OBForceField and OBFFConstraints

OBForceField
OBFFConstraints

Documentation

class OBForceField

AddInterGroup(self: pyOBabel.pyOBabel.OBForceField, group: pyOBabel.pyOBabel.OBBitVec) → None

AddInterGroups(self: pyOBabel.pyOBabel.OBForceField, group1: pyOBabel.pyOBabel.OBBitVec, group2: pyOBabel.pyOBabel.OBBitVec) → None

AddIntraGroup(self: pyOBabel.pyOBabel.OBForceField, group: pyOBabel.pyOBabel.OBBitVec) → None

ClearGroups(self: pyOBabel.pyOBabel.OBForceField) → None

ConjugateGradients(self: pyOBabel.pyOBabel.OBForceField, steps: int, econv: float=9.999999974752427e-07, method: int=2) → None

ConjugateGradientsInitialize(self: pyOBabel.pyOBabel.OBForceField, steps: int, econv: float=9.999999974752427e-07, method: int=2) → None

ConjugateGradientsTakeNSteps(self: pyOBabel.pyOBabel.OBForceField, n: int) → bool

CorrectVelocities(self: pyOBabel.pyOBabel.OBForceField) → None

DetectExplosion(self: pyOBabel.pyOBabel.OBForceField) → bool

DistanceGeometry(self: pyOBabel.pyOBabel.OBForceField) → None

E_Angle(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

E_Bond(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

E_Electrostatic(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

E_OOP(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

E_StrBnd(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

E_Torsion(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

E_VDW(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

EnableAllPairs(self: pyOBabel.pyOBabel.OBForceField) → None

EnableCutOff(self: pyOBabel.pyOBabel.OBForceField, enable: bool) → None

Energy(self: pyOBabel.pyOBabel.OBForceField, arg0: bool) → float

FastRotorSearch(self: pyOBabel.pyOBabel.OBForceField, permute: bool=True) → int

FindForceField(arg0: str) → pyOBabel.pyOBabel.OBForceField

FindType(arg0: str) → pyOBabel.pyOBabel.OBForceField

GenerateVelocities(self: pyOBabel.pyOBabel.OBForceField) → None

GetAtomTypes(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

GetConformers(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

GetConstraints(self: pyOBabel.pyOBabel.OBForceField) → pyOBabel.pyOBabel.OBFFConstraints

GetCoordinates(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

GetElectrostaticCutOff(self: pyOBabel.pyOBabel.OBForceField) → float

GetLineSearchType(self: pyOBabel.pyOBabel.OBForceField) → int

GetLogLevel(self: pyOBabel.pyOBabel.OBForceField) → int

GetNumElectrostaticPairs(self: pyOBabel.pyOBabel.OBForceField) → int

GetNumPairs(self: pyOBabel.pyOBabel.OBForceField) → int

GetNumVDWPairs(self: pyOBabel.pyOBabel.OBForceField) → int

GetUnit(self: pyOBabel.pyOBabel.OBForceField) → str

GetUpdateFrequency(self: pyOBabel.pyOBabel.OBForceField) → int

GetVDWCutOff(self: pyOBabel.pyOBabel.OBForceField) → float

HasAnalyticalGradients(self: pyOBabel.pyOBabel.OBForceField) → bool

HasGroups(self: pyOBabel.pyOBabel.OBForceField) → bool

IsCutOffEnabled(self: pyOBabel.pyOBabel.OBForceField) → bool

IsSetupNeeded(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

LineSearch(self: pyOBabel.pyOBabel.OBForceField, atom: pyOBabel.pyOBabel.OBAtom, direction: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

MakeNewInstance(self: pyOBabel.pyOBabel.OBForceField) → pyOBabel.pyOBabel.OBForceField

MolecularDynamicsTakeNSteps(self: pyOBabel.pyOBabel.OBForceField, steps: int, Temperature: float, timestep: float=0.001, method: int=2) → None

OBFFLog(self: pyOBabel.pyOBabel.OBForceField, msg: str) → None

ParseParamFile(self: pyOBabel.pyOBabel.OBForceField) → bool

PrintFormalCharges(self: pyOBabel.pyOBabel.OBForceField) → None

PrintPartialCharges(self: pyOBabel.pyOBabel.OBForceField) → None

PrintTypes(self: pyOBabel.pyOBabel.OBForceField) → None

PrintVelocities(self: pyOBabel.pyOBabel.OBForceField) → None

RandomRotorSearch(self: pyOBabel.pyOBabel.OBForceField, conformers: int, geomSteps: int=2500, sampleRingBonds: bool=False) → None

RandomRotorSearchInitialize(self: pyOBabel.pyOBabel.OBForceField, conformers: int, geomSteps: int=2500, sampleRingBonds: bool=False) → None

RandomRotorSearchNextConformer(self: pyOBabel.pyOBabel.OBForceField, geomSteps: int=2500) → bool

SetConformers(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

SetConstraints(self: pyOBabel.pyOBabel.OBForceField, constraints: pyOBabel.pyOBabel.OBFFConstraints) → None

