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 *) 0, unsigned int correctvalence=1, std::vector< unsigned int > *atomorder=(std::vector< unsigned int > *) 0, std::vector< unsigned int > *bondorder=(std::vector< unsigned int > *) 0)	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
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
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	inlinevirtual
~OBMol()	OBMol	virtual