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OBMol Member List

This is the complete list of members for OBMol, including all inherited members.

_atomIds | OBMol | protected
_autoFormalCharge | OBMol | protected
_autoPartialCharge | OBMol | protected
_bondIds | OBMol | protected
_c | OBMol | protected
_dimension | OBMol | protected
_energy | OBMol | protected
_flags | OBMol | protected
_internals | OBMol | protected
_mod | OBMol | protected
_natoms | OBMol | protected
_nbonds | OBMol | protected
_residue | OBMol | protected
_title | OBMol | protected
_totalCharge | OBMol | protected
_totalSpin | OBMol | protected
_vatom | OBMol | protected
_vbond | OBMol | protected
_vconf | OBMol | protected
_vdata | OBBase | protected
AddAtom(OBAtom &atom, bool forceNewId=false) | OBMol |
AddBond(int beginIdx, int endIdx, int order, int flags=0, int insertpos=-1) | OBMol |
AddBond(OBBond &) | OBMol |
AddConformer(double *f) | OBMol | inline
AddHydrogens(bool polaronly=false, bool correctForPH=false, double pH=7.4) | OBMol |
AddHydrogens(OBAtom *) | OBMol |
AddNewHydrogens(HydrogenType whichHydrogen, bool correctForPH=false, double pH=7.4) | OBMol |
AddNonPolarHydrogens() | OBMol |
AddPolarHydrogens() | OBMol |
AddResidue(OBResidue &) | OBMol |
Align(OBAtom *, OBAtom *, vector3 &, vector3 &) | OBMol |
AreInSameRing(OBAtom *a, OBAtom *b) | OBMol |
AssignSpinMultiplicity(bool NoImplicitH=false) | OBMol |
AssignTotalChargeToAtoms(int charge) | OBMol |
AutomaticFormalCharge() | OBMol | inline
AutomaticPartialCharge() | OBMol | inline
BeginAtom(OBAtomIterator &i) | OBMol |
BeginAtoms() | OBMol | inline
BeginBond(OBBondIterator &i) | OBMol |
BeginBonds() | OBMol | inline
BeginConformer(std::vector< double * >::iterator &i) | OBMol | inline
BeginData() | OBBase | inline
BeginInternalCoord(std::vector< OBInternalCoord * >::iterator &i) | OBMol | inline
BeginModify(void) | OBMol | virtual
BeginResidue(OBResidueIterator &i) | OBMol | inline
BeginResidues() | OBMol | inline
CastAndClear(bool clear=true) | OBBase | inline
Center() | OBMol |
Center(int nconf) | OBMol |
ClassDescription() | OBMol | static
Clear() | OBMol | virtual
CloneData(OBGenericData *d) | OBBase |
ConnectTheDots() | OBMol |
ContigFragList(std::vector< std::vector< int > > &) | OBMol |
ConvertDativeBonds() | OBMol |
ConvertZeroBonds() | OBMol |
CopyConformer(double *c, int nconf) | OBMol |
CopySubstructure(OBMol &newmol, OBBitVec *includeatoms, OBBitVec *excludebonds=(OBBitVec *) nullptr, unsigned int correctvalence=1, std::vector< unsigned int > *atomorder=(std::vector< unsigned int > *) nullptr, std::vector< unsigned int > *bondorder=(std::vector< unsigned int > *) nullptr) | OBMol |
CorrectForPH(double pH=7.4) | OBMol |
DataSize() const | OBBase | inline
DecrementMod() | OBMol | inline
DeleteAtom(OBAtom *, bool destroyAtom=true) | OBMol |
DeleteBond(OBBond *, bool destroyBond=true) | OBMol |
DeleteConformer(int nconf) | OBMol |
DeleteData(unsigned int type) | OBBase |
DeleteData(OBGenericData *) | OBBase |
DeleteData(std::vector< OBGenericData * > &) | OBBase |
DeleteData(const std::string &s) | OBBase |
DeleteHydrogen(OBAtom *) | OBMol |
DeleteHydrogens() | OBMol |
DeleteHydrogens(OBAtom *) | OBMol |
DeleteNonPolarHydrogens() | OBMol |
DeletePolarHydrogens() | OBMol |
