pdbfixer.patch

diff --git a/home/anja/miniconda3/envs/engens-conda-env/lib/python3.6/site-packages/pdbfixer/pdbfixer.py b/../pdbfixer.py
index 2cd4d8d..a72173c 100644
--- a/home/anja/miniconda3/envs/engens-conda-env/lib/python3.6/site-packages/pdbfixer/pdbfixer.py
+++ b/../pdbfixer.py
@@ -927,18 +927,20 @@ class PDBFixer(object):
             system = forcefield.createSystem(newTopology)
 
             # Set any previously existing atoms to be massless, they so won't move.
-
-            for atom in existingAtomMap.values():
-                system.setParticleMass(atom.index, 0.0)
+            [system.setParticleMass(atom.index, 0.0) for atom in existingAtomMap.values()]
+           # for atom in existingAtomMap.values():
+             #   system.setParticleMass(atom.index, 0.0)
 
             # If any heavy atoms were omitted, add them back to avoid steric clashes.
 
             nonbonded = [f for f in system.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
-            for atom in self.topology.atoms():
-                if atom.element not in (None, hydrogen) and atom not in existingAtomMap:
-                    system.addParticle(0.0)
-                    nonbonded.addParticle([])
-                    newPositions.append(self.positions[atom.index])
+
+            [(system.addParticle(0.0), nonbonded.addParticle([]), newPositions.append(self.positions[atom.index])) for atom in self.topology.atoms() if atom.element not in (None, hydrogen) and atom not in existingAtomMap]
+            #for atom in self.topology.atoms():
+           #     if atom.element not in (None, hydrogen) and atom not in existingAtomMap:
+           #         system.addParticle(0.0)
+            #        nonbonded.addParticle([])
+            #        newPositions.append(self.positions[atom.index])
 
             # For efficiency, only compute interactions that involve a new atom.
 
@@ -949,7 +951,7 @@ class PDBFixer(object):
             integrator = mm.LangevinIntegrator(300*unit.kelvin, 10/unit.picosecond, 5*unit.femtosecond)
             if seed is not None:
                 integrator.setRandomNumberSeed(seed)
-            context = mm.Context(system, integrator)
+            context = mm.Context(system, integrator, mm.Platform.getPlatformByName('CUDA'))
             context.setPositions(newPositions)
             mm.LocalEnergyMinimizer.minimize(context)
             state = context.getState(getPositions=True)
@@ -979,7 +981,6 @@ class PDBFixer(object):
             (newTopology2, newPositions2, newAtoms2, existingAtomMap2) = self._addAtomsToTopology(False, False)
 
             # Copy over the minimized positions for the new atoms.
-
             for a1, a2 in zip(newAtoms, newAtoms2):
                 newPositions2[a2.index] = state.getPositions()[a1.index]
             self.topology = newTopology2