pyOBabel

It is a Python interface for openbabel chemical toolbox.

It is not the official Python interface of openbabel and may lack many functionality of openbabel. If you are looking for official Python, Please follow this pybel link.

Why another Python interface

The official Python interface to openbabel was built using SWIG. However, I used pybind11 to built the Python interface. It gives flexibility in building Python interface such that the obtained Python interface can be used in pythonic way.

Please cite the original publication of the openbabel:

• O’Boyle et al (2011)

  Open Babel: An open chemical toolbox Journal of Cheminformatics 2011 3:33 https://doi.org/10.1186/1758-2946-3-33 .

Contents

Summary of available classes

OBMol	Molecule Class
OBAtom
OBBond
OBResidue
vector3	Represents a vector in 3-dimensional real space.
OBBitVec
OBConversion
OBBuilder
OBForceField
OBFFConstraints
OBError
OBMessageHandler

Summary of available classes and functions

Classes

OBMol

OBMol	Molecule Class
OBMol.atoms	List of the atoms – OBAtom.
OBMol.bonds	List of the bonds – OBBond.
OBMol.residues	List of the residues - OBResidue.

Documentation

class OBMol

Molecule Class

The most important class in Open Babel is OBMol, or the molecule class. The OBMol class is designed to store all the basic information associated with a molecule, to make manipulations on the connection table of a molecule facile, and to provide member functions which automatically perceive information about a molecule. A guided tour of the OBMol class is a good place to start.

Example

import pyOBabel as ob

# An OBMol class can be instantiated by
mol = OBMol()

conv = ob.OBConversion()
conv.SetInFormat("MOL2")
conv.ReadFile(mol, filename)

# Print index and atomic number
for atom in mol.atoms:
    print(atom.GetIndex(), atom.GetAtomicNum())

# Print bond order, first atom index and second atom index
for bond in mol.bonds:
    print(bond.GetBondOrder(), bond.GetBeginAtom().GetIndex(),
        bond.GetEndAtom().GetIndex())

AddAtom(self: pyOBabel.pyOBabel.OBMol, atom: OpenBabel::OBAtom, forceNewId: bool=False) → bool

AddBond(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBBond) → bool

AddBondBetweenAtoms(self: pyOBabel.pyOBabel.OBMol, beginIdx: int, endIdx: int, order: int, flags: int=0, insertpos: int=-1) → bool

AddConformerCoords(self: pyOBabel.pyOBabel.OBMol, arg0: list) → None

AddHydrogens(*args, **kwargs)

Overloaded function.

1. AddHydrogens(self: pyOBabel.pyOBabel.OBMol, polaronly: bool=False, correctForPH: bool=False, pH: float=7.4) -> bool
2. AddHydrogens(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom) -> bool

AddNewHydrogens(self: pyOBabel.pyOBabel.OBMol, whichHydrogen: pyOBabel.pyOBabel.HydrogenType, correctForPH: bool=False, pH: float=7.4) → bool

AddNonPolarHydrogens(self: pyOBabel.pyOBabel.OBMol) → bool

AddPolarHydrogens(self: pyOBabel.pyOBabel.OBMol) → bool

AddResidue(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBResidue) → bool

Align(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom, arg1: OpenBabel::OBAtom, arg2: pyOBabel.pyOBabel.vector3, arg3: pyOBabel.pyOBabel.vector3) → None

AreInSameRing(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom, arg1: OpenBabel::OBAtom) → int

AssignSpinMultiplicity(self: pyOBabel.pyOBabel.OBMol, NoImplicitH: bool=False) → bool

AssignTotalChargeToAtoms(self: pyOBabel.pyOBabel.OBMol, arg0: int) → bool

AutomaticFormalCharge(self: pyOBabel.pyOBabel.OBMol) → bool

AutomaticPartialCharge(self: pyOBabel.pyOBabel.OBMol) → bool

BeginModify(self: pyOBabel.pyOBabel.OBMol) → None

Center(self: pyOBabel.pyOBabel.OBMol) → None

CenterOfConformer(self: pyOBabel.pyOBabel.OBMol, arg0: int) → pyOBabel.pyOBabel.vector3

Clear(self: pyOBabel.pyOBabel.OBMol) → bool

ConnectTheDots(self: pyOBabel.pyOBabel.OBMol) → None

ContigFragList(self: pyOBabel.pyOBabel.OBMol, arg0: List[List[int]]) → None

ConvertDativeBonds(self: pyOBabel.pyOBabel.OBMol) → bool

ConvertZeroBonds(self: pyOBabel.pyOBabel.OBMol) → bool

CorrectForPH(self: pyOBabel.pyOBabel.OBMol, pH: float=7.4) → bool

DeleteAtom(self: pyOBabel.pyOBabel.OBMol, atom: OpenBabel::OBAtom, destroyAtom: bool=False) → bool

DeleteBond(self: pyOBabel.pyOBabel.OBMol, bond: OpenBabel::OBBond, destroyBond: bool=False) → bool

DeleteConformerByIndex(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

DeleteHydrogen(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom) → bool

DeleteHydrogensAll(self: pyOBabel.pyOBabel.OBMol) → bool

DeleteHydrogensFromAtom(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom) → bool

DeleteNonPolarHydrogens(self: pyOBabel.pyOBabel.OBMol) → bool

DeletePolarHydrogens(self: pyOBabel.pyOBabel.OBMol) → bool

DeleteResidue(self: pyOBabel.pyOBabel.OBMol, residue: OpenBabel::OBResidue, destroyResidue: bool=False) → bool

Empty(self: pyOBabel.pyOBabel.OBMol) → bool

EndModify(self: pyOBabel.pyOBabel.OBMol, nukePerceivedData: bool=True) → None

FindAngles(self: pyOBabel.pyOBabel.OBMol) → None

FindChiralCenters(self: pyOBabel.pyOBabel.OBMol) → None

FindLSSR(self: pyOBabel.pyOBabel.OBMol) → None

FindRingAtomsAndBonds(self: pyOBabel.pyOBabel.OBMol) → None

FindSSSR(self: pyOBabel.pyOBabel.OBMol) → None

FindTorsions(self: pyOBabel.pyOBabel.OBMol) → None

GetAngle(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom, arg1: OpenBabel::OBAtom, arg2: OpenBabel::OBAtom) → float

