| AddAllMissingAtoms(ADD_ATOM_TYPE atom_type) | HaMolecule | |
| AddAtomFromTempl(HaAtom *aptr2, HaAtom *aptr3, HaAtom *aptr4, const HaAtom *aptr_templ, const HaAtom *aptr_templ_2, const HaAtom *aptr_templ_3, const HaAtom *aptr_templ_4) | HaMolecule | |
| AddBond(HaAtom *src, HaAtom *dst, int flag) | HaMolecule | |
| AddChain(char ident) | HaMolecule | |
| AddFeature() (defined in HaMolecule) | HaMolecule | |
| AddHBond(HaAtom *src, HaAtom *dst) | HaMolecule | |
| AddMissingAtoms(HaResidue *pres, ADD_ATOM_TYPE atom_type) | HaMolecule | |
| AddMissingAtoms_2(HaResidue *pres, HaResidue *prtempl, ADD_ATOM_TYPE atom_type) (defined in HaMolecule) | HaMolecule | [protected] |
| AddMolCopy(const HaMolecule &Mol_ref, bool create_new_chain=true, map< HaAtom *, HaAtom *, less< HaAtom * > > *ptr_atom_map=NULL) (defined in HaMolecule) | HaMolecule | |
| AddSSBond(HaAtom *src, HaAtom *dst) | HaMolecule | |
| AddWaterHydrogens(HaResidue *pres) | HaMolecule | |
| AreHBonded(HaAtom *src, HaAtom *dst) const | HaMolecule | |
| AreHBondsFound() const | HaMolecule | [inline] |
| AreSSBondsFound() const | HaMolecule | [inline] |
| Atoms | HaMolecule | |
| AttachFragment(HaAtom *catom_host, HaAtom *catom_frag) (defined in HaMolecule) | HaMolecule | [static] |
| BondIfClose(HaAtom *sptr, HaAtom *dptr) | HaMolecule | |
| BondIterator typedef | HaMolecule | |
| Bonds | HaMolecule | |
| CalcHydrogenBonds() | HaMolecule | |
| CalcNucleicHBonds(HaChain *chn1) (defined in HaMolecule) | HaMolecule | |
| CalcProteinHBonds(HaChain *chn1) (defined in HaMolecule) | HaMolecule | |
| CalculateBondEnergy(HaResidue *group) (defined in HaMolecule) | HaMolecule | |
| Chains | HaMolecule | |
| classification (defined in HaMolecule) | HaMolecule | |
| CombineMolecules(HaMolecule *frag_mol, HaAtom *catom_host, HaAtom *catom_frag) (defined in HaMolecule) | HaMolecule | |
| connect_flag (defined in Object3D) | Object3D | [protected] |
| CreateHydrogenBond(HaAtom *src, HaAtom *dst, int energy, int offset) (defined in HaMolecule) | HaMolecule | |
| CreateMoleculeBonds() (defined in HaMolecule) | HaMolecule | |
| CreateMolResidue() | HaMolecule | |
| CurChain | HaMolecule | |
| CurChainItr (defined in HaMolecule) | HaMolecule | [protected] |
| CurResidue | HaMolecule | |
| DeleteBond(HaAtom *src, HaAtom *dst) (defined in HaMolecule) | HaMolecule | |
| DescribeMolecule() (defined in HaMolecule) | HaMolecule | |
| DescribeSequence() (defined in HaMolecule) | HaMolecule | |
| DetermineStructure(int flag) | HaMolecule | |
| displayed_flag (defined in Object3D) | Object3D | [protected] |
| Features (defined in HaMolecule) | HaMolecule | |
| FillRef(char *buf, int mode=0) const | HaMolecule | |
| FindAlphaHelix(int pitch, int flag) (defined in HaMolecule) | HaMolecule | [protected] |
| FindBetaSheets() (defined in HaMolecule) | HaMolecule | [protected] |
| FindBetaTurns() (defined in HaMolecule) | HaMolecule | [protected] |
| FindDisulphideBridges() | HaMolecule | |
| FindTurnStructure() (defined in HaMolecule) | HaMolecule | [protected] |
| FixChainsIdent() | HaMolecule | |
| GetAtomByRef(const char *at_ref) | HaMolecule | |
| GetAtomBySeqNum(const int index) | HaMolecule | |
| GetAtomBySeqNum(const int index) const | HaMolecule | |
| GetAtomIterator() | HaMolecule | [virtual] |
| GetAverageCoord(double &avx, double &avy, double &avz) | HaMolecule | |
| GetChain(const char chain_id) | HaMolecule | |
| GetFirstChain() | HaMolecule | |
| GetHostMolSet() (defined in HaMolecule) | HaMolecule | [inline] |
| GetHostMolSet() const (defined in HaMolecule) | HaMolecule | [inline] |
| GetMinMaxCrd(double &MinX_v, double &MinY_v, double &MinZ_v, double &MaxX_v, double &MaxY_v, double &MaxZ_v) | HaMolecule | |
| GetNAtoms() const | HaMolecule | [virtual] |
| GetNBonds() const | HaMolecule | |
| GetNChains() | HaMolecule | [inline] |
| GetNextChain() | HaMolecule | |
| GetNHBonds() const | HaMolecule | |
| GetNRes() const | HaMolecule | |
| GetNSSBonds() const | HaMolecule | |
