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Commit b2212517 authored by peastman's avatar peastman
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Merge pull request #506 from peastman/forcefield 

Began creating API for programmatically building and editing ForceFields
parents e62739d2 9bce462d
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wrappers/python/simtk/openmm/app/forcefield.py
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......@@ -40,6 +40,11 @@ import simtk.unit as unit
import element as elem
from simtk.openmm.app import Topology
def _convertParameterToNumber(param):
if unit.is_quantity(param):
return mm.stripUnits((param,))[0]
return float(param)
# Enumerated values for nonbonded method
class NoCutoff(object):
......@@ -115,13 +120,7 @@ class ForceField(object):
if tree.getroot().find('AtomTypes') is not None:
for type in tree.getroot().find('AtomTypes').findall('Type'):
element = None
if 'element' in type.attrib:
element = elem.get_by_symbol(type.attrib['element'])
name = type.attrib['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: '+name)
self._atomTypes[name] = (type.attrib['class'], float(type.attrib['mass']), element)
self.registerAtomType(type.attrib)
# Load the residue templates.
......@@ -129,38 +128,17 @@ class ForceField(object):
for residue in root.find('Residues').findall('Residue'):
resName = residue.attrib['name']
template = ForceField._TemplateData(resName)
self._templates[resName] = template
for atom in residue.findall('Atom'):
template.atoms.append(ForceField._TemplateAtomData(atom.attrib['name'], atom.attrib['type'], self._atomTypes[atom.attrib['type']][2]))
for site in residue.findall('VirtualSite'):
template.virtualSites.append(ForceField._VirtualSiteData(site))
for bond in residue.findall('Bond'):
b = (int(bond.attrib['from']), int(bond.attrib['to']))
template.bonds.append(b)
template.atoms[b[0]].bondedTo.append(b[1])
template.atoms[b[1]].bondedTo.append(b[0])
template.addBond(int(bond.attrib['from']), int(bond.attrib['to']))
for bond in residue.findall('ExternalBond'):
b = int(bond.attrib['from'])
template.externalBonds.append(b)
template.atoms[b].externalBonds += 1
for template in self._templates.values():
signature = _createResidueSignature([atom.element for atom in template.atoms])
if signature in self._templateSignatures:
self._templateSignatures[signature].append(template)
else:
self._templateSignatures[signature] = [template]
# Build sets of every atom type belonging to each class
for type in self._atomTypes:
atomClass = self._atomTypes[type][0]
if atomClass in self._atomClasses:
typeSet = self._atomClasses[atomClass]
else:
typeSet = set()
self._atomClasses[atomClass] = typeSet
typeSet.add(type)
self._atomClasses[''].add(type)
self.registerResidueTemplate(template)
# Load force definitions
......@@ -171,12 +149,53 @@ class ForceField(object):
# Load scripts
for node in tree.getroot().findall('Script'):
self._scripts.append(node.text)
self.registerScript(node.text)
def _findAtomTypes(self, node, num):
def getGenerators(self):
"""Get the list of all registered generators."""
return self._forces
def registerGenerator(self, generator):
"""Register a new generator."""
self._forces.append(generator)
def registerAtomType(self, parameters):
"""Register a new atom type."""
name = parameters['name']
if name in self._atomTypes:
raise ValueError('Found multiple definitions for atom type: '+name)
atomClass = parameters['class']
mass = _convertParameterToNumber(parameters['mass'])
element = None
if 'element' in parameters:
element = parameters['element']
if not isinstance(element, elem.Element):
element = elem.get_by_symbol(element)
self._atomTypes[name] = (atomClass, mass, element)
if atomClass in self._atomClasses:
typeSet = self._atomClasses[atomClass]
else:
typeSet = set()
self._atomClasses[atomClass] = typeSet
typeSet.add(name)
self._atomClasses[''].add(name)
def registerResidueTemplate(self, template):
"""Register a new residue template."""