GetConformerCoordsByIndex(self: pyOBabel.pyOBabel.OBMol, arg0: int) → list

GetConformerEnergies(self: pyOBabel.pyOBabel.OBMol) → List[float]

GetConformerEnergy(self: pyOBabel.pyOBabel.OBMol, arg0: int) → float

GetConformersAllCoords(self: pyOBabel.pyOBabel.OBMol) → list

GetCoordinates(self: pyOBabel.pyOBabel.OBMol) → list

GetDimension(self: pyOBabel.pyOBabel.OBMol) → int

GetExactMass(self: pyOBabel.pyOBabel.OBMol, arg0: bool) → float

GetFormula(self: pyOBabel.pyOBabel.OBMol) → str

GetHeatFormation(self: pyOBabel.pyOBabel.OBMol) → float

GetMolWt(self: pyOBabel.pyOBabel.OBMol, implicitH: bool=True) → float

GetSpacedFormula(self: pyOBabel.pyOBabel.OBMol, ones: int=0, sp: str=' ', implicitH: bool=True) → str

GetTitle(self: pyOBabel.pyOBabel.OBMol, replaceNewlines: bool=True) → str

GetTorsionByAtoms(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom, arg1: OpenBabel::OBAtom, arg2: OpenBabel::OBAtom, arg3: OpenBabel::OBAtom) → float

GetTorsionByIndex(self: pyOBabel.pyOBabel.OBMol, arg0: int, arg1: int, arg2: int, arg3: int) → float

GetTotalCharge(self: pyOBabel.pyOBabel.OBMol) → int

GetTotalSpinMultiplicity(self: pyOBabel.pyOBabel.OBMol) → int

Has2D(self: pyOBabel.pyOBabel.OBMol, Not3D: bool=False) → bool

Has3D(self: pyOBabel.pyOBabel.OBMol) → bool

HasAromaticPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasAtomTypesPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasChainsPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasChiralityPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasClosureBondsPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasHybridizationPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasHydrogensAdded(self: pyOBabel.pyOBabel.OBMol) → bool

HasLSSRPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasNonZeroCoords(self: pyOBabel.pyOBabel.OBMol) → bool

HasPartialChargesPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasRingAtomsAndBondsPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasRingTypesPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasSSSRPerceived(self: pyOBabel.pyOBabel.OBMol) → bool

HasSpinMultiplicityAssigned(self: pyOBabel.pyOBabel.OBMol) → bool

InsertAtom(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom) → bool

IsChiral(self: pyOBabel.pyOBabel.OBMol) → bool

IsCorrectedForPH(self: pyOBabel.pyOBabel.OBMol) → bool

MakeDativeBonds(self: pyOBabel.pyOBabel.OBMol) → bool

NewAtom(self: pyOBabel.pyOBabel.OBMol) → OpenBabel::OBAtom

NewAtomById(self: pyOBabel.pyOBabel.OBMol, arg0: int) → OpenBabel::OBAtom

NewBond(self: pyOBabel.pyOBabel.OBMol) → OpenBabel::OBBond

NewBondById(self: pyOBabel.pyOBabel.OBMol, arg0: int) → OpenBabel::OBBond

NewResidue(self: pyOBabel.pyOBabel.OBMol) → OpenBabel::OBResidue

NumAtoms(self: pyOBabel.pyOBabel.OBMol) → int

NumBonds(self: pyOBabel.pyOBabel.OBMol) → int

NumConformers(self: pyOBabel.pyOBabel.OBMol) → int

NumHvyAtoms(self: pyOBabel.pyOBabel.OBMol) → int

NumResidues(self: pyOBabel.pyOBabel.OBMol) → int

NumRotors(self: pyOBabel.pyOBabel.OBMol, sampleRingBonds: bool=False) → int

PerceiveBondOrders(self: pyOBabel.pyOBabel.OBMol) → None

RenumberAtomsByAtoms(self: pyOBabel.pyOBabel.OBMol, arg0: List[OpenBabel::OBAtom]) → None

RenumberAtomsByIndex(self: pyOBabel.pyOBabel.OBMol, arg0: List[int]) → None

ReserveAtoms(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

Separate(self: pyOBabel.pyOBabel.OBMol, StartIndex: int=1) → List[pyOBabel.pyOBabel.OBMol]

SetAromaticPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetAtomTypesPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetAutomaticFormalCharge(self: pyOBabel.pyOBabel.OBMol, arg0: bool) → None

SetAutomaticPartialCharge(self: pyOBabel.pyOBabel.OBMol, arg0: bool) → None

SetChainsPerceived(self: pyOBabel.pyOBabel.OBMol, arg0: bool) → None

SetChiralityPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetClosureBondsPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetConformerByIndex(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

SetConformerEnergies(self: pyOBabel.pyOBabel.OBMol, arg0: List[float]) → None

SetConformersCoords(self: pyOBabel.pyOBabel.OBMol, arg0: list) → None

SetCoordinates(self: pyOBabel.pyOBabel.OBMol, arg0: list) → None

SetCorrectedForPH(self: pyOBabel.pyOBabel.OBMol) → None

SetDimension(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

SetFlags(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

SetFormula(self: pyOBabel.pyOBabel.OBMol, arg0: str) → None

SetHeatFormation(self: pyOBabel.pyOBabel.OBMol, arg0: float) → None

SetHybridizationPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetHydrogensAdded(self: pyOBabel.pyOBabel.OBMol) → None

SetIsPatternStructure(self: pyOBabel.pyOBabel.OBMol) → None

SetLSSRPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetPartialChargesPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetRingAtomsAndBondsPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetRingTypesPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetSSSRPerceived(self: pyOBabel.pyOBabel.OBMol) → None

