUpOnExit() +{ + QMutexLocker lkr(&caches_mutex); + + for (auto &cache : caches) + { + auto c = cache.lock(); + + if (c.get() != nullptr) + { + // interupt the thread so that it will stop + c->requestInterruption(); + + // clean up all of the pages associated with this cache + QMutexLocker lkr2(&(c->page_mutex)); + + for (auto &page : c->pages) + { + auto p = page.lock(); + + if (p.get() != nullptr) + { + p->cleanUpOnExit(); + } + } + + lkr2.unlock(); + + auto handler = c->page_handler.lock(); + + if (handler.get() != nullptr) + { + handler->cleanUpOnExit(); + } + } + } + + // wait for all of the threads to stop, and if they don't + // then kill them + for (auto &cache : caches) + { + auto c = cache.lock(); + + if (c.get() != nullptr) + { + if (QThread::currentThread() != c.get()) + { + if (not c->wait(50)) + { + // kill it + c->terminate(); + } + } + } + } +} + +/** This is the clean-up function that is registered with the + * atexit function. It will call the cleanUpOnExit function + * of CacheData + */ +void clean_up_pagecache() +{ + CacheData::cleanUpOnExit(); +} + +static const RegisterExitFunction clean_up_pagecache_instance(clean_up_pagecache); + /** Set the maximum page size to the passed value */ void CacheData::setMaxPageSize(unsigned int size, bool update_existing) { @@ -1087,6 +1182,27 @@ PageData::~PageData() delete[] d; } +/** Called when the program is exiting - makes sure that page file is + * deleted + */ +void PageData::cleanUpOnExit() +{ + QMutexLocker lkr(&mutex); + + if (cache_file != 0) + { + cache_file->remove(); + delete cache_file; + cache_file = 0; + } + + if (d != 0) + { + delete[] d; + d = 0; + } +} + /** Return the maximum number of bytes that can be stored in this page */ unsigned int PageData::maxBytes() const { From 2e57dff32ef127cae0b00647cacae47517d89be2 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 21 Apr 2024 18:33:50 +0100 Subject: [PATCH 245/468] Added unit tests that validate that the cache is working as expected, and that it is running correctly when used as part of a dynamics trajectory --- tests/base/test_pagecache.py | 69 +++++++++++++++++++++++++ tests/convert/test_openmm_trajectory.py | 38 ++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 tests/base/test_pagecache.py create mode 100644 tests/convert/test_openmm_trajectory.py diff --git a/tests/base/test_pagecache.py b/tests/base/test_pagecache.py new file mode 100644 index 000000000..2fef80522 --- /dev/null +++ b/tests/base/test_pagecache.py @@ -0,0 +1,69 @@ +import sire as sr +import pytest + + +def test_pagecache(ala_mols): + mols = ala_mols + + PageCache = sr.base.PageCache + + c = PageCache("temp_pagecache_XXXXXX", 32 * 1024) + + assert c.page_size() == 32 * 1024 + assert c.num_pages() == 0 + assert c.num_bytes() == 0 + + assert "temp_pagecache_" in c.cache_dir() + + h1 = c.store(42) + + assert h1.fetch() == 42 + + h2 = c.store("Hello Python Page Cache") + + assert h2.fetch() == "Hello Python Page Cache" + + assert h1.fetch() == 42 + + h3 = c.store(mols) + + mols2 = h3.fetch() + + assert mols2.num_molecules() == mols.num_molecules() + assert mols2.num_atoms() == mols.num_atoms() + + assert c.num_pages() > 0 + cache_dir = c.cache_dir() + + assert "temp_pagecache_" in cache_dir + + handles = [] + + for i in range(0, 5000): + handles.append(c.store(i)) + + for i, h in enumerate(handles): + assert h.fetch() == i + + # the cache may not have flushed to pages or disk yet + # so we should wait a little bit of time to let it do that... + import time + + n_sleeps = 0 + + while c.num_pages() < 2: + time.sleep(0.1) + n_sleeps += 1 + + if n_sleeps > 50: + break + + assert c.num_pages() >= 2 + + cache_dir = c.cache_dir() + + assert "temp_pagecache_" in cache_dir + + import os + + assert os.path.exists(cache_dir) diff --git a/tests/convert/test_openmm_trajectory.py b/tests/convert/test_openmm_trajectory.py new file mode 100644 index 000000000..8b0ac6590 --- /dev/null +++ b/tests/convert/test_openmm_trajectory.py @@ -0,0 +1,38 @@ +import sire as sr +import pytest + + +@pytest.mark.veryslow +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats(), + reason="openmm support is not available", +) +def test_openmm_trajectory(ala_mols, openmm_platform, tmpdir): + mols = ala_mols + + mols = mols.minimisation().run().commit() + + d = mols.dynamics(timestep="1fs", temperature="25oC") + + d.run("0.1ps", save_frequency="0.01ps") + + mols = d.commit() + + assert mols.num_frames() == 10 + + rmsd = mols.trajectory().rmsd() + + assert len(rmsd) == 10 + + d = tmpdir.mkdir("test_openmm_trajectory") + + f = sr.save(mols.trajectory(), d.join("test"), format=["PRMTOP", "RST"]) + + mols2 = sr.load(f) + + rmsd2 = mols2.trajectory().rmsd() + + assert len(rmsd2) == 10 + + for r1, r2 in zip(rmsd, rmsd2): + assert r1.value() == pytest.approx(r2.value(), abs=1e-3) From c408bc47ea3f3088ca421a366032e6c572ed8e3e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 21 Apr 2024 19:52:27 +0100 Subject: [PATCH 246/468] Finished everything - added the ability to set the root page cache directory, and to also read this from an environment variable. Added lots of docs about this and the PageCache class to cheatsheet/trajectory.rst Updated the tests, and added a changelog entry. --- corelib/src/libs/SireBase/pagecache.cpp | 49 ++++++++++++++++++- corelib/src/libs/SireBase/pagecache.h | 3 ++ .../src/libs/SireSystem/systemtrajectory.cpp | 2 +- doc/source/changelog.rst | 25 +++++++++- doc/source/cheatsheet/trajectory.rst | 49 +++++++++++++++++++ tests/base/test_pagecache.py | 29 +++++++++-- wrapper/Base/PageCache.pypp.cpp | 33 +++++++++++++ wrapper/Base/_Base_free_functions.pypp.cpp | 6 +++ 8 files changed, 189 insertions(+), 7 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index 4eabdc8fb..ade55b8d5 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -824,7 +824,7 @@ CacheData::CacheData(QString c, unsigned int p) if (c.simplified().isEmpty()) { // by default, go into the current directory - c = "temp_XXXXXX"; + c = QDir(PageCache::rootDirectory()).filePath("temp_XXXXXX"); } if (page_size < 1024) @@ -839,6 +839,19 @@ CacheData::CacheData(QString c, unsigned int p) } cache_dir_template = c; + + // make sure that we can actually create a cache directory in this + // space - do this by creating a test directory and then deleting it + QTemporaryDir test_dir(c); + + if (not test_dir.isValid()) + { + throw SireError::io_error(QObject::tr( + "Failed to create cache directory %1. %2") + .arg(c) + .arg(test_dir.errorString()), + CODELOC); + } } /** Destructor */ @@ -1975,3 +1988,37 @@ PageCache::Handle PageCache::store(const QByteArray &data) return Handle(d->store(data)); } + +static QString cache_root_dir = QString(); + +/** Set the root directory that should be used for all new caches, + * when the cache directory is not specified + */ +void PageCache::setRootDirectory(const QString &dir) +{ + QDir d; + + if (not d.mkpath(QDir(dir).absolutePath())) + { + throw SireError::io_error(QObject::tr( + "Failed to create cache root directory %1") + .arg(dir), + CODELOC); + } + + cache_root_dir = QDir(dir).absolutePath(); +} + +/** Get the root directory that should be used for all new caches, + * when the cache directory is not specified + */ +QString PageCache::rootDirectory() +{ + if (cache_root_dir.isEmpty()) + { + auto env = qEnvironmentVariable("SIRE_PAGECACHE_ROOT", "."); + PageCache::setRootDirectory(env); + } + + return cache_root_dir; +} diff --git a/corelib/src/libs/SireBase/pagecache.h b/corelib/src/libs/SireBase/pagecache.h index 93e61a891..b951a7214 100644 --- a/corelib/src/libs/SireBase/pagecache.h +++ b/corelib/src/libs/SireBase/pagecache.h @@ -83,6 +83,9 @@ namespace SireBase static void setMaxResidentPages(unsigned int n_pages); static unsigned int maxResidentPages(); + static void setRootDirectory(const QString &cache_dir); + static QString rootDirectory(); + PageCache *clone() const; QString toString() const; diff --git a/corelib/src/libs/SireSystem/systemtrajectory.cpp b/corelib/src/libs/SireSystem/systemtrajectory.cpp index f880c554e..1c57da68b 100644 --- a/corelib/src/libs/SireSystem/systemtrajectory.cpp +++ b/corelib/src/libs/SireSystem/systemtrajectory.cpp @@ -66,7 +66,7 @@ namespace SireSystem if (not cache) { - QString cache_dir = QDir::current().absoluteFilePath("temp_traj_XXXXXX"); + QString cache_dir = QDir(PageCache::rootDirectory()).absoluteFilePath("temp_traj_XXXXXX"); cache = std::make_shared(cache_dir); shared_cache = cache; } diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 5e528c5d1..b2586c4a2 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -15,9 +15,32 @@ organisation on `GitHub `__. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- -* Please add an item to this changelog when you create your PR * Correctly set the ``element1`` property in ``sire.morph.create_from_pertfile``. +* Added a :class:`sire.base.PageCache` class which can be used to cache and + restore objects to memory pages which are automatically paged to and from + disk as needed. This lets you work on data that can't fit in memory. + +* Updated the way that :class:`sire.system.System` objects hold the + set of temporary frames in a trajectory. Rather than each molecule holding + its own temporary frame, now the :class:`~sire.system.System` object holds + a ``SystemTrajectory`` object. This holds the frame data for all molecules + in the :class:`~sire.system.System` in a single binary array. The data + for this array is paged to disk as needed via the above + :class:`sire.base.PageCache` class. This both significantly speeds up + processing of these temporary frames, and ensures that long simulations + do not fill memory, causing the system to crash. In addition, the + ``SystemTrajectory`` object is NOT streamed to a S3 file. This means that + the S3 file (used normally for restarts) won't grow unbounded with + temporary frames, meaning that it is safe to create restarts of + long-running simulations. Note that this does mean that the temporary + directory is lost. You **must** save the trajectory to a file at the + end of your simulation or it will be lost. You can do this using the + standard trajectory save functions, e.g. + ``sire.save(mols.trajectory(), "output", format=["PRMTOP", "RST"])``. + +* Please add an item to this changelog when you create your PR + `2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ diff --git a/doc/source/cheatsheet/trajectory.rst b/doc/source/cheatsheet/trajectory.rst index 4981383be..967ccf708 100644 --- a/doc/source/cheatsheet/trajectory.rst +++ b/doc/source/cheatsheet/trajectory.rst @@ -436,3 +436,52 @@ and all of the water molecules. 498 498 99.800003 -12.226096 -35.170080 -47.396176 499 499 100.000000 -7.356142 -41.265345 -48.621487 [500 rows x 5 columns] + +Trajectories and PageCache +-------------------------- + +When you run a molecular dynamics simulation, you will typically generate +a lot of frames, which will become too large to fit in memory. To handle +this, a :class:`sire.base.PageCache` is used. This class provides a +:class:`~sire.base.PageCache` to which objects can be stored and fetched. +The memory for those objects is automatically paged back to disk, meaning +that it doesn't need to stay resident in memory. + +The :class:`~sire.system.System` class automatically uses a +:class:`~sire.base.PageCache` to manage the frames involved in its +:meth:`~sire.system.System.save_frame` and +:meth:`~sire.system.System.load_frame` function calls. This page cache +will page data larger than ~256MB to disk, into a directory called +``temp_trajectory_XXXXXX`` in the current working directory +(where ``XXXXXX`` is replaced with a random string). This directory +will be automatically cleaned up when the program exits, and potentially +earlier when the system is deleted and then garbage collected by python. + +You can change the location of the page cache in two ways. Either, +you can set the environment variable ``SIRE_PAGECACHE_ROOT`` to the directory +where you want the page cache to be stored, or you can call the +:meth:`~sire.base.PageCache.set_root_directory` function to set the +root directory in your script. + +You can also use the :class:`~sire.base.PageCache` class directly to +create caches for your own objects. For example, here we will create a +cache into which we will place some data. + +>>> import sire as sr +>>> cache = sr.base.PageCache() +>>> handle1 = cache.store("Hello World") +>>> mols = sr.load_test_files("ala.top", "ala.crd") +>>> handle2 = cache.store(mols) +>>> print(handle1.fetch()) +Hello World +>>> print(handle2.fetch()) +System( name=ACE num_molecules=631 num_residues=633 num_atoms=1912 ) +>>> print(sr.base.PageCache.get_statistics()) +Cache: /path/to/cache_root/temp_XXXXXX + Current Page: 977.279 KB : is_resident 1 + Total size: 977.279 KB + +.. note:: + + The :class:`~sire.base.PageCache` class can hold any object that is + picklable. diff --git a/tests/base/test_pagecache.py b/tests/base/test_pagecache.py index 2fef80522..5d219ef49 100644 --- a/tests/base/test_pagecache.py +++ b/tests/base/test_pagecache.py @@ -1,12 +1,35 @@ import sire as sr -import pytest +import os -def test_pagecache(ala_mols): +def test_pagecache(ala_mols, tmpdir): mols = ala_mols PageCache = sr.base.PageCache + root_dir = PageCache.root_directory() + + assert os.path.exists(root_dir) + + # should be the current path + assert root_dir == os.getcwd() + + d = tmpdir.mkdir("test_pagecache") + + PageCache.set_root_directory(d.strpath) + + root_dir2 = PageCache.root_directory() + + assert os.path.exists(root_dir2) + + # should be the tempdir + assert root_dir2 == d.strpath + + # restore to the original root dir + PageCache.set_root_directory(root_dir) + + assert PageCache.root_directory() == root_dir + c = PageCache("temp_pagecache_XXXXXX", 32 * 1024) assert c.page_size() == 32 * 1024 @@ -64,6 +87,4 @@ def test_pagecache(ala_mols): assert "temp_pagecache_" in cache_dir - import os - assert os.path.exists(cache_dir) diff --git a/wrapper/Base/PageCache.pypp.cpp b/wrapper/Base/PageCache.pypp.cpp index 1c296e45d..eba18819a 100644 --- a/wrapper/Base/PageCache.pypp.cpp +++ b/wrapper/Base/PageCache.pypp.cpp @@ -7,6 +7,8 @@ namespace bp = boost::python; +#include "SireBase/atexit.h" + #include "SireBase/console.h" #include "SireBase/parallel.h" @@ -43,6 +45,8 @@ const char* pvt_get_name(const SireBase::PageCache&){ return "SireBase::PageCach #include "Helpers/release_gil_policy.hpp" +#include "SireBase/atexit.h" + #include "SireBase/console.h" #include "SireBase/parallel.h" @@ -81,6 +85,8 @@ SireBase::PageCache::Handle __copy__(const SireBase::PageCache::Handle &other){ #include "Helpers/len.hpp" +#include "SireBase/atexit.h" + #include "SireBase/console.h" #include "SireBase/parallel.h" @@ -616,6 +622,18 @@ void register_PageCache_class(){ , bp::release_gil_policy() , "Return the suggested maximum page size for this cache" ); + } + { //::SireBase::PageCache::rootDirectory + + typedef ::QString ( *rootDirectory_function_type )( ); + rootDirectory_function_type rootDirectory_function_value( &::SireBase::PageCache::rootDirectory ); + + PageCache_exposer.def( + "rootDirectory" + , rootDirectory_function_value + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::setMaxPageSize @@ -641,6 +659,19 @@ void register_PageCache_class(){ , bp::release_gil_policy() , "Set the maximum number of resident pages per cache" ); + } + { //::SireBase::PageCache::setRootDirectory + + typedef void ( *setRootDirectory_function_type )( ::QString const & ); + setRootDirectory_function_type setRootDirectory_function_value( &::SireBase::PageCache::setRootDirectory ); + + PageCache_exposer.def( + "setRootDirectory" + , setRootDirectory_function_value + , ( bp::arg("cache_dir") ) + , bp::release_gil_policy() + , "" ); + } { //::SireBase::PageCache::size @@ -706,8 +737,10 @@ void register_PageCache_class(){ PageCache_exposer.staticmethod( "getStatistics" ); PageCache_exposer.staticmethod( "maxPageSize" ); PageCache_exposer.staticmethod( "maxResidentPages" ); + PageCache_exposer.staticmethod( "rootDirectory" ); PageCache_exposer.staticmethod( "setMaxPageSize" ); PageCache_exposer.staticmethod( "setMaxResidentPages" ); + PageCache_exposer.staticmethod( "setRootDirectory" ); PageCache_exposer.staticmethod( "typeName" ); PageCache_exposer.def( "__copy__", &__copy__); PageCache_exposer.def( "__deepcopy__", &__copy__); diff --git a/wrapper/Base/_Base_free_functions.pypp.cpp b/wrapper/Base/_Base_free_functions.pypp.cpp index 7a1d1d9aa..bb6da7b77 100644 --- a/wrapper/Base/_Base_free_functions.pypp.cpp +++ b/wrapper/Base/_Base_free_functions.pypp.cpp @@ -7,8 +7,14 @@ namespace bp = boost::python; +#include "SireBase/atexit.h" + #include "atexit.h" +#include + +#include + #include "atexit.h" #include "SireError/errors.h" From fcdd71bf3b2410ee677e018e95738c7ac2c43d3f Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 21 Apr 2024 22:42:24 +0100 Subject: [PATCH 247/468] Fixed issues identified by GH Actions. Added as a header so that memcpy is found on Linux. Added platform=openmm_platform so that the OpenCL platform is not used on the MacOS runner. And added pathlib path handling in test_pagecache.py as the test got tripped up by differences in posix and Windows paths (despite this working on my Windows VM...) --- corelib/src/libs/SireBase/pagecache.cpp | 10 +++++---- tests/base/test_pagecache.py | 27 +++++++++++++++---------- tests/convert/test_openmm_trajectory.py | 8 ++++---- 3 files changed, 26 insertions(+), 19 deletions(-) diff --git a/corelib/src/libs/SireBase/pagecache.cpp b/corelib/src/libs/SireBase/pagecache.cpp index ade55b8d5..d2d6f2ee9 100644 --- a/corelib/src/libs/SireBase/pagecache.cpp +++ b/corelib/src/libs/SireBase/pagecache.cpp @@ -45,6 +45,8 @@ #include +#include // needed for memcpy + namespace SireBase { namespace detail @@ -356,7 +358,7 @@ int RestoredPage::timeToLive() const /** Fetch 'n_bytes' bytes of data starting at 'offset' */ QByteArray RestoredPage::fetch(unsigned int offset, unsigned int n_bytes) const { - if (offset + n_bytes > d.size()) + if (offset + n_bytes > static_cast(d.size())) { throw SireError::invalid_arg( QObject::tr("Impossible to fetch %1 bytes starting at " @@ -453,7 +455,7 @@ void PageHandler::_lkr_addToRestored(const std::shared_ptr &restor // check to see if we need to replace an old page auto max_resident = max_resident_pages; - if (restored_pages.count() < max_resident) + if (static_cast(restored_pages.count()) < max_resident) { restored_pages.append(restored); return; @@ -1051,7 +1053,7 @@ void CacheData::run() // get the data QByteArray data = handle->fetch(); - const int n_bytes = data.size(); + const unsigned int n_bytes = static_cast(data.size()); if (n_bytes >= page_size) { @@ -1268,7 +1270,7 @@ bool PageData::isCached() const unsigned int PageData::store(const QByteArray &data) { // this test will fail if the page is frozen - if (data.size() > this->bytesRemaining()) + if (static_cast(data.size()) > this->bytesRemaining()) { QString message = QObject::tr("Data is too large to fit on this page!"); Console::error(message); diff --git a/tests/base/test_pagecache.py b/tests/base/test_pagecache.py index 5d219ef49..ea480a54c 100644 --- a/tests/base/test_pagecache.py +++ b/tests/base/test_pagecache.py @@ -1,34 +1,39 @@ import sire as sr -import os def test_pagecache(ala_mols, tmpdir): + import pathlib + mols = ala_mols PageCache = sr.base.PageCache - root_dir = PageCache.root_directory() + root_dir = pathlib.PurePath(PageCache.root_directory()).as_posix() - assert os.path.exists(root_dir) + assert pathlib.Path(root_dir).exists() # should be the current path - assert root_dir == os.getcwd() + cwd = pathlib.Path().cwd().as_posix() + + assert root_dir == cwd d = tmpdir.mkdir("test_pagecache") - PageCache.set_root_directory(d.strpath) + new_root_dir = pathlib.PurePath(d.strpath).as_posix() - root_dir2 = PageCache.root_directory() + PageCache.set_root_directory(new_root_dir) - assert os.path.exists(root_dir2) + root_dir2 = pathlib.PurePath(PageCache.root_directory()).as_posix() + + assert pathlib.Path(root_dir2).exists() # should be the tempdir - assert root_dir2 == d.strpath + assert root_dir2 == new_root_dir # restore to the original root dir PageCache.set_root_directory(root_dir) - assert PageCache.root_directory() == root_dir + assert pathlib.PurePath(PageCache.root_directory()).as_posix() == root_dir c = PageCache("temp_pagecache_XXXXXX", 32 * 1024) @@ -83,8 +88,8 @@ def test_pagecache(ala_mols, tmpdir): assert c.num_pages() >= 2 - cache_dir = c.cache_dir() + cache_dir = pathlib.PurePath(c.cache_dir()).as_posix() assert "temp_pagecache_" in cache_dir - assert os.path.exists(cache_dir) + assert pathlib.Path(cache_dir).exists() diff --git a/tests/convert/test_openmm_trajectory.py b/tests/convert/test_openmm_trajectory.py index 8b0ac6590..2f57eba9d 100644 --- a/tests/convert/test_openmm_trajectory.py +++ b/tests/convert/test_openmm_trajectory.py @@ -10,9 +10,9 @@ def test_openmm_trajectory(ala_mols, openmm_platform, tmpdir): mols = ala_mols - mols = mols.minimisation().run().commit() + mols = mols.minimisation(platform=openmm_platform).run().commit() - d = mols.dynamics(timestep="1fs", temperature="25oC") + d = mols.dynamics(timestep="1fs", temperature="25oC", platform=openmm_platform) d.run("0.1ps", save_frequency="0.01ps") @@ -24,9 +24,9 @@ def test_openmm_trajectory(ala_mols, openmm_platform, tmpdir): assert len(rmsd) == 10 - d = tmpdir.mkdir("test_openmm_trajectory") + dir = tmpdir.mkdir("test_openmm_trajectory") - f = sr.save(mols.trajectory(), d.join("test"), format=["PRMTOP", "RST"]) + f = sr.save(mols.trajectory(), dir.join("test"), format=["PRMTOP", "RST"]) mols2 = sr.load(f) From 4ddb6e41df067216b1bebf3b8eb36d6cc5309056 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 21 Apr 2024 22:51:26 +0100 Subject: [PATCH 248/468] Update SECURITY.md Updated with the new version numbers for the 2024 releases [ci skip] Signed-off-by: Christopher Woods --- SECURITY.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/SECURITY.md b/SECURITY.md index a084c17cc..3a2828e33 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -4,13 +4,13 @@ As we have limited resource, we only support the latest major release of sire with security updates. For example, if the current version -is 2023.5.0, then only versions 2023.5.0 to 2023.5.X wil have updates, -which will be released as 2023.5.X+1. +is 2024.1.0, then only versions 2024.1.0 to 2024.1.X wil have updates, +which will be released as 2024.1.X+1. | Version | Supported | | ------- | ------------------ | -| 2023.5.x | :white_check_mark: | -| < 2023.5.x| :x: | +| 2024.1.x | :white_check_mark: | +| < 2024.1.x| :x: | ## Reporting a Vulnerability From ec6279767e1bb981cfba71a10c72f62f1049f435 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 09:33:28 +0100 Subject: [PATCH 249/468] Move Python object registry into EMLECallback serialization. --- wrapper/Convert/SireOpenMM/emle.cpp | 97 +++++++++++++++-------------- 1 file changed, 51 insertions(+), 46 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 16a993f8a..35eae4403 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -64,6 +64,34 @@ class GILLock ///////// Implementation of EMLECallback ///////// +// A registry to store Python callback objects. +QHash py_object_registry; + +// A mutex to protect the registry. +std::mutex py_object_mutex; + +// Set a callback Python object in the registry using a mutex. +void setPyObject(bp::object cb, QString uuid) +{ + std::lock_guard lock(py_object_mutex); + py_object_registry[uuid] = cb; +}; + +// Get a callback object from the registry using a mutex. +bp::object getPythonObject(QString uuid) +{ + std::lock_guard lock(py_object_mutex); + + if (not py_object_registry.contains(uuid)) + { + throw SireError::invalid_key(QObject::tr( + "Unable to find UUID %1 in the EMLEForce callback registry.").arg(uuid), + CODELOC); + } + + return py_object_registry[uuid]; +} + static const RegisterMetaType r_emlecallback(NO_ROOT); QDataStream &operator<<(QDataStream &ds, const EMLECallback &emlecallback) @@ -72,7 +100,13 @@ QDataStream &operator<<(QDataStream &ds, const EMLECallback &emlecallback) SharedDataStream sds(ds); - sds << emlecallback.callback; + // Generate a unique identifier for the callback. + auto uuid = QUuid::createUuid().toString(); + + sds << uuid << emlecallback.callback; + + // Set the Python object in the registry. + setPyObject(emlecallback.py_object, uuid); return ds; } @@ -85,7 +119,13 @@ QDataStream &operator>>(QDataStream &ds, EMLECallback &emlecallback) { SharedDataStream sds(ds); - sds >> emlecallback.callback; + QString uuid; + + // Get the UUID of the Python object and the callback name. + sds >> uuid >> emlecallback.callback; + + // Set the Python object. + emlecallback.py_object = getPythonObject(uuid); } else throw version_error(v, "1", r_emlecallback, CODELOC); @@ -323,31 +363,6 @@ EMLEForce::call( namespace OpenMM { - // A callback registry; - QHash callback_registry; - - // A mutex to protect the registry. - std::mutex callback_mutex; - - // Set a callback in the registry using a mutex. - void setCallback(EMLECallback cb, QString uuid) - { - std::lock_guard lock(callback_mutex); - callback_registry[uuid] = cb; - }; - - // Get a callback from the registry using a mutex. - EMLECallback getCallback(QString uuid) - { - std::lock_guard lock(callback_mutex); - - if (not callback_registry.contains(uuid)) - { - throw OpenMM::OpenMMException("Unable to find UUID in the EMLEForce callback registry."); - } - - return callback_registry[uuid]; - } class EMLEForceProxy : public SerializationProxy { public: @@ -363,20 +378,11 @@ namespace OpenMM EMLEForce emleforce = *static_cast(object); ds << emleforce; - // Generate a unique identifier for the callback. - auto uuid = QUuid::createUuid().toString(); - // Set the version. node.setIntProperty("version", 0); // Set the data by converting the QByteArray to a hexidecimal string. node.setStringProperty("data", data.toHex().data()); - - // Set the UID. - node.setStringProperty("uuid", uuid.toStdString()); - - // Set the callback. - setCallback(emleforce.getCallback(), uuid); }; void* deserialize(const SerializationNode& node) const @@ -400,18 +406,17 @@ namespace OpenMM // Deserialize the object. QDataStream ds(data); EMLEForce emleforce; - ds >> emleforce; - - // Get the UID string. - auto uuid = QString::fromStdString(node.getStringProperty("uuid")); - - // Create a new EMLEForce object. - auto emleforce_ptr = new EMLEForce(emleforce); - // Set the callback. - emleforce_ptr->setCallback(getCallback(uuid)); + try + { + ds >> emleforce; + } + catch (...) + { + throw OpenMM::OpenMMException("Unable to find UUID in the EMLEForce callback registry."); + } - return emleforce_ptr; + return new EMLEForce(emleforce); }; }; From 89828aaaa49a5659ac689e7db4a00884749f98eb Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 09:36:41 +0100 Subject: [PATCH 250/468] Add note regarding partial serialization. --- wrapper/Convert/SireOpenMM/emle.cpp | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 35eae4403..580c923fd 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -381,6 +381,11 @@ namespace OpenMM // Set the version. node.setIntProperty("version", 0); + // Set the note attributer. + node.setStringProperty("note", + "This force only supports partial serialization, so can only be used " + "within the same session and memory space."); + // Set the data by converting the QByteArray to a hexidecimal string. node.setStringProperty("data", data.toHex().data()); }; From e5bba90087a791e0c1f64c3e1e7f1005cd37f3e5 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 09:58:39 +0100 Subject: [PATCH 251/468] Add get_force monkey-patch to get OpenMM force from EMLEEngine. --- src/sire/qm/_emle.py | 36 ++++++++++++++++++- src/sire/qm/_utils.py | 9 ++++- .../Convert/SireOpenMM/EMLEEngine.pypp.cpp | 12 ------- wrapper/Convert/SireOpenMM/emle.cpp | 17 --------- wrapper/Convert/SireOpenMM/emle.h | 3 -- 5 files changed, 43 insertions(+), 34 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index bfcf82b3a..6765e4baf 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -9,6 +9,37 @@ _EMLEEngine = _Convert._SireOpenMM.EMLEEngine +# Monkey-patch to get the underlying OpenMM force of the EMLEEngine. +def _get_openmm_force(self): + """ + Get the OpenMM Force for this engine. + + Returns + ------- + + force : openmm.Force + The OpenMM Force object. + """ + + # Create a dynamics object for the QM region. + d = self._mols["property is_perturbable"].dynamics( + timestep="1fs", + constraint="none", + platform="cpu", + qm_engine=self, + ) + + from copy import deepcopy as _deepcopy + + # Return a copy of the OpenMM EMLEForce. + # (For now this is set as the fourth force in the system.) + return _deepcopy(d._d._omm_mols.getSystem().getForce(4)) + + +# Bind the monkey-patched function to the EMLEEngine. +_EMLEEngine.get_force = _get_openmm_force + + def emle( mols, qm_atoms, @@ -139,4 +170,7 @@ def emle( # Update the molecule in the system. mols.update(qm_mols) - return engine + # Bind the system as a private attribute of the engine. + engine._mols = mols + + return mols, engine diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 2331dd6ee..f24c0d996 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -665,6 +665,13 @@ def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_length map: sire.legacy.Base.PropertyMap The property map for the system. + + + Returns + ------- + + engine: sire.legacy.QM.Engine + The configured QM engine. """ # Work out the indices of the QM atoms. @@ -696,4 +703,4 @@ def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_length except: raise Exception("Unable to set link atom information.") - return mols, engine + return engine diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp index e6016d97c..ea7edc728 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp @@ -105,18 +105,6 @@ void register_EMLEEngine_class(){ , bp::release_gil_policy() , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); - } - { //::SireOpenMM::EMLEEngine::getForce - - typedef ::SireOpenMM::EMLEForce ( ::SireOpenMM::EMLEEngine::*getForce_function_type)( ) const; - getForce_function_type getForce_function_value( &::SireOpenMM::EMLEEngine::getForce ); - - EMLEEngine_exposer.def( - "getForce" - , getForce_function_value - , bp::release_gil_policy() - , "Get the EMLE force object." ); - } { //::SireOpenMM::EMLEEngine::getLambda diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 580c923fd..c4bdc9c72 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -1006,20 +1006,3 @@ QMForce* EMLEEngine::createForce() const this->charges ); } - -EMLEForce EMLEEngine::getForce() const -{ - return EMLEForce( - this->callback, - this->cutoff, - this->neighbour_list_frequency, - this->lambda, - this->atoms, - this->mm1_to_qm, - this->mm1_to_mm2, - this->bond_scale_factors, - this->mm2_atoms, - this->numbers, - this->charges - ); -} diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/emle.h index 963b7c64e..c8bde98cc 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/emle.h @@ -555,9 +555,6 @@ namespace SireOpenMM //! Create an EMLE force object. QMForce* createForce() const; - //! Get the EMLE force object. - EMLEForce getForce() const; - private: EMLECallback callback; SireUnits::Dimension::Length cutoff; From 7fb96b67f121fbce04250bebcec9f09478907308 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 13:26:55 +0100 Subject: [PATCH 252/468] Add support for using OpenMM-ML lambda_emle global parameter. --- wrapper/Convert/SireOpenMM/emle.cpp | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index c4bdc9c72..976902306 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -736,8 +736,19 @@ double EMLEForceImpl::computeForce( auto forces_qm = result.get<1>(); auto forces_mm = result.get<2>(); - // Store the current lambda weighting factor. - const auto lambda = this->owner.getLambda(); + // The current interpolation (weighting) parameter. + double lambda; + + // Try to get the "lambda_emle" global parameter from the context. + try + { + lambda = context.getParameter("lambda_emle"); + } + // Fall back on the lambda value stored in the EMLEForce object. + catch (...) + { + lambda = this->owner.getLambda(); + } // Now update the force vector. From fcdc2fe7c0d294ead21a03df6dea17099be2b338 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 13:45:11 +0100 Subject: [PATCH 253/468] Allow decoupling of electrostatics from ML potential. --- wrapper/Convert/SireOpenMM/emle.cpp | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 976902306..fa5dc65ae 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -744,10 +744,18 @@ double EMLEForceImpl::computeForce( { lambda = context.getParameter("lambda_emle"); } - // Fall back on the lambda value stored in the EMLEForce object. catch (...) { - lambda = this->owner.getLambda(); + // Try to get the "lambda_interpolate" global parameter from the context. + try + { + lambda = context.getParameter("lambda_interpolate"); + } + // Fall back on the lambda value stored in the EMLEForce object. + catch (...) + { + lambda = this->owner.getLambda(); + } } // Now update the force vector. From 506d234b6de8336890ec5d8d0533b8fbe231dd7f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 20:43:17 +0100 Subject: [PATCH 254/468] Add QMForce first so position is guaranteed. --- .../Convert/SireOpenMM/sire_to_openmm_system.cpp | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 8837a878c..a8c83bed0 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -763,6 +763,13 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, LambdaSchedule::standard_morph()); } + // Add any QM force first so that we can guarantee that it is index zero. + if (qmff != 0) + { + lambda_lever.setForceIndex("qmff", system.addForce(qmff)); + lambda_lever.addLever("qm_scale"); + } + // We can now add the standard forces to the OpenMM::System. // We do this here, so that we can capture the index of the // force and associate it with a name in the lever. @@ -791,12 +798,6 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, lambda_lever.addLever("torsion_phase"); lambda_lever.addLever("torsion_k"); - if (qmff != 0) - { - lambda_lever.setForceIndex("qmff", system.addForce(qmff)); - lambda_lever.addLever("qm_scale"); - } - /// /// Stage 4 - define the forces for ghost atoms /// From 4ec9b788f10c72c7aacf7e4c1f490362daf4cf96 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 20:44:05 +0100 Subject: [PATCH 255/468] Add a null CustomBondForce to enable lambda_emle global parameter. --- src/sire/qm/_emle.py | 26 +++++++++++++++++--------- 1 file changed, 17 insertions(+), 9 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 6765e4baf..863d2a22e 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -10,17 +10,20 @@ # Monkey-patch to get the underlying OpenMM force of the EMLEEngine. -def _get_openmm_force(self): +def _get_openmm_forces(self): """ - Get the OpenMM Force for this engine. + Get the OpenMM forces for this engine. Returns ------- - force : openmm.Force - The OpenMM Force object. + force : [openmm.Force] + The OpenMM forces. """ + from copy import deepcopy as _deepcopy + from openmm import CustomBondForce as _CustomBondForce + # Create a dynamics object for the QM region. d = self._mols["property is_perturbable"].dynamics( timestep="1fs", @@ -29,15 +32,20 @@ def _get_openmm_force(self): qm_engine=self, ) - from copy import deepcopy as _deepcopy + # Get the OpenMM EMLEForce. + emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) + + # Create a null CustomBondForce to add the EMLE interpolation + # parameter. + cv_force = _CustomBondForce("") + cv_force.addGlobalParameter("lambda_emle", 1.0) - # Return a copy of the OpenMM EMLEForce. - # (For now this is set as the fourth force in the system.) - return _deepcopy(d._d._omm_mols.getSystem().getForce(4)) + # Return the forces. + return [emle_force, cv_force] # Bind the monkey-patched function to the EMLEEngine. -_EMLEEngine.get_force = _get_openmm_force +_EMLEEngine.get_forces = _get_openmm_forces def emle( From 37fe9d80f82227e7fa67365f435b45e0a90a58e8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 20:49:44 +0100 Subject: [PATCH 256/468] Clamp the lambda value to between 0 and 1. --- wrapper/Convert/SireOpenMM/emle.cpp | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index fa5dc65ae..0169dea4d 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -758,6 +758,16 @@ double EMLEForceImpl::computeForce( } } + // Clamp the lambda value. + if (lambda < 0.0) + { + lambda = 0.0; + } + else if (lambda > 1.0) + { + lambda = 1.0; + } + // Now update the force vector. // First the QM atoms. From 56ac6c6a717903b28f028fe9f3f02109f173ffc7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 22 Apr 2024 20:49:59 +0100 Subject: [PATCH 257/468] Improve docstring. --- src/sire/qm/_emle.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 863d2a22e..84ad4548d 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -12,7 +12,11 @@ # Monkey-patch to get the underlying OpenMM force of the EMLEEngine. def _get_openmm_forces(self): """ - Get the OpenMM forces for this engine. + Get the OpenMM forces for this engine. The first force is the actual + EMLEForce, which uses a CustomCPPForceImpl to calculate the electrostatic + embedding force. The second is a null CustomBondForce that can be used to + add a "lambda_emle" global parameter to a context to allow the force to be + scaled. Returns ------- From e5c97ad57efa0608648e9b14a57d8e269b2e80b4 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Apr 2024 09:01:25 +0100 Subject: [PATCH 258/468] Improve docstring for get_forces and return forces as a tuple. --- src/sire/qm/_emle.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 84ad4548d..9a6db3ef6 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -21,8 +21,13 @@ def _get_openmm_forces(self): Returns ------- - force : [openmm.Force] - The OpenMM forces. + emle_force : openmm.Force + The EMLEForce object to compute the electrostatic embedding force. + + interpolation_force : openmm.CustomBondForce + A null CustomBondForce object that can be used to add a "lambda_emle" + global parameter to an OpenMM context. This allows the electrostatic + embedding force to be scaled. """ from copy import deepcopy as _deepcopy @@ -41,11 +46,11 @@ def _get_openmm_forces(self): # Create a null CustomBondForce to add the EMLE interpolation # parameter. - cv_force = _CustomBondForce("") - cv_force.addGlobalParameter("lambda_emle", 1.0) + interpolation_force = _CustomBondForce("") + interpolation_force.addGlobalParameter("lambda_emle", 1.0) # Return the forces. - return [emle_force, cv_force] + return emle_force, interpolation_force # Bind the monkey-patched function to the EMLEEngine. From 999f20648b58cfbcd2aff7a0cdeb86f925c091b2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Apr 2024 09:30:25 +0100 Subject: [PATCH 259/468] Add unit test for use of EMLEForce with OpenMM-ML. --- tests/qm/test_emle.py | 111 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 110 insertions(+), 1 deletion(-) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 2a6034033..2d214db7f 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -13,6 +13,13 @@ except: has_emle = False +try: + from openmmml import MLPotential + + has_openmm_ml = True +except: + has_openmm_ml = False + def test_callback(): """Makes sure that a callback method works correctly""" @@ -104,7 +111,7 @@ def test_interpolate(ala_mols, selection): """ # Create a local copy of the test system. - mols = ala_mols.__copy__() + mols = ala_mols.clone() # Create an EMLE calculator. calculator = EMLECalculator(device="cpu") @@ -141,3 +148,105 @@ def test_interpolate(ala_mols, selection): assert math.isclose( nrg_interp.value(), 0.5 * (nrg_mm + nrg_emle).value(), rel_tol=1e-4 ) + + +@pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") +@pytest.mark.skipif(not has_openmm_ml, reason="openmm-ml is not installed") +def test_openmm_ml(ala_mols): + """ + Make sure that the EMLE engine can be used with OpenMM-ML. + """ + + import openmm + import sire as sr + + # Create a local copy of the test system. + mols = ala_mols.clone() + + # Create an EMLE calculator. + calculator = EMLECalculator(backend="torchani", device="cpu") + + # Create an EMLE engine bound to the calculator. + emle_mols, engine = emle(mols, mols[0], calculator) + + # Create a QM/MM capable dynamics object. + d = emle_mols.dynamics( + timestep="1fs", + constraint="none", + qm_engine=engine, + cutoff_type="pme", + platform="cpu", + ) + + # Get the energy. + nrg_sire = d.current_potential_energy().to("kJ_per_mol") + + with tempfile.TemporaryDirectory() as tmpdir: + # Create a new EMLECalculator without a backend. + calculator = EMLECalculator(backend=None, device="cpu") + + # Create an EMLE engine bound to the calculator. + emle_mols, engine = emle(mols, mols[0], calculator) + + # The first molecule (the dipeptide) is the QM region. This is + # perturbable and can be interpolated between MM (the reference state) + # and QM (the perturbed state). Here we want the QM state, which has + # zeroed charges for the QM region. This means that the entire + # intermolecular electrostatic interaction will be computed by + # EMLE, rather than using the MM charges for mechanical embedding. + qm_mol = sr.morph.link_to_perturbed(emle_mols[0]) + emle_mols.update(qm_mol) + + # Write the sytem to an AMBER coordinate and topology file. + files = sr.expand(tmpdir, ["ala.rst7", "ala.prm7"]) + for file in files: + sr.save(emle_mols, file) + + # Load back the files and create an OpenMM topology. + inpcrd = openmm.app.AmberInpcrdFile(f"{tmpdir}/ala.rst7") + prmtop = openmm.app.AmberPrmtopFile(f"{tmpdir}/ala.prm7") + topology = prmtop.topology + + # Create the MM system. + mm_system = prmtop.createSystem( + nonbondedMethod=openmm.app.PME, + nonbondedCutoff=1 * openmm.unit.nanometer, + constraints=openmm.app.HBonds, + ) + + # Define the ML region. + ml_atoms = list(range(mols[0].num_atoms())) + + # Create the mixed ML/MM system. + potential = MLPotential("ani2x") + ml_system = potential.createMixedSystem( + topology, mm_system, ml_atoms, interpolate=False + ) + + # Get the OpenMM forces from the engine. + emle_force, interpolation_force = engine.get_forces() + + # Add the EMLE force to the system. + ml_system.addForce(emle_force) + + # Create the integrator. + integrator = openmm.LangevinMiddleIntegrator( + 300 * openmm.unit.kelvin, + 1.0 / openmm.unit.picosecond, + 0.002 * openmm.unit.picosecond, + ) + + # Create the context. + context = openmm.Context(ml_system, integrator) + + # Set the positions. + context.setPositions(inpcrd.positions) + + # Get the energy. + state = context.getState(getEnergy=True) + nrg_openmm = state.getPotentialEnergy().value_in_unit( + openmm.unit.kilojoules_per_mole + ) + + # Make sure the energies are close. + assert math.isclose(nrg_openmm, nrg_sire, rel_tol=1e-3) From 5cdda56de1b4a57fbbfc881779c22b91a3d04707 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Apr 2024 15:51:58 +0100 Subject: [PATCH 260/468] Add maximumCutoff method to TriclinicBox class. [closes #189] --- corelib/src/libs/SireVol/triclinicbox.cpp | 15 +++++++++++ corelib/src/libs/SireVol/triclinicbox.h | 3 +++ doc/source/changelog.rst | 3 +++ tests/vol/test_triclinic.py | 31 +++++++++++++++++++++++ 4 files changed, 52 insertions(+) diff --git a/corelib/src/libs/SireVol/triclinicbox.cpp b/corelib/src/libs/SireVol/triclinicbox.cpp index 413b5f2fc..e8faba888 100644 --- a/corelib/src/libs/SireVol/triclinicbox.cpp +++ b/corelib/src/libs/SireVol/triclinicbox.cpp @@ -565,6 +565,21 @@ Matrix TriclinicBox::boxMatrix() const return this->cellMatrix(); } +SireUnits::Dimension::Length TriclinicBox::maximumCutoff() const +{ + // If the box is reduced, then use the minumum diagonal element. + if (this->isReduced()) + { + QList diagonals = {this->v0.x(), this->v1.y(), this->v2.z()}; + return SireUnits::Dimension::Length(*std::min_element(diagonals.begin(), diagonals.end())/2.0); + } + // Otherwise, use half the norm of the smallest box vector. + else + { + return SireUnits::Dimension::Length(this->dist_max); + } +} + /** Return the volume of the central box of this space. */ SireUnits::Dimension::Volume TriclinicBox::volume() const { diff --git a/corelib/src/libs/SireVol/triclinicbox.h b/corelib/src/libs/SireVol/triclinicbox.h index a39028f52..bc3706ada 100644 --- a/corelib/src/libs/SireVol/triclinicbox.h +++ b/corelib/src/libs/SireVol/triclinicbox.h @@ -153,6 +153,9 @@ namespace SireVol QString toString() const; + /** Get the maximum cutoff distance for the triclinic box. */ + SireUnits::Dimension::Length maximumCutoff() const; + /** Get the volume of the triclinic box. */ SireUnits::Dimension::Volume volume() const; diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 5e528c5d1..ca25501ce 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -17,6 +17,9 @@ organisation on `GitHub `__. * Please add an item to this changelog when you create your PR * Correctly set the ``element1`` property in ``sire.morph.create_from_pertfile``. +* Added mising :meth:`~sire.vol.TriclinicBox.maximum_cutoff` method so that + the cutoff is set correctly when creating a :obj:`~sire.system.ForceFieldInfo` + object. `2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ diff --git a/tests/vol/test_triclinic.py b/tests/vol/test_triclinic.py index 52691eb64..b79ebd140 100644 --- a/tests/vol/test_triclinic.py +++ b/tests/vol/test_triclinic.py @@ -141,3 +141,34 @@ def test_stream(): # Make sure the boxes are the same. assert recovered_box == box + + +def test_max_cutoff(ala_mols): + """ + Test that the maximum cutoff is set correctly. + """ + + # Create a local + mols = ala_mols.clone() + + # Create a cubic triclinic space. + + # Set the vectors. + v0 = sr.maths.Vector(50, 0, 0) + v1 = sr.maths.Vector(0, 50, 0) + v2 = sr.maths.Vector(0, 0, 50) + + # Create the space. + space = sr.vol.TriclinicBox(v0, v1, v2) + + # Check the maximum cutoff. + assert space.maximum_cutoff() == 25 * sr.units.angstroms + + # Now set the space property on the molecules. + mols.set_property("space", space) + + # Create a ForceFieldInfo object. + ffinfo = sr.system.ForceFieldInfo(mols) + + # Check the cutoff. This is the maximum cutoff minus 1 angstrom. + assert ffinfo.cutoff() == 24 * sr.units.angstroms From 38940355d93423cf87da9271bdfa004812305b15 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 23 Apr 2024 15:59:59 +0100 Subject: [PATCH 261/468] Typos. --- corelib/src/libs/SireVol/triclinicbox.cpp | 2 +- tests/vol/test_triclinic.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/corelib/src/libs/SireVol/triclinicbox.cpp b/corelib/src/libs/SireVol/triclinicbox.cpp index e8faba888..9f6ddad85 100644 --- a/corelib/src/libs/SireVol/triclinicbox.cpp +++ b/corelib/src/libs/SireVol/triclinicbox.cpp @@ -567,7 +567,7 @@ Matrix TriclinicBox::boxMatrix() const SireUnits::Dimension::Length TriclinicBox::maximumCutoff() const { - // If the box is reduced, then use the minumum diagonal element. + // If the box is reduced, then use half the minimum diagonal element. if (this->isReduced()) { QList diagonals = {this->v0.x(), this->v1.y(), this->v2.z()}; diff --git a/tests/vol/test_triclinic.py b/tests/vol/test_triclinic.py index b79ebd140..c9e929ea5 100644 --- a/tests/vol/test_triclinic.py +++ b/tests/vol/test_triclinic.py @@ -148,7 +148,7 @@ def test_max_cutoff(ala_mols): Test that the maximum cutoff is set correctly. """ - # Create a local + # Create a local copy of the molecules. mols = ala_mols.clone() # Create a cubic triclinic space. From ef5225dbd411d17857fd118c109140e4bdb8a279 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 24 Apr 2024 12:13:46 +0100 Subject: [PATCH 262/468] Add section about using an EMLEForce with OpenMM-ML. --- doc/source/tutorial/partXX/01_emle.rst | 137 ++++++++++++++++++++++++- 1 file changed, 134 insertions(+), 3 deletions(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 13ea73b51..097e73f8d 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -30,6 +30,9 @@ in water. First, let us load the molecular system: >>> import sire as sr >>> mols = sr.load_test_files("ala.crd", "ala.top") +Creating an EMLE calculator +--------------------------- + Next we will create an ``emle-engine`` calculator to perform the QM (or ML) calculation for the dipeptide along with the ML electrostatic embedding. Since this is a small molecule it isn't beneficial to perform the calculation on a GPU, so we will use the CPU instead. @@ -47,10 +50,13 @@ section of the ``emle-engine`` documentation. At present, the default embedding model provided with ``emle-engine`` supports only the elements H, C, N, O, and S. We plan on adding support for other elements in the near future. +Creating a QM engine +-------------------- + We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation: ->>> mols, engine = sr.qm.emle(mols, mols[0], calculator, "7.5A", 20) +>>> qm_mols, engine = sr.qm.emle(mols, mols[0], calculator, "7.5A", 20) Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule), and @@ -58,7 +64,7 @@ the third is calculator that was created above. The fourth and fifth arguments are optional, and specify the QM cutoff distance and the neigbour list update frequency respectively. (Shown are the default values.) The function returns a modified version of the molecules containing a "merged" dipeptide that can be -interpolated between QM and MM levels of theory, along with an engine. The +interpolated between MM and QM levels of theory, along with an engine. The engine registers a Python callback that uses ``emle-engine`` to perform the QM calculation. @@ -70,6 +76,9 @@ see, e.g., the NAMD user guide `here `_. While we support multiple QM fragments, we do not currently support multiple *independent* QM regions. We plan on adding support for this in the near future. +Running a QM/MM simulation +-------------------------- + Next we need to create a dynamics object to perform the simulation. For QM/MM simulations it is recommended to use a 1 femtosecond timestep and no constraints. In this example we will use the ``lambda_interpolate`` keyword to interpolate @@ -77,7 +86,7 @@ the dipeptide potential between pure MM (λ=0) and QM (λ=1) over the course of the simulation, which can be used for end-state correction of binding free energy calculations. ->>> d = mols.dynamics(timestep="1fs", constraint="none", qm_engine=engine, lambda_interpolate=[0, 1]) +>>> d = qm_mols.dynamics(timestep="1fs", constraint="none", qm_engine=engine, lambda_interpolate=[0, 1]) We can now run the simulation. The options below specify the run time, the frequency at which trajectory frames are saved, and the frequency at which @@ -143,3 +152,125 @@ time In the table above, the time doesn't start from zero because the example molecular system was loaded from an existing trajectory restart file. + +Interfacing with OpenMM-ML +-------------------------- + +In the example above we used a sire dynamics object ``d`` to run the simulation. +This is wrapper around a standard OpenMM context object, providing a simple +convenience functions to make it easier to run and analyse simulations. However, +if you are already familiar with OpenMM, then it is possible to use ``emle-engine`` +with OpenMM directly. This allows for fully customised simulations, or the use +of `OpenMM-ML `_ as the backend for +calculation of the intramolecular force for the QM region. + +To use ``OpenMM-ML`` as the backend for the QM calculation, you will first need +to install the package: + +.. code-block:: bash + + $ conda install -c conda-forge openmm-ml + +Next, you will need to create an ``MLPotential`` for desired backend. Here we +will use the ``ani2x``, as was used for the ``EMLECalculator`` above. The + +>>> import openmm +>>> from openmmml import MLPotential +>>> potential = MLPotential("ani2x") + +Since we are now using the ``MLPotential`` for the QM calculation, we need to +create a new ``EMLECalculator`` object with no backend, i.e. one that only +computes the electrostatic embedding: + +>>> calculator = EMLECalculator(backend=None, device="cpu") + +Next we create a new engine bound to the calculator: + +>>> qm_mols, engine = sr.qm.emle(mols, mols[0], calculator, "7.5A", 20) + +Rather than using this engine with a ``sire`` dynamics object, we can instead +extract the underlying ``OpenMM`` force object and add it to an existing +``OpenMM`` system. The forces can be extracted from the engine as follows: + +>>> emle_force, interpolation_force = engine.get_forces() + +The ``emle_force`` object is the ``OpenMM`` force object that calculates the +electrostatic embedding interaction. The ``interpolation_force`` is a null +``CustomBondForce`` object that contains a ``lambda_emle`` global parameter +than can be used to scale the electrostatic embedding interaction. (By default, +this is set to 1, but can be set to any value between 0 and 1.) + +.. note:: + + The ``interpolation_force`` has no energy contribution. It is only required + as there is currently no way to add global parameters to the ``EMLEForce``. + +Since we want to use electrostatic embedding, we will also need to zero the charges +on the atoms within the QM region before creating an ``OpenMM`` system. If not, +then we would also calculate the mechanical embedding interaction. This can be +done using the ``qm_mols`` object generated above. This system is *perturbable* +so can be converted between an MM reference state and QM perturbed state. Here +we require the perturbed state, which has zeroed charges for the QM region: + +>>> qm_mol = sr.morph.link_to_perturbed(qm_mols[0]) +>>> qm_mols.update(qm_mol) + +We now write the modified system to an AMBER format topology and coordinate file +so that we can load them with ``OpenMM``: + +>>> sr.save(qm_mols, "ala_qm.prm7") +>>> sr.save(qm_mols, "ala_qm.rst7") + +We can now read them back in with ``OpenMM``: + +>>> prmtop = openmm.app.AmberPrmtopFile("ala_qm.prm7") +>>> inpcrd = openmm.app.AmberInpcrdFile("ala_qm.rst7") + +Next we use the ``prmtop`` to create the MM system: + +>>> mm_system = prmtop.createSystem( +... nonbondedMethod=openmm.app.PME, +... nonbondedCutoff=1 * openmm.unit.nanometer, +... constraints=openmm.app.HBonds, +... ) + +In oder to create the ML system, we first define the ML region. This is a list +of atom indices that are to be treated with the ML model. + +>>> ml_atoms = list(range(qm_mols[0].num_atoms())) + +We can now create the ML system: + +>>> ml_system = potential.createMixedSystem( +... topology, mm_system, ml_atoms, interpolate=True +... ) + +By setting ``interpolate=True`` we are telling the ``MLPotential`` to create +a *mixed* system that can be interpolated between MM and ML levels of theory +using the ``lambda_interpolate`` global parameter. (By default this is set to 1.) + +.. note:: + + If you choose not to add the ``emle`` interpolation force to the system, then + the ``EMLEForce`` will also use the ``lambda_interpolate`` global parameter. + This allows for the electrostatic embedding to be alongside or independent of + the ML model. + +We can now add the ``emle`` forces to the system: + +>>> ml_system.addForce(emle_force) +>>> ml_system.addForce(interpolation_force) + +In oder to run a simulation we need to create an integrator and context. First +we create the integrator: + +>>> integrator = openmm.LangevinMiddleIntegrator( +... 300 * openmm.unit.kelvin, +... 1.0 / openmm.unit.picosecond, +... 0.002 * openmm.unit.picosecond, +... ) + +And finally the context: + +>>> context = openmm.Context(ml_system, integrator) +>>> context.setPositions(inpcrd.positions) From 56489a41853bc2de16e07f8442422195306e0d4f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Apr 2024 10:22:26 +0100 Subject: [PATCH 263/468] Added alanine-dipeptide conformational sampling tutorial. --- doc/source/tutorial/index_partXX.rst | 2 + doc/source/tutorial/partXX/02_adp_pmf.rst | 179 ++++++++++++++++++++++ doc/source/tutorial/partXX/images/pmf.png | Bin 0 -> 21011 bytes 3 files changed, 181 insertions(+) create mode 100644 doc/source/tutorial/partXX/02_adp_pmf.rst create mode 100644 doc/source/tutorial/partXX/images/pmf.png diff --git a/doc/source/tutorial/index_partXX.rst b/doc/source/tutorial/index_partXX.rst index 413e59783..7d20030a5 100644 --- a/doc/source/tutorial/index_partXX.rst +++ b/doc/source/tutorial/index_partXX.rst @@ -16,3 +16,5 @@ QM/MM simulations using ``sire``. :maxdepth: 1 partXX/01_emle + partXX/02_adp_pmf + partXX/03_diels_alder diff --git a/doc/source/tutorial/partXX/02_adp_pmf.rst b/doc/source/tutorial/partXX/02_adp_pmf.rst new file mode 100644 index 000000000..40255b520 --- /dev/null +++ b/doc/source/tutorial/partXX/02_adp_pmf.rst @@ -0,0 +1,179 @@ +========================================== +Alanine-dipeptide conformational landscape +========================================== + +..note:: + + The code in this tutorial was adapted from `FastMBAR `_. + +In a recent `preprint `_ +we used the ``emle-engine`` interface to ``sander`` to compute free-energy +surfaces for alanine-dipeptide as a function of the Φ and Ψ dihedral +angles shown below. Compared to regular mechanical embedding, ``EMLE`` was +found to be closer to the reference density-functional theory (DFT) surface. +In this tutorial we will show how to use the ``sire-emle`` interface to set +up and run the same calculations using ``OpenMM``. + +.. image:: https://raw.githubusercontent.com/CCPBioSim/biosimspace-advanced-simulation/de3f65372b49879b788f46618e0bfef78b2559b9/metadynamics/assets/alanine_dipeptide.png + :target: https://raw.githubusercontent.com/CCPBioSim/biosimspace-advanced-simulation/de3f65372b49879b788f46618e0bfef78b2559b9/metadynamics/assets/alanine_dipeptide.png + :alt: Alanine-dipeptide backbone angles + +Creating a context with sire-emle +--------------------------------- + +As in the previous section, we can first use ``sire-emle`` to create +a QM/MM capabable dynamics object for the alanine-dipeptide example +system. We can then extract the underlying ``OpenMM`` context from +this. + +First we will create an ``EMLECalculator`` to compute the QM intramolecular +interaction using `ANI-2x `_ along with +the electrostatic embedding interaction. + +>>> from emle import EMLECalculator +>>> calculator = EMLECalculator(device="cpu") + +Next we will load the alanine-dipeptide system using ``sire``: + +>> import sire as sr +>>> mols = sr.load_test_files("ala.crd", "ala.top") + +We can then create an ``EMLEEngine`` that can be be used to perform QM/MM +with ``sire``: + +>>> qm_mols, engine = sr.qm.emle(mols, mols[0], calculator) + +Here the first argument is the molecules that we are simulating, the second +selection coresponding to the QM region (here this is the first molecule), and +the third is calculator that was created above. The fourth and fifth arguments +are optional, and specify the QM cutoff distance and the neigbour list update +frequency respectively. (Shown are the default values.) The function returns a +modified version of the molecules containing a "merged" dipeptide that can be +interpolated between MM and QM levels of theory, along with an engine. The +engine registers a Python callback that uses ``emle-engine`` to perform the QM +calculation. + +We can now create a ``dynamics`` that will create an ``OpenMM`` context for us +and can be used to run a simulation: + +>>> d = mols.dynamics( +... timestep="1fs", +... constraint="none", +... ) + +Before extracting the context we will use the dynamics object to minimise the +alanine-dipeptide system: + +>> d.minimise() + +Setting up umbrella sampling with OpenMM +---------------------------------------- + +We can now extract the underlying ``OpenMM`` context from the dynamics object, +then create a copy of the integrator and system. + +>>> from copy import deepcopy +>>> context = d._d._omm_mols +>>> omm_system = context.getSystem() +>>> integrator = deepcopy(context.getIntegrator()) + +In order to perform umbrella sampling we will need to add a biasing potentials +for the two dihedral angles. Here we will use simple harmonic biasing potentials: + +First the Φ dihedral, which is formed by atom indices 4, 6, 8, and 14: + +>>> import openmm +>>> bias_torsion_phi = openmm.CustomTorsionForce( +... "0.5*k_phi*dtheta^2; dtheta = min(tmp, 2*pi-tmp); tmp = abs(theta - phi)" +... ) +>>> bias_torsion_phi.addGlobalParameter("pi", math.pi) +>>> bias_torsion_phi.addGlobalParameter("k_phi", 100.0) +>>> bias_torsion_phi.addGlobalParameter("phi", 0.0) +>>> bias_torsion_phi.addTorsion(4, 6, 8, 14) + +Next the Ψ dihedral, which is formed by atom indices 6, 8, 14, and 16: + +>>> bias_torsion_psi = openmm.CustomTorsionForce( +... "0.5*k_psi*dtheta^2; dtheta = min(tmp, 2*pi-tmp); tmp = abs(theta - psi)" +... ) +>>> bias_torsion_psi.addGlobalParameter("pi", math.pi) +>>> bias_torsion_psi.addGlobalParameter("k_psi", 100.0) +>>> bias_torsion_psi.addGlobalParameter("psi", 0.0) +>>> bias_torsion_psi.addTorsion(6, 8, 14, 16) + +We can now add these forces to the system: + +>>> omm_system.addForce(bias_torsion_phi) +>>> omm_system.addForce(bias_torsion_psi) + +In order to run the simulation we will create a new context using the system +and integrator and set the initial positions. + +>>> new_context = openmm.Context(omm_system, integrator, context.getPlatform()) +>>> new_context.setPositions(context.getState(getPositions=True).getPositions()) + +Running the simulation +---------------------- + +We are almost ready to run an umbrella sampling simulation. In this example we +will sample the Φ and Ψ dihedral angles on a 36x36 grid. We will first set the +biasing potential centers: + +>>> m = 36 +>>> M = m * m +>>> phi = np.linspace(-math.pi, math.pi, m, endpoint=False) +>>> psi = np.linspace(-math.pi, math.pi, m, endpoint=False) + +During the simulation we will save trajectories to disk which can later be +post-processed to compute the dihedral angles. We will create a directory +in which to store the files: + +>>> os.makedirs("./output/traj", exist_ok=True) + +The sampling is performed by looping over each of the umbrella windows +sequentially. For each window we set the biasing potential center and run +an initial equilibration of 5000 steps. We then run a production simulation +of 100 cycles of 100 steps each, saving trajectory after each cycle: + +>>> for idx in range(M): +... phi_index = idx // m +... psi_index = idx % m +... +... # Set the center of the biasing potentials. +... new_context.setParameter("phi", phi[phi_index]) +... new_context.setParameter("psi", psi[psi_index]) +... +... # Initial equilibrium. +... integrator.step(5000) +... +... # Production sampling. +... file_handle = open(f"./output/traj/phi_{phi_index}_phi_{psi_index}.dcd", "bw") +... dcd_file = DCDFile(file_handle, prm.topology, dt=integrator.getStepSize()) +... for x in range(100): +... integrator.step(100) +... state = new_context.getState(getPositions=True) +... positions = state.getPositions() +... dcd_file.writeModel(positions) +... file_handle.close() + +..note:: + + This is not a particulary efficient way to perform the sampling. In practice, + since it's possible to get good single core performance it is better to run + the windows in parallel, either individually, or in blocks. + +Analysing the results +--------------------- + +The trajectories saved to disk can be post-processed to compute the dihedral +angles, for example using the approach +`here `_. +The free-energy surface can then be compute using MBAR, or UWHAM. Example code +is provided in the `FastMBAR `_ +tutorial `here https://fastmbar.readthedocs.io/en/latest/dialanine_PMF.html#use-fastmbar-to-solve-mbar-uwham-equations-and-compute-the-pmf>`_. + +The resulting free-energy surface should look similar to the one shown below: + +.. image:: images/pmf.png + :target: images/pmf.png + :alt: Free-energy surface for alanine-dipeptide dihedral angles. diff --git a/doc/source/tutorial/partXX/images/pmf.png b/doc/source/tutorial/partXX/images/pmf.png new file mode 100644 index 0000000000000000000000000000000000000000..307d643c9d5cd3fba2e6ca17648ca6f8785f319b GIT binary patch literal 21011 zcmeHvcU%)$yZ@O4f^?DI0*Zpt6=~8eARq!ZigZOmq(y0wI*JNX7f}#ttD-C*MO1o; zeQlt)6s3)zB7zVEOhn2rBs1~7>+9Zo-_QN?w;$FdGp9V~so&>0XXeZf8*_dhDINd- zzomugE&#Y-062eNf@fTbw=ElCd~lO2_67j}sWSf$iXUdQ!h;>#_n0j#EHLh`4o@Lw zC79|SH(yOwicDE`BE?+!n3*=b#UNJhT;h87WV3ZK#+GLkkEg6iNH*0!p?Li`@j`-z zPqM+z1VuPy?ZIT_uoQEpFthbBa+l&Z8=o@TcE&==Z+S|Rna*+I#WO35PpmwZygVsc 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z4EndH9NT>$%gqIr<58uQ;0?+B_28bBAa(dy(3FBJFIUZiThcwRbXO6iG;{duq6UO$ z(X5LWls~@Q$CE1Am7r$QB2UTYtjVq=?G3^=@G3sNLxbFp`ZgVctKF_yscT6`#eB4c zgRI8!c|=8r7&+=+Ycm=JCEiSXwbg$tv+duJaUxx`LFm!cg}?;WSN2L188*+fTHES{ z%tYgrio|_dMY8$$8qt&AX)5|w)Q{R6(Y;3NnyZ!ZA4YK}e@lE#<`A8R= zVs}oYnm>P)zu7IAsd9CuYBD~LLjKV6dRL)r;B`PnXI2lN{dwlC8prO&$(OH%1ARzA zJ-e8i*S6~LTO55y3|ry99wDf|o-UMgPH!DQ+QUDlo)s2TNIPRz%=8#F>*{pqv5us3w>-GN7mu%Y3l z%&hBSb=T{+-|V#XwAwRxk!E~1RZek7&@;O@yR@|q{trSKir9O#t*h{XbyU=7`4cmx zhz7ntv|q~ym+}RL>*VJZ&j@AsrZApjR$lj^xU{QfkZ-hlaIvWukKL z7^v=ZioVJA_O;%rH?D~-{k04JH+RSn%L4Xtg4H9vZ%H*(d|-!t6F;ev4^S7rj>(&E zUK)=(6tTc7ky>yj?l;ek&z2;-$}-Z6aDl;y=2V5vv;{Ekxu`0X~{ zUe7W)+NN8|Vj!vN*0bI`fsVQSEr)=Fikt&7_H8oDnXjMwIv+pqES+nkk>?e?UjWTW ze2;F!xXktTjjABN3smdEnN1VD9GW00bV|BEOu$}<0yG_?4O&CQ%!e&U1th>$f_drr%OQ$K;F~7d>yfF96WusmO`ci)T%v#&xX(fDzO&8f3fdCrmmPx# literal 0 HcmV?d00001 From 08bfad3724dc9e2f1a4be025cb316789f7d35b46 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Apr 2024 11:20:49 +0100 Subject: [PATCH 264/468] Save topology and coordinate file in same function call. --- doc/source/tutorial/partXX/01_emle.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 097e73f8d..0b734abca 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -218,8 +218,7 @@ we require the perturbed state, which has zeroed charges for the QM region: We now write the modified system to an AMBER format topology and coordinate file so that we can load them with ``OpenMM``: ->>> sr.save(qm_mols, "ala_qm.prm7") ->>> sr.save(qm_mols, "ala_qm.rst7") +>>> sr.save(qm_mols, "ala_qm", ["prm7", "rst7"]) We can now read them back in with ``OpenMM``: From 62f5d22b14b56a1411839f7d5b752144e4c7c9c0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Apr 2024 12:45:05 +0100 Subject: [PATCH 265/468] Add section on diels-alder reaction. --- doc/source/tutorial/partXX/02_adp_pmf.rst | 1 + doc/source/tutorial/partXX/03_diels_alder.rst | 215 ++++++++++++++++++ doc/source/tutorial/partXX/images/abyu.png | Bin 0 -> 204647 bytes 3 files changed, 216 insertions(+) create mode 100644 doc/source/tutorial/partXX/03_diels_alder.rst create mode 100644 doc/source/tutorial/partXX/images/abyu.png diff --git a/doc/source/tutorial/partXX/02_adp_pmf.rst b/doc/source/tutorial/partXX/02_adp_pmf.rst index 40255b520..bd9dff260 100644 --- a/doc/source/tutorial/partXX/02_adp_pmf.rst +++ b/doc/source/tutorial/partXX/02_adp_pmf.rst @@ -83,6 +83,7 @@ for the two dihedral angles. Here we will use simple harmonic biasing potentials First the Φ dihedral, which is formed by atom indices 4, 6, 8, and 14: >>> import openmm +>>> import openmm.app >>> bias_torsion_phi = openmm.CustomTorsionForce( ... "0.5*k_phi*dtheta^2; dtheta = min(tmp, 2*pi-tmp); tmp = abs(theta - phi)" ... ) diff --git a/doc/source/tutorial/partXX/03_diels_alder.rst b/doc/source/tutorial/partXX/03_diels_alder.rst new file mode 100644 index 000000000..d0f665ef2 --- /dev/null +++ b/doc/source/tutorial/partXX/03_diels_alder.rst @@ -0,0 +1,215 @@ +==================== +Diels-Alder reaction +==================== + +In this section we will show how to use the ``sire-emle`` interface to set up +simulations of the Diels-Alder reaction catalsed by the +`AbyU `_ enzyme. +This tutorial is intented to show how to set up the simulation in a similar +manner to how it would be performed in a standard QM/MM code, such as ``sander`` +from the `AmberTools `_ suite. + +Setting up the system +--------------------- + +Since the system is quite large it is convenient to restrict the simulation to +simulate solvent within a restricted region around the reaction site. In +``sander`` this can be performed by creating a solvent sphere and using +``ibelly`` to keep solvent molecules outside of this sphere fixed. The same +approach is easy to implement using ``sire`` and ``OpenMM``. First let us +load the full AbyU system: + +>>> import sire as sr +>>> mols = sr.load_test_files("abyu.prm7", "abyu.rst7") + +Next we use a ``sire`` selection to create a sphere around the reaction site: + +>>> water_sphere = mols["water within 22A of atomidx 3 in molidx 1"] + +.. note:: + + Here we choose a sphere of radius 22 Å around atom 3 in the first molecule. + This is the reaction site in the AbyU system. In the simulation we will fix + all atoms more than 20 Å from this site. + +Next, we need to recreate the system by adding the water sphere to protein and +enzyme molecules: + +>>> new_mols = mols[:2] + water_sphere +>>> system = sr.system.System() +>>> for mol in new_mols: +... system.add(mol) + +.. note:: + + Here we add the molecules to the new system one-by-one to ensure that + the order is preserved. + +Now we'll add the original simulation box to the new system: + +>>> system.set_property("space", mols.property("space")) + +Next we'll minimise the system ready for simulation: + +>>> m = system.minimisation() +>>> m.run() +>>> mols = m.commit() + +Let's take a look at the system: + +.. image:: images/abyu.png + :target: images/abyu.png + :alt: AbyU system with a sphere of water molecules around the reaction site. + +Finally, we will write the system to an AMBER topology file for later use: + +>>> sr.save(mols, "abyu_sphere.prm7") + +Setting up the EMLE engine +-------------------------- + +We can now create an ``EMLECalculator`` to compute the QM intramolecular +interaction and the electrostatic embedding interaction. Here we will use +`xtb `_ as the QM backend: + +>>> from emle import EMLECalculator +>>> calculator = EMLECalculator(backend="xtb", device="cpu") + +Next we will create an ``EMLEEngine`` that can be be used to perform QM/MM +calculation: + +>>> qm_mols, engine = sr.qm.emle(mols, mols[1], calculator) + +Here are specifying that molecule index 1, the enzyme, is the QM region. + +Creating a context +------------------ + +We can now create a ``dynamics`` that will create an ``OpenMM`` context for us. +In order to use the solvent sphere we will need to specify the ``fixed`` keyword +argument. This specifies a selection for the atoms that should be fixed during +simulation. Here we will fix all atoms more than 20 Å from the reaction site: + +>>> d = mols.dynamics( +... timestep="1fs", +... constraint="none", +... perturbable_constraint="none", +... integrator="langevin_middle", +... cutoff_type="rf", +... qm_engine=engine, +... platform="cpu", +... fixed="not atoms within 20A of atomidx 3 in molidx 1", +) + +.. note:: + + In ``OpenMM``, fixed atoms are implemented by setting atomic masses to zero. + This means that the atoms are still involved in interactions, but do not move. + +Now we will extract the context from the dynamics object: + +>>> context = d._d._omm_mols + +Creating a reaction coordinate +------------------------------ + +In order to study the Diels-Alder reaction we need to define a reaction coordinate. +With ``sander``, a typical choice is to use a generalised distance coordinate +restraint, using a weighted sum of distances between specific atom pairs involved +in the reaction. It is easy to implement this in ``OpenMM`` using a ``CustomBondForce`` +combined with a ``CustomCVForce``. + +First we will specify the the atom pairs involved in the bonds, along with the weights. + +>> pairs = ((2125, 2094, 0.7), (2119, 2087, 0.3)) + +We will now define a force constant for our collective variable and an initial +equilibrium value: + +>>> import openmm +>>> import openmm.app +>>> from openmm import unit as unit +>>> k = (200 * unit.kilocalorie_per_mole / unit.angstrom**2).value_in_unit( +... unit.kilojoule_per_mole / unit.nanometer**2 +... ) +... r = 2.9 * unit.angstroms + +Next we will create a ``CustomBondForce`` to calculate the distance between the +atom pairs: + +>>> cv = openmm.CustomBondForce("weight*r") +>>> cv.addPerBondParameter("weight") +>>> for atom1, atom2, weight in pairs: +... cv.addBond(atom1, atom2, [weight]) + +We will also create two null forces to monitor the individual bond distances: + +>>> bond1 = openmm.CustomBondForce("r") +>>> bond1.addBond(2125, 2094) +>>> bond2 = openmm.CustomBondForce("r") +>>> bond2.addBond(2119, 2087) + +We can now create our restraint force using the collective variable. First let +us define the energy expression. This is a simple harmonic potential: + +>>> energy_expression = "k*(weighted_distance-r0)^2" + +Next we will create the force: + +>>> restraint_force = openmm.CustomCVForce(energy_expression) +>>> restraint_force.addCollectiveVariable("weighted_distance", cv) +>>> restraint_force.addCollectiveVariable("bond1", bond1) +>>> restraint_force.addCollectiveVariable("bond2", bond2) +>>> restraint_force.addGlobalParameter("k", k) +>>> restraint_force.addGlobalParameter("r0", r) + +Setting up a new OpenMM context +------------------------------- + +We can now create a new OpenMM context with the restraint force to the system +from the original context. First let us extract the original system and integrator: + +>>> from copy import deepcopy +>>> system = context.getSystem() +>>> integrator = deepcopy(context.getIntegrator()) + +Next we will add the restraint force to the system: + +>>> system.addForce(restraint_force) + +Finally we will create a new context with the modified system and integrator, +setting the platform to the same as the original context: + +>>> new_context = openmm.Context(system, integrator, context.getPlatform()) +>>> new_context.setPositions(context.getState(getPositions=True).getPositions()) + +Running the simulation +---------------------- + +We can now run the simulation. Here we will run a short umbrella sampling +simpluation for a single window using 100 cycles of 100 integration steps. +After each cycle we will save append to a trajectory file and print the +current values of the collective variables. + +First we will create a trajectory file using the topology saved earlier as +a reference: + +>>> prm = openmm.app.AmberPrmtopFile("abyu_sphere.prm7") +>>> file_handle = open("traj.dcd", "wb") +>>> dcd_file = openmm.app.DCDFile(file_handle, prm.topology, dt=integrator.getStepSize()) + +Next we will run the simulation: + +>>> for x in range(100): +... integrator.step(10) +... state = new_context.getState(getPositions=True) +... positions = state.getPositions() +... dcd_file.writeModel(positions) +... cv_vals = restraint_force.getCollectiveVariableValues(new_context) +... print(f"Step {x:>3} of 100: CVs = {cv_vals[0]:.3f}, {cv_vals[1]:.3f}, {cv_vals[2]:.3f}") +... file_handle.close() + +.. note:: + + In order to compute the free energy profile of the 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We can then extract the underlying ``OpenMM`` context from this. @@ -35,11 +35,10 @@ the electrostatic embedding interaction. Next we will load the alanine-dipeptide system using ``sire``: ->> import sire as sr +>>> import sire as sr >>> mols = sr.load_test_files("ala.crd", "ala.top") -We can then create an ``EMLEEngine`` that can be be used to perform QM/MM -with ``sire``: +We can then create an ``EMLEEngine`` that can be be used to perform QM/MM: >>> qm_mols, engine = sr.qm.emle(mols, mols[0], calculator) @@ -59,12 +58,14 @@ and can be used to run a simulation: >>> d = mols.dynamics( ... timestep="1fs", ... constraint="none", +... engine=engine, +... platform="cpu", ... ) Before extracting the context we will use the dynamics object to minimise the alanine-dipeptide system: ->> d.minimise() +>>> d.minimise() Setting up umbrella sampling with OpenMM ---------------------------------------- @@ -170,8 +171,7 @@ The trajectories saved to disk can be post-processed to compute the dihedral angles, for example using the approach `here `_. The free-energy surface can then be compute using MBAR, or UWHAM. Example code -is provided in the `FastMBAR `_ -tutorial `here https://fastmbar.readthedocs.io/en/latest/dialanine_PMF.html#use-fastmbar-to-solve-mbar-uwham-equations-and-compute-the-pmf>`_. +is provided in the `FastMBAR tutorial `_. The resulting free-energy surface should look similar to the one shown below: diff --git a/doc/source/tutorial/partXX/03_diels_alder.rst b/doc/source/tutorial/partXX/03_diels_alder.rst index d0f665ef2..92cb3a999 100644 --- a/doc/source/tutorial/partXX/03_diels_alder.rst +++ b/doc/source/tutorial/partXX/03_diels_alder.rst @@ -5,24 +5,25 @@ Diels-Alder reaction In this section we will show how to use the ``sire-emle`` interface to set up simulations of the Diels-Alder reaction catalsed by the `AbyU `_ enzyme. -This tutorial is intented to show how to set up the simulation in a similar -manner to how it would be performed in a standard QM/MM code, such as ``sander`` +This tutorial is intended to show how to set up a simulation in a similar +manner to how it would be performed with a standard QM/MM code, such as ``sander`` from the `AmberTools `_ suite. Setting up the system --------------------- Since the system is quite large it is convenient to restrict the simulation to -simulate solvent within a restricted region around the reaction site. In -``sander`` this can be performed by creating a solvent sphere and using -``ibelly`` to keep solvent molecules outside of this sphere fixed. The same -approach is easy to implement using ``sire`` and ``OpenMM``. First let us -load the full AbyU system: +only consider solvent within a restricted region around the reaction site. In +``sander`` this can be performed by creating a solvent sphere and using an +``ibelly`` restraint to keep solvent molecules outside of this sphere fixed. +The same approach is easy to implement using ``sire`` and ``OpenMM``. First +let us load the full AbyU system: >>> import sire as sr >>> mols = sr.load_test_files("abyu.prm7", "abyu.rst7") -Next we use a ``sire`` selection to create a sphere around the reaction site: +Next we use a ``sire`` `selection `_ +to create a sphere around the reaction site: >>> water_sphere = mols["water within 22A of atomidx 3 in molidx 1"] @@ -80,15 +81,16 @@ calculation: >>> qm_mols, engine = sr.qm.emle(mols, mols[1], calculator) -Here are specifying that molecule index 1, the enzyme, is the QM region. +Here are specifying that molecule index 1, i.e. the enzyme, is the QM region. Creating a context ------------------ -We can now create a ``dynamics`` that will create an ``OpenMM`` context for us. -In order to use the solvent sphere we will need to specify the ``fixed`` keyword -argument. This specifies a selection for the atoms that should be fixed during -simulation. Here we will fix all atoms more than 20 Å from the reaction site: +We can now create a dynamics object that will create an ``OpenMM`` context for +us. In order to use the solvent sphere we will need to specify the ``fixed`` +keyword argument. This specifies a selection for the atoms that should be +fixed during simulation. Here we will fix all atoms more than 20 Å from the +reaction site: >>> d = mols.dynamics( ... timestep="1fs", @@ -123,6 +125,9 @@ First we will specify the the atom pairs involved in the bonds, along with the w >> pairs = ((2125, 2094, 0.7), (2119, 2087, 0.3)) +Here the first two values in each tuple are the atom indices of the atoms involved +in the bond, and the third value is the weight of the bond. + We will now define a force constant for our collective variable and an initial equilibrium value: @@ -149,8 +154,8 @@ We will also create two null forces to monitor the individual bond distances: >>> bond2 = openmm.CustomBondForce("r") >>> bond2.addBond(2119, 2087) -We can now create our restraint force using the collective variable. First let -us define the energy expression. This is a simple harmonic potential: +We can now create our restraint force using the collective variables above. +First let us define the energy expression. This is a simple harmonic potential: >>> energy_expression = "k*(weighted_distance-r0)^2" @@ -166,8 +171,9 @@ Next we will create the force: Setting up a new OpenMM context ------------------------------- -We can now create a new OpenMM context with the restraint force to the system -from the original context. First let us extract the original system and integrator: +We can now create a new OpenMM context with the restraint force added to the +system from the original context. First let us extract copies of the original +system and integrator: >>> from copy import deepcopy >>> system = context.getSystem() @@ -188,8 +194,8 @@ Running the simulation We can now run the simulation. Here we will run a short umbrella sampling simpluation for a single window using 100 cycles of 100 integration steps. -After each cycle we will save append to a trajectory file and print the -current values of the collective variables. +After each cycle we will append to a trajectory file and print the current +values of the collective variables. First we will create a trajectory file using the topology saved earlier as a reference: @@ -198,7 +204,7 @@ a reference: >>> file_handle = open("traj.dcd", "wb") >>> dcd_file = openmm.app.DCDFile(file_handle, prm.topology, dt=integrator.getStepSize()) -Next we will run the simulation: +And now we will run the simulation: >>> for x in range(100): ... integrator.step(10) From dd0e75a2a009f48d97720b2babdd04526cf9f55b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Apr 2024 19:27:05 +0100 Subject: [PATCH 267/468] Add note that OpenMM-ML isn't installed by default. --- doc/source/tutorial/partXX/01_emle.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 0b734abca..e8c25b0e3 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -178,6 +178,11 @@ will use the ``ani2x``, as was used for the ``EMLECalculator`` above. The >>> from openmmml import MLPotential >>> potential = MLPotential("ani2x") +.. note:: + + ``OpenMM-ML`` isn't installed by default in the ``emle-sire`` environment. + To install it, use ``conda install -c conda-forge openmm-ml``. + Since we are now using the ``MLPotential`` for the QM calculation, we need to create a new ``EMLECalculator`` object with no backend, i.e. one that only computes the electrostatic embedding: From 4732fc6dad9cec903b699ab09e5730dd660492a2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 09:06:18 +0100 Subject: [PATCH 268/468] Use CPU platform for tutorial. --- doc/source/tutorial/partXX/01_emle.rst | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index e8c25b0e3..49f2bbef5 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -86,7 +86,13 @@ the dipeptide potential between pure MM (λ=0) and QM (λ=1) over the course of the simulation, which can be used for end-state correction of binding free energy calculations. ->>> d = qm_mols.dynamics(timestep="1fs", constraint="none", qm_engine=engine, lambda_interpolate=[0, 1]) +>>> d = qm_mols.dynamics( +... timestep="1fs", +... constraint="none", +... qm_engine=engine, +... lambda_interpolate=[0, 1], +... platform="cpu", +... ) We can now run the simulation. The options below specify the run time, the frequency at which trajectory frames are saved, and the frequency at which From 4c2d8a111bd91e5d496d2357b25e419e0c6f0d4f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 09:13:14 +0100 Subject: [PATCH 269/468] Formatting tweak. --- doc/source/tutorial/partXX/01_emle.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 49f2bbef5..3af3b483f 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -178,7 +178,7 @@ to install the package: $ conda install -c conda-forge openmm-ml Next, you will need to create an ``MLPotential`` for desired backend. Here we -will use the ``ani2x``, as was used for the ``EMLECalculator`` above. The +will use the ANI-2x, as was used for the ``EMLECalculator`` above. The >>> import openmm >>> from openmmml import MLPotential From 38eed227e1230cf987c5f1a04e130bf0bc17308b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 09:20:05 +0100 Subject: [PATCH 270/468] Remove redundant note. --- doc/source/tutorial/partXX/01_emle.rst | 5 ----- 1 file changed, 5 deletions(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 3af3b483f..49a908d14 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -184,11 +184,6 @@ will use the ANI-2x, as was used for the ``EMLECalculator`` above. The >>> from openmmml import MLPotential >>> potential = MLPotential("ani2x") -.. note:: - - ``OpenMM-ML`` isn't installed by default in the ``emle-sire`` environment. - To install it, use ``conda install -c conda-forge openmm-ml``. - Since we are now using the ``MLPotential`` for the QM calculation, we need to create a new ``EMLECalculator`` object with no backend, i.e. one that only computes the electrostatic embedding: From a89be39a6e60f30aafbc8aafa76b3fc6ad65b18a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 09:29:44 +0100 Subject: [PATCH 271/468] Typos. --- doc/source/tutorial/partXX/01_emle.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 49a908d14..ed0d04ffc 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -247,7 +247,7 @@ of atom indices that are to be treated with the ML model. We can now create the ML system: >>> ml_system = potential.createMixedSystem( -... topology, mm_system, ml_atoms, interpolate=True +... prmtop.topology, mm_system, ml_atoms, interpolate=True ... ) By setting ``interpolate=True`` we are telling the ``MLPotential`` to create @@ -266,7 +266,7 @@ We can now add the ``emle`` forces to the system: >>> ml_system.addForce(emle_force) >>> ml_system.addForce(interpolation_force) -In oder to run a simulation we need to create an integrator and context. First +In order to run a simulation we need to create an integrator and context. First we create the integrator: >>> integrator = openmm.LangevinMiddleIntegrator( From 360db61673f7a8c1f9d0a2b44bbb8578815ed4a1 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 11:57:53 +0100 Subject: [PATCH 272/468] Add introduction sire-emle notebook. --- doc/source/tutorial/partXX/sire_emle.ipynb | 773 +++++++++++++++++++++ 1 file changed, 773 insertions(+) create mode 100644 doc/source/tutorial/partXX/sire_emle.ipynb diff --git a/doc/source/tutorial/partXX/sire_emle.ipynb b/doc/source/tutorial/partXX/sire_emle.ipynb new file mode 100644 index 000000000..80b93a9c8 --- /dev/null +++ b/doc/source/tutorial/partXX/sire_emle.ipynb @@ -0,0 +1,773 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "653dd6e1-f537-4a7c-b708-0652f3aea7c2", + "metadata": {}, + "source": [ + "# Sire-EMLE\n", + "\n", + "The `sire` QM/MM implementation takes advantage of the new means of writing [platform independent force calculations](http://docs.openmm.org/development/developerguide/09_customcppforceimpl.html) introduced in [OpenMM](http://openmm.org/) 8.1. This allows us to interface with any external package to modify atomic forces within the OpenMM context. While OpenMM already directly supports ML/MM simulations via the [OpenMM-ML](https://github.com/openmm/openmm-ml) package, it is currently limited to specific backends and only supports mechanical embedding. The `sire` QM/MM implementation performs the QM calculation using the [emle-engine](https://github.com/chemle/emle-engine) package, which has support for a wide range of backends and embedding models, importantly providing a simple and efficient ML model for electrostatic embedding.\n", + "\n", + "Here are some useful links:\n", + "\n", + "* [Paper](https://doi.org/10.26434/chemrxiv-2022-rknwt-v3) on the original EMLE methodology.\n", + "* [emle-engine](https://github.com/chemle/emle-engine) GitHub repository.\n", + "* [Preprint](https://doi.org/10.26434/chemrxiv-2023-6rng3-v2) on alanine-dipeptide conformational landscape study.\n", + "* Sire-EMLE [tutorials](https://github.com/OpenBioSim/sire/blob/feature_emle/doc/source/tutorial/partXX).\n", + "\n", + "In order to use QM/MM functionality within `sire` you will first need to create the following `conda` environment:\n", + "\n", + "```bash\n", + "$ git clone https://github.com/chemle/emle-engine.git\n", + "$ cd emle-engine\n", + "$ conda env create -f environment_sire.yaml\n", + "$ conda activate emle-sire\n", + "$ pip install -e .\n", + "```\n", + "\n", + "In this tutorial, we will perform a short ML/MM simulation of alanine dipeptide in water. First, let us load the molecular system:" + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "ab513df4-dce9-4650-96d2-8b64ffd25c17", + "metadata": {}, + "outputs": [ + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "e74cb328add74fe28a55a1445302924d", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:rdkit:Enabling RDKit 2023.09.4 jupyter extensions\n" + ] + } + ], + "source": [ + "import sire as sr\n", + "mols = sr.load_test_files(\"ala.crd\", \"ala.top\")" + ] + }, + { + "cell_type": "markdown", + "id": "aec5d4db-64f7-4540-a695-02953ce38ed9", + "metadata": {}, + "source": [ + "## Creating an EMLE calculator\n", + "\n", + "Next we will create an `emle-engine` calculator to perform the QM (or ML) calculation for the dipeptide along with the ML electrostatic embedding. Since this is a small molecule it isn't beneficial to perform the calculation on a GPU, so we will use the CPU instead." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "1e7a8d25-eae9-434c-9293-cf6058aa5690", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:549: UserWarning: The value of the smallest subnormal for type is zero.\n", + " setattr(self, word, getattr(machar, word).flat[0])\n", + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero.\n", + " return self._float_to_str(self.smallest_subnormal)\n", + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:549: UserWarning: The value of the smallest subnormal for type is zero.\n", + " setattr(self, word, getattr(machar, word).flat[0])\n", + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero.\n", + " return self._float_to_str(self.smallest_subnormal)\n", + "WARNING:rascal.utils.filter:Warning: skmatter module not found. CUR and FPS filters will be unavailable.\n", + "WARNING:rascal.utils.filter:Original error:\n", + "No module named 'skmatter'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/torchani/resources/\n" + ] + } + ], + "source": [ + "from emle.calculator import EMLECalculator\n", + "calculator = EMLECalculator(device=\"cpu\")" + ] + }, + { + "cell_type": "markdown", + "id": "11d55aa7-c355-4f0a-a4bf-ea53cdeaa7a6", + "metadata": {}, + "source": [ + "By default, `emle-engine` will use [TorchANI](https://aiqm.github.io/torchani/) as the backend for in vacuo calculation of energies and gradients using the ANI-2x model. However, it is possible to use a wide variety of other backends, including your own as long as it supports the standand [Atomic Simulation Environment (ASE) calculator interface](https://wiki.fysik.dtu.dk/ase/). For details, see the [backends](https://github.com/chemle/emle-engine#backends) section of the emle-engine documentation. At present, the default embedding model provided with emle-engine supports only the elements H, C, N, O, and S. We plan on adding support for other elements in the near future.\n", + "\n", + "## Creating a QM engine\n", + "\n", + "We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation:" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "7ef98e4b-2458-4e7a-8404-32141f7654a2", + "metadata": {}, + "outputs": [], + "source": [ + "qm_mols, engine = sr.qm.emle(mols, mols[0], calculator, \"7.5A\", 20)" + ] + }, + { + "cell_type": "markdown", + "id": "b4dd507a-20b5-41be-98f8-d0cf57f0dfe0", + "metadata": {}, + "source": [ + "Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule), and the third is calculator that was created above. The fourth and fifth arguments are optional, and specify the QM cutoff distance and the neigbour list update frequency respectively. (Shown are the default values.) The function returns a modified version of the molecules containing a \"merged\" dipeptide that can be interpolated between MM and QM levels of theory, along with an engine. The engine registers a Python callback that uses `emle-engine` to perform the QM calculation.\n", + "\n", + "The selection syntax for QM atoms is extremely flexible. Any valid search string, atom index, list of atom indicies, or molecule view/container that can be used. Support for modelling partial molecules at the QM level is provided via the link atom approach, via the charge shifting method. For details of this implementation, see, e.g., the NAMD user guide [here](https://www.ks.uiuc.edu/Research/qmmm/). While we support multiple QM fragments, we do not currently support multiple independent QM regions. We plan on adding support for this in the near future.\n", + "\n", + "## Running a QM/MM simulation\n", + "\n", + "Next we need to create a dynamics object to perform the simulation. For QM/MM simulations it is recommended to use a 1 femtosecond timestep and no constraints. In this example we will use the `lambda_interpolate` keyword to interpolate the dipeptide potential between pure MM (λ=0) and QM (λ=1) over the course of the simulation, which can be used for end-state correction of binding free energy calculations." + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "d25b14ba-c0da-4e7f-868b-b86ecf791bfc", + "metadata": {}, + "outputs": [], + "source": [ + "d = qm_mols.dynamics(\n", + " timestep=\"1fs\",\n", + " constraint=\"none\",\n", + " qm_engine=engine,\n", + " lambda_interpolate=[0, 1],\n", + " platform=\"cpu\",\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "4d97d2f4-c686-4e20-99c6-d76b9b6c41f9", + "metadata": {}, + "source": [ + "We can now run the simulation. The options below specify the run time, the frequency at which trajectory frames are saved, and the frequency at which energies are recorded. The energy_frequency also specifies the frequency at which the λ value is updated." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "29224f7c-e3c4-4131-a406-17af3af980d3", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "dynamics \u001b[37;42m \u001b[0m \u001b[35m 21 s\u001b[0m \u001b[36m 4.7 steps / s\u001b[0m \n" + ] + }, + { + "data": { + "text/plain": [ + "Dynamics(completed=6000.1 ps, energy=-317033 kcal mol-1, speed=0.4 ns day-1)" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import os\n", + "os.environ[\"OMP_NUM_THREADS\"] = \"1\"\n", + "d.run(\"0.1ps\", frame_frequency=\"0.01ps\", energy_frequency=\"0.01ps\")" + ] + }, + { + "cell_type": "markdown", + "id": "1101ac69-5701-473e-971f-bb8d2cba0923", + "metadata": {}, + "source": [ + "\n", + "\n", + "
    \n", + "⚠️ If you don't require a trajectory file, then better performance can be achieved leaving the frame_frequency keyword argument unset.\n", + "
    \n", + "\n", + "
    \n", + "⚠️ Currently requires the use of librascal for the calculation of SOAP (Smooth Overlap of Atomic Positions) descriptors. This is a serial code, so you may see better performance by restricting the number of OpenMP threads to 1, e.g. by setting the OMP_NUM_THREADS environment variable.\n", + "
    " + ] + }, + { + "cell_type": "markdown", + "id": "47c807f2-6f9b-4b0d-88c2-3ff11e458c10", + "metadata": {}, + "source": [ + "Once the simulation has finished we can get back the trajectory of energy values. This can be obtained as a [pandas](https://pandas.pydata.org/) `DataFrame`, allowing for easy plotting and analysis. The table below shows the instantaneous kintetic and potential energies as a function of λ, along with the pure MM and QM potential energies. (Times are in picoseconds and energies are in kcal/mol.)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "2f0b7725-f272-439f-8f72-ae6fe954d2e4", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:numexpr.utils:Note: NumExpr detected 20 cores but \"NUMEXPR_MAX_THREADS\" not set, so enforcing safe limit of 8.\n", + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/pandas/core/computation/expressions.py:21: UserWarning: Pandas requires version '2.8.0' or newer of 'numexpr' (version '2.7.3' currently installed).\n", + " from pandas.core.computation.check import NUMEXPR_INSTALLED\n" + ] + }, + { + "data": { + "text/html": [ + "
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    \n", + "⚠️ The interpolation_force has no energy contribution. It is only required as there is currently no way to add global parameters to the EMLEForce.\n", + "
    \n", + "\n", + "Since we want to use electrostatic embedding, we will also need to zero the charges on the atoms within the QM region before creating an `OpenMM` system. If not, then we would also calculate the mechanical embedding interaction. This can be done using the `qm_mols` object generated above. This system is *perturbable* so can be converted between an MM reference state and QM perturbed state. Here we require the perturbed state, which has zeroed charges for the QM region:" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "3c4429bd-d9a2-4a46-af2c-d33921e47f64", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "SireMol::AtomCharges( size=22\n", + "0: 0 |e|\n", + "1: 0 |e|\n", + "2: 0 |e|\n", + "3: 0 |e|\n", + "4: 0 |e|\n", + "...\n", + "17: 0 |e|\n", + "18: 0 |e|\n", + "19: 0 |e|\n", + "20: 0 |e|\n", + "21: 0 |e|\n", + ")" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "qm_mol = sr.morph.link_to_perturbed(qm_mols[0])\n", + "qm_mols.update(qm_mol)\n", + "qm_mol.property(\"charge\")" + ] + }, + { + "cell_type": "markdown", + "id": "448cb006-5ea5-46ae-9f19-f6060ae520e4", + "metadata": {}, + "source": [ + "We now write the modified system to an AMBER format topology and coordinate file so that we can load them with `OpenMM`:" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "e9c636fe-92f2-4546-98e7-49c6a6f91ccb", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['/home/lester/Code/openbiosim/sire-emle/ala_qm.prm7',\n", + " '/home/lester/Code/openbiosim/sire-emle/ala_qm.rst7']" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "sr.save(qm_mols, \"ala_qm\", [\"prm7\", \"rst7\"])" + ] + }, + { + "cell_type": "markdown", + "id": "a18835fd-0eca-4424-910e-274dffbeda08", + "metadata": {}, + "source": [ + "We can now read them back in with OpenMM:" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "e933ff6d-2d81-4d6a-af16-8a61e3cf0ea3", + "metadata": {}, + "outputs": [], + "source": [ + "prmtop = openmm.app.AmberPrmtopFile(\"ala_qm.prm7\")\n", + "inpcrd = openmm.app.AmberInpcrdFile(\"ala_qm.rst7\")" + ] + }, + { + "cell_type": "markdown", + "id": "827c4965-e53a-427c-b855-294d4d4a1761", + "metadata": {}, + "source": [ + "Next we use the prmtop to create the MM system:" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "38ec7d50-44a3-46ea-83be-031230b568c1", + "metadata": {}, + "outputs": [], + "source": [ + "mm_system = prmtop.createSystem(\n", + " nonbondedMethod=openmm.app.PME,\n", + " nonbondedCutoff=7.5 * openmm.unit.angstrom,\n", + " constraints=openmm.app.HBonds\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "4453c713-8b9d-4289-b420-ab01c0c20869", + "metadata": {}, + "source": [ + "In oder to create the ML system, we first define the ML region. This is a list of atom indices that are to be treated with the ML model." + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "7921e1a5-76ce-4a11-abf0-99919c8ad5bf", + "metadata": {}, + "outputs": [], + "source": [ + "ml_atoms = list(range(qm_mols[0].num_atoms()))" + ] + }, + { + "cell_type": "markdown", + "id": "0426b8e5-0c51-46f5-861e-71501b222508", + "metadata": {}, + "source": [ + "We can now create the ML system:" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "952cb2fe-ca9e-46d8-a0b9-b6646449ccfd", + "metadata": {}, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/torchani/resources/\n" + ] + } + ], + "source": [ + "ml_system = potential.createMixedSystem(prmtop.topology, mm_system, ml_atoms, interpolate=True)" + ] + }, + { + "cell_type": "markdown", + "id": "4396f10b-0d29-452d-bb2f-4bb494e95619", + "metadata": {}, + "source": [ + "By setting `interpolate=True` we are telling the `MLPotential` to create a mixed system that can be interpolated between MM and ML levels of theory using the `lambda_interpolate` global parameter. (By default this is set to 1.)\n", + "\n", + "
    \n", + "⚠️ If you choose not to add the emle interpolation force to the system, then the EMLEForce will also use the lambda_interpolate global parameter. This allows for the electrostatic embedding to be alongside or independent of the ML model.\n", + "
    " + ] + }, + { + "cell_type": "markdown", + "id": "e1d45ac2-f34f-48e1-884a-243b63ddf9af", + "metadata": {}, + "source": [ + "We can now add the `emle` forces to the system:" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "63ab7538-9267-43ae-8ae7-1317438d41c9", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "7" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "ml_system.addForce(emle_force)\n", + "ml_system.addForce(interpolation_force)" + ] + }, + { + "cell_type": "markdown", + "id": "11cda2ef-e907-4e8f-8f79-1ab158f6188d", + "metadata": {}, + "source": [ + "In order to run a simulation we need to create an integrator and context. First we create the integrator:" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "ed684bf8-c8e3-40d7-88d1-7231217de606", + "metadata": {}, + "outputs": [], + "source": [ + "integrator = openmm.LangevinMiddleIntegrator(\n", + " 300 * openmm.unit.kelvin,\n", + " 1.0 / openmm.unit.picosecond,\n", + " 0.002 * openmm.unit.picosecond\n", + ")" + ] + }, + { + "cell_type": "markdown", + "id": "fbad1f00-b2cc-42b4-93ee-43b87bd7053b", + "metadata": {}, + "source": [ + "And finally the context:" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "266bb2bd-0797-4f7d-bc27-35524dd85513", + "metadata": {}, + "outputs": [], + "source": [ + "context = openmm.Context(ml_system, integrator)\n", + "context.setPositions(inpcrd.positions)" + ] + }, + { + "cell_type": "markdown", + "id": "7c2ecc57-61a2-409d-a434-b880ccf37262", + "metadata": {}, + "source": [ + "Let's check the global parameters:" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "539a8f46-1205-4c96-92e4-f97d346d70e1", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "lambda_emle 1.0\n", + "lambda_interpolate 1.0\n" + ] + } + ], + "source": [ + "for param in context.getParameters():\n", + " print(param, context.getParameter(param))" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} From e52e10a768d17b67d2fc4ab17bd58da9146d7d34 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 12:11:27 +0100 Subject: [PATCH 273/468] Use comparable settings. --- tests/qm/test_emle.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 2d214db7f..ad4d0865c 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -175,6 +175,7 @@ def test_openmm_ml(ala_mols): constraint="none", qm_engine=engine, cutoff_type="pme", + cutoff="7.5 A", platform="cpu", ) @@ -210,7 +211,7 @@ def test_openmm_ml(ala_mols): # Create the MM system. mm_system = prmtop.createSystem( nonbondedMethod=openmm.app.PME, - nonbondedCutoff=1 * openmm.unit.nanometer, + nonbondedCutoff=7.5 * openmm.unit.angstrom, constraints=openmm.app.HBonds, ) From b71b1e7c6f4cdcf3249b2cc2a28e5939d0237384 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 13:46:30 +0100 Subject: [PATCH 274/468] QM region is the substrate, not enzyme. --- doc/source/tutorial/partXX/03_diels_alder.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/partXX/03_diels_alder.rst b/doc/source/tutorial/partXX/03_diels_alder.rst index 92cb3a999..8c1822a78 100644 --- a/doc/source/tutorial/partXX/03_diels_alder.rst +++ b/doc/source/tutorial/partXX/03_diels_alder.rst @@ -81,7 +81,7 @@ calculation: >>> qm_mols, engine = sr.qm.emle(mols, mols[1], calculator) -Here are specifying that molecule index 1, i.e. the enzyme, is the QM region. +Here are specifying that molecule index 1, i.e. the substrate, is the QM region. Creating a context ------------------ From 343fdb9dfd28b121a84bd192946ddabe01e16ec7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 13:58:21 +0100 Subject: [PATCH 275/468] Clean example notebook. --- doc/source/tutorial/partXX/sire_emle.ipynb | 341 ++------------------- 1 file changed, 29 insertions(+), 312 deletions(-) diff --git a/doc/source/tutorial/partXX/sire_emle.ipynb b/doc/source/tutorial/partXX/sire_emle.ipynb index 80b93a9c8..cb81ba340 100644 --- a/doc/source/tutorial/partXX/sire_emle.ipynb +++ b/doc/source/tutorial/partXX/sire_emle.ipynb @@ -31,30 +31,10 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "ab513df4-dce9-4650-96d2-8b64ffd25c17", "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "e74cb328add74fe28a55a1445302924d", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "INFO:rdkit:Enabling RDKit 2023.09.4 jupyter extensions\n" - ] - } - ], + "outputs": [], "source": [ "import sire as sr\n", "mols = sr.load_test_files(\"ala.crd\", \"ala.top\")" @@ -72,35 +52,10 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "1e7a8d25-eae9-434c-9293-cf6058aa5690", "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:549: UserWarning: The value of the smallest subnormal for type is zero.\n", - " setattr(self, word, getattr(machar, word).flat[0])\n", - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero.\n", - " return self._float_to_str(self.smallest_subnormal)\n", - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:549: UserWarning: The value of the smallest subnormal for type is zero.\n", - " setattr(self, word, getattr(machar, word).flat[0])\n", - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero.\n", - " return self._float_to_str(self.smallest_subnormal)\n", - "WARNING:rascal.utils.filter:Warning: skmatter module not found. CUR and FPS filters will be unavailable.\n", - "WARNING:rascal.utils.filter:Original error:\n", - "No module named 'skmatter'\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/torchani/resources/\n" - ] - } - ], + "outputs": [], "source": [ "from emle.calculator import EMLECalculator\n", "calculator = EMLECalculator(device=\"cpu\")" @@ -120,7 +75,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "7ef98e4b-2458-4e7a-8404-32141f7654a2", "metadata": {}, "outputs": [], @@ -144,7 +99,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "d25b14ba-c0da-4e7f-868b-b86ecf791bfc", "metadata": {}, "outputs": [], @@ -168,28 +123,10 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "id": "29224f7c-e3c4-4131-a406-17af3af980d3", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "dynamics \u001b[37;42m \u001b[0m \u001b[35m 21 s\u001b[0m \u001b[36m 4.7 steps / s\u001b[0m \n" - ] - }, - { - "data": { - "text/plain": [ - "Dynamics(completed=6000.1 ps, energy=-317033 kcal mol-1, speed=0.4 ns day-1)" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "import os\n", "os.environ[\"OMP_NUM_THREADS\"] = \"1\"\n", @@ -224,160 +161,10 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "2f0b7725-f272-439f-8f72-ae6fe954d2e4", "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "INFO:numexpr.utils:Note: NumExpr detected 20 cores but \"NUMEXPR_MAX_THREADS\" not set, so enforcing safe limit of 8.\n", - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/pandas/core/computation/expressions.py:21: UserWarning: Pandas requires version '2.8.0' or newer of 'numexpr' (version '2.7.3' currently installed).\n", - " from pandas.core.computation.check import NUMEXPR_INSTALLED\n" - ] - }, - { - "data": { - "text/html": [ - "
