| add_macrocycle_constraints(core::pose::Pose &pose, utility::vector1< core::Size > const &ligids) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| advanced_map_erosion_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| align_reference_atom_ids_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| aligner_fastmode_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| altcrossover_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| apply(Pose &pose) override | protocols::ligand_docking::ga_ligand_dock::GALigandDock | virtual |
| apply_coord_cst_to_sctip(core::pose::PoseOP pose, utility::vector1< core::Size > const &moving_scs) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| auto_determine_optH_mode(core::pose::Pose const &pose, utility::vector1< core::Size > const &movable_scs) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| auto_final_optH_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| calculate_free_ligand_score(core::pose::Pose pose, utility::vector1< core::Size > const &lig_resnos) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| calculate_free_receptor_score(core::pose::Pose pose, utility::vector1< core::Size > const &lig_resnos, utility::vector1< core::Size > const &moving_scs, bool simple=true) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| calculate_native_density_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| cartmin_lig_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::ligand_docking::ga_ligand_dock::GALigandDock | virtual |
| compare_hbonds_to_native(HbondMap const &native_hbond_map, HbondMap const &lig_hbond_map) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| contact_distance_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| create() | protocols::moves::Mover | virtual |
| current_job_ | protocols::moves::Mover | private |
| current_tag_ | protocols::moves::Mover | private |
| debug_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| debug_report_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| entropy_method_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| estimate_buns_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| estimate_dG_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| eval_docked_pose(core::pose::Pose &pose, utility::vector1< core::Size > const &lig_ids) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| eval_docked_pose_helper(core::pose::Pose &pose, utility::vector1< core::Size > const &lig_ids, utility::vector1< core::Size > &movable_scs) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| exact_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| fa_rep_grid_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| fast_relax_lines_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| fast_relax_script_file_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| favor_native_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_cartligmin(LigandConformer const &gene, core::pose::Pose &pose) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_exact_cartmin(core::Size nneigh, LigandConformer &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_exact_ligmin(LigandConformer const &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_exact_ligmin_helper(LigandConformer const &gene, core::pose::Pose &pose, core::kinematics::MoveMapOP movemap, core::scoring::ScoreFunctionOP scfxn_local, core::Real const &fa_rep_weight, core::Real const &coordinate_cst_weight, core::Real const &torlerance, core::Size const &maxiter) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_exact_minimize_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_exact_scmin(LigandConformer const &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_optH(core::Size const &optH_mode, LigandConformer const &gene, core::pose::Pose &pose, core::pack::task::PackerTaskOP task, utility::vector1< core::Size > &contact_scs) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_optH_mode_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_solvate(LigandConformer &gene, core::pose::Pose &pose) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| final_solvate_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| freeze_ligand_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| freeze_ligand_backbone_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| fresh_instance() const override | protocols::ligand_docking::ga_ligand_dock::GALigandDock | virtual |
| frozen_residues_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| full_repack_before_finalmin_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| GALigandDock() | protocols::ligand_docking::ga_ligand_dock::GALigandDock | |
| generate_perturbed_structures(LigandConformer const &gene_initial, GridScorerOP gridscorer, core::Size npool, LigandAligner aligner) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| get_additional_output() override | protocols::ligand_docking::ga_ligand_dock::GALigandDock | virtual |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_ligand_resids(core::pose::Pose const &pose, utility::vector1< core::Size > &lig_resids) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| get_movable_scs(core::pose::Pose const &pose, GridScorerCOP gridscore, utility::vector1< core::Size > const &lig_resnos) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| get_name() const override | protocols::ligand_docking::ga_ligand_dock::GALigandDock | virtual |
| get_native_pose() const | protocols::moves::Mover | |
| get_optimizer(LigandConformer const &gene_initial, GridScorerOP gridscorer) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_type() const | protocols::moves::Mover | inline |
| grid_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| grid_bound_penalty_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| grid_radius_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| has_density_map_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| hashsize_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| hb_resids_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| hb_resids_include_bb_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| hb_resids_metric_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| idealize_and_repack_pose(core::pose::Pose &pose, utility::vector1< core::Size > const &movable_scs, utility::vector1< core::Size > const &lig_resnos) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| info_ | protocols::moves::Mover | private |
| init_dens_weight_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| initial_pool_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| input_fold_tree_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| input_pose_ | protocols::moves::Mover | private |