DeleteResidue(OBResidue *, bool destroyResidue=true) | OBMol |
DestroyAtom(OBAtom *) | OBMol | virtual
DestroyBond(OBBond *) | OBMol | virtual
DestroyResidue(OBResidue *) | OBMol | virtual
DoTransformations(const std::map< std::string, std::string > *pOptions, OBConversion *pConv) | OBMol | virtual
Empty() | OBMol | inline
EndAtoms() | OBMol | inline
EndBonds() | OBMol | inline
EndData() | OBBase | inline
EndModify(bool nukePerceivedData=true) | OBMol | virtual
EndResidues() | OBMol | inline
FindAngles() | OBMol |
FindChildren(std::vector< int > &children, int bgnIdx, int endIdx) | OBMol |
FindChildren(std::vector< OBAtom * > &children, OBAtom *bgn, OBAtom *end) | OBMol |
FindLargestFragment(OBBitVec &frag) | OBMol |
FindLSSR() | OBMol |
FindRingAtomsAndBonds() | OBMol |
FindSSSR() | OBMol |
FindTorsions() | OBMol |
GetAllData(const unsigned int type) | OBBase |
GetAngle(OBAtom *a, OBAtom *b, OBAtom *c) | OBMol |
GetAtom(int idx) const | OBMol |
GetAtomById(unsigned long id) const | OBMol |
GetBond(int idx) const | OBMol |
GetBond(int a, int b) const | OBMol |
GetBond(OBAtom *bgn, OBAtom *end) const | OBMol |
GetBondById(unsigned long id) const | OBMol |
GetConformer(int i) | OBMol | inline
GetConformers() | OBMol | inline
GetCoordinates() | OBMol | inline
GetData(const unsigned int type) | OBBase |
GetData(const std::string &) | OBBase |
GetData(const char *) | OBBase |
GetData() | OBBase | inline
GetData(DataOrigin source) | OBBase |
GetDimension() const | OBMol | inline
GetEnergies() | OBMol |
GetEnergy() const | OBMol | inline
GetEnergy(int ci) | OBMol |
GetExactMass(bool implicitH=true) | OBMol |
GetFirstAtom() const | OBMol |
GetFlags() | OBMol | inline
GetFormula() | OBMol |
GetGIDVector(std::vector< unsigned int > &) | OBMol |
GetGIVector(std::vector< unsigned int > &) | OBMol |
GetGTDVector(std::vector< int > &) | OBMol |
GetInternalCoord() | OBMol |
GetLSSR() | OBMol |
GetMod() | OBMol | inline
GetMolWt(bool implicitH=true) | OBMol |
GetNextFragment(OpenBabel::OBMolAtomDFSIter &iter, OBMol &newMol) | OBMol |
GetResidue(int idx) const | OBMol |
GetSpacedFormula(int ones=0, const char *sp=" ", bool implicitH=true) | OBMol |
GetSSSR() | OBMol |
GetTitle(bool replaceNewlines=true) const | OBMol | virtual
GetTorsion(int, int, int, int) | OBMol |
GetTorsion(OBAtom *a, OBAtom *b, OBAtom *c, OBAtom *d) | OBMol |
GetTotalCharge() | OBMol |
GetTotalSpinMultiplicity() | OBMol |
Has2D(bool Not3D=false) | OBMol |
Has3D() | OBMol |
HasAromaticPerceived() | OBMol | inline
HasAtomTypesPerceived() | OBMol | inline
HasChainsPerceived() | OBMol | inline
HasChiralityPerceived() | OBMol | inline
HasClosureBondsPerceived() | OBMol | inline
HasData(const std::string &) | OBBase |
HasData(const char *) | OBBase |
HasData(const unsigned int type) | OBBase |
HasFlag(int flag) | OBMol | inline
HasHybridizationPerceived() | OBMol | inline
HasHydrogensAdded() | OBMol | inline
HasLSSRPerceived() | OBMol | inline
HasNonZeroCoords() | OBMol |
HasPartialChargesPerceived() | OBMol | inline
HasRingAtomsAndBondsPerceived() | OBMol | inline
HasRingTypesPerceived() | OBMol | inline
HasSpinMultiplicityAssigned() | OBMol | inline
HasSSSRPerceived() | OBMol | inline
IncrementMod() | OBMol | inline
InsertAtom(OBAtom &) | OBMol |
IsCorrectedForPH() | OBMol | inline
