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Unverified Commit ba907d8a authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Added residueTemplates argument to more methods (#4211)

parent 0a3a914f
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Showing with 64 additions and 23 deletions
wrappers/python/openmm/app/forcefield.py
View file @ ba907d8a
......@@ -1042,7 +1042,7 @@ class ForceField(object):
bondedToAtom = [sorted(b) for b in bondedToAtom]
return bondedToAtom
def getUnmatchedResidues(self, topology):
def getUnmatchedResidues(self, topology, residueTemplates=dict()):
"""Return a list of Residue objects from specified topology for which no forcefield templates are available.
.. CAUTION:: This method is experimental, and its API is subject to change.
......@@ -1051,6 +1051,12 @@ class ForceField(object):
----------
topology : Topology
The Topology whose residues are to be checked against the forcefield residue templates.
residueTemplates : dict=dict()
Specifies which template to use for particular residues. The keys should be Residue
objects from the Topology, and the values should be the names of the templates to
use for them. This is useful when a ForceField contains multiple templates that
can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
Returns
-------
......@@ -1064,6 +1070,11 @@ class ForceField(object):
bondedToAtom = self._buildBondedToAtomList(topology)
unmatched_residues = list() # list of unmatched residues
for res in topology.residues():
if res in residueTemplates:
# Make sure the specified template matches.
template = self._templates[residueTemplates[res]]
matches = compiled.matchResidueToTemplate(res, template, bondedToAtom, False, False)
else:
# Attempt to match one of the existing templates.
[template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
if matches is None:
......@@ -1179,11 +1190,11 @@ class ForceField(object):
their total mass the same. If rigidWater is used to make water molecules
rigid, then water hydrogens are not altered.
residueTemplates : dict=dict()
Key: Topology Residue object
Value: string, name of _TemplateData residue template object to use for (Key) residue.
This allows user to specify which template to apply to particular Residues
in the event that multiple matching templates are available (e.g Fe2+ and Fe3+
templates in the ForceField for a monoatomic iron ion in the topology).
Specifies which template to use for particular residues. The keys should be Residue
objects from the Topology, and the values should be the names of the templates to
use for them. This is useful when a ForceField contains multiple templates that
can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
ignoreExternalBonds : boolean=False
If true, ignore external bonds when matching residues to templates. This is
useful when the Topology represents one piece of a larger molecule, so chains are
......
wrappers/python/openmm/app/modeller.py
View file @ ba907d8a
......@@ -257,7 +257,7 @@ class Modeller(object):
self.topology = newTopology
self.positions = newPositions
def _addIons(self, forcefield, numWaters, replaceableMols, ionCutoff=0.05*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
def _addIons(self, forcefield, numWaters, replaceableMols, ionCutoff=0.05*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True, residueTemplates=dict()):
"""Adds ions to the system by replacing certain molecules.
Parameters
......@@ -281,6 +281,12 @@ class Modeller(object):
Note that only monovalent ions are currently supported.
neutralize : bool=True
whether to add ions to neutralize the system
residueTemplates : dict=dict()
specifies which template the ForceField should use for particular residues. The keys
should be Residue objects from the Topology, and the values should be the names of the
templates to use for them. This is useful when a ForceField contains multiple templates
that can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
"""
posIonElements = {'Cs+': elem.cesium, 'K+': elem.potassium,
......@@ -302,7 +308,7 @@ class Modeller(object):
negativeElement = negIonElements[negativeIon]
# Determine the total charge of the system
system = forcefield.createSystem(self.topology)
system = forcefield.createSystem(self.topology, residueTemplates=residueTemplates)
for i in range(system.getNumForces()):
if isinstance(system.getForce(i), NonbondedForce):
nonbonded = system.getForce(i)
......@@ -375,7 +381,7 @@ class Modeller(object):
self.topology = modeller.topology
self.positions = modeller.positions
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, boxShape='cube', positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
def addSolvent(self, forcefield, model='tip3p', boxSize=None, boxVectors=None, padding=None, numAdded=None, boxShape='cube', positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True, residueTemplates=dict()):
"""Add solvent (both water and ions) to the model to fill a periodic box.
The algorithm works as follows:
......@@ -439,6 +445,12 @@ class Modeller(object):
Note that only monovalent ions are currently supported.
neutralize : bool=True
whether to add ions to neutralize the system
residueTemplates : dict=dict()
specifies which template the ForceField should use for particular residues. The keys
should be Residue objects from the Topology, and the values should be the names of the
templates to use for them. This is useful when a ForceField contains multiple templates
that can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
"""
if len([x for x in (boxSize, boxVectors, padding, numAdded) if x is not None]) > 1:
raise ValueError('At most one of the following arguments may be specified: boxSize, boxVectors, padding, numAdded')
......@@ -504,7 +516,7 @@ class Modeller(object):
# Have the ForceField build a System for the solute from which we can determine van der Waals radii.
system = forcefield.createSystem(self.topology)
system = forcefield.createSystem(self.topology, residueTemplates=residueTemplates)
nonbonded = None
for i in range(system.getNumForces()):
if isinstance(system.getForce(i), NonbondedForce):
......@@ -644,7 +656,7 @@ class Modeller(object):
numTotalWaters = len(waterPos)
# Add ions to neutralize the system.
self._addIons(forcefield, numTotalWaters, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize)
self._addIons(forcefield, numTotalWaters, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize, residueTemplates=residueTemplates)
def _computeBoxVectors(self, width, boxShape):
"""Compute the periodic box vectors given a box width and shape."""