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Import 'openmm' instead.\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ - "/home/lester/.conda/envs/sire-emle/lib/python3.10/site-packages/torchani/resources/\n" - ] - } - ], + "outputs": [], "source": [ "ml_system = potential.createMixedSystem(prmtop.topology, mm_system, ml_atoms, interpolate=True)" ] @@ -659,21 +396,10 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "id": "63ab7538-9267-43ae-8ae7-1317438d41c9", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "7" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "ml_system.addForce(emle_force)\n", "ml_system.addForce(interpolation_force)" @@ -689,7 +415,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "id": "ed684bf8-c8e3-40d7-88d1-7231217de606", "metadata": {}, "outputs": [], @@ -711,7 +437,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "id": "266bb2bd-0797-4f7d-bc27-35524dd85513", "metadata": {}, "outputs": [], @@ -730,19 +456,10 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "id": "539a8f46-1205-4c96-92e4-f97d346d70e1", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "lambda_emle 1.0\n", - "lambda_interpolate 1.0\n" - ] - } - ], + "outputs": [], "source": [ "for param in context.getParameters():\n", " print(param, context.getParameter(param))" From b05c9e76243f1413fe7baebe55113dbf7ac78ba1 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 15:56:37 +0100 Subject: [PATCH 276/468] Add option to redistribute excess QM charge. --- src/sire/qm/_emle.py | 11 +++++++- src/sire/qm/_utils.py | 62 +++++++++++++++++++++++++++++++++++++++---- tests/qm/test_emle.py | 45 +++++++++++++++++++++++++++++++ 3 files changed, 112 insertions(+), 6 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 9a6db3ef6..6cef477b0 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -63,6 +63,7 @@ def emle( calculator, cutoff="7.5A", neighbourlist_update_frequency=20, + redistribute_charge=False, map=None, ): """ @@ -88,6 +89,11 @@ def emle( neighbourlist_update_frequency : int, optional, default=20 The frequency with which to update the neighbourlist. + redistribute_charge : bool + Whether to redistribute charge of the QM atoms to ensure that the total + charge of the QM region is an integer. Excess charge is redistributed + over the non QM atoms within the residues involved in the QM region. + Returns ------- @@ -145,6 +151,9 @@ def emle( if neighbourlist_update_frequency < 0: raise ValueError("'neighbourlist_update_frequency' must be >= 0") + if not isinstance(redistribute_charge, bool): + raise TypeError("'redistribute_charge' must be of type 'bool'") + if map is not None: if not isinstance(map, dict): raise TypeError("'map' must be of type 'dict'") @@ -166,7 +175,7 @@ def emle( ) # Check that the charge of the QM region is integer valued. - _check_charge(qm_atoms, map) + _check_charge(mols, qm_atoms, map, redistribute_charge) # Get the mapping between molecule numbers and QM atoms. qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index f24c0d996..4872190ff 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,30 +1,44 @@ -def _check_charge(qm_atoms, map, tol=1e-6): +def _check_charge(mols, qm_atoms, map, redistribute_charge=False, tol=1e-6): """ Internal helper function to check that the QM region has integer charge. Parameters ---------- + mols : sire.system.System + The system containing the QM atoms. + qm_atoms: [sire.legacy.Mol.AtomIdx] A list of QM atoms. + redistribute_charge: bool + Whether to redistribute charge to ensure that the QM region has an + integer charge. + map: sire.legacy.Base.PropertyMap The property map for the molecule. tol: float The tolerance for the charge check. + Returns + ------- + Raises ------ Exception - If the charge of the QM region is not an integer. + If the charge of the QM region is not an integer and charge redistribution + is not allowed. + """ import math as _math + from sire.units import e_charge as _e_charge + # Get the charge property. - charge_prop = map["charge"] + charge_prop = map["charge"].source() # Work out the charge of the QM atoms. qm_charge = 0 @@ -32,8 +46,46 @@ def _check_charge(qm_atoms, map, tol=1e-6): qm_charge += atom.property(charge_prop).value() # Check that the charge is an integer. - if not _math.isclose(qm_charge, round(qm_charge), abs_tol=tol): - raise Exception(f"Charge of the QM region ({qm_charge}) is not an integer!") + if _math.isclose(qm_charge, round(qm_charge), abs_tol=tol): + return + else: + if redistribute_charge: + # Find the residues containing the QM atoms. + residues = qm_atoms.residues() + + # Work out the fractional excess charge to the nearest integer. + excess_charge = (round(qm_charge) - qm_charge) * _e_charge + + # Redistribute the charge over the QM atoms. + qm_frac = excess_charge / len(qm_atoms) + + # Redistribute the charge over the non QM atoms. + rem_frac = excess_charge / (residues.num_atoms() - len(qm_atoms)) + + # Loop over the residues. + for res in residues: + # Get the molecule from the system. + mol = mols[res.molecule()] + + # Create a cursor for the molecule. + cursor = mol.cursor() + + # Loop over the atoms in the residue. + for atom in res: + # Shift the charge. + if atom in qm_atoms: + cursor[atom][charge_prop] -= qm_frac + else: + cursor[atom][charge_prop] += rem_frac + + # Commit the changes. + mol = cursor.commit() + + # Update the molecule in the system. + mols.update(mol) + + else: + raise Exception(f"Charge of the QM region ({qm_charge}) is not an integer!") def _create_qm_mol_to_atoms(qm_atoms): diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index ad4d0865c..a313b6273 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -103,6 +103,51 @@ def test_link_atoms(ala_mols, selection, expected): assert bond_scale_factors == expected[2] +def test_charge_redistribution(): + """ + Make sure that charge redistribution works correctly. + """ + + import sire as sr + + from sire.base import create_map + from sire.qm._utils import _check_charge + from sire.mol import selection_to_atoms + + # A selection for the QM region. This is a subset of a TRP residue. + selection = "residx 118 and not atomname CA, C, HA, O, H" + + # The inverse selection. + not_selection = f"not ({selection})" + + # Load the AbyU test system. + mols = sr.load_test_files("abyu.prm7", "abyu.rst7") + + # Selet the QM atoms. + qm_atoms = selection_to_atoms(mols, selection) + + # Get the charges of both regions. + charge0 = mols[selection].charge() + charge1 = mols[not_selection].charge() + + # Check the charges, redistributing to the nearest integer. + _check_charge(mols, qm_atoms, create_map({}), redistribute_charge=True) + + # Get the new charges. + new_charge0 = mols[selection].charge() + new_charge1 = mols[not_selection].charge() + + # Make sure the QM charge has been redistributed to the nearest integer. + assert math.isclose(round(charge0.value()), new_charge0.value(), rel_tol=1e-4) + + # Make sure the remainder has beeen redistributed to the other atoms. + assert math.isclose((charge0 + charge1).value(), new_charge1.value(), rel_tol=1e-4) + + # Make sure the check fails if we don't redistribute the charge. + with pytest.raises(Exception): + _check_charge(mols, qm_atoms, create_map({}), redistribute_charge=False) + + @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") @pytest.mark.parametrize("selection", ["molidx 0", "resname ALA"]) def test_interpolate(ala_mols, selection): From 99eb489dd2dd9da1099150a5cde25b716621e399 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 16:18:22 +0100 Subject: [PATCH 277/468] Formatting tweak. --- wrapper/Convert/SireOpenMM/emle.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/emle.cpp index 0169dea4d..6c1cc75c8 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/emle.cpp @@ -676,7 +676,7 @@ double EMLEForceImpl::computeForce( // virtual point charges. const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; - // Loop over the MM2 atoms and perform charge shifting. Here the MM1 + // Loop over the MM2 atoms and perform charge shifting. Here the MM1 // charge is redistributed over the MM2 atoms and two virtual point // charges are added either side of the MM2 atoms in order to preserve // the MM1-MM2 dipole. From 3160719cd65aa4e80d10c18504802b83215f02f3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 26 Apr 2024 16:40:19 +0100 Subject: [PATCH 278/468] Use np.isclose to avoid precision overflow. --- src/sire/qm/_utils.py | 4 +++- tests/qm/test_emle.py | 16 +++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 4872190ff..33ccb87bd 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -85,7 +85,9 @@ def _check_charge(mols, qm_atoms, map, redistribute_charge=False, tol=1e-6): mols.update(mol) else: - raise Exception(f"Charge of the QM region ({qm_charge}) is not an integer!") + raise Exception( + f"Charge of the QM region ({qm_charge:.5f}) is not an integer!" + ) def _create_qm_mol_to_atoms(qm_atoms): diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index a313b6273..41773d5a3 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -1,4 +1,4 @@ -import math +import numpy as np import pytest import tempfile @@ -115,7 +115,7 @@ def test_charge_redistribution(): from sire.mol import selection_to_atoms # A selection for the QM region. This is a subset of a TRP residue. - selection = "residx 118 and not atomname CA, C, HA, O, H" + selection = "residx 118 and not atomname C, CA, H, HA, N, O" # The inverse selection. not_selection = f"not ({selection})" @@ -138,10 +138,10 @@ def test_charge_redistribution(): new_charge1 = mols[not_selection].charge() # Make sure the QM charge has been redistributed to the nearest integer. - assert math.isclose(round(charge0.value()), new_charge0.value(), rel_tol=1e-4) + assert np.isclose(round(charge0.value()), new_charge0.value(), rtol=1e-4) # Make sure the remainder has beeen redistributed to the other atoms. - assert math.isclose((charge0 + charge1).value(), new_charge1.value(), rel_tol=1e-4) + assert np.isclose((charge0 + charge1).value(), new_charge1.value(), rtol=1e-4) # Make sure the check fails if we don't redistribute the charge. with pytest.raises(Exception): @@ -183,16 +183,14 @@ def test_interpolate(ala_mols, selection): nrg_mm_interp = d.current_potential_energy() # Make sure this agrees with the standard MM energy. - assert math.isclose(nrg_mm_interp.value(), nrg_mm.value(), rel_tol=1e-4) + assert np.isclose(nrg_mm_interp.value(), nrg_mm.value(), rtol=1e-4) # Now get the interpolated energy at lambda = 0.5. d.set_lambda(0.5) nrg_interp = d.current_potential_energy() # Make sure the interpolated energy is correct. - assert math.isclose( - nrg_interp.value(), 0.5 * (nrg_mm + nrg_emle).value(), rel_tol=1e-4 - ) + assert np.isclose(nrg_interp.value(), 0.5 * (nrg_mm + nrg_emle).value(), rtol=1e-4) @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") @@ -295,4 +293,4 @@ def test_openmm_ml(ala_mols): ) # Make sure the energies are close. - assert math.isclose(nrg_openmm, nrg_sire, rel_tol=1e-3) + assert np.isclose(nrg_openmm, nrg_sire, rtol=1e-3) From 92ac9691e503f2f62798b4969bde7c281f28dd92 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 29 Apr 2024 09:43:55 +0100 Subject: [PATCH 279/468] Try removing GROMACS. --- requirements_bss.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index 98a166778..71f06244e 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -12,7 +12,7 @@ openmmtools >= 0.21.5 # Both ambertools and gromacs aren't available on Windows ambertools >= 22 ; sys_platform != "win32" -gromacs ; sys_platform != "win32" +#gromacs ; sys_platform != "win32" # kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools From 12a853817e5415d830dfa5334e3e50f8d0981605 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 30 Apr 2024 10:40:05 +0100 Subject: [PATCH 280/468] Ignore BioSimSpace format position restraint include directives. [closes #194] --- corelib/src/libs/SireIO/grotop.cpp | 6 ++++++ doc/source/changelog.rst | 3 +++ tests/io/test_grotop.py | 6 ++++++ 3 files changed, 15 insertions(+) diff --git a/corelib/src/libs/SireIO/grotop.cpp b/corelib/src/libs/SireIO/grotop.cpp index 5446c47bc..43c169a15 100644 --- a/corelib/src/libs/SireIO/grotop.cpp +++ b/corelib/src/libs/SireIO/grotop.cpp @@ -5399,6 +5399,12 @@ QVector GroTop::preprocess(const QVector &lines, QHash`__. standard trajectory save functions, e.g. ``sire.save(mols.trajectory(), "output", format=["PRMTOP", "RST"])``. +* Ignore BioSimSpace format position restraint include directives when + parsing GROMACS topology files. + * Please add an item to this changelog when you create your PR `2024.1.0 `__ - April 2024 diff --git a/tests/io/test_grotop.py b/tests/io/test_grotop.py index 1d4c47d28..5a23a87e4 100644 --- a/tests/io/test_grotop.py +++ b/tests/io/test_grotop.py @@ -33,3 +33,9 @@ def test_grospace(tmpdir, kigaki_mols): mols = sr.load(f, show_warnings=False) assert energy.value() == pytest.approx(mols.energy().value()) + + +def test_posre(): + # Make sure we can parse a file with BioSimSpace position restraint include + # directives. + mols = sr.load_test_files("posre.top") From 0ea9bf63132d9afc2d6e0b041a01cdc5b5b17f99 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 1 May 2024 10:16:58 +0100 Subject: [PATCH 281/468] Only exclude GROMACS on Windows and macOS arm64. --- requirements_bss.txt | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index 71f06244e..81fd6fe82 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -10,9 +10,10 @@ openmmtools >= 0.21.5 -# Both ambertools and gromacs aren't available on Windows +# Both ambertools and gromacs aren't available on Windows. +# The arm64 gromacs package is current broken. ambertools >= 22 ; sys_platform != "win32" -#gromacs ; sys_platform != "win32" +gromacs ; sys_platform != "win32" and platform_machine != "arm64" # kartograf on Windows pulls in an openfe that has an old / incompatble # ambertools From 0a4ab08ac60315d3cdc3fb713cbb25d5276b5a1c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 1 May 2024 11:20:08 +0100 Subject: [PATCH 282/468] Update format of lambda interpolation energy trajectory. --- doc/source/tutorial/partXX/01_emle.rst | 46 +++++------ doc/source/tutorial/partXX/sire_emle.ipynb | 2 +- src/sire/mol/_dynamics.py | 95 +++++++++------------- 3 files changed, 64 insertions(+), 79 deletions(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index ed0d04ffc..b5505805f 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -126,33 +126,33 @@ at which the λ value is updated. Once the simulation has finished we can get back the trajectory of energy values. This can be obtained as a `pandas `_ ``DataFrame``, allowing for easy plotting and analysis. The table below shows the instantaneous -kintetic and potential energies as a function of λ, along with the pure MM and -QM potential energies. (Times are in picoseconds and energies are in kcal/mol.) +kinetic and potential energies as a function of λ, along with the accumulated +non-equilibrium work. (Times are in picoseconds and energies are in kcal/mol.) >>> nrg_traj = d.energy_trajectory(to_pandas=True) >>> print(nrg_traj) - lambda KE PE(lambda) PE(lambda=0) PE(lambda=1) + lambda kinetic potential work time -6000.05 0.000000 980.181564 -6954.938694 -6954.938694 -318014.135823 -6000.10 0.052632 871.904630 -23214.139963 -6843.385099 -317910.734657 -6000.15 0.105263 1074.693130 -39796.029943 -7056.370765 -318111.343285 -6000.20 0.157895 979.813677 -56061.595767 -6952.183998 -318008.475588 -6000.25 0.210526 1009.571276 -72462.277097 -6981.451657 -318040.986409 -6000.30 0.263158 1016.026458 -88842.745858 -6991.337337 -318046.238677 -6000.35 0.315789 1003.273813 -105199.347795 -6976.690749 -318031.016925 -6000.40 0.368421 1021.295211 -121583.564572 -6991.838146 -318041.438719 -6000.45 0.421053 1027.366329 -137961.602333 -7000.530076 -318049.949920 -6000.50 0.473684 1049.387973 -154355.318394 -7023.254018 -318072.387286 -6000.55 0.526316 1040.626785 -170718.777695 -7016.367279 -318066.329145 -6000.60 0.578947 1047.005579 -187097.460730 -7015.987089 -318076.072803 -6000.65 0.631579 1030.218148 -203453.572350 -6997.132190 -318063.875864 -6000.70 0.684211 1022.362023 -219819.959312 -6994.205184 -318058.533453 -6000.75 0.736842 1044.950320 -236216.451165 -7012.311296 -318084.096807 -6000.80 0.789474 1024.087813 -252561.720268 -6985.090189 -318055.746705 -6000.85 0.842105 1056.241205 -268962.249393 -7016.702075 -318082.555659 -6000.90 0.894737 1053.591066 -285328.646842 -7013.509852 -318075.626766 -6000.95 0.947368 1033.013716 -301672.026582 -6986.164439 -318045.397622 -6001.00 1.000000 1045.687318 -318056.550581 -6991.865785 -318056.550599 +6000.05 0.000000 1004.360323 -6929.923522 0.000000 +6000.10 0.052632 907.430686 -23199.383591 -856.287372 +6000.15 0.105263 1103.734847 -39773.815961 -1728.625918 +6000.20 0.157895 982.097859 -56012.557224 -2583.296511 +6000.25 0.210526 1035.727824 -72437.484783 -3447.766382 +6000.30 0.263158 1029.009153 -88803.629979 -4309.142445 +6000.35 0.315789 1014.269847 -105159.643486 -5169.985261 +6000.40 0.368421 1021.246476 -121532.624612 -6031.721110 +6000.45 0.421053 1022.233858 -137904.993921 -6893.424758 +6000.50 0.473684 1025.310039 -154284.677129 -7755.513348 +6000.55 0.526316 1025.001630 -170655.548776 -8617.138171 +6000.60 0.578947 1016.891585 -187011.341345 -9477.969359 +6000.65 0.631579 1022.910901 -203389.408932 -10339.972916 +6000.70 0.684211 1024.431575 -219765.627241 -11201.879143 +6000.75 0.736842 1052.484710 -236168.647435 -12065.195995 +6000.80 0.789474 1032.732604 -252520.971205 -12925.844615 +6000.85 0.842105 1061.216013 -268919.903129 -13788.946295 +6000.90 0.894737 1062.979311 -285305.108112 -14651.325505 +6000.95 0.947368 1057.025646 -301673.184597 -15512.803215 +6001.00 1.000000 1024.034371 -318006.345331 -16372.443253 .. note:: diff --git a/doc/source/tutorial/partXX/sire_emle.ipynb b/doc/source/tutorial/partXX/sire_emle.ipynb index cb81ba340..4f31e074c 100644 --- a/doc/source/tutorial/partXX/sire_emle.ipynb +++ b/doc/source/tutorial/partXX/sire_emle.ipynb @@ -156,7 +156,7 @@ "id": "47c807f2-6f9b-4b0d-88c2-3ff11e458c10", "metadata": {}, "source": [ - "Once the simulation has finished we can get back the trajectory of energy values. This can be obtained as a [pandas](https://pandas.pydata.org/) `DataFrame`, allowing for easy plotting and analysis. The table below shows the instantaneous kintetic and potential energies as a function of λ, along with the pure MM and QM potential energies. (Times are in picoseconds and energies are in kcal/mol.)" + "Once the simulation has finished we can get back the trajectory of energy values. This can be obtained as a [pandas](https://pandas.pydata.org/) `DataFrame`, allowing for easy plotting and analysis. The table below shows the instantaneous kinetic and potential energies as a function of λ, along with the accumulated non-equilibrium work. (Times are in picoseconds and energies are in kcal/mol.)" ] }, { diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 8c2c43d91..24597dc49 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -75,33 +75,6 @@ def __init__(self, mols=None, map=None, **kwargs): "region is not recommended." ) - # see if this is an interpolation simulation - if map.specified("lambda_interpolate"): - if map["lambda_interpolate"].has_value(): - lambda_interpolate = map["lambda_interpolate"].value() - else: - lambda_interpolate = map["lambda_interpolate"].source() - - # Single lambda value. - try: - lambda_interpolate = float(lambda_interpolate) - map.set("lambda_value", lambda_interpolate) - # Two lambda values. - except: - try: - if not len(lambda_interpolate) == 2: - raise - lambda_interpolate = [float(x) for x in lambda_interpolate] - map.set("lambda_value", lambda_interpolate[0]) - except: - raise ValueError( - "'lambda_interpolate' must be a float or a list of two floats" - ) - self._is_interpolate = True - self._lambda_interpolate = lambda_interpolate - else: - self._is_interpolate = False - if map.specified("cutoff"): cutoff = map["cutoff"] @@ -135,6 +108,39 @@ def __init__(self, mols=None, map=None, **kwargs): self._sire_mols._system.add(mols.molecules().to_molecule_group()) self._sire_mols._system.set_property("space", self._ffinfo.space()) + # see if this is an interpolation simulation + if map.specified("lambda_interpolate"): + if map["lambda_interpolate"].has_value(): + lambda_interpolate = map["lambda_interpolate"].value() + else: + lambda_interpolate = map["lambda_interpolate"].source() + + # Single lambda value. + try: + lambda_interpolate = float(lambda_interpolate) + map.set("lambda_value", lambda_interpolate) + # Two lambda values. + except: + try: + if not len(lambda_interpolate) == 2: + raise + lambda_interpolate = [float(x) for x in lambda_interpolate] + map.set("lambda_value", lambda_interpolate[0]) + except: + raise ValueError( + "'lambda_interpolate' must be a float or a list of two floats" + ) + + from ..units import kcal_per_mol + + self._is_interpolate = True + self._lambda_interpolate = lambda_interpolate + self._work = 0*kcal_per_mol + self._nrg_prev = 0*kcal_per_mol + + else: + self._is_interpolate = False + # find the existing energy trajectory - we will build on this self._energy_trajectory = self._sire_mols.energy_trajectory( to_pandas=False, map=self._map @@ -294,12 +300,7 @@ def _exit_dynamics_block( # should save energy here nrgs = {} - if self._is_interpolate: - ke = "KE" - else: - ke = "kinetic" - - nrgs[ke] = ( + nrgs["kinetic"] = ( self._omm_state.getKineticEnergy().value_in_unit( openmm.unit.kilocalorie_per_mole ) @@ -315,30 +316,14 @@ def _exit_dynamics_block( sim_lambda_value = self._omm_mols.get_lambda() + # Store the potential energy and accumulated non-equilibrium work. if self._is_interpolate: - nrgs["PE(lambda)"] = nrgs["potential"] - nrgs.pop("potential") - if sim_lambda_value != 0.0: - self._omm_mols.set_lambda(0.0) - nrgs["PE(lambda=0)"] = ( - self._omm_mols.get_potential_energy( - to_sire_units=False - ).value_in_unit(openmm.unit.kilocalorie_per_mole) - * kcal_per_mol - ) - else: - nrgs["PE(lambda=0)"] = nrgs["PE(lambda)"] - if sim_lambda_value != 1.0: - self._omm_mols.set_lambda(1.0) - nrgs["PE(lambda=1)"] = ( - self._omm_mols.get_potential_energy( - to_sire_units=False - ).value_in_unit(openmm.unit.kilocalorie_per_mole) - * kcal_per_mol - ) - else: - nrgs["PE(lambda=1)"] = nrgs["PE(lambda)"] + nrg = nrgs["potential"] + if sim_lambda_value != 0.0: + self._work += delta_lambda*(nrg - self._nrg_prev) + self._nrg_prev = nrg + nrgs["work"] = self._work else: nrgs[str(sim_lambda_value)] = nrgs["potential"] From 1ad5ad8ca289df6970086ddc4bfe74737eb49328 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 1 May 2024 11:29:25 +0100 Subject: [PATCH 283/468] Add note regarding interpolation being non-linear. --- tests/qm/test_emle.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 41773d5a3..98ec82cc6 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -189,7 +189,9 @@ def test_interpolate(ala_mols, selection): d.set_lambda(0.5) nrg_interp = d.current_potential_energy() - # Make sure the interpolated energy is correct. + # Make sure the interpolated energy is correct. Note that the interpolation + # is actually non-linear so the energies are not exactly the average of the + # two states. assert np.isclose(nrg_interp.value(), 0.5 * (nrg_mm + nrg_emle).value(), rtol=1e-4) From b7c1cf540169b3600202bb01f44f475b49d56606 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 2 May 2024 06:42:34 +0100 Subject: [PATCH 284/468] Sire will add missing bonded terms will correct nulls. --- src/sire/qm/_utils.py | 59 +++++++++++++------------------------------ 1 file changed, 18 insertions(+), 41 deletions(-) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 33ccb87bd..ca440aa56 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -466,7 +466,6 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): A list of merged molecules. """ - from ..legacy import CAS as _CAS from ..legacy import Mol as _Mol from ..legacy import MM as _MM from ..morph import link_to_reference as _link_to_reference @@ -517,11 +516,8 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): atom0 = info.atom_idx(bond.atom0()) atom1 = info.atom_idx(bond.atom1()) - if atom0 in qm_idxs and atom1 in qm_idxs: - r = _CAS.Symbol("r") - amber_bond = _MM.AmberBond(0, r) - bonds.set(atom0, atom1, amber_bond.to_expression(r)) - else: + # This bond doesn't only involve QM atoms. + if atom0 not in qm_idxs or atom1 not in qm_idxs: bonds.set(atom0, atom1, bond.function()) edit_mol = edit_mol.set_property(prop + "1", bonds).molecule() @@ -540,13 +536,12 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): atom1 = info.atom_idx(angle.atom1()) atom2 = info.atom_idx(angle.atom2()) - if atom0 in qm_idxs and atom1 in qm_idxs and atom2 in qm_idxs: - theta = _CAS.Symbol("theta") - amber_angle = _MM.AmberAngle(0.0, theta) - angles.set( - atom0, atom1, atom2, amber_angle.to_expression(theta) - ) - else: + # This angle doesn't only involve QM atoms. + if ( + atom0 not in qm_idxs + or atom1 not in qm_idxs + or atom2 not in qm_idxs + ): angles.set(atom0, atom1, atom2, angle.function()) edit_mol = edit_mol.set_property(prop + "1", angles).molecule() @@ -566,22 +561,13 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): atom2 = info.atom_idx(dihedral.atom2()) atom3 = info.atom_idx(dihedral.atom3()) + # This dihedral doesn't only involve QM atoms. if ( - atom0 in qm_idxs - and atom1 in qm_idxs - and atom2 in qm_idxs - and atom3 in qm_idxs + atom0 not in qm_idxs + or atom1 not in qm_idxs + or atom2 not in qm_idxs + or atom3 not in qm_idxs ): - phi = _CAS.Symbol("phi") - amber_dihedral = _MM.AmberDihedral(0, phi) - dihedrals.set( - atom0, - atom1, - atom2, - atom3, - amber_dihedral.to_expression(phi), - ) - else: dihedrals.set(atom0, atom1, atom2, atom3, dihedral.function()) edit_mol = edit_mol.set_property(prop + "1", dihedrals).molecule() @@ -601,22 +587,13 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): atom2 = info.atom_idx(improper.atom2()) atom3 = info.atom_idx(improper.atom3()) + # This improper doesn't only involve QM atoms. if ( - atom0 in qm_idxs - and atom1 in qm_idxs - and atom2 in qm_idxs - and atom3 in qm_idxs + atom0 not in qm_idxs + or atom1 not in qm_idxs + or atom2 not in qm_idxs + or atom3 not in qm_idxs ): - psi = _CAS.Symbol("psi") - amber_improper = _MM.AmberDihedral(0, psi) - impropers.set( - atom0, - atom1, - atom2, - atom3, - amber_improper.to_expression(psi), - ) - else: impropers.set(atom0, atom1, atom2, atom3, improper.function()) edit_mol = edit_mol.set_property(prop + "1", impropers).molecule() From a4af636c56aa19e7b25fe234cacbcfc2a3df021e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 2 May 2024 11:29:08 +0100 Subject: [PATCH 285/468] Add function to zero the charge on the QM region. --- src/sire/qm/__init__.py | 1 + src/sire/qm/_utils.py | 68 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index a677d3e0a..527ee003d 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -1,3 +1,4 @@ __all__ = ["emle"] from ._emle import emle +from ._utils import _zero_charge as zero_charge diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index ca440aa56..1e3043724 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -1,3 +1,71 @@ +def _zero_charge(mols, qm_atoms, map=None): + """ + Zero the charge for the QM atoms in the system. + + Parameters + ---------- + + mols : sire.system.System + The molecular system. + + qm_atoms : str, int, list, molecule view/collection etc. + Any valid search string, atom index, list of atom indicies, + or molecule view/container that can be used to select + qm_atoms from 'mols'. + + Returns + ------- + + mols : sire.system.System + The molecular system with the QM atom charges zeroed. + """ + + from ..base import create_map as _create_map + from ..mol import selection_to_atoms as _selection_to_atoms + from ..morph import extract_reference as _extract_reference + from ..units import e_charge as _e_charge + + # Clone the molecules. + mols = mols.clone() + + # Try to extract the reference state. + try: + mols = _extract_reference(mols) + # This is a regular molecule, so pass. + except: + pass + + try: + qm_atoms = _selection_to_atoms(mols, qm_atoms) + except: + raise ValueError("Unable to select 'qm_atoms' from 'mols'") + + if map is not None: + if not isinstance(map, dict): + raise TypeError("'map' must be of type 'dict'") + map = _create_map(map) + + # Create a dictionary mapping molecular numbers to QM atoms. + qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) + + # Get the charge property. + charge_prop = map["charge"].source() + + # Loop over the molecules. + for mol_num, qm_atoms in qm_mol_to_atoms.items(): + # Create a cursor for the molecule. + cursor = mols[mol_num].cursor() + + # Zero the charges for the QM atoms. + for atom in qm_atoms: + cursor[atom][charge_prop] = 0.0 * _e_charge + + # Commit the changes. + mols.update(cursor.commit()) + + return mols + + def _check_charge(mols, qm_atoms, map, redistribute_charge=False, tol=1e-6): """ Internal helper function to check that the QM region has integer charge. From ddbd389ef4b5b42e0ba867718ce0634c301e7242 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 2 May 2024 11:34:07 +0100 Subject: [PATCH 286/468] Update documentation and test with new sr.qm.zero_charge function. --- doc/source/tutorial/partXX/01_emle.rst | 8 +++----- doc/source/tutorial/partXX/sire_emle.ipynb | 6 ++---- tests/qm/test_emle.py | 5 ++--- 3 files changed, 7 insertions(+), 12 deletions(-) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index b5505805f..230938dbf 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -214,12 +214,10 @@ this is set to 1, but can be set to any value between 0 and 1.) Since we want to use electrostatic embedding, we will also need to zero the charges on the atoms within the QM region before creating an ``OpenMM`` system. If not, then we would also calculate the mechanical embedding interaction. This can be -done using the ``qm_mols`` object generated above. This system is *perturbable* -so can be converted between an MM reference state and QM perturbed state. Here -we require the perturbed state, which has zeroed charges for the QM region: +done by passing the molecules through the ``sr.qm.zero_charge`` function along with +the selection for the QM region: ->>> qm_mol = sr.morph.link_to_perturbed(qm_mols[0]) ->>> qm_mols.update(qm_mol) +>>> qm_mols = sr.qm.zero_charge(qm_mols, qm_mols[0]) We now write the modified system to an AMBER format topology and coordinate file so that we can load them with ``OpenMM``: diff --git a/doc/source/tutorial/partXX/sire_emle.ipynb b/doc/source/tutorial/partXX/sire_emle.ipynb index 4f31e074c..596c0addd 100644 --- a/doc/source/tutorial/partXX/sire_emle.ipynb +++ b/doc/source/tutorial/partXX/sire_emle.ipynb @@ -264,7 +264,7 @@ "⚠️ The interpolation_force has no energy contribution. It is only required as there is currently no way to add global parameters to the EMLEForce.\n", "\n", "\n", - "Since we want to use electrostatic embedding, we will also need to zero the charges on the atoms within the QM region before creating an `OpenMM` system. If not, then we would also calculate the mechanical embedding interaction. This can be done using the `qm_mols` object generated above. This system is *perturbable* so can be converted between an MM reference state and QM perturbed state. Here we require the perturbed state, which has zeroed charges for the QM region:" + "Since we want to use electrostatic embedding, we will also need to zero the charges on the atoms within the QM region before creating an `OpenMM` system. This can be done by passing the molecules through the ``sr.qm.zero_charge`` function along with the selection for the QM region:" ] }, { @@ -274,9 +274,7 @@ "metadata": {}, "outputs": [], "source": [ - "qm_mol = sr.morph.link_to_perturbed(qm_mols[0])\n", - "qm_mols.update(qm_mol)\n", - "qm_mol.property(\"charge\")" + "qm_mols = sr.qm.zero_charge(qm_mols, qm_mols[0])" ] }, { diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 98ec82cc6..6205bb8b0 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -240,13 +240,12 @@ def test_openmm_ml(ala_mols): # zeroed charges for the QM region. This means that the entire # intermolecular electrostatic interaction will be computed by # EMLE, rather than using the MM charges for mechanical embedding. - qm_mol = sr.morph.link_to_perturbed(emle_mols[0]) - emle_mols.update(qm_mol) + omm_mols = sr.qm.zero_charge(mols, mols[0]) # Write the sytem to an AMBER coordinate and topology file. files = sr.expand(tmpdir, ["ala.rst7", "ala.prm7"]) for file in files: - sr.save(emle_mols, file) + sr.save(omm_mols, file) # Load back the files and create an OpenMM topology. inpcrd = openmm.app.AmberInpcrdFile(f"{tmpdir}/ala.rst7") From 71c07f111b462c439de4e28d1761c57407a1eb04 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 3 May 2024 12:05:02 +0100 Subject: [PATCH 287/468] Add note regarding non-linearity of energy interpolation. --- doc/source/tutorial/partXX/01_emle.rst | 10 ++++++++++ doc/source/tutorial/partXX/sire_emle.ipynb | 14 ++++++++++++++ 2 files changed, 24 insertions(+) diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/01_emle.rst index 230938dbf..da5763778 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/01_emle.rst @@ -159,6 +159,16 @@ time In the table above, the time doesn't start from zero because the example molecular system was loaded from an existing trajectory restart file. +.. note:: + + Unlike the ``sander`` interface of ``emle-engine``, the interpolated potential + energy is non-linear with respect to λ, i.e. it is not precisely a linear + combination of MM and QM energies. This is because the ``sire`` interface + performs a *perturbation* of the system parameters from MM to QM as λ is + changed, e.g. scaling down the force constants for bonded terms in the QM + region and scaling down the charges. Perturbing charges linearly results in + an energy change *between* charges that is quadratic in λ. + Interfacing with OpenMM-ML -------------------------- diff --git a/doc/source/tutorial/partXX/sire_emle.ipynb b/doc/source/tutorial/partXX/sire_emle.ipynb index 596c0addd..c5795a00b 100644 --- a/doc/source/tutorial/partXX/sire_emle.ipynb +++ b/doc/source/tutorial/partXX/sire_emle.ipynb @@ -169,6 +169,20 @@ "d.energy_trajectory(to_pandas=True)" ] }, + { + "cell_type": "markdown", + "id": "ae5d0547-e6f5-424c-ba56-193b6ad34bd7", + "metadata": {}, + "source": [ + "
    \n", + "⚠️ In the table above, the time doesn't start from zero because the example molecular system was loaded from an existing trajectory restart file.\n", + "
    \n", + "\n", + "
    \n", + "⚠️ Unlike the sander interface of emle-engine, the interpolated potential energy is non-linear with respect to λ, i.e. it is not precisely a linear combination of MM and QM energies. This is because the sire interface performs a *perturbation* of the system parameters from MM to QM as λ is changed, e.g. scaling down the force constants for bonded terms in the QM region and scaling down the charges. Perturbing charges linearly results in an energy change between charges that is quadratic in λ.\n", + "
    " + ] + }, { "cell_type": "markdown", "id": "ccfa5f0c-5f41-4353-88c4-b4784ccba1f3", From a0c88a1312283f9453507c65f83a34812246b271 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 3 May 2024 14:40:21 +0100 Subject: [PATCH 288/468] Rename ADP PMF plot. --- doc/source/tutorial/partXX/02_adp_pmf.rst | 4 ++-- .../tutorial/partXX/images/{pmf.png => pmf_adp.png} | Bin 2 files changed, 2 insertions(+), 2 deletions(-) rename doc/source/tutorial/partXX/images/{pmf.png => pmf_adp.png} (100%) diff --git a/doc/source/tutorial/partXX/02_adp_pmf.rst b/doc/source/tutorial/partXX/02_adp_pmf.rst index 9fec41c78..807ba46d0 100644 --- a/doc/source/tutorial/partXX/02_adp_pmf.rst +++ b/doc/source/tutorial/partXX/02_adp_pmf.rst @@ -175,6 +175,6 @@ is provided in the `FastMBAR tutorial Date: Fri, 3 May 2024 15:39:34 +0100 Subject: [PATCH 289/468] Update AbyU tutorial with results. --- doc/source/tutorial/partXX/03_diels_alder.rst | 70 +++++++++++++----- .../tutorial/partXX/images/pmf_abyu.png | Bin 0 -> 458496 bytes 2 files changed, 50 insertions(+), 20 deletions(-) create mode 100644 doc/source/tutorial/partXX/images/pmf_abyu.png diff --git a/doc/source/tutorial/partXX/03_diels_alder.rst b/doc/source/tutorial/partXX/03_diels_alder.rst index 8c1822a78..ae22af5bf 100644 --- a/doc/source/tutorial/partXX/03_diels_alder.rst +++ b/doc/source/tutorial/partXX/03_diels_alder.rst @@ -79,9 +79,18 @@ interaction and the electrostatic embedding interaction. Here we will use Next we will create an ``EMLEEngine`` that can be be used to perform QM/MM calculation: ->>> qm_mols, engine = sr.qm.emle(mols, mols[1], calculator) +>>> qm_mols, engine = sr.qm.emle( +... mols, + "atomnum 1804:1822,2083:2132", + calculator, + redistribute_charge=True +... ) -Here are specifying that molecule index 1, i.e. the substrate, is the QM region. +Here the selection for the QM region includes tryptophan side-chain atoms +(1804-1822) and the substrate (2083-2132). The ``redistribute_charge`` keyword +ensures that the charge on atoms in the QM region is integer valued by +redistributing the remaining fractional charge over MM atoms within the +residues containing the QM atoms. Creating a context ------------------ @@ -134,18 +143,18 @@ equilibrium value: >>> import openmm >>> import openmm.app >>> from openmm import unit as unit ->>> k = (200 * unit.kilocalorie_per_mole / unit.angstrom**2).value_in_unit( +>>> k0 = (200 * unit.kilocalorie_per_mole / unit.angstrom**2).value_in_unit( ... unit.kilojoule_per_mole / unit.nanometer**2 ... ) -... r = 2.9 * unit.angstroms +... r0 = 2.9 * unit.angstroms Next we will create a ``CustomBondForce`` to calculate the distance between the atom pairs: ->>> cv = openmm.CustomBondForce("weight*r") ->>> cv.addPerBondParameter("weight") +>>> cv0 = openmm.CustomBondForce("weight*r") +>>> cv0.addPerBondParameter("weight") >>> for atom1, atom2, weight in pairs: -... cv.addBond(atom1, atom2, [weight]) +... cv0.addBond(atom1, atom2, [weight]) We will also create two null forces to monitor the individual bond distances: @@ -157,16 +166,31 @@ We will also create two null forces to monitor the individual bond distances: We can now create our restraint force using the collective variables above. First let us define the energy expression. This is a simple harmonic potential: ->>> energy_expression = "k*(weighted_distance-r0)^2" +>>> energy_expression0 = "k0*(weighted_distance-r0)^2" Next we will create the force: ->>> restraint_force = openmm.CustomCVForce(energy_expression) ->>> restraint_force.addCollectiveVariable("weighted_distance", cv) ->>> restraint_force.addCollectiveVariable("bond1", bond1) ->>> restraint_force.addCollectiveVariable("bond2", bond2) ->>> restraint_force.addGlobalParameter("k", k) ->>> restraint_force.addGlobalParameter("r0", r) +>>> restraint_force0 = openmm.CustomCVForce(energy_expression0) +>>> restraint_force0.addCollectiveVariable("weighted_distance", cv0) +>>> restraint_force0.addCollectiveVariable("bond1", bond1) +>>> restraint_force0.addCollectiveVariable("bond2", bond2) +>>> restraint_force0.addGlobalParameter("k0", k0) +>>> restraint_force0.addGlobalParameter("r0", r0) + +During simulation we might also wish to prevent the formation of a spurious bond +between atoms 2115 and 2084. We can do this by adding an additional ``CustomCVForce``: + +>>> k1 = (100*unit.kilocalorie_per_mole/unit.angstrom**2).value_in_unit( +... unit.kilojoule_per_mole/unit.nanometer**2 +... ) +... r1 = 3.2*unit.angstroms +... cv1 = CustomBondForce("r") +... cv1..addBond(2115, 2084) +... energy_expression1 =("k1*(dist-r1)^2") +... restraint_force1 = openmm.CustomCVForce(energy_expression1) +... restraint_force1.addCollectiveVariable("dist", cv1) +... restraint_force1.addGlobalParameter("k1", k1) +... restraint_force1.addGlobalParameter("r1", r1) Setting up a new OpenMM context ------------------------------- @@ -179,9 +203,10 @@ system and integrator: >>> system = context.getSystem() >>> integrator = deepcopy(context.getIntegrator()) -Next we will add the restraint force to the system: +Next we will add the restraint forces to the system: ->>> system.addForce(restraint_force) +>>> system.addForce(restraint_force0) +>>> system.addForce(restraint_force1) Finally we will create a new context with the modified system and integrator, setting the platform to the same as the original context: @@ -211,11 +236,16 @@ And now we will run the simulation: ... state = new_context.getState(getPositions=True) ... positions = state.getPositions() ... dcd_file.writeModel(positions) -... cv_vals = restraint_force.getCollectiveVariableValues(new_context) +... cv_vals = restraint_force0.getCollectiveVariableValues(new_context) ... print(f"Step {x:>3} of 100: CVs = {cv_vals[0]:.3f}, {cv_vals[1]:.3f}, {cv_vals[2]:.3f}") ... file_handle.close() -.. note:: +In order to compute the free energy profile of the reaction we would need to +perform umbrella sampling simulations along the reaction coordinate. The resulting +free energy profile should looks similar to the one shown in the left panel of +the figure below. The right panel shows the two bond distances of interest +monitored within each sampling window. - In order to compute the free energy profile of the reaction we would need to - perform umbrella sampling simulations along the reaction coordinate. +.. image:: images/pmf_abyu.png + :target: images/pmf_abyu.png + :alt: Free-energy profile for diels-alder reaction catalysed by AbyU. diff --git a/doc/source/tutorial/partXX/images/pmf_abyu.png b/doc/source/tutorial/partXX/images/pmf_abyu.png new file mode 100644 index 0000000000000000000000000000000000000000..e82117dcdd1a8ea3f6428c1534ebe2d504b25f95 GIT binary patch literal 458496 zcmeFZWmp{Dny`yIfj|frECkm;aEIXTZovrwf;H|QEVx^64em~GcXw~xov%9Y?3vkn zexHA*?h6`L_tjms)>DtK4pER3M@Jz*fr5fUmz4Od1O)|;2L%OVi3tOYWaOL40uQ7{ z5=y|MD)l6I8ZA5DR4$FGF^5K%FG;p(E`q{r5d2|jdC2-<>> zkLg?cHh%NZJUxG8b?dv}+4UHSiAhD?dOmdgjx#;ItUArw#OeW3r3o~|3-rMhMk4e7 zw_j&LN*=n<|1k*sdqRaQf%<=jZQUqr9vC z?GzxN5-bn^mlN=Rh97A@kTU%H2?MX*kSBw-_&?`{>4ozDpYp$E@c-LcZfn!2w{@Ao 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z3!ZZ%_RP}K)H)^>P;&ZzuGHS748L_z2yw$Wz+Yu{O*P1!FgM!noD3^FG)zMtT*X)A z)coO|qxC+ZLzc`xC8HgzOm>R4vAC2?b9S)prcz)hat0;0g5*u5(}MV6W71)2B6w<) zazf^gYvZ0h@vy4GjuL)^i42$EADL26ifh5mid`uE$%J{sOI*Bv%{)83SCnwp?CNb+uM({55w7D+7WGg!{`$M!A>X1X52bg_m|NS`;vnqYe zOXadhW+A$n&hxT);m1gP5=TuH zBld%Vj9e&`8>(r25`2?RAo&hAXJYHvy(#6##q6eI;b3Cehs>!2jZ}bHZ1{b?){8hQ zT+BQB&wrAPKzHU}2lj04rBnL&5V20CI(%;M(hXT)U07W_9rudU#cX#-a2@ynbybi3 zVk2#5ldX;_Hg<8IK%Q*og>QmWr|yWksnofuz{kBY?Ah{ioO6H0$M?k@#`rc#o!y0- z(&t%`Q&*;k>H36?FJ0g5XV8SiG3h)Lrt}iMx-XmSB%2EjrBL*^FOoxncE^Xs*N5|e z?%AE!4Yi+0YDNC!AE~)lCkn;p9;mH-aS-PlfqULR^LQHA@y=e0AU|YGf?o-t0#49O zzOqXbje#G6&w{}Jz8ziWF;V7KnY2|I(~ZZeW!hHw$r5ToFO=7IcYxyGZ$8j- Date: Tue, 21 May 2024 11:50:34 +0100 Subject: [PATCH 290/468] Add map option to fix LJ sigma for ghost atoms. --- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 7062c1451..5ce40d59d 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -559,6 +559,9 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, check_for_h_by_ambertype = map["check_for_h_by_ambertype"].value().asABoolean(); } + // a list to store ghost atom indices + QList ghost_atoms; + if (is_perturbable) { const auto params1_masses = params1.masses(); @@ -638,6 +641,14 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, light_atoms.insert(i); } } + + // check for ghost atoms + const auto charge0 = params.charges().at(cgatomidx); + const auto lj0 = params.ljs().at(cgatomidx); + if (charge0 == 0 and lj0.epsilon().value() == 0) + { + ghost_atoms.append(i); + } } } else @@ -686,6 +697,13 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, this->cljs = QVector>(nats, boost::make_tuple(0.0, 0.0, 0.0)); auto cljs_data = cljs.data(); + // whether the user doesn't want to perturb the LJ sigma for ghost atoms + bool fix_ghost_sigmas = false; + if (map.specified("fix_ghost_sigmas")) + { + fix_ghost_sigmas = map["fix_ghost_sigmas"].value().asABoolean(); + } + for (int i = 0; i < nats; ++i) { const auto &cgatomidx = idx_to_cgatomidx_data[i]; @@ -696,6 +714,13 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, double sig = lj.sigma().to(SireUnits::nanometer); double eps = lj.epsilon().to(SireUnits::kJ_per_mol); + if (fix_ghost_sigmas and ghost_atoms.contains(i)) + { + // use the sigma from the opposite state + const auto &lj1 = params1.ljs().at(idx_to_cgatomidx_data[i]); + sig = lj1.sigma().to(SireUnits::nanometer); + } + if (sig == 0) { // this must be a null parameter From 6a7ba68125a78eee488df1874cb7689859b03c03 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 23 May 2024 15:15:51 +0100 Subject: [PATCH 291/468] Update CHANGELOG. --- doc/source/changelog.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 81afaff8f..610a343d8 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -45,6 +45,9 @@ organisation on `GitHub `__. * Ignore BioSimSpace format position restraint include directives when parsing GROMACS topology files. +* Add a map option to prevent perturbation of the Lennard-Jones sigma + parameter for ghost atoms during alchemical free energy simulations. + * Please add an item to this changelog when you create your PR `2024.1.0 `__ - April 2024 From 5b077138acd2226443436424cb8551fcdd648c9b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 26 May 2024 17:33:20 +0100 Subject: [PATCH 292/468] Changed `isDummy` to check epsilon values only. Changed `fix_ghost_sigmas` into `fix_perturbable_zero_sigmas` and moved the test into PerturbableOpenMMMolecule. Added ability to pass `map` to this constructor so that the option can be passed through to the right place. Most of the diff is because I had to regeneate the wrappers, and so the MM wrappers all got the new copy() functions for their copy and deepcopy functions. --- corelib/src/libs/SireMM/ljparameter.h | 10 +-- .../Convert/SireOpenMM/LambdaLever.pypp.cpp | 15 ++-- .../SireOpenMM/OpenMMMetaData.pypp.cpp | 8 ++- .../PerturbableOpenMMMolecule.pypp.cpp | 24 +++++-- wrapper/Convert/SireOpenMM/lambdalever.cpp | 5 +- wrapper/Convert/SireOpenMM/lambdalever.h | 3 +- wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 69 +++++++++++-------- wrapper/Convert/SireOpenMM/openmmmolecule.h | 5 +- .../SireOpenMM/sire_to_openmm_system.cpp | 3 +- wrapper/MM/AmberAngle.pypp.cpp | 8 ++- wrapper/MM/AmberBond.pypp.cpp | 8 ++- wrapper/MM/AmberDihPart.pypp.cpp | 8 ++- wrapper/MM/AmberDihedral.pypp.cpp | 8 ++- wrapper/MM/AmberNB14.pypp.cpp | 8 ++- wrapper/MM/AmberParams.pypp.cpp | 8 ++- wrapper/MM/Angle.pypp.cpp | 8 ++- wrapper/MM/AngleComponent.pypp.cpp | 8 ++- wrapper/MM/AngleParameterName.pypp.cpp | 8 ++- wrapper/MM/AngleRestraint.pypp.cpp | 8 ++- wrapper/MM/AngleSymbols.pypp.cpp | 8 ++- wrapper/MM/AtomLJs.pypp.cpp | 8 ++- wrapper/MM/BendBendComponent.pypp.cpp | 8 ++- wrapper/MM/BendBendParameterName.pypp.cpp | 8 ++- wrapper/MM/BendBendSymbols.pypp.cpp | 8 ++- wrapper/MM/Bond.pypp.cpp | 8 ++- wrapper/MM/BondComponent.pypp.cpp | 8 ++- wrapper/MM/BondParameterName.pypp.cpp | 8 ++- wrapper/MM/BondRestraint.pypp.cpp | 8 ++- wrapper/MM/BondRestraints.pypp.cpp | 8 ++- wrapper/MM/BondSymbols.pypp.cpp | 8 ++- wrapper/MM/BoreschRestraint.pypp.cpp | 8 ++- wrapper/MM/BoreschRestraints.pypp.cpp | 8 ++- wrapper/MM/CHARMMSwitchingFunction.pypp.cpp | 8 ++- wrapper/MM/CLJ14Group.pypp.cpp | 8 ++- wrapper/MM/CLJAtom.pypp.cpp | 8 ++- wrapper/MM/CLJAtoms.pypp.cpp | 8 ++- wrapper/MM/CLJBox.pypp.cpp | 8 ++- wrapper/MM/CLJBoxDistance.pypp.cpp | 8 ++- wrapper/MM/CLJBoxIndex.pypp.cpp | 8 ++- wrapper/MM/CLJBoxes.pypp.cpp | 8 ++- wrapper/MM/CLJCalculator.pypp.cpp | 8 ++- wrapper/MM/CLJComponent.pypp.cpp | 8 ++- wrapper/MM/CLJDelta.pypp.cpp | 8 ++- wrapper/MM/CLJExtractor.pypp.cpp | 8 ++- wrapper/MM/CLJGrid.pypp.cpp | 8 ++- wrapper/MM/CLJGroup.pypp.cpp | 8 ++- wrapper/MM/CLJIntraRFFunction.pypp.cpp | 8 ++- wrapper/MM/CLJIntraShiftFunction.pypp.cpp | 8 ++- wrapper/MM/CLJNBPairs.pypp.cpp | 10 +-- wrapper/MM/CLJParameterNames.pypp.cpp | 8 ++- wrapper/MM/CLJParameterNames3D.pypp.cpp | 8 ++- wrapper/MM/CLJProbe.pypp.cpp | 8 ++- wrapper/MM/CLJRFFunction.pypp.cpp | 8 ++- wrapper/MM/CLJScaleFactor.pypp.cpp | 8 ++- wrapper/MM/CLJShiftFunction.pypp.cpp | 8 ++- wrapper/MM/CLJSoftIntraRFFunction.pypp.cpp | 8 ++- wrapper/MM/CLJSoftIntraShiftFunction.pypp.cpp | 8 ++- wrapper/MM/CLJSoftRFFunction.pypp.cpp | 8 ++- wrapper/MM/CLJSoftShiftFunction.pypp.cpp | 8 ++- wrapper/MM/CLJWorkspace.pypp.cpp | 8 ++- wrapper/MM/ChargeParameterName.pypp.cpp | 8 ++- wrapper/MM/ChargeParameterName3D.pypp.cpp | 8 ++- wrapper/MM/CoulombComponent.pypp.cpp | 8 ++- wrapper/MM/CoulombNBPairs.pypp.cpp | 8 ++- wrapper/MM/CoulombProbe.pypp.cpp | 8 ++- wrapper/MM/CoulombScaleFactor.pypp.cpp | 8 ++- wrapper/MM/Dihedral.pypp.cpp | 8 ++- wrapper/MM/DihedralComponent.pypp.cpp | 8 ++- wrapper/MM/DihedralParameterName.pypp.cpp | 8 ++- wrapper/MM/DihedralRestraint.pypp.cpp | 8 ++- wrapper/MM/DihedralSymbols.pypp.cpp | 8 ++- wrapper/MM/DistanceRestraint.pypp.cpp | 8 ++- wrapper/MM/DoubleDistanceRestraint.pypp.cpp | 8 ++- wrapper/MM/ExcludedPairs.pypp.cpp | 8 ++- wrapper/MM/FourAtomFunction.pypp.cpp | 8 ++- wrapper/MM/FourAtomFunctions.pypp.cpp | 8 ++- wrapper/MM/FourAtomPerturbation.pypp.cpp | 8 ++- wrapper/MM/GridFF.pypp.cpp | 8 ++- wrapper/MM/GridFF2.pypp.cpp | 8 ++- wrapper/MM/GromacsAngle.pypp.cpp | 8 ++- wrapper/MM/GromacsAtomType.pypp.cpp | 8 ++- wrapper/MM/GromacsBond.pypp.cpp | 8 ++- wrapper/MM/GromacsDihedral.pypp.cpp | 8 ++- wrapper/MM/GroupInternalParameters.pypp.cpp | 8 ++- wrapper/MM/HarmonicSwitchingFunction.pypp.cpp | 8 ++- wrapper/MM/Improper.pypp.cpp | 8 ++- wrapper/MM/ImproperComponent.pypp.cpp | 8 ++- wrapper/MM/ImproperParameterName.pypp.cpp | 8 ++- wrapper/MM/ImproperSymbols.pypp.cpp | 8 ++- wrapper/MM/InterCLJFF.pypp.cpp | 8 ++- wrapper/MM/InterCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/InterCoulombFF.pypp.cpp | 8 ++- wrapper/MM/InterCoulombFFBase.pypp.cpp | 8 ++- wrapper/MM/InterFF.pypp.cpp | 8 ++- wrapper/MM/InterGroupCLJFF.pypp.cpp | 8 ++- wrapper/MM/InterGroupCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/InterGroupCoulombFF.pypp.cpp | 8 ++- wrapper/MM/InterGroupCoulombFFBase.pypp.cpp | 8 ++- wrapper/MM/InterGroupFF.pypp.cpp | 8 ++- wrapper/MM/InterGroupLJFF.pypp.cpp | 8 ++- wrapper/MM/InterGroupLJFFBase.pypp.cpp | 8 ++- wrapper/MM/InterGroupSoftCLJFF.pypp.cpp | 8 ++- wrapper/MM/InterGroupSoftCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/InterLJFF.pypp.cpp | 8 ++- wrapper/MM/InterLJFFBase.pypp.cpp | 8 ++- wrapper/MM/InterSoftCLJFF.pypp.cpp | 8 ++- wrapper/MM/InterSoftCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/InternalComponent.pypp.cpp | 8 ++- wrapper/MM/InternalFF.pypp.cpp | 8 ++- wrapper/MM/InternalGroupFF.pypp.cpp | 8 ++- wrapper/MM/InternalParameterNames.pypp.cpp | 8 ++- wrapper/MM/InternalParameterNames3D.pypp.cpp | 8 ++- wrapper/MM/InternalParameters.pypp.cpp | 8 ++- wrapper/MM/InternalParameters3D.pypp.cpp | 8 ++- wrapper/MM/InternalSymbols.pypp.cpp | 8 ++- wrapper/MM/Intra14Component.pypp.cpp | 8 ++- wrapper/MM/Intra14CoulombComponent.pypp.cpp | 8 ++- wrapper/MM/Intra14LJComponent.pypp.cpp | 8 ++- wrapper/MM/IntraCLJFF.pypp.cpp | 8 ++- wrapper/MM/IntraCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraCoulombFF.pypp.cpp | 8 ++- wrapper/MM/IntraCoulombFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraFF.pypp.cpp | 8 ++- wrapper/MM/IntraGroupCLJFF.pypp.cpp | 8 ++- wrapper/MM/IntraGroupCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraGroupCoulombFF.pypp.cpp | 8 ++- wrapper/MM/IntraGroupCoulombFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraGroupFF.pypp.cpp | 8 ++- wrapper/MM/IntraGroupLJFF.pypp.cpp | 8 ++- wrapper/MM/IntraGroupLJFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraGroupSoftCLJFF.pypp.cpp | 8 ++- wrapper/MM/IntraGroupSoftCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraLJFF.pypp.cpp | 8 ++- wrapper/MM/IntraLJFFBase.pypp.cpp | 8 ++- wrapper/MM/IntraSoftCLJFF.pypp.cpp | 8 ++- wrapper/MM/IntraSoftCLJFFBase.pypp.cpp | 8 ++- wrapper/MM/LJ1264Parameter.pypp.cpp | 8 ++- wrapper/MM/LJComponent.pypp.cpp | 8 ++- wrapper/MM/LJException.pypp.cpp | 8 ++- wrapper/MM/LJExceptionID.pypp.cpp | 8 ++- wrapper/MM/LJNBPairs.pypp.cpp | 8 ++- wrapper/MM/LJParameter.pypp.cpp | 8 ++- wrapper/MM/LJParameterName.pypp.cpp | 8 ++- wrapper/MM/LJParameterName3D.pypp.cpp | 8 ++- wrapper/MM/LJPerturbation.pypp.cpp | 8 ++- wrapper/MM/LJProbe.pypp.cpp | 8 ++- wrapper/MM/LJScaleFactor.pypp.cpp | 8 ++- wrapper/MM/MMDetail.pypp.cpp | 8 ++- wrapper/MM/Mover_Angle_.pypp.cpp | 8 ++- wrapper/MM/Mover_Bond_.pypp.cpp | 8 ++- wrapper/MM/Mover_Dihedral_.pypp.cpp | 8 ++- wrapper/MM/Mover_Improper_.pypp.cpp | 8 ++- wrapper/MM/Mover_SelectorAngle_.pypp.cpp | 8 ++- wrapper/MM/Mover_SelectorBond_.pypp.cpp | 8 ++- wrapper/MM/Mover_SelectorDihedral_.pypp.cpp | 8 ++- wrapper/MM/Mover_SelectorImproper_.pypp.cpp | 8 ++- wrapper/MM/MultiCLJComponent.pypp.cpp | 8 ++- wrapper/MM/NoCutoff.pypp.cpp | 8 ++- wrapper/MM/NullCLJFunction.pypp.cpp | 8 ++- wrapper/MM/NullRestraint.pypp.cpp | 8 ++- wrapper/MM/PositionalRestraint.pypp.cpp | 8 ++- wrapper/MM/PositionalRestraints.pypp.cpp | 8 ++- wrapper/MM/RestraintComponent.pypp.cpp | 8 ++- wrapper/MM/RestraintFF.pypp.cpp | 8 ++- wrapper/MM/ScaledCLJParameterNames3D.pypp.cpp | 8 ++- .../MM/ScaledChargeParameterNames3D.pypp.cpp | 8 ++- wrapper/MM/ScaledLJParameterNames3D.pypp.cpp | 8 ++- wrapper/MM/SelectorAngle.pypp.cpp | 8 ++- wrapper/MM/SelectorBond.pypp.cpp | 8 ++- wrapper/MM/SelectorDihedral.pypp.cpp | 8 ++- wrapper/MM/SelectorImproper.pypp.cpp | 8 ++- wrapper/MM/SelectorMAngle.pypp.cpp | 8 ++- wrapper/MM/SelectorMBond.pypp.cpp | 8 ++- wrapper/MM/SelectorMDihedral.pypp.cpp | 8 ++- wrapper/MM/SelectorMImproper.pypp.cpp | 8 ++- wrapper/MM/SoftCLJComponent.pypp.cpp | 8 ++- wrapper/MM/StretchBendComponent.pypp.cpp | 8 ++- wrapper/MM/StretchBendParameterName.pypp.cpp | 8 ++- wrapper/MM/StretchBendSymbols.pypp.cpp | 8 ++- .../MM/StretchBendTorsionComponent.pypp.cpp | 8 ++- .../StretchBendTorsionParameterName.pypp.cpp | 8 ++- wrapper/MM/StretchBendTorsionSymbols.pypp.cpp | 8 ++- wrapper/MM/StretchStretchComponent.pypp.cpp | 8 ++- .../MM/StretchStretchParameterName.pypp.cpp | 8 ++- wrapper/MM/StretchStretchSymbols.pypp.cpp | 8 ++- wrapper/MM/TestFF.pypp.cpp | 8 ++- wrapper/MM/ThreeAtomFunction.pypp.cpp | 8 ++- wrapper/MM/ThreeAtomFunctions.pypp.cpp | 8 ++- wrapper/MM/ThreeAtomPerturbation.pypp.cpp | 8 ++- wrapper/MM/TripleDistanceRestraint.pypp.cpp | 8 ++- wrapper/MM/TwoAtomFunction.pypp.cpp | 8 ++- wrapper/MM/TwoAtomFunctions.pypp.cpp | 8 ++- wrapper/MM/TwoAtomPerturbation.pypp.cpp | 8 ++- wrapper/MM/UreyBradleyComponent.pypp.cpp | 8 ++- wrapper/MM/UreyBradleyParameterName.pypp.cpp | 8 ++- 195 files changed, 1021 insertions(+), 611 deletions(-) diff --git a/corelib/src/libs/SireMM/ljparameter.h b/corelib/src/libs/SireMM/ljparameter.h index dc13a0e19..ee30661a4 100644 --- a/corelib/src/libs/SireMM/ljparameter.h +++ b/corelib/src/libs/SireMM/ljparameter.h @@ -141,12 +141,14 @@ namespace SireMM return not operator==(other); } - /** Return whether or not this is a dummy LJ parameter */ + /** Return whether or not this is a dummy LJ parameter. A dummy LJ + * parameter is one with a zero epsilon value (i.e. it will have a + * a zero LJ interaction energy with all other particles, regardless + * of their LJ parameters) + */ SIRE_ALWAYS_INLINE bool LJParameter::isDummy() const { - // we only need to compare sqrtsig as this will be set to zero if - // sqrteps is zero - return sqrtsig == 0.0; + return sqrteps == 0.0; } /** Return whether or not this parameter has non-zero LJ parameters */ diff --git a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp index ac45c54ee..85786b4a2 100644 --- a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireOpenMM::LambdaLever __copy__(const SireOpenMM::LambdaLever &other){ return SireOpenMM::LambdaLever(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -55,14 +57,13 @@ void register_LambdaLever_class(){ } { //::SireOpenMM::LambdaLever::addPerturbableMolecule - typedef int ( ::SireOpenMM::LambdaLever::*addPerturbableMolecule_function_type)( ::SireOpenMM::OpenMMMolecule const &,::QHash< QString, int > const & ) ; + typedef int ( ::SireOpenMM::LambdaLever::*addPerturbableMolecule_function_type)( ::SireOpenMM::OpenMMMolecule const &,::QHash< QString, int > const &,::SireBase::PropertyMap const & ) ; addPerturbableMolecule_function_type addPerturbableMolecule_function_value( &::SireOpenMM::LambdaLever::addPerturbableMolecule ); LambdaLever_exposer.def( "addPerturbableMolecule" , addPerturbableMolecule_function_value - , ( bp::arg("molecule"), bp::arg("start_indicies") ) - , bp::release_gil_policy() + , ( bp::arg("molecule"), bp::arg("start_indicies"), bp::arg("map")=SireBase::PropertyMap() ) , "Add info for the passed perturbable OpenMMMolecule, returning\n its index in the list of perturbable molecules\n" ); } @@ -115,7 +116,7 @@ void register_LambdaLever_class(){ , getLeverValues_function_value , ( bp::arg("lambda_values"), bp::arg("mol") ) , bp::release_gil_policy() - , "" ); + , "Get all of the lever values that would be set for the passed\n lambda values using the current context. This returns a PropertyList\n of columns, where each column is a PropertyMap with the column name\n and either double or QString array property of values.\n\n This is designed to be used by a higher-level python function that\n will convert this output into, e.g. a pandas DataFrame\n" ); } { //::SireOpenMM::LambdaLever::getPerturbableMoleculeMaps @@ -272,9 +273,9 @@ void register_LambdaLever_class(){ } LambdaLever_exposer.staticmethod( "typeName" ); - LambdaLever_exposer.def( "__copy__", &__copy__); - LambdaLever_exposer.def( "__deepcopy__", &__copy__); - LambdaLever_exposer.def( "clone", &__copy__); + LambdaLever_exposer.def( "__copy__", &__copy__); + LambdaLever_exposer.def( "__deepcopy__", &__copy__); + LambdaLever_exposer.def( "clone", &__copy__); LambdaLever_exposer.def( "__str__", &__str__< ::SireOpenMM::LambdaLever > ); LambdaLever_exposer.def( "__repr__", &__str__< ::SireOpenMM::LambdaLever > ); } diff --git a/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp b/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp index eb68e6a3f..07b317ddb 100644 --- a/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/OpenMMMetaData.pypp.cpp @@ -129,6 +129,8 @@ namespace bp = boost::python; SireOpenMM::OpenMMMetaData __copy__(const SireOpenMM::OpenMMMetaData &other){ return SireOpenMM::OpenMMMetaData(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -273,9 +275,9 @@ void register_OpenMMMetaData_class(){ } OpenMMMetaData_exposer.staticmethod( "typeName" ); - OpenMMMetaData_exposer.def( "__copy__", &__copy__); - OpenMMMetaData_exposer.def( "__deepcopy__", &__copy__); - OpenMMMetaData_exposer.def( "clone", &__copy__); + OpenMMMetaData_exposer.def( "__copy__", &__copy__); + OpenMMMetaData_exposer.def( "__deepcopy__", &__copy__); + OpenMMMetaData_exposer.def( "clone", &__copy__); OpenMMMetaData_exposer.def( "__str__", &__str__< ::SireOpenMM::OpenMMMetaData > ); OpenMMMetaData_exposer.def( "__repr__", &__str__< ::SireOpenMM::OpenMMMetaData > ); } diff --git a/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp b/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp index b24f08114..2c8453127 100644 --- a/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PerturbableOpenMMMolecule.pypp.cpp @@ -113,6 +113,8 @@ namespace bp = boost::python; SireOpenMM::PerturbableOpenMMMolecule __copy__(const SireOpenMM::PerturbableOpenMMMolecule &other){ return SireOpenMM::PerturbableOpenMMMolecule(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -123,8 +125,8 @@ void register_PerturbableOpenMMMolecule_class(){ typedef bp::class_< SireOpenMM::PerturbableOpenMMMolecule > PerturbableOpenMMMolecule_exposer_t; PerturbableOpenMMMolecule_exposer_t PerturbableOpenMMMolecule_exposer = PerturbableOpenMMMolecule_exposer_t( "PerturbableOpenMMMolecule", "This class holds all of the information of an OpenMM molecule\nthat can be perturbed using a LambdaSchedule. The data is held\nin easy-to-access arrays, with guarantees that the arrays are\ncompatible and the data is aligned.\n", bp::init< >("Null constructor") ); bp::scope PerturbableOpenMMMolecule_scope( PerturbableOpenMMMolecule_exposer ); - PerturbableOpenMMMolecule_exposer.def( bp::init< SireOpenMM::OpenMMMolecule const & >(( bp::arg("mol") ), "Construct from the passed OpenMMMolecule") ); - PerturbableOpenMMMolecule_exposer.def( bp::init< SireMol::Molecule const &, SireBase::PropertyMap const & >(( bp::arg("mol"), bp::arg("map") ), "Construct from a passed molecule and map") ); + PerturbableOpenMMMolecule_exposer.def( bp::init< SireOpenMM::OpenMMMolecule const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("mol"), bp::arg("map")=SireBase::PropertyMap() ), "Construct from the passed OpenMMMolecule") ); + PerturbableOpenMMMolecule_exposer.def( bp::init< SireMol::Molecule const &, bp::optional< SireBase::PropertyMap const & > >(( bp::arg("mol"), bp::arg("map")=SireBase::PropertyMap() ), "Construct from a passed molecule and map") ); PerturbableOpenMMMolecule_exposer.def( bp::init< SireOpenMM::PerturbableOpenMMMolecule const & >(( bp::arg("other") ), "Copy constructor") ); { //::SireOpenMM::PerturbableOpenMMMolecule::angles @@ -595,6 +597,18 @@ void register_PerturbableOpenMMMolecule_class(){ , bp::release_gil_policy() , "Return true if the atom is a ghost atom in the\n referenece or perturbed states" ); + } + { //::SireOpenMM::PerturbableOpenMMMolecule::isNull + + typedef bool ( ::SireOpenMM::PerturbableOpenMMMolecule::*isNull_function_type)( ) const; + isNull_function_type isNull_function_value( &::SireOpenMM::PerturbableOpenMMMolecule::isNull ); + + PerturbableOpenMMMolecule_exposer.def( + "isNull" + , isNull_function_value + , bp::release_gil_policy() + , "Return whether or not this is null" ); + } PerturbableOpenMMMolecule_exposer.def( bp::self != bp::self ); { //::SireOpenMM::PerturbableOpenMMMolecule::operator= @@ -686,9 +700,9 @@ void register_PerturbableOpenMMMolecule_class(){ } PerturbableOpenMMMolecule_exposer.staticmethod( "typeName" ); - PerturbableOpenMMMolecule_exposer.def( "__copy__", &__copy__); - PerturbableOpenMMMolecule_exposer.def( "__deepcopy__", &__copy__); - PerturbableOpenMMMolecule_exposer.def( "clone", &__copy__); + PerturbableOpenMMMolecule_exposer.def( "__copy__", &__copy__); + PerturbableOpenMMMolecule_exposer.def( "__deepcopy__", &__copy__); + PerturbableOpenMMMolecule_exposer.def( "clone", &__copy__); PerturbableOpenMMMolecule_exposer.def( "__str__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > ); PerturbableOpenMMMolecule_exposer.def( "__repr__", &__str__< ::SireOpenMM::PerturbableOpenMMMolecule > ); } diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index f44b38f90..a70a0c18f 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -1964,10 +1964,11 @@ QList LambdaLever::getRestraints(const QString &name, * its index in the list of perturbable molecules */ int LambdaLever::addPerturbableMolecule(const OpenMMMolecule &molecule, - const QHash &starts) + const QHash &starts, + const PropertyMap &map) { // should add in some sanity checks for these inputs - this->perturbable_mols.append(PerturbableOpenMMMolecule(molecule)); + this->perturbable_mols.append(PerturbableOpenMMMolecule(molecule, map)); this->start_indicies.append(starts); this->perturbable_maps.insert(molecule.number, molecule.perturtable_map); this->lambda_cache.clear(); diff --git a/wrapper/Convert/SireOpenMM/lambdalever.h b/wrapper/Convert/SireOpenMM/lambdalever.h index 9bf0b60d7..46cb254d1 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.h +++ b/wrapper/Convert/SireOpenMM/lambdalever.h @@ -123,7 +123,8 @@ namespace SireOpenMM void addRestraintIndex(const QString &force, int index); int addPerturbableMolecule(const OpenMMMolecule &molecule, - const QHash &start_indicies); + const QHash &start_indicies, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); void setExceptionIndicies(int idx, const QString &ff, const QVector> &exception_idxs); diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 5ce40d59d..ceedf8e6f 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -559,9 +559,6 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, check_for_h_by_ambertype = map["check_for_h_by_ambertype"].value().asABoolean(); } - // a list to store ghost atom indices - QList ghost_atoms; - if (is_perturbable) { const auto params1_masses = params1.masses(); @@ -641,14 +638,6 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, light_atoms.insert(i); } } - - // check for ghost atoms - const auto charge0 = params.charges().at(cgatomidx); - const auto lj0 = params.ljs().at(cgatomidx); - if (charge0 == 0 and lj0.epsilon().value() == 0) - { - ghost_atoms.append(i); - } } } else @@ -697,13 +686,6 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, this->cljs = QVector>(nats, boost::make_tuple(0.0, 0.0, 0.0)); auto cljs_data = cljs.data(); - // whether the user doesn't want to perturb the LJ sigma for ghost atoms - bool fix_ghost_sigmas = false; - if (map.specified("fix_ghost_sigmas")) - { - fix_ghost_sigmas = map["fix_ghost_sigmas"].value().asABoolean(); - } - for (int i = 0; i < nats; ++i) { const auto &cgatomidx = idx_to_cgatomidx_data[i]; @@ -714,13 +696,6 @@ void OpenMMMolecule::constructFromAmber(const Molecule &mol, double sig = lj.sigma().to(SireUnits::nanometer); double eps = lj.epsilon().to(SireUnits::kJ_per_mol); - if (fix_ghost_sigmas and ghost_atoms.contains(i)) - { - // use the sigma from the opposite state - const auto &lj1 = params1.ljs().at(idx_to_cgatomidx_data[i]); - sig = lj1.sigma().to(SireUnits::nanometer); - } - if (sig == 0) { // this must be a null parameter @@ -2098,7 +2073,7 @@ PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const Molecule &mol, const PropertyMap &map) : ConcreteProperty() { - this->operator=(PerturbableOpenMMMolecule(OpenMMMolecule(mol, map))); + this->operator=(PerturbableOpenMMMolecule(OpenMMMolecule(mol, map), map)); } /** Return whether or not this is null */ @@ -2110,7 +2085,8 @@ bool PerturbableOpenMMMolecule::isNull() const } /** Construct from the passed OpenMMMolecule */ -PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const OpenMMMolecule &mol) +PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const OpenMMMolecule &mol, + const PropertyMap &map) : ConcreteProperty() { if (mol.perturbed.get() == 0) @@ -2200,6 +2176,45 @@ PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const OpenMMMolecule &mol) from_ghost_idxs = mol.from_ghost_idxs; perturbable_constraints = mol.perturbable_constraints; + + bool fix_perturbable_zero_sigmas = false; + + if (map.specified("fix_perturbable_zero_sigmas")) + { + fix_perturbable_zero_sigmas = map["fix_perturbable_zero_sigmas"].value().asABoolean(); + } + + if (fix_perturbable_zero_sigmas) + { + const int nats = sig0.count(); + + if (sig1.count() != nats) + { + throw SireError::program_bug(QObject::tr( + "The number of atoms in the reference (%1) and perturbed (%2) " + "states do not match.") + .arg(nats) + .arg(sig1.count()), + CODELOC); + } + + const auto *sig0_data = sig0.constData(); + const auto *sig1_data = sig1.constData(); + + for (int i = 0; i < nats; ++i) + { + if (std::abs(sig0_data[i]) < 1e-9) + { + sig0[i] = sig1_data[i]; + sig0_data = sig0.constData(); + } + else if (std::abs(sig1_data[i] < 1e-9)) + { + sig1[i] = sig0_data[i]; + sig1_data = sig1.constData(); + } + } + } } /** Copy constructor */ diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 30420f0be..39dd5e905 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -204,10 +204,11 @@ namespace SireOpenMM public: PerturbableOpenMMMolecule(); - PerturbableOpenMMMolecule(const OpenMMMolecule &mol); + PerturbableOpenMMMolecule(const OpenMMMolecule &mol, + const SireBase::PropertyMap &map = SireBase::PropertyMap()); PerturbableOpenMMMolecule(const SireMol::Molecule &mol, - const SireBase::PropertyMap &map); + const SireBase::PropertyMap &map = SireBase::PropertyMap()); PerturbableOpenMMMolecule(const PerturbableOpenMMMolecule &other); diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index bb4733f93..e3a0c59ff 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1144,7 +1144,8 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // of perturbable molecules (e.g. the first perturbable // molecule we find has index 0) auto pert_idx = lambda_lever.addPerturbableMolecule(mol, - start_indicies); + start_indicies, + map); // and we can record the map from the molecule index // to the perturbable molecule index diff --git a/wrapper/MM/AmberAngle.pypp.cpp b/wrapper/MM/AmberAngle.pypp.cpp index 3a0c92514..b134b5ff4 100644 --- a/wrapper/MM/AmberAngle.pypp.cpp +++ b/wrapper/MM/AmberAngle.pypp.cpp @@ -73,6 +73,8 @@ namespace bp = boost::python; SireMM::AmberAngle __copy__(const SireMM::AmberAngle &other){ return SireMM::AmberAngle(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -217,9 +219,9 @@ void register_AmberAngle_class(){ } AmberAngle_exposer.staticmethod( "typeName" ); - AmberAngle_exposer.def( "__copy__", &__copy__); - AmberAngle_exposer.def( "__deepcopy__", &__copy__); - AmberAngle_exposer.def( "clone", &__copy__); + AmberAngle_exposer.def( "__copy__", &__copy__); + AmberAngle_exposer.def( "__deepcopy__", &__copy__); + AmberAngle_exposer.def( "clone", &__copy__); AmberAngle_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AmberAngle >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AmberAngle_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AmberAngle >, diff --git a/wrapper/MM/AmberBond.pypp.cpp b/wrapper/MM/AmberBond.pypp.cpp index cd1d926e2..765eecf22 100644 --- a/wrapper/MM/AmberBond.pypp.cpp +++ b/wrapper/MM/AmberBond.pypp.cpp @@ -73,6 +73,8 @@ namespace bp = boost::python; SireMM::AmberBond __copy__(const SireMM::AmberBond &other){ return SireMM::AmberBond(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -217,9 +219,9 @@ void register_AmberBond_class(){ } AmberBond_exposer.staticmethod( "typeName" ); - AmberBond_exposer.def( "__copy__", &__copy__); - AmberBond_exposer.def( "__deepcopy__", &__copy__); - AmberBond_exposer.def( "clone", &__copy__); + AmberBond_exposer.def( "__copy__", &__copy__); + AmberBond_exposer.def( "__deepcopy__", &__copy__); + AmberBond_exposer.def( "clone", &__copy__); AmberBond_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AmberBond >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AmberBond_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AmberBond >, diff --git a/wrapper/MM/AmberDihPart.pypp.cpp b/wrapper/MM/AmberDihPart.pypp.cpp index 901450127..215e9cba4 100644 --- a/wrapper/MM/AmberDihPart.pypp.cpp +++ b/wrapper/MM/AmberDihPart.pypp.cpp @@ -73,6 +73,8 @@ namespace bp = boost::python; SireMM::AmberDihPart __copy__(const SireMM::AmberDihPart &other){ return SireMM::AmberDihPart(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -215,9 +217,9 @@ void register_AmberDihPart_class(){ } AmberDihPart_exposer.staticmethod( "typeName" ); - AmberDihPart_exposer.def( "__copy__", &__copy__); - AmberDihPart_exposer.def( "__deepcopy__", &__copy__); - AmberDihPart_exposer.def( "clone", &__copy__); + AmberDihPart_exposer.def( "__copy__", &__copy__); + AmberDihPart_exposer.def( "__deepcopy__", &__copy__); + AmberDihPart_exposer.def( "clone", &__copy__); AmberDihPart_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AmberDihPart >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AmberDihPart_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AmberDihPart >, diff --git a/wrapper/MM/AmberDihedral.pypp.cpp b/wrapper/MM/AmberDihedral.pypp.cpp index de9fce62c..3f89d3c57 100644 --- a/wrapper/MM/AmberDihedral.pypp.cpp +++ b/wrapper/MM/AmberDihedral.pypp.cpp @@ -73,6 +73,8 @@ namespace bp = boost::python; SireMM::AmberDihedral __copy__(const SireMM::AmberDihedral &other){ return SireMM::AmberDihedral(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -203,9 +205,9 @@ void register_AmberDihedral_class(){ } AmberDihedral_exposer.staticmethod( "typeName" ); - AmberDihedral_exposer.def( "__copy__", &__copy__); - AmberDihedral_exposer.def( "__deepcopy__", &__copy__); - AmberDihedral_exposer.def( "clone", &__copy__); + AmberDihedral_exposer.def( "__copy__", &__copy__); + AmberDihedral_exposer.def( "__deepcopy__", &__copy__); + AmberDihedral_exposer.def( "clone", &__copy__); AmberDihedral_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AmberDihedral >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AmberDihedral_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AmberDihedral >, diff --git a/wrapper/MM/AmberNB14.pypp.cpp b/wrapper/MM/AmberNB14.pypp.cpp index de9f3bd99..dd427c21b 100644 --- a/wrapper/MM/AmberNB14.pypp.cpp +++ b/wrapper/MM/AmberNB14.pypp.cpp @@ -73,6 +73,8 @@ namespace bp = boost::python; SireMM::AmberNB14 __copy__(const SireMM::AmberNB14 &other){ return SireMM::AmberNB14(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -190,9 +192,9 @@ void register_AmberNB14_class(){ } AmberNB14_exposer.staticmethod( "typeName" ); - AmberNB14_exposer.def( "__copy__", &__copy__); - AmberNB14_exposer.def( "__deepcopy__", &__copy__); - AmberNB14_exposer.def( "clone", &__copy__); + AmberNB14_exposer.def( "__copy__", &__copy__); + AmberNB14_exposer.def( "__deepcopy__", &__copy__); + AmberNB14_exposer.def( "clone", &__copy__); AmberNB14_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AmberNB14 >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AmberNB14_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AmberNB14 >, diff --git a/wrapper/MM/AmberParams.pypp.cpp b/wrapper/MM/AmberParams.pypp.cpp index a1306fe96..8ec4a0bb8 100644 --- a/wrapper/MM/AmberParams.pypp.cpp +++ b/wrapper/MM/AmberParams.pypp.cpp @@ -73,6 +73,8 @@ namespace bp = boost::python; SireMM::AmberParams __copy__(const SireMM::AmberParams &other){ return SireMM::AmberParams(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -858,9 +860,9 @@ void register_AmberParams_class(){ } AmberParams_exposer.staticmethod( "typeName" ); - AmberParams_exposer.def( "__copy__", &__copy__); - AmberParams_exposer.def( "__deepcopy__", &__copy__); - AmberParams_exposer.def( "clone", &__copy__); + AmberParams_exposer.def( "__copy__", &__copy__); + AmberParams_exposer.def( "__deepcopy__", &__copy__); + AmberParams_exposer.def( "clone", &__copy__); AmberParams_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AmberParams >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AmberParams_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AmberParams >, diff --git a/wrapper/MM/Angle.pypp.cpp b/wrapper/MM/Angle.pypp.cpp index 0cbb033a4..873a8449d 100644 --- a/wrapper/MM/Angle.pypp.cpp +++ b/wrapper/MM/Angle.pypp.cpp @@ -42,6 +42,8 @@ namespace bp = boost::python; SireMM::Angle __copy__(const SireMM::Angle &other){ return SireMM::Angle(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -471,9 +473,9 @@ void register_Angle_class(){ } Angle_exposer.staticmethod( "typeName" ); - Angle_exposer.def( "__copy__", &__copy__); - Angle_exposer.def( "__deepcopy__", &__copy__); - Angle_exposer.def( "clone", &__copy__); + Angle_exposer.def( "__copy__", &__copy__); + Angle_exposer.def( "__deepcopy__", &__copy__); + Angle_exposer.def( "clone", &__copy__); Angle_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Angle >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Angle_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Angle >, diff --git a/wrapper/MM/AngleComponent.pypp.cpp b/wrapper/MM/AngleComponent.pypp.cpp index b2f107988..5e9944b2c 100644 --- a/wrapper/MM/AngleComponent.pypp.cpp +++ b/wrapper/MM/AngleComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::AngleComponent __copy__(const SireMM::AngleComponent &other){ return SireMM::AngleComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_AngleComponent_class(){ } AngleComponent_exposer.staticmethod( "typeName" ); - AngleComponent_exposer.def( "__copy__", &__copy__); - AngleComponent_exposer.def( "__deepcopy__", &__copy__); - AngleComponent_exposer.def( "clone", &__copy__); + AngleComponent_exposer.def( "__copy__", &__copy__); + AngleComponent_exposer.def( "__deepcopy__", &__copy__); + AngleComponent_exposer.def( "clone", &__copy__); AngleComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AngleComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AngleComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AngleComponent >, diff --git a/wrapper/MM/AngleParameterName.pypp.cpp b/wrapper/MM/AngleParameterName.pypp.cpp index 416ccd350..1a357b7d6 100644 --- a/wrapper/MM/AngleParameterName.pypp.cpp +++ b/wrapper/MM/AngleParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::AngleParameterName __copy__(const SireMM::AngleParameterName &other){ return SireMM::AngleParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::AngleParameterName&){ return "SireMM::AngleParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_AngleParameterName_class(){ , "" ); } - AngleParameterName_exposer.def( "__copy__", &__copy__); - AngleParameterName_exposer.def( "__deepcopy__", &__copy__); - AngleParameterName_exposer.def( "clone", &__copy__); + AngleParameterName_exposer.def( "__copy__", &__copy__); + AngleParameterName_exposer.def( "__deepcopy__", &__copy__); + AngleParameterName_exposer.def( "clone", &__copy__); AngleParameterName_exposer.def( "__str__", &pvt_get_name); AngleParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/AngleRestraint.pypp.cpp b/wrapper/MM/AngleRestraint.pypp.cpp index 45e37f153..052916bb4 100644 --- a/wrapper/MM/AngleRestraint.pypp.cpp +++ b/wrapper/MM/AngleRestraint.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireMM::AngleRestraint __copy__(const SireMM::AngleRestraint &other){ return SireMM::AngleRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -357,9 +359,9 @@ void register_AngleRestraint_class(){ AngleRestraint_exposer.staticmethod( "harmonic" ); AngleRestraint_exposer.staticmethod( "theta" ); AngleRestraint_exposer.staticmethod( "typeName" ); - AngleRestraint_exposer.def( "__copy__", &__copy__); - AngleRestraint_exposer.def( "__deepcopy__", &__copy__); - AngleRestraint_exposer.def( "clone", &__copy__); + AngleRestraint_exposer.def( "__copy__", &__copy__); + AngleRestraint_exposer.def( "__deepcopy__", &__copy__); + AngleRestraint_exposer.def( "clone", &__copy__); AngleRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::AngleRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AngleRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::AngleRestraint >, diff --git a/wrapper/MM/AngleSymbols.pypp.cpp b/wrapper/MM/AngleSymbols.pypp.cpp index fe0e656bc..deecfb934 100644 --- a/wrapper/MM/AngleSymbols.pypp.cpp +++ b/wrapper/MM/AngleSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::AngleSymbols __copy__(const SireMM::AngleSymbols &other){ return SireMM::AngleSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::AngleSymbols&){ return "SireMM::AngleSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -56,9 +58,9 @@ void register_AngleSymbols_class(){ , "Return the symbols representing the angle (theta)" ); } - AngleSymbols_exposer.def( "__copy__", &__copy__); - AngleSymbols_exposer.def( "__deepcopy__", &__copy__); - AngleSymbols_exposer.def( "clone", &__copy__); + AngleSymbols_exposer.def( "__copy__", &__copy__); + AngleSymbols_exposer.def( "__deepcopy__", &__copy__); + AngleSymbols_exposer.def( "clone", &__copy__); AngleSymbols_exposer.def( "__str__", &pvt_get_name); AngleSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/AtomLJs.pypp.cpp b/wrapper/MM/AtomLJs.pypp.cpp index 44b00dc65..977ec7fcd 100644 --- a/wrapper/MM/AtomLJs.pypp.cpp +++ b/wrapper/MM/AtomLJs.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMol::AtomProperty __copy__(const SireMol::AtomProperty &other){ return SireMol::AtomProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -827,9 +829,9 @@ void register_AtomLJs_class(){ } AtomLJs_exposer.staticmethod( "fromVariant" ); AtomLJs_exposer.staticmethod( "typeName" ); - AtomLJs_exposer.def( "__copy__", &__copy__); - AtomLJs_exposer.def( "__deepcopy__", &__copy__); - AtomLJs_exposer.def( "clone", &__copy__); + AtomLJs_exposer.def( "__copy__", &__copy__>); + AtomLJs_exposer.def( "__deepcopy__", &__copy__>); + AtomLJs_exposer.def( "clone", &__copy__>); AtomLJs_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMol::AtomProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AtomLJs_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMol::AtomProperty >, diff --git a/wrapper/MM/BendBendComponent.pypp.cpp b/wrapper/MM/BendBendComponent.pypp.cpp index 3288b5fe8..9415ade51 100644 --- a/wrapper/MM/BendBendComponent.pypp.cpp +++ b/wrapper/MM/BendBendComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::BendBendComponent __copy__(const SireMM::BendBendComponent &other){ return SireMM::BendBendComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_BendBendComponent_class(){ } BendBendComponent_exposer.staticmethod( "typeName" ); - BendBendComponent_exposer.def( "__copy__", &__copy__); - BendBendComponent_exposer.def( "__deepcopy__", &__copy__); - BendBendComponent_exposer.def( "clone", &__copy__); + BendBendComponent_exposer.def( "__copy__", &__copy__); + BendBendComponent_exposer.def( "__deepcopy__", &__copy__); + BendBendComponent_exposer.def( "clone", &__copy__); BendBendComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::BendBendComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BendBendComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::BendBendComponent >, diff --git a/wrapper/MM/BendBendParameterName.pypp.cpp b/wrapper/MM/BendBendParameterName.pypp.cpp index f8048aa5d..298608a79 100644 --- a/wrapper/MM/BendBendParameterName.pypp.cpp +++ b/wrapper/MM/BendBendParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::BendBendParameterName __copy__(const SireMM::BendBendParameterName &other){ return SireMM::BendBendParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::BendBendParameterName&){ return "SireMM::BendBendParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_BendBendParameterName_class(){ , "" ); } - BendBendParameterName_exposer.def( "__copy__", &__copy__); - BendBendParameterName_exposer.def( "__deepcopy__", &__copy__); - BendBendParameterName_exposer.def( "clone", &__copy__); + BendBendParameterName_exposer.def( "__copy__", &__copy__); + BendBendParameterName_exposer.def( "__deepcopy__", &__copy__); + BendBendParameterName_exposer.def( "clone", &__copy__); BendBendParameterName_exposer.def( "__str__", &pvt_get_name); BendBendParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/BendBendSymbols.pypp.cpp b/wrapper/MM/BendBendSymbols.pypp.cpp index 04754de27..57d536d17 100644 --- a/wrapper/MM/BendBendSymbols.pypp.cpp +++ b/wrapper/MM/BendBendSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::BendBendSymbols __copy__(const SireMM::BendBendSymbols &other){ return SireMM::BendBendSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::BendBendSymbols&){ return "SireMM::BendBendSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -80,9 +82,9 @@ void register_BendBendSymbols_class(){ , "Return the symbol representing the angle between atoms 3-1-0, theta_\n{310}" ); } - BendBendSymbols_exposer.def( "__copy__", &__copy__); - BendBendSymbols_exposer.def( "__deepcopy__", &__copy__); - BendBendSymbols_exposer.def( "clone", &__copy__); + BendBendSymbols_exposer.def( "__copy__", &__copy__); + BendBendSymbols_exposer.def( "__deepcopy__", &__copy__); + BendBendSymbols_exposer.def( "clone", &__copy__); BendBendSymbols_exposer.def( "__str__", &pvt_get_name); BendBendSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/Bond.pypp.cpp b/wrapper/MM/Bond.pypp.cpp index f4fd7545b..9bd466fea 100644 --- a/wrapper/MM/Bond.pypp.cpp +++ b/wrapper/MM/Bond.pypp.cpp @@ -42,6 +42,8 @@ namespace bp = boost::python; SireMM::Bond __copy__(const SireMM::Bond &other){ return SireMM::Bond(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -459,9 +461,9 @@ void register_Bond_class(){ } Bond_exposer.staticmethod( "typeName" ); - Bond_exposer.def( "__copy__", &__copy__); - Bond_exposer.def( "__deepcopy__", &__copy__); - Bond_exposer.def( "clone", &__copy__); + Bond_exposer.def( "__copy__", &__copy__); + Bond_exposer.def( "__deepcopy__", &__copy__); + Bond_exposer.def( "clone", &__copy__); Bond_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Bond >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Bond_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Bond >, diff --git a/wrapper/MM/BondComponent.pypp.cpp b/wrapper/MM/BondComponent.pypp.cpp index 1b6b00c9c..94621c39a 100644 --- a/wrapper/MM/BondComponent.pypp.cpp +++ b/wrapper/MM/BondComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::BondComponent __copy__(const SireMM::BondComponent &other){ return SireMM::BondComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_BondComponent_class(){ } BondComponent_exposer.staticmethod( "typeName" ); - BondComponent_exposer.def( "__copy__", &__copy__); - BondComponent_exposer.def( "__deepcopy__", &__copy__); - BondComponent_exposer.def( "clone", &__copy__); + BondComponent_exposer.def( "__copy__", &__copy__); + BondComponent_exposer.def( "__deepcopy__", &__copy__); + BondComponent_exposer.def( "clone", &__copy__); BondComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::BondComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BondComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::BondComponent >, diff --git a/wrapper/MM/BondParameterName.pypp.cpp b/wrapper/MM/BondParameterName.pypp.cpp index 19a44a2ab..1ae851160 100644 --- a/wrapper/MM/BondParameterName.pypp.cpp +++ b/wrapper/MM/BondParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::BondParameterName __copy__(const SireMM::BondParameterName &other){ return SireMM::BondParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::BondParameterName&){ return "SireMM::BondParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_BondParameterName_class(){ , "" ); } - BondParameterName_exposer.def( "__copy__", &__copy__); - BondParameterName_exposer.def( "__deepcopy__", &__copy__); - BondParameterName_exposer.def( "clone", &__copy__); + BondParameterName_exposer.def( "__copy__", &__copy__); + BondParameterName_exposer.def( "__deepcopy__", &__copy__); + BondParameterName_exposer.def( "clone", &__copy__); BondParameterName_exposer.def( "__str__", &pvt_get_name); BondParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/BondRestraint.pypp.cpp b/wrapper/MM/BondRestraint.pypp.cpp index c680cfb17..ea5e7fbed 100644 --- a/wrapper/MM/BondRestraint.pypp.cpp +++ b/wrapper/MM/BondRestraint.pypp.cpp @@ -25,6 +25,8 @@ namespace bp = boost::python; SireMM::BondRestraint __copy__(const SireMM::BondRestraint &other){ return SireMM::BondRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -202,9 +204,9 @@ void register_BondRestraint_class(){ } BondRestraint_exposer.staticmethod( "typeName" ); - BondRestraint_exposer.def( "__copy__", &__copy__); - BondRestraint_exposer.def( "__deepcopy__", &__copy__); - BondRestraint_exposer.def( "clone", &__copy__); + BondRestraint_exposer.def( "__copy__", &__copy__); + BondRestraint_exposer.def( "__deepcopy__", &__copy__); + BondRestraint_exposer.def( "clone", &__copy__); BondRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::BondRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BondRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::BondRestraint >, diff --git a/wrapper/MM/BondRestraints.pypp.cpp b/wrapper/MM/BondRestraints.pypp.cpp index 5bc3ea598..1e3cfbde4 100644 --- a/wrapper/MM/BondRestraints.pypp.cpp +++ b/wrapper/MM/BondRestraints.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireMM::BondRestraints __copy__(const SireMM::BondRestraints &other){ return SireMM::BondRestraints(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -296,9 +298,9 @@ void register_BondRestraints_class(){ } BondRestraints_exposer.staticmethod( "typeName" ); - BondRestraints_exposer.def( "__copy__", &__copy__); - BondRestraints_exposer.def( "__deepcopy__", &__copy__); - BondRestraints_exposer.def( "clone", &__copy__); + BondRestraints_exposer.def( "__copy__", &__copy__); + BondRestraints_exposer.def( "__deepcopy__", &__copy__); + BondRestraints_exposer.def( "clone", &__copy__); BondRestraints_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::BondRestraints >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BondRestraints_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::BondRestraints >, diff --git a/wrapper/MM/BondSymbols.pypp.cpp b/wrapper/MM/BondSymbols.pypp.cpp index b9feb17f3..71815128c 100644 --- a/wrapper/MM/BondSymbols.pypp.cpp +++ b/wrapper/MM/BondSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::BondSymbols __copy__(const SireMM::BondSymbols &other){ return SireMM::BondSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::BondSymbols&){ return "SireMM::BondSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -56,9 +58,9 @@ void register_BondSymbols_class(){ , "Return the symbol representing the vector along the bond (r)" ); } - BondSymbols_exposer.def( "__copy__", &__copy__); - BondSymbols_exposer.def( "__deepcopy__", &__copy__); - BondSymbols_exposer.def( "clone", &__copy__); + BondSymbols_exposer.def( "__copy__", &__copy__); + BondSymbols_exposer.def( "__deepcopy__", &__copy__); + BondSymbols_exposer.def( "clone", &__copy__); BondSymbols_exposer.def( "__str__", &pvt_get_name); BondSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/BoreschRestraint.pypp.cpp b/wrapper/MM/BoreschRestraint.pypp.cpp index e9bbc0d19..2e1e94b19 100644 --- a/wrapper/MM/BoreschRestraint.pypp.cpp +++ b/wrapper/MM/BoreschRestraint.pypp.cpp @@ -25,6 +25,8 @@ namespace bp = boost::python; SireMM::BoreschRestraint __copy__(const SireMM::BoreschRestraint &other){ return SireMM::BoreschRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -201,9 +203,9 @@ void register_BoreschRestraint_class(){ } BoreschRestraint_exposer.staticmethod( "typeName" ); - BoreschRestraint_exposer.def( "__copy__", &__copy__); - BoreschRestraint_exposer.def( "__deepcopy__", &__copy__); - BoreschRestraint_exposer.def( "clone", &__copy__); + BoreschRestraint_exposer.def( "__copy__", &__copy__); + BoreschRestraint_exposer.def( "__deepcopy__", &__copy__); + BoreschRestraint_exposer.def( "clone", &__copy__); BoreschRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::BoreschRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BoreschRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::BoreschRestraint >, diff --git a/wrapper/MM/BoreschRestraints.pypp.cpp b/wrapper/MM/BoreschRestraints.pypp.cpp index 9f45de923..09ca8e9ad 100644 --- a/wrapper/MM/BoreschRestraints.pypp.cpp +++ b/wrapper/MM/BoreschRestraints.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireMM::BoreschRestraints __copy__(const SireMM::BoreschRestraints &other){ return SireMM::BoreschRestraints(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -224,9 +226,9 @@ void register_BoreschRestraints_class(){ } BoreschRestraints_exposer.staticmethod( "typeName" ); - BoreschRestraints_exposer.def( "__copy__", &__copy__); - BoreschRestraints_exposer.def( "__deepcopy__", &__copy__); - BoreschRestraints_exposer.def( "clone", &__copy__); + BoreschRestraints_exposer.def( "__copy__", &__copy__); + BoreschRestraints_exposer.def( "__deepcopy__", &__copy__); + BoreschRestraints_exposer.def( "clone", &__copy__); BoreschRestraints_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::BoreschRestraints >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); BoreschRestraints_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::BoreschRestraints >, diff --git a/wrapper/MM/CHARMMSwitchingFunction.pypp.cpp b/wrapper/MM/CHARMMSwitchingFunction.pypp.cpp index abd025786..185203bea 100644 --- a/wrapper/MM/CHARMMSwitchingFunction.pypp.cpp +++ b/wrapper/MM/CHARMMSwitchingFunction.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireMM::CHARMMSwitchingFunction __copy__(const SireMM::CHARMMSwitchingFunction &other){ return SireMM::CHARMMSwitchingFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -138,9 +140,9 @@ void register_CHARMMSwitchingFunction_class(){ } CHARMMSwitchingFunction_exposer.staticmethod( "typeName" ); - CHARMMSwitchingFunction_exposer.def( "__copy__", &__copy__); - CHARMMSwitchingFunction_exposer.def( "__deepcopy__", &__copy__); - CHARMMSwitchingFunction_exposer.def( "clone", &__copy__); + CHARMMSwitchingFunction_exposer.def( "__copy__", &__copy__); + CHARMMSwitchingFunction_exposer.def( "__deepcopy__", &__copy__); + CHARMMSwitchingFunction_exposer.def( "clone", &__copy__); CHARMMSwitchingFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CHARMMSwitchingFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CHARMMSwitchingFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CHARMMSwitchingFunction >, diff --git a/wrapper/MM/CLJ14Group.pypp.cpp b/wrapper/MM/CLJ14Group.pypp.cpp index 4bf4b90e7..1a8c3c7c1 100644 --- a/wrapper/MM/CLJ14Group.pypp.cpp +++ b/wrapper/MM/CLJ14Group.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireMM::CLJ14Group __copy__(const SireMM::CLJ14Group &other){ return SireMM::CLJ14Group(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -378,9 +380,9 @@ void register_CLJ14Group_class(){ } CLJ14Group_exposer.staticmethod( "typeName" ); - CLJ14Group_exposer.def( "__copy__", &__copy__); - CLJ14Group_exposer.def( "__deepcopy__", &__copy__); - CLJ14Group_exposer.def( "clone", &__copy__); + CLJ14Group_exposer.def( "__copy__", &__copy__); + CLJ14Group_exposer.def( "__deepcopy__", &__copy__); + CLJ14Group_exposer.def( "clone", &__copy__); CLJ14Group_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJ14Group >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJ14Group_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJ14Group >, diff --git a/wrapper/MM/CLJAtom.pypp.cpp b/wrapper/MM/CLJAtom.pypp.cpp index 94938ef32..2c15d1f1e 100644 --- a/wrapper/MM/CLJAtom.pypp.cpp +++ b/wrapper/MM/CLJAtom.pypp.cpp @@ -45,6 +45,8 @@ namespace bp = boost::python; SireMM::CLJAtom __copy__(const SireMM::CLJAtom &other){ return SireMM::CLJAtom(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -208,9 +210,9 @@ void register_CLJAtom_class(){ } CLJAtom_exposer.staticmethod( "buildFrom" ); CLJAtom_exposer.staticmethod( "typeName" ); - CLJAtom_exposer.def( "__copy__", &__copy__); - CLJAtom_exposer.def( "__deepcopy__", &__copy__); - CLJAtom_exposer.def( "clone", &__copy__); + CLJAtom_exposer.def( "__copy__", &__copy__); + CLJAtom_exposer.def( "__deepcopy__", &__copy__); + CLJAtom_exposer.def( "clone", &__copy__); CLJAtom_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJAtom >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJAtom_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJAtom >, diff --git a/wrapper/MM/CLJAtoms.pypp.cpp b/wrapper/MM/CLJAtoms.pypp.cpp index b69079ed8..4678aaafe 100644 --- a/wrapper/MM/CLJAtoms.pypp.cpp +++ b/wrapper/MM/CLJAtoms.pypp.cpp @@ -45,6 +45,8 @@ namespace bp = boost::python; SireMM::CLJAtoms __copy__(const SireMM::CLJAtoms &other){ return SireMM::CLJAtoms(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -650,9 +652,9 @@ void register_CLJAtoms_class(){ } CLJAtoms_exposer.staticmethod( "idOfDummy" ); CLJAtoms_exposer.staticmethod( "typeName" ); - CLJAtoms_exposer.def( "__copy__", &__copy__); - CLJAtoms_exposer.def( "__deepcopy__", &__copy__); - CLJAtoms_exposer.def( "clone", &__copy__); + CLJAtoms_exposer.def( "__copy__", &__copy__); + CLJAtoms_exposer.def( "__deepcopy__", &__copy__); + CLJAtoms_exposer.def( "clone", &__copy__); CLJAtoms_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJAtoms >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJAtoms_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJAtoms >, diff --git a/wrapper/MM/CLJBox.pypp.cpp b/wrapper/MM/CLJBox.pypp.cpp index 8e1d1beb8..974f838d3 100644 --- a/wrapper/MM/CLJBox.pypp.cpp +++ b/wrapper/MM/CLJBox.pypp.cpp @@ -37,6 +37,8 @@ namespace bp = boost::python; SireMM::CLJBox __copy__(const SireMM::CLJBox &other){ return SireMM::CLJBox(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -331,9 +333,9 @@ void register_CLJBox_class(){ } CLJBox_exposer.staticmethod( "typeName" ); - CLJBox_exposer.def( "__copy__", &__copy__); - CLJBox_exposer.def( "__deepcopy__", &__copy__); - CLJBox_exposer.def( "clone", &__copy__); + CLJBox_exposer.def( "__copy__", &__copy__); + CLJBox_exposer.def( "__deepcopy__", &__copy__); + CLJBox_exposer.def( "clone", &__copy__); CLJBox_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJBox >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJBox_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJBox >, diff --git a/wrapper/MM/CLJBoxDistance.pypp.cpp b/wrapper/MM/CLJBoxDistance.pypp.cpp index 1b9476b60..c11a7a398 100644 --- a/wrapper/MM/CLJBoxDistance.pypp.cpp +++ b/wrapper/MM/CLJBoxDistance.pypp.cpp @@ -37,6 +37,8 @@ namespace bp = boost::python; SireMM::CLJBoxDistance __copy__(const SireMM::CLJBoxDistance &other){ return SireMM::CLJBoxDistance(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -141,9 +143,9 @@ void register_CLJBoxDistance_class(){ } CLJBoxDistance_exposer.staticmethod( "typeName" ); - CLJBoxDistance_exposer.def( "__copy__", &__copy__); - CLJBoxDistance_exposer.def( "__deepcopy__", &__copy__); - CLJBoxDistance_exposer.def( "clone", &__copy__); + CLJBoxDistance_exposer.def( "__copy__", &__copy__); + CLJBoxDistance_exposer.def( "__deepcopy__", &__copy__); + CLJBoxDistance_exposer.def( "clone", &__copy__); CLJBoxDistance_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJBoxDistance >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJBoxDistance_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJBoxDistance >, diff --git a/wrapper/MM/CLJBoxIndex.pypp.cpp b/wrapper/MM/CLJBoxIndex.pypp.cpp index 9f6709450..ff2415b67 100644 --- a/wrapper/MM/CLJBoxIndex.pypp.cpp +++ b/wrapper/MM/CLJBoxIndex.pypp.cpp @@ -37,6 +37,8 @@ namespace bp = boost::python; SireMM::CLJBoxIndex __copy__(const SireMM::CLJBoxIndex &other){ return SireMM::CLJBoxIndex(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -336,9 +338,9 @@ void register_CLJBoxIndex_class(){ CLJBoxIndex_exposer.staticmethod( "createWithInverseBoxLength" ); CLJBoxIndex_exposer.staticmethod( "null" ); CLJBoxIndex_exposer.staticmethod( "typeName" ); - CLJBoxIndex_exposer.def( "__copy__", &__copy__); - CLJBoxIndex_exposer.def( "__deepcopy__", &__copy__); - CLJBoxIndex_exposer.def( "clone", &__copy__); + CLJBoxIndex_exposer.def( "__copy__", &__copy__); + CLJBoxIndex_exposer.def( "__deepcopy__", &__copy__); + CLJBoxIndex_exposer.def( "clone", &__copy__); CLJBoxIndex_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJBoxIndex >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJBoxIndex_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJBoxIndex >, diff --git a/wrapper/MM/CLJBoxes.pypp.cpp b/wrapper/MM/CLJBoxes.pypp.cpp index da35c1204..34648c630 100644 --- a/wrapper/MM/CLJBoxes.pypp.cpp +++ b/wrapper/MM/CLJBoxes.pypp.cpp @@ -37,6 +37,8 @@ namespace bp = boost::python; SireMM::CLJBoxes __copy__(const SireMM::CLJBoxes &other){ return SireMM::CLJBoxes(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -527,9 +529,9 @@ void register_CLJBoxes_class(){ } CLJBoxes_exposer.staticmethod( "getDistances" ); CLJBoxes_exposer.staticmethod( "typeName" ); - CLJBoxes_exposer.def( "__copy__", &__copy__); - CLJBoxes_exposer.def( "__deepcopy__", &__copy__); - CLJBoxes_exposer.def( "clone", &__copy__); + CLJBoxes_exposer.def( "__copy__", &__copy__); + CLJBoxes_exposer.def( "__deepcopy__", &__copy__); + CLJBoxes_exposer.def( "clone", &__copy__); CLJBoxes_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJBoxes >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJBoxes_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJBoxes >, diff --git a/wrapper/MM/CLJCalculator.pypp.cpp b/wrapper/MM/CLJCalculator.pypp.cpp index 02d8c7667..b5e6ff362 100644 --- a/wrapper/MM/CLJCalculator.pypp.cpp +++ b/wrapper/MM/CLJCalculator.pypp.cpp @@ -27,6 +27,8 @@ namespace bp = boost::python; SireMM::CLJCalculator __copy__(const SireMM::CLJCalculator &other){ return SireMM::CLJCalculator(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -170,9 +172,9 @@ void register_CLJCalculator_class(){ } CLJCalculator_exposer.staticmethod( "typeName" ); - CLJCalculator_exposer.def( "__copy__", &__copy__); - CLJCalculator_exposer.def( "__deepcopy__", &__copy__); - CLJCalculator_exposer.def( "clone", &__copy__); + CLJCalculator_exposer.def( "__copy__", &__copy__); + CLJCalculator_exposer.def( "__deepcopy__", &__copy__); + CLJCalculator_exposer.def( "clone", &__copy__); CLJCalculator_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJCalculator >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJCalculator_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJCalculator >, diff --git a/wrapper/MM/CLJComponent.pypp.cpp b/wrapper/MM/CLJComponent.pypp.cpp index fda2f73c9..27468c4b3 100644 --- a/wrapper/MM/CLJComponent.pypp.cpp +++ b/wrapper/MM/CLJComponent.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; SireMM::CLJComponent __copy__(const SireMM::CLJComponent &other){ return SireMM::CLJComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -130,9 +132,9 @@ void register_CLJComponent_class(){ } CLJComponent_exposer.staticmethod( "typeName" ); - CLJComponent_exposer.def( "__copy__", &__copy__); - CLJComponent_exposer.def( "__deepcopy__", &__copy__); - CLJComponent_exposer.def( "clone", &__copy__); + CLJComponent_exposer.def( "__copy__", &__copy__); + CLJComponent_exposer.def( "__deepcopy__", &__copy__); + CLJComponent_exposer.def( "clone", &__copy__); CLJComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJComponent >, diff --git a/wrapper/MM/CLJDelta.pypp.cpp b/wrapper/MM/CLJDelta.pypp.cpp index 9be4626ec..012e49f5a 100644 --- a/wrapper/MM/CLJDelta.pypp.cpp +++ b/wrapper/MM/CLJDelta.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireMM::CLJDelta __copy__(const SireMM::CLJDelta &other){ return SireMM::CLJDelta(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -280,9 +282,9 @@ void register_CLJDelta_class(){ CLJDelta_exposer.staticmethod( "mergeNew" ); CLJDelta_exposer.staticmethod( "mergeOld" ); CLJDelta_exposer.staticmethod( "typeName" ); - CLJDelta_exposer.def( "__copy__", &__copy__); - CLJDelta_exposer.def( "__deepcopy__", &__copy__); - CLJDelta_exposer.def( "clone", &__copy__); + CLJDelta_exposer.def( "__copy__", &__copy__); + CLJDelta_exposer.def( "__deepcopy__", &__copy__); + CLJDelta_exposer.def( "clone", &__copy__); CLJDelta_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJDelta >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJDelta_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJDelta >, diff --git a/wrapper/MM/CLJExtractor.pypp.cpp b/wrapper/MM/CLJExtractor.pypp.cpp index 2c454d863..91e2e04a2 100644 --- a/wrapper/MM/CLJExtractor.pypp.cpp +++ b/wrapper/MM/CLJExtractor.pypp.cpp @@ -37,6 +37,8 @@ namespace bp = boost::python; SireMM::CLJExtractor __copy__(const SireMM::CLJExtractor &other){ return SireMM::CLJExtractor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -409,9 +411,9 @@ void register_CLJExtractor_class(){ } CLJExtractor_exposer.staticmethod( "typeName" ); - CLJExtractor_exposer.def( "__copy__", &__copy__); - CLJExtractor_exposer.def( "__deepcopy__", &__copy__); - CLJExtractor_exposer.def( "clone", &__copy__); + CLJExtractor_exposer.def( "__copy__", &__copy__); + CLJExtractor_exposer.def( "__deepcopy__", &__copy__); + CLJExtractor_exposer.def( "clone", &__copy__); CLJExtractor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJExtractor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJExtractor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJExtractor >, diff --git a/wrapper/MM/CLJGrid.pypp.cpp b/wrapper/MM/CLJGrid.pypp.cpp index 7b0246536..988a53c9e 100644 --- a/wrapper/MM/CLJGrid.pypp.cpp +++ b/wrapper/MM/CLJGrid.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::CLJGrid __copy__(const SireMM::CLJGrid &other){ return SireMM::CLJGrid(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -621,9 +623,9 @@ void register_CLJGrid_class(){ } CLJGrid_exposer.staticmethod( "idOfFixedAtom" ); CLJGrid_exposer.staticmethod( "typeName" ); - CLJGrid_exposer.def( "__copy__", &__copy__); - CLJGrid_exposer.def( "__deepcopy__", &__copy__); - CLJGrid_exposer.def( "clone", &__copy__); + CLJGrid_exposer.def( "__copy__", &__copy__); + CLJGrid_exposer.def( "__deepcopy__", &__copy__); + CLJGrid_exposer.def( "clone", &__copy__); CLJGrid_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJGrid >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJGrid_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJGrid >, diff --git a/wrapper/MM/CLJGroup.pypp.cpp b/wrapper/MM/CLJGroup.pypp.cpp index 9680cb2b3..17c1097b0 100644 --- a/wrapper/MM/CLJGroup.pypp.cpp +++ b/wrapper/MM/CLJGroup.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireMM::CLJGroup __copy__(const SireMM::CLJGroup &other){ return SireMM::CLJGroup(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -458,9 +460,9 @@ void register_CLJGroup_class(){ } CLJGroup_exposer.staticmethod( "typeName" ); - CLJGroup_exposer.def( "__copy__", &__copy__); - CLJGroup_exposer.def( "__deepcopy__", &__copy__); - CLJGroup_exposer.def( "clone", &__copy__); + CLJGroup_exposer.def( "__copy__", &__copy__); + CLJGroup_exposer.def( "__deepcopy__", &__copy__); + CLJGroup_exposer.def( "clone", &__copy__); CLJGroup_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJGroup >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJGroup_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJGroup >, diff --git a/wrapper/MM/CLJIntraRFFunction.pypp.cpp b/wrapper/MM/CLJIntraRFFunction.pypp.cpp index 472bb1b4a..274b71f7a 100644 --- a/wrapper/MM/CLJIntraRFFunction.pypp.cpp +++ b/wrapper/MM/CLJIntraRFFunction.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::CLJIntraRFFunction __copy__(const SireMM::CLJIntraRFFunction &other){ return SireMM::CLJIntraRFFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -186,9 +188,9 @@ void register_CLJIntraRFFunction_class(){ } CLJIntraRFFunction_exposer.staticmethod( "defaultRFFunction" ); CLJIntraRFFunction_exposer.staticmethod( "typeName" ); - CLJIntraRFFunction_exposer.def( "__copy__", &__copy__); - CLJIntraRFFunction_exposer.def( "__deepcopy__", &__copy__); - CLJIntraRFFunction_exposer.def( "clone", &__copy__); + CLJIntraRFFunction_exposer.def( "__copy__", &__copy__); + CLJIntraRFFunction_exposer.def( "__deepcopy__", &__copy__); + CLJIntraRFFunction_exposer.def( "clone", &__copy__); CLJIntraRFFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJIntraRFFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJIntraRFFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJIntraRFFunction >, diff --git a/wrapper/MM/CLJIntraShiftFunction.pypp.cpp b/wrapper/MM/CLJIntraShiftFunction.pypp.cpp index 1044ce451..1cd139361 100644 --- a/wrapper/MM/CLJIntraShiftFunction.pypp.cpp +++ b/wrapper/MM/CLJIntraShiftFunction.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::CLJIntraShiftFunction __copy__(const SireMM::CLJIntraShiftFunction &other){ return SireMM::CLJIntraShiftFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -108,9 +110,9 @@ void register_CLJIntraShiftFunction_class(){ } CLJIntraShiftFunction_exposer.staticmethod( "defaultShiftFunction" ); CLJIntraShiftFunction_exposer.staticmethod( "typeName" ); - CLJIntraShiftFunction_exposer.def( "__copy__", &__copy__); - CLJIntraShiftFunction_exposer.def( "__deepcopy__", &__copy__); - CLJIntraShiftFunction_exposer.def( "clone", &__copy__); + CLJIntraShiftFunction_exposer.def( "__copy__", &__copy__); + CLJIntraShiftFunction_exposer.def( "__deepcopy__", &__copy__); + CLJIntraShiftFunction_exposer.def( "clone", &__copy__); CLJIntraShiftFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJIntraShiftFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJIntraShiftFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJIntraShiftFunction >, diff --git a/wrapper/MM/CLJNBPairs.pypp.cpp b/wrapper/MM/CLJNBPairs.pypp.cpp index c918920de..bf6577f63 100644 --- a/wrapper/MM/CLJNBPairs.pypp.cpp +++ b/wrapper/MM/CLJNBPairs.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::CLJNBPairs __copy__(const SireMM::CLJNBPairs &other){ return SireMM::CLJNBPairs(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -83,7 +85,7 @@ void register_CLJNBPairs_class(){ "merge" , merge_function_value , ( bp::arg("other"), bp::arg("mapping"), bp::arg("ghost")=::QString( ), bp::arg("map")=SireBase::PropertyMap() ) - , "" ); + , "Merge this property with another property" ); } { //::SireMM::CLJNBPairs::nExcludedAtoms @@ -151,9 +153,9 @@ void register_CLJNBPairs_class(){ } CLJNBPairs_exposer.staticmethod( "typeName" ); - CLJNBPairs_exposer.def( "__copy__", &__copy__); - CLJNBPairs_exposer.def( "__deepcopy__", &__copy__); - CLJNBPairs_exposer.def( "clone", &__copy__); + CLJNBPairs_exposer.def( "__copy__", &__copy__); + CLJNBPairs_exposer.def( "__deepcopy__", &__copy__); + CLJNBPairs_exposer.def( "clone", &__copy__); CLJNBPairs_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJNBPairs >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJNBPairs_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJNBPairs >, diff --git a/wrapper/MM/CLJParameterNames.pypp.cpp b/wrapper/MM/CLJParameterNames.pypp.cpp index b93550b69..b4aba2539 100644 --- a/wrapper/MM/CLJParameterNames.pypp.cpp +++ b/wrapper/MM/CLJParameterNames.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; SireMM::CLJParameterNames __copy__(const SireMM::CLJParameterNames &other){ return SireMM::CLJParameterNames(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::CLJParameterNames&){ return "SireMM::CLJParameterNames";} #include "Helpers/release_gil_policy.hpp" @@ -53,9 +55,9 @@ void register_CLJParameterNames_class(){ typedef bp::class_< SireMM::CLJParameterNames, bp::bases< SireMM::LJParameterName, SireMM::ChargeParameterName > > CLJParameterNames_exposer_t; CLJParameterNames_exposer_t CLJParameterNames_exposer = CLJParameterNames_exposer_t( "CLJParameterNames", "This class provides the default name of the properties\nthat contain the charge and LJ parameters", bp::init< >("") ); bp::scope CLJParameterNames_scope( CLJParameterNames_exposer ); - CLJParameterNames_exposer.def( "__copy__", &__copy__); - CLJParameterNames_exposer.def( "__deepcopy__", &__copy__); - CLJParameterNames_exposer.def( "clone", &__copy__); + CLJParameterNames_exposer.def( "__copy__", &__copy__); + CLJParameterNames_exposer.def( "__deepcopy__", &__copy__); + CLJParameterNames_exposer.def( "clone", &__copy__); CLJParameterNames_exposer.def( "__str__", &pvt_get_name); CLJParameterNames_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/CLJParameterNames3D.pypp.cpp b/wrapper/MM/CLJParameterNames3D.pypp.cpp index 24cd8003e..d47c55640 100644 --- a/wrapper/MM/CLJParameterNames3D.pypp.cpp +++ b/wrapper/MM/CLJParameterNames3D.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; SireMM::CLJParameterNames3D __copy__(const SireMM::CLJParameterNames3D &other){ return SireMM::CLJParameterNames3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::CLJParameterNames3D&){ return "SireMM::CLJParameterNames3D";} #include "Helpers/release_gil_policy.hpp" @@ -53,9 +55,9 @@ void register_CLJParameterNames3D_class(){ typedef bp::class_< SireMM::CLJParameterNames3D, bp::bases< SireMM::CLJParameterNames, SireMM::LJParameterName, SireMM::ChargeParameterName > > CLJParameterNames3D_exposer_t; CLJParameterNames3D_exposer_t CLJParameterNames3D_exposer = CLJParameterNames3D_exposer_t( "CLJParameterNames3D", "This class provides the default name of the properties\nthat contain the charge, LJ and 3D coordinates properties", bp::init< >("") ); bp::scope CLJParameterNames3D_scope( CLJParameterNames3D_exposer ); - CLJParameterNames3D_exposer.def( "__copy__", &__copy__); - CLJParameterNames3D_exposer.def( "__deepcopy__", &__copy__); - CLJParameterNames3D_exposer.def( "clone", &__copy__); + CLJParameterNames3D_exposer.def( "__copy__", &__copy__); + CLJParameterNames3D_exposer.def( "__deepcopy__", &__copy__); + CLJParameterNames3D_exposer.def( "clone", &__copy__); CLJParameterNames3D_exposer.def( "__str__", &pvt_get_name); CLJParameterNames3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/CLJProbe.pypp.cpp b/wrapper/MM/CLJProbe.pypp.cpp index 04bc5e992..06baa5a33 100644 --- a/wrapper/MM/CLJProbe.pypp.cpp +++ b/wrapper/MM/CLJProbe.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireMM::CLJProbe __copy__(const SireMM::CLJProbe &other){ return SireMM::CLJProbe(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -100,9 +102,9 @@ void register_CLJProbe_class(){ } CLJProbe_exposer.staticmethod( "typeName" ); - CLJProbe_exposer.def( "__copy__", &__copy__); - CLJProbe_exposer.def( "__deepcopy__", &__copy__); - CLJProbe_exposer.def( "clone", &__copy__); + CLJProbe_exposer.def( "__copy__", &__copy__); + CLJProbe_exposer.def( "__deepcopy__", &__copy__); + CLJProbe_exposer.def( "clone", &__copy__); CLJProbe_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJProbe >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJProbe_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJProbe >, diff --git a/wrapper/MM/CLJRFFunction.pypp.cpp b/wrapper/MM/CLJRFFunction.pypp.cpp index 97bf5289d..c1605c4bf 100644 --- a/wrapper/MM/CLJRFFunction.pypp.cpp +++ b/wrapper/MM/CLJRFFunction.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::CLJRFFunction __copy__(const SireMM::CLJRFFunction &other){ return SireMM::CLJRFFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -210,9 +212,9 @@ void register_CLJRFFunction_class(){ } CLJRFFunction_exposer.staticmethod( "defaultRFFunction" ); CLJRFFunction_exposer.staticmethod( "typeName" ); - CLJRFFunction_exposer.def( "__copy__", &__copy__); - CLJRFFunction_exposer.def( "__deepcopy__", &__copy__); - CLJRFFunction_exposer.def( "clone", &__copy__); + CLJRFFunction_exposer.def( "__copy__", &__copy__); + CLJRFFunction_exposer.def( "__deepcopy__", &__copy__); + CLJRFFunction_exposer.def( "clone", &__copy__); CLJRFFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJRFFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJRFFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJRFFunction >, diff --git a/wrapper/MM/CLJScaleFactor.pypp.cpp b/wrapper/MM/CLJScaleFactor.pypp.cpp index c5f83d9eb..e66756e5c 100644 --- a/wrapper/MM/CLJScaleFactor.pypp.cpp +++ b/wrapper/MM/CLJScaleFactor.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::CLJScaleFactor __copy__(const SireMM::CLJScaleFactor &other){ return SireMM::CLJScaleFactor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -85,9 +87,9 @@ void register_CLJScaleFactor_class(){ } CLJScaleFactor_exposer.staticmethod( "typeName" ); - CLJScaleFactor_exposer.def( "__copy__", &__copy__); - CLJScaleFactor_exposer.def( "__deepcopy__", &__copy__); - CLJScaleFactor_exposer.def( "clone", &__copy__); + CLJScaleFactor_exposer.def( "__copy__", &__copy__); + CLJScaleFactor_exposer.def( "__deepcopy__", &__copy__); + CLJScaleFactor_exposer.def( "clone", &__copy__); CLJScaleFactor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJScaleFactor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJScaleFactor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJScaleFactor >, diff --git a/wrapper/MM/CLJShiftFunction.pypp.cpp b/wrapper/MM/CLJShiftFunction.pypp.cpp index cc21dae29..8cd87291b 100644 --- a/wrapper/MM/CLJShiftFunction.pypp.cpp +++ b/wrapper/MM/CLJShiftFunction.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::CLJShiftFunction __copy__(const SireMM::CLJShiftFunction &other){ return SireMM::CLJShiftFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -132,9 +134,9 @@ void register_CLJShiftFunction_class(){ } CLJShiftFunction_exposer.staticmethod( "defaultShiftFunction" ); CLJShiftFunction_exposer.staticmethod( "typeName" ); - CLJShiftFunction_exposer.def( "__copy__", &__copy__); - CLJShiftFunction_exposer.def( "__deepcopy__", &__copy__); - CLJShiftFunction_exposer.def( "clone", &__copy__); + CLJShiftFunction_exposer.def( "__copy__", &__copy__); + CLJShiftFunction_exposer.def( "__deepcopy__", &__copy__); + CLJShiftFunction_exposer.def( "clone", &__copy__); CLJShiftFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJShiftFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJShiftFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJShiftFunction >, diff --git a/wrapper/MM/CLJSoftIntraRFFunction.pypp.cpp b/wrapper/MM/CLJSoftIntraRFFunction.pypp.cpp index 783f2b1be..5fbb00091 100644 --- a/wrapper/MM/CLJSoftIntraRFFunction.pypp.cpp +++ b/wrapper/MM/CLJSoftIntraRFFunction.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::CLJSoftIntraRFFunction __copy__(const SireMM::CLJSoftIntraRFFunction &other){ return SireMM::CLJSoftIntraRFFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -186,9 +188,9 @@ void register_CLJSoftIntraRFFunction_class(){ } CLJSoftIntraRFFunction_exposer.staticmethod( "defaultRFFunction" ); CLJSoftIntraRFFunction_exposer.staticmethod( "typeName" ); - CLJSoftIntraRFFunction_exposer.def( "__copy__", &__copy__); - CLJSoftIntraRFFunction_exposer.def( "__deepcopy__", &__copy__); - CLJSoftIntraRFFunction_exposer.def( "clone", &__copy__); + CLJSoftIntraRFFunction_exposer.def( "__copy__", &__copy__); + CLJSoftIntraRFFunction_exposer.def( "__deepcopy__", &__copy__); + CLJSoftIntraRFFunction_exposer.def( "clone", &__copy__); CLJSoftIntraRFFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJSoftIntraRFFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJSoftIntraRFFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJSoftIntraRFFunction >, diff --git a/wrapper/MM/CLJSoftIntraShiftFunction.pypp.cpp b/wrapper/MM/CLJSoftIntraShiftFunction.pypp.cpp index 49534fbb8..8cd02ab93 100644 --- a/wrapper/MM/CLJSoftIntraShiftFunction.pypp.cpp +++ b/wrapper/MM/CLJSoftIntraShiftFunction.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::CLJSoftIntraShiftFunction __copy__(const SireMM::CLJSoftIntraShiftFunction &other){ return SireMM::CLJSoftIntraShiftFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -108,9 +110,9 @@ void register_CLJSoftIntraShiftFunction_class(){ } CLJSoftIntraShiftFunction_exposer.staticmethod( "defaultShiftFunction" ); CLJSoftIntraShiftFunction_exposer.staticmethod( "typeName" ); - CLJSoftIntraShiftFunction_exposer.def( "__copy__", &__copy__); - CLJSoftIntraShiftFunction_exposer.def( "__deepcopy__", &__copy__); - CLJSoftIntraShiftFunction_exposer.def( "clone", &__copy__); + CLJSoftIntraShiftFunction_exposer.def( "__copy__", &__copy__); + CLJSoftIntraShiftFunction_exposer.def( "__deepcopy__", &__copy__); + CLJSoftIntraShiftFunction_exposer.def( "clone", &__copy__); CLJSoftIntraShiftFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJSoftIntraShiftFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJSoftIntraShiftFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJSoftIntraShiftFunction >, diff --git a/wrapper/MM/CLJSoftRFFunction.pypp.cpp b/wrapper/MM/CLJSoftRFFunction.pypp.cpp index 21605ad1c..c0461ef4b 100644 --- a/wrapper/MM/CLJSoftRFFunction.pypp.cpp +++ b/wrapper/MM/CLJSoftRFFunction.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::CLJSoftRFFunction __copy__(const SireMM::CLJSoftRFFunction &other){ return SireMM::CLJSoftRFFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -198,9 +200,9 @@ void register_CLJSoftRFFunction_class(){ } CLJSoftRFFunction_exposer.staticmethod( "defaultRFFunction" ); CLJSoftRFFunction_exposer.staticmethod( "typeName" ); - CLJSoftRFFunction_exposer.def( "__copy__", &__copy__); - CLJSoftRFFunction_exposer.def( "__deepcopy__", &__copy__); - CLJSoftRFFunction_exposer.def( "clone", &__copy__); + CLJSoftRFFunction_exposer.def( "__copy__", &__copy__); + CLJSoftRFFunction_exposer.def( "__deepcopy__", &__copy__); + CLJSoftRFFunction_exposer.def( "clone", &__copy__); CLJSoftRFFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJSoftRFFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJSoftRFFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJSoftRFFunction >, diff --git a/wrapper/MM/CLJSoftShiftFunction.pypp.cpp b/wrapper/MM/CLJSoftShiftFunction.pypp.cpp index f561e3ed0..ffcab1e0a 100644 --- a/wrapper/MM/CLJSoftShiftFunction.pypp.cpp +++ b/wrapper/MM/CLJSoftShiftFunction.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::CLJSoftShiftFunction __copy__(const SireMM::CLJSoftShiftFunction &other){ return SireMM::CLJSoftShiftFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -120,9 +122,9 @@ void register_CLJSoftShiftFunction_class(){ } CLJSoftShiftFunction_exposer.staticmethod( "defaultShiftFunction" ); CLJSoftShiftFunction_exposer.staticmethod( "typeName" ); - CLJSoftShiftFunction_exposer.def( "__copy__", &__copy__); - CLJSoftShiftFunction_exposer.def( "__deepcopy__", &__copy__); - CLJSoftShiftFunction_exposer.def( "clone", &__copy__); + CLJSoftShiftFunction_exposer.def( "__copy__", &__copy__); + CLJSoftShiftFunction_exposer.def( "__deepcopy__", &__copy__); + CLJSoftShiftFunction_exposer.def( "clone", &__copy__); CLJSoftShiftFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJSoftShiftFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJSoftShiftFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJSoftShiftFunction >, diff --git a/wrapper/MM/CLJWorkspace.pypp.cpp b/wrapper/MM/CLJWorkspace.pypp.cpp index 3cbb6a1bc..a478e200f 100644 --- a/wrapper/MM/CLJWorkspace.pypp.cpp +++ b/wrapper/MM/CLJWorkspace.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireMM::CLJWorkspace __copy__(const SireMM::CLJWorkspace &other){ return SireMM::CLJWorkspace(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -351,9 +353,9 @@ void register_CLJWorkspace_class(){ } CLJWorkspace_exposer.staticmethod( "typeName" ); - CLJWorkspace_exposer.def( "__copy__", &__copy__); - CLJWorkspace_exposer.def( "__deepcopy__", &__copy__); - CLJWorkspace_exposer.def( "clone", &__copy__); + CLJWorkspace_exposer.def( "__copy__", &__copy__); + CLJWorkspace_exposer.def( "__deepcopy__", &__copy__); + CLJWorkspace_exposer.def( "clone", &__copy__); CLJWorkspace_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CLJWorkspace >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CLJWorkspace_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CLJWorkspace >, diff --git a/wrapper/MM/ChargeParameterName.pypp.cpp b/wrapper/MM/ChargeParameterName.pypp.cpp index a324d88dc..7932d34ed 100644 --- a/wrapper/MM/ChargeParameterName.pypp.cpp +++ b/wrapper/MM/ChargeParameterName.pypp.cpp @@ -41,6 +41,8 @@ namespace bp = boost::python; SireMM::ChargeParameterName __copy__(const SireMM::ChargeParameterName &other){ return SireMM::ChargeParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ChargeParameterName&){ return "SireMM::ChargeParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -63,9 +65,9 @@ void register_ChargeParameterName_class(){ , "" ); } - ChargeParameterName_exposer.def( "__copy__", &__copy__); - ChargeParameterName_exposer.def( "__deepcopy__", &__copy__); - ChargeParameterName_exposer.def( "clone", &__copy__); + ChargeParameterName_exposer.def( "__copy__", &__copy__); + ChargeParameterName_exposer.def( "__deepcopy__", &__copy__); + ChargeParameterName_exposer.def( "clone", &__copy__); ChargeParameterName_exposer.def( "__str__", &pvt_get_name); ChargeParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/ChargeParameterName3D.pypp.cpp b/wrapper/MM/ChargeParameterName3D.pypp.cpp index 8db9d1cbf..6ccb96d4c 100644 --- a/wrapper/MM/ChargeParameterName3D.pypp.cpp +++ b/wrapper/MM/ChargeParameterName3D.pypp.cpp @@ -41,6 +41,8 @@ namespace bp = boost::python; SireMM::ChargeParameterName3D __copy__(const SireMM::ChargeParameterName3D &other){ return SireMM::ChargeParameterName3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ChargeParameterName3D&){ return "SireMM::ChargeParameterName3D";} #include "Helpers/release_gil_policy.hpp" @@ -51,9 +53,9 @@ void register_ChargeParameterName3D_class(){ typedef bp::class_< SireMM::ChargeParameterName3D, bp::bases< SireMM::ChargeParameterName > > ChargeParameterName3D_exposer_t; ChargeParameterName3D_exposer_t ChargeParameterName3D_exposer = ChargeParameterName3D_exposer_t( "ChargeParameterName3D", "This class provides the default name of the properties\nthat contain the charge, LJ and 3D coordinates properties", bp::init< >("") ); bp::scope ChargeParameterName3D_scope( ChargeParameterName3D_exposer ); - ChargeParameterName3D_exposer.def( "__copy__", &__copy__); - ChargeParameterName3D_exposer.def( "__deepcopy__", &__copy__); - ChargeParameterName3D_exposer.def( "clone", &__copy__); + ChargeParameterName3D_exposer.def( "__copy__", &__copy__); + ChargeParameterName3D_exposer.def( "__deepcopy__", &__copy__); + ChargeParameterName3D_exposer.def( "clone", &__copy__); ChargeParameterName3D_exposer.def( "__str__", &pvt_get_name); ChargeParameterName3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/CoulombComponent.pypp.cpp b/wrapper/MM/CoulombComponent.pypp.cpp index 683f83e5f..965ab6f78 100644 --- a/wrapper/MM/CoulombComponent.pypp.cpp +++ b/wrapper/MM/CoulombComponent.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; SireMM::CoulombComponent __copy__(const SireMM::CoulombComponent &other){ return SireMM::CoulombComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -106,9 +108,9 @@ void register_CoulombComponent_class(){ } CoulombComponent_exposer.staticmethod( "typeName" ); - CoulombComponent_exposer.def( "__copy__", &__copy__); - CoulombComponent_exposer.def( "__deepcopy__", &__copy__); - CoulombComponent_exposer.def( "clone", &__copy__); + CoulombComponent_exposer.def( "__copy__", &__copy__); + CoulombComponent_exposer.def( "__deepcopy__", &__copy__); + CoulombComponent_exposer.def( "clone", &__copy__); CoulombComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CoulombComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CoulombComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CoulombComponent >, diff --git a/wrapper/MM/CoulombNBPairs.pypp.cpp b/wrapper/MM/CoulombNBPairs.pypp.cpp index a80af7324..cf40221c1 100644 --- a/wrapper/MM/CoulombNBPairs.pypp.cpp +++ b/wrapper/MM/CoulombNBPairs.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::CoulombNBPairs __copy__(const SireMM::CoulombNBPairs &other){ return SireMM::CoulombNBPairs(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -76,9 +78,9 @@ void register_CoulombNBPairs_class(){ } CoulombNBPairs_exposer.staticmethod( "typeName" ); - CoulombNBPairs_exposer.def( "__copy__", &__copy__); - CoulombNBPairs_exposer.def( "__deepcopy__", &__copy__); - CoulombNBPairs_exposer.def( "clone", &__copy__); + CoulombNBPairs_exposer.def( "__copy__", &__copy__); + CoulombNBPairs_exposer.def( "__deepcopy__", &__copy__); + CoulombNBPairs_exposer.def( "clone", &__copy__); CoulombNBPairs_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CoulombNBPairs >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CoulombNBPairs_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CoulombNBPairs >, diff --git a/wrapper/MM/CoulombProbe.pypp.cpp b/wrapper/MM/CoulombProbe.pypp.cpp index 2e51a8328..f820958b1 100644 --- a/wrapper/MM/CoulombProbe.pypp.cpp +++ b/wrapper/MM/CoulombProbe.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireMM::CoulombProbe __copy__(const SireMM::CoulombProbe &other){ return SireMM::CoulombProbe(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -85,9 +87,9 @@ void register_CoulombProbe_class(){ } CoulombProbe_exposer.staticmethod( "typeName" ); - CoulombProbe_exposer.def( "__copy__", &__copy__); - CoulombProbe_exposer.def( "__deepcopy__", &__copy__); - CoulombProbe_exposer.def( "clone", &__copy__); + CoulombProbe_exposer.def( "__copy__", &__copy__); + CoulombProbe_exposer.def( "__deepcopy__", &__copy__); + CoulombProbe_exposer.def( "clone", &__copy__); CoulombProbe_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CoulombProbe >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CoulombProbe_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CoulombProbe >, diff --git a/wrapper/MM/CoulombScaleFactor.pypp.cpp b/wrapper/MM/CoulombScaleFactor.pypp.cpp index 299db676a..3072d6dbf 100644 --- a/wrapper/MM/CoulombScaleFactor.pypp.cpp +++ b/wrapper/MM/CoulombScaleFactor.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::CoulombScaleFactor __copy__(const SireMM::CoulombScaleFactor &other){ return SireMM::CoulombScaleFactor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireMM::CoulombScaleFactor&){ return "SireMM::CoulombScaleFactor";} @@ -84,9 +86,9 @@ void register_CoulombScaleFactor_class(){ } CoulombScaleFactor_exposer.staticmethod( "typeName" ); - CoulombScaleFactor_exposer.def( "__copy__", &__copy__); - CoulombScaleFactor_exposer.def( "__deepcopy__", &__copy__); - CoulombScaleFactor_exposer.def( "clone", &__copy__); + CoulombScaleFactor_exposer.def( "__copy__", &__copy__); + CoulombScaleFactor_exposer.def( "__deepcopy__", &__copy__); + CoulombScaleFactor_exposer.def( "clone", &__copy__); CoulombScaleFactor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::CoulombScaleFactor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CoulombScaleFactor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::CoulombScaleFactor >, diff --git a/wrapper/MM/Dihedral.pypp.cpp b/wrapper/MM/Dihedral.pypp.cpp index abf7cdd74..380f98f90 100644 --- a/wrapper/MM/Dihedral.pypp.cpp +++ b/wrapper/MM/Dihedral.pypp.cpp @@ -42,6 +42,8 @@ namespace bp = boost::python; SireMM::Dihedral __copy__(const SireMM::Dihedral &other){ return SireMM::Dihedral(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -483,9 +485,9 @@ void register_Dihedral_class(){ } Dihedral_exposer.staticmethod( "typeName" ); - Dihedral_exposer.def( "__copy__", &__copy__); - Dihedral_exposer.def( "__deepcopy__", &__copy__); - Dihedral_exposer.def( "clone", &__copy__); + Dihedral_exposer.def( "__copy__", &__copy__); + Dihedral_exposer.def( "__deepcopy__", &__copy__); + Dihedral_exposer.def( "clone", &__copy__); Dihedral_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Dihedral >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Dihedral_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Dihedral >, diff --git a/wrapper/MM/DihedralComponent.pypp.cpp b/wrapper/MM/DihedralComponent.pypp.cpp index 537830aca..8d10f067b 100644 --- a/wrapper/MM/DihedralComponent.pypp.cpp +++ b/wrapper/MM/DihedralComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::DihedralComponent __copy__(const SireMM::DihedralComponent &other){ return SireMM::DihedralComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_DihedralComponent_class(){ } DihedralComponent_exposer.staticmethod( "typeName" ); - DihedralComponent_exposer.def( "__copy__", &__copy__); - DihedralComponent_exposer.def( "__deepcopy__", &__copy__); - DihedralComponent_exposer.def( "clone", &__copy__); + DihedralComponent_exposer.def( "__copy__", &__copy__); + DihedralComponent_exposer.def( "__deepcopy__", &__copy__); + DihedralComponent_exposer.def( "clone", &__copy__); DihedralComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::DihedralComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DihedralComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::DihedralComponent >, diff --git a/wrapper/MM/DihedralParameterName.pypp.cpp b/wrapper/MM/DihedralParameterName.pypp.cpp index 36ddb6c5f..f2eb7e9dc 100644 --- a/wrapper/MM/DihedralParameterName.pypp.cpp +++ b/wrapper/MM/DihedralParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::DihedralParameterName __copy__(const SireMM::DihedralParameterName &other){ return SireMM::DihedralParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::DihedralParameterName&){ return "SireMM::DihedralParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_DihedralParameterName_class(){ , "" ); } - DihedralParameterName_exposer.def( "__copy__", &__copy__); - DihedralParameterName_exposer.def( "__deepcopy__", &__copy__); - DihedralParameterName_exposer.def( "clone", &__copy__); + DihedralParameterName_exposer.def( "__copy__", &__copy__); + DihedralParameterName_exposer.def( "__deepcopy__", &__copy__); + DihedralParameterName_exposer.def( "clone", &__copy__); DihedralParameterName_exposer.def( "__str__", &pvt_get_name); DihedralParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/DihedralRestraint.pypp.cpp b/wrapper/MM/DihedralRestraint.pypp.cpp index e133849e6..65ed2feb1 100644 --- a/wrapper/MM/DihedralRestraint.pypp.cpp +++ b/wrapper/MM/DihedralRestraint.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireMM::DihedralRestraint __copy__(const SireMM::DihedralRestraint &other){ return SireMM::DihedralRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -369,9 +371,9 @@ void register_DihedralRestraint_class(){ DihedralRestraint_exposer.staticmethod( "harmonic" ); DihedralRestraint_exposer.staticmethod( "phi" ); DihedralRestraint_exposer.staticmethod( "typeName" ); - DihedralRestraint_exposer.def( "__copy__", &__copy__); - DihedralRestraint_exposer.def( "__deepcopy__", &__copy__); - DihedralRestraint_exposer.def( "clone", &__copy__); + DihedralRestraint_exposer.def( "__copy__", &__copy__); + DihedralRestraint_exposer.def( "__deepcopy__", &__copy__); + DihedralRestraint_exposer.def( "clone", &__copy__); DihedralRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::DihedralRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DihedralRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::DihedralRestraint >, diff --git a/wrapper/MM/DihedralSymbols.pypp.cpp b/wrapper/MM/DihedralSymbols.pypp.cpp index 9e0259739..3d7fa0d59 100644 --- a/wrapper/MM/DihedralSymbols.pypp.cpp +++ b/wrapper/MM/DihedralSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::DihedralSymbols __copy__(const SireMM::DihedralSymbols &other){ return SireMM::DihedralSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::DihedralSymbols&){ return "SireMM::DihedralSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -56,9 +58,9 @@ void register_DihedralSymbols_class(){ , "Return the symbol representing the torsion (phi)" ); } - DihedralSymbols_exposer.def( "__copy__", &__copy__); - DihedralSymbols_exposer.def( "__deepcopy__", &__copy__); - DihedralSymbols_exposer.def( "clone", &__copy__); + DihedralSymbols_exposer.def( "__copy__", &__copy__); + DihedralSymbols_exposer.def( "__deepcopy__", &__copy__); + DihedralSymbols_exposer.def( "clone", &__copy__); DihedralSymbols_exposer.def( "__str__", &pvt_get_name); DihedralSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/DistanceRestraint.pypp.cpp b/wrapper/MM/DistanceRestraint.pypp.cpp index 1f59e2873..752ae2b93 100644 --- a/wrapper/MM/DistanceRestraint.pypp.cpp +++ b/wrapper/MM/DistanceRestraint.pypp.cpp @@ -32,6 +32,8 @@ namespace bp = boost::python; SireMM::DistanceRestraint __copy__(const SireMM::DistanceRestraint &other){ return SireMM::DistanceRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -341,9 +343,9 @@ void register_DistanceRestraint_class(){ DistanceRestraint_exposer.staticmethod( "harmonic" ); DistanceRestraint_exposer.staticmethod( "r" ); DistanceRestraint_exposer.staticmethod( "typeName" ); - DistanceRestraint_exposer.def( "__copy__", &__copy__); - DistanceRestraint_exposer.def( "__deepcopy__", &__copy__); - DistanceRestraint_exposer.def( "clone", &__copy__); + DistanceRestraint_exposer.def( "__copy__", &__copy__); + DistanceRestraint_exposer.def( "__deepcopy__", &__copy__); + DistanceRestraint_exposer.def( "clone", &__copy__); DistanceRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::DistanceRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DistanceRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::DistanceRestraint >, diff --git a/wrapper/MM/DoubleDistanceRestraint.pypp.cpp b/wrapper/MM/DoubleDistanceRestraint.pypp.cpp index 47595c01b..585f63ed8 100644 --- a/wrapper/MM/DoubleDistanceRestraint.pypp.cpp +++ b/wrapper/MM/DoubleDistanceRestraint.pypp.cpp @@ -32,6 +32,8 @@ namespace bp = boost::python; SireMM::DoubleDistanceRestraint __copy__(const SireMM::DoubleDistanceRestraint &other){ return SireMM::DoubleDistanceRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -362,9 +364,9 @@ void register_DoubleDistanceRestraint_class(){ DoubleDistanceRestraint_exposer.staticmethod( "r01" ); DoubleDistanceRestraint_exposer.staticmethod( "r23" ); DoubleDistanceRestraint_exposer.staticmethod( "typeName" ); - DoubleDistanceRestraint_exposer.def( "__copy__", &__copy__); - DoubleDistanceRestraint_exposer.def( "__deepcopy__", &__copy__); - DoubleDistanceRestraint_exposer.def( "clone", &__copy__); + DoubleDistanceRestraint_exposer.def( "__copy__", &__copy__); + DoubleDistanceRestraint_exposer.def( "__deepcopy__", &__copy__); + DoubleDistanceRestraint_exposer.def( "clone", &__copy__); DoubleDistanceRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::DoubleDistanceRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DoubleDistanceRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::DoubleDistanceRestraint >, diff --git a/wrapper/MM/ExcludedPairs.pypp.cpp b/wrapper/MM/ExcludedPairs.pypp.cpp index 3b4c4d621..b480d1a38 100644 --- a/wrapper/MM/ExcludedPairs.pypp.cpp +++ b/wrapper/MM/ExcludedPairs.