| AddHarmConstraint(HaAtom *atom1, HaAtom *atom2, double eq_dist, double force_const ) | HaMolMechMod | |
| AddImprDihedral(MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, MatPoint *pt4) (defined in HaMolMechMod) | HaMolMechMod | |
| amber_constr_crd_file | HaMolMechMod | |
| amber_crd_file | HaMolMechMod | |
| amber_inp_file | HaMolMechMod | |
| amber_out_file | HaMolMechMod | |
| amber_proc_id (defined in HaMolMechMod) | HaMolMechMod | |
| amber_rst_file | HaMolMechMod | |
| amber_run_file | HaMolMechMod | |
| amber_top_file | HaMolMechMod | |
| amber_trj_coord_file | HaMolMechMod | |
| amber_trj_ene_file | HaMolMechMod | |
| amber_trj_vel_file | HaMolMechMod | |
| amber_version | HaMolMechMod | |
| atom2_3body | HaMolMechMod | |
| atom3_3body | HaMolMechMod | |
| atom_restr_const | HaMolMechMod | |
| beta_3body | HaMolMechMod | |
| bond_ene | HaMolMechMod | |
| bond_param_map | HaMolMechMod | [static] |
| BondConstrains | HaMolMechMod | |
| build_nb_contact_list_flag | HaMolMechMod | |
| BuildExcludedAtomList() | HaMolMechMod | |
| BuildGrpGrpNonBondList(AtomList *group1, AtomList *group2) | HaMolMechMod | |
| BuildNonBondContactList() | HaMolMechMod | |
| calc_electr_flag | HaMolMechMod | |
| calc_vdw_flag | HaMolMechMod | |
| CalcNonBondPt(const MatPoint *pt1, const MatPoint *pt2, double &vdw_at_ene, double &el_at_ene) | HaMolMechMod | |
| CalculateEnergy() | HaMolMechMod | |
| cap_atom_num | HaMolMechMod | |
| cap_fconst | HaMolMechMod | |
| ClearConstraints() | HaMolMechMod | |
| compressibility | HaMolMechMod | |
| constraint_ene | HaMolMechMod | |
| CreateCompMod(const int mtype, HaMolSet *new_phost_mset=NULL) | HaCompMod | [static] |
| cur_energy | HaMolMechMod | |
| cur_nstep | HaMolMechMod | |
| debug_level (defined in HaCompMod) | HaCompMod | |
| delay_time | HaMolMechMod | |
| DeletePoints(set< MatPoint *, less< MatPoint * > > *pt_set) | HaMolMechMod | |
| density | HaMolMechMod | |
| diel_const | HaMolMechMod | |
| dih_param_map | HaMolMechMod | [static] |
| dihed_ene | HaMolMechMod | |
| Dihedrals | HaMolMechMod | |
| electr_ene | HaMolMechMod | |
| electr_ene_14 | HaMolMechMod | |
| electr_ene_nb | HaMolMechMod | |
| electr_model | HaMolMechMod | |
| exact_ewald_flag | HaMolMechMod | |
| excluded_atom_list | HaMolMechMod | |
| fast_water_method | HaMolMechMod | |
| FindBondParamFromSymbol(const char *ats1, const char *ats2) (defined in HaMolMechMod) | HaMolMechMod | [static] |
| FindDihedralParamFromSymbol(const char *ats1, const char *ats2, const char *ats3, const char *ats4, bool improper_flag=false) (defined in HaMolMechMod) | HaMolMechMod | [static] |
| FindPointParamFromSymbol(const char *ats1) | HaMolMechMod | [static] |
| FindValAngleParamFromSymbol(const char *ats1, const char *ats2, const char *ats3) (defined in HaMolMechMod) | HaMolMechMod | [static] |
| gamma_3body | HaMolMechMod | |
| GetDihedral(MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, MatPoint *pt4) | HaMolMechMod | |
| GetImprDihedral(MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, MatPoint *pt4) | HaMolMechMod | |
| GetMMBond(MatPoint *pt1, MatPoint *pt2) | HaMolMechMod | |
| GetMolSet() | HaCompMod | [inline] |
| GetMolSet() const | HaCompMod | [inline] |
| GetMovingAtoms() | HaMolMechMod | |
| GetResImprAngles(HaResidue *pres, list< MMDihedral * > &res_idih_list) | HaMolMechMod | |
| GetRestrAtoms() | HaMolMechMod | |
