| add_molset_copies(int nx, int ny, int nz) | HaMolSet | |
| AddAtomList(const char *id="") | HaMolSet | |
| AddBlankChemGroup(const HaString &gid="") | HaMolSet | |
| AddElectrSurf(int add_surf_below_flag, int add_surf_top_flag, int add_atom_top_flag, int add_atom_below_flag) | HaMolSet | |
| AddHydrogens() | HaMolSet | |
| AddHydrogensHybrid() | HaMolSet | |
| AddMissingAtoms() | HaMolSet | |
| AddObject3D(Object3D *new_view_object) | HaMolSet | |
| AddPolarHydrogens() | HaMolSet | |
| AlignOverlapMol(AtomList &fmolatset, HaMolecule *pMol2, PtrPtrMap *fit=NULL, HaVec_double *p_trans=NULL, HaMat_double *p_rot=NULL) | HaMolSet | |
| AnnounceGeomChange() | HaMolSet | [virtual] |
| AreHBonded(HaAtom *src, HaAtom *dst) const | HaMolSet | |
| BondIterator typedef (defined in HaMolSet) | HaMolSet | |
| CalcDipole() | HaMolSet | |
| CalcHBonds(bool recalc=false) (defined in HaMolSet) | HaMolSet | |
| CalcMolSurface() | HaMolSet | |
| CalcMolSurfDens() | HaMolSet | |
| CalcPKsForSelection() | HaMolSet | |
| CalcSCFPK(VecPtr &act_chem_st, HaMat_double &inter_mat) | HaMolSet | |
| CalculatePotential(double x, double y, double z) | HaMolSet | |
| ChargeMaps | HaMolSet | |
| CheckUniqChemGrpID(const HaString &gid) (defined in HaMolSet) | HaMolSet | |
| chemg_idx (defined in HaMolSet) | HaMolSet | |
| ChemGroups | HaMolSet | |
| ChemGroupsType typedef (defined in HaMolSet) | HaMolSet | |
| ClearPickedAtoms() | HaMolSet | |
| CompModules | HaMolSet | |
| Create2DMolArray(HaMolecule *pMol_ref, const double deltx, const double delty, const int nx, const int ny, const double alpha, const double tilt) | HaMolSet | |
| CreateChargeMap(const char *map_name) | HaMolSet | |
| CreateMolecule() | HaMolSet | |
| CreateSurf(const int num_layers, const HaString name="GOLD") | HaMolSet | |
| CreateTransAlk(const int nunit, const HaString name="ALK") | HaMolSet | |
| debug_flag (defined in HaMolSet) | HaMolSet | |
| DEBUG_FLAG_PARAMS enum name (defined in HaMolSet) | HaMolSet | |
| DeleteAll() | HaMolSet | |
| DeleteAtom(HaAtom *aptr) | HaMolSet | |
| DeleteAtomList(const HaString &gid) | HaMolSet | |
| DeleteAtomListPtr(AtomList *alist_ptr) | HaMolSet | |
| DeleteAtoms(AtomCollection &atset) | HaMolSet | |
| DeleteAtomWithRef(const char *atref) | HaMolSet | |
| DeleteChemGroup(const HaString &gid) | HaMolSet | |
| DeleteChemGroupPtr(ChemGroup *grp_ptr) | HaMolSet | |
| DeleteExtraAtoms() | HaMolSet | |
| DeleteMol(HaMolecule *pMol) | HaMolSet | |
| DeleteObject3D(Object3D *pobj) | HaMolSet | |
| DeleteObject3D(const HaString obj_name) | HaMolSet | |
| DisplaySelectCount() | HaMolSet | |
| ExecuteCommand(CmdParser &cmd_pr) (defined in HaMolSet) | HaMolSet | |
| ExecuteShowCommand(CmdParser &cmd_pr) (defined in HaMolSet) | HaMolSet | |
| FetchFile(int format, const char *file_name) | HaMolSet | |
| file_reading_debug enum value (defined in HaMolSet) | HaMolSet | |
| FindClosestContact(HaAtom *atc1, HaAtom *atc2) | HaMolSet | |
| Fragments (defined in HaMolSet) | HaMolSet | |
| GetActiveMolView() | HaMolSet | |
| GetAtomByRef(const char *at_ref) | HaMolSet | |
| GetAtomListByID(const char *id) | HaMolSet | |
| GetAtomsByRef(const char *at_ref, AtomList &at_set) | HaMolSet | |
| GetChargeMapByName(const char *map_name) | HaMolSet | |