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::ExcludedPairs __copy__(const SireMM::ExcludedPairs &other){ return SireMM::ExcludedPairs(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -199,9 +201,9 @@ void register_ExcludedPairs_class(){ } ExcludedPairs_exposer.staticmethod( "typeName" ); - ExcludedPairs_exposer.def( "__copy__", &__copy__); - ExcludedPairs_exposer.def( "__deepcopy__", &__copy__); - ExcludedPairs_exposer.def( "clone", &__copy__); + ExcludedPairs_exposer.def( "__copy__", &__copy__); + ExcludedPairs_exposer.def( "__deepcopy__", &__copy__); + ExcludedPairs_exposer.def( "clone", &__copy__); ExcludedPairs_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::ExcludedPairs >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ExcludedPairs_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::ExcludedPairs >, diff --git a/wrapper/MM/FourAtomFunction.pypp.cpp b/wrapper/MM/FourAtomFunction.pypp.cpp index 2456677e9..29b950c0c 100644 --- a/wrapper/MM/FourAtomFunction.pypp.cpp +++ b/wrapper/MM/FourAtomFunction.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::FourAtomFunction __copy__(const SireMM::FourAtomFunction &other){ return SireMM::FourAtomFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -123,9 +125,9 @@ void register_FourAtomFunction_class(){ , "Return a string representation" ); } - FourAtomFunction_exposer.def( "__copy__", &__copy__); - FourAtomFunction_exposer.def( "__deepcopy__", &__copy__); - FourAtomFunction_exposer.def( "clone", &__copy__); + FourAtomFunction_exposer.def( "__copy__", &__copy__); + FourAtomFunction_exposer.def( "__deepcopy__", &__copy__); + FourAtomFunction_exposer.def( "clone", &__copy__); FourAtomFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::FourAtomFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); FourAtomFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::FourAtomFunction >, diff --git a/wrapper/MM/FourAtomFunctions.pypp.cpp b/wrapper/MM/FourAtomFunctions.pypp.cpp index ff40dfe7d..ae875205c 100644 --- a/wrapper/MM/FourAtomFunctions.pypp.cpp +++ b/wrapper/MM/FourAtomFunctions.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::FourAtomFunctions __copy__(const SireMM::FourAtomFunctions &other){ return SireMM::FourAtomFunctions(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -446,9 +448,9 @@ void register_FourAtomFunctions_class(){ } FourAtomFunctions_exposer.staticmethod( "typeName" ); - FourAtomFunctions_exposer.def( "__copy__", &__copy__); - FourAtomFunctions_exposer.def( "__deepcopy__", &__copy__); - FourAtomFunctions_exposer.def( "clone", &__copy__); + FourAtomFunctions_exposer.def( "__copy__", &__copy__); + FourAtomFunctions_exposer.def( "__deepcopy__", &__copy__); + FourAtomFunctions_exposer.def( "clone", &__copy__); FourAtomFunctions_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::FourAtomFunctions >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); FourAtomFunctions_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::FourAtomFunctions >, diff --git a/wrapper/MM/FourAtomPerturbation.pypp.cpp b/wrapper/MM/FourAtomPerturbation.pypp.cpp index 2b454fa66..64d0fea73 100644 --- a/wrapper/MM/FourAtomPerturbation.pypp.cpp +++ b/wrapper/MM/FourAtomPerturbation.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::FourAtomPerturbation __copy__(const SireMM::FourAtomPerturbation &other){ return SireMM::FourAtomPerturbation(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -164,9 +166,9 @@ void register_FourAtomPerturbation_class(){ } FourAtomPerturbation_exposer.staticmethod( "typeName" ); - FourAtomPerturbation_exposer.def( "__copy__", &__copy__); - FourAtomPerturbation_exposer.def( "__deepcopy__", &__copy__); - FourAtomPerturbation_exposer.def( "clone", &__copy__); + FourAtomPerturbation_exposer.def( "__copy__", &__copy__); + FourAtomPerturbation_exposer.def( "__deepcopy__", &__copy__); + FourAtomPerturbation_exposer.def( "clone", &__copy__); FourAtomPerturbation_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::FourAtomPerturbation >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); FourAtomPerturbation_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::FourAtomPerturbation >, diff --git a/wrapper/MM/GridFF.pypp.cpp b/wrapper/MM/GridFF.pypp.cpp index ad2bdeb63..01605f874 100644 --- a/wrapper/MM/GridFF.pypp.cpp +++ b/wrapper/MM/GridFF.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::GridFF __copy__(const SireMM::GridFF &other){ return SireMM::GridFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -291,9 +293,9 @@ void register_GridFF_class(){ } GridFF_exposer.staticmethod( "typeName" ); - GridFF_exposer.def( "__copy__", &__copy__); - GridFF_exposer.def( "__deepcopy__", &__copy__); - GridFF_exposer.def( "clone", &__copy__); + GridFF_exposer.def( "__copy__", &__copy__); + GridFF_exposer.def( "__deepcopy__", &__copy__); + GridFF_exposer.def( "clone", &__copy__); GridFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GridFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GridFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GridFF >, diff --git a/wrapper/MM/GridFF2.pypp.cpp b/wrapper/MM/GridFF2.pypp.cpp index ad07adb20..07e9b0438 100644 --- a/wrapper/MM/GridFF2.pypp.cpp +++ b/wrapper/MM/GridFF2.pypp.cpp @@ -41,6 +41,8 @@ namespace bp = boost::python; SireMM::GridFF2 __copy__(const SireMM::GridFF2 &other){ return SireMM::GridFF2(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -297,9 +299,9 @@ void register_GridFF2_class(){ } GridFF2_exposer.staticmethod( "typeName" ); - GridFF2_exposer.def( "__copy__", &__copy__); - GridFF2_exposer.def( "__deepcopy__", &__copy__); - GridFF2_exposer.def( "clone", &__copy__); + GridFF2_exposer.def( "__copy__", &__copy__); + GridFF2_exposer.def( "__deepcopy__", &__copy__); + GridFF2_exposer.def( "clone", &__copy__); GridFF2_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GridFF2 >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GridFF2_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GridFF2 >, diff --git a/wrapper/MM/GromacsAngle.pypp.cpp b/wrapper/MM/GromacsAngle.pypp.cpp index 9592ba546..7036e338e 100644 --- a/wrapper/MM/GromacsAngle.pypp.cpp +++ b/wrapper/MM/GromacsAngle.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::GromacsAngle __copy__(const SireMM::GromacsAngle &other){ return SireMM::GromacsAngle(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -355,9 +357,9 @@ void register_GromacsAngle_class(){ } GromacsAngle_exposer.staticmethod( "typeName" ); - GromacsAngle_exposer.def( "__copy__", &__copy__); - GromacsAngle_exposer.def( "__deepcopy__", &__copy__); - GromacsAngle_exposer.def( "clone", &__copy__); + GromacsAngle_exposer.def( "__copy__", &__copy__); + GromacsAngle_exposer.def( "__deepcopy__", &__copy__); + GromacsAngle_exposer.def( "clone", &__copy__); GromacsAngle_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GromacsAngle >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GromacsAngle_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GromacsAngle >, diff --git a/wrapper/MM/GromacsAtomType.pypp.cpp b/wrapper/MM/GromacsAtomType.pypp.cpp index 3cd7fdf25..2a87ede39 100644 --- a/wrapper/MM/GromacsAtomType.pypp.cpp +++ b/wrapper/MM/GromacsAtomType.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::GromacsAtomType __copy__(const SireMM::GromacsAtomType &other){ return SireMM::GromacsAtomType(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -281,9 +283,9 @@ void register_GromacsAtomType_class(){ } GromacsAtomType_exposer.staticmethod( "toParticleType" ); GromacsAtomType_exposer.staticmethod( "typeName" ); - GromacsAtomType_exposer.def( "__copy__", &__copy__); - GromacsAtomType_exposer.def( "__deepcopy__", &__copy__); - GromacsAtomType_exposer.def( "clone", &__copy__); + GromacsAtomType_exposer.def( "__copy__", &__copy__); + GromacsAtomType_exposer.def( "__deepcopy__", &__copy__); + GromacsAtomType_exposer.def( "clone", &__copy__); GromacsAtomType_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GromacsAtomType >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GromacsAtomType_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GromacsAtomType >, diff --git a/wrapper/MM/GromacsBond.pypp.cpp b/wrapper/MM/GromacsBond.pypp.cpp index 5a895a96f..6a792f3f9 100644 --- a/wrapper/MM/GromacsBond.pypp.cpp +++ b/wrapper/MM/GromacsBond.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::GromacsBond __copy__(const SireMM::GromacsBond &other){ return SireMM::GromacsBond(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -304,9 +306,9 @@ void register_GromacsBond_class(){ } GromacsBond_exposer.staticmethod( "typeName" ); - GromacsBond_exposer.def( "__copy__", &__copy__); - GromacsBond_exposer.def( "__deepcopy__", &__copy__); - GromacsBond_exposer.def( "clone", &__copy__); + GromacsBond_exposer.def( "__copy__", &__copy__); + GromacsBond_exposer.def( "__deepcopy__", &__copy__); + GromacsBond_exposer.def( "clone", &__copy__); GromacsBond_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GromacsBond >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GromacsBond_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GromacsBond >, diff --git a/wrapper/MM/GromacsDihedral.pypp.cpp b/wrapper/MM/GromacsDihedral.pypp.cpp index f0bd9ce1a..d93d1e524 100644 --- a/wrapper/MM/GromacsDihedral.pypp.cpp +++ b/wrapper/MM/GromacsDihedral.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::GromacsDihedral __copy__(const SireMM::GromacsDihedral &other){ return SireMM::GromacsDihedral(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -358,9 +360,9 @@ void register_GromacsDihedral_class(){ GromacsDihedral_exposer.staticmethod( "construct" ); GromacsDihedral_exposer.staticmethod( "constructImproper" ); GromacsDihedral_exposer.staticmethod( "typeName" ); - GromacsDihedral_exposer.def( "__copy__", &__copy__); - GromacsDihedral_exposer.def( "__deepcopy__", &__copy__); - GromacsDihedral_exposer.def( "clone", &__copy__); + GromacsDihedral_exposer.def( "__copy__", &__copy__); + GromacsDihedral_exposer.def( "__deepcopy__", &__copy__); + GromacsDihedral_exposer.def( "clone", &__copy__); GromacsDihedral_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GromacsDihedral >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GromacsDihedral_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GromacsDihedral >, diff --git a/wrapper/MM/GroupInternalParameters.pypp.cpp b/wrapper/MM/GroupInternalParameters.pypp.cpp index 865302bbe..b70f2e4ee 100644 --- a/wrapper/MM/GroupInternalParameters.pypp.cpp +++ b/wrapper/MM/GroupInternalParameters.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::GroupInternalParameters __copy__(const SireMM::GroupInternalParameters &other){ return SireMM::GroupInternalParameters(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireMM::GroupInternalParameters&){ return "SireMM::GroupInternalParameters";} @@ -643,9 +645,9 @@ void register_GroupInternalParameters_class(){ , "Return the Urey-Bradley potentials for this group" ); } - GroupInternalParameters_exposer.def( "__copy__", &__copy__); - GroupInternalParameters_exposer.def( "__deepcopy__", &__copy__); - GroupInternalParameters_exposer.def( "clone", &__copy__); + GroupInternalParameters_exposer.def( "__copy__", &__copy__); + GroupInternalParameters_exposer.def( "__deepcopy__", &__copy__); + GroupInternalParameters_exposer.def( "clone", &__copy__); GroupInternalParameters_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::GroupInternalParameters >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); GroupInternalParameters_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::GroupInternalParameters >, diff --git a/wrapper/MM/HarmonicSwitchingFunction.pypp.cpp b/wrapper/MM/HarmonicSwitchingFunction.pypp.cpp index 9ce77c4ad..18e95b56d 100644 --- a/wrapper/MM/HarmonicSwitchingFunction.pypp.cpp +++ b/wrapper/MM/HarmonicSwitchingFunction.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireMM::HarmonicSwitchingFunction __copy__(const SireMM::HarmonicSwitchingFunction &other){ return SireMM::HarmonicSwitchingFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -138,9 +140,9 @@ void register_HarmonicSwitchingFunction_class(){ } HarmonicSwitchingFunction_exposer.staticmethod( "typeName" ); - HarmonicSwitchingFunction_exposer.def( "__copy__", &__copy__); - HarmonicSwitchingFunction_exposer.def( "__deepcopy__", &__copy__); - HarmonicSwitchingFunction_exposer.def( "clone", &__copy__); + HarmonicSwitchingFunction_exposer.def( "__copy__", &__copy__); + HarmonicSwitchingFunction_exposer.def( "__deepcopy__", &__copy__); + HarmonicSwitchingFunction_exposer.def( "clone", &__copy__); HarmonicSwitchingFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::HarmonicSwitchingFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); HarmonicSwitchingFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::HarmonicSwitchingFunction >, diff --git a/wrapper/MM/Improper.pypp.cpp b/wrapper/MM/Improper.pypp.cpp index ac555b29e..a303e869e 100644 --- a/wrapper/MM/Improper.pypp.cpp +++ b/wrapper/MM/Improper.pypp.cpp @@ -44,6 +44,8 @@ namespace bp = boost::python; SireMM::Improper __copy__(const SireMM::Improper &other){ return SireMM::Improper(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -535,9 +537,9 @@ void register_Improper_class(){ } Improper_exposer.staticmethod( "typeName" ); - Improper_exposer.def( "__copy__", &__copy__); - Improper_exposer.def( "__deepcopy__", &__copy__); - Improper_exposer.def( "clone", &__copy__); + Improper_exposer.def( "__copy__", &__copy__); + Improper_exposer.def( "__deepcopy__", &__copy__); + Improper_exposer.def( "clone", &__copy__); Improper_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Improper >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Improper_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Improper >, diff --git a/wrapper/MM/ImproperComponent.pypp.cpp b/wrapper/MM/ImproperComponent.pypp.cpp index 85b7ffbda..9c7759ffc 100644 --- a/wrapper/MM/ImproperComponent.pypp.cpp +++ b/wrapper/MM/ImproperComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::ImproperComponent __copy__(const SireMM::ImproperComponent &other){ return SireMM::ImproperComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_ImproperComponent_class(){ } ImproperComponent_exposer.staticmethod( "typeName" ); - ImproperComponent_exposer.def( "__copy__", &__copy__); - ImproperComponent_exposer.def( "__deepcopy__", &__copy__); - ImproperComponent_exposer.def( "clone", &__copy__); + ImproperComponent_exposer.def( "__copy__", &__copy__); + ImproperComponent_exposer.def( "__deepcopy__", &__copy__); + ImproperComponent_exposer.def( "clone", &__copy__); ImproperComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::ImproperComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ImproperComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::ImproperComponent >, diff --git a/wrapper/MM/ImproperParameterName.pypp.cpp b/wrapper/MM/ImproperParameterName.pypp.cpp index 186b7e3f9..aa5bd0bab 100644 --- a/wrapper/MM/ImproperParameterName.pypp.cpp +++ b/wrapper/MM/ImproperParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::ImproperParameterName __copy__(const SireMM::ImproperParameterName &other){ return SireMM::ImproperParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ImproperParameterName&){ return "SireMM::ImproperParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_ImproperParameterName_class(){ , "" ); } - ImproperParameterName_exposer.def( "__copy__", &__copy__); - ImproperParameterName_exposer.def( "__deepcopy__", &__copy__); - ImproperParameterName_exposer.def( "clone", &__copy__); + ImproperParameterName_exposer.def( "__copy__", &__copy__); + ImproperParameterName_exposer.def( "__deepcopy__", &__copy__); + ImproperParameterName_exposer.def( "clone", &__copy__); ImproperParameterName_exposer.def( "__str__", &pvt_get_name); ImproperParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/ImproperSymbols.pypp.cpp b/wrapper/MM/ImproperSymbols.pypp.cpp index 59f6d1c89..874441c73 100644 --- a/wrapper/MM/ImproperSymbols.pypp.cpp +++ b/wrapper/MM/ImproperSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::ImproperSymbols __copy__(const SireMM::ImproperSymbols &other){ return SireMM::ImproperSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ImproperSymbols&){ return "SireMM::ImproperSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -68,9 +70,9 @@ void register_ImproperSymbols_class(){ , "Return the symbol representing the angle between the improper\nand the plane formed by atoms 1-3" ); } - ImproperSymbols_exposer.def( "__copy__", &__copy__); - ImproperSymbols_exposer.def( "__deepcopy__", &__copy__); - ImproperSymbols_exposer.def( "clone", &__copy__); + ImproperSymbols_exposer.def( "__copy__", &__copy__); + ImproperSymbols_exposer.def( "__deepcopy__", &__copy__); + ImproperSymbols_exposer.def( "clone", &__copy__); ImproperSymbols_exposer.def( "__str__", &pvt_get_name); ImproperSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/InterCLJFF.pypp.cpp b/wrapper/MM/InterCLJFF.pypp.cpp index 52b082f90..103b690c0 100644 --- a/wrapper/MM/InterCLJFF.pypp.cpp +++ b/wrapper/MM/InterCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B3DFF > __copy__(const SireFF::Inter2B3DFF > &other){ return SireFF::Inter2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -270,9 +272,9 @@ void register_InterCLJFF_class(){ } InterCLJFF_exposer.staticmethod( "typeName" ); - InterCLJFF_exposer.def( "__copy__", &__copy__); - InterCLJFF_exposer.def( "__deepcopy__", &__copy__); - InterCLJFF_exposer.def( "clone", &__copy__); + InterCLJFF_exposer.def( "__copy__", &__copy__ >>); + InterCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterCLJFF_exposer.def( "clone", &__copy__ >>); InterCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B3DFF > > ); InterCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B3DFF > > ); InterCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B3DFF > > ); diff --git a/wrapper/MM/InterCLJFFBase.pypp.cpp b/wrapper/MM/InterCLJFFBase.pypp.cpp index de6b53e3f..8c6d22c64 100644 --- a/wrapper/MM/InterCLJFFBase.pypp.cpp +++ b/wrapper/MM/InterCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2BFF > __copy__(const SireFF::Inter2BFF > &other){ return SireFF::Inter2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterCLJFFBase_class(){ } InterCLJFFBase_exposer.staticmethod( "typeName" ); - InterCLJFFBase_exposer.def( "__copy__", &__copy__); - InterCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - InterCLJFFBase_exposer.def( "clone", &__copy__); + InterCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + InterCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterCLJFFBase_exposer.def( "clone", &__copy__ >>); InterCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2BFF > >, diff --git a/wrapper/MM/InterCoulombFF.pypp.cpp b/wrapper/MM/InterCoulombFF.pypp.cpp index 083ed15ec..b26cf2f9e 100644 --- a/wrapper/MM/InterCoulombFF.pypp.cpp +++ b/wrapper/MM/InterCoulombFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B3DFF > __copy__(const SireFF::Inter2B3DFF > &other){ return SireFF::Inter2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -270,9 +272,9 @@ void register_InterCoulombFF_class(){ } InterCoulombFF_exposer.staticmethod( "typeName" ); - InterCoulombFF_exposer.def( "__copy__", &__copy__); - InterCoulombFF_exposer.def( "__deepcopy__", &__copy__); - InterCoulombFF_exposer.def( "clone", &__copy__); + InterCoulombFF_exposer.def( "__copy__", &__copy__ >>); + InterCoulombFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterCoulombFF_exposer.def( "clone", &__copy__ >>); InterCoulombFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B3DFF > > ); InterCoulombFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B3DFF > > ); InterCoulombFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B3DFF > > ); diff --git a/wrapper/MM/InterCoulombFFBase.pypp.cpp b/wrapper/MM/InterCoulombFFBase.pypp.cpp index 34e2b0ffe..54ef981e6 100644 --- a/wrapper/MM/InterCoulombFFBase.pypp.cpp +++ b/wrapper/MM/InterCoulombFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2BFF > __copy__(const SireFF::Inter2BFF > &other){ return SireFF::Inter2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterCoulombFFBase_class(){ } InterCoulombFFBase_exposer.staticmethod( "typeName" ); - InterCoulombFFBase_exposer.def( "__copy__", &__copy__); - InterCoulombFFBase_exposer.def( "__deepcopy__", &__copy__); - InterCoulombFFBase_exposer.def( "clone", &__copy__); + InterCoulombFFBase_exposer.def( "__copy__", &__copy__ >>); + InterCoulombFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterCoulombFFBase_exposer.def( "clone", &__copy__ >>); InterCoulombFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterCoulombFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2BFF > >, diff --git a/wrapper/MM/InterFF.pypp.cpp b/wrapper/MM/InterFF.pypp.cpp index 08aea6060..10720107e 100644 --- a/wrapper/MM/InterFF.pypp.cpp +++ b/wrapper/MM/InterFF.pypp.cpp @@ -54,6 +54,8 @@ namespace bp = boost::python; SireMM::InterFF __copy__(const SireMM::InterFF &other){ return SireMM::InterFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -629,9 +631,9 @@ void register_InterFF_class(){ } InterFF_exposer.staticmethod( "typeName" ); - InterFF_exposer.def( "__copy__", &__copy__); - InterFF_exposer.def( "__deepcopy__", &__copy__); - InterFF_exposer.def( "clone", &__copy__); + InterFF_exposer.def( "__copy__", &__copy__); + InterFF_exposer.def( "__deepcopy__", &__copy__); + InterFF_exposer.def( "clone", &__copy__); InterFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InterFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InterFF >, diff --git a/wrapper/MM/InterGroupCLJFF.pypp.cpp b/wrapper/MM/InterGroupCLJFF.pypp.cpp index 4410cdf3e..644c9af1c 100644 --- a/wrapper/MM/InterGroupCLJFF.pypp.cpp +++ b/wrapper/MM/InterGroupCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B2G3DFF > __copy__(const SireFF::Inter2B2G3DFF > &other){ return SireFF::Inter2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_InterGroupCLJFF_class(){ } InterGroupCLJFF_exposer.staticmethod( "typeName" ); - InterGroupCLJFF_exposer.def( "__copy__", &__copy__); - InterGroupCLJFF_exposer.def( "__deepcopy__", &__copy__); - InterGroupCLJFF_exposer.def( "clone", &__copy__); + InterGroupCLJFF_exposer.def( "__copy__", &__copy__ >>); + InterGroupCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupCLJFF_exposer.def( "clone", &__copy__ >>); InterGroupCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B2G3DFF > > ); diff --git a/wrapper/MM/InterGroupCLJFFBase.pypp.cpp b/wrapper/MM/InterGroupCLJFFBase.pypp.cpp index 47f0639da..27fce5373 100644 --- a/wrapper/MM/InterGroupCLJFFBase.pypp.cpp +++ b/wrapper/MM/InterGroupCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2B2GFF > __copy__(const SireFF::Inter2B2GFF > &other){ return SireFF::Inter2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterGroupCLJFFBase_class(){ } InterGroupCLJFFBase_exposer.staticmethod( "typeName" ); - InterGroupCLJFFBase_exposer.def( "__copy__", &__copy__); - InterGroupCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - InterGroupCLJFFBase_exposer.def( "clone", &__copy__); + InterGroupCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + InterGroupCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupCLJFFBase_exposer.def( "clone", &__copy__ >>); InterGroupCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterGroupCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2B2GFF > >, diff --git a/wrapper/MM/InterGroupCoulombFF.pypp.cpp b/wrapper/MM/InterGroupCoulombFF.pypp.cpp index bef5e2291..96719d9ad 100644 --- a/wrapper/MM/InterGroupCoulombFF.pypp.cpp +++ b/wrapper/MM/InterGroupCoulombFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B2G3DFF > __copy__(const SireFF::Inter2B2G3DFF > &other){ return SireFF::Inter2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_InterGroupCoulombFF_class(){ } InterGroupCoulombFF_exposer.staticmethod( "typeName" ); - InterGroupCoulombFF_exposer.def( "__copy__", &__copy__); - InterGroupCoulombFF_exposer.def( "__deepcopy__", &__copy__); - InterGroupCoulombFF_exposer.def( "clone", &__copy__); + InterGroupCoulombFF_exposer.def( "__copy__", &__copy__ >>); + InterGroupCoulombFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupCoulombFF_exposer.def( "clone", &__copy__ >>); InterGroupCoulombFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupCoulombFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupCoulombFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B2G3DFF > > ); diff --git a/wrapper/MM/InterGroupCoulombFFBase.pypp.cpp b/wrapper/MM/InterGroupCoulombFFBase.pypp.cpp index 122ab43ff..3706753b6 100644 --- a/wrapper/MM/InterGroupCoulombFFBase.pypp.cpp +++ b/wrapper/MM/InterGroupCoulombFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2B2GFF > __copy__(const SireFF::Inter2B2GFF > &other){ return SireFF::Inter2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterGroupCoulombFFBase_class(){ } InterGroupCoulombFFBase_exposer.staticmethod( "typeName" ); - InterGroupCoulombFFBase_exposer.def( "__copy__", &__copy__); - InterGroupCoulombFFBase_exposer.def( "__deepcopy__", &__copy__); - InterGroupCoulombFFBase_exposer.def( "clone", &__copy__); + InterGroupCoulombFFBase_exposer.def( "__copy__", &__copy__ >>); + InterGroupCoulombFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupCoulombFFBase_exposer.def( "clone", &__copy__ >>); InterGroupCoulombFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterGroupCoulombFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2B2GFF > >, diff --git a/wrapper/MM/InterGroupFF.pypp.cpp b/wrapper/MM/InterGroupFF.pypp.cpp index ca17ca66d..f9d33edc1 100644 --- a/wrapper/MM/InterGroupFF.pypp.cpp +++ b/wrapper/MM/InterGroupFF.pypp.cpp @@ -52,6 +52,8 @@ namespace bp = boost::python; SireMM::InterGroupFF __copy__(const SireMM::InterGroupFF &other){ return SireMM::InterGroupFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -627,9 +629,9 @@ void register_InterGroupFF_class(){ } InterGroupFF_exposer.staticmethod( "typeName" ); - InterGroupFF_exposer.def( "__copy__", &__copy__); - InterGroupFF_exposer.def( "__deepcopy__", &__copy__); - InterGroupFF_exposer.def( "clone", &__copy__); + InterGroupFF_exposer.def( "__copy__", &__copy__); + InterGroupFF_exposer.def( "__deepcopy__", &__copy__); + InterGroupFF_exposer.def( "clone", &__copy__); InterGroupFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InterGroupFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterGroupFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InterGroupFF >, diff --git a/wrapper/MM/InterGroupLJFF.pypp.cpp b/wrapper/MM/InterGroupLJFF.pypp.cpp index b9c84d2b0..afc759e82 100644 --- a/wrapper/MM/InterGroupLJFF.pypp.cpp +++ b/wrapper/MM/InterGroupLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B2G3DFF > __copy__(const SireFF::Inter2B2G3DFF > &other){ return SireFF::Inter2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_InterGroupLJFF_class(){ } InterGroupLJFF_exposer.staticmethod( "typeName" ); - InterGroupLJFF_exposer.def( "__copy__", &__copy__); - InterGroupLJFF_exposer.def( "__deepcopy__", &__copy__); - InterGroupLJFF_exposer.def( "clone", &__copy__); + InterGroupLJFF_exposer.def( "__copy__", &__copy__ >>); + InterGroupLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupLJFF_exposer.def( "clone", &__copy__ >>); InterGroupLJFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B2G3DFF > > ); diff --git a/wrapper/MM/InterGroupLJFFBase.pypp.cpp b/wrapper/MM/InterGroupLJFFBase.pypp.cpp index 78696b9e3..af2a0cecb 100644 --- a/wrapper/MM/InterGroupLJFFBase.pypp.cpp +++ b/wrapper/MM/InterGroupLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2B2GFF > __copy__(const SireFF::Inter2B2GFF > &other){ return SireFF::Inter2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterGroupLJFFBase_class(){ } InterGroupLJFFBase_exposer.staticmethod( "typeName" ); - InterGroupLJFFBase_exposer.def( "__copy__", &__copy__); - InterGroupLJFFBase_exposer.def( "__deepcopy__", &__copy__); - InterGroupLJFFBase_exposer.def( "clone", &__copy__); + InterGroupLJFFBase_exposer.def( "__copy__", &__copy__ >>); + InterGroupLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupLJFFBase_exposer.def( "clone", &__copy__ >>); InterGroupLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterGroupLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2B2GFF > >, diff --git a/wrapper/MM/InterGroupSoftCLJFF.pypp.cpp b/wrapper/MM/InterGroupSoftCLJFF.pypp.cpp index 42cb7f5e7..e6d470d78 100644 --- a/wrapper/MM/InterGroupSoftCLJFF.pypp.cpp +++ b/wrapper/MM/InterGroupSoftCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B2G3DFF > __copy__(const SireFF::Inter2B2G3DFF > &other){ return SireFF::Inter2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_InterGroupSoftCLJFF_class(){ } InterGroupSoftCLJFF_exposer.staticmethod( "typeName" ); - InterGroupSoftCLJFF_exposer.def( "__copy__", &__copy__); - InterGroupSoftCLJFF_exposer.def( "__deepcopy__", &__copy__); - InterGroupSoftCLJFF_exposer.def( "clone", &__copy__); + InterGroupSoftCLJFF_exposer.def( "__copy__", &__copy__ >>); + InterGroupSoftCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupSoftCLJFF_exposer.def( "clone", &__copy__ >>); InterGroupSoftCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupSoftCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B2G3DFF > > ); InterGroupSoftCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B2G3DFF > > ); diff --git a/wrapper/MM/InterGroupSoftCLJFFBase.pypp.cpp b/wrapper/MM/InterGroupSoftCLJFFBase.pypp.cpp index aaa12628c..125b09618 100644 --- a/wrapper/MM/InterGroupSoftCLJFFBase.pypp.cpp +++ b/wrapper/MM/InterGroupSoftCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2B2GFF > __copy__(const SireFF::Inter2B2GFF > &other){ return SireFF::Inter2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterGroupSoftCLJFFBase_class(){ } InterGroupSoftCLJFFBase_exposer.staticmethod( "typeName" ); - InterGroupSoftCLJFFBase_exposer.def( "__copy__", &__copy__); - InterGroupSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - InterGroupSoftCLJFFBase_exposer.def( "clone", &__copy__); + InterGroupSoftCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + InterGroupSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterGroupSoftCLJFFBase_exposer.def( "clone", &__copy__ >>); InterGroupSoftCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterGroupSoftCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2B2GFF > >, diff --git a/wrapper/MM/InterLJFF.pypp.cpp b/wrapper/MM/InterLJFF.pypp.cpp index 4b4d46c30..93a39986b 100644 --- a/wrapper/MM/InterLJFF.pypp.cpp +++ b/wrapper/MM/InterLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B3DFF > __copy__(const SireFF::Inter2B3DFF > &other){ return SireFF::Inter2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -270,9 +272,9 @@ void register_InterLJFF_class(){ } InterLJFF_exposer.staticmethod( "typeName" ); - InterLJFF_exposer.def( "__copy__", &__copy__); - InterLJFF_exposer.def( "__deepcopy__", &__copy__); - InterLJFF_exposer.def( "clone", &__copy__); + InterLJFF_exposer.def( "__copy__", &__copy__ >>); + InterLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterLJFF_exposer.def( "clone", &__copy__ >>); InterLJFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B3DFF > > ); InterLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B3DFF > > ); InterLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B3DFF > > ); diff --git a/wrapper/MM/InterLJFFBase.pypp.cpp b/wrapper/MM/InterLJFFBase.pypp.cpp index 37707906d..ee818f2e5 100644 --- a/wrapper/MM/InterLJFFBase.pypp.cpp +++ b/wrapper/MM/InterLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2BFF > __copy__(const SireFF::Inter2BFF > &other){ return SireFF::Inter2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterLJFFBase_class(){ } InterLJFFBase_exposer.staticmethod( "typeName" ); - InterLJFFBase_exposer.def( "__copy__", &__copy__); - InterLJFFBase_exposer.def( "__deepcopy__", &__copy__); - InterLJFFBase_exposer.def( "clone", &__copy__); + InterLJFFBase_exposer.def( "__copy__", &__copy__ >>); + InterLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterLJFFBase_exposer.def( "clone", &__copy__ >>); InterLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2BFF > >, diff --git a/wrapper/MM/InterSoftCLJFF.pypp.cpp b/wrapper/MM/InterSoftCLJFF.pypp.cpp index 61e1b67f2..dda8c6948 100644 --- a/wrapper/MM/InterSoftCLJFF.pypp.cpp +++ b/wrapper/MM/InterSoftCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Inter2B3DFF > __copy__(const SireFF::Inter2B3DFF > &other){ return SireFF::Inter2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -270,9 +272,9 @@ void register_InterSoftCLJFF_class(){ } InterSoftCLJFF_exposer.staticmethod( "typeName" ); - InterSoftCLJFF_exposer.def( "__copy__", &__copy__); - InterSoftCLJFF_exposer.def( "__deepcopy__", &__copy__); - InterSoftCLJFF_exposer.def( "clone", &__copy__); + InterSoftCLJFF_exposer.def( "__copy__", &__copy__ >>); + InterSoftCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + InterSoftCLJFF_exposer.def( "clone", &__copy__ >>); InterSoftCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Inter2B3DFF > > ); InterSoftCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Inter2B3DFF > > ); InterSoftCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Inter2B3DFF > > ); diff --git a/wrapper/MM/InterSoftCLJFFBase.pypp.cpp b/wrapper/MM/InterSoftCLJFFBase.pypp.cpp index 59f35125c..0955c7431 100644 --- a/wrapper/MM/InterSoftCLJFFBase.pypp.cpp +++ b/wrapper/MM/InterSoftCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Inter2BFF > __copy__(const SireFF::Inter2BFF > &other){ return SireFF::Inter2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_InterSoftCLJFFBase_class(){ } InterSoftCLJFFBase_exposer.staticmethod( "typeName" ); - InterSoftCLJFFBase_exposer.def( "__copy__", &__copy__); - InterSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - InterSoftCLJFFBase_exposer.def( "clone", &__copy__); + InterSoftCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + InterSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + InterSoftCLJFFBase_exposer.def( "clone", &__copy__ >>); InterSoftCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Inter2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InterSoftCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Inter2BFF > >, diff --git a/wrapper/MM/InternalComponent.pypp.cpp b/wrapper/MM/InternalComponent.pypp.cpp index 34433d8ca..b91ef3aee 100644 --- a/wrapper/MM/InternalComponent.pypp.cpp +++ b/wrapper/MM/InternalComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::InternalComponent __copy__(const SireMM::InternalComponent &other){ return SireMM::InternalComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -251,9 +253,9 @@ void register_InternalComponent_class(){ } InternalComponent_exposer.staticmethod( "typeName" ); - InternalComponent_exposer.def( "__copy__", &__copy__); - InternalComponent_exposer.def( "__deepcopy__", &__copy__); - InternalComponent_exposer.def( "clone", &__copy__); + InternalComponent_exposer.def( "__copy__", &__copy__); + InternalComponent_exposer.def( "__deepcopy__", &__copy__); + InternalComponent_exposer.def( "clone", &__copy__); InternalComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InternalComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InternalComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InternalComponent >, diff --git a/wrapper/MM/InternalFF.pypp.cpp b/wrapper/MM/InternalFF.pypp.cpp index 09b4a45b5..7c8646c14 100644 --- a/wrapper/MM/InternalFF.pypp.cpp +++ b/wrapper/MM/InternalFF.pypp.cpp @@ -50,6 +50,8 @@ namespace bp = boost::python; SireMM::InternalFF __copy__(const SireMM::InternalFF &other){ return SireMM::InternalFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -511,9 +513,9 @@ void register_InternalFF_class(){ } InternalFF_exposer.staticmethod( "typeName" ); - InternalFF_exposer.def( "__copy__", &__copy__); - InternalFF_exposer.def( "__deepcopy__", &__copy__); - InternalFF_exposer.def( "clone", &__copy__); + InternalFF_exposer.def( "__copy__", &__copy__); + InternalFF_exposer.def( "__deepcopy__", &__copy__); + InternalFF_exposer.def( "clone", &__copy__); InternalFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InternalFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InternalFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InternalFF >, diff --git a/wrapper/MM/InternalGroupFF.pypp.cpp b/wrapper/MM/InternalGroupFF.pypp.cpp index b4044f694..49d07307d 100644 --- a/wrapper/MM/InternalGroupFF.pypp.cpp +++ b/wrapper/MM/InternalGroupFF.pypp.cpp @@ -54,6 +54,8 @@ namespace bp = boost::python; SireMM::InternalGroupFF __copy__(const SireMM::InternalGroupFF &other){ return SireMM::InternalGroupFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -490,9 +492,9 @@ void register_InternalGroupFF_class(){ } InternalGroupFF_exposer.staticmethod( "typeName" ); - InternalGroupFF_exposer.def( "__copy__", &__copy__); - InternalGroupFF_exposer.def( "__deepcopy__", &__copy__); - InternalGroupFF_exposer.def( "clone", &__copy__); + InternalGroupFF_exposer.def( "__copy__", &__copy__); + InternalGroupFF_exposer.def( "__deepcopy__", &__copy__); + InternalGroupFF_exposer.def( "clone", &__copy__); InternalGroupFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InternalGroupFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InternalGroupFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InternalGroupFF >, diff --git a/wrapper/MM/InternalParameterNames.pypp.cpp b/wrapper/MM/InternalParameterNames.pypp.cpp index 1edfad66a..3a1c47cfb 100644 --- a/wrapper/MM/InternalParameterNames.pypp.cpp +++ b/wrapper/MM/InternalParameterNames.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::InternalParameterNames __copy__(const SireMM::InternalParameterNames &other){ return SireMM::InternalParameterNames(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::InternalParameterNames&){ return "SireMM::InternalParameterNames";} #include "Helpers/release_gil_policy.hpp" @@ -59,9 +61,9 @@ void register_InternalParameterNames_class(){ typedef bp::class_< SireMM::InternalParameterNames, bp::bases< SireMM::StretchBendTorsionParameterName, SireMM::BendBendParameterName, SireMM::StretchBendParameterName, SireMM::StretchStretchParameterName, SireMM::UreyBradleyParameterName, SireMM::ImproperParameterName, SireMM::DihedralParameterName, SireMM::AngleParameterName, SireMM::BondParameterName > > InternalParameterNames_exposer_t; InternalParameterNames_exposer_t InternalParameterNames_exposer = InternalParameterNames_exposer_t( "InternalParameterNames", "This class provides the default name of the properties\nthat contain the bond, angle, dihedral and Urey-Bradley parameters", bp::init< >("") ); bp::scope InternalParameterNames_scope( InternalParameterNames_exposer ); - InternalParameterNames_exposer.def( "__copy__", &__copy__); - InternalParameterNames_exposer.def( "__deepcopy__", &__copy__); - InternalParameterNames_exposer.def( "clone", &__copy__); + InternalParameterNames_exposer.def( "__copy__", &__copy__); + InternalParameterNames_exposer.def( "__deepcopy__", &__copy__); + InternalParameterNames_exposer.def( "clone", &__copy__); InternalParameterNames_exposer.def( "__str__", &pvt_get_name); InternalParameterNames_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/InternalParameterNames3D.pypp.cpp b/wrapper/MM/InternalParameterNames3D.pypp.cpp index d9f73cc21..7558e2898 100644 --- a/wrapper/MM/InternalParameterNames3D.pypp.cpp +++ b/wrapper/MM/InternalParameterNames3D.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::InternalParameterNames3D __copy__(const SireMM::InternalParameterNames3D &other){ return SireMM::InternalParameterNames3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::InternalParameterNames3D&){ return "SireMM::InternalParameterNames3D";} #include "Helpers/release_gil_policy.hpp" @@ -59,9 +61,9 @@ void register_InternalParameterNames3D_class(){ typedef bp::class_< SireMM::InternalParameterNames3D, bp::bases< SireMM::InternalParameterNames, SireMM::StretchBendTorsionParameterName, SireMM::BendBendParameterName, SireMM::StretchBendParameterName, SireMM::StretchStretchParameterName, SireMM::UreyBradleyParameterName, SireMM::ImproperParameterName, SireMM::DihedralParameterName, SireMM::AngleParameterName, SireMM::BondParameterName > > InternalParameterNames3D_exposer_t; InternalParameterNames3D_exposer_t InternalParameterNames3D_exposer = InternalParameterNames3D_exposer_t( "InternalParameterNames3D", "This class provides the default name of the properties\nthat contain the internal and 3D coordinates properties", bp::init< >("") ); bp::scope InternalParameterNames3D_scope( InternalParameterNames3D_exposer ); - InternalParameterNames3D_exposer.def( "__copy__", &__copy__); - InternalParameterNames3D_exposer.def( "__deepcopy__", &__copy__); - InternalParameterNames3D_exposer.def( "clone", &__copy__); + InternalParameterNames3D_exposer.def( "__copy__", &__copy__); + InternalParameterNames3D_exposer.def( "__deepcopy__", &__copy__); + InternalParameterNames3D_exposer.def( "clone", &__copy__); InternalParameterNames3D_exposer.def( "__str__", &pvt_get_name); InternalParameterNames3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/InternalParameters.pypp.cpp b/wrapper/MM/InternalParameters.pypp.cpp index d084d4d4c..590f2ec58 100644 --- a/wrapper/MM/InternalParameters.pypp.cpp +++ b/wrapper/MM/InternalParameters.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::InternalParameters __copy__(const SireMM::InternalParameters &other){ return SireMM::InternalParameters(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireMM::InternalParameters&){ return "SireMM::InternalParameters";} @@ -345,9 +347,9 @@ void register_InternalParameters_class(){ } InternalParameters_exposer.staticmethod( "typeName" ); - InternalParameters_exposer.def( "__copy__", &__copy__); - InternalParameters_exposer.def( "__deepcopy__", &__copy__); - InternalParameters_exposer.def( "clone", &__copy__); + InternalParameters_exposer.def( "__copy__", &__copy__); + InternalParameters_exposer.def( "__deepcopy__", &__copy__); + InternalParameters_exposer.def( "clone", &__copy__); InternalParameters_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InternalParameters >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InternalParameters_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InternalParameters >, diff --git a/wrapper/MM/InternalParameters3D.pypp.cpp b/wrapper/MM/InternalParameters3D.pypp.cpp index 08daae968..f69413720 100644 --- a/wrapper/MM/InternalParameters3D.pypp.cpp +++ b/wrapper/MM/InternalParameters3D.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::InternalParameters3D __copy__(const SireMM::InternalParameters3D &other){ return SireMM::InternalParameters3D(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireMM::InternalParameters3D&){ return "SireMM::InternalParameters3D";} @@ -188,9 +190,9 @@ void register_InternalParameters3D_class(){ } InternalParameters3D_exposer.staticmethod( "typeName" ); - InternalParameters3D_exposer.def( "__copy__", &__copy__); - InternalParameters3D_exposer.def( "__deepcopy__", &__copy__); - InternalParameters3D_exposer.def( "clone", &__copy__); + InternalParameters3D_exposer.def( "__copy__", &__copy__); + InternalParameters3D_exposer.def( "__deepcopy__", &__copy__); + InternalParameters3D_exposer.def( "clone", &__copy__); InternalParameters3D_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::InternalParameters3D >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); InternalParameters3D_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::InternalParameters3D >, diff --git a/wrapper/MM/InternalSymbols.pypp.cpp b/wrapper/MM/InternalSymbols.pypp.cpp index 949e3bc0c..1ba64a907 100644 --- a/wrapper/MM/InternalSymbols.pypp.cpp +++ b/wrapper/MM/InternalSymbols.pypp.cpp @@ -33,6 +33,8 @@ namespace bp = boost::python; SireMM::InternalSymbols __copy__(const SireMM::InternalSymbols &other){ return SireMM::InternalSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::InternalSymbols&){ return "SireMM::InternalSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -151,9 +153,9 @@ void register_InternalSymbols_class(){ , "Return all of the symbols used in the Urey-Bradley parameters" ); } - InternalSymbols_exposer.def( "__copy__", &__copy__); - InternalSymbols_exposer.def( "__deepcopy__", &__copy__); - InternalSymbols_exposer.def( "clone", &__copy__); + InternalSymbols_exposer.def( "__copy__", &__copy__); + InternalSymbols_exposer.def( "__deepcopy__", &__copy__); + InternalSymbols_exposer.def( "clone", &__copy__); InternalSymbols_exposer.def( "__str__", &pvt_get_name); InternalSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/Intra14Component.pypp.cpp b/wrapper/MM/Intra14Component.pypp.cpp index 1a51dfacf..e5f4f402c 100644 --- a/wrapper/MM/Intra14Component.pypp.cpp +++ b/wrapper/MM/Intra14Component.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::Intra14Component __copy__(const SireMM::Intra14Component &other){ return SireMM::Intra14Component(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -131,9 +133,9 @@ void register_Intra14Component_class(){ } Intra14Component_exposer.staticmethod( "typeName" ); - Intra14Component_exposer.def( "__copy__", &__copy__); - Intra14Component_exposer.def( "__deepcopy__", &__copy__); - Intra14Component_exposer.def( "clone", &__copy__); + Intra14Component_exposer.def( "__copy__", &__copy__); + Intra14Component_exposer.def( "__deepcopy__", &__copy__); + Intra14Component_exposer.def( "clone", &__copy__); Intra14Component_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Intra14Component >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Intra14Component_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Intra14Component >, diff --git a/wrapper/MM/Intra14CoulombComponent.pypp.cpp b/wrapper/MM/Intra14CoulombComponent.pypp.cpp index 410d6eef9..b686bcfd2 100644 --- a/wrapper/MM/Intra14CoulombComponent.pypp.cpp +++ b/wrapper/MM/Intra14CoulombComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::Intra14CoulombComponent __copy__(const SireMM::Intra14CoulombComponent &other){ return SireMM::Intra14CoulombComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_Intra14CoulombComponent_class(){ } Intra14CoulombComponent_exposer.staticmethod( "typeName" ); - Intra14CoulombComponent_exposer.def( "__copy__", &__copy__); - Intra14CoulombComponent_exposer.def( "__deepcopy__", &__copy__); - Intra14CoulombComponent_exposer.def( "clone", &__copy__); + Intra14CoulombComponent_exposer.def( "__copy__", &__copy__); + Intra14CoulombComponent_exposer.def( "__deepcopy__", &__copy__); + Intra14CoulombComponent_exposer.def( "clone", &__copy__); Intra14CoulombComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Intra14CoulombComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Intra14CoulombComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Intra14CoulombComponent >, diff --git a/wrapper/MM/Intra14LJComponent.pypp.cpp b/wrapper/MM/Intra14LJComponent.pypp.cpp index 5216f3dbf..128c38718 100644 --- a/wrapper/MM/Intra14LJComponent.pypp.cpp +++ b/wrapper/MM/Intra14LJComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::Intra14LJComponent __copy__(const SireMM::Intra14LJComponent &other){ return SireMM::Intra14LJComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_Intra14LJComponent_class(){ } Intra14LJComponent_exposer.staticmethod( "typeName" ); - Intra14LJComponent_exposer.def( "__copy__", &__copy__); - Intra14LJComponent_exposer.def( "__deepcopy__", &__copy__); - Intra14LJComponent_exposer.def( "clone", &__copy__); + Intra14LJComponent_exposer.def( "__copy__", &__copy__); + Intra14LJComponent_exposer.def( "__deepcopy__", &__copy__); + Intra14LJComponent_exposer.def( "clone", &__copy__); Intra14LJComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::Intra14LJComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Intra14LJComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::Intra14LJComponent >, diff --git a/wrapper/MM/IntraCLJFF.pypp.cpp b/wrapper/MM/IntraCLJFF.pypp.cpp index 6f12aa84f..dee12dea3 100644 --- a/wrapper/MM/IntraCLJFF.pypp.cpp +++ b/wrapper/MM/IntraCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B3DFF > __copy__(const SireFF::Intra2B3DFF > &other){ return SireFF::Intra2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraCLJFF_class(){ } IntraCLJFF_exposer.staticmethod( "typeName" ); - IntraCLJFF_exposer.def( "__copy__", &__copy__); - IntraCLJFF_exposer.def( "__deepcopy__", &__copy__); - IntraCLJFF_exposer.def( "clone", &__copy__); + IntraCLJFF_exposer.def( "__copy__", &__copy__ >>); + IntraCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraCLJFF_exposer.def( "clone", &__copy__ >>); IntraCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B3DFF > > ); diff --git a/wrapper/MM/IntraCLJFFBase.pypp.cpp b/wrapper/MM/IntraCLJFFBase.pypp.cpp index 0201a35e7..def5eddf0 100644 --- a/wrapper/MM/IntraCLJFFBase.pypp.cpp +++ b/wrapper/MM/IntraCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2BFF > __copy__(const SireFF::Intra2BFF > &other){ return SireFF::Intra2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraCLJFFBase_class(){ } IntraCLJFFBase_exposer.staticmethod( "typeName" ); - IntraCLJFFBase_exposer.def( "__copy__", &__copy__); - IntraCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraCLJFFBase_exposer.def( "clone", &__copy__); + IntraCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraCLJFFBase_exposer.def( "clone", &__copy__ >>); IntraCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2BFF > >, diff --git a/wrapper/MM/IntraCoulombFF.pypp.cpp b/wrapper/MM/IntraCoulombFF.pypp.cpp index 4f48f5197..b291aa559 100644 --- a/wrapper/MM/IntraCoulombFF.pypp.cpp +++ b/wrapper/MM/IntraCoulombFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B3DFF > __copy__(const SireFF::Intra2B3DFF > &other){ return SireFF::Intra2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraCoulombFF_class(){ } IntraCoulombFF_exposer.staticmethod( "typeName" ); - IntraCoulombFF_exposer.def( "__copy__", &__copy__); - IntraCoulombFF_exposer.def( "__deepcopy__", &__copy__); - IntraCoulombFF_exposer.def( "clone", &__copy__); + IntraCoulombFF_exposer.def( "__copy__", &__copy__ >>); + IntraCoulombFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraCoulombFF_exposer.def( "clone", &__copy__ >>); IntraCoulombFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraCoulombFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraCoulombFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B3DFF > > ); diff --git a/wrapper/MM/IntraCoulombFFBase.pypp.cpp b/wrapper/MM/IntraCoulombFFBase.pypp.cpp index 110439c7a..f727b2ea3 100644 --- a/wrapper/MM/IntraCoulombFFBase.pypp.cpp +++ b/wrapper/MM/IntraCoulombFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2BFF > __copy__(const SireFF::Intra2BFF > &other){ return SireFF::Intra2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraCoulombFFBase_class(){ } IntraCoulombFFBase_exposer.staticmethod( "typeName" ); - IntraCoulombFFBase_exposer.def( "__copy__", &__copy__); - IntraCoulombFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraCoulombFFBase_exposer.def( "clone", &__copy__); + IntraCoulombFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraCoulombFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraCoulombFFBase_exposer.def( "clone", &__copy__ >>); IntraCoulombFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraCoulombFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2BFF > >, diff --git a/wrapper/MM/IntraFF.pypp.cpp b/wrapper/MM/IntraFF.pypp.cpp index b3f37ffc4..746b9cdb0 100644 --- a/wrapper/MM/IntraFF.pypp.cpp +++ b/wrapper/MM/IntraFF.pypp.cpp @@ -52,6 +52,8 @@ namespace bp = boost::python; SireMM::IntraFF __copy__(const SireMM::IntraFF &other){ return SireMM::IntraFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -417,9 +419,9 @@ void register_IntraFF_class(){ } IntraFF_exposer.staticmethod( "typeName" ); - IntraFF_exposer.def( "__copy__", &__copy__); - IntraFF_exposer.def( "__deepcopy__", &__copy__); - IntraFF_exposer.def( "clone", &__copy__); + IntraFF_exposer.def( "__copy__", &__copy__); + IntraFF_exposer.def( "__deepcopy__", &__copy__); + IntraFF_exposer.def( "clone", &__copy__); IntraFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::IntraFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::IntraFF >, diff --git a/wrapper/MM/IntraGroupCLJFF.pypp.cpp b/wrapper/MM/IntraGroupCLJFF.pypp.cpp index 97a0eddc2..788e6d2b4 100644 --- a/wrapper/MM/IntraGroupCLJFF.pypp.cpp +++ b/wrapper/MM/IntraGroupCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B2G3DFF > __copy__(const SireFF::Intra2B2G3DFF > &other){ return SireFF::Intra2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraGroupCLJFF_class(){ } IntraGroupCLJFF_exposer.staticmethod( "typeName" ); - IntraGroupCLJFF_exposer.def( "__copy__", &__copy__); - IntraGroupCLJFF_exposer.def( "__deepcopy__", &__copy__); - IntraGroupCLJFF_exposer.def( "clone", &__copy__); + IntraGroupCLJFF_exposer.def( "__copy__", &__copy__ >>); + IntraGroupCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupCLJFF_exposer.def( "clone", &__copy__ >>); IntraGroupCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B2G3DFF > > ); diff --git a/wrapper/MM/IntraGroupCLJFFBase.pypp.cpp b/wrapper/MM/IntraGroupCLJFFBase.pypp.cpp index 89c219106..14a42e154 100644 --- a/wrapper/MM/IntraGroupCLJFFBase.pypp.cpp +++ b/wrapper/MM/IntraGroupCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2B2GFF > __copy__(const SireFF::Intra2B2GFF > &other){ return SireFF::Intra2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraGroupCLJFFBase_class(){ } IntraGroupCLJFFBase_exposer.staticmethod( "typeName" ); - IntraGroupCLJFFBase_exposer.def( "__copy__", &__copy__); - IntraGroupCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraGroupCLJFFBase_exposer.def( "clone", &__copy__); + IntraGroupCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraGroupCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupCLJFFBase_exposer.def( "clone", &__copy__ >>); IntraGroupCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraGroupCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2B2GFF > >, diff --git a/wrapper/MM/IntraGroupCoulombFF.pypp.cpp b/wrapper/MM/IntraGroupCoulombFF.pypp.cpp index a40c7dfd3..26deed2ce 100644 --- a/wrapper/MM/IntraGroupCoulombFF.pypp.cpp +++ b/wrapper/MM/IntraGroupCoulombFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B2G3DFF > __copy__(const SireFF::Intra2B2G3DFF > &other){ return SireFF::Intra2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraGroupCoulombFF_class(){ } IntraGroupCoulombFF_exposer.staticmethod( "typeName" ); - IntraGroupCoulombFF_exposer.def( "__copy__", &__copy__); - IntraGroupCoulombFF_exposer.def( "__deepcopy__", &__copy__); - IntraGroupCoulombFF_exposer.def( "clone", &__copy__); + IntraGroupCoulombFF_exposer.def( "__copy__", &__copy__ >>); + IntraGroupCoulombFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupCoulombFF_exposer.def( "clone", &__copy__ >>); IntraGroupCoulombFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupCoulombFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupCoulombFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B2G3DFF > > ); diff --git a/wrapper/MM/IntraGroupCoulombFFBase.pypp.cpp b/wrapper/MM/IntraGroupCoulombFFBase.pypp.cpp index a677dda73..51a526e33 100644 --- a/wrapper/MM/IntraGroupCoulombFFBase.pypp.cpp +++ b/wrapper/MM/IntraGroupCoulombFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2B2GFF > __copy__(const SireFF::Intra2B2GFF > &other){ return SireFF::Intra2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraGroupCoulombFFBase_class(){ } IntraGroupCoulombFFBase_exposer.staticmethod( "typeName" ); - IntraGroupCoulombFFBase_exposer.def( "__copy__", &__copy__); - IntraGroupCoulombFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraGroupCoulombFFBase_exposer.def( "clone", &__copy__); + IntraGroupCoulombFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraGroupCoulombFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupCoulombFFBase_exposer.def( "clone", &__copy__ >>); IntraGroupCoulombFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraGroupCoulombFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2B2GFF > >, diff --git a/wrapper/MM/IntraGroupFF.pypp.cpp b/wrapper/MM/IntraGroupFF.pypp.cpp index 55ae07e2b..b304e485e 100644 --- a/wrapper/MM/IntraGroupFF.pypp.cpp +++ b/wrapper/MM/IntraGroupFF.pypp.cpp @@ -52,6 +52,8 @@ namespace bp = boost::python; SireMM::IntraGroupFF __copy__(const SireMM::IntraGroupFF &other){ return SireMM::IntraGroupFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -417,9 +419,9 @@ void register_IntraGroupFF_class(){ } IntraGroupFF_exposer.staticmethod( "typeName" ); - IntraGroupFF_exposer.def( "__copy__", &__copy__); - IntraGroupFF_exposer.def( "__deepcopy__", &__copy__); - IntraGroupFF_exposer.def( "clone", &__copy__); + IntraGroupFF_exposer.def( "__copy__", &__copy__); + IntraGroupFF_exposer.def( "__deepcopy__", &__copy__); + IntraGroupFF_exposer.def( "clone", &__copy__); IntraGroupFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::IntraGroupFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraGroupFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::IntraGroupFF >, diff --git a/wrapper/MM/IntraGroupLJFF.pypp.cpp b/wrapper/MM/IntraGroupLJFF.pypp.cpp index 5b230790a..9d57fc55d 100644 --- a/wrapper/MM/IntraGroupLJFF.pypp.cpp +++ b/wrapper/MM/IntraGroupLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B2G3DFF > __copy__(const SireFF::Intra2B2G3DFF > &other){ return SireFF::Intra2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraGroupLJFF_class(){ } IntraGroupLJFF_exposer.staticmethod( "typeName" ); - IntraGroupLJFF_exposer.def( "__copy__", &__copy__); - IntraGroupLJFF_exposer.def( "__deepcopy__", &__copy__); - IntraGroupLJFF_exposer.def( "clone", &__copy__); + IntraGroupLJFF_exposer.def( "__copy__", &__copy__ >>); + IntraGroupLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupLJFF_exposer.def( "clone", &__copy__ >>); IntraGroupLJFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B2G3DFF > > ); diff --git a/wrapper/MM/IntraGroupLJFFBase.pypp.cpp b/wrapper/MM/IntraGroupLJFFBase.pypp.cpp index a09391fc1..3fe5023a1 100644 --- a/wrapper/MM/IntraGroupLJFFBase.pypp.cpp +++ b/wrapper/MM/IntraGroupLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2B2GFF > __copy__(const SireFF::Intra2B2GFF > &other){ return SireFF::Intra2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraGroupLJFFBase_class(){ } IntraGroupLJFFBase_exposer.staticmethod( "typeName" ); - IntraGroupLJFFBase_exposer.def( "__copy__", &__copy__); - IntraGroupLJFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraGroupLJFFBase_exposer.def( "clone", &__copy__); + IntraGroupLJFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraGroupLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupLJFFBase_exposer.def( "clone", &__copy__ >>); IntraGroupLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraGroupLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2B2GFF > >, diff --git a/wrapper/MM/IntraGroupSoftCLJFF.pypp.cpp b/wrapper/MM/IntraGroupSoftCLJFF.pypp.cpp index c94e4e885..d47af10cd 100644 --- a/wrapper/MM/IntraGroupSoftCLJFF.pypp.cpp +++ b/wrapper/MM/IntraGroupSoftCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B2G3DFF > __copy__(const SireFF::Intra2B2G3DFF > &other){ return SireFF::Intra2B2G3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraGroupSoftCLJFF_class(){ } IntraGroupSoftCLJFF_exposer.staticmethod( "typeName" ); - IntraGroupSoftCLJFF_exposer.def( "__copy__", &__copy__); - IntraGroupSoftCLJFF_exposer.def( "__deepcopy__", &__copy__); - IntraGroupSoftCLJFF_exposer.def( "clone", &__copy__); + IntraGroupSoftCLJFF_exposer.def( "__copy__", &__copy__ >>); + IntraGroupSoftCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupSoftCLJFF_exposer.def( "clone", &__copy__ >>); IntraGroupSoftCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupSoftCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B2G3DFF > > ); IntraGroupSoftCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B2G3DFF > > ); diff --git a/wrapper/MM/IntraGroupSoftCLJFFBase.pypp.cpp b/wrapper/MM/IntraGroupSoftCLJFFBase.pypp.cpp index d893546d4..9a59c5988 100644 --- a/wrapper/MM/IntraGroupSoftCLJFFBase.pypp.cpp +++ b/wrapper/MM/IntraGroupSoftCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2B2GFF > __copy__(const SireFF::Intra2B2GFF > &other){ return SireFF::Intra2B2GFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraGroupSoftCLJFFBase_class(){ } IntraGroupSoftCLJFFBase_exposer.staticmethod( "typeName" ); - IntraGroupSoftCLJFFBase_exposer.def( "__copy__", &__copy__); - IntraGroupSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraGroupSoftCLJFFBase_exposer.def( "clone", &__copy__); + IntraGroupSoftCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraGroupSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraGroupSoftCLJFFBase_exposer.def( "clone", &__copy__ >>); IntraGroupSoftCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2B2GFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraGroupSoftCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2B2GFF > >, diff --git a/wrapper/MM/IntraLJFF.pypp.cpp b/wrapper/MM/IntraLJFF.pypp.cpp index ba11d2313..cf8b5090a 100644 --- a/wrapper/MM/IntraLJFF.pypp.cpp +++ b/wrapper/MM/IntraLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B3DFF > __copy__(const SireFF::Intra2B3DFF > &other){ return SireFF::Intra2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraLJFF_class(){ } IntraLJFF_exposer.staticmethod( "typeName" ); - IntraLJFF_exposer.def( "__copy__", &__copy__); - IntraLJFF_exposer.def( "__deepcopy__", &__copy__); - IntraLJFF_exposer.def( "clone", &__copy__); + IntraLJFF_exposer.def( "__copy__", &__copy__ >>); + IntraLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraLJFF_exposer.def( "clone", &__copy__ >>); IntraLJFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B3DFF > > ); diff --git a/wrapper/MM/IntraLJFFBase.pypp.cpp b/wrapper/MM/IntraLJFFBase.pypp.cpp index 46856d0c6..c364de7f3 100644 --- a/wrapper/MM/IntraLJFFBase.pypp.cpp +++ b/wrapper/MM/IntraLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2BFF > __copy__(const SireFF::Intra2BFF > &other){ return SireFF::Intra2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraLJFFBase_class(){ } IntraLJFFBase_exposer.staticmethod( "typeName" ); - IntraLJFFBase_exposer.def( "__copy__", &__copy__); - IntraLJFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraLJFFBase_exposer.def( "clone", &__copy__); + IntraLJFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraLJFFBase_exposer.def( "clone", &__copy__ >>); IntraLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2BFF > >, diff --git a/wrapper/MM/IntraSoftCLJFF.pypp.cpp b/wrapper/MM/IntraSoftCLJFF.pypp.cpp index 2204a400e..5356437b2 100644 --- a/wrapper/MM/IntraSoftCLJFF.pypp.cpp +++ b/wrapper/MM/IntraSoftCLJFF.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireFF::Intra2B3DFF > __copy__(const SireFF::Intra2B3DFF > &other){ return SireFF::Intra2B3DFF >(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -257,9 +259,9 @@ void register_IntraSoftCLJFF_class(){ } IntraSoftCLJFF_exposer.staticmethod( "typeName" ); - IntraSoftCLJFF_exposer.def( "__copy__", &__copy__); - IntraSoftCLJFF_exposer.def( "__deepcopy__", &__copy__); - IntraSoftCLJFF_exposer.def( "clone", &__copy__); + IntraSoftCLJFF_exposer.def( "__copy__", &__copy__ >>); + IntraSoftCLJFF_exposer.def( "__deepcopy__", &__copy__ >>); + IntraSoftCLJFF_exposer.def( "clone", &__copy__ >>); IntraSoftCLJFF_exposer.def( "__str__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraSoftCLJFF_exposer.def( "__repr__", &__str__< ::SireFF::Intra2B3DFF > > ); IntraSoftCLJFF_exposer.def( "__len__", &__len_count< ::SireFF::Intra2B3DFF > > ); diff --git a/wrapper/MM/IntraSoftCLJFFBase.pypp.cpp b/wrapper/MM/IntraSoftCLJFFBase.pypp.cpp index ac7889f67..6d994839b 100644 --- a/wrapper/MM/IntraSoftCLJFFBase.pypp.cpp +++ b/wrapper/MM/IntraSoftCLJFFBase.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireFF::Intra2BFF > __copy__(const SireFF::Intra2BFF > &other){ return SireFF::Intra2BFF >(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -158,9 +160,9 @@ void register_IntraSoftCLJFFBase_class(){ } IntraSoftCLJFFBase_exposer.staticmethod( "typeName" ); - IntraSoftCLJFFBase_exposer.def( "__copy__", &__copy__); - IntraSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__); - IntraSoftCLJFFBase_exposer.def( "clone", &__copy__); + IntraSoftCLJFFBase_exposer.def( "__copy__", &__copy__ >>); + IntraSoftCLJFFBase_exposer.def( "__deepcopy__", &__copy__ >>); + IntraSoftCLJFFBase_exposer.def( "clone", &__copy__ >>); IntraSoftCLJFFBase_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireFF::Intra2BFF > >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IntraSoftCLJFFBase_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireFF::Intra2BFF > >, diff --git a/wrapper/MM/LJ1264Parameter.pypp.cpp b/wrapper/MM/LJ1264Parameter.pypp.cpp index 9fe0a8c69..c5ac70af3 100644 --- a/wrapper/MM/LJ1264Parameter.pypp.cpp +++ b/wrapper/MM/LJ1264Parameter.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::LJ1264Parameter __copy__(const SireMM::LJ1264Parameter &other){ return SireMM::LJ1264Parameter(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -260,9 +262,9 @@ void register_LJ1264Parameter_class(){ LJ1264Parameter_exposer.staticmethod( "CUnit" ); LJ1264Parameter_exposer.staticmethod( "dummy" ); LJ1264Parameter_exposer.staticmethod( "typeName" ); - LJ1264Parameter_exposer.def( "__copy__", &__copy__); - LJ1264Parameter_exposer.def( "__deepcopy__", &__copy__); - LJ1264Parameter_exposer.def( "clone", &__copy__); + LJ1264Parameter_exposer.def( "__copy__", &__copy__); + LJ1264Parameter_exposer.def( "__deepcopy__", &__copy__); + LJ1264Parameter_exposer.def( "clone", &__copy__); LJ1264Parameter_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJ1264Parameter >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJ1264Parameter_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJ1264Parameter >, diff --git a/wrapper/MM/LJComponent.pypp.cpp b/wrapper/MM/LJComponent.pypp.cpp index bb86a3723..f2775c928 100644 --- a/wrapper/MM/LJComponent.pypp.cpp +++ b/wrapper/MM/LJComponent.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; SireMM::LJComponent __copy__(const SireMM::LJComponent &other){ return SireMM::LJComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -106,9 +108,9 @@ void register_LJComponent_class(){ } LJComponent_exposer.staticmethod( "typeName" ); - LJComponent_exposer.def( "__copy__", &__copy__); - LJComponent_exposer.def( "__deepcopy__", &__copy__); - LJComponent_exposer.def( "clone", &__copy__); + LJComponent_exposer.def( "__copy__", &__copy__); + LJComponent_exposer.def( "__deepcopy__", &__copy__); + LJComponent_exposer.def( "clone", &__copy__); LJComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJComponent >, diff --git a/wrapper/MM/LJException.pypp.cpp b/wrapper/MM/LJException.pypp.cpp index cf1805cc4..30005f7ed 100644 --- a/wrapper/MM/LJException.pypp.cpp +++ b/wrapper/MM/LJException.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireMM::LJException __copy__(const SireMM::LJException &other){ return SireMM::LJException(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -147,9 +149,9 @@ void register_LJException_class(){ } LJException_exposer.staticmethod( "typeName" ); - LJException_exposer.def( "__copy__", &__copy__); - LJException_exposer.def( "__deepcopy__", &__copy__); - LJException_exposer.def( "clone", &__copy__); + LJException_exposer.def( "__copy__", &__copy__); + LJException_exposer.def( "__deepcopy__", &__copy__); + LJException_exposer.def( "clone", &__copy__); LJException_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJException >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJException_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJException >, diff --git a/wrapper/MM/LJExceptionID.pypp.cpp b/wrapper/MM/LJExceptionID.pypp.cpp index cc5842269..6faa936b3 100644 --- a/wrapper/MM/LJExceptionID.pypp.cpp +++ b/wrapper/MM/LJExceptionID.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireMM::LJExceptionID __copy__(const SireMM::LJExceptionID &other){ return SireMM::LJExceptionID(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -134,9 +136,9 @@ void register_LJExceptionID_class(){ } LJExceptionID_exposer.staticmethod( "generate" ); LJExceptionID_exposer.staticmethod( "typeName" ); - LJExceptionID_exposer.def( "__copy__", &__copy__); - LJExceptionID_exposer.def( "__deepcopy__", &__copy__); - LJExceptionID_exposer.def( "clone", &__copy__); + LJExceptionID_exposer.def( "__copy__", &__copy__); + LJExceptionID_exposer.def( "__deepcopy__", &__copy__); + LJExceptionID_exposer.def( "clone", &__copy__); LJExceptionID_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJExceptionID >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJExceptionID_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJExceptionID >, diff --git a/wrapper/MM/LJNBPairs.pypp.cpp b/wrapper/MM/LJNBPairs.pypp.cpp index 35d645d87..a4e88a009 100644 --- a/wrapper/MM/LJNBPairs.pypp.cpp +++ b/wrapper/MM/LJNBPairs.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::LJNBPairs __copy__(const SireMM::LJNBPairs &other){ return SireMM::LJNBPairs(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -76,9 +78,9 @@ void register_LJNBPairs_class(){ } LJNBPairs_exposer.staticmethod( "typeName" ); - LJNBPairs_exposer.def( "__copy__", &__copy__); - LJNBPairs_exposer.def( "__deepcopy__", &__copy__); - LJNBPairs_exposer.def( "clone", &__copy__); + LJNBPairs_exposer.def( "__copy__", &__copy__); + LJNBPairs_exposer.def( "__deepcopy__", &__copy__); + LJNBPairs_exposer.def( "clone", &__copy__); LJNBPairs_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJNBPairs >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJNBPairs_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJNBPairs >, diff --git a/wrapper/MM/LJParameter.pypp.cpp b/wrapper/MM/LJParameter.pypp.cpp index 4854a2988..7dcef8cb0 100644 --- a/wrapper/MM/LJParameter.pypp.cpp +++ b/wrapper/MM/LJParameter.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::LJParameter __copy__(const SireMM::LJParameter &other){ return SireMM::LJParameter(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -280,9 +282,9 @@ void register_LJParameter_class(){ LJParameter_exposer.staticmethod( "fromRMinAndEpsilon" ); LJParameter_exposer.staticmethod( "fromSigmaAndEpsilon" ); LJParameter_exposer.staticmethod( "typeName" ); - LJParameter_exposer.def( "__copy__", &__copy__); - LJParameter_exposer.def( "__deepcopy__", &__copy__); - LJParameter_exposer.def( "clone", &__copy__); + LJParameter_exposer.def( "__copy__", &__copy__); + LJParameter_exposer.def( "__deepcopy__", &__copy__); + LJParameter_exposer.def( "clone", &__copy__); LJParameter_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJParameter >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJParameter_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJParameter >, diff --git a/wrapper/MM/LJParameterName.pypp.cpp b/wrapper/MM/LJParameterName.pypp.cpp index 3c980d478..ceb899c56 100644 --- a/wrapper/MM/LJParameterName.pypp.cpp +++ b/wrapper/MM/LJParameterName.pypp.cpp @@ -45,6 +45,8 @@ namespace bp = boost::python; SireMM::LJParameterName __copy__(const SireMM::LJParameterName &other){ return SireMM::LJParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::LJParameterName&){ return "SireMM::LJParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -67,9 +69,9 @@ void register_LJParameterName_class(){ , "" ); } - LJParameterName_exposer.def( "__copy__", &__copy__); - LJParameterName_exposer.def( "__deepcopy__", &__copy__); - LJParameterName_exposer.def( "clone", &__copy__); + LJParameterName_exposer.def( "__copy__", &__copy__); + LJParameterName_exposer.def( "__deepcopy__", &__copy__); + LJParameterName_exposer.def( "clone", &__copy__); LJParameterName_exposer.def( "__str__", &pvt_get_name); LJParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/LJParameterName3D.pypp.cpp b/wrapper/MM/LJParameterName3D.pypp.cpp index 5e463fa96..bce566119 100644 --- a/wrapper/MM/LJParameterName3D.pypp.cpp +++ b/wrapper/MM/LJParameterName3D.pypp.cpp @@ -45,6 +45,8 @@ namespace bp = boost::python; SireMM::LJParameterName3D __copy__(const SireMM::LJParameterName3D &other){ return SireMM::LJParameterName3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::LJParameterName3D&){ return "SireMM::LJParameterName3D";} #include "Helpers/release_gil_policy.hpp" @@ -55,9 +57,9 @@ void register_LJParameterName3D_class(){ typedef bp::class_< SireMM::LJParameterName3D, bp::bases< SireMM::LJParameterName > > LJParameterName3D_exposer_t; LJParameterName3D_exposer_t LJParameterName3D_exposer = LJParameterName3D_exposer_t( "LJParameterName3D", "This class provides the default name of the properties\nthat contain the LJ and 3D coordinates properties", bp::init< >("") ); bp::scope LJParameterName3D_scope( LJParameterName3D_exposer ); - LJParameterName3D_exposer.def( "__copy__", &__copy__); - LJParameterName3D_exposer.def( "__deepcopy__", &__copy__); - LJParameterName3D_exposer.def( "clone", &__copy__); + LJParameterName3D_exposer.def( "__copy__", &__copy__); + LJParameterName3D_exposer.def( "__deepcopy__", &__copy__); + LJParameterName3D_exposer.def( "clone", &__copy__); LJParameterName3D_exposer.def( "__str__", &pvt_get_name); LJParameterName3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/LJPerturbation.pypp.cpp b/wrapper/MM/LJPerturbation.pypp.cpp index 48e353733..c39218299 100644 --- a/wrapper/MM/LJPerturbation.pypp.cpp +++ b/wrapper/MM/LJPerturbation.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireMM::LJPerturbation __copy__(const SireMM::LJPerturbation &other){ return SireMM::LJPerturbation(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -267,9 +269,9 @@ void register_LJPerturbation_class(){ } LJPerturbation_exposer.staticmethod( "typeName" ); - LJPerturbation_exposer.def( "__copy__", &__copy__); - LJPerturbation_exposer.def( "__deepcopy__", &__copy__); - LJPerturbation_exposer.def( "clone", &__copy__); + LJPerturbation_exposer.def( "__copy__", &__copy__); + LJPerturbation_exposer.def( "__deepcopy__", &__copy__); + LJPerturbation_exposer.def( "clone", &__copy__); LJPerturbation_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJPerturbation >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJPerturbation_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJPerturbation >, diff --git a/wrapper/MM/LJProbe.pypp.cpp b/wrapper/MM/LJProbe.pypp.cpp index 5a81755cb..9f6f633ca 100644 --- a/wrapper/MM/LJProbe.pypp.cpp +++ b/wrapper/MM/LJProbe.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireMM::LJProbe __copy__(const SireMM::LJProbe &other){ return SireMM::LJProbe(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -73,9 +75,9 @@ void register_LJProbe_class(){ } LJProbe_exposer.staticmethod( "typeName" ); - LJProbe_exposer.def( "__copy__", &__copy__); - LJProbe_exposer.def( "__deepcopy__", &__copy__); - LJProbe_exposer.def( "clone", &__copy__); + LJProbe_exposer.def( "__copy__", &__copy__); + LJProbe_exposer.def( "__deepcopy__", &__copy__); + LJProbe_exposer.def( "clone", &__copy__); LJProbe_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJProbe >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJProbe_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJProbe >, diff --git a/wrapper/MM/LJScaleFactor.pypp.cpp b/wrapper/MM/LJScaleFactor.pypp.cpp index 5d7743add..dc63a3679 100644 --- a/wrapper/MM/LJScaleFactor.pypp.cpp +++ b/wrapper/MM/LJScaleFactor.pypp.cpp @@ -19,6 +19,8 @@ namespace bp = boost::python; SireMM::LJScaleFactor __copy__(const SireMM::LJScaleFactor &other){ return SireMM::LJScaleFactor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireMM::LJScaleFactor&){ return "SireMM::LJScaleFactor";} @@ -84,9 +86,9 @@ void register_LJScaleFactor_class(){ } LJScaleFactor_exposer.staticmethod( "typeName" ); - LJScaleFactor_exposer.def( "__copy__", &__copy__); - LJScaleFactor_exposer.def( "__deepcopy__", &__copy__); - LJScaleFactor_exposer.def( "clone", &__copy__); + LJScaleFactor_exposer.def( "__copy__", &__copy__); + LJScaleFactor_exposer.def( "__deepcopy__", &__copy__); + LJScaleFactor_exposer.def( "clone", &__copy__); LJScaleFactor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::LJScaleFactor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); LJScaleFactor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::LJScaleFactor >, diff --git a/wrapper/MM/MMDetail.pypp.cpp b/wrapper/MM/MMDetail.pypp.cpp index 7b7b37087..5c6a4ef5f 100644 --- a/wrapper/MM/MMDetail.pypp.cpp +++ b/wrapper/MM/MMDetail.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireMM::MMDetail __copy__(const SireMM::MMDetail &other){ return SireMM::MMDetail(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -330,9 +332,9 @@ void register_MMDetail_class(){ } MMDetail_exposer.staticmethod( "guessFrom" ); MMDetail_exposer.staticmethod( "typeName" ); - MMDetail_exposer.def( "__copy__", &__copy__); - MMDetail_exposer.def( "__deepcopy__", &__copy__); - MMDetail_exposer.def( "clone", &__copy__); + MMDetail_exposer.def( "__copy__", &__copy__); + MMDetail_exposer.def( "__deepcopy__", &__copy__); + MMDetail_exposer.def( "clone", &__copy__); MMDetail_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::MMDetail >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MMDetail_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::MMDetail >, diff --git a/wrapper/MM/Mover_Angle_.pypp.cpp b/wrapper/MM/Mover_Angle_.pypp.cpp index 022dfd89f..f4bbc2dfd 100644 --- a/wrapper/MM/Mover_Angle_.pypp.cpp +++ b/wrapper/MM/Mover_Angle_.pypp.cpp @@ -87,6 +87,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -478,9 +480,9 @@ void register_Mover_Angle__class(){ } Mover_Angle__exposer.staticmethod( "typeName" ); - Mover_Angle__exposer.def( "__copy__", &__copy__); - Mover_Angle__exposer.def( "__deepcopy__", &__copy__); - Mover_Angle__exposer.def( "clone", &__copy__); + Mover_Angle__exposer.def( "__copy__", &__copy__>); + Mover_Angle__exposer.def( "__deepcopy__", &__copy__>); + Mover_Angle__exposer.def( "clone", &__copy__>); Mover_Angle__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_Angle__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_Angle__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_Bond_.pypp.cpp b/wrapper/MM/Mover_Bond_.pypp.cpp index 16c12f527..e839ee37b 100644 --- a/wrapper/MM/Mover_Bond_.pypp.cpp +++ b/wrapper/MM/Mover_Bond_.pypp.cpp @@ -87,6 +87,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -478,9 +480,9 @@ void register_Mover_Bond__class(){ } Mover_Bond__exposer.staticmethod( "typeName" ); - Mover_Bond__exposer.def( "__copy__", &__copy__); - Mover_Bond__exposer.def( "__deepcopy__", &__copy__); - Mover_Bond__exposer.def( "clone", &__copy__); + Mover_Bond__exposer.def( "__copy__", &__copy__>); + Mover_Bond__exposer.def( "__deepcopy__", &__copy__>); + Mover_Bond__exposer.def( "clone", &__copy__>); Mover_Bond__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_Bond__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_Bond__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_Dihedral_.pypp.cpp b/wrapper/MM/Mover_Dihedral_.pypp.cpp index 3f85c2020..a7a76d031 100644 --- a/wrapper/MM/Mover_Dihedral_.pypp.cpp +++ b/wrapper/MM/Mover_Dihedral_.pypp.cpp @@ -87,6 +87,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -478,9 +480,9 @@ void register_Mover_Dihedral__class(){ } Mover_Dihedral__exposer.staticmethod( "typeName" ); - Mover_Dihedral__exposer.def( "__copy__", &__copy__); - Mover_Dihedral__exposer.def( "__deepcopy__", &__copy__); - Mover_Dihedral__exposer.def( "clone", &__copy__); + Mover_Dihedral__exposer.def( "__copy__", &__copy__>); + Mover_Dihedral__exposer.def( "__deepcopy__", &__copy__>); + Mover_Dihedral__exposer.def( "clone", &__copy__>); Mover_Dihedral__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_Dihedral__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_Dihedral__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_Improper_.pypp.cpp b/wrapper/MM/Mover_Improper_.pypp.cpp index 842c27e46..babf94157 100644 --- a/wrapper/MM/Mover_Improper_.pypp.cpp +++ b/wrapper/MM/Mover_Improper_.pypp.cpp @@ -89,6 +89,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -480,9 +482,9 @@ void register_Mover_Improper__class(){ } Mover_Improper__exposer.staticmethod( "typeName" ); - Mover_Improper__exposer.def( "__copy__", &__copy__); - Mover_Improper__exposer.def( "__deepcopy__", &__copy__); - Mover_Improper__exposer.def( "clone", &__copy__); + Mover_Improper__exposer.def( "__copy__", &__copy__>); + Mover_Improper__exposer.def( "__deepcopy__", &__copy__>); + Mover_Improper__exposer.def( "clone", &__copy__>); Mover_Improper__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_Improper__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_Improper__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_SelectorAngle_.pypp.cpp b/wrapper/MM/Mover_SelectorAngle_.pypp.cpp index b1c13727e..1530a7fed 100644 --- a/wrapper/MM/Mover_SelectorAngle_.pypp.cpp +++ b/wrapper/MM/Mover_SelectorAngle_.pypp.cpp @@ -87,6 +87,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -478,9 +480,9 @@ void register_Mover_SelectorAngle__class(){ } Mover_SelectorAngle__exposer.staticmethod( "typeName" ); - Mover_SelectorAngle__exposer.def( "__copy__", &__copy__); - Mover_SelectorAngle__exposer.def( "__deepcopy__", &__copy__); - Mover_SelectorAngle__exposer.def( "clone", &__copy__); + Mover_SelectorAngle__exposer.def( "__copy__", &__copy__>); + Mover_SelectorAngle__exposer.def( "__deepcopy__", &__copy__>); + Mover_SelectorAngle__exposer.def( "clone", &__copy__>); Mover_SelectorAngle__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_SelectorAngle__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_SelectorAngle__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_SelectorBond_.pypp.cpp b/wrapper/MM/Mover_SelectorBond_.pypp.cpp index a1d736498..ca3b20263 100644 --- a/wrapper/MM/Mover_SelectorBond_.pypp.cpp +++ b/wrapper/MM/Mover_SelectorBond_.pypp.cpp @@ -85,6 +85,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -476,9 +478,9 @@ void register_Mover_SelectorBond__class(){ } Mover_SelectorBond__exposer.staticmethod( "typeName" ); - Mover_SelectorBond__exposer.def( "__copy__", &__copy__); - Mover_SelectorBond__exposer.def( "__deepcopy__", &__copy__); - Mover_SelectorBond__exposer.def( "clone", &__copy__); + Mover_SelectorBond__exposer.def( "__copy__", &__copy__>); + Mover_SelectorBond__exposer.def( "__deepcopy__", &__copy__>); + Mover_SelectorBond__exposer.def( "clone", &__copy__>); Mover_SelectorBond__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_SelectorBond__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_SelectorBond__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_SelectorDihedral_.pypp.cpp b/wrapper/MM/Mover_SelectorDihedral_.pypp.cpp index da9090ad3..c29eab659 100644 --- a/wrapper/MM/Mover_SelectorDihedral_.pypp.cpp +++ b/wrapper/MM/Mover_SelectorDihedral_.pypp.cpp @@ -85,6 +85,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -476,9 +478,9 @@ void register_Mover_SelectorDihedral__class(){ } Mover_SelectorDihedral__exposer.staticmethod( "typeName" ); - Mover_SelectorDihedral__exposer.def( "__copy__", &__copy__); - Mover_SelectorDihedral__exposer.def( "__deepcopy__", &__copy__); - Mover_SelectorDihedral__exposer.def( "clone", &__copy__); + Mover_SelectorDihedral__exposer.def( "__copy__", &__copy__>); + Mover_SelectorDihedral__exposer.def( "__deepcopy__", &__copy__>); + Mover_SelectorDihedral__exposer.def( "clone", &__copy__>); Mover_SelectorDihedral__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_SelectorDihedral__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_SelectorDihedral__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/Mover_SelectorImproper_.pypp.cpp b/wrapper/MM/Mover_SelectorImproper_.pypp.cpp index 8e7d5b724..55bfe92d5 100644 --- a/wrapper/MM/Mover_SelectorImproper_.pypp.cpp +++ b/wrapper/MM/Mover_SelectorImproper_.pypp.cpp @@ -85,6 +85,8 @@ namespace bp = boost::python; SireMol::Mover __copy__(const SireMol::Mover &other){ return SireMol::Mover(other); } +#include "Helpers/copy.hpp" + #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" @@ -476,9 +478,9 @@ void register_Mover_SelectorImproper__class(){ } Mover_SelectorImproper__exposer.staticmethod( "typeName" ); - Mover_SelectorImproper__exposer.def( "__copy__", &__copy__); - Mover_SelectorImproper__exposer.def( "__deepcopy__", &__copy__); - Mover_SelectorImproper__exposer.def( "clone", &__copy__); + Mover_SelectorImproper__exposer.def( "__copy__", &__copy__>); + Mover_SelectorImproper__exposer.def( "__deepcopy__", &__copy__>); + Mover_SelectorImproper__exposer.def( "clone", &__copy__>); Mover_SelectorImproper__exposer.def( "__str__", &__str__< ::SireMol::Mover > ); Mover_SelectorImproper__exposer.def( "__repr__", &__str__< ::SireMol::Mover > ); Mover_SelectorImproper__exposer.def( "__len__", &__len_size< ::SireMol::Mover > ); diff --git a/wrapper/MM/MultiCLJComponent.pypp.cpp b/wrapper/MM/MultiCLJComponent.pypp.cpp index 212d5557e..11862456b 100644 --- a/wrapper/MM/MultiCLJComponent.pypp.cpp +++ b/wrapper/MM/MultiCLJComponent.pypp.cpp @@ -20,6 +20,8 @@ namespace bp = boost::python; SireMM::MultiCLJComponent __copy__(const SireMM::MultiCLJComponent &other){ return SireMM::MultiCLJComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -325,9 +327,9 @@ void register_MultiCLJComponent_class(){ } MultiCLJComponent_exposer.staticmethod( "typeName" ); - MultiCLJComponent_exposer.def( "__copy__", &__copy__); - MultiCLJComponent_exposer.def( "__deepcopy__", &__copy__); - MultiCLJComponent_exposer.def( "clone", &__copy__); + MultiCLJComponent_exposer.def( "__copy__", &__copy__); + MultiCLJComponent_exposer.def( "__deepcopy__", &__copy__); + MultiCLJComponent_exposer.def( "clone", &__copy__); MultiCLJComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::MultiCLJComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MultiCLJComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::MultiCLJComponent >, diff --git a/wrapper/MM/NoCutoff.pypp.cpp b/wrapper/MM/NoCutoff.pypp.cpp index a0b00cfd3..20de913c9 100644 --- a/wrapper/MM/NoCutoff.pypp.cpp +++ b/wrapper/MM/NoCutoff.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireMM::NoCutoff __copy__(const SireMM::NoCutoff &other){ return SireMM::NoCutoff(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -134,9 +136,9 @@ void register_NoCutoff_class(){ } NoCutoff_exposer.staticmethod( "typeName" ); - NoCutoff_exposer.def( "__copy__", &__copy__); - NoCutoff_exposer.def( "__deepcopy__", &__copy__); - NoCutoff_exposer.def( "clone", &__copy__); + NoCutoff_exposer.def( "__copy__", &__copy__); + NoCutoff_exposer.def( "__deepcopy__", &__copy__); + NoCutoff_exposer.def( "clone", &__copy__); NoCutoff_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::NoCutoff >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NoCutoff_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::NoCutoff >, diff --git a/wrapper/MM/NullCLJFunction.pypp.cpp b/wrapper/MM/NullCLJFunction.pypp.cpp index e48e94e36..e3ee99fd7 100644 --- a/wrapper/MM/NullCLJFunction.pypp.cpp +++ b/wrapper/MM/NullCLJFunction.pypp.cpp @@ -53,6 +53,8 @@ namespace bp = boost::python; SireMM::NullCLJFunction __copy__(const SireMM::NullCLJFunction &other){ return SireMM::NullCLJFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -106,9 +108,9 @@ void register_NullCLJFunction_class(){ } NullCLJFunction_exposer.staticmethod( "typeName" ); - NullCLJFunction_exposer.def( "__copy__", &__copy__); - NullCLJFunction_exposer.def( "__deepcopy__", &__copy__); - NullCLJFunction_exposer.def( "clone", &__copy__); + NullCLJFunction_exposer.def( "__copy__", &__copy__); + NullCLJFunction_exposer.def( "__deepcopy__", &__copy__); + NullCLJFunction_exposer.def( "clone", &__copy__); NullCLJFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::NullCLJFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NullCLJFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::NullCLJFunction >, diff --git a/wrapper/MM/NullRestraint.pypp.cpp b/wrapper/MM/NullRestraint.pypp.cpp index 8ea61ddd4..45e130aa8 100644 --- a/wrapper/MM/NullRestraint.pypp.cpp +++ b/wrapper/MM/NullRestraint.pypp.cpp @@ -37,6 +37,8 @@ namespace bp = boost::python; SireMM::NullRestraint __copy__(const SireMM::NullRestraint &other){ return SireMM::NullRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -340,9 +342,9 @@ void register_NullRestraint_class(){ } NullRestraint_exposer.staticmethod( "typeName" ); - NullRestraint_exposer.def( "__copy__", &__copy__); - NullRestraint_exposer.def( "__deepcopy__", &__copy__); - NullRestraint_exposer.def( "clone", &__copy__); + NullRestraint_exposer.def( "__copy__", &__copy__); + NullRestraint_exposer.def( "__deepcopy__", &__copy__); + NullRestraint_exposer.def( "clone", &__copy__); NullRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::NullRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NullRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::NullRestraint >, diff --git a/wrapper/MM/PositionalRestraint.pypp.cpp b/wrapper/MM/PositionalRestraint.pypp.cpp index dbae9b973..7e7d58491 100644 --- a/wrapper/MM/PositionalRestraint.pypp.cpp +++ b/wrapper/MM/PositionalRestraint.pypp.cpp @@ -25,6 +25,8 @@ namespace bp = boost::python; SireMM::PositionalRestraint __copy__(const SireMM::PositionalRestraint &other){ return SireMM::PositionalRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -190,9 +192,9 @@ void register_PositionalRestraint_class(){ } PositionalRestraint_exposer.staticmethod( "typeName" ); - PositionalRestraint_exposer.def( "__copy__", &__copy__); - PositionalRestraint_exposer.def( "__deepcopy__", &__copy__); - PositionalRestraint_exposer.def( "clone", &__copy__); + PositionalRestraint_exposer.def( "__copy__", &__copy__); + PositionalRestraint_exposer.def( "__deepcopy__", &__copy__); + PositionalRestraint_exposer.def( "clone", &__copy__); PositionalRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::PositionalRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PositionalRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::PositionalRestraint >, diff --git a/wrapper/MM/PositionalRestraints.pypp.cpp b/wrapper/MM/PositionalRestraints.pypp.cpp index ade356fbb..787f32e66 100644 --- a/wrapper/MM/PositionalRestraints.pypp.cpp +++ b/wrapper/MM/PositionalRestraints.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireMM::PositionalRestraints __copy__(const SireMM::PositionalRestraints &other){ return SireMM::PositionalRestraints(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -296,9 +298,9 @@ void register_PositionalRestraints_class(){ } PositionalRestraints_exposer.staticmethod( "typeName" ); - PositionalRestraints_exposer.def( "__copy__", &__copy__); - PositionalRestraints_exposer.def( "__deepcopy__", &__copy__); - PositionalRestraints_exposer.def( "clone", &__copy__); + PositionalRestraints_exposer.def( "__copy__", &__copy__); + PositionalRestraints_exposer.def( "__deepcopy__", &__copy__); + PositionalRestraints_exposer.def( "clone", &__copy__); PositionalRestraints_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::PositionalRestraints >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PositionalRestraints_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::PositionalRestraints >, diff --git a/wrapper/MM/RestraintComponent.pypp.cpp b/wrapper/MM/RestraintComponent.pypp.cpp index 6abf1e672..1d0cabc40 100644 --- a/wrapper/MM/RestraintComponent.pypp.cpp +++ b/wrapper/MM/RestraintComponent.pypp.cpp @@ -16,6 +16,8 @@ namespace bp = boost::python; SireMM::RestraintComponent __copy__(const SireMM::RestraintComponent &other){ return SireMM::RestraintComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -106,9 +108,9 @@ void register_RestraintComponent_class(){ } RestraintComponent_exposer.staticmethod( "typeName" ); - RestraintComponent_exposer.def( "__copy__", &__copy__); - RestraintComponent_exposer.def( "__deepcopy__", &__copy__); - RestraintComponent_exposer.def( "clone", &__copy__); + RestraintComponent_exposer.def( "__copy__", &__copy__); + RestraintComponent_exposer.def( "__deepcopy__", &__copy__); + RestraintComponent_exposer.def( "clone", &__copy__); RestraintComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::RestraintComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); RestraintComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::RestraintComponent >, diff --git a/wrapper/MM/RestraintFF.pypp.cpp b/wrapper/MM/RestraintFF.pypp.cpp index 8e6675fae..d3076139a 100644 --- a/wrapper/MM/RestraintFF.pypp.cpp +++ b/wrapper/MM/RestraintFF.pypp.cpp @@ -40,6 +40,8 @@ namespace bp = boost::python; SireMM::RestraintFF __copy__(const SireMM::RestraintFF &other){ return SireMM::RestraintFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -517,9 +519,9 @@ void register_RestraintFF_class(){ } RestraintFF_exposer.staticmethod( "typeName" ); - RestraintFF_exposer.def( "__copy__", &__copy__); - RestraintFF_exposer.def( "__deepcopy__", &__copy__); - RestraintFF_exposer.def( "clone", &__copy__); + RestraintFF_exposer.def( "__copy__", &__copy__); + RestraintFF_exposer.def( "__deepcopy__", &__copy__); + RestraintFF_exposer.def( "clone", &__copy__); RestraintFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::RestraintFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); RestraintFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::RestraintFF >, diff --git a/wrapper/MM/ScaledCLJParameterNames3D.pypp.cpp b/wrapper/MM/ScaledCLJParameterNames3D.pypp.cpp index a394439ee..78803ecd2 100644 --- a/wrapper/MM/ScaledCLJParameterNames3D.pypp.cpp +++ b/wrapper/MM/ScaledCLJParameterNames3D.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; SireMM::ScaledCLJParameterNames3D __copy__(const SireMM::ScaledCLJParameterNames3D &other){ return SireMM::ScaledCLJParameterNames3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ScaledCLJParameterNames3D&){ return "SireMM::ScaledCLJParameterNames3D";} #include "Helpers/release_gil_policy.hpp" @@ -53,9 +55,9 @@ void register_ScaledCLJParameterNames3D_class(){ typedef bp::class_< SireMM::ScaledCLJParameterNames3D, bp::bases< SireMM::CLJParameterNames3D, SireMM::CLJParameterNames, SireMM::LJParameterName, SireMM::ChargeParameterName > > ScaledCLJParameterNames3D_exposer_t; ScaledCLJParameterNames3D_exposer_t ScaledCLJParameterNames3D_exposer = ScaledCLJParameterNames3D_exposer_t( "ScaledCLJParameterNames3D", "This class provides the default name of the properties\nthat contain the charge, LJ, intramolecular NB scale parameters and\n3D coordinates properties", bp::init< >("") ); bp::scope ScaledCLJParameterNames3D_scope( ScaledCLJParameterNames3D_exposer ); - ScaledCLJParameterNames3D_exposer.def( "__copy__", &__copy__); - ScaledCLJParameterNames3D_exposer.def( "__deepcopy__", &__copy__); - ScaledCLJParameterNames3D_exposer.def( "clone", &__copy__); + ScaledCLJParameterNames3D_exposer.def( "__copy__", &__copy__); + ScaledCLJParameterNames3D_exposer.def( "__deepcopy__", &__copy__); + ScaledCLJParameterNames3D_exposer.def( "clone", &__copy__); ScaledCLJParameterNames3D_exposer.def( "__str__", &pvt_get_name); ScaledCLJParameterNames3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/ScaledChargeParameterNames3D.pypp.cpp b/wrapper/MM/ScaledChargeParameterNames3D.pypp.cpp index 8ed635a48..df91591c0 100644 --- a/wrapper/MM/ScaledChargeParameterNames3D.pypp.cpp +++ b/wrapper/MM/ScaledChargeParameterNames3D.pypp.cpp @@ -41,6 +41,8 @@ namespace bp = boost::python; SireMM::ScaledChargeParameterNames3D __copy__(const SireMM::ScaledChargeParameterNames3D &other){ return SireMM::ScaledChargeParameterNames3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ScaledChargeParameterNames3D&){ return "SireMM::ScaledChargeParameterNames3D";} #include "Helpers/release_gil_policy.hpp" @@ -51,9 +53,9 @@ void register_ScaledChargeParameterNames3D_class(){ typedef bp::class_< SireMM::ScaledChargeParameterNames3D, bp::bases< SireMM::ChargeParameterName3D, SireMM::ChargeParameterName > > ScaledChargeParameterNames3D_exposer_t; ScaledChargeParameterNames3D_exposer_t ScaledChargeParameterNames3D_exposer = ScaledChargeParameterNames3D_exposer_t( "ScaledChargeParameterNames3D", "This class provides the default name of the properties\nthat contain the charge and intramolecular NB scale parameters and\n3D coordinates properties", bp::init< >("") ); bp::scope ScaledChargeParameterNames3D_scope( ScaledChargeParameterNames3D_exposer ); - ScaledChargeParameterNames3D_exposer.def( "__copy__", &__copy__); - ScaledChargeParameterNames3D_exposer.def( "__deepcopy__", &__copy__); - ScaledChargeParameterNames3D_exposer.def( "clone", &__copy__); + ScaledChargeParameterNames3D_exposer.def( "__copy__", &__copy__); + ScaledChargeParameterNames3D_exposer.def( "__deepcopy__", &__copy__); + ScaledChargeParameterNames3D_exposer.def( "clone", &__copy__); ScaledChargeParameterNames3D_exposer.def( "__str__", &pvt_get_name); ScaledChargeParameterNames3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/ScaledLJParameterNames3D.pypp.cpp b/wrapper/MM/ScaledLJParameterNames3D.pypp.cpp index 7c6716542..73806852b 100644 --- a/wrapper/MM/ScaledLJParameterNames3D.pypp.cpp +++ b/wrapper/MM/ScaledLJParameterNames3D.pypp.cpp @@ -45,6 +45,8 @@ namespace bp = boost::python; SireMM::ScaledLJParameterNames3D __copy__(const SireMM::ScaledLJParameterNames3D &other){ return SireMM::ScaledLJParameterNames3D(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::ScaledLJParameterNames3D&){ return "SireMM::ScaledLJParameterNames3D";} #include "Helpers/release_gil_policy.hpp" @@ -55,9 +57,9 @@ void register_ScaledLJParameterNames3D_class(){ typedef bp::class_< SireMM::ScaledLJParameterNames3D, bp::bases< SireMM::LJParameterName3D, SireMM::LJParameterName > > ScaledLJParameterNames3D_exposer_t; ScaledLJParameterNames3D_exposer_t ScaledLJParameterNames3D_exposer = ScaledLJParameterNames3D_exposer_t( "ScaledLJParameterNames3D", "This class provides the default name of the properties\nthat contain the LJ, intramolecular NB scale parameters and\n3D coordinates properties", bp::init< >("") ); bp::scope ScaledLJParameterNames3D_scope( ScaledLJParameterNames3D_exposer ); - ScaledLJParameterNames3D_exposer.def( "__copy__", &__copy__); - ScaledLJParameterNames3D_exposer.def( "__deepcopy__", &__copy__); - ScaledLJParameterNames3D_exposer.def( "clone", &__copy__); + ScaledLJParameterNames3D_exposer.def( "__copy__", &__copy__); + ScaledLJParameterNames3D_exposer.def( "__deepcopy__", &__copy__); + ScaledLJParameterNames3D_exposer.def( "clone", &__copy__); ScaledLJParameterNames3D_exposer.def( "__str__", &pvt_get_name); ScaledLJParameterNames3D_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/SelectorAngle.pypp.cpp b/wrapper/MM/SelectorAngle.pypp.cpp index 61215fb5e..9d003366b 100644 --- a/wrapper/MM/SelectorAngle.pypp.cpp +++ b/wrapper/MM/SelectorAngle.pypp.cpp @@ -41,6 +41,8 @@ namespace bp = boost::python; SireMM::SelectorAngle __copy__(const SireMM::SelectorAngle &other){ return SireMM::SelectorAngle(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -677,9 +679,9 @@ void register_SelectorAngle_class(){ } SelectorAngle_exposer.staticmethod( "typeName" ); - SelectorAngle_exposer.def( "__copy__", &__copy__); - SelectorAngle_exposer.def( "__deepcopy__", &__copy__); - SelectorAngle_exposer.def( "clone", &__copy__); + SelectorAngle_exposer.def( "__copy__", &__copy__); + SelectorAngle_exposer.def( "__deepcopy__", &__copy__); + SelectorAngle_exposer.def( "clone", &__copy__); SelectorAngle_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorAngle >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorAngle_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorAngle >, diff --git a/wrapper/MM/SelectorBond.pypp.cpp b/wrapper/MM/SelectorBond.pypp.cpp index 311a277e5..600c1235f 100644 --- a/wrapper/MM/SelectorBond.pypp.cpp +++ b/wrapper/MM/SelectorBond.pypp.cpp @@ -39,6 +39,8 @@ namespace bp = boost::python; SireMM::SelectorBond __copy__(const SireMM::SelectorBond &other){ return SireMM::SelectorBond(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -672,9 +674,9 @@ void register_SelectorBond_class(){ } SelectorBond_exposer.staticmethod( "typeName" ); - SelectorBond_exposer.def( "__copy__", &__copy__); - SelectorBond_exposer.def( "__deepcopy__", &__copy__); - SelectorBond_exposer.def( "clone", &__copy__); + SelectorBond_exposer.def( "__copy__", &__copy__); + SelectorBond_exposer.def( "__deepcopy__", &__copy__); + SelectorBond_exposer.def( "clone", &__copy__); SelectorBond_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorBond >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorBond_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorBond >, diff --git a/wrapper/MM/SelectorDihedral.pypp.cpp b/wrapper/MM/SelectorDihedral.pypp.cpp index af5ad8d40..769d7409c 100644 --- a/wrapper/MM/SelectorDihedral.pypp.cpp +++ b/wrapper/MM/SelectorDihedral.pypp.cpp @@ -39,6 +39,8 @@ namespace bp = boost::python; SireMM::SelectorDihedral __copy__(const SireMM::SelectorDihedral &other){ return SireMM::SelectorDihedral(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -678,9 +680,9 @@ void register_SelectorDihedral_class(){ } SelectorDihedral_exposer.staticmethod( "typeName" ); - SelectorDihedral_exposer.def( "__copy__", &__copy__); - SelectorDihedral_exposer.def( "__deepcopy__", &__copy__); - SelectorDihedral_exposer.def( "clone", &__copy__); + SelectorDihedral_exposer.def( "__copy__", &__copy__); + SelectorDihedral_exposer.def( "__deepcopy__", &__copy__); + SelectorDihedral_exposer.def( "clone", &__copy__); SelectorDihedral_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorDihedral >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorDihedral_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorDihedral >, diff --git a/wrapper/MM/SelectorImproper.pypp.cpp b/wrapper/MM/SelectorImproper.pypp.cpp index 331a8012d..5e9ea3ed8 100644 --- a/wrapper/MM/SelectorImproper.pypp.cpp +++ b/wrapper/MM/SelectorImproper.pypp.cpp @@ -39,6 +39,8 @@ namespace bp = boost::python; SireMM::SelectorImproper __copy__(const SireMM::SelectorImproper &other){ return SireMM::SelectorImproper(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -678,9 +680,9 @@ void register_SelectorImproper_class(){ } SelectorImproper_exposer.staticmethod( "typeName" ); - SelectorImproper_exposer.def( "__copy__", &__copy__); - SelectorImproper_exposer.def( "__deepcopy__", &__copy__); - SelectorImproper_exposer.def( "clone", &__copy__); + SelectorImproper_exposer.def( "__copy__", &__copy__); + SelectorImproper_exposer.def( "__deepcopy__", &__copy__); + SelectorImproper_exposer.def( "clone", &__copy__); SelectorImproper_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorImproper >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorImproper_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorImproper >, diff --git a/wrapper/MM/SelectorMAngle.pypp.cpp b/wrapper/MM/SelectorMAngle.pypp.cpp index 70e54ea1b..d3fa06483 100644 --- a/wrapper/MM/SelectorMAngle.pypp.cpp +++ b/wrapper/MM/SelectorMAngle.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireMM::SelectorMAngle __copy__(const SireMM::SelectorMAngle &other){ return SireMM::SelectorMAngle(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -1566,9 +1568,9 @@ void register_SelectorMAngle_class(){ } SelectorMAngle_exposer.staticmethod( "typeName" ); - SelectorMAngle_exposer.def( "__copy__", &__copy__); - SelectorMAngle_exposer.def( "__deepcopy__", &__copy__); - SelectorMAngle_exposer.def( "clone", &__copy__); + SelectorMAngle_exposer.def( "__copy__", &__copy__); + SelectorMAngle_exposer.def( "__deepcopy__", &__copy__); + SelectorMAngle_exposer.def( "clone", &__copy__); SelectorMAngle_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorMAngle >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorMAngle_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorMAngle >, diff --git a/wrapper/MM/SelectorMBond.pypp.cpp b/wrapper/MM/SelectorMBond.pypp.cpp index ef4ceb005..6a4b27847 100644 --- a/wrapper/MM/SelectorMBond.pypp.cpp +++ b/wrapper/MM/SelectorMBond.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireMM::SelectorMBond __copy__(const SireMM::SelectorMBond &other){ return SireMM::SelectorMBond(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -1565,9 +1567,9 @@ void register_SelectorMBond_class(){ } SelectorMBond_exposer.staticmethod( "typeName" ); - SelectorMBond_exposer.def( "__copy__", &__copy__); - SelectorMBond_exposer.def( "__deepcopy__", &__copy__); - SelectorMBond_exposer.def( "clone", &__copy__); + SelectorMBond_exposer.def( "__copy__", &__copy__); + SelectorMBond_exposer.def( "__deepcopy__", &__copy__); + SelectorMBond_exposer.def( "clone", &__copy__); SelectorMBond_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorMBond >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorMBond_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorMBond >, diff --git a/wrapper/MM/SelectorMDihedral.pypp.cpp b/wrapper/MM/SelectorMDihedral.pypp.cpp index 6b1b024b7..10e356f56 100644 --- a/wrapper/MM/SelectorMDihedral.pypp.cpp +++ b/wrapper/MM/SelectorMDihedral.pypp.cpp @@ -27,6 +27,8 @@ namespace bp = boost::python; SireMM::SelectorMDihedral __copy__(const SireMM::SelectorMDihedral &other){ return SireMM::SelectorMDihedral(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -1565,9 +1567,9 @@ void register_SelectorMDihedral_class(){ } SelectorMDihedral_exposer.staticmethod( "typeName" ); - SelectorMDihedral_exposer.def( "__copy__", &__copy__); - SelectorMDihedral_exposer.def( "__deepcopy__", &__copy__); - SelectorMDihedral_exposer.def( "clone", &__copy__); + SelectorMDihedral_exposer.def( "__copy__", &__copy__); + SelectorMDihedral_exposer.def( "__deepcopy__", &__copy__); + SelectorMDihedral_exposer.def( "clone", &__copy__); SelectorMDihedral_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorMDihedral >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorMDihedral_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorMDihedral >, diff --git a/wrapper/MM/SelectorMImproper.pypp.cpp b/wrapper/MM/SelectorMImproper.pypp.cpp index 883cb3613..ebce1472a 100644 --- a/wrapper/MM/SelectorMImproper.pypp.cpp +++ b/wrapper/MM/SelectorMImproper.pypp.cpp @@ -29,6 +29,8 @@ namespace bp = boost::python; SireMM::SelectorMImproper __copy__(const SireMM::SelectorMImproper &other){ return SireMM::SelectorMImproper(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -1567,9 +1569,9 @@ void register_SelectorMImproper_class(){ } SelectorMImproper_exposer.staticmethod( "typeName" ); - SelectorMImproper_exposer.def( "__copy__", &__copy__); - SelectorMImproper_exposer.def( "__deepcopy__", &__copy__); - SelectorMImproper_exposer.def( "clone", &__copy__); + SelectorMImproper_exposer.def( "__copy__", &__copy__); + SelectorMImproper_exposer.def( "__deepcopy__", &__copy__); + SelectorMImproper_exposer.def( "clone", &__copy__); SelectorMImproper_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SelectorMImproper >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SelectorMImproper_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SelectorMImproper >, diff --git a/wrapper/MM/SoftCLJComponent.pypp.cpp b/wrapper/MM/SoftCLJComponent.pypp.cpp index 2bedc3aea..8a107ee10 100644 --- a/wrapper/MM/SoftCLJComponent.pypp.cpp +++ b/wrapper/MM/SoftCLJComponent.pypp.cpp @@ -22,6 +22,8 @@ namespace bp = boost::python; SireMM::SoftCLJComponent __copy__(const SireMM::SoftCLJComponent &other){ return SireMM::SoftCLJComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -227,9 +229,9 @@ void register_SoftCLJComponent_class(){ } SoftCLJComponent_exposer.staticmethod( "nAlphaValues" ); SoftCLJComponent_exposer.staticmethod( "typeName" ); - SoftCLJComponent_exposer.def( "__copy__", &__copy__); - SoftCLJComponent_exposer.def( "__deepcopy__", &__copy__); - SoftCLJComponent_exposer.def( "clone", &__copy__); + SoftCLJComponent_exposer.def( "__copy__", &__copy__); + SoftCLJComponent_exposer.def( "__deepcopy__", &__copy__); + SoftCLJComponent_exposer.def( "clone", &__copy__); SoftCLJComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::SoftCLJComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SoftCLJComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::SoftCLJComponent >, diff --git a/wrapper/MM/StretchBendComponent.pypp.cpp b/wrapper/MM/StretchBendComponent.pypp.cpp index e05eaddfb..bc29c6b58 100644 --- a/wrapper/MM/StretchBendComponent.pypp.cpp +++ b/wrapper/MM/StretchBendComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::StretchBendComponent __copy__(const SireMM::StretchBendComponent &other){ return SireMM::StretchBendComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_StretchBendComponent_class(){ } StretchBendComponent_exposer.staticmethod( "typeName" ); - StretchBendComponent_exposer.def( "__copy__", &__copy__); - StretchBendComponent_exposer.def( "__deepcopy__", &__copy__); - StretchBendComponent_exposer.def( "clone", &__copy__); + StretchBendComponent_exposer.def( "__copy__", &__copy__); + StretchBendComponent_exposer.def( "__deepcopy__", &__copy__); + StretchBendComponent_exposer.def( "clone", &__copy__); StretchBendComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::StretchBendComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); StretchBendComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::StretchBendComponent >, diff --git a/wrapper/MM/StretchBendParameterName.pypp.cpp b/wrapper/MM/StretchBendParameterName.pypp.cpp index 5cb0819e1..e0785cae0 100644 --- a/wrapper/MM/StretchBendParameterName.pypp.cpp +++ b/wrapper/MM/StretchBendParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::StretchBendParameterName __copy__(const SireMM::StretchBendParameterName &other){ return SireMM::StretchBendParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::StretchBendParameterName&){ return "SireMM::StretchBendParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_StretchBendParameterName_class(){ , "" ); } - StretchBendParameterName_exposer.def( "__copy__", &__copy__); - StretchBendParameterName_exposer.def( "__deepcopy__", &__copy__); - StretchBendParameterName_exposer.def( "clone", &__copy__); + StretchBendParameterName_exposer.def( "__copy__", &__copy__); + StretchBendParameterName_exposer.def( "__deepcopy__", &__copy__); + StretchBendParameterName_exposer.def( "clone", &__copy__); StretchBendParameterName_exposer.def( "__str__", &pvt_get_name); StretchBendParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/StretchBendSymbols.pypp.cpp b/wrapper/MM/StretchBendSymbols.pypp.cpp index bcaea365d..45b42fdae 100644 --- a/wrapper/MM/StretchBendSymbols.pypp.cpp +++ b/wrapper/MM/StretchBendSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::StretchBendSymbols __copy__(const SireMM::StretchBendSymbols &other){ return SireMM::StretchBendSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::StretchBendSymbols&){ return "SireMM::StretchBendSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -92,9 +94,9 @@ void register_StretchBendSymbols_class(){ , "Return the symbol representing the angle, theta" ); } - StretchBendSymbols_exposer.def( "__copy__", &__copy__); - StretchBendSymbols_exposer.def( "__deepcopy__", &__copy__); - StretchBendSymbols_exposer.def( "clone", &__copy__); + StretchBendSymbols_exposer.def( "__copy__", &__copy__); + StretchBendSymbols_exposer.def( "__deepcopy__", &__copy__); + StretchBendSymbols_exposer.def( "clone", &__copy__); StretchBendSymbols_exposer.def( "__str__", &pvt_get_name); StretchBendSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/StretchBendTorsionComponent.pypp.cpp b/wrapper/MM/StretchBendTorsionComponent.pypp.cpp index 4003ba51d..4fa6c9d8e 100644 --- a/wrapper/MM/StretchBendTorsionComponent.pypp.cpp +++ b/wrapper/MM/StretchBendTorsionComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::StretchBendTorsionComponent __copy__(const SireMM::StretchBendTorsionComponent &other){ return SireMM::StretchBendTorsionComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_StretchBendTorsionComponent_class(){ } StretchBendTorsionComponent_exposer.staticmethod( "typeName" ); - StretchBendTorsionComponent_exposer.def( "__copy__", &__copy__); - StretchBendTorsionComponent_exposer.def( "__deepcopy__", &__copy__); - StretchBendTorsionComponent_exposer.def( "clone", &__copy__); + StretchBendTorsionComponent_exposer.def( "__copy__", &__copy__); + StretchBendTorsionComponent_exposer.def( "__deepcopy__", &__copy__); + StretchBendTorsionComponent_exposer.def( "clone", &__copy__); StretchBendTorsionComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::StretchBendTorsionComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); StretchBendTorsionComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::StretchBendTorsionComponent >, diff --git a/wrapper/MM/StretchBendTorsionParameterName.pypp.cpp b/wrapper/MM/StretchBendTorsionParameterName.pypp.cpp index d6daaf024..bac7b183e 100644 --- a/wrapper/MM/StretchBendTorsionParameterName.pypp.cpp +++ b/wrapper/MM/StretchBendTorsionParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::StretchBendTorsionParameterName __copy__(const SireMM::StretchBendTorsionParameterName &other){ return SireMM::StretchBendTorsionParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::StretchBendTorsionParameterName&){ return "SireMM::StretchBendTorsionParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_StretchBendTorsionParameterName_class(){ , "" ); } - StretchBendTorsionParameterName_exposer.def( "__copy__", &__copy__); - StretchBendTorsionParameterName_exposer.def( "__deepcopy__", &__copy__); - StretchBendTorsionParameterName_exposer.def( "clone", &__copy__); + StretchBendTorsionParameterName_exposer.def( "__copy__", &__copy__); + StretchBendTorsionParameterName_exposer.def( "__deepcopy__", &__copy__); + StretchBendTorsionParameterName_exposer.def( "clone", &__copy__); StretchBendTorsionParameterName_exposer.def( "__str__", &pvt_get_name); StretchBendTorsionParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/StretchBendTorsionSymbols.pypp.cpp b/wrapper/MM/StretchBendTorsionSymbols.pypp.cpp index c7a6d88d8..af17e6f57 100644 --- a/wrapper/MM/StretchBendTorsionSymbols.pypp.cpp +++ b/wrapper/MM/StretchBendTorsionSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::StretchBendTorsionSymbols __copy__(const SireMM::StretchBendTorsionSymbols &other){ return SireMM::StretchBendTorsionSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::StretchBendTorsionSymbols&){ return "SireMM::StretchBendTorsionSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -128,9 +130,9 @@ void register_StretchBendTorsionSymbols_class(){ , "Return the symbol representing the angle between atoms 3-2-1, theta_\n{321}" ); } - StretchBendTorsionSymbols_exposer.def( "__copy__", &__copy__); - StretchBendTorsionSymbols_exposer.def( "__deepcopy__", &__copy__); - StretchBendTorsionSymbols_exposer.def( "clone", &__copy__); + StretchBendTorsionSymbols_exposer.def( "__copy__", &__copy__); + StretchBendTorsionSymbols_exposer.def( "__deepcopy__", &__copy__); + StretchBendTorsionSymbols_exposer.def( "clone", &__copy__); StretchBendTorsionSymbols_exposer.def( "__str__", &pvt_get_name); StretchBendTorsionSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/StretchStretchComponent.pypp.cpp b/wrapper/MM/StretchStretchComponent.pypp.cpp index 9b28ea3eb..9450a83a8 100644 --- a/wrapper/MM/StretchStretchComponent.pypp.cpp +++ b/wrapper/MM/StretchStretchComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::StretchStretchComponent __copy__(const SireMM::StretchStretchComponent &other){ return SireMM::StretchStretchComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_StretchStretchComponent_class(){ } StretchStretchComponent_exposer.staticmethod( "typeName" ); - StretchStretchComponent_exposer.def( "__copy__", &__copy__); - StretchStretchComponent_exposer.def( "__deepcopy__", &__copy__); - StretchStretchComponent_exposer.def( "clone", &__copy__); + StretchStretchComponent_exposer.def( "__copy__", &__copy__); + StretchStretchComponent_exposer.def( "__deepcopy__", &__copy__); + StretchStretchComponent_exposer.def( "clone", &__copy__); StretchStretchComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::StretchStretchComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); StretchStretchComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::StretchStretchComponent >, diff --git a/wrapper/MM/StretchStretchParameterName.pypp.cpp b/wrapper/MM/StretchStretchParameterName.pypp.cpp index fa9593ce3..f7b02cb41 100644 --- a/wrapper/MM/StretchStretchParameterName.pypp.cpp +++ b/wrapper/MM/StretchStretchParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::StretchStretchParameterName __copy__(const SireMM::StretchStretchParameterName &other){ return SireMM::StretchStretchParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::StretchStretchParameterName&){ return "SireMM::StretchStretchParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_StretchStretchParameterName_class(){ , "" ); } - StretchStretchParameterName_exposer.def( "__copy__", &__copy__); - StretchStretchParameterName_exposer.def( "__deepcopy__", &__copy__); - StretchStretchParameterName_exposer.def( "clone", &__copy__); + StretchStretchParameterName_exposer.def( "__copy__", &__copy__); + StretchStretchParameterName_exposer.def( "__deepcopy__", &__copy__); + StretchStretchParameterName_exposer.def( "clone", &__copy__); StretchStretchParameterName_exposer.def( "__str__", &pvt_get_name); StretchStretchParameterName_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/StretchStretchSymbols.pypp.cpp b/wrapper/MM/StretchStretchSymbols.pypp.cpp index c20c6ad2f..82808bf93 100644 --- a/wrapper/MM/StretchStretchSymbols.pypp.cpp +++ b/wrapper/MM/StretchStretchSymbols.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::StretchStretchSymbols __copy__(const SireMM::StretchStretchSymbols &other){ return SireMM::StretchStretchSymbols(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::StretchStretchSymbols&){ return "SireMM::StretchStretchSymbols";} #include "Helpers/release_gil_policy.hpp" @@ -80,9 +82,9 @@ void register_StretchStretchSymbols_class(){ , "Return the symbol representing the bond length r_\n{21}" ); } - StretchStretchSymbols_exposer.def( "__copy__", &__copy__); - StretchStretchSymbols_exposer.def( "__deepcopy__", &__copy__); - StretchStretchSymbols_exposer.def( "clone", &__copy__); + StretchStretchSymbols_exposer.def( "__copy__", &__copy__); + StretchStretchSymbols_exposer.def( "__deepcopy__", &__copy__); + StretchStretchSymbols_exposer.def( "clone", &__copy__); StretchStretchSymbols_exposer.def( "__str__", &pvt_get_name); StretchStretchSymbols_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/TestFF.pypp.cpp b/wrapper/MM/TestFF.pypp.cpp index 584f22548..5d99d77cd 100644 --- a/wrapper/MM/TestFF.pypp.cpp +++ b/wrapper/MM/TestFF.pypp.cpp @@ -31,6 +31,8 @@ namespace bp = boost::python; SireMM::TestFF __copy__(const SireMM::TestFF &other){ return SireMM::TestFF(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::TestFF&){ return "SireMM::TestFF";} #include "Helpers/release_gil_policy.hpp" @@ -106,9 +108,9 @@ void register_TestFF_class(){ , "" ); } - TestFF_exposer.def( "__copy__", &__copy__); - TestFF_exposer.def( "__deepcopy__", &__copy__); - TestFF_exposer.def( "clone", &__copy__); + TestFF_exposer.def( "__copy__", &__copy__); + TestFF_exposer.def( "__deepcopy__", &__copy__); + TestFF_exposer.def( "clone", &__copy__); TestFF_exposer.def( "__str__", &pvt_get_name); TestFF_exposer.def( "__repr__", &pvt_get_name); } diff --git a/wrapper/MM/ThreeAtomFunction.pypp.cpp b/wrapper/MM/ThreeAtomFunction.pypp.cpp index 96a5d3b2c..9d9edee4b 100644 --- a/wrapper/MM/ThreeAtomFunction.pypp.cpp +++ b/wrapper/MM/ThreeAtomFunction.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::ThreeAtomFunction __copy__(const SireMM::ThreeAtomFunction &other){ return SireMM::ThreeAtomFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -111,9 +113,9 @@ void register_ThreeAtomFunction_class(){ , "Return a string representation" ); } - ThreeAtomFunction_exposer.def( "__copy__", &__copy__); - ThreeAtomFunction_exposer.def( "__deepcopy__", &__copy__); - ThreeAtomFunction_exposer.def( "clone", &__copy__); + ThreeAtomFunction_exposer.def( "__copy__", &__copy__); + ThreeAtomFunction_exposer.def( "__deepcopy__", &__copy__); + ThreeAtomFunction_exposer.def( "clone", &__copy__); ThreeAtomFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::ThreeAtomFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ThreeAtomFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::ThreeAtomFunction >, diff --git a/wrapper/MM/ThreeAtomFunctions.pypp.cpp b/wrapper/MM/ThreeAtomFunctions.pypp.cpp index 5dfeb3e2c..aee2881db 100644 --- a/wrapper/MM/ThreeAtomFunctions.pypp.cpp +++ b/wrapper/MM/ThreeAtomFunctions.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::ThreeAtomFunctions __copy__(const SireMM::ThreeAtomFunctions &other){ return SireMM::ThreeAtomFunctions(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -394,9 +396,9 @@ void register_ThreeAtomFunctions_class(){ } ThreeAtomFunctions_exposer.staticmethod( "typeName" ); - ThreeAtomFunctions_exposer.def( "__copy__", &__copy__); - ThreeAtomFunctions_exposer.def( "__deepcopy__", &__copy__); - ThreeAtomFunctions_exposer.def( "clone", &__copy__); + ThreeAtomFunctions_exposer.def( "__copy__", &__copy__); + ThreeAtomFunctions_exposer.def( "__deepcopy__", &__copy__); + ThreeAtomFunctions_exposer.def( "clone", &__copy__); ThreeAtomFunctions_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::ThreeAtomFunctions >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ThreeAtomFunctions_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::ThreeAtomFunctions >, diff --git a/wrapper/MM/ThreeAtomPerturbation.pypp.cpp b/wrapper/MM/ThreeAtomPerturbation.pypp.cpp index 3ac723697..3a9ab0a1c 100644 --- a/wrapper/MM/ThreeAtomPerturbation.pypp.cpp +++ b/wrapper/MM/ThreeAtomPerturbation.