| GetNumFeatures(const int itype) const (defined in HaMolecule) | HaMolecule | |
| GetObjName() const (defined in Object3D) | Object3D | [inline, virtual] |
| GetObjType() const (defined in Object3D) | Object3D | [inline] |
| GetPointIterator() | HaMolecule | [virtual] |
| GetPosEulerTrans(double &phi, double &cos_theta, double &psi, Vec3D &trans) | HaMolecule | |
| GetPtNum() | HaMolecule | [inline, virtual] |
| GetRef() const | HaMolecule | |
| GetResByRef(const HaString &res_str) | HaMolecule | |
| GetSeqNumOfAtom(const HaAtom *aptr) const | HaMolecule | |
| GetStdPosition(HaMat_double &rot_std, Vec3D &trans_std) | HaMolecule | |
| GetStdRotMat(HaMat_double &rot_mat) | HaMolecule | |
| HaMolecule(HaMolSet *new_phost_mset, HaString new_name="HARLEMMOL") (defined in HaMolecule) | HaMolecule | |
| HaMolecule(const HaMolecule &Mol_ref) (defined in HaMolecule) | HaMolecule | |
| HBonds | HaMolecule | |
| HBonds_found | HaMolecule | |
| identcode (defined in HaMolecule) | HaMolecule | |
| InitAtoms(GauFile &gfile) | HaMolecule | |
| InitAtomsGRWF() | HaMolecule | |
| IsConnected() (defined in Object3D) | Object3D | [inline] |
| IsDisplayed() (defined in Object3D) | Object3D | [inline] |
| IsMember(const HaAtom *aptr) const | HaMolecule | [virtual] |
| IsSecStructFound() (defined in HaMolecule) | HaMolecule | [inline] |
| IsWithinRadius(Vec3D *pptr, double limit) | PointCollection | |
| name (defined in Object3D) | Object3D | [protected] |
| nodes (defined in HaMolecule) | HaMolecule | [protected] |
| obj_type | Object3D | [protected] |
| Object3D(const int new_obj_type, const char *new_name="GEN_Object3D") (defined in Object3D) | Object3D | |
| Object3D(const Object3D &obj_ref) (defined in Object3D) | Object3D | |
| phost_mset (defined in HaMolecule) | HaMolecule | [protected] |
| Print_info(ostream &sout, const int level) const | HaMolecule | |
| ProcessFeatures() (defined in HaMolecule) | HaMolecule | |
| Renumber(int start) (defined in HaMolecule) | HaMolecule | |
| ResidueIterator typedef | HaMolecule | |
| RotateObj(const HaMat_double &rot_mat, const Vec3D &cnt) | HaMolecule | [virtual] |
| RotateX(double theta, const Vec3D &cnt) | Object3D | [virtual] |
| RotateY(double theta, const Vec3D &cnt) | Object3D | [virtual] |
| RotateZ(double theta, const Vec3D &cnt) | Object3D | [virtual] |
| sec_struct_found | HaMolecule | |
| SeqFormat | HaMolecule | [static] |
| SetAtomScreenCoord(HaMolView *pview) | HaMolecule | |
| SetConnected(const bool status) (defined in Object3D) | Object3D | [inline] |
| SetCoordSubstH(const HaAtom *aptr1, const HaAtom *aptr2, HaAtom *haptr) | HaMolecule | [static] |
| SetCysBridgeNames() | HaMolecule | |
| SetDisplayed(const bool status) (defined in Object3D) | Object3D | [inline] |
| SetIntCoordFromStr(const char *int_crd_str) | HaMolecule | |
| SetObjName(const char *new_name) | HaMolecule | [virtual] |
| SetPosEulerTrans(double phi, double cos_theta, double psi, const Vec3D &trans) | HaMolecule | |
| SetPosition(const HaMat_double &rot_new, const Vec3D &trans_new) | HaMolecule | |
| SetTermResNames() | HaMolecule | |
| SetUniqueAtomNames() (defined in HaMolecule) | HaMolecule | |
| SSBonds | HaMolecule | |
| SSBonds_found (defined in HaMolecule) | HaMolecule | |
| structsource | HaMolecule | |
| Superimpose(PointCollection &grp1, PointCollection &grp2, HaMat_double &rot_mat, HaVec_double &transl_vec, double &eps) | PointCollection | [static] |
| TestDisulphideBridge(HaResidue *group1, HaResidue *group2, HaAtom *cys1) (defined in HaMolecule) | HaMolecule | |
| TestLadder(list< HaChain >::iterator chain_ref, HaResidue *prevri, HaResidue *curri, HaResidue *nexti) (defined in HaMolecule) | HaMolecule | [protected] |
| Translate(const Vec3D &tr_vec) | HaMolecule | [virtual] |
| UpdateFeature(FeatEntry *ptr, int mask) (defined in HaMolecule) | HaMolecule | |
| ~HaMolecule() (defined in HaMolecule) | HaMolecule | [virtual] |
| ~Object3D() (defined in Object3D) | Object3D | [virtual] |
