| _autoFormalCharge | OBMol | [protected] |
| _autoPartialCharge | 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 &) | 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=true) | OBMol | |
| AddHydrogens(OBAtom *) | OBMol | |
| AddPolarHydrogens() | OBMol | |
| AddResidue(OBResidue &) | OBMol | |
| Align(OBAtom *, OBAtom *, vector3 &, vector3 &) | OBMol | |
| AssignSpinMultiplicity() | 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] |
| ConnectTheDots() | OBMol | |
| ContigFragList(std::vector< std::vector< int > > &) | OBMol | |
| ConvertDativeBonds() | OBMol | |
| CopyConformer(double *c, int nconf) | OBMol | |
| CorrectForPH() | OBMol | |
| CreateAtom(void) | OBMol | [virtual] |
| CreateBond(void) | OBMol | [virtual] |
| CreateResidue(void) | OBMol | [virtual] |
| DataSize() const | OBBase | [inline] |
| DecrementMod() | OBMol | [inline] |
| DeleteAtom(OBAtom *) | OBMol | |
| DeleteBond(OBBond *) | OBMol | |
| DeleteConformer(int nconf) | OBMol | |
| DeleteData(unsigned int type) | OBBase | |
| DeleteData(OBGenericData *) | OBBase | |
| DeleteData(std::vector< OBGenericData * > &) | OBBase | |
| DeleteHydrogen(OBAtom *) | OBMol | |
| DeleteHydrogens() | OBMol | |
| DeleteHydrogens(OBAtom *) | OBMol | |
| DeleteNonPolarHydrogens() | OBMol | |
| DeleteResidue(OBResidue *) | OBMol | |
| DestroyAtom(OBAtom *) | OBMol | [virtual] |
| DestroyBond(OBBond *) | OBMol | [virtual] |
| DestroyResidue(OBResidue *) | OBMol | [virtual] |
| DoTransformations(const std::map< std::string, std::string > *pOptions) | 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(OBAtom *atom1, OBAtom *atom2, std::vector< int > ¤tState, std::vector< int > &initState, std::vector< int > &bcurrentState, std::vector< int > &binitState, std::vector< bool > &mark) | OBMol | [protected] |
| expandcycle(OBAtom *atom, OBBitVec &avisit) | 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 | |
| FindLargestFragment(OBBitVec &frag) | OBMol | |
| FindRingAtomsAndBonds() | OBMol | |
| FindSSSR() | OBMol | |
| FindTorsions() | OBMol | |
| GetAngle(OBAtom *a, OBAtom *b, OBAtom *c) | OBMol | |
| GetAtom(int idx) | OBMol | |
| GetBond(int idx) | OBMol | |
| GetBond(int a, int b) | OBMol | |
| GetBond(OBAtom *bgn, OBAtom *end) | 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] |
| GetEnergy() const | OBMol | [inline] |
| GetExactMass() | OBMol | |
| GetFirstAtom() | 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 | |
| GetMod() | OBMol | [inline] |
| GetMolWt() | OBMol | |
| getorden(OBAtom *atom) | OBMol | [protected] |
| GetResidue(int) | OBMol | |
| GetSpacedFormula(int ones=0, const char *sp=" ") | OBMol | |
| GetSSSR() | OBMol | |
| GetTitle() const | OBMol | [inline] |
| GetTorsion(int, int, int, int) | OBMol | |
| GetTorsion(OBAtom *a, OBAtom *b, OBAtom *c, OBAtom *d) | OBMol | |
| GetTotalCharge() | OBMol | |
| GetTotalSpinMultiplicity() | OBMol | |
| Has2D() | OBMol | |
| Has3D() | OBMol | |
| 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] |
| HasNonZeroCoords() | OBMol | |
| HasPartialChargesPerceived() | OBMol | [inline] |
| HasRingAtomsAndBondsPerceived() | OBMol | [inline] |
| HasSpinMultiplicityAssigned() | OBMol | [inline] |
| HasSSSRPerceived() | OBMol | [inline] |
| IncrementMod() | OBMol | [inline] |
| InsertAtom(OBAtom &) | OBMol | |
| IsChiral() | OBMol | |
| IsCorrectedForPH() | OBMol | [inline] |
| Kekulize() | OBMol | |
| NewAtom() | OBMol | [virtual] |
| NewBond() | OBMol | [virtual] |
| NewPerceiveKekuleBonds() | OBMol | |
| NewResidue() | OBMol | [virtual] |
| 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 | |
| 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 | |
| SetCorrectedForPH() | OBMol | [inline] |
| SetData(OBGenericData *d) | OBBase | [inline] |
| SetDimension(unsigned short int d) | OBMol | [inline] |
| 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 | [inline] |
| SetKekulePerceived() | OBMol | [inline] |
| SetPartialChargesPerceived() | OBMol | [inline] |
| SetRingAtomsAndBondsPerceived() | OBMol | [inline] |
| SetSpinMultiplicityAssigned() | OBMol | [inline] |
| SetSSSRPerceived() | OBMol | [inline] |
| SetTitle(const char *title) | OBMol | |
| SetTitle(std::string &title) | OBMol | |
| SetTorsion(OBAtom *, OBAtom *, OBAtom *, OBAtom *, double) | OBMol | |
| SetTotalCharge(int charge) | OBMol | |
| SetTotalSpinMultiplicity(unsigned int spin) | OBMol | |
| start_kekulize(std::vector< OBAtom * > &cycle, std::vector< int > &electron) | OBMol | [protected] |
| StripSalts() | 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] |
| UnsetPartialChargesPerceived() | OBMol | [inline] |
| ~OBBase() | OBBase | [inline, virtual] |
| ~OBMol() | OBMol | [virtual] |
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.