| GetChemGroupByAtom(const HaAtom *aptr) | HaMolSet | |
| GetChemGroupByID(const HaString &gid) | HaMolSet | |
| GetChemGroupByIdx(int index) | HaMolSet | |
| GetCompModule(const int mtype, const bool create_module=false) | HaMolSet | |
| GetDaltonMod(const bool create_module=false) | HaMolSet | |
| GetElectrostMod(const bool create_module=false) | HaMolSet | |
| GetETCouplMod(const bool create_module=false) | HaMolSet | |
| GetFirstMolecule() | HaMolSet | |
| GetGaussMod(const bool create_module=false) | HaMolSet | |
| GetInterMolMod(const bool create_module=false) | HaMolSet | |
| GetLastFragment() (defined in HaMolSet) | HaMolSet | |
| GetMinMaxCrd(double &MinX_v, double &MinY_v, double &MinZ_v, double &MaxX_v, double &MaxY_v, double &MaxZ_v) | HaMolSet | |
| GetMinMaxCrdSelected(double &MinX_v, double &MinY_v, double &MinZ_v, double &MaxX_v, double &MaxY_v, double &MaxZ_v) | HaMolSet | |
| GetMolByName(const char *mol_name) | HaMolSet | |
| GetMoleculeNum(int imol) | HaMolSet | |
| GetMolMechMod(const bool create_module=false) | HaMolSet | |
| GetMolTemplForRes(const char *res_templ_name) | HaResDB | |
| GetName() | HaMolSet | |
| GetNAtoms() const | HaMolSet | |
| GetNBonds() const | HaMolSet | |
| GetNChains() const | HaMolSet | |
| GetNChemGroups() const | HaMolSet | |
| GetNMol() const | HaMolSet | |
| GetNRes() const | HaMolSet | |
| GetNuclAcidMod(const bool create_module=false) | HaMolSet | |
| GetPH() const | HaMolSet | |
| GetQCMod(const bool create_module=false) | HaMolSet | |
| GetResByRef(const char *res_ref) | HaMolSet | |
| GetScatterMod(const bool create_module=false) | HaMolSet | |
| GetSeqNumOfAtom(const HaAtom *aptr) const | HaMolSet | |
| GetSTMMod(const bool create_module=false) | HaMolSet | |
| GetTemplateForAtom(HaAtom *aptr) | HaResDB | |
| GetTemplateForResidue(const char *res_full_name) | HaResDB | |
| GetTemplResAtomMaps(HaResidue *pres, map< MatPoint *, MatPoint *, less< MatPoint * > > &res_to_templ_map, map< MatPoint *, MatPoint *, less< MatPoint * > > &templ_to_res_map) | HaResDB | |
| GetUniqChemGrpID(int buf_reg_flag) (defined in HaMolSet) | HaMolSet | |
| GetUniqueMolName(const HaString suggest_name) | HaMolSet | |
| HaMolSet() (defined in HaMolSet) | HaMolSet | |
| HaMolSet(const HaString &new_name) (defined in HaMolSet) | HaMolSet | |
| HaResDB() (defined in HaResDB) | HaResDB | |
| HostMolecules | HaMolSet | |
| info_str | HaMolSet | |
| Init() (defined in HaResDB) | HaResDB | |
| init_flag (defined in HaResDB) | HaResDB | |
| IsInitiated() (defined in HaResDB) | HaResDB | [inline] |
| LoadAmberPrepFile(const char *fname) | HaMolSet | |
| LoadHarlemFile(const char *fname) | HaMolSet | |
| LoadMDLFile(const char *fname) | HaMolSet | |
| LoadMol2File(const char *fname) | HaMolSet | |
| LoadPDBFile(const char *fname, int flag=0) | HaMolSet | |
| LoadRWFMolecule(const char *fname) | HaMolSet | |
| LoadXYZFile(const char *fname) | HaMolSet | |
| m_calc_bonds_flag | HaMolSet | [static] |
| m_calc_s_hbonds_flag | HaMolSet | [static] |
| m_save_connect | HaMolSet | |
| m_save_mol_name (defined in HaMolSet) | HaMolSet | |
| m_save_selected | HaMolSet | |
| m_save_transform | HaMolSet | |
| m_unique_atom_names_flag | HaMolSet | |
| MergeMolecules(HaMolecule *pMol1, HaMolecule *pMol2) | HaMolSet | |