SetSpinMultiplicityAssigned(self: pyOBabel.pyOBabel.OBMol) → None

SetTitle(self: pyOBabel.pyOBabel.OBMol, arg0: str) → None

SetTorsion(self: pyOBabel.pyOBabel.OBMol, arg0: OpenBabel::OBAtom, arg1: OpenBabel::OBAtom, arg2: OpenBabel::OBAtom, arg3: OpenBabel::OBAtom, arg4: float) → None

SetTotalCharge(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

SetTotalSpinMultiplicity(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

StripSalts(self: pyOBabel.pyOBabel.OBMol, threshold: int=0) → bool

ToInertialFrameForAllConformers(self: pyOBabel.pyOBabel.OBMol) → None

ToInertialFrameForOneConformer(self: pyOBabel.pyOBabel.OBMol, arg0: int, arg1: float) → None

TranslateAllConformers(self: pyOBabel.pyOBabel.OBMol, arg0: pyOBabel.pyOBabel.vector3) → None

TranslateOneConformer(self: pyOBabel.pyOBabel.OBMol, arg0: pyOBabel.pyOBabel.vector3, arg1: int) → None

UnsetAromaticPerceived(self: pyOBabel.pyOBabel.OBMol) → None

UnsetFlag(self: pyOBabel.pyOBabel.OBMol, arg0: int) → None

UnsetHydrogensAdded(self: pyOBabel.pyOBabel.OBMol) → None

UnsetLSSRPerceived(self: pyOBabel.pyOBabel.OBMol) → None

UnsetPartialChargesPerceived(self: pyOBabel.pyOBabel.OBMol) → None

UnsetRingTypesPerceived(self: pyOBabel.pyOBabel.OBMol) → None

UnsetSSSRPerceived(self: pyOBabel.pyOBabel.OBMol) → None

atoms

List of the atoms – OBAtom. It yields a read-only list.

Example

# Print index and atomic number
for atom in mol.atoms:
    print(atom.GetIndex(), atom.GetAtomicNum())

bonds

List of the bonds – OBBond. It yields a read-only list.

Example

# Print bond order, first atom index and second atom index
for bond in mol.bonds:
    print(bond.GetBondOrder(), bond.GetBeginAtom().GetIndex(),
            bond.GetEndAtom().GetIndex())

copy(self: pyOBabel.pyOBabel.OBMol) → pyOBabel.pyOBabel.OBMol

residues

List of the residues - OBResidue.

Example

# Print Residue name
for residue in mol.residues:
    print(residue.GetName())

OBAtom

OBAtom

Documentation

class OBAtom

AddBond(self: pyOBabel.pyOBabel.OBAtom, arg0: OpenBabel::OBBond) → None

AddResidue(self: pyOBabel.pyOBabel.OBAtom, arg0: OpenBabel::OBResidue) → None

AverageBondAngle(self: pyOBabel.pyOBabel.OBAtom) → float

BOSum(self: pyOBabel.pyOBabel.OBAtom) → int

Clear(self: pyOBabel.pyOBabel.OBAtom) → bool

ClearBond(self: pyOBabel.pyOBabel.OBAtom) → None

CountBondsOfOrder(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → int

CountFreeOxygens(self: pyOBabel.pyOBabel.OBAtom) → int

CountFreeSulfurs(self: pyOBabel.pyOBabel.OBAtom) → int

CountRingBonds(self: pyOBabel.pyOBabel.OBAtom) → int

DeleteResidue(self: pyOBabel.pyOBabel.OBAtom) → None

Duplicate(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom) → None

ExplicitHydrogenCount(self: pyOBabel.pyOBabel.OBAtom, arg0: bool) → int

GetAngle(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom, arg1: pyOBabel.pyOBabel.OBAtom) → float

GetAngleBetweenAtoms(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom, arg1: pyOBabel.pyOBabel.OBAtom) → float

GetAtomicMass(self: pyOBabel.pyOBabel.OBAtom) → float

GetAtomicNum(self: pyOBabel.pyOBabel.OBAtom) → int

GetBond(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom) → OpenBabel::OBBond

GetDistanceFromAtom(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom) → float

GetDistanceFromIndex(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → float

GetDistanceFromVector(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.vector3) → float

GetExactMass(self: pyOBabel.pyOBabel.OBAtom) → float

GetFormalCharge(self: pyOBabel.pyOBabel.OBAtom) → int

GetHeteroValence(self: pyOBabel.pyOBabel.OBAtom) → int

GetHvyValence(self: pyOBabel.pyOBabel.OBAtom) → int

GetHyb(self: pyOBabel.pyOBabel.OBAtom) → int

GetId(self: pyOBabel.pyOBabel.OBAtom) → int

GetIdx(self: pyOBabel.pyOBabel.OBAtom) → int

GetImplicitHCount(self: pyOBabel.pyOBabel.OBAtom) → int

GetIndex(self: pyOBabel.pyOBabel.OBAtom) → int

GetIsotope(self: pyOBabel.pyOBabel.OBAtom) → int

GetNewBondVector(self: pyOBabel.pyOBabel.OBAtom, arg0: float) → pyOBabel.pyOBabel.vector3

