pyOBabel
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Module Documentation
pyOBabel
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A
AddAngleConstraint() (OBFFConstraints method)
AddAtom() (OBMol method)
AddAtomConstraint() (OBFFConstraints method)
AddAtomXConstraint() (OBFFConstraints method)
AddAtomYConstraint() (OBFFConstraints method)
AddAtomZConstraint() (OBFFConstraints method)
AddBond() (OBAtom method)
(OBMol method)
AddBondBetweenAtoms() (OBMol method)
AddChemObject() (OBConversion method)
AddConformerCoords() (OBMol method)
AddDistanceConstraint() (OBFFConstraints method)
AddHydrogens() (OBMol method)
AddIgnore() (OBFFConstraints method)
AddInterGroup() (OBForceField method)
AddInterGroups() (OBForceField method)
AddIntraGroup() (OBForceField method)
AddNbrs() (OBBuilder method)
AddNewHydrogens() (OBMol method)
AddNonPolarHydrogens() (OBMol method)
AddOption() (OBConversion method)
AddPolarHydrogens() (OBMol method)
AddResidue() (OBAtom method)
(OBMol method)
AddTorsionConstraint() (OBFFConstraints method)
Align() (OBMol method)
AreInSameRing() (OBMol method)
AssignSpinMultiplicity() (OBMol method)
AssignTotalChargeToAtoms() (OBMol method)
atoms (OBMol attribute)
AutomaticFormalCharge() (OBMol method)
AutomaticPartialCharge() (OBMol method)
AverageBondAngle() (OBAtom method)
B
BeginModify() (OBMol method)
BitIsOn() (OBBitVec method)
bonds (OBMol attribute)
BOSum() (OBAtom method)
Build() (OBBuilder method)
C
CalcTorsionAngle() (in module pyOBabel)
CanBeNormalized() (vector3 method)
Center() (OBMol method)
CenterOfConformer() (OBMol method)
Clear() (OBAtom method)
(OBBitVec method)
(OBFFConstraints method)
(OBMol method)
ClearBond() (OBAtom method)
ClearGroups() (OBForceField method)
ClearLog() (OBMessageHandler method)
CloseOutFile() (OBConversion method)
ConjugateGradients() (OBForceField method)
ConjugateGradientsInitialize() (OBForceField method)
ConjugateGradientsTakeNSteps() (OBForceField method)
Connect() (OBBuilder method)
ConnectTheDots() (OBMol method)
ContigFragList() (OBMol method)
Convert() (OBConversion method)
ConvertDativeBonds() (OBMol method)
ConvertZeroBonds() (OBMol method)
copy() (OBMol method)
(vector3 method)
CorrectForPH() (OBMol method)
CorrectStereoAtoms() (OBBuilder method)
CorrectVelocities() (OBForceField method)
CountBits() (OBBitVec method)
CountBondsOfOrder() (OBAtom method)
CountFreeOxygens() (OBAtom method)
CountFreeSulfurs() (OBAtom method)
CountRingBonds() (OBAtom method)
createOrthoVector() (vector3 method)
cross() (in module pyOBabel)
D
DeleteAtom() (OBMol method)
DeleteBond() (OBMol method)
DeleteConformerByIndex() (OBMol method)
DeleteConstraint() (OBFFConstraints method)
DeleteHydrogen() (OBMol method)
DeleteHydrogensAll() (OBMol method)
DeleteHydrogensFromAtom() (OBMol method)
DeleteNonPolarHydrogens() (OBMol method)
DeletePolarHydrogens() (OBMol method)
DeleteResidue() (OBAtom method)
(OBMol method)
DetectExplosion() (OBForceField method)
DistanceGeometry() (OBForceField method)
distSq() (vector3 method)
dot() (in module pyOBabel)
Duplicate() (OBAtom method)
E