self._templates[template.name] = template
signature = _createResidueSignature([atom.element for atom in template.atoms])
if signature in self._templateSignatures:
self._templateSignatures[signature].append(template)
else:
self._templateSignatures[signature] = [template]
def registerScript(self, script):
"""Register a new script to be executed after building the System."""
self._scripts.append(script)
def _findAtomTypes(self, attrib, num):
"""Parse the attributes on an XML tag to find the set of atom types for each atom it involves."""
types = []
attrib = node.attrib
for i in range(num):
if num == 1:
suffix = ''
......@@ -186,7 +205,7 @@ class ForceField(object):
typeAttrib = 'type'+suffix
if classAttrib in attrib:
if typeAttrib in attrib:
raise ValueError('Tag specifies both a type and a class for the same atom: '+etree.tostring(node))
raise ValueError('Specified both a type and a class for the same atom: '+str(attrib))
if attrib[classAttrib] not in self._atomClasses:
types.append(None) # Unknown atom class
else:
......@@ -198,18 +217,17 @@ class ForceField(object):
types.append([attrib[typeAttrib]])
return types
def _parseTorsion(self, node):
def _parseTorsion(self, attrib):
"""Parse the node defining a torsion."""
types = self._findAtomTypes(node, 4)
types = self._findAtomTypes(attrib, 4)
if None in types:
return None
torsion = PeriodicTorsion(types)
attrib = node.attrib
index = 1
while 'phase%d'%index in attrib:
torsion.periodicity.append(int(attrib['periodicity%d'%index]))
torsion.phase.append(float(attrib['phase%d'%index]))
torsion.k.append(float(attrib['k%d'%index]))
torsion.phase.append(_convertParameterToNumber(attrib['phase%d'%index]))
torsion.k.append(_convertParameterToNumber(attrib['k%d'%index]))
index += 1
return torsion
......@@ -235,6 +253,11 @@ class ForceField(object):
self.bonds = []
self.externalBonds = []
def addBond(self, atom1, atom2):
self.bonds.append((atom1, atom2))
self.atoms[atom1].bondedTo.append(atom2)
self.atoms[atom2].bondedTo.append(atom1)
class _TemplateAtomData:
"""Inner class used to encapsulate data about an atom in a residue template definition."""
def __init__(self, name, type, element):
......@@ -660,23 +683,27 @@ def _findMatchErrors(forcefield, res):
class HarmonicBondGenerator:
"""A HarmonicBondGenerator constructs a HarmonicBondForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.types1 = []
self.types2 = []
self.length = []
self.k = []
def registerBond(self, parameters):
types = self.ff._findAtomTypes(parameters, 2)
if None not in types:
self.types1.append(types[0])
self.types2.append(types[1])
self.length.append(_convertParameterToNumber(parameters['length']))
self.k.append(_convertParameterToNumber(parameters['k']))
@staticmethod
def parseElement(element, ff):
generator = HarmonicBondGenerator()
ff._forces.append(generator)
generator = HarmonicBondGenerator(ff)
ff.registerGenerator(generator)
for bond in element.findall('Bond'):
types = ff._findAtomTypes(bond, 2)
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.length.append(float(bond.attrib['length']))
generator.k.append(float(bond.attrib['k']))
generator.registerBond(bond.attrib)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
existing = [sys.getForce(i) for i in range(sys.getNumForces())]
......@@ -707,25 +734,29 @@ parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement
class HarmonicAngleGenerator:
"""A HarmonicAngleGenerator constructs a HarmonicAngleForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.types1 = []
self.types2 = []
self.types3 = []
self.angle = []
self.k = []
def registerAngle(self, parameters):
types = self.ff._findAtomTypes(parameters, 3)
if None not in types:
self.types1.append(types[0])
self.types2.append(types[1])
self.types3.append(types[2])
self.angle.append(_convertParameterToNumber(parameters['angle']))
