| active_site_grid_ | protocols::match::Matcher | private |
| add_external_geometry_samples_for_constraint(core::Size cst_id, core::chemical::ResidueTypeCOP restype, utility::vector1< std::string > const &upstream_launch_atoms, utility::vector1< core::id::AtomID > const &downstream_3atoms, utility::vector1< toolbox::match_enzdes_util::ExternalGeomSampler > const &exgeom_list, core::Size const exgeom_id, bool enumerate_ligand_rotamers=false, bool catalytic_bond=false, bool build_round1_hits_twice=false) | protocols::match::Matcher | |
| add_secondary_downstream_match_geometry_for_constraint(core::Size geom_cst_id, core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP downstream_restype, utility::vector1< core::Size > const &candidate_atids, utility::vector1< core::Size > const &target_atids, toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi, std::string SecMatchStr, core::pose::Pose const &upstream_pose, bool catalytic_bond) | protocols::match::Matcher | |
| add_secondary_upstream_match_geometry_for_constraint(core::Size geom_cst_id, core::Size target_geom_cst_id, core::chemical::ResidueTypeCOP candidate_restype, core::chemical::ResidueTypeCOP target_restype, utility::vector1< core::Size > const &candidate_atids, utility::vector1< core::Size > const &target_atids, toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi, std::string SecMatchStr, core::pose::Pose const &upstream_pose) | protocols::match::Matcher | |
| add_upstream_restype_for_constraint(core::Size cst_id, core::chemical::ResidueTypeCOP restype) | protocols::match::Matcher | |
| all_build_points_ | protocols::match::Matcher | private |
| all_downstream_algorithms_ | protocols::match::Matcher | private |
| all_downstream_builders_ | protocols::match::Matcher | private |
| bb_grid_ | protocols::match::Matcher | private |
| BoundingBox typedef | protocols::match::Matcher | |
| build_point(core::Size index) const | protocols::match::Matcher | |
| build_point(core::Size index) | protocols::match::Matcher | |
| build_round1_hits_twice_ | protocols::match::Matcher | private |
| build_set_id_for_restype_ | protocols::match::Matcher | private |
| check_downstream_hit_incompatibility(match const &m, utility::LexicographicalIterator &lex) const | protocols::match::Matcher | private |
| check_non_upstream_only_hit_incompatibility(match_dspos1 const &m1, utility::LexicographicalIterator &lex, output::MatchProcessor const &processor) const | protocols::match::Matcher | private |
| check_potential_dsbuilder_incompatibility_ | protocols::match::Matcher | mutableprivate |
| create_ds_builder(core::Size const cst_id, core::chemical::ResidueTypeCOP restype, utility::vector1< std::string > const &upstream_launch_atoms, utility::vector1< core::id::AtomID > const &downstream_3atoms, bool enumerate_ligand_rotamers, bool catalytic_bond) | protocols::match::Matcher | private |
| desymmeterize_upstream_restype_for_constraint(core::Size cst_id) | protocols::match::Matcher | |
| downstream_algorithms(core::Size cst_id) const | protocols::match::Matcher | |
| downstream_algorithms_ | protocols::match::Matcher | private |
| downstream_atoms_required_inside_active_site_ | protocols::match::Matcher | private |
| downstream_builder(core::Size cst_id) const | protocols::match::Matcher | |
| downstream_builder(core::Size) | protocols::match::Matcher | |
| downstream_builders(core::Size cst_id) const | protocols::match::Matcher | |
| downstream_builders_ | protocols::match::Matcher | private |
| downstream_orientation_atoms_ | protocols::match::Matcher | private |
| downstream_pose() const | protocols::match::Matcher | |
| downstream_pose_ | protocols::match::Matcher | private |
| dynamic_grid_refinement_ | protocols::match::Matcher | private |
| erase_hit(downstream::DownstreamAlgorithm const &dsalg, core::Size geom_cst_id_for_hit, HitListIterator const &iter) | protocols::match::Matcher | |