GetNextAtom(self: pyOBabel.pyOBabel.OBAtom) → pyOBabel.pyOBabel.OBAtom

GetParent(self: pyOBabel.pyOBabel.OBAtom) → pyOBabel.pyOBabel.OBMol

GetPartialCharge(self: pyOBabel.pyOBabel.OBAtom) → float

GetResidue(self: pyOBabel.pyOBabel.OBAtom) → OpenBabel::OBResidue

GetSpinMultiplicity(self: pyOBabel.pyOBabel.OBAtom) → int

GetType(self: pyOBabel.pyOBabel.OBAtom) → str

GetValence(self: pyOBabel.pyOBabel.OBAtom) → int

GetVector(self: pyOBabel.pyOBabel.OBAtom) → pyOBabel.pyOBabel.vector3

GetX(self: pyOBabel.pyOBabel.OBAtom) → float

GetY(self: pyOBabel.pyOBabel.OBAtom) → float

GetZ(self: pyOBabel.pyOBabel.OBAtom) → float

HasAlphaBetaUnsat(self: pyOBabel.pyOBabel.OBAtom, arg0: bool) → bool

HasAromaticBond(self: pyOBabel.pyOBabel.OBAtom) → bool

HasBondOfOrder(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → bool

HasChiralVolume(self: pyOBabel.pyOBabel.OBAtom) → bool

HasChiralitySpecified(self: pyOBabel.pyOBabel.OBAtom) → bool

HasDoubleBond(self: pyOBabel.pyOBabel.OBAtom) → bool

HasNonSingleBond(self: pyOBabel.pyOBabel.OBAtom) → bool

HasResidue(self: pyOBabel.pyOBabel.OBAtom) → bool

HasSingleBond(self: pyOBabel.pyOBabel.OBAtom) → bool

HighestBondOrder(self: pyOBabel.pyOBabel.OBAtom) → int

HtoMethyl(self: pyOBabel.pyOBabel.OBAtom) → bool

IsAmideNitrogen(self: pyOBabel.pyOBabel.OBAtom) → bool

IsAntiClockwise(self: pyOBabel.pyOBabel.OBAtom) → bool

IsAromatic(self: pyOBabel.pyOBabel.OBAtom) → bool

IsAromaticNOxide(self: pyOBabel.pyOBabel.OBAtom) → bool

IsAxial(self: pyOBabel.pyOBabel.OBAtom) → bool

IsCarboxylOxygen(self: pyOBabel.pyOBabel.OBAtom) → bool

IsChiral(self: pyOBabel.pyOBabel.OBAtom) → bool

IsClockwise(self: pyOBabel.pyOBabel.OBAtom) → bool

IsConnected(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom) → bool

IsHbondAcceptor(self: pyOBabel.pyOBabel.OBAtom) → bool

IsHbondAcceptorSimple(self: pyOBabel.pyOBabel.OBAtom) → bool

IsHbondDonor(self: pyOBabel.pyOBabel.OBAtom) → bool

IsHbondDonorH(self: pyOBabel.pyOBabel.OBAtom) → bool

IsHetAtom(self: pyOBabel.pyOBabel.OBAtom) → bool

IsHeteroatom(self: pyOBabel.pyOBabel.OBAtom) → bool

IsInRing(self: pyOBabel.pyOBabel.OBAtom) → bool

IsInRingSize(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → bool

IsNegativeStereo(self: pyOBabel.pyOBabel.OBAtom) → bool

IsNitroOxygen(self: pyOBabel.pyOBabel.OBAtom) → bool

IsNonPolarHydrogen(self: pyOBabel.pyOBabel.OBAtom) → bool

IsOneFour(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom) → bool

IsOneThree(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBAtom) → bool

IsPhosphateOxygen(self: pyOBabel.pyOBabel.OBAtom) → bool

IsPolarHydrogen(self: pyOBabel.pyOBabel.OBAtom) → bool

IsPositiveStereo(self: pyOBabel.pyOBabel.OBAtom) → bool

IsSulfateOxygen(self: pyOBabel.pyOBabel.OBAtom) → bool

LewisAcidBaseCounts(self: pyOBabel.pyOBabel.OBAtom) → Tuple[int, int]

MatchesSMARTS(self: pyOBabel.pyOBabel.OBAtom, arg0: str) → bool

MemberOfRingCount(self: pyOBabel.pyOBabel.OBAtom) → int

MemberOfRingSize(self: pyOBabel.pyOBabel.OBAtom) → int

NewResidue(self: pyOBabel.pyOBabel.OBAtom) → None

SetAntiClockwiseStereo(self: pyOBabel.pyOBabel.OBAtom) → None

SetAromatic(self: pyOBabel.pyOBabel.OBAtom) → None

SetAtomicNum(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetChiral(self: pyOBabel.pyOBabel.OBAtom) → None

SetClockwiseStereo(self: pyOBabel.pyOBabel.OBAtom) → None

SetFormalCharge(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetHyb(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetHybAndGeom(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → bool

SetId(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetIdx(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetImplicitHCount(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetInRing(self: pyOBabel.pyOBabel.OBAtom, arg0: bool) → None

SetIsotope(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetNegativeStereo(self: pyOBabel.pyOBabel.OBAtom) → None

SetParent(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.OBMol) → None

SetPartialCharge(self: pyOBabel.pyOBabel.OBAtom, arg0: float) → None

SetPositiveStereo(self: pyOBabel.pyOBabel.OBAtom) → None

SetResidue(self: pyOBabel.pyOBabel.OBAtom, arg0: OpenBabel::OBResidue) → None

SetSpinMultiplicity(self: pyOBabel.pyOBabel.OBAtom, arg0: int) → None

SetType(self: pyOBabel.pyOBabel.OBAtom, arg0: str) → None

SetVector(*args, **kwargs)

Overloaded function.