......@@ -721,7 +733,7 @@ class Modeller(object):
terminal = hydrogen.attrib['terminal']
data.hydrogens.append(Modeller._Hydrogen(hydrogen.attrib['name'], hydrogen.attrib['parent'], maxph, atomVariants, terminal))
def addHydrogens(self, forcefield=None, pH=7.0, variants=None, platform=None):
def addHydrogens(self, forcefield=None, pH=7.0, variants=None, platform=None, residueTemplates=dict()):
"""Add missing hydrogens to the model.
Some residues can exist in multiple forms depending on the pH and properties of the local environment. These
......@@ -787,6 +799,12 @@ class Modeller(object):
platform : Platform=None
the Platform to use when computing the hydrogen atom positions. If
this is None, the default Platform will be used.
residueTemplates : dict=dict()
specifies which template the ForceField should use for particular residues. The keys
should be Residue objects from the Topology, and the values should be the names of the
templates to use for them. This is useful when a ForceField contains multiple templates
that can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
Returns
-------
......@@ -991,7 +1009,7 @@ class Modeller(object):
if forcefield is not None:
# Use the ForceField the user specified.
system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic)
system = forcefield.createSystem(newTopology, rigidWater=False, nonbondedMethod=CutoffNonPeriodic, residueTemplates=residueTemplates)
atoms = list(newTopology.atoms())
for i in range(system.getNumParticles()):
if i not in addedH:
......@@ -1051,7 +1069,7 @@ class Modeller(object):
del context
return actualVariants
def addExtraParticles(self, forcefield, ignoreExternalBonds=False):
def addExtraParticles(self, forcefield, ignoreExternalBonds=False, residueTemplates=dict()):
"""Add missing extra particles to the model that are required by a force
field.
......@@ -1074,6 +1092,12 @@ class Modeller(object):
If true, ignore external bonds when matching residues to templates.
This is useful when the Topology represents one piece of a larger
molecule, so chains are not terminated properly.
residueTemplates : dict=dict()
specifies which template the ForceField should use for particular residues. The keys
should be Residue objects from the Topology, and the values should be the names of the
templates to use for them. This is useful when a ForceField contains multiple templates
that can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
"""
# Record which atoms are bonded to each other atom.
......@@ -1093,7 +1117,7 @@ class Modeller(object):
# Identify the template to use for each residue.
templates = forcefield._matchAllResiduesToTemplates(ForceField._SystemData(self.topology), self.topology, {}, False, True, False)
templates = forcefield._matchAllResiduesToTemplates(ForceField._SystemData(self.topology), self.topology, residueTemplates, False, True, False)
# Create the new Topology.
......@@ -1206,7 +1230,7 @@ class Modeller(object):
# There were particles whose position we couldn't identify before, since they were neither virtual sites nor Drude particles.
# Try to figure them out based on bonds. First, use the ForceField to create a list of every bond involving one of them.
system = forcefield.createSystem(newTopology, constraints=AllBonds)
system = forcefield.createSystem(newTopology, constraints=AllBonds, residueTemplates=residueTemplates)
bonds = []
for i in range(system.getNumConstraints()):
bond = system.getConstraintParameters(i)
......@@ -1234,7 +1258,7 @@ class Modeller(object):
self.positions = newPositions
def addMembrane(self, forcefield, lipidType='POPC', membraneCenterZ=0*nanometer, minimumPadding=1*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True):
def addMembrane(self, forcefield, lipidType='POPC', membraneCenterZ=0*nanometer, minimumPadding=1*nanometer, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*molar, neutralize=True, residueTemplates=dict()):
"""Add a lipid membrane to the model.
This method actually adds both a membrane and a water box. It is best to build them together,
......@@ -1286,6 +1310,12 @@ class Modeller(object):
Note that only monovalent ions are currently supported.
neutralize : bool=True
whether to add ions to neutralize the system
residueTemplates : dict=dict()
specifies which template the ForceField should use for particular residues. The keys
should be Residue objects from the Topology, and the values should be the names of the
templates to use for them. This is useful when a ForceField contains multiple templates
that can match the same residue (e.g Fe2+ and Fe3+ templates in the ForceField for a
monoatomic iron ion in the Topology).
"""
if 'topology' in dir(lipidType) and 'positions' in dir(lipidType):
patch = lipidType
......@@ -1451,8 +1481,8 @@ class Modeller(object):
# Create a System for the lipids, then add in the protein as stationary particles.
system = forcefield.createSystem(membraneTopology, nonbondedMethod=CutoffPeriodic)
proteinSystem = forcefield.createSystem(self.topology, nonbondedMethod=CutoffNonPeriodic)
system = forcefield.createSystem(membraneTopology, nonbondedMethod=CutoffPeriodic, residueTemplates=residueTemplates)
proteinSystem = forcefield.createSystem(self.topology, nonbondedMethod=CutoffNonPeriodic, residueTemplates=residueTemplates)
numMembraneParticles = system.getNumParticles()
numProteinParticles = proteinSystem.getNumParticles()
for i in range(numProteinParticles):
......@@ -1520,7 +1550,7 @@ class Modeller(object):
needExtraWater = (boxSizeZ > patchSize[2])
if needExtraWater:
modeller.addSolvent(forcefield, neutralize=False)
modeller.addSolvent(forcefield, neutralize=False, residueTemplates=residueTemplates)
# Record the positions of all waters that have been added.
......@@ -1587,7 +1617,7 @@ class Modeller(object):
if lowerZBoundary < waterZ.value_in_unit(nanometer) < upperZBoundary:
del waterPos[wRes]
self._addIons(forcefield, numTotalWaters, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize)
self._addIons(forcefield, numTotalWaters, waterPos, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength, neutralize=neutralize, residueTemplates=residueTemplates)
class _CellList(object):
......
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