| MOL_SAVE_FLAG enum name (defined in HaMolSet) | HaMolSet | |
| mset_pview | HaMolSet | |
| name | HaMolSet | |
| NamedAtomLists | HaMolSet | |
| NamedAtomListsType typedef (defined in HaMolSet) | HaMolSet | |
| OverlapMol(AtomList &fmolatset, AtomList &smolatset) | HaMolSet | |
| pbox_alpha (defined in HaMolSet) | HaMolSet | |
| pbox_beta (defined in HaMolSet) | HaMolSet | |
| pbox_gamma | HaMolSet | |
| pbox_x (defined in HaMolSet) | HaMolSet | |
| pbox_y (defined in HaMolSet) | HaMolSet | |
| pbox_z | HaMolSet | |
| ph | HaMolSet | |
| picked_atoms (defined in HaMolSet) | HaMolSet | |
| place_to_orig() | HaMolSet | |
| pmsetdoc | HaMolSet | |
| Print_info(ostream &sout, const int level) | HaMolSet | |
| ProcessPDBAtom(int heta, IntPtrMap &id_at_map, HaMolecule *pMol) (defined in HaMolSet) | HaMolSet | [protected] |
| RefreshAllViews(long lHint=0L) | HaMolSet | |
| RenumberGrp() (defined in HaMolSet) | HaMolSet | |
| res_db_dir (defined in HaResDB) | HaResDB | [static] |
| res_db_files (defined in HaResDB) | HaResDB | |
| ResetETModule() | HaMolSet | |
| ResidueIterator typedef (defined in HaMolSet) | HaMolSet | |
| ReverseAtomSelection() | HaMolSet | |
| SAVE_AS_ONE_MOL enum value (defined in HaMolSet) | HaMolSet | |
| save_flags (defined in HaMolSet) | HaMolSet | |
| SAVE_SELECTED enum value (defined in HaMolSet) | HaMolSet | |
| SAVE_TRANSFORMED enum value (defined in HaMolSet) | HaMolSet | |
| SaveHarlemFile(const char *filename) | HaMolSet | |
| SavePDBFile(const char *filename) | HaMolSet | |
| SaveXYZFile(const char *filename) | HaMolSet | |
| SaveXYZRadFile(const char *filename) | HaMolSet | |
| SelectAllAtoms() | HaMolSet | |
| SelectOnly(AtomCollection *atom_coll) | HaMolSet | |
| SelectZone(int mask) | HaMolSet | |
| SelectZoneExpr(Expr *expr) | HaMolSet | |
| set_fragment_selected(const char *frag_name) (defined in HaMolSet) | HaMolSet | |
| set_min_max | HaMolSet | |
| SetAltStatesActive(int set_flag) | HaMolSet | |
| SetAngle(HaAtom *aptr1, HaAtom *aptr2, HaAtom *aptr3, double ang_new) | HaMolSet | |
| SetAtomListFromSelection(const HaString &id) | HaMolSet | |
| SetBondDist(HaAtom *aptr1, HaAtom *aptr2, double new_dist) | HaMolSet | |
| SetChargeMapByCurrentCharges(const char *map_name) | HaMolSet | |
| SetChargesForCurrentPH() | HaMolSet | |
| SetChargesForPH(double pH_val) | HaMolSet | |
| SetChargesFromChargeMap(MatPoint_double_map *charge_map) | HaMolSet | |
| SetChemGrpSelected(const HaString &gid) | HaMolSet | |
| SetName(const char *new_name) | HaMolSet | |
| SetParseRadii() | HaMolSet | |
| SetPH(double new_ph) | HaMolSet | |
| SetStdAtomicParams(const int at_params_type) | HaMolSet | |
| SetStdChemGroups() | HaMolSet | |
| SetStdParams() (defined in HaResDB) | HaResDB | [protected] |
| SetStdResPK() | HaMolSet | |
| SetStdResPK_G1() | HaMolSet | |
| SetTorsion(HaAtom *aptr1, HaAtom *aptr2, HaAtom *aptr3, HaAtom *aptr4, double tors_new) | HaMolSet | |
| SetVdwRadii() | HaMolSet | |
| solv_buffer_dist | HaMolSet | |
| solv_name | HaMolSet | |
| solvate() | HaMolSet | |
| spacegroup (defined in HaMolSet) | HaMolSet | |
| UnSelectAllAtoms() | HaMolSet | |
| ViewObjects | HaMolSet | |
| ~HaMolSet() (defined in HaMolSet) | HaMolSet | [virtual] |
| ~HaResDB() (defined in HaResDB) | HaResDB | [virtual] |