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::ThreeAtomPerturbation __copy__(const SireMM::ThreeAtomPerturbation &other){ return SireMM::ThreeAtomPerturbation(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -152,9 +154,9 @@ void register_ThreeAtomPerturbation_class(){ } ThreeAtomPerturbation_exposer.staticmethod( "typeName" ); - ThreeAtomPerturbation_exposer.def( "__copy__", &__copy__); - ThreeAtomPerturbation_exposer.def( "__deepcopy__", &__copy__); - ThreeAtomPerturbation_exposer.def( "clone", &__copy__); + ThreeAtomPerturbation_exposer.def( "__copy__", &__copy__); + ThreeAtomPerturbation_exposer.def( "__deepcopy__", &__copy__); + ThreeAtomPerturbation_exposer.def( "clone", &__copy__); ThreeAtomPerturbation_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::ThreeAtomPerturbation >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ThreeAtomPerturbation_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::ThreeAtomPerturbation >, diff --git a/wrapper/MM/TripleDistanceRestraint.pypp.cpp b/wrapper/MM/TripleDistanceRestraint.pypp.cpp index e8e37178f..a61554fd4 100644 --- a/wrapper/MM/TripleDistanceRestraint.pypp.cpp +++ b/wrapper/MM/TripleDistanceRestraint.pypp.cpp @@ -32,6 +32,8 @@ namespace bp = boost::python; SireMM::TripleDistanceRestraint __copy__(const SireMM::TripleDistanceRestraint &other){ return SireMM::TripleDistanceRestraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -411,9 +413,9 @@ void register_TripleDistanceRestraint_class(){ TripleDistanceRestraint_exposer.staticmethod( "r23" ); TripleDistanceRestraint_exposer.staticmethod( "r45" ); TripleDistanceRestraint_exposer.staticmethod( "typeName" ); - TripleDistanceRestraint_exposer.def( "__copy__", &__copy__); - TripleDistanceRestraint_exposer.def( "__deepcopy__", &__copy__); - TripleDistanceRestraint_exposer.def( "clone", &__copy__); + TripleDistanceRestraint_exposer.def( "__copy__", &__copy__); + TripleDistanceRestraint_exposer.def( "__deepcopy__", &__copy__); + TripleDistanceRestraint_exposer.def( "clone", &__copy__); TripleDistanceRestraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::TripleDistanceRestraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TripleDistanceRestraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::TripleDistanceRestraint >, diff --git a/wrapper/MM/TwoAtomFunction.pypp.cpp b/wrapper/MM/TwoAtomFunction.pypp.cpp index a21e15e4d..4c48d652a 100644 --- a/wrapper/MM/TwoAtomFunction.pypp.cpp +++ b/wrapper/MM/TwoAtomFunction.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::TwoAtomFunction __copy__(const SireMM::TwoAtomFunction &other){ return SireMM::TwoAtomFunction(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -99,9 +101,9 @@ void register_TwoAtomFunction_class(){ , "Return a string representation" ); } - TwoAtomFunction_exposer.def( "__copy__", &__copy__); - TwoAtomFunction_exposer.def( "__deepcopy__", &__copy__); - TwoAtomFunction_exposer.def( "clone", &__copy__); + TwoAtomFunction_exposer.def( "__copy__", &__copy__); + TwoAtomFunction_exposer.def( "__deepcopy__", &__copy__); + TwoAtomFunction_exposer.def( "clone", &__copy__); TwoAtomFunction_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::TwoAtomFunction >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TwoAtomFunction_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::TwoAtomFunction >, diff --git a/wrapper/MM/TwoAtomFunctions.pypp.cpp b/wrapper/MM/TwoAtomFunctions.pypp.cpp index 45c42139c..ae6e351b6 100644 --- a/wrapper/MM/TwoAtomFunctions.pypp.cpp +++ b/wrapper/MM/TwoAtomFunctions.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireMM::TwoAtomFunctions __copy__(const SireMM::TwoAtomFunctions &other){ return SireMM::TwoAtomFunctions(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -394,9 +396,9 @@ void register_TwoAtomFunctions_class(){ } TwoAtomFunctions_exposer.staticmethod( "typeName" ); - TwoAtomFunctions_exposer.def( "__copy__", &__copy__); - TwoAtomFunctions_exposer.def( "__deepcopy__", &__copy__); - TwoAtomFunctions_exposer.def( "clone", &__copy__); + TwoAtomFunctions_exposer.def( "__copy__", &__copy__); + TwoAtomFunctions_exposer.def( "__deepcopy__", &__copy__); + TwoAtomFunctions_exposer.def( "clone", &__copy__); TwoAtomFunctions_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::TwoAtomFunctions >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TwoAtomFunctions_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::TwoAtomFunctions >, diff --git a/wrapper/MM/TwoAtomPerturbation.pypp.cpp b/wrapper/MM/TwoAtomPerturbation.pypp.cpp index e79156068..e0e0b2630 100644 --- a/wrapper/MM/TwoAtomPerturbation.pypp.cpp +++ b/wrapper/MM/TwoAtomPerturbation.pypp.cpp @@ -34,6 +34,8 @@ namespace bp = boost::python; SireMM::TwoAtomPerturbation __copy__(const SireMM::TwoAtomPerturbation &other){ return SireMM::TwoAtomPerturbation(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -140,9 +142,9 @@ void register_TwoAtomPerturbation_class(){ } TwoAtomPerturbation_exposer.staticmethod( "typeName" ); - TwoAtomPerturbation_exposer.def( "__copy__", &__copy__); - TwoAtomPerturbation_exposer.def( "__deepcopy__", &__copy__); - TwoAtomPerturbation_exposer.def( "clone", &__copy__); + TwoAtomPerturbation_exposer.def( "__copy__", &__copy__); + TwoAtomPerturbation_exposer.def( "__deepcopy__", &__copy__); + TwoAtomPerturbation_exposer.def( "clone", &__copy__); TwoAtomPerturbation_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::TwoAtomPerturbation >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TwoAtomPerturbation_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::TwoAtomPerturbation >, diff --git a/wrapper/MM/UreyBradleyComponent.pypp.cpp b/wrapper/MM/UreyBradleyComponent.pypp.cpp index e1f3f067e..2e2e2d9fc 100644 --- a/wrapper/MM/UreyBradleyComponent.pypp.cpp +++ b/wrapper/MM/UreyBradleyComponent.pypp.cpp @@ -18,6 +18,8 @@ namespace bp = boost::python; SireMM::UreyBradleyComponent __copy__(const SireMM::UreyBradleyComponent &other){ return SireMM::UreyBradleyComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -107,9 +109,9 @@ void register_UreyBradleyComponent_class(){ } UreyBradleyComponent_exposer.staticmethod( "typeName" ); - UreyBradleyComponent_exposer.def( "__copy__", &__copy__); - UreyBradleyComponent_exposer.def( "__deepcopy__", &__copy__); - UreyBradleyComponent_exposer.def( "clone", &__copy__); + UreyBradleyComponent_exposer.def( "__copy__", &__copy__); + UreyBradleyComponent_exposer.def( "__deepcopy__", &__copy__); + UreyBradleyComponent_exposer.def( "clone", &__copy__); UreyBradleyComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireMM::UreyBradleyComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); UreyBradleyComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireMM::UreyBradleyComponent >, diff --git a/wrapper/MM/UreyBradleyParameterName.pypp.cpp b/wrapper/MM/UreyBradleyParameterName.pypp.cpp index b2cb09004..21a320049 100644 --- a/wrapper/MM/UreyBradleyParameterName.pypp.cpp +++ b/wrapper/MM/UreyBradleyParameterName.pypp.cpp @@ -49,6 +49,8 @@ namespace bp = boost::python; SireMM::UreyBradleyParameterName __copy__(const SireMM::UreyBradleyParameterName &other){ return SireMM::UreyBradleyParameterName(other); } +#include "Helpers/copy.hpp" + const char* pvt_get_name(const SireMM::UreyBradleyParameterName&){ return "SireMM::UreyBradleyParameterName";} #include "Helpers/release_gil_policy.hpp" @@ -71,9 +73,9 @@ void register_UreyBradleyParameterName_class(){ , "" ); } - UreyBradleyParameterName_exposer.def( "__copy__", &__copy__); - UreyBradleyParameterName_exposer.def( "__deepcopy__", &__copy__); - UreyBradleyParameterName_exposer.def( "clone", &__copy__); + UreyBradleyParameterName_exposer.def( "__copy__", &__copy__); + UreyBradleyParameterName_exposer.def( "__deepcopy__", &__copy__); + UreyBradleyParameterName_exposer.def( "clone", &__copy__); UreyBradleyParameterName_exposer.def( "__str__", &pvt_get_name); UreyBradleyParameterName_exposer.def( "__repr__", &pvt_get_name); } From 002ada426bb79d58f1b688fa48fbbd8936ec5d8e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 27 May 2024 19:07:20 +0100 Subject: [PATCH 293/468] Minor bugfix when there are no available OpenMM platforms - the dictkeys is not iterable, so should be a list. Not triggering CI as this is a minor fix. Adding it here as it isn't big enough to warrant a new branch and PR [ci skip] --- wrapper/Convert/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 31f915362..cf71f3f31 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -398,7 +398,7 @@ def sire_to_openmm(mols, map): platform = platforms["cpu"] elif len(platforms) > 0: - platform = platforms[platforms.keys()[0]] + platform = platforms[list(platforms.keys())[0]] if platform is None: raise ValueError( From 44ce0e7cee9d2ed3d8a296fbfe13ae76f5f8df6d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 18:32:11 +0100 Subject: [PATCH 294/468] Added code that excludes the to_ghost / from_ghost non-bonded interactions. --- doc/source/changelog.rst | 7 ++ wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 33 +++++-- wrapper/Convert/SireOpenMM/openmmmolecule.h | 3 + .../SireOpenMM/sire_to_openmm_system.cpp | 99 +++++++++++++++++-- 4 files changed, 126 insertions(+), 16 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 610a343d8..e420840de 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -16,6 +16,7 @@ organisation on `GitHub `__. ----------------------------------------------------------------------------------------- * Correctly set the ``element1`` property in ``sire.morph.create_from_pertfile``. + * Added mising :meth:`~sire.vol.TriclinicBox.maximum_cutoff` method so that the cutoff is set correctly when creating a :obj:`~sire.system.ForceFieldInfo` object. @@ -42,6 +43,12 @@ organisation on `GitHub `__. standard trajectory save functions, e.g. ``sire.save(mols.trajectory(), "output", format=["PRMTOP", "RST"])``. +* Added code that automatically excludes non-bonded interactions between + from_ghost and to_ghost atoms in the OpenMM layer. This is to prevent + crashes caused by poor interactions between from_ghost atoms appearing + over the top of to_ghost atoms during a perturbation where one group + is grown over another. + * Ignore BioSimSpace format position restraint include directives when parsing GROMACS topology files. diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index ceedf8e6f..36e16e3da 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -1193,15 +1193,22 @@ void OpenMMMolecule::alignInternals(const PropertyMap &map) { if (is_ghost(clj0)) { - from_ghost_idxs.insert(i); + // ghost atoms are only ghosts is they are real in at + // least one end state (cannot be both a to_ghost and + // a from_ghost atom - this is also implicitly tested + // for above in the clj0 != clj1) + if (not is_ghost(clj1)) + { + from_ghost_idxs.insert(i); - // alpha is 1 for the reference state for ghost atoms - // (and will be 0 for the perturbed state) - this->alphas[i] = 1.0; + // alpha is 1 for the reference state for ghost atoms + // (and will be 0 for the perturbed state) + this->alphas[i] = 1.0; - // kappa is 1 for both end states for ghost atoms - this->kappas[i] = 1.0; - this->perturbed->kappas[i] = 1.0; + // kappa is 1 for both end states for ghost atoms + this->kappas[i] = 1.0; + this->perturbed->kappas[i] = 1.0; + } } else if (is_ghost(clj1)) { @@ -1795,6 +1802,18 @@ void OpenMMMolecule::copyInCoordsAndVelocities(OpenMM::Vec3 *c, OpenMM::Vec3 *v) } } +/** Return the number of atoms in this molecule */ +int OpenMMMolecule::nAtoms() const +{ + return this->coords.count(); +} + +/** Return the number of ghost atoms (sum of to_ghosts and from_ghosts) */ +int OpenMMMolecule::nGhostAtoms() const +{ + return from_ghost_idxs.count() + to_ghost_idxs.count(); +} + /** Return the alpha parameters of all atoms in atom order for * this molecule */ diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.h b/wrapper/Convert/SireOpenMM/openmmmolecule.h index 39dd5e905..f21c44746 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.h +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.h @@ -79,6 +79,9 @@ namespace SireOpenMM bool isGhostAtom(int atom) const; + int nAtoms() const; + int nGhostAtoms() const; + boost::tuple getException(int atom0, int atom1, int start_index, diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index e3a0c59ff..03e2ad242 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -547,6 +547,31 @@ _set_box_vectors(OpenMM::System &system, return boxvecs; } +class IndexPair +{ +public: + IndexPair(int atom0 = 0, int atom1 = 0) : _atom0(atom0), _atom1(atom1) + { + if (atom1 < atom0) + { + std::swap(_atom0, _atom1); + } + } + + bool operator==(const IndexPair &other) const + { + return _atom0 == other._atom0 and _atom1 == other._atom1; + } + + int _atom0; + int _atom1; +}; + +uint qHash(const IndexPair &pair) +{ + return qHash(pair._atom0) ^ qHash(pair._atom1); +} + /** This is the (monster) function that converts a passed set of Sire @@ -1082,13 +1107,32 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, std::vector custom_params = {0.0, 0.0, 0.0, 0.0, 0.0}; // the sets of particle indexes for the ghost atoms and non-ghost atoms - std::set ghost_atoms; - std::set non_ghost_atoms; + QVector ghost_atoms; + QVector non_ghost_atoms; + + // count the number of atoms and ghost atoms + int n_atoms = 0; + int n_ghost_atoms = 0; + + for (int i = 0; i < nmols; ++i) + { + const auto &mol = openmm_mols_data[i]; + n_atoms += mol.nAtoms(); + n_ghost_atoms += mol.nGhostAtoms(); + } + + // there's probably lots of optimisations we can make if the + // number of ghost atoms is zero... + ghost_atoms.reserve(n_ghost_atoms); + non_ghost_atoms.reserve(n_atoms - n_ghost_atoms); // the set of all ghost atoms, with the value // indicating if this is a from-ghost (true) or // a to-ghost (false) - QHash ghost_is_from; + QVector from_ghost_idxs; + QVector to_ghost_idxs; + from_ghost_idxs.reserve(n_ghost_atoms); + to_ghost_idxs.reserve(n_ghost_atoms); // loop over every molecule and add them one by one for (int i = 0; i < nmols; ++i) @@ -1218,8 +1262,16 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // this is a ghost atom! We need to record this // fact and make sure that we don't calculate // the LJ energy using the standard cljff - ghost_atoms.insert(atom_index); - ghost_is_from.insert(atom_index, is_from_ghost); + ghost_atoms.append(atom_index); + + if (is_from_ghost) + { + from_ghost_idxs.append(atom_index); + } + else + { + to_ghost_idxs.append(atom_index); + } // don't include the LJ energy as this will be // calculated using the ghost forcefields @@ -1233,7 +1285,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // just add it to the standard cljff as normal cljff->addParticle(charge, boost::get<1>(clj), boost::get<2>(clj)); - non_ghost_atoms.insert(atom_index); + non_ghost_atoms.append(atom_index); } } } @@ -1279,7 +1331,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, custom_params[4] = 0.0; ghost_ghostff->addParticle(custom_params); ghost_nonghostff->addParticle(custom_params); - non_ghost_atoms.insert(atom_index); + non_ghost_atoms.append(atom_index); } } } @@ -1340,8 +1392,10 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { // set up the interaction groups - ghost / non-ghost // ghost / ghost - ghost_ghostff->addInteractionGroup(ghost_atoms, ghost_atoms); - ghost_nonghostff->addInteractionGroup(ghost_atoms, non_ghost_atoms); + std::set ghost_atoms_set(ghost_atoms.begin(), ghost_atoms.end()); + std::set non_ghost_atoms_set(non_ghost_atoms.begin(), non_ghost_atoms.end()); + ghost_ghostff->addInteractionGroup(ghost_atoms_set, ghost_atoms_set); + ghost_nonghostff->addInteractionGroup(ghost_atoms_set, non_ghost_atoms_set); } // see if we want to remove COM motion @@ -1373,6 +1427,11 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, /// /// We will also add all of the perturbable constraints here /// + /// (we need to remember which ghost-ghost interactions we have + /// excluded, so that we don't double-exclude them later) + QSet excluded_ghost_pairs; + excluded_ghost_pairs.reserve((n_ghost_atoms * n_ghost_atoms) / 2); + for (int i = 0; i < nmols; ++i) { int start_index = start_indexes[i]; @@ -1468,6 +1527,12 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, params14); } } + + if (atom0_is_ghost and atom1_is_ghost) + { + // remember that this ghost-ghost interaction is already excluded + excluded_ghost_pairs.insert(IndexPair(boost::get<0>(p), boost::get<1>(p))); + } } else { @@ -1507,6 +1572,22 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } } + // go through all of the ghost atoms and exclude interactions + // between from_ghosts and to_ghosts + for (const auto &from_ghost_idx : from_ghost_idxs) + { + for (const auto &to_ghost_idx : to_ghost_idxs) + { + if (not excluded_ghost_pairs.contains(IndexPair(from_ghost_idx, to_ghost_idx))) + { + ghost_ghostff->addExclusion(from_ghost_idx, to_ghost_idx); + ghost_nonghostff->addExclusion(from_ghost_idx, to_ghost_idx); + cljff->addException(from_ghost_idx, to_ghost_idx, + 0.0, 1e-9, 1e-9, true); + } + } + } + // Stage 6 is complete. We have set up all of the exceptions. The // total energy / force calculated for the system should now be // correct. From e92b1dd890b47b66c689091eab95904057ae44f2 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:24:20 +0100 Subject: [PATCH 295/468] Added paper citation and removed mamba build --- .github/workflows/devel.yaml | 8 +++----- .github/workflows/main.yaml | 8 +++----- .github/workflows/pr.yaml | 8 +++----- README.rst | 28 ++++++++++++++++++++++++++-- doc/source/index.rst | 24 ++++++++++++++++++++++++ 5 files changed, 59 insertions(+), 17 deletions(-) diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index e63e5072a..830e22773 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -50,14 +50,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the devel branch (push to devel) run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -65,8 +63,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 76732f2ec..cff88bd43 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -50,14 +50,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the main branch (push to main) run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -65,8 +63,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # upload to the 'test' channel diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index e1a45542b..7834f1541 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -52,14 +52,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the feature branch (pull request to devel) run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -67,5 +65,5 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire diff --git a/README.rst b/README.rst index 4689732d8..f4c3220dc 100644 --- a/README.rst +++ b/README.rst @@ -2,8 +2,8 @@ `Sire `__ ====================================== -.. image:: https://github.com/openbiosim/sire/workflows/Build/badge.svg - :target: https://github.com/openbiosim/sire/actions?query=workflow%3ABuild +.. image:: https://github.com/OpenBioSim/sire/actions/workflows/devel.yaml/badge.svg + :target: https://github.com/OpenBioSim/sire/actions/workflows/devel.yaml :alt: Build status .. image:: https://anaconda.org/openbiosim/sire/badges/downloads.svg @@ -14,6 +14,30 @@ :target: https://www.gnu.org/licenses/gpl-3.0.en.html :alt: License +Citation +======== + +If you use sire in your work, please cite the +`following paper `__: + +.. code-block:: bibtex + + @article{10.1063/5.0200458, + author = {Woods, Christopher J. and Hedges, Lester O. and Mulholland, Adrian J. and Malaisree, Maturos and Tosco, Paolo and Loeffler, Hannes H. and Suruzhon, Miroslav and Burman, Matthew and Bariami, Sofia and Bosisio, Stefano and Calabro, Gaetano and Clark, Finlay and Mey, Antonia S. J. S. and Michel, Julien}, + title = "{Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs}", + journal = {The Journal of Chemical Physics}, + volume = {160}, + number = {20}, + pages = {202503}, + year = {2024}, + month = {05}, + abstract = "{Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire’s molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber, and AmberTools for automated molecular parameterization and the running of molecular dynamics, metadynamics, and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis, and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit, and combine molecular information from multiple sources and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https://try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company.}", + issn = {0021-9606}, + doi = {10.1063/5.0200458}, + url = {https://doi.org/10.1063/5.0200458}, + eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0200458/19969848/202503\_1\_5.0200458.pdf}, + } + About ===== diff --git a/doc/source/index.rst b/doc/source/index.rst index ce6e90c6a..f5577315a 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -9,6 +9,30 @@ It is used as a key component of `BioSimSpace `__, and is distributed and supported as an open source community project by `OpenBioSim `__. +Citation +======== + +If you use sire in your work, please cite the +`following paper `__: + +.. code-block:: bibtex + + @article{10.1063/5.0200458, + author = {Woods, Christopher J. and Hedges, Lester O. and Mulholland, Adrian J. and Malaisree, Maturos and Tosco, Paolo and Loeffler, Hannes H. and Suruzhon, Miroslav and Burman, Matthew and Bariami, Sofia and Bosisio, Stefano and Calabro, Gaetano and Clark, Finlay and Mey, Antonia S. J. S. and Michel, Julien}, + title = "{Sire: An interoperability engine for prototyping algorithms and exchanging information between molecular simulation programs}", + journal = {The Journal of Chemical Physics}, + volume = {160}, + number = {20}, + pages = {202503}, + year = {2024}, + month = {05}, + abstract = "{Sire is a Python/C++ library that is used both to prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of many other programs and libraries. This empowers researchers to use sire to write a single script that can, for example, load a molecule from a PDBx/mmCIF file via Gemmi, perform SMARTS searches via RDKit, parameterize molecules using BioSimSpace, run GPU-accelerated molecular dynamics via OpenMM, and then display the resulting dynamics trajectory in a NGLView Jupyter notebook 3D molecular viewer. This functionality is built on by BioSimSpace, which uses sire’s molecular information engine to interconvert with programs such as GROMACS, NAMD, Amber, and AmberTools for automated molecular parameterization and the running of molecular dynamics, metadynamics, and alchemical free energy workflows. Sire comes complete with a powerful molecular information search engine, plus trajectory loading and editing, analysis, and energy evaluation engines. This, when combined with an in-built computer algebra system, gives substantial flexibility to researchers to load, search for, edit, and combine molecular information from multiple sources and use that to drive novel algorithms by combining functionality from other programs. Sire is open source (GPL3) and is available via conda and at a free Jupyter notebook server at https://try.openbiosim.org. Sire is supported by the not-for-profit OpenBioSim community interest company.}", + issn = {0021-9606}, + doi = {10.1063/5.0200458}, + url = {https://doi.org/10.1063/5.0200458}, + eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0200458/19969848/202503\_1\_5.0200458.pdf}, + } + Quick Start =========== From abee11bc3e6b57b1f71379da48e811573b160397 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:25:04 +0100 Subject: [PATCH 296/468] Removed mamba from build - will debug broken windows build --- .github/workflows/devel.yaml | 8 +++----- .github/workflows/main.yaml | 8 +++----- .github/workflows/pr.yaml | 8 +++----- 3 files changed, 9 insertions(+), 15 deletions(-) diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index e63e5072a..830e22773 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -50,14 +50,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the devel branch (push to devel) run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -65,8 +63,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 76732f2ec..cff88bd43 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -50,14 +50,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the main branch (push to main) run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -65,8 +63,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # upload to the 'test' channel diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index e1a45542b..7834f1541 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -52,14 +52,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the feature branch (pull request to devel) run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -67,5 +65,5 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire From f1fa9dc7283c6b43f1f0e0682e7ee47b87c34bd9 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:26:32 +0100 Subject: [PATCH 297/468] Removed badges as they don't render well --- README.rst | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/README.rst b/README.rst index f4c3220dc..8d1aa9ce2 100644 --- a/README.rst +++ b/README.rst @@ -2,18 +2,6 @@ `Sire `__ ====================================== -.. image:: https://github.com/OpenBioSim/sire/actions/workflows/devel.yaml/badge.svg - :target: https://github.com/OpenBioSim/sire/actions/workflows/devel.yaml - :alt: Build status - -.. image:: https://anaconda.org/openbiosim/sire/badges/downloads.svg - :target: https://anaconda.org/openbiosim/sire - :alt: Downloads - -.. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg - :target: https://www.gnu.org/licenses/gpl-3.0.en.html - :alt: License - Citation ======== From 3ddca08ce40de7e3a89d5f5e29bea86e37e21cbe Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:28:52 +0100 Subject: [PATCH 298/468] Workflow update --- .github/workflows/devel.yaml | 2 +- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 830e22773..7c603c15a 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -55,7 +55,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index cff88bd43..ee70f5118 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -55,7 +55,7 @@ jobs: run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 7834f1541..5840e5009 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -57,7 +57,7 @@ jobs: run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py From 19e06e65bad15ade340aad175ef3e022424a73b0 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:29:25 +0100 Subject: [PATCH 299/468] Fix --- .github/workflows/devel.yaml | 2 +- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 830e22773..7c603c15a 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -55,7 +55,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index cff88bd43..ee70f5118 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -55,7 +55,7 @@ jobs: run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 7834f1541..5840e5009 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -57,7 +57,7 @@ jobs: run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py From a662bfb3c55a88e248b5b55674af6dbc8c0399d9 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:40:37 +0100 Subject: [PATCH 300/468] Removed mamba from everything --- .github/workflows/choose_branch.yaml | 8 +++----- .github/workflows/devel.yaml | 2 +- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 2 +- src/sire/utils/_try_import.py | 28 +++++++--------------------- wrapper/__init__.py | 22 ++++------------------ 6 files changed, 17 insertions(+), 47 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 534742c71..41541f42d 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -55,14 +55,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the desired branch run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -70,8 +68,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 7c603c15a..9f623d3e2 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -55,7 +55,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index ee70f5118..0b2c9ad5e 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -55,7 +55,7 @@ jobs: run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 5840e5009..a49c5cc71 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -57,7 +57,7 @@ jobs: run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/src/sire/utils/_try_import.py b/src/sire/utils/_try_import.py index 2b7060718..b6a927f92 100644 --- a/src/sire/utils/_try_import.py +++ b/src/sire/utils/_try_import.py @@ -40,15 +40,7 @@ def _find_conda(): ) return None - if conda.endswith(".exe"): - m = os.path.join(os.path.dirname(conda), "mamba.exe") - else: - m = os.path.join(os.path.dirname(conda), "mamba") - - if os.path.exists(m): - return m - else: - return conda + return conda def _install_package(name, package_registry, version=None): @@ -98,10 +90,7 @@ def _install_package(name, package_registry, version=None): except Exception: pass - print( - "\nWARNING: Unable to install '%s' from package '%s'\n" - % (name, package) - ) + print("\nWARNING: Unable to install '%s' from package '%s'\n" % (name, package)) class _ModuleStub: @@ -109,7 +98,7 @@ def __init__(self, name: str, install_command: str = None): self._name = name if install_command is None: - self._install_command = f"mamba install {name}" + self._install_command = f"conda install {name}" else: self._install_command = install_command @@ -135,7 +124,7 @@ def try_import(name, package_registry=_module_to_package, version=None): the package to install using "package_registry" (or if this is not available, using just the name of the module). This will then be installed using - "mamba", then "conda" (first one that works will return). + "conda" (first one that works will return). For example, use this via @@ -176,9 +165,7 @@ def try_import(name, package_registry=_module_to_package, version=None): return _ModuleStub(name) -def try_import_from( - name, fromlist, package_registry=_module_to_package, version=None -): +def try_import_from(name, fromlist, package_registry=_module_to_package, version=None): """Try to import from the module called 'name' the passed symbol (or list of symbols) contained in 'fromlist', returning the symbol (or list of symbols). @@ -224,15 +211,14 @@ def try_import_from( return try_import_from(name, fromlist, package_registry=None) else: m = " ".join(fromlist) - return _ModuleStub(name, f"mamba install {m}") + return _ModuleStub(name, f"conda install {m}") if nsyms == 1: try: return getattr(mod, fromlist[0]) except Exception: raise ImportError( - "Cannot find the symbol '%s' in module '%s'" - % (fromlist[0], name) + "Cannot find the symbol '%s' in module '%s'" % (fromlist[0], name) ) else: ret = [] diff --git a/wrapper/__init__.py b/wrapper/__init__.py index 5124caf4b..6eec87f6d 100644 --- a/wrapper/__init__.py +++ b/wrapper/__init__.py @@ -85,15 +85,7 @@ def _find_conda(): ) return None - if conda.endswith(".exe"): - m = os.path.join(os.path.dirname(conda), "mamba.exe") - else: - m = os.path.join(os.path.dirname(conda), "mamba") - - if os.path.exists(m): - return m - else: - return conda + return conda def _install_package(name, package_registry, version=None): @@ -143,10 +135,7 @@ def _install_package(name, package_registry, version=None): except Exception: pass - print( - "\nWARNING: Unable to install '%s' from package '%s'\n" - % (name, package) - ) + print("\nWARNING: Unable to install '%s' from package '%s'\n" % (name, package)) def try_import(name, package_registry=_module_to_package, version=None): @@ -187,9 +176,7 @@ def try_import(name, package_registry=_module_to_package, version=None): raise ImportError("Failed to install module %s" % name) -def try_import_from( - name, fromlist, package_registry=_module_to_package, version=None -): +def try_import_from(name, fromlist, package_registry=_module_to_package, version=None): """Try to import from the module called 'name' the passed symbol (or list of symbols) contained in 'fromlist', returning the symbol (or list of symbols). @@ -242,8 +229,7 @@ def try_import_from( return getattr(mod, fromlist[0]) except Exception: raise ImportError( - "Cannot find the symbol '%s' in module '%s'" - % (fromlist[0], name) + "Cannot find the symbol '%s' in module '%s'" % (fromlist[0], name) ) else: ret = [] From 94827a7a60853963e88e21d48375f6fe3735199c Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 19:41:22 +0100 Subject: [PATCH 301/468] Does this work? --- .github/workflows/choose_branch.yaml | 8 +++----- .github/workflows/devel.yaml | 2 +- .github/workflows/main.yaml | 2 +- .github/workflows/pr.yaml | 2 +- 4 files changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 534742c71..41541f42d 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -55,14 +55,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the desired branch run: git clone https://github.com/${{ env.REPO }} -b ${{ github.event.inputs.branch }} sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -70,8 +68,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # Maybe add the logic here that this is a dev package? diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 7c603c15a..9f623d3e2 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -55,7 +55,7 @@ jobs: run: git clone https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index ee70f5118..0b2c9ad5e 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -55,7 +55,7 @@ jobs: run: git clone -b main https://github.com/openbiosim/sire sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index 5840e5009..a49c5cc71 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -57,7 +57,7 @@ jobs: run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} sire # - name: Setup Conda - run: conda install -y -c conda-forge conda-build anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge conda-build boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py From a21e38117548cf14b26d50bc89ed39cacf01db6d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 2 Jun 2024 22:43:14 +0100 Subject: [PATCH 302/468] Setting compilers on each OS explicitly - hopefully this will help GH on Windows find MSVC --- recipes/sire/conda_build_config.yaml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/recipes/sire/conda_build_config.yaml b/recipes/sire/conda_build_config.yaml index f45e1ecfa..e8bc0c8bf 100644 --- a/recipes/sire/conda_build_config.yaml +++ b/recipes/sire/conda_build_config.yaml @@ -1,3 +1,13 @@ +c_compiler: + - gcc # [linux] + - clang # [osx] + - vs2019 # [win] + +cxx_compiler: + - gxx # [linux] + - clangxx # [osx] + - vs2019 # [win] + c_compiler_version: - 12.3.0 # [linux] From 88ee896b50ba10f2c0276e13a8d1fecd0d761c9e Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 3 Jun 2024 07:56:10 +0100 Subject: [PATCH 303/468] Silencing warnings and skippnig gemmi tests on Windows (not fully supported at the moment) --- corelib/CMakeLists.txt | 2 +- tests/convert/test_gemmi.py | 10 +++++++--- tests/io/test_pdbx.py | 7 +++++-- 3 files changed, 13 insertions(+), 6 deletions(-) diff --git a/corelib/CMakeLists.txt b/corelib/CMakeLists.txt index 23f60519a..d659f70bd 100644 --- a/corelib/CMakeLists.txt +++ b/corelib/CMakeLists.txt @@ -631,7 +631,7 @@ elseif (MSVC) set ( SIRE_SMALL_FLAGS "/O1" ) set ( SIRE_WARNALL_FLAGS "" ) - set ( SIRE_RELEASE_FLAGS "/O2 /GL /Gw" ) + set ( SIRE_RELEASE_FLAGS "/O2 /GL /Gw /D_SILENCE_STDEXT_ARR_ITERS_DEPRECATION_WARNING" ) set ( SIRE_DEBUG_FLAGS "/Zi" ) set ( SIRE_VISIBILITY_FLAGS "/DSIRE_NO_VISIBILITY_AVAILABLE" ) GET_SIRE_VECTOR_FLAGS( "/openmp:experimental" "/arch:SSE2" "/arch:AVX" "/arch:AVX512" "/arch:NEON" ) diff --git a/tests/convert/test_gemmi.py b/tests/convert/test_gemmi.py index c4da5827f..01fb4b0f3 100644 --- a/tests/convert/test_gemmi.py +++ b/tests/convert/test_gemmi.py @@ -1,6 +1,7 @@ import sire as sr import pytest +import sys def _assert_equal(v0, v1, tol): @@ -10,7 +11,8 @@ def _assert_equal(v0, v1, tol): @pytest.mark.skipif( - "gemmi" not in sr.convert.supported_formats(), reason="gemmi not available" + ("gemmi" not in sr.convert.supported_formats()) or (sys.platform == "win32"), + reason="gemmi not available", ) def test_gemmi(testfile_cache_dir, pdbx_3nss): mols = pdbx_3nss @@ -45,7 +47,8 @@ def test_gemmi(testfile_cache_dir, pdbx_3nss): @pytest.mark.skipif( - "gemmi" not in sr.convert.supported_formats(), reason="gemmi not available" + ("gemmi" not in sr.convert.supported_formats()) or (sys.platform == "win32"), + reason="gemmi not available", ) def test_gemmi_roundtrip(tmpdir, pdbx_3nss): mols = pdbx_3nss.clone() @@ -97,7 +100,8 @@ def test_gemmi_roundtrip(tmpdir, pdbx_3nss): @pytest.mark.skipif( - "gemmi" not in sr.convert.supported_formats(), reason="gemmi not available" + ("gemmi" not in sr.convert.supported_formats()) or (sys.platform == "win32"), + reason="gemmi not available", ) def test_gemmi_complex_metadata(tmpdir, ala_mols): mols = ala_mols.clone() diff --git a/tests/io/test_pdbx.py b/tests/io/test_pdbx.py index 5d30f19bb..b7f09809e 100644 --- a/tests/io/test_pdbx.py +++ b/tests/io/test_pdbx.py @@ -1,6 +1,7 @@ import sire as sr import pytest +import sys def _assert_equal(v0, v1, tol): @@ -10,7 +11,8 @@ def _assert_equal(v0, v1, tol): @pytest.mark.skipif( - "gemmi" not in sr.convert.supported_formats(), reason="gemmi not available" + ("gemmi" not in sr.convert.supported_formats()) or (sys.platform == "win32"), + reason="gemmi not available", ) def test_pdbx(tmpdir, ala_mols): mols = ala_mols @@ -36,7 +38,8 @@ def test_pdbx(tmpdir, ala_mols): @pytest.mark.skipif( - "gemmi" not in sr.convert.supported_formats(), reason="gemmi not available" + ("gemmi" not in sr.convert.supported_formats()) or (sys.platform == "win32"), + reason="gemmi not available", ) def test_pdbx_pdb(pdb_3nss, pdbx_3nss): mols = pdb_3nss From 9a39dede88ccbdd06b2e990456eb0e2488df6f7b Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Mon, 3 Jun 2024 19:25:21 +0100 Subject: [PATCH 304/468] Silencing warnings for the wrapper compilation too --- wrapper/CMakeLists.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wrapper/CMakeLists.txt b/wrapper/CMakeLists.txt index bcc167150..77ac9bde9 100644 --- a/wrapper/CMakeLists.txt +++ b/wrapper/CMakeLists.txt @@ -283,6 +283,8 @@ if(CMAKE_GENERATOR MATCHES "Visual Studio") # MSBuild message(STATUS "Turning on bigobj") # needed to link _Mol.pyd add_compile_options("/bigobj") + message(STATUS "Silencing deprecation warning: D_SILENCE_STDEXT_ARR_ITERS_DEPRECATION_WARNING") + add_compile_definitions("/D_SILENCE_STDEXT_ARR_ITERS_DEPRECATION_WARNING") endif() # Conda can mess up our include paths. This makes sure that every From 089c3c341d87abfdb70e3422ffb1b09307fc102f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 13 Jun 2024 09:51:38 +0100 Subject: [PATCH 305/468] Pin RDKit to the patch release. [closes #200] [ci skip] --- recipes/sire/template.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/sire/template.yaml b/recipes/sire/template.yaml index a2f6535b5..9a33377bb 100644 --- a/recipes/sire/template.yaml +++ b/recipes/sire/template.yaml @@ -21,7 +21,7 @@ requirements: run: SIRE_RUN_REQUIREMENTS run_constrained: - - {{ pin_compatible('rdkit', max_pin='x.x') }} + - {{ pin_compatible('rdkit', max_pin='x.x.x') }} test: script_env: From bef34f93ef90b0a7a659a1dac9b0c4dbc98e4005 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 20 Jun 2024 16:04:14 +0100 Subject: [PATCH 306/468] Generalise OpenMM QM interface to work with any Python callback. --- src/sire/_pythonize.py | 8 +- src/sire/qm/__init__.py | 150 +++++++++++ src/sire/qm/_emle.py | 25 +- src/sire/qm/_utils.py | 3 +- tests/qm/test_emle.py | 28 +- .../Convert/SireOpenMM/CMakeAutogenFile.txt | 6 +- wrapper/Convert/SireOpenMM/CMakeLists.txt | 2 +- .../Convert/SireOpenMM/EMLECallback.pypp.cpp | 99 ------- .../Convert/SireOpenMM/EMLECallback.pypp.hpp | 10 - .../Convert/SireOpenMM/EMLEEngine.pypp.hpp | 10 - wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp | 10 - .../Convert/SireOpenMM/LambdaLever.pypp.cpp | 8 +- .../Convert/SireOpenMM/PyQMCallback.pypp.cpp | 119 ++++++++ .../Convert/SireOpenMM/PyQMCallback.pypp.hpp | 10 + ...MLEEngine.pypp.cpp => PyQMEngine.pypp.cpp} | 222 ++++++++------- .../Convert/SireOpenMM/PyQMEngine.pypp.hpp | 10 + ...{EMLEForce.pypp.cpp => PyQMForce.pypp.cpp} | 198 ++++++++------ wrapper/Convert/SireOpenMM/PyQMForce.pypp.hpp | 10 + .../SireOpenMM/SireOpenMM_registrars.cpp | 14 +- .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 28 +- wrapper/Convert/SireOpenMM/active_headers.h | 4 +- wrapper/Convert/SireOpenMM/lambdalever.cpp | 2 +- .../Convert/SireOpenMM/{emle.cpp => pyqm.cpp} | 255 ++++++++++-------- wrapper/Convert/SireOpenMM/{emle.h => pyqm.h} | 101 +++---- wrapper/Convert/SireOpenMM/qmmm.cpp | 1 - wrapper/Convert/SireOpenMM/qmmm.h | 7 - .../Convert/SireOpenMM/register_extras.cpp | 4 +- .../SireOpenMM/sire_to_openmm_system.cpp | 2 +- wrapper/Convert/__init__.py | 12 +- 29 files changed, 805 insertions(+), 553 deletions(-) delete mode 100644 wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp delete mode 100644 wrapper/Convert/SireOpenMM/EMLECallback.pypp.hpp delete mode 100644 wrapper/Convert/SireOpenMM/EMLEEngine.pypp.hpp delete mode 100644 wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp create mode 100644 wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp create mode 100644 wrapper/Convert/SireOpenMM/PyQMCallback.pypp.hpp rename wrapper/Convert/SireOpenMM/{EMLEEngine.pypp.cpp => PyQMEngine.pypp.cpp} (64%) create mode 100644 wrapper/Convert/SireOpenMM/PyQMEngine.pypp.hpp rename wrapper/Convert/SireOpenMM/{EMLEForce.pypp.cpp => PyQMForce.pypp.cpp} (67%) create mode 100644 wrapper/Convert/SireOpenMM/PyQMForce.pypp.hpp rename wrapper/Convert/SireOpenMM/{emle.cpp => pyqm.cpp} (80%) rename wrapper/Convert/SireOpenMM/{emle.h => pyqm.h} (88%) diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index c624b4be9..de6613070 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -238,10 +238,10 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): delete_old=delete_old, ) - # Pythonize the EMLE classes. - _pythonize(Convert._SireOpenMM.EMLECallback, delete_old=delete_old) - _pythonize(Convert._SireOpenMM.EMLEEngine, delete_old=delete_old) - _pythonize(Convert._SireOpenMM.EMLEForce, delete_old=delete_old) + # Pythonize the QM classes. + _pythonize(Convert._SireOpenMM.PyQMCallback, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.PyQMEngine, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.PyQMForce, delete_old=delete_old) try: import lazy_import diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index 527ee003d..aafeeb448 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -2,3 +2,153 @@ from ._emle import emle from ._utils import _zero_charge as zero_charge + +def create_engine( + mols, + qm_atoms, + py_object, + name=None, + cutoff="7.5A", + neighbourlist_update_frequency=20, + redistribute_charge=False, + map=None, +): + """ + Create a QM engine object to allow QM/MM simulations using sire.mol.dynamics. + + Parameters + ---------- + + mols : sire.system.System + The molecular system. + + qm_atoms : str, int, list, molecule view/collection etc. + Any valid search string, atom index, list of atom indicies, + or molecule view/container that can be used to select + qm_atoms from 'mols'. + + py_object : object + The Python object that will contains the callback for the QM calculation. + + name : str, optional, default=None + The name of the callback method. If None, then the py_object is assumed to + be a callable. + + cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" + The cutoff to use for the QM/MM calculation. + + neighbourlist_update_frequency : int, optional, default=20 + The frequency with which to update the neighbourlist. + + redistribute_charge : bool + Whether to redistribute charge of the QM atoms to ensure that the total + charge of the QM region is an integer. Excess charge is redistributed + over the non QM atoms within the residues involved in the QM region. + + Returns + ------- + + engine : sire.legacy.Convert._SireOpenMM.PyQMEngine + The QM engine. + """ + + from ..base import create_map as _create_map + from ..mol import selection_to_atoms as _selection_to_atoms + from ..system import System as _System + from ..legacy import Units as _Units + from ..units import angstrom as _angstrom + from .. import u as _u + + if not isinstance(mols, _System): + raise TypeError("mols must be a of type 'sire.System'") + + # Clone the system. + mols = mols.clone() + + try: + qm_atoms = _selection_to_atoms(mols, qm_atoms) + except: + raise ValueError("Unable to select 'qm_atoms' from 'mols'") + + from inspect import isclass, isfunction + + if isclass(py_object): + if name is None: + raise ValueError("name must be provided if 'py_object' is a class.") + if not hasattr(py_object, name): + raise ValueError(f"'py_object' does not have a method called '{name}'.") + elif isfunction(py_object): + name = "" + else: + raise ValueError("'py_object' must be a class or function.") + + if not isinstance(cutoff, (str, _Units.GeneralUnit)): + raise TypeError( + "cutoff must be of type 'str' or 'sire.legacy.Units.GeneralUnit'" + ) + + if isinstance(cutoff, str): + try: + cutoff = _u(cutoff) + except: + raise ValueError("Unable to parse cutoff as a GeneralUnit") + + if not cutoff.has_same_units(_angstrom): + raise ValueError("'cutoff' must be in units of length") + + if not isinstance(neighbourlist_update_frequency, int): + raise TypeError("'neighbourlist_update_frequency' must be of type 'int'") + + if neighbourlist_update_frequency < 0: + raise ValueError("'neighbourlist_update_frequency' must be >= 0") + + if not isinstance(redistribute_charge, bool): + raise TypeError("'redistribute_charge' must be of type 'bool'") + + if map is not None: + if not isinstance(map, dict): + raise TypeError("'map' must be of type 'dict'") + map = _create_map(map) + + # Create the EMLE engine. + engine = _PyQMEngine( + calculator, + name, + cutoff, + neighbourlist_update_frequency, + ) + + from ._utils import ( + _check_charge, + _create_qm_mol_to_atoms, + _configure_engine, + _create_merged_mols, + _get_link_atoms, + ) + + # Check that the charge of the QM region is integer valued. + _check_charge(mols, qm_atoms, map, redistribute_charge) + + # Get the mapping between molecule numbers and QM atoms. + qm_mol_to_atoms = _create_qm_mol_to_atoms(qm_atoms) + + # Get link atom information. + mm1_to_qm, mm1_to_mm2, bond_scale_factors, mm1_indices = _get_link_atoms( + mols, qm_mol_to_atoms, map + ) + + # Configure the engine. + engine = _configure_engine( + engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_scale_factors, map + ) + + # Create the merged molecule. + qm_mols = _create_merged_mols(qm_mol_to_atoms, mm1_indices, map) + + # Update the molecule in the system. + mols.update(qm_mols) + + # Bind the system as a private attribute of the engine. + engine._mols = mols + + return mols, engine diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 6cef477b0..ff0c20753 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -6,14 +6,14 @@ _use_new_api() -_EMLEEngine = _Convert._SireOpenMM.EMLEEngine +_PyQMEngine = _Convert._SireOpenMM.PyQMEngine -# Monkey-patch to get the underlying OpenMM force of the EMLEEngine. +# Monkey-patch to get the underlying OpenMM force of the EMLE engine. def _get_openmm_forces(self): """ Get the OpenMM forces for this engine. The first force is the actual - EMLEForce, which uses a CustomCPPForceImpl to calculate the electrostatic + EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic embedding force. The second is a null CustomBondForce that can be used to add a "lambda_emle" global parameter to a context to allow the force to be scaled. @@ -22,7 +22,7 @@ def _get_openmm_forces(self): ------- emle_force : openmm.Force - The EMLEForce object to compute the electrostatic embedding force. + The EMLE force object to compute the electrostatic embedding force. interpolation_force : openmm.CustomBondForce A null CustomBondForce object that can be used to add a "lambda_emle" @@ -41,7 +41,7 @@ def _get_openmm_forces(self): qm_engine=self, ) - # Get the OpenMM EMLEForce. + # Get the OpenMM EMLE force. emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) # Create a null CustomBondForce to add the EMLE interpolation @@ -53,8 +53,8 @@ def _get_openmm_forces(self): return emle_force, interpolation_force -# Bind the monkey-patched function to the EMLEEngine. -_EMLEEngine.get_forces = _get_openmm_forces +# Bind the monkey-patched function to the PyQMEngine. +_PyQMEngine.get_forces = _get_openmm_forces def emle( @@ -67,7 +67,7 @@ def emle( map=None, ): """ - Create an EMLEEngine object to allow QM/MM simulations using sire.mol.dynamics. + Create an EMLE engine object to allow QM/MM simulations using sire.mol.dynamics. Parameters ---------- @@ -97,8 +97,8 @@ def emle( Returns ------- - engine : sire.legacy.Convert._SireOpenMM.EMLEEngine - The EMLEEngine object. + engine : sire.legacy.Convert._SireOpenMM.PyQMEngine + The EMLE engine object. """ try: @@ -159,9 +159,10 @@ def emle( raise TypeError("'map' must be of type 'dict'") map = _create_map(map) - # Create the EMLEEngine. - engine = _EMLEEngine( + # Create the EMLE engine. + engine = _PyQMEngine( calculator, + "_sire_callback", cutoff, neighbourlist_update_frequency, ) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 1e3043724..655639a0e 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -765,11 +765,10 @@ def _configure_engine(engine, mols, qm_atoms, mm1_to_qm, mm1_to_mm2, bond_length map: sire.legacy.Base.PropertyMap The property map for the system. - Returns ------- - engine: sire.legacy.QM.Engine + engine: sire.legacy.Convert.PyQMEngine The configured QM engine. """ diff --git a/tests/qm/test_emle.py b/tests/qm/test_emle.py index 6205bb8b0..82a254e2f 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_emle.py @@ -2,7 +2,7 @@ import pytest import tempfile -from sire.legacy.Convert import EMLECallback, EMLEEngine +from sire.legacy.Convert import PyQMCallback from sire.qm import emle @@ -21,7 +21,7 @@ has_openmm_ml = False -def test_callback(): +def test_callback_method(): """Makes sure that a callback method works correctly""" class Test: @@ -32,7 +32,7 @@ def callback(self, a, b, c, d): test = Test() # Create a callback object. - cb = EMLECallback(test, "callback") + cb = PyQMCallback(test, "callback") # Create some lists to hold test data. a = [1, 2] @@ -47,6 +47,28 @@ def callback(self, a, b, c, d): assert result == (42, d, c) == test.callback(a, b, c, d) +def test_callback_function(): + """Makes sure that a callback function works correctly""" + + def callback(a, b, c, d): + return (42, d, c) + + # Create a callback object. + cb = PyQMCallback(callback, "") + + # Create some lists to hold test data. + a = [1, 2] + b = [3, 4] + c = [a, b] + d = [b, a] + + # Call the callback. + result = cb.call(a, b, c, d) + + # Make sure the result is correct. + assert result == (42, d, c) == callback(a, b, c, d) + + @pytest.mark.parametrize( "selection, expected", [ diff --git a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt index 14b187087..9e443e04c 100644 --- a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt +++ b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt @@ -2,10 +2,10 @@ set ( PYPP_SOURCES LambdaLever.pypp.cpp PerturbableOpenMMMolecule.pypp.cpp + PyQMCallback.pypp.cpp + PyQMForce.pypp.cpp + PyQMEngine.pypp.cpp QMEngine.pypp.cpp - EMLEForce.pypp.cpp - EMLEEngine.pypp.cpp - EMLECallback.pypp.cpp _SireOpenMM_free_functions.pypp.cpp QMForce.pypp.cpp vector_less__OpenMM_scope_Vec3__greater_.pypp.cpp diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 479deda47..19c40b45e 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -79,7 +79,7 @@ if (${SIRE_USE_OPENMM}) # Define the sources in SireOpenMM set ( SIREOPENMM_SOURCES - emle.cpp + pyqm.cpp lambdalever.cpp openmmminimise.cpp openmmmolecule.cpp diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp deleted file mode 100644 index c0863c5db..000000000 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.cpp +++ /dev/null @@ -1,99 +0,0 @@ -// This file has been generated by Py++. - -// (C) Christopher Woods, GPL >= 3 License - -#include "boost/python.hpp" -#include "EMLECallback.pypp.hpp" - -namespace bp = boost::python; - -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -#include "SireError/errors.h" - -#include "SireMaths/vector.h" - -#include "SireStream/datastream.h" - -#include "SireStream/shareddatastream.h" - -#include "SireVol/triclinicbox.h" - -#include "emle.h" - -SireOpenMM::EMLECallback __copy__(const SireOpenMM::EMLECallback &other){ return SireOpenMM::EMLECallback(other); } - -#include "Qt/qdatastream.hpp" - -const char* pvt_get_name(const SireOpenMM::EMLECallback&){ return "SireOpenMM::EMLECallback";} - -#include "Helpers/release_gil_policy.hpp" - -void register_EMLECallback_class(){ - - { //::SireOpenMM::EMLECallback - typedef bp::class_< SireOpenMM::EMLECallback > EMLECallback_exposer_t; - EMLECallback_exposer_t EMLECallback_exposer = EMLECallback_exposer_t( "EMLECallback", "A callback wrapper class to allow use of electrostatic embedding of\nmachine learning potentials via emle-engine.", bp::init< >("Default constructor.") ); - bp::scope EMLECallback_scope( EMLECallback_exposer ); - EMLECallback_exposer.def( bp::init< bp::api::object, bp::optional< QString > >(( bp::arg("arg0"), bp::arg("callback")="_sire_callback" ), "Constructor\nPar:am py_object\nA Python object that contains the callback function.\n\nPar:am callback\nThe name of a callback method that take the following arguments:\n- numbers_qm: A list of atomic numbers for the atoms in the ML region.\n- charges_mm: A list of the MM charges in mod electron charge.\n- xyz_qm: A vector of positions for the atoms in the ML region in Angstrom.\n- xyz_mm: A vector of positions for the atoms in the MM region in Angstrom.\n") ); - { //::SireOpenMM::EMLECallback::call - - typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLECallback::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; - call_function_type call_function_value( &::SireOpenMM::EMLECallback::call ); - - EMLECallback_exposer.def( - "call" - , call_function_value - , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) - , bp::release_gil_policy() - , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); - - } - { //::SireOpenMM::EMLECallback::typeName - - typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireOpenMM::EMLECallback::typeName ); - - EMLECallback_exposer.def( - "typeName" - , typeName_function_value - , bp::release_gil_policy() - , "Return the C++ name for this class." ); - - } - { //::SireOpenMM::EMLECallback::what - - typedef char const * ( ::SireOpenMM::EMLECallback::*what_function_type)( ) const; - what_function_type what_function_value( &::SireOpenMM::EMLECallback::what ); - - EMLECallback_exposer.def( - "what" - , what_function_value - , bp::release_gil_policy() - , "Return the C++ name for this class." ); - - } - EMLECallback_exposer.staticmethod( "typeName" ); - EMLECallback_exposer.def( "__copy__", &__copy__); - EMLECallback_exposer.def( "__deepcopy__", &__copy__); - EMLECallback_exposer.def( "clone", &__copy__); - EMLECallback_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::EMLECallback >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - EMLECallback_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::EMLECallback >, - bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - EMLECallback_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::EMLECallback >()); - EMLECallback_exposer.def( "__str__", &pvt_get_name); - EMLECallback_exposer.def( "__repr__", &pvt_get_name); - } - -} diff --git a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.hpp b/wrapper/Convert/SireOpenMM/EMLECallback.pypp.hpp deleted file mode 100644 index c42426360..000000000 --- a/wrapper/Convert/SireOpenMM/EMLECallback.pypp.hpp +++ /dev/null @@ -1,10 +0,0 @@ -// This file has been generated by Py++. - -// (C) Christopher Woods, GPL >= 3 License - -#ifndef EMLECallback_hpp__pyplusplus_wrapper -#define EMLECallback_hpp__pyplusplus_wrapper - -void register_EMLECallback_class(); - -#endif//EMLECallback_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.hpp b/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.hpp deleted file mode 100644 index ee44f3d23..000000000 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.hpp +++ /dev/null @@ -1,10 +0,0 @@ -// This file has been generated by Py++. - -// (C) Christopher Woods, GPL >= 3 License - -#ifndef EMLEEngine_hpp__pyplusplus_wrapper -#define EMLEEngine_hpp__pyplusplus_wrapper - -void register_EMLEEngine_class(); - -#endif//EMLEEngine_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp b/wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp deleted file mode 100644 index 05d6d9265..000000000 --- a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.hpp +++ /dev/null @@ -1,10 +0,0 @@ -// This file has been generated by Py++. - -// (C) Christopher Woods, GPL >= 3 License - -#ifndef EMLEForce_hpp__pyplusplus_wrapper -#define EMLEForce_hpp__pyplusplus_wrapper - -void register_EMLEForce_class(); - -#endif//EMLEForce_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp index 5be152634..d063ae6e2 100644 --- a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp @@ -13,10 +13,10 @@ namespace bp = boost::python; #include "SireCAS/values.h" -#include "emle.h" - #include "lambdalever.h" +#include "pyqm.h" + #include "tostring.h" #include "SireBase/arrayproperty.hpp" @@ -25,10 +25,10 @@ namespace bp = boost::python; #include "SireCAS/values.h" -#include "emle.h" - #include "lambdalever.h" +#include "pyqm.h" + #include "tostring.h" SireOpenMM::LambdaLever __copy__(const SireOpenMM::LambdaLever &other){ return SireOpenMM::LambdaLever(other); } diff --git a/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp new file mode 100644 index 000000000..f4089d479 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp @@ -0,0 +1,119 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "PyQMCallback.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireVol/triclinicbox.h" + +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "pyqm.h" + +#include + +#include + +#include + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireVol/triclinicbox.h" + +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "pyqm.h" + +#include + +#include + +#include + +SireOpenMM::PyQMCallback __copy__(const SireOpenMM::PyQMCallback &other){ return SireOpenMM::PyQMCallback(other); } + +#include "Qt/qdatastream.hpp" + +const char* pvt_get_name(const SireOpenMM::PyQMCallback&){ return "SireOpenMM::PyQMCallback";} + +#include "Helpers/release_gil_policy.hpp" + +void register_PyQMCallback_class(){ + + { //::SireOpenMM::PyQMCallback + typedef bp::class_< SireOpenMM::PyQMCallback > PyQMCallback_exposer_t; + PyQMCallback_exposer_t PyQMCallback_exposer = PyQMCallback_exposer_t( "PyQMCallback", "A callback wrapper class to interface with external QM engines\nvia the CustomCPPForceImpl.", bp::init< >("Default constructor.") ); + bp::scope PyQMCallback_scope( PyQMCallback_exposer ); + PyQMCallback_exposer.def( bp::init< bp::api::object, bp::optional< QString > >(( bp::arg("arg0"), bp::arg("name")="" ), "Constructor\nPar:am py_object\nA Python object that contains the callback function.\n\nPar:am name\nThe name of a callback method that take the following arguments:\n- numbers_qm: A list of atomic numbers for the atoms in the ML region.\n- charges_mm: A list of the MM charges in mod electron charge.\n- xyz_qm: A vector of positions for the atoms in the ML region in Angstrom.\n- xyz_mm: A vector of positions for the atoms in the MM region in Angstrom.\nIf empty, then the object is assumed to be a callable.\n") ); + { //::SireOpenMM::PyQMCallback::call + + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMCallback::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + call_function_type call_function_value( &::SireOpenMM::PyQMCallback::call ); + + PyQMCallback_exposer.def( + "call" + , call_function_value + , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) + , bp::release_gil_policy() + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + + } + { //::SireOpenMM::PyQMCallback::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireOpenMM::PyQMCallback::typeName ); + + PyQMCallback_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + { //::SireOpenMM::PyQMCallback::what + + typedef char const * ( ::SireOpenMM::PyQMCallback::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::PyQMCallback::what ); + + PyQMCallback_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + PyQMCallback_exposer.staticmethod( "typeName" ); + PyQMCallback_exposer.def( "__copy__", &__copy__); + PyQMCallback_exposer.def( "__deepcopy__", &__copy__); + PyQMCallback_exposer.def( "clone", &__copy__); + PyQMCallback_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::PyQMCallback >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + PyQMCallback_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::PyQMCallback >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + PyQMCallback_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::PyQMCallback >()); + PyQMCallback_exposer.def( "__str__", &pvt_get_name); + PyQMCallback_exposer.def( "__repr__", &pvt_get_name); + } + +} diff --git a/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.hpp b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.hpp new file mode 100644 index 000000000..f3b426b39 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef PyQMCallback_hpp__pyplusplus_wrapper +#define PyQMCallback_hpp__pyplusplus_wrapper + +void register_PyQMCallback_class(); + +#endif//PyQMCallback_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp similarity index 64% rename from wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp rename to wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp index ea7edc728..c68954bd8 100644 --- a/wrapper/Convert/SireOpenMM/EMLEEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp @@ -3,7 +3,7 @@ // (C) Christopher Woods, GPL >= 3 License #include "boost/python.hpp" -#include "EMLEEngine.pypp.hpp" +#include "PyQMEngine.pypp.hpp" namespace bp = boost::python; @@ -17,7 +17,17 @@ namespace bp = boost::python; #include "SireVol/triclinicbox.h" -#include "emle.h" +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "pyqm.h" + +#include + +#include + +#include #include "SireError/errors.h" @@ -29,28 +39,38 @@ namespace bp = boost::python; #include "SireVol/triclinicbox.h" -#include "emle.h" +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "pyqm.h" + +#include + +#include + +#include -SireOpenMM::EMLEEngine __copy__(const SireOpenMM::EMLEEngine &other){ return SireOpenMM::EMLEEngine(other); } +SireOpenMM::PyQMEngine __copy__(const SireOpenMM::PyQMEngine &other){ return SireOpenMM::PyQMEngine(other); } #include "Helpers/str.hpp" #include "Helpers/release_gil_policy.hpp" -void register_EMLEEngine_class(){ +void register_PyQMEngine_class(){ - { //::SireOpenMM::EMLEEngine - typedef bp::class_< SireOpenMM::EMLEEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > EMLEEngine_exposer_t; - EMLEEngine_exposer_t EMLEEngine_exposer = EMLEEngine_exposer_t( "EMLEEngine", "", bp::init< >("Default constructor.") ); - bp::scope EMLEEngine_scope( EMLEEngine_exposer ); - EMLEEngine_exposer.def( bp::init< bp::api::object, bp::optional< SireUnits::Dimension::Length, int, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nAn EMLECalculator Python object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); - EMLEEngine_exposer.def( bp::init< SireOpenMM::EMLEEngine const & >(( bp::arg("other") ), "Copy constructor.") ); - { //::SireOpenMM::EMLEEngine::call - - typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLEEngine::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; - call_function_type call_function_value( &::SireOpenMM::EMLEEngine::call ); + { //::SireOpenMM::PyQMEngine + typedef bp::class_< SireOpenMM::PyQMEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > PyQMEngine_exposer_t; + PyQMEngine_exposer_t PyQMEngine_exposer = PyQMEngine_exposer_t( "PyQMEngine", "", bp::init< >("Default constructor.") ); + bp::scope PyQMEngine_scope( PyQMEngine_exposer ); + PyQMEngine_exposer.def( bp::init< bp::api::object, bp::optional< QString, SireUnits::Dimension::Length, int, double > >(( bp::arg("arg0"), bp::arg("method")="", bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nA Python object.\n\nPar:am name\nThe name of the callback method. If empty, then the object is\nassumed to be a callable.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); + PyQMEngine_exposer.def( bp::init< SireOpenMM::PyQMEngine const & >(( bp::arg("other") ), "Copy constructor.") ); + { //::SireOpenMM::PyQMEngine::call + + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMEngine::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + call_function_type call_function_value( &::SireOpenMM::PyQMEngine::call ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "call" , call_function_value , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) @@ -58,120 +78,120 @@ void register_EMLEEngine_class(){ , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } - { //::SireOpenMM::EMLEEngine::getAtoms + { //::SireOpenMM::PyQMEngine::getAtoms - typedef ::QVector< int > ( ::SireOpenMM::EMLEEngine::*getAtoms_function_type)( ) const; - getAtoms_function_type getAtoms_function_value( &::SireOpenMM::EMLEEngine::getAtoms ); + typedef ::QVector< int > ( ::SireOpenMM::PyQMEngine::*getAtoms_function_type)( ) const; + getAtoms_function_type getAtoms_function_value( &::SireOpenMM::PyQMEngine::getAtoms ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getAtoms" , getAtoms_function_value , bp::release_gil_policy() , "Get the indices of the atoms in the QM region.\nReturn:s\nA vector of atom indices for the QM region.\n" ); } - { //::SireOpenMM::EMLEEngine::getCallback + { //::SireOpenMM::PyQMEngine::getCallback - typedef ::SireOpenMM::EMLECallback ( ::SireOpenMM::EMLEEngine::*getCallback_function_type)( ) const; - getCallback_function_type getCallback_function_value( &::SireOpenMM::EMLEEngine::getCallback ); + typedef ::SireOpenMM::PyQMCallback ( ::SireOpenMM::PyQMEngine::*getCallback_function_type)( ) const; + getCallback_function_type getCallback_function_value( &::SireOpenMM::PyQMEngine::getCallback ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getCallback" , getCallback_function_value , bp::release_gil_policy() , "Get the callback object.\nReturn:s\nA Python object that contains the callback function.\n" ); } - { //::SireOpenMM::EMLEEngine::getCharges + { //::SireOpenMM::PyQMEngine::getCharges - typedef ::QVector< double > ( ::SireOpenMM::EMLEEngine::*getCharges_function_type)( ) const; - getCharges_function_type getCharges_function_value( &::SireOpenMM::EMLEEngine::getCharges ); + typedef ::QVector< double > ( ::SireOpenMM::PyQMEngine::*getCharges_function_type)( ) const; + getCharges_function_type getCharges_function_value( &::SireOpenMM::PyQMEngine::getCharges ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getCharges" , getCharges_function_value , bp::release_gil_policy() , "Get the atomic charges of all atoms in the system.\nReturn:s\nA vector of atomic charges for all atoms in the system.\n" ); } - { //::SireOpenMM::EMLEEngine::getCutoff + { //::SireOpenMM::PyQMEngine::getCutoff - typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::EMLEEngine::*getCutoff_function_type)( ) const; - getCutoff_function_type getCutoff_function_value( &::SireOpenMM::EMLEEngine::getCutoff ); + typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::PyQMEngine::*getCutoff_function_type)( ) const; + getCutoff_function_type getCutoff_function_value( &::SireOpenMM::PyQMEngine::getCutoff ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getCutoff" , getCutoff_function_value , bp::release_gil_policy() , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); } - { //::SireOpenMM::EMLEEngine::getLambda + { //::SireOpenMM::PyQMEngine::getLambda - typedef double ( ::SireOpenMM::EMLEEngine::*getLambda_function_type)( ) const; - getLambda_function_type getLambda_function_value( &::SireOpenMM::EMLEEngine::getLambda ); + typedef double ( ::SireOpenMM::PyQMEngine::*getLambda_function_type)( ) const; + getLambda_function_type getLambda_function_value( &::SireOpenMM::PyQMEngine::getLambda ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getLambda" , getLambda_function_value , bp::release_gil_policy() , "Get the lambda weighting factor.\nReturn:s\nThe lambda weighting factor.\n" ); } - { //::SireOpenMM::EMLEEngine::getLinkAtoms + { //::SireOpenMM::PyQMEngine::getLinkAtoms - typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLEEngine::*getLinkAtoms_function_type)( ) const; - getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::EMLEEngine::getLinkAtoms ); + typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMEngine::*getLinkAtoms_function_type)( ) const; + getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::PyQMEngine::getLinkAtoms ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getLinkAtoms" , getLinkAtoms_function_value , bp::release_gil_policy() , "Get the link atoms associated with each QM atom.\nReturn:s\nA tuple containing:\n\nmm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nmm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nbond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); } - { //::SireOpenMM::EMLEEngine::getMM2Atoms + { //::SireOpenMM::PyQMEngine::getMM2Atoms - typedef ::QVector< int > ( ::SireOpenMM::EMLEEngine::*getMM2Atoms_function_type)( ) const; - getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::EMLEEngine::getMM2Atoms ); + typedef ::QVector< int > ( ::SireOpenMM::PyQMEngine::*getMM2Atoms_function_type)( ) const; + getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::PyQMEngine::getMM2Atoms ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getMM2Atoms" , getMM2Atoms_function_value , bp::release_gil_policy() , "Get the vector of MM2 atoms.\nReturn:s\nA vector of MM2 atom indices.\n" ); } - { //::SireOpenMM::EMLEEngine::getNeighbourListFrequency + { //::SireOpenMM::PyQMEngine::getNeighbourListFrequency - typedef int ( ::SireOpenMM::EMLEEngine::*getNeighbourListFrequency_function_type)( ) const; - getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::EMLEEngine::getNeighbourListFrequency ); + typedef int ( ::SireOpenMM::PyQMEngine::*getNeighbourListFrequency_function_type)( ) const; + getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::PyQMEngine::getNeighbourListFrequency ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getNeighbourListFrequency" , getNeighbourListFrequency_function_value , bp::release_gil_policy() , "Get the neighbour list frequency.\nReturn:s\nThe neighbour list frequency.\n" ); } - { //::SireOpenMM::EMLEEngine::getNumbers + { //::SireOpenMM::PyQMEngine::getNumbers - typedef ::QVector< int > ( ::SireOpenMM::EMLEEngine::*getNumbers_function_type)( ) const; - getNumbers_function_type getNumbers_function_value( &::SireOpenMM::EMLEEngine::getNumbers ); + typedef ::QVector< int > ( ::SireOpenMM::PyQMEngine::*getNumbers_function_type)( ) const; + getNumbers_function_type getNumbers_function_value( &::SireOpenMM::PyQMEngine::getNumbers ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "getNumbers" , getNumbers_function_value , bp::release_gil_policy() , "Get the atomic numbers for the atoms in the QM region.\nReturn:s\nA vector of atomic numbers for the atoms in the QM region.\n" ); } - { //::SireOpenMM::EMLEEngine::operator= + { //::SireOpenMM::PyQMEngine::operator= - typedef ::SireOpenMM::EMLEEngine & ( ::SireOpenMM::EMLEEngine::*assign_function_type)( ::SireOpenMM::EMLEEngine const & ) ; - assign_function_type assign_function_value( &::SireOpenMM::EMLEEngine::operator= ); + typedef ::SireOpenMM::PyQMEngine & ( ::SireOpenMM::PyQMEngine::*assign_function_type)( ::SireOpenMM::PyQMEngine const & ) ; + assign_function_type assign_function_value( &::SireOpenMM::PyQMEngine::operator= ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "assign" , assign_function_value , ( bp::arg("other") ) @@ -179,12 +199,12 @@ void register_EMLEEngine_class(){ , "Assignment operator." ); } - { //::SireOpenMM::EMLEEngine::setAtoms + { //::SireOpenMM::PyQMEngine::setAtoms - typedef void ( ::SireOpenMM::EMLEEngine::*setAtoms_function_type)( ::QVector< int > ) ; - setAtoms_function_type setAtoms_function_value( &::SireOpenMM::EMLEEngine::setAtoms ); + typedef void ( ::SireOpenMM::PyQMEngine::*setAtoms_function_type)( ::QVector< int > ) ; + setAtoms_function_type setAtoms_function_value( &::SireOpenMM::PyQMEngine::setAtoms ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setAtoms" , setAtoms_function_value , ( bp::arg("atoms") ) @@ -192,12 +212,12 @@ void register_EMLEEngine_class(){ , "Set the list of atom indices for the QM region.\nPar:am atoms\nA vector of atom indices for the QM region.\n" ); } - { //::SireOpenMM::EMLEEngine::setCallback + { //::SireOpenMM::PyQMEngine::setCallback - typedef void ( ::SireOpenMM::EMLEEngine::*setCallback_function_type)( ::SireOpenMM::EMLECallback ) ; - setCallback_function_type setCallback_function_value( &::SireOpenMM::EMLEEngine::setCallback ); + typedef void ( ::SireOpenMM::PyQMEngine::*setCallback_function_type)( ::SireOpenMM::PyQMCallback ) ; + setCallback_function_type setCallback_function_value( &::SireOpenMM::PyQMEngine::setCallback ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setCallback" , setCallback_function_value , ( bp::arg("callback") ) @@ -205,12 +225,12 @@ void register_EMLEEngine_class(){ , "Set the callback object.\nPar:am callback\nA Python object that contains the callback function.\n" ); } - { //::SireOpenMM::EMLEEngine::setCharges + { //::SireOpenMM::PyQMEngine::setCharges - typedef void ( ::SireOpenMM::EMLEEngine::*setCharges_function_type)( ::QVector< double > ) ; - setCharges_function_type setCharges_function_value( &::SireOpenMM::EMLEEngine::setCharges ); + typedef void ( ::SireOpenMM::PyQMEngine::*setCharges_function_type)( ::QVector< double > ) ; + setCharges_function_type setCharges_function_value( &::SireOpenMM::PyQMEngine::setCharges ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setCharges" , setCharges_function_value , ( bp::arg("charges") ) @@ -218,12 +238,12 @@ void register_EMLEEngine_class(){ , "Set the atomic charges of all atoms in the system.\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n" ); } - { //::SireOpenMM::EMLEEngine::setCutoff + { //::SireOpenMM::PyQMEngine::setCutoff - typedef void ( ::SireOpenMM::EMLEEngine::*setCutoff_function_type)( ::SireUnits::Dimension::Length ) ; - setCutoff_function_type setCutoff_function_value( &::SireOpenMM::EMLEEngine::setCutoff ); + typedef void ( ::SireOpenMM::PyQMEngine::*setCutoff_function_type)( ::SireUnits::Dimension::Length ) ; + setCutoff_function_type setCutoff_function_value( &::SireOpenMM::PyQMEngine::setCutoff ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setCutoff" , setCutoff_function_value , ( bp::arg("cutoff") ) @@ -231,12 +251,12 @@ void register_EMLEEngine_class(){ , "Set the QM cutoff distance.\nPar:am cutoff\nThe QM cutoff distance.\n" ); } - { //::SireOpenMM::EMLEEngine::setLambda + { //::SireOpenMM::PyQMEngine::setLambda - typedef void ( ::SireOpenMM::EMLEEngine::*setLambda_function_type)( double ) ; - setLambda_function_type setLambda_function_value( &::SireOpenMM::EMLEEngine::setLambda ); + typedef void ( ::SireOpenMM::PyQMEngine::*setLambda_function_type)( double ) ; + setLambda_function_type setLambda_function_value( &::SireOpenMM::PyQMEngine::setLambda ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setLambda" , setLambda_function_value , ( bp::arg("lambda") ) @@ -244,12 +264,12 @@ void register_EMLEEngine_class(){ , "Set the lambda weighting factor.\nPar:am lambda\nThe lambda weighting factor.\n" ); } - { //::SireOpenMM::EMLEEngine::setLinkAtoms + { //::SireOpenMM::PyQMEngine::setLinkAtoms - typedef void ( ::SireOpenMM::EMLEEngine::*setLinkAtoms_function_type)( ::QMap< int, int >,::QMap< int, QVector< int > >,::QMap< int, double > ) ; - setLinkAtoms_function_type setLinkAtoms_function_value( &::SireOpenMM::EMLEEngine::setLinkAtoms ); + typedef void ( ::SireOpenMM::PyQMEngine::*setLinkAtoms_function_type)( ::QMap< int, int >,::QMap< int, QVector< int > >,::QMap< int, double > ) ; + setLinkAtoms_function_type setLinkAtoms_function_value( &::SireOpenMM::PyQMEngine::setLinkAtoms ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setLinkAtoms" , setLinkAtoms_function_value , ( bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors") ) @@ -257,12 +277,12 @@ void register_EMLEEngine_class(){ , "Set the link atoms associated with each QM atom.\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); } - { //::SireOpenMM::EMLEEngine::setNeighbourListFrequency + { //::SireOpenMM::PyQMEngine::setNeighbourListFrequency - typedef void ( ::SireOpenMM::EMLEEngine::*setNeighbourListFrequency_function_type)( int ) ; - setNeighbourListFrequency_function_type setNeighbourListFrequency_function_value( &::SireOpenMM::EMLEEngine::setNeighbourListFrequency ); + typedef void ( ::SireOpenMM::PyQMEngine::*setNeighbourListFrequency_function_type)( int ) ; + setNeighbourListFrequency_function_type setNeighbourListFrequency_function_value( &::SireOpenMM::PyQMEngine::setNeighbourListFrequency ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setNeighbourListFrequency" , setNeighbourListFrequency_function_value , ( bp::arg("neighbour_list_frequency") ) @@ -270,12 +290,12 @@ void register_EMLEEngine_class(){ , "Set the neighbour list frequency.\nPar:am neighbour_list_frequency\nThe neighbour list frequency.\n" ); } - { //::SireOpenMM::EMLEEngine::setNumbers + { //::SireOpenMM::PyQMEngine::setNumbers - typedef void ( ::SireOpenMM::EMLEEngine::*setNumbers_function_type)( ::QVector< int > ) ; - setNumbers_function_type setNumbers_function_value( &::SireOpenMM::EMLEEngine::setNumbers ); + typedef void ( ::SireOpenMM::PyQMEngine::*setNumbers_function_type)( ::QVector< int > ) ; + setNumbers_function_type setNumbers_function_value( &::SireOpenMM::PyQMEngine::setNumbers ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "setNumbers" , setNumbers_function_value , ( bp::arg("numbers") ) @@ -283,36 +303,36 @@ void register_EMLEEngine_class(){ , "Set the atomic numbers for the atoms in the QM region.\nPar:am numbers\nA vector of atomic numbers for the atoms in the QM region.\n" ); } - { //::SireOpenMM::EMLEEngine::typeName + { //::SireOpenMM::PyQMEngine::typeName typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireOpenMM::EMLEEngine::typeName ); + typeName_function_type typeName_function_value( &::SireOpenMM::PyQMEngine::typeName ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "typeName" , typeName_function_value , bp::release_gil_policy() , "Return the C++ name for this class." ); } - { //::SireOpenMM::EMLEEngine::what + { //::SireOpenMM::PyQMEngine::what - typedef char const * ( ::SireOpenMM::EMLEEngine::*what_function_type)( ) const; - what_function_type what_function_value( &::SireOpenMM::EMLEEngine::what ); + typedef char const * ( ::SireOpenMM::PyQMEngine::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::PyQMEngine::what ); - EMLEEngine_exposer.def( + PyQMEngine_exposer.def( "what" , what_function_value , bp::release_gil_policy() , "Return the C++ name for this class." ); } - EMLEEngine_exposer.staticmethod( "typeName" ); - EMLEEngine_exposer.def( "__copy__", &__copy__); - EMLEEngine_exposer.def( "__deepcopy__", &__copy__); - EMLEEngine_exposer.def( "clone", &__copy__); - EMLEEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::EMLEEngine > ); - EMLEEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::EMLEEngine > ); + PyQMEngine_exposer.staticmethod( "typeName" ); + PyQMEngine_exposer.def( "__copy__", &__copy__); + PyQMEngine_exposer.def( "__deepcopy__", &__copy__); + PyQMEngine_exposer.def( "clone", &__copy__); + PyQMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::PyQMEngine > ); + PyQMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::PyQMEngine > ); } } diff --git a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.hpp b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.hpp new file mode 100644 index 000000000..e49bc2a0f --- /dev/null +++ b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef PyQMEngine_hpp__pyplusplus_wrapper +#define PyQMEngine_hpp__pyplusplus_wrapper + +void register_PyQMEngine_class(); + +#endif//PyQMEngine_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp similarity index 67% rename from wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp rename to wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp index 4e9f2c3b2..ad1a17d2a 100644 --- a/wrapper/Convert/SireOpenMM/EMLEForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp @@ -3,7 +3,7 @@ // (C) Christopher Woods, GPL >= 3 License #include "boost/python.hpp" -#include "EMLEForce.pypp.hpp" +#include "PyQMForce.pypp.hpp" namespace bp = boost::python; @@ -17,7 +17,17 @@ namespace bp = boost::python; #include "SireVol/triclinicbox.h" -#include "emle.h" +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "pyqm.h" + +#include + +#include + +#include #include "SireError/errors.h" @@ -29,30 +39,40 @@ namespace bp = boost::python; #include "SireVol/triclinicbox.h" -#include "emle.h" +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "pyqm.h" -SireOpenMM::EMLEForce __copy__(const SireOpenMM::EMLEForce &other){ return SireOpenMM::EMLEForce(other); } +#include + +#include + +#include + +SireOpenMM::PyQMForce __copy__(const SireOpenMM::PyQMForce &other){ return SireOpenMM::PyQMForce(other); } #include "Qt/qdatastream.hpp" -const char* pvt_get_name(const SireOpenMM::EMLEForce&){ return "SireOpenMM::EMLEForce";} +const char* pvt_get_name(const SireOpenMM::PyQMForce&){ return "SireOpenMM::PyQMForce";} #include "Helpers/release_gil_policy.hpp" -void register_EMLEForce_class(){ +void register_PyQMForce_class(){ - { //::SireOpenMM::EMLEForce - typedef bp::class_< SireOpenMM::EMLEForce, bp::bases< SireOpenMM::QMForce > > EMLEForce_exposer_t; - EMLEForce_exposer_t EMLEForce_exposer = EMLEForce_exposer_t( "EMLEForce", "", bp::init< >("Default constructor.") ); - bp::scope EMLEForce_scope( EMLEForce_exposer ); - EMLEForce_exposer.def( bp::init< SireOpenMM::EMLECallback, SireUnits::Dimension::Length, int, double, QVector< int >, QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, QVector< int >, QVector< int >, QVector< double > >(( bp::arg("callback"), bp::arg("cutoff"), bp::arg("neighbour_list_frequency"), bp::arg("lambda"), bp::arg("atoms"), bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors"), bp::arg("mm2_atoms"), bp::arg("numbers"), bp::arg("charges") ), "Constructor.\nPar:am callback\nThe EMLECallback object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n\nPar:am atoms\nA vector of atom indices for the QM region.\n\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\nPar:am mm2_atoms\nA vector of MM2 atom indices.\n\nPar:am numbers\nA vector of atomic charges for all atoms in the system.\n\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n") ); - EMLEForce_exposer.def( bp::init< SireOpenMM::EMLEForce const & >(( bp::arg("other") ), "Copy constructor.") ); - { //::SireOpenMM::EMLEForce::call + { //::SireOpenMM::PyQMForce + typedef bp::class_< SireOpenMM::PyQMForce, bp::bases< SireOpenMM::QMForce > > PyQMForce_exposer_t; + PyQMForce_exposer_t PyQMForce_exposer = PyQMForce_exposer_t( "PyQMForce", "", bp::init< >("Default constructor.") ); + bp::scope PyQMForce_scope( PyQMForce_exposer ); + PyQMForce_exposer.def( bp::init< SireOpenMM::PyQMCallback, SireUnits::Dimension::Length, int, double, QVector< int >, QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, QVector< int >, QVector< int >, QVector< double > >(( bp::arg("callback"), bp::arg("cutoff"), bp::arg("neighbour_list_frequency"), bp::arg("lambda"), bp::arg("atoms"), bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors"), bp::arg("mm2_atoms"), bp::arg("numbers"), bp::arg("charges") ), "Constructor.\nPar:am callback\nThe PyQMCallback object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n\nPar:am atoms\nA vector of atom indices for the QM region.\n\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\nPar:am mm2_atoms\nA vector of MM2 atom indices.\n\nPar:am numbers\nA vector of atomic charges for all atoms in the system.\n\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n") ); + PyQMForce_exposer.def( bp::init< SireOpenMM::PyQMForce const & >(( bp::arg("other") ), "Copy constructor.") ); + { //::SireOpenMM::PyQMForce::call - typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLEForce::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; - call_function_type call_function_value( &::SireOpenMM::EMLEForce::call ); + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMForce::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + call_function_type call_function_value( &::SireOpenMM::PyQMForce::call ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "call" , call_function_value , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) @@ -60,133 +80,120 @@ void register_EMLEForce_class(){ , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } - { //::SireOpenMM::EMLEForce::getAtoms + { //::SireOpenMM::PyQMForce::getAtoms - typedef ::QVector< int > ( ::SireOpenMM::EMLEForce::*getAtoms_function_type)( ) const; - getAtoms_function_type getAtoms_function_value( &::SireOpenMM::EMLEForce::getAtoms ); + typedef ::QVector< int > ( ::SireOpenMM::PyQMForce::*getAtoms_function_type)( ) const; + getAtoms_function_type getAtoms_function_value( &::SireOpenMM::PyQMForce::getAtoms ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getAtoms" , getAtoms_function_value , bp::release_gil_policy() , "Get the indices of the atoms in the QM region.\nReturn:s\nA vector of atom indices for the QM region.\n" ); } - { //::SireOpenMM::EMLEForce::setCallback - - typedef void ( ::SireOpenMM::EMLEForce::*setCallback_function_type)( ::SireOpenMM::EMLECallback ) ; - setCallback_function_type setCallback_function_value( &::SireOpenMM::EMLEForce::setCallback ); - - EMLEForce_exposer.def( - "setCallback" - , setCallback_function_value - , ( bp::arg("callback") ) - , bp::release_gil_policy() - , "Set the callback object.\nPar:am callback\nA Python object that contains the callback function.\n" ); - - } - { //::SireOpenMM::EMLEForce::getCallback + { //::SireOpenMM::PyQMForce::getCallback - typedef ::SireOpenMM::EMLECallback ( ::SireOpenMM::EMLEForce::*getCallback_function_type)( ) const; - getCallback_function_type getCallback_function_value( &::SireOpenMM::EMLEForce::getCallback ); + typedef ::SireOpenMM::PyQMCallback ( ::SireOpenMM::PyQMForce::*getCallback_function_type)( ) const; + getCallback_function_type getCallback_function_value( &::SireOpenMM::PyQMForce::getCallback ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getCallback" , getCallback_function_value , bp::release_gil_policy() , "Get the callback object.\nReturn:s\nA Python object that contains the callback function.\n" ); } - { //::SireOpenMM::EMLEForce::getCharges + { //::SireOpenMM::PyQMForce::getCharges - typedef ::QVector< double > ( ::SireOpenMM::EMLEForce::*getCharges_function_type)( ) const; - getCharges_function_type getCharges_function_value( &::SireOpenMM::EMLEForce::getCharges ); + typedef ::QVector< double > ( ::SireOpenMM::PyQMForce::*getCharges_function_type)( ) const; + getCharges_function_type getCharges_function_value( &::SireOpenMM::PyQMForce::getCharges ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getCharges" , getCharges_function_value , bp::release_gil_policy() , "Get the atomic charges of all atoms in the system.\nReturn:s\nA vector of atomic charges for all atoms in the system.\n" ); } - { //::SireOpenMM::EMLEForce::getCutoff + { //::SireOpenMM::PyQMForce::getCutoff - typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::EMLEForce::*getCutoff_function_type)( ) const; - getCutoff_function_type getCutoff_function_value( &::SireOpenMM::EMLEForce::getCutoff ); + typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::PyQMForce::*getCutoff_function_type)( ) const; + getCutoff_function_type getCutoff_function_value( &::SireOpenMM::PyQMForce::getCutoff ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getCutoff" , getCutoff_function_value , bp::release_gil_policy() , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); } - { //::SireOpenMM::EMLEForce::getLambda + { //::SireOpenMM::PyQMForce::getLambda - typedef double ( ::SireOpenMM::EMLEForce::*getLambda_function_type)( ) const; - getLambda_function_type getLambda_function_value( &::SireOpenMM::EMLEForce::getLambda ); + typedef double ( ::SireOpenMM::PyQMForce::*getLambda_function_type)( ) const; + getLambda_function_type getLambda_function_value( &::SireOpenMM::PyQMForce::getLambda ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getLambda" , getLambda_function_value , bp::release_gil_policy() , "Get the lambda weighting factor.\nReturn:s\nThe lambda weighting factor.\n" ); } - { //::SireOpenMM::EMLEForce::getLinkAtoms + { //::SireOpenMM::PyQMForce::getLinkAtoms - typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::EMLEForce::*getLinkAtoms_function_type)( ) const; - getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::EMLEForce::getLinkAtoms ); + typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMForce::*getLinkAtoms_function_type)( ) const; + getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::PyQMForce::getLinkAtoms ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getLinkAtoms" , getLinkAtoms_function_value , bp::release_gil_policy() , "Get the link atoms associated with each QM atom.\nReturn:s\nA tuple containing:\n\nmm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nmm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nbond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); } - { //::SireOpenMM::EMLEForce::getMM2Atoms + { //::SireOpenMM::PyQMForce::getMM2Atoms - typedef ::QVector< int > ( ::SireOpenMM::EMLEForce::*getMM2Atoms_function_type)( ) const; - getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::EMLEForce::getMM2Atoms ); + typedef ::QVector< int > ( ::SireOpenMM::PyQMForce::*getMM2Atoms_function_type)( ) const; + getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::PyQMForce::getMM2Atoms ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getMM2Atoms" , getMM2Atoms_function_value , bp::release_gil_policy() , "Get the vector of MM2 atoms.\nReturn:s\nA vector of MM2 atom indices.\n" ); } - { //::SireOpenMM::EMLEForce::getNeighbourListFrequency + { //::SireOpenMM::PyQMForce::getNeighbourListFrequency - typedef int ( ::SireOpenMM::EMLEForce::*getNeighbourListFrequency_function_type)( ) const; - getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::EMLEForce::getNeighbourListFrequency ); + typedef int ( ::SireOpenMM::PyQMForce::*getNeighbourListFrequency_function_type)( ) const; + getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::PyQMForce::getNeighbourListFrequency ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getNeighbourListFrequency" , getNeighbourListFrequency_function_value , bp::release_gil_policy() , "Get the neighbour list frequency.\nReturn:s\nThe neighbour list frequency.\n" ); } - { //::SireOpenMM::EMLEForce::getNumbers + { //::SireOpenMM::PyQMForce::getNumbers - typedef ::QVector< int > ( ::SireOpenMM::EMLEForce::*getNumbers_function_type)( ) const; - getNumbers_function_type getNumbers_function_value( &::SireOpenMM::EMLEForce::getNumbers ); + typedef ::QVector< int > ( ::SireOpenMM::PyQMForce::*getNumbers_function_type)( ) const; + getNumbers_function_type getNumbers_function_value( &::SireOpenMM::PyQMForce::getNumbers ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "getNumbers" , getNumbers_function_value , bp::release_gil_policy() , "Get the atomic numbers for the atoms in the QM region.\nReturn:s\nA vector of atomic numbers for the atoms in the QM region.\n" ); } - { //::SireOpenMM::EMLEForce::operator= + { //::SireOpenMM::PyQMForce::operator= - typedef ::SireOpenMM::EMLEForce & ( ::SireOpenMM::EMLEForce::*assign_function_type)( ::SireOpenMM::EMLEForce const & ) ; - assign_function_type assign_function_value( &::SireOpenMM::EMLEForce::operator= ); + typedef ::SireOpenMM::PyQMForce & ( ::SireOpenMM::PyQMForce::*assign_function_type)( ::SireOpenMM::PyQMForce const & ) ; + assign_function_type assign_function_value( &::SireOpenMM::PyQMForce::operator= ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "assign" , assign_function_value , ( bp::arg("other") ) @@ -194,12 +201,25 @@ void register_EMLEForce_class(){ , "Assignment operator." ); } - { //::SireOpenMM::EMLEForce::setLambda + { //::SireOpenMM::PyQMForce::setCallback + + typedef void ( ::SireOpenMM::PyQMForce::*setCallback_function_type)( ::SireOpenMM::PyQMCallback ) ; + setCallback_function_type setCallback_function_value( &::SireOpenMM::PyQMForce::setCallback ); + + PyQMForce_exposer.def( + "setCallback" + , setCallback_function_value + , ( bp::arg("callback") ) + , bp::release_gil_policy() + , "Set the callback object.\nPar:am callback\nA Python object that contains the callback function.\n" ); + + } + { //::SireOpenMM::PyQMForce::setLambda - typedef void ( ::SireOpenMM::EMLEForce::*setLambda_function_type)( double ) ; - setLambda_function_type setLambda_function_value( &::SireOpenMM::EMLEForce::setLambda ); + typedef void ( ::SireOpenMM::PyQMForce::*setLambda_function_type)( double ) ; + setLambda_function_type setLambda_function_value( &::SireOpenMM::PyQMForce::setLambda ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "setLambda" , setLambda_function_value , ( bp::arg("lambda") ) @@ -207,41 +227,41 @@ void register_EMLEForce_class(){ , "Set the lambda weighting factor\nPar:am lambda\nThe lambda weighting factor.\n" ); } - { //::SireOpenMM::EMLEForce::typeName + { //::SireOpenMM::PyQMForce::typeName typedef char const * ( *typeName_function_type )( ); - typeName_function_type typeName_function_value( &::SireOpenMM::EMLEForce::typeName ); + typeName_function_type typeName_function_value( &::SireOpenMM::PyQMForce::typeName ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "typeName" , typeName_function_value , bp::release_gil_policy() , "Return the C++ name for this class." ); } - { //::SireOpenMM::EMLEForce::what + { //::SireOpenMM::PyQMForce::what - typedef char const * ( ::SireOpenMM::EMLEForce::*what_function_type)( ) const; - what_function_type what_function_value( &::SireOpenMM::EMLEForce::what ); + typedef char const * ( ::SireOpenMM::PyQMForce::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::PyQMForce::what ); - EMLEForce_exposer.def( + PyQMForce_exposer.def( "what" , what_function_value , bp::release_gil_policy() , "Return the C++ name for this class." ); } - EMLEForce_exposer.staticmethod( "typeName" ); - EMLEForce_exposer.def( "__copy__", &__copy__); - EMLEForce_exposer.def( "__deepcopy__", &__copy__); - EMLEForce_exposer.def( "clone", &__copy__); - EMLEForce_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::EMLEForce >, + PyQMForce_exposer.staticmethod( "typeName" ); + PyQMForce_exposer.def( "__copy__", &__copy__); + PyQMForce_exposer.def( "__deepcopy__", &__copy__); + PyQMForce_exposer.def( "clone", &__copy__); + PyQMForce_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::PyQMForce >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - EMLEForce_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::EMLEForce >, + PyQMForce_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::PyQMForce >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); - EMLEForce_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::EMLEForce >()); - EMLEForce_exposer.def( "__str__", &pvt_get_name); - EMLEForce_exposer.def( "__repr__", &pvt_get_name); + PyQMForce_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::PyQMForce >()); + PyQMForce_exposer.def( "__str__", &pvt_get_name); + PyQMForce_exposer.def( "__repr__", &pvt_get_name); } } diff --git a/wrapper/Convert/SireOpenMM/PyQMForce.pypp.hpp b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.hpp new file mode 100644 index 000000000..40b5f0f11 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef PyQMForce_hpp__pyplusplus_wrapper +#define PyQMForce_hpp__pyplusplus_wrapper + +void register_PyQMForce_class(); + +#endif//PyQMForce_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index 4145761c4..2f68bd88d 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -4,7 +4,7 @@ #include "SireOpenMM_registrars.h" #include "qmmm.h" -#include "emle.h" +#include "pyqm.h" #include "lambdalever.h" #include "openmmmolecule.h" @@ -15,12 +15,12 @@ void register_SireOpenMM_objects() ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::NullQMEngine >(); - ObjectRegistry::registerConverterFor< SireOpenMM::EMLECallback >(); - ObjectRegistry::registerConverterFor< SireOpenMM::EMLEForce >(); - ObjectRegistry::registerConverterFor< SireOpenMM::EMLEEngine >(); - ObjectRegistry::registerConverterFor< SireOpenMM::EMLECallback >(); - ObjectRegistry::registerConverterFor< SireOpenMM::EMLEForce >(); - ObjectRegistry::registerConverterFor< SireOpenMM::EMLEEngine >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PyQMCallback >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PyQMForce >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PyQMEngine >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PyQMCallback >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PyQMForce >(); + ObjectRegistry::registerConverterFor< SireOpenMM::PyQMEngine >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index e1ac8a459..e65bfbfbd 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -7,12 +7,6 @@ #include "boost/python/suite/indexing/vector_indexing_suite.hpp" -#include "EMLECallback.pypp.hpp" - -#include "EMLEEngine.pypp.hpp" - -#include "EMLEForce.pypp.hpp" - #include "LambdaLever.pypp.hpp" #include "NullQMEngine.pypp.hpp" @@ -21,6 +15,12 @@ #include "PerturbableOpenMMMolecule.pypp.hpp" +#include "PyQMCallback.pypp.hpp" + +#include "PyQMEngine.pypp.hpp" + +#include "PyQMForce.pypp.hpp" + #include "QMEngine.pypp.hpp" #include "QMForce.pypp.hpp" @@ -42,23 +42,23 @@ BOOST_PYTHON_MODULE(_SireOpenMM){ register_vector_less__OpenMM_scope_Vec3__greater__class(); - register_EMLECallback_class(); + register_LambdaLever_class(); register_QMEngine_class(); - register_EMLEEngine_class(); + register_NullQMEngine_class(); - register_QMForce_class(); + register_OpenMMMetaData_class(); - register_EMLEForce_class(); + register_PerturbableOpenMMMolecule_class(); - register_LambdaLever_class(); + register_PyQMCallback_class(); - register_NullQMEngine_class(); + register_PyQMEngine_class(); - register_OpenMMMetaData_class(); + register_QMForce_class(); - register_PerturbableOpenMMMolecule_class(); + register_PyQMForce_class(); register_SireOpenMM_properties(); diff --git a/wrapper/Convert/SireOpenMM/active_headers.h b/wrapper/Convert/SireOpenMM/active_headers.h index 9da80fe28..b867c53c5 100644 --- a/wrapper/Convert/SireOpenMM/active_headers.h +++ b/wrapper/Convert/SireOpenMM/active_headers.h @@ -1,12 +1,14 @@ #ifndef ACTIVE_HEADERS_H #define ACTIVE_HEADERS_H +#define QT_NO_SIGNALS_SLOTS_KEYWORDS = 1 + #ifdef GCCXML_PARSE -#include "emle.h" #include "lambdalever.h" #include "openmmminimise.h" #include "openmmmolecule.h" +#include "pyqm.h" #include "qmmm.h" #include "sire_openmm.h" diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index b75e2a606..85eee4aca 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -26,7 +26,7 @@ * \*********************************************/ -#include "emle.h" +#include "pyqm.h" #include "lambdalever.h" #include "SireBase/propertymap.h" diff --git a/wrapper/Convert/SireOpenMM/emle.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp similarity index 80% rename from wrapper/Convert/SireOpenMM/emle.cpp rename to wrapper/Convert/SireOpenMM/pyqm.cpp index 6c1cc75c8..087ad889e 100644 --- a/wrapper/Convert/SireOpenMM/emle.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -40,7 +40,7 @@ #include "SireStream/shareddatastream.h" #include "SireVol/triclinicbox.h" -#include "emle.h" +#include "pyqm.h" using namespace SireMaths; using namespace SireOpenMM; @@ -61,7 +61,7 @@ class GILLock }; ///////// -///////// Implementation of EMLECallback +///////// Implementation of PyQMCallback ///////// // A registry to store Python callback objects. @@ -85,35 +85,35 @@ bp::object getPythonObject(QString uuid) if (not py_object_registry.contains(uuid)) { throw SireError::invalid_key(QObject::tr( - "Unable to find UUID %1 in the EMLEForce callback registry.").arg(uuid), + "Unable to find UUID %1 in the PyQMForce callback registry.").arg(uuid), CODELOC); } return py_object_registry[uuid]; } -static const RegisterMetaType r_emlecallback(NO_ROOT); +static const RegisterMetaType r_pyqmcallback(NO_ROOT); -QDataStream &operator<<(QDataStream &ds, const EMLECallback &emlecallback) +QDataStream &operator<<(QDataStream &ds, const PyQMCallback &pyqmcallback) { - writeHeader(ds, r_emlecallback, 1); + writeHeader(ds, r_pyqmcallback, 1); SharedDataStream sds(ds); // Generate a unique identifier for the callback. auto uuid = QUuid::createUuid().toString(); - sds << uuid << emlecallback.callback; + sds << uuid << pyqmcallback.name << pyqmcallback.is_method; // Set the Python object in the registry. - setPyObject(emlecallback.py_object, uuid); + setPyObject(pyqmcallback.py_object, uuid); return ds; } -QDataStream &operator>>(QDataStream &ds, EMLECallback &emlecallback) +QDataStream &operator>>(QDataStream &ds, PyQMCallback &pyqmcallback) { - VersionID v = readHeader(ds, r_emlecallback); + VersionID v = readHeader(ds, r_pyqmcallback); if (v == 1) { @@ -122,28 +122,33 @@ QDataStream &operator>>(QDataStream &ds, EMLECallback &emlecallback) QString uuid; // Get the UUID of the Python object and the callback name. - sds >> uuid >> emlecallback.callback; + sds >> uuid >> pyqmcallback.name >> pyqmcallback.is_method; // Set the Python object. - emlecallback.py_object = getPythonObject(uuid); + pyqmcallback.py_object = getPythonObject(uuid); } else - throw version_error(v, "1", r_emlecallback, CODELOC); + throw version_error(v, "1", r_pyqmcallback, CODELOC); return ds; } -EMLECallback::EMLECallback() +PyQMCallback::PyQMCallback() { } -EMLECallback::EMLECallback(bp::object py_object, QString callback) : - py_object(py_object), callback(callback) +PyQMCallback::PyQMCallback(bp::object py_object, QString name) : + py_object(py_object), name(name) { + // Is this a method or free function. + if (name.isEmpty()) + { + this->is_method = false; + } } boost::tuple>, QVector>> -EMLECallback::call( +PyQMCallback::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, @@ -153,71 +158,84 @@ EMLECallback::call( // Acquire GIL before calling Python code. GILLock lock; - return bp::call_method>, QVector>>>( - this->py_object.ptr(), - this->callback.toStdString().c_str(), - numbers_qm, - charges_mm, - xyz_qm, - xyz_mm - ); + if (this->is_method) + { + return bp::call_method>, QVector>>>( + this->py_object.ptr(), + this->name.toStdString().c_str(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm + ); + } + else + { + return bp::call>, QVector>>>( + this->py_object.ptr(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm + ); + } } -const char *EMLECallback::typeName() +const char *PyQMCallback::typeName() { - return QMetaType::typeName(qMetaTypeId()); + return QMetaType::typeName(qMetaTypeId()); } -const char *EMLECallback::what() const +const char *PyQMCallback::what() const { - return EMLECallback::typeName(); + return PyQMCallback::typeName(); } ///////// -///////// Implementation of EMLEForce +///////// Implementation of PyQMForce ///////// -static const RegisterMetaType r_emleforce(NO_ROOT); +static const RegisterMetaType r_pyqmforce(NO_ROOT); -QDataStream &operator<<(QDataStream &ds, const EMLEForce &emleforce) +QDataStream &operator<<(QDataStream &ds, const PyQMForce &pyqmforce) { - writeHeader(ds, r_emleforce, 1); + writeHeader(ds, r_pyqmforce, 1); SharedDataStream sds(ds); - sds << emleforce.callback << emleforce.cutoff << emleforce.neighbour_list_frequency - << emleforce.lambda << emleforce.atoms << emleforce.mm1_to_qm - << emleforce.mm1_to_mm2 << emleforce.bond_scale_factors << emleforce.mm2_atoms - << emleforce.numbers << emleforce.charges; + sds << pyqmforce.callback << pyqmforce.cutoff << pyqmforce.neighbour_list_frequency + << pyqmforce.lambda << pyqmforce.atoms << pyqmforce.mm1_to_qm + << pyqmforce.mm1_to_mm2 << pyqmforce.bond_scale_factors << pyqmforce.mm2_atoms + << pyqmforce.numbers << pyqmforce.charges; return ds; } -QDataStream &operator>>(QDataStream &ds, EMLEForce &emleforce) +QDataStream &operator>>(QDataStream &ds, PyQMForce &pyqmforce) { - VersionID v = readHeader(ds, r_emleforce); + VersionID v = readHeader(ds, r_pyqmforce); if (v == 1) { SharedDataStream sds(ds); - sds >> emleforce.callback >> emleforce.cutoff >> emleforce.neighbour_list_frequency - >> emleforce.lambda >> emleforce.atoms >> emleforce.mm1_to_qm - >> emleforce.mm1_to_mm2 >> emleforce.bond_scale_factors >> emleforce.mm2_atoms - >> emleforce.numbers >> emleforce.charges; + sds >> pyqmforce.callback >> pyqmforce.cutoff >> pyqmforce.neighbour_list_frequency + >> pyqmforce.lambda >> pyqmforce.atoms >> pyqmforce.mm1_to_qm + >> pyqmforce.mm1_to_mm2 >> pyqmforce.bond_scale_factors >> pyqmforce.mm2_atoms + >> pyqmforce.numbers >> pyqmforce.charges; } else - throw version_error(v, "1", r_emleforce, CODELOC); + throw version_error(v, "1", r_pyqmforce, CODELOC); return ds; } -EMLEForce::EMLEForce() +PyQMForce::PyQMForce() { } -EMLEForce::EMLEForce( - EMLECallback callback, +PyQMForce::PyQMForce( + PyQMCallback callback, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, double lambda, @@ -242,7 +260,7 @@ EMLEForce::EMLEForce( { } -EMLEForce::EMLEForce(const EMLEForce &other) : +PyQMForce::PyQMForce(const PyQMForce &other) : callback(other.callback), cutoff(other.cutoff), neighbour_list_frequency(other.neighbour_list_frequency), @@ -257,7 +275,7 @@ EMLEForce::EMLEForce(const EMLEForce &other) : { } -EMLEForce &EMLEForce::operator=(const EMLEForce &other) +PyQMForce &PyQMForce::operator=(const PyQMForce &other) { this->callback = other.callback; this->cutoff = other.cutoff; @@ -273,17 +291,17 @@ EMLEForce &EMLEForce::operator=(const EMLEForce &other) return *this; } -void EMLEForce::setCallback(EMLECallback callback) +void PyQMForce::setCallback(PyQMCallback callback) { this->callback = callback; } -EMLECallback EMLEForce::getCallback() const +PyQMCallback PyQMForce::getCallback() const { return this->callback; } -void EMLEForce::setLambda(double lambda) +void PyQMForce::setLambda(double lambda) { // Clamp the lambda value. if (lambda < 0.0) @@ -297,58 +315,58 @@ void EMLEForce::setLambda(double lambda) this->lambda = lambda; } -double EMLEForce::getLambda() const +double PyQMForce::getLambda() const { return this->lambda; } -SireUnits::Dimension::Length EMLEForce::getCutoff() const +SireUnits::Dimension::Length PyQMForce::getCutoff() const { return this->cutoff; } -int EMLEForce::getNeighbourListFrequency() const +int PyQMForce::getNeighbourListFrequency() const { return this->neighbour_list_frequency; } -QVector EMLEForce::getAtoms() const +QVector PyQMForce::getAtoms() const { return this->atoms; } -boost::tuple, QMap>, QMap> EMLEForce::getLinkAtoms() const +boost::tuple, QMap>, QMap> PyQMForce::getLinkAtoms() const { return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); } -QVector EMLEForce::getMM2Atoms() const +QVector PyQMForce::getMM2Atoms() const { return this->mm2_atoms; } -QVector EMLEForce::getNumbers() const +QVector PyQMForce::getNumbers() const { return this->numbers; } -QVector EMLEForce::getCharges() const +QVector PyQMForce::getCharges() const { return this->charges; } -const char *EMLEForce::typeName() +const char *PyQMForce::typeName() { - return QMetaType::typeName(qMetaTypeId()); + return QMetaType::typeName(qMetaTypeId()); } -const char *EMLEForce::what() const +const char *PyQMForce::what() const { - return EMLEForce::typeName(); + return PyQMForce::typeName(); } boost::tuple>, QVector>> -EMLEForce::call( +PyQMForce::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, @@ -364,9 +382,9 @@ EMLEForce::call( namespace OpenMM { - class EMLEForceProxy : public SerializationProxy { + class PyQMForceProxy : public SerializationProxy { public: - EMLEForceProxy() : SerializationProxy("EMLEForce") + PyQMForceProxy() : SerializationProxy("PyQMForce") { }; @@ -375,8 +393,8 @@ namespace OpenMM // Serialize the object. QByteArray data; QDataStream ds(&data, QIODevice::WriteOnly); - EMLEForce emleforce = *static_cast(object); - ds << emleforce; + PyQMForce pyqmforce = *static_cast(object); + ds << pyqmforce; // Set the version. node.setIntProperty("version", 0); @@ -410,60 +428,60 @@ namespace OpenMM // Deserialize the object. QDataStream ds(data); - EMLEForce emleforce; + PyQMForce pyqmforce; try { - ds >> emleforce; + ds >> pyqmforce; } catch (...) { - throw OpenMM::OpenMMException("Unable to find UUID in the EMLEForce callback registry."); + throw OpenMM::OpenMMException("Unable to find UUID in the PyQMForce callback registry."); } - return new EMLEForce(emleforce); + return new PyQMForce(pyqmforce); }; }; - // Register the EMLEForce serialization proxy. - extern "C" void registerEmleSerializationProxies() { - SerializationProxy::registerProxy(typeid(EMLEForce), new EMLEForceProxy()); + // Register the PyQMForce serialization proxy. + extern "C" void registerPyQMSerializationProxies() { + SerializationProxy::registerProxy(typeid(PyQMForce), new PyQMForceProxy()); } }; ///////// -///////// Implementation of EMLEForceImpl +///////// Implementation of PyQMForceImpl ///////// -OpenMM::ForceImpl *EMLEForce::createImpl() const +OpenMM::ForceImpl *PyQMForce::createImpl() const { #ifdef SIRE_USE_CUSTOMCPPFORCE - return new EMLEForceImpl(*this); + return new PyQMForceImpl(*this); #else throw SireError::unsupported(QObject::tr( - "Unable to create an EMLEForceImpl because OpenMM::CustomCPPForceImpl " + "Unable to create an PyQMForceImpl because OpenMM::CustomCPPForceImpl " "is not available. You need to use OpenMM 8.1 or later."), CODELOC); return 0; #endif } -EMLEForceImpl::EMLEForceImpl(const EMLEForce &owner) : +PyQMForceImpl::PyQMForceImpl(const PyQMForce &owner) : OpenMM::CustomCPPForceImpl(owner), owner(owner) { } -EMLEForceImpl::~EMLEForceImpl() +PyQMForceImpl::~PyQMForceImpl() { } -const EMLEForce &EMLEForceImpl::getOwner() const +const PyQMForce &PyQMForceImpl::getOwner() const { return this->owner; } -double EMLEForceImpl::computeForce( +double PyQMForceImpl::computeForce( OpenMM::ContextImpl &context, const std::vector &positions, std::vector &forces) @@ -751,7 +769,7 @@ double EMLEForceImpl::computeForce( { lambda = context.getParameter("lambda_interpolate"); } - // Fall back on the lambda value stored in the EMLEForce object. + // Fall back on the lambda value stored in the PyQMForce object. catch (...) { lambda = this->owner.getLambda(); @@ -820,28 +838,29 @@ double EMLEForceImpl::computeForce( } ///////// -///////// Implementation of EMLEEngine +///////// Implementation of PyQMEngine ///////// -EMLEEngine::EMLEEngine() : ConcreteProperty() +PyQMEngine::PyQMEngine() : ConcreteProperty() { // Register the serialization proxies. - OpenMM::registerEmleSerializationProxies(); + OpenMM::registerPyQMSerializationProxies(); } -EMLEEngine::EMLEEngine( +PyQMEngine::PyQMEngine( bp::object py_object, + QString name, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, double lambda) : - ConcreteProperty(), - callback(py_object, "_sire_callback"), + ConcreteProperty(), + callback(py_object, name), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), lambda(lambda) { // Register the serialization proxies. - OpenMM::registerEmleSerializationProxies(); + OpenMM::registerPyQMSerializationProxies(); if (this->neighbour_list_frequency < 0) { @@ -857,7 +876,7 @@ EMLEEngine::EMLEEngine( } } -EMLEEngine::EMLEEngine(const EMLEEngine &other) : +PyQMEngine::PyQMEngine(const PyQMEngine &other) : callback(other.callback), cutoff(other.cutoff), neighbour_list_frequency(other.neighbour_list_frequency), @@ -872,7 +891,7 @@ EMLEEngine::EMLEEngine(const EMLEEngine &other) : { } -EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) +PyQMEngine &PyQMEngine::operator=(const PyQMEngine &other) { this->callback = other.callback; this->cutoff = other.cutoff; @@ -888,17 +907,17 @@ EMLEEngine &EMLEEngine::operator=(const EMLEEngine &other) return *this; } -void EMLEEngine::setCallback(EMLECallback callback) +void PyQMEngine::setCallback(PyQMCallback callback) { this->callback = callback; } -EMLECallback EMLEEngine::getCallback() const +PyQMCallback PyQMEngine::getCallback() const { return this->callback; } -void EMLEEngine::setLambda(double lambda) +void PyQMEngine::setLambda(double lambda) { // Clamp the lambda value. if (lambda < 0.0) @@ -912,27 +931,27 @@ void EMLEEngine::setLambda(double lambda) this->lambda = lambda; } -double EMLEEngine::getLambda() const +double PyQMEngine::getLambda() const { return this->lambda; } -void EMLEEngine::setCutoff(SireUnits::Dimension::Length cutoff) +void PyQMEngine::setCutoff(SireUnits::Dimension::Length cutoff) { this->cutoff = cutoff; } -SireUnits::Dimension::Length EMLEEngine::getCutoff() const +SireUnits::Dimension::Length PyQMEngine::getCutoff() const { return this->cutoff; } -int EMLEEngine::getNeighbourListFrequency() const +int PyQMEngine::getNeighbourListFrequency() const { return this->neighbour_list_frequency; } -void EMLEEngine::setNeighbourListFrequency(int neighbour_list_frequency) +void PyQMEngine::setNeighbourListFrequency(int neighbour_list_frequency) { // Assume anything less than zero means no neighbour list. if (neighbour_list_frequency < 0) @@ -942,22 +961,22 @@ void EMLEEngine::setNeighbourListFrequency(int neighbour_list_frequency) this->neighbour_list_frequency = neighbour_list_frequency; } -QVector EMLEEngine::getAtoms() const +QVector PyQMEngine::getAtoms() const { return this->atoms; } -void EMLEEngine::setAtoms(QVector atoms) +void PyQMEngine::setAtoms(QVector atoms) { this->atoms = atoms; } -boost::tuple, QMap>, QMap> EMLEEngine::getLinkAtoms() const +boost::tuple, QMap>, QMap> PyQMEngine::getLinkAtoms() const { return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); } -void EMLEEngine::setLinkAtoms( +void PyQMEngine::setLinkAtoms( QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_scale_factors) @@ -974,43 +993,43 @@ void EMLEEngine::setLinkAtoms( } } -QVector EMLEEngine::getMM2Atoms() const +QVector PyQMEngine::getMM2Atoms() const { return this->mm2_atoms; } -QVector EMLEEngine::getNumbers() const +QVector PyQMEngine::getNumbers() const { return this->numbers; } -void EMLEEngine::setNumbers(QVector numbers) +void PyQMEngine::setNumbers(QVector numbers) { this->numbers = numbers; } -QVector EMLEEngine::getCharges() const +QVector PyQMEngine::getCharges() const { return this->charges; } -void EMLEEngine::setCharges(QVector charges) +void PyQMEngine::setCharges(QVector charges) { this->charges = charges; } -const char *EMLEEngine::typeName() +const char *PyQMEngine::typeName() { - return QMetaType::typeName(qMetaTypeId()); + return QMetaType::typeName(qMetaTypeId()); } -const char *EMLEEngine::what() const +const char *PyQMEngine::what() const { - return EMLEEngine::typeName(); + return PyQMEngine::typeName(); } boost::tuple>, QVector>> -EMLEEngine::call( +PyQMEngine::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, @@ -1019,9 +1038,9 @@ EMLEEngine::call( return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); } -QMForce* EMLEEngine::createForce() const +QMForce* PyQMEngine::createForce() const { - return new EMLEForce( + return new PyQMForce( this->callback, this->cutoff, this->neighbour_list_frequency, diff --git a/wrapper/Convert/SireOpenMM/emle.h b/wrapper/Convert/SireOpenMM/pyqm.h similarity index 88% rename from wrapper/Convert/SireOpenMM/emle.h rename to wrapper/Convert/SireOpenMM/pyqm.h index c8bde98cc..50c44122c 100644 --- a/wrapper/Convert/SireOpenMM/emle.h +++ b/wrapper/Convert/SireOpenMM/pyqm.h @@ -55,41 +55,42 @@ SIRE_BEGIN_HEADER namespace SireOpenMM { - class EMLECallback; - class EMLEForce; + class PyQMCallback; + class PyQMForce; } -QDataStream &operator<<(QDataStream &, const SireOpenMM::EMLECallback &); -QDataStream &operator>>(QDataStream &, SireOpenMM::EMLECallback &); +QDataStream &operator<<(QDataStream &, const SireOpenMM::PyQMCallback &); +QDataStream &operator>>(QDataStream &, SireOpenMM::PyQMCallback &); -QDataStream &operator<<(QDataStream &, const SireOpenMM::EMLEForce &); -QDataStream &operator>>(QDataStream &, SireOpenMM::EMLEForce &); +QDataStream &operator<<(QDataStream &, const SireOpenMM::PyQMForce &); +QDataStream &operator>>(QDataStream &, SireOpenMM::PyQMForce &); namespace SireOpenMM { - // A callback wrapper class to allow use of electrostatic embedding of - // machine learning potentials via emle-engine. - class EMLECallback + // A callback wrapper class to interface with external QM engines + // via the CustomCPPForceImpl. + class PyQMCallback { - friend QDataStream & ::operator<<(QDataStream &, const EMLECallback &); - friend QDataStream & ::operator>>(QDataStream &, EMLECallback &); + friend QDataStream & ::operator<<(QDataStream &, const PyQMCallback &); + friend QDataStream & ::operator>>(QDataStream &, PyQMCallback &); public: //! Default constructor. - EMLECallback(); + PyQMCallback(); //! Constructor /*! \param py_object A Python object that contains the callback function. - \param callback + \param name The name of a callback method that take the following arguments: - numbers_qm: A list of atomic numbers for the atoms in the ML region. - charges_mm: A list of the MM charges in mod electron charge. - xyz_qm: A vector of positions for the atoms in the ML region in Angstrom. - xyz_mm: A vector of positions for the atoms in the MM region in Angstrom. + If empty, then the object is assumed to be a callable. */ - EMLECallback(bp::object, QString callback="_sire_callback"); + PyQMCallback(bp::object, QString name=""); //! Call the callback function. /*! \param numbers_qm @@ -125,21 +126,22 @@ namespace SireOpenMM private: bp::object py_object; - QString callback; + QString name; + bool is_method = true; }; - class EMLEForce : public QMForce + class PyQMForce : public QMForce { - friend QDataStream & ::operator<<(QDataStream &, const EMLEForce &); - friend QDataStream & ::operator>>(QDataStream &, EMLEForce &); + friend QDataStream & ::operator<<(QDataStream &, const PyQMForce &); + friend QDataStream & ::operator>>(QDataStream &, PyQMForce &); public: //! Default constructor. - EMLEForce(); + PyQMForce(); //! Constructor. /* \param callback - The EMLECallback object. + The PyQMCallback object. \param cutoff The ML cutoff distance. @@ -179,8 +181,8 @@ namespace SireOpenMM \param charges A vector of atomic charges for all atoms in the system. */ - EMLEForce( - EMLECallback callback, + PyQMForce( + PyQMCallback callback, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, double lambda, @@ -194,22 +196,22 @@ namespace SireOpenMM ); //! Copy constructor. - EMLEForce(const EMLEForce &other); + PyQMForce(const PyQMForce &other); //! Assignment operator. - EMLEForce &operator=(const EMLEForce &other); + PyQMForce &operator=(const PyQMForce &other); //! Set the callback object. /*! \param callback A Python object that contains the callback function. */ - void setCallback(EMLECallback callback); + void setCallback(PyQMCallback callback); //! Get the callback object. /*! \returns A Python object that contains the callback function. */ - EMLECallback getCallback() const; + PyQMCallback getCallback() const; //! Get the lambda weighting factor. /*! \returns @@ -317,7 +319,7 @@ namespace SireOpenMM OpenMM::ForceImpl *createImpl() const; private: - EMLECallback callback; + PyQMCallback callback; SireUnits::Dimension::Length cutoff; int neighbour_list_frequency; double lambda; @@ -331,21 +333,21 @@ namespace SireOpenMM }; #ifdef SIRE_USE_CUSTOMCPPFORCE - class EMLEForceImpl : public OpenMM::CustomCPPForceImpl + class PyQMForceImpl : public OpenMM::CustomCPPForceImpl { public: - EMLEForceImpl(const EMLEForce &owner); + PyQMForceImpl(const PyQMForce &owner); - ~EMLEForceImpl(); + ~PyQMForceImpl(); double computeForce(OpenMM::ContextImpl &context, const std::vector &positions, std::vector &forces); - const EMLEForce &getOwner() const; + const PyQMForce &getOwner() const; private: - const EMLEForce &owner; + const PyQMForce &owner; unsigned long long step_count=0; double cutoff; bool is_neighbour_list; @@ -355,15 +357,19 @@ namespace SireOpenMM }; #endif - class EMLEEngine : public SireBase::ConcreteProperty + class PyQMEngine : public SireBase::ConcreteProperty { public: //! Default constructor. - EMLEEngine(); + PyQMEngine(); //! Constructor /*! \param py_object - An EMLECalculator Python object. + A Python object. + + \param name + The name of the callback method. If empty, then the object is + assumed to be a callable. \param cutoff The ML cutoff distance. @@ -376,30 +382,31 @@ namespace SireOpenMM The lambda weighting factor. This can be used to interpolate between potentials for end-state correction calculations. */ - EMLEEngine( + PyQMEngine( bp::object, + QString method="", SireUnits::Dimension::Length cutoff=7.5*SireUnits::angstrom, int neighbour_list_frequency=20, double lambda=1.0 ); //! Copy constructor. - EMLEEngine(const EMLEEngine &other); + PyQMEngine(const PyQMEngine &other); //! Assignment operator. - EMLEEngine &operator=(const EMLEEngine &other); + PyQMEngine &operator=(const PyQMEngine &other); //! Set the callback object. /*! \param callback A Python object that contains the callback function. */ - void setCallback(EMLECallback callback); + void setCallback(PyQMCallback callback); //! Get the callback object. /*! \returns A Python object that contains the callback function. */ - EMLECallback getCallback() const; + PyQMCallback getCallback() const; //! Get the lambda weighting factor. /*! \returns @@ -556,7 +563,7 @@ namespace SireOpenMM QMForce* createForce() const; private: - EMLECallback callback; + PyQMCallback callback; SireUnits::Dimension::Length cutoff; int neighbour_list_frequency; double lambda; @@ -570,13 +577,13 @@ namespace SireOpenMM }; } -Q_DECLARE_METATYPE(SireOpenMM::EMLECallback) -Q_DECLARE_METATYPE(SireOpenMM::EMLEForce) -Q_DECLARE_METATYPE(SireOpenMM::EMLEEngine) +Q_DECLARE_METATYPE(SireOpenMM::PyQMCallback) +Q_DECLARE_METATYPE(SireOpenMM::PyQMForce) +Q_DECLARE_METATYPE(SireOpenMM::PyQMEngine) -SIRE_EXPOSE_CLASS(SireOpenMM::EMLECallback) -SIRE_EXPOSE_CLASS(SireOpenMM::EMLEForce) -SIRE_EXPOSE_CLASS(SireOpenMM::EMLEEngine) +SIRE_EXPOSE_CLASS(SireOpenMM::PyQMCallback) +SIRE_EXPOSE_CLASS(SireOpenMM::PyQMForce) +SIRE_EXPOSE_CLASS(SireOpenMM::PyQMEngine) SIRE_END_HEADER