self.k.append(_convertParameterToNumber(parameters['k']))
@staticmethod
def parseElement(element, ff):
generator = HarmonicAngleGenerator()
ff._forces.append(generator)
generator = HarmonicAngleGenerator(ff)
ff.registerGenerator(generator)
for angle in element.findall('Angle'):
types = ff._findAtomTypes(angle, 3)
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
generator.types3.append(types[2])
generator.angle.append(float(angle.attrib['angle']))
generator.k.append(float(angle.attrib['k']))
generator.registerAngle(angle.attrib)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
existing = [sys.getForce(i) for i in range(sys.getNumForces())]
......@@ -789,23 +820,29 @@ class PeriodicTorsion:
class PeriodicTorsionGenerator:
"""A PeriodicTorsionGenerator constructs a PeriodicTorsionForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.proper = []
self.improper = []
def registerProperTorsion(self, parameters):
torsion = self.ff._parseTorsion(parameters)
if torsion is not None:
self.proper.append(torsion)
def registerImproperTorsion(self, parameters):
torsion = self.ff._parseTorsion(parameters)
if torsion is not None:
self.improper.append(torsion)
@staticmethod
def parseElement(element, ff):
generator = PeriodicTorsionGenerator()
generator.ff = ff
ff._forces.append(generator)
generator = PeriodicTorsionGenerator(ff)
ff.registerGenerator(generator)
for torsion in element.findall('Proper'):
torsion = ff._parseTorsion(torsion)
if torsion is not None:
generator.proper.append(torsion)
generator.registerProperTorsion(torsion.attrib)
for torsion in element.findall('Improper'):
torsion = ff._parseTorsion(torsion)
if torsion is not None:
generator.improper.append(torsion)
generator.registerImproperTorsion(torsion.attrib)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
existing = [sys.getForce(i) for i in range(sys.getNumForces())]
......@@ -888,21 +925,21 @@ class RBTorsion:
class RBTorsionGenerator:
"""An RBTorsionGenerator constructs an RBTorsionForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.proper = []
self.improper = []
@staticmethod
def parseElement(element, ff):
generator = RBTorsionGenerator()
generator.ff = ff
ff._forces.append(generator)
generator = RBTorsionGenerator(ff)
ff.registerGenerator(generator)
for torsion in element.findall('Proper'):
types = ff._findAtomTypes(torsion, 4)
types = ff._findAtomTypes(torsion.attrib, 4)
if None not in types:
generator.proper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
for torsion in element.findall('Improper'):
types = ff._findAtomTypes(torsion, 4)
types = ff._findAtomTypes(torsion.attrib, 4)
if None not in types:
generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
......@@ -984,15 +1021,15 @@ class CMAPTorsion:
class CMAPTorsionGenerator:
"""A CMAPTorsionGenerator constructs a CMAPTorsionForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.torsions = []
self.maps = []
@staticmethod
def parseElement(element, ff):
generator = CMAPTorsionGenerator()
generator.ff = ff
ff._forces.append(generator)
generator = CMAPTorsionGenerator(ff)
ff.registerGenerator(generator)
for map in element.findall('Map'):
values = [float(x) for x in map.text.split()]
size = sqrt(len(values))
......@@ -1000,7 +1037,7 @@ class CMAPTorsionGenerator:
raise ValueError('CMAP must have the same number of elements along each dimension')
generator.maps.append(values)
for torsion in element.findall('Torsion'):
types = ff._findAtomTypes(torsion, 5)
types = ff._findAtomTypes(torsion.attrib, 5)
if None not in types:
generator.torsions.append(CMAPTorsion(types, int(torsion.attrib['map'])))
......@@ -1064,28 +1101,32 @@ parsers["CMAPTorsionForce"] = CMAPTorsionGenerator.parseElement
class NonbondedGenerator:
"""A NonbondedGenerator constructs a NonbondedForce."""