| GetType() | HaCompMod | [inline] |
| GetValAngle(MatPoint *pt1, MatPoint *pt2, MatPoint *pt3) | HaMolMechMod | |
| grad_ene_max | HaMolMechMod | |
| HaCompMod(const int new_mtype, HaMolSet *new_phost_mset=NULL) | HaCompMod | |
| HaMolMechMod(HaMolSet *new_pmset=NULL) (defined in HaMolMechMod) | HaMolMechMod | |
| hbond_ene | HaMolMechMod | |
| HBondParams | HaMolMechMod | |
| impdih_param_map | HaMolMechMod | [static] |
| ImprDihedrals | HaMolMechMod | |
| init_charges_flag | HaMolMechMod | |
| init_ff_maps | HaMolMechMod | [static] |
| init_min_step | HaMolMechMod | |
| init_read_coord | HaMolMechMod | |
| init_temp | HaMolMechMod | |
| Initialize() | HaMolMechMod | |
| InitParamSet() | HaMolMechMod | |
| kin_ene | HaMolMechMod | |
| last_solute_atom | HaMolMechMod | |
| length_md_run | HaMolMechMod | |
| limit_wrt_atoms | HaMolMechMod | |
| LoadAmberMDInfoFile() | HaMolMechMod | |
| LoadAmberRestartFile() | HaMolMechMod | |
| max_comp_cycles | HaMolMechMod | |
| max_min_step | HaMolMechMod | |
| MBonds | HaMolMechMod | |
| md_time_step | HaMolMechMod | |
| min_cnvrg_criterium | HaMolMechMod | |
| min_type | HaMolMechMod | |
| module_to_init_flag | HaMolMechMod | |
| moving_atoms | HaMolMechMod | |
| mtype | HaCompMod | [protected] |
| nbstp_wrt_coord | HaMolMechMod | |
| nbstp_wrt_ener | HaMolMechMod | |
| nbstp_wrt_rstrt | HaMolMechMod | |
| nbstp_wrt_vel | HaMolMechMod | |
| neutral_end_hydr_flag | HaMolMechMod | |
| nmr_max_num_submol | HaMolMechMod | |
| nmr_penalty_min_method | HaMolMechMod | |
| nmr_restrain | HaMolMechMod | |
| noesy_vol_freq | HaMolMechMod | |
| nonb_cutoff_dist | HaMolMechMod | |
| nonb_list_flag | HaMolMechMod | |
| nonb_list_update_freq | HaMolMechMod | |
| nonbond_contact_list | HaMolMechMod | |
| num_3body_inter | HaMolMechMod | |
| num_dfreedom_sub | HaMolMechMod | |
| num_ions | HaMolMechMod | |
| num_md_run | HaMolMechMod | |
| num_step_steep_descent | HaMolMechMod | |
| omit_interactions | HaMolMechMod | |
| OnDelAtoms(AtomCollection &del_atoms) | HaMolMechMod | [virtual] |
| OpenSanderFilesToRead() | HaMolMechMod | |
| param_to_init_flag | HaMolMechMod | |
| peaks_coupling | HaMolMechMod | |
| peaks_init_pot | HaMolMechMod | |
| peaks_rate | HaMolMechMod | |
| period_bcond | HaMolMechMod | |
| pexp_3body | HaMolMechMod | |
| phost_mset | HaCompMod | [protected] |
| play_back_flag | HaMolMechMod | |
| pme_box_alpha | HaMolMechMod | |
| pme_box_beta (defined in HaMolMechMod) | HaMolMechMod | |
| pme_box_gamma | HaMolMechMod | |
| pme_box_x | HaMolMechMod | |
| pme_box_y (defined in HaMolMechMod) | HaMolMechMod | |
| pme_box_z | HaMolMechMod | |
| pme_dsum_tol | HaMolMechMod | |
| pme_grid_nx | HaMolMechMod | |
| pme_grid_ny (defined in HaMolMechMod) | HaMolMechMod | |
| pme_grid_nz | HaMolMechMod | |
| pme_neutralize_system | HaMolMechMod | |
| pme_spline_order | HaMolMechMod | |
| pme_verbose | HaMolMechMod | |
| pmesh_ewald_flag | HaMolMechMod | |
| Points | HaMolMechMod | |
| POINTS_TYPE typedef (defined in HaMolMechMod) | HaMolMechMod | |
| polar_ene | HaMolMechMod | |
| polar_method | HaMolMechMod | |
| pot_ene | HaMolMechMod | |
| press | HaMolMechMod | |
| pressure_reg_method | HaMolMechMod | |
| pressure_relax_time | HaMolMechMod | |
| pressure_scale_method | HaMolMechMod | |
| print_freq | HaMolMechMod | |
| Print_info(ostream &sout, const int level) | HaMolMechMod | |