diff --git a/wrapper/Convert/SireOpenMM/qmmm.cpp b/wrapper/Convert/SireOpenMM/qmmm.cpp index 227c92695..e73844a65 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.cpp +++ b/wrapper/Convert/SireOpenMM/qmmm.cpp @@ -32,7 +32,6 @@ using namespace SireBase; using namespace SireOpenMM; -using namespace SireStream; ///////// ///////// Implementation of QMForce diff --git a/wrapper/Convert/SireOpenMM/qmmm.h b/wrapper/Convert/SireOpenMM/qmmm.h index f7108c1ad..ba662949b 100644 --- a/wrapper/Convert/SireOpenMM/qmmm.h +++ b/wrapper/Convert/SireOpenMM/qmmm.h @@ -32,17 +32,10 @@ #include "OpenMM.h" #include "openmm/Force.h" -#include - -#include -#include - #include "sireglobal.h" #include "SireBase/property.h" -#include "SireUnits/dimensions.h" - SIRE_BEGIN_HEADER namespace SireOpenMM diff --git a/wrapper/Convert/SireOpenMM/register_extras.cpp b/wrapper/Convert/SireOpenMM/register_extras.cpp index 998fc1301..1a18f9497 100644 --- a/wrapper/Convert/SireOpenMM/register_extras.cpp +++ b/wrapper/Convert/SireOpenMM/register_extras.cpp @@ -51,7 +51,7 @@ namespace SireOpenMM bp::converter::registry::insert(&extract_swig_wrapped_pointer, bp::type_id()); bp::converter::registry::insert(&extract_swig_wrapped_pointer, bp::type_id()); - // A tuple return type container for EMLECallback. (Energy, QM forces, MM forces) + // A tuple return type container for the PyQMCallback. (Energy, QM forces, MM forces) bp::register_tuple>, QVector>>>(); // Dictionary for mapping link atoms to QM and MM2 atoms. @@ -59,7 +59,7 @@ namespace SireOpenMM register_dict>(); register_dict>>(); - // A tuple for passing link atom information to EMLEEngine. + // A tuple for passing link atom information to PyQMEngine. bp::register_tuple, QMap>>>(); } } diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index a8c83bed0..79438b42b 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -47,7 +47,7 @@ #include "tostring.h" #include "openmmmolecule.h" -#include "emle.h" +#include "pyqm.h" #include diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 15e9314c9..f77f51069 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -19,8 +19,8 @@ "OpenMMMetaData", "SOMMContext", "QMEngine", - "EMLECallback", - "EMLEEngine", + "PyQMCallback", + "PyQMEngine", ] try: @@ -100,8 +100,8 @@ def smarts_to_rdkit(*args, **kwargs): PerturbableOpenMMMolecule, OpenMMMetaData, QMEngine, - EMLECallback, - EMLEEngine, + PyQMCallback, + PyQMEngine, ) from ..._pythonize import _pythonize @@ -112,8 +112,8 @@ def smarts_to_rdkit(*args, **kwargs): PerturbableOpenMMMolecule, OpenMMMetaData, QMEngine, - EMLECallback, - EMLEEngine, + PyQMCallback, + PyQMEngine, ], delete_old=True, ) From ade5d791a9ed1a792a4d25a78cb47d12ad9cb395 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 21 Jun 2024 09:24:19 +0100 Subject: [PATCH 307/468] Create a derived EMLEEngine class with EMLE specific attributes. --- src/sire/qm/__init__.py | 1 + src/sire/qm/_emle.py | 90 ++++++++++++++++++++--------------------- 2 files changed, 44 insertions(+), 47 deletions(-) diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index aafeeb448..f88fa8454 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -3,6 +3,7 @@ from ._emle import emle from ._utils import _zero_charge as zero_charge + def create_engine( mols, qm_atoms, diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index ff0c20753..57f864718 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -6,55 +6,51 @@ _use_new_api() -_PyQMEngine = _Convert._SireOpenMM.PyQMEngine +class EMLEEngine(_Convert._SireOpenMM.PyQMEngine): + """A class to enable use of EMLE as a QM engine.""" + + def get_forces(self): + """ + Get the OpenMM forces for this engine. The first force is the actual + EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic + embedding force. The second is a null CustomBondForce that can be used to + add a "lambda_emle" global parameter to a context to allow the force to be + scaled. + + Returns + ------- + + emle_force : openmm.Force + The EMLE force object to compute the electrostatic embedding force. + + interpolation_force : openmm.CustomBondForce + A null CustomBondForce object that can be used to add a "lambda_emle" + global parameter to an OpenMM context. This allows the electrostatic + embedding force to be scaled. + """ + + from copy import deepcopy as _deepcopy + from openmm import CustomBondForce as _CustomBondForce + + # Create a dynamics object for the QM region. + d = self._mols["property is_perturbable"].dynamics( + timestep="1fs", + constraint="none", + platform="cpu", + qm_engine=self, + ) -# Monkey-patch to get the underlying OpenMM force of the EMLE engine. -def _get_openmm_forces(self): - """ - Get the OpenMM forces for this engine. The first force is the actual - EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic - embedding force. The second is a null CustomBondForce that can be used to - add a "lambda_emle" global parameter to a context to allow the force to be - scaled. - - Returns - ------- - - emle_force : openmm.Force - The EMLE force object to compute the electrostatic embedding force. - - interpolation_force : openmm.CustomBondForce - A null CustomBondForce object that can be used to add a "lambda_emle" - global parameter to an OpenMM context. This allows the electrostatic - embedding force to be scaled. - """ - - from copy import deepcopy as _deepcopy - from openmm import CustomBondForce as _CustomBondForce - - # Create a dynamics object for the QM region. - d = self._mols["property is_perturbable"].dynamics( - timestep="1fs", - constraint="none", - platform="cpu", - qm_engine=self, - ) - - # Get the OpenMM EMLE force. - emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) - - # Create a null CustomBondForce to add the EMLE interpolation - # parameter. - interpolation_force = _CustomBondForce("") - interpolation_force.addGlobalParameter("lambda_emle", 1.0) - - # Return the forces. - return emle_force, interpolation_force + # Get the OpenMM EMLE force. + emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) + # Create a null CustomBondForce to add the EMLE interpolation + # parameter. + interpolation_force = _CustomBondForce("") + interpolation_force.addGlobalParameter("lambda_emle", 1.0) -# Bind the monkey-patched function to the PyQMEngine. -_PyQMEngine.get_forces = _get_openmm_forces + # Return the forces. + return emle_force, interpolation_force def emle( @@ -97,7 +93,7 @@ def emle( Returns ------- - engine : sire.legacy.Convert._SireOpenMM.PyQMEngine + engine : sire.qm.EMLEEngine The EMLE engine object. """ @@ -160,7 +156,7 @@ def emle( map = _create_map(map) # Create the EMLE engine. - engine = _PyQMEngine( + engine = EMLEEngine( calculator, "_sire_callback", cutoff, From f8d993ae4be39a69067c17c3593ea52721b575d9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 21 Jun 2024 09:46:33 +0100 Subject: [PATCH 308/468] Add test for indirect method of creating an EMLE engine. --- src/sire/qm/__init__.py | 41 ++++++++++++++------------- src/sire/qm/_emle.py | 4 --- tests/qm/{test_emle.py => test_qm.py} | 39 +++++++++++++++++++++++-- 3 files changed, 59 insertions(+), 25 deletions(-) rename tests/qm/{test_emle.py => test_qm.py} (89%) diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index f88fa8454..c598799c6 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -1,4 +1,10 @@ -__all__ = ["emle"] +__all__ = ["create_engine", "emle", "zero_charge"] + +from .. import use_new_api as _use_new_api + +_use_new_api() + +from ..legacy import Convert as _Convert from ._emle import emle from ._utils import _zero_charge as zero_charge @@ -8,14 +14,14 @@ def create_engine( mols, qm_atoms, py_object, - name=None, + callback=None, cutoff="7.5A", neighbourlist_update_frequency=20, redistribute_charge=False, map=None, ): """ - Create a QM engine object to allow QM/MM simulations using sire.mol.dynamics. + Create a QM engine to that can be used for QM/MM simulations with sire.mol.dynamics. Parameters ---------- @@ -30,10 +36,11 @@ def create_engine( py_object : object The Python object that will contains the callback for the QM calculation. + This can be a class instance with a "callback" method, or a callable. - name : str, optional, default=None - The name of the callback method. If None, then the py_object is assumed to - be a callable. + callback : str, optional, default=None + The name of the callback. If None, then the py_object is assumed to + be a callable, i.e. it is itself the callback. cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. @@ -71,17 +78,13 @@ def create_engine( except: raise ValueError("Unable to select 'qm_atoms' from 'mols'") - from inspect import isclass, isfunction - - if isclass(py_object): - if name is None: - raise ValueError("name must be provided if 'py_object' is a class.") - if not hasattr(py_object, name): - raise ValueError(f"'py_object' does not have a method called '{name}'.") - elif isfunction(py_object): - name = "" + if callback is not None: + if not isinstance(callback, str): + raise TypeError("'callback' must be of type 'str'") + if not hasattr(py_object, callback): + raise ValueError(f"'py_object' does not have a method called '{callback}'.") else: - raise ValueError("'py_object' must be a class or function.") + callback = "" if not isinstance(cutoff, (str, _Units.GeneralUnit)): raise TypeError( @@ -112,9 +115,9 @@ def create_engine( map = _create_map(map) # Create the EMLE engine. - engine = _PyQMEngine( - calculator, - name, + engine = _Convert.PyQMEngine( + py_object, + callback, cutoff, neighbourlist_update_frequency, ) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 57f864718..fa84c5a1b 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -2,10 +2,6 @@ from ..legacy import Convert as _Convert -from .. import use_new_api as _use_new_api - -_use_new_api() - class EMLEEngine(_Convert._SireOpenMM.PyQMEngine): """A class to enable use of EMLE as a QM engine.""" diff --git a/tests/qm/test_emle.py b/tests/qm/test_qm.py similarity index 89% rename from tests/qm/test_emle.py rename to tests/qm/test_qm.py index 82a254e2f..9316dc1e7 100644 --- a/tests/qm/test_emle.py +++ b/tests/qm/test_qm.py @@ -172,7 +172,7 @@ def test_charge_redistribution(): @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") @pytest.mark.parametrize("selection", ["molidx 0", "resname ALA"]) -def test_interpolate(ala_mols, selection): +def test_emle_interpolate(ala_mols, selection): """ Make sure that lambda interpolation between pure MM and EMLE potentials works. """ @@ -219,7 +219,7 @@ def test_interpolate(ala_mols, selection): @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") @pytest.mark.skipif(not has_openmm_ml, reason="openmm-ml is not installed") -def test_openmm_ml(ala_mols): +def test_emle_openmm_ml(ala_mols): """ Make sure that the EMLE engine can be used with OpenMM-ML. """ @@ -317,3 +317,38 @@ def test_openmm_ml(ala_mols): # Make sure the energies are close. assert np.isclose(nrg_openmm, nrg_sire, rtol=1e-3) + + +@pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") +def test_emle_indirect(ala_mols): + """ + Make sure that a QM/MM dynamics object can be created using the indirect + setup for EMLE engines. + """ + + import openmm + import sire as sr + + # Create a local copy of the test system. + mols = ala_mols.clone() + + # Create an EMLE calculator. + calculator = EMLECalculator(backend="torchani", device="cpu") + + # Create an EMLE engine bound to the calculator. + emle_mols, engine = sr.qm.create_engine( + mols, mols[0], calculator, callback="_sire_callback" + ) + + # Create a QM/MM capable dynamics object. + d = emle_mols.dynamics( + timestep="1fs", + constraint="none", + qm_engine=engine, + cutoff_type="pme", + cutoff="7.5 A", + platform="cpu", + ) + + # Get the potential energy. This will fail if the callback can't be found. + d.current_potential_energy() From ec482d2db1ebfac83b0f2b5870a0241fe82ec47f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 21 Jun 2024 09:56:47 +0100 Subject: [PATCH 309/468] Document the form of the callback function. --- src/sire/qm/__init__.py | 13 +++++++++++-- wrapper/Convert/SireOpenMM/pyqm.h | 8 ++++++-- 2 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index c598799c6..73adb9bf3 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -40,7 +40,16 @@ def create_engine( callback : str, optional, default=None The name of the callback. If None, then the py_object is assumed to - be a callable, i.e. it is itself the callback. + be a callable, i.e. it is itself the callback. The callback should + take the following arguments: + - numbers_qm: A list of atomic numbers for the atoms in the QM region. + - charges_mm: A list of the MM charges in mod electron charge. + - xyz_qm: A list of positions for the atoms in the QM region in Angstrom. + - xyz_mm: A list of positions for the atoms in the MM region in Angstrom. + In addition, it should return a tuple containing the following: + - energy: The QM energy in kJ/mol. + - forces_qm: A list of forces on the atoms in the QM region in kJ/mol/nm. + - forces_mm: A list of forces on the atoms in the MM region in kJ/mol/nm. cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. @@ -114,7 +123,7 @@ def create_engine( raise TypeError("'map' must be of type 'dict'") map = _create_map(map) - # Create the EMLE engine. + # Create the QM engine. engine = _Convert.PyQMEngine( py_object, callback, diff --git a/wrapper/Convert/SireOpenMM/pyqm.h b/wrapper/Convert/SireOpenMM/pyqm.h index 50c44122c..53df067cc 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.h +++ b/wrapper/Convert/SireOpenMM/pyqm.h @@ -86,8 +86,12 @@ namespace SireOpenMM The name of a callback method that take the following arguments: - numbers_qm: A list of atomic numbers for the atoms in the ML region. - charges_mm: A list of the MM charges in mod electron charge. - - xyz_qm: A vector of positions for the atoms in the ML region in Angstrom. - - xyz_mm: A vector of positions for the atoms in the MM region in Angstrom. + - xyz_qm: A list of positions for the atoms in the ML region in Angstrom. + - xyz_mm: A list of positions for the atoms in the MM region in Angstrom. + The callback shoul return a tuple containing: + - The energy in kJ/mol. + - A list of forces for the QM atoms in kJ/mol/nm. + - A list of forces for the MM atoms in kJ/mol/nm. If empty, then the object is assumed to be a callable. */ PyQMCallback(bp::object, QString name=""); From f20776433f4749cb69fc67e66e6dffcc2ea115a9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 21 Jun 2024 12:44:22 +0100 Subject: [PATCH 310/468] Add support for QM/MM with mechanical embedding. --- src/sire/qm/__init__.py | 16 +- src/sire/qm/_emle.py | 3 +- src/sire/qm/_utils.py | 7 +- .../Convert/SireOpenMM/PyQMCallback.pypp.cpp | 2 +- .../Convert/SireOpenMM/PyQMEngine.pypp.cpp | 27 +- wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp | 14 +- wrapper/Convert/SireOpenMM/active_headers.h | 4 +- wrapper/Convert/SireOpenMM/pyqm.cpp | 311 ++++++++++-------- wrapper/Convert/SireOpenMM/pyqm.h | 28 ++ 9 files changed, 262 insertions(+), 150 deletions(-) diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index 73adb9bf3..d9b0917c6 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -17,6 +17,7 @@ def create_engine( callback=None, cutoff="7.5A", neighbourlist_update_frequency=20, + mechanical_embedding=False, redistribute_charge=False, map=None, ): @@ -57,6 +58,13 @@ def create_engine( neighbourlist_update_frequency : int, optional, default=20 The frequency with which to update the neighbourlist. + mechanical_embedding: bool, optional, default=False + Whether to use mechanical embedding. If True, then electrostatics will + be computed at the MM level by OpenMM. Note that the signature of the + callback does not change when mechanical embedding is used, i.e. it will + take an empty lists for the MM charges and positions and return an empty + list of forces for the MM region. + redistribute_charge : bool Whether to redistribute charge of the QM atoms to ensure that the total charge of the QM region is an integer. Excess charge is redistributed @@ -115,6 +123,9 @@ def create_engine( if neighbourlist_update_frequency < 0: raise ValueError("'neighbourlist_update_frequency' must be >= 0") + if not isinstance(mechanical_embedding, bool): + raise TypeError("'mechanical_embedding' must be of type 'bool'") + if not isinstance(redistribute_charge, bool): raise TypeError("'redistribute_charge' must be of type 'bool'") @@ -129,6 +140,7 @@ def create_engine( callback, cutoff, neighbourlist_update_frequency, + mechanical_embedding, ) from ._utils import ( @@ -156,7 +168,9 @@ def create_engine( ) # Create the merged molecule. - qm_mols = _create_merged_mols(qm_mol_to_atoms, mm1_indices, map) + qm_mols = _create_merged_mols( + qm_mol_to_atoms, mm1_indices, mechanical_embedding, map + ) # Update the molecule in the system. mols.update(qm_mols) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index fa84c5a1b..9aedad47c 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -157,6 +157,7 @@ def emle( "_sire_callback", cutoff, neighbourlist_update_frequency, + False, ) from ._utils import ( @@ -184,7 +185,7 @@ def emle( ) # Create the merged molecule. - qm_mols = _create_merged_mols(qm_mol_to_atoms, mm1_indices, map) + qm_mols = _create_merged_mols(qm_mol_to_atoms, mm1_indices, False, map) # Update the molecule in the system. mols.update(qm_mols) diff --git a/src/sire/qm/_utils.py b/src/sire/qm/_utils.py index 655639a0e..5dfe95455 100644 --- a/src/sire/qm/_utils.py +++ b/src/sire/qm/_utils.py @@ -510,7 +510,7 @@ def _get_link_atoms(mols, qm_mol_to_atoms, map): return mm1_to_qm, mm1_to_mm2, bond_scale_factors, mm1_indices -def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): +def _create_merged_mols(qm_mol_to_atoms, mm1_indices, mechanical_embedding, map): """ Internal helper function to create a merged molecule from the QM molecule. @@ -524,6 +524,9 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): mm1_indices: [[sire.legacy.Mol.AtomIdx]] A list of lists of MM1 atom indices. + mechanical_embedding: bool + Whether mechanical embedding is being used. + map: sire.legacy.Base.PropertyMap The property map for the system. @@ -668,7 +671,7 @@ def _create_merged_mols(qm_mol_to_atoms, mm1_indices, map): edit_mol = edit_mol.remove_property(prop).molecule() # Charge. - elif prop == charge_prop: + elif not mechanical_embedding and prop == charge_prop: edit_mol = edit_mol.set_property( prop + "0", qm_mol.property(prop) ).molecule() diff --git a/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp index f4089d479..d31a885de 100644 --- a/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp @@ -65,7 +65,7 @@ void register_PyQMCallback_class(){ typedef bp::class_< SireOpenMM::PyQMCallback > PyQMCallback_exposer_t; PyQMCallback_exposer_t PyQMCallback_exposer = PyQMCallback_exposer_t( "PyQMCallback", "A callback wrapper class to interface with external QM engines\nvia the CustomCPPForceImpl.", bp::init< >("Default constructor.") ); bp::scope PyQMCallback_scope( PyQMCallback_exposer ); - PyQMCallback_exposer.def( bp::init< bp::api::object, bp::optional< QString > >(( bp::arg("arg0"), bp::arg("name")="" ), "Constructor\nPar:am py_object\nA Python object that contains the callback function.\n\nPar:am name\nThe name of a callback method that take the following arguments:\n- numbers_qm: A list of atomic numbers for the atoms in the ML region.\n- charges_mm: A list of the MM charges in mod electron charge.\n- xyz_qm: A vector of positions for the atoms in the ML region in Angstrom.\n- xyz_mm: A vector of positions for the atoms in the MM region in Angstrom.\nIf empty, then the object is assumed to be a callable.\n") ); + PyQMCallback_exposer.def( bp::init< bp::api::object, bp::optional< QString > >(( bp::arg("arg0"), bp::arg("name")="" ), "Constructor\nPar:am py_object\nA Python object that contains the callback function.\n\nPar:am name\nThe name of a callback method that take the following arguments:\n- numbers_qm: A list of atomic numbers for the atoms in the ML region.\n- charges_mm: A list of the MM charges in mod electron charge.\n- xyz_qm: A list of positions for the atoms in the ML region in Angstrom.\n- xyz_mm: A list of positions for the atoms in the MM region in Angstrom.\nThe callback shoul return a tuple containing:\n- The energy in kJmol.\n- A list of forces for the QM atoms in kJmolnm.\n- A list of forces for the MM atoms in kJmolnm.\nIf empty, then the object is assumed to be a callable.\n") ); { //::SireOpenMM::PyQMCallback::call typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMCallback::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; diff --git a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp index c68954bd8..1b2780dfc 100644 --- a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp @@ -63,7 +63,7 @@ void register_PyQMEngine_class(){ typedef bp::class_< SireOpenMM::PyQMEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > PyQMEngine_exposer_t; PyQMEngine_exposer_t PyQMEngine_exposer = PyQMEngine_exposer_t( "PyQMEngine", "", bp::init< >("Default constructor.") ); bp::scope PyQMEngine_scope( PyQMEngine_exposer ); - PyQMEngine_exposer.def( bp::init< bp::api::object, bp::optional< QString, SireUnits::Dimension::Length, int, double > >(( bp::arg("arg0"), bp::arg("method")="", bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nA Python object.\n\nPar:am name\nThe name of the callback method. If empty, then the object is\nassumed to be a callable.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); + PyQMEngine_exposer.def( bp::init< bp::api::object, bp::optional< QString, SireUnits::Dimension::Length, int, bool, double > >(( bp::arg("arg0"), bp::arg("method")="", bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("is_mechanical")=(bool)(false), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nA Python object.\n\nPar:am name\nThe name of the callback method. If empty, then the object is\nassumed to be a callable.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); PyQMEngine_exposer.def( bp::init< SireOpenMM::PyQMEngine const & >(( bp::arg("other") ), "Copy constructor.") ); { //::SireOpenMM::PyQMEngine::call @@ -125,6 +125,18 @@ void register_PyQMEngine_class(){ , bp::release_gil_policy() , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); + } + { //::SireOpenMM::PyQMEngine::getIsMechanical + + typedef bool ( ::SireOpenMM::PyQMEngine::*getIsMechanical_function_type)( ) const; + getIsMechanical_function_type getIsMechanical_function_value( &::SireOpenMM::PyQMEngine::getIsMechanical ); + + PyQMEngine_exposer.def( + "getIsMechanical" + , getIsMechanical_function_value + , bp::release_gil_policy() + , "Get the mechanical embedding flag.\nReturn:s\nA flag to indicate if mechanical embedding is being used.\n" ); + } { //::SireOpenMM::PyQMEngine::getLambda @@ -250,6 +262,19 @@ void register_PyQMEngine_class(){ , bp::release_gil_policy() , "Set the QM cutoff distance.\nPar:am cutoff\nThe QM cutoff distance.\n" ); + } + { //::SireOpenMM::PyQMEngine::setIsMechanical + + typedef void ( ::SireOpenMM::PyQMEngine::*setIsMechanical_function_type)( bool ) ; + setIsMechanical_function_type setIsMechanical_function_value( &::SireOpenMM::PyQMEngine::setIsMechanical ); + + PyQMEngine_exposer.def( + "setIsMechanical" + , setIsMechanical_function_value + , ( bp::arg("is_mechanical") ) + , bp::release_gil_policy() + , "Set the mechanical embedding flag.\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n" ); + } { //::SireOpenMM::PyQMEngine::setLambda diff --git a/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp index ad1a17d2a..1f25099bc 100644 --- a/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp @@ -65,7 +65,7 @@ void register_PyQMForce_class(){ typedef bp::class_< SireOpenMM::PyQMForce, bp::bases< SireOpenMM::QMForce > > PyQMForce_exposer_t; PyQMForce_exposer_t PyQMForce_exposer = PyQMForce_exposer_t( "PyQMForce", "", bp::init< >("Default constructor.") ); bp::scope PyQMForce_scope( PyQMForce_exposer ); - PyQMForce_exposer.def( bp::init< SireOpenMM::PyQMCallback, SireUnits::Dimension::Length, int, double, QVector< int >, QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, QVector< int >, QVector< int >, QVector< double > >(( bp::arg("callback"), bp::arg("cutoff"), bp::arg("neighbour_list_frequency"), bp::arg("lambda"), bp::arg("atoms"), bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors"), bp::arg("mm2_atoms"), bp::arg("numbers"), bp::arg("charges") ), "Constructor.\nPar:am callback\nThe PyQMCallback object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n\nPar:am atoms\nA vector of atom indices for the QM region.\n\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\nPar:am mm2_atoms\nA vector of MM2 atom indices.\n\nPar:am numbers\nA vector of atomic charges for all atoms in the system.\n\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n") ); + PyQMForce_exposer.def( bp::init< SireOpenMM::PyQMCallback, SireUnits::Dimension::Length, int, bool, double, QVector< int >, QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, QVector< int >, QVector< int >, QVector< double > >(( bp::arg("callback"), bp::arg("cutoff"), bp::arg("neighbour_list_frequency"), bp::arg("is_mechanical"), bp::arg("lambda"), bp::arg("atoms"), bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors"), bp::arg("mm2_atoms"), bp::arg("numbers"), bp::arg("charges") ), "Constructor.\nPar:am callback\nThe PyQMCallback object.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n\nPar:am atoms\nA vector of atom indices for the QM region.\n\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\nPar:am mm2_atoms\nA vector of MM2 atom indices.\n\nPar:am numbers\nA vector of atomic charges for all atoms in the system.\n\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n") ); PyQMForce_exposer.def( bp::init< SireOpenMM::PyQMForce const & >(( bp::arg("other") ), "Copy constructor.") ); { //::SireOpenMM::PyQMForce::call @@ -127,6 +127,18 @@ void register_PyQMForce_class(){ , bp::release_gil_policy() , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); + } + { //::SireOpenMM::PyQMForce::getIsMechanical + + typedef bool ( ::SireOpenMM::PyQMForce::*getIsMechanical_function_type)( ) const; + getIsMechanical_function_type getIsMechanical_function_value( &::SireOpenMM::PyQMForce::getIsMechanical ); + + PyQMForce_exposer.def( + "getIsMechanical" + , getIsMechanical_function_value + , bp::release_gil_policy() + , "Get the mechanical embedding flag.\nReturn:s\nA flag to indicate if mechanical embedding is being used.\n" ); + } { //::SireOpenMM::PyQMForce::getLambda diff --git a/wrapper/Convert/SireOpenMM/active_headers.h b/wrapper/Convert/SireOpenMM/active_headers.h index b867c53c5..4ea67d542 100644 --- a/wrapper/Convert/SireOpenMM/active_headers.h +++ b/wrapper/Convert/SireOpenMM/active_headers.h @@ -1,10 +1,10 @@ #ifndef ACTIVE_HEADERS_H #define ACTIVE_HEADERS_H -#define QT_NO_SIGNALS_SLOTS_KEYWORDS = 1 - #ifdef GCCXML_PARSE +#define QT_NO_SIGNALS_SLOTS_KEYWORDS = 1 + #include "lambdalever.h" #include "openmmminimise.h" #include "openmmmolecule.h" diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index 087ad889e..718fca995 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -238,6 +238,7 @@ PyQMForce::PyQMForce( PyQMCallback callback, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, + bool is_mechanical, double lambda, QVector atoms, QMap mm1_to_qm, @@ -249,6 +250,7 @@ PyQMForce::PyQMForce( callback(callback), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), + is_mechanical(is_mechanical), lambda(lambda), atoms(atoms), mm1_to_qm(mm1_to_qm), @@ -264,6 +266,7 @@ PyQMForce::PyQMForce(const PyQMForce &other) : callback(other.callback), cutoff(other.cutoff), neighbour_list_frequency(other.neighbour_list_frequency), + is_mechanical(other.is_mechanical), lambda(other.lambda), atoms(other.atoms), mm1_to_qm(other.mm1_to_qm), @@ -330,6 +333,11 @@ int PyQMForce::getNeighbourListFrequency() const return this->neighbour_list_frequency; } +bool PyQMForce::getIsMechanical() const +{ + return this->is_mechanical;; +} + QVector PyQMForce::getAtoms() const { return this->atoms; @@ -555,55 +563,95 @@ double PyQMForceImpl::computeForce( } center /= i; - // Initialise a vector to hold the current positions for the MM atoms. - // and virtual point charges. + // Initialise a vector to hold the current positions and charges for the MM atoms. QVector> xyz_mm; - QVector> xyz_virtual; - - // Initialise a vector to hold the charges for the MM atoms and virtual - // point charges. QVector charges_mm; - QVector charges_virtual; // Initialise a list to hold the indices of the MM atoms. QVector idx_mm; - // Manually work out the MM point charges and build the neigbour list. - if (not this->is_neighbour_list or this->step_count % this->neighbour_list_frequency == 0) + // Store the current number of MM atoms. + unsigned int num_mm = 0; + + // If we are using electrostatic embedding, the work out the MM point charges and + // build the neighbour list. + if (not this->owner.getIsMechanical()) { - // Clear the neighbour list. - if (this->is_neighbour_list) - { - this->neighbour_list.clear(); - } + // Initialise a vector to hold the current positions and charges for the virtual + // point charges. + QVector> xyz_virtual; + QVector charges_virtual; - i = 0; - // Loop over all of the OpenMM positions. - for (const auto &pos : positions) + // Manually work out the MM point charges and build the neigbour list. + if (not this->is_neighbour_list or this->step_count % this->neighbour_list_frequency == 0) { - // Exclude QM atoms or link atoms, which are handled later. - if (not qm_atoms.contains(i) and - not mm1_to_mm2.contains(i) and - not mm2_atoms.contains(i)) + // Clear the neighbour list. + if (this->is_neighbour_list) { - // Store the MM atom position in Sire Vector format. - Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + this->neighbour_list.clear(); + } - // Loop over all of the QM atoms. - for (const auto &qm_vec : xyz_qm_vec) + i = 0; + // Loop over all of the OpenMM positions. + for (const auto &pos : positions) + { + // Exclude QM atoms or link atoms, which are handled later. + if (not qm_atoms.contains(i) and + not mm1_to_mm2.contains(i) and + not mm2_atoms.contains(i)) { - // Work out the distance between the current MM atom and QM atoms. - const auto dist = space.calcDist(mm_vec, qm_vec); + // Store the MM atom position in Sire Vector format. + Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); - // The current MM atom is within the neighbour list cutoff. - if (this->is_neighbour_list and dist < this->neighbour_list_cutoff) + // Loop over all of the QM atoms. + for (const auto &qm_vec : xyz_qm_vec) { - // Insert the MM atom index into the neighbour list. - this->neighbour_list.insert(i); + // Work out the distance between the current MM atom and QM atoms. + const auto dist = space.calcDist(mm_vec, qm_vec); + + // The current MM atom is within the neighbour list cutoff. + if (this->is_neighbour_list and dist < this->neighbour_list_cutoff) + { + // Insert the MM atom index into the neighbour list. + this->neighbour_list.insert(i); + } + + // The current MM atom is within the cutoff, add it. + if (dist < cutoff) + { + // Work out the minimum image position with respect to the + // reference position and add to the vector. + mm_vec = space.getMinimumImage(mm_vec, center); + xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[i]); + idx_mm.append(i); + + // Exit the inner loop. + break; + } } + } + // Update the atom index. + i++; + } + } + // Use the neighbour list. + else + { + // Loop over the MM atoms in the neighbour list. + for (const auto &idx : this->neighbour_list) + { + // Store the MM atom position in Sire Vector format. + Vector mm_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); + + // Loop over all of the QM atoms. + for (const auto &qm_vec : xyz_qm_vec) + { // The current MM atom is within the cutoff, add it. - if (dist < cutoff) + if (space.calcDist(mm_vec, qm_vec) < cutoff) { // Work out the minimum image position with respect to the // reference position and add to the vector. @@ -611,134 +659,101 @@ double PyQMForceImpl::computeForce( xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); // Add the charge and index. - charges_mm.append(this->owner.getCharges()[i]); - idx_mm.append(i); + charges_mm.append(this->owner.getCharges()[idx]); + idx_mm.append(idx); // Exit the inner loop. break; } } } - - // Update the atom index. - i++; - } - } - // Use the neighbour list. - else - { - // Loop over the MM atoms in the neighbour list. - for (const auto &idx : this->neighbour_list) - { - // Store the MM atom position in Sire Vector format. - Vector mm_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); - - // Loop over all of the QM atoms. - for (const auto &qm_vec : xyz_qm_vec) - { - // The current MM atom is within the cutoff, add it. - if (space.calcDist(mm_vec, qm_vec) < cutoff) - { - // Work out the minimum image position with respect to the - // reference position and add to the vector. - mm_vec = space.getMinimumImage(mm_vec, center); - xyz_mm.append(QVector({mm_vec[0], mm_vec[1], mm_vec[2]})); - - // Add the charge and index. - charges_mm.append(this->owner.getCharges()[idx]); - idx_mm.append(idx); - - // Exit the inner loop. - break; - } - } } - } - // Handle link atoms via the Charge Shift method. - // See: https://www.ks.uiuc.edu/Research/qmmm - for (const auto &idx: mm1_to_mm2.keys()) - { - // Get the QM atom to which the current MM atom is bonded. - const auto qm_idx = mm1_to_qm[idx]; - - // Store the MM1 position in Sire Vector format, along with the - // position of the QM atom to which it is bonded. - Vector mm1_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); - Vector qm_vec(10*positions[qm_idx][0], 10*positions[qm_idx][1], 10*positions[qm_idx][2]); - - // Work out the minimum image positions with respect to the reference position. - mm1_vec = space.getMinimumImage(mm1_vec, center); - qm_vec = space.getMinimumImage(qm_vec, center); - - // Work out the position of the link atom. Here we use a bond length - // scale factor taken from the MM bond potential, i.e. R0(QM-L) / R0(QM-MM1), - // where R0(QM-L) is the equilibrium bond length for the QM and link (L) - // elements, and R0(QM-MM1) is the equilibrium bond length for the QM - // and MM1 elements. - const auto link_vec = qm_vec + bond_scale_factors[idx]*(mm1_vec - qm_vec); - - // Add to the QM positions. - xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); - - // Add the MM1 index to the QM atoms vector. - qm_atoms.append(qm_idx); - - // Append a hydrogen element to the numbers vector. - numbers.append(1); - - // Store the number of MM2 atoms. - const auto num_mm2 = mm1_to_mm2[idx].size(); - - // Store the fractional charge contribution to the MM2 atoms and - // virtual point charges. - const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; - - // Loop over the MM2 atoms and perform charge shifting. Here the MM1 - // charge is redistributed over the MM2 atoms and two virtual point - // charges are added either side of the MM2 atoms in order to preserve - // the MM1-MM2 dipole. - for (const auto& mm2_idx : mm1_to_mm2[idx]) + // Handle link atoms via the Charge Shift method. + // See: https://www.ks.uiuc.edu/Research/qmmm + for (const auto &idx: mm1_to_mm2.keys()) { - // Store the MM2 position in Sire Vector format. - Vector mm2_vec(10*positions[mm2_idx][0], 10*positions[mm2_idx][1], 10*positions[mm2_idx][2]); + // Get the QM atom to which the current MM atom is bonded. + const auto qm_idx = mm1_to_qm[idx]; + + // Store the MM1 position in Sire Vector format, along with the + // position of the QM atom to which it is bonded. + Vector mm1_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); + Vector qm_vec(10*positions[qm_idx][0], 10*positions[qm_idx][1], 10*positions[qm_idx][2]); + + // Work out the minimum image positions with respect to the reference position. + mm1_vec = space.getMinimumImage(mm1_vec, center); + qm_vec = space.getMinimumImage(qm_vec, center); + + // Work out the position of the link atom. Here we use a bond length + // scale factor taken from the MM bond potential, i.e. R0(QM-L) / R0(QM-MM1), + // where R0(QM-L) is the equilibrium bond length for the QM and link (L) + // elements, and R0(QM-MM1) is the equilibrium bond length for the QM + // and MM1 elements. + const auto link_vec = qm_vec + bond_scale_factors[idx]*(mm1_vec - qm_vec); + + // Add to the QM positions. + xyz_qm.append(QVector({link_vec[0], link_vec[1], link_vec[2]})); + + // Add the MM1 index to the QM atoms vector. + qm_atoms.append(qm_idx); + + // Append a hydrogen element to the numbers vector. + numbers.append(1); + + // Store the number of MM2 atoms. + const auto num_mm2 = mm1_to_mm2[idx].size(); + + // Store the fractional charge contribution to the MM2 atoms and + // virtual point charges. + const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; + + // Loop over the MM2 atoms and perform charge shifting. Here the MM1 + // charge is redistributed over the MM2 atoms and two virtual point + // charges are added either side of the MM2 atoms in order to preserve + // the MM1-MM2 dipole. + for (const auto& mm2_idx : mm1_to_mm2[idx]) + { + // Store the MM2 position in Sire Vector format. + Vector mm2_vec(10*positions[mm2_idx][0], 10*positions[mm2_idx][1], 10*positions[mm2_idx][2]); - // Work out the minimum image position with respect to the reference position. - mm2_vec = space.getMinimumImage(mm2_vec, center); + // Work out the minimum image position with respect to the reference position. + mm2_vec = space.getMinimumImage(mm2_vec, center); - // Add to the MM positions. - xyz_mm.append(QVector({mm2_vec[0], mm2_vec[1], mm2_vec[2]})); + // Add to the MM positions. + xyz_mm.append(QVector({mm2_vec[0], mm2_vec[1], mm2_vec[2]})); - // Add the charge and index. - charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); - idx_mm.append(mm2_idx); + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); + idx_mm.append(mm2_idx); - // Now add the virtual point charges. + // Now add the virtual point charges. - // Compute the normal vector from the MM1 to MM2 atom. - const auto normal = (mm2_vec - mm1_vec).normalise(); + // Compute the normal vector from the MM1 to MM2 atom. + const auto normal = (mm2_vec - mm1_vec).normalise(); - // Positive direction. (Away from MM1 atom.) - auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; - xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); - charges_virtual.append(-frac_charge); + // Positive direction. (Away from MM1 atom.) + auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; + xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_virtual.append(-frac_charge); - // Negative direction (Towards MM1 atom.) - xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; - xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); - charges_virtual.append(frac_charge); + // Negative direction (Towards MM1 atom.) + xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; + xyz_virtual.append(QVector({xyz[0], xyz[1], xyz[2]})); + charges_virtual.append(frac_charge); + } } - } - // Store the current number of MM atoms. - const auto num_mm = xyz_mm.size(); + // Store the current number of MM atoms. + num_mm = xyz_mm.size(); - // If there are any virtual point charges, then add to the MM positions - // and charges. - if (xyz_virtual.size() > 0) - { - xyz_mm.append(xyz_virtual); - charges_mm.append(charges_virtual); + // If there are any virtual point charges, then add to the MM positions + // and charges. + if (xyz_virtual.size() > 0) + { + xyz_mm.append(xyz_virtual); + charges_mm.append(charges_virtual); + } } // Call the callback. @@ -852,11 +867,13 @@ PyQMEngine::PyQMEngine( QString name, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, + bool is_mechanical, double lambda) : ConcreteProperty(), callback(py_object, name), cutoff(cutoff), neighbour_list_frequency(neighbour_list_frequency), + is_mechanical(is_mechanical), lambda(lambda) { // Register the serialization proxies. @@ -880,6 +897,7 @@ PyQMEngine::PyQMEngine(const PyQMEngine &other) : callback(other.callback), cutoff(other.cutoff), neighbour_list_frequency(other.neighbour_list_frequency), + is_mechanical(other.is_mechanical), lambda(other.lambda), atoms(other.atoms), mm1_to_qm(other.mm1_to_qm), @@ -961,6 +979,16 @@ void PyQMEngine::setNeighbourListFrequency(int neighbour_list_frequency) this->neighbour_list_frequency = neighbour_list_frequency; } +bool PyQMEngine::getIsMechanical() const +{ + return this->is_mechanical; +} + +void PyQMEngine::setIsMechanical(bool is_mechanical) +{ + this->is_mechanical = is_mechanical; +} + QVector PyQMEngine::getAtoms() const { return this->atoms; @@ -1044,6 +1072,7 @@ QMForce* PyQMEngine::createForce() const this->callback, this->cutoff, this->neighbour_list_frequency, + this->is_mechanical, this->lambda, this->atoms, this->mm1_to_qm, diff --git a/wrapper/Convert/SireOpenMM/pyqm.h b/wrapper/Convert/SireOpenMM/pyqm.h index 53df067cc..402966dfe 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.h +++ b/wrapper/Convert/SireOpenMM/pyqm.h @@ -154,6 +154,9 @@ namespace SireOpenMM The frequency at which the neighbour list is updated. (Number of steps.) If zero, then no neighbour list is used. + \param is_mechanical + A flag to indicate if mechanical embedding is being used. + \param lambda The lambda weighting factor. This can be used to interpolate between potentials for end-state correction calculations. @@ -189,6 +192,7 @@ namespace SireOpenMM PyQMCallback callback, SireUnits::Dimension::Length cutoff, int neighbour_list_frequency, + bool is_mechanical, double lambda, QVector atoms, QMap mm1_to_qm, @@ -241,6 +245,12 @@ namespace SireOpenMM */ int getNeighbourListFrequency() const; + //! Get the mechanical embedding flag. + /*! \returns + A flag to indicate if mechanical embedding is being used. + */ + bool getIsMechanical() const; + //! Get the indices of the atoms in the QM region. /*! \returns A vector of atom indices for the QM region. @@ -326,6 +336,7 @@ namespace SireOpenMM PyQMCallback callback; SireUnits::Dimension::Length cutoff; int neighbour_list_frequency; + bool is_mechanical; double lambda; QVector atoms; QMap mm1_to_qm; @@ -382,6 +393,9 @@ namespace SireOpenMM The frequency at which the neighbour list is updated. (Number of steps.) If zero, then no neighbour list is used. + \param is_mechanical + A flag to indicate if mechanical embedding is being used. + \param lambda The lambda weighting factor. This can be used to interpolate between potentials for end-state correction calculations. @@ -391,6 +405,7 @@ namespace SireOpenMM QString method="", SireUnits::Dimension::Length cutoff=7.5*SireUnits::angstrom, int neighbour_list_frequency=20, + bool is_mechanical=false, double lambda=1.0 ); @@ -448,6 +463,18 @@ namespace SireOpenMM */ void setNeighbourListFrequency(int neighbour_list_frequency); + //! Get the mechanical embedding flag. + /*! \returns + A flag to indicate if mechanical embedding is being used. + */ + bool getIsMechanical() const; + + //! Set the mechanical embedding flag. + /*! \param is_mechanical + A flag to indicate if mechanical embedding is being used. + */ + void setIsMechanical(bool is_mechanical); + //! Get the indices of the atoms in the QM region. /*! \returns A vector of atom indices for the QM region. @@ -570,6 +597,7 @@ namespace SireOpenMM PyQMCallback callback; SireUnits::Dimension::Length cutoff; int neighbour_list_frequency; + bool is_mechanical; double lambda; QVector atoms; QMap mm1_to_qm; From 3759d413fd227a6d7a38be1ab9c13b203a80df65 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 21 Jun 2024 13:30:24 +0100 Subject: [PATCH 311/468] Whitespace trim. --- wrapper/Convert/SireOpenMM/pyqm.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index 718fca995..74db8513a 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -389,7 +389,6 @@ PyQMForce::call( namespace OpenMM { - class PyQMForceProxy : public SerializationProxy { public: PyQMForceProxy() : SerializationProxy("PyQMForce") From 643747cb1ccdc6bffa24b72d75519d5bd3d5defc Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 21 Jun 2024 13:30:44 +0100 Subject: [PATCH 312/468] Add QM/MM intro section and renumber other sections. --- doc/source/tutorial/index_partXX.rst | 7 +- doc/source/tutorial/partXX/01_intro.rst | 99 +++++++++++++++++++ .../partXX/{01_emle.rst => 02_emle.rst} | 22 ++--- .../partXX/{02_adp_pmf.rst => 03_adp_pmf.rst} | 0 ...{03_diels_alder.rst => 04_diels_alder.rst} | 0 5 files changed, 114 insertions(+), 14 deletions(-) create mode 100644 doc/source/tutorial/partXX/01_intro.rst rename doc/source/tutorial/partXX/{01_emle.rst => 02_emle.rst} (93%) rename doc/source/tutorial/partXX/{02_adp_pmf.rst => 03_adp_pmf.rst} (100%) rename doc/source/tutorial/partXX/{03_diels_alder.rst => 04_diels_alder.rst} (100%) diff --git a/doc/source/tutorial/index_partXX.rst b/doc/source/tutorial/index_partXX.rst index 7d20030a5..6587de731 100644 --- a/doc/source/tutorial/index_partXX.rst +++ b/doc/source/tutorial/index_partXX.rst @@ -15,6 +15,7 @@ QM/MM simulations using ``sire``. .. toctree:: :maxdepth: 1 - partXX/01_emle - partXX/02_adp_pmf - partXX/03_diels_alder + partXX/01_intro + partXX/02_emle + partXX/03_adp_pmf + partXX/04_diels_alder diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst new file mode 100644 index 000000000..03080cfca --- /dev/null +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -0,0 +1,99 @@ +============ +Introduction +============ + +The ``sire`` QM/MM implementation takes advantage of the new means of writing +`platform independent force calculations `_ +introduced in `OpenMM `_ 8.1. This allows us to interface +with any external package to modify atomic forces within the ``OpenMM`` context. +While OpenMM already directly supports ML/MM simulations via the `OpenMM-ML `_ +package, it is currently limited to specific backends and only supports mechanical +embedding. The ``sire`` QM/MM implementation provides a simple way to interface +with any external QM package using a simple Python callback. This approach is +designed with generarilty and flexibility in mind, rather than performance, +allowing a user to quickly prototype new ideas. + +Creating a QM engine +-------------------- + +In order to run QM/MM with ``sire``, we first need to create a QM engine. This +is passed as a keword argument to the ``dynamics`` function and is used to +perform the QM part of the calculation at each timestep. + +As an example, we will consider the case of running a QM/MM simulation of alanine +dipeptide in water. First, let us load the molecular system: + +>>> import sire as sr +>>> mols = sr.load_test_files("ala.crd", "ala.top") + +We now need to set up the molecular system for the QM/MM simulation and create +an engine to perform the calculation: + +>>> qm_mols, engine = sr.qm.create_engine( +>>> ... mols, +>>> ... mols[0], +>>> ... py_object, +>>> ... callback="callback", +>>> ... cutoff="7.5A", +>>> ... neighbour_list_update_frequency=20, +>>> ... mechanical_embedding=False, +>>> ... ) + +Here the first argument is the molecules that we are simulating, the second +selection coresponding to the QM region (here this is the first molecule). +The third argument is the Python object that will be used to perform the QM +calculation. The fourth argument is the name of the callback function that will +be used. If ``None``, then it assumed that the ``py_object`` itself is a callable, +i.e. it is the callback function. The callback function should have the following +signature: + +.. code-block:: python + + def callback( + numbers_qm: List[int], + charges_mm: List[float], + xyz_qm: List[List[float]], + xyz_mm: List[List[float]], + ) -> Tuple[float, List[List[float]], List[List[float]]]: + +The function takes the atomic numbers of the QM atoms, the charges of the MM +atoms in mod electron charge, the coordinates of the QM atoms in Angstrom, and +the coordinates of the MM atoms in Angstrom. It should return the calculated +energy in kJ/mol, the forces on the QM atoms in kJ/mol/nm, and the forces +on the MM atoms in kJ/mol/nm. The remaining arguments are optional and specify +the QM cutoff distance, the neigbour list update frequency, and whether the +electrostatics should be treated with mechanical embedding. When mechanical +embedding is used, the electrostatics are treated at the MM level by ``OpenMM``. +Note that this doesn't change the signature of the callback function, i.e. it +will be passed empty lists for the MM specific arguments and should return an +empty list for the MM forces. Atomic positions passed to the callback function +will already be unwrapped with the QM region in the center. + +The ``create_engine`` function returns a modified version of the molecules +containing a "merged" dipeptide that can be interpolated between MM and QM +levels of theory, along with the QM engine. This approach is extremely flexible +and allows the user to easily create a QM engine for a wide variety of QM packages. + +Running a QM/MM simulation +-------------------------- + +In order to run a QM/MM simulation with ``sire`` we just need to specify our +QM engine when creating a dynamics object, for example: + +>>> d = qm_mols.dynamics( +... timestep="1fs", +... constraint="none", +... qm_engine=engine, +... platform="cpu", +... ) + +For QM/MM simulations it is recommended to use a 1 femtosecond timestep and no +constraints. The simulation can then be run as usual: + +>>> d.run("100ps", energy_frequency="1ps", frame_frequency="1ps") + +This will run 100 picoseconds of dynamics, recording the energy and coordinates +every picosecond. + +In next section we will show how to use `emle-engine `_ +package as QM engine via a simple specialisation of the interface shown above. diff --git a/doc/source/tutorial/partXX/01_emle.rst b/doc/source/tutorial/partXX/02_emle.rst similarity index 93% rename from doc/source/tutorial/partXX/01_emle.rst rename to doc/source/tutorial/partXX/02_emle.rst index da5763778..3900f8974 100644 --- a/doc/source/tutorial/partXX/01_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -2,19 +2,13 @@ Sire-EMLE ========= -The ``sire`` QM/MM implementation takes advantage of the new means of writing -`platform independent force calculations `_ -introduced in `OpenMM `_ 8.1. This allows us to interface -with any external package to modify atomic forces within the ``OpenMM`` context. -While OpenMM already directly supports ML/MM simulations via the `OpenMM-ML `_ -package, it is currently limited to specific backends and only supports mechanical -embedding. The ``sire`` QM/MM implementation performs the QM calculation using -the `emle-engine `_ package, which has +In this section we will show how to use the `emle-engine `_ +package as a QM/MM engine within ``sire``. The ``emle-engine`` package provides support for a wide range of backends and embedding models, importantly providing a simple and efficient ML model for electrostatic embedding. -In order to use QM/MM functionality within ``sire`` you will first need to -create the following ``conda`` environment: +In order to use EMLE you will first need to create the following ``conda`` +environment: .. code-block:: bash @@ -56,7 +50,13 @@ Creating a QM engine We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation: ->>> qm_mols, engine = sr.qm.emle(mols, mols[0], calculator, "7.5A", 20) +>>> qm_mols, engine = sr.qm.emle( +>>> ... mols, +>>> ... mols[0], +>>> ... calculator, +>>> ... cutoff="7.5A", +>>> ... neighbour_list_update_frequency=20 +>>> ) Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule), and diff --git a/doc/source/tutorial/partXX/02_adp_pmf.rst b/doc/source/tutorial/partXX/03_adp_pmf.rst similarity index 100% rename from doc/source/tutorial/partXX/02_adp_pmf.rst rename to doc/source/tutorial/partXX/03_adp_pmf.rst diff --git a/doc/source/tutorial/partXX/03_diels_alder.rst b/doc/source/tutorial/partXX/04_diels_alder.rst similarity index 100% rename from doc/source/tutorial/partXX/03_diels_alder.rst rename to doc/source/tutorial/partXX/04_diels_alder.rst From 082bc1a8937de736035717846098bb177d31560d Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 22 Jun 2024 17:30:59 +0100 Subject: [PATCH 313/468] Changed mirror ghost sigma test to <=1e-9, added more detail to the changelog and defined QT_NO_SIGNALS_SLOTS_KEYWORDS at the gccxml level when generating headers. [ci skip] --- doc/source/changelog.rst | 4 ++-- wrapper/AutoGenerate/create_wrappers.py | 2 ++ wrapper/Convert/SireOpenMM/openmmmolecule.cpp | 4 ++-- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index e420840de..6af579eef 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -52,8 +52,8 @@ organisation on `GitHub `__. * Ignore BioSimSpace format position restraint include directives when parsing GROMACS topology files. -* Add a map option to prevent perturbation of the Lennard-Jones sigma - parameter for ghost atoms during alchemical free energy simulations. +* Added a map option (fix_perturbable_zero_sigmas) to prevent perturbation of + the Lennard-Jones sigma parameter for ghost atoms during alchemical free energy simulations. * Please add an item to this changelog when you create your PR diff --git a/wrapper/AutoGenerate/create_wrappers.py b/wrapper/AutoGenerate/create_wrappers.py index 9f719bfdc..40a27bbe0 100644 --- a/wrapper/AutoGenerate/create_wrappers.py +++ b/wrapper/AutoGenerate/create_wrappers.py @@ -828,6 +828,7 @@ def fixMB(mb): define_symbols=[ "GCCXML_PARSE", "__PIC__", + "QT_NO_SIGNALS_SLOTS_KEYWORDS=1", "SIRE_ALWAYS_INLINE=inline", "SIRE_SKIP_INLINE_FUNCTIONS", "SIREN_SKIP_INLINE_FUNCTIONS", @@ -854,6 +855,7 @@ def fixMB(mb): define_symbols=[ "GCCXML_PARSE", "__PIC__", + "QT_NO_SIGNALS_SLOTS_KEYWORDS=1", "SIRE_USE_OPENMM", "SIRE_ALWAYS_INLINE=inline", "SIRE_SKIP_INLINE_FUNCTIONS", diff --git a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp index 36e16e3da..40979610d 100644 --- a/wrapper/Convert/SireOpenMM/openmmmolecule.cpp +++ b/wrapper/Convert/SireOpenMM/openmmmolecule.cpp @@ -2222,12 +2222,12 @@ PerturbableOpenMMMolecule::PerturbableOpenMMMolecule(const OpenMMMolecule &mol, for (int i = 0; i < nats; ++i) { - if (std::abs(sig0_data[i]) < 1e-9) + if (std::abs(sig0_data[i]) <= 1e-9) { sig0[i] = sig1_data[i]; sig0_data = sig0.constData(); } - else if (std::abs(sig1_data[i] < 1e-9)) + else if (std::abs(sig1_data[i] <= 1e-9)) { sig1[i] = sig0_data[i]; sig1_data = sig1.constData(); From b1db53ceba941a2f0d8be648d21e475c58f420ea Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 22 Jun 2024 18:30:02 +0100 Subject: [PATCH 314/468] Now reorder cutgroups so that the CGAtomIdx order always matches the AtomIdx order. This works really well, except that it fails when merging submolecules, because the CGAtomIdx order changes on commit. I need to fix this. I suspect it will be by converting merged proteins into a single cutgroup? --- corelib/src/libs/SireMol/structureeditor.cpp | 128 +++++++++++++++++++ tests/mol/test_reorder.py | 36 ++++++ 2 files changed, 164 insertions(+) create mode 100644 tests/mol/test_reorder.py diff --git a/corelib/src/libs/SireMol/structureeditor.cpp b/corelib/src/libs/SireMol/structureeditor.cpp index df276c401..0452b4e8e 100644 --- a/corelib/src/libs/SireMol/structureeditor.cpp +++ b/corelib/src/libs/SireMol/structureeditor.cpp @@ -3210,6 +3210,134 @@ const MoleculeInfoData &StructureEditor::commitInfo() } } + // make sure that the AtomIdx order matches the CGAtomIdx order + // This is needed to remove confusion in code that assumes + // AtomIdx order is always correct. This is a big change in code + // behaviour, but it is necessary to make the code more robust, + // and also recognises the reality that CutGroups are now "under + // the hood" in the code and not really visible or known about by + // end users. + int atom_count = 0; + bool in_atomidx_order = true; + + for (int i = 0; i < this->nCutGroupsInMolecule(); ++i) + { + const auto cgdata = this->getCGData(CGIdx(i)); + + for (const auto &atomidx : cgdata.get<1>()) + { + if (atomidx != AtomIdx(atom_count)) + { + in_atomidx_order = false; + break; + } + + ++atom_count; + } + } + + if (atom_count != this->nAtomsInMolecule()) + { + in_atomidx_order = false; + } + + if (not in_atomidx_order) + { + SireBase::Console::warning(QObject::tr( + "The atoms in the CutGroups are not in the same order as the atoms in the molecule. " + "Rebuilding CutGroups so that the CGAtomIdx order matches the AtomIdx order.")); + + // are the atoms contiguous in residues? + bool contiguous_residues = true; + QSet seen_residues; + seen_residues.reserve(this->nResiduesInMolecule()); + ResIdx prev_residx = ResIdx::null(); + + for (int i = 0; i < this->nAtomsInMolecule(); ++i) + { + const auto info = this->getAtomData(AtomIdx(i)); + + if (prev_residx.isNull()) + { + prev_residx = info.get<4>(); + seen_residues.insert(prev_residx); + } + else + { + if (info.get<4>() != prev_residx) + { + prev_residx = info.get<4>(); + + if (seen_residues.contains(prev_residx)) + { + contiguous_residues = false; + break; + } + else + { + seen_residues.insert(prev_residx); + } + } + } + } + + // delete all existing CutGroups + this->removeAllCutGroups(); + + if (contiguous_residues) + { + prev_residx = ResIdx::null(); + int cgcount = 0; + + for (int i = 0; i < this->nAtomsInMolecule(); ++i) + { + const auto info = this->getAtomData(AtomIdx(i)); + + if (prev_residx.isNull() or info.get<4>() != prev_residx) + { + prev_residx = info.get<4>(); + this->addCutGroup().rename(CGName(QString::number(cgcount))); + cgcount += 1; + } + + this->reparentAtom(this->getUID(AtomIdx(i)), CGIdx(cgcount - 1)); + } + + if (cgcount != this->nResiduesInMolecule()) + { + SireBase::Console::warning(QObject::tr( + "The number of CutGroups created (%1) does not match " + "the number of residues in the molecule (%2)! Rebuilding " + "into a single CutGroup.") + .arg(cgcount) + .arg(this->nResiduesInMolecule())); + + this->removeAllCutGroups(); + + this->addCutGroup().rename(CGName("0")); + + for (int i = 0; i < this->nAtomsInMolecule(); ++i) + { + this->reparentAtom(this->getUID(AtomIdx(i)), CGIdx(0)); + } + } + } + else + { + // create a new CutGroup and add all atoms to it + SireBase::Console::warning(QObject::tr( + "The atoms in the molecule are not contiguous in residues. " + "Rebuilding into a single CutGroup.")); + + this->addCutGroup().rename(CGName("0")); + + for (int i = 0; i < this->nAtomsInMolecule(); ++i) + { + this->reparentAtom(this->getUID(AtomIdx(i)), CGIdx(0)); + } + } + } + d->cached_molinfo = new MoleculeInfoData(*this); } diff --git a/tests/mol/test_reorder.py b/tests/mol/test_reorder.py new file mode 100644 index 000000000..e04325da8 --- /dev/null +++ b/tests/mol/test_reorder.py @@ -0,0 +1,36 @@ +def test_reorder_atoms(ala_mols): + mols = ala_mols + + mol = mols[0] + + # check that reorder preserves residue cutting + mol = mol.edit() + atom = mol.atom(2) + atom = atom.reindex(0) + mol = atom.molecule().commit() + + assert mol.num_residues() == 3 + assert mol.num_cutgroups() == mol.num_residues() + + atomidx = 0 + + for cutgroup in mol.cutgroups(): + for atom in cutgroup.atoms(): + assert atom.index().value() == atomidx + atomidx += 1 + + # now check with reordering that break residue cutting + mol = mols[0] + + mol = mol.edit() + atom = mol.atom("HA") + atom = atom.reindex(0) + mol = atom.molecule().commit() + + assert mol.num_cutgroups() == 1 + + atomidx = 0 + + for atom in mol.cutgroups()[0].atoms(): + assert atom.index().value() == atomidx + atomidx += 1 From 26a79eeca9ed143b73e9f1a595fc58a8065db942 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 22 Jun 2024 22:55:08 +0100 Subject: [PATCH 315/468] Fixed the merge code by making sure that the AtomIdx of the added atom is correct for its position in the molecule (i.e. is one higher than the AtomIdx of the last atom in the residue) --- corelib/src/libs/SireSystem/merge.cpp | 14 ++++++++++++++ doc/source/changelog.rst | 13 +++++++++++++ 2 files changed, 27 insertions(+) diff --git a/corelib/src/libs/SireSystem/merge.cpp b/corelib/src/libs/SireSystem/merge.cpp index 5031f81d8..d01703f76 100644 --- a/corelib/src/libs/SireSystem/merge.cpp +++ b/corelib/src/libs/SireSystem/merge.cpp @@ -390,12 +390,26 @@ namespace SireSystem auto res = mol.residue(residx); + // get the AtomIdx of the last atom in this residue + AtomIdx last_atomidx(0); + + if (res.nAtoms() > 0) + { + last_atomidx = res.atom(res.nAtoms() - 1).index(); + } + // add the atom - it has the name "Xxx" as it doesn't exist // in the reference state auto atom = res.add(AtomName("Xxx")); largest_atomnum = AtomNum(largest_atomnum.value() + 1); atom.renumber(largest_atomnum); + // ensure that its index follows on from the index of the + // last atom in the residue - this is so that we keep + // the AtomIdx and CGAtomIdx orders in sync, and don't + // force a complex reordering of the atoms when we commit + atom.reindex(last_atomidx + 1); + // reparent this atom to the CutGroup for this residue atom.reparent(cgidx); diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 6af579eef..ac86ad415 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -55,6 +55,19 @@ organisation on `GitHub `__. * Added a map option (fix_perturbable_zero_sigmas) to prevent perturbation of the Lennard-Jones sigma parameter for ghost atoms during alchemical free energy simulations. +* [CHANGE IN BEHAVIOUR] - added code that ensures that, when editing molecules, + the CGAtomIdx order will always follow the AtomIdx order of atoms. This is + because a lot of code had implicitly assumed this, and so it was a cause + of bugs when this wasn't the case. Now, when you edit a molecule, on committing, + the orders will be checked. If they don't agree, then the CutGroups will be + reordered, with atoms reordered as necessary to make the CGAtomIdx order match + the AtomIdx order. If this isn't possible (e.g. because atoms in CutGroups + are not contiguous), then the molecule will be converted to a single-cutgroup + molecule, with the atoms placed in AtomIdx order. As part of this change, + the merge code will now also ensure that added atoms are added with the + correct AtomIdx, rather than added as the last atoms in the molecule. This + is also more natural. This fixes issue #202. + * Please add an item to this changelog when you create your PR `2024.1.0 `__ - April 2024 From 89ae69e2d30c182f0bdb18a2adea31b2204a2d4a Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 23 Jun 2024 17:46:26 +0100 Subject: [PATCH 316/468] Added the "center" keyword argument to Cursors, CursorsM and System (plus legacy.System.System). Also added "origin" and "zero" as recognised options for constructing vectors, e.g. ``` c = mols.cursor() c.make_whole(center="origin") ``` will work. --- corelib/src/libs/SireSystem/system.cpp | 59 +++++++++++++++++++ corelib/src/libs/SireSystem/system.h | 4 ++ src/sire/maths/_vector.py | 7 +++ src/sire/mol/_cursor.py | 8 +-- src/sire/system/_system.py | 22 +++++-- tests/mol/test_make_whole.py | 20 ++++++- wrapper/System/AngleComponent.pypp.cpp | 8 ++- wrapper/System/AssignerGroup.pypp.cpp | 8 ++- wrapper/System/CheckPoint.pypp.cpp | 8 ++- wrapper/System/CloseMols.pypp.cpp | 8 ++- wrapper/System/ComponentConstraint.pypp.cpp | 8 ++- wrapper/System/Constraints.pypp.cpp | 8 ++- wrapper/System/DihedralComponent.pypp.cpp | 8 ++- wrapper/System/DistanceComponent.pypp.cpp | 8 ++- .../System/DoubleDistanceComponent.pypp.cpp | 8 ++- wrapper/System/EnergyMonitor.pypp.cpp | 8 ++- wrapper/System/ForceFieldInfo.pypp.cpp | 8 ++- wrapper/System/FreeEnergyMonitor.pypp.cpp | 8 ++- wrapper/System/IDAndSet_MonitorID_.pypp.cpp | 8 ++- wrapper/System/IDAndSet_SysID_.pypp.cpp | 8 ++- wrapper/System/IDAssigner.pypp.cpp | 8 ++- wrapper/System/IDOrSet_MonitorID_.pypp.cpp | 8 ++- wrapper/System/IDOrSet_SysID_.pypp.cpp | 8 ++- wrapper/System/IdentityConstraint.pypp.cpp | 8 ++- wrapper/System/MonitorComponent.pypp.cpp | 8 ++- wrapper/System/MonitorComponents.pypp.cpp | 8 ++- wrapper/System/MonitorIdx.pypp.cpp | 8 ++- wrapper/System/MonitorMonitor.pypp.cpp | 8 ++- wrapper/System/MonitorName.pypp.cpp | 8 ++- wrapper/System/MonitorProperty.pypp.cpp | 8 ++- wrapper/System/NullConstraint.pypp.cpp | 8 ++- wrapper/System/NullMonitor.pypp.cpp | 8 ++- .../System/PerturbationConstraint.pypp.cpp | 8 ++- wrapper/System/PolariseCharges.pypp.cpp | 8 ++- wrapper/System/PolariseChargesFF.pypp.cpp | 8 ++- wrapper/System/PropertyConstraint.pypp.cpp | 8 ++- wrapper/System/SireSystem_registrars.cpp | 3 + wrapper/System/SpaceWrapper.pypp.cpp | 8 ++- wrapper/System/Specify_MonitorID_.pypp.cpp | 8 ++- wrapper/System/Specify_SysID_.pypp.cpp | 8 ++- wrapper/System/SysIdx.pypp.cpp | 8 ++- wrapper/System/SysName.pypp.cpp | 8 ++- wrapper/System/System.pypp.cpp | 34 ++++++++++- wrapper/System/SystemMonitors.pypp.cpp | 8 ++- .../System/TripleDistanceComponent.pypp.cpp | 8 ++- wrapper/System/VolMapMonitor.pypp.cpp | 8 ++- wrapper/System/WindowedComponent.pypp.cpp | 8 ++- 47 files changed, 337 insertions(+), 132 deletions(-) diff --git a/corelib/src/libs/SireSystem/system.cpp b/corelib/src/libs/SireSystem/system.cpp index d64c3996b..874d0abb1 100644 --- a/corelib/src/libs/SireSystem/system.cpp +++ b/corelib/src/libs/SireSystem/system.cpp @@ -4162,6 +4162,65 @@ void System::makeWhole() this->makeWhole(PropertyMap()); } +void System::makeWhole(const Vector ¢er, const PropertyMap &map) +{ + if (this->needsAccepting()) + { + this->accept(); + } + + if (not this->containsProperty(map["space"])) + return; + + if (not this->property(map["space"]).isA()) + return; + + const auto &space = this->property(map["space"]).asA(); + + if (not space.isPeriodic()) + return; + + PropertyMap m = map; + m.set("space", space); + + // get a list of all molecules in the system + const SelectorMol mols(*this); + + SelectorMol changed_mols; + + for (const auto &mol : mols) + { + auto new_mol = mol.move().makeWhole(center, m).commit(); + + if (new_mol.data().version() != mol.data().version()) + { + changed_mols.append(new_mol); + } + } + + if (not changed_mols.isEmpty()) + { + Delta delta(*this, true); + + // this ensures that only a single copy of System is used - prevents + // unnecessary copying + this->operator=(System()); + delta.update(changed_mols.toMolecules()); + this->operator=(delta.apply()); + + if (this->needsAccepting()) + { + delta = Delta(); + this->accept(); + } + } +} + +void System::makeWhole(const Vector ¢er) +{ + this->makeWhole(center, PropertyMap()); +} + const char *System::typeName() { return QMetaType::typeName(qMetaTypeId()); diff --git a/corelib/src/libs/SireSystem/system.h b/corelib/src/libs/SireSystem/system.h index 83d5f3698..6d726fdd4 100644 --- a/corelib/src/libs/SireSystem/system.h +++ b/corelib/src/libs/SireSystem/system.h @@ -443,6 +443,10 @@ namespace SireSystem void makeWhole(); void makeWhole(const SireBase::PropertyMap &map); + void makeWhole(const SireMaths::Vector ¢er); + void makeWhole(const SireMaths::Vector ¢er, + const SireBase::PropertyMap &map); + static const System &null(); protected: diff --git a/src/sire/maths/_vector.py b/src/sire/maths/_vector.py index 85c10aaf6..79edd1286 100644 --- a/src/sire/maths/_vector.py +++ b/src/sire/maths/_vector.py @@ -237,6 +237,13 @@ class containing 3 double precision values. These values """ def __init__(self, *args, **kwargs): + if len(args) == 1: + # check for "zero" or "origin" + arg0 = str(args[0]).strip().lower() + + if arg0 == "zero" or arg0 == "origin": + args = [0.0, 0.0, 0.0] + from ..units import angstrom from .. import u diff --git a/src/sire/mol/_cursor.py b/src/sire/mol/_cursor.py index 26e88d1eb..600c12ffa 100644 --- a/src/sire/mol/_cursor.py +++ b/src/sire/mol/_cursor.py @@ -2624,7 +2624,7 @@ def delete_frame(self, *args, **kwargs): return self - def make_whole(self, *args, map=None): + def make_whole(self, center=None, map=None): """ Make all of the atoms operated on by this cursor whole (they won't be broken across a periodic box boundary) @@ -2634,7 +2634,7 @@ def make_whole(self, *args, map=None): which they should be wrapped. """ for cursor in self._cursors: - cursor.make_whole(*args, map=map) + cursor.make_whole(center=center, map=map) return self @@ -3779,7 +3779,7 @@ def delete_frame(self, *args, **kwargs): return self - def make_whole(self, *args, map=None): + def make_whole(self, center=None, map=None): """ Make all of the atoms operated on by this cursor whole (they won't be broken across a periodic box boundary) @@ -3789,7 +3789,7 @@ def make_whole(self, *args, map=None): which they should be wrapped. """ for cursor in self._cursors: - cursor.make_whole(*args, map=map) + cursor.make_whole(center=center, map=map) return self diff --git a/src/sire/system/_system.py b/src/sire/system/_system.py index a2eb05a77..9f00b81ea 100644 --- a/src/sire/system/_system.py +++ b/src/sire/system/_system.py @@ -145,18 +145,30 @@ def numbers(self): """Return the numbers of all of the molecules in this System""" return self.molecules().numbers() - def make_whole(self, map=None): + def make_whole(self, center=None, map=None): """ Make all of the molecules in this system whole. This maps each molecule into the current space, such that no molecule is broken across a periodic box boundary """ - if map is None: - self._system.make_whole() + if center is None: + if map is None: + self._system.make_whole() + else: + from ..base import create_map + + self._system.make_whole(map=create_map(map)) else: - from ..base import create_map + from ..maths import Vector + + center = Vector(center) + + if map is None: + self._system.make_whole(center=center) + else: + from ..base import create_map - self._system.make_whole(map=create_map(map)) + self._system.make_whole(center=center, map=create_map(map)) self._molecules = None diff --git a/tests/mol/test_make_whole.py b/tests/mol/test_make_whole.py index cc00792db..78c4898f1 100644 --- a/tests/mol/test_make_whole.py +++ b/tests/mol/test_make_whole.py @@ -59,9 +59,7 @@ def test_auto_make_whole_on_load_frame(wrapped_mols): def test_auto_make_whole_on_load(): - mols = sr.load_test_files( - "wrapped.rst7", "wrapped.prm7", map={"make_whole": True} - ) + mols = sr.load_test_files("wrapped.rst7", "wrapped.prm7", map={"make_whole": True}) _assert_correct_com(mols[0].evaluate().center_of_mass()) @@ -84,3 +82,19 @@ def test_auto_make_whole_on_load_no_breakage(kigaki_mols): kigaki_mols[0].evaluate().center_of_mass() == mols[0].evaluate().center_of_mass() ) + + +def test_make_whole_center_args(ala_mols): + mols = ala_mols + + c = mols[0].cursor() + c.make_whole(center="origin") + + c = mols.cursor() + c.make_whole(center=0) + + c = mols[0].atoms().cursor() + c.make_whole(center=(1, 2, 3)) + + mols = mols.clone() + mols.make_whole(center=("1A", "2A", "3A")) diff --git a/wrapper/System/AngleComponent.pypp.cpp b/wrapper/System/AngleComponent.pypp.cpp index bf494bd7d..35cf5b2a7 100644 --- a/wrapper/System/AngleComponent.pypp.cpp +++ b/wrapper/System/AngleComponent.pypp.cpp @@ -30,6 +30,8 @@ namespace bp = boost::python; SireSystem::AngleComponent __copy__(const SireSystem::AngleComponent &other){ return SireSystem::AngleComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -237,9 +239,9 @@ void register_AngleComponent_class(){ AngleComponent_exposer.staticmethod( "theta021" ); AngleComponent_exposer.staticmethod( "theta102" ); AngleComponent_exposer.staticmethod( "typeName" ); - AngleComponent_exposer.def( "__copy__", &__copy__); - AngleComponent_exposer.def( "__deepcopy__", &__copy__); - AngleComponent_exposer.def( "clone", &__copy__); + AngleComponent_exposer.def( "__copy__", &__copy__); + AngleComponent_exposer.def( "__deepcopy__", &__copy__); + AngleComponent_exposer.def( "clone", &__copy__); AngleComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::AngleComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AngleComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::AngleComponent >, diff --git a/wrapper/System/AssignerGroup.pypp.cpp b/wrapper/System/AssignerGroup.pypp.cpp index 651cdaf56..b3946f03a 100644 --- a/wrapper/System/AssignerGroup.pypp.cpp +++ b/wrapper/System/AssignerGroup.pypp.cpp @@ -44,6 +44,8 @@ namespace bp = boost::python; SireSystem::AssignerGroup __copy__(const SireSystem::AssignerGroup &other){ return SireSystem::AssignerGroup(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireSystem::AssignerGroup&){ return "SireSystem::AssignerGroup";} @@ -197,9 +199,9 @@ void register_AssignerGroup_class(){ } AssignerGroup_exposer.staticmethod( "typeName" ); - AssignerGroup_exposer.def( "__copy__", &__copy__); - AssignerGroup_exposer.def( "__deepcopy__", &__copy__); - AssignerGroup_exposer.def( "clone", &__copy__); + AssignerGroup_exposer.def( "__copy__", &__copy__); + AssignerGroup_exposer.def( "__deepcopy__", &__copy__); + AssignerGroup_exposer.def( "clone", &__copy__); AssignerGroup_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::AssignerGroup >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); AssignerGroup_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::AssignerGroup >, diff --git a/wrapper/System/CheckPoint.pypp.cpp b/wrapper/System/CheckPoint.pypp.cpp index 306ff5f73..09ee88b27 100644 --- a/wrapper/System/CheckPoint.pypp.cpp +++ b/wrapper/System/CheckPoint.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireSystem::CheckPoint __copy__(const SireSystem::CheckPoint &other){ return SireSystem::CheckPoint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -72,9 +74,9 @@ void register_CheckPoint_class(){ } CheckPoint_exposer.staticmethod( "typeName" ); - CheckPoint_exposer.def( "__copy__", &__copy__); - CheckPoint_exposer.def( "__deepcopy__", &__copy__); - CheckPoint_exposer.def( "clone", &__copy__); + CheckPoint_exposer.def( "__copy__", &__copy__); + CheckPoint_exposer.def( "__deepcopy__", &__copy__); + CheckPoint_exposer.def( "clone", &__copy__); CheckPoint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::CheckPoint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CheckPoint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::CheckPoint >, diff --git a/wrapper/System/CloseMols.pypp.cpp b/wrapper/System/CloseMols.pypp.cpp index 22aafe076..fc54e9802 100644 --- a/wrapper/System/CloseMols.pypp.cpp +++ b/wrapper/System/CloseMols.pypp.cpp @@ -28,6 +28,8 @@ namespace bp = boost::python; SireSystem::CloseMols __copy__(const SireSystem::CloseMols &other){ return SireSystem::CloseMols(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireSystem::CloseMols&){ return "SireSystem::CloseMols";} @@ -207,9 +209,9 @@ void register_CloseMols_class(){ } CloseMols_exposer.staticmethod( "typeName" ); - CloseMols_exposer.def( "__copy__", &__copy__); - CloseMols_exposer.def( "__deepcopy__", &__copy__); - CloseMols_exposer.def( "clone", &__copy__); + CloseMols_exposer.def( "__copy__", &__copy__); + CloseMols_exposer.def( "__deepcopy__", &__copy__); + CloseMols_exposer.def( "clone", &__copy__); CloseMols_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::CloseMols >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); CloseMols_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::CloseMols >, diff --git a/wrapper/System/ComponentConstraint.pypp.cpp b/wrapper/System/ComponentConstraint.pypp.cpp index bd24e732e..3aba0a6d6 100644 --- a/wrapper/System/ComponentConstraint.pypp.cpp +++ b/wrapper/System/ComponentConstraint.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireSystem::ComponentConstraint __copy__(const SireSystem::ComponentConstraint &other){ return SireSystem::ComponentConstraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -114,9 +116,9 @@ void register_ComponentConstraint_class(){ } ComponentConstraint_exposer.staticmethod( "typeName" ); - ComponentConstraint_exposer.def( "__copy__", &__copy__); - ComponentConstraint_exposer.def( "__deepcopy__", &__copy__); - ComponentConstraint_exposer.def( "clone", &__copy__); + ComponentConstraint_exposer.def( "__copy__", &__copy__); + ComponentConstraint_exposer.def( "__deepcopy__", &__copy__); + ComponentConstraint_exposer.def( "clone", &__copy__); ComponentConstraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::ComponentConstraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ComponentConstraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::ComponentConstraint >, diff --git a/wrapper/System/Constraints.pypp.cpp b/wrapper/System/Constraints.pypp.cpp index 02065e84b..df0853950 100644 --- a/wrapper/System/Constraints.pypp.cpp +++ b/wrapper/System/Constraints.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireSystem::Constraints __copy__(const SireSystem::Constraints &other){ return SireSystem::Constraints(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -271,9 +273,9 @@ void register_Constraints_class(){ } Constraints_exposer.staticmethod( "typeName" ); - Constraints_exposer.def( "__copy__", &__copy__); - Constraints_exposer.def( "__deepcopy__", &__copy__); - Constraints_exposer.def( "clone", &__copy__); + Constraints_exposer.def( "__copy__", &__copy__); + Constraints_exposer.def( "__deepcopy__", &__copy__); + Constraints_exposer.def( "clone", &__copy__); Constraints_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::Constraints >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Constraints_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::Constraints >, diff --git a/wrapper/System/DihedralComponent.pypp.cpp b/wrapper/System/DihedralComponent.pypp.cpp index 3e968952e..7f526cb8a 100644 --- a/wrapper/System/DihedralComponent.pypp.cpp +++ b/wrapper/System/DihedralComponent.pypp.cpp @@ -30,6 +30,8 @@ namespace bp = boost::python; SireSystem::DihedralComponent __copy__(const SireSystem::DihedralComponent &other){ return SireSystem::DihedralComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -249,9 +251,9 @@ void register_DihedralComponent_class(){ DihedralComponent_exposer.staticmethod( "theta012" ); DihedralComponent_exposer.staticmethod( "theta123" ); DihedralComponent_exposer.staticmethod( "typeName" ); - DihedralComponent_exposer.def( "__copy__", &__copy__); - DihedralComponent_exposer.def( "__deepcopy__", &__copy__); - DihedralComponent_exposer.def( "clone", &__copy__); + DihedralComponent_exposer.def( "__copy__", &__copy__); + DihedralComponent_exposer.def( "__deepcopy__", &__copy__); + DihedralComponent_exposer.def( "clone", &__copy__); DihedralComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::DihedralComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DihedralComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::DihedralComponent >, diff --git a/wrapper/System/DistanceComponent.pypp.cpp b/wrapper/System/DistanceComponent.pypp.cpp index 69245cb0e..e6a939d04 100644 --- a/wrapper/System/DistanceComponent.pypp.cpp +++ b/wrapper/System/DistanceComponent.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireSystem::DistanceComponent __copy__(const SireSystem::DistanceComponent &other){ return SireSystem::DistanceComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -143,9 +145,9 @@ void register_DistanceComponent_class(){ } DistanceComponent_exposer.staticmethod( "r" ); DistanceComponent_exposer.staticmethod( "typeName" ); - DistanceComponent_exposer.def( "__copy__", &__copy__); - DistanceComponent_exposer.def( "__deepcopy__", &__copy__); - DistanceComponent_exposer.def( "clone", &__copy__); + DistanceComponent_exposer.def( "__copy__", &__copy__); + DistanceComponent_exposer.def( "__deepcopy__", &__copy__); + DistanceComponent_exposer.def( "clone", &__copy__); DistanceComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::DistanceComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DistanceComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::DistanceComponent >, diff --git a/wrapper/System/DoubleDistanceComponent.pypp.cpp b/wrapper/System/DoubleDistanceComponent.pypp.cpp index 7013a9a35..703203939 100644 --- a/wrapper/System/DoubleDistanceComponent.pypp.cpp +++ b/wrapper/System/DoubleDistanceComponent.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireSystem::DoubleDistanceComponent __copy__(const SireSystem::DoubleDistanceComponent &other){ return SireSystem::DoubleDistanceComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -180,9 +182,9 @@ void register_DoubleDistanceComponent_class(){ DoubleDistanceComponent_exposer.staticmethod( "r01" ); DoubleDistanceComponent_exposer.staticmethod( "r23" ); DoubleDistanceComponent_exposer.staticmethod( "typeName" ); - DoubleDistanceComponent_exposer.def( "__copy__", &__copy__); - DoubleDistanceComponent_exposer.def( "__deepcopy__", &__copy__); - DoubleDistanceComponent_exposer.def( "clone", &__copy__); + DoubleDistanceComponent_exposer.def( "__copy__", &__copy__); + DoubleDistanceComponent_exposer.def( "__deepcopy__", &__copy__); + DoubleDistanceComponent_exposer.def( "clone", &__copy__); DoubleDistanceComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::DoubleDistanceComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); DoubleDistanceComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::DoubleDistanceComponent >, diff --git a/wrapper/System/EnergyMonitor.pypp.cpp b/wrapper/System/EnergyMonitor.pypp.cpp index 45119994d..922d5441b 100644 --- a/wrapper/System/EnergyMonitor.pypp.cpp +++ b/wrapper/System/EnergyMonitor.pypp.cpp @@ -40,6 +40,8 @@ namespace bp = boost::python; SireSystem::EnergyMonitor __copy__(const SireSystem::EnergyMonitor &other){ return SireSystem::EnergyMonitor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -310,9 +312,9 @@ void register_EnergyMonitor_class(){ } EnergyMonitor_exposer.staticmethod( "typeName" ); - EnergyMonitor_exposer.def( "__copy__", &__copy__); - EnergyMonitor_exposer.def( "__deepcopy__", &__copy__); - EnergyMonitor_exposer.def( "clone", &__copy__); + EnergyMonitor_exposer.def( "__copy__", &__copy__); + EnergyMonitor_exposer.def( "__deepcopy__", &__copy__); + EnergyMonitor_exposer.def( "clone", &__copy__); EnergyMonitor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::EnergyMonitor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); EnergyMonitor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::EnergyMonitor >, diff --git a/wrapper/System/ForceFieldInfo.pypp.cpp b/wrapper/System/ForceFieldInfo.pypp.cpp index 2a2bff054..bed27e18f 100644 --- a/wrapper/System/ForceFieldInfo.pypp.cpp +++ b/wrapper/System/ForceFieldInfo.pypp.cpp @@ -32,6 +32,8 @@ namespace bp = boost::python; SireSystem::ForceFieldInfo __copy__(const SireSystem::ForceFieldInfo &other){ return SireSystem::ForceFieldInfo(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -312,9 +314,9 @@ void register_ForceFieldInfo_class(){ } ForceFieldInfo_exposer.staticmethod( "cutoffTypes" ); ForceFieldInfo_exposer.staticmethod( "typeName" ); - ForceFieldInfo_exposer.def( "__copy__", &__copy__); - ForceFieldInfo_exposer.def( "__deepcopy__", &__copy__); - ForceFieldInfo_exposer.def( "clone", &__copy__); + ForceFieldInfo_exposer.def( "__copy__", &__copy__); + ForceFieldInfo_exposer.def( "__deepcopy__", &__copy__); + ForceFieldInfo_exposer.def( "clone", &__copy__); ForceFieldInfo_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::ForceFieldInfo >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); ForceFieldInfo_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::ForceFieldInfo >, diff --git a/wrapper/System/FreeEnergyMonitor.pypp.cpp b/wrapper/System/FreeEnergyMonitor.pypp.cpp index ce6dcecb3..dc9f1b1f8 100644 --- a/wrapper/System/FreeEnergyMonitor.pypp.cpp +++ b/wrapper/System/FreeEnergyMonitor.pypp.cpp @@ -43,6 +43,8 @@ namespace bp = boost::python; SireSystem::FreeEnergyMonitor __copy__(const SireSystem::FreeEnergyMonitor &other){ return SireSystem::FreeEnergyMonitor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -446,9 +448,9 @@ void register_FreeEnergyMonitor_class(){ } FreeEnergyMonitor_exposer.staticmethod( "merge" ); FreeEnergyMonitor_exposer.staticmethod( "typeName" ); - FreeEnergyMonitor_exposer.def( "__copy__", &__copy__); - FreeEnergyMonitor_exposer.def( "__deepcopy__", &__copy__); - FreeEnergyMonitor_exposer.def( "clone", &__copy__); + FreeEnergyMonitor_exposer.def( "__copy__", &__copy__); + FreeEnergyMonitor_exposer.def( "__deepcopy__", &__copy__); + FreeEnergyMonitor_exposer.def( "clone", &__copy__); FreeEnergyMonitor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::FreeEnergyMonitor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); FreeEnergyMonitor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::FreeEnergyMonitor >, diff --git a/wrapper/System/IDAndSet_MonitorID_.pypp.cpp b/wrapper/System/IDAndSet_MonitorID_.pypp.cpp index 978e3221b..46fcaa58d 100644 --- a/wrapper/System/IDAndSet_MonitorID_.pypp.cpp +++ b/wrapper/System/IDAndSet_MonitorID_.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireID::IDAndSet __copy__(const SireID::IDAndSet &other){ return SireID::IDAndSet(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -167,9 +169,9 @@ void register_IDAndSet_MonitorID__class(){ } IDAndSet_MonitorID__exposer.staticmethod( "typeName" ); - IDAndSet_MonitorID__exposer.def( "__copy__", &__copy__); - IDAndSet_MonitorID__exposer.def( "__deepcopy__", &__copy__); - IDAndSet_MonitorID__exposer.def( "clone", &__copy__); + IDAndSet_MonitorID__exposer.def( "__copy__", &__copy__>); + IDAndSet_MonitorID__exposer.def( "__deepcopy__", &__copy__>); + IDAndSet_MonitorID__exposer.def( "clone", &__copy__>); IDAndSet_MonitorID__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireID::IDAndSet >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IDAndSet_MonitorID__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireID::IDAndSet >, diff --git a/wrapper/System/IDAndSet_SysID_.pypp.cpp b/wrapper/System/IDAndSet_SysID_.pypp.cpp index f9b0546c8..a9e7a80c7 100644 --- a/wrapper/System/IDAndSet_SysID_.pypp.cpp +++ b/wrapper/System/IDAndSet_SysID_.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireID::IDAndSet __copy__(const SireID::IDAndSet &other){ return SireID::IDAndSet(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -165,9 +167,9 @@ void register_IDAndSet_SysID__class(){ } IDAndSet_SysID__exposer.staticmethod( "typeName" ); - IDAndSet_SysID__exposer.def( "__copy__", &__copy__); - IDAndSet_SysID__exposer.def( "__deepcopy__", &__copy__); - IDAndSet_SysID__exposer.def( "clone", &__copy__); + IDAndSet_SysID__exposer.def( "__copy__", &__copy__>); + IDAndSet_SysID__exposer.def( "__deepcopy__", &__copy__>); + IDAndSet_SysID__exposer.def( "clone", &__copy__>); IDAndSet_SysID__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireID::IDAndSet >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IDAndSet_SysID__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireID::IDAndSet >, diff --git a/wrapper/System/IDAssigner.pypp.cpp b/wrapper/System/IDAssigner.pypp.cpp index 9af711af5..c678bd6aa 100644 --- a/wrapper/System/IDAssigner.pypp.cpp +++ b/wrapper/System/IDAssigner.pypp.cpp @@ -52,6 +52,8 @@ namespace bp = boost::python; SireSystem::IDAssigner __copy__(const SireSystem::IDAssigner &other){ return SireSystem::IDAssigner(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -206,9 +208,9 @@ void register_IDAssigner_class(){ } IDAssigner_exposer.staticmethod( "typeName" ); - IDAssigner_exposer.def( "__copy__", &__copy__); - IDAssigner_exposer.def( "__deepcopy__", &__copy__); - IDAssigner_exposer.def( "clone", &__copy__); + IDAssigner_exposer.def( "__copy__", &__copy__); + IDAssigner_exposer.def( "__deepcopy__", &__copy__); + IDAssigner_exposer.def( "clone", &__copy__); IDAssigner_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::IDAssigner >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IDAssigner_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::IDAssigner >, diff --git a/wrapper/System/IDOrSet_MonitorID_.pypp.cpp b/wrapper/System/IDOrSet_MonitorID_.pypp.cpp index c0c263d0d..54981fefa 100644 --- a/wrapper/System/IDOrSet_MonitorID_.pypp.cpp +++ b/wrapper/System/IDOrSet_MonitorID_.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireID::IDOrSet __copy__(const SireID::IDOrSet &other){ return SireID::IDOrSet(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -167,9 +169,9 @@ void register_IDOrSet_MonitorID__class(){ } IDOrSet_MonitorID__exposer.staticmethod( "typeName" ); - IDOrSet_MonitorID__exposer.def( "__copy__", &__copy__); - IDOrSet_MonitorID__exposer.def( "__deepcopy__", &__copy__); - IDOrSet_MonitorID__exposer.def( "clone", &__copy__); + IDOrSet_MonitorID__exposer.def( "__copy__", &__copy__>); + IDOrSet_MonitorID__exposer.def( "__deepcopy__", &__copy__>); + IDOrSet_MonitorID__exposer.def( "clone", &__copy__>); IDOrSet_MonitorID__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireID::IDOrSet >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IDOrSet_MonitorID__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireID::IDOrSet >, diff --git a/wrapper/System/IDOrSet_SysID_.pypp.cpp b/wrapper/System/IDOrSet_SysID_.pypp.cpp index 1da113c03..8c3d1756d 100644 --- a/wrapper/System/IDOrSet_SysID_.pypp.cpp +++ b/wrapper/System/IDOrSet_SysID_.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireID::IDOrSet __copy__(const SireID::IDOrSet &other){ return SireID::IDOrSet(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -165,9 +167,9 @@ void register_IDOrSet_SysID__class(){ } IDOrSet_SysID__exposer.staticmethod( "typeName" ); - IDOrSet_SysID__exposer.def( "__copy__", &__copy__); - IDOrSet_SysID__exposer.def( "__deepcopy__", &__copy__); - IDOrSet_SysID__exposer.def( "clone", &__copy__); + IDOrSet_SysID__exposer.def( "__copy__", &__copy__>); + IDOrSet_SysID__exposer.def( "__deepcopy__", &__copy__>); + IDOrSet_SysID__exposer.def( "clone", &__copy__>); IDOrSet_SysID__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireID::IDOrSet >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IDOrSet_SysID__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireID::IDOrSet >, diff --git a/wrapper/System/IdentityConstraint.pypp.cpp b/wrapper/System/IdentityConstraint.pypp.cpp index e13c3b9d4..a00fc7f05 100644 --- a/wrapper/System/IdentityConstraint.pypp.cpp +++ b/wrapper/System/IdentityConstraint.pypp.cpp @@ -54,6 +54,8 @@ namespace bp = boost::python; SireSystem::IdentityConstraint __copy__(const SireSystem::IdentityConstraint &other){ return SireSystem::IdentityConstraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -220,9 +222,9 @@ void register_IdentityConstraint_class(){ } IdentityConstraint_exposer.staticmethod( "constrain" ); IdentityConstraint_exposer.staticmethod( "typeName" ); - IdentityConstraint_exposer.def( "__copy__", &__copy__); - IdentityConstraint_exposer.def( "__deepcopy__", &__copy__); - IdentityConstraint_exposer.def( "clone", &__copy__); + IdentityConstraint_exposer.def( "__copy__", &__copy__); + IdentityConstraint_exposer.def( "__deepcopy__", &__copy__); + IdentityConstraint_exposer.def( "clone", &__copy__); IdentityConstraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::IdentityConstraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); IdentityConstraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::IdentityConstraint >, diff --git a/wrapper/System/MonitorComponent.pypp.cpp b/wrapper/System/MonitorComponent.pypp.cpp index b452ea47a..473c52b35 100644 --- a/wrapper/System/MonitorComponent.pypp.cpp +++ b/wrapper/System/MonitorComponent.pypp.cpp @@ -20,6 +20,8 @@ namespace bp = boost::python; SireSystem::MonitorComponent __copy__(const SireSystem::MonitorComponent &other){ return SireSystem::MonitorComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -112,9 +114,9 @@ void register_MonitorComponent_class(){ } MonitorComponent_exposer.staticmethod( "typeName" ); - MonitorComponent_exposer.def( "__copy__", &__copy__); - MonitorComponent_exposer.def( "__deepcopy__", &__copy__); - MonitorComponent_exposer.def( "clone", &__copy__); + MonitorComponent_exposer.def( "__copy__", &__copy__); + MonitorComponent_exposer.def( "__deepcopy__", &__copy__); + MonitorComponent_exposer.def( "clone", &__copy__); MonitorComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::MonitorComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MonitorComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::MonitorComponent >, diff --git a/wrapper/System/MonitorComponents.pypp.cpp b/wrapper/System/MonitorComponents.pypp.cpp index 1687174f7..29e031701 100644 --- a/wrapper/System/MonitorComponents.pypp.cpp +++ b/wrapper/System/MonitorComponents.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireSystem::MonitorComponents __copy__(const SireSystem::MonitorComponents &other){ return SireSystem::MonitorComponents(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -183,9 +185,9 @@ void register_MonitorComponents_class(){ } MonitorComponents_exposer.staticmethod( "typeName" ); - MonitorComponents_exposer.def( "__copy__", &__copy__); - MonitorComponents_exposer.def( "__deepcopy__", &__copy__); - MonitorComponents_exposer.def( "clone", &__copy__); + MonitorComponents_exposer.def( "__copy__", &__copy__); + MonitorComponents_exposer.def( "__deepcopy__", &__copy__); + MonitorComponents_exposer.def( "clone", &__copy__); MonitorComponents_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::MonitorComponents >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MonitorComponents_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::MonitorComponents >, diff --git a/wrapper/System/MonitorIdx.pypp.cpp b/wrapper/System/MonitorIdx.pypp.cpp index 211f4d0c3..d0f3dfe0e 100644 --- a/wrapper/System/MonitorIdx.pypp.cpp +++ b/wrapper/System/MonitorIdx.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireSystem::MonitorIdx __copy__(const SireSystem::MonitorIdx &other){ return SireSystem::MonitorIdx(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -132,9 +134,9 @@ void register_MonitorIdx_class(){ } MonitorIdx_exposer.staticmethod( "null" ); MonitorIdx_exposer.staticmethod( "typeName" ); - MonitorIdx_exposer.def( "__copy__", &__copy__); - MonitorIdx_exposer.def( "__deepcopy__", &__copy__); - MonitorIdx_exposer.def( "clone", &__copy__); + MonitorIdx_exposer.def( "__copy__", &__copy__); + MonitorIdx_exposer.def( "__deepcopy__", &__copy__); + MonitorIdx_exposer.def( "clone", &__copy__); MonitorIdx_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::MonitorIdx >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MonitorIdx_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::MonitorIdx >, diff --git a/wrapper/System/MonitorMonitor.pypp.cpp b/wrapper/System/MonitorMonitor.pypp.cpp index f25a05c53..61bbfde7b 100644 --- a/wrapper/System/MonitorMonitor.pypp.cpp +++ b/wrapper/System/MonitorMonitor.pypp.cpp @@ -22,6 +22,8 @@ namespace bp = boost::python; SireSystem::MonitorMonitor __copy__(const SireSystem::MonitorMonitor &other){ return SireSystem::MonitorMonitor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -215,9 +217,9 @@ void register_MonitorMonitor_class(){ } MonitorMonitor_exposer.staticmethod( "typeName" ); - MonitorMonitor_exposer.def( "__copy__", &__copy__); - MonitorMonitor_exposer.def( "__deepcopy__", &__copy__); - MonitorMonitor_exposer.def( "clone", &__copy__); + MonitorMonitor_exposer.def( "__copy__", &__copy__); + MonitorMonitor_exposer.def( "__deepcopy__", &__copy__); + MonitorMonitor_exposer.def( "clone", &__copy__); MonitorMonitor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::MonitorMonitor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MonitorMonitor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::MonitorMonitor >, diff --git a/wrapper/System/MonitorName.pypp.cpp b/wrapper/System/MonitorName.pypp.cpp index 02d751bb5..e3580573b 100644 --- a/wrapper/System/MonitorName.pypp.cpp +++ b/wrapper/System/MonitorName.pypp.cpp @@ -17,6 +17,8 @@ namespace bp = boost::python; SireSystem::MonitorName __copy__(const SireSystem::MonitorName &other){ return SireSystem::MonitorName(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -122,9 +124,9 @@ void register_MonitorName_class(){ } MonitorName_exposer.staticmethod( "typeName" ); - MonitorName_exposer.def( "__copy__", &__copy__); - MonitorName_exposer.def( "__deepcopy__", &__copy__); - MonitorName_exposer.def( "clone", &__copy__); + MonitorName_exposer.def( "__copy__", &__copy__); + MonitorName_exposer.def( "__deepcopy__", &__copy__); + MonitorName_exposer.def( "clone", &__copy__); MonitorName_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::MonitorName >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MonitorName_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::MonitorName >, diff --git a/wrapper/System/MonitorProperty.pypp.cpp b/wrapper/System/MonitorProperty.pypp.cpp index 03c2e539c..4c5562f66 100644 --- a/wrapper/System/MonitorProperty.pypp.cpp +++ b/wrapper/System/MonitorProperty.pypp.cpp @@ -32,6 +32,8 @@ namespace bp = boost::python; SireSystem::MonitorProperty __copy__(const SireSystem::MonitorProperty &other){ return SireSystem::MonitorProperty(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -237,9 +239,9 @@ void register_MonitorProperty_class(){ } MonitorProperty_exposer.staticmethod( "typeName" ); - MonitorProperty_exposer.def( "__copy__", &__copy__); - MonitorProperty_exposer.def( "__deepcopy__", &__copy__); - MonitorProperty_exposer.def( "clone", &__copy__); + MonitorProperty_exposer.def( "__copy__", &__copy__); + MonitorProperty_exposer.def( "__deepcopy__", &__copy__); + MonitorProperty_exposer.def( "clone", &__copy__); MonitorProperty_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::MonitorProperty >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); MonitorProperty_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::MonitorProperty >, diff --git a/wrapper/System/NullConstraint.pypp.cpp b/wrapper/System/NullConstraint.pypp.cpp index 1e2774cf5..30a1f2f77 100644 --- a/wrapper/System/NullConstraint.pypp.cpp +++ b/wrapper/System/NullConstraint.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireSystem::NullConstraint __copy__(const SireSystem::NullConstraint &other){ return SireSystem::NullConstraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -88,9 +90,9 @@ void register_NullConstraint_class(){ } NullConstraint_exposer.staticmethod( "typeName" ); - NullConstraint_exposer.def( "__copy__", &__copy__); - NullConstraint_exposer.def( "__deepcopy__", &__copy__); - NullConstraint_exposer.def( "clone", &__copy__); + NullConstraint_exposer.def( "__copy__", &__copy__); + NullConstraint_exposer.def( "__deepcopy__", &__copy__); + NullConstraint_exposer.def( "clone", &__copy__); NullConstraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::NullConstraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NullConstraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::NullConstraint >, diff --git a/wrapper/System/NullMonitor.pypp.cpp b/wrapper/System/NullMonitor.pypp.cpp index 23fa38097..e68a63933 100644 --- a/wrapper/System/NullMonitor.pypp.cpp +++ b/wrapper/System/NullMonitor.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireSystem::NullMonitor __copy__(const SireSystem::NullMonitor &other){ return SireSystem::NullMonitor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -87,9 +89,9 @@ void register_NullMonitor_class(){ } NullMonitor_exposer.staticmethod( "typeName" ); - NullMonitor_exposer.def( "__copy__", &__copy__); - NullMonitor_exposer.def( "__deepcopy__", &__copy__); - NullMonitor_exposer.def( "clone", &__copy__); + NullMonitor_exposer.def( "__copy__", &__copy__); + NullMonitor_exposer.def( "__deepcopy__", &__copy__); + NullMonitor_exposer.def( "clone", &__copy__); NullMonitor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::NullMonitor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); NullMonitor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::NullMonitor >, diff --git a/wrapper/System/PerturbationConstraint.pypp.cpp b/wrapper/System/PerturbationConstraint.pypp.cpp index 3b78bbd41..36653e9c4 100644 --- a/wrapper/System/PerturbationConstraint.pypp.cpp +++ b/wrapper/System/PerturbationConstraint.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireSystem::PerturbationConstraint __copy__(const SireSystem::PerturbationConstraint &other){ return SireSystem::PerturbationConstraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -114,9 +116,9 @@ void register_PerturbationConstraint_class(){ } PerturbationConstraint_exposer.staticmethod( "typeName" ); - PerturbationConstraint_exposer.def( "__copy__", &__copy__); - PerturbationConstraint_exposer.def( "__deepcopy__", &__copy__); - PerturbationConstraint_exposer.def( "clone", &__copy__); + PerturbationConstraint_exposer.def( "__copy__", &__copy__); + PerturbationConstraint_exposer.def( "__deepcopy__", &__copy__); + PerturbationConstraint_exposer.def( "clone", &__copy__); PerturbationConstraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::PerturbationConstraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PerturbationConstraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::PerturbationConstraint >, diff --git a/wrapper/System/PolariseCharges.pypp.cpp b/wrapper/System/PolariseCharges.pypp.cpp index 560661a0c..4a588d976 100644 --- a/wrapper/System/PolariseCharges.pypp.cpp +++ b/wrapper/System/PolariseCharges.pypp.cpp @@ -64,6 +64,8 @@ namespace bp = boost::python; SireSystem::PolariseCharges __copy__(const SireSystem::PolariseCharges &other){ return SireSystem::PolariseCharges(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -182,9 +184,9 @@ void register_PolariseCharges_class(){ } PolariseCharges_exposer.staticmethod( "typeName" ); - PolariseCharges_exposer.def( "__copy__", &__copy__); - PolariseCharges_exposer.def( "__deepcopy__", &__copy__); - PolariseCharges_exposer.def( "clone", &__copy__); + PolariseCharges_exposer.def( "__copy__", &__copy__); + PolariseCharges_exposer.def( "__deepcopy__", &__copy__); + PolariseCharges_exposer.def( "clone", &__copy__); PolariseCharges_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::PolariseCharges >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PolariseCharges_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::PolariseCharges >, diff --git a/wrapper/System/PolariseChargesFF.pypp.cpp b/wrapper/System/PolariseChargesFF.pypp.cpp index 3c370c15a..fb6b47adb 100644 --- a/wrapper/System/PolariseChargesFF.pypp.cpp +++ b/wrapper/System/PolariseChargesFF.pypp.cpp @@ -64,6 +64,8 @@ namespace bp = boost::python; SireSystem::PolariseChargesFF __copy__(const SireSystem::PolariseChargesFF &other){ return SireSystem::PolariseChargesFF(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -184,9 +186,9 @@ void register_PolariseChargesFF_class(){ } PolariseChargesFF_exposer.staticmethod( "typeName" ); - PolariseChargesFF_exposer.def( "__copy__", &__copy__); - PolariseChargesFF_exposer.def( "__deepcopy__", &__copy__); - PolariseChargesFF_exposer.def( "clone", &__copy__); + PolariseChargesFF_exposer.def( "__copy__", &__copy__); + PolariseChargesFF_exposer.def( "__deepcopy__", &__copy__); + PolariseChargesFF_exposer.def( "clone", &__copy__); PolariseChargesFF_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::PolariseChargesFF >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PolariseChargesFF_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::PolariseChargesFF >, diff --git a/wrapper/System/PropertyConstraint.pypp.cpp b/wrapper/System/PropertyConstraint.pypp.cpp index c5921ba2e..a2c529ab8 100644 --- a/wrapper/System/PropertyConstraint.pypp.cpp +++ b/wrapper/System/PropertyConstraint.pypp.cpp @@ -35,6 +35,8 @@ namespace bp = boost::python; SireSystem::PropertyConstraint __copy__(const SireSystem::PropertyConstraint &other){ return SireSystem::PropertyConstraint(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -90,9 +92,9 @@ void register_PropertyConstraint_class(){ } PropertyConstraint_exposer.staticmethod( "typeName" ); - PropertyConstraint_exposer.def( "__copy__", &__copy__); - PropertyConstraint_exposer.def( "__deepcopy__", &__copy__); - PropertyConstraint_exposer.def( "clone", &__copy__); + PropertyConstraint_exposer.def( "__copy__", &__copy__); + PropertyConstraint_exposer.def( "__deepcopy__", &__copy__); + PropertyConstraint_exposer.def( "clone", &__copy__); PropertyConstraint_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::PropertyConstraint >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); PropertyConstraint_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::PropertyConstraint >, diff --git a/wrapper/System/SireSystem_registrars.cpp b/wrapper/System/SireSystem_registrars.cpp index 78bae3b56..596197b4a 100644 --- a/wrapper/System/SireSystem_registrars.cpp +++ b/wrapper/System/SireSystem_registrars.cpp @@ -27,6 +27,7 @@ #include "distancecomponent.h" #include "closemols.h" #include "system.h" +#include "systemtrajectory.h" #include "monitorproperty.h" #include "volmapmonitor.h" #include "monitorname.h" @@ -74,6 +75,8 @@ void register_SireSystem_objects() ObjectRegistry::registerConverterFor< SireSystem::TripleDistanceComponent >(); ObjectRegistry::registerConverterFor< SireSystem::CloseMols >(); ObjectRegistry::registerConverterFor< SireSystem::System >(); + ObjectRegistry::registerConverterFor< SireSystem::SystemTrajectory >(); + ObjectRegistry::registerConverterFor< SireSystem::MolSystemTrajectory >(); ObjectRegistry::registerConverterFor< SireSystem::MonitorProperty >(); ObjectRegistry::registerConverterFor< SireSystem::VolMapMonitor >(); ObjectRegistry::registerConverterFor< SireSystem::MonitorName >(); diff --git a/wrapper/System/SpaceWrapper.pypp.cpp b/wrapper/System/SpaceWrapper.pypp.cpp index a2a74572b..5adbeb296 100644 --- a/wrapper/System/SpaceWrapper.pypp.cpp +++ b/wrapper/System/SpaceWrapper.pypp.cpp @@ -30,6 +30,8 @@ namespace bp = boost::python; SireSystem::SpaceWrapper __copy__(const SireSystem::SpaceWrapper &other){ return SireSystem::SpaceWrapper(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -108,9 +110,9 @@ void register_SpaceWrapper_class(){ } SpaceWrapper_exposer.staticmethod( "typeName" ); - SpaceWrapper_exposer.def( "__copy__", &__copy__); - SpaceWrapper_exposer.def( "__deepcopy__", &__copy__); - SpaceWrapper_exposer.def( "clone", &__copy__); + SpaceWrapper_exposer.def( "__copy__", &__copy__); + SpaceWrapper_exposer.def( "__deepcopy__", &__copy__); + SpaceWrapper_exposer.def( "clone", &__copy__); SpaceWrapper_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::SpaceWrapper >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SpaceWrapper_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::SpaceWrapper >, diff --git a/wrapper/System/Specify_MonitorID_.pypp.cpp b/wrapper/System/Specify_MonitorID_.pypp.cpp index ad8a803a9..ccf575686 100644 --- a/wrapper/System/Specify_MonitorID_.pypp.cpp +++ b/wrapper/System/Specify_MonitorID_.pypp.cpp @@ -23,6 +23,8 @@ namespace bp = boost::python; SireID::Specify __copy__(const SireID::Specify &other){ return SireID::Specify(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -216,9 +218,9 @@ void register_Specify_MonitorID__class(){ } Specify_MonitorID__exposer.staticmethod( "typeName" ); - Specify_MonitorID__exposer.def( "__copy__", &__copy__); - Specify_MonitorID__exposer.def( "__deepcopy__", &__copy__); - Specify_MonitorID__exposer.def( "clone", &__copy__); + Specify_MonitorID__exposer.def( "__copy__", &__copy__>); + Specify_MonitorID__exposer.def( "__deepcopy__", &__copy__>); + Specify_MonitorID__exposer.def( "clone", &__copy__>); Specify_MonitorID__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireID::Specify >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Specify_MonitorID__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireID::Specify >, diff --git a/wrapper/System/Specify_SysID_.pypp.cpp b/wrapper/System/Specify_SysID_.pypp.cpp index 0393793d7..edd900dea 100644 --- a/wrapper/System/Specify_SysID_.pypp.cpp +++ b/wrapper/System/Specify_SysID_.pypp.cpp @@ -21,6 +21,8 @@ namespace bp = boost::python; SireID::Specify __copy__(const SireID::Specify &other){ return SireID::Specify(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -214,9 +216,9 @@ void register_Specify_SysID__class(){ } Specify_SysID__exposer.staticmethod( "typeName" ); - Specify_SysID__exposer.def( "__copy__", &__copy__); - Specify_SysID__exposer.def( "__deepcopy__", &__copy__); - Specify_SysID__exposer.def( "clone", &__copy__); + Specify_SysID__exposer.def( "__copy__", &__copy__>); + Specify_SysID__exposer.def( "__deepcopy__", &__copy__>); + Specify_SysID__exposer.def( "clone", &__copy__>); Specify_SysID__exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireID::Specify >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); Specify_SysID__exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireID::Specify >, diff --git a/wrapper/System/SysIdx.pypp.cpp b/wrapper/System/SysIdx.pypp.cpp index e185ba62e..5e6fade82 100644 --- a/wrapper/System/SysIdx.pypp.cpp +++ b/wrapper/System/SysIdx.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireSystem::SysIdx __copy__(const SireSystem::SysIdx &other){ return SireSystem::SysIdx(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -128,9 +130,9 @@ void register_SysIdx_class(){ } SysIdx_exposer.staticmethod( "null" ); SysIdx_exposer.staticmethod( "typeName" ); - SysIdx_exposer.def( "__copy__", &__copy__); - SysIdx_exposer.def( "__deepcopy__", &__copy__); - SysIdx_exposer.def( "clone", &__copy__); + SysIdx_exposer.def( "__copy__", &__copy__); + SysIdx_exposer.def( "__deepcopy__", &__copy__); + SysIdx_exposer.def( "clone", &__copy__); SysIdx_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::SysIdx >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SysIdx_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::SysIdx >, diff --git a/wrapper/System/SysName.pypp.cpp b/wrapper/System/SysName.pypp.cpp index 7d238a215..8c9cc4c62 100644 --- a/wrapper/System/SysName.pypp.cpp +++ b/wrapper/System/SysName.pypp.cpp @@ -13,6 +13,8 @@ namespace bp = boost::python; SireSystem::SysName __copy__(const SireSystem::SysName &other){ return SireSystem::SysName(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -118,9 +120,9 @@ void register_SysName_class(){ } SysName_exposer.staticmethod( "typeName" ); - SysName_exposer.def( "__copy__", &__copy__); - SysName_exposer.def( "__deepcopy__", &__copy__); - SysName_exposer.def( "clone", &__copy__); + SysName_exposer.def( "__copy__", &__copy__); + SysName_exposer.def( "__deepcopy__", &__copy__); + SysName_exposer.def( "clone", &__copy__); SysName_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::SysName >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SysName_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::SysName >, diff --git a/wrapper/System/System.pypp.cpp b/wrapper/System/System.pypp.cpp index 99f71009f..f798d4e61 100644 --- a/wrapper/System/System.pypp.cpp +++ b/wrapper/System/System.pypp.cpp @@ -76,6 +76,8 @@ namespace bp = boost::python; SireSystem::System __copy__(const SireSystem::System &other){ return SireSystem::System(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -1369,6 +1371,32 @@ void register_System_class(){ , bp::release_gil_policy() , "" ); + } + { //::SireSystem::System::makeWhole + + typedef void ( ::SireSystem::System::*makeWhole_function_type)( ::SireMaths::Vector const & ) ; + makeWhole_function_type makeWhole_function_value( &::SireSystem::System::makeWhole ); + + System_exposer.def( + "makeWhole" + , makeWhole_function_value + , ( bp::arg("center") ) + , bp::release_gil_policy() + , "" ); + + } + { //::SireSystem::System::makeWhole + + typedef void ( ::SireSystem::System::*makeWhole_function_type)( ::SireMaths::Vector const &,::SireBase::PropertyMap const & ) ; + makeWhole_function_type makeWhole_function_value( &::SireSystem::System::makeWhole ); + + System_exposer.def( + "makeWhole" + , makeWhole_function_value + , ( bp::arg("center"), bp::arg("map") ) + , bp::release_gil_policy() + , "" ); + } { //::SireSystem::System::monitor @@ -2622,9 +2650,9 @@ void register_System_class(){ } System_exposer.staticmethod( "null" ); System_exposer.staticmethod( "typeName" ); - System_exposer.def( "__copy__", &__copy__); - System_exposer.def( "__deepcopy__", &__copy__); - System_exposer.def( "clone", &__copy__); + System_exposer.def( "__copy__", &__copy__); + System_exposer.def( "__deepcopy__", &__copy__); + System_exposer.def( "clone", &__copy__); System_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::System >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); System_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::System >, diff --git a/wrapper/System/SystemMonitors.pypp.cpp b/wrapper/System/SystemMonitors.pypp.cpp index 2ff15bf90..e2870b87c 100644 --- a/wrapper/System/SystemMonitors.pypp.cpp +++ b/wrapper/System/SystemMonitors.pypp.cpp @@ -28,6 +28,8 @@ namespace bp = boost::python; SireSystem::SystemMonitors __copy__(const SireSystem::SystemMonitors &other){ return SireSystem::SystemMonitors(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" const char* pvt_get_name(const SireSystem::SystemMonitors&){ return "SireSystem::SystemMonitors";} @@ -423,9 +425,9 @@ void register_SystemMonitors_class(){ } SystemMonitors_exposer.staticmethod( "typeName" ); - SystemMonitors_exposer.def( "__copy__", &__copy__); - SystemMonitors_exposer.def( "__deepcopy__", &__copy__); - SystemMonitors_exposer.def( "clone", &__copy__); + SystemMonitors_exposer.def( "__copy__", &__copy__); + SystemMonitors_exposer.def( "__deepcopy__", &__copy__); + SystemMonitors_exposer.def( "clone", &__copy__); SystemMonitors_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::SystemMonitors >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); SystemMonitors_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::SystemMonitors >, diff --git a/wrapper/System/TripleDistanceComponent.pypp.cpp b/wrapper/System/TripleDistanceComponent.pypp.cpp index d9c7750ec..c12d81f58 100644 --- a/wrapper/System/TripleDistanceComponent.pypp.cpp +++ b/wrapper/System/TripleDistanceComponent.pypp.cpp @@ -26,6 +26,8 @@ namespace bp = boost::python; SireSystem::TripleDistanceComponent __copy__(const SireSystem::TripleDistanceComponent &other){ return SireSystem::TripleDistanceComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -217,9 +219,9 @@ void register_TripleDistanceComponent_class(){ TripleDistanceComponent_exposer.staticmethod( "r23" ); TripleDistanceComponent_exposer.staticmethod( "r45" ); TripleDistanceComponent_exposer.staticmethod( "typeName" ); - TripleDistanceComponent_exposer.def( "__copy__", &__copy__); - TripleDistanceComponent_exposer.def( "__deepcopy__", &__copy__); - TripleDistanceComponent_exposer.def( "clone", &__copy__); + TripleDistanceComponent_exposer.def( "__copy__", &__copy__); + TripleDistanceComponent_exposer.def( "__deepcopy__", &__copy__); + TripleDistanceComponent_exposer.def( "clone", &__copy__); TripleDistanceComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::TripleDistanceComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); TripleDistanceComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::TripleDistanceComponent >, diff --git a/wrapper/System/VolMapMonitor.pypp.cpp b/wrapper/System/VolMapMonitor.pypp.cpp index c1efc7489..29192b7b2 100644 --- a/wrapper/System/VolMapMonitor.pypp.cpp +++ b/wrapper/System/VolMapMonitor.pypp.cpp @@ -40,6 +40,8 @@ namespace bp = boost::python; SireSystem::VolMapMonitor __copy__(const SireSystem::VolMapMonitor &other){ return SireSystem::VolMapMonitor(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -282,9 +284,9 @@ void register_VolMapMonitor_class(){ } VolMapMonitor_exposer.staticmethod( "typeName" ); - VolMapMonitor_exposer.def( "__copy__", &__copy__); - VolMapMonitor_exposer.def( "__deepcopy__", &__copy__); - VolMapMonitor_exposer.def( "clone", &__copy__); + VolMapMonitor_exposer.def( "__copy__", &__copy__); + VolMapMonitor_exposer.def( "__deepcopy__", &__copy__); + VolMapMonitor_exposer.def( "clone", &__copy__); VolMapMonitor_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::VolMapMonitor >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); VolMapMonitor_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::VolMapMonitor >, diff --git a/wrapper/System/WindowedComponent.pypp.cpp b/wrapper/System/WindowedComponent.pypp.cpp index 3e7c40cf1..282203fff 100644 --- a/wrapper/System/WindowedComponent.pypp.cpp +++ b/wrapper/System/WindowedComponent.pypp.cpp @@ -36,6 +36,8 @@ namespace bp = boost::python; SireSystem::WindowedComponent __copy__(const SireSystem::WindowedComponent &other){ return SireSystem::WindowedComponent(other); } +#include "Helpers/copy.hpp" + #include "Qt/qdatastream.hpp" #include "Helpers/str.hpp" @@ -138,9 +140,9 @@ void register_WindowedComponent_class(){ } WindowedComponent_exposer.staticmethod( "typeName" ); - WindowedComponent_exposer.def( "__copy__", &__copy__); - WindowedComponent_exposer.def( "__deepcopy__", &__copy__); - WindowedComponent_exposer.def( "clone", &__copy__); + WindowedComponent_exposer.def( "__copy__", &__copy__); + WindowedComponent_exposer.def( "__deepcopy__", &__copy__); + WindowedComponent_exposer.def( "clone", &__copy__); WindowedComponent_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireSystem::WindowedComponent >, bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); WindowedComponent_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireSystem::WindowedComponent >, From 7074b84a101ccbbc1efc37cd5d986663344311eb Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 23 Jun 2024 17:56:01 +0100 Subject: [PATCH 317/468] Adding a changelog entry --- doc/source/changelog.rst | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index ac86ad415..95045e4ec 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -68,6 +68,13 @@ organisation on `GitHub `__. correct AtomIdx, rather than added as the last atoms in the molecule. This is also more natural. This fixes issue #202. +* Added the "center" keyword argument to the ``make_whole`` functions of + :class:`~sire.mol.Cursors`, :class:`~sire.mol.CursorsM` and + :class:`~sire.system.System` (as well as to the legacy System class). + Also allowed the constructor of :class:`~sire.maths.Vector` to recognise + ``origin`` and ``zero`` as arguments, meaning you can write + ``cursor.make_whole(center="origin")``. This fixes issue #199. + * Please add an item to this changelog when you create your PR `2024.1.0 `__ - April 2024 From 594f0ffbff58276cae8c2aa53253b93bfb4fd370 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 24 Jun 2024 10:24:50 +0100 Subject: [PATCH 318/468] Move info regarding selection and link atoms into intro. --- doc/source/tutorial/partXX/01_intro.rst | 7 +++++++ doc/source/tutorial/partXX/02_emle.rst | 8 -------- 2 files changed, 7 insertions(+), 8 deletions(-) diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst index 03080cfca..86b11fde5 100644 --- a/doc/source/tutorial/partXX/01_intro.rst +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -41,6 +41,13 @@ an engine to perform the calculation: Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule). +The selection syntax for QM atoms is extremely flexible. Any valid search string, +atom index, list of atom indicies, or molecule view/container that can be used. +Support for modelling partial molecules at the QM level is provided via the link +atom approach, via the charge shifting method. For details of this implementation, +see, e.g., the NAMD user guide `here `_. +While we support multiple QM fragments, we do not currently support multiple +*independent* QM regions. We plan on adding support for this in the near future. The third argument is the Python object that will be used to perform the QM calculation. The fourth argument is the name of the callback function that will be used. If ``None``, then it assumed that the ``py_object`` itself is a callable, diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index 3900f8974..87092e9fb 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -68,14 +68,6 @@ interpolated between MM and QM levels of theory, along with an engine. The engine registers a Python callback that uses ``emle-engine`` to perform the QM calculation. -The selection syntax for QM atoms is extremely flexible. Any valid search string, -atom index, list of atom indicies, or molecule view/container that can be used. -Support for modelling partial molecules at the QM level is provided via the link -atom approach, via the charge shifting method. For details of this implementation, -see, e.g., the NAMD user guide `here `_. -While we support multiple QM fragments, we do not currently support multiple -*independent* QM regions. We plan on adding support for this in the near future. - Running a QM/MM simulation -------------------------- From 1eb82ffb3dc368a9ebef5e2620ae5877da7daf5d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 24 Jun 2024 10:33:14 +0100 Subject: [PATCH 319/468] Catch errors from callback. --- wrapper/Convert/SireOpenMM/pyqm.cpp | 50 ++++++++++++++++++++--------- 1 file changed, 35 insertions(+), 15 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index 74db8513a..4e7402e19 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -160,24 +160,44 @@ PyQMCallback::call( if (this->is_method) { - return bp::call_method>, QVector>>>( - this->py_object.ptr(), - this->name.toStdString().c_str(), - numbers_qm, - charges_mm, - xyz_qm, - xyz_mm - ); + try + { + return bp::call_method>, QVector>>>( + this->py_object.ptr(), + this->name.toStdString().c_str(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm + ); + } + catch (const bp::error_already_set &) + { + PyErr_Print(); + throw SireError::process_error(QObject::tr( + "An error occurred when calling the QM Python callback method"), + CODELOC); + } } else { - return bp::call>, QVector>>>( - this->py_object.ptr(), - numbers_qm, - charges_mm, - xyz_qm, - xyz_mm - ); + try + { + return bp::call>, QVector>>>( + this->py_object.ptr(), + numbers_qm, + charges_mm, + xyz_qm, + xyz_mm + ); + } + catch (const bp::error_already_set &) + { + PyErr_Print(); + throw SireError::process_error(QObject::tr( + "An error occurred when calling the QM Python callback method"), + CODELOC); + } } } From 5e013d3ef2b4dcf30b33ef2899ca6d4ae4ee2c7e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 24 Jun 2024 11:55:52 +0100 Subject: [PATCH 320/468] Add test for using a simple callback with create_engine. --- tests/qm/test_qm.py | 50 ++++++++++++++++++++++++++++++++++++++------- 1 file changed, 43 insertions(+), 7 deletions(-) diff --git a/tests/qm/test_qm.py b/tests/qm/test_qm.py index 9316dc1e7..f3ea81e66 100644 --- a/tests/qm/test_qm.py +++ b/tests/qm/test_qm.py @@ -4,7 +4,7 @@ from sire.legacy.Convert import PyQMCallback -from sire.qm import emle +import sire as sr try: from emle.calculator import EMLECalculator @@ -190,7 +190,7 @@ def test_emle_interpolate(ala_mols, selection): nrg_mm = d.current_potential_energy() # Create an EMLE engine bound to the calculator. - mols, engine = emle(mols, selection, calculator) + mols, engine = sr.qm.emle(mols, selection, calculator) # Create a QM/MM capable dynamics object. d = mols.dynamics( @@ -234,7 +234,7 @@ def test_emle_openmm_ml(ala_mols): calculator = EMLECalculator(backend="torchani", device="cpu") # Create an EMLE engine bound to the calculator. - emle_mols, engine = emle(mols, mols[0], calculator) + emle_mols, engine = sr.qm.emle(mols, mols[0], calculator) # Create a QM/MM capable dynamics object. d = emle_mols.dynamics( @@ -254,7 +254,7 @@ def test_emle_openmm_ml(ala_mols): calculator = EMLECalculator(backend=None, device="cpu") # Create an EMLE engine bound to the calculator. - emle_mols, engine = emle(mols, mols[0], calculator) + emle_mols, engine = sr.qm.emle(mols, mols[0], calculator) # The first molecule (the dipeptide) is the QM region. This is # perturbable and can be interpolated between MM (the reference state) @@ -326,9 +326,6 @@ def test_emle_indirect(ala_mols): setup for EMLE engines. """ - import openmm - import sire as sr - # Create a local copy of the test system. mols = ala_mols.clone() @@ -352,3 +349,42 @@ def test_emle_indirect(ala_mols): # Get the potential energy. This will fail if the callback can't be found. d.current_potential_energy() + + +def test_create_engine(ala_mols): + """ + Make sure that a QM/MM engine can be created and used via a simple callback + function. + """ + + # A test callback function. Returns a known energy and dummy forces. + def callback(numbers_qm, charges_mm, xyz_qm, xyz_mm): + return (42, xyz_qm, xyz_mm) + + # Create a local copy of the test system. + mols = ala_mols.clone() + + # Create a QM engine bound to the callback. + qm_mols, engine = sr.qm.create_engine( + mols, + mols[0], + callback, + callback=None, + ) + + # Create a QM/MM capable dynamics object for the QM molecule only. + d = qm_mols[0].dynamics( + timestep="1fs", + constraint="none", + qm_engine=engine, + cutoff_type="pme", + cutoff="7.5 A", + platform="cpu", + ) + + # Get the potential energy. This should equal the value returned by the + # callback, i.e. 42. + nrg = d.current_potential_energy().to("kJ_per_mol") + + # Make sure the energy is correct. + assert nrg == 42 From 71b354057f42aab774c9321ae669be65cce803f2 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sat, 29 Jun 2024 18:31:38 +0100 Subject: [PATCH 321/468] Updated for 2024.3.0 development [ci skip] --- doc/source/changelog.rst | 7 +++++-- version.txt | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 95045e4ec..72ad734b3 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -12,6 +12,11 @@ Development was migrated into the `OpenBioSim `__ organisation on `GitHub `__. +`2024.3.0 `__ - September 2024 +---------------------------------------------------------------------------------------------- + +* Please add an item to this changelog when you create your PR + `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- @@ -75,8 +80,6 @@ organisation on `GitHub `__. ``origin`` and ``zero`` as arguments, meaning you can write ``cursor.make_whole(center="origin")``. This fixes issue #199. -* Please add an item to this changelog when you create your PR - `2024.1.0 `__ - April 2024 ------------------------------------------------------------------------------------------ diff --git a/version.txt b/version.txt index 5dc9f0c61..3cb3977c1 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -2024.2.0.dev +2024.3.0.dev From e235e51253c2fd55ebb57f372cb3b8c5008fed64 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sun, 30 Jun 2024 11:39:49 +0100 Subject: [PATCH 322/468] Add support for optimised Sire callback using ANI2xEMLE model. --- src/sire/qm/_emle.