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Rework tinkerxyz conversion code, now dataframe based
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@jessbade
jessbade committed Feb 23, 2024
1 parent 692f247 commit 63a3929
Showing 1 changed file with 49 additions and 223 deletions.
272 changes: 49 additions & 223 deletions isicle/md.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@
from isicle.geometry import Geometry, XYZGeometry
from isicle.interfaces import WrapperInterface
from isicle.parse import XTBParser, TINKERParser
from isicle.utils import tinkerxyz_lookup

"""
Files resulting from an xtb job always run in the same directory that the command is
Expand Down Expand Up @@ -762,233 +763,53 @@ def _convert_to_tinkerxyz(self):
"""

# getting MMFF values for large atom types
def getMMFF_large_atom_type(mmff_props, atom, m):
small_to_large_list = [
[[]],
[[1]],
[[3, "C"], [2, "C=C"]],
[
[4, "C=O"],
[5, "C=N"],
[6, "NC(N)=N"],
[7, "CC=O"],
[8, "NC=O"],
[10, "NC(=O)N"],
[11, "OC=O"],
[12, "NC(=O)O"],
[13, "NC(=O)O"],
[14, "OC(=O)O"],
[15, "SC=O"],
[16, "NC=S"],
[17, "C=S(O)O"],
[18, "C=S=O"],
[19, "SC=S"],
[20, "C=P"],
],
[[21, "C#[C,N]"], [22, "[C,N,O]=C=[C,N,O]"]],
[[23, "C[H]"], [24, "[Si][H]"]],
[
[41, "O"],
[25, "OC"],
[26, "OC=O"],
[27, "OC=C"],
[27, "Occ"],
[28, "OC=N"],
[29, "OC=S"],
[31, "ON=O"],
[30, "O[N+]([O-])=O"],
[36, "OS"],
[34, "OSO"],
[35, "OS=O"],
[33, "OS(O)=O"],
[32, "OS(O)(=O)=O"],
[40, "OP"],
[39, "OPO"],
[38, "OP(=O)O"],
[37, "OP(=O)(=O)O"],
],
[
[42, "C=O"],
[44, "CC=O"],
[43, "NC=O"],
[45, "OC=O"],
[46, "O=N"],
[47, "S=O"],
[48, "[C,N]=S=O"],
],
[[49]],
[[50, "C=N"], [51, "N=N"]],
[[52, "NC=O"], [53, "NC=S"], [54, "NN=C"], [55, "NN=N"]],
[[56]],
[[57]],
[[58]],
[[59]],
[[60]],
[[61]],
[[62, "S=O"], [63, "S=N"]],
[
[64, "O=S=O"],
[70, "OSN"],
[65, "N-S(=O)=O"],
[66, "OS(O)O"],
[67, "C"],
[68, "OS(O)(O)O"],
[69, "CS(O)(O)C"],
],
[[71]],
[[72]],
[[74, "[H]O"], [73, "[H]OC"], [75, "[H][O-]"]],
[[76]],
[
[82, "[H]N"],
[77, "[H]N(C)C"],
[78, "[H]N([H])[H]"],
[79, "[H]n1cccc1"],
[80, "[H]NO"],
[81, "[H][N-]"],
],
[[83, "[H]OC=O"], [84, "[H]OP"]],
[[89, "P"], [88, "PO"], [87, "OPO"], [86, "OP(O)O"], [89, "OP(O)(O)O"]],
[[90]],
[[91, "[H]N=N"], [92, "[H]N=C"]],
[
[102, "[H]N"],
[93, "[H]NC=O"],
[94, "[H]NC=S"],
[95, "[H]NC=C"],
[96, "[H]NC=N"],
[97, "[H]NN=C"],
[98, "[H]NN=N"],
[99, "[H]NS=O"],
[100, "[H]NP=O"],
[101, "[H]N#[C,N]"],
],
[[103, "[H]OC=C"], [104, "[C]OC=N"]],
[[105]],
[[106]],
[
[107, "[O-]C=O"],
[108, "NO"],
[109, "ON=O"],
[110, "O[N+]([O-])=O"],
[111, "[O-][N+]([O-])=O"],
[112, "OS"],
[113, "OS=O"],
[114, "OS(=O)=O"],
[115, "OS(=O)(=O)O"],
[116, "O=[S-]S"],
[117, "OP"],
[118, "OPO"],
[119, "OP(=O)O"],
[120, "OP(=O)(=O)"],
[121, "OCl(=O)(=O)[O-]"],
],
[[122]],
[[123]],
[[124, "[O-]"], [125, "[O-]C=[C,N]"]],
[
[126, "[H][N+][H,C][H,C][H,C]"],
[127, "C1=[NH+]C=CN1"],
[128, "C1=C[NH+]=CC=C1"],
[129, "CC(N)=[NH2+]"],
[130, "C=[NH2+]"],
[131, "NC(N)=[NH2+]"],
[132, "[H]N([H])([H])([H])[H]"],
],
[[133]],
[[134]],
[[135]],
[[136, "NC=C"], [137, "NC=N"], [138, "NC=P"], [139, "NC#C"]],
[[140, "[O-]C=O"], [141, "[S-]C=S"]],
[[142]],
[
[143, "NS(=O)O"],
[144, "NS(=O)(=O)O"],
[145, "NP(=O)O"],
[146, "NP(=O)(=O)O"],
[147, "NC#N"],
],
[[148]],
[[149, "ON=O"], [150, "O[N+][O-]=O"]],
[[151]],
[[152]],
[[153]],
[[154]],
[[155]],
[[156]],
[[157]],
[[158]],
[[159, "[N+]=C"], [160, "[N+]=N"]],
[[161]],
[[162]],
[[163, "NC(N)=[NH2+]"], [164, "[N+]=CN"]],
[[165]],
[[166]],
[[167]],
[[168]],
[[169]],
[[170]],
[[171]],
[[172]],
[[173]],
[[174]],
[[175]],
[[176]],
[[177]],
[[178, "[H]S"], [179, "[H]S=N"], [180, "[H]P"]],
[[181, "SP"], [183, "[S-]"], [182, "[S-]C=S"], [184, "[S-]S(=O)"]],
[[185, "[O-]S=O"], [186, "[O-]S=S"]],
[[187]],
[[188]],
[[189]],
[[190]],
[[191]],
[[192]],
[[193]],
[
[194, "N[N+]1=CNC=C1"],
[195, "[H][N+]([H])([H])([H])[H]"],
[196, "[H][N+]([H])([H])([H])[H]"],
[197, "[H][N+]([H])([H])([H])[H]"],
],
[
[198, "[H][N+]([H])([H])([H])[H]"],
[199, "[H][N+]([H])([H])([H])[H]"],
[200, "[H][N+]([H])([H])([H])[H]"],
],
[[-1]],
[[-1]],
[[-1]],
[[-1]],
[[201]],
[[202]],
[[203]],
[[204]],
[[205]],
[[206]],
[[207]],
[[208]],
[[209, "[Zn]"], [210, "[Zn++]"]],
[[211]],
[[212]],
[[213]],
[[214]],
]
def getMMFF_large_atom_type(mmff_props, atom, mol, xyzref):
def split_lookup(x):
if len(x) == 2:
return [x[0], x[1]]
elif len(x) == 1:
return [x[0], ""]
elif len(x) == 0:
return [None, ""]
else:
raise ValueError("Unexpected length from lookup file.")