1. SetVector(self: pyOBabel.pyOBabel.OBAtom, arg0: pyOBabel.pyOBabel.vector3) -> None
2. SetVector(self: pyOBabel.pyOBabel.OBAtom, arg0: float, arg1: float, arg2: float) -> None

SmallestBondAngle(self: pyOBabel.pyOBabel.OBAtom) → float

UnsetAromatic(self: pyOBabel.pyOBabel.OBAtom) → None

UnsetStereo(self: pyOBabel.pyOBabel.OBAtom) → None

OBBond

OBBond

Documentation

class OBBond

GetBO(self: pyOBabel.pyOBabel.OBBond) → int

GetBeginAtom(self: pyOBabel.pyOBabel.OBBond) → pyOBabel.pyOBabel.OBAtom

GetBeginAtomIdx(self: pyOBabel.pyOBabel.OBBond) → int

GetBondOrder(self: pyOBabel.pyOBabel.OBBond) → int

GetEndAtom(self: pyOBabel.pyOBabel.OBBond) → pyOBabel.pyOBabel.OBAtom

GetEndAtomIdx(self: pyOBabel.pyOBabel.OBBond) → int

GetEquibLength(self: pyOBabel.pyOBabel.OBBond) → float

GetFlags(self: pyOBabel.pyOBabel.OBBond) → int

GetId(self: pyOBabel.pyOBabel.OBBond) → int

GetIdx(self: pyOBabel.pyOBabel.OBBond) → int

GetLength(self: pyOBabel.pyOBabel.OBBond) → float

GetNbrAtom(self: pyOBabel.pyOBabel.OBBond, arg0: pyOBabel.pyOBabel.OBAtom) → pyOBabel.pyOBabel.OBAtom

GetNbrAtomIdx(self: pyOBabel.pyOBabel.OBBond, arg0: pyOBabel.pyOBabel.OBAtom) → int

GetParent(self: pyOBabel.pyOBabel.OBBond) → pyOBabel.pyOBabel.OBMol

IsAmide(self: pyOBabel.pyOBabel.OBBond) → bool

IsAromatic(self: pyOBabel.pyOBabel.OBBond) → bool

IsCarbonyl(self: pyOBabel.pyOBabel.OBBond) → bool

IsCisOrTrans(self: pyOBabel.pyOBabel.OBBond) → bool

IsClosure(self: pyOBabel.pyOBabel.OBBond) → bool

IsDoubleBondGeometry(self: pyOBabel.pyOBabel.OBBond) → bool

IsDown(self: pyOBabel.pyOBabel.OBBond) → bool

IsEster(self: pyOBabel.pyOBabel.OBBond) → bool

IsHash(self: pyOBabel.pyOBabel.OBBond) → bool

IsInRing(self: pyOBabel.pyOBabel.OBBond) → bool

IsPrimaryAmide(self: pyOBabel.pyOBabel.OBBond) → bool

IsRotor(self: pyOBabel.pyOBabel.OBBond, arg0: bool) → bool

IsSecondaryAmide(self: pyOBabel.pyOBabel.OBBond) → bool

IsTertiaryAmide(self: pyOBabel.pyOBabel.OBBond) → bool

IsUp(self: pyOBabel.pyOBabel.OBBond) → bool

IsWedge(self: pyOBabel.pyOBabel.OBBond) → bool

IsWedgeOrHash(self: pyOBabel.pyOBabel.OBBond) → bool

SetAromatic(self: pyOBabel.pyOBabel.OBBond) → None

SetBO(self: pyOBabel.pyOBabel.OBBond, arg0: int) → None

SetBegin(self: pyOBabel.pyOBabel.OBBond, arg0: pyOBabel.pyOBabel.OBAtom) → None

SetBondOrder(self: pyOBabel.pyOBabel.OBBond, arg0: int) → None

SetClosure(self: pyOBabel.pyOBabel.OBBond, arg0: bool) → None

SetDown(self: pyOBabel.pyOBabel.OBBond) → None

SetEnd(self: pyOBabel.pyOBabel.OBBond, arg0: pyOBabel.pyOBabel.OBAtom) → None

SetHash(self: pyOBabel.pyOBabel.OBBond) → None

SetId(self: pyOBabel.pyOBabel.OBBond, arg0: int) → None

SetInRing(self: pyOBabel.pyOBabel.OBBond, arg0: bool) → None

SetLength(*args, **kwargs)

Overloaded function.

1. SetLength(self: pyOBabel.pyOBabel.OBBond, arg0: pyOBabel.pyOBabel.OBAtom, arg1: float) -> None
2. SetLength(self: pyOBabel.pyOBabel.OBBond, arg0: float) -> None

SetParent(self: pyOBabel.pyOBabel.OBBond, arg0: pyOBabel.pyOBabel.OBMol) → None

SetUp(self: pyOBabel.pyOBabel.OBBond) → None

SetWedge(self: pyOBabel.pyOBabel.OBBond) → None

SetWedgeOrHash(self: pyOBabel.pyOBabel.OBBond) → None

UnsetAromatic(self: pyOBabel.pyOBabel.OBBond) → None

UnsetDown(self: pyOBabel.pyOBabel.OBBond) → None

UnsetHash(self: pyOBabel.pyOBabel.OBBond) → None

UnsetUp(self: pyOBabel.pyOBabel.OBBond) → None

UnsetWedge(self: pyOBabel.pyOBabel.OBBond) → None

OBResidue

OBResidue

Documentation

class OBResidue

GetName(self: pyOBabel.pyOBabel.OBResidue) → str

SetName(self: pyOBabel.pyOBabel.OBResidue, arg0: str) → None

vector3

vector3	Represents a vector in 3-dimensional real space.
vector3.Set(self, inX, inY, inZ)	Set x,y and z-component of a vector :param inX: Input X-coordinate :type inX: float :param inY: Input Y-coordinate :type inY: float :param inZ: Input Z-coordinate :type inZ: float
vector3.SetX(self, inX)	To set the x-coordinate of the vector :param inX: Input X-coordinate :type inX: float
vector3.SetY(self, inY)	To set the y-coordinate of the vector :param inX: Input Y-coordinate :type inX: float
vector3.SetZ(self, inZ)	To set the z-coordinate of the vector :param inX: Input Z-coordinate :type inX: float
vector3.GetX(self)	to Get the x-coordinate of the vector
vector3.GetY(self)	to Get the y-coordinate of the vector
vector3.GetZ(self)	to Get the z-coordinate of the vector
vector3.Get(self)	To Get coordinates as a list
vector3.copy(self)	To copy this vector
vector3.normalize(self)	Normalize the vector
vector3.CanBeNormalized(self)	Whether a vector can be normalized
vector3.length_2(self)	The length of the vector squared
vector3.length(self)	The length of the vector
vector3.IsApprox(self, arg0, arg1)	Safe comparison for floating-point vector3
vector3.distSq(self, v)	Square of distance between self and input vector.
vector3.createOrthoVector(self)	Creates a vector of length one, orthogonal to this
dot(v1, v2)	Dot product of two vectors
cross(v1, v2)	Cross product of two vectors
vectorAngle(v1, v2)	Calculate the angle between vectors (in degrees)
CalcTorsionAngle(a, b, c, d)	Calculate the torsion angle between vectors (in degrees)
Point2PlaneSigned(a, b, c, d)	Calculate the signed distance of point a to the plane determined by b,c,d
Point2Plane(a, b, c, d)	Calculate the distance of point a to the plane determined by b,c,d
Point2PlaneAngle(a, b, c, d)	Calculate the angle between point a and the plane determined by b,c,d
Point2Line(a, b, c)	Calculate the distance of a point a to a line determined by b and c

