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.

AddHydrogens(self: pyOBabel.pyOBabel.OBMol, polaronly: bool=False, correctForPH: bool=False, pH: float=7.4) -> bool
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())