| estimate_n_matches_for_hit_subsets(Vector const &euclidean_bin_widths, Vector const &euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits, core::Size accuracy_threshold) const | protocols::match::Matcher | private |
| euclidean_bin_widths_ | protocols::match::Matcher | private |
| euler_bin_widths_ | protocols::match::Matcher | private |
| find_hits() | protocols::match::Matcher | |
| finish_hit_generation_for_constraint(core::Size cst_id) | protocols::match::Matcher | private |
| generate_hits() | protocols::match::Matcher | private |
| generate_hits_for_constraint(core::Size cst_id) | protocols::match::Matcher | private |
| geom_cst_has_primary_modification_ | protocols::match::Matcher | private |
| geom_csts_with_primary_hitlist_modificiations_ | protocols::match::Matcher | private |
| geomcst_is_upstream_only_ | protocols::match::Matcher | private |
| get_pose_build_resids() const | protocols::match::Matcher | |
| gridlig_fname_ | protocols::match::Matcher | private |
| has_upstream_only_geomcsts() const | protocols::match::Matcher | |
| hit_list_begin(core::Size geom_cst_id) | protocols::match::Matcher | |
| hit_list_end(core::Size geom_cst_id) | protocols::match::Matcher | |
| HitList typedef | protocols::match::Matcher | |
| HitListConstIterator typedef | protocols::match::Matcher | |
| HitListIterator typedef | protocols::match::Matcher | |
| hits(core::Size cst_id) const | protocols::match::Matcher | |
| hits_ | protocols::match::Matcher | private |
| increment_upstream_only_hit_combination(utility::vector1< HitPtrListCOP > const &upstream_only_hits, core::Size starting_point, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, core::Size &last_upstream_only_geomcst_advanced) const | protocols::match::Matcher | private |
| initialize_active_site_grid() | protocols::match::Matcher | private |
| initialize_bump_grids() | protocols::match::Matcher | private |
| initialize_downstream_algorithms() | protocols::match::Matcher | private |
| initialize_from_file(toolbox::match_enzdes_util::EnzConstraintIO const &enz_data, MatcherTask const &task) | protocols::match::Matcher | |
| initialize_from_task(MatcherTask const &task) | protocols::match::Matcher | |
| initialize_occupied_space_hash() | protocols::match::Matcher | private |
| initialize_scaffold_build_points() | protocols::match::Matcher | private |
| Matcher() | protocols::match::Matcher | |
| Matcher(Matcher const &) | protocols::match::Matcher | private |
| n_geometric_constraints() const | protocols::match::Matcher | inline |
| n_geometric_constraints_ | protocols::match::Matcher | private |
| nonconst_downstream_algorithms(core::Size cst_id) | protocols::match::Matcher | |
| note_primary_change_to_geom_csts_hitlist(core::Size geom_cst_id) | protocols::match::Matcher | private |
| occ_space_bounding_box_ | protocols::match::Matcher | private |
| occ_space_hash() const | protocols::match::Matcher | |
| occ_space_hash() | protocols::match::Matcher | |
| occ_space_hash_ | protocols::match::Matcher | private |
| operator=(Matcher const &rhs) | protocols::match::Matcher | private |
| original_scaffold_residue_bump_grids_ | protocols::match::Matcher | private |
| output_match_dspos1_for_geomcst_ | protocols::match::Matcher | private |
| output_matches_as_singular_downstream_positioning_ | protocols::match::Matcher | private |
| per_constraint_build_points(core::Size cst_id) const | protocols::match::Matcher | |
| per_constraint_build_points_ | protocols::match::Matcher | private |
| per_cst_build_resids_ | protocols::match::Matcher | private |
| pose_build_resids_ | protocols::match::Matcher | private |
| prepare_for_hit_generation_for_constraint(core::Size cst_id) | protocols::match::Matcher | private |
| process_matches(output::MatchProcessor &processor) const | protocols::match::Matcher | |
| process_matches_all_hit_combos_for_hit_subsets(output::MatchProcessor &processor, HitHasher &hit_hasher, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const | protocols::match::Matcher | private |
| process_matches_main_loop_enumerating_all_hit_combos(output::MatchProcessor &processor) const | protocols::match::Matcher | private |