E_Angle() (OBForceField method)
E_Bond() (OBForceField method)
E_Electrostatic() (OBForceField method)
E_OOP() (OBForceField method)
E_StrBnd() (OBForceField method)
E_Torsion() (OBForceField method)
E_VDW() (OBForceField method)
Empty() (OBMol method)
EnableAllPairs() (OBForceField method)
EnableCutOff() (OBForceField method)
EndBit() (OBBitVec method)
EndModify() (OBMol method)
Energy() (OBForceField method)
ExplicitHydrogenCount() (OBAtom method)
F
FastRotorSearch() (OBForceField method)
FindAngles() (OBMol method)
FindChiralCenters() (OBMol method)
FindForceField() (OBForceField method)
FindLSSR() (OBMol method)
FindRingAtomsAndBonds() (OBMol method)
FindSSSR() (OBMol method)
FindTorsions() (OBMol method)
FindType() (OBForceField method)
FirstBit() (OBBitVec method)
Fold() (OBBitVec method)
FromString() (OBBitVec method)
FromVecInt() (OBBitVec method)
FullConvert() (OBConversion method)
G
GenerateVelocities() (OBForceField method)
Get() (vector3 method)
GetAngle() (OBAtom method)
(OBMol method)
GetAngleBetweenAtoms() (OBAtom method)
GetAtomicMass() (OBAtom method)
GetAtomicNum() (OBAtom method)
GetAtomTypes() (OBForceField method)
GetAuditMessageCount() (OBMessageHandler method)
GetBeginAtom() (OBBond method)
GetBeginAtomIdx() (OBBond method)
GetBO() (OBBond method)
GetBond() (OBAtom method)
GetBondOrder() (OBBond method)
GetChemObject() (OBConversion method)
GetConformerCoordsByIndex() (OBMol method)
GetConformerEnergies() (OBMol method)
GetConformerEnergy() (OBMol method)
GetConformers() (OBForceField method)
GetConformersAllCoords() (OBMol method)
GetConstraintAtomA() (OBFFConstraints method)
GetConstraintAtomB() (OBFFConstraints method)
GetConstraintAtomC() (OBFFConstraints method)
GetConstraintAtomD() (OBFFConstraints method)
GetConstraintEnergy() (OBFFConstraints method)
GetConstraints() (OBForceField method)
GetConstraintType() (OBFFConstraints method)
GetConstraintValue() (OBFFConstraints method)
GetCoordinates() (OBForceField method)
(OBMol method)
GetCount() (OBConversion method)
GetDebugMessageCount() (OBMessageHandler method)
GetDimension() (OBMol method)
GetDistanceFromAtom() (OBAtom method)
GetDistanceFromIndex() (OBAtom method)
GetDistanceFromVector() (OBAtom method)
GetElectrostaticCutOff() (OBForceField method)
GetEndAtom() (OBBond method)
GetEndAtomIdx() (OBBond method)
GetEquibLength() (OBBond method)
GetError() (OBError method)
GetErrorMessageCount() (OBMessageHandler method)
GetExactMass() (OBAtom method)
(OBMol method)
GetExplanation() (OBError method)
GetFactor() (OBFFConstraints method)
GetFixedBitVec() (OBFFConstraints method)
GetFlags() (OBBond method)
GetFormalCharge() (OBAtom method)
GetFormula() (OBMol method)
GetFragment() (OBBuilder method)
GetGradient() (OBFFConstraints method)
GetHeatFormation() (OBMol method)
GetHeteroValence() (OBAtom method)
GetHvyValence() (OBAtom method)
GetHyb() (OBAtom method)
GetId() (OBAtom method)
(OBBond method)
GetIdx() (OBAtom method)
(OBBond method)
GetIgnoredBitVec() (OBFFConstraints method)
GetImplicitHCount() (OBAtom method)
GetIndex() (OBAtom method)
GetInfoMessageCount() (OBMessageHandler method)
