def ToSystem ( self, mmModel = None ):
"""Create a system."""
system = None
if self.QPARSED:
# . Sequence data and then basic system.
sequence = self.ToSequence ( )
system = System.FromSequence ( sequence )
system.label = " ".join ( self.title )
# . Assign atomic numbers using atomic numbers if they exist, otherwise masses.
atomicNumbers = getattr ( self, "atomic_number", None )
if atomicNumbers is None:
for ( mass, atom ) in zip ( self.mass, system.atoms ):
atom.atomicNumber = PeriodicTable.AtomicNumberFromMass ( mass )
else:
for ( n, atom ) in zip ( atomicNumbers, system.atoms ):
atom.atomicNumber = n
# . The MM model (with some options).
if mmModel is None: mmModel = MMModelAMBER ( )
# . 1-4 scaling factors.
if hasattr ( self, "scee_scale_factor" ): mmModel.electrostaticScale14 = 1.0 / self.scee_scale_factor[0]
if hasattr ( self, "scnb_scale_factor" ): mmModel.lennardJonesScale14 = 1.0 / self.scnb_scale_factor[0]
# . Define the model.
system.DefineMMModel ( mmModel, buildModel = False )
# . The MM atoms.
mm = self.ToMMAtomContainer ( )
if mm is not None: system.energyModel.mmAtoms = mm
# . Various MM terms.
mmTerms = []
mm = self.ToHarmonicBondContainer ( )
if mm is not None: mmTerms.append ( mm )
mm = self.ToHarmonicAngleContainer ( )
if mm is not None: mmTerms.append ( mm )
self.UntangleDihedralsAnd14s ( )
if self.dihedrals is not None: mmTerms.append ( self.dihedrals )
if self.impropers is not None: mmTerms.append ( self.impropers )
if len ( mmTerms ) > 0: system.energyModel.mmTerms = MMTermContainer ( mmTerms )
# . Remaining MM data.
if self.interactions14 is not None: system.energyModel.interactions14 = self.interactions14
mm = self.ToExclusionsPairList ( )
if mm is not None: system.energyModel.exclusions = mm
mm = self.ToLJParameterContainer ( mmModel.lennardJonesStyle )
if mm is not None:
system.energyModel.ljParameters = mm
# . 1-4 parameters.
scale = mmModel.lennardJonesScale14
if scale != 0.0:
lj14 = Clone ( mm )
lj14.label = "1-4 Lennard-Jones"
lj14.Scale ( scale )
system.energyModel.ljParameters14 = lj14
# . Symmetry data.
self.ToSymmetry ( system )
return system
def ParseMass(self, tokens):
"""Mass line."""
if len(tokens) < 3: self.Warning("Invalid MASS line.", False)
else:
index = int(tokens[0])
label = tokens[1]
mass = float(tokens[2])
if len(tokens) > 3:
atomicNumber = PeriodicTable.AtomicNumber(tokens[3])
else:
atomicNumber = PeriodicTable.AtomicNumberFromMass(mass)
self.atomTypes[label] = CHARMMTopologyAtomType(
atomicNumber=atomicNumber, index=index, label=label, mass=mass)
def ToSystem(self, mmModel=None, parameters=None):
"""Create a system."""
system = None
if self.QPARSED:
# . Get the sequence.
sequence = self.ToSequence()
# . Basic system.
system = System.FromSequence(sequence)
system.label = " ".join(self.title)
# . Assign atomic numbers from masses.
for (datum, atom) in zip(self.atoms, system.atoms):
atom.atomicNumber = PeriodicTable.AtomicNumberFromMass(
datum[7])
# . The MM model.
if mmModel is None: mmModel = MMModelCHARMM()
# . Build the model but only when PSF files are in XPLOR format.
if (mmModel is not None) and (parameters
is not None) and (self.isXPLOR):
system.DefineMMModel(mmModel, buildModel=False)
# . The MM atoms.
mm = self.ToMMAtomContainer()
if mm is not None: system.energyModel.mmAtoms = mm
# . Various MM terms.
mmTerms = []
mm = self.ToHarmonicBondContainer(
rawParameters=parameters.bonds)
if mm is not None: mmTerms.append(mm)
mm = self.ToHarmonicAngleContainer(
rawParameters=parameters.angles)
if mm is not None: mmTerms.append(mm)
mm = self.ToHarmonicUreyBradleyContainer(
rawParameters=parameters.ureybradleys)
if mm is not None: mmTerms.append(mm)
mm = self.ToFourierDihedralContainer(
rawParameters=parameters.dihedrals,
rawParametersWild=parameters.dihedralwilds)
if mm is not None: mmTerms.append(mm)
mm = self.ToHarmonicImproperContainer(
rawParameters=parameters.impropers,
rawParametersWild=parameters.improperwilds)
if mm is not None: mmTerms.append(mm)
mm = self.ToCMAPDihedralContainer(
rawParameters=parameters.cmaps)
if mm is not None: mmTerms.append(mm)
if len(mmTerms) > 0:
system.energyModel.mmTerms = MMTermContainer(mmTerms)
# . Exclusions.
(exclusions, interactions14) = self.ToExclusionPairLists()
if exclusions is not None:
system.energyModel.exclusions = exclusions
if interactions14 is not None:
system.energyModel.interactions14 = interactions14
# . LJ terms.
( ljParameters, ljParameters14 ) = self.ToLJParameterContainers ( parameters = parameters.nonbonds , parametersWild = parameters.nonbondwilds, \
parameters14 = parameters.nonbond14s, parameters14Wild = parameters.nonbond14wilds )
if ljParameters is not None:
system.energyModel.ljParameters = ljParameters
if ljParameters14 is not None:
system.energyModel.ljParameters14 = ljParameters14
# . Fixed atoms - do after MM model so MM terms are appropriately affected.
self.ToFixedAtoms(system)
return system