| process_matches_where_one_geomcst_defines_downstream_location(output::MatchProcessor &processor) const | protocols::match::Matcher | private |
| read_gridlig_file_ | protocols::match::Matcher | private |
| Real typedef | protocols::match::Matcher | |
| refine_grid_and_subsample_for_hit_subsets(Vector &good_euclidean_bin_widths, Vector &good_euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const | protocols::match::Matcher | private |
| regenerate_round1_hits() | protocols::match::Matcher | private |
| relevant_downstream_atoms_ | protocols::match::Matcher | private |
| representative_downstream_algorithm(core::Size cst_id) const | protocols::match::Matcher | |
| representative_downstream_algorithm_ | protocols::match::Matcher | private |
| same_build_resids_for_all_csts_ | protocols::match::Matcher | private |
| select_hit_representatives(utility::vector1< utility::vector1< Hit const * > > const &hit_vectors, utility::vector1< core::Size > &n_hits_per_geomcst, utility::vector1< utility::vector1< core::Size > > &reps) const | protocols::match::Matcher | private |
| set_bump_tolerance(Real permitted_overlap) | protocols::match::Matcher | |
| set_downstream_pose(core::pose::Pose const &pose, utility::vector1< core::id::AtomID > orientation_atoms) | protocols::match::Matcher | |
| set_fa_dun_cutoff_for_constraint(core::Size cst_id, core::chemical::ResidueTypeCOP restype, core::Real fa_dun_cutoff) | protocols::match::Matcher | |
| set_hash_euclidean_bin_width(Real width) | protocols::match::Matcher | |
| set_hash_euclidean_bin_widths(Vector widths) | protocols::match::Matcher | |
| set_hash_euler_bin_width(Real width) | protocols::match::Matcher | |
| set_hash_euler_bin_widths(Vector widths) | protocols::match::Matcher | |
| set_n_geometric_constraints(core::Size n_constraints) | protocols::match::Matcher | |
| set_occupied_space_bounding_box(BoundingBox const &bb) | protocols::match::Matcher | |
| set_original_scaffold_build_points(utility::vector1< core::Size > const &resids) | protocols::match::Matcher | |
| set_original_scaffold_build_points_for_constraint(core::Size cst_id, utility::vector1< core::Size > const &resids) | protocols::match::Matcher | |
| set_sample_startegy_for_constraint(core::Size cst_id, core::chemical::ResidueTypeCOP restype, core::Size chi, upstream::SampleStrategyData const &strat) | protocols::match::Matcher | |
| set_upstream_pose(core::pose::Pose const &pose) | protocols::match::Matcher | |
| Size typedef | protocols::match::Matcher | |
| subsample_hits(Vector const &euclidean_bin_widths, Vector const &euler_bin_widths, utility::vector1< std::list< Hit const * > > const &neighbor_hits) const | protocols::match::Matcher | private |
| test_upstream_only_hit_incompatibility(match const &m, utility::vector1< HitPtrListCOP > const &upstream_only_hits, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, core::Size &last_upstream_only_geomcst_advanced, output::MatchProcessor const &processor) const | protocols::match::Matcher | private |
| test_upstream_only_hit_incompatibility(match_dspos1 const &m1, utility::vector1< HitPtrListCOP > const &upstream_only_hits, utility::vector1< std::list< Hit const * >::const_iterator > &upstream_only_hit_iterators, core::Size &last_upstream_only_geomcst_advanced, output::MatchProcessor const &processor) const | protocols::match::Matcher | private |
| upstream_builder(core::Size cst_id) const | protocols::match::Matcher | |
| upstream_builder(core::Size cst_id) | protocols::match::Matcher | |
| upstream_builders_ | protocols::match::Matcher | private |
| upstream_pose() const | protocols::match::Matcher | |
| upstream_pose_ | protocols::match::Matcher | private |
| upstream_resids_and_radii_defining_active_site_ | protocols::match::Matcher | private |
| use_input_sc_ | protocols::match::Matcher | private |
| Vector typedef | protocols::match::Matcher | |
| ~Matcher() override | protocols::match::Matcher | |
1.8.7