def __init__(self, coulomb14scale, lj14scale):
def __init__(self, forcefield, coulomb14scale, lj14scale):
self.ff = forcefield
self.coulomb14scale = coulomb14scale
self.lj14scale = lj14scale
self.typeMap = {}
def registerAtom(self, parameters):
types = self.ff._findAtomTypes(parameters, 1)
if None not in types:
values = (_convertParameterToNumber(parameters['charge']), _convertParameterToNumber(parameters['sigma']), _convertParameterToNumber(parameters['epsilon']))
for t in types[0]:
self.typeMap[t] = values
@staticmethod
def parseElement(element, ff):
existing = [f for f in ff._forces if isinstance(f, NonbondedGenerator)]
if len(existing) == 0:
generator = NonbondedGenerator(float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale']))
ff._forces.append(generator)
generator = NonbondedGenerator(ff, float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale']))
ff.registerGenerator(generator)
else:
# Multiple <NonbondedForce> tags were found, probably in different files. Simply add more types to the existing one.
generator = existing[0]
if generator.coulomb14scale != float(element.attrib['coulomb14scale']) or generator.lj14scale != float(element.attrib['lj14scale']):
raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['sigma']), float(atom.attrib['epsilon']))
for t in types[0]:
generator.typeMap[t] = values
generator.registerAtom(atom.attrib)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
......@@ -1149,24 +1190,28 @@ parsers["NonbondedForce"] = NonbondedGenerator.parseElement
class GBSAOBCGenerator:
"""A GBSAOBCGenerator constructs a GBSAOBCForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.typeMap = {}
def registerAtom(self, parameters):
types = self.ff._findAtomTypes(parameters, 1)
if None not in types:
values = (_convertParameterToNumber(parameters['charge']), _convertParameterToNumber(parameters['radius']), _convertParameterToNumber(parameters['scale']))
for t in types[0]:
self.typeMap[t] = values
@staticmethod
def parseElement(element, ff):
existing = [f for f in ff._forces if isinstance(f, GBSAOBCGenerator)]
if len(existing) == 0:
generator = GBSAOBCGenerator()
ff._forces.append(generator)
generator = GBSAOBCGenerator(ff)
ff.registerGenerator(generator)
else:
# Multiple <GBSAOBCForce> tags were found, probably in different files. Simply add more types to the existing one.
generator = existing[0]
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['scale']))
for t in types[0]:
generator.typeMap[t] = values
generator.registerAtom(atom.attrib)
def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
......@@ -1206,7 +1251,6 @@ class GBVIGenerator:
"""A GBVIGenerator constructs a GBVIForce."""
def __init__(self,ff):
self.ff = ff
self.fixedParameters = {}
self.fixedParameters['soluteDielectric'] = 1.0
......@@ -1224,9 +1268,9 @@ class GBVIGenerator:
if (key in element.attrib):
generator.fixedParameters[key] = float(element.attrib[key])
ff._forces.append(generator)
ff.registerGenerator(generator)
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
types = ff._findAtomTypes(atom.attrib, 1)
if None not in types:
values = (float(atom.attrib['charge']), float(atom.attrib['radius']), float(atom.attrib['gamma']))
for t in types[0]:
......@@ -1292,7 +1336,8 @@ parsers["GBVIForce"] = GBVIGenerator.parseElement
class CustomBondGenerator:
"""A CustomBondGenerator constructs a CustomBondForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.types1 = []
self.types2 = []
self.globalParams = {}
......@@ -1301,15 +1346,15 @@ class CustomBondGenerator:
@staticmethod
def parseElement(element, ff):
generator = CustomBondGenerator()
ff._forces.append(generator)
generator = CustomBondGenerator(ff)
ff.registerGenerator(generator)
generator.energy = element.attrib['energy']
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerBondParameter'):
generator.perBondParams.append(param.attrib['name'])
for bond in element.findall('Bond'):
types = ff._findAtomTypes(bond, 2)
types = ff._findAtomTypes(bond.attrib, 2)