Documentation

class vector3

Represents a vector in 3-dimensional real space.

The vector3 class was designed to simplify operations with floating point coordinates. To this end many of the common operations have been overloaded for simplicity. Vector addition, subtraction, scalar multiplication, dot product, cross product, magnitude and a number of other utility functions are built in to the vector class. For a full description of the class member functions please consult the documentation. The following code demonstrates several of the functions of the vector class:

Example

v1, v2, v3 = vector3(), vector3(), vector3()
v1.Set([1, 2, 3])
v2.Set([4 ,5, 6])
v3 = cross(v1,v2)
v3 *= 2.5
v3.normalize()

CanBeNormalized(self: pyOBabel.pyOBabel.vector3) → bool

Whether a vector can be normalized

Returns:CanBeNormalize – True or False Return type:bool

Get(self: pyOBabel.pyOBabel.vector3) → list

To Get coordinates as a list

Returns:list – coordinates as a list Return type:list

GetX(self: pyOBabel.pyOBabel.vector3) → float

to Get the x-coordinate of the vector

Returns:outX – x-coordinate of the vector Return type:float

GetY(self: pyOBabel.pyOBabel.vector3) → float

to Get the y-coordinate of the vector

Returns:outY – y-coordinate of the vector Return type:float

GetZ(self: pyOBabel.pyOBabel.vector3) → float

to Get the z-coordinate of the vector

Returns:outZ – z-coordinate of the vector Return type:float

IsApprox(self: pyOBabel.pyOBabel.vector3, arg0: pyOBabel.pyOBabel.vector3, arg1: float) → bool

Safe comparison for floating-point vector3

True if this vector is approximately equal to the other vector to the input precision. More specifically, this method works exactly like the pyOBabel.IsApprox() function, replacing the absolute value for doubles by the norm for vectors.

Parameters:

• other (vector3) – The vector for comparison
• precision (float) – This parameter plays the same role as in pyOBabel.IsApprox()

Returns:

IsApprox – True or False

Return type:

bool

Set(self: pyOBabel.pyOBabel.vector3, inX: float, inY: float, inZ: float) → None

Set x,y and z-component of a vector :param inX: Input X-coordinate :type inX: float :param inY: Input Y-coordinate :type inY: float :param inZ: Input Z-coordinate :type inZ: float

Returns: Return type:None

SetX(self: pyOBabel.pyOBabel.vector3, inX: float) → None

To set the x-coordinate of the vector :param inX: Input X-coordinate :type inX: float

Returns: Return type:None

SetY(self: pyOBabel.pyOBabel.vector3, inY: float) → None

To set the y-coordinate of the vector :param inX: Input Y-coordinate :type inX: float

Returns: Return type:None

SetZ(self: pyOBabel.pyOBabel.vector3, inZ: float) → None

To set the z-coordinate of the vector :param inX: Input Z-coordinate :type inX: float

Returns: Return type:None

copy(self: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

To copy this vector

Parameters:inpVector (vector3) – Vector to copy Returns: Return type:None

createOrthoVector(self: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

Creates a vector of length one, orthogonal to this

Create a unit orthogonal vector

Returns:v – Unit orthogonal vector or None if not successfull Return type:vector3

distSq(self: pyOBabel.pyOBabel.vector3, v: pyOBabel.pyOBabel.vector3) → float

Square of distance between self and input vector.

square of the distance between self and vv. equivalent to length_2(self-vv)

Parameters:v (vector3) – Vector to copy Returns:length – The square of distance between self and input vector Return type:float

length(self: pyOBabel.pyOBabel.vector3) → float

The length of the vector

Returns:length – The length of the vector Return type:float

length_2(self: pyOBabel.pyOBabel.vector3) → float

The length of the vector squared

Returns:length2 – The squared length of the vector Return type:float

normalize(self: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

Normalize the vector

Scales a vector to give it length one.

Returns:normalized – The normalized vector Return type:vector3

dot(v1: pyOBabel.pyOBabel.vector3, v2: pyOBabel.pyOBabel.vector3) → float

Dot product of two vectors

Parameters:

• v1 (vector3) – First vector
• v2 (vector3) – Second vector

Returns:

product – Dot product of two vectors

Return type:

float

cross(v1: pyOBabel.pyOBabel.vector3, v2: pyOBabel.pyOBabel.vector3) → pyOBabel.pyOBabel.vector3

Cross product of two vectors

Parameters:

• v1 (vector3) – First vector
• v2 (vector3) – Second vector

Returns:

cross – Cross product of two vectors

Return type:

vector3

vectorAngle(v1: pyOBabel.pyOBabel.vector3, v2: pyOBabel.pyOBabel.vector3) → float

Calculate the angle between vectors (in degrees)

Parameters:

• v1 (vector3) – First vector
• v2 (vector3) – Second vector

Returns:

angle – Angle between vectors (in degrees)

Return type:

float

CalcTorsionAngle(a: pyOBabel.pyOBabel.vector3, b: pyOBabel.pyOBabel.vector3, c: pyOBabel.pyOBabel.vector3, d: pyOBabel.pyOBabel.vector3) → float