SetCoordinates(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

SetElectrostaticCutOff(self: pyOBabel.pyOBabel.OBForceField, r: float) → None

SetFixAtom(self: pyOBabel.pyOBabel.OBForceField, index: int) → None

SetFormalCharges(self: pyOBabel.pyOBabel.OBForceField) → bool

SetIgnoreAtom(self: pyOBabel.pyOBabel.OBForceField, arg0: int) → None

SetLineSearchType(self: pyOBabel.pyOBabel.OBForceField, type: int) → None

SetLogLevel(self: pyOBabel.pyOBabel.OBForceField, arg0: int) → bool

SetParameterFile(self: pyOBabel.pyOBabel.OBForceField, filename: str) → None

SetPartialCharges(self: pyOBabel.pyOBabel.OBForceField) → bool

SetTypes(self: pyOBabel.pyOBabel.OBForceField) → bool

SetUpdateFrequency(self: pyOBabel.pyOBabel.OBForceField, f: int) → None

SetVDWCutOff(self: pyOBabel.pyOBabel.OBForceField, r: float) → None

Setup(self: pyOBabel.pyOBabel.OBForceField, arg0: pyOBabel.pyOBabel.OBMol) → bool

SetupCalculations(self: pyOBabel.pyOBabel.OBForceField) → bool

SetupPointers(self: pyOBabel.pyOBabel.OBForceField) → bool

SetupWithConstraints(self: pyOBabel.pyOBabel.OBForceField, arg0: pyOBabel.pyOBabel.OBMol, arg1: pyOBabel.pyOBabel.OBFFConstraints) → bool

SteepestDescent(self: pyOBabel.pyOBabel.OBForceField, steps: int, econv: float=9.999999974752427e-07, method: int=2) → None

SteepestDescentInitialize(self: pyOBabel.pyOBabel.OBForceField, steps: int, econv: float=9.999999974752427e-07, method: int=2) → None

SteepestDescentTakeNSteps(self: pyOBabel.pyOBabel.OBForceField, n: int) → bool

SystematicRotorSearch(self: pyOBabel.pyOBabel.OBForceField, geomSteps: int=2500, sampleRingBonds: bool=False) → None

SystematicRotorSearchInitialize(self: pyOBabel.pyOBabel.OBForceField, geomSteps: int=2500, sampleRingBonds: bool=False) → int

SystematicRotorSearchNextConformer(self: pyOBabel.pyOBabel.OBForceField, geomSteps: int=2500) → bool

UnsetFixAtom(self: pyOBabel.pyOBabel.OBForceField) → None

UnsetIgnoreAtom(self: pyOBabel.pyOBabel.OBForceField) → None

UpdateConformers(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

UpdateCoordinates(self: pyOBabel.pyOBabel.OBForceField, mol: pyOBabel.pyOBabel.OBMol) → bool

UpdatePairsSimple(self: pyOBabel.pyOBabel.OBForceField) → None

Validate(self: pyOBabel.pyOBabel.OBForceField) → bool

ValidateConjugateGradients(self: pyOBabel.pyOBabel.OBForceField, steps: int) → None

ValidateGradientError(self: pyOBabel.pyOBabel.OBForceField, numgrad: pyOBabel.pyOBabel.vector3, anagrad: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

ValidateGradients(self: pyOBabel.pyOBabel.OBForceField) → bool

ValidateLineSearch(self: pyOBabel.pyOBabel.OBForceField, atom: pyOBabel.pyOBabel.OBAtom, direction: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

ValidateSteepestDescent(self: pyOBabel.pyOBabel.OBForceField, steps: int) → None

WeightedRotorSearch(self: pyOBabel.pyOBabel.OBForceField, conformers: int, geomSteps: int=2500, sampleRingBonds: bool=False) → None

class OBFFConstraints

AddAngleConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int, b: int, c: int, angle: float) → None

AddAtomConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → None

AddAtomXConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → None

AddAtomYConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → None

AddAtomZConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → None

AddDistanceConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int, b: int, length: float) → None

AddIgnore(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → None

AddTorsionConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, a: int, b: int, b: int, d: int, torsion: float) → None

Clear(self: pyOBabel.pyOBabel.OBFFConstraints) → None

DeleteConstraint(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → None

GetConstraintAtomA(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → int

GetConstraintAtomB(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → int

GetConstraintAtomC(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → int

GetConstraintAtomD(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → int

GetConstraintEnergy(self: pyOBabel.pyOBabel.OBFFConstraints) → float

GetConstraintType(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → int

GetConstraintValue(self: pyOBabel.pyOBabel.OBFFConstraints, index: int) → float

GetFactor(self: pyOBabel.pyOBabel.OBFFConstraints) → float

GetFixedBitVec(self: pyOBabel.pyOBabel.OBFFConstraints) → pyOBabel.pyOBabel.OBBitVec

GetGradient(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → pyOBabel.pyOBabel.vector3

GetIgnoredBitVec(self: pyOBabel.pyOBabel.OBFFConstraints) → pyOBabel.pyOBabel.OBBitVec

IsFixed(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → bool

IsIgnored(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → bool

IsXFixed(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → bool

IsYFixed(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → bool

IsZFixed(self: pyOBabel.pyOBabel.OBFFConstraints, a: int) → bool

SetFactor(self: pyOBabel.pyOBabel.OBFFConstraints, factor: float) → None

Setup(self: pyOBabel.pyOBabel.OBFFConstraints, mol: pyOBabel.pyOBabel.OBMol) → None