IsPeriodic() | OBMol | inline
IsReaction() | OBMol | inline
MakeDativeBonds() | OBMol |
NewAtom() | OBMol |
NewAtom(unsigned long id) | OBMol |
NewBond() | OBMol |
NewBond(unsigned long id) | OBMol |
NewResidue() | OBMol |
NextAtom(OBAtomIterator &i) | OBMol |
NextBond(OBBondIterator &i) | OBMol |
NextConformer(std::vector< double * >::iterator &i) | OBMol | inline
NextInternalCoord(std::vector< OBInternalCoord * >::iterator &i) | OBMol | inline
NextResidue(OBResidueIterator &i) | OBMol | inline
NumAtoms() const | OBMol | inline
NumBonds() const | OBMol | inline
NumConformers() | OBMol | inline
NumHvyAtoms() | OBMol |
NumResidues() const | OBMol | inline
NumRotors(bool sampleRingBonds=false) | OBMol |
OBMol() | OBMol |
OBMol(const OBMol &) | OBMol |
operator+=(const OBMol &mol) | OBMol |
operator=(const OBMol &mol) | OBMol |
PerceiveBondOrders() | OBMol |
RenumberAtoms(std::vector< OBAtom * > &) | OBMol |
RenumberAtoms(std::vector< int >) | OBMol |
ReserveAtoms(int natoms) | OBMol | inline
Rotate(const double u[3][3]) | OBMol |
Rotate(const double m[9]) | OBMol |
Rotate(const double m[9], int nconf) | OBMol |
Separate(int StartIndex=1) | OBMol |
SetAromaticPerceived(bool value=true) | OBMol | inline
SetAtomTypesPerceived(bool value=true) | OBMol | inline
SetAutomaticFormalCharge(bool val) | OBMol | inline
SetAutomaticPartialCharge(bool val) | OBMol | inline
SetChainsPerceived(bool value=true) | OBMol | inline
SetChiralityPerceived(bool value=true) | OBMol | inline
SetClosureBondsPerceived(bool value=true) | OBMol | inline
SetConformer(unsigned int i) | OBMol |
SetConformers(std::vector< double * > &v) | OBMol |
SetCoordinates(double *c) | OBMol |
SetCorrectedForPH(bool value=true) | OBMol | inline
SetData(OBGenericData *d) | OBBase | inline
SetDimension(unsigned short int d) | OBMol | inline
SetEnergies(std::vector< double > &energies) | OBMol |
SetEnergy(double energy) | OBMol | inline
SetFlag(int flag) | OBMol | inline
SetFlags(int flags) | OBMol | inline
SetFormula(std::string molFormula) | OBMol |
SetHybridizationPerceived(bool value=true) | OBMol | inline
SetHydrogensAdded(bool value=true) | OBMol | inline
SetInternalCoord(std::vector< OBInternalCoord * > int_coord) | OBMol |
SetIsPatternStructure(bool value=true) | OBMol | inline
SetIsReaction(bool value=true) | OBMol | inline
SetLSSRPerceived(bool value=true) | OBMol | inline
SetPartialChargesPerceived(bool value=true) | OBMol | inline
SetPeriodicMol(bool value=true) | OBMol | inline
SetRingAtomsAndBondsPerceived(bool value=true) | OBMol | inline
SetRingTypesPerceived(bool value=true) | OBMol | inline
SetSpinMultiplicityAssigned(bool value=true) | OBMol | inline
SetSSSRPerceived(bool value=true) | OBMol | inline
SetTitle(const char *title) | OBMol | virtual
SetTitle(std::string &title) | OBMol |
SetTorsion(OBAtom *, OBAtom *, OBAtom *, OBAtom *, double ang) | OBMol |
SetTotalCharge(int charge) | OBMol |
SetTotalSpinMultiplicity(unsigned int spinMultiplicity) | OBMol |
StripSalts(unsigned int threshold=0) | OBMol |
ToInertialFrame(int conf, double *rmat) | OBMol |
ToInertialFrame() | OBMol |
Translate(const vector3 &v) | OBMol |
Translate(const vector3 &v, int conf) | OBMol |
UnsetFlag(int flag) | OBMol | inline
~OBBase() | OBBase | inline virtual
~OBMol() | OBMol | virtual