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -1339,7 +1384,8 @@ parsers["CustomBondForce"] = CustomBondGenerator.parseElement
class CustomAngleGenerator:
"""A CustomAngleGenerator constructs a CustomAngleForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.types1 = []
self.types2 = []
self.types3 = []
......@@ -1349,15 +1395,15 @@ class CustomAngleGenerator:
@staticmethod
def parseElement(element, ff):
generator = CustomAngleGenerator()
ff._forces.append(generator)
generator = CustomAngleGenerator(ff)
ff.registerGenerator(generator)
generator.energy = element.attrib['energy']
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerAngleParameter'):
generator.perAngleParams.append(param.attrib['name'])
for angle in element.findall('Angle'):
types = ff._findAtomTypes(angle, 3)
types = ff._findAtomTypes(angle.attrib, 3)
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -1401,7 +1447,8 @@ class CustomTorsion:
class CustomTorsionGenerator:
"""A CustomTorsionGenerator constructs a CustomTorsionForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.proper = []
self.improper = []
self.globalParams = {}
......@@ -1409,20 +1456,19 @@ class CustomTorsionGenerator:
@staticmethod
def parseElement(element, ff):
generator = CustomTorsionGenerator()
generator.ff = ff
ff._forces.append(generator)
generator = CustomTorsionGenerator(ff)
ff.registerGenerator(generator)
generator.energy = element.attrib['energy']
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerTorsionParameter'):
generator.perTorsionParams.append(param.attrib['name'])
for torsion in element.findall('Proper'):
types = ff._findAtomTypes(torsion, 4)
types = ff._findAtomTypes(torsion.attrib, 4)
if None not in types:
generator.proper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
for torsion in element.findall('Improper'):
types = ff._findAtomTypes(torsion, 4)
types = ff._findAtomTypes(torsion.attrib, 4)
if None not in types:
generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
......@@ -1491,7 +1537,8 @@ parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement
class CustomNonbondedGenerator:
"""A CustomNonbondedGenerator constructs a CustomNonbondedForce."""
def __init__(self, energy, bondCutoff):
def __init__(self, forcefield, energy, bondCutoff):
self.ff = forcefield
self.energy = energy
self.bondCutoff = bondCutoff
self.typeMap = {}
......@@ -1501,14 +1548,14 @@ class CustomNonbondedGenerator:
@staticmethod
def parseElement(element, ff):
generator = CustomNonbondedGenerator(element.attrib['energy'], int(element.attrib['bondCutoff']))
ff._forces.append(generator)
generator = CustomNonbondedGenerator(ff, element.attrib['energy'], int(element.attrib['bondCutoff']))
ff.registerGenerator(generator)
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerParticleParameter'):
generator.perParticleParams.append(param.attrib['name'])
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
types = ff._findAtomTypes(atom.attrib, 1)
if None not in types:
values = [float(atom.attrib[param]) for param in generator.perParticleParams]
for t in types[0]:
......@@ -1589,7 +1636,8 @@ parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement
class CustomGBGenerator:
"""A CustomGBGenerator constructs a CustomGBForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.typeMap = {}
self.globalParams = {}
self.perParticleParams = []
......@@ -1599,14 +1647,14 @@ class CustomGBGenerator:
@staticmethod
def parseElement(element, ff):
generator = CustomGBGenerator()
ff._forces.append(generator)
generator = CustomGBGenerator(ff)
ff.registerGenerator(generator)
for param in element.findall('GlobalParameter'):
generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
for param in element.findall('PerParticleParameter'):
generator.perParticleParams.append(param.attrib['name'])
for atom in element.findall('Atom'):
types = ff._findAtomTypes(atom, 1)
types = ff._findAtomTypes(atom.attrib, 1)
if None not in types:
values = [float(atom.attrib[param]) for param in generator.perParticleParams]
for t in types[0]:
......@@ -1729,7 +1777,7 @@ class AmoebaBondGenerator:
generator = AmoebaBondGenerator(float(element.attrib['bond-cubic']), float(element.attrib['bond-quartic']))
forceField._forces.append(generator)
for bond in element.findall('Bond'):
types = forceField._findAtomTypes(bond, 2)
types = forceField._findAtomTypes(bond.attrib, 2)
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -1842,7 +1890,7 @@ class AmoebaAngleGenerator:
generator = AmoebaAngleGenerator(forceField, float(element.attrib['angle-cubic']), float(element.attrib['angle-quartic']), float(element.attrib['angle-pentic']), float(element.attrib['angle-sextic']))
forceField._forces.append(generator)
for angle in element.findall('Angle'):
types = forceField._findAtomTypes(angle, 3)
types = forceField._findAtomTypes(angle.attrib, 3)
if None not in types:
generator.types1.append(types[0])
......@@ -2327,7 +2375,7 @@ class AmoebaTorsionGenerator:
# where ti=[amplitude_i,angle_i]
for torsion in element.findall('Torsion'):
types = forceField._findAtomTypes(torsion, 4)
types = forceField._findAtomTypes(torsion.attrib, 4)
if None not in types:
generator.types1.append(types[0])
......@@ -2438,7 +2486,7 @@ class AmoebaPiTorsionGenerator:
forceField._forces.append(generator)
for piTorsion in element.findall('PiTorsion'):
types = forceField._findAtomTypes(piTorsion, 2)
types = forceField._findAtomTypes(piTorsion.attrib, 2)
if None not in types:
generator.types1.append(types[0])
generator.types2.append(types[1])
......@@ -2557,7 +2605,7 @@ class AmoebaTorsionTorsionGenerator:
# <TorsionTorsion class1="3" class2="1" class3="2" class4="3" class5="1" grid="0" nx="25" ny="25" />
for torsionTorsion in element.findall('TorsionTorsion'):
types = forceField._findAtomTypes(torsionTorsion, 5)
types = forceField._findAtomTypes(torsionTorsion.attrib, 5)
if None not in types:
generator.types1.append(types[0])
......@@ -2795,7 +2843,7 @@ class AmoebaStretchBendGenerator:
# <StretchBend class1="2" class2="1" class3="4" k1="3.14005676385" k2="3.14005676385" />
for stretchBend in element.findall('StretchBend'):
types = forceField._findAtomTypes(stretchBend, 3)
types = forceField._findAtomTypes(stretchBend.attrib, 3)
if None not in types:
generator.types1.append(types[0])
......@@ -2952,7 +3000,7 @@ class AmoebaVdwGenerator:
# sigma is modified based on radiustype and radiussize
for atom in element.findall('Vdw'):
types = forceField._findAtomTypes(atom, 1)
types = forceField._findAtomTypes(atom.attrib, 1)
if None not in types:
values = [float(atom.attrib['sigma']), float(atom.attrib['epsilon']), float(atom.attrib['reduction'])]
......@@ -3225,7 +3273,7 @@ class AmoebaMultipoleGenerator:
# set type map: [ kIndices, multipoles, AMOEBA/OpenMM axis type]
for atom in element.findall('Multipole'):
types = forceField._findAtomTypes(atom, 1)
types = forceField._findAtomTypes(atom.attrib, 1)
if None not in types:
# k-indices not provided default to 0
......@@ -3282,7 +3330,7 @@ class AmoebaMultipoleGenerator:
# polarization parameters
for atom in element.findall('Polarize'):
types = forceField._findAtomTypes(atom, 1)
types = forceField._findAtomTypes(atom.attrib, 1)
if None not in types:
classIndex = atom.attrib['type']
......@@ -3810,7 +3858,7 @@ class AmoebaWcaDispersionGenerator:
# typeMap[] = [ radius, epsilon ]
for atom in element.findall('WcaDispersion'):
types = forceField._findAtomTypes(atom, 1)
types = forceField._findAtomTypes(atom.attrib, 1)
if None not in types:
values = [float(atom.attrib['radius']), float(atom.attrib['epsilon'])]
......@@ -4154,7 +4202,7 @@ class AmoebaUreyBradleyGenerator:
generator = AmoebaUreyBradleyGenerator()
forceField._forces.append(generator)
for bond in element.findall('UreyBradley'):
types = forceField._findAtomTypes(bond, 3)
types = forceField._findAtomTypes(bond.attrib, 3)
if None not in types:
generator.types1.append(types[0])
......@@ -4205,20 +4253,21 @@ parsers["AmoebaUreyBradleyForce"] = AmoebaUreyBradleyGenerator.parseElement
class DrudeGenerator:
"""A DrudeGenerator constructs a DrudeForce."""