| random_seed | HaMolMechMod | |
| ReadTrajPoint() | HaMolMechMod | |
| ref_pressure | HaMolMechMod | |
| ref_temp | HaMolMechMod | |
| remove_init_motion_flag | HaMolMechMod | |
| remove_motion_freq | HaMolMechMod | |
| remove_solute_nb_cut_flag | HaMolMechMod | |
| res_impr_dih_map | HaMolMechMod | |
| restart_flag | HaMolMechMod | |
| restrained_atoms | HaMolMechMod | |
| restraint_format | HaMolMechMod | |
| rms_ene | HaMolMechMod | |
| run_amber_thread | HaMolMechMod | |
| run_internal_flag | HaMolMechMod | |
| run_type | HaMolMechMod | |
| RunAmber() | HaMolMechMod | |
| RunAmberThread() | HaMolMechMod | |
| RunSanderInt() | HaMolMechMod | |
| sander_exe_fname | HaMolMechMod | |
| SaveAmberAllInpFiles() | HaMolMechMod | |
| SaveAmberCrdFile() | HaMolMechMod | |
| SaveAmberInpFile() | HaMolMechMod | |
| SaveAmberRunFile() | HaMolMechMod | |
| SaveAmberTopFile() | HaMolMechMod | |
| scale_14_electr | HaMolMechMod | |
| scale_14_vdw | HaMolMechMod | |
| scale_init_vel | HaMolMechMod | |
| Set14interDihFlags() | HaMolMechMod | |
| SetDebugLevel(int new_debug_level) (defined in HaCompMod) | HaCompMod | [virtual] |
| SetHBondConstraints(double force_const ) | HaMolMechMod | |
| SetMMBond(MatPoint *pt1, MatPoint *pt2, double r0, double fc, int set_type=NOT_SET) (defined in HaMolMechMod) | HaMolMechMod | |
| SetMolHost(HaMolSet *new_phost_mset) (defined in HaCompMod) | HaCompMod | [inline] |
| SetMoveAll() | HaMolMechMod | |
| SetMoveOnly(const HaString &new_mov_atom_list_name) | HaMolMechMod | |
| SetRestrainedAtoms(const char *restr_atom_list_name) | HaMolMechMod | |
| SetStdParams() (defined in HaMolMechMod) | HaMolMechMod | |
| SetStdValParams() | HaMolMechMod | |
| SetStdVdWParams() | HaMolMechMod | |
| SetValAngle(MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, double a0, double fc, int set_type=NOT_SET) | HaMolMechMod | |
| shake_constr | HaMolMechMod | |
| shake_tol | HaMolMechMod | |
| skip_pt_between | HaMolMechMod | |
| skip_pt_init | HaMolMechMod | |
| soft_repulsion | HaMolMechMod | |
| soft_repulsion_const | HaMolMechMod | |
| solute_solvent_image_flag | HaMolMechMod | |
| start_time | HaMolMechMod | |
| start_vel_method | HaMolMechMod | |
| stop_calc_flag | HaMolMechMod | |
| StopCalc() | HaMolMechMod | |
| symb_ppar_map | HaMolMechMod | [static] |
| temp | HaMolMechMod | |
| temp_deviation | HaMolMechMod | |
| temp_relax_time_solute | HaMolMechMod | |
| temp_relax_time_solvent | HaMolMechMod | |
| temp_scale_method | HaMolMechMod | |
| time | HaMolMechMod | |
| time_limit | HaMolMechMod | |
| traj_script | HaMolMechMod | |
| traj_wrt_format | HaMolMechMod | |
| trj_coord_fp | HaMolMechMod | |
| trj_ene_fp | HaMolMechMod | |
| trj_vel_fp | HaMolMechMod | |
| ValAngles | HaMolMechMod | |
| vang_ene | HaMolMechMod | |
| vang_param_map | HaMolMechMod | [static] |
| vdw_ene | HaMolMechMod | |
| vdw_ene_14 | HaMolMechMod | |
| vdw_ene_nb | HaMolMechMod | |
| vel_limit | HaMolMechMod | |
| wat_h1_name | HaMolMechMod | |
| wat_h2_name | HaMolMechMod | |
| wat_ox_name | HaMolMechMod | |
| wat_res_name | HaMolMechMod | |
| water_cap_flag | HaMolMechMod | |
| water_pairlist_method | HaMolMechMod | |
| wrap_coord | HaMolMechMod | |
| write_coord_format | HaMolMechMod | |
| ~HaCompMod() (defined in HaCompMod) | HaCompMod | [virtual] |
| ~HaMolMechMod() (defined in HaMolMechMod) | HaMolMechMod | |
