OBMol Member List

This is the complete list of members for OBMol, including all inherited members.
_atomIdsOBMol [protected]
_autoFormalChargeOBMol [protected]
_autoPartialChargeOBMol [protected]
_bondIdsOBMol [protected]
_cOBMol [protected]
_dimensionOBMol [protected]
_energyOBMol [protected]
_flagsOBMol [protected]
_internalsOBMol [protected]
_modOBMol [protected]
_natomsOBMol [protected]
_nbondsOBMol [protected]
_residueOBMol [protected]
_titleOBMol [protected]
_totalChargeOBMol [protected]
_totalSpinOBMol [protected]
_vatomOBMol [protected]
_vbondOBMol [protected]
_vconfOBMol [protected]
_vdataOBBase [protected]
AddAtom(OBAtom &)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
AddPolarHydrogens()OBMol
AddResidue(OBResidue &)OBMol
Align(OBAtom *, OBAtom *, vector3 &, vector3 &)OBMol
AssignSpinMultiplicity(bool NoImplicitH=false)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
CopyConformer(double *c, int nconf)OBMol
CorrectForPH(double pH=7.4)OBMol
CreateAtom(void)OBMol [virtual]
CreateBond(void)OBMol [virtual]
CreateResidue(void)OBMol [virtual]
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
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]
expand_kekulize(int bond_idx, std::vector< int > &atomState, std::vector< int > &bondState)OBMol [protected]
expandcycle(OBAtom *atom, OBBitVec &avisit, const OBBitVec &potAromBonds)OBMol [protected]
FindAngles()OBMol
FindChildren(std::vector< int > &children, int bgnIdx, int endIdx)OBMol
FindChildren(std::vector< OBAtom * > &children, OBAtom *bgn, OBAtom *end)OBMol
FindChiralCenters()OBMol [inline]
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
getorden(OBAtom *atom)OBMol [protected]
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
has_no_leftover_electrons(std::vector< int > &atomState)OBMol [protected]
HasAromaticCorrected()OBMol [inline]
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, protected]
HasHybridizationPerceived()OBMol [inline]
HasHydrogensAdded()OBMol [inline]
HasImplicitValencePerceived()OBMol [inline]
HasKekulePerceived()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
IsChiral()OBMol
IsCorrectedForPH()OBMol [inline]
Kekulize()OBMol
NewAtom()OBMol
NewAtom(unsigned long id)OBMol
NewBond()OBMol
NewBond(unsigned long id)OBMol
NewPerceiveKekuleBonds()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()OBMol
OBMol()OBMol
OBMol(const OBMol &)OBMol
operator+=(const OBMol &mol)OBMol
operator=(const OBMol &mol)OBMol
PerceiveBondOrders()OBMol
PerceiveKekuleBonds()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
SetAromaticCorrected()OBMol [inline]
SetAromaticPerceived()OBMol [inline]
SetAtomTypesPerceived()OBMol [inline]
SetAutomaticFormalCharge(bool val)OBMol [inline]
SetAutomaticPartialCharge(bool val)OBMol [inline]
SetChainsPerceived()OBMol [inline]
SetChiralityPerceived()OBMol [inline]
SetClosureBondsPerceived()OBMol [inline]
SetConformer(int i)OBMol
SetConformers(std::vector< double * > &v)OBMol
SetCoordinates(double *c)OBMol
SetCorrectedForPH()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, protected]
SetFlags(int flags)OBMol [inline]
SetFormula(std::string molFormula)OBMol
SetHybridizationPerceived()OBMol [inline]
SetHydrogensAdded()OBMol [inline]
SetImplicitValencePerceived()OBMol [inline]
SetInternalCoord(std::vector< OBInternalCoord * > int_coord)OBMol
SetIsPatternStructure()OBMol [inline]
SetKekulePerceived()OBMol [inline]
SetLSSRPerceived()OBMol [inline]
SetPartialChargesPerceived()OBMol [inline]
SetRingAtomsAndBondsPerceived()OBMol [inline]
SetRingTypesPerceived()OBMol [inline]
SetSpinMultiplicityAssigned()OBMol [inline]
SetSSSRPerceived()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
start_kekulize(std::vector< OBAtom * > &cycle, std::vector< int > &electron)OBMol [protected]
StripSalts(int threshold=0)OBMol
ToInertialFrame(int conf, double *rmat)OBMol
ToInertialFrame()OBMol
Translate(const vector3 &v)OBMol
Translate(const vector3 &v, int conf)OBMol
UnsetAromaticPerceived()OBMol [inline]
UnsetFlag(int flag)OBMol [inline]
UnsetHydrogensAdded()OBMol [inline]
UnsetImplicitValencePerceived()OBMol [inline]
UnsetLSSRPerceived()OBMol [inline]
UnsetPartialChargesPerceived()OBMol [inline]
UnsetRingTypesPerceived()OBMol [inline]
UnsetSSSRPerceived()OBMol [inline]
~OBBase()OBBase [inline, virtual]
~OBMol()OBMol [virtual]
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