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 9aedad47c..243deb67d 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -151,10 +151,22 @@ def emle( raise TypeError("'map' must be of type 'dict'") map = _create_map(map) + # Determine the callback name. Use an optimised version of the callback + # if the user has specified "torchani" as the backend and is using + # "electrostatic" embedding. + if calculator._backend == "torchani" and calculator._method == "electrostatic": + try: + from emle.models import ANI2xEMLE as _ANI2xEMLE + callback = "_sire_callback_optimised" + except: + callback = "_sire_callback" + else: + callback = "_sire_callback" + # Create the EMLE engine. engine = EMLEEngine( calculator, - "_sire_callback", + callback, cutoff, neighbourlist_update_frequency, False, From f23de21ccaa9c027c26779df146650579f1d3fb4 Mon Sep 17 00:00:00 2001 From: Christopher Woods Date: Sun, 30 Jun 2024 12:37:43 +0100 Subject: [PATCH 323/468] Python 3.12 fully supported now on MacOS ARM64 [ci skip] --- .github/workflows/main.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 0b2c9ad5e..158f4e438 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -29,10 +29,6 @@ jobs: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - exclude: - - platform: - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.12" # MacOS can't run 3.12 yet... environment: name: sire-build defaults: From dd24ebf851eea7d88b252a658843979aaa4d5a6d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 2 Jul 2024 15:02:32 +0100 Subject: [PATCH 324/468] Standardise neighbour_list_frequency kwarg. --- doc/source/tutorial/partXX/01_intro.rst | 4 ++-- doc/source/tutorial/partXX/02_emle.rst | 4 ++-- src/sire/qm/__init__.py | 16 ++++++++-------- src/sire/qm/_emle.py | 17 +++++++++-------- 4 files changed, 21 insertions(+), 20 deletions(-) diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst index 86b11fde5..6bda650bb 100644 --- a/doc/source/tutorial/partXX/01_intro.rst +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -35,7 +35,7 @@ an engine to perform the calculation: >>> ... py_object, >>> ... callback="callback", >>> ... cutoff="7.5A", ->>> ... neighbour_list_update_frequency=20, +>>> ... neighbour_list_frequency=20, >>> ... mechanical_embedding=False, >>> ... ) @@ -68,7 +68,7 @@ atoms in mod electron charge, the coordinates of the QM atoms in Angstrom, and the coordinates of the MM atoms in Angstrom. It should return the calculated energy in kJ/mol, the forces on the QM atoms in kJ/mol/nm, and the forces on the MM atoms in kJ/mol/nm. The remaining arguments are optional and specify -the QM cutoff distance, the neigbour list update frequency, and whether the +the QM cutoff distance, the neighbour list update frequency, and whether the electrostatics should be treated with mechanical embedding. When mechanical embedding is used, the electrostatics are treated at the MM level by ``OpenMM``. Note that this doesn't change the signature of the callback function, i.e. it diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index 87092e9fb..112e3b450 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -55,13 +55,13 @@ an engine to perform the calculation: >>> ... mols[0], >>> ... calculator, >>> ... cutoff="7.5A", ->>> ... neighbour_list_update_frequency=20 +>>> ... neighbour_list_frequency=20 >>> ) Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule), and the third is calculator that was created above. The fourth and fifth arguments -are optional, and specify the QM cutoff distance and the neigbour list update +are optional, and specify the QM cutoff distance and the neighbour list update frequency respectively. (Shown are the default values.) The function returns a modified version of the molecules containing a "merged" dipeptide that can be interpolated between MM and QM levels of theory, along with an engine. The diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index d9b0917c6..3137d1401 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -16,7 +16,7 @@ def create_engine( py_object, callback=None, cutoff="7.5A", - neighbourlist_update_frequency=20, + neighbour_list_frequency=20, mechanical_embedding=False, redistribute_charge=False, map=None, @@ -55,8 +55,8 @@ def create_engine( cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. - neighbourlist_update_frequency : int, optional, default=20 - The frequency with which to update the neighbourlist. + neighbour_list_frequency : int, optional, default=20 + The frequency with which to update the neighbour list. mechanical_embedding: bool, optional, default=False Whether to use mechanical embedding. If True, then electrostatics will @@ -117,11 +117,11 @@ def create_engine( if not cutoff.has_same_units(_angstrom): raise ValueError("'cutoff' must be in units of length") - if not isinstance(neighbourlist_update_frequency, int): - raise TypeError("'neighbourlist_update_frequency' must be of type 'int'") + if not isinstance(neighbour_list_frequency, int): + raise TypeError("'neighbour_list_frequency' must be of type 'int'") - if neighbourlist_update_frequency < 0: - raise ValueError("'neighbourlist_update_frequency' must be >= 0") + if neighbour_list_frequency < 0: + raise ValueError("'neighbour_list_frequency' must be >= 0") if not isinstance(mechanical_embedding, bool): raise TypeError("'mechanical_embedding' must be of type 'bool'") @@ -139,7 +139,7 @@ def create_engine( py_object, callback, cutoff, - neighbourlist_update_frequency, + neighbour_list_frequency, mechanical_embedding, ) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 243deb67d..b4c2612da 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -54,7 +54,7 @@ def emle( qm_atoms, calculator, cutoff="7.5A", - neighbourlist_update_frequency=20, + neighbour_list_frequency=20, redistribute_charge=False, map=None, ): @@ -78,8 +78,8 @@ def emle( cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. - neighbourlist_update_frequency : int, optional, default=20 - The frequency with which to update the neighbourlist. + neighbour_list_frequency : int, optional, default=20 + The frequency with which to update the neighbour list. redistribute_charge : bool Whether to redistribute charge of the QM atoms to ensure that the total @@ -137,11 +137,11 @@ def emle( if not cutoff.has_same_units(_angstrom): raise ValueError("'cutoff' must be in units of length") - if not isinstance(neighbourlist_update_frequency, int): - raise TypeError("'neighbourlist_update_frequency' must be of type 'int'") + if not isinstance(neighbour_list_frequency, int): + raise TypeError("'neighbour_list_frequency' must be of type 'int'") - if neighbourlist_update_frequency < 0: - raise ValueError("'neighbourlist_update_frequency' must be >= 0") + if neighbour_list_frequency < 0: + raise ValueError("'neighbour_list_frequency' must be >= 0") if not isinstance(redistribute_charge, bool): raise TypeError("'redistribute_charge' must be of type 'bool'") @@ -157,6 +157,7 @@ def emle( if calculator._backend == "torchani" and calculator._method == "electrostatic": try: from emle.models import ANI2xEMLE as _ANI2xEMLE + callback = "_sire_callback_optimised" except: callback = "_sire_callback" @@ -168,7 +169,7 @@ def emle( calculator, callback, cutoff, - neighbourlist_update_frequency, + neighbour_list_frequency, False, ) From 4ba9b9751a4422c2969a0c7a3c04c6f3c10e8c02 Mon Sep 17 00:00:00 2001 From: jmichel80 Date: Wed, 10 Jul 2024 12:54:56 +0100 Subject: [PATCH 325/468] now printing to stdout the identify of the water molecules that are perturbed into ions if a co-alchemical water perturbation has been activated --- wrapper/Tools/OpenMMMD.py | 1 + 1 file changed, 1 insertion(+) diff --git a/wrapper/Tools/OpenMMMD.py b/wrapper/Tools/OpenMMMD.py index 6114c80f3..82a38d4b0 100644 --- a/wrapper/Tools/OpenMMMD.py +++ b/wrapper/Tools/OpenMMMD.py @@ -2505,6 +2505,7 @@ def selectWatersForPerturbation(system, charge_diff): # FIXME: select waters according to distance criterion # if mol.residue().name() == water_resname and cnt < nions: if mol.residues()[0].name() == water_resname and cnt < nions: + print ("Selected water %s for perturbation into ion" % mol) cnt += 1 perturbed_water = mol.edit() From db0d862f702b7ba3c1a4ec7901fa19baeab69bdc Mon Sep 17 00:00:00 2001 From: jmichel80 Date: Wed, 10 Jul 2024 14:14:33 +0100 Subject: [PATCH 326/468] print the first residue of the molecule instead of the molecule for easier cross referencing to the loaded prm7 input --- wrapper/Tools/OpenMMMD.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Tools/OpenMMMD.py b/wrapper/Tools/OpenMMMD.py index 82a38d4b0..45f7017ee 100644 --- a/wrapper/Tools/OpenMMMD.py +++ b/wrapper/Tools/OpenMMMD.py @@ -2505,7 +2505,7 @@ def selectWatersForPerturbation(system, charge_diff): # FIXME: select waters according to distance criterion # if mol.residue().name() == water_resname and cnt < nions: if mol.residues()[0].name() == water_resname and cnt < nions: - print ("Selected water %s for perturbation into ion" % mol) + print ("Selected water residue %s for perturbation into ion" % (mol.residues()[0])) cnt += 1 perturbed_water = mol.edit() From a74235737d223d19624bc6ea171c6c3f5b1e6b06 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 10 Jul 2024 15:49:55 +0100 Subject: [PATCH 327/468] Add function to create ions from AMBER templates. --- corelib/src/libs/SireIO/biosimspace.cpp | 62 +++++++++++ corelib/src/libs/SireIO/biosimspace.h | 34 +++++++ corelib/templates/ions/cl_tip3p.prm7 | 130 ++++++++++++++++++++++++ corelib/templates/ions/cl_tip4p.prm7 | 130 ++++++++++++++++++++++++ corelib/templates/ions/na_tip3p.prm7 | 130 ++++++++++++++++++++++++ corelib/templates/ions/na_tip4p.prm7 | 130 ++++++++++++++++++++++++ wrapper/IO/_IO_free_functions.pypp.cpp | 90 ++++++++++++++++ 7 files changed, 706 insertions(+) create mode 100644 corelib/templates/ions/cl_tip3p.prm7 create mode 100644 corelib/templates/ions/cl_tip4p.prm7 create mode 100644 corelib/templates/ions/na_tip3p.prm7 create mode 100644 corelib/templates/ions/na_tip4p.prm7 diff --git a/corelib/src/libs/SireIO/biosimspace.cpp b/corelib/src/libs/SireIO/biosimspace.cpp index 94a9a74cf..0eb4ade06 100644 --- a/corelib/src/libs/SireIO/biosimspace.cpp +++ b/corelib/src/libs/SireIO/biosimspace.cpp @@ -1589,6 +1589,68 @@ namespace SireIO return retval; } + Molecule createSodiumIon(const Vector &coords, const QString model, const PropertyMap &map) + { + // Strip all whitespace from the model name and convert to upper case. + auto _model = model.simplified().replace(" ", "").toUpper(); + + // Create a hash between the allowed model names and their templace files. + QHash models; + models["TIP3P"] = getShareDir() + "/templates/ions/na_tip3p"; + models["TIP4P"] = getShareDir() + "/templates/ions/na_tip4p"; + + // Make sure the user has passed a valid water model. + if (not models.contains(_model)) + { + throw SireError::incompatible_error(QObject::tr("Unsupported AMBER ion model '%1'").arg(model), CODELOC); + } + + // Extract the water model template path. + auto path = models[_model]; + + // Load the ion template. + auto ion_template = MoleculeParser::read(path + ".prm7", map); + + // Extract the ion the template. + auto ion = ion_template[MolIdx(0)].molecule(); + + // Set the coordinates of the ion. + ion = ion.edit().atom(AtomIdx(0)).setProperty(map["coordinates"], coords).molecule().commit(); + + return ion; + } + + Molecule createChlorineIon(const Vector &coords, const QString model, const PropertyMap &map) + { + // Strip all whitespace from the model name and convert to upper case. + auto _model = model.simplified().replace(" ", "").toUpper(); + + // Create a hash between the allowed model names and their templace files. + QHash models; + models["TIP3P"] = getShareDir() + "/templates/ions/cl_tip3p"; + models["TIP4P"] = getShareDir() + "/templates/ions/cl_tip4p"; + + // Make sure the user has passed a valid water model. + if (not models.contains(_model)) + { + throw SireError::incompatible_error(QObject::tr("Unsupported AMBER ion model '%1'").arg(model), CODELOC); + } + + // Extract the water model template path. + auto path = models[_model]; + + // Load the ion template. + auto ion_template = MoleculeParser::read(path + ".prm7"); + + // Extract the ion the template. + auto ion = ion_template[MolIdx(0)].molecule(); + + // Set the coordinates of the ion. + ion = ion.edit().atom(AtomIdx(0)).setProperty(map["coordinates"], coords).molecule().commit(); + + return ion; + } + Vector cross(const Vector &v0, const Vector &v1) { double nx = v0.y() * v1.z() - v0.z() * v1.y(); diff --git a/corelib/src/libs/SireIO/biosimspace.h b/corelib/src/libs/SireIO/biosimspace.h index 5f7541c5a..b90c6db8a 100644 --- a/corelib/src/libs/SireIO/biosimspace.h +++ b/corelib/src/libs/SireIO/biosimspace.h @@ -319,6 +319,38 @@ namespace SireIO const QHash &molecule_mapping, const bool is_lambda1 = false, const PropertyMap &map0 = PropertyMap(), const PropertyMap &map1 = PropertyMap()); + //! Create a sodium ion at the specified position. + /*! \param position + The position of the sodium ion. + + \param model + The name of the water model. + + \param map + A dictionary of user-defined molecular property names. + + \retval sodium + The sodium ion. + */ + SIREIO_EXPORT Molecule createSodiumIon( + const Vector &coords, const QString model, const PropertyMap &map = PropertyMap()); + + //! Create a chlorine ion at the specified position. + /*! \param position + The position of the chlorine ion. + + \param model + The name of the water model. + + \param map + A dictionary of user-defined molecular property names. + + \retval chlorine + The chlorine ion. + */ + SIREIO_EXPORT Molecule createChlorineIon( + const Vector &coords, const QString model, const PropertyMap &map = PropertyMap()); + Vector cross(const Vector &v0, const Vector &v1); } // namespace SireIO @@ -332,6 +364,8 @@ SIRE_EXPOSE_FUNCTION(SireIO::setAmberWater) SIRE_EXPOSE_FUNCTION(SireIO::setGromacsWater) SIRE_EXPOSE_FUNCTION(SireIO::updateAndPreserveOrder) SIRE_EXPOSE_FUNCTION(SireIO::updateCoordinatesAndVelocities) +SIRE_EXPOSE_FUNCTION(SireIO::createSodiumIon) +SIRE_EXPOSE_FUNCTION(SireIO::createChlorineIon) SIRE_END_HEADER diff --git a/corelib/templates/ions/cl_tip3p.prm7 b/corelib/templates/ions/cl_tip3p.prm7 new file mode 100644 index 000000000..ac016b750 --- /dev/null +++ b/corelib/templates/ions/cl_tip3p.prm7 @@ -0,0 +1,130 @@ +%VERSION VERSION_STAMP = V0001.000 DATE = 07/10/24 14:04:15 +%FLAG TITLE +%FORMAT(20a4) + +%FLAG POINTERS +%FORMAT(10I8) + 1 1 0 0 0 0 0 0 0 0 + 1 1 0 0 0 0 0 0 1 0 + 0 0 0 0 0 0 0 0 1 0 + 0 0 0 +%FLAG ATOM_NAME +%FORMAT(20a4) +Cl- +%FLAG CHARGE +%FORMAT(5E16.8) + -1.82223000E+01 +%FLAG ATOMIC_NUMBER +%FORMAT(10I8) + 17 +%FLAG MASS +%FORMAT(5E16.8) + 3.54500000E+01 +%FLAG ATOM_TYPE_INDEX +%FORMAT(10I8) + 1 +%FLAG NUMBER_EXCLUDED_ATOMS +%FORMAT(10I8) + 1 +%FLAG NONBONDED_PARM_INDEX +%FORMAT(10I8) + 1 +%FLAG RESIDUE_LABEL +%FORMAT(20a4) +Cl- +%FLAG RESIDUE_POINTER +%FORMAT(10I8) + 1 +%FLAG BOND_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG BOND_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG ANGLE_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG ANGLE_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PERIODICITY +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PHASE +%FORMAT(5E16.8) + +%FLAG SCEE_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SCNB_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SOLTY +%FORMAT(5E16.8) + 0.00000000E+00 +%FLAG LENNARD_JONES_ACOEF +%FORMAT(5E16.8) + 9.24719470E+06 +%FLAG LENNARD_JONES_BCOEF +%FORMAT(5E16.8) + 1.14737423E+03 +%FLAG BONDS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG BONDS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG EXCLUDED_ATOMS_LIST +%FORMAT(10I8) + 0 +%FLAG HBOND_ACOEF +%FORMAT(5E16.8) + +%FLAG HBOND_BCOEF +%FORMAT(5E16.8) + +%FLAG HBCUT +%FORMAT(5E16.8) + +%FLAG AMBER_ATOM_TYPE +%FORMAT(20a4) +Cl- +%FLAG TREE_CHAIN_CLASSIFICATION +%FORMAT(20a4) +M +%FLAG JOIN_ARRAY +%FORMAT(10I8) + 0 +%FLAG IROTAT +%FORMAT(10I8) + 0 +%FLAG RADIUS_SET +%FORMAT(1a80) +modified Bondi radii (mbondi) +%FLAG RADII +%FORMAT(5E16.8) + 1.70000000E+00 +%FLAG SCREEN +%FORMAT(5E16.8) + 8.00000000E-01 +%FLAG ATOMS_PER_MOLECULE +%FORMAT(10I8) + 1 +%FLAG IPOL +%FORMAT(1I8) + 0 diff --git a/corelib/templates/ions/cl_tip4p.prm7 b/corelib/templates/ions/cl_tip4p.prm7 new file mode 100644 index 000000000..2a91cfd7d --- /dev/null +++ b/corelib/templates/ions/cl_tip4p.prm7 @@ -0,0 +1,130 @@ +%VERSION VERSION_STAMP = V0001.000 DATE = 07/10/24 14:04:34 +%FLAG TITLE +%FORMAT(20a4) + +%FLAG POINTERS +%FORMAT(10I8) + 1 1 0 0 0 0 0 0 0 0 + 1 1 0 0 0 0 0 0 1 0 + 0 0 0 0 0 0 0 0 1 0 + 0 0 0 +%FLAG ATOM_NAME +%FORMAT(20a4) +Cl- +%FLAG CHARGE +%FORMAT(5E16.8) + -1.82223000E+01 +%FLAG ATOMIC_NUMBER +%FORMAT(10I8) + 17 +%FLAG MASS +%FORMAT(5E16.8) + 3.54500000E+01 +%FLAG ATOM_TYPE_INDEX +%FORMAT(10I8) + 1 +%FLAG NUMBER_EXCLUDED_ATOMS +%FORMAT(10I8) + 1 +%FLAG NONBONDED_PARM_INDEX +%FORMAT(10I8) + 1 +%FLAG RESIDUE_LABEL +%FORMAT(20a4) +Cl- +%FLAG RESIDUE_POINTER +%FORMAT(10I8) + 1 +%FLAG BOND_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG BOND_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG ANGLE_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG ANGLE_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PERIODICITY +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PHASE +%FORMAT(5E16.8) + +%FLAG SCEE_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SCNB_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SOLTY +%FORMAT(5E16.8) + 0.00000000E+00 +%FLAG LENNARD_JONES_ACOEF +%FORMAT(5E16.8) + 9.33304478E+06 +%FLAG LENNARD_JONES_BCOEF +%FORMAT(5E16.8) + 6.59809978E+02 +%FLAG BONDS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG BONDS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG EXCLUDED_ATOMS_LIST +%FORMAT(10I8) + 0 +%FLAG HBOND_ACOEF +%FORMAT(5E16.8) + +%FLAG HBOND_BCOEF +%FORMAT(5E16.8) + +%FLAG HBCUT +%FORMAT(5E16.8) + +%FLAG AMBER_ATOM_TYPE +%FORMAT(20a4) +Cl- +%FLAG TREE_CHAIN_CLASSIFICATION +%FORMAT(20a4) +M +%FLAG JOIN_ARRAY +%FORMAT(10I8) + 0 +%FLAG IROTAT +%FORMAT(10I8) + 0 +%FLAG RADIUS_SET +%FORMAT(1a80) +modified Bondi radii (mbondi) +%FLAG RADII +%FORMAT(5E16.8) + 1.70000000E+00 +%FLAG SCREEN +%FORMAT(5E16.8) + 8.00000000E-01 +%FLAG ATOMS_PER_MOLECULE +%FORMAT(10I8) + 1 +%FLAG IPOL +%FORMAT(1I8) + 0 diff --git a/corelib/templates/ions/na_tip3p.prm7 b/corelib/templates/ions/na_tip3p.prm7 new file mode 100644 index 000000000..0ef0e27e4 --- /dev/null +++ b/corelib/templates/ions/na_tip3p.prm7 @@ -0,0 +1,130 @@ +%VERSION VERSION_STAMP = V0001.000 DATE = 07/10/24 14:04:59 +%FLAG TITLE +%FORMAT(20a4) + +%FLAG POINTERS +%FORMAT(10I8) + 1 1 0 0 0 0 0 0 0 0 + 1 1 0 0 0 0 0 0 1 0 + 0 0 0 0 0 0 0 0 1 0 + 0 0 0 +%FLAG ATOM_NAME +%FORMAT(20a4) +Na+ +%FLAG CHARGE +%FORMAT(5E16.8) + 1.82223000E+01 +%FLAG ATOMIC_NUMBER +%FORMAT(10I8) + 11 +%FLAG MASS +%FORMAT(5E16.8) + 2.29900000E+01 +%FLAG ATOM_TYPE_INDEX +%FORMAT(10I8) + 1 +%FLAG NUMBER_EXCLUDED_ATOMS +%FORMAT(10I8) + 1 +%FLAG NONBONDED_PARM_INDEX +%FORMAT(10I8) + 1 +%FLAG RESIDUE_LABEL +%FORMAT(20a4) +Na+ +%FLAG RESIDUE_POINTER +%FORMAT(10I8) + 1 +%FLAG BOND_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG BOND_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG ANGLE_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG ANGLE_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PERIODICITY +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PHASE +%FORMAT(5E16.8) + +%FLAG SCEE_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SCNB_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SOLTY +%FORMAT(5E16.8) + 0.00000000E+00 +%FLAG LENNARD_JONES_ACOEF +%FORMAT(5E16.8) + 1.55205818E+04 +%FLAG LENNARD_JONES_BCOEF +%FORMAT(5E16.8) + 7.36779156E+01 +%FLAG BONDS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG BONDS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG EXCLUDED_ATOMS_LIST +%FORMAT(10I8) + 0 +%FLAG HBOND_ACOEF +%FORMAT(5E16.8) + +%FLAG HBOND_BCOEF +%FORMAT(5E16.8) + +%FLAG HBCUT +%FORMAT(5E16.8) + +%FLAG AMBER_ATOM_TYPE +%FORMAT(20a4) +Na+ +%FLAG TREE_CHAIN_CLASSIFICATION +%FORMAT(20a4) +M +%FLAG JOIN_ARRAY +%FORMAT(10I8) + 0 +%FLAG IROTAT +%FORMAT(10I8) + 0 +%FLAG RADIUS_SET +%FORMAT(1a80) +modified Bondi radii (mbondi) +%FLAG RADII +%FORMAT(5E16.8) + 1.50000000E+00 +%FLAG SCREEN +%FORMAT(5E16.8) + 8.00000000E-01 +%FLAG ATOMS_PER_MOLECULE +%FORMAT(10I8) + 1 +%FLAG IPOL +%FORMAT(1I8) + 0 diff --git a/corelib/templates/ions/na_tip4p.prm7 b/corelib/templates/ions/na_tip4p.prm7 new file mode 100644 index 000000000..543f65f71 --- /dev/null +++ b/corelib/templates/ions/na_tip4p.prm7 @@ -0,0 +1,130 @@ +%VERSION VERSION_STAMP = V0001.000 DATE = 07/10/24 14:04:42 +%FLAG TITLE +%FORMAT(20a4) + +%FLAG POINTERS +%FORMAT(10I8) + 1 1 0 0 0 0 0 0 0 0 + 1 1 0 0 0 0 0 0 1 0 + 0 0 0 0 0 0 0 0 1 0 + 0 0 0 +%FLAG ATOM_NAME +%FORMAT(20a4) +Na+ +%FLAG CHARGE +%FORMAT(5E16.8) + 1.82223000E+01 +%FLAG ATOMIC_NUMBER +%FORMAT(10I8) + 11 +%FLAG MASS +%FORMAT(5E16.8) + 2.29900000E+01 +%FLAG ATOM_TYPE_INDEX +%FORMAT(10I8) + 1 +%FLAG NUMBER_EXCLUDED_ATOMS +%FORMAT(10I8) + 1 +%FLAG NONBONDED_PARM_INDEX +%FORMAT(10I8) + 1 +%FLAG RESIDUE_LABEL +%FORMAT(20a4) +Na+ +%FLAG RESIDUE_POINTER +%FORMAT(10I8) + 1 +%FLAG BOND_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG BOND_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG ANGLE_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG ANGLE_EQUIL_VALUE +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_FORCE_CONSTANT +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PERIODICITY +%FORMAT(5E16.8) + +%FLAG DIHEDRAL_PHASE +%FORMAT(5E16.8) + +%FLAG SCEE_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SCNB_SCALE_FACTOR +%FORMAT(5E16.8) + +%FLAG SOLTY +%FORMAT(5E16.8) + 0.00000000E+00 +%FLAG LENNARD_JONES_ACOEF +%FORMAT(5E16.8) + 7.95580953E+03 +%FLAG LENNARD_JONES_BCOEF +%FORMAT(5E16.8) + 7.32135689E+01 +%FLAG BONDS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG BONDS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG ANGLES_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_INC_HYDROGEN +%FORMAT(10I8) + +%FLAG DIHEDRALS_WITHOUT_HYDROGEN +%FORMAT(10I8) + +%FLAG EXCLUDED_ATOMS_LIST +%FORMAT(10I8) + 0 +%FLAG HBOND_ACOEF +%FORMAT(5E16.8) + +%FLAG HBOND_BCOEF +%FORMAT(5E16.8) + +%FLAG HBCUT +%FORMAT(5E16.8) + +%FLAG AMBER_ATOM_TYPE +%FORMAT(20a4) +Na+ +%FLAG TREE_CHAIN_CLASSIFICATION +%FORMAT(20a4) +M +%FLAG JOIN_ARRAY +%FORMAT(10I8) + 0 +%FLAG IROTAT +%FORMAT(10I8) + 0 +%FLAG RADIUS_SET +%FORMAT(1a80) +modified Bondi radii (mbondi) +%FLAG RADII +%FORMAT(5E16.8) + 1.50000000E+00 +%FLAG SCREEN +%FORMAT(5E16.8) + 8.00000000E-01 +%FLAG ATOMS_PER_MOLECULE +%FORMAT(10I8) + 1 +%FLAG IPOL +%FORMAT(1I8) + 0 diff --git a/wrapper/IO/_IO_free_functions.pypp.cpp b/wrapper/IO/_IO_free_functions.pypp.cpp index 4787605a1..fa5466500 100644 --- a/wrapper/IO/_IO_free_functions.pypp.cpp +++ b/wrapper/IO/_IO_free_functions.pypp.cpp @@ -7,6 +7,70 @@ namespace bp = boost::python; +#include "SireBase/getinstalldir.h" + +#include "SireError/errors.h" + +#include "SireMol/atomelements.h" + +#include "SireMol/atommasses.h" + +#include "SireMol/connectivity.h" + +#include "SireMol/core.h" + +#include "SireMol/mgname.h" + +#include "SireMol/moleditor.h" + +#include "SireMol/molidx.h" + +#include "SireSystem/system.h" + +#include "SireUnits/units.h" + +#include "SireVol/periodicbox.h" + +#include "SireVol/triclinicbox.h" + +#include "biosimspace.h" + +#include "moleculeparser.h" + +#include "biosimspace.h" + +#include "SireBase/getinstalldir.h" + +#include "SireError/errors.h" + +#include "SireMol/atomelements.h" + +#include "SireMol/atommasses.h" + +#include "SireMol/connectivity.h" + +#include "SireMol/core.h" + +#include "SireMol/mgname.h" + +#include "SireMol/moleditor.h" + +#include "SireMol/molidx.h" + +#include "SireSystem/system.h" + +#include "SireUnits/units.h" + +#include "SireVol/periodicbox.h" + +#include "SireVol/triclinicbox.h" + +#include "biosimspace.h" + +#include "moleculeparser.h" + +#include "biosimspace.h" + #include "SireBase/parallel.h" #include "SireMol/core.h" @@ -493,6 +557,32 @@ namespace bp = boost::python; void register_free_functions(){ + { //::SireIO::createChlorineIon + + typedef ::SireMol::Molecule ( *createChlorineIon_function_type )( ::SireMaths::Vector const &,::QString const,::SireBase::PropertyMap const & ); + createChlorineIon_function_type createChlorineIon_function_value( &::SireIO::createChlorineIon ); + + bp::def( + "createChlorineIon" + , createChlorineIon_function_value + , ( bp::arg("coords"), bp::arg("model"), bp::arg("map")=SireBase::PropertyMap() ) + , "Create a chlorine ion at the specified position.\nPar:am position\nThe position of the chlorine ion.\n\nPar:am model\nThe name of the water model.\n\nPar:am map\nA dictionary of user-defined molecular property names.\n\nRetval: chlorine\nThe chlorine ion.\n" ); + + } + + { //::SireIO::createSodiumIon + + typedef ::SireMol::Molecule ( *createSodiumIon_function_type )( ::SireMaths::Vector const &,::QString const,::SireBase::PropertyMap const & ); + createSodiumIon_function_type createSodiumIon_function_value( &::SireIO::createSodiumIon ); + + bp::def( + "createSodiumIon" + , createSodiumIon_function_value + , ( bp::arg("coords"), bp::arg("model"), bp::arg("map")=SireBase::PropertyMap() ) + , "Create a sodium ion at the specified position.\nPar:am position\nThe position of the sodium ion.\n\nPar:am model\nThe name of the water model.\n\nPar:am map\nA dictionary of user-defined molecular property names.\n\nRetval: sodium\nThe sodium ion.\n" ); + + } + { //::SireIO::getCoordsArray typedef ::QVector< float > ( *getCoordsArray_function_type )( ::SireMol::MoleculeView const &,::SireUnits::Dimension::Length const &,::SireBase::PropertyMap const & ); From 8a74d0c3910b9029ee786197b453885251e6d976 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 11 Jul 2024 09:57:48 +0100 Subject: [PATCH 328/468] Add missing CHANGELOG entries. [ci skip] --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 72ad734b3..cee9ded34 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -16,6 +16,8 @@ organisation on `GitHub `__. ---------------------------------------------------------------------------------------------- * Please add an item to this changelog when you create your PR +* Print residue indices of perturbed water molecules to SOMD1 log. +* Add support for creating Na+ and Cl- ions. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From d83b63f5e0c2151c509b9fc87dc17a6cd2fe4fae Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 11 Jul 2024 14:15:18 +0100 Subject: [PATCH 329/468] Fix merging of monatomic ions. --- corelib/src/libs/SireMol/atommapping.cpp | 69 +++++++++++++++++++----- doc/source/changelog.rst | 1 + tests/morph/test_merge.py | 19 +++++++ 3 files changed, 75 insertions(+), 14 deletions(-) diff --git a/corelib/src/libs/SireMol/atommapping.cpp b/corelib/src/libs/SireMol/atommapping.cpp index c38616017..5722d1de8 100644 --- a/corelib/src/libs/SireMol/atommapping.cpp +++ b/corelib/src/libs/SireMol/atommapping.cpp @@ -31,6 +31,7 @@ #include "SireMaths/align.h" #include "SireMol/core.h" +#include "SireMol/moleditor.h" #include "SireStream/datastream.h" #include "SireStream/shareddatastream.h" @@ -723,20 +724,40 @@ AtomMapping AtomMapping::alignTo0() const QVector coords0 = this->atms0.property(map0["coordinates"]).toVector(); QVector coords1 = this->atms1.property(map1["coordinates"]).toVector(); - // calculate the transform to do a RMSD aligment of the two sets of coordinates - auto transform = SireMaths::getAlignment(coords0, coords1, true); - - auto mols1 = this->orig_atms1.molecules(); - AtomMapping ret(*this); - for (int i = 0; i < mols1.count(); ++i) + if ((this->count() == 1) and ((coords0.count() == 1) or (coords1.count() == 1))) { - auto mol = mols1[i].move().transform(transform, map1).commit(); + // if we've only mapped a single atom and one molecule is a monatomic ion, + // then simply replace the coordinates of the mapped atom. + + auto atom0 = this->atms0[0]; + auto atom1 = this->atms1[0]; + + auto mol = this->orig_atms1.molecules()[0]; + + mol = mol.edit().atom(atom1.index()) + .setProperty(map1["coordinates"].source(), coords0[0]) + .molecule().commit(); ret.atms1.update(mol); ret.orig_atms1.update(mol); } + else + { + // calculate the transform to do a RMSD aligment of the two sets of coordinates + auto transform = SireMaths::getAlignment(coords0, coords1, true); + + auto mols1 = this->orig_atms1.molecules(); + + for (int i = 0; i < mols1.count(); ++i) + { + auto mol = mols1[i].move().transform(transform, map1).commit(); + + ret.atms1.update(mol); + ret.orig_atms1.update(mol); + } + } return ret; } @@ -754,20 +775,40 @@ AtomMapping AtomMapping::alignTo1() const QVector coords0 = this->atms0.property(map0["coordinates"]).toVector(); QVector coords1 = this->atms1.property(map1["coordinates"]).toVector(); - // calculate the transform to do a RMSD aligment of the two sets of coordinates - auto transform = SireMaths::getAlignment(coords1, coords0, true); - - auto mols0 = this->orig_atms0.molecules(); - AtomMapping ret(*this); - for (int i = 0; i < mols0.count(); ++i) + if ((this->count() == 1) and ((coords0.count() == 1) or (coords1.count() == 1))) { - auto mol = mols0[i].move().transform(transform, map0).commit(); + // if we've only mapped a single atom and one molecule is a monatomic ion, + // then simply replace the coordinates of the mapped atom. + + auto atom0 = this->atms0[0]; + auto atom1 = this->atms1[0]; + + auto mol = this->orig_atms0.molecules()[0]; + + mol = mol.edit().atom(atom0.index()) + .setProperty(map0["coordinates"].source(), coords0[0]) + .molecule().commit(); ret.atms0.update(mol); ret.orig_atms0.update(mol); } + else + { + // calculate the transform to do a RMSD aligment of the two sets of coordinates + auto transform = SireMaths::getAlignment(coords1, coords0, true); + + auto mols0 = this->orig_atms0.molecules(); + + for (int i = 0; i < mols0.count(); ++i) + { + auto mol = mols0[i].move().transform(transform, map0).commit(); + + ret.atms0.update(mol); + ret.orig_atms0.update(mol); + } + } return ret; } diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index cee9ded34..b55abf931 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -18,6 +18,7 @@ organisation on `GitHub `__. * Please add an item to this changelog when you create your PR * Print residue indices of perturbed water molecules to SOMD1 log. * Add support for creating Na+ and Cl- ions. +* Fix ``sire.morph.merge`` function when one molecule is a monatomic ion. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index 8d5311569..238c4481f 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -202,3 +202,22 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform): # These energies aren't correct - extra ghost atom internals? assert nrg_neo.value() == pytest.approx(nrg_merged_0.value(), abs=1e-3) # assert nrg_met.value() == pytest.approx(nrg_merged_1.value(), abs=1e-3) + + +def test_ion_merge(ala_mols): + water = ala_mols[-1] + ion = sr.legacy.IO.createSodiumIon(water.atoms()[-1].coordinates(), "tip3p") + + merged = sr.morph.merge(water, ion) + + coords0 = merged.property("coordinates0").to_vector()[0] + coords1 = merged.property("coordinates1").to_vector()[0] + + assert coords0 == coords1 + + merged = sr.morph.merge(ion, water) + + coords0 = merged.property("coordinates0").to_vector()[0] + coords1 = merged.property("coordinates1").to_vector()[0] + + assert coords0 == coords1 From f23acd39fe01b505a442043a6e3a2a5ec01e68da Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 12 Jul 2024 08:38:36 +0100 Subject: [PATCH 330/468] Skip test on Windows. [ci skip] --- tests/morph/test_merge.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/morph/test_merge.py b/tests/morph/test_merge.py index 238c4481f..25f9550b6 100644 --- a/tests/morph/test_merge.py +++ b/tests/morph/test_merge.py @@ -204,6 +204,7 @@ def test_merge_neopentane_methane(neopentane_methane, openmm_platform): # assert nrg_met.value() == pytest.approx(nrg_merged_1.value(), abs=1e-3) +@pytest.mark.skipif(sys.platform == "win32", reason="Not supported on Windows") def test_ion_merge(ala_mols): water = ala_mols[-1] ion = sr.legacy.IO.createSodiumIon(water.atoms()[-1].coordinates(), "tip3p") From 36ac725b73ea39412bb53737951647686b73730b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 12 Jul 2024 13:53:04 +0100 Subject: [PATCH 331/468] Typo. [ci skip] --- wrapper/Convert/SireOpenMM/pyqm.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index 4e7402e19..b28be4bac 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -426,7 +426,7 @@ namespace OpenMM // Set the version. node.setIntProperty("version", 0); - // Set the note attributer. + // Set the note attribute. node.setStringProperty("note", "This force only supports partial serialization, so can only be used " "within the same session and memory space."); From a632ed5ab5156b8972c081c7d9097ae231f2b950 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 12 Jul 2024 14:54:37 +0100 Subject: [PATCH 332/468] Simplify loops. [ci skip] --- wrapper/Convert/SireOpenMM/pyqm.cpp | 23 ++++------------------- 1 file changed, 4 insertions(+), 19 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index b28be4bac..d7034cec7 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -823,44 +823,29 @@ double PyQMForceImpl::computeForce( // Now update the force vector. // First the QM atoms. - i = 0; - for (const auto &force : forces_qm) + for (int i=0; i Date: Fri, 12 Jul 2024 15:13:26 +0100 Subject: [PATCH 333/468] Fix header guard. [ci skip] --- wrapper/Convert/SireOpenMM/pyqm.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.h b/wrapper/Convert/SireOpenMM/pyqm.h index 402966dfe..7088a1b9a 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.h +++ b/wrapper/Convert/SireOpenMM/pyqm.h @@ -26,8 +26,8 @@ * \*********************************************/ -#ifndef SIREOPENMM_EMLE_H -#define SIREOPENMM_EMLE_H +#ifndef SIREOPENMM_PYQM_H +#define SIREOPENMM_PYQM_H #include "OpenMM.h" #include "openmm/Force.h" From 8ddd63ac76d4d3951bcbe5b8e29c949ced94bb96 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 12 Jul 2024 16:48:48 +0100 Subject: [PATCH 334/468] Added Torch QM/MM implementation. --- src/sire/_pythonize.py | 2 + src/sire/qm/_emle.py | 119 +- .../Convert/SireOpenMM/CMakeAutogenFile.txt | 2 + wrapper/Convert/SireOpenMM/CMakeLists.txt | 5 + .../SireOpenMM/SireOpenMM_registrars.cpp | 3 + .../Convert/SireOpenMM/TorchQMEngine.pypp.cpp | 338 ++++++ .../Convert/SireOpenMM/TorchQMEngine.pypp.hpp | 10 + .../Convert/SireOpenMM/TorchQMForce.pypp.cpp | 254 ++++ .../Convert/SireOpenMM/TorchQMForce.pypp.hpp | 10 + .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 8 + wrapper/Convert/SireOpenMM/active_headers.h | 2 - wrapper/Convert/SireOpenMM/torchqm.cpp | 1021 +++++++++++++++++ wrapper/Convert/SireOpenMM/torchqm.h | 506 ++++++++ wrapper/Convert/__init__.py | 3 + 14 files changed, 2258 insertions(+), 25 deletions(-) create mode 100644 wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp create mode 100644 wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.hpp create mode 100644 wrapper/Convert/SireOpenMM/TorchQMForce.pypp.cpp create mode 100644 wrapper/Convert/SireOpenMM/TorchQMForce.pypp.hpp create mode 100644 wrapper/Convert/SireOpenMM/torchqm.cpp create mode 100644 wrapper/Convert/SireOpenMM/torchqm.h diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index de6613070..00378867f 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -242,6 +242,8 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): _pythonize(Convert._SireOpenMM.PyQMCallback, delete_old=delete_old) _pythonize(Convert._SireOpenMM.PyQMEngine, delete_old=delete_old) _pythonize(Convert._SireOpenMM.PyQMForce, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.TorchQMEngine, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.TorchQMForce, delete_old=delete_old) try: import lazy_import diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index b4c2612da..60fb8fb9b 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -49,6 +49,52 @@ def get_forces(self): return emle_force, interpolation_force +class TorchEMLEEngine(_Convert._SireOpenMM.TorchQMEngine): + """A class to enable use of EMLE as a QM engine using C++ Torch.""" + + def get_forces(self): + """ + Get the OpenMM forces for this engine. The first force is the actual + EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic + embedding force. The second is a null CustomBondForce that can be used to + add a "lambda_emle" global parameter to a context to allow the force to be + scaled. + + Returns + ------- + + emle_force : openmm.Force + The EMLE force object to compute the electrostatic embedding force. + + interpolation_force : openmm.CustomBondForce + A null CustomBondForce object that can be used to add a "lambda_emle" + global parameter to an OpenMM context. This allows the electrostatic + embedding force to be scaled. + """ + + from copy import deepcopy as _deepcopy + from openmm import CustomBondForce as _CustomBondForce + + # Create a dynamics object for the QM region. + d = self._mols["property is_perturbable"].dynamics( + timestep="1fs", + constraint="none", + platform="cpu", + qm_engine=self, + ) + + # Get the OpenMM EMLE force. + emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) + + # Create a null CustomBondForce to add the EMLE interpolation + # parameter. + interpolation_force = _CustomBondForce("") + interpolation_force.addGlobalParameter("lambda_emle", 1.0) + + # Return the forces. + return emle_force, interpolation_force + + def emle( mols, qm_atoms, @@ -72,8 +118,9 @@ def emle( or molecule view/container that can be used to select qm_atoms from 'mols'. - calculator : emle.calculator.EMLECalculator - The EMLECalculator object to use for elecotrostatic embedding calculations. + calculator : emle.calculator.EMLECalculator, emle.models.EMLE + The EMLE calculator or model to use for elecotrostatic embedding + calculations. cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. @@ -95,6 +142,7 @@ def emle( try: from emle.calculator import EMLECalculator as _EMLECalculator + from emle.models import EMLE as _EMLE except: raise ImportError( "Could not import emle. Please install emle-engine and try again." @@ -118,9 +166,9 @@ def emle( except: raise ValueError("Unable to select 'qm_atoms' from 'mols'") - if not isinstance(calculator, _EMLECalculator): + if not isinstance(calculator, (_EMLECalculator, _EMLE)): raise TypeError( - "'calculator' must be a of type 'emle.calculator.EMLECalculator'" + "'calculator' must be a of type 'emle.calculator.EMLECalculator' or 'emle.models.EMLE'" ) if not isinstance(cutoff, (str, _Units.GeneralUnit)): @@ -151,27 +199,52 @@ def emle( raise TypeError("'map' must be of type 'dict'") map = _create_map(map) - # Determine the callback name. Use an optimised version of the callback - # if the user has specified "torchani" as the backend and is using - # "electrostatic" embedding. - if calculator._backend == "torchani" and calculator._method == "electrostatic": - try: - from emle.models import ANI2xEMLE as _ANI2xEMLE - - callback = "_sire_callback_optimised" - except: + # Create an engine from an EMLE calculator. + if isinstance(calculator, _EMLECalculator): + # Determine the callback name. Use an optimised version of the callback + # if the user has specified "torchani" as the backend and is using + # "electrostatic" embedding. + if calculator._backend == "torchani" and calculator._method == "electrostatic": + try: + from emle.models import ANI2xEMLE as _ANI2xEMLE + + callback = "_sire_callback_optimised" + except: + callback = "_sire_callback" + else: callback = "_sire_callback" + + # Create the EMLE engine. + engine = EMLEEngine( + calculator, + callback, + cutoff, + neighbour_list_frequency, + False, + ) + + # Create an engine from an EMLE model. else: - callback = "_sire_callback" - - # Create the EMLE engine. - engine = EMLEEngine( - calculator, - callback, - cutoff, - neighbour_list_frequency, - False, - ) + import torch as _torch + + try: + script_module = _torch.jit.script(calculator) + except: + raise ValueError( + "Unable to compile the EMLE model to a TorchScript module." + ) + + # Save the script module to a file. + module_path = calculator.__class__.__name__ + ".pt" + _torch.jit.save(script_module, calculator.__class__.__name__ + ".pt") + + # Create the EMLE engine. + engine = TorchEMLEEngine( + module_path, + cutoff, + neighbour_list_frequency, + False, + ) from ._utils import ( _check_charge, diff --git a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt index 9e443e04c..0a7247be3 100644 --- a/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt +++ b/wrapper/Convert/SireOpenMM/CMakeAutogenFile.txt @@ -5,6 +5,8 @@ set ( PYPP_SOURCES PyQMCallback.pypp.cpp PyQMForce.pypp.cpp PyQMEngine.pypp.cpp + TorchQMForce.pypp.cpp + TorchQMEngine.pypp.cpp QMEngine.pypp.cpp _SireOpenMM_free_functions.pypp.cpp QMForce.pypp.cpp diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 19c40b45e..dac13252b 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -50,6 +50,9 @@ if (${SIRE_USE_OPENMM}) #if (CAN_USE_CUSTOMCPPFORCE) message(STATUS "OpenMM version supports CustomCPPForce") add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") + + find_package(Torch REQUIRED) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}") #else() #message(STATUS "OpenMM version does not support CustomCPPForce") #endif() @@ -80,6 +83,7 @@ if (${SIRE_USE_OPENMM}) set ( SIREOPENMM_SOURCES pyqm.cpp + torchqm.cpp lambdalever.cpp openmmminimise.cpp openmmmolecule.cpp @@ -120,6 +124,7 @@ if (${SIRE_USE_OPENMM}) SIRE_SireStream SIRE_SireError ${OpenMM_LIBRARIES} + ${TORCH_LIBRARIES} ) include( LimitSirePythonExportSymbols ) diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index 2f68bd88d..7a88a370c 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -7,6 +7,7 @@ #include "pyqm.h" #include "lambdalever.h" #include "openmmmolecule.h" +#include "torchqm.h" #include "Helpers/objectregistry.hpp" @@ -25,6 +26,8 @@ void register_SireOpenMM_objects() ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); + ObjectRegistry::registerConverterFor< SireOpenMM::TorchQMForce >(); + ObjectRegistry::registerConverterFor< SireOpenMM::TorchQMEngine >(); } diff --git a/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp new file mode 100644 index 000000000..8a5676264 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp @@ -0,0 +1,338 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "TorchQMEngine.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireVol/triclinicbox.h" + +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "torchqm.h" + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireVol/triclinicbox.h" + +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "torchqm.h" + +SireOpenMM::TorchQMEngine __copy__(const SireOpenMM::TorchQMEngine &other){ return SireOpenMM::TorchQMEngine(other); } + +#include "Helpers/str.hpp" + +#include "Helpers/release_gil_policy.hpp" + +void register_TorchQMEngine_class(){ + + { //::SireOpenMM::TorchQMEngine + typedef bp::class_< SireOpenMM::TorchQMEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > TorchQMEngine_exposer_t; + TorchQMEngine_exposer_t TorchQMEngine_exposer = TorchQMEngine_exposer_t( "TorchQMEngine", "", bp::init< >("Default constructor.") ); + bp::scope TorchQMEngine_scope( TorchQMEngine_exposer ); + TorchQMEngine_exposer.def( bp::init< QString, bp::optional< SireUnits::Dimension::Length, int, bool, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("is_mechanical")=(bool)(false), bp::arg("lambda")=1. ), "Constructor\nPar:am module_path\nThe path to the serialised TorchScript module.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); + TorchQMEngine_exposer.def( bp::init< SireOpenMM::TorchQMEngine const & >(( bp::arg("other") ), "Copy constructor.") ); + { //::SireOpenMM::TorchQMEngine::getModulePath + + typedef ::QString ( ::SireOpenMM::TorchQMEngine::*getModulePath_function_type)( ) const; + getModulePath_function_type getModulePath_function_value( &::SireOpenMM::TorchQMEngine::getModulePath ); + + TorchQMEngine_exposer.def( + "getModulePath" + , getModulePath_function_value + , bp::release_gil_policy() + , "Get the path to the serialised TorchScript module.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getAtoms + + typedef ::QVector< int > ( ::SireOpenMM::TorchQMEngine::*getAtoms_function_type)( ) const; + getAtoms_function_type getAtoms_function_value( &::SireOpenMM::TorchQMEngine::getAtoms ); + + TorchQMEngine_exposer.def( + "getAtoms" + , getAtoms_function_value + , bp::release_gil_policy() + , "Get the indices of the atoms in the QM region.\nReturn:s\nA vector of atom indices for the QM region.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getCharges + + typedef ::QVector< double > ( ::SireOpenMM::TorchQMEngine::*getCharges_function_type)( ) const; + getCharges_function_type getCharges_function_value( &::SireOpenMM::TorchQMEngine::getCharges ); + + TorchQMEngine_exposer.def( + "getCharges" + , getCharges_function_value + , bp::release_gil_policy() + , "Get the atomic charges of all atoms in the system.\nReturn:s\nA vector of atomic charges for all atoms in the system.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getCutoff + + typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::TorchQMEngine::*getCutoff_function_type)( ) const; + getCutoff_function_type getCutoff_function_value( &::SireOpenMM::TorchQMEngine::getCutoff ); + + TorchQMEngine_exposer.def( + "getCutoff" + , getCutoff_function_value + , bp::release_gil_policy() + , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getIsMechanical + + typedef bool ( ::SireOpenMM::TorchQMEngine::*getIsMechanical_function_type)( ) const; + getIsMechanical_function_type getIsMechanical_function_value( &::SireOpenMM::TorchQMEngine::getIsMechanical ); + + TorchQMEngine_exposer.def( + "getIsMechanical" + , getIsMechanical_function_value + , bp::release_gil_policy() + , "Get the mechanical embedding flag.\nReturn:s\nA flag to indicate if mechanical embedding is being used.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getLambda + + typedef double ( ::SireOpenMM::TorchQMEngine::*getLambda_function_type)( ) const; + getLambda_function_type getLambda_function_value( &::SireOpenMM::TorchQMEngine::getLambda ); + + TorchQMEngine_exposer.def( + "getLambda" + , getLambda_function_value + , bp::release_gil_policy() + , "Get the lambda weighting factor.\nReturn:s\nThe lambda weighting factor.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getLinkAtoms + + typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::TorchQMEngine::*getLinkAtoms_function_type)( ) const; + getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::TorchQMEngine::getLinkAtoms ); + + TorchQMEngine_exposer.def( + "getLinkAtoms" + , getLinkAtoms_function_value + , bp::release_gil_policy() + , "Get the link atoms associated with each QM atom.\nReturn:s\nA tuple containing:\n\nmm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nmm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nbond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getMM2Atoms + + typedef ::QVector< int > ( ::SireOpenMM::TorchQMEngine::*getMM2Atoms_function_type)( ) const; + getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::TorchQMEngine::getMM2Atoms ); + + TorchQMEngine_exposer.def( + "getMM2Atoms" + , getMM2Atoms_function_value + , bp::release_gil_policy() + , "Get the vector of MM2 atoms.\nReturn:s\nA vector of MM2 atom indices.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getNeighbourListFrequency + + typedef int ( ::SireOpenMM::TorchQMEngine::*getNeighbourListFrequency_function_type)( ) const; + getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::TorchQMEngine::getNeighbourListFrequency ); + + TorchQMEngine_exposer.def( + "getNeighbourListFrequency" + , getNeighbourListFrequency_function_value + , bp::release_gil_policy() + , "Get the neighbour list frequency.\nReturn:s\nThe neighbour list frequency.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::getNumbers + + typedef ::QVector< int > ( ::SireOpenMM::TorchQMEngine::*getNumbers_function_type)( ) const; + getNumbers_function_type getNumbers_function_value( &::SireOpenMM::TorchQMEngine::getNumbers ); + + TorchQMEngine_exposer.def( + "getNumbers" + , getNumbers_function_value + , bp::release_gil_policy() + , "Get the atomic numbers for the atoms in the QM region.\nReturn:s\nA vector of atomic numbers for the atoms in the QM region.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::operator= + + typedef ::SireOpenMM::TorchQMEngine & ( ::SireOpenMM::TorchQMEngine::*assign_function_type)( ::SireOpenMM::TorchQMEngine const & ) ; + assign_function_type assign_function_value( &::SireOpenMM::TorchQMEngine::operator= ); + + TorchQMEngine_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "Assignment operator." ); + + } + { //::SireOpenMM::TorchQMEngine::setModulePath + + typedef void ( ::SireOpenMM::TorchQMEngine::*setModulePath_function_type)( ::QString ) ; + setModulePath_function_type setModulePath_function_value( &::SireOpenMM::TorchQMEngine::setModulePath ); + + TorchQMEngine_exposer.def( + "setModulePath" + , setModulePath_function_value + , ( bp::arg("module_path") ) + , bp::release_gil_policy() + , "Set the path to the serialised TorchScript module.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setAtoms + + typedef void ( ::SireOpenMM::TorchQMEngine::*setAtoms_function_type)( ::QVector< int > ) ; + setAtoms_function_type setAtoms_function_value( &::SireOpenMM::TorchQMEngine::setAtoms ); + + TorchQMEngine_exposer.def( + "setAtoms" + , setAtoms_function_value + , ( bp::arg("atoms") ) + , bp::release_gil_policy() + , "Set the list of atom indices for the QM region.\nPar:am atoms\nA vector of atom indices for the QM region.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setCharges + + typedef void ( ::SireOpenMM::TorchQMEngine::*setCharges_function_type)( ::QVector< double > ) ; + setCharges_function_type setCharges_function_value( &::SireOpenMM::TorchQMEngine::setCharges ); + + TorchQMEngine_exposer.def( + "setCharges" + , setCharges_function_value + , ( bp::arg("charges") ) + , bp::release_gil_policy() + , "Set the atomic charges of all atoms in the system.\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setCutoff + + typedef void ( ::SireOpenMM::TorchQMEngine::*setCutoff_function_type)( ::SireUnits::Dimension::Length ) ; + setCutoff_function_type setCutoff_function_value( &::SireOpenMM::TorchQMEngine::setCutoff ); + + TorchQMEngine_exposer.def( + "setCutoff" + , setCutoff_function_value + , ( bp::arg("cutoff") ) + , bp::release_gil_policy() + , "Set the QM cutoff distance.\nPar:am cutoff\nThe QM cutoff distance.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setIsMechanical + + typedef void ( ::SireOpenMM::TorchQMEngine::*setIsMechanical_function_type)( bool ) ; + setIsMechanical_function_type setIsMechanical_function_value( &::SireOpenMM::TorchQMEngine::setIsMechanical ); + + TorchQMEngine_exposer.def( + "setIsMechanical" + , setIsMechanical_function_value + , ( bp::arg("is_mechanical") ) + , bp::release_gil_policy() + , "Set the mechanical embedding flag.\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setLambda + + typedef void ( ::SireOpenMM::TorchQMEngine::*setLambda_function_type)( double ) ; + setLambda_function_type setLambda_function_value( &::SireOpenMM::TorchQMEngine::setLambda ); + + TorchQMEngine_exposer.def( + "setLambda" + , setLambda_function_value + , ( bp::arg("lambda") ) + , bp::release_gil_policy() + , "Set the lambda weighting factor.\nPar:am lambda\nThe lambda weighting factor.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setLinkAtoms + + typedef void ( ::SireOpenMM::TorchQMEngine::*setLinkAtoms_function_type)( ::QMap< int, int >,::QMap< int, QVector< int > >,::QMap< int, double > ) ; + setLinkAtoms_function_type setLinkAtoms_function_value( &::SireOpenMM::TorchQMEngine::setLinkAtoms ); + + TorchQMEngine_exposer.def( + "setLinkAtoms" + , setLinkAtoms_function_value + , ( bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors") ) + , bp::release_gil_policy() + , "Set the link atoms associated with each QM atom.\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setNeighbourListFrequency + + typedef void ( ::SireOpenMM::TorchQMEngine::*setNeighbourListFrequency_function_type)( int ) ; + setNeighbourListFrequency_function_type setNeighbourListFrequency_function_value( &::SireOpenMM::TorchQMEngine::setNeighbourListFrequency ); + + TorchQMEngine_exposer.def( + "setNeighbourListFrequency" + , setNeighbourListFrequency_function_value + , ( bp::arg("neighbour_list_frequency") ) + , bp::release_gil_policy() + , "Set the neighbour list frequency.\nPar:am neighbour_list_frequency\nThe neighbour list frequency.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::setNumbers + + typedef void ( ::SireOpenMM::TorchQMEngine::*setNumbers_function_type)( ::QVector< int > ) ; + setNumbers_function_type setNumbers_function_value( &::SireOpenMM::TorchQMEngine::setNumbers ); + + TorchQMEngine_exposer.def( + "setNumbers" + , setNumbers_function_value + , ( bp::arg("numbers") ) + , bp::release_gil_policy() + , "Set the atomic numbers for the atoms in the QM region.\nPar:am numbers\nA vector of atomic numbers for the atoms in the QM region.\n" ); + + } + { //::SireOpenMM::TorchQMEngine::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireOpenMM::TorchQMEngine::typeName ); + + TorchQMEngine_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + { //::SireOpenMM::TorchQMEngine::what + + typedef char const * ( ::SireOpenMM::TorchQMEngine::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::TorchQMEngine::what ); + + TorchQMEngine_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + TorchQMEngine_exposer.staticmethod( "typeName" ); + TorchQMEngine_exposer.def( "__copy__", &__copy__); + TorchQMEngine_exposer.def( "__deepcopy__", &__copy__); + TorchQMEngine_exposer.def( "clone", &__copy__); + TorchQMEngine_exposer.def( "__str__", &__str__< ::SireOpenMM::TorchQMEngine > ); + TorchQMEngine_exposer.def( "__repr__", &__str__< ::SireOpenMM::TorchQMEngine > ); + } + +} diff --git a/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.hpp b/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.hpp new file mode 100644 index 000000000..30458e40a --- /dev/null +++ b/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef TorchQMEngine_hpp__pyplusplus_wrapper +#define TorchQMEngine_hpp__pyplusplus_wrapper + +void register_TorchQMEngine_class(); + +#endif//TorchQMEngine_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/TorchQMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/TorchQMForce.pypp.cpp new file mode 100644 index 000000000..7e13a3dda --- /dev/null +++ b/wrapper/Convert/SireOpenMM/TorchQMForce.pypp.cpp @@ -0,0 +1,254 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "TorchQMForce.pypp.hpp" + +namespace bp = boost::python; + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireVol/triclinicbox.h" + +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "torchqm.h" + +#include "SireError/errors.h" + +#include "SireMaths/vector.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireVol/triclinicbox.h" + +#include "openmm/serialization/SerializationNode.h" + +#include "openmm/serialization/SerializationProxy.h" + +#include "torchqm.h" + +SireOpenMM::TorchQMForce __copy__(const SireOpenMM::TorchQMForce &other){ return SireOpenMM::TorchQMForce(other); } + +#include "Qt/qdatastream.hpp" + +const char* pvt_get_name(const SireOpenMM::TorchQMForce&){ return "SireOpenMM::TorchQMForce";} + +#include "Helpers/release_gil_policy.hpp" + +void register_TorchQMForce_class(){ + + { //::SireOpenMM::TorchQMForce + typedef bp::class_< SireOpenMM::TorchQMForce, bp::bases< SireOpenMM::QMForce > > TorchQMForce_exposer_t; + TorchQMForce_exposer_t TorchQMForce_exposer = TorchQMForce_exposer_t( "TorchQMForce", "", bp::init< >("Default constructor.") ); + bp::scope TorchQMForce_scope( TorchQMForce_exposer ); + TorchQMForce_exposer.def( bp::init< QString, SireUnits::Dimension::Length, int, bool, double, QVector< int >, QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, QVector< int >, QVector< int >, QVector< double > >(( bp::arg("module_path"), bp::arg("cutoff"), bp::arg("neighbour_list_frequency"), bp::arg("is_mechanical"), bp::arg("lambda"), bp::arg("atoms"), bp::arg("mm1_to_qm"), bp::arg("mm1_to_mm2"), bp::arg("bond_scale_factors"), bp::arg("mm2_atoms"), bp::arg("numbers"), bp::arg("charges") ), "Constructor.\nPar:am module_path\nThe path to the serialised TorchScript module.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n\nPar:am atoms\nA vector of atom indices for the QM region.\n\nPar:am mm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nPar:am mm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nPar:am bond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\nPar:am mm2_atoms\nA vector of MM2 atom indices.\n\nPar:am numbers\nA vector of atomic charges for all atoms in the system.\n\nPar:am charges\nA vector of atomic charges for all atoms in the system.\n") ); + TorchQMForce_exposer.def( bp::init< SireOpenMM::TorchQMForce const & >(( bp::arg("other") ), "Copy constructor.") ); + { //::SireOpenMM::TorchQMForce::getModulePath + + typedef ::QString ( ::SireOpenMM::TorchQMForce::*getModulePath_function_type)( ) const; + getModulePath_function_type getModulePath_function_value( &::SireOpenMM::TorchQMForce::getModulePath ); + + TorchQMForce_exposer.def( + "getModulePath" + , getModulePath_function_value + , bp::release_gil_policy() + , "Get the path to the serialised TorchScript module.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getAtoms + + typedef ::QVector< int > ( ::SireOpenMM::TorchQMForce::*getAtoms_function_type)( ) const; + getAtoms_function_type getAtoms_function_value( &::SireOpenMM::TorchQMForce::getAtoms ); + + TorchQMForce_exposer.def( + "getAtoms" + , getAtoms_function_value + , bp::release_gil_policy() + , "Get the indices of the atoms in the QM region.\nReturn:s\nA vector of atom indices for the QM region.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getCharges + + typedef ::QVector< double > ( ::SireOpenMM::TorchQMForce::*getCharges_function_type)( ) const; + getCharges_function_type getCharges_function_value( &::SireOpenMM::TorchQMForce::getCharges ); + + TorchQMForce_exposer.def( + "getCharges" + , getCharges_function_value + , bp::release_gil_policy() + , "Get the atomic charges of all atoms in the system.\nReturn:s\nA vector of atomic charges for all atoms in the system.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getCutoff + + typedef ::SireUnits::Dimension::Length ( ::SireOpenMM::TorchQMForce::*getCutoff_function_type)( ) const; + getCutoff_function_type getCutoff_function_value( &::SireOpenMM::TorchQMForce::getCutoff ); + + TorchQMForce_exposer.def( + "getCutoff" + , getCutoff_function_value + , bp::release_gil_policy() + , "Get the QM cutoff distance.\nReturn:s\nThe QM cutoff distance.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getIsMechanical + + typedef bool ( ::SireOpenMM::TorchQMForce::*getIsMechanical_function_type)( ) const; + getIsMechanical_function_type getIsMechanical_function_value( &::SireOpenMM::TorchQMForce::getIsMechanical ); + + TorchQMForce_exposer.def( + "getIsMechanical" + , getIsMechanical_function_value + , bp::release_gil_policy() + , "Get the mechanical embedding flag.\nReturn:s\nA flag to indicate if mechanical embedding is being used.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getLambda + + typedef double ( ::SireOpenMM::TorchQMForce::*getLambda_function_type)( ) const; + getLambda_function_type getLambda_function_value( &::SireOpenMM::TorchQMForce::getLambda ); + + TorchQMForce_exposer.def( + "getLambda" + , getLambda_function_value + , bp::release_gil_policy() + , "Get the lambda weighting factor.\nReturn:s\nThe lambda weighting factor.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getLinkAtoms + + typedef ::boost::tuples::tuple< QMap< int, int >, QMap< int, QVector< int > >, QMap< int, double >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::TorchQMForce::*getLinkAtoms_function_type)( ) const; + getLinkAtoms_function_type getLinkAtoms_function_value( &::SireOpenMM::TorchQMForce::getLinkAtoms ); + + TorchQMForce_exposer.def( + "getLinkAtoms" + , getLinkAtoms_function_value + , bp::release_gil_policy() + , "Get the link atoms associated with each QM atom.\nReturn:s\nA tuple containing:\n\nmm1_to_qm\nA dictionary mapping link atom (MM1) indices to the QM atoms to\nwhich they are bonded.\n\nmm1_to_mm2\nA dictionary of link atoms indices (MM1) to a list of the MM\natoms to which they are bonded (MM2).\n\nbond_scale_factors\nA dictionary of link atom indices (MM1) to a list of the bond\nlength scale factors between the QM and MM1 atoms. The scale\nfactors are the ratio of the equilibrium bond lengths for the\nQM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) R0(QM-MM1),\ntaken from the MM force field parameters for the molecule.\n\n" ); + + } + { //::SireOpenMM::TorchQMForce::getMM2Atoms + + typedef ::QVector< int > ( ::SireOpenMM::TorchQMForce::*getMM2Atoms_function_type)( ) const; + getMM2Atoms_function_type getMM2Atoms_function_value( &::SireOpenMM::TorchQMForce::getMM2Atoms ); + + TorchQMForce_exposer.def( + "getMM2Atoms" + , getMM2Atoms_function_value + , bp::release_gil_policy() + , "Get the vector of MM2 atoms.\nReturn:s\nA vector of MM2 atom indices.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getNeighbourListFrequency + + typedef int ( ::SireOpenMM::TorchQMForce::*getNeighbourListFrequency_function_type)( ) const; + getNeighbourListFrequency_function_type getNeighbourListFrequency_function_value( &::SireOpenMM::TorchQMForce::getNeighbourListFrequency ); + + TorchQMForce_exposer.def( + "getNeighbourListFrequency" + , getNeighbourListFrequency_function_value + , bp::release_gil_policy() + , "Get the neighbour list frequency.\nReturn:s\nThe neighbour list frequency.\n" ); + + } + { //::SireOpenMM::TorchQMForce::getNumbers + + typedef ::QVector< int > ( ::SireOpenMM::TorchQMForce::*getNumbers_function_type)( ) const; + getNumbers_function_type getNumbers_function_value( &::SireOpenMM::TorchQMForce::getNumbers ); + + TorchQMForce_exposer.def( + "getNumbers" + , getNumbers_function_value + , bp::release_gil_policy() + , "Get the atomic numbers for the atoms in the QM region.\nReturn:s\nA vector of atomic numbers for the atoms in the QM region.\n" ); + + } + { //::SireOpenMM::TorchQMForce::operator= + + typedef ::SireOpenMM::TorchQMForce & ( ::SireOpenMM::TorchQMForce::*assign_function_type)( ::SireOpenMM::TorchQMForce const & ) ; + assign_function_type assign_function_value( &::SireOpenMM::TorchQMForce::operator= ); + + TorchQMForce_exposer.def( + "assign" + , assign_function_value + , ( bp::arg("other") ) + , bp::return_self< >() + , "Assignment operator." ); + + } + { //::SireOpenMM::TorchQMForce::setLambda + + typedef void ( ::SireOpenMM::TorchQMForce::*setLambda_function_type)( double ) ; + setLambda_function_type setLambda_function_value( &::SireOpenMM::TorchQMForce::setLambda ); + + TorchQMForce_exposer.def( + "setLambda" + , setLambda_function_value + , ( bp::arg("lambda") ) + , bp::release_gil_policy() + , "Set the lambda weighting factor\nPar:am lambda\nThe lambda weighting factor.\n" ); + + } + { //::SireOpenMM::TorchQMForce::setModulePath + + typedef void ( ::SireOpenMM::TorchQMForce::*setModulePath_function_type)( ::QString ) ; + setModulePath_function_type setModulePath_function_value( &::SireOpenMM::TorchQMForce::setModulePath ); + + TorchQMForce_exposer.def( + "setModulePath" + , setModulePath_function_value + , ( bp::arg("module_path") ) + , bp::release_gil_policy() + , "Set the path to the serialised TorchScript module.\n" ); + + } + { //::SireOpenMM::TorchQMForce::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireOpenMM::TorchQMForce::typeName ); + + TorchQMForce_exposer.def( + "typeName" + , typeName_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + { //::SireOpenMM::TorchQMForce::what + + typedef char const * ( ::SireOpenMM::TorchQMForce::*what_function_type)( ) const; + what_function_type what_function_value( &::SireOpenMM::TorchQMForce::what ); + + TorchQMForce_exposer.def( + "what" + , what_function_value + , bp::release_gil_policy() + , "Return the C++ name for this class." ); + + } + TorchQMForce_exposer.staticmethod( "typeName" ); + TorchQMForce_exposer.def( "__copy__", &__copy__); + TorchQMForce_exposer.def( "__deepcopy__", &__copy__); + TorchQMForce_exposer.def( "clone", &__copy__); + TorchQMForce_exposer.def( "__rlshift__", &__rlshift__QDataStream< ::SireOpenMM::TorchQMForce >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + TorchQMForce_exposer.def( "__rrshift__", &__rrshift__QDataStream< ::SireOpenMM::TorchQMForce >, + bp::return_internal_reference<1, bp::with_custodian_and_ward<1,2> >() ); + TorchQMForce_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::TorchQMForce >()); + TorchQMForce_exposer.def( "__str__", &pvt_get_name); + TorchQMForce_exposer.def( "__repr__", &pvt_get_name); + } + +} diff --git a/wrapper/Convert/SireOpenMM/TorchQMForce.pypp.hpp b/wrapper/Convert/SireOpenMM/TorchQMForce.pypp.hpp new file mode 100644 index 000000000..6bba6b23d --- /dev/null +++ b/wrapper/Convert/SireOpenMM/TorchQMForce.pypp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef TorchQMForce_hpp__pyplusplus_wrapper +#define TorchQMForce_hpp__pyplusplus_wrapper + +void register_TorchQMForce_class(); + +#endif//TorchQMForce_hpp__pyplusplus_wrapper diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index e65bfbfbd..ea0fa865a 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -25,6 +25,10 @@ #include "QMForce.pypp.hpp" +#include "TorchQMEngine.pypp.hpp" + +#include "TorchQMForce.pypp.hpp" + #include "_SireOpenMM_free_functions.pypp.hpp" #include "vector_less__OpenMM_scope_Vec3__greater_.pypp.hpp" @@ -56,10 +60,14 @@ BOOST_PYTHON_MODULE(_SireOpenMM){ register_PyQMEngine_class(); + register_TorchQMEngine_class(); + register_QMForce_class(); register_PyQMForce_class(); + register_TorchQMForce_class(); + register_SireOpenMM_properties(); SireOpenMM::register_extras(); diff --git a/wrapper/Convert/SireOpenMM/active_headers.h b/wrapper/Convert/SireOpenMM/active_headers.h index 4ea67d542..afb0de961 100644 --- a/wrapper/Convert/SireOpenMM/active_headers.h +++ b/wrapper/Convert/SireOpenMM/active_headers.h @@ -3,8 +3,6 @@ #ifdef GCCXML_PARSE -#define QT_NO_SIGNALS_SLOTS_KEYWORDS = 1 - #include "lambdalever.h" #include "openmmminimise.h" #include "openmmmolecule.h" diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp new file mode 100644 index 000000000..a1170c131 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -0,0 +1,1021 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2023 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#include "openmm/serialization/SerializationNode.h" +#include "openmm/serialization/SerializationProxy.h" + +#include "SireError/errors.h" +#include "SireMaths/vector.h" +#include "SireStream/datastream.h" +#include "SireStream/shareddatastream.h" +#include "SireVol/triclinicbox.h" + +#include "torchqm.h" + +using namespace SireMaths; +using namespace SireOpenMM; +using namespace SireStream; +using namespace SireVol; + +// The delta used to place virtual point charges either side of the MM2 +// atoms, in nanometers. +static const double VIRTUAL_PC_DELTA = 0.01; + +// Conversion factor from Hartree to kJ/mol. +static const double HARTREE_TO_KJ_MOL = 2625.499638755248; + +///////// +///////// Implementation of TorchQMForce +///////// + +static const RegisterMetaType r_torchqmforce(NO_ROOT); + +QDataStream &operator<<(QDataStream &ds, const TorchQMForce &torchqmforce) +{ + writeHeader(ds, r_torchqmforce, 1); + + SharedDataStream sds(ds); + + sds << torchqmforce.module_path << torchqmforce.cutoff << torchqmforce.neighbour_list_frequency + << torchqmforce.lambda << torchqmforce.atoms << torchqmforce.mm1_to_qm + << torchqmforce.mm1_to_mm2 << torchqmforce.bond_scale_factors << torchqmforce.mm2_atoms + << torchqmforce.numbers << torchqmforce.charges; + + return ds; +} + +QDataStream &operator>>(QDataStream &ds, TorchQMForce &torchqmforce) +{ + VersionID v = readHeader(ds, r_torchqmforce); + + if (v == 1) + { + SharedDataStream sds(ds); + + sds >> torchqmforce.module_path >> torchqmforce.cutoff >> torchqmforce.neighbour_list_frequency + >> torchqmforce.lambda >> torchqmforce.atoms >> torchqmforce.mm1_to_qm + >> torchqmforce.mm1_to_mm2 >> torchqmforce.bond_scale_factors >> torchqmforce.mm2_atoms + >> torchqmforce.numbers >> torchqmforce.charges; + + // Re-load the Torch module. + torchqmforce.setModulePath(torchqmforce.getModulePath()); + } + else + throw version_error(v, "1", r_torchqmforce, CODELOC); + + return ds; +} + +TorchQMForce::TorchQMForce() +{ +} + +TorchQMForce::TorchQMForce( + QString module_path, + SireUnits::Dimension::Length cutoff, + int neighbour_list_frequency, + bool is_mechanical, + double lambda, + QVector atoms, + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_scale_factors, + QVector mm2_atoms, + QVector numbers, + QVector charges) : + cutoff(cutoff), + neighbour_list_frequency(neighbour_list_frequency), + is_mechanical(is_mechanical), + lambda(lambda), + atoms(atoms), + mm1_to_qm(mm1_to_qm), + mm1_to_mm2(mm1_to_mm2), + bond_scale_factors(bond_scale_factors), + mm2_atoms(mm2_atoms), + numbers(numbers), + charges(charges) +{ + // Try to load the Torch module. + this->setModulePath(module_path); +} + +TorchQMForce::TorchQMForce(const TorchQMForce &other) : + module_path(other.module_path), + torch_module(other.torch_module), + cutoff(other.cutoff), + neighbour_list_frequency(other.neighbour_list_frequency), + is_mechanical(other.is_mechanical), + lambda(other.lambda), + atoms(other.atoms), + mm1_to_qm(other.mm1_to_qm), + mm1_to_mm2(other.mm1_to_mm2), + mm2_atoms(other.mm2_atoms), + bond_scale_factors(other.bond_scale_factors), + numbers(other.numbers), + charges(other.charges) +{ +} + +TorchQMForce &TorchQMForce::operator=(const TorchQMForce &other) +{ + this->module_path = other.module_path; + this->torch_module = other.torch_module; + this->cutoff = other.cutoff; + this->neighbour_list_frequency = other.neighbour_list_frequency; + this->lambda = other.lambda; + this->atoms = other.atoms; + this->mm1_to_qm = other.mm1_to_qm; + this->mm1_to_mm2 = other.mm1_to_mm2; + this->mm2_atoms = other.mm2_atoms; + this->bond_scale_factors = other.bond_scale_factors; + this->numbers = other.numbers; + this->charges = other.charges; + return *this; +} + +void TorchQMForce::setModulePath(QString module_path) +{ + // Try to load the Torch module. + try + { + this->torch_module = torch::jit::load(module_path.toStdString()); + torch::jit::getProfilingMode() = false; + torch::jit::setGraphExecutorOptimize(false); + } + catch (const c10::Error& e) + { + throw SireError::io_error( + QObject::tr( + "Unable to load the TorchScript module '%1'. The error was '%2'.") + .arg(module_path).arg(e.what()), + CODELOC); + } + + this->module_path = module_path; +} + +QString TorchQMForce::getModulePath() const +{ + return this->module_path; +} + +torch::jit::script::Module TorchQMForce::getTorchModule() const +{ + return this->torch_module; +} + +void TorchQMForce::setLambda(double lambda) +{ + // Clamp the lambda value. + if (lambda < 0.0) + { + lambda = 0.0; + } + else if (lambda > 1.0) + { + lambda = 1.0; + } + this->lambda = lambda; +} + +double TorchQMForce::getLambda() const +{ + return this->lambda; +} + +SireUnits::Dimension::Length TorchQMForce::getCutoff() const +{ + return this->cutoff; +} + +int TorchQMForce::getNeighbourListFrequency() const +{ + return this->neighbour_list_frequency; +} + +bool TorchQMForce::getIsMechanical() const +{ + return this->is_mechanical;; +} + +QVector TorchQMForce::getAtoms() const +{ + return this->atoms; +} + +boost::tuple, QMap>, QMap> TorchQMForce::getLinkAtoms() const +{ + return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); +} + +QVector TorchQMForce::getMM2Atoms() const +{ + return this->mm2_atoms; +} + +QVector TorchQMForce::getNumbers() const +{ + return this->numbers; +} + +QVector TorchQMForce::getCharges() const +{ + return this->charges; +} + +const char *TorchQMForce::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *TorchQMForce::what() const +{ + return TorchQMForce::typeName(); +} + +///////// +///////// OpenMM Serialization +///////// + +namespace OpenMM +{ + class TorchQMForceProxy : public SerializationProxy { + public: + TorchQMForceProxy() : SerializationProxy("TorchQMForce") + { + }; + + void serialize(const void* object, SerializationNode& node) const + { + // Serialize the object. + QByteArray data; + QDataStream ds(&data, QIODevice::WriteOnly); + TorchQMForce torchqmforce = *static_cast(object); + ds << torchqmforce; + + // Set the version. + node.setIntProperty("version", 0); + + // Set the note attribute. + node.setStringProperty("note", + "This force only supports partial serialization, so can only be used " + "within the same session and memory space."); + + // Set the data by converting the QByteArray to a hexidecimal string. + node.setStringProperty("data", data.toHex().data()); + }; + + void* deserialize(const SerializationNode& node) const + { + // Check the version. + int version = node.getIntProperty("version"); + if (version != 0) + { + throw OpenMM::OpenMMException("Unsupported version number"); + } + + // Get the data as a std::string. + auto string = node.getStringProperty("data"); + + // Convert to hexidecimal. + auto hex = QByteArray::fromRawData(string.data(), string.size()); + + // Convert to a QByteArray. + auto data = QByteArray::fromHex(hex); + + // Deserialize the object. + QDataStream ds(data); + TorchQMForce torchqmforce; + + try + { + ds >> torchqmforce; + } + catch (...) + { + throw OpenMM::OpenMMException("Unable deserialize TorchQMForce"); + } + + return new TorchQMForce(torchqmforce); + }; + }; + + // Register the TorchQMForce serialization proxy. + extern "C" void registerTorchQMSerializationProxies() { + SerializationProxy::registerProxy(typeid(TorchQMForce), new TorchQMForceProxy()); + } +}; + +///////// +///////// Implementation of TorchQMForceImpl +///////// + +OpenMM::ForceImpl *TorchQMForce::createImpl() const +{ +#ifdef SIRE_USE_CUSTOMCPPFORCE + return new TorchQMForceImpl(*this); +#else + throw SireError::unsupported(QObject::tr( + "Unable to create an TorchQMForceImpl because OpenMM::CustomCPPForceImpl " + "is not available. You need to use OpenMM 8.1 or later."), + CODELOC); + return 0; +#endif +} + +TorchQMForceImpl::TorchQMForceImpl(const TorchQMForce &owner) : + OpenMM::CustomCPPForceImpl(owner), + owner(owner) +{ + this->torch_module = owner.getTorchModule(); +} + +TorchQMForceImpl::~TorchQMForceImpl() +{ +} + +const TorchQMForce &TorchQMForceImpl::getOwner() const +{ + return this->owner; +} + +double TorchQMForceImpl::computeForce( + OpenMM::ContextImpl &context, + const std::vector &positions, + std::vector &forces) +{ +#ifdef SIRE_USE_CUSTOMCPPFORCE + // Get the platform name from the context. + const auto platform = context.getPlatform().getName(); + + // Set the Torch device. + auto device = torch::kCUDA; + if (platform != "CUDA") + { + device = torch::kCPU; + } + + // If this is the first step, then setup information for the neighbour list. + if (this->step_count == 0) + { + // Move the Torch module to the correct device. + this->torch_module.to(device); + + // Store the cutoff as a double in Angstom. + this->cutoff = this->owner.getCutoff().value(); + + // The neighbour list cutoff is 20% larger than the cutoff. + this->neighbour_list_cutoff = 1.2*this->cutoff; + + // Store the neighbour list update frequency. + this->neighbour_list_frequency = this->owner.getNeighbourListFrequency(); + + // Flag whether a neighbour list is used. + this->is_neighbour_list = this->neighbour_list_frequency > 0; + } + + // Get the current box vectors in nanometers. + OpenMM::Vec3 box_x, box_y, box_z; + context.getPeriodicBoxVectors(box_x, box_y, box_z); + + // Create a triclinic space, converting to Angstrom. + TriclinicBox space( + Vector(10*box_x[0], 10*box_x[1], 10*box_x[2]), + Vector(10*box_y[0], 10*box_y[1], 10*box_y[2]), + Vector(10*box_z[0], 10*box_z[1], 10*box_z[2]) + ); + + // Store the QM atomic indices and numbers. + auto qm_atoms = this->owner.getAtoms(); + auto numbers = this->owner.getNumbers(); + + // Store the link atom info. Link atoms are handled using the Charge Shift + // method. See: https://www.ks.uiuc.edu/Research/qmmm + const auto link_atoms = this->owner.getLinkAtoms(); + const auto mm1_to_qm = link_atoms.get<0>(); + const auto mm1_to_mm2 = link_atoms.get<1>(); + const auto bond_scale_factors = link_atoms.get<2>(); + const auto mm2_atoms = this->owner.getMM2Atoms(); + + // Initialise a vector to hold the current positions for the QM atoms. + QVector xyz_qm_vec(qm_atoms.size()); + std::vector xyz_qm(3*qm_atoms.size()); + + // First loop over all QM atoms and store the positions. + int i = 0; + for (const auto &idx : qm_atoms) + { + const auto &pos = positions[idx]; + Vector qm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + xyz_qm_vec[i] = qm_vec; + i++; + } + + // Next sure that the QM atoms are whole (unwrapped). + xyz_qm_vec = space.makeWhole(xyz_qm_vec); + + // Get the center of the QM atoms. We will use this as a reference when + // re-imaging the MM atoms. Also store the QM atoms in the xyz_qm vector. + Vector center; + i = 0; + for (const auto &qm_vec : xyz_qm_vec) + { + xyz_qm[3*i] = qm_vec[0]; + xyz_qm[3*i+1] = qm_vec[1]; + xyz_qm[3*i+2] = qm_vec[2]; + center += qm_vec; + i++; + } + center /= i; + + // Initialise a vector to hold the current positions and charges for the MM atoms. + std::vector xyz_mm; + QVector charges_mm; + + // Initialise a list to hold the indices of the MM atoms. + QVector idx_mm; + + // Store the current number of MM atoms. + unsigned int num_mm = 0; + + // If we are using electrostatic embedding, the work out the MM point charges and + // build the neighbour list. + if (not this->owner.getIsMechanical()) + { + // Initialise a vector to hold the current positions and charges for the virtual + // point charges. + std::vector xyz_virtual_flat; + QVector charges_virtual; + + // Manually work out the MM point charges and build the neigbour list. + if (not this->is_neighbour_list or this->step_count % this->neighbour_list_frequency == 0) + { + // Clear the neighbour list. + if (this->is_neighbour_list) + { + this->neighbour_list.clear(); + } + + i = 0; + // Loop over all of the OpenMM positions. + for (const auto &pos : positions) + { + // Exclude QM atoms or link atoms, which are handled later. + if (not qm_atoms.contains(i) and + not mm1_to_mm2.contains(i) and + not mm2_atoms.contains(i)) + { + // Store the MM atom position in Sire Vector format. + Vector mm_vec(10*pos[0], 10*pos[1], 10*pos[2]); + + // Loop over all of the QM atoms. + for (const auto &qm_vec : xyz_qm_vec) + { + // Work out the distance between the current MM atom and QM atoms. + const auto dist = space.calcDist(mm_vec, qm_vec); + + // The current MM atom is within the neighbour list cutoff. + if (this->is_neighbour_list and dist < this->neighbour_list_cutoff) + { + // Insert the MM atom index into the neighbour list. + this->neighbour_list.insert(i); + } + + // The current MM atom is within the cutoff, add it. + if (dist < cutoff) + { + // Work out the minimum image position with respect to the + // reference position and add to the vector. + mm_vec = space.getMinimumImage(mm_vec, center); + xyz_mm.push_back(mm_vec[0]); + xyz_mm.push_back(mm_vec[1]); + xyz_mm.push_back(mm_vec[2]); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[i]); + idx_mm.append(i); + + // Exit the inner loop. + break; + } + } + } + + // Update the atom index. + i++; + } + } + // Use the neighbour list. + else + { + // Loop over the MM atoms in the neighbour list. + for (const auto &idx : this->neighbour_list) + { + // Store the MM atom position in Sire Vector format. + Vector mm_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); + + // Loop over all of the QM atoms. + for (const auto &qm_vec : xyz_qm_vec) + { + // The current MM atom is within the cutoff, add it. + if (space.calcDist(mm_vec, qm_vec) < cutoff) + { + // Work out the minimum image position with respect to the + // reference position and add to the vector. + mm_vec = space.getMinimumImage(mm_vec, center); + xyz_mm.push_back(mm_vec[0]); + xyz_mm.push_back(mm_vec[1]); + xyz_mm.push_back(mm_vec[2]); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[idx]); + idx_mm.append(idx); + + // Exit the inner loop. + break; + } + } + } + } + + // Handle link atoms via the Charge Shift method. + // See: https://www.ks.uiuc.edu/Research/qmmm + for (const auto &idx: mm1_to_mm2.keys()) + { + // Get the QM atom to which the current MM atom is bonded. + const auto qm_idx = mm1_to_qm[idx]; + + // Store the MM1 position in Sire Vector format, along with the + // position of the QM atom to which it is bonded. + Vector mm1_vec(10*positions[idx][0], 10*positions[idx][1], 10*positions[idx][2]); + Vector qm_vec(10*positions[qm_idx][0], 10*positions[qm_idx][1], 10*positions[qm_idx][2]); + + // Work out the minimum image positions with respect to the reference position. + mm1_vec = space.getMinimumImage(mm1_vec, center); + qm_vec = space.getMinimumImage(qm_vec, center); + + // Work out the position of the link atom. Here we use a bond length + // scale factor taken from the MM bond potential, i.e. R0(QM-L) / R0(QM-MM1), + // where R0(QM-L) is the equilibrium bond length for the QM and link (L) + // elements, and R0(QM-MM1) is the equilibrium bond length for the QM + // and MM1 elements. + const auto link_vec = qm_vec + bond_scale_factors[idx]*(mm1_vec - qm_vec); + + // Add to the QM positions. + xyz_qm.push_back(link_vec[0]); + xyz_qm.push_back(link_vec[1]); + xyz_qm.push_back(link_vec[2]); + + // Add the MM1 index to the QM atoms vector. + qm_atoms.append(qm_idx); + + // Append a hydrogen element to the numbers vector. + numbers.append(1); + + // Store the number of MM2 atoms. + const auto num_mm2 = mm1_to_mm2[idx].size(); + + // Store the fractional charge contribution to the MM2 atoms and + // virtual point charges. + const auto frac_charge = this->owner.getCharges()[idx] / num_mm2; + + // Loop over the MM2 atoms and perform charge shifting. Here the MM1 + // charge is redistributed over the MM2 atoms and two virtual point + // charges are added either side of the MM2 atoms in order to preserve + // the MM1-MM2 dipole. + for (const auto& mm2_idx : mm1_to_mm2[idx]) + { + // Store the MM2 position in Sire Vector format. + Vector mm2_vec(10*positions[mm2_idx][0], 10*positions[mm2_idx][1], 10*positions[mm2_idx][2]); + + // Work out the minimum image position with respect to the reference position. + mm2_vec = space.getMinimumImage(mm2_vec, center); + + // Add to the MM positions. + xyz_mm.push_back(mm2_vec[0]); + xyz_mm.push_back(mm2_vec[1]); + xyz_mm.push_back(mm2_vec[2]); + + // Add the charge and index. + charges_mm.append(this->owner.getCharges()[mm2_idx] + frac_charge); + idx_mm.append(mm2_idx); + + // Now add the virtual point charges. + + // Compute the normal vector from the MM1 to MM2 atom. + const auto normal = (mm2_vec - mm1_vec).normalise(); + + // Positive direction. (Away from MM1 atom.) + auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; + xyz_virtual_flat.push_back(xyz[0]); + xyz_virtual_flat.push_back(xyz[1]); + xyz_virtual_flat.push_back(xyz[2]); + charges_virtual.append(-frac_charge); + + // Negative direction (Towards MM1 atom.) + xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; + xyz_virtual_flat.push_back(xyz[0]); + xyz_virtual_flat.push_back(xyz[1]); + xyz_virtual_flat.push_back(xyz[2]); + charges_virtual.append(frac_charge); + } + } + + // Store the current number of MM atoms. + num_mm = charges_mm.size(); + + // If there are any virtual point charges, then add to the MM positions + // and charges. + if (xyz_virtual_flat.size() > 0) + { + xyz_mm.reserve(xyz_mm.size() + xyz_virtual_flat.size()); + xyz_mm.insert(xyz_mm.end(), xyz_virtual_flat.begin(), xyz_virtual_flat.end()); + charges_mm.append(charges_virtual); + } + + // Update the maximum number of MM atoms that we've seen. + if (charges_mm.size() > this->max_num_mm) + { + this->max_num_mm = charges_mm.size(); + } + else + { + // Resize the charges and positions vectors to the maximum number of MM atoms. + // This is to try to preserve a static compute graph to avoid re-jitting. + charges_mm.resize(this->max_num_mm); + xyz_mm.resize(3*this->max_num_mm); + } + } + + // Convert input to Torch tensors. + + // MM charges. + torch::Tensor charges_mm_torch = torch::from_blob(charges_mm.data(), {charges_mm.size()}, + torch::TensorOptions().dtype(torch::kFloat64)) + .to(torch::kFloat32).to(device); + + // Atomic numbers. + torch::Tensor atomic_numbers_torch = torch::from_blob(numbers.data(), {numbers.size()}, + torch::TensorOptions().dtype(torch::kInt32)) + .to(torch::kInt64).to(device); + + // QM positions. + torch::Tensor xyz_qm_torch = torch::from_blob(xyz_qm.data(), {numbers.size(), 3}, + torch::TensorOptions().dtype(torch::kFloat32)) + .to(device); + xyz_qm_torch.requires_grad_(true); + + // MM positions. + torch::Tensor xyz_mm_torch = torch::from_blob(xyz_mm.data(), {charges_mm.size(), 3}, + torch::TensorOptions().dtype(torch::kFloat32)) + .to(device); + xyz_mm_torch.requires_grad_(true); + + // Create the input vector. + auto input = std::vector{ + atomic_numbers_torch, + charges_mm_torch, + xyz_qm_torch, + xyz_mm_torch + }; + + // Compute the energies. + auto energies = this->torch_module.forward(input).toTensor(); + + // Store the sum of the energy in kJ. + const auto energy = energies.sum().item() * HARTREE_TO_KJ_MOL; + + // Compute the gradients. + energies.sum().backward(); + + // Compute the forces, converting from Hatree/Anstrom to kJ/mol/nm. + const auto forces_qm = (-xyz_qm_torch.grad() * HARTREE_TO_KJ_MOL * 10).cpu();; + const auto forces_mm = (-xyz_mm_torch.grad() * HARTREE_TO_KJ_MOL * 10).cpu();; + + // The current interpolation (weighting) parameter. + double lambda; + + // Try to get the "lambda_emle" global parameter from the context. + try + { + lambda = context.getParameter("lambda_emle"); + } + catch (...) + { + // Try to get the "lambda_interpolate" global parameter from the context. + try + { + lambda = context.getParameter("lambda_interpolate"); + } + // Fall back on the lambda value stored in the TorchQMForce object. + catch (...) + { + lambda = this->owner.getLambda(); + } + } + + // Clamp the lambda value. + if (lambda < 0.0) + { + lambda = 0.0; + } + else if (lambda > 1.0) + { + lambda = 1.0; + } + + // Now update the force vector. + + // Flatten the forces to std::vector. + std::vector forces_qm_flat( + forces_qm.data_ptr(), + forces_qm.data_ptr() + forces_qm.numel()); + std::vector forces_mm_flat( + forces_mm.data_ptr(), + forces_mm.data_ptr() + forces_mm.numel()); + + // First the QM atoms. + for (int i=0; istep_count++; + + // Finally, return the energy. + return lambda * energy; +#endif +} + +///////// +///////// Implementation of TorchQMEngine +///////// + +TorchQMEngine::TorchQMEngine() : ConcreteProperty() +{ + // Register the serialization proxies. + OpenMM::registerTorchQMSerializationProxies(); +} + +TorchQMEngine::TorchQMEngine( + QString module_path, + SireUnits::Dimension::Length cutoff, + int neighbour_list_frequency, + bool is_mechanical, + double lambda) : + ConcreteProperty(), + module_path(module_path), + cutoff(cutoff), + neighbour_list_frequency(neighbour_list_frequency), + is_mechanical(is_mechanical), + lambda(lambda) +{ + // Register the serialization proxies. + OpenMM::registerTorchQMSerializationProxies(); + + if (this->neighbour_list_frequency < 0) + { + neighbour_list_frequency = 0; + } + if (this->lambda < 0.0) + { + this->lambda = 0.0; + } + else if (this->lambda > 1.0) + { + this->lambda = 1.0; + } +} + +TorchQMEngine::TorchQMEngine(const TorchQMEngine &other) : + module_path(other.module_path), + cutoff(other.cutoff), + neighbour_list_frequency(other.neighbour_list_frequency), + is_mechanical(other.is_mechanical), + lambda(other.lambda), + atoms(other.atoms), + mm1_to_qm(other.mm1_to_qm), + mm1_to_mm2(other.mm1_to_mm2), + mm2_atoms(other.mm2_atoms), + bond_scale_factors(other.bond_scale_factors), + numbers(other.numbers), + charges(other.charges) +{ +} + +TorchQMEngine &TorchQMEngine::operator=(const TorchQMEngine &other) +{ + this->module_path = other.module_path; + this->cutoff = other.cutoff; + this->neighbour_list_frequency = other.neighbour_list_frequency; + this->lambda = other.lambda; + this->atoms = other.atoms; + this->mm1_to_qm = other.mm1_to_qm; + this->mm1_to_mm2 = other.mm1_to_mm2; + this->mm2_atoms = other.mm2_atoms; + this->bond_scale_factors = other.bond_scale_factors; + this->numbers = other.numbers; + this->charges = other.charges; + return *this; +} + +void TorchQMEngine::setModulePath(QString module_path) +{ + this->module_path = module_path; +} + +QString TorchQMEngine::getModulePath() const +{ + return this->module_path; +} + +void TorchQMEngine::setLambda(double lambda) +{ + // Clamp the lambda value. + if (lambda < 0.0) + { + lambda = 0.0; + } + else if (lambda > 1.0) + { + lambda = 1.0; + } + this->lambda = lambda; +} + +double TorchQMEngine::getLambda() const +{ + return this->lambda; +} + +void TorchQMEngine::setCutoff(SireUnits::Dimension::Length cutoff) +{ + this->cutoff = cutoff; +} + +SireUnits::Dimension::Length TorchQMEngine::getCutoff() const +{ + return this->cutoff; +} + +int TorchQMEngine::getNeighbourListFrequency() const +{ + return this->neighbour_list_frequency; +} + +void TorchQMEngine::setNeighbourListFrequency(int neighbour_list_frequency) +{ + // Assume anything less than zero means no neighbour list. + if (neighbour_list_frequency < 0) + { + neighbour_list_frequency = 0; + } + this->neighbour_list_frequency = neighbour_list_frequency; +} + +bool TorchQMEngine::getIsMechanical() const +{ + return this->is_mechanical; +} + +void TorchQMEngine::setIsMechanical(bool is_mechanical) +{ + this->is_mechanical = is_mechanical; +} + +QVector TorchQMEngine::getAtoms() const +{ + return this->atoms; +} + +void TorchQMEngine::setAtoms(QVector atoms) +{ + this->atoms = atoms; +} + +boost::tuple, QMap>, QMap> TorchQMEngine::getLinkAtoms() const +{ + return boost::make_tuple(this->mm1_to_qm, this->mm1_to_mm2, this->bond_scale_factors); +} + +void TorchQMEngine::setLinkAtoms( + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_scale_factors) +{ + this->mm1_to_qm = mm1_to_qm; + this->mm1_to_mm2 = mm1_to_mm2; + this->bond_scale_factors = bond_scale_factors; + + // Build a vector of all of the MM2 atoms. + this->mm2_atoms.clear(); + for (const auto &mm2 : this->mm1_to_mm2.values()) + { + this->mm2_atoms.append(mm2); + } +} + +QVector TorchQMEngine::getMM2Atoms() const +{ + return this->mm2_atoms; +} + +QVector TorchQMEngine::getNumbers() const +{ + return this->numbers; +} + +void TorchQMEngine::setNumbers(QVector numbers) +{ + this->numbers = numbers; +} + +QVector TorchQMEngine::getCharges() const +{ + return this->charges; +} + +void TorchQMEngine::setCharges(QVector charges) +{ + this->charges = charges; +} + +const char *TorchQMEngine::typeName() +{ + return QMetaType::typeName(qMetaTypeId()); +} + +const char *TorchQMEngine::what() const +{ + return TorchQMEngine::typeName(); +} + +QMForce* TorchQMEngine::createForce() const +{ + return new TorchQMForce( + this->module_path, + this->cutoff, + this->neighbour_list_frequency, + this->is_mechanical, + this->lambda, + this->atoms, + this->mm1_to_qm, + this->mm1_to_mm2, + this->bond_scale_factors, + this->mm2_atoms, + this->numbers, + this->charges + ); +} diff --git a/wrapper/Convert/SireOpenMM/torchqm.h b/wrapper/Convert/SireOpenMM/torchqm.h new file mode 100644 index 000000000..7b11ef088 --- /dev/null +++ b/wrapper/Convert/SireOpenMM/torchqm.h @@ -0,0 +1,506 @@ +/********************************************\ + * + * Sire - Molecular Simulation Framework + * + * Copyright (C) 2023 Christopher Woods + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + * + * For full details of the license please see the COPYING file + * that should have come with this distribution. + * + * You can contact the authors via the website + * at https://sire.openbiosim.org + * +\*********************************************/ + +#ifndef SIREOPENMM_TORCHQM_H +#define SIREOPENMM_TORCHQM_H + +#include "OpenMM.h" +#include "openmm/Force.h" +#ifdef SIRE_USE_CUSTOMCPPFORCE +#include "openmm/internal/ContextImpl.h" +#include "openmm/internal/CustomCPPForceImpl.h" +#endif + +#include "boost/python.hpp" +#include + +#include + +#include +#include + +#include "sireglobal.h" + +#include "SireUnits/dimensions.h" +#include "SireUnits/units.h" + +#include "qmmm.h" + +namespace bp = boost::python; + +SIRE_BEGIN_HEADER + +namespace SireOpenMM +{ + class TorchQMForce; +} + +QDataStream &operator<<(QDataStream &, const SireOpenMM::TorchQMForce &); +QDataStream &operator>>(QDataStream &, SireOpenMM::TorchQMForce &); + +namespace SireOpenMM +{ + class TorchQMForce : public QMForce + { + friend QDataStream & ::operator<<(QDataStream &, const TorchQMForce &); + friend QDataStream & ::operator>>(QDataStream &, TorchQMForce &); + + public: + //! Default constructor. + TorchQMForce(); + + //! Constructor. + /* \param module_path + The path to the serialised TorchScript module. + + \param torch_module + The TorchScript module. + + \param cutoff + The ML cutoff distance. + + \param neighbour_list_frequency + The frequency at which the neighbour list is updated. (Number of steps.) + If zero, then no neighbour list is used. + + \param is_mechanical + A flag to indicate if mechanical embedding is being used. + + \param lambda + The lambda weighting factor. This can be used to interpolate between + potentials for end-state correction calculations. + + \param atoms + A vector of atom indices for the QM region. + + \param mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + \param mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + \param bond_scale_factors + A dictionary of link atom indices (MM1) to a list of the bond + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + + \param mm2_atoms + A vector of MM2 atom indices. + + \param numbers + A vector of atomic charges for all atoms in the system. + + \param charges + A vector of atomic charges for all atoms in the system. + */ + TorchQMForce( + QString module_path, + SireUnits::Dimension::Length cutoff, + int neighbour_list_frequency, + bool is_mechanical, + double lambda, + QVector atoms, + QMap mm1_to_qm, + QMap> mm1_to_mm2, + QMap bond_scale_factors, + QVector mm2_atoms, + QVector numbers, + QVector charges + ); + + //! Copy constructor. + TorchQMForce(const TorchQMForce &other); + + //! Assignment operator. + TorchQMForce &operator=(const TorchQMForce &other); + + //! Get the path to the serialised TorchScript module. + /*! \returns + The path to the serialised TorchScript module. + */ + QString getModulePath() const; + + //! Set the path to the serialised TorchScript module. + /*! \param module_path + The path to the serialised TorchScript module. + */ + void setModulePath(QString module_path); + + //! Get the TorchScript module. + /*! \returns + The TorchScript module. + */ + torch::jit::script::Module getTorchModule() const; + + //! Get the lambda weighting factor. + /*! \returns + The lambda weighting factor. + */ + double getLambda() const; + + //! Set the lambda weighting factor + /* \param lambda + The lambda weighting factor. + */ + void setLambda(double lambda); + + //! Get the QM cutoff distance. + /*! \returns + The QM cutoff distance. + */ + SireUnits::Dimension::Length getCutoff() const; + + //! Get the neighbour list frequency. + /*! \returns + The neighbour list frequency. + */ + int getNeighbourListFrequency() const; + + //! Get the mechanical embedding flag. + /*! \returns + A flag to indicate if mechanical embedding is being used. + */ + bool getIsMechanical() const; + + //! Get the indices of the atoms in the QM region. + /*! \returns + A vector of atom indices for the QM region. + */ + QVector getAtoms() const; + + //! Get the link atoms associated with each QM atom. + /*! \returns + A tuple containing: + + mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + bond_scale_factors + A dictionary of link atom indices (MM1) to a list of the bond + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + + */ + boost::tuple, QMap>, QMap> getLinkAtoms() const; + + //! Get the vector of MM2 atoms. + /*! \returns + A vector of MM2 atom indices. + */ + QVector getMM2Atoms() const; + + //! Get the atomic numbers for the atoms in the QM region. + /*! \returns + A vector of atomic numbers for the atoms in the QM region. + */ + QVector getNumbers() const; + + //! Get the atomic charges of all atoms in the system. + /*! \returns + A vector of atomic charges for all atoms in the system. + */ + QVector getCharges() const; + + //! Return the C++ name for this class. + static const char *typeName(); + + //! Return the C++ name for this class. + const char *what() const; + + protected: + OpenMM::ForceImpl *createImpl() const; + + private: + QString module_path; + torch::jit::script::Module torch_module; + SireUnits::Dimension::Length cutoff; + int neighbour_list_frequency; + bool is_mechanical; + double lambda; + QVector atoms; + QMap mm1_to_qm; + QMap> mm1_to_mm2; + QMap bond_scale_factors; + QVector mm2_atoms; + QVector numbers; + QVector charges; + }; + +#ifdef SIRE_USE_CUSTOMCPPFORCE + class TorchQMForceImpl : public OpenMM::CustomCPPForceImpl + { + public: + TorchQMForceImpl(const TorchQMForce &owner); + + ~TorchQMForceImpl(); + + double computeForce(OpenMM::ContextImpl &context, + const std::vector &positions, + std::vector &forces); + + const TorchQMForce &getOwner() const; + + private: + const TorchQMForce &owner; + torch::jit::script::Module torch_module; + unsigned long long step_count=0; + double cutoff; + bool is_neighbour_list; + int neighbour_list_frequency; + double neighbour_list_cutoff; + QSet neighbour_list; + int max_num_mm=0; + }; +#endif + + class TorchQMEngine : public SireBase::ConcreteProperty + { + public: + //! Default constructor. + TorchQMEngine(); + + //! Constructor + /*! \param module_path + The path to the serialised TorchScript module. + + \param cutoff + The ML cutoff distance. + + \param neighbour_list_frequency + The frequency at which the neighbour list is updated. (Number of steps.) + If zero, then no neighbour list is used. + + \param is_mechanical + A flag to indicate if mechanical embedding is being used. + + \param lambda + The lambda weighting factor. This can be used to interpolate between + potentials for end-state correction calculations. + */ + TorchQMEngine( + QString module_path, + SireUnits::Dimension::Length cutoff=7.5*SireUnits::angstrom, + int neighbour_list_frequency=20, + bool is_mechanical=false, + double lambda=1.0 + ); + + //! Copy constructor. + TorchQMEngine(const TorchQMEngine &other); + + //! Assignment operator. + TorchQMEngine &operator=(const TorchQMEngine &other); + + //! Get the path to the serialised TorchScript module. + /*! \returns + The path to the serialised TorchScript module. + */ + QString getModulePath() const; + + //! Set the path to the serialised TorchScript module. + /*! \param module_path + The path to the serialised TorchScript module. + */ + void setModulePath(QString module_path); + + //! Get the lambda weighting factor. + /*! \returns + The lambda weighting factor. + */ + double getLambda() const; + + //! Set the lambda weighting factor. + /*! \param lambda + The lambda weighting factor. + */ + void setLambda(double lambda); + + //! Get the QM cutoff distance. + /*! \returns + The QM cutoff distance. + */ + SireUnits::Dimension::Length getCutoff() const; + + //! Set the QM cutoff distance. + /*! \param cutoff + The QM cutoff distance. + */ + void setCutoff(SireUnits::Dimension::Length cutoff); + + //! Get the neighbour list frequency. + /*! \returns + The neighbour list frequency. + */ + int getNeighbourListFrequency() const; + + //! Set the neighbour list frequency. + /*! \param neighbour_list_frequency + The neighbour list frequency. + */ + void setNeighbourListFrequency(int neighbour_list_frequency); + + //! Get the mechanical embedding flag. + /*! \returns + A flag to indicate if mechanical embedding is being used. + */ + bool getIsMechanical() const; + + //! Set the mechanical embedding flag. + /*! \param is_mechanical + A flag to indicate if mechanical embedding is being used. + */ + void setIsMechanical(bool is_mechanical); + + //! Get the indices of the atoms in the QM region. + /*! \returns + A vector of atom indices for the QM region. + */ + QVector getAtoms() const; + + //! Set the list of atom indices for the QM region. + /*! \param atoms + A vector of atom indices for the QM region. + */ + void setAtoms(QVector atoms); + + //! Get the link atoms associated with each QM atom. + /*! \returns + A tuple containing: + + mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + bond_scale_factors + A dictionary of link atom indices (MM1) to a list of the bond + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + + */ + boost::tuple, QMap>, QMap> getLinkAtoms() const; + + //! Set the link atoms associated with each QM atom. + /*! \param mm1_to_qm + A dictionary mapping link atom (MM1) indices to the QM atoms to + which they are bonded. + + \param mm1_to_mm2 + A dictionary of link atoms indices (MM1) to a list of the MM + atoms to which they are bonded (MM2). + + \param bond_scale_factors + A dictionary of link atom indices (MM1) to a list of the bond + length scale factors between the QM and MM1 atoms. The scale + factors are the ratio of the equilibrium bond lengths for the + QM-L (QM-link) atom and QM-MM1 atom, i.e. R0(QM-L) / R0(QM-MM1), + taken from the MM force field parameters for the molecule. + + */ + void setLinkAtoms(QMap mm1_to_qm, QMap> mm1_to_mm2, QMap bond_scale_factors); + + //! Get the vector of MM2 atoms. + /*! \returns + A vector of MM2 atom indices. + */ + QVector getMM2Atoms() const; + + //! Get the atomic numbers for the atoms in the QM region. + /*! \returns + A vector of atomic numbers for the atoms in the QM region. + */ + QVector getNumbers() const; + + //! Set the atomic numbers for the atoms in the QM region. + /*! \param numbers + A vector of atomic numbers for the atoms in the QM region. + */ + void setNumbers(QVector numbers); + + //! Get the atomic charges of all atoms in the system. + /*! \returns + A vector of atomic charges for all atoms in the system. + */ + QVector getCharges() const; + + //! Set the atomic charges of all atoms in the system. + /*! \param charges + A vector of atomic charges for all atoms in the system. + */ + void setCharges(QVector charges); + + //! Return the C++ name for this class. + static const char *typeName(); + + //! Return the C++ name for this class. + const char *what() const; + + //! Create an EMLE force object. + QMForce* createForce() const; + + private: + QString module_path; + SireUnits::Dimension::Length cutoff; + int neighbour_list_frequency; + bool is_mechanical; + double lambda; + QVector atoms; + QMap mm1_to_qm; + QMap> mm1_to_mm2; + QMap bond_scale_factors; + QVector mm2_atoms; + QVector numbers; + QVector charges; + }; +} + +Q_DECLARE_METATYPE(SireOpenMM::TorchQMForce) +Q_DECLARE_METATYPE(SireOpenMM::TorchQMEngine) + +SIRE_EXPOSE_CLASS(SireOpenMM::TorchQMForce) +SIRE_EXPOSE_CLASS(SireOpenMM::TorchQMEngine) + +SIRE_END_HEADER + +#endif diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 37e1103ff..a94ea4700 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -21,6 +21,7 @@ "QMEngine", "PyQMCallback", "PyQMEngine", + "TorchQMEngine", ] try: @@ -102,6 +103,7 @@ def smarts_to_rdkit(*args, **kwargs): QMEngine, PyQMCallback, PyQMEngine, + TorchQMEngine, ) from ..._pythonize import _pythonize @@ -114,6 +116,7 @@ def smarts_to_rdkit(*args, **kwargs): QMEngine, PyQMCallback, PyQMEngine, + TorchQMEngine, ], delete_old=True, ) From 3b7b303746f4f9252b634de543d9cadf3149acb1 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 13 Jul 2024 13:29:05 +0100 Subject: [PATCH 335/468] Call .eval() on module. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index a1170c131..3abd7f913 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -163,9 +163,10 @@ void TorchQMForce::setModulePath(QString module_path) // Try to load the Torch module. try { - this->torch_module = torch::jit::load(module_path.toStdString()); torch::jit::getProfilingMode() = false; torch::jit::setGraphExecutorOptimize(false); + this->torch_module = torch::jit::load(module_path.toStdString()); + this->torch_module.eval(); } catch (const c10::Error& e) { From b8304f7c6cf8ca6be80736ce9c9f5df2e2fd928d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 13 Jul 2024 14:02:39 +0100 Subject: [PATCH 336/468] Use torch::autograd::grad rather than backward. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index 3abd7f913..2661653ad 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -29,6 +29,8 @@ #include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationProxy.h" +#include + #include "SireError/errors.h" #include "SireMaths/vector.h" #include "SireStream/datastream.h" @@ -712,11 +714,11 @@ double TorchQMForceImpl::computeForce( const auto energy = energies.sum().item() * HARTREE_TO_KJ_MOL; // Compute the gradients. - energies.sum().backward(); + const auto gradients = torch::autograd::grad({energies.sum()}, {xyz_qm_torch, xyz_mm_torch}); // Compute the forces, converting from Hatree/Anstrom to kJ/mol/nm. - const auto forces_qm = (-xyz_qm_torch.grad() * HARTREE_TO_KJ_MOL * 10).cpu();; - const auto forces_mm = (-xyz_mm_torch.grad() * HARTREE_TO_KJ_MOL * 10).cpu();; + const auto forces_qm = -(gradients[0] * HARTREE_TO_KJ_MOL * 10).cpu(); + const auto forces_mm = -(gradients[1] * HARTREE_TO_KJ_MOL * 10).cpu(); // The current interpolation (weighting) parameter. double lambda; From 2f00fc30fef592adfaea57f3bd2e894eddf5c931 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 15 Jul 2024 15:26:06 +0100 Subject: [PATCH 337/468] Update vector name. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index 2661653ad..443b8651b 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -472,7 +472,7 @@ double TorchQMForceImpl::computeForce( { // Initialise a vector to hold the current positions and charges for the virtual // point charges. - std::vector xyz_virtual_flat; + std::vector xyz_virtual; QVector charges_virtual; // Manually work out the MM point charges and build the neigbour list. @@ -635,16 +635,16 @@ double TorchQMForceImpl::computeForce( // Positive direction. (Away from MM1 atom.) auto xyz = mm2_vec + VIRTUAL_PC_DELTA*normal; - xyz_virtual_flat.push_back(xyz[0]); - xyz_virtual_flat.push_back(xyz[1]); - xyz_virtual_flat.push_back(xyz[2]); + xyz_virtual.push_back(xyz[0]); + xyz_virtual.push_back(xyz[1]); + xyz_virtual.push_back(xyz[2]); charges_virtual.append(-frac_charge); // Negative direction (Towards MM1 atom.) xyz = mm2_vec - VIRTUAL_PC_DELTA*normal; - xyz_virtual_flat.push_back(xyz[0]); - xyz_virtual_flat.push_back(xyz[1]); - xyz_virtual_flat.push_back(xyz[2]); + xyz_virtual.push_back(xyz[0]); + xyz_virtual.push_back(xyz[1]); + xyz_virtual.push_back(xyz[2]); charges_virtual.append(frac_charge); } } @@ -654,10 +654,10 @@ double TorchQMForceImpl::computeForce( // If there are any virtual point charges, then add to the MM positions // and charges. - if (xyz_virtual_flat.size() > 0) + if (xyz_virtual.size() > 0) { - xyz_mm.reserve(xyz_mm.size() + xyz_virtual_flat.size()); - xyz_mm.insert(xyz_mm.end(), xyz_virtual_flat.begin(), xyz_virtual_flat.end()); + xyz_mm.reserve(xyz_mm.size() + xyz_virtual.size()); + xyz_mm.insert(xyz_mm.end(), xyz_virtual.begin(), xyz_virtual.end()); charges_mm.append(charges_virtual); } From d36b3aae6283661fa4173c63fbfc202581b918fb Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 16 Jul 2024 11:12:24 +0100 Subject: [PATCH 338/468] Remove librascal and associated dependencies. --- requirements_emle.txt | 5 +---- setup.py | 14 +------------- 2 files changed, 2 insertions(+), 17 deletions(-) diff --git a/requirements_emle.txt b/requirements_emle.txt index 61a260174..2f08283f5 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -1,12 +1,9 @@ ambertools ase deepmd-kit -eigen loguru -pip -pybind11 pytorch -python < 3.11 +python pyyaml torchani xtb-python diff --git a/setup.py b/setup.py index c40192055..128607fcc 100644 --- a/setup.py +++ b/setup.py @@ -417,20 +417,8 @@ def conda_install( print("from running again. Please re-execute this script.") sys.exit(-1) - # Install additional requirements for EMLE. + # Install emle-engine. if install_emle_reqs: - # librascal. - cmd = [ - "pip", - "install", - "git+https://github.com/lab-cosmo/librascal.git", - ] - status = subprocess.run(cmd) - if status.returncode != 0: - print("Something went wrong installing librascal!") - sys.exit(-1) - - # emle-engine. cmd = [ "pip", "install", From ef00217d21ea9e28fbaf9aae6528494a9a8e9808 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 17 Jul 2024 08:44:10 +0100 Subject: [PATCH 339/468] Update workflow now that we support more Python variants and platforms. --- .github/workflows/emle.yaml | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 1ef7362b0..7728349e6 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -21,13 +21,24 @@ jobs: name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) runs-on: ${{ matrix.platform.os }} strategy: - max-parallel: 9 + max-parallel: 6 fail-fast: false matrix: - python-version: ["3.10"] + python-version: ["3.10", "3.11", "3.12"] platform: + - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + exclude: + # Exclude all but the latest Python from all + # but Linux + - platform: + { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11 + - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } + python-version: "3.10" + - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } + python-version: "3.11" environment: name: sire-build defaults: @@ -46,14 +57,12 @@ jobs: python-version: ${{ matrix.python-version }} activate-environment: sire_build miniforge-version: latest - miniforge-variant: Mambaforge - use-mamba: true # - name: Clone the feature_emle branch run: git clone -b feature_emle https://github.com/openbiosim/sire sire # - name: Setup Conda - run: mamba install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser + run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser # - name: Update Conda recipe run: python ${{ github.workspace }}/sire/actions/update_recipe.py @@ -61,8 +70,8 @@ jobs: - name: Prepare build location run: mkdir ${{ github.workspace }}/build # - - name: Build Conda package using mamba build - run: conda mambabuild -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire + - name: Build Conda package using conda build + run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire # - name: Upload Conda package # upload to the 'test' channel From e3cbfa2aa2f72abfdb941ab25bdb4e21add709c4 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 17 Jul 2024 14:41:41 +0100 Subject: [PATCH 340/468] Detach tensors from graph. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index 443b8651b..6704b5142 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -717,8 +717,8 @@ double TorchQMForceImpl::computeForce( const auto gradients = torch::autograd::grad({energies.sum()}, {xyz_qm_torch, xyz_mm_torch}); // Compute the forces, converting from Hatree/Anstrom to kJ/mol/nm. - const auto forces_qm = -(gradients[0] * HARTREE_TO_KJ_MOL * 10).cpu(); - const auto forces_mm = -(gradients[1] * HARTREE_TO_KJ_MOL * 10).cpu(); + const auto forces_qm = -(gradients[0] * HARTREE_TO_KJ_MOL * 10).detach().cpu(); + const auto forces_mm = -(gradients[1] * HARTREE_TO_KJ_MOL * 10).detach().cpu(); // The current interpolation (weighting) parameter. double lambda; From 464c680c6caba06331dd58203dc6aec334a6b833 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 24 Jul 2024 15:40:55 +0100 Subject: [PATCH 341/468] Exclude OpenMMPMEFEP.pypp.cpp when OpenMM is missing. [closes #213] [ci skip] --- wrapper/Move/CMakeNoOpenMM.txt | 1 + wrapper/Move/CMakeNoOpenMMFile.txt | 1 + wrapper/Move/CMakeOpenMM.txt | 1 + wrapper/Move/CMakeOpenMMFile.txt | 1 + 4 files changed, 4 insertions(+) diff --git a/wrapper/Move/CMakeNoOpenMM.txt b/wrapper/Move/CMakeNoOpenMM.txt index 833386a2a..1f5c40eac 100644 --- a/wrapper/Move/CMakeNoOpenMM.txt +++ b/wrapper/Move/CMakeNoOpenMM.txt @@ -3,4 +3,5 @@ set ( SIRE_OPENMM_WRAPPERS NoOpenMM/OpenMMFrEnergyST.pypp.cpp NoOpenMM/OpenMMFrEnergyDT.pypp.cpp NoOpenMM/OpenMMMDIntegrator.pypp.cpp + NoOpenMM/OpenMMPMEFEP.pypp.cpp ) diff --git a/wrapper/Move/CMakeNoOpenMMFile.txt b/wrapper/Move/CMakeNoOpenMMFile.txt index 11f644756..c4fd3a780 100644 --- a/wrapper/Move/CMakeNoOpenMMFile.txt +++ b/wrapper/Move/CMakeNoOpenMMFile.txt @@ -3,6 +3,7 @@ set ( PYPP_OPENMM_SOURCES NoOpenMM/OpenMMFrEnergyST.pypp.cpp NoOpenMM/OpenMMFrEnergyDT.pypp.cpp NoOpenMM/OpenMMMDIntegrator.pypp.cpp + NoOpenMM/OpenMMPMEFEP.pypp.cpp ) set( SIRE_OPENMM_LIBRARIES "" ) diff --git a/wrapper/Move/CMakeOpenMM.txt b/wrapper/Move/CMakeOpenMM.txt index a4dc0fd98..5d72e5a88 100644 --- a/wrapper/Move/CMakeOpenMM.txt +++ b/wrapper/Move/CMakeOpenMM.txt @@ -3,4 +3,5 @@ set ( SIRE_OPENMM_WRAPPERS OpenMMFrEnergyST.pypp.cpp OpenMMFrEnergyDT.pypp.cpp OpenMMMDIntegrator.pypp.cpp + OpenMMPMEFEP.pypp.cpp ) diff --git a/wrapper/Move/CMakeOpenMMFile.txt b/wrapper/Move/CMakeOpenMMFile.txt index cb3d0ff95..00cb8fd84 100644 --- a/wrapper/Move/CMakeOpenMMFile.txt +++ b/wrapper/Move/CMakeOpenMMFile.txt @@ -3,4 +3,5 @@ set ( PYPP_OPENMM_SOURCES OpenMMMDIntegrator.pypp.cpp OpenMMFrEnergyDT.pypp.cpp OpenMMFrEnergyST.pypp.cpp + OpenMMPMEFEP.pypp.cpp ) From 8b8a8d9f01cb505fa991d0d4ae82fe9f7cb39ecf Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 24 Jul 2024 16:45:33 +0100 Subject: [PATCH 342/468] Add missing NoOpenMM/OpenMMPMEFEP wrappers. --- wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.cpp | 108 +++++++++++++++++++ wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.hpp | 10 ++ 2 files changed, 118 insertions(+) create mode 100644 wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.cpp create mode 100644 wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.hpp diff --git a/wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.cpp b/wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.cpp new file mode 100644 index 000000000..864d0bb09 --- /dev/null +++ b/wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.cpp @@ -0,0 +1,108 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#include "boost/python.hpp" +#include "OpenMMPMEFEP.pypp.hpp" + +namespace bp = boost::python; + +#include "SireFF/forcetable.h" + +#include "SireIO/amber.h" + +#include "SireMM/atomljs.h" + +#include "SireMM/internalff.h" + +#include "SireMM/internalperturbation.h" + +#include "SireMaths/constants.h" + +#include "SireMaths/rangenerator.h" + +#include "SireMaths/vector.h" + +#include "SireMol/amberparameters.h" + +#include "SireMol/atomcharges.h" + +#include "SireMol/atomcoords.h" + +#include "SireMol/atommasses.h" + +#include "SireMol/bondid.h" + +#include "SireMol/connectivity.h" + +#include "SireMol/mgname.h" + +#include "SireMol/molecule.h" + +#include "SireMol/core.h" + +#include "SireMol/moleculegroup.h" + +#include "SireMol/moleditor.h" + +#include "SireMol/partialmolecule.h" + +#include "SireMol/perturbation.h" + +#include "SireMove/flexibility.h" + +#include "SireStream/datastream.h" + +#include "SireStream/shareddatastream.h" + +#include "SireSystem/system.h" + +#include "SireUnits/convert.h" + +#include "SireUnits/temperature.h" + +#include "SireUnits/units.h" + +#include "SireVol/periodicbox.h" + +#include "ensemble.h" + +#include "openmmfrenergyst.h" + +#include + +#include + +#include + +#include "openmmfrenergyst.h" + +SireMove::OpenMMPMEFEP __copy__(const SireMove::OpenMMPMEFEP &other){ return SireMove::OpenMMPMEFEP(other); } + +const char* pvt_get_name(const SireMove::OpenMMPMEFEP&){ return "SireMove::OpenMMPMEFEP";} + +void register_OpenMMPMEFEP_class(){ + + { //::SireMove::OpenMMPMEFEP + typedef bp::class_< SireMove::OpenMMPMEFEP > OpenMMPMEFEP_exposer_t; + OpenMMPMEFEP_exposer_t OpenMMPMEFEP_exposer = OpenMMPMEFEP_exposer_t( "OpenMMPMEFEP", bp::init< >() ); + bp::scope OpenMMPMEFEP_scope( OpenMMPMEFEP_exposer ); + { //::SireMove::OpenMMPMEFEP::typeName + + typedef char const * ( *typeName_function_type )( ); + typeName_function_type typeName_function_value( &::SireMove::OpenMMPMEFEP::typeName ); + + OpenMMPMEFEP_exposer.def( + "typeName" + , typeName_function_value ); + + } + OpenMMPMEFEP_exposer.staticmethod( "typeName" ); + OpenMMPMEFEP_exposer.def( "__copy__", &__copy__); + OpenMMPMEFEP_exposer.def( "__deepcopy__", &__copy__); + OpenMMPMEFEP_exposer.def( "clone", &__copy__); + OpenMMPMEFEP_exposer.def( "__str__", &pvt_get_name); + OpenMMPMEFEP_exposer.def( "__repr__", &pvt_get_name); + } + +} diff --git a/wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.hpp b/wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.hpp new file mode 100644 index 000000000..3b3ee9cdc --- /dev/null +++ b/wrapper/Move/NoOpenMM/OpenMMPMEFEP.pycpp.hpp @@ -0,0 +1,10 @@ +// This file has been generated by Py++. + +// (C) Christopher Woods, GPL >= 3 License + +#ifndef OpenMMPMEFEP_hpp__pyplusplus_wrapper +#define OpenMMPMEFEP_hpp__pyplusplus_wrapper + +void register_OpenMMPMEFEP_class(); + +#endif//OpenMMPMEFEP_hpp__pyplusplus_wrapper From 629ad4e48247c7123815c6a4cba5a8d00f8eb475 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 24 Jul 2024 16:49:34 +0100 Subject: [PATCH 343/468] Use IFBOX=3 for general triclinic space. [closes #215] --- corelib/src/libs/SireIO/amberprm.cpp | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/corelib/src/libs/SireIO/amberprm.cpp b/corelib/src/libs/SireIO/amberprm.cpp index e3a1071d2..21a926d63 100644 --- a/corelib/src/libs/SireIO/amberprm.cpp +++ b/corelib/src/libs/SireIO/amberprm.cpp @@ -2181,7 +2181,16 @@ QStringList toLines(const QVector ¶ms, const Space &space, int if (has_periodic_box) { - pointers[27] = 1; + // Orthorhombic box. + if (space.isA()) + { + pointers[27] = 1; + } + // General triclinic box. + else if (space.isA()) + { + pointers[27] = 3; + } } // here is the number of solvent molecules, and the index of the last From 2a5c9e4652fe50f04d3615c308cc2c8b139eb8a3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 24 Jul 2024 16:51:16 +0100 Subject: [PATCH 344/468] Update CHANGELOG. --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index b55abf931..8c63444f3 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -19,6 +19,8 @@ organisation on `GitHub `__. * Print residue indices of perturbed water molecules to SOMD1 log. * Add support for creating Na+ and Cl- ions. * Fix ``sire.morph.merge`` function when one molecule is a monatomic ion. +* Remove ``sire.move.OpenMMPMEFEP`` wrappers from build when OpenMM is not available. +* Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From 5030be924126a59efdd475af49794de05d02eef0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Jul 2024 13:40:17 +0100 Subject: [PATCH 345/468] Headers are now part of librdkit-dev package. --- requirements_build.