| is_virtual_root_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| last_status_ | protocols::moves::Mover | private |
| ligand_file_list_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| ligid_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| load_initial_pool(LigandConformer const &gene_initial, LigandConformers &genes_sel) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| load_reference_pool(LigandConformer const &gene_initial, utility::vector1< ConstraintInfo > &ref_ligs) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| load_template_pool(LigandConformer const &gene_initial, LigandConformers &genes_sel, core::Size nsel, utility::vector1< ConstraintInfo > &template_cst_infos) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| local_res_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| macrocycle_ligand_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| make_starting_pose_for_virtual_screening(core::pose::Pose const &pose_apo, core::Size const &lig_resno, std::string const ligand_name) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| match_by_atomtype(core::conformation::Residue const &rsd1, core::conformation::Residue const &rsd2) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| max_rot_cumulative_prob_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| maxiter_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| method_for_radius_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| min_neighbor_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| move_water_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::ligand_docking::ga_ligand_dock::GALigandDock | static |
| multi_ligands_maxRad_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| multiple_ligands_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| n_template_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| name() | protocols::moves::Mover | inlinestatic |
| native_pose_ | protocols::moves::Mover | private |
| neighborhood_size_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| ngen_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| npool_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| nrelax_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| nreport_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| optimize_input_H_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| output_ligand_only_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| packer_cycles_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| padding_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::ligand_docking::ga_ligand_dock::GALigandDock | virtual |
| pmut_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| Pose typedef | protocols::moves::Mover | |
| pose_native_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| PoseCOP typedef | protocols::moves::Mover | |
| pre_optH_relax_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| premin_ligand(core::pose::Pose &pose, utility::vector1< core::Size > const &lig_resnos) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| premin_ligand_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| print_initial_pool_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| protocol_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | static |
| ramp_schedule_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| random_oversample_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| redefine_flexscs_at_relax_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| reference_frac_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| reference_frac_auto_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| reference_oversample_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| reference_pool_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| remaining_outputs_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| replace_ligand(core::pose::Pose pose_complex, core::pose::Pose &pose_ligand, bool align=true) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| reset_status() | protocols::moves::Mover | |
| rmsdthreshold_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| rot_energy_cutoff_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| run_docking(LigandConformer const &gene_initial, GridScorerOP gridscore, LigandAligner &aligner, OutputStructureStore &outputs) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| runmode_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| sample_ring_conformers_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| sc_edge_buffer_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| scfxn_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| scfxn_relax_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| setup_ligand_aligner(core::pose::Pose const &pose, utility::vector1< core::Size > const &lig_resnos, utility::vector1< core::Size > movable_scs_in_ref, utility::vector1< core::conformation::Residue > const &rsds_to_build_grids, utility::vector1< bool > const &use_sc_only_in_grid) const | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| setup_params_for_runmode(std::string runmode) | protocols::ligand_docking::ga_ligand_dock::GALigandDock | |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| shuffle_ligands_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| sidechains_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| single_mutation_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| skeleton_radius_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| skeleton_threshold_const_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| smoothing_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| stdev_multiplier_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| Strings typedef | protocols::moves::Mover | |
| subhash_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| TagCOP typedef | protocols::moves::Mover | |
| template_pool_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| top_pose_metric_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| torsion_sampler_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| torsion_sampler_percentage_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| turnon_flexscs_at_relax_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| type_ | protocols::moves::Mover | private |
| use_dalphaball_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| use_mean_maxRad_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
| use_pharmacophore_ | protocols::ligand_docking::ga_ligand_dock::GALigandDock | private |
