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Allow selecting the Platform to use #324

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Allow selecting the Platform to use #324

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da6761c
Fix exception with unknown residues
peastman Jan 6, 2025
05d9ab5
Merge branch 'master' of github.com:openmm/pdbfixer
peastman Jan 6, 2025
670a428
Allow selecting the Platform to use
peastman Jan 21, 2025
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14 changes: 10 additions & 4 deletions pdbfixer/pdbfixer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.

Portions copyright (c) 2013-2024 Stanford University and the Authors.
Portions copyright (c) 2013-2025 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:

Expand Down Expand Up @@ -295,7 +295,7 @@ class PDBFixer(object):
"""PDBFixer implements many tools for fixing problems in PDB and PDBx/mmCIF files.
"""

def __init__(self, filename=None, pdbfile=None, pdbxfile=None, url=None, pdbid=None):
def __init__(self, filename=None, pdbfile=None, pdbxfile=None, url=None, pdbid=None, platform=None):
"""Create a new PDBFixer instance to fix problems in a PDB or PDBx/mmCIF file.

Parameters
Expand All @@ -315,6 +315,8 @@ def __init__(self, filename=None, pdbfile=None, pdbxfile=None, url=None, pdbid=N
at the file content.
pdbid : str, optional, default=None
A four-letter PDB code specifying the structure to be retrieved from the RCSB.
platform: openmm.Platform, optional, default=None
The Platform to use for running calculations. If None, a Platform will be chosen automatically.

Notes
-----
Expand Down Expand Up @@ -347,6 +349,7 @@ def __init__(self, filename=None, pdbfile=None, pdbxfile=None, url=None, pdbid=N
if bool(filename) + bool(pdbfile) + bool(pdbxfile) + bool(url) + bool(pdbid) != 1:
raise Exception("Exactly one option [filename, pdbfile, pdbxfile, url, pdbid] must be specified.")

self.platform = platform
self.source = None
if pdbid:
# A PDB id has been specified.
Expand Down Expand Up @@ -1280,7 +1283,10 @@ def addMissingAtoms(self, seed=None):
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)
if self.platform is None:
context = mm.Context(system, integrator)
else:
context = mm.Context(system, integrator, self.platform)
context.setPositions(newPositions)
mm.LocalEnergyMinimizer.minimize(context)
state = context.getState(getPositions=True)
Expand Down Expand Up @@ -1389,7 +1395,7 @@ def addMissingHydrogens(self, pH=7.0, forcefield=None):
extraDefinitions = self._downloadNonstandardDefinitions()
variants = [self._describeVariant(res, extraDefinitions) for res in self.topology.residues()]
modeller = app.Modeller(self.topology, self.positions)
modeller.addHydrogens(pH=pH, forcefield=forcefield, variants=variants)
modeller.addHydrogens(pH=pH, forcefield=forcefield, variants=variants, platform=self.platform)
self.topology = modeller.topology
self.positions = modeller.positions

Expand Down
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