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_build.txt b/requirements_build.txt index a9ea6f100..9389de249 100644 --- a/requirements_build.txt +++ b/requirements_build.txt @@ -14,7 +14,7 @@ sysroot_linux-64==2.17 ; sys_platform == "linux" # These packages are needed to compile # the SireRDKit plugin rdkit >=2023.0.0 -rdkit-dev >=2023.0.0 +librdkit-dev >=2023.0.0 # These packages are needed to compile # the SireGemmi plugin From 7185ec62f772a0bd98105f0dcd699b9db174235e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Jul 2024 13:59:46 +0100 Subject: [PATCH 346/468] Move librdkit-dev to host section. --- requirements_build.txt | 5 ----- requirements_host.txt | 2 +- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/requirements_build.txt b/requirements_build.txt index 9389de249..1ab5d8a1a 100644 --- a/requirements_build.txt +++ b/requirements_build.txt @@ -11,11 +11,6 @@ make ; sys_platform == "linux" libtool ; sys_platform == "linux" sysroot_linux-64==2.17 ; sys_platform == "linux" -# These packages are needed to compile -# the SireRDKit plugin -rdkit >=2023.0.0 -librdkit-dev >=2023.0.0 - # These packages are needed to compile # the SireGemmi plugin gemmi >=0.6.4 diff --git a/requirements_host.txt b/requirements_host.txt index 9b0e2a797..a431aacc9 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -12,7 +12,7 @@ qt-main rich tbb tbb-devel -rdkit >=2023.0.0 +librdkit-dev >=2023.0.0 gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble From 09a0879f6b33157f1f790a0fc6ce18db67b24fa8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 25 Jul 2024 14:56:14 +0100 Subject: [PATCH 347/468] Handle IFBOX pointer values other than 1. --- corelib/src/libs/SireIO/amber.cpp | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/corelib/src/libs/SireIO/amber.cpp b/corelib/src/libs/SireIO/amber.cpp index 4f6c824e4..f42ffe5d2 100644 --- a/corelib/src/libs/SireIO/amber.cpp +++ b/corelib/src/libs/SireIO/amber.cpp @@ -2151,7 +2151,7 @@ tuple Amber::readCrdTop(const QString &crdfile, const Q // Now the box information SpacePtr spce; - if (pointers[IFBOX] == 1) + if (pointers[IFBOX] == 1 or pointers[IFBOX] == 2 or pointers[IFBOX] == 3) { /** Rectangular box, dimensions read from the crd file */ Vector dimensions(crd_box[0], crd_box[1], crd_box[2]); @@ -2173,12 +2173,6 @@ tuple Amber::readCrdTop(const QString &crdfile, const Q // spce = PeriodicBox( Vector ( crdBox[0], crdBox[1], crdBox[2] ) ).asA() ; // qDebug() << " periodic box " << spce.toString() ; } - else if (pointers[IFBOX] == 2) - { - /** Truncated Octahedral box*/ - throw SireError::incompatible_error(QObject::tr("Sire does not yet support a truncated octahedral box"), - CODELOC); - } else { /** Default is a non periodic system */ From 890ae4e59abba13c120159373c18377283004744 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 29 Jul 2024 16:05:39 +0100 Subject: [PATCH 348/468] Only exclude from/to ghost nonbonded interactions in the same molecule. [closes #219] [ci skip] --- .../SireOpenMM/sire_to_openmm_system.cpp | 23 +++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 03e2ad242..684b9a58b 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1576,14 +1576,29 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // between from_ghosts and to_ghosts for (const auto &from_ghost_idx : from_ghost_idxs) { + // work out the molecule index for the from ghost atom + int mol_from = 0; + while (start_indexes[mol_from] <= from_ghost_idx) + mol_from++; + for (const auto &to_ghost_idx : to_ghost_idxs) { + // work out the molecule index for the to ghost atom + int mol_to = 0; + while (start_indexes[mol_to] <= to_ghost_idx) + mol_to++; + if (not excluded_ghost_pairs.contains(IndexPair(from_ghost_idx, to_ghost_idx))) { - ghost_ghostff->addExclusion(from_ghost_idx, to_ghost_idx); - ghost_nonghostff->addExclusion(from_ghost_idx, to_ghost_idx); - cljff->addException(from_ghost_idx, to_ghost_idx, - 0.0, 1e-9, 1e-9, true); + // only exclude if we haven't already excluded this pair + // and if the two atoms are in the same molecule + if (mol_from == mol_to) + { + ghost_ghostff->addExclusion(from_ghost_idx, to_ghost_idx); + ghost_nonghostff->addExclusion(from_ghost_idx, to_ghost_idx); + cljff->addException(from_ghost_idx, to_ghost_idx, + 0.0, 1e-9, 1e-9, true); + } } } } From dc0e6dd7333790630cc1b2338ddfae53e4cff8dd Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 29 Jul 2024 16:12:39 +0100 Subject: [PATCH 349/468] Update the CHANGELOG. [ci skip] --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 8c63444f3..ef66695cc 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -21,6 +21,8 @@ organisation on `GitHub `__. * Fix ``sire.morph.merge`` function when one molecule is a monatomic ion. * Remove ``sire.move.OpenMMPMEFEP`` wrappers from build when OpenMM is not available. * Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser. +* Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule. + `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From 294e294e6f44e5e6663b4d2bf9ecd44a0d2963c4 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 29 Jul 2024 16:49:47 +0100 Subject: [PATCH 350/468] Make calculator type check backwards compatible. --- src/sire/qm/_emle.py | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 60fb8fb9b..42d9027c1 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -142,12 +142,18 @@ def emle( try: from emle.calculator import EMLECalculator as _EMLECalculator - from emle.models import EMLE as _EMLE except: raise ImportError( "Could not import emle. Please install emle-engine and try again." ) + try: + from emle.models import EMLE as _EMLE + + has_model = True + except: + has_model = False + from ..base import create_map as _create_map from ..mol import selection_to_atoms as _selection_to_atoms from ..system import System as _System @@ -166,10 +172,16 @@ def emle( except: raise ValueError("Unable to select 'qm_atoms' from 'mols'") - if not isinstance(calculator, (_EMLECalculator, _EMLE)): - raise TypeError( - "'calculator' must be a of type 'emle.calculator.EMLECalculator' or 'emle.models.EMLE'" - ) + if has_model: + if not isinstance(calculator, (_EMLECalculator, _EMLE)): + raise TypeError( + "'calculator' must be a of type 'emle.calculator.EMLECalculator' or 'emle.models.EMLE'" + ) + else: + if not isinstance(calculator, _EMLECalculator): + raise TypeError( + "'calculator' must be a of type 'emle.calculator.EMLECalculator'" + ) if not isinstance(cutoff, (str, _Units.GeneralUnit)): raise TypeError( From 7c9d84e5630384e2a87fc15d8c25a4fc3ace7859 Mon Sep 17 00:00:00 2001 From: Joao Morado Date: Mon, 29 Jul 2024 21:49:27 +0100 Subject: [PATCH 351/468] Fix missing is_mechanical from (de)serialization and assignment operators --- wrapper/Convert/SireOpenMM/pyqm.cpp | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index d7034cec7..ba40ece19 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -224,9 +224,9 @@ QDataStream &operator<<(QDataStream &ds, const PyQMForce &pyqmforce) SharedDataStream sds(ds); sds << pyqmforce.callback << pyqmforce.cutoff << pyqmforce.neighbour_list_frequency - << pyqmforce.lambda << pyqmforce.atoms << pyqmforce.mm1_to_qm - << pyqmforce.mm1_to_mm2 << pyqmforce.bond_scale_factors << pyqmforce.mm2_atoms - << pyqmforce.numbers << pyqmforce.charges; + << pyqmforce.is_mechanical << pyqmforce.lambda << pyqmforce.atoms + << pyqmforce.mm1_to_qm << pyqmforce.mm1_to_mm2 << pyqmforce.bond_scale_factors + << pyqmforce.mm2_atoms << pyqmforce.numbers << pyqmforce.charges; return ds; } @@ -240,9 +240,9 @@ QDataStream &operator>>(QDataStream &ds, PyQMForce &pyqmforce) SharedDataStream sds(ds); sds >> pyqmforce.callback >> pyqmforce.cutoff >> pyqmforce.neighbour_list_frequency - >> pyqmforce.lambda >> pyqmforce.atoms >> pyqmforce.mm1_to_qm - >> pyqmforce.mm1_to_mm2 >> pyqmforce.bond_scale_factors >> pyqmforce.mm2_atoms - >> pyqmforce.numbers >> pyqmforce.charges; + >> pyqmforce.is_mechanical >> >> pyqmforce.lambda >> pyqmforce.atoms + >> pyqmforce.mm1_to_qm >> pyqmforce.mm1_to_mm2 >> pyqmforce.bond_scale_factors + >> pyqmforce.mm2_atoms >> pyqmforce.numbers >> pyqmforce.charges; } else throw version_error(v, "1", r_pyqmforce, CODELOC); @@ -303,6 +303,7 @@ PyQMForce &PyQMForce::operator=(const PyQMForce &other) this->callback = other.callback; this->cutoff = other.cutoff; this->neighbour_list_frequency = other.neighbour_list_frequency; + this->is_mechanical = other.is_mechanical; this->lambda = other.lambda; this->atoms = other.atoms; this->mm1_to_qm = other.mm1_to_qm; @@ -918,6 +919,7 @@ PyQMEngine &PyQMEngine::operator=(const PyQMEngine &other) this->callback = other.callback; this->cutoff = other.cutoff; this->neighbour_list_frequency = other.neighbour_list_frequency; + this->is_mechanical = other.is_mechanical; this->lambda = other.lambda; this->atoms = other.atoms; this->mm1_to_qm = other.mm1_to_qm; From 5f1d4bf0be040a2fc8a80282258da6a3b2b7528e Mon Sep 17 00:00:00 2001 From: Joao Morado Date: Mon, 29 Jul 2024 22:00:34 +0100 Subject: [PATCH 352/468] Update changelog --- doc/source/changelog.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 72ad734b3..720f76331 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -15,7 +15,7 @@ organisation on `GitHub `__. `2024.3.0 `__ - September 2024 ---------------------------------------------------------------------------------------------- -* Please add an item to this changelog when you create your PR +* Fixed missing `is_mechanical`` from (de)serialization and assignment operators. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From 0a01de53a4ca454443cbb0ef82e7936b7d1d6fca Mon Sep 17 00:00:00 2001 From: Joao Morado Date: Mon, 29 Jul 2024 22:18:37 +0100 Subject: [PATCH 353/468] Fix double "<<" --- wrapper/Convert/SireOpenMM/pyqm.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index ba40ece19..ebb1f75c0 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -240,7 +240,7 @@ QDataStream &operator>>(QDataStream &ds, PyQMForce &pyqmforce) SharedDataStream sds(ds); sds >> pyqmforce.callback >> pyqmforce.cutoff >> pyqmforce.neighbour_list_frequency - >> pyqmforce.is_mechanical >> >> pyqmforce.lambda >> pyqmforce.atoms + >> pyqmforce.is_mechanical >> pyqmforce.lambda >> pyqmforce.atoms >> pyqmforce.mm1_to_qm >> pyqmforce.mm1_to_mm2 >> pyqmforce.bond_scale_factors >> pyqmforce.mm2_atoms >> pyqmforce.numbers >> pyqmforce.charges; } From f06aefa66f83a8ef1c000521ffefb6054fd54527 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 30 Jul 2024 09:13:06 +0100 Subject: [PATCH 354/468] No need for CHANGELOG entry until feature_emle PR is made. [ci skip] --- doc/source/changelog.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 720f76331..1e9a2c35d 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -15,8 +15,6 @@ organisation on `GitHub `__. `2024.3.0 `__ - September 2024 ---------------------------------------------------------------------------------------------- -* Fixed missing `is_mechanical`` from (de)serialization and assignment operators. - `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From 5afad08839c746dc3189c33e03fad687cc46eab0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 30 Jul 2024 09:15:38 +0100 Subject: [PATCH 355/468] Add missing is_mechanical attribute to streaming operators. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index 6704b5142..ab5f22d95 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -64,9 +64,9 @@ QDataStream &operator<<(QDataStream &ds, const TorchQMForce &torchqmforce) SharedDataStream sds(ds); sds << torchqmforce.module_path << torchqmforce.cutoff << torchqmforce.neighbour_list_frequency - << torchqmforce.lambda << torchqmforce.atoms << torchqmforce.mm1_to_qm - << torchqmforce.mm1_to_mm2 << torchqmforce.bond_scale_factors << torchqmforce.mm2_atoms - << torchqmforce.numbers << torchqmforce.charges; + << torchqmforce.is_mechanical << torchqmforce.lambda << torchqmforce.atoms + << torchqmforce.mm1_to_qm << torchqmforce.mm1_to_mm2 << torchqmforce.bond_scale_factors + << torchqmforce.mm2_atoms << torchqmforce.numbers << torchqmforce.charges; return ds; } @@ -80,9 +80,9 @@ QDataStream &operator>>(QDataStream &ds, TorchQMForce &torchqmforce) SharedDataStream sds(ds); sds >> torchqmforce.module_path >> torchqmforce.cutoff >> torchqmforce.neighbour_list_frequency - >> torchqmforce.lambda >> torchqmforce.atoms >> torchqmforce.mm1_to_qm - >> torchqmforce.mm1_to_mm2 >> torchqmforce.bond_scale_factors >> torchqmforce.mm2_atoms - >> torchqmforce.numbers >> torchqmforce.charges; + >> torchqmforce.is_mechanical >> torchqmforce.lambda >> torchqmforce.atoms + >> torchqmforce.mm1_to_qm >> torchqmforce.mm1_to_mm2 >> torchqmforce.bond_scale_factors + >> torchqmforce.mm2_atoms >> torchqmforce.numbers >> torchqmforce.charges; // Re-load the Torch module. torchqmforce.setModulePath(torchqmforce.getModulePath()); From dfafe55bc42283c4c71781c1876cb60c8c08f21f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 30 Jul 2024 09:41:21 +0100 Subject: [PATCH 356/468] Add is_mechanical to assignment operators. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index ab5f22d95..87c2a5074 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -149,6 +149,7 @@ TorchQMForce &TorchQMForce::operator=(const TorchQMForce &other) this->torch_module = other.torch_module; this->cutoff = other.cutoff; this->neighbour_list_frequency = other.neighbour_list_frequency; + this->is_mechanical = other.is_mechanical; this->lambda = other.lambda; this->atoms = other.atoms; this->mm1_to_qm = other.mm1_to_qm; @@ -863,6 +864,7 @@ TorchQMEngine &TorchQMEngine::operator=(const TorchQMEngine &other) this->module_path = other.module_path; this->cutoff = other.cutoff; this->neighbour_list_frequency = other.neighbour_list_frequency; + this->is_mechanical = other.is_mechanical; this->lambda = other.lambda; this->atoms = other.atoms; this->mm1_to_qm = other.mm1_to_qm; From a42866875a93e6d1366accb1aa0c476bc10816f0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 31 Jul 2024 14:39:18 +0100 Subject: [PATCH 357/468] Update EMLE requirements. [ci skip] --- requirements_emle.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements_emle.txt b/requirements_emle.txt index 2f08283f5..48ff9407c 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -2,6 +2,7 @@ ambertools ase deepmd-kit loguru +pygit2 pytorch python pyyaml From 25c121ab18983db7dbdfc36e6fb230643130601a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 31 Jul 2024 15:11:31 +0100 Subject: [PATCH 358/468] Handle vacuum simulations. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index 87c2a5074..be7b911de 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -714,12 +714,24 @@ double TorchQMForceImpl::computeForce( // Store the sum of the energy in kJ. const auto energy = energies.sum().item() * HARTREE_TO_KJ_MOL; + // If there are no MM atoms, then we need to allow unused tensors. + bool allow_unused = num_mm == 0; + // Compute the gradients. - const auto gradients = torch::autograd::grad({energies.sum()}, {xyz_qm_torch, xyz_mm_torch}); + const auto gradients = torch::autograd::grad( + {energies.sum()}, {xyz_qm_torch, xyz_mm_torch}, {}, c10::nullopt, false, allow_unused); // Compute the forces, converting from Hatree/Anstrom to kJ/mol/nm. const auto forces_qm = -(gradients[0] * HARTREE_TO_KJ_MOL * 10).detach().cpu(); - const auto forces_mm = -(gradients[1] * HARTREE_TO_KJ_MOL * 10).detach().cpu(); + torch::Tensor forces_mm; + if (num_mm > 0) + { + forces_mm = -(gradients[1] * HARTREE_TO_KJ_MOL * 10).detach().cpu(); + } + else + { + forces_mm = torch::zeros({0, 3}, torch::TensorOptions().dtype(torch::kFloat32)); + } // The current interpolation (weighting) parameter. double lambda; From c9c254f2352709797ff7c89f6556b56d21529741 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 31 Jul 2024 15:19:47 +0100 Subject: [PATCH 359/468] Error if mols doesn't contain a perturbable molecule for QM/MM. --- src/sire/mol/_dynamics.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 24597dc49..739fb7620 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -47,6 +47,16 @@ def __init__(self, mols=None, map=None, **kwargs): "'qm_engine' must be an instance of 'sire.legacy.Convert.QMEngine'" ) + # If a QM/MM engine is specified, then we need to check that there is a + # perturbable molecule. + try: + pert_mol = mols["property is_perturbable"] + except: + raise ValueError( + "You are trying to run QM/MM dynamics for a system without " + "a QM/MM enabled molecule!" + ) + # Check the constraints and raise a warning if the perturbable_constraint # is not "none". @@ -135,8 +145,8 @@ def __init__(self, mols=None, map=None, **kwargs): self._is_interpolate = True self._lambda_interpolate = lambda_interpolate - self._work = 0*kcal_per_mol - self._nrg_prev = 0*kcal_per_mol + self._work = 0 * kcal_per_mol + self._nrg_prev = 0 * kcal_per_mol else: self._is_interpolate = False @@ -321,7 +331,7 @@ def _exit_dynamics_block( nrg = nrgs["potential"] if sim_lambda_value != 0.0: - self._work += delta_lambda*(nrg - self._nrg_prev) + self._work += delta_lambda * (nrg - self._nrg_prev) self._nrg_prev = nrg nrgs["work"] = self._work else: From 6db1e3090290ea6c39e938b4d037ee94a0a0b162 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 10:45:40 +0100 Subject: [PATCH 360/468] Add support for conditionally installing TorchQM interface. --- src/sire/_pythonize.py | 7 +- src/sire/qm/_emle.py | 94 +++++++++++-------- wrapper/Convert/SireOpenMM/CMakeLists.txt | 19 +++- .../SireOpenMM/SireOpenMM_registrars.cpp | 2 + .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 12 ++- wrapper/Convert/SireOpenMM/active_headers.h | 1 + wrapper/Convert/SireOpenMM/torchqm.cpp | 4 + wrapper/Convert/SireOpenMM/torchqm.h | 3 + wrapper/Convert/__init__.py | 14 ++- 9 files changed, 104 insertions(+), 52 deletions(-) diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index 00378867f..ca7856402 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -242,8 +242,11 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): _pythonize(Convert._SireOpenMM.PyQMCallback, delete_old=delete_old) _pythonize(Convert._SireOpenMM.PyQMEngine, delete_old=delete_old) _pythonize(Convert._SireOpenMM.PyQMForce, delete_old=delete_old) - _pythonize(Convert._SireOpenMM.TorchQMEngine, delete_old=delete_old) - _pythonize(Convert._SireOpenMM.TorchQMForce, delete_old=delete_old) + try: + _pythonize(Convert._SireOpenMM.TorchQMEngine, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.TorchQMForce, delete_old=delete_old) + except: + pass try: import lazy_import diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 42d9027c1..95c164496 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -49,50 +49,58 @@ def get_forces(self): return emle_force, interpolation_force -class TorchEMLEEngine(_Convert._SireOpenMM.TorchQMEngine): - """A class to enable use of EMLE as a QM engine using C++ Torch.""" - - def get_forces(self): - """ - Get the OpenMM forces for this engine. The first force is the actual - EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic - embedding force. The second is a null CustomBondForce that can be used to - add a "lambda_emle" global parameter to a context to allow the force to be - scaled. - - Returns - ------- - - emle_force : openmm.Force - The EMLE force object to compute the electrostatic embedding force. - - interpolation_force : openmm.CustomBondForce - A null CustomBondForce object that can be used to add a "lambda_emle" - global parameter to an OpenMM context. This allows the electrostatic - embedding force to be scaled. - """ - - from copy import deepcopy as _deepcopy - from openmm import CustomBondForce as _CustomBondForce +# Conditionally create a TorchEMLEEngine class if Torch is available. +try: + + class TorchEMLEEngine(_Convert._SireOpenMM.TorchQMEngine): + """A class to enable use of EMLE as a QM engine using C++ Torch.""" + + def get_forces(self): + """ + Get the OpenMM forces for this engine. The first force is the actual + EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic + embedding force. The second is a null CustomBondForce that can be used to + add a "lambda_emle" global parameter to a context to allow the force to be + scaled. + + Returns + ------- + + emle_force : openmm.Force + The EMLE force object to compute the electrostatic embedding force. + + interpolation_force : openmm.CustomBondForce + A null CustomBondForce object that can be used to add a "lambda_emle" + global parameter to an OpenMM context. This allows the electrostatic + embedding force to be scaled. + """ + + from copy import deepcopy as _deepcopy + from openmm import CustomBondForce as _CustomBondForce + + # Create a dynamics object for the QM region. + d = self._mols["property is_perturbable"].dynamics( + timestep="1fs", + constraint="none", + platform="cpu", + qm_engine=self, + ) - # Create a dynamics object for the QM region. - d = self._mols["property is_perturbable"].dynamics( - timestep="1fs", - constraint="none", - platform="cpu", - qm_engine=self, - ) + # Get the OpenMM EMLE force. + emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) - # Get the OpenMM EMLE force. - emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) + # Create a null CustomBondForce to add the EMLE interpolation + # parameter. + interpolation_force = _CustomBondForce("") + interpolation_force.addGlobalParameter("lambda_emle", 1.0) - # Create a null CustomBondForce to add the EMLE interpolation - # parameter. - interpolation_force = _CustomBondForce("") - interpolation_force.addGlobalParameter("lambda_emle", 1.0) + # Return the forces. + return emle_force, interpolation_force - # Return the forces. - return emle_force, interpolation_force + _has_torchqmengine = True +except: + _has_torchqmengine = False + pass def emle( @@ -237,6 +245,12 @@ def emle( # Create an engine from an EMLE model. else: + if not _has_torchqmengine: + raise ValueError( + "Sire hasn't been compiled with support for TorchQMEngine. " + "Please install libtorch and recompile." + ) + import torch as _torch try: diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index dac13252b..5894fe0a8 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -51,8 +51,16 @@ if (${SIRE_USE_OPENMM}) message(STATUS "OpenMM version supports CustomCPPForce") add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") - find_package(Torch REQUIRED) - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}") + if (NOT DEFINED ENV{SIRE_NO_TORCH}) + find_package(Torch) + if (TORCH_FOUND) + message(STATUS "Torch found") + add_definitions("-DSIRE_USE_TORCH") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}") + else() + message(STATUS "Torch not found") + endif() + endif() #else() #message(STATUS "OpenMM version does not support CustomCPPForce") #endif() @@ -102,6 +110,13 @@ if (${SIRE_USE_OPENMM}) ${PYPP_SOURCES} ) + # Remove any Torch specific files if Torch is not found. + if (NOT TORCH_FOUND) + list(REMOVE_ITEM SIREOPENMM_SOURCES torchqm.cpp) + list(REMOVE_ITEM SIREOPENMM_SOURCES TorchQMEngine.pypp.cpp) + list(REMOVE_ITEM SIREOPENMM_SOURCES TorchQMForce.pypp.cpp) + endif() + # Create the library that holds all of the class wrappers add_library (SireOpenMM ${SIREOPENMM_SOURCES}) diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index 7a88a370c..a9983dace 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -26,8 +26,10 @@ void register_SireOpenMM_objects() ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); +#ifdef SIRE_USE_TORCH ObjectRegistry::registerConverterFor< SireOpenMM::TorchQMForce >(); ObjectRegistry::registerConverterFor< SireOpenMM::TorchQMEngine >(); +#endif } diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index ea0fa865a..458b3b2d5 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -25,9 +25,10 @@ #include "QMForce.pypp.hpp" +#ifdef SIRE_USE_TORCH #include "TorchQMEngine.pypp.hpp" - #include "TorchQMForce.pypp.hpp" +#endif #include "_SireOpenMM_free_functions.pypp.hpp" @@ -60,18 +61,19 @@ BOOST_PYTHON_MODULE(_SireOpenMM){ register_PyQMEngine_class(); - register_TorchQMEngine_class(); - register_QMForce_class(); register_PyQMForce_class(); - register_TorchQMForce_class(); - register_SireOpenMM_properties(); SireOpenMM::register_extras(); register_free_functions(); + +#ifdef SIRE_USE_TORCH + register_TorchQMEngine_class(); + register_TorchQMForce_class(); +#endif } diff --git a/wrapper/Convert/SireOpenMM/active_headers.h b/wrapper/Convert/SireOpenMM/active_headers.h index afb0de961..8338cbad1 100644 --- a/wrapper/Convert/SireOpenMM/active_headers.h +++ b/wrapper/Convert/SireOpenMM/active_headers.h @@ -9,6 +9,7 @@ #include "pyqm.h" #include "qmmm.h" #include "sire_openmm.h" +#include "torchqm.h" #endif diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index be7b911de..b3d8b8be9 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -26,6 +26,8 @@ * \*********************************************/ +#ifdef SIRE_USE_TORCH + #include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationProxy.h" @@ -1036,3 +1038,5 @@ QMForce* TorchQMEngine::createForce() const this->charges ); } + +#endif diff --git a/wrapper/Convert/SireOpenMM/torchqm.h b/wrapper/Convert/SireOpenMM/torchqm.h index 7b11ef088..314ce99dd 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.h +++ b/wrapper/Convert/SireOpenMM/torchqm.h @@ -29,6 +29,8 @@ #ifndef SIREOPENMM_TORCHQM_H #define SIREOPENMM_TORCHQM_H +#ifdef SIRE_USE_TORCH + #include "OpenMM.h" #include "openmm/Force.h" #ifdef SIRE_USE_CUSTOMCPPFORCE @@ -504,3 +506,4 @@ SIRE_EXPOSE_CLASS(SireOpenMM::TorchQMEngine) SIRE_END_HEADER #endif +#endif diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index a94ea4700..dbca6a2ee 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -21,7 +21,6 @@ "QMEngine", "PyQMCallback", "PyQMEngine", - "TorchQMEngine", ] try: @@ -103,9 +102,14 @@ def smarts_to_rdkit(*args, **kwargs): QMEngine, PyQMCallback, PyQMEngine, - TorchQMEngine, ) + try: + from ._SireOpenMM import TorchQMEngine + __all__.append("TorchQMEngine") + except: + pass + from ..._pythonize import _pythonize _pythonize( @@ -116,11 +120,15 @@ def smarts_to_rdkit(*args, **kwargs): QMEngine, PyQMCallback, PyQMEngine, - TorchQMEngine, ], delete_old=True, ) + try: + _pythonize(TorchQMEngine, delete_old=True) + except: + pass + PerturbableOpenMMMolecule.changed_atoms = _changed_atoms PerturbableOpenMMMolecule.changed_bonds = _changed_bonds PerturbableOpenMMMolecule.changed_angles = _changed_angles From acec6ee0afbb279bfa50c5d4dd3fe03894ccdcb4 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 11:16:59 +0100 Subject: [PATCH 361/468] Guard against missing emle.models module. --- src/sire/qm/_emle.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 95c164496..77c592aed 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -251,6 +251,13 @@ def emle( "Please install libtorch and recompile." ) + try: + from emle.models import EMLE as _EMLE + except: + raise ImportError( + "Could not import emle.models. Please reinstall emle-engine and try again." + ) + import torch as _torch try: From 522011f677e393230e0bc7e9908ba186de0fd0ea Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 11:40:47 +0100 Subject: [PATCH 362/468] Fix RDKit requirement. --- requirements_build.txt | 5 ----- requirements_host.txt | 2 +- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/requirements_build.txt b/requirements_build.txt index a9ea6f100..1ab5d8a1a 100644 --- a/requirements_build.txt +++ b/requirements_build.txt @@ -11,11 +11,6 @@ make ; sys_platform == "linux" libtool ; sys_platform == "linux" sysroot_linux-64==2.17 ; sys_platform == "linux" -# These packages are needed to compile -# the SireRDKit plugin -rdkit >=2023.0.0 -rdkit-dev >=2023.0.0 - # These packages are needed to compile # the SireGemmi plugin gemmi >=0.6.4 diff --git a/requirements_host.txt b/requirements_host.txt index 9b0e2a797..a431aacc9 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -12,7 +12,7 @@ qt-main rich tbb tbb-devel -rdkit >=2023.0.0 +librdkit-dev >=2023.0.0 gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble From 0120ebe7e1bb51e09c536251150fbe03d09d30d5 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 11:41:07 +0100 Subject: [PATCH 363/468] The xtb-python package isn't available on Windows. --- requirements_emle.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_emle.txt b/requirements_emle.txt index 48ff9407c..96b1c727f 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -7,7 +7,7 @@ pytorch python pyyaml torchani -xtb-python +xtb-python ; sys_platform != "win32" gcc< 13 ; sys_platform == "linux" gxx< 13 ; sys_platform == "linux" From 291d481d29a169f3db10ddf8d62b2f05f4f807dc Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 12:00:01 +0100 Subject: [PATCH 364/468] Not (yet) able to build on Windows or Python 3.12. --- .github/workflows/emle.yaml | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 7728349e6..28be43639 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -21,24 +21,13 @@ jobs: name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) runs-on: ${{ matrix.platform.os }} strategy: - max-parallel: 6 + max-parallel: 9 fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.11"] platform: - - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - exclude: - # Exclude all but the latest Python from all - # but Linux - - platform: - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11 - - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.10" - - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.11" environment: name: sire-build defaults: From 2c0aa2648f12760fee92698c0f238ad74a40a8df Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 12:24:39 +0100 Subject: [PATCH 365/468] Trying previous RDKit packages. --- requirements_host.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/requirements_host.txt b/requirements_host.txt index a431aacc9..112eadb3f 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -12,7 +12,8 @@ qt-main rich tbb tbb-devel -librdkit-dev >=2023.0.0 +rdkit <=2024.03.4 +rdkit-dev <=2024.03.4 gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble From 29c995f52d067caa5aaa3c0ee224a1ef8e7def9b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 12:49:24 +0100 Subject: [PATCH 366/468] Don't duplicate RDKit requirement. --- requirements_bss.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index 98a166778..d63d7087a 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -32,7 +32,6 @@ py3dmol pydot pygtail pyyaml -rdkit >=2023.0.0 gemmi >=0.6.4 # The below are packages that aren't available on all From bc785d241c512a6885c505ad4e46433f3108acd8 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 12:52:36 +0100 Subject: [PATCH 367/468] Don't duplicate gemmi requirement either. --- requirements_bss.txt | 1 - 1 file changed, 1 deletion(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index d63d7087a..3b622a2ab 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -32,7 +32,6 @@ py3dmol pydot pygtail pyyaml -gemmi >=0.6.4 # The below are packages that aren't available on all # platforms/OSs and so need to be conditionally included From 4768ff7ded67aa5f9ef658b0b9844e126751bd2a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 12:52:56 +0100 Subject: [PATCH 368/468] Try librdkit-dev again. --- requirements_host.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/requirements_host.txt b/requirements_host.txt index 112eadb3f..40e3ecf8d 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -5,6 +5,7 @@ gsl lazy_import libcblas libnetcdf +librdkit-dev openmm pandas python @@ -12,8 +13,6 @@ qt-main rich tbb tbb-devel -rdkit <=2024.03.4 -rdkit-dev <=2024.03.4 gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble From fcaed49ba7d6829ebd351782dcb2a116064b989b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 13:41:21 +0100 Subject: [PATCH 369/468] Avoid duplicate requirements and refactor. --- requirements_bss.txt | 2 -- requirements_emle.txt | 2 +- requirements_host.txt | 2 +- 3 files changed, 2 insertions(+), 4 deletions(-) diff --git a/requirements_bss.txt b/requirements_bss.txt index 81fd6fe82..33ae86a9f 100644 --- a/requirements_bss.txt +++ b/requirements_bss.txt @@ -33,8 +33,6 @@ py3dmol pydot pygtail pyyaml -rdkit >=2023.0.0 -gemmi >=0.6.4 # The below are packages that aren't available on all # platforms/OSs and so need to be conditionally included diff --git a/requirements_emle.txt b/requirements_emle.txt index 96b1c727f..48ff9407c 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -7,7 +7,7 @@ pytorch python pyyaml torchani -xtb-python ; sys_platform != "win32" +xtb-python gcc< 13 ; sys_platform == "linux" gxx< 13 ; sys_platform == "linux" diff --git a/requirements_host.txt b/requirements_host.txt index a431aacc9..a1d7605dc 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -5,6 +5,7 @@ gsl lazy_import libcblas libnetcdf +librdkit-dev >=2023.0.0 openmm pandas python @@ -12,7 +13,6 @@ qt-main rich tbb tbb-devel -librdkit-dev >=2023.0.0 gemmi >=0.6.4 # kartograf on Windows pulls in an openfe that has an old / incompatble From 5b5c92b4bf543d477780dd67ee9607aa978a9baa Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 1 Aug 2024 18:20:47 +0100 Subject: [PATCH 370/468] Add NNPOps to EMLE requirements. --- requirements_emle.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/requirements_emle.txt b/requirements_emle.txt index 48ff9407c..68dc7083d 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -2,6 +2,7 @@ ambertools ase deepmd-kit loguru +nnpops pygit2 pytorch python From da84a18c46776b3811a051784249e61c5cc10e04 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 2 Aug 2024 12:32:12 +0100 Subject: [PATCH 371/468] Add example for how to use EMLE Torch modules. [ci skip] --- doc/source/tutorial/partXX/02_emle.rst | 147 +++++++++++++++++++++- doc/source/tutorial/partXX/images/ala.png | Bin 0 -> 13549 bytes 2 files changed, 146 insertions(+), 1 deletion(-) create mode 100644 doc/source/tutorial/partXX/images/ala.png diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index 112e3b450..7a608fb88 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -194,7 +194,9 @@ computes the electrostatic embedding: Next we create a new engine bound to the calculator: ->>> qm_mols, engine = sr.qm.emle(mols, mols[0], calculator, "7.5A", 20) +>>> qm_mols, engine = sr.qm.emle( +>>> ... mols, mols[0], calculator, cutoff="7.5A", neighbour_list_frequency=20 +>>> ... ) Rather than using this engine with a ``sire`` dynamics object, we can instead extract the underlying ``OpenMM`` force object and add it to an existing @@ -279,3 +281,146 @@ And finally the context: >>> context = openmm.Context(ml_system, integrator) >>> context.setPositions(inpcrd.positions) + +Creating an EMLE torch module +----------------------------- + +As well as the ``EMLECalculator``, the ``emle-engine`` package provides Torch +modules for the calculation of the electrostatic embedding. These can be used +to create derived modules for the calculation of in vacuo and electrostatic +embedding energies for different backends. For example, we provide an optimised +``ANI2xEMLE`` module that can be used to add electrostatic embedding to the +existing ``ANI2x`` model from `TorchANI `_. + +As an example for how to use the module, let's again use the example alanine +dipeptide system. First, let's reload the system and center the solute within +the simulation box: + +>>> mols = sr.load_test_files("ala.crd", "ala.top") +>>> center = mols[0].coordinates() +>>> mols.make_whole(center=center) + +To obtain the point charges around the QM region we can take advantage of +Sire's powerful search syntax, e.g: + +>>> mols["mols within 7.5 of molidx 0"].view() + +.. image:: images/ala.png + :target: images/ala.png + :alt: Alanine-dipeptide in water. + +Next we will set the device and dtype for our Torch tensors: + +>>> import torch +>>> device = torch.device("cuda") +>>> dtype = torch.float32 + +Now we can create the input tensors for our calculation. First the coordinates +of the QM region: + +>>> coords_qm = torch.tensor( +>>> ... sr.io.get_coords_array(mols[0]), +>>> ... device=device, +>>> ... dtype=dtype, +>>> ... requires_grad=True, +>>> ) + +Next the coordinates of the MM region, which can be obtained using the search +term above: + +>>> mm_atoms = mols["water within 7.5 of molidx 0"].atoms() +>>> coords_mm = torch.tensor( +>>> ... sr.io.get_coords_array(mm_atoms), +>>> ... device=device, +>>> ... dtype=dtype, +>>> ... requires_grad=True, +>>> ... ) + +Now the atomic numbers for the atoms within the QM region: + +>>> atomic_numbers = torch.tensor( +>>> ... [element.num_protons() for element in mols[0].property("element")], +>>> ... device=device, +>>> ... dtype=torch.int64, +>>> ... ) + +And finally the charges of the MM atoms: + +>>> charges_mm = torch.tensor([atom.property("charge").value() for atom in mm_atoms], +>>> ... device=device, +>>> ... dtype=dtype +>>> ... ) + +In order to perform a calculation we need to create an instance of the +``ANI2xEMLE`` module: + +>>> from emle.models import ANI2xEMLE +>>> model = ANI2xEMLE().to(device) + +.. note:: + + The ``ANI2xEMLE`` model currently requires the ``feature_aev`` branch of + ``emle-engine``, which can be installed with the following command: + ``pip install git+https://github.com/chemle/emle-engine.git@feature_aev`` + +We can now calculate the in vacuo and electrostatic embedding energies: + +>>> energies = model(atomic_numbers, charges_mm, coords_qm, coords_mm) +>>> print(energies) +tensor([-4.9570e+02, -4.2597e-02, -1.2952e-02], device='cuda:0', + dtype=torch.float64, grad_fn=) + +The first element of the tensor is the in vacuo energy of the QM region, the +second is the static electrostatic embedding energy, and the third is the +induced electrostatic embedding energy. + +Then we can use ``autograd`` to compute the gradients of the energies with respect +to the QM and MM coordinates: + +>>> grad_qm, grad_mm = torch.autograd.grad(energies.sum(), (coords_qm, coords_mm)) +>>> print(grad_qm) +>>> print(grad_mm) +tensor([[-2.4745e-03, -1.2421e-02, 1.1079e-02], + [-7.0100e-03, -2.9659e-02, -6.8182e-03], + [-1.8393e-03, 1.1682e-02, 1.1509e-02], + [-3.4777e-03, 1.5750e-03, -1.9650e-02], + [-3.4737e-02, 7.3493e-02, 3.7996e-02], + [-9.3575e-03, -3.7101e-02, -2.0774e-02], + [ 9.2816e-02, -7.5343e-03, -5.0656e-02], + [ 4.9443e-03, 1.1114e-02, -4.0737e-04], + [-1.6362e-03, 3.0464e-03, 3.0192e-02], + [-6.2813e-03, -1.3678e-02, -3.4606e-03], + [ 4.5878e-03, 3.0234e-02, -2.9871e-02], + [-3.8999e-03, -1.3376e-02, -2.6382e-03], + [ 4.4184e-03, -7.4247e-03, 5.1742e-04], + [ 8.8851e-05, -8.5786e-03, 1.2712e-02], + [-5.9939e-02, 1.1648e-01, 1.6692e-01], + [-6.4231e-03, -4.4771e-02, 3.0655e-03], + [ 1.1274e-01, -6.4833e-02, -1.5494e-01], + [ 1.8500e-03, 5.5206e-03, -7.0060e-03], + [-6.3634e-02, -1.5340e-02, -2.7031e-03], + [ 7.7061e-03, 3.7852e-02, 6.0927e-03], + [-2.9915e-03, -3.5084e-02, 2.3909e-02], + [-1.5018e-02, 8.6911e-03, -2.5789e-03]], device='cuda:0') +tensor([[ 1.8065e-03, -1.4048e-03, -6.0694e-04], + [-9.0640e-04, 5.1307e-04, 9.6374e-06], + [-8.4827e-04, 9.5815e-04, 1.7164e-04], + ..., + [-5.7833e-04, -1.9125e-04, 2.0395e-03], + [ 3.2311e-04, 2.1525e-04, -7.8029e-04], + [ 3.5424e-04, 4.0781e-04, -1.5014e-03]], device='cuda:0') + +The model is serialisable, so can be saved and loaded using the standard +``torch.jit`` functions, e.g.: + +>>> script_model = torch.jit.script(model) +>>> torch.jit.save(script_model, "ani2xemle.pt") + +It is also possible to use the model with Sire when performing QM/MM dynamics: + +>>> qm_mols, engine = sr.qm.emle( +>>> ... mols, mols[0], model, cutoff="7.5A", neighbour_list_frequency=20 +>>> ... ) + +The model will be serialised and loaded into a C++ ``TorchQMEngine`` object, +bypassing the need for a Python callback. diff --git a/doc/source/tutorial/partXX/images/ala.png b/doc/source/tutorial/partXX/images/ala.png new file mode 100644 index 0000000000000000000000000000000000000000..3e7c85489acf1d922d58f863469f95c0138f181f GIT binary patch literal 13549 zcmeHucTkht_I9NA7CO>Jii9LUfY7_3^bXQO5_<0-AWeD)rAw6}B2{`9klv&TiXezI z=}koVMbEkCo;%-f=9@d;cmKPYNwUkcp1szy*532JlQ+>?8h1&F7>NJ?0I8~qq7DFX zg8aGfCTRRnh zceJj*h91)20SQNO$Vd}O`if%+oY0;KHeV-4XAf~-DURQ~;+XcYVK4{VZ-}RZ6o-+z z7Mp^LJDN>cKv)0*Qu4L)7UYm7Vv}@7S&Qo^D*s7==}B?edV0EwgTX#NJ_0^M0xs@0 zU??082SWtGf`T9n0_5T6?1}INIeT#aqWFVD5$%C=w{!Khb8%+-#fh+T@$!`7;K0nY z{lh;eS9SHj=$$?OQ~{$0*cagnh6+HyPEO#zTX=XXd1FZabm)Jz@X+&fMT2$F9xh() zNVJkS+S!xy?-VHHU-qtE?vB61K_S6tN3;_L>Va7m`Y%h~RaMve%i@;=Hg-;~zpXH0 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changed, 36 insertions(+), 36 deletions(-) diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst index 6bda650bb..4e7f652df 100644 --- a/doc/source/tutorial/partXX/01_intro.rst +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -30,14 +30,14 @@ We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation: >>> qm_mols, engine = sr.qm.create_engine( ->>> ... mols, ->>> ... mols[0], ->>> ... py_object, ->>> ... callback="callback", ->>> ... cutoff="7.5A", ->>> ... neighbour_list_frequency=20, ->>> ... mechanical_embedding=False, ->>> ... ) +... mols, +... mols[0], +... py_object, +... callback="callback", +... cutoff="7.5A", +... neighbour_list_frequency=20, +... mechanical_embedding=False, +... ) Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule). diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index 7a608fb88..8061776f5 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -51,12 +51,12 @@ We now need to set up the molecular system for the QM/MM simulation and create an engine to perform the calculation: >>> qm_mols, engine = sr.qm.emle( ->>> ... mols, ->>> ... mols[0], ->>> ... calculator, ->>> ... cutoff="7.5A", ->>> ... neighbour_list_frequency=20 ->>> ) +... mols, +... mols[0], +... calculator, +... cutoff="7.5A", +... neighbour_list_frequency=20 +... ) Here the first argument is the molecules that we are simulating, the second selection coresponding to the QM region (here this is the first molecule), and @@ -319,37 +319,37 @@ Now we can create the input tensors for our calculation. First the coordinates of the QM region: >>> coords_qm = torch.tensor( ->>> ... sr.io.get_coords_array(mols[0]), ->>> ... device=device, ->>> ... dtype=dtype, ->>> ... requires_grad=True, ->>> ) +... sr.io.get_coords_array(mols[0]), +... device=device, +... dtype=dtype, +... requires_grad=True, +... ) Next the coordinates of the MM region, which can be obtained using the search term above: >>> mm_atoms = mols["water within 7.5 of molidx 0"].atoms() >>> coords_mm = torch.tensor( ->>> ... sr.io.get_coords_array(mm_atoms), ->>> ... device=device, ->>> ... dtype=dtype, ->>> ... requires_grad=True, ->>> ... ) +... sr.io.get_coords_array(mm_atoms), +... device=device, +... dtype=dtype, +... requires_grad=True, +... ) Now the atomic numbers for the atoms within the QM region: >>> atomic_numbers = torch.tensor( ->>> ... [element.num_protons() for element in mols[0].property("element")], ->>> ... device=device, ->>> ... dtype=torch.int64, ->>> ... ) +... [element.num_protons() for element in mols[0].property("element")], +... device=device, +... dtype=torch.int64, +... ) And finally the charges of the MM atoms: >>> charges_mm = torch.tensor([atom.property("charge").value() for atom in mm_atoms], ->>> ... device=device, ->>> ... dtype=dtype ->>> ... ) +... device=device, +... dtype=dtype +... ) In order to perform a calculation we need to create an instance of the ``ANI2xEMLE`` module: @@ -419,8 +419,8 @@ The model is serialisable, so can be saved and loaded using the standard It is also possible to use the model with Sire when performing QM/MM dynamics: >>> qm_mols, engine = sr.qm.emle( ->>> ... mols, mols[0], model, cutoff="7.5A", neighbour_list_frequency=20 ->>> ... ) +... mols, mols[0], model, cutoff="7.5A", neighbour_list_frequency=20 +... ) The model will be serialised and loaded into a C++ ``TorchQMEngine`` object, bypassing the need for a Python callback. diff --git a/doc/source/tutorial/partXX/04_diels_alder.rst b/doc/source/tutorial/partXX/04_diels_alder.rst index ae22af5bf..c685d44de 100644 --- a/doc/source/tutorial/partXX/04_diels_alder.rst +++ b/doc/source/tutorial/partXX/04_diels_alder.rst @@ -81,9 +81,9 @@ calculation: >>> qm_mols, engine = sr.qm.emle( ... mols, - "atomnum 1804:1822,2083:2132", - calculator, - redistribute_charge=True +... "atomnum 1804:1822,2083:2132", +... calculator, +... redistribute_charge=True ... ) Here the selection for the QM region includes tryptophan side-chain atoms From e8d0ef81965a23e4a66f20f47d566a9cb948b821 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 09:42:08 +0100 Subject: [PATCH 373/468] Import objects needed for type hinting. --- doc/source/tutorial/partXX/01_intro.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst index 4e7f652df..f45d58745 100644 --- a/doc/source/tutorial/partXX/01_intro.rst +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -56,6 +56,8 @@ signature: .. code-block:: python + from typing import List, Tuple + def callback( numbers_qm: List[int], charges_mm: List[float], From bc93b9adccc77b7175de859f6596383efb50bf10 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 13:39:53 +0100 Subject: [PATCH 374/468] Allow user to build wrappers for a specificy library. [ci skip] --- .../sire-generate-wrappers/generate_wrappers | 21 +++++++++++++++++-- 1 file changed, 19 insertions(+), 2 deletions(-) diff --git a/docker/sire-generate-wrappers/generate_wrappers b/docker/sire-generate-wrappers/generate_wrappers index b6d8e0218..4f5c38e4a 100755 --- a/docker/sire-generate-wrappers/generate_wrappers +++ b/docker/sire-generate-wrappers/generate_wrappers @@ -11,6 +11,16 @@ while (( "$#" )); do exit 1 fi ;; + -l|--lib) + if [ -n "$2" ] && [ ${2:0:1} != "-" ]; then + LIB=$2 + shift 2 + else + echo "Error: Argument for $1 is missing" >&2 + exit 1 + fi + ;; + -*|--*=) # unsupported flags echo "Error: Unsupported flag $1" >&2 exit 1 @@ -50,7 +60,14 @@ cd sire/wrapper echo "Running scanheaders..." python AutoGenerate/scanheaders.py $HOME/sire/corelib/src/libs . -echo "Now generating all of the headers..." -python create_all_wrappers.py +if [ -z "$LIB" ] +then + echo "No library specified, generating all wrappers..." + python create_all_wrappers.py +else + echo "Generating wrappers for $LIB..." + cd $LIB + python ../AutoGenerate/create_wrappers.py +fi echo "Complete" From 367843967ae6c06535410275c8017cabc690f0b6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 13:40:27 +0100 Subject: [PATCH 375/468] Rename existing Docker file. [ci skip] --- .../sire-generate-wrappers/Dockerfile_arm64 | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 docker/sire-generate-wrappers/Dockerfile_arm64 diff --git a/docker/sire-generate-wrappers/Dockerfile_arm64 b/docker/sire-generate-wrappers/Dockerfile_arm64 new file mode 100644 index 000000000..b4ed37642 --- /dev/null +++ b/docker/sire-generate-wrappers/Dockerfile_arm64 @@ -0,0 +1,45 @@ +FROM continuumio/miniconda3:latest + +RUN apt-get update && apt-get -y upgrade \ + && apt-get install -y --no-install-recommends \ + git \ + wget \ + g++ \ + gcc \ + nano \ + ca-certificates \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +WORKDIR /root + +RUN conda install make clang clangdev llvmdev cmake + +RUN conda install -c conda-forge python-levenshtein && \ + conda clean -a -f -y + +RUN pip install pyplusplus pygccxml fuzzywuzzy && \ + rm -fr ~/.cache/pip /tmp* + +RUN git clone https://github.com/CastXML/CastXML && \ + cd CastXML && \ + mkdir build && \ + cd build && \ + cmake -DCMAKE_INSTALL_PREFIX=/opt/conda/ .. && \ + make -j 4 && \ + make -j 4 install && \ + cd $HOME && \ + rm -rf CastXML + +# Need to fix an exception that is raised on Apple M1 +COPY scanner.py /opt/conda/lib/python3.9/site-packages/pygccxml/parser + +COPY includes.tar.bz2 /opt/conda +COPY generate_wrappers /usr/bin +COPY unpack_headers /usr/bin +RUN chmod a+x /usr/bin/generate_wrappers +COPY bashrc /root/.bashrc +COPY push_wrappers /usr/bin +RUN chmod a+x /usr/bin/push_wrappers + +RUN mkdir /tmp From 6e154f37b40a6618927f8f6e76f8cbff07b1caff Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 13:40:48 +0100 Subject: [PATCH 376/468] Add Linux x86 Dockerfile. [ci skip] --- docker/sire-generate-wrappers/Dockerfile_x86 | 42 ++++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 docker/sire-generate-wrappers/Dockerfile_x86 diff --git a/docker/sire-generate-wrappers/Dockerfile_x86 b/docker/sire-generate-wrappers/Dockerfile_x86 new file mode 100644 index 000000000..d225a62f7 --- /dev/null +++ b/docker/sire-generate-wrappers/Dockerfile_x86 @@ -0,0 +1,42 @@ +FROM continuumio/miniconda3:4.12.0 + +RUN apt-get update && apt-get -y upgrade \ + && apt-get install -y --no-install-recommends \ + git \ + wget \ + g++ \ + gcc \ + nano \ + ca-certificates \ + && apt-get clean \ + && rm -rf /var/lib/apt/lists/* + +WORKDIR /root + +RUN conda install make clang clangdev llvmdev cmake python=3.7 + +RUN conda install -c conda-forge python-levenshtein && \ + conda clean -a -f -y + +RUN pip install pyplusplus==1.8.2 pygccxml==1.8.5 fuzzywuzzy && \ + rm -fr ~/.cache/pip /tmp* + +RUN git clone https://github.com/CastXML/CastXML && \ + cd CastXML && \ + mkdir build && \ + cd build && \ + cmake -DCMAKE_INSTALL_PREFIX=/opt/conda/ .. && \ + make -j 4 && \ + make -j 4 install && \ + cd $HOME && \ + rm -rf CastXML + +COPY includes.tar.bz2 /opt/conda +COPY generate_wrappers /usr/bin +COPY unpack_headers /usr/bin +RUN chmod a+x /usr/bin/generate_wrappers +COPY bashrc /root/.bashrc +COPY push_wrappers /usr/bin +RUN chmod a+x /usr/bin/push_wrappers + +RUN mkdir /tmp From 4798f4d88428286725a2b95a6c96f0c8b58b6147 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 13:41:06 +0100 Subject: [PATCH 377/468] Remove old Dockerfile. [ci skip] --- docker/sire-generate-wrappers/Dockerfile | 45 ------------------------ 1 file changed, 45 deletions(-) delete mode 100644 docker/sire-generate-wrappers/Dockerfile diff --git a/docker/sire-generate-wrappers/Dockerfile b/docker/sire-generate-wrappers/Dockerfile deleted file mode 100644 index b4ed37642..000000000 --- a/docker/sire-generate-wrappers/Dockerfile +++ /dev/null @@ -1,45 +0,0 @@ -FROM continuumio/miniconda3:latest - -RUN apt-get update && apt-get -y upgrade \ - && apt-get install -y --no-install-recommends \ - git \ - wget \ - g++ \ - gcc \ - nano \ - ca-certificates \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* - -WORKDIR /root - -RUN conda install make clang clangdev llvmdev cmake - -RUN conda install -c conda-forge python-levenshtein && \ - conda clean -a -f -y - -RUN pip install pyplusplus pygccxml fuzzywuzzy && \ - rm -fr ~/.cache/pip /tmp* - -RUN git clone https://github.com/CastXML/CastXML && \ - cd CastXML && \ - mkdir build && \ - cd build && \ - cmake -DCMAKE_INSTALL_PREFIX=/opt/conda/ .. && \ - make -j 4 && \ - make -j 4 install && \ - cd $HOME && \ - rm -rf CastXML - -# Need to fix an exception that is raised on Apple M1 -COPY scanner.py /opt/conda/lib/python3.9/site-packages/pygccxml/parser - -COPY includes.tar.bz2 /opt/conda -COPY generate_wrappers /usr/bin -COPY unpack_headers /usr/bin -RUN chmod a+x /usr/bin/generate_wrappers -COPY bashrc /root/.bashrc -COPY push_wrappers /usr/bin -RUN chmod a+x /usr/bin/push_wrappers - -RUN mkdir /tmp From 625bb733473c8bdec5e5715c5691c17cb16d40ef Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 13:44:55 +0100 Subject: [PATCH 378/468] Add note about single library wrappers and update Dockerfile name. [ci skip] --- docker/sire-generate-wrappers/README.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/docker/sire-generate-wrappers/README.md b/docker/sire-generate-wrappers/README.md index 5a2d7547e..13fd3e624 100644 --- a/docker/sire-generate-wrappers/README.md +++ b/docker/sire-generate-wrappers/README.md @@ -66,6 +66,15 @@ would type This will run in parallel, but be aware that this can take a long time! +If you only wish to build the wrappers for a specificy library, this can +be done by passing the ``--lib`` argument, e.g.: + +``` +(base) root:~# generate_wrappers --lib IO +``` + +would only generate the wrappers for the `IO` library. + ## Checking the wrappers The `generate_wrappers` command will check out your branch @@ -174,10 +183,10 @@ Create the `includes.tar.bz2` file by running the ./create_includes_tarball --sire $HOME/sire.app ``` -Next, create the container via +Next, create the container via, e.g: ``` -docker build -t siremol/sire-generate-wrappers . +docker build -t siremol/sire-generate-wrappers -f Dockerfile_x86 ``` Assuming this worked, you can run the container via From 7c81259352fb39131ed26a605156a92296833dc3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 13:52:59 +0100 Subject: [PATCH 379/468] Update CHANGELOG. [ci skip] --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index ef66695cc..3a1d98aba 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -22,6 +22,7 @@ organisation on `GitHub `__. * Remove ``sire.move.OpenMMPMEFEP`` wrappers from build when OpenMM is not available. * Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser. * Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule. +* Add Docker support for building wrappers on Linux x86. `2024.2.0 `__ - June 2024 From 125340d180fb05957fb50b8056d36010ace0f3c2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 5 Aug 2024 14:35:50 +0100 Subject: [PATCH 380/468] Replace old references to siremol with openbiosim. [ci skip] --- docker/sire-generate-wrappers/README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docker/sire-generate-wrappers/README.md b/docker/sire-generate-wrappers/README.md index 13fd3e624..4bf3a342a 100644 --- a/docker/sire-generate-wrappers/README.md +++ b/docker/sire-generate-wrappers/README.md @@ -29,8 +29,8 @@ this; ``` Unable to find image 'openbiosim/sire-generate-wrappers:arm64' locally -Trying to pull repository docker.io/siremol/sire-generate-wrappers ... -latest: Pulling from docker.io/siremol/sire-generate-wrappers +Trying to pull repository docker.io/openbiosim/sire-generate-wrappers ... +latest: Pulling from docker.io/openbiosim/sire-generate-wrappers a2abf6c4d29d: Pull complete c256cb8a03f5: Pull complete 96470ebef4ad: Pull complete @@ -43,7 +43,7 @@ d719333d5423: Pull complete 4642f7c70ef4: Pull complete b70e0e58d6c8: Pull complete Digest: sha256:a8a4513655dd43cebac306f77ac85a3fd953802759029bc771fe51db058eea95 -Status: Downloaded newer image for siremol/sire-generate-wrappers:latest +Status: Downloaded newer image for openbiosim/sire-generate-wrappers:latest (base) root:~# ``` @@ -186,14 +186,14 @@ Create the `includes.tar.bz2` file by running the Next, create the container via, e.g: ``` -docker build -t siremol/sire-generate-wrappers -f Dockerfile_x86 +docker build -t openbiosim/sire-generate-wrappers -f Dockerfile_x86 ``` Assuming this worked, you can run the container via the same command as at the top, e.g. ``` -docker run -it siremol/sire-generate-wrappers +docker run -it openbiosim/sire-generate-wrappers ``` and the follow the rest of the instructions. From d6c9e493d7bf678f5ef43d12b614be012beb70cd Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 6 Aug 2024 11:59:05 +0100 Subject: [PATCH 381/468] Formatting tweaks. [ci skip] --- doc/source/tutorial/partXX/02_emle.rst | 28 +++++++++++++------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index 8061776f5..a491793e0 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -319,10 +319,10 @@ Now we can create the input tensors for our calculation. First the coordinates of the QM region: >>> coords_qm = torch.tensor( -... sr.io.get_coords_array(mols[0]), -... device=device, -... dtype=dtype, -... requires_grad=True, +... sr.io.get_coords_array(mols[0]), +... device=device, +... dtype=dtype, +... requires_grad=True, ... ) Next the coordinates of the MM region, which can be obtained using the search @@ -330,25 +330,25 @@ term above: >>> mm_atoms = mols["water within 7.5 of molidx 0"].atoms() >>> coords_mm = torch.tensor( -... sr.io.get_coords_array(mm_atoms), -... device=device, -... dtype=dtype, -... requires_grad=True, +... sr.io.get_coords_array(mm_atoms), +... device=device, +... dtype=dtype, +... requires_grad=True, ... ) Now the atomic numbers for the atoms within the QM region: >>> atomic_numbers = torch.tensor( -... [element.num_protons() for element in mols[0].property("element")], -... device=device, -... dtype=torch.int64, +... [element.num_protons() for element in mols[0].property("element")], +... device=device, +... dtype=torch.int64, ... ) And finally the charges of the MM atoms: >>> charges_mm = torch.tensor([atom.property("charge").value() for atom in mm_atoms], -... device=device, -... dtype=dtype +... device=device, +... dtype=dtype ... ) In order to perform a calculation we need to create an instance of the @@ -419,7 +419,7 @@ The model is serialisable, so can be saved and loaded using the standard It is also possible to use the model with Sire when performing QM/MM dynamics: >>> qm_mols, engine = sr.qm.emle( -... mols, mols[0], model, cutoff="7.5A", neighbour_list_frequency=20 +... mols, mols[0], model, cutoff="7.5A", neighbour_list_frequency=20 ... ) The model will be serialised and loaded into a C++ ``TorchQMEngine`` object, From 1d9f02fb0a7cc6c87f8643508268dc1ad178122b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 6 Aug 2024 18:53:50 +0100 Subject: [PATCH 382/468] No need to set graph mode optimisations to false. --- wrapper/Convert/SireOpenMM/torchqm.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index b3d8b8be9..aeb498e2d 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -169,7 +169,6 @@ void TorchQMForce::setModulePath(QString module_path) try { torch::jit::getProfilingMode() = false; - torch::jit::setGraphExecutorOptimize(false); this->torch_module = torch::jit::load(module_path.toStdString()); this->torch_module.eval(); } From 0f83efbda8cff01e814844ee649335a703d15bb0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 9 Aug 2024 10:45:15 +0100 Subject: [PATCH 383/468] Port RF torsion fix to PME code. [ci skip] --- corelib/src/libs/SireMove/openmmpmefep.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/corelib/src/libs/SireMove/openmmpmefep.cpp b/corelib/src/libs/SireMove/openmmpmefep.cpp index 6c2c8096d..68a017d4f 100644 --- a/corelib/src/libs/SireMove/openmmpmefep.cpp +++ b/corelib/src/libs/SireMove/openmmpmefep.cpp @@ -1853,7 +1853,7 @@ void OpenMMPMEFEP::initialise(bool fullPME) dihedral_pert_list.append(DihedralID(four.atom0(), four.atom1(), four.atom2(), four.atom3())); dihedral_pert_swap_list.append( - DihedralID(four.atom3(), four.atom1(), four.atom2(), four.atom0())); + DihedralID(four.atom3(), four.atom2(), four.atom1(), four.atom0())); improper_pert_list.append(ImproperID(four.atom0(), four.atom1(), four.atom2(), four.atom3())); improper_pert_swap_list.append( From c168d9d1ba58050b8b895056014cdd17ae9cbb2c Mon Sep 17 00:00:00 2001 From: Nigel Palmer Date: Fri, 2 Aug 2024 13:23:44 +0100 Subject: [PATCH 384/468] Port RF Boresch restraints to PME Based of Boresch restraints for RF in src/libs/SireMove/openmmfrenergyst.cpp and https://github.com/OpenBioSim/sire/commit/43ed4bc57fa9f407e13621de1420550c154131c9 --- corelib/src/libs/SireMove/openmmpmefep.cpp | 258 ++++++++++++++++++++- doc/source/changelog.rst | 1 + 2 files changed, 254 insertions(+), 5 deletions(-) diff --git a/corelib/src/libs/SireMove/openmmpmefep.cpp b/corelib/src/libs/SireMove/openmmpmefep.cpp index 6c2c8096d..654706c21 100644 --- a/corelib/src/libs/SireMove/openmmpmefep.cpp +++ b/corelib/src/libs/SireMove/openmmpmefep.cpp @@ -836,15 +836,80 @@ void OpenMMPMEFEP::initialise(bool fullPME) qDebug() << "\n\nRestraint is ON\n\n"; } + /************************************RECEPTOR-lIGAND RESTRAINTS**************************/ + // Check if we are in turn on receptor-ligand restraint mode + + bool turn_on_restraints_mode{false}; + + for (int i = 0; i < nmols; i++) + { + Molecule molecule = moleculegroup.moleculeAt(i).molecule(); + + if (molecule.hasProperty("turn_on_restraints_mode")) + { + turn_on_restraints_mode = true; // Lambda will be used to turn on the receptor-ligand restraints + if (Debug) + qDebug() << "Lambda will be used to turn on the receptor-ligand restraints"; + break; // We've found the solute - exit loop over molecules in system. + } + } + /*** BOND LINK FORCE FIELD ***/ - /* NOTE: CustomBondForce does not (OpenMM 6.2) apply PBC checks so code will be buggy if - restraints involve one atom that diffuses out of the box. */ + /* FC 12/21 CustomBondForce now (OpenMM 7.4.0) allows application of PBC checks*/ - auto custom_link_bond = new OpenMM::CustomBondForce("kl * max(0, d - dl*dl);" - "d = (r-reql) * (r-reql)"); + OpenMM::CustomBondForce * custom_link_bond = new OpenMM::CustomBondForce("lamrest*kl*max(0,d-dl*dl);" + "d=(r-reql)*(r-reql)"); custom_link_bond->addPerBondParameter("reql"); custom_link_bond->addPerBondParameter("kl"); custom_link_bond->addPerBondParameter("dl"); + custom_link_bond->setUsesPeriodicBoundaryConditions(true); + // If in turn on receptor-ligand restraints mode, default value of lamrest needs to be lambda, because + // the default value is used for the first nrg_freq timesteps before being set by updateOpenMMContextLambda + if (turn_on_restraints_mode) + custom_link_bond->addGlobalParameter("lamrest", current_lambda); + // We are not in turn on receptor-ligand restraints mode - set lamrest to 1 + else + custom_link_bond->addGlobalParameter("lamrest", 1); + + /****************************************BORESCH DISTANCE POTENTIAL*****************************/ + + OpenMM::CustomBondForce *custom_boresch_dist_rest = + new OpenMM::CustomBondForce("lamrest*force_const*(r-equil_val)^2"); + custom_boresch_dist_rest->addPerBondParameter("force_const"); + custom_boresch_dist_rest->addPerBondParameter("equil_val"); + custom_boresch_dist_rest->setUsesPeriodicBoundaryConditions(true); + if (turn_on_restraints_mode) + custom_boresch_dist_rest->addGlobalParameter("lamrest", current_lambda); + // We are not in turn on receptor-ligand restraints mode - set lamrest to 1 + else + custom_boresch_dist_rest->addGlobalParameter("lamrest", 1); + + /****************************************BORESCH ANGLE POTENTIAL*****************************/ + + OpenMM::CustomAngleForce *custom_boresch_angle_rest = + new OpenMM::CustomAngleForce("lamrest*force_const*(theta-equil_val)^2"); + custom_boresch_angle_rest->addPerAngleParameter("force_const"); + custom_boresch_angle_rest->addPerAngleParameter("equil_val"); + custom_boresch_angle_rest->setUsesPeriodicBoundaryConditions(true); + if (turn_on_restraints_mode) + custom_boresch_angle_rest->addGlobalParameter("lamrest", current_lambda); + // We are not in turn on receptor-ligand restraints mode - set lamrest to 1 + else + custom_boresch_angle_rest->addGlobalParameter("lamrest", 1); + + /****************************************BORESCH DIHEDRAL POTENTIAL*****************************/ + + OpenMM::CustomTorsionForce *custom_boresch_dihedral_rest = + new OpenMM::CustomTorsionForce("lamrest*force_const*min(dtheta, 2*pi-dtheta)^2;" + "dtheta = abs(theta-equil_val); pi = 3.1415926535"); + custom_boresch_dihedral_rest->addPerTorsionParameter("force_const"); + custom_boresch_dihedral_rest->addPerTorsionParameter("equil_val"); + custom_boresch_dihedral_rest->setUsesPeriodicBoundaryConditions(true); + if (turn_on_restraints_mode) + custom_boresch_dihedral_rest->addGlobalParameter("lamrest", current_lambda); + // We are not in turn on receptor-ligand restraints mode - set lamrest to 1 + else + custom_boresch_dihedral_rest->addGlobalParameter("lamrest", 1); /*** BUILD OpenMM SYSTEM ***/ @@ -970,7 +1035,10 @@ void OpenMMPMEFEP::initialise(bool fullPME) // Molecule solutemol = solute.moleculeAt(0).molecule(); int nions = 0; - QVector perturbed_energies_tmp{false, false, false, false, false, false, false, false, false}; + QVector perturbed_energies_tmp(10); + + for (int i = 0; i < perturbed_energies_tmp.size(); i++) + perturbed_energies_tmp[i] = false; // the default AMBER 1-4 scaling factors double const Coulomb14Scale = 1.0 / 1.2; @@ -2501,6 +2569,14 @@ void OpenMMPMEFEP::initialise(bool fullPME) } } // if (!fullPME) + + if (turn_on_restraints_mode) + { + perturbed_energies_tmp[9] = true; //Lambda will be used to turn on the receptor-ligand restraints + if (Debug) + qDebug() << "Added Perturbed Receptor-Ligand Restraint energy term"; + } + perturbed_energies = perturbed_energies_tmp; // IMPORTANT: PERTURBED ENERGY TORSIONS ARE ADDED ABOVE @@ -2556,6 +2632,174 @@ void OpenMMPMEFEP::initialise(bool fullPME) } // end of bond link flag + bool UseBoresch_flag = true; + + // Boresch Restraints. All the information is stored in the solute only. + + if (UseBoresch_flag == true) + { + bool found_solute{false}; + for (int i = 0; i < nmols; i++) + { + Molecule molecule = moleculegroup.moleculeAt(i).molecule(); + + bool has_boresch_dist = molecule.hasProperty("boresch_dist_restraint"); + bool has_boresch_angle = molecule.hasProperty("boresch_angle_restraints"); + bool has_boresch_dihedral = molecule.hasProperty("boresch_dihedral_restraints"); + + if (has_boresch_dist) + { + found_solute = true; // We have found the solute, but before breaking we must also check + // if there are Boresch angle and torsion restraints. + + if (Debug) + { + qDebug() << "Boresch distance restraint properties stored = true"; + qDebug() << "Boresch angle restraint properties stored = " << has_boresch_angle; + qDebug() << "Boresch dihedral restraint properties stored = " << has_boresch_dihedral; + } + + std::vector custom_boresch_dist_par(2); + + const auto boresch_dist_prop = molecule.property("boresch_dist_restraint").asA(); + + const auto atomnum0 = boresch_dist_prop.property(QString("AtomNum0")).asA().toInt(); + const auto atomnum1 = boresch_dist_prop.property(QString("AtomNum1")).asA().toInt(); + const auto force_const = + boresch_dist_prop.property(QString("force_const")).asA().toDouble(); + const auto equil_val = + boresch_dist_prop.property(QString("equil_val")).asA().toDouble(); + + const auto openmmindex0 = AtomNumToOpenMMIndex[atomnum0]; + const auto openmmindex1 = AtomNumToOpenMMIndex[atomnum1]; + + custom_boresch_dist_par[0] = + force_const * (OpenMM::KJPerKcal * OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm); // force_const + custom_boresch_dist_par[1] = equil_val * OpenMM::NmPerAngstrom; // equil_val + + if (Debug) + { + qDebug() << "Boresch distance restraint implemented"; + qDebug() << "atomnum0 = " << atomnum0 << " openmmindex0 =" << openmmindex0; + qDebug() << "atomnum1 = " << atomnum1 << " openmmindex1 =" << openmmindex1; + qDebug() << "force_const = " << force_const << " equil_val = " << equil_val; + } + + custom_boresch_dist_rest->addBond(openmmindex0, openmmindex1, custom_boresch_dist_par); + + system_openmm->addForce(custom_boresch_dist_rest); + } + + if (has_boresch_angle) + { + std::vector custom_boresch_angle_par(2); + + const auto boresch_angle_prop = molecule.property("boresch_angle_restraints").asA(); + + const auto n_angles = + boresch_angle_prop.property(QString("n_boresch_angle_restraints")).asA().toInt(); + + if (Debug) + qDebug() << "Number of Boresch angle restraints = " << n_angles; + + for (int i = 0; i < n_angles; i++) + { + const auto atomnum0 = + boresch_angle_prop.property(QString("AtomNum0-%1").arg(i)).asA().toInt(); + const auto atomnum1 = + boresch_angle_prop.property(QString("AtomNum1-%1").arg(i)).asA().toInt(); + const auto atomnum2 = + boresch_angle_prop.property(QString("AtomNum2-%1").arg(i)).asA().toInt(); + const auto force_const = + boresch_angle_prop.property(QString("force_const-%1").arg(i)).asA().toDouble(); + const auto equil_val = + boresch_angle_prop.property(QString("equil_val-%1").arg(i)).asA().toDouble(); + + const auto openmmindex0 = AtomNumToOpenMMIndex[atomnum0]; + const auto openmmindex1 = AtomNumToOpenMMIndex[atomnum1]; + const auto openmmindex2 = AtomNumToOpenMMIndex[atomnum2]; + + custom_boresch_angle_par[0] = force_const * (OpenMM::KJPerKcal); // force_const + custom_boresch_angle_par[1] = equil_val; // equil_val + + if (Debug) + { + qDebug() << "atomnum0 = " << atomnum0 << " openmmindex0 =" << openmmindex0; + qDebug() << "atomnum1 = " << atomnum1 << " openmmindex1 =" << openmmindex1; + qDebug() << "atomnum2 = " << atomnum2 << " openmmindex2 =" << openmmindex2; + qDebug() << "force_const = " << force_const << " equil_val = " << equil_val; + } + + custom_boresch_angle_rest->addAngle(openmmindex0, openmmindex1, openmmindex2, + custom_boresch_angle_par); + } + + system_openmm->addForce(custom_boresch_angle_rest); + } + + if (has_boresch_dihedral) + { + std::vector custom_boresch_dihedral_par(2); + + const auto boresch_dihedral_prop = molecule.property("boresch_dihedral_restraints").asA(); + + const auto n_dihedrals = boresch_dihedral_prop.property(QString("n_boresch_dihedral_restraints")) + .asA() + .toInt(); + + if (Debug) + qDebug() << "Number of Boresch dihedral restraints = " << n_dihedrals; + + for (int i = 0; i < n_dihedrals; i++) + { + const auto atomnum0 = + boresch_dihedral_prop.property(QString("AtomNum0-%1").arg(i)).asA().toInt(); + const auto atomnum1 = + boresch_dihedral_prop.property(QString("AtomNum1-%1").arg(i)).asA().toInt(); + const auto atomnum2 = + boresch_dihedral_prop.property(QString("AtomNum2-%1").arg(i)).asA().toInt(); + const auto atomnum3 = + boresch_dihedral_prop.property(QString("AtomNum3-%1").arg(i)).asA().toInt(); + const auto force_const = boresch_dihedral_prop.property(QString("force_const-%1").arg(i)) + .asA() + .toDouble(); + const auto equil_val = boresch_dihedral_prop.property(QString("equil_val-%1").arg(i)) + .asA() + .toDouble(); + + const auto openmmindex0 = AtomNumToOpenMMIndex[atomnum0]; + const auto openmmindex1 = AtomNumToOpenMMIndex[atomnum1]; + const auto openmmindex2 = AtomNumToOpenMMIndex[atomnum2]; + const auto openmmindex3 = AtomNumToOpenMMIndex[atomnum3]; + + custom_boresch_dihedral_par[0] = force_const * (OpenMM::KJPerKcal); // force_const + custom_boresch_dihedral_par[1] = equil_val; // equil_val + + if (Debug) + { + qDebug() << "atomnum0 = " << atomnum0 << " openmmindex0 =" << openmmindex0; + qDebug() << "atomnum1 = " << atomnum1 << " openmmindex1 =" << openmmindex1; + qDebug() << "atomnum2 = " << atomnum2 << " openmmindex2 =" << openmmindex2; + qDebug() << "atomnum3 = " << atomnum3 << " openmmindex3 =" << openmmindex3; + qDebug() << "force_const = " << force_const << " equil_val = " << equil_val; + } + + custom_boresch_dihedral_rest->addTorsion(openmmindex0, openmmindex1, openmmindex2, openmmindex3, + custom_boresch_dihedral_par); + } + + system_openmm->addForce(custom_boresch_dihedral_rest); + } + + if (found_solute) + break; // We've found the molecule, exit the outer loop. If a molecule has Boresch + // distance restraints it must be the solute, but we cannot break immediately + // because it may also have angle/ dihedral restraints + + } // End of loop over molecules in system + + } // End of Boresch flag + this->openmm_system = system_openmm; this->isSystemInitialised = true; } // OpenMMPMEFEP::initialise END @@ -3414,6 +3658,10 @@ void OpenMMPMEFEP::updateOpenMMContextLambda(double lambda) if (perturbed_energies[7]) openmm_context->setParameter("lamdih", lambda); // Torsions + // RECEPTOR-LIGAND RESTRAINTS + if (perturbed_energies[9]) + openmm_context->setParameter("lamrest", lambda); //Receptor-ligand restraints + // lambda for the offsets (linear scaling) of the charges in // reciprocal space openmm_context->setParameter("lambda_offset", lambda); diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 3a1d98aba..54835e82f 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -23,6 +23,7 @@ organisation on `GitHub `__. * Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser. * Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule. * Add Docker support for building wrappers on Linux x86. +* Add support for boresch restraints to PME. `2024.2.0 `__ - June 2024 From 6d19c276aac2c0d6cc0d9a7ef32a236bb5816cda Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 12 Aug 2024 10:09:19 +0100 Subject: [PATCH 385/468] Work around lack of inheritance in TorchScript. --- src/sire/qm/_emle.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 77c592aed..769046d58 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -156,6 +156,7 @@ def emle( ) try: + import torch as _torch from emle.models import EMLE as _EMLE has_model = True @@ -181,7 +182,17 @@ def emle( raise ValueError("Unable to select 'qm_atoms' from 'mols'") if has_model: - if not isinstance(calculator, (_EMLECalculator, _EMLE)): + # EMLECalculator. + if isinstance(calculator, _EMLECalculator): + pass + # EMLE model. Note that TorchScript doesn't support inheritance, so + # we need to check whether this is a torch.nn.Module and whether it + # has the "_is_emle" attribute, which is added to all EMLE models. + elif isinstance(calculator, _torch.nn.Module) and hasattr( + calculator, "_is_emle" + ): + pass + else: raise TypeError( "'calculator' must be a of type 'emle.calculator.EMLECalculator' or 'emle.models.EMLE'" ) From acb6ba33e04f66dfe2ee2ff21d7cdffe6225285e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Aug 2024 13:25:22 +0100 Subject: [PATCH 386/468] Update CHANGELOG. [ci skip] --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 54835e82f..475654df7 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -24,6 +24,7 @@ organisation on `GitHub `__. * Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule. * Add Docker support for building wrappers on Linux x86. * Add support for boresch restraints to PME. +* Port SOMD torsion fix to PME code. `2024.2.0 `__ - June 2024 From 2b126dfe976a39687a44f9277c749853537e1977 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Aug 2024 14:07:56 +0100 Subject: [PATCH 387/468] Fix OpenMM-ML section. [closes #227] --- doc/source/tutorial/partXX/02_emle.rst | 26 ++++++++++++-------------- 1 file changed, 12 insertions(+), 14 deletions(-) diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index a491793e0..cef392abf 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -194,10 +194,15 @@ computes the electrostatic embedding: Next we create a new engine bound to the calculator: ->>> qm_mols, engine = sr.qm.emle( +>>> _, engine = sr.qm.emle( >>> ... mols, mols[0], calculator, cutoff="7.5A", neighbour_list_frequency=20 >>> ... ) +.. note:: + + ``qm_mols`` is not needed when using ``OpenMM-ML``, since it will perform + its own internal modifications for performing interpolation. + Rather than using this engine with a ``sire`` dynamics object, we can instead extract the underlying ``OpenMM`` force object and add it to an existing ``OpenMM`` system. The forces can be extracted from the engine as follows: @@ -215,23 +220,16 @@ this is set to 1, but can be set to any value between 0 and 1.) The ``interpolation_force`` has no energy contribution. It is only required as there is currently no way to add global parameters to the ``EMLEForce``. -Since we want to use electrostatic embedding, we will also need to zero the charges -on the atoms within the QM region before creating an ``OpenMM`` system. If not, -then we would also calculate the mechanical embedding interaction. This can be -done by passing the molecules through the ``sr.qm.zero_charge`` function along with -the selection for the QM region: - ->>> qm_mols = sr.qm.zero_charge(qm_mols, qm_mols[0]) - -We now write the modified system to an AMBER format topology and coordinate file -so that we can load them with ``OpenMM``: +Next we need to save the original molecular system to disk so that we can load it +with ``OpenMM``. Here we will use AMBER format files, but any format supported by +``OpenMM`` can be used. ->>> sr.save(qm_mols, "ala_qm", ["prm7", "rst7"]) +>>> sr.save(qm_mols, "ala", ["prm7", "rst7"]) We can now read them back in with ``OpenMM``: ->>> prmtop = openmm.app.AmberPrmtopFile("ala_qm.prm7") ->>> inpcrd = openmm.app.AmberInpcrdFile("ala_qm.rst7") +>>> prmtop = openmm.app.AmberPrmtopFile("ala.prm7") +>>> inpcrd = openmm.app.AmberInpcrdFile("ala.rst7") Next we use the ``prmtop`` to create the MM system: From 6804fb87981e76a1d3fb5f1a4784a1e3da631162 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Aug 2024 14:13:53 +0100 Subject: [PATCH 388/468] Update EMLE-OpenMM-ML test. --- tests/qm/test_qm.py | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/tests/qm/test_qm.py b/tests/qm/test_qm.py index f3ea81e66..339375ba7 100644 --- a/tests/qm/test_qm.py +++ b/tests/qm/test_qm.py @@ -256,18 +256,10 @@ def test_emle_openmm_ml(ala_mols): # Create an EMLE engine bound to the calculator. emle_mols, engine = sr.qm.emle(mols, mols[0], calculator) - # The first molecule (the dipeptide) is the QM region. This is - # perturbable and can be interpolated between MM (the reference state) - # and QM (the perturbed state). Here we want the QM state, which has - # zeroed charges for the QM region. This means that the entire - # intermolecular electrostatic interaction will be computed by - # EMLE, rather than using the MM charges for mechanical embedding. - omm_mols = sr.qm.zero_charge(mols, mols[0]) - # Write the sytem to an AMBER coordinate and topology file. files = sr.expand(tmpdir, ["ala.rst7", "ala.prm7"]) for file in files: - sr.save(omm_mols, file) + sr.save(mols, file) # Load back the files and create an OpenMM topology. inpcrd = openmm.app.AmberInpcrdFile(f"{tmpdir}/ala.rst7") From 0baeb3e4fe25a9fd7349d819e397dd172167bdee Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Aug 2024 14:25:34 +0100 Subject: [PATCH 389/468] Show how to disable mechanical embedding with OpenMM-ML. --- doc/source/tutorial/partXX/02_emle.rst | 9 +++++++++ tests/qm/test_qm.py | 11 ++++++++++- 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index cef392abf..998dc0807 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -266,6 +266,15 @@ We can now add the ``emle`` forces to the system: >>> ml_system.addForce(emle_force) >>> ml_system.addForce(interpolation_force) +In order to ensure that ``OpenMM-ML`` doesn't perform mechanical embedding, we +next need to zero the charges of the QM atoms in the MM system: + +>>> for force in ml_system.getForces(): +... if isinstance(force, mm.NonbondedForce): +... for i in ml_atoms: +... _, sigma, epsilon = force.getParticleParameters(i) +... force.setParticleParameters(i, 0, sigma, epsilon) + In order to run a simulation we need to create an integrator and context. First we create the integrator: diff --git a/tests/qm/test_qm.py b/tests/qm/test_qm.py index 339375ba7..964aea012 100644 --- a/tests/qm/test_qm.py +++ b/tests/qm/test_qm.py @@ -288,6 +288,15 @@ def test_emle_openmm_ml(ala_mols): # Add the EMLE force to the system. ml_system.addForce(emle_force) + # Turn off the dispersion correction to match Sire's calculation + # Set the MM charges to zero + for force in ml_system.getForces(): + if isinstance(force, openmm.NonbondedForce): + for i in ml_atoms: + _, sigma, epsilon = force.getParticleParameters(i) + force.setParticleParameters(i, 0, sigma, epsilon) + force.setUseDispersionCorrection(False) + # Create the integrator. integrator = openmm.LangevinMiddleIntegrator( 300 * openmm.unit.kelvin, @@ -308,7 +317,7 @@ def test_emle_openmm_ml(ala_mols): ) # Make sure the energies are close. - assert np.isclose(nrg_openmm, nrg_sire, rtol=1e-3) + assert np.isclose(nrg_openmm, nrg_sire, rtol=1e-6) @pytest.mark.skipif(not has_emle, reason="emle-engine is not installed") From c70dd1488831c5e57466e59825373e149e1edc8c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Aug 2024 14:29:04 +0100 Subject: [PATCH 390/468] Formatting tweak. [ci skip] --- tests/qm/test_qm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/qm/test_qm.py b/tests/qm/test_qm.py index 964aea012..61ec67732 100644 --- a/tests/qm/test_qm.py +++ b/tests/qm/test_qm.py @@ -289,7 +289,7 @@ def test_emle_openmm_ml(ala_mols): ml_system.addForce(emle_force) # Turn off the dispersion correction to match Sire's calculation - # Set the MM charges to zero + # and set the QM atoms to have zero charge. for force in ml_system.getForces(): if isinstance(force, openmm.NonbondedForce): for i in ml_atoms: From 199f732f801237960b64d3002a8fde9d634e403b Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 14 Aug 2024 15:15:00 +0100 Subject: [PATCH 391/468] Use mols rather than qm_mols. [ci skip] --- doc/source/tutorial/partXX/02_emle.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index 998dc0807..c038a7be6 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -224,7 +224,7 @@ Next we need to save the original molecular system to disk so that we can load i with ``OpenMM``. Here we will use AMBER format files, but any format supported by ``OpenMM`` can be used. ->>> sr.save(qm_mols, "ala", ["prm7", "rst7"]) +>>> sr.save(mols, "ala", ["prm7", "rst7"]) We can now read them back in with ``OpenMM``: From e287cd3644887adc8c74e08fb33bbd27a2644ee1 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 16 Aug 2024 09:26:39 +0100 Subject: [PATCH 392/468] Add note on generality of callback interface. --- doc/source/tutorial/partXX/01_intro.rst | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst index f45d58745..e0e3ef161 100644 --- a/doc/source/tutorial/partXX/01_intro.rst +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -83,6 +83,11 @@ containing a "merged" dipeptide that can be interpolated between MM and QM levels of theory, along with the QM engine. This approach is extremely flexible and allows the user to easily create a QM engine for a wide variety of QM packages. +Note that while the callback interface described above is designed to be used +for QM/MM, it is completely general so could be used to apply *any* external +force based on the local environment around a subset of atoms. For example, you +could apply a biasing potential on top of the regular MM force field. + Running a QM/MM simulation -------------------------- @@ -104,5 +109,12 @@ constraints. The simulation can then be run as usual: This will run 100 picoseconds of dynamics, recording the energy and coordinates every picosecond. +If you are using the callback interface and wish to apply a force on top of the +existing MM force field, rather than perform QM/MM, then you can pass +``swap_end_states=True`` to the ``dynamics`` function. This will swap the QM and +MM end states of all *perturbable* molecules within ``qm_mols``, so that the MM +state corresponds to λ = 1. More details on on λ interpolation can be found in +the `next section `_. + In next section we will show how to use `emle-engine `_ package as QM engine via a simple specialisation of the interface shown above. From 1f360250eef71001d0643db41db094558c2a49fa Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 19 Aug 2024 18:37:44 +0100 Subject: [PATCH 393/468] Remove duplicate "_du" suffix for dummy atoms. [ref #228] --- corelib/src/libs/SireIO/grotop.cpp | 8 -------- 1 file changed, 8 deletions(-) diff --git a/corelib/src/libs/SireIO/grotop.cpp b/corelib/src/libs/SireIO/grotop.cpp index 43c169a15..025c26786 100644 --- a/corelib/src/libs/SireIO/grotop.cpp +++ b/corelib/src/libs/SireIO/grotop.cpp @@ -3217,14 +3217,6 @@ static QStringList writeMolType(const QString &name, const GroMolType &moltype, elem1 = Element::elementWithMass(mol.property("mass1").asA()[cgatomidx]); } - // Update the atom types. - - if (elem0.nProtons() == 0) - atomtype0 += "_du"; - - if (elem1.nProtons() == 0) - atomtype1 += "_du"; - QString resnum = QString::number(atom0.residueNumber().value()); if (not atom0.chainName().isNull()) From d722c2937df7a06f25a06993df409122746811f9 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 19 Aug 2024 19:38:11 +0100 Subject: [PATCH 394/468] Fix deduplication of atomtype records. [ref #228] --- corelib/src/libs/SireIO/grotop.cpp | 50 ++++++++++++++++++++++++++++++ 1 file changed, 50 insertions(+) diff --git a/corelib/src/libs/SireIO/grotop.cpp b/corelib/src/libs/SireIO/grotop.cpp index 025c26786..87908ea6b 100644 --- a/corelib/src/libs/SireIO/grotop.cpp +++ b/corelib/src/libs/SireIO/grotop.cpp @@ -2869,6 +2869,7 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps QString particle_type = "A"; // A is for Atom + // This is a dummy atom. if (elem.nProtons() == 0 and lj.isDummy()) { if (is_perturbable) @@ -2877,6 +2878,9 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps // Only label dummies for regular simulations. else if (not was_perturbable) particle_type = "D"; + + // Flag that we need to update the atoms. + update_atoms0 = true; } // This is a new atom type. @@ -2893,6 +2897,15 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps // Hash the atom type against its parameter string, minus the type. param_hash.insert(atomtypes[atomtype].mid(6), atomtype); + + if (update_atoms0) + { + // Set the type. + atom.setAtomType(atomtype); + + // Update the atoms in the vector. + atoms[i] = atom; + } } // This type has been seen before. else @@ -2977,6 +2990,17 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps update_atoms0 = true; } } + else + { + if (update_atoms0) + { + // Set the type. + atom.setAtomType(atomtype); + + // Update the atoms in the vector. + atoms[i] = atom; + } + } } } @@ -3019,9 +3043,15 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps QString particle_type = "A"; // A is for Atom + // This is a dummy atom. if (elem.nProtons() == 0 and lj.isDummy()) + { atomtype += "_du"; + // Flag that we need to update the atoms. + update_atoms1 = true; + } + // This is a new atom type. if (not atomtypes.contains(atomtype)) { @@ -3036,6 +3066,15 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps // Hash the atom type against its parameter string, minus the type. param_hash.insert(atomtypes[atomtype].mid(6), atomtype); + + if (update_atoms1) + { + // Set the type. + atom.setAtomType(atomtype); + + // Update the atoms in the vector. + atoms[i] = atom; + } } // This type has been seen before. @@ -3121,6 +3160,17 @@ static QStringList writeAtomTypes(QMap, GroMolType> &moltyps update_atoms1 = true; } } + else + { + if (update_atoms1) + { + // Set the type. + atom.setAtomType(atomtype); + + // Update the atoms in the vector. + atoms[i] = atom; + } + } } } From c7a93a78fb9cfb95772205a4006d6e86b2a29f7e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 19 Aug 2024 19:42:36 +0100 Subject: [PATCH 395/468] Update CHANGELOG. --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 3a1d98aba..33d9808b0 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -23,6 +23,7 @@ organisation on `GitHub `__. * Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser. * Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule. * Add Docker support for building wrappers on Linux x86. +* Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. `2024.2.0 `__ - June 2024 From 1902d6d7ab544d2f350ccdc5dbb52bafb88a5c48 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 19 Aug 2024 20:10:55 +0100 Subject: [PATCH 396/468] Add unit test for GROMACS FEP atomtypes and atoms records. [ref #228] --- tests/io/test_grotop.py | 128 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 128 insertions(+) diff --git a/tests/io/test_grotop.py b/tests/io/test_grotop.py index 5a23a87e4..09d93a603 100644 --- a/tests/io/test_grotop.py +++ b/tests/io/test_grotop.py @@ -39,3 +39,131 @@ def test_posre(): # Make sure we can parse a file with BioSimSpace position restraint include # directives. mols = sr.load_test_files("posre.top") + + +def test_fep_atoms(): + """ + Test that GROMACS FEP atomtypes and atoms are created correctly. + """ + + import os + import tempfile + + atomtypes = """[ atomtypes ] + ; name at.num mass charge ptype sigma epsilon + C1 6 12.010700 0.000000 A 0.348065 0.363503 + C1_du 0 0.000000 0.000000 A 0.348065 0.000000 + C2 6 12.010700 0.000000 A 0.337953 0.455389 + H1 1 1.007940 0.000000 A 0.110343 0.058956 + H1_du 0 0.000000 0.000000 A 0.110343 0.000000 + H2 1 1.007940 0.000000 A 0.257258 0.065318 + H2_du 0 0.000000 0.000000 A 0.264454 0.000000 + H2_dux 0 0.000000 0.000000 A 0.257258 0.000000 + H3 1 1.007940 0.000000 A 0.264454 0.066021 + H3_du 0 0.000000 0.000000 A 0.258323 0.000000 + H4 1 1.007940 0.000000 A 0.258323 0.068656 + H5 1 1.007940 0.000000 A 0.245363 0.054840 + N1 7 14.006700 0.000000 A 0.320688 0.701621 + O1 8 15.999400 0.000000 A 0.303981 0.879502 + O1_du 0 0.000000 0.000000 A 0.303981 0.000000 + O2 8 15.999400 0.000000 A 0.302511 0.704858 + """ + + atoms = """[ atoms ] + ; nr type0 resnr residue atom cgnr charge0 mass0 type1 charge1 mass1 + 1 O1 1 LIG O1x 1 -0.803190 15.999430 O1_du 0.000000 15.999430 + 2 C1 1 LIG C1x 2 0.916780 12.010780 N1 -0.662150 14.006720 + 3 O1 1 LIG O2x 3 -0.803190 15.999430 O1_du 0.000000 15.999430 + 4 C1 1 LIG C2x 4 0.082410 12.010780 C1 -0.105710 12.010780 + 5 N1 1 LIG N1x 5 -0.564860 14.006720 N1 -0.484790 14.006720 + 6 H1 1 LIG H1x 6 0.449360 1.007947 H1 0.407460 1.007947 + 7 C1 1 LIG C3x 7 0.061040 12.010780 C1 0.001920 12.010780 + 8 C1 1 LIG C4x 8 -0.087870 12.010780 C1 -0.087450 12.010780 + 9 C1 1 LIG C5x 9 -0.101450 12.010780 N1 -0.015090 14.006720 + 10 C1 1 LIG C6x 10 -0.165020 12.010780 C1 -0.045730 12.010780 + 11 H2 1 LIG H2x 11 0.106400 1.007947 H5 0.196160 1.007947 + 12 C1 1 LIG C7x 12 -0.107040 12.010780 C1_du 0.000000 12.010780 + 13 H2 1 LIG H3x 13 0.120980 1.007947 H2_dux 0.000000 1.007947 + 14 C1 1 LIG C8x 14 -0.057540 12.010780 C1 -0.204760 12.010780 + 15 C1 1 LIG C9x 15 -0.203310 12.010780 C1 0.114810 12.010780 + 16 C2 1 LIG C10x 16 0.013180 12.010780 C2 -0.054450 12.010780 + 17 H3 1 LIG H4x 17 0.044890 1.007947 H3 0.058540 1.007947 + 18 H3 1 LIG H5x 18 0.044890 1.007947 H3 0.058540 1.007947 + 19 C2 1 LIG C11x 19 -0.084960 12.010780 C2 -0.080770 12.010780 + 20 H3 1 LIG H6x 20 0.058790 1.007947 H3 0.071370 1.007947 + 21 H3 1 LIG H7x 21 0.058790 1.007947 H3 0.071370 1.007947 + 22 C2 1 LIG C12x 22 0.126550 12.010780 C2 0.130690 12.010780 + 23 H4 1 LIG H8x 23 0.037860 1.007947 H4 0.038330 1.007947 + 24 H4 1 LIG H9x 24 0.037860 1.007947 H4 0.038330 1.007947 + 25 O2 1 LIG O3x 25 -0.332540 15.999430 O2 -0.334080 15.999430 + 26 C1 1 LIG C13x 26 0.142880 12.010780 C1 0.108960 12.010780 + 27 C1 1 LIG C14x 27 -0.181170 12.010780 C1 -0.171770 12.010780 + 28 H2 1 LIG H10x 28 0.144890 1.007947 H2 0.138510 1.007947 + 29 C1 1 LIG C15x 29 -0.052890 12.010780 C1 -0.042000 12.010780 + 30 C2 1 LIG C16x 30 -0.051460 12.010780 C2 -0.059900 12.010780 + 31 H3 1 LIG H11x 31 0.040320 1.007947 H3 0.050460 1.007947 + 32 H3 1 LIG H12x 32 0.040320 1.007947 H3 0.050460 1.007947 + 33 H3 1 LIG H13x 33 0.040320 1.007947 H3 0.050460 1.007947 + 34 C1 1 LIG C17x 34 -0.175410 12.010780 C1 -0.147890 12.010780 + 35 H2 1 LIG H14x 35 0.122060 1.007947 H2 0.142460 1.007947 + 36 C1 1 LIG C18x 36 -0.101660 12.010780 C1 -0.094400 12.010780 + 37 H2 1 LIG H15x 37 0.123170 1.007947 H2 0.139870 1.007947 + 38 C1 1 LIG C19x 38 -0.184410 12.010780 C1 -0.174770 12.010780 + 39 H2 1 LIG H16x 39 0.144680 1.007947 H2 0.138300 1.007947 + 40 C2 1 LIG C20x 40 -0.038120 12.010780 C2 -0.032020 12.010780 + 41 H3 1 LIG H17x 41 0.030840 1.007947 H2_du 0.000000 1.007947 + 42 H3 1 LIG H18x 42 0.030840 1.007947 H2_du 0.000000 1.007947 + 43 H3 1 LIG H19x 43 0.030840 1.007947 H2_du 0.000000 1.007947 + 44 C2 1 LIG C21x 44 -0.035100 12.010780 C2 0.001470 12.010780 + 45 H3 1 LIG H20x 45 0.026750 1.007947 H2_du 0.000000 1.007947 + 46 H3 1 LIG H21x 46 0.026750 1.007947 H2_du 0.000000 1.007947 + 47 H3 1 LIG H22x 47 0.026750 1.007947 H2_du 0.000000 1.007947 + 48 H1_du 1 LIG H1x 48 0.000000 1.007947 H1 0.459340 1.007947 + 49 H1_du 1 LIG H2x 49 0.000000 1.007947 H1 0.459340 1.007947 + 50 H1_du 1 LIG H3x 50 0.000000 1.007947 H1 0.459340 1.007947 + 51 H2_du 1 LIG H19x 51 0.000000 1.007947 H3 0.062430 1.007947 + 52 H2_du 1 LIG H20x 52 0.000000 1.007947 H3 0.062430 1.007947 + 53 H2_du 1 LIG H21x 53 0.000000 1.007947 H3 0.062430 1.007947 + 54 H3_du 1 LIG H22x 54 0.000000 1.007947 H4 0.074650 1.007947 + 55 H3_du 1 LIG H23x 55 0.000000 1.007947 H4 0.074650 1.007947 + 56 H3_du 1 LIG H24x 56 0.000000 1.007947 H4 0.074650 1.007947 + """ + + # Load the molecule. + merged_mol = sr.load_test_files("merged_molecule_grotop.s3") + + # Save to a temporary file. + with tempfile.TemporaryDirectory() as tmpdir: + sr.save(merged_mol, os.path.join(tmpdir, "merged_molecule"), format="GroTop") + + # Read the [ atomtypes ] and [ atoms ] sections from the file. + with open(os.path.join(tmpdir, "merged_molecule.grotop"), "r") as f: + atomtypes_lines = [] + atoms_lines = [] + found_atomtypes = False + found_atoms = False + for line in f: + if line.startswith("[ atomtypes ]"): + found_atomtypes = True + elif line.startswith("[ atoms ]"): + found_atoms = True + + if found_atomtypes and not found_atoms: + if line != "\n": + atomtypes_lines.append(line) + else: + found_atomtypes = False + + if found_atoms: + if line != "\n": + atoms_lines.append(line) + else: + found_atoms = False + + # Check that the atomtypes and atoms are as expected. + atomtypes_list = atomtypes.split("\n") + for a, b in zip(atomtypes_list, atomtypes_lines): + assert a.strip() == b.strip() + atoms_list = atoms.split("\n") + for a, b in zip(atoms_list, atoms_lines): + assert a.strip() == b.strip() From a5bdb62a3a2205fc60c569121b633ed474f245e4 Mon Sep 17 00:00:00 2001 From: Nigel Palmer Date: Tue, 27 Aug 2024 14:27:47 +0100 Subject: [PATCH 397/468] Updated flat-bottomed distance restraint for PME to match RF Updated to match the equation in openmmfrenergyst.cpp. This is due to a minor issue with the older version where the potential is not harmonic with equilibrium position dl. --- corelib/src/libs/SireMove/openmmpmefep.cpp | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/corelib/src/libs/SireMove/openmmpmefep.cpp b/corelib/src/libs/SireMove/openmmpmefep.cpp index 654706c21..1ceb95d83 100644 --- a/corelib/src/libs/SireMove/openmmpmefep.cpp +++ b/corelib/src/libs/SireMove/openmmpmefep.cpp @@ -857,8 +857,8 @@ void OpenMMPMEFEP::initialise(bool fullPME) /*** BOND LINK FORCE FIELD ***/ /* FC 12/21 CustomBondForce now (OpenMM 7.4.0) allows application of PBC checks*/ - OpenMM::CustomBondForce * custom_link_bond = new OpenMM::CustomBondForce("lamrest*kl*max(0,d-dl*dl);" - "d=(r-reql)*(r-reql)"); + OpenMM::CustomBondForce * custom_link_bond = new OpenMM::CustomBondForce("delta(min(0, r_eff))*(lamrest^5)*kl*r_eff^2;" + "r_eff=abs(r-reql)-dl"); custom_link_bond->addPerBondParameter("reql"); custom_link_bond->addPerBondParameter("kl"); custom_link_bond->addPerBondParameter("dl"); From 9982f5906360108335efb42e3553141bcbd7f52c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 2 Sep 2024 13:38:05 +0100 Subject: [PATCH 398/468] Add Python 3.10 to allow SOAP based EMLE models with Rascal. --- .github/workflows/emle.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 28be43639..39366ac7d 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -24,7 +24,7 @@ jobs: max-parallel: 9 fail-fast: false matrix: - python-version: ["3.11"] + python-version: ["3.10", "3.11"] platform: - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } From 17915cf139140b6c3c0aafd86b1812520d070091 Mon Sep 17 00:00:00 2001 From: Matthew Date: Thu, 26 Sep 2024 15:02:08 +0100 Subject: [PATCH 399/468] Proper length of the custom_clj_params used for positional restraint ghost atoms --- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 684b9a58b..60228871a 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -315,7 +315,8 @@ void _add_positional_restraints(const SireMM::PositionalRestraints &restraints, auto ghost_nonghostff = lambda_lever.getForce("ghost/non-ghost", system); std::vector custom_params = {1.0, 0.0, 0.0}; - std::vector custom_clj_params = {0.0, 0.0, 0.0, 0.0}; + // Define null parameters used to add these particles to the ghost forces (5 total) + std::vector custom_clj_params = {0.0, 0.0, 0.0, 0.0, 0.0}; // we need to add all of the positions as anchor particles for (const auto &restraint : atom_restraints) From 0a7fe8de5e7f17f978f08ddd2793c1124da11e48 Mon Sep 17 00:00:00 2001 From: Matthew Date: Thu, 26 Sep 2024 15:06:23 +0100 Subject: [PATCH 400/468] Updates changelog --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 915311990..e400d02ec 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -26,6 +26,7 @@ organisation on `GitHub `__. * Add support for boresch restraints to PME. * Port SOMD torsion fix to PME code. * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. +* Fix issues with positionally restrainted atoms in perturbable systems. `2024.2.0 `__ - June 2024 From 265bf8137f922511b5f989ee6ac4073de92236cd Mon Sep 17 00:00:00 2001 From: Matthew Date: Thu, 26 Sep 2024 16:44:26 +0100 Subject: [PATCH 401/468] Fix for repex in NPT ensemble --- src/sire/morph/_repex.py | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/src/sire/morph/_repex.py b/src/sire/morph/_repex.py index ffd328063..dd0e80c5a 100644 --- a/src/sire/morph/_repex.py +++ b/src/sire/morph/_repex.py @@ -87,7 +87,9 @@ def replica_exchange( # delta = beta_b * [ H_b_i - H_b_j + P_b (V_b_i - V_b_j) ] + # beta_a * [ H_a_i - H_a_j + P_a (V_a_i - V_a_j) ] - from ..units import k_boltz + from ..units import k_boltz, mole + + N_A = 6.02214076e23 / mole beta0 = 1.0 / (k_boltz * temperature0) beta1 = 1.0 / (k_boltz * temperature1) @@ -102,8 +104,8 @@ def replica_exchange( pressure1 = ensemble1.pressure() delta = beta1 * ( - nrgs1[0] - nrgs1[1] + pressure1 * (volume1 - volume0) - ) + beta0 * (nrgs0[0] - nrgs0[1] + pressure0 * (volume0 - volume1)) + nrgs1[0] - nrgs1[1] + (pressure1 * (volume1 - volume0) * N_A) + ) + beta0 * (nrgs0[0] - nrgs0[1] + (pressure0 * (volume0 - volume1) * N_A)) from math import exp @@ -118,12 +120,8 @@ def replica_exchange( replica1.set_lambda(lam0) if ensemble0 != ensemble1: - replica0.set_ensemble( - ensemble1, rescale_velocities=rescale_velocities - ) - replica1.set_ensemble( - ensemble0, rescale_velocities=rescale_velocities - ) + replica0.set_ensemble(ensemble1, rescale_velocities=rescale_velocities) + replica1.set_ensemble(ensemble0, rescale_velocities=rescale_velocities) return (replica1, replica0, True) else: From 2a0c15d3816b3856e256d778201995695d9bbaaa Mon Sep 17 00:00:00 2001 From: Matthew Date: Thu, 26 Sep 2024 16:49:45 +0100 Subject: [PATCH 402/468] Changelog --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 915311990..b26941653 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -26,6 +26,7 @@ organisation on `GitHub `__. * Add support for boresch restraints to PME. * Port SOMD torsion fix to PME code. * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. +* Fixes issue with runnning ``sire.morph.replica_exchange`` on systems in an NPT ensemble. `2024.2.0 `__ - June 2024 From 8836f9216c2f034add1754a37bca48d45418e770 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 27 Sep 2024 09:27:35 +0100 Subject: [PATCH 403/468] Fix buffer overflow. [closes #236] --- doc/source/changelog.rst | 1 + wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 915311990..2a16019d3 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -26,6 +26,7 @@ organisation on `GitHub `__. * Add support for boresch restraints to PME. * Port SOMD torsion fix to PME code. * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. +* Fixed buffer overflow when computing molecule indices to excluded to/from ghost atom interactions. `2024.2.0 `__ - June 2024 diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 684b9a58b..847ef0dfb 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1578,14 +1578,14 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { // work out the molecule index for the from ghost atom int mol_from = 0; - while (start_indexes[mol_from] <= from_ghost_idx) + while (start_indexes[mol_from] <= from_ghost_idx and mol_from < nmols) mol_from++; for (const auto &to_ghost_idx : to_ghost_idxs) { // work out the molecule index for the to ghost atom int mol_to = 0; - while (start_indexes[mol_to] <= to_ghost_idx) + while (start_indexes[mol_to] <= to_ghost_idx and mol_to < nmols) mol_to++; if (not excluded_ghost_pairs.contains(IndexPair(from_ghost_idx, to_ghost_idx))) From 1028bcaf5b79d42eae53329f2a1e138bab58f9fb Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 27 Sep 2024 12:33:38 +0100 Subject: [PATCH 404/468] Fix delta squared parameter in nonbonded expressions. [closes #238] --- wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index 847ef0dfb..f7c7a0468 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -916,7 +916,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { nb14_expression = QString( "coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));" + "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha*alpha)+r_safe^2))-(kappa/r_safe));" "lj_nrg=four_epsilon*sig6*(sig6-1);" "sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);" "r_safe=max(r, 0.001);") @@ -929,7 +929,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { nb14_expression = QString( "coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha)+r_safe^2))-(kappa/r_safe));" + "coul_nrg=138.9354558466661*q*(((%1)/sqrt((%2*alpha*alpha)+r_safe^2))-(kappa/r_safe));" "lj_nrg=four_epsilon*sig6*(sig6-1);" "sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);" "r_safe=max(r, 0.001);" @@ -976,7 +976,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // kJ mol-1 given the units of charge (|e|) and distance (nm) // clj_expression = QString("coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));" + "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha*max_alpha)+r_safe^2))-(max_kappa/r_safe));" "lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);" "sig6=(sigma^6)/(%3*sigma^6 + r_safe^6);" "r_safe=max(r, 0.001);" @@ -1014,7 +1014,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, // kJ mol-1 given the units of charge (|e|) and distance (nm) // clj_expression = QString("coul_nrg+lj_nrg;" - "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha)+r_safe^2))-(max_kappa/r_safe));" + "coul_nrg=138.9354558466661*q1*q2*(((%1)/sqrt((%2*max_alpha*max_alpha)+r_safe^2))-(max_kappa/r_safe));" "lj_nrg=two_sqrt_epsilon1*two_sqrt_epsilon2*sig6*(sig6-1);" "sig6=(sigma^6)/(((sigma*delta) + r_safe^2)^3);" "delta=%3*max_alpha;" From b8c23a330d0498732f54656cdefe7110ef1b0536 Mon Sep 17 00:00:00 2001 From: Matthew Date: Fri, 27 Sep 2024 14:25:53 +0100 Subject: [PATCH 405/468] Adds test for positional restraints on perturbed molecules --- tests/convert/test_openmm_restraints.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tests/convert/test_openmm_restraints.py b/tests/convert/test_openmm_restraints.py index 7f2b5ee2e..c7dcd8bf7 100644 --- a/tests/convert/test_openmm_restraints.py +++ b/tests/convert/test_openmm_restraints.py @@ -6,8 +6,12 @@ "openmm" not in sr.convert.supported_formats(), reason="openmm support is not available", ) -def test_openmm_positional_restraints(kigaki_mols, openmm_platform): - mols = kigaki_mols +@pytest.mark.parametrize("molecules", ["kigaki_mols", "merged_ethane_methanol"]) +def test_openmm_positional_restraints(molecules, openmm_platform, request): + mols = request.getfixturevalue(molecules) + + if mols[0].is_perturbable(): + mols = sr.morph.link_to_reference(mols) mol = mols[0] From e699235571b0831828882082d505eb83d801af2c Mon Sep 17 00:00:00 2001 From: Matthew Date: Fri, 27 Sep 2024 14:27:32 +0100 Subject: [PATCH 406/468] Fixed typo in changelog --- doc/source/changelog.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index e400d02ec..8f0c435ae 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -26,7 +26,7 @@ organisation on `GitHub `__. * Add support for boresch restraints to PME. * Port SOMD torsion fix to PME code. * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. -* Fix issues with positionally restrainted atoms in perturbable systems. +* Fix issues with positionally restrained atoms in perturbable systems. `2024.2.0 `__ - June 2024 From 1894153b75897d00505ab4254a5b65763b874f48 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 27 Sep 2024 15:16:14 +0100 Subject: [PATCH 407/468] Exclude to/from ghost interactions from ghost_14ff. [closes #239] --- wrapper/Convert/SireOpenMM/lambdalever.cpp | 13 ++++++++++++- .../Convert/SireOpenMM/sire_to_openmm_system.cpp | 6 +++++- 2 files changed, 17 insertions(+), 2 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index a70a0c18f..acca98d81 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -1438,12 +1438,23 @@ double LambdaLever::setLambda(OpenMM::Context &context, // don't set LJ terms for ghost atoms if (atom0_is_ghost or atom1_is_ghost) { + // are the atoms perturbing from ghosts? + const auto from_ghost0 = perturbable_mol.getFromGhostIdxs().contains(atom0); + const auto from_ghost1 = perturbable_mol.getFromGhostIdxs().contains(atom1); + // are the atoms perturbing to ghosts? + const auto to_ghost0 = perturbable_mol.getToGhostIdxs().contains(atom0); + const auto to_ghost1 = perturbable_mol.getToGhostIdxs().contains(atom1); + + // is this interaction between an to/from ghost atom? + const auto to_from_ghost = (from_ghost0 and to_ghost1) or (from_ghost1 and to_ghost0); + cljff->setExceptionParameters( boost::get<0>(idxs[j]), boost::get<0>(p), boost::get<1>(p), boost::get<2>(p), 1e-9, 1e-9); - if (ghost_14ff != 0) + // exclude 14s for to/from ghost interactions + if (not to_from_ghost and ghost_14ff != 0) { // this is a 1-4 parameter - need to update // the ghost 1-4 forcefield diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index f7c7a0468..5a94e9252 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -1503,7 +1503,11 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, boost::get<2>(p), 1e-9, 1e-9, true); - if (coul_14_scl != 0 or lj_14_scl != 0) + // Whether this is a to/from ghost interaction. + auto to_from_ghost = (from_ghost_idxs.contains(atom0) and to_ghost_idxs.contains(atom1)) or + (from_ghost_idxs.contains(atom1) and to_ghost_idxs.contains(atom0)); + + if (not to_from_ghost and (coul_14_scl != 0 or lj_14_scl != 0)) { // this is a 1-4 interaction that should be added // to the ghost-14 forcefield From 9e529ea22150a1c8fa96d85dd08ea31688a5833d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 27 Sep 2024 16:28:02 +0100 Subject: [PATCH 408/468] Update CHANGELOG. [ci skip] --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 2a16019d3..2512c46b1 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -27,6 +27,8 @@ organisation on `GitHub `__. * Port SOMD torsion fix to PME code. * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. * Fixed buffer overflow when computing molecule indices to excluded to/from ghost atom interactions. +* Fixed calculation of ``delta^2`` in soft-core Couloumb potential. +* Excluded to/from ghost atom interactions from ``ghost_14ff``. `2024.2.0 `__ - June 2024 From 132055eb7979a014fc75904589a03562fe605304 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 30 Sep 2024 09:16:34 +0100 Subject: [PATCH 409/468] Fix definition of ghost alpha parameter. [ci skip] --- doc/source/tutorial/part07/03_ghosts.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/source/tutorial/part07/03_ghosts.rst b/doc/source/tutorial/part07/03_ghosts.rst index c044b1057..ba24b459b 100644 --- a/doc/source/tutorial/part07/03_ghosts.rst +++ b/doc/source/tutorial/part07/03_ghosts.rst @@ -97,10 +97,10 @@ The soft-core parameters are: * ``α_i`` and ``α_j`` control the amount of "softening" of the electrostatic and LJ interactions. A value of 0 means no softening (fully hard), while a value of 1 means fully soft. Ghost atoms which - disappear as a function of λ have a value of α of 0 in the - reference state, and 1 in the perturbed state. Ghost atoms which appear - as a function of λ have a value of α of 1 in the reference - state, and 0 in the perturbed state. These values can be perturbed + disappear as a function of λ have a value of α of 1 in the + reference state, and 0 in the perturbed state. Ghost atoms which appear + as a function of λ have a value of α of 0 in the reference + state, and 1 in the perturbed state. These values can be perturbed via the ``alpha`` lever in the λ-schedule. * ``n`` is the "coulomb power", and is set to 0 by default. It can be @@ -159,10 +159,10 @@ The soft-core parameters are: * ``α_i`` and ``α_j`` control the amount of "softening" of the electrostatic and LJ interactions. A value of 0 means no softening (fully hard), while a value of 1 means fully soft. Ghost atoms which - disappear as a function of λ have a value of α of 0 in the - reference state, and 1 in the perturbed state. Ghost atoms which appear - as a function of λ have a value of α of 1 in the reference - state, and 0 in the perturbed state. These values can be perturbed + disappear as a function of λ have a value of α of 1 in the + reference state, and 0 in the perturbed state. Ghost atoms which appear + as a function of λ have a value of α of 0 in the reference + state, and 1 in the perturbed state. These values can be perturbed via the ``alpha`` lever in the λ-schedule. * ``m`` is the "taylor power", and is set to 1 by default. It can be From 0e242058761c7bae0793f3e9f5eaf3d6060b374f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 30 Sep 2024 11:01:23 +0100 Subject: [PATCH 410/468] Add function for evaluating custom XML forces. [ci skip] --- src/sire/morph/CMakeLists.txt | 1 + src/sire/morph/__init__.py | 3 + src/sire/morph/_xml.py | 256 ++++++++++++++++++++++++++++++++++ 3 files changed, 260 insertions(+) create mode 100644 src/sire/morph/_xml.py diff --git a/src/sire/morph/CMakeLists.txt b/src/sire/morph/CMakeLists.txt index 11ea25882..3c63ff840 100644 --- a/src/sire/morph/CMakeLists.txt +++ b/src/sire/morph/CMakeLists.txt @@ -16,6 +16,7 @@ set ( SCRIPTS _pertfile.py _perturbation.py _repex.py + _xml.py ) # installation diff --git a/src/sire/morph/__init__.py b/src/sire/morph/__init__.py index e5931ee5e..caf66cb84 100644 --- a/src/sire/morph/__init__.py +++ b/src/sire/morph/__init__.py @@ -16,6 +16,7 @@ "zero_ghost_bonds", "zero_ghost_angles", "zero_ghost_torsions", + "evaluate_xml_force", "Perturbation", ] @@ -48,3 +49,5 @@ from ._mutate import mutate from ._decouple import annihilate, decouple + +from ._xml import evaluate_xml_force diff --git a/src/sire/morph/_xml.py b/src/sire/morph/_xml.py new file mode 100644 index 000000000..f0412d55a --- /dev/null +++ b/src/sire/morph/_xml.py @@ -0,0 +1,256 @@ +__all__ = ["evaluate_xml_force"] + + +def evaluate_xml_force(mols, xml, force): + """ + Evaluate the custom force defined in the passed XML file. + The passed molecules must be the ones used to create the + OpenMM context associated with the XML file. + + + Parameters + ---------- + + mols : sire.system.System, sire.mol.Molecule + The perturbable molecular system or molecule to evaluate the force on. + This should have already been linked to the appropriate end state. + + xml : str + The path to the XML file containing the custom force. + + force : str + The name of the custom force to evaluate. Options are: + "ghost-ghost", "ghost-nonghost", "ghost-14". + + Returns + ------- + + [((sire.mol.Atom, sr.mol.Atom), (sr.units.GeneralUnit, sr.units.GeneralUnit))] + The atom pairs and pairwise Coulomb and Lennard-Jones energies. + """ + + from math import sqrt + + import xml.etree.ElementTree as ET + import sys + + from .._measure import measure + from ..legacy.Mol import Molecule + from ..system import System + from ..units import nanometer, kJ_per_mol + + # Store the name of the current module. + module = sys.modules[__name__] + + # Validate the molecules. + if not isinstance(mols, (System, Molecule)): + raise TypeError( + "'mols' must be of type 'sire.system.System' or 'sire.mol.Molecule'." + ) + + # Validate the XML file. + if not isinstance(xml, str): + raise TypeError("'xml' must be of type 'str'.") + + # Try to parse the XML file. + try: + tree = ET.parse(xml) + except: + raise ValueError(f"Could not parse the XML file: {xml}") + + # Validate the force type. + if not isinstance(force, str): + raise TypeError("'force' must be of type 'str'.") + + # Sanitize the force name. + force = ( + force.lower() + .replace(" ", "") + .replace("-", "") + .replace("_", "") + .replace("/", "") + ) + + # Validate the force name. + if not force in ["ghostghost", "ghostnonghost", "ghost14"]: + raise ValueError( + "'force' must be one of 'ghost-ghost', 'ghost-nonghost', or 'ghost-14'." + ) + + # Create the name and index based on the force type. + if force == "ghostghost": + name = "CustomNonbondedForce" + index = 0 + elif force == "ghostnonghost": + name = "CustomNonbondedForce" + index = 1 + elif force == "ghost14": + name = "CustomBondForce" + index = 0 + + # Get the root of the XML tree. + root = tree.getroot() + + # Loop over the forces until we find the first CustomNonbondedForce. + force_index = 0 + for force in tree.find("Forces"): + if force.get("name") == name: + if force_index == index: + break + force_index += 1 + + # Get the energy terms. + terms = list(reversed(force.get("energy").split(";")[1:-1])) + + # Create a list to store the results. + results = [] + + # CustomNonbondedForce: ghost-ghost or ghost-nonghost. + if name == "CustomNonbondedForce": + # Get the parameters for this force. + parameters = [p.get("name") for p in force.find("PerParticleParameters")] + + # Get all the particle parameters. + particles = force.find("Particles") + + # Get the two sets of particles that interact. + set1 = [ + int(p.get("index")) + for p in force.find("InteractionGroups") + .find("InteractionGroup") + .find("Set1") + ] + set2 = [ + int(p.get("index")) + for p in force.find("InteractionGroups") + .find("InteractionGroup") + .find("Set2") + ] + + # Get the exclusions. + exclusions = [ + (int(e.get("p1")), int(e.get("p2"))) + for e in force.find("Exclusions").findall("Exclusion") + ] + for x, (i, j) in enumerate(exclusions): + if i > j: + exclusions[x] = (j, i) + exclusions = set(exclusions) + + # Get the cutoff distance. + cutoff = float(force.get("cutoff")) + + # Get the list of atoms. + atoms = mols.atoms() + + # Loop over all particles in set1. + for x in range(len(set1)): + # Get the index from set1. + i = set1[x] + + # Get the parameters for this particle. + particle_i = particles[i] + + # Get the atom. + atom_i = atoms[i] + + # Set the parameters for this particle. + setattr(module, parameters[0] + "1", float(particle_i.get("param1"))) + setattr(module, parameters[1] + "1", float(particle_i.get("param2"))) + setattr(module, parameters[2] + "1", float(particle_i.get("param3"))) + setattr(module, parameters[3] + "1", float(particle_i.get("param4"))) + setattr(module, parameters[4] + "1", float(particle_i.get("param5"))) + + # Loop over all other particles in set1. + for y in range(x + 1, len(set1)): + # Get the index from set2. + j = set1[y] + + # Check if this pair is excluded. + pair = (i, j) if i < j else (j, i) + if pair in exclusions: + continue + + # Get the parameters for this particle. + particle_j = particles[j] + + # Get the atom. + atom_j = atoms[j] + + # Set the parameters for this particle. + setattr(module, parameters[0] + "2", float(particle_j.get("param1"))) + setattr(module, parameters[1] + "2", float(particle_j.get("param2"))) + setattr(module, parameters[2] + "2", float(particle_j.get("param3"))) + setattr(module, parameters[3] + "2", float(particle_j.get("param4"))) + setattr(module, parameters[4] + "2", float(particle_j.get("param5"))) + + # Get the distance between the particles. + r = measure(atom_i, atom_j).to(nanometer) + + # Atoms are within the cutoff. + if r < cutoff: + # Evaluate the energy term by term. + for term in terms: + # Replace any instances of ^ with **. + term = term.replace("^", "**") + + # Split the term into the result and the expression. + result, expression = term.split("=") + + # Evaluate the expression. + setattr(module, result, eval(expression)) + + # Give energies units. + coul_nrg = module.coul_nrg * kJ_per_mol + lj_nrg = module.lj_nrg * kJ_per_mol + + # Append the results for this pair. + results.append(((atom_i, atom_j), (coul_nrg, lj_nrg))) + + # CustomBondForce: ghost-14. + else: + # Get the parameters for this force. + parameters = [p.get("name") for p in force.find("PerBondParameters")] + + # Get all the bond parameters. + bonds = force.find("Bonds").findall("Bond") + + # Get the list of atoms. + atoms = mols.atoms() + + # Loop over all bonds. + for bond in bonds: + # Get the atoms involved in the bond. + atom_i = atoms[int(bond.get("p1"))] + atom_j = atoms[int(bond.get("p2"))] + + # Set the parameters for this bond. + setattr(module, parameters[0], float(bond.get("param1"))) + setattr(module, parameters[1], float(bond.get("param2"))) + setattr(module, parameters[2], float(bond.get("param3"))) + setattr(module, parameters[3], float(bond.get("param4"))) + setattr(module, parameters[4], float(bond.get("param5"))) + + # Get the distance between the particles. + r = measure(atom_i, atom_j).to(nanometer) + + # Evaluate the energy term by term. + for term in terms: + # Replace any instances of ^ with **. + term = term.replace("^", "**") + + # Split the term into the result and the expression. + result, expression = term.split("=") + + # Evaluate the expression. + setattr(module, result, eval(expression)) + + # Give energies units. + coul_nrg = module.coul_nrg * kJ_per_mol + lj_nrg = module.lj_nrg * kJ_per_mol + + # Append the results for this bond. + results.append(((atom_i, atom_j), (coul_nrg, lj_nrg))) + + # Return the results. + return results From 3d9fe403bb96522b5e595d1f1212bb99afd5c448 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 30 Sep 2024 11:03:22 +0100 Subject: [PATCH 411/468] Update CHANGELOG. [ci skip] --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 2512c46b1..5509f7d58 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -29,6 +29,8 @@ organisation on `GitHub `__. * Fixed buffer overflow when computing molecule indices to excluded to/from ghost atom interactions. * Fixed calculation of ``delta^2`` in soft-core Couloumb potential. * Excluded to/from ghost atom interactions from ``ghost_14ff``. +* Fixed description of soft-core alpha parameter in tutorial. +* Added debugging function to evaluate custom forces in OpenMM XML files. `2024.2.0 `__ - June 2024 From 4fcce0f04381df4c1b0d3450ca56dfe4db2f2bb4 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 30 Sep 2024 11:13:56 +0100 Subject: [PATCH 412/468] Return pairs and energy components separately. [ci skip] --- src/sire/morph/_xml.py | 24 ++++++++++++++++++------ 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/src/sire/morph/_xml.py b/src/sire/morph/_xml.py index f0412d55a..3128f8a5a 100644 --- a/src/sire/morph/_xml.py +++ b/src/sire/morph/_xml.py @@ -25,8 +25,14 @@ def evaluate_xml_force(mols, xml, force): Returns ------- - [((sire.mol.Atom, sr.mol.Atom), (sr.units.GeneralUnit, sr.units.GeneralUnit))] - The atom pairs and pairwise Coulomb and Lennard-Jones energies. + pairs : [(sire.mol.Atom, sire.mol.Atom)] + The atom pairs that interacted. + + nrg_coul : [sr.units.GeneralUnit] + The Coulomb energies for each atom pair. + + nrg_lj : [sr.units.GeneralUnit] + The Lennard-Jones energies for each atom pair. """ from math import sqrt @@ -103,7 +109,9 @@ def evaluate_xml_force(mols, xml, force): terms = list(reversed(force.get("energy").split(";")[1:-1])) # Create a list to store the results. - results = [] + pairs = [] + nrg_coul_list = [] + nrg_lj_list = [] # CustomNonbondedForce: ghost-ghost or ghost-nonghost. if name == "CustomNonbondedForce": @@ -205,7 +213,9 @@ def evaluate_xml_force(mols, xml, force): lj_nrg = module.lj_nrg * kJ_per_mol # Append the results for this pair. - results.append(((atom_i, atom_j), (coul_nrg, lj_nrg))) + pairs.append((atom_i, atom_j)) + nrg_coul_list.append(coul_nrg) + nrg_lj_list.append(lj_nrg) # CustomBondForce: ghost-14. else: @@ -250,7 +260,9 @@ def evaluate_xml_force(mols, xml, force): lj_nrg = module.lj_nrg * kJ_per_mol # Append the results for this bond. - results.append(((atom_i, atom_j), (coul_nrg, lj_nrg))) + pairs.append((atom_i, atom_j)) + nrg_coul_list.append(coul_nrg) + nrg_lj_list.append(lj_nrg) # Return the results. - return results + return pairs, nrg_coul_list, nrg_lj_list From 998293230439472dd86f3e783cdc2cb777c88a32 Mon Sep 17 00:00:00 2001 From: Matthew Date: Mon, 30 Sep 2024 16:15:20 +0100 Subject: [PATCH 413/468] Replica exchange now has the correct signs --- src/sire/morph/_repex.