GetIsotope() (OBAtom method)
GetLength() (OBBond method)
GetLevel() (OBError method)
GetLineSearchType() (OBForceField method)
GetLogLevel() (OBForceField method)
GetMaxLogEntries() (OBMessageHandler method)
GetMessagesOfLevel() (OBMessageHandler method)
GetMessageSummary() (OBMessageHandler method)
GetMethod() (OBError method)
GetMolWt() (OBMol method)
GetName() (OBResidue method)
GetNbrAtom() (OBBond method)
GetNbrAtomIdx() (OBBond method)
GetNewBondVector() (OBAtom method)
(OBBuilder method)
GetNextAtom() (OBAtom method)
GetNumElectrostaticPairs() (OBForceField method)
GetNumPairs() (OBForceField method)
GetNumVDWPairs() (OBForceField method)
GetOptions() (OBConversion method)
GetOutputIndex() (OBConversion method)
GetOutputLevel() (OBMessageHandler method)
GetOutputStream() (OBMessageHandler method)
GetParent() (OBAtom method)
(OBBond method)
GetPartialCharge() (OBAtom method)
GetPossibleCause() (OBError method)
GetResidue() (OBAtom method)
GetSize() (OBBitVec method)
GetSpacedFormula() (OBMol method)
GetSpinMultiplicity() (OBAtom method)
GetSuggestedRemedy() (OBError method)
GetSupportedInputFormat() (OBConversion method)
GetSupportedOutputFormat() (OBConversion method)
GetTitle() (OBMol method)
GetTorsionByAtoms() (OBMol method)
GetTorsionByIndex() (OBMol method)
GetTotalCharge() (OBMol method)
GetTotalSpinMultiplicity() (OBMol method)
GetType() (OBAtom method)
GetUnit() (OBForceField method)
GetUpdateFrequency() (OBForceField method)
GetValence() (OBAtom method)
GetVDWCutOff() (OBForceField method)
GetVector() (OBAtom method)
GetWarningMessageCount() (OBMessageHandler method)
GetX() (OBAtom method)
(vector3 method)
GetY() (OBAtom method)
(vector3 method)
GetZ() (OBAtom method)
(vector3 method)
H
Has2D() (OBMol method)
Has3D() (OBMol method)
HasAlphaBetaUnsat() (OBAtom method)
HasAnalyticalGradients() (OBForceField method)
HasAromaticBond() (OBAtom method)
HasAromaticPerceived() (OBMol method)
HasAtomTypesPerceived() (OBMol method)
HasBondOfOrder() (OBAtom method)
HasChainsPerceived() (OBMol method)
HasChiralityPerceived() (OBMol method)
HasChiralitySpecified() (OBAtom method)
HasChiralVolume() (OBAtom method)
HasClosureBondsPerceived() (OBMol method)
HasDoubleBond() (OBAtom method)
HasGroups() (OBForceField method)
HasHybridizationPerceived() (OBMol method)
HasHydrogensAdded() (OBMol method)
HasLSSRPerceived() (OBMol method)
HasNonSingleBond() (OBAtom method)
HasNonZeroCoords() (OBMol method)
HasPartialChargesPerceived() (OBMol method)
HasResidue() (OBAtom method)
HasRingAtomsAndBondsPerceived() (OBMol method)
HasRingTypesPerceived() (OBMol method)
HasSingleBond() (OBAtom method)
HasSpinMultiplicityAssigned() (OBMol method)
HasSSSRPerceived() (OBMol method)
HighestBondOrder() (OBAtom method)
HtoMethyl() (OBAtom method)
I
InsertAtom() (OBMol method)
IsAmide() (OBBond method)
IsAmideNitrogen() (OBAtom method)
IsAntiClockwise() (OBAtom method)
IsApprox() (vector3 method)
IsAromatic() (OBAtom method)
(OBBond method)
IsAromaticNOxide() (OBAtom method)
IsAxial() (OBAtom method)
IsCarbonyl() (OBBond method)
