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cbc-univie · Oct 25, 2023 · c83fe0f · c83fe0f
1 parent f99cb3c
commit c83fe0f
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Showing 3 changed files with 7 additions and 9 deletions.
diff --git a/protex/system.py b/protex/system.py
@@ -400,7 +400,7 @@ def __init__(
         self.residues: list[Residue] = self._set_initial_states()
         self.boxlength: openmm.Quantity = (
             simulation.context.getState().getPeriodicBoxVectors()[0][0] # NOTE: supports only cubic boxes and nVT -> changed in update.py to get at every step for npT
-        )  
+        )
 
     def dump(self, fname: str) -> None:
         """Pickle the current ProtexSystem object.

diff --git a/protex/testsystems.py b/protex/testsystems.py
@@ -7,11 +7,10 @@
     from openmm import (
         Context,
         DrudeNoseHooverIntegrator,
+        MonteCarloBarostat,
         OpenMMException,
         Platform,
         XmlSerializer,
-        MonteCarloBarostat
-
     )
     from openmm.app import (
         PME,
@@ -21,7 +20,7 @@
         HBonds,
         Simulation,
     )
-    from openmm.unit import angstroms, kelvin, picoseconds, atmosphere
+    from openmm.unit import angstroms, atmosphere, kelvin, picoseconds
 except ImportError:
     import simtk.openmm as mm
     from simtk.openmm import (

diff --git a/protex/update.py b/protex/update.py
@@ -336,16 +336,16 @@ def _update(self, candidates: list[tuple], nr_of_steps: int) -> None:
         initial_e = state.getPotentialEnergy()
         if np.isnan(initial_e._value):
             raise RuntimeError(f"Energy is {initial_e}")
-        
+
         # get the boxlength depending on ensemble
         if self.ionic_liquid.ensemble == "nVT":
             self.boxl_vec = (
                 self.ionic_liquid.boxlength
             )  # changed to store boxl as quantity in system class
         elif self.ionic_liquid.ensemble == "npT":
-            self.boxl_vec = self.ionic_liquid.simulation.context.getState().getPeriodicBoxVectors()[0][0] 
+            self.boxl_vec = self.ionic_liquid.simulation.context.getState().getPeriodicBoxVectors()[0][0]
         self.boxl = self.boxl_vec.value_in_unit(nanometers)
-        
+
         logger.info("Start changing states ...")
         assert nr_of_steps > 1, "Use an update step number of at least 2."
         for lamb in np.linspace(0, 1, nr_of_steps):
@@ -710,14 +710,13 @@ def update(self, nr_of_steps: int = 2) -> list[tuple[Residue, Residue]]:
         list[tuple[Residue, Residue]]
             A list with all the updated residue tuples
         """
-
         # get the boxlength depending on ensemble
         if self.ionic_liquid.ensemble == "nVT":
             self.boxl_vec = (
                 self.ionic_liquid.boxlength
             )  # changed to store boxl as quantity in system class
         elif self.ionic_liquid.ensemble == "npT":
-            self.boxl_vec = self.ionic_liquid.simulation.context.getState().getPeriodicBoxVectors()[0][0] 
+            self.boxl_vec = self.ionic_liquid.simulation.context.getState().getPeriodicBoxVectors()[0][0]
         self.boxl = self.boxl_vec.value_in_unit(nanometers)
         print(f"{self.boxl=}")