| bb_crd | NuclAcidMod | |
| bb_sidx | NuclAcidMod | |
| BBOffset(int ir) | NuclAcidMod | |
| bend (defined in NuclAcidMod) | NuclAcidMod | |
| bs_bs_pars (defined in NuclAcidMod) | NuclAcidMod | |
| BuildNuclAcid() | NuclAcidMod | |
| CalcAxis() | NuclAcidMod | |
| CalcAxisPar1(HaMat_double &ax_hlxc, double &sum, HaVec_double &gra, HaVec_double &scp) | NuclAcidMod | |
| CalcBBCrd() | NuclAcidMod | |
| CalcBend() | NuclAcidMod | |
| CalcEne() | NuclAcidMod | |
| CalcGlobHlxCrd() | NuclAcidMod | |
| CalcLocCrdSys() | NuclAcidMod | |
| CalcLocHlxCrd(int for_bp=TRUE) | NuclAcidMod | |
| CalcPdistToShlxCnt() | NuclAcidMod | |
| ChainIdxOfRes(int ir) | NuclAcidMod | |
| CreateCompMod(const int mtype, HaMolSet *new_phost_mset=NULL) | HaCompMod | [static] |
| CreateMolFromJumna() | NuclAcidMod | |
| cur_energy | NuclAcidMod | |
| debug_level (defined in HaCompMod) | HaCompMod | |
| diel_slope | NuclAcidMod | |
| dif | NuclAcidMod | |
| dir_strand | NuclAcidMod | |
| ene_per_unit_flag | NuclAcidMod | |
| FindDNAMol() | NuclAcidMod | |
| force_field | NuclAcidMod | |
| fst_twist | NuclAcidMod | |
| GenComplStrand() | NuclAcidMod | |
| GetAtomCrd(int at_num, int coord_num) | NuclAcidMod | |
| GetMolSet() | HaCompMod | [inline] |
| GetMolSet() const | HaCompMod | [inline] |
| GetNRes() const | NuclAcidMod | |
| GetType() | HaCompMod | [inline] |
| GetVarNum(int crd_num) | NuclAcidMod | |
| h (defined in NuclAcidMod) | NuclAcidMod | |
| HaCompMod(const int new_mtype, HaMolSet *new_phost_mset=NULL) | HaCompMod | |
| hel (defined in NuclAcidMod) | NuclAcidMod | |
| hel_crd | NuclAcidMod | |
| hho (defined in NuclAcidMod) | NuclAcidMod | |
| hold (defined in NuclAcidMod) | NuclAcidMod | |
| homon_symm_flags | NuclAcidMod | |
| homon_symm_offs | NuclAcidMod | |
| IdxLastFreeHelCoord() | NuclAcidMod | |
| IdxLastHelCoord() | NuclAcidMod | |
| IdxResInChain(int ir) | NuclAcidMod | |
| init_flag | NuclAcidMod | |
| Is3endRes(int ir) | NuclAcidMod | |
| IsFstResInChain(int ir) | NuclAcidMod | |
| IsHelCoordLocked(int ir, int i_crd) | NuclAcidMod | |
| IsRibRes(int ir) | NuclAcidMod | |
| IsSupHlxConstr() | NuclAcidMod | |
| IsThymineRes(int ir) | NuclAcidMod | |
| lock_bb | NuclAcidMod | |
| lock_hel | NuclAcidMod | |
| LockBBCoord(int i_strand, int i_res, int i_crd, int do_lock) | NuclAcidMod | |
| LockHelCoord(int i_strand, int i_res, int i_crd, int do_lock) | NuclAcidMod | |
| max_iter | NuclAcidMod | |
| MinEne() | NuclAcidMod | |
| mtype | HaCompMod | [protected] |
| nbreak_1 | NuclAcidMod | |
| nbreak_2 | NuclAcidMod | |
| ncrd_ind_res | NuclAcidMod | |
| ncrd_res | NuclAcidMod | |
| nsym_unit | NuclAcidMod | |
| NuclAcidMod(HaMolSet *new_pmset=NULL) (defined in NuclAcidMod) | NuclAcidMod | |
| NumAllBBVarRes(int ir) | NuclAcidMod | |
| NumBBCoord() | NuclAcidMod | |
| NumFreeBBCoord() | NuclAcidMod | |
| NumIndBBVarRes(int ir) | NuclAcidMod | |
| o | NuclAcidMod | |
| OnDelAtoms(AtomCollection &del_atoms) | HaCompMod | [virtual] |
| out_prefix | NuclAcidMod | |
| p_dna_mol | NuclAcidMod | |
| pdb_prefix | NuclAcidMod | |
| phos_chrg | NuclAcidMod | |
| phost_mset | HaCompMod | [protected] |
| ReadAXEfile(const char *axe_file) | NuclAcidMod | |
| RestoreConfig() | NuclAcidMod | |
| SaveAXEfile(const char *axe_file) | NuclAcidMod | |
| SaveConfig() | NuclAcidMod | |
| seq | NuclAcidMod | |
| SetBBCoord(int i_strand, int i_res, int i_crd, double crd_val) | NuclAcidMod | |
| SetCoordsFromJumna() | NuclAcidMod | |
| SetDebugLevel(int new_debug_level) (defined in HaCompMod) | HaCompMod | [virtual] |
| SetDielSlope(double slope_new) | NuclAcidMod | |
| SetFFtype(const char *new_ff_type) | NuclAcidMod | |
| SetFFtypeIdx(const int i_ff_type) | NuclAcidMod | |
| SetHelCoord(int i_strand, int i_res, int i_crd, double crd_val) | NuclAcidMod | |
| SetIntCoordsToJumna() | NuclAcidMod | |
| SetMolHost(HaMolSet *new_phost_mset) (defined in HaCompMod) | HaCompMod | [inline] |
| SetPhosChrg(double phos_chrg_new) | NuclAcidMod | |
| SetSeq(const char *seq_str) | NuclAcidMod | |
| SetShlxTwist(double shlx_tw) | NuclAcidMod | |
| SetStdParams() (defined in NuclAcidMod) | NuclAcidMod | |
| sug (defined in NuclAcidMod) | NuclAcidMod | |
| sup_helix_pit | NuclAcidMod | |
| sup_helix_rad | NuclAcidMod | |
| tor (defined in NuclAcidMod) | NuclAcidMod | |
| u (defined in NuclAcidMod) | NuclAcidMod | |
| uho (defined in NuclAcidMod) | NuclAcidMod | |
| ul | NuclAcidMod | |
| update_var_flag | NuclAcidMod | |
| UpdateVarCoord() | NuclAcidMod | |
| UpdateXYZ() | NuclAcidMod | |
| vkin (defined in NuclAcidMod) | NuclAcidMod | |
| vold (defined in NuclAcidMod) | NuclAcidMod | |
| ~HaCompMod() (defined in HaCompMod) | HaCompMod | [virtual] |
| ~NuclAcidMod() (defined in NuclAcidMod) | NuclAcidMod | |