IsCarboxylOxygen() (OBAtom method)
IsChiral() (OBAtom method)
(OBMol method)
IsCisOrTrans() (OBBond method)
IsClockwise() (OBAtom method)
IsClosure() (OBBond method)
IsConnected() (OBAtom method)
IsCorrectedForPH() (OBMol method)
IsCutOffEnabled() (OBForceField method)
IsDoubleBondGeometry() (OBBond method)
IsDown() (OBBond method)
IsEmpty() (OBBitVec method)
IsEster() (OBBond method)
IsFirstInput() (OBConversion method)
IsFixed() (OBFFConstraints method)
IsHash() (OBBond method)
IsHbondAcceptor() (OBAtom method)
IsHbondAcceptorSimple() (OBAtom method)
IsHbondDonor() (OBAtom method)
IsHbondDonorH() (OBAtom method)
IsHetAtom() (OBAtom method)
IsHeteroatom() (OBAtom method)
IsIgnored() (OBFFConstraints method)
IsInRing() (OBAtom method)
(OBBond method)
IsInRingSize() (OBAtom method)
IsLast() (OBConversion method)
IsLastFile() (OBConversion method)
IsNegativeStereo() (OBAtom method)
IsNitroOxygen() (OBAtom method)
IsNonPolarHydrogen() (OBAtom method)
IsOneFour() (OBAtom method)
IsOneThree() (OBAtom method)
IsOption() (OBConversion method)
IsPhosphateOxygen() (OBAtom method)
IsPolarHydrogen() (OBAtom method)
IsPositiveStereo() (OBAtom method)
IsPrimaryAmide() (OBBond method)
IsRotor() (OBBond method)
IsSecondaryAmide() (OBBond method)
IsSetupNeeded() (OBForceField method)
IsSpiroAtom() (OBBuilder method)
IsSulfateOxygen() (OBAtom method)
IsTertiaryAmide() (OBBond method)
IsUp() (OBBond method)
IsWedge() (OBBond method)
IsWedgeOrHash() (OBBond method)
IsXFixed() (OBFFConstraints method)
IsYFixed() (OBFFConstraints method)
IsZFixed() (OBFFConstraints method)
L
length() (vector3 method)
length_2() (vector3 method)
LewisAcidBaseCounts() (OBAtom method)
LineSearch() (OBForceField method)
LoadFragments() (OBBuilder method)
M
MakeDativeBonds() (OBMol method)
MakeNewInstance() (OBForceField method)
MatchesSMARTS() (OBAtom method)
MemberOfRingCount() (OBAtom method)
MemberOfRingSize() (OBAtom method)
message() (OBError method)
MolecularDynamicsTakeNSteps() (OBForceField method)
N
Negate() (OBBitVec method)
NewAtom() (OBMol method)
NewAtomById() (OBMol method)
NewBond() (OBMol method)
NewBondById() (OBMol method)
NewResidue() (OBAtom method)
(OBMol method)
NextBit() (OBBitVec method)
normalize() (vector3 method)
NumAtoms() (OBMol method)
NumBonds() (OBMol method)
NumConformers() (OBMol method)
NumHvyAtoms() (OBMol method)
NumResidues() (OBMol method)
NumRotors() (OBMol method)
O
OBAtom (class in pyOBabel)
OBBitVec (class in pyOBabel)
OBBond (class in pyOBabel)
OBBuilder (class in pyOBabel)
OBConversion (class in pyOBabel)
OBError (class in pyOBabel)
OBFFConstraints (class in pyOBabel)
OBFFLog() (OBForceField method)
OBForceField (class in pyOBabel)
OBMessageHandler (class in pyOBabel)
OBMol (class in pyOBabel)
OBResidue (class in pyOBabel)
OpenInAndOutFiles() (OBConversion method)
P
ParseParamFile() (OBForceField method)
PerceiveBondOrders() (OBMol method)
Point2Line() (in module pyOBabel)
Point2Plane() (in module pyOBabel)
Point2PlaneAngle() (in module pyOBabel)
Point2PlaneSigned() (in module pyOBabel)
PrintFormalCharges() (OBForceField method)