Calculate the torsion angle between vectors (in degrees)

Parameters:

• a (vector3) – First vector
• b (vector3) – Second vector
• c (vector3) – Third vector
• d (vector3) – fourth vector

Returns:

angle – Torsion angle between vectors (in degrees)

Return type:

float

Point2PlaneSigned(a: pyOBabel.pyOBabel.vector3, b: pyOBabel.pyOBabel.vector3, c: pyOBabel.pyOBabel.vector3, d: pyOBabel.pyOBabel.vector3) → float

Calculate the signed distance of point a to the plane determined by b,c,d

Parameters:

• a (vector3) – First vector
• b (vector3) – Second vector
• c (vector3) – Third vector
• d (vector3) – fourth vector

Returns:

distance – Signed distance between point to a plane

Return type:

float

Point2Plane(a: pyOBabel.pyOBabel.vector3, b: pyOBabel.pyOBabel.vector3, c: pyOBabel.pyOBabel.vector3, d: pyOBabel.pyOBabel.vector3) → float

Calculate the distance of point a to the plane determined by b,c,d

Parameters:

• a (vector3) – First vector
• b (vector3) – Second vector
• c (vector3) – Third vector
• d (vector3) – fourth vector

Returns:

distance – Distance between point to a plane

Return type:

float

Point2PlaneAngle(a: pyOBabel.pyOBabel.vector3, b: pyOBabel.pyOBabel.vector3, c: pyOBabel.pyOBabel.vector3, d: pyOBabel.pyOBabel.vector3) → float

Calculate the angle between point a and the plane determined by b,c,d

Parameters:

• a (vector3) – First vector
• b (vector3) – Second vector
• c (vector3) – Third vector
• d (vector3) – fourth vector

Returns:

angle – angle between a point and plane

Return type:

float

Point2Line(a: pyOBabel.pyOBabel.vector3, b: pyOBabel.pyOBabel.vector3, c: pyOBabel.pyOBabel.vector3) → float

Calculate the distance of a point a to a line determined by b and c

Parameters:

• a (vector3) – First vector
• b (vector3) – Second vector
• c (vector3) – Third vector

Returns:

distance – Distance between a point and a line

Return type:

float

OBBitVec

OBBitVec

Documentation

class OBBitVec

BitIsOn(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → bool

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

CountBits(self: pyOBabel.pyOBabel.OBBitVec) → int

EndBit(self: pyOBabel.pyOBabel.OBBitVec) → int

FirstBit(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → int

Fold(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → None

FromString(self: pyOBabel.pyOBabel.OBBitVec, arg0: str, arg1: int) → None

FromVecInt(self: pyOBabel.pyOBabel.OBBitVec, arg0: List[int]) → None

GetSize(self: pyOBabel.pyOBabel.OBBitVec) → int

IsEmpty(self: pyOBabel.pyOBabel.OBBitVec) → bool

Negate(self: pyOBabel.pyOBabel.OBBitVec) → None

NextBit(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → int

Resize(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → bool

ResizeWords(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → bool

SetBitOff(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → None

SetBitOn(self: pyOBabel.pyOBabel.OBBitVec, arg0: int) → None

SetRangeOff(self: pyOBabel.pyOBabel.OBBitVec, arg0: int, arg1: int) → None

SetRangeOn(self: pyOBabel.pyOBabel.OBBitVec, arg0: int, arg1: int) → None

OBConversion

OBConversion

Documentation

class OBConversion

AddChemObject(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBBase) → int

AddOption(self: pyOBabel.pyOBabel.OBConversion, opt: str, opttyp: pyOBabel.pyOBabel.OBConversion.Option_type=Option_type.OUTOPTIONS, txt: str=0) → None

CloseOutFile(self: pyOBabel.pyOBabel.OBConversion) → None

Convert(self: pyOBabel.pyOBabel.OBConversion) → int

FullConvert(self: pyOBabel.pyOBabel.OBConversion, arg0: List[str], arg1: str, arg2: List[str]) → int

GetChemObject(self: pyOBabel.pyOBabel.OBConversion) → pyOBabel.pyOBabel.OBBase

GetCount(self: pyOBabel.pyOBabel.OBConversion) → int

GetOptions(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBConversion.Option_type) → Dict[str, str]

GetOutputIndex(self: pyOBabel.pyOBabel.OBConversion) → int

GetSupportedInputFormat(self: pyOBabel.pyOBabel.OBConversion) → List[str]

GetSupportedOutputFormat(self: pyOBabel.pyOBabel.OBConversion) → List[str]

IsFirstInput(self: pyOBabel.pyOBabel.OBConversion) → bool

IsLast(self: pyOBabel.pyOBabel.OBConversion) → bool

IsLastFile(self: pyOBabel.pyOBabel.OBConversion) → bool

IsOption(self: pyOBabel.pyOBabel.OBConversion, opt: str, opttyp: pyOBabel.pyOBabel.OBConversion.Option_type=Option_type.OUTOPTIONS) → str

OpenInAndOutFiles(self: pyOBabel.pyOBabel.OBConversion, arg0: str, arg1: str) → bool

Read(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBBase) → bool

ReadFile(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBBase, arg1: str) → bool

ReadString(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBBase, arg1: str) → bool

RemoveOption(self: pyOBabel.pyOBabel.OBConversion, arg0: str, arg1: pyOBabel.pyOBabel.OBConversion.Option_type) → bool

SetFirstInput(self: pyOBabel.pyOBabel.OBConversion, arg0: bool) → None

SetInAndOutFormats(self: pyOBabel.pyOBabel.OBConversion, inID: str, outID: str, ingzip: bool=False, outgzip: bool=False) → None

SetInFormat(self: pyOBabel.pyOBabel.OBConversion, inID: str, isgzip: bool=False) → bool