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/sire/morph/_repex.py b/src/sire/morph/_repex.py index dd0e80c5a..6818022ba 100644 --- a/src/sire/morph/_repex.py +++ b/src/sire/morph/_repex.py @@ -95,7 +95,7 @@ def replica_exchange( beta1 = 1.0 / (k_boltz * temperature1) if not ensemble0.is_constant_pressure(): - delta = beta1 * (nrgs1[0] - nrgs1[1]) + beta0 * (nrgs0[0] - nrgs0[1]) + delta = beta1 * (nrgs1[1] - nrgs1[0]) + beta0 * (nrgs0[0] - nrgs0[1]) else: volume0 = replica0.current_space().volume() volume1 = replica1.current_space().volume() @@ -103,9 +103,10 @@ def replica_exchange( pressure0 = ensemble0.pressure() pressure1 = ensemble1.pressure() - delta = beta1 * ( - nrgs1[0] - nrgs1[1] + (pressure1 * (volume1 - volume0) * N_A) - ) + beta0 * (nrgs0[0] - nrgs0[1] + (pressure0 * (volume0 - volume1) * N_A)) + delta = -1.0 * ( + beta1 * (nrgs1[0] - nrgs1[1] + (pressure1 * (volume1 - volume0) * N_A)) + + beta0 * (nrgs0[1] - nrgs0[0] + (pressure0 * (volume0 - volume1) * N_A)) + ) from math import exp From af242974c1d10d622d8132a8598a73d32cfac675 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 2 Oct 2024 15:03:37 +0100 Subject: [PATCH 414/468] Add timeout to OpenMM minimiser. [closes #230] --- src/sire/mol/_dynamics.py | 14 ++++++++ src/sire/mol/_minimisation.py | 4 +++ .../_SireOpenMM_free_functions.pypp.cpp | 4 +-- wrapper/Convert/SireOpenMM/openmmminimise.cpp | 34 ++++++++++++++++++- wrapper/Convert/SireOpenMM/openmmminimise.h | 3 +- wrapper/Convert/__init__.py | 2 ++ 6 files changed, 57 insertions(+), 4 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 71c98b52c..4cc7544d2 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -586,6 +586,7 @@ def run_minimisation( starting_k: float = 100.0, ratchet_scale: float = 2.0, max_constraint_error: float = 0.001, + timeout: str = "60s", ): """ Internal method that runs minimisation on the molecules. @@ -619,12 +620,24 @@ def run_minimisation( - starting_k (float): The starting value of k for the minimisation - ratchet_scale (float): The amount to scale k at each ratchet - max_constraint_error (float): The maximum error in the constraint in nm + - timeout (float): The maximum time to run the minimisation for in seconds. + A value of <=0 will disable the timeout. """ from ..legacy.Convert import minimise_openmm_context if max_iterations <= 0: max_iterations = 0 + try: + from ..units import second + from .. import u + + timeout = u(timeout) + if not timeout.has_same_units(second): + raise ValueError("'timeout' must have units of time") + except: + raise ValueError("Unable to parse 'timeout' as a time") + self._minimisation_log = minimise_openmm_context( self._omm_mols, tolerance=tolerance, @@ -635,6 +648,7 @@ def run_minimisation( starting_k=starting_k, ratchet_scale=ratchet_scale, max_constraint_error=max_constraint_error, + timeout=timeout.to(second), ) def _rebuild_and_minimise(self): diff --git a/src/sire/mol/_minimisation.py b/src/sire/mol/_minimisation.py index 514523f69..969286c95 100644 --- a/src/sire/mol/_minimisation.py +++ b/src/sire/mol/_minimisation.py @@ -96,6 +96,7 @@ def run( starting_k: float = 400.0, ratchet_scale: float = 10.0, max_constraint_error: float = 0.001, + timeout: str = "60s", ): """ Internal method that runs minimisation on the molecules. @@ -129,6 +130,8 @@ def run( - starting_k (float): The starting value of k for the minimisation - ratchet_scale (float): The amount to scale k at each ratchet - max_constraint_error (float): The maximum error in the constraint in nm + - timeout (float): The maximum time to run the minimisation for in seconds. + A value of <=0 will disable the timeout. """ if not self._d.is_null(): self._d.run_minimisation( @@ -140,6 +143,7 @@ def run( starting_k=starting_k, ratchet_scale=ratchet_scale, max_constraint_error=max_constraint_error, + timeout=timeout, ) return self diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp index e75947576..995a5bdf9 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp @@ -2143,13 +2143,13 @@ void register_free_functions(){ { //::SireOpenMM::minimise_openmm_context - typedef ::QString ( *minimise_openmm_context_function_type )( ::OpenMM::Context &,double,int,int,int,int,double,double,double ); + typedef ::QString ( *minimise_openmm_context_function_type )( ::OpenMM::Context &,double,int,int,int,int,double,double,double,double ); minimise_openmm_context_function_type minimise_openmm_context_function_value( &::SireOpenMM::minimise_openmm_context ); bp::def( "minimise_openmm_context" , minimise_openmm_context_function_value - , ( bp::arg("context"), bp::arg("tolerance")=10., bp::arg("max_iterations")=(int)(-1), bp::arg("max_restarts")=(int)(10), bp::arg("max_ratchets")=(int)(20), bp::arg("ratchet_frequency")=(int)(500), bp::arg("starting_k")=100., bp::arg("ratchet_scale")=2., bp::arg("max_constraint_error")=0.01 ) + , ( bp::arg("context"), bp::arg("tolerance")=10., bp::arg("max_iterations")=(int)(-1), bp::arg("max_restarts")=(int)(10), bp::arg("max_ratchets")=(int)(20), bp::arg("ratchet_frequency")=(int)(500), bp::arg("starting_k")=100., bp::arg("ratchet_scale")=2., bp::arg("max_constraint_error")=0.01, bp::arg("timeout")=60. ) , "This is a minimiser heavily inspired by the\nLocalEnergyMinimizer included in OpenMM. This is re-written\nfor sire to;\n\n1. Better integrate minimisation into the sire progress\nmonitoring interupting framework.\n2. Avoid errors caused by OpenMM switching from the desired\ncontext to the CPU context, thus triggering spurious exceptions\nrelated to exclusions exceptions not matching\n\nThis exposes more controls from the underlying minimisation\nlibrary, and also logs events and progress, which is returned\nas a string.\n\nThis raises an exception if minimisation fails.\n" ); } diff --git a/wrapper/Convert/SireOpenMM/openmmminimise.cpp b/wrapper/Convert/SireOpenMM/openmmminimise.cpp index 949b27eb3..7d5fa4045 100644 --- a/wrapper/Convert/SireOpenMM/openmmminimise.cpp +++ b/wrapper/Convert/SireOpenMM/openmmminimise.cpp @@ -42,6 +42,7 @@ // COPIED FROM SO POST - https://stackoverflow.com/questions/570669/checking-if-a-double-or-float-is-nan-in-c +#include #include // std::isnan, std::fpclassify #include #include // std::setw @@ -616,13 +617,18 @@ namespace SireOpenMM int max_restarts, int max_ratchets, int ratchet_frequency, double starting_k, double ratchet_scale, - double max_constraint_error) + double max_constraint_error, double timeout) { if (max_iterations < 0) { max_iterations = std::numeric_limits::max(); } + if (timeout <= 0) + { + timeout = std::numeric_limits::max(); + } + auto gil = SireBase::release_gil(); const OpenMM::System &system = context.getSystem(); @@ -650,6 +656,7 @@ namespace SireOpenMM data.addLog(QString("Minimising with a tolerance of %1").arg(tolerance)); data.addLog(QString("Minimising with constraint tolerance %1").arg(working_constraint_tol)); + data.addLog(QString("Minimising with a timeout of %1 seconds").arg(timeout)); data.addLog(QString("Minimising with k = %1").arg(k)); data.addLog(QString("Minimising with %1 particles").arg(num_particles)); data.addLog(QString("Minimising with a maximum of %1 iterations").arg(max_iterations)); @@ -679,6 +686,9 @@ namespace SireOpenMM int max_linesearch = 100; const int max_linesearch_delta = 100; + // Store the starting time. + auto start_time = std::chrono::high_resolution_clock::now(); + while (data.getIteration() < data.getMaxIterations()) { if (not is_success) @@ -686,6 +696,16 @@ namespace SireOpenMM // try one more time with the real starting positions if (not have_hard_reset) { + // Check the current time and see if we've exceeded the timeout. + auto current_time = std::chrono::high_resolution_clock::now(); + auto elapsed_time = std::chrono::duration_cast(current_time - start_time).count(); + + if (elapsed_time > timeout) + { + data.addLog("Minimisation timed out!"); + break; + } + data.hardReset(); context.setPositions(starting_pos); @@ -709,6 +729,7 @@ namespace SireOpenMM } } + data.addLog(QString("Minimisation loop - %1 steps from %2").arg(data.getIteration()).arg(data.getMaxIterations())); try @@ -762,6 +783,17 @@ namespace SireOpenMM // Repeatedly minimize, steadily increasing the strength of the springs until all constraints are satisfied. while (data.getIteration() < data.getMaxIterations()) { + // Check the current time and see if we've exceeded the timeout. + auto current_time = std::chrono::high_resolution_clock::now(); + auto elapsed_time = std::chrono::duration_cast(current_time - start_time).count(); + + if (elapsed_time > timeout) + { + data.addLog("Minimisation timed out!"); + is_success = false; + break; + } + param.max_iterations = data.getMaxIterations() - data.getIteration(); lbfgsfloatval_t fx; // final energy auto last_it = data.getIteration(); diff --git a/wrapper/Convert/SireOpenMM/openmmminimise.h b/wrapper/Convert/SireOpenMM/openmmminimise.h index 3e8a04a84..ab8b6c247 100644 --- a/wrapper/Convert/SireOpenMM/openmmminimise.h +++ b/wrapper/Convert/SireOpenMM/openmmminimise.h @@ -33,7 +33,8 @@ namespace SireOpenMM int ratchet_frequency = 500, double starting_k = 100.0, double ratchet_scale = 2.0, - double max_constraint_error = 0.01); + double max_constraint_error = 0.01, + double timeout = 60.0); } diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index cf71f3f31..d3edce1bf 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -492,6 +492,7 @@ def minimise_openmm_context( starting_k: float = 100.0, ratchet_scale: float = 2.0, max_constraint_error: float = 0.01, + timeout: str = "60s", ): return _minimise_openmm_context( context, @@ -503,6 +504,7 @@ def minimise_openmm_context( starting_k=starting_k, ratchet_scale=ratchet_scale, max_constraint_error=max_constraint_error, + timeout=timeout, ) except Exception as e: From 9c9bc3278d4cfe155ea7e22fe865cf0664d2cfa7 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 2 Oct 2024 15:05:03 +0100 Subject: [PATCH 415/468] Expose pickle operator on LambdaLever. --- wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp index 85786b4a2..b019312b6 100644 --- a/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/LambdaLever.pypp.cpp @@ -35,6 +35,8 @@ SireOpenMM::LambdaLever __copy__(const SireOpenMM::LambdaLever &other){ return S #include "Helpers/release_gil_policy.hpp" +#include "Qt/qdatastream.hpp" + void register_LambdaLever_class(){ { //::SireOpenMM::LambdaLever @@ -275,6 +277,7 @@ void register_LambdaLever_class(){ LambdaLever_exposer.staticmethod( "typeName" ); LambdaLever_exposer.def( "__copy__", &__copy__); LambdaLever_exposer.def( "__deepcopy__", &__copy__); + LambdaLever_exposer.def_pickle(sire_pickle_suite< ::SireOpenMM::LambdaLever >()); LambdaLever_exposer.def( "clone", &__copy__); LambdaLever_exposer.def( "__str__", &__str__< ::SireOpenMM::LambdaLever > ); LambdaLever_exposer.def( "__repr__", &__str__< ::SireOpenMM::LambdaLever > ); From 0162be36e86a0beb63a20e866d8d0ff7bee48686 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 2 Oct 2024 15:30:22 +0100 Subject: [PATCH 416/468] Remove debugging statement. [ci skip] --- wrapper/Convert/SireOpenMM/openmmminimise.cpp | 1 - 1 file changed, 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/openmmminimise.cpp b/wrapper/Convert/SireOpenMM/openmmminimise.cpp index 7d5fa4045..aa84026ad 100644 --- a/wrapper/Convert/SireOpenMM/openmmminimise.cpp +++ b/wrapper/Convert/SireOpenMM/openmmminimise.cpp @@ -1095,7 +1095,6 @@ namespace SireOpenMM { data.addLog("Minimisation failed!"); bar.failure("Minimisation failed! Could not satisfy constraints!"); - qDebug() << data.getLog().join("\n"); throw SireError::invalid_state(QObject::tr( "Despite repeated attempts, the minimiser could not minimise the system " "while simultaneously satisfying the constraints."), From 4c3effa9898b3e2bf1de94e502c04b84a15c5866 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 2 Oct 2024 15:41:15 +0100 Subject: [PATCH 417/468] Update CHANGELOG. [ci skip] --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 5509f7d58..209277b11 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -31,6 +31,8 @@ organisation on `GitHub `__. * Excluded to/from ghost atom interactions from ``ghost_14ff``. * Fixed description of soft-core alpha parameter in tutorial. * Added debugging function to evaluate custom forces in OpenMM XML files. +* Added a timeout to the OpenMM minimiser function. +* Exposed the pickle operator on the LambdaLever class. `2024.2.0 `__ - June 2024 From 9d520c9e295997f9653e0db49e423bde381e14e0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 3 Oct 2024 12:52:11 +0100 Subject: [PATCH 418/468] Increase default minimiser timeout. [ci skip] --- src/sire/mol/_dynamics.py | 2 +- src/sire/mol/_minimisation.py | 2 +- wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp | 2 +- wrapper/Convert/SireOpenMM/openmmminimise.h | 2 +- wrapper/Convert/__init__.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 4cc7544d2..383a74631 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -586,7 +586,7 @@ def run_minimisation( starting_k: float = 100.0, ratchet_scale: float = 2.0, max_constraint_error: float = 0.001, - timeout: str = "60s", + timeout: str = "300s", ): """ Internal method that runs minimisation on the molecules. diff --git a/src/sire/mol/_minimisation.py b/src/sire/mol/_minimisation.py index 969286c95..32e3dc8f9 100644 --- a/src/sire/mol/_minimisation.py +++ b/src/sire/mol/_minimisation.py @@ -96,7 +96,7 @@ def run( starting_k: float = 400.0, ratchet_scale: float = 10.0, max_constraint_error: float = 0.001, - timeout: str = "60s", + timeout: str = "300s", ): """ Internal method that runs minimisation on the molecules. diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp index 995a5bdf9..21d3bd539 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM_free_functions.pypp.cpp @@ -2149,7 +2149,7 @@ void register_free_functions(){ bp::def( "minimise_openmm_context" , minimise_openmm_context_function_value - , ( bp::arg("context"), bp::arg("tolerance")=10., bp::arg("max_iterations")=(int)(-1), bp::arg("max_restarts")=(int)(10), bp::arg("max_ratchets")=(int)(20), bp::arg("ratchet_frequency")=(int)(500), bp::arg("starting_k")=100., bp::arg("ratchet_scale")=2., bp::arg("max_constraint_error")=0.01, bp::arg("timeout")=60. ) + , ( bp::arg("context"), bp::arg("tolerance")=10., bp::arg("max_iterations")=(int)(-1), bp::arg("max_restarts")=(int)(10), bp::arg("max_ratchets")=(int)(20), bp::arg("ratchet_frequency")=(int)(500), bp::arg("starting_k")=100., bp::arg("ratchet_scale")=2., bp::arg("max_constraint_error")=0.01, bp::arg("timeout")=300. ) , "This is a minimiser heavily inspired by the\nLocalEnergyMinimizer included in OpenMM. This is re-written\nfor sire to;\n\n1. Better integrate minimisation into the sire progress\nmonitoring interupting framework.\n2. Avoid errors caused by OpenMM switching from the desired\ncontext to the CPU context, thus triggering spurious exceptions\nrelated to exclusions exceptions not matching\n\nThis exposes more controls from the underlying minimisation\nlibrary, and also logs events and progress, which is returned\nas a string.\n\nThis raises an exception if minimisation fails.\n" ); } diff --git a/wrapper/Convert/SireOpenMM/openmmminimise.h b/wrapper/Convert/SireOpenMM/openmmminimise.h index ab8b6c247..b9a09e073 100644 --- a/wrapper/Convert/SireOpenMM/openmmminimise.h +++ b/wrapper/Convert/SireOpenMM/openmmminimise.h @@ -34,7 +34,7 @@ namespace SireOpenMM double starting_k = 100.0, double ratchet_scale = 2.0, double max_constraint_error = 0.01, - double timeout = 60.0); + double timeout = 300.0); } diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index d3edce1bf..ffd82899d 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -492,7 +492,7 @@ def minimise_openmm_context( starting_k: float = 100.0, ratchet_scale: float = 2.0, max_constraint_error: float = 0.01, - timeout: str = "60s", + timeout: str = "300s", ): return _minimise_openmm_context( context, From d4f7e83a7208943dadf5b1389b64b2de62b71212 Mon Sep 17 00:00:00 2001 From: Matthew Date: Fri, 4 Oct 2024 15:14:23 +0100 Subject: [PATCH 419/468] Multiply out -1 to simplify expression --- src/sire/morph/_repex.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/sire/morph/_repex.py b/src/sire/morph/_repex.py index 6818022ba..d350a4870 100644 --- a/src/sire/morph/_repex.py +++ b/src/sire/morph/_repex.py @@ -103,10 +103,9 @@ def replica_exchange( pressure0 = ensemble0.pressure() pressure1 = ensemble1.pressure() - delta = -1.0 * ( - beta1 * (nrgs1[0] - nrgs1[1] + (pressure1 * (volume1 - volume0) * N_A)) - + beta0 * (nrgs0[1] - nrgs0[0] + (pressure0 * (volume0 - volume1) * N_A)) - ) + delta = beta1 * ( + nrgs1[1] - nrgs1[0] - (pressure1 * (volume1 - volume0) * N_A) + ) + beta0 * (nrgs0[0] - nrgs0[1] - (pressure0 * (volume0 - volume1) * N_A)) from math import exp From 03b7b902c3c4af889af3ad075b9151c2a1b0721e Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 4 Oct 2024 16:36:35 +0100 Subject: [PATCH 420/468] Fix sign in volume correction term. [ci skip] --- src/sire/morph/_repex.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/sire/morph/_repex.py b/src/sire/morph/_repex.py index d350a4870..8edbd6057 100644 --- a/src/sire/morph/_repex.py +++ b/src/sire/morph/_repex.py @@ -104,8 +104,8 @@ def replica_exchange( pressure1 = ensemble1.pressure() delta = beta1 * ( - nrgs1[1] - nrgs1[0] - (pressure1 * (volume1 - volume0) * N_A) - ) + beta0 * (nrgs0[0] - nrgs0[1] - (pressure0 * (volume0 - volume1) * N_A)) + (nrgs1[1] - nrgs1[0]) + (pressure1 * (volume1 - volume0) * N_A) + ) + beta0 * ((nrgs0[0] - nrgs0[1]) + (pressure0 * (volume0 - volume1) * N_A)) from math import exp From fe30263a3d5cb81a0d328678f3d5baa834a53e24 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 8 Oct 2024 12:15:04 +0100 Subject: [PATCH 421/468] Re-calculate energy after constraint projection. [closes #241] [ci skip] --- wrapper/Convert/SireOpenMM/openmmminimise.cpp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/wrapper/Convert/SireOpenMM/openmmminimise.cpp b/wrapper/Convert/SireOpenMM/openmmminimise.cpp index aa84026ad..7253b6ca6 100644 --- a/wrapper/Convert/SireOpenMM/openmmminimise.cpp +++ b/wrapper/Convert/SireOpenMM/openmmminimise.cpp @@ -1025,6 +1025,10 @@ namespace SireOpenMM // to the full precision requested by the user. context.applyConstraints(working_constraint_tol); + // Recalculate the energy after the constraints have been applied. + energy_before = energy_after; + energy_after = context.getState(OpenMM::State::Energy).getPotentialEnergy(); + const auto delta_energy = energy_after - energy_before; data.addLog(QString("Change in energy: %1 kJ mol-1").arg(delta_energy)); From 18cb0524dff3f3dde2d18bcbd72bde3324d634c6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Tue, 8 Oct 2024 12:42:23 +0100 Subject: [PATCH 422/468] Update minimisation log message. [ci skip] --- wrapper/Convert/SireOpenMM/openmmminimise.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wrapper/Convert/SireOpenMM/openmmminimise.cpp b/wrapper/Convert/SireOpenMM/openmmminimise.cpp index 7253b6ca6..dd5a5f536 100644 --- a/wrapper/Convert/SireOpenMM/openmmminimise.cpp +++ b/wrapper/Convert/SireOpenMM/openmmminimise.cpp @@ -1031,7 +1031,7 @@ namespace SireOpenMM const auto delta_energy = energy_after - energy_before; - data.addLog(QString("Change in energy: %1 kJ mol-1").arg(delta_energy)); + data.addLog(QString("Change in energy following constraint projection: %1 kJ mol-1").arg(delta_energy)); if (std::abs(delta_energy) < 1000.0) { From 481afe11636c36fd9593b67242736dd35e9e6b87 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 09:16:54 +0100 Subject: [PATCH 423/468] Clear OpenMM state when minimising. [closes #242] --- src/sire/mol/_dynamics.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 383a74631..ea9845df5 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -99,8 +99,7 @@ def __init__(self, mols=None, map=None, **kwargs): from ..convert import to self._omm_mols = to(self._sire_mols, "openmm", map=self._map) - self._omm_state = None - self._omm_state_has_cv = (False, False) + self._clear_state() if self._ffinfo.space().is_periodic(): self._enforce_periodic_box = True @@ -174,8 +173,7 @@ def _enter_dynamics_block(self): raise SystemError("Cannot start dynamics while it is already running!") self._is_running = True - self._omm_state = None - self._omm_state_has_cv = (False, False) + self._clear_state() def _exit_dynamics_block( self, @@ -559,8 +557,7 @@ def step(self, num_steps: int = 1): if self._is_running: raise SystemError("Cannot step dynamics while it is already running!") - self._omm_state = None - self._omm_state_has_cv = (False, False) + self._clear_state() self._omm_mols.getIntegrator().step(num_steps) @@ -638,6 +635,8 @@ def run_minimisation( except: raise ValueError("Unable to parse 'timeout' as a time") + self._clear_state() + self._minimisation_log = minimise_openmm_context( self._omm_mols, tolerance=tolerance, @@ -976,8 +975,7 @@ class NeedsMinimiseError(Exception): # try to fix this problem by minimising, # then running again self._is_running = False - self._omm_state = None - self._omm_state_has_cv = (False, False) + self._clear_state() self._rebuild_and_minimise() orig_args["auto_fix_minimise"] = False self.run(**orig_args) From 0d2297c71a537c678ea49f26bb98ab6192b082df Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 09:17:25 +0100 Subject: [PATCH 424/468] Update CHANGELOG. --- doc/source/changelog.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index de68c5a17..41d3fe077 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -35,6 +35,8 @@ organisation on `GitHub `__. * Exposed the pickle operator on the LambdaLever class. * Fix issues with positionally restrained atoms in perturbable systems. * Fix exchange probability equations in ``sire.morph.replica_exchange`` function. +* Fix calculation of energy change following final constraint projection after energy minimisation. +* Clear internal OpenMM state from dynamics object following a successful minimisation. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From f4c68dea7b8b6df292c201f4541c47d60edd6949 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 13:46:10 +0100 Subject: [PATCH 425/468] Add xfail unit test for crazy constraint bug. [ci skip] --- tests/convert/test_openmm_constraints.py | 70 ++++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index a8cf77371..a19d27eb8 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -451,3 +451,73 @@ def test_auto_constraints(ala_mols, openmm_platform): constraint[0].atom(0).index(), constraint[0].atom(1).index() ) assert bond in constrained + + +@pytest.mark.xfail(reason="Unresolved bug.") +def test_asymmetric_constraints(): + # This test is for debugging a peculiar issue with one of the perturbations + # from the MCL1 test suite. Here there are no ghost atoms and a single atom + # changes type during the perturbation, from H to Cl. The constraints are + # different for the two end states. Currently, the minimised energy at + # lambda=1 does not match the minimised energy at lambda=0 when the end + # states are swapped. From debugging, it seems that this is the caused by + # calling context.applyConstraints() for the final constraint projection + # following succesful minimisation. It's not clear if the bug lies in Sire, + # or OpenMM. + + from math import isclose + + # Load the MCL1 perturbation. (Perturbable ligand is the last molecule.) + mol = sr.load_test_files("mcl1_60_61.s3")[-1] + + # Create dynamics objects for the forward and backward perturbations. + d_forwards = mol.dynamics( + perturbable_constraint="h_bonds_not_heavy_perturbed", + dynamic_constraints=True, + include_constrained_energies=False, + ) + d_backwards = mol.dynamics( + perturbable_constraint="h_bonds_not_heavy_perturbed", + include_constrained_energies=False, + dynamic_constraints=True, + swap_end_states=True, + ) + + # Set lambda so the dynamics states are equivalent. + d_forwards.set_lambda(1.0, update_constraints=True) + d_backwards.set_lambda(0.0, update_constraints=True) + + # Get the initial potential energies. + nrg_forwards = d_forwards.current_potential_energy().value() + nrg_backwards = d_backwards.current_potential_energy().value() + + # Check the potential energies are the same. + assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-5) + + # Minimise both dynamics objects. + d_forwards.minimise() + d_backwards.minimise() + + # Get the minimisation logs. + log_forwards = d_forwards._d.get_minimisation_log() + log_backwards = d_backwards._d.get_minimisation_log() + + lines_forward = log_forwards.split("\n") + for line in lines_forward: + if "Final energy" in line: + nrg_forwards = float(line.split()[2]) + + lines_backward = log_backwards.split("\n") + for line in lines_backward: + if "Final energy" in line: + nrg_backwards = float(line.split()[2]) + + # Check the final energies from the logs are the same. + assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) + + # Now get the final potential energies. (Post constraint projection.) + nrg_forwards = d_forwards.current_potential_energy().value() + nrg_backwards = d_backwards.current_potential_energy().value() + + # Check the minimised potential energies are the same. + assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) From c0c559a5d628f20e6fab68b91cde48425b3a88af Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 14:18:42 +0100 Subject: [PATCH 426/468] Add missing skipif decorator. --- tests/convert/test_openmm_constraints.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index a19d27eb8..0ed402693 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -453,6 +453,10 @@ def test_auto_constraints(ala_mols, openmm_platform): assert bond in constrained +@pytest.mark.skipif( + "openmm" not in sr.convert.supported_formats(), + reason="openmm support is not available", +) @pytest.mark.xfail(reason="Unresolved bug.") def test_asymmetric_constraints(): # This test is for debugging a peculiar issue with one of the perturbations From b208bf8657d5016dde78296a3229b892b2209a28 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 15:21:42 +0100 Subject: [PATCH 427/468] Default to using no neighbour list. --- doc/source/tutorial/partXX/01_intro.rst | 7 ++++++- src/sire/qm/__init__.py | 7 ++++--- src/sire/qm/_emle.py | 7 ++++--- wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp | 2 +- wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp | 2 +- wrapper/Convert/SireOpenMM/pyqm.h | 2 +- wrapper/Convert/SireOpenMM/torchqm.h | 2 +- 7 files changed, 18 insertions(+), 11 deletions(-) diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/partXX/01_intro.rst index e0e3ef161..8ff871d5b 100644 --- a/doc/source/tutorial/partXX/01_intro.rst +++ b/doc/source/tutorial/partXX/01_intro.rst @@ -76,7 +76,12 @@ embedding is used, the electrostatics are treated at the MM level by ``OpenMM``. Note that this doesn't change the signature of the callback function, i.e. it will be passed empty lists for the MM specific arguments and should return an empty list for the MM forces. Atomic positions passed to the callback function -will already be unwrapped with the QM region in the center. +will already be unwrapped with the QM region in the center. By default, no +neighbour list will be used. (The same thing can be achieved by passing +``neighbour_list_frequency=0``.) This is useful when using the engine as +a calculator for different input structures, where there may be no correlation +between coordinates. For regular molecular dynamics simulations, setting a +non-zero neighbour list frequency can improve performance. The ``create_engine`` function returns a modified version of the molecules containing a "merged" dipeptide that can be interpolated between MM and QM diff --git a/src/sire/qm/__init__.py b/src/sire/qm/__init__.py index 3137d1401..cb79a420a 100644 --- a/src/sire/qm/__init__.py +++ b/src/sire/qm/__init__.py @@ -16,7 +16,7 @@ def create_engine( py_object, callback=None, cutoff="7.5A", - neighbour_list_frequency=20, + neighbour_list_frequency=0, mechanical_embedding=False, redistribute_charge=False, map=None, @@ -55,8 +55,9 @@ def create_engine( cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. - neighbour_list_frequency : int, optional, default=20 - The frequency with which to update the neighbour list. + neighbour_list_frequency : int, optional, default=0 + The frequency with which to update the neighbour list. A value of + zero means that no neighbour list will be used. mechanical_embedding: bool, optional, default=False Whether to use mechanical embedding. If True, then electrostatics will diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index 769046d58..c370350a8 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -108,7 +108,7 @@ def emle( qm_atoms, calculator, cutoff="7.5A", - neighbour_list_frequency=20, + neighbour_list_frequency=0, redistribute_charge=False, map=None, ): @@ -133,8 +133,9 @@ def emle( cutoff : str or sire.legacy.Units.GeneralUnit, optional, default="7.5A" The cutoff to use for the QM/MM calculation. - neighbour_list_frequency : int, optional, default=20 - The frequency with which to update the neighbour list. + neighbour_list_frequency : int, optional, default=0 + The frequency with which to update the neighbour list. A value of + zero means that no neighbour list will be used. redistribute_charge : bool Whether to redistribute charge of the QM atoms to ensure that the total diff --git a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp index 1b2780dfc..45708bb7e 100644 --- a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp @@ -63,7 +63,7 @@ void register_PyQMEngine_class(){ typedef bp::class_< SireOpenMM::PyQMEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > PyQMEngine_exposer_t; PyQMEngine_exposer_t PyQMEngine_exposer = PyQMEngine_exposer_t( "PyQMEngine", "", bp::init< >("Default constructor.") ); bp::scope PyQMEngine_scope( PyQMEngine_exposer ); - PyQMEngine_exposer.def( bp::init< bp::api::object, bp::optional< QString, SireUnits::Dimension::Length, int, bool, double > >(( bp::arg("arg0"), bp::arg("method")="", bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("is_mechanical")=(bool)(false), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nA Python object.\n\nPar:am name\nThe name of the callback method. If empty, then the object is\nassumed to be a callable.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); + PyQMEngine_exposer.def( bp::init< bp::api::object, bp::optional< QString, SireUnits::Dimension::Length, int, bool, double > >(( bp::arg("arg0"), bp::arg("method")="", bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(0), bp::arg("is_mechanical")=(bool)(false), bp::arg("lambda")=1. ), "Constructor\nPar:am py_object\nA Python object.\n\nPar:am name\nThe name of the callback method. If empty, then the object is\nassumed to be a callable.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); PyQMEngine_exposer.def( bp::init< SireOpenMM::PyQMEngine const & >(( bp::arg("other") ), "Copy constructor.") ); { //::SireOpenMM::PyQMEngine::call diff --git a/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp index 8a5676264..29847e98d 100644 --- a/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/TorchQMEngine.pypp.cpp @@ -51,7 +51,7 @@ void register_TorchQMEngine_class(){ typedef bp::class_< SireOpenMM::TorchQMEngine, bp::bases< SireBase::Property, SireOpenMM::QMEngine > > TorchQMEngine_exposer_t; TorchQMEngine_exposer_t TorchQMEngine_exposer = TorchQMEngine_exposer_t( "TorchQMEngine", "", bp::init< >("Default constructor.") ); bp::scope TorchQMEngine_scope( TorchQMEngine_exposer ); - TorchQMEngine_exposer.def( bp::init< QString, bp::optional< SireUnits::Dimension::Length, int, bool, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(20), bp::arg("is_mechanical")=(bool)(false), bp::arg("lambda")=1. ), "Constructor\nPar:am module_path\nThe path to the serialised TorchScript module.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); + TorchQMEngine_exposer.def( bp::init< QString, bp::optional< SireUnits::Dimension::Length, int, bool, double > >(( bp::arg("arg0"), bp::arg("cutoff")=7.5 * SireUnits::angstrom, bp::arg("neighbour_list_frequency")=(int)(0), bp::arg("is_mechanical")=(bool)(false), bp::arg("lambda")=1. ), "Constructor\nPar:am module_path\nThe path to the serialised TorchScript module.\n\nPar:am cutoff\nThe ML cutoff distance.\n\nPar:am neighbour_list_frequency\nThe frequency at which the neighbour list is updated. (Number of steps.)\nIf zero, then no neighbour list is used.\n\nPar:am is_mechanical\nA flag to indicate if mechanical embedding is being used.\n\nPar:am lambda\nThe lambda weighting factor. This can be used to interpolate between\npotentials for end-state correction calculations.\n") ); TorchQMEngine_exposer.def( bp::init< SireOpenMM::TorchQMEngine const & >(( bp::arg("other") ), "Copy constructor.") ); { //::SireOpenMM::TorchQMEngine::getModulePath diff --git a/wrapper/Convert/SireOpenMM/pyqm.h b/wrapper/Convert/SireOpenMM/pyqm.h index 7088a1b9a..016cd2744 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.h +++ b/wrapper/Convert/SireOpenMM/pyqm.h @@ -404,7 +404,7 @@ namespace SireOpenMM bp::object, QString method="", SireUnits::Dimension::Length cutoff=7.5*SireUnits::angstrom, - int neighbour_list_frequency=20, + int neighbour_list_frequency=0, bool is_mechanical=false, double lambda=1.0 ); diff --git a/wrapper/Convert/SireOpenMM/torchqm.h b/wrapper/Convert/SireOpenMM/torchqm.h index 314ce99dd..2d631cfd1 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.h +++ b/wrapper/Convert/SireOpenMM/torchqm.h @@ -318,7 +318,7 @@ namespace SireOpenMM TorchQMEngine( QString module_path, SireUnits::Dimension::Length cutoff=7.5*SireUnits::angstrom, - int neighbour_list_frequency=20, + int neighbour_list_frequency=0, bool is_mechanical=false, double lambda=1.0 ); From efc3c3c67a057d7b4405c0c22f1c5dfa5ac76b98 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 15:40:05 +0100 Subject: [PATCH 428/468] Remove non-working CustomCPPForceImpl support CMake check. --- wrapper/Convert/SireOpenMM/CMakeLists.txt | 35 ++++------------------- 1 file changed, 5 insertions(+), 30 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 5894fe0a8..0428f8ef1 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -25,33 +25,11 @@ if (${SIRE_USE_OPENMM}) # Other python wrapping directories include_directories(${CMAKE_SOURCE_DIR}) - #include(CheckCXXSourceRuns) + # We're only building against OpenMM 8.1+, so include CustomCPPForce support. + add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") - # Temporarily add OpenMM include directory to CMAKE_REQUIRED_INCLUDES. - #set(CMAKE_OLD_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES}) - #set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${OpenMM_INCLUDE_DIR}) - - # Whether or not we have CustomCPPForceImpl (OpenMM 8.1+) - #CHECK_CXX_SOURCE_RUNS(" - #include \"openmm/internal/ContextImpl.h\" - #include \"openmm/internal/CustomCPPForceImpl.h\" - - # int main() - #{ - # OpenMM::ContextImpl* context = NULL; - # OpenMM::CustomCPPForceImpl* force = NULL; - # return 0; - #}" - #CAN_USE_CUSTOMCPPFORCE) - - # Restore CMAKE_REQUIRED_INCLUDES. - #set(CMAKE_REQUIRED_INCLUDES ${CMAKE_OLD_REQUIRED_INCLUDES}) - - #if (CAN_USE_CUSTOMCPPFORCE) - message(STATUS "OpenMM version supports CustomCPPForce") - add_definitions("-DSIRE_USE_CUSTOMCPPFORCE") - - if (NOT DEFINED ENV{SIRE_NO_TORCH}) + # Check to see if Torch support has been disabled. + if (NOT DEFINED ENV{SIRE_NO_TORCH}) find_package(Torch) if (TORCH_FOUND) message(STATUS "Torch found") @@ -60,10 +38,7 @@ if (${SIRE_USE_OPENMM}) else() message(STATUS "Torch not found") endif() - endif() - #else() - #message(STATUS "OpenMM version does not support CustomCPPForce") - #endif() + endif() # Check to see if we have support for updating some parameters in context include(CheckCXXSourceCompiles) From 136a47e86689cdf0e77cb8dc322fedf553e81c58 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 16:19:48 +0100 Subject: [PATCH 429/468] Add conditions to emle requirements. --- requirements_emle.txt | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/requirements_emle.txt b/requirements_emle.txt index 68dc7083d..a3c1d6df8 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -1,14 +1,14 @@ -ambertools +ambertools >= 22 ; sys_platform != "win32" ase -deepmd-kit +deepmd-kit ; platform_machine != "aarch64" and sys_platform != "win32" loguru -nnpops +nnpops ; platform_machine != "aarch64" and sys_platform != "win32" pygit2 pytorch python pyyaml -torchani -xtb-python +torchani ; sys_platform != "win32" and (sys_platform != "linux" and platform_machine != "aarch64") +xtb-python ; sys_platform != "win32" gcc< 13 ; sys_platform == "linux" gxx< 13 ; sys_platform == "linux" From c312a5efbf7db69d768bba1f4a0dcdb97ed40eee Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 16:24:30 +0100 Subject: [PATCH 430/468] Try full platform and variant build to check for failures. --- .github/workflows/emle.yaml | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 39366ac7d..7728349e6 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -21,13 +21,24 @@ jobs: name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) runs-on: ${{ matrix.platform.os }} strategy: - max-parallel: 9 + max-parallel: 6 fail-fast: false matrix: - python-version: ["3.10", "3.11"] + python-version: ["3.10", "3.11", "3.12"] platform: + - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + exclude: + # Exclude all but the latest Python from all + # but Linux + - platform: + { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11 + - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } + python-version: "3.10" + - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } + python-version: "3.11" environment: name: sire-build defaults: From 127e2181f8d1f39d4886c54815d3af6878e81799 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 16:32:37 +0100 Subject: [PATCH 431/468] PyTorch is unavailable on Windows. --- requirements_emle.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_emle.txt b/requirements_emle.txt index a3c1d6df8..e6521e4cf 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -4,7 +4,7 @@ deepmd-kit ; platform_machine != "aarch64" and sys_platform != "win32" loguru nnpops ; platform_machine != "aarch64" and sys_platform != "win32" pygit2 -pytorch +pytorch ; sys_platform != "win32" python pyyaml torchani ; sys_platform != "win32" and (sys_platform != "linux" and platform_machine != "aarch64") From 9987e500a6f9ea5c2d76403b3b47734a21c71f47 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 16:37:32 +0100 Subject: [PATCH 432/468] Crudely disable Torch support on Windows for now. --- setup.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/setup.py b/setup.py index 128607fcc..568fdaa92 100644 --- a/setup.py +++ b/setup.py @@ -27,6 +27,10 @@ import shutil import glob +# Disable Torch support if using Windows. +if platform.system() == "Windows": + os.environ["SIRE_NO_TORCH"] = 1 + try: # We have to check the version, but we can't do this by # importing sire (this will block installing of files on From 6493dbfaf9920fa85f087cd635bf6ab721f231d0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 20:33:13 +0100 Subject: [PATCH 433/468] xtb-python causes conflicts for Linux Python 3.12. --- requirements_emle.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_emle.txt b/requirements_emle.txt index e6521e4cf..c88c93010 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -8,7 +8,7 @@ pytorch ; sys_platform != "win32" python pyyaml torchani ; sys_platform != "win32" and (sys_platform != "linux" and platform_machine != "aarch64") -xtb-python ; sys_platform != "win32" +xtb-python ; sys_platform != "win32" and (sys_platform != "linux" and python_version != "3.12") gcc< 13 ; sys_platform == "linux" gxx< 13 ; sys_platform == "linux" From 748eb4df50d36035047632f59e3e3ca0861d2075 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 20:34:17 +0100 Subject: [PATCH 434/468] Windows requries that environment variable is a string. --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 568fdaa92..b55963489 100644 --- a/setup.py +++ b/setup.py @@ -29,7 +29,7 @@ # Disable Torch support if using Windows. if platform.system() == "Windows": - os.environ["SIRE_NO_TORCH"] = 1 + os.environ["SIRE_NO_TORCH"] = "1" try: # We have to check the version, but we can't do this by From 928565679c8123974f521084f5f302eb11801869 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 20:35:56 +0100 Subject: [PATCH 435/468] Try unpinning gcc on Linux. --- requirements_emle.txt | 3 --- 1 file changed, 3 deletions(-) diff --git a/requirements_emle.txt b/requirements_emle.txt index c88c93010..23f445dcd 100644 --- a/requirements_emle.txt +++ b/requirements_emle.txt @@ -9,6 +9,3 @@ python pyyaml torchani ; sys_platform != "win32" and (sys_platform != "linux" and platform_machine != "aarch64") xtb-python ; sys_platform != "win32" and (sys_platform != "linux" and python_version != "3.12") - -gcc< 13 ; sys_platform == "linux" -gxx< 13 ; sys_platform == "linux" From c8ecad7f2118751962cd1cc864d73c7e688620a2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 9 Oct 2024 20:49:04 +0100 Subject: [PATCH 436/468] Only avoid TorchQMForce build for Windows during CI. --- .github/workflows/emle.yaml | 1 + setup.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 7728349e6..2109e5f82 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -48,6 +48,7 @@ jobs: SIRE_DONT_PHONEHOME: 1 SIRE_SILENT_PHONEHOME: 1 SIRE_EMLE: 1 + SIRE_CI: 1 REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # diff --git a/setup.py b/setup.py index b55963489..6c66638b7 100644 --- a/setup.py +++ b/setup.py @@ -27,8 +27,8 @@ import shutil import glob -# Disable Torch support if using Windows. -if platform.system() == "Windows": +# Disable Torch support for Windows during CI builds. +if "SIRE_CI" in os.environ and platform.system() == "Windows": os.environ["SIRE_NO_TORCH"] = "1" try: From 3ad642bc2c41043a56a7711aacfde49ef762718d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 10:03:17 +0100 Subject: [PATCH 437/468] Rework conditional Torch support implementation. --- .github/workflows/emle.yaml | 1 - setup.py | 4 - src/sire/_pythonize.py | 7 +- src/sire/qm/_emle.py | 111 ++++++++---------- wrapper/Convert/SireOpenMM/CMakeLists.txt | 7 -- .../SireOpenMM/SireOpenMM_registrars.cpp | 2 - .../Convert/SireOpenMM/_SireOpenMM.main.cpp | 6 +- wrapper/Convert/SireOpenMM/pyqm.cpp | 12 +- wrapper/Convert/SireOpenMM/torchqm.cpp | 25 ++-- wrapper/Convert/SireOpenMM/torchqm.h | 15 ++- wrapper/Convert/__init__.py | 14 +-- 11 files changed, 92 insertions(+), 112 deletions(-) diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml index 2109e5f82..7728349e6 100644 --- a/.github/workflows/emle.yaml +++ b/.github/workflows/emle.yaml @@ -48,7 +48,6 @@ jobs: SIRE_DONT_PHONEHOME: 1 SIRE_SILENT_PHONEHOME: 1 SIRE_EMLE: 1 - SIRE_CI: 1 REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # diff --git a/setup.py b/setup.py index 6c66638b7..128607fcc 100644 --- a/setup.py +++ b/setup.py @@ -27,10 +27,6 @@ import shutil import glob -# Disable Torch support for Windows during CI builds. -if "SIRE_CI" in os.environ and platform.system() == "Windows": - os.environ["SIRE_NO_TORCH"] = "1" - try: # We have to check the version, but we can't do this by # importing sire (this will block installing of files on diff --git a/src/sire/_pythonize.py b/src/sire/_pythonize.py index ca7856402..00378867f 100644 --- a/src/sire/_pythonize.py +++ b/src/sire/_pythonize.py @@ -242,11 +242,8 @@ def _load_new_api_modules(delete_old: bool = True, is_base: bool = False): _pythonize(Convert._SireOpenMM.PyQMCallback, delete_old=delete_old) _pythonize(Convert._SireOpenMM.PyQMEngine, delete_old=delete_old) _pythonize(Convert._SireOpenMM.PyQMForce, delete_old=delete_old) - try: - _pythonize(Convert._SireOpenMM.TorchQMEngine, delete_old=delete_old) - _pythonize(Convert._SireOpenMM.TorchQMForce, delete_old=delete_old) - except: - pass + _pythonize(Convert._SireOpenMM.TorchQMEngine, delete_old=delete_old) + _pythonize(Convert._SireOpenMM.TorchQMForce, delete_old=delete_old) try: import lazy_import diff --git a/src/sire/qm/_emle.py b/src/sire/qm/_emle.py index c370350a8..591ac599d 100644 --- a/src/sire/qm/_emle.py +++ b/src/sire/qm/_emle.py @@ -49,58 +49,50 @@ def get_forces(self): return emle_force, interpolation_force -# Conditionally create a TorchEMLEEngine class if Torch is available. -try: - - class TorchEMLEEngine(_Convert._SireOpenMM.TorchQMEngine): - """A class to enable use of EMLE as a QM engine using C++ Torch.""" - - def get_forces(self): - """ - Get the OpenMM forces for this engine. The first force is the actual - EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic - embedding force. The second is a null CustomBondForce that can be used to - add a "lambda_emle" global parameter to a context to allow the force to be - scaled. - - Returns - ------- - - emle_force : openmm.Force - The EMLE force object to compute the electrostatic embedding force. - - interpolation_force : openmm.CustomBondForce - A null CustomBondForce object that can be used to add a "lambda_emle" - global parameter to an OpenMM context. This allows the electrostatic - embedding force to be scaled. - """ - - from copy import deepcopy as _deepcopy - from openmm import CustomBondForce as _CustomBondForce - - # Create a dynamics object for the QM region. - d = self._mols["property is_perturbable"].dynamics( - timestep="1fs", - constraint="none", - platform="cpu", - qm_engine=self, - ) +class TorchEMLEEngine(_Convert._SireOpenMM.TorchQMEngine): + """A class to enable use of EMLE as a QM engine using C++ Torch.""" - # Get the OpenMM EMLE force. - emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) + def get_forces(self): + """ + Get the OpenMM forces for this engine. The first force is the actual + EMLE force, which uses a CustomCPPForceImpl to calculate the electrostatic + embedding force. The second is a null CustomBondForce that can be used to + add a "lambda_emle" global parameter to a context to allow the force to be + scaled. - # Create a null CustomBondForce to add the EMLE interpolation - # parameter. - interpolation_force = _CustomBondForce("") - interpolation_force.addGlobalParameter("lambda_emle", 1.0) + Returns + ------- - # Return the forces. - return emle_force, interpolation_force + emle_force : openmm.Force + The EMLE force object to compute the electrostatic embedding force. - _has_torchqmengine = True -except: - _has_torchqmengine = False - pass + interpolation_force : openmm.CustomBondForce + A null CustomBondForce object that can be used to add a "lambda_emle" + global parameter to an OpenMM context. This allows the electrostatic + embedding force to be scaled. + """ + + from copy import deepcopy as _deepcopy + from openmm import CustomBondForce as _CustomBondForce + + # Create a dynamics object for the QM region. + d = self._mols["property is_perturbable"].dynamics( + timestep="1fs", + constraint="none", + platform="cpu", + qm_engine=self, + ) + + # Get the OpenMM EMLE force. + emle_force = _deepcopy(d._d._omm_mols.getSystem().getForce(0)) + + # Create a null CustomBondForce to add the EMLE interpolation + # parameter. + interpolation_force = _CustomBondForce("") + interpolation_force.addGlobalParameter("lambda_emle", 1.0) + + # Return the forces. + return emle_force, interpolation_force def emle( @@ -257,12 +249,6 @@ def emle( # Create an engine from an EMLE model. else: - if not _has_torchqmengine: - raise ValueError( - "Sire hasn't been compiled with support for TorchQMEngine. " - "Please install libtorch and recompile." - ) - try: from emle.models import EMLE as _EMLE except: @@ -283,13 +269,16 @@ def emle( module_path = calculator.__class__.__name__ + ".pt" _torch.jit.save(script_module, calculator.__class__.__name__ + ".pt") - # Create the EMLE engine. - engine = TorchEMLEEngine( - module_path, - cutoff, - neighbour_list_frequency, - False, - ) + try: + # Create the EMLE engine. + engine = TorchEMLEEngine( + module_path, + cutoff, + neighbour_list_frequency, + False, + ) + except Exception as e: + raise ValueError("Unable to create a TorchEMLEEngine: " + str(e)) from ._utils import ( _check_charge, diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt index 0428f8ef1..61d30e978 100644 --- a/wrapper/Convert/SireOpenMM/CMakeLists.txt +++ b/wrapper/Convert/SireOpenMM/CMakeLists.txt @@ -85,13 +85,6 @@ if (${SIRE_USE_OPENMM}) ${PYPP_SOURCES} ) - # Remove any Torch specific files if Torch is not found. - if (NOT TORCH_FOUND) - list(REMOVE_ITEM SIREOPENMM_SOURCES torchqm.cpp) - list(REMOVE_ITEM SIREOPENMM_SOURCES TorchQMEngine.pypp.cpp) - list(REMOVE_ITEM SIREOPENMM_SOURCES TorchQMForce.pypp.cpp) - endif() - # Create the library that holds all of the class wrappers add_library (SireOpenMM ${SIREOPENMM_SOURCES}) diff --git a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp index a9983dace..7a88a370c 100644 --- a/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp +++ b/wrapper/Convert/SireOpenMM/SireOpenMM_registrars.cpp @@ -26,10 +26,8 @@ void register_SireOpenMM_objects() ObjectRegistry::registerConverterFor< SireOpenMM::LambdaLever >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); ObjectRegistry::registerConverterFor< SireOpenMM::PerturbableOpenMMMolecule >(); -#ifdef SIRE_USE_TORCH ObjectRegistry::registerConverterFor< SireOpenMM::TorchQMForce >(); ObjectRegistry::registerConverterFor< SireOpenMM::TorchQMEngine >(); -#endif } diff --git a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp index 458b3b2d5..b686def19 100644 --- a/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp +++ b/wrapper/Convert/SireOpenMM/_SireOpenMM.main.cpp @@ -25,10 +25,9 @@ #include "QMForce.pypp.hpp" -#ifdef SIRE_USE_TORCH #include "TorchQMEngine.pypp.hpp" + #include "TorchQMForce.pypp.hpp" -#endif #include "_SireOpenMM_free_functions.pypp.hpp" @@ -71,9 +70,8 @@ BOOST_PYTHON_MODULE(_SireOpenMM){ register_free_functions(); -#ifdef SIRE_USE_TORCH register_TorchQMEngine_class(); + register_TorchQMForce_class(); -#endif } diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index ebb1f75c0..5a1e5a78a 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -224,8 +224,8 @@ QDataStream &operator<<(QDataStream &ds, const PyQMForce &pyqmforce) SharedDataStream sds(ds); sds << pyqmforce.callback << pyqmforce.cutoff << pyqmforce.neighbour_list_frequency - << pyqmforce.is_mechanical << pyqmforce.lambda << pyqmforce.atoms - << pyqmforce.mm1_to_qm << pyqmforce.mm1_to_mm2 << pyqmforce.bond_scale_factors + << pyqmforce.is_mechanical << pyqmforce.lambda << pyqmforce.atoms + << pyqmforce.mm1_to_qm << pyqmforce.mm1_to_mm2 << pyqmforce.bond_scale_factors << pyqmforce.mm2_atoms << pyqmforce.numbers << pyqmforce.charges; return ds; @@ -240,8 +240,8 @@ QDataStream &operator>>(QDataStream &ds, PyQMForce &pyqmforce) SharedDataStream sds(ds); sds >> pyqmforce.callback >> pyqmforce.cutoff >> pyqmforce.neighbour_list_frequency - >> pyqmforce.is_mechanical >> pyqmforce.lambda >> pyqmforce.atoms - >> pyqmforce.mm1_to_qm >> pyqmforce.mm1_to_mm2 >> pyqmforce.bond_scale_factors + >> pyqmforce.is_mechanical >> pyqmforce.lambda >> pyqmforce.atoms + >> pyqmforce.mm1_to_qm >> pyqmforce.mm1_to_mm2 >> pyqmforce.bond_scale_factors >> pyqmforce.mm2_atoms >> pyqmforce.numbers >> pyqmforce.charges; } else @@ -494,6 +494,7 @@ OpenMM::ForceImpl *PyQMForce::createImpl() const #endif } +#ifdef SIRE_USE_CUSTOMCPPFORCE PyQMForceImpl::PyQMForceImpl(const PyQMForce &owner) : OpenMM::CustomCPPForceImpl(owner), owner(owner) @@ -514,7 +515,6 @@ double PyQMForceImpl::computeForce( const std::vector &positions, std::vector &forces) { -#ifdef SIRE_USE_CUSTOMCPPFORCE // If this is the first step, then setup information for the neighbour list. if (this->step_count == 0) { @@ -854,8 +854,8 @@ double PyQMForceImpl::computeForce( // Finally, return the energy. return lambda * energy; -#endif } +#endif ///////// ///////// Implementation of PyQMEngine diff --git a/wrapper/Convert/SireOpenMM/torchqm.cpp b/wrapper/Convert/SireOpenMM/torchqm.cpp index aeb498e2d..1332c91c7 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.cpp +++ b/wrapper/Convert/SireOpenMM/torchqm.cpp @@ -26,12 +26,12 @@ * \*********************************************/ -#ifdef SIRE_USE_TORCH - #include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationProxy.h" +#ifdef SIRE_USE_TORCH #include +#endif #include "SireError/errors.h" #include "SireMaths/vector.h" @@ -165,6 +165,7 @@ TorchQMForce &TorchQMForce::operator=(const TorchQMForce &other) void TorchQMForce::setModulePath(QString module_path) { +#ifdef SIRE_USE_TORCH // Try to load the Torch module. try { @@ -180,6 +181,7 @@ void TorchQMForce::setModulePath(QString module_path) .arg(module_path).arg(e.what()), CODELOC); } +#endif this->module_path = module_path; } @@ -189,7 +191,11 @@ QString TorchQMForce::getModulePath() const return this->module_path; } +#ifdef SIRE_USE_TORCH torch::jit::script::Module TorchQMForce::getTorchModule() const +#else +void* TorchQMForce::getTorchModule() const +#endif { return this->torch_module; } @@ -342,7 +348,7 @@ namespace OpenMM OpenMM::ForceImpl *TorchQMForce::createImpl() const { -#ifdef SIRE_USE_CUSTOMCPPFORCE +#if defined(SIRE_USE_CUSTOMCPPFORCE) and defined(SIRE_USE_TORCH) return new TorchQMForceImpl(*this); #else throw SireError::unsupported(QObject::tr( @@ -353,6 +359,7 @@ OpenMM::ForceImpl *TorchQMForce::createImpl() const #endif } +#if defined(SIRE_USE_CUSTOMCPPFORCE) and defined(SIRE_USE_TORCH) TorchQMForceImpl::TorchQMForceImpl(const TorchQMForce &owner) : OpenMM::CustomCPPForceImpl(owner), owner(owner) @@ -374,7 +381,6 @@ double TorchQMForceImpl::computeForce( const std::vector &positions, std::vector &forces) { -#ifdef SIRE_USE_CUSTOMCPPFORCE // Get the platform name from the context. const auto platform = context.getPlatform().getName(); @@ -813,8 +819,8 @@ double TorchQMForceImpl::computeForce( // Finally, return the energy. return lambda * energy; -#endif } +#endif ///////// ///////// Implementation of TorchQMEngine @@ -839,6 +845,13 @@ TorchQMEngine::TorchQMEngine( is_mechanical(is_mechanical), lambda(lambda) { +#ifndef SIRE_USE_TORCH + throw SireError::unsupported(QObject::tr( + "Unable to create an TorchQMEngine because Sire has been compiled " + "without Torch support."), + CODELOC); +#endif + // Register the serialization proxies. OpenMM::registerTorchQMSerializationProxies(); @@ -1037,5 +1050,3 @@ QMForce* TorchQMEngine::createForce() const this->charges ); } - -#endif diff --git a/wrapper/Convert/SireOpenMM/torchqm.h b/wrapper/Convert/SireOpenMM/torchqm.h index 2d631cfd1..839ecf071 100644 --- a/wrapper/Convert/SireOpenMM/torchqm.h +++ b/wrapper/Convert/SireOpenMM/torchqm.h @@ -29,8 +29,6 @@ #ifndef SIREOPENMM_TORCHQM_H #define SIREOPENMM_TORCHQM_H -#ifdef SIRE_USE_TORCH - #include "OpenMM.h" #include "openmm/Force.h" #ifdef SIRE_USE_CUSTOMCPPFORCE @@ -41,7 +39,9 @@ #include "boost/python.hpp" #include +#ifdef SIRE_USE_TORCH #include +#endif #include #include @@ -161,7 +161,11 @@ namespace SireOpenMM /*! \returns The TorchScript module. */ +#ifdef SIRE_USE_TORCH torch::jit::script::Module getTorchModule() const; +#else + void* getTorchModule() const; +#endif //! Get the lambda weighting factor. /*! \returns @@ -250,7 +254,11 @@ namespace SireOpenMM private: QString module_path; +#ifdef SIRE_USE_TORCH torch::jit::script::Module torch_module; +#else + void *torch_module; +#endif SireUnits::Dimension::Length cutoff; int neighbour_list_frequency; bool is_mechanical; @@ -264,7 +272,7 @@ namespace SireOpenMM QVector charges; }; -#ifdef SIRE_USE_CUSTOMCPPFORCE +#if defined(SIRE_USE_CUSTOMCPPFORCE) && defined(SIRE_USE_TORCH) class TorchQMForceImpl : public OpenMM::CustomCPPForceImpl { public: @@ -506,4 +514,3 @@ SIRE_EXPOSE_CLASS(SireOpenMM::TorchQMEngine) SIRE_END_HEADER #endif -#endif diff --git a/wrapper/Convert/__init__.py b/wrapper/Convert/__init__.py index 46153eec2..a481b4b86 100644 --- a/wrapper/Convert/__init__.py +++ b/wrapper/Convert/__init__.py @@ -21,6 +21,7 @@ "QMEngine", "PyQMCallback", "PyQMEngine", + "TorchQMEngine", ] try: @@ -102,14 +103,9 @@ def smarts_to_rdkit(*args, **kwargs): QMEngine, PyQMCallback, PyQMEngine, + TorchQMEngine, ) - try: - from ._SireOpenMM import TorchQMEngine - __all__.append("TorchQMEngine") - except: - pass - from ..._pythonize import _pythonize _pythonize( @@ -120,15 +116,11 @@ def smarts_to_rdkit(*args, **kwargs): QMEngine, PyQMCallback, PyQMEngine, + TorchQMEngine, ], delete_old=True, ) - try: - _pythonize(TorchQMEngine, delete_old=True) - except: - pass - PerturbableOpenMMMolecule.changed_atoms = _changed_atoms PerturbableOpenMMMolecule.changed_bonds = _changed_bonds PerturbableOpenMMMolecule.changed_angles = _changed_angles From 502d0312e3c982842d4c0247b27bba7df8045106 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 10:05:31 +0100 Subject: [PATCH 438/468] Add EMLE support to all CI builds. --- .github/workflows/choose_branch.yaml | 1 + .github/workflows/devel.yaml | 1 + .github/workflows/main.yaml | 1 + .github/workflows/pr.yaml | 1 + 4 files changed, 4 insertions(+) diff --git a/.github/workflows/choose_branch.yaml b/.github/workflows/choose_branch.yaml index 41541f42d..4d95e94b4 100644 --- a/.github/workflows/choose_branch.yaml +++ b/.github/workflows/choose_branch.yaml @@ -46,6 +46,7 @@ jobs: env: SIRE_DONT_PHONEHOME: 1 SIRE_SILENT_PHONEHOME: 1 + SIRE_EMLE: 1 REPO: "${{ github.repository }}" steps: # diff --git a/.github/workflows/devel.yaml b/.github/workflows/devel.yaml index 9f623d3e2..bf520b79a 100644 --- a/.github/workflows/devel.yaml +++ b/.github/workflows/devel.yaml @@ -41,6 +41,7 @@ jobs: env: SIRE_DONT_PHONEHOME: 1 SIRE_SILENT_PHONEHOME: 1 + SIRE_EMLE: 1 REPO: "${{ github.repository }}" steps: # diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 158f4e438..12aa105de 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -37,6 +37,7 @@ jobs: env: SIRE_DONT_PHONEHOME: 1 SIRE_SILENT_PHONEHOME: 1 + SIRE_EMLE: 1 REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index a49c5cc71..4b4dd4a45 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -43,6 +43,7 @@ jobs: env: SIRE_DONT_PHONEHOME: 1 SIRE_SILENT_PHONEHOME: 1 + SIRE_EMLE: 1 REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" steps: # From 210fc632a3c307c62769ddeecd0dcd0db621958f Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 10:12:26 +0100 Subject: [PATCH 439/468] Add note about lack of Torch support on Windows. --- doc/source/tutorial/partXX/02_emle.rst | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/partXX/02_emle.rst index c038a7be6..cd01b687b 100644 --- a/doc/source/tutorial/partXX/02_emle.rst +++ b/doc/source/tutorial/partXX/02_emle.rst @@ -299,6 +299,14 @@ embedding energies for different backends. For example, we provide an optimised ``ANI2xEMLE`` module that can be used to add electrostatic embedding to the existing ``ANI2x`` model from `TorchANI `_. +.. note:: + + Torch support is currently not available for our Windows conda pacakge + since ``pytorch`` is not available for Windows on the ``conda-forge``. + It is possible to compile Sire from source using a local ``pytorch`` + installation, or using the pacakge from the official ``pytorch`` conda + channel. + As an example for how to use the module, let's again use the example alanine dipeptide system. First, let's reload the system and center the solute within the simulation box: From 9024411c0a55c84f56d32af49f7dd419d9b82263 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 13:08:02 +0100 Subject: [PATCH 440/468] Move placeholder documentation to correct path. --- .../tutorial/{index_partXX.rst => index_part08.rst} | 10 +++++----- doc/source/tutorial/{partXX => part08}/01_intro.rst | 0 doc/source/tutorial/{partXX => part08}/02_emle.rst | 0 .../tutorial/{partXX => part08}/03_adp_pmf.rst | 0 .../tutorial/{partXX => part08}/04_diels_alder.rst | 0 .../tutorial/{partXX => part08}/images/abyu.png | Bin .../tutorial/{partXX => part08}/images/ala.png | Bin .../tutorial/{partXX => part08}/images/pmf_abyu.png | Bin .../tutorial/{partXX => part08}/images/pmf_adp.png | Bin .../tutorial/{partXX => part08}/sire_emle.ipynb | 0 10 files changed, 5 insertions(+), 5 deletions(-) rename doc/source/tutorial/{index_partXX.rst => index_part08.rst} (87%) rename doc/source/tutorial/{partXX => part08}/01_intro.rst (100%) rename doc/source/tutorial/{partXX => part08}/02_emle.rst (100%) rename doc/source/tutorial/{partXX => part08}/03_adp_pmf.rst (100%) rename doc/source/tutorial/{partXX => part08}/04_diels_alder.rst (100%) rename doc/source/tutorial/{partXX => part08}/images/abyu.png (100%) rename doc/source/tutorial/{partXX => part08}/images/ala.png (100%) rename doc/source/tutorial/{partXX => part08}/images/pmf_abyu.png (100%) rename doc/source/tutorial/{partXX => part08}/images/pmf_adp.png (100%) rename doc/source/tutorial/{partXX => part08}/sire_emle.ipynb (100%) diff --git a/doc/source/tutorial/index_partXX.rst b/doc/source/tutorial/index_part08.rst similarity index 87% rename from doc/source/tutorial/index_partXX.rst rename to doc/source/tutorial/index_part08.rst index 6587de731..d2629dc51 100644 --- a/doc/source/tutorial/index_partXX.rst +++ b/doc/source/tutorial/index_part08.rst @@ -1,5 +1,5 @@ =============== -Part XX - QM/MM +Part 08 - QM/MM =============== QM/MM is a method that combines the accuracy of quantum mechanics with the @@ -15,7 +15,7 @@ QM/MM simulations using ``sire``. .. toctree:: :maxdepth: 1 - partXX/01_intro - partXX/02_emle - partXX/03_adp_pmf - partXX/04_diels_alder + part08/01_intro + part08/02_emle + part08/03_adp_pmf + part08/04_diels_alder diff --git a/doc/source/tutorial/partXX/01_intro.rst b/doc/source/tutorial/part08/01_intro.rst similarity index 100% rename from doc/source/tutorial/partXX/01_intro.rst rename to doc/source/tutorial/part08/01_intro.rst diff --git a/doc/source/tutorial/partXX/02_emle.rst b/doc/source/tutorial/part08/02_emle.rst similarity index 100% rename from doc/source/tutorial/partXX/02_emle.rst rename to doc/source/tutorial/part08/02_emle.rst diff --git a/doc/source/tutorial/partXX/03_adp_pmf.rst b/doc/source/tutorial/part08/03_adp_pmf.rst similarity index 100% rename from doc/source/tutorial/partXX/03_adp_pmf.rst rename to doc/source/tutorial/part08/03_adp_pmf.rst diff --git a/doc/source/tutorial/partXX/04_diels_alder.rst b/doc/source/tutorial/part08/04_diels_alder.rst similarity index 100% rename from doc/source/tutorial/partXX/04_diels_alder.rst rename to doc/source/tutorial/part08/04_diels_alder.rst diff --git a/doc/source/tutorial/partXX/images/abyu.png b/doc/source/tutorial/part08/images/abyu.png similarity index 100% rename from doc/source/tutorial/partXX/images/abyu.png rename to doc/source/tutorial/part08/images/abyu.png diff --git a/doc/source/tutorial/partXX/images/ala.png b/doc/source/tutorial/part08/images/ala.png similarity index 100% rename from doc/source/tutorial/partXX/images/ala.png rename to doc/source/tutorial/part08/images/ala.png diff --git a/doc/source/tutorial/partXX/images/pmf_abyu.png b/doc/source/tutorial/part08/images/pmf_abyu.png similarity index 100% rename from doc/source/tutorial/partXX/images/pmf_abyu.png rename to doc/source/tutorial/part08/images/pmf_abyu.png diff --git a/doc/source/tutorial/partXX/images/pmf_adp.png b/doc/source/tutorial/part08/images/pmf_adp.png similarity index 100% rename from doc/source/tutorial/partXX/images/pmf_adp.png rename to doc/source/tutorial/part08/images/pmf_adp.png diff --git a/doc/source/tutorial/partXX/sire_emle.ipynb b/doc/source/tutorial/part08/sire_emle.ipynb similarity index 100% rename from doc/source/tutorial/partXX/sire_emle.ipynb rename to doc/source/tutorial/part08/sire_emle.ipynb From 8527f7c20262cd903bf5a92a0248f1ee10bef706 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 13:09:54 +0100 Subject: [PATCH 441/468] Update CHANGELOG. --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 41d3fe077..16c468c23 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -37,6 +37,7 @@ organisation on `GitHub `__. * Fix exchange probability equations in ``sire.morph.replica_exchange`` function. * Fix calculation of energy change following final constraint projection after energy minimisation. * Clear internal OpenMM state from dynamics object following a successful minimisation. +* Add support for QM/MM simulations using OpenMM. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From ef637609c12dabf85d5814d10949d517de008ad3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 13:12:12 +0100 Subject: [PATCH 442/468] Remove redundant workflow script. --- .github/workflows/emle.yaml | 82 ------------------------------------- 1 file changed, 82 deletions(-) delete mode 100644 .github/workflows/emle.yaml diff --git a/.github/workflows/emle.yaml b/.github/workflows/emle.yaml deleted file mode 100644 index 7728349e6..000000000 --- a/.github/workflows/emle.yaml +++ /dev/null @@ -1,82 +0,0 @@ -name: Release sire-emle - -# Note that push and pull-request builds are automatically -# now skipped by GitHub if -# [skip ci], [ci skip], [no ci], [skip actions], or [actions skip] -# are in the commit message. We don't need to check for this ourselves. - -# Only allow this action to run on a manual run. -# We should specify when run whether or not we want -# to upload the packages at the end. -on: - workflow_dispatch: - inputs: - upload_packages: - description: "Upload packages to anaconda (yes/no)?" - required: true - default: "no" - -jobs: - build: - name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }}) - runs-on: ${{ matrix.platform.os }} - strategy: - max-parallel: 6 - fail-fast: false - matrix: - python-version: ["3.10", "3.11", "3.12"] - platform: - - { name: "windows", os: "windows-latest", shell: "pwsh" } - - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - exclude: - # Exclude all but the latest Python from all - # but Linux - - platform: - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } - python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11 - - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.10" - - platform: { name: "windows", os: "windows-latest", shell: "pwsh" } - python-version: "3.11" - environment: - name: sire-build - defaults: - run: - shell: ${{ matrix.platform.shell }} - env: - SIRE_DONT_PHONEHOME: 1 - SIRE_SILENT_PHONEHOME: 1 - SIRE_EMLE: 1 - REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}" - steps: - # - - uses: conda-incubator/setup-miniconda@v3 - with: - auto-update-conda: true - python-version: ${{ matrix.python-version }} - activate-environment: sire_build - miniforge-version: latest - # - - name: Clone the feature_emle branch - run: git clone -b feature_emle https://github.com/openbiosim/sire sire - # - - name: Setup Conda - run: conda install -y -c conda-forge boa anaconda-client packaging pip-requirements-parser - # - - name: Update Conda recipe - run: python ${{ github.workspace }}/sire/actions/update_recipe.py - # - - name: Prepare build location - run: mkdir ${{ github.workspace }}/build - # - - name: Build Conda package using conda build - run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/sire/recipes/sire - # - - name: Upload Conda package - # upload to the 'test' channel - run: python ${{ github.workspace }}/sire/actions/upload_package.py emle - env: - SRC_DIR: ${{ github.workspace }}/sire - ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - if: github.event.inputs.upload_packages == 'yes' From fa2aec7a8ac740a4b185f63d45943c7a93719499 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 13:17:12 +0100 Subject: [PATCH 443/468] Test that serialised OpenMM systems are identical. --- tests/convert/test_openmm_constraints.py | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index 0ed402693..6e1169298 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -470,6 +470,8 @@ def test_asymmetric_constraints(): # or OpenMM. from math import isclose + from openmm import XmlSerializer + from tempfile import NamedTemporaryFile # Load the MCL1 perturbation. (Perturbable ligand is the last molecule.) mol = sr.load_test_files("mcl1_60_61.s3")[-1] @@ -519,9 +521,27 @@ def test_asymmetric_constraints(): # Check the final energies from the logs are the same. assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) + # Serialise the systems in the contexts. + xml0 = NamedTemporaryFile() + xml1 = NamedTemporaryFile() + with open(xml0.name, "w") as f: + f.write(XmlSerializer.serialize(d_forwards._d._omm_mols.getSystem())) + with open(xml1.name, "w") as f: + f.write(XmlSerializer.serialize(d_backwards._d._omm_mols.getSystem())) + + # Load the serialised systems and sort. + with open(xml0.name, "r") as f: + xml0_lines = sorted(f.readlines()) + with open(xml1.name, "r") as f: + xml1_lines = sorted(f.readlines()) + + # Check the serialised systems are the same. + assert xml0_lines == xml1_lines + # Now get the final potential energies. (Post constraint projection.) nrg_forwards = d_forwards.current_potential_energy().value() nrg_backwards = d_backwards.current_potential_energy().value() - # Check the minimised potential energies are the same. + # Check the minimised potential energies are the same. (Post constraint projection.) + # This currently fails, which is inexplicable given evertyhing else above agrees. assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) From 75b3d09b002c237b50c22aa693f252034b4868a3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 13:19:42 +0100 Subject: [PATCH 444/468] Remove note about AEV feature branch. --- doc/source/tutorial/part08/02_emle.rst | 6 ------ 1 file changed, 6 deletions(-) diff --git a/doc/source/tutorial/part08/02_emle.rst b/doc/source/tutorial/part08/02_emle.rst index cd01b687b..6bf2b1c9d 100644 --- a/doc/source/tutorial/part08/02_emle.rst +++ b/doc/source/tutorial/part08/02_emle.rst @@ -372,12 +372,6 @@ In order to perform a calculation we need to create an instance of the >>> from emle.models import ANI2xEMLE >>> model = ANI2xEMLE().to(device) -.. note:: - - The ``ANI2xEMLE`` model currently requires the ``feature_aev`` branch of - ``emle-engine``, which can be installed with the following command: - ``pip install git+https://github.com/chemle/emle-engine.git@feature_aev`` - We can now calculate the in vacuo and electrostatic embedding energies: >>> energies = model(atomic_numbers, charges_mm, coords_qm, coords_mm) From 577cfd2b4830dd9fb884c4c268e6f86ca391c8c4 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 10 Oct 2024 15:35:29 +0100 Subject: [PATCH 445/468] Typo. [ci skip] --- tests/convert/test_openmm_constraints.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index 6e1169298..a58d662b9 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -543,5 +543,5 @@ def test_asymmetric_constraints(): nrg_backwards = d_backwards.current_potential_energy().value() # Check the minimised potential energies are the same. (Post constraint projection.) - # This currently fails, which is inexplicable given evertyhing else above agrees. + # This currently fails, which is inexplicable given everything else above agrees. assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) From bca81c51d159357fa766f71baba019e1bf5612e1 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 11 Oct 2024 17:16:41 +0100 Subject: [PATCH 446/468] Update constraint test with fix. [ci skip] --- tests/convert/test_openmm_constraints.py | 25 +++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index a58d662b9..c733f4fe5 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -457,17 +457,9 @@ def test_auto_constraints(ala_mols, openmm_platform): "openmm" not in sr.convert.supported_formats(), reason="openmm support is not available", ) -@pytest.mark.xfail(reason="Unresolved bug.") def test_asymmetric_constraints(): - # This test is for debugging a peculiar issue with one of the perturbations - # from the MCL1 test suite. Here there are no ghost atoms and a single atom - # changes type during the perturbation, from H to Cl. The constraints are - # different for the two end states. Currently, the minimised energy at - # lambda=1 does not match the minimised energy at lambda=0 when the end - # states are swapped. From debugging, it seems that this is the caused by - # calling context.applyConstraints() for the final constraint projection - # following succesful minimisation. It's not clear if the bug lies in Sire, - # or OpenMM. + # Test that constraints are updated correctly when the end states have + # different constraints. from math import isclose from openmm import XmlSerializer @@ -493,6 +485,18 @@ def test_asymmetric_constraints(): d_forwards.set_lambda(1.0, update_constraints=True) d_backwards.set_lambda(0.0, update_constraints=True) + # We need to reinitialise the forwards context for the constraints to be + # updated. + + # Store the positions. + pos = d_forwards._d._omm_mols.getState(getPositions=True).getPositions() + + # Reinitialise the context. + d_forwards._d._omm_mols.reinitialize() + + # Set the positions. + d_forwards._d._omm_mols.setPositions(pos) + # Get the initial potential energies. nrg_forwards = d_forwards.current_potential_energy().value() nrg_backwards = d_backwards.current_potential_energy().value() @@ -543,5 +547,4 @@ def test_asymmetric_constraints(): nrg_backwards = d_backwards.current_potential_energy().value() # Check the minimised potential energies are the same. (Post constraint projection.) - # This currently fails, which is inexplicable given everything else above agrees. assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) From 52626111bfaf5ecbc6cc46f4cb6d216dd4e375c2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 12 Oct 2024 13:32:33 +0100 Subject: [PATCH 447/468] Require OpenMM >= 8.1. --- requirements_host.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements_host.txt b/requirements_host.txt index 40e3ecf8d..9d6ca6ca9 100644 --- a/requirements_host.txt +++ b/requirements_host.txt @@ -6,7 +6,7 @@ lazy_import libcblas libnetcdf librdkit-dev -openmm +openmm >= 8.1 pandas python qt-main From 5a7a281ccc8dd315cd8b882a4d39bdb864852b6a Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 12 Oct 2024 13:43:26 +0100 Subject: [PATCH 448/468] Reinitialize the context if constraints change. [closes #244] --- tests/convert/test_openmm_constraints.py | 52 +++++----------------- wrapper/Convert/SireOpenMM/lambdalever.cpp | 26 +++++++++++ 2 files changed, 37 insertions(+), 41 deletions(-) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index c733f4fe5..3c525de2e 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -485,46 +485,6 @@ def test_asymmetric_constraints(): d_forwards.set_lambda(1.0, update_constraints=True) d_backwards.set_lambda(0.0, update_constraints=True) - # We need to reinitialise the forwards context for the constraints to be - # updated. - - # Store the positions. - pos = d_forwards._d._omm_mols.getState(getPositions=True).getPositions() - - # Reinitialise the context. - d_forwards._d._omm_mols.reinitialize() - - # Set the positions. - d_forwards._d._omm_mols.setPositions(pos) - - # Get the initial potential energies. - nrg_forwards = d_forwards.current_potential_energy().value() - nrg_backwards = d_backwards.current_potential_energy().value() - - # Check the potential energies are the same. - assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-5) - - # Minimise both dynamics objects. - d_forwards.minimise() - d_backwards.minimise() - - # Get the minimisation logs. - log_forwards = d_forwards._d.get_minimisation_log() - log_backwards = d_backwards._d.get_minimisation_log() - - lines_forward = log_forwards.split("\n") - for line in lines_forward: - if "Final energy" in line: - nrg_forwards = float(line.split()[2]) - - lines_backward = log_backwards.split("\n") - for line in lines_backward: - if "Final energy" in line: - nrg_backwards = float(line.split()[2]) - - # Check the final energies from the logs are the same. - assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) - # Serialise the systems in the contexts. xml0 = NamedTemporaryFile() xml1 = NamedTemporaryFile() @@ -539,6 +499,16 @@ def test_asymmetric_constraints(): with open(xml1.name, "r") as f: xml1_lines = sorted(f.readlines()) + nrg_forwards = d_forwards.current_potential_energy().value() + nrg_backwards = d_backwards.current_potential_energy().value() + + # Check the potential energies are the same. + assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-5) + + # Minimise both dynamics objects. + d_forwards.minimise() + d_backwards.minimise() + # Check the serialised systems are the same. assert xml0_lines == xml1_lines @@ -547,4 +517,4 @@ def test_asymmetric_constraints(): nrg_backwards = d_backwards.current_potential_energy().value() # Check the minimised potential energies are the same. (Post constraint projection.) - assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-3) + assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-1) diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 7eecab49a..47829c81c 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -1152,6 +1152,9 @@ double LambdaLever::setLambda(OpenMM::Context &context, // we know if we have peturbable ghost atoms if we have the ghost forcefields const bool have_ghost_atoms = (ghost_ghostff != 0 or ghost_nonghostff != 0); + // whether the constraints have changed + bool have_constraints_changed = false; + std::vector custom_params = {0.0, 0.0, 0.0, 0.0, 0.0}; if (qmff != 0) @@ -1552,6 +1555,7 @@ double LambdaLever::setLambda(OpenMM::Context &context, if (orig_distance != constraint_length) { system.setConstraintParameters(idx, particle1, particle2, constraint_length); + have_constraints_changed = true; } } } @@ -1792,6 +1796,28 @@ double LambdaLever::setLambda(OpenMM::Context &context, } } + // reinitialize the context if the constraints have changed + if (have_constraints_changed) + { + // we need to reinitialize the context if the constraints have changed + // since updating the parameters in the system will not update the context + // itself + + // get the current state + const auto state = context.getState(OpenMM::State::Positions | OpenMM::State::Velocities); + + // store the current positions and velocities + const auto positions = state.getPositions(); + const auto velocities = state.getVelocities(); + + // reinitialize the context + context.reinitialize(); + + // set the positions and velocities back to what they were + context.setPositions(positions); + context.setVelocities(velocities); + } + return lambda_value; } From ffd44d7f87472dd274beedad6494eef60f7197b3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 12 Oct 2024 13:47:51 +0100 Subject: [PATCH 449/468] Update CHANGELOG. [ci skip] --- doc/source/changelog.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 16c468c23..6d9e76188 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -38,6 +38,7 @@ organisation on `GitHub `__. * Fix calculation of energy change following final constraint projection after energy minimisation. * Clear internal OpenMM state from dynamics object following a successful minimisation. * Add support for QM/MM simulations using OpenMM. +* Reinitialise OpenMM context if constraints change when setting lambda. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From 53dcfb768958bc138669965a2124d6c1331d5673 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 12 Oct 2024 15:13:48 +0100 Subject: [PATCH 450/468] Use CPU platform for test. --- tests/convert/test_openmm_constraints.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index 3c525de2e..ef2fdb184 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -473,12 +473,14 @@ def test_asymmetric_constraints(): perturbable_constraint="h_bonds_not_heavy_perturbed", dynamic_constraints=True, include_constrained_energies=False, + platform="CPU", ) d_backwards = mol.dynamics( perturbable_constraint="h_bonds_not_heavy_perturbed", include_constrained_energies=False, dynamic_constraints=True, swap_end_states=True, + platform="CPU", ) # Set lambda so the dynamics states are equivalent. From 48bb4227a6d0b5a86b100572a94527363cc2da03 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Sat, 12 Oct 2024 16:44:30 +0100 Subject: [PATCH 451/468] Only run test on Linux. --- tests/convert/test_openmm_constraints.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index ef2fdb184..0e269bc6b 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -1,5 +1,6 @@ import sire as sr import pytest +import platform @pytest.mark.skipif( @@ -457,6 +458,7 @@ def test_auto_constraints(ala_mols, openmm_platform): "openmm" not in sr.convert.supported_formats(), reason="openmm support is not available", ) +@pytest.mark.skipif(platform.system() != "Linux", reason="Minimisation is platform dependent") def test_asymmetric_constraints(): # Test that constraints are updated correctly when the end states have # different constraints. From 6b57a66d0988ee90a0ac4aa3294dda571a9d8696 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 14 Oct 2024 11:17:17 +0100 Subject: [PATCH 452/468] Update callback to take optional list of MM atom indices. --- doc/source/tutorial/part08/01_intro.rst | 8 ++++-- .../Convert/SireOpenMM/PyQMCallback.pypp.cpp | 8 +++--- .../Convert/SireOpenMM/PyQMEngine.pypp.cpp | 6 ++--- wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp | 6 ++--- wrapper/Convert/SireOpenMM/pyqm.cpp | 22 +++++++++------ wrapper/Convert/SireOpenMM/pyqm.h | 27 ++++++++++++++++--- 6 files changed, 53 insertions(+), 24 deletions(-) diff --git a/doc/source/tutorial/part08/01_intro.rst b/doc/source/tutorial/part08/01_intro.rst index 8ff871d5b..3a86040a5 100644 --- a/doc/source/tutorial/part08/01_intro.rst +++ b/doc/source/tutorial/part08/01_intro.rst @@ -56,18 +56,22 @@ signature: .. code-block:: python - from typing import List, Tuple + from typing import List, Optional, Tuple def callback( numbers_qm: List[int], charges_mm: List[float], xyz_qm: List[List[float]], xyz_mm: List[List[float]], + idx_mm: Optional[List[int]] = None, ) -> Tuple[float, List[List[float]], List[List[float]]]: The function takes the atomic numbers of the QM atoms, the charges of the MM atoms in mod electron charge, the coordinates of the QM atoms in Angstrom, and -the coordinates of the MM atoms in Angstrom. It should return the calculated +the coordinates of the MM atoms in Angstrom. Optionally, it should also take the +indices of the true MM atoms (not link atoms or virtual charges) within the +QM/MM region. This is useful for obtaining any additional atomic properties +that may be required by the callback. The function should return the calculated energy in kJ/mol, the forces on the QM atoms in kJ/mol/nm, and the forces on the MM atoms in kJ/mol/nm. The remaining arguments are optional and specify the QM cutoff distance, the neighbour list update frequency, and whether the diff --git a/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp index d31a885de..1264f0745 100644 --- a/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMCallback.pypp.cpp @@ -65,18 +65,18 @@ void register_PyQMCallback_class(){ typedef bp::class_< SireOpenMM::PyQMCallback > PyQMCallback_exposer_t; PyQMCallback_exposer_t PyQMCallback_exposer = PyQMCallback_exposer_t( "PyQMCallback", "A callback wrapper class to interface with external QM engines\nvia the CustomCPPForceImpl.", bp::init< >("Default constructor.") ); bp::scope PyQMCallback_scope( PyQMCallback_exposer ); - PyQMCallback_exposer.def( bp::init< bp::api::object, bp::optional< QString > >(( bp::arg("arg0"), bp::arg("name")="" ), "Constructor\nPar:am py_object\nA Python object that contains the callback function.\n\nPar:am name\nThe name of a callback method that take the following arguments:\n- numbers_qm: A list of atomic numbers for the atoms in the ML region.\n- charges_mm: A list of the MM charges in mod electron charge.\n- xyz_qm: A list of positions for the atoms in the ML region in Angstrom.\n- xyz_mm: A list of positions for the atoms in the MM region in Angstrom.\nThe callback shoul return a tuple containing:\n- The energy in kJmol.\n- A list of forces for the QM atoms in kJmolnm.\n- A list of forces for the MM atoms in kJmolnm.\nIf empty, then the object is assumed to be a callable.\n") ); + PyQMCallback_exposer.def( bp::init< bp::api::object, bp::optional< QString > >(( bp::arg("arg0"), bp::arg("name")="" ), "Constructor\nPar:am py_object\nA Python object that contains the callback function.\n\nPar:am name\nThe name of a callback method that take the following arguments:\n- numbers_qm: A list of atomic numbers for the atoms in the ML region.\n- charges_mm: A list of the MM charges in mod electron charge.\n- xyz_qm: A list of positions for the atoms in the ML region in Angstrom.\n- xyz_mm: A list of positions for the atoms in the MM region in Angstrom.\n- idx_mm: A list of indices for the MM atoms in the QM/MM region.\nThe callback should return a tuple containing:\n- The energy in kJmol.\n- A list of forces for the QM atoms in kJmolnm.\n- A list of forces for the MM atoms in kJmolnm.\nIf empty, then the object is assumed to be a callable.\n") ); { //::SireOpenMM::PyQMCallback::call - typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMCallback::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMCallback::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > >,::QVector< int > ) const; call_function_type call_function_value( &::SireOpenMM::PyQMCallback::call ); PyQMCallback_exposer.def( "call" , call_function_value - , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) + , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm"), bp::arg("idx_mm") ) , bp::release_gil_policy() - , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nPar:am idx_mm A vector of indices for the MM atoms in the QM/MM region. Note that len(idx_mm) <= len(charges_mm) since it only contains the indices of true MM atoms, not link atoms or virtual charges.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } { //::SireOpenMM::PyQMCallback::typeName diff --git a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp index 45708bb7e..b4589667e 100644 --- a/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMEngine.pypp.cpp @@ -67,15 +67,15 @@ void register_PyQMEngine_class(){ PyQMEngine_exposer.def( bp::init< SireOpenMM::PyQMEngine const & >(( bp::arg("other") ), "Copy constructor.") ); { //::SireOpenMM::PyQMEngine::call - typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMEngine::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMEngine::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > >,::QVector < int > ) const; call_function_type call_function_value( &::SireOpenMM::PyQMEngine::call ); PyQMEngine_exposer.def( "call" , call_function_value - , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) + , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm"), bp::arg("idx_mm") ) , bp::release_gil_policy() - , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nPar:am idx_mm A vector of indices for the MM atoms in the QM/MM region. Note that len(idx_mm) <= len(charges_mm) since it only contains the indices of the true MM atoms, not link atoms or virtual charges.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } { //::SireOpenMM::PyQMEngine::getAtoms diff --git a/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp index 1f25099bc..18797552d 100644 --- a/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp +++ b/wrapper/Convert/SireOpenMM/PyQMForce.pypp.cpp @@ -69,15 +69,15 @@ void register_PyQMForce_class(){ PyQMForce_exposer.def( bp::init< SireOpenMM::PyQMForce const & >(( bp::arg("other") ), "Copy constructor.") ); { //::SireOpenMM::PyQMForce::call - typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMForce::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > > ) const; + typedef ::boost::tuples::tuple< double, QVector< QVector< double > >, QVector< QVector< double > >, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type > ( ::SireOpenMM::PyQMForce::*call_function_type)( ::QVector< int >,::QVector< double >,::QVector< QVector< double > >,::QVector< QVector< double > >, ::QVector < int > ) const; call_function_type call_function_value( &::SireOpenMM::PyQMForce::call ); PyQMForce_exposer.def( "call" , call_function_value - , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm") ) + , ( bp::arg("numbers_qm"), bp::arg("charges_mm"), bp::arg("xyz_qm"), bp::arg("xyz_mm"), bp::arg("idx_mm") ) , bp::release_gil_policy() - , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); + , "Call the callback function.\nPar:am numbers_qm\nA vector of atomic numbers for the atoms in the ML region.\n\nPar:am charges_mm\nA vector of the charges on the MM atoms in mod electron charge.\n\nPar:am xyz_qm\nA vector of positions for the atoms in the ML region in Angstrom.\n\nPar:am xyz_mm\nA vector of positions for the atoms in the MM region in Angstrom.\n\nPar:am idx_mm A vector of indices for the MM atoms in the QM/MM region. Note that len(idx_mm) <= len(charges_mm) since it only contains the indices of true MM atoms, not link atoms or virtual charges.\n\nReturn:s\nA tuple containing:\n- The energy in kJmol.\n- A vector of forces for the QM atoms in kJmolnm.\n- A vector of forces for the MM atoms in kJmolnm.\n" ); } { //::SireOpenMM::PyQMForce::getAtoms diff --git a/wrapper/Convert/SireOpenMM/pyqm.cpp b/wrapper/Convert/SireOpenMM/pyqm.cpp index 5a1e5a78a..8c37cc2ad 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.cpp +++ b/wrapper/Convert/SireOpenMM/pyqm.cpp @@ -152,7 +152,8 @@ PyQMCallback::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm) const + QVector> xyz_mm, + QVector idx_mm) const { // Acquire GIL before calling Python code. @@ -168,7 +169,8 @@ PyQMCallback::call( numbers_qm, charges_mm, xyz_qm, - xyz_mm + xyz_mm, + idx_mm ); } catch (const bp::error_already_set &) @@ -188,7 +190,8 @@ PyQMCallback::call( numbers_qm, charges_mm, xyz_qm, - xyz_mm + xyz_mm, + idx_mm ); } catch (const bp::error_already_set &) @@ -399,9 +402,10 @@ PyQMForce::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm) const + QVector> xyz_mm, + QVector idx_mm) const { - return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); + return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm, idx_mm); } ///////// @@ -781,7 +785,8 @@ double PyQMForceImpl::computeForce( numbers, charges_mm, xyz_qm, - xyz_mm + xyz_mm, + idx_mm ); // Extract the results. These will automatically be returned in OpenMM units. @@ -1067,9 +1072,10 @@ PyQMEngine::call( QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm) const + QVector> xyz_mm, + QVector idx_mm) const { - return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm); + return this->callback.call(numbers_qm, charges_mm, xyz_qm, xyz_mm, idx_mm); } QMForce* PyQMEngine::createForce() const diff --git a/wrapper/Convert/SireOpenMM/pyqm.h b/wrapper/Convert/SireOpenMM/pyqm.h index 016cd2744..f4e94a658 100644 --- a/wrapper/Convert/SireOpenMM/pyqm.h +++ b/wrapper/Convert/SireOpenMM/pyqm.h @@ -88,7 +88,8 @@ namespace SireOpenMM - charges_mm: A list of the MM charges in mod electron charge. - xyz_qm: A list of positions for the atoms in the ML region in Angstrom. - xyz_mm: A list of positions for the atoms in the MM region in Angstrom. - The callback shoul return a tuple containing: + - idx_mm: A list of indices for MM atom indices in the QM/MM region. + The callback should return a tuple containing: - The energy in kJ/mol. - A list of forces for the QM atoms in kJ/mol/nm. - A list of forces for the MM atoms in kJ/mol/nm. @@ -109,6 +110,11 @@ namespace SireOpenMM \param xyz_mm A vector of positions for the atoms in the MM region in Angstrom. + \param idx_mm + A vector of MM atom indices. Note that len(idx_mm) <= len(charges_mm) + since it only contains the indices of true MM atoms, not link atoms + or virtual charges. + \returns A tuple containing: - The energy in kJ/mol. @@ -119,7 +125,8 @@ namespace SireOpenMM QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm + QVector> xyz_mm, + QVector idx_mm ) const; //! Return the C++ name for this class. @@ -316,6 +323,11 @@ namespace SireOpenMM \param xyz_mm A vector of positions for the atoms in the MM region in Angstrom. + \param idx_mm + A vector of MM atom indices. Note that len(idx_mm) <= len(charges_mm) + since it only contains the indices of true MM atoms, not link atoms + or virtual charges. + \returns A tuple containing: - The energy in kJ/mol. @@ -326,7 +338,8 @@ namespace SireOpenMM QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm + QVector> xyz_mm, + QVector idx_mm ) const; protected: @@ -577,6 +590,11 @@ namespace SireOpenMM \param xyz_mm A vector of positions for the atoms in the MM region in Angstrom. + \param idx_mm + A vector of MM atom indices. Note that len(idx_mm) <= len(charges_mm) + since it only contains the indices of true MM atoms, not link atoms + or virtual charges. + \returns A tuple containing: - The energy in kJ/mol. @@ -587,7 +605,8 @@ namespace SireOpenMM QVector numbers_qm, QVector charges_mm, QVector> xyz_qm, - QVector> xyz_mm + QVector> xyz_mm, + QVector idx_mm ) const; //! Create an EMLE force object. From 852e37a21cedfcf663c54d3c3d223c7dbed0777d Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 14 Oct 2024 11:33:11 +0100 Subject: [PATCH 453/468] Clarify that link atoms & virtual charges are at end of lists. [ci skip] --- doc/source/tutorial/part08/01_intro.rst | 32 +++++++++++++------------ 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/doc/source/tutorial/part08/01_intro.rst b/doc/source/tutorial/part08/01_intro.rst index 3a86040a5..c9172300a 100644 --- a/doc/source/tutorial/part08/01_intro.rst +++ b/doc/source/tutorial/part08/01_intro.rst @@ -71,21 +71,23 @@ atoms in mod electron charge, the coordinates of the QM atoms in Angstrom, and the coordinates of the MM atoms in Angstrom. Optionally, it should also take the indices of the true MM atoms (not link atoms or virtual charges) within the QM/MM region. This is useful for obtaining any additional atomic properties -that may be required by the callback. The function should return the calculated -energy in kJ/mol, the forces on the QM atoms in kJ/mol/nm, and the forces -on the MM atoms in kJ/mol/nm. The remaining arguments are optional and specify -the QM cutoff distance, the neighbour list update frequency, and whether the -electrostatics should be treated with mechanical embedding. When mechanical -embedding is used, the electrostatics are treated at the MM level by ``OpenMM``. -Note that this doesn't change the signature of the callback function, i.e. it -will be passed empty lists for the MM specific arguments and should return an -empty list for the MM forces. Atomic positions passed to the callback function -will already be unwrapped with the QM region in the center. By default, no -neighbour list will be used. (The same thing can be achieved by passing -``neighbour_list_frequency=0``.) This is useful when using the engine as -a calculator for different input structures, where there may be no correlation -between coordinates. For regular molecular dynamics simulations, setting a -non-zero neighbour list frequency can improve performance. +that may be required by the callback. (Note that link atoms and virtual charges +are always placed last in the list of MM charges and positions.) The function +should return the calculated energy in kJ/mol, the forces on the QM atoms in +kJ/mol/nm, and the forces on the MM atoms in kJ/mol/nm. The remaining arguments +are optional and specify the QM cutoff distance, the neighbour list update +frequency, and whether the electrostatics should be treated with mechanical +embedding. When mechanical embedding is used, the electrostatics are treated +at the MM level by ``OpenMM``. Note that this doesn't change the signature of +the callback function, i.e. it will be passed empty lists for the MM specific +arguments and should return an empty list for the MM forces. Atomic positions +passed to the callback function will already be unwrapped with the QM region +in the center. By default, no neighbour list will be used. (The same thing +can be achieved by passing ``neighbour_list_frequency=0``.) This is useful +when using the engine as a calculator for different input structures, where +there may be no correlation between coordinates. For regular molecular +dynamics simulations, setting a non-zero neighbour list frequency can +improve performance. The ``create_engine`` function returns a modified version of the molecules containing a "merged" dipeptide that can be interpolated between MM and QM From d4e8c2d9f3821ab771e586b32b3ee2bfd6caeffb Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 14 Oct 2024 12:26:39 +0100 Subject: [PATCH 454/468] Update callback signature in tests. --- tests/qm/test_qm.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/tests/qm/test_qm.py b/tests/qm/test_qm.py index 61ec67732..11318986e 100644 --- a/tests/qm/test_qm.py +++ b/tests/qm/test_qm.py @@ -25,7 +25,7 @@ def test_callback_method(): """Makes sure that a callback method works correctly""" class Test: - def callback(self, a, b, c, d): + def callback(self, a, b, c, d, e=None): return (42, d, c) # Instantiate the class. @@ -39,9 +39,10 @@ def callback(self, a, b, c, d): b = [3, 4] c = [a, b] d = [b, a] + e = [4, 5] # Call the callback. - result = cb.call(a, b, c, d) + result = cb.call(a, b, c, d, e) # Make sure the result is correct. assert result == (42, d, c) == test.callback(a, b, c, d) @@ -50,7 +51,7 @@ def callback(self, a, b, c, d): def test_callback_function(): """Makes sure that a callback function works correctly""" - def callback(a, b, c, d): + def callback(a, b, c, d, e=None): return (42, d, c) # Create a callback object. @@ -61,9 +62,10 @@ def callback(a, b, c, d): b = [3, 4] c = [a, b] d = [b, a] + e = [4, 5] # Call the callback. - result = cb.call(a, b, c, d) + result = cb.call(a, b, c, d, e) # Make sure the result is correct. assert result == (42, d, c) == callback(a, b, c, d) @@ -359,7 +361,7 @@ def test_create_engine(ala_mols): """ # A test callback function. Returns a known energy and dummy forces. - def callback(numbers_qm, charges_mm, xyz_qm, xyz_mm): + def callback(numbers_qm, charges_mm, xyz_qm, xyz_mm, idx_mm=None): return (42, xyz_qm, xyz_mm) # Create a local copy of the test system. From c58fc13f9522256e31b468bd209da5112c073742 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 14 Oct 2024 14:30:18 +0100 Subject: [PATCH 455/468] Use ethane~methanol perturbation and reference platform. --- tests/convert/test_openmm_constraints.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index 0e269bc6b..123dbb7d4 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -458,8 +458,7 @@ def test_auto_constraints(ala_mols, openmm_platform): "openmm" not in sr.convert.supported_formats(), reason="openmm support is not available", ) -@pytest.mark.skipif(platform.system() != "Linux", reason="Minimisation is platform dependent") -def test_asymmetric_constraints(): +def test_asymmetric_constraints(merged_ethane_methanol): # Test that constraints are updated correctly when the end states have # different constraints. @@ -467,22 +466,23 @@ def test_asymmetric_constraints(): from openmm import XmlSerializer from tempfile import NamedTemporaryFile - # Load the MCL1 perturbation. (Perturbable ligand is the last molecule.) - mol = sr.load_test_files("mcl1_60_61.s3")[-1] + # Extract the molecule. + mol = merged_ethane_methanol.clone()[0] + mol = sr.morph.link_to_reference(mol) # Create dynamics objects for the forward and backward perturbations. d_forwards = mol.dynamics( perturbable_constraint="h_bonds_not_heavy_perturbed", dynamic_constraints=True, include_constrained_energies=False, - platform="CPU", + platform="Reference", ) d_backwards = mol.dynamics( perturbable_constraint="h_bonds_not_heavy_perturbed", include_constrained_energies=False, dynamic_constraints=True, swap_end_states=True, - platform="CPU", + platform="Reference", ) # Set lambda so the dynamics states are equivalent. @@ -521,4 +521,4 @@ def test_asymmetric_constraints(): nrg_backwards = d_backwards.current_potential_energy().value() # Check the minimised potential energies are the same. (Post constraint projection.) - assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-1) + assert isclose(nrg_forwards, nrg_backwards, rel_tol=1e-4) From 152ab025d14aa27ebc3efc82c2abab60208c04db Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 14 Oct 2024 16:40:15 +0100 Subject: [PATCH 456/468] Use preserveState=True rather than saving state ourselves. --- wrapper/Convert/SireOpenMM/lambdalever.cpp | 23 +++++----------------- 1 file changed, 5 insertions(+), 18 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 47829c81c..436f4ee0b 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -1796,26 +1796,13 @@ double LambdaLever::setLambda(OpenMM::Context &context, } } - // reinitialize the context if the constraints have changed + // we need to reinitialize the context if the constraints have changed + // since updating the parameters in the system will not update the context + // itself if (have_constraints_changed) { - // we need to reinitialize the context if the constraints have changed - // since updating the parameters in the system will not update the context - // itself - - // get the current state - const auto state = context.getState(OpenMM::State::Positions | OpenMM::State::Velocities); - - // store the current positions and velocities - const auto positions = state.getPositions(); - const auto velocities = state.getVelocities(); - - // reinitialize the context - context.reinitialize(); - - // set the positions and velocities back to what they were - context.setPositions(positions); - context.setVelocities(velocities); + // reinitialize the context, preserving the state + context.reinitialize(true); } return lambda_value; From dcc71645e050014aab071a0e55cf60efc0509b10 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 14 Oct 2024 16:53:36 +0100 Subject: [PATCH 457/468] Only run constraint check on Linux. --- tests/convert/test_openmm_constraints.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/tests/convert/test_openmm_constraints.py b/tests/convert/test_openmm_constraints.py index 123dbb7d4..c7427391a 100644 --- a/tests/convert/test_openmm_constraints.py +++ b/tests/convert/test_openmm_constraints.py @@ -458,8 +458,12 @@ def test_auto_constraints(ala_mols, openmm_platform): "openmm" not in sr.convert.supported_formats(), reason="openmm support is not available", ) +@pytest.mark.skipif( + platform.system() != "Linux", + reason="XMLSerializer doesn't preserve precision on Windows and macOS", +) def test_asymmetric_constraints(merged_ethane_methanol): - # Test that constraints are updated correctly when the end states have + # Check that constraints are updated correctly when the end states have # different constraints. from math import isclose From 26b5008ab99f29c0618f72733ac0a891a26e8277 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 16 Oct 2024 11:14:41 +0100 Subject: [PATCH 458/468] Give custom OpenMM forces meaningful names. --- doc/source/changelog.rst | 1 + src/sire/morph/_xml.py | 22 +++++++++---------- .../SireOpenMM/sire_to_openmm_system.cpp | 7 ++++++ 3 files changed, 19 insertions(+), 11 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index 6d9e76188..e6470b933 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -39,6 +39,7 @@ organisation on `GitHub `__. * Clear internal OpenMM state from dynamics object following a successful minimisation. * Add support for QM/MM simulations using OpenMM. * Reinitialise OpenMM context if constraints change when setting lambda. +* Give custom OpenMM forces meaningful names. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- diff --git a/src/sire/morph/_xml.py b/src/sire/morph/_xml.py index 3128f8a5a..2e61b2276 100644 --- a/src/sire/morph/_xml.py +++ b/src/sire/morph/_xml.py @@ -85,25 +85,25 @@ def evaluate_xml_force(mols, xml, force): # Create the name and index based on the force type. if force == "ghostghost": - name = "CustomNonbondedForce" - index = 0 + name = "GhostGhostNonbondedForce" elif force == "ghostnonghost": - name = "CustomNonbondedForce" - index = 1 + name = "GhostNonGhostNonbondedForce" elif force == "ghost14": - name = "CustomBondForce" - index = 0 + name = "Ghost14BondForce" # Get the root of the XML tree. root = tree.getroot() # Loop over the forces until we find the first CustomNonbondedForce. - force_index = 0 + is_found = False for force in tree.find("Forces"): if force.get("name") == name: - if force_index == index: - break - force_index += 1 + is_found = True + break + + # Raise an error if the force was not found. + if not is_found: + raise ValueError(f"Could not find the force: {name}") # Get the energy terms. terms = list(reversed(force.get("energy").split(";")[1:-1])) @@ -114,7 +114,7 @@ def evaluate_xml_force(mols, xml, force): nrg_lj_list = [] # CustomNonbondedForce: ghost-ghost or ghost-nonghost. - if name == "CustomNonbondedForce": + if name != "Ghost14BondForce": # Get the parameters for this force. parameters = [p.get("name") for p in force.find("PerParticleParameters")] diff --git a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp index a10f64652..e3c46a03e 100644 --- a/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp +++ b/wrapper/Convert/SireOpenMM/sire_to_openmm_system.cpp @@ -113,6 +113,7 @@ void _add_boresch_restraints(const SireMM::BoreschRestraints &restraints, .toStdString(); auto *restraintff = new OpenMM::CustomCompoundBondForce(6, energy_expression); + restraintff->setName("BoreschRestraintForce"); restraintff->addPerBondParameter("rho"); restraintff->addPerBondParameter("kr"); @@ -209,6 +210,7 @@ void _add_bond_restraints(const SireMM::BondRestraints &restraints, .toStdString(); auto *restraintff = new OpenMM::CustomBondForce(energy_expression); + restraintff->setName("BondRestraintForce"); restraintff->addPerBondParameter("rho"); restraintff->addPerBondParameter("k"); @@ -283,6 +285,7 @@ void _add_positional_restraints(const SireMM::PositionalRestraints &restraints, .toStdString(); auto *restraintff = new OpenMM::CustomBondForce(energy_expression); + restraintff->setName("PositionalRestraintForce"); restraintff->addPerBondParameter("rho"); restraintff->addPerBondParameter("k"); @@ -755,6 +758,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, { auto &engine = map["qm_engine"].value().asA(); qmff = engine.createForce(); + qmff->setName("QMForce"); } catch (...) { @@ -966,6 +970,7 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } ghost_14ff = new OpenMM::CustomBondForce(nb14_expression); + ghost_14ff->setName("Ghost14BondForce"); ghost_14ff->addPerBondParameter("q"); ghost_14ff->addPerBondParameter("sigma"); @@ -1054,7 +1059,9 @@ OpenMMMetaData SireOpenMM::sire_to_openmm_system(OpenMM::System &system, } ghost_ghostff = new OpenMM::CustomNonbondedForce(clj_expression); + ghost_ghostff->setName("GhostGhostNonbondedForce"); ghost_nonghostff = new OpenMM::CustomNonbondedForce(clj_expression); + ghost_nonghostff->setName("GhostNonGhostNonbondedForce"); ghost_ghostff->addPerParticleParameter("q"); ghost_ghostff->addPerParticleParameter("half_sigma"); From 718d573bff3adc45ce9cede3eb29b562ac215f0c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Wed, 16 Oct 2024 12:44:12 +0100 Subject: [PATCH 459/468] Use named restraint forces. --- wrapper/Convert/SireOpenMM/lambdalever.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/wrapper/Convert/SireOpenMM/lambdalever.cpp b/wrapper/Convert/SireOpenMM/lambdalever.cpp index 436f4ee0b..67707a398 100644 --- a/wrapper/Convert/SireOpenMM/lambdalever.cpp +++ b/wrapper/Convert/SireOpenMM/lambdalever.cpp @@ -1912,13 +1912,13 @@ void LambdaLever::updateRestraintInContext(OpenMM::Force &ff, double rho, // what is the type of this force...? const auto ff_type = ff.getName(); - if (ff_type == "CustomBondForce") + if (ff_type == "BondRestraintForce" or ff_type == "PositionalRestraintForce") { _update_restraint_in_context( dynamic_cast(&ff), rho, context); } - else if (ff_type == "CustomCompoundBondForce") + else if (ff_type == "BoreschRestraintForce") { _update_restraint_in_context( dynamic_cast(&ff), @@ -1929,7 +1929,7 @@ void LambdaLever::updateRestraintInContext(OpenMM::Force &ff, double rho, throw SireError::unknown_type(QObject::tr( "Unable to update the restraints for the passed force as it has " "an unknown type (%1). We currently only support a limited number " - "of force types, e.g. CustomBondForce etc") + "of force types, e.g. BondRestraintForce etc") .arg(QString::fromStdString(ff_type)), CODELOC); } From 34df271ed3e852a863633623b4047915d99051b0 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 17 Oct 2024 15:49:10 +0100 Subject: [PATCH 460/468] Correct molecule index. [ci skip] --- doc/source/tutorial/part08/04_diels_alder.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/part08/04_diels_alder.rst b/doc/source/tutorial/part08/04_diels_alder.rst index c685d44de..db2baed14 100644 --- a/doc/source/tutorial/part08/04_diels_alder.rst +++ b/doc/source/tutorial/part08/04_diels_alder.rst @@ -29,7 +29,7 @@ to create a sphere around the reaction site: .. note:: - Here we choose a sphere of radius 22 Å around atom 3 in the first molecule. + Here we choose a sphere of radius 22 Å around atom 3 in the second molecule. This is the reaction site in the AbyU system. In the simulation we will fix all atoms more than 20 Å from this site. From c23b78a2bdab98579ac57d54e8d4760cabe9f9e2 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 17 Oct 2024 15:49:52 +0100 Subject: [PATCH 461/468] Remove redundant notes. [ci skip] --- doc/source/tutorial/part08/02_emle.rst | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/doc/source/tutorial/part08/02_emle.rst b/doc/source/tutorial/part08/02_emle.rst index 6bf2b1c9d..84305c4c5 100644 --- a/doc/source/tutorial/part08/02_emle.rst +++ b/doc/source/tutorial/part08/02_emle.rst @@ -93,28 +93,11 @@ at which the λ value is updated. >>> d.run("1ps", frame_frequency="0.05ps", energy_frequency="0.05ps") -.. note:: - - Updating λ requires the updating of force field parameters in the ``OpenMM`` - context. For large systems, this can be quite slow so it isn't recommended - to set the ``energy_frequency`` to a value that is too small. We have a custom - `fork `_ of ``OpenMM`` that provides a - significant speedup for this operation by only updating a subset of the parameters. - Installation instructions can be provided on request. - .. note:: If you don't require a trajectory file, then better performance can be achieved leaving the ``frame_frequency`` keyword argument unset. -.. note:: - - ``emle-engine`` currently requires the use of `librascal `_ - for the calculation of SOAP (Smooth Overlap of Atomic Positions) descriptors. - This is a serial code, so you may see better performance by restricting the - number of ``OpenMP`` threads to 1, e.g. by setting the ``OMP_NUM_THREADS`` - environment variable. - Once the simulation has finished we can get back the trajectory of energy values. This can be obtained as a `pandas `_ ``DataFrame``, allowing for easy plotting and analysis. The table below shows the instantaneous From 223f90caa22b01591b98289dfa4a12d15e8791e6 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 17 Oct 2024 15:50:29 +0100 Subject: [PATCH 462/468] Typo. [ci skip] --- doc/source/tutorial/part08/01_intro.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tutorial/part08/01_intro.rst b/doc/source/tutorial/part08/01_intro.rst index c9172300a..166b27e17 100644 --- a/doc/source/tutorial/part08/01_intro.rst +++ b/doc/source/tutorial/part08/01_intro.rst @@ -17,7 +17,7 @@ Creating a QM engine -------------------- In order to run QM/MM with ``sire``, we first need to create a QM engine. This -is passed as a keword argument to the ``dynamics`` function and is used to +is passed as a keyword argument to the ``dynamics`` function and is used to perform the QM part of the calculation at each timestep. As an example, we will consider the case of running a QM/MM simulation of alanine From 4cd098e0e3588e7f30c442d19d619ea7bdd39e40 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 17 Oct 2024 15:51:32 +0100 Subject: [PATCH 463/468] Return clone of molecules. [ref #218] --- src/sire/mol/_dynamics.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index cdb8a56b5..965a67f95 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -1144,7 +1144,7 @@ def commit(self, return_as_system: bool = False): from ..system import System if System.is_system(self._orig_mols): - return self._sire_mols + return self._sire_mols.clone() else: r = self._orig_mols.clone() r.update(self._sire_mols.molecules()) From 41b381f5131da7df25d336f91c9095724d65a51c Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Thu, 17 Oct 2024 15:57:07 +0100 Subject: [PATCH 464/468] Add method to return underlying context from dynamics object. [ci skip] --- doc/source/tutorial/part08/03_adp_pmf.rst | 2 +- doc/source/tutorial/part08/04_diels_alder.rst | 2 +- src/sire/mol/_dynamics.py | 7 +++++++ 3 files changed, 9 insertions(+), 2 deletions(-) diff --git a/doc/source/tutorial/part08/03_adp_pmf.rst b/doc/source/tutorial/part08/03_adp_pmf.rst index 807ba46d0..d016a1735 100644 --- a/doc/source/tutorial/part08/03_adp_pmf.rst +++ b/doc/source/tutorial/part08/03_adp_pmf.rst @@ -74,7 +74,7 @@ We can now extract the underlying ``OpenMM`` context from the dynamics object, then create a copy of the integrator and system. >>> from copy import deepcopy ->>> context = d._d._omm_mols +>>> context = d.context() >>> omm_system = context.getSystem() >>> integrator = deepcopy(context.getIntegrator()) diff --git a/doc/source/tutorial/part08/04_diels_alder.rst b/doc/source/tutorial/part08/04_diels_alder.rst index db2baed14..a32eb781e 100644 --- a/doc/source/tutorial/part08/04_diels_alder.rst +++ b/doc/source/tutorial/part08/04_diels_alder.rst @@ -119,7 +119,7 @@ reaction site: Now we will extract the context from the dynamics object: ->>> context = d._d._omm_mols +>>> context = d.context() Creating a reaction coordinate ------------------------------ diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 965a67f95..666f048b0 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -1531,6 +1531,13 @@ def integrator(self): """ return self._d.integrator() + def context(self): + """ + Return the underlying OpenMM context that is being driven by this + dynamics object. + """ + return self._d._omm_mols + def info(self): """ Return the information that describes the forcefield that will From 2dc4c6e946b54632cd74c2aca0640d678b8f9ce3 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Fri, 18 Oct 2024 16:07:45 +0100 Subject: [PATCH 465/468] Don't udpate constraints when computing energy trajectory. --- src/sire/mol/_dynamics.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/sire/mol/_dynamics.py b/src/sire/mol/_dynamics.py index 666f048b0..ca23bceb0 100644 --- a/src/sire/mol/_dynamics.py +++ b/src/sire/mol/_dynamics.py @@ -338,7 +338,9 @@ def _exit_dynamics_block( if lambda_windows is not None: for lambda_value in lambda_windows: if lambda_value != sim_lambda_value: - self._omm_mols.set_lambda(lambda_value) + self._omm_mols.set_lambda( + lambda_value, update_constraints=False + ) nrgs[str(lambda_value)] = ( self._omm_mols.get_potential_energy( to_sire_units=False From 8a2f67c0fd1fa2f9930ea0d74b6f3bca08bfda03 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 21 Oct 2024 09:48:28 +0100 Subject: [PATCH 466/468] Update CHANGELOG for the 2024.3.0 release. --- doc/source/changelog.rst | 90 ++++++++++++++++++++++++++++++---------- 1 file changed, 69 insertions(+), 21 deletions(-) diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst index e6470b933..8d01fad32 100644 --- a/doc/source/changelog.rst +++ b/doc/source/changelog.rst @@ -12,34 +12,82 @@ Development was migrated into the `OpenBioSim `__ organisation on `GitHub `__. -`2024.3.0 `__ - September 2024 ----------------------------------------------------------------------------------------------- +`2024.3.0 `__ - October 2024 +-------------------------------------------------------------------------------------------- + +* Print residue indices of perturbed water molecules to SOMD1 log to allow + for easier debugging. + +* Add support for creating Na+ and Cl- ions as a means of generating templates for + uses as alchemical ions. + +* Fix ``sire.morph.merge`` function when one molecule is a monatomic ion. This prevents + the attempted rigid-body alignment, which would fail due to there being too few + degrees of freedom. -* Please add an item to this changelog when you create your PR -* Print residue indices of perturbed water molecules to SOMD1 log. -* Add support for creating Na+ and Cl- ions. -* Fix ``sire.morph.merge`` function when one molecule is a monatomic ion. * Remove ``sire.move.OpenMMPMEFEP`` wrappers from build when OpenMM is not available. + * Set ``IFBOX`` pointer to 3 for general triclinic boxes in ``sire.IO.AmberPrm`` parser. -* Only excluded nonbonded interactions between from_ghost and to_ghost atoms if they are in the same molecule. + +* Only exclude nonbonded interactions between ``from_ghost`` and ``to_ghost`` atoms + if they are in the same molecule. This prevents spurious intermolcular interactions + between molecules containing ghost atoms, e.g. a ligand and an alchemical water. + * Add Docker support for building wrappers on Linux x86. -* Add support for boresch restraints to PME. -* Port SOMD torsion fix to PME code. + +* Port SOMD1 Boresch restraint implementation to PME code. (This feature was present + in the reaction field implementation, but not for PME.) + +* Port SOMD1 torsion fix to PME code. (This had been fixed for the reaction field implementation, + but not for PME.) + * Fix issues with ``atomtype`` and ``atom`` records for dummy atoms in GROMACS topology files. -* Fixed buffer overflow when computing molecule indices to excluded to/from ghost atom interactions. + +* Fixed buffer overflow when computing molecule indices to excluded to/from + ghost atom interactions which caused corruption of the exclusion list. + * Fixed calculation of ``delta^2`` in soft-core Couloumb potential. -* Excluded to/from ghost atom interactions from ``ghost_14ff``. -* Fixed description of soft-core alpha parameter in tutorial. -* Added debugging function to evaluate custom forces in OpenMM XML files. -* Added a timeout to the OpenMM minimiser function. -* Exposed the pickle operator on the LambdaLever class. -* Fix issues with positionally restrained atoms in perturbable systems. + +* Exclude to/from ghost atom interactions from the ``ghost_14ff``. Exclusions were + already added to the ``ghost_ghostff``, but not the ``ghost_14ff``. + +* Fixed description of soft-core alpha parameter in :doc:`tutorial `. + +* Added debugging function to evaluate custom forces in OpenMM XML files. This + allows a user to decompose the pair-wise contribtions to the custom OpenMM + forces created by :mod:`sire`. + +* Added a timeout to the OpenMM minimiser function. This gives the user a single tunable + parameter to control roughly how long a minimisation should last before being aborted. + +* Exposed missing pickle operator on the ``LambdaLever`` class. + +* Fix bug setting custom nonbonded parameters for ghost atoms used in + positional restraints in OpenMM. + * Fix exchange probability equations in ``sire.morph.replica_exchange`` function. -* Fix calculation of energy change following final constraint projection after energy minimisation. -* Clear internal OpenMM state from dynamics object following a successful minimisation. -* Add support for QM/MM simulations using OpenMM. -* Reinitialise OpenMM context if constraints change when setting lambda. -* Give custom OpenMM forces meaningful names. + +* Fix calculation of energy change following final constraint projection + after energy minimisation. Previously the energy change was calculated from + the final step of the minimisation, rather than the change in energy + following the application of the constraints. + +* Clear internal OpenMM state from dynamics object during minimisation, + preventing the previous, pre-minimisation, state from being used when + ``get_state()`` is called. + +* Add support for QM/MM simulations using OpenMM. This uses the recent ``CustomCPPForceImpl`` + introduced in OpenMM 8.1 to allow an interface between OpenMM and external + QM or ML codes. We support a generic Python callback interface and a ``Torch`` + based interface for ML models. This is documented in the new :doc:`tutorial `. + +* Reinitialise OpenMM context if constraints change when setting lambda. Updating + constraints in an OpenMM system does not update the associated data structures + in the context. A full reinitialiasation is required. + +* Give custom OpenMM forces meaningful names. This makes it easier to parse OpenMM + XML files and debug custom forces, particularly when multiple forces of the same + type are present. `2024.2.0 `__ - June 2024 ----------------------------------------------------------------------------------------- From b52e4bfd059caf9200c60bd4d3ee71e1e1836111 Mon Sep 17 00:00:00 2001 From: Lester Hedges Date: Mon, 21 Oct 2024 09:56:49 +0100 Subject: [PATCH 467/468] Re-add Python 3.12 CI exclusions for macOS. --- .github/workflows/main.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml index 12aa105de..3a1f0761f 100644 --- a/.github/workflows/main.yaml +++ b/.github/workflows/main.yaml @@ -29,6 +29,10 @@ jobs: - { name: "windows", os: "windows-latest", shell: "pwsh" } - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" } - { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + exclude: + - platform: + { name: "macos", os: "macos-latest", shell: "bash -l {0}" } + python-version: "3.12" # MacOS can't run 3.12 yet... environment: name: sire-build defaults: From cd33b56019e53ad7425a64ad07f9320d77371a1c Mon Sep 17 00:00:00 2001 From: finlayclark Date: Mon, 21 Oct 2024 10:48:53 +0100 Subject: [PATCH 468/468] Improve annihilate docstring [ci skip] Make it clear that annihilate removes intramolecular bonded interactions, not just intramolecular nonbonded interactions, as might be expected from some of the ABFE literature. --- src/sire/morph/_decouple.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/sire/morph/_decouple.py b/src/sire/morph/_decouple.py index d7ca2e98c..a414aad35 100644 --- a/src/sire/morph/_decouple.py +++ b/src/sire/morph/_decouple.py @@ -6,7 +6,10 @@ def annihilate(mol, as_new_molecule: bool = True, map=None): Return a merged molecule that represents the perturbation that completely annihilates the molecule. The returned merged molecule will be suitable for using in a double-annihilation free energy - simulation, e.g. to calculate absolute binding free energies. + simulation, e.g. to calculate absolute binding free energies. Note that + this perturbation will remove all intramolecular interactions, not just + nonbonded intramolecular interactions. You should add positional restraints + to all atoms in the molecule to prevent to prevent it drifting apart. Parameters ----------

    \n", + "⚠️ Updating λ requires the updating of force field parameters in the OpenMM context. For large systems, this can be quite slow so it isn't recommended to set the energy_frequency to a value that is too small. We have a custom fork of OpenMM that provides a significant speedup for this operation by only updating a subset of the parameters. Installation instructions can be provided on request.\n", + "