PrintPartialCharges() (OBForceField method)
PrintTypes() (OBForceField method)
PrintVelocities() (OBForceField method)
pyOBabel (module)
R
RandomRotorSearch() (OBForceField method)
RandomRotorSearchInitialize() (OBForceField method)
RandomRotorSearchNextConformer() (OBForceField method)
Read() (OBConversion method)
ReadFile() (OBConversion method)
ReadString() (OBConversion method)
RemoveOption() (OBConversion method)
RenumberAtomsByAtoms() (OBMol method)
RenumberAtomsByIndex() (OBMol method)
ReserveAtoms() (OBMol method)
residues (OBMol attribute)
Resize() (OBBitVec method)
ResizeWords() (OBBitVec method)
S
Separate() (OBMol method)
Set() (vector3 method)
SetAntiClockwiseStereo() (OBAtom method)
SetAromatic() (OBAtom method)
(OBBond method)
SetAromaticPerceived() (OBMol method)
SetAtomicNum() (OBAtom method)
SetAtomTypesPerceived() (OBMol method)
SetAutomaticFormalCharge() (OBMol method)
SetAutomaticPartialCharge() (OBMol method)
SetBegin() (OBBond method)
SetBitOff() (OBBitVec method)
SetBitOn() (OBBitVec method)
SetBO() (OBBond method)
SetBondOrder() (OBBond method)
SetChainsPerceived() (OBMol method)
SetChiral() (OBAtom method)
SetChiralityPerceived() (OBMol method)
SetClockwiseStereo() (OBAtom method)
SetClosure() (OBBond method)
SetClosureBondsPerceived() (OBMol method)
SetConformerByIndex() (OBMol method)
SetConformerEnergies() (OBMol method)
SetConformers() (OBForceField method)
SetConformersCoords() (OBMol method)
SetConstraints() (OBForceField method)
SetCoordinates() (OBForceField method)
(OBMol method)
SetCorrectedForPH() (OBMol method)
SetDimension() (OBMol method)
SetDown() (OBBond method)
SetElectrostaticCutOff() (OBForceField method)
SetEnd() (OBBond method)
SetFactor() (OBFFConstraints method)
SetFirstInput() (OBConversion method)
SetFixAtom() (OBForceField method)
SetFlags() (OBMol method)
SetFormalCharge() (OBAtom method)
SetFormalCharges() (OBForceField method)
SetFormula() (OBMol method)
SetHash() (OBBond method)
SetHeatFormation() (OBMol method)
SetHyb() (OBAtom method)
SetHybAndGeom() (OBAtom method)
SetHybridizationPerceived() (OBMol method)
SetHydrogensAdded() (OBMol method)
SetId() (OBAtom method)
(OBBond method)
SetIdx() (OBAtom method)
SetIgnoreAtom() (OBForceField method)
SetImplicitHCount() (OBAtom method)
SetInAndOutFormats() (OBConversion method)
SetInFormat() (OBConversion method)
SetInRing() (OBAtom method)
(OBBond method)
SetIsotope() (OBAtom method)
SetIsPatternStructure() (OBMol method)
SetKeepRings() (OBBuilder method)
SetLast() (OBConversion method)
SetLength() (OBBond method)
SetLineSearchType() (OBForceField method)
SetLogLevel() (OBForceField method)
SetLSSRPerceived() (OBMol method)
SetMaxLogEntries() (OBMessageHandler method)
SetMoreFilesToCome() (OBConversion method)
SetName() (OBResidue method)
SetNegativeStereo() (OBAtom method)
SetOneObjectOnly() (OBConversion method)
SetOptions() (OBConversion method)
SetOutFormat() (OBConversion method)
SetOutputIndex() (OBConversion method)
SetOutputLevel() (OBMessageHandler method)
SetOutputStream() (OBMessageHandler method)
SetParameterFile() (OBForceField method)