SetLast(self: pyOBabel.pyOBabel.OBConversion, arg0: bool) → None

SetMoreFilesToCome(self: pyOBabel.pyOBabel.OBConversion) → None

SetOneObjectOnly(self: pyOBabel.pyOBabel.OBConversion, arg0: bool) → None

SetOptions(self: pyOBabel.pyOBabel.OBConversion, arg0: str, arg1: pyOBabel.pyOBabel.OBConversion.Option_type) → None

SetOutFormat(self: pyOBabel.pyOBabel.OBConversion, inID: str, isgzip: bool=False) → bool

SetOutputIndex(self: pyOBabel.pyOBabel.OBConversion, arg0: int) → None

Write(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBBase) → bool

WriteFile(self: pyOBabel.pyOBabel.OBConversion, arg0: pyOBabel.pyOBabel.OBBase, arg1: str) → bool

WriteString(self: pyOBabel.pyOBabel.OBConversion, obmol: pyOBabel.pyOBabel.OBBase, trimWhitespace: bool=False) → str

OBBuilder

OBBuilder

Documentation

class OBBuilder

AddNbrs(fragment: pyOBabel.pyOBabel.OBBitVec, atom: pyOBabel.pyOBabel.OBAtom) → None

Build(self: pyOBabel.pyOBabel.OBBuilder, mol: pyOBabel.pyOBabel.OBMol, stereoWarnings: bool=True) → bool

Connect(*args, **kwargs)

Overloaded function.

1. Connect(mol: pyOBabel.pyOBabel.OBMol, a: int, b: int, newpos: pyOBabel.pyOBabel.vector3, bondOrder: int=1) -> bool
2. Connect(mol: pyOBabel.pyOBabel.OBMol, a: int, b: int, bondOrder: int=1) -> bool

CorrectStereoAtoms(*args, **kwargs)

Overloaded function.

1. CorrectStereoAtoms(mol: pyOBabel.pyOBabel.OBMol) -> bool
2. CorrectStereoAtoms(mol: pyOBabel.pyOBabel.OBMol, warn: bool=True) -> bool

GetFragment(atom: pyOBabel.pyOBabel.OBAtom) → pyOBabel.pyOBabel.OBBitVec

GetNewBondVector(*args, **kwargs)

Overloaded function.

1. GetNewBondVector(atom: pyOBabel.pyOBabel.OBAtom) -> pyOBabel.pyOBabel.vector3
2. GetNewBondVector(atom: pyOBabel.pyOBabel.OBAtom, length: float) -> pyOBabel.pyOBabel.vector3

IsSpiroAtom(atomId: int, mol: pyOBabel.pyOBabel.OBMol) → bool

LoadFragments(self: pyOBabel.pyOBabel.OBBuilder) → None

SetKeepRings(self: pyOBabel.pyOBabel.OBBuilder) → None

Swap(mol: pyOBabel.pyOBabel.OBMol, a: int, b: int, c: int, d: int) → bool

UnsetKeepRings(self: pyOBabel.pyOBabel.OBBuilder) → None

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

OBError and OBMessageHandler

OBError
OBMessageHandler

Documentation

class OBError

GetError(self: pyOBabel.pyOBabel.OBError) → str

GetExplanation(self: pyOBabel.pyOBabel.OBError) → str

GetLevel(self: pyOBabel.pyOBabel.OBError) → pyOBabel.pyOBabel.obMessageLevel

GetMethod(self: pyOBabel.pyOBabel.OBError) → str

GetPossibleCause(self: pyOBabel.pyOBabel.OBError) → str

GetSuggestedRemedy(self: pyOBabel.pyOBabel.OBError) → str

message(self: pyOBabel.pyOBabel.OBError) → str

class OBMessageHandler

ClearLog(self: pyOBabel.pyOBabel.OBMessageHandler) → None

GetAuditMessageCount(self: pyOBabel.pyOBabel.OBMessageHandler) → int

GetDebugMessageCount(self: pyOBabel.pyOBabel.OBMessageHandler) → int

GetErrorMessageCount(self: pyOBabel.pyOBabel.OBMessageHandler) → int

GetInfoMessageCount(self: pyOBabel.pyOBabel.OBMessageHandler) → int

GetMaxLogEntries(self: pyOBabel.pyOBabel.OBMessageHandler) → int

GetMessageSummary(self: pyOBabel.pyOBabel.OBMessageHandler) → str

GetMessagesOfLevel(self: pyOBabel.pyOBabel.OBMessageHandler, arg0: pyOBabel.pyOBabel.obMessageLevel) → List[str]

GetOutputLevel(self: pyOBabel.pyOBabel.OBMessageHandler) → pyOBabel.pyOBabel.obMessageLevel

GetOutputStream(self: pyOBabel.pyOBabel.OBMessageHandler) → object

GetWarningMessageCount(self: pyOBabel.pyOBabel.OBMessageHandler) → int

SetMaxLogEntries(self: pyOBabel.pyOBabel.OBMessageHandler, arg0: int) → None

SetOutputLevel(self: pyOBabel.pyOBabel.OBMessageHandler, arg0: pyOBabel.pyOBabel.obMessageLevel) → None

SetOutputStream(self: pyOBabel.pyOBabel.OBMessageHandler, arg0: object) → None

StartLogging(self: pyOBabel.pyOBabel.OBMessageHandler) → None

StopErrorWrap(self: pyOBabel.pyOBabel.OBMessageHandler) → bool

ThrowErrorByMessage(self: pyOBabel.pyOBabel.OBMessageHandler, method: str, errorMsg: str, level: pyOBabel.pyOBabel.obMessageLevel=obMessageLevel.obDebug, qualifier: pyOBabel.pyOBabel.errorQualifier=errorQualifier.always) → None

ThrowErrorByOBError(self: pyOBabel.pyOBabel.OBMessageHandler, err: pyOBabel.pyOBabel.OBError, qqualifier: pyOBabel.pyOBabel.errorQualifier=errorQualifier.always) → None

Indices and tables

• Index
• Module Index
• Search Page