def substructure_check(x, m):
substruc = Chem.MolFromSmarts(x)
return m.GetSubstructMatches(substruc)

def update_large_atom(x, atom):
for elem in x["check"]:
if elem.count(atom.GetIdx()) > 0:
return 1
return 0

MMFF_small_atom_type = mmff_props.GetMMFFAtomType(atom.GetIdx())
MMFF_large_atom_type = small_to_large_list[MMFF_small_atom_type][0][0]
if len(small_to_large_list[MMFF_small_atom_type]) > 1:
for atom_info in small_to_large_list[MMFF_small_atom_type]:
substructure = Chem.MolFromSmarts(atom_info[1])
for substructure_match in m.GetSubstructMatches(substructure):
if substructure_match.count(atom.GetIdx()) > 0:
MMFF_large_atom_type = atom_info[0]
return MMFF_large_atom_type
xyzref_subset = xyzref.loc[MMFF_small_atom_type,]
xyzref_subset = xyzref_subset.reset_index()
check_len = len(xyzref_subset)
if check_len > 1:
xyzref_subset[["id", "substructure"]] = xyzref_subset.apply(
lambda x: split_lookup(x.lookup),
axis="columns",
result_type="expand",
)
xyzref_subset["check"] = xyzref_subset["substructure"].apply(
lambda x: substructure_check(x, mol)
)
xyzref_subset["update"] = xyzref_subset.apply(
lambda x: update_large_atom(x, atom), axis="columns"
)
return (
xyzref_subset[xyzref_subset["update"] > 0].tail(1)["id"].values[0]
)
else:
return xyzref_subset["lookup"].values[0][0]

mol = self.geom.mol
conf = mol.GetConformer()
mmff_props = AllChem.MMFFGetMoleculeProperties(mol)

xyzref = tinkerxyz_lookup()
xyz = ""

# Set header line with number of atoms and basename
Expand All @@ -1011,13 +832,13 @@ def getMMFF_large_atom_type(mmff_props, atom, m):
list(conf.GetAtomPosition(atom.GetIdx()))[0],
list(conf.GetAtomPosition(atom.GetIdx()))[1],
list(conf.GetAtomPosition(atom.GetIdx()))[2],
getMMFF_large_atom_type(mmff_props, atom, mol),
getMMFF_large_atom_type(mmff_props, atom, mol, xyzref),
attached_atoms,
)

return xyz

def set_geometry(self, geom):
def set_geometry(self, geom, forcefield="UFF", ff_iter=200):
"""
Set :obj:`~isicle.geometry.Geometry` instance for simulation.
Expand All @@ -1029,6 +850,11 @@ def set_geometry(self, geom):
"""

# Assign geometry
if not geom._is_embedded(geom.mol):
geom = geom.initial_optimize(
embed=True, forcefield=forcefield, ff_iter=ff_iter
)

self.geom = geom
self.basename = self.geom.basename

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