SetParent() (OBAtom method)
(OBBond method)
SetPartialCharge() (OBAtom method)
SetPartialCharges() (OBForceField method)
SetPartialChargesPerceived() (OBMol method)
SetPositiveStereo() (OBAtom method)
SetRangeOff() (OBBitVec method)
SetRangeOn() (OBBitVec method)
SetResidue() (OBAtom method)
SetRingAtomsAndBondsPerceived() (OBMol method)
SetRingTypesPerceived() (OBMol method)
SetSpinMultiplicity() (OBAtom method)
SetSpinMultiplicityAssigned() (OBMol method)
SetSSSRPerceived() (OBMol method)
SetTitle() (OBMol method)
SetTorsion() (OBMol method)
SetTotalCharge() (OBMol method)
SetTotalSpinMultiplicity() (OBMol method)
SetType() (OBAtom method)
SetTypes() (OBForceField method)
SetUp() (OBBond method)
Setup() (OBFFConstraints method)
(OBForceField method)
SetupCalculations() (OBForceField method)
SetUpdateFrequency() (OBForceField method)
SetupPointers() (OBForceField method)
SetupWithConstraints() (OBForceField method)
SetVDWCutOff() (OBForceField method)
SetVector() (OBAtom method)
SetWedge() (OBBond method)
SetWedgeOrHash() (OBBond method)
SetX() (vector3 method)
SetY() (vector3 method)
SetZ() (vector3 method)
SmallestBondAngle() (OBAtom method)
StartLogging() (OBMessageHandler method)
SteepestDescent() (OBForceField method)
SteepestDescentInitialize() (OBForceField method)
SteepestDescentTakeNSteps() (OBForceField method)
StopErrorWrap() (OBMessageHandler method)
StripSalts() (OBMol method)
Swap() (OBBuilder method)
SystematicRotorSearch() (OBForceField method)
SystematicRotorSearchInitialize() (OBForceField method)
SystematicRotorSearchNextConformer() (OBForceField method)
T
ThrowErrorByMessage() (OBMessageHandler method)
ThrowErrorByOBError() (OBMessageHandler method)
ToInertialFrameForAllConformers() (OBMol method)
ToInertialFrameForOneConformer() (OBMol method)
TranslateAllConformers() (OBMol method)
TranslateOneConformer() (OBMol method)
U
UnsetAromatic() (OBAtom method)
(OBBond method)
UnsetAromaticPerceived() (OBMol method)
UnsetDown() (OBBond method)
UnsetFixAtom() (OBForceField method)
UnsetFlag() (OBMol method)
UnsetHash() (OBBond method)
UnsetHydrogensAdded() (OBMol method)
UnsetIgnoreAtom() (OBForceField method)
UnsetKeepRings() (OBBuilder method)
UnsetLSSRPerceived() (OBMol method)
UnsetPartialChargesPerceived() (OBMol method)
UnsetRingTypesPerceived() (OBMol method)
UnsetSSSRPerceived() (OBMol method)
UnsetStereo() (OBAtom method)
UnsetUp() (OBBond method)
UnsetWedge() (OBBond method)
UpdateConformers() (OBForceField method)
UpdateCoordinates() (OBForceField method)
UpdatePairsSimple() (OBForceField method)
V
Validate() (OBForceField method)
ValidateConjugateGradients() (OBForceField method)
ValidateGradientError() (OBForceField method)
ValidateGradients() (OBForceField method)
ValidateLineSearch() (OBForceField method)
ValidateSteepestDescent() (OBForceField method)
vector3 (class in pyOBabel)
vectorAngle() (in module pyOBabel)
W
WeightedRotorSearch() (OBForceField method)
Write() (OBConversion method)
WriteFile() (OBConversion method)
WriteString() (OBConversion method)
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