def __init__(self):
def __init__(self, forcefield):
self.ff = forcefield
self.typeMap = {}
@staticmethod
def parseElement(element, ff):
existing = [f for f in ff._forces if isinstance(f, DrudeGenerator)]
if len(existing) == 0:
generator = DrudeGenerator()
ff._forces.append(generator)
generator = DrudeGenerator(ff)
ff.registerGenerator(generator)
else:
# Multiple <DrudeForce> tags were found, probably in different files. Simply add more types to the existing one.
generator = existing[0]
for particle in element.findall('Particle'):
types = ff._findAtomTypes(particle, 5)
types = ff._findAtomTypes(particle.attrib, 5)
if None not in types[:2]:
aniso12 = 0.0
aniso34 = 0.0
......
wrappers/python/tests/TestForceField.py
View file @ b2212517
......@@ -4,6 +4,7 @@ from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.app.element as elem
import simtk.openmm.app.forcefield as forcefield
class TestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method."""
......@@ -150,6 +151,41 @@ class TestForceField(unittest.TestCase):
numDifferences += 1
self.assertTrue(numDifferences < system.getNumParticles()/20) # Tolerate occasional differences from numerical error
def test_ProgrammaticForceField(self):
"""Test building a ForceField programmatically."""
# Build the ForceField for TIP3P programmatically.
ff = ForceField()
ff.registerAtomType({'name':'tip3p-O', 'class':'OW', 'mass':15.99943*daltons, 'element':elem.oxygen})
ff.registerAtomType({'name':'tip3p-H', 'class':'HW', 'mass':1.007947*daltons, 'element':elem.hydrogen})
residue = ForceField._TemplateData('HOH')
residue.atoms.append(ForceField._TemplateAtomData('O', 'tip3p-O', elem.oxygen))
residue.atoms.append(ForceField._TemplateAtomData('H1', 'tip3p-H', elem.hydrogen))
residue.atoms.append(ForceField._TemplateAtomData('H2', 'tip3p-H', elem.hydrogen))
residue.addBond(0, 1)
residue.addBond(0, 2)
ff.registerResidueTemplate(residue)
bonds = forcefield.HarmonicBondGenerator(ff)
bonds.registerBond({'class1':'OW', 'class2':'HW', 'length':0.09572*nanometers, 'k':462750.4*kilojoules_per_mole/nanometer})
ff.registerGenerator(bonds)
angles = forcefield.HarmonicAngleGenerator(ff)
angles.registerAngle({'class1':'HW', 'class2':'OW', 'class3':'HW', 'angle':1.82421813418*radians, 'k':836.8*kilojoules_per_mole/radian})
ff.registerGenerator(angles)
nonbonded = forcefield.NonbondedGenerator(ff, 0.833333, 0.5)
nonbonded.registerAtom({'type':'tip3p-O', 'charge':-0.834, 'sigma':0.31507524065751241*nanometers, 'epsilon':0.635968*kilojoules_per_mole})
nonbonded.registerAtom({'type':'tip3p-H', 'charge':0.417, 'sigma':1*nanometers, 'epsilon':0*kilojoules_per_mole})
ff.registerGenerator(nonbonded)
# Build a water box.
modeller = Modeller(Topology(), [])
modeller.addSolvent(ff, boxSize=Vec3(3, 3, 3)*nanometers)
# Create a system using the programmatic force field as well as one from an XML file.
system1 = ff.createSystem(modeller.topology)
ff2 = ForceField('tip3p.xml')
system2 = ff2.createSystem(modeller.topology)
self.assertEqual(XmlSerializer.serialize(system1), XmlSerializer.serialize(system2))
class AmoebaTestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method with the AMOEBA forcefield."""
......
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