Index

A

api (C++ type) api::cell_t (C++ class) api::cell_t::a (C++ member) api::cell_t::alpha (C++ member) api::cell_t::b (C++ member)

api::cell_t::beta (C++ member) api::cell_t::c (C++ member) api::cell_t::cell_t (C++ function), [1] api::cell_t::gamma (C++ member) api::cell_t::is_set (C++ member)

C

Cell_Translation (C++ class) Cell_Translation::Cell_Translation (C++ function), [1] Cell_Translation::inv (C++ function) Cell_Translation::operator<< (C++ function) Cell_Translation::us (C++ member) Cell_Translation::vs (C++ member) Cell_Translation::ws (C++ member) coot (C++ type), [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] coot::api (C++ type) coot::api::vertex_with_rotation_translation (C++ class) coot::api::vertex_with_rotation_translation::colour (C++ member) coot::api::vertex_with_rotation_translation::model_rotation_matrix (C++ member) coot::api::vertex_with_rotation_translation::model_translation (C++ member) coot::api::vertex_with_rotation_translation::normal (C++ member) coot::api::vertex_with_rotation_translation::pos (C++ member) coot::api::vertex_with_rotation_translation::vertex_with_rotation_translation (C++ function), [1], [2] coot::api::vn_vertex (C++ class) coot::api::vn_vertex::normal (C++ member) coot::api::vn_vertex::pos (C++ member) coot::api::vn_vertex::vn_vertex (C++ function), [1] coot::api::vnc_vertex (C++ class) coot::api::vnc_vertex::color (C++ member) coot::api::vnc_vertex::normal (C++ member) coot::api::vnc_vertex::pos (C++ member) coot::api::vnc_vertex::vnc_vertex (C++ function), [1], [2], [3] coot::atom_spec_t (C++ class) coot::atom_spec_t::alt_conf (C++ member) coot::atom_spec_t::atom_name (C++ member) coot::atom_spec_t::atom_spec_t (C++ function), [1], [2], [3] coot::atom_spec_t::chain_id (C++ member) coot::atom_spec_t::empty (C++ function) coot::atom_spec_t::float_user_data (C++ member) coot::atom_spec_t::format (C++ function) coot::atom_spec_t::get_atom (C++ function) coot::atom_spec_t::ins_code (C++ member) coot::atom_spec_t::int_user_data (C++ member) coot::atom_spec_t::is_same (C++ function) coot::atom_spec_t::label (C++ function), [1] coot::atom_spec_t::matches_spec (C++ function) coot::atom_spec_t::model_number (C++ member) coot::atom_spec_t::res_no (C++ member) coot::atom_spec_t::selectatoms (C++ function) coot::atom_spec_t::simple_label (C++ function) coot::atom_spec_t::string_user_data (C++ member) coot::Cartesian (C++ class) coot::Cartesian::amplitude (C++ function) coot::Cartesian::amplitude_squared (C++ function) coot::Cartesian::Angle (C++ function) coot::Cartesian::by_scalar (C++ function) coot::Cartesian::Cartesian (C++ function), [1], [2] coot::Cartesian::cos_angle_btwn_vecs (C++ function) coot::Cartesian::cross_product (C++ function) coot::Cartesian::CrossProduct (C++ function) coot::Cartesian::DihedralAngle (C++ function) coot::Cartesian::distance_to_line (C++ function) coot::Cartesian::dot_product (C++ function) coot::Cartesian::get_x (C++ function) coot::Cartesian::get_y (C++ function) coot::Cartesian::get_z (C++ function) coot::Cartesian::GetCartFrom3Carts (C++ function) coot::Cartesian::GetCartFrom3Carts_intermediate (C++ function) coot::Cartesian::invert_z (C++ function) coot::Cartesian::length (C++ function) coot::Cartesian::lengthsq (C++ function) coot::Cartesian::LineLength (C++ function) coot::Cartesian::mid_point (C++ function) coot::Cartesian::normalize (C++ function) coot::Cartesian::on_a_face (C++ function) coot::Cartesian::operator* (C++ function) coot::Cartesian::operator*= (C++ function) coot::Cartesian::operator+ (C++ function) coot::Cartesian::operator+= (C++ function) coot::Cartesian::operator- (C++ function) coot::Cartesian::operator-= (C++ function) coot::Cartesian::operator/= (C++ function) coot::Cartesian::operator<< (C++ function), [1] coot::Cartesian::operator= (C++ function) coot::Cartesian::position_by_torsion (C++ function) coot::Cartesian::rotate_about_vector (C++ function) coot::Cartesian::set_them (C++ function) coot::Cartesian::third_points (C++ function) coot::Cartesian::unit (C++ function) coot::Cartesian::unit_vector_yourself (C++ function) coot::Cartesian::within_box (C++ function) coot::Cartesian::x (C++ function) coot::Cartesian::x_ (C++ member) coot::Cartesian::y (C++ function) coot::Cartesian::y_ (C++ member) coot::Cartesian::z (C++ function) coot::Cartesian::z_ (C++ member) coot::CartesianPair (C++ class) coot::CartesianPair::amplitude (C++ function) coot::CartesianPair::CartesianPair (C++ function), [1] coot::CartesianPair::extentsBox (C++ function) coot::CartesianPair::finish (C++ member) coot::CartesianPair::getFinish (C++ function) coot::CartesianPair::getStart (C++ function) coot::CartesianPair::operator<< (C++ function), [1] coot::CartesianPair::start (C++ member) coot::CartesianPairInfo (C++ class) coot::CartesianPairInfo::CartesianPairInfo (C++ function) coot::CartesianPairInfo::data (C++ member) coot::CartesianPairInfo::size (C++ member) coot::chain_validation_information_t (C++ class) coot::chain_validation_information_t::add (C++ function) coot::chain_validation_information_t::add_residue_validation_information (C++ function) coot::chain_validation_information_t::chain_id (C++ member) coot::chain_validation_information_t::chain_validation_information_t (C++ function), [1] coot::chain_validation_information_t::rviv (C++ member) coot::colour_t (C++ class) coot::colour_t::average (C++ function) coot::colour_t::brighter (C++ function) coot::colour_t::col (C++ member) coot::colour_t::colour_t (C++ function), [1] coot::colour_t::convert_from_hsv (C++ function) coot::colour_t::convert_to_hsv (C++ function) coot::colour_t::init (C++ function) coot::colour_t::operator[] (C++ function), [1] coot::colour_t::rotate (C++ function) coot::colour_t::set (C++ function) coot::colour_t::to_colour_holder (C++ function) coot::colour_t::to_glm (C++ function) coot::compare_atom_specs_user_float (C++ function) coot::compare_atom_specs_user_float_in_pair (C++ function) coot::coot_mat44 (C++ class) coot::coot_mat44::coot_mat44 (C++ function) coot::coot_mat44::is_close_to_unit_matrix (C++ function) coot::coot_mat44::m (C++ member) coot::coot_v4 (C++ class) coot::coot_v4::v4 (C++ member) coot::cos_angle_btwn_vecs (C++ function) coot::cross_product (C++ function) coot::dot_product (C++ function) coot::graph_data_type (C++ enum) coot::graph_data_type::CORRELATION (C++ enumerator) coot::graph_data_type::DENSITY (C++ enumerator) coot::graph_data_type::DISTORTION (C++ enumerator) coot::graph_data_type::ENERGY (C++ enumerator) coot::graph_data_type::LOG_PROBABILITY (C++ enumerator) coot::graph_data_type::PROBABILITY (C++ enumerator) coot::graph_data_type::TORSION_ANGLE (C++ enumerator) coot::graph_data_type::UNSET (C++ enumerator) coot::instanced_geometry_t (C++ class) coot::instanced_geometry_t::empty (C++ function) coot::instanced_geometry_t::instanced_geometry_t (C++ function), [1], [2] coot::instanced_geometry_t::instancing_data_A (C++ member) coot::instanced_geometry_t::instancing_data_B (C++ member) coot::instanced_geometry_t::name (C++ member) coot::instanced_geometry_t::triangles (C++ member) coot::instanced_geometry_t::vertices (C++ member) coot::instanced_mesh_t (C++ class) coot::instanced_mesh_t::add (C++ function) coot::instanced_mesh_t::clear (C++ function) coot::instanced_mesh_t::export_to_glTF (C++ function) coot::instanced_mesh_t::geom (C++ member) coot::instanced_mesh_t::instanced_mesh_t (C++ function) coot::instanced_mesh_t::markup (C++ member) coot::instanced_mesh_to_simple_mesh (C++ function) coot::instancing_data_type_A_t (C++ class) coot::instancing_data_type_A_t::colour (C++ member) coot::instancing_data_type_A_t::instancing_data_type_A_t (C++ function), [1] coot::instancing_data_type_A_t::position (C++ member) coot::instancing_data_type_A_t::size (C++ member) coot::instancing_data_type_B_t (C++ class) coot::instancing_data_type_B_t::colour (C++ member) coot::instancing_data_type_B_t::instancing_data_type_B_t (C++ function), [1] coot::instancing_data_type_B_t::orientation (C++ member) coot::instancing_data_type_B_t::position (C++ member) coot::instancing_data_type_B_t::size (C++ member) coot::is_an_in_triangle (C++ function) coot::link_atoms (C++ function), [1] coot::map_stats_t (C++ enum) coot::map_stats_t::SIMPLE (C++ enumerator) coot::map_stats_t::WITH_KOLMOGOROV_SMIRNOV_DIFFERENCE_MAP_TEST (C++ enumerator) coot::molecule_t (C++ class) coot::molecule_t::add_alternative_conformation (C++ function) coot::molecule_t::add_colour_rule (C++ function) coot::molecule_t::add_compound (C++ function) coot::molecule_t::add_hydrogen_atoms (C++ function) coot::molecule_t::add_neighbor_residues_for_refinement_help (C++ function) coot::molecule_t::add_parallel_plane_restraint (C++ function) coot::molecule_t::add_shelx_string_to_molecule (C++ function) coot::molecule_t::add_target_position_restraint (C++ function) coot::molecule_t::add_target_position_restraint_and_refine (C++ function) coot::molecule_t::add_terminal_residue_directly (C++ function) coot::molecule_t::add_to_non_drawn_bonds (C++ function) coot::molecule_t::adjust_occupancy_other_residue_atoms (C++ function) coot::molecule_t::all_molecule_contact_dots (C++ function) coot::molecule_t::append_to_molecule (C++ function) coot::molecule_t::apply_transformation_to_atom_selection (C++ function) coot::molecule_t::apply_user_defined_atom_colour_selections (C++ function) coot::molecule_t::assign_sequence (C++ function) coot::molecule_t::associate_data_mtz_file_with_map (C++ function) coot::molecule_t::associate_sequence_with_molecule (C++ function) coot::molecule_t::atom_sel (C++ member) coot::molecule_t::atoms_with_position_restraints (C++ member) coot::molecule_t::auto_fit_rotamer (C++ function) coot::molecule_t::backrub_rotamer (C++ function), [1] coot::molecule_t::base_colour_for_bonds (C++ member) coot::molecule_t::bespoke_carbon_atoms_colour (C++ member) coot::molecule_t::blender_mesh (C++ member) coot::molecule_t::bonds_box (C++ member) coot::molecule_t::bonds_box_type (C++ member) coot::molecule_t::bonds_colour_map_rotation (C++ member) coot::molecule_t::chains_in_model (C++ function) coot::molecule_t::change_chain_id (C++ function) coot::molecule_t::change_chain_id_with_residue_range (C++ function) coot::molecule_t::change_chain_id_with_residue_range_helper_insert_or_add (C++ function) coot::molecule_t::change_rotamer_number (C++ function) coot::molecule_t::change_to_first_rotamer (C++ function) coot::molecule_t::change_to_next_rotamer (C++ function) coot::molecule_t::change_to_previous_rotamer (C++ function) coot::molecule_t::cid_to_atom (C++ function) coot::molecule_t::cid_to_atom_spec (C++ function) coot::molecule_t::cid_to_residue (C++ function) coot::molecule_t::cid_to_residue_spec (C++ function) coot::molecule_t::cid_to_residues (C++ function) coot::molecule_t::cis_trans_conversion (C++ function) coot::molecule_t::clear_diff_map_draw_vecs (C++ function) coot::molecule_t::clear_draw_vecs (C++ function) coot::molecule_t::clear_extra_restraints (C++ function) coot::molecule_t::clear_non_drawn_bonds (C++ function) coot::molecule_t::clear_refinement (C++ function) coot::molecule_t::clear_target_position_restraint (C++ function) coot::molecule_t::clear_target_position_restraints (C++ function) coot::molecule_t::close_yourself (C++ function) coot::molecule_t::colour_holder_to_glm (C++ function) coot::molecule_t::colour_rules (C++ member) coot::molecule_t::contact_dots_for_ligand (C++ function) coot::molecule_t::copy_and_add_chain_residues_to_chain (C++ function) coot::molecule_t::copy_and_add_residue_to_chain (C++ function) coot::molecule_t::current_rotamer_map (C++ member) coot::molecule_t::default_temperature_factor_for_new_atoms (C++ member) coot::molecule_t::delete_any_link_containing_residue (C++ function) coot::molecule_t::delete_atom (C++ function) coot::molecule_t::delete_atoms (C++ function) coot::molecule_t::delete_chain_using_atom_cid (C++ function) coot::molecule_t::delete_colour_rules (C++ function) coot::molecule_t::delete_ghost_selections (C++ function) coot::molecule_t::delete_hydrogen_atoms (C++ function) coot::molecule_t::delete_link (C++ function) coot::molecule_t::delete_literal_using_cid (C++ function) coot::molecule_t::delete_residue (C++ function) coot::molecule_t::delete_residue_atoms_with_alt_conf (C++ function) coot::molecule_t::delete_side_chain (C++ function) coot::molecule_t::difference_map_peaks (C++ function) coot::molecule_t::difference_map_peaks_info_t (C++ class) coot::molecule_t::difference_map_peaks_info_t::difference_map_peaks_info_t (C++ function) coot::molecule_t::difference_map_peaks_info_t::peak_height (C++ member) coot::molecule_t::difference_map_peaks_info_t::pos (C++ member) coot::molecule_t::dotted_chopped_name (C++ function) coot::molecule_t::draw_diff_map_vector_sets (C++ member) coot::molecule_t::draw_vector_sets (C++ member) coot::molecule_t::draw_vector_sets_lock (C++ member) coot::molecule_t::eigen_flip_residue (C++ function) coot::molecule_t::export_chemical_features_as_gltf (C++ function) coot::molecule_t::export_map_molecule_as_gltf (C++ function) coot::molecule_t::export_model_molecule_as_gltf (C++ function) coot::molecule_t::export_molecular_representation_as_gltf (C++ function) coot::molecule_t::extra_restraints (C++ member) coot::molecule_t::file_to_string (C++ function) coot::molecule_t::fill_default_colour_rules (C++ function) coot::molecule_t::fill_fobs_sigfobs (C++ function) coot::molecule_t::fill_partial_residue (C++ function) coot::molecule_t::fill_partial_residues (C++ function) coot::molecule_t::find_serial_number_for_insert (C++ function) coot::molecule_t::fit_to_map_by_random_jiggle (C++ function), [1] coot::molecule_t::fit_to_map_by_random_jiggle_using_atom_selection (C++ function) coot::molecule_t::fix_atom_selection_during_refinement (C++ function) coot::molecule_t::fixed_atom_specs (C++ member) coot::molecule_t::flip_peptide (C++ function) coot::molecule_t::fraction_to_colour (C++ function) coot::molecule_t::full_atom_spec_to_atom_index (C++ function), [1] coot::molecule_t::generate_chain_self_restraints (C++ function) coot::molecule_t::generate_local_self_restraints (C++ function), [1], [2] coot::molecule_t::generate_self_restraints (C++ function) coot::molecule_t::geometric_distortions_from_mol (C++ function), [1] coot::molecule_t::get_atom (C++ function) coot::molecule_t::get_bond_colour_basic (C++ function) coot::molecule_t::get_bond_colour_by_colour_wheel_position (C++ function) coot::molecule_t::get_bond_colour_by_mol_no (C++ function) coot::molecule_t::get_bonds_box_type (C++ function) coot::molecule_t::get_bonds_mesh (C++ function) coot::molecule_t::get_bonds_mesh_for_selection_instanced (C++ function) coot::molecule_t::get_bonds_mesh_instanced (C++ function) coot::molecule_t::get_chain_ids (C++ function) coot::molecule_t::get_chemical_features_mesh (C++ function) coot::molecule_t::get_colour_rules (C++ function) coot::molecule_t::get_colour_table_for_blender (C++ function) coot::molecule_t::get_density_at_position (C++ function) coot::molecule_t::get_extra_restraints_mesh (C++ function) coot::molecule_t::get_fixed_atoms (C++ function) coot::molecule_t::get_gaussian_surface (C++ function) coot::molecule_t::get_goodsell_style_mesh (C++ function) coot::molecule_t::get_goodsell_style_mesh_instanced (C++ function) coot::molecule_t::get_HA_unit_vector (C++ function) coot::molecule_t::get_last_restraints (C++ function) coot::molecule_t::get_map_contours_mesh (C++ function) coot::molecule_t::get_map_contours_mesh_using_other_map_for_colours (C++ function) coot::molecule_t::get_map_histogram (C++ function) coot::molecule_t::get_map_mean (C++ function) coot::molecule_t::get_map_molecule_centre (C++ function) coot::molecule_t::get_map_rmsd_approx (C++ function) coot::molecule_t::get_map_section_texture (C++ function) coot::molecule_t::get_median_temperature_factor (C++ function) coot::molecule_t::get_mesh_for_ligand_validation_vs_dictionary (C++ function) coot::molecule_t::get_molecular_representation_mesh (C++ function) coot::molecule_t::get_molecule_centre (C++ function) coot::molecule_t::get_molecule_diameter (C++ function) coot::molecule_t::get_molecule_index (C++ function) coot::molecule_t::get_name (C++ function) coot::molecule_t::get_ncs_related_chains (C++ function) coot::molecule_t::get_non_standard_residues_in_molecule (C++ function) coot::molecule_t::get_number_of_atoms (C++ function) coot::molecule_t::get_number_of_hydrogen_atoms (C++ function) coot::molecule_t::get_number_of_map_sections (C++ function) coot::molecule_t::get_original_fobs_sigfobs (C++ function) coot::molecule_t::get_original_rfree_flags (C++ function) coot::molecule_t::get_overlap_dots (C++ function) coot::molecule_t::get_overlap_dots_for_ligand (C++ function) coot::molecule_t::get_overlaps (C++ function) coot::molecule_t::get_overlaps_for_ligand (C++ function) coot::molecule_t::get_residue (C++ function), [1] coot::molecule_t::get_residue_average_position (C++ function) coot::molecule_t::get_residue_CA_position (C++ function) coot::molecule_t::get_residue_closest_to (C++ function) coot::molecule_t::get_residue_name (C++ function) coot::molecule_t::get_residue_names_with_no_dictionary (C++ function) coot::molecule_t::get_residue_sidechain_average_position (C++ function) coot::molecule_t::get_rotamer_dodecs (C++ function) coot::molecule_t::get_rotamer_dodecs_instanced (C++ function) coot::molecule_t::get_show_symmetry (C++ function) coot::molecule_t::get_simple_molecule (C++ function), [1] coot::molecule_t::get_single_letter_codes_for_chain (C++ function) coot::molecule_t::get_suggested_initial_contour_level (C++ function) coot::molecule_t::get_symmetry (C++ function) coot::molecule_t::get_triangles_for_blender (C++ function) coot::molecule_t::get_updating_maps_diff_diff_map_peaks (C++ function) coot::molecule_t::get_vertices_for_blender (C++ function) coot::molecule_t::has_xmap (C++ function) coot::molecule_t::have_unsaved_changes (C++ function) coot::molecule_t::histogram_info_t (C++ class) coot::molecule_t::histogram_info_t::base (C++ member) coot::molecule_t::histogram_info_t::bin_width (C++ member) coot::molecule_t::histogram_info_t::counts (C++ member) coot::molecule_t::histogram_info_t::histogram_info_t (C++ function), [1] coot::molecule_t::histogram_info_t::mean (C++ member) coot::molecule_t::histogram_info_t::variance (C++ member) coot::molecule_t::history_filename_vec (C++ member) coot::molecule_t::hydrogen_atom_should_be_drawn (C++ function) coot::molecule_t::imol_no (C++ member) coot::molecule_t::indexed_user_defined_colour_selection_cids (C++ member) coot::molecule_t::indexed_user_defined_colour_selection_cids_apply_to_non_carbon_atoms_also (C++ member) coot::molecule_t::init (C++ function) coot::molecule_t::init_all_molecule_refinement (C++ function) coot::molecule_t::insert_waters_into_molecule (C++ function) coot::molecule_t::interesting_place_t (C++ class) coot::molecule_t::interesting_place_t::badness (C++ member) coot::molecule_t::interesting_place_t::button_label (C++ member) coot::molecule_t::interesting_place_t::feature_type (C++ member) coot::molecule_t::interesting_place_t::feature_value (C++ member) coot::molecule_t::interesting_place_t::interesting_place_t (C++ function), [1], [2] coot::molecule_t::interesting_place_t::residue_spec (C++ member) coot::molecule_t::interesting_place_t::set_badness_value (C++ function) coot::molecule_t::interesting_place_t::set_feature_value (C++ function) coot::molecule_t::interesting_place_t::x (C++ member) coot::molecule_t::interesting_place_t::y (C++ member) coot::molecule_t::interesting_place_t::z (C++ member) coot::molecule_t::is_closed (C++ function) coot::molecule_t::is_closed_flag (C++ member) coot::molecule_t::is_difference_map_p (C++ function) coot::molecule_t::is_EM_map (C++ function) coot::molecule_t::is_em_map_cached_flag (C++ member) coot::molecule_t::is_em_map_cached_state (C++ function) coot::molecule_t::is_from_shelx_ins (C++ function) coot::molecule_t::is_from_shelx_ins_flag (C++ member) coot::molecule_t::is_het_residue (C++ function) coot::molecule_t::is_valid_map_molecule (C++ function) coot::molecule_t::is_valid_model_molecule (C++ function) coot::molecule_t::jed_flip (C++ function) coot::molecule_t::jed_flip_internal (C++ function), [1] coot::molecule_t::last_restraints (C++ member) coot::molecule_t::ligand_flip_number (C++ member) coot::molecule_t::M2T_float_params (C++ member) coot::molecule_t::M2T_int_params (C++ member) coot::molecule_t::M2T_updateFloatParameter (C++ function), [1] coot::molecule_t::M2T_updateIntParameter (C++ function) coot::molecule_t::make_backup (C++ function) coot::molecule_t::make_bonds (C++ function) coot::molecule_t::make_bonds_type_checked (C++ function), [1] coot::molecule_t::make_ca_bonds (C++ function) coot::molecule_t::make_colour_by_chain_bonds (C++ function) coot::molecule_t::make_colour_table (C++ function) coot::molecule_t::make_colour_table_for_goodsell_style (C++ function) coot::molecule_t::make_exportable_environment_bond_box (C++ function) coot::molecule_t::make_import_datanames (C++ function) coot::molecule_t::make_mesh_for_bonds_for_blender (C++ function) coot::molecule_t::make_mesh_for_gaussian_surface_for_blender (C++ function) coot::molecule_t::make_mesh_for_goodsell_style_for_blender (C++ function) coot::molecule_t::make_mesh_for_map_contours_for_blender (C++ function) coot::molecule_t::make_mesh_for_molecular_representation_for_blender (C++ function) coot::molecule_t::makebonds (C++ function) coot::molecule_t::map_chains_to_new_chains (C++ function) coot::molecule_t::map_colour (C++ member) coot::molecule_t::map_ghost_info (C++ member) coot::molecule_t::map_triangle_centres (C++ member) coot::molecule_t::match_torsions (C++ function) coot::molecule_t::merge_ligand_to_near_chain (C++ function) coot::molecule_t::merge_molecules (C++ function), [1] coot::molecule_t::merge_molecules_just_one_residue_at_given_spec (C++ function) coot::molecule_t::merge_molecules_just_one_residue_homogeneous (C++ function) coot::molecule_t::minimize (C++ function) coot::molecule_t::modification_info (C++ member) coot::molecule_t::modification_info_t (C++ class) coot::molecule_t::modification_info_t::backup_dir (C++ member) coot::molecule_t::modification_info_t::get_backup_file_name_from_index (C++ function) coot::molecule_t::modification_info_t::get_index_string (C++ function) coot::molecule_t::modification_info_t::have_unsaved_changes (C++ function)

coot::molecule_t::modification_info_t::init (C++ function) coot::molecule_t::modification_info_t::is_mmcif_flag (C++ member) coot::molecule_t::modification_info_t::make_backup (C++ function) coot::molecule_t::modification_info_t::max_modification_index (C++ member) coot::molecule_t::modification_info_t::modification_index (C++ member) coot::molecule_t::modification_info_t::modification_info_t (C++ function), [1] coot::molecule_t::modification_info_t::mol_name (C++ member) coot::molecule_t::modification_info_t::print_save_info (C++ function) coot::molecule_t::modification_info_t::redo (C++ function) coot::molecule_t::modification_info_t::save_info (C++ member) coot::molecule_t::modification_info_t::save_info_t (C++ class) coot::molecule_t::modification_info_t::save_info_t::file_name (C++ member) coot::molecule_t::modification_info_t::save_info_t::get_mol (C++ function) coot::molecule_t::modification_info_t::save_info_t::modification_info_string (C++ member) coot::molecule_t::modification_info_t::save_info_t::save_info_t (C++ function) coot::molecule_t::modification_info_t::set_molecule_name (C++ function) coot::molecule_t::modification_info_t::undo (C++ function) coot::molecule_t::molecule_save_info_t (C++ class) coot::molecule_t::molecule_save_info_t::get_next_modification_index (C++ function) coot::molecule_t::molecule_save_info_t::get_previous_modification_index (C++ function) coot::molecule_t::molecule_save_info_t::have_unsaved_changes (C++ function) coot::molecule_t::molecule_save_info_t::index_string (C++ function) coot::molecule_t::molecule_save_info_t::last_saved (C++ member) coot::molecule_t::molecule_save_info_t::made_a_save (C++ function) coot::molecule_t::molecule_save_info_t::max_modification_index (C++ member) coot::molecule_t::molecule_save_info_t::modification_index (C++ member) coot::molecule_t::molecule_save_info_t::molecule_save_info_t (C++ function) coot::molecule_t::molecule_save_info_t::new_modification (C++ function) coot::molecule_t::molecule_save_info_t::set_modification_index (C++ function) coot::molecule_t::molecule_t (C++ function), [1], [2], [3] coot::molecule_t::molecule_to_mmCIF_string (C++ function) coot::molecule_t::molecule_to_PDB_string (C++ function) coot::molecule_t::movable_atom (C++ function) coot::molecule_t::move_molecule_to_new_centre (C++ function) coot::molecule_t::moving_atom_matches (C++ function) coot::molecule_t::multi_fasta_seq (C++ member) coot::molecule_t::multiply_residue_temperature_factors (C++ function) coot::molecule_t::mutate (C++ function) coot::molecule_t::mutate_by_overlap (C++ function) coot::molecule_t::name (C++ member) coot::molecule_t::name_for_display_manager (C++ function) coot::molecule_t::neighbouring_residues (C++ member) coot::molecule_t::new_positions_for_atoms_in_residues (C++ function) coot::molecule_t::new_positions_for_residue_atoms (C++ function), [1] coot::molecule_t::next_residue_number_in_chain (C++ function) coot::molecule_t::no_bonds_to_these_atom_indices (C++ member) coot::molecule_t::non_standard_residue_types_in_model (C++ function) coot::molecule_t::nucelotide_residue_name_to_base_atom_names (C++ function) coot::molecule_t::original_fobs_sigfobs_fill_tried_and_failed (C++ member) coot::molecule_t::original_fobs_sigfobs_filled (C++ member) coot::molecule_t::original_fobs_sigfobs_p (C++ member) coot::molecule_t::original_fphis_filled (C++ member) coot::molecule_t::original_fphis_p (C++ member) coot::molecule_t::original_r_free_flags_p (C++ member) coot::molecule_t::other_map_for_colouring_max_value (C++ member) coot::molecule_t::other_map_for_colouring_min_value (C++ member) coot::molecule_t::peptide_omega_analysis (C++ function) coot::molecule_t::position_to_colour_using_other_map (C++ function) coot::molecule_t::print_colour_rules (C++ function) coot::molecule_t::print_colour_table (C++ function) coot::molecule_t::print_M2T_FloatParameters (C++ function) coot::molecule_t::print_M2T_IntParameters (C++ function) coot::molecule_t::print_non_drawn_bonds (C++ function) coot::molecule_t::print_secondary_structure_info (C++ function) coot::molecule_t::radial_map_colour_invert_flag (C++ member) coot::molecule_t::radial_map_colour_saturation (C++ member) coot::molecule_t::ramachandran_validation (C++ function) coot::molecule_t::read_extra_restraints (C++ function) coot::molecule_t::read_shelx_ins_file (C++ function) coot::molecule_t::really_do_backups (C++ member) coot::molecule_t::redo (C++ function) coot::molecule_t::refine_direct (C++ function) coot::molecule_t::refine_using_last_restraints (C++ function) coot::molecule_t::Refmac_fobs_col (C++ function) coot::molecule_t::refmac_fobs_col (C++ member) coot::molecule_t::Refmac_mtz_filename (C++ function) coot::molecule_t::refmac_mtz_filename (C++ member) coot::molecule_t::refmac_r_free_col (C++ member) coot::molecule_t::refmac_r_free_flag_sensible (C++ member) coot::molecule_t::Refmac_sigfobs_col (C++ function) coot::molecule_t::refmac_sigfobs_col (C++ member) coot::molecule_t::remove_TER_internal (C++ function) coot::molecule_t::remove_TER_on_last_residue (C++ function) coot::molecule_t::replace_coords (C++ function) coot::molecule_t::replace_fragment (C++ function), [1] coot::molecule_t::replace_molecule_by_model_from_file (C++ function) coot::molecule_t::replace_residue (C++ function) coot::molecule_t::residue_name_to_plane_atom_names (C++ function) coot::molecule_t::residues_near_residue (C++ function) coot::molecule_t::restore_from_backup (C++ function) coot::molecule_t::rigid_body_fit (C++ function), [1] coot::molecule_t::rotamer_change_info_t (C++ class) coot::molecule_t::rotamer_change_info_t::name (C++ member) coot::molecule_t::rotamer_change_info_t::rank (C++ member) coot::molecule_t::rotamer_change_info_t::richardson_probability (C++ member) coot::molecule_t::rotamer_change_info_t::rotamer_change_info_t (C++ function), [1] coot::molecule_t::rotamer_change_info_t::status (C++ member) coot::molecule_t::rotate_around_bond (C++ function) coot::molecule_t::sanity_check_atoms (C++ function) coot::molecule_t::save_history_file_name (C++ function) coot::molecule_t::save_time_string (C++ member) coot::molecule_t::select_residues (C++ function), [1], [2] coot::molecule_t::set_base_colour_for_bonds (C++ function) coot::molecule_t::set_bespoke_carbon_atom_colour (C++ function) coot::molecule_t::set_colour_wheel_rotation_base (C++ function) coot::molecule_t::set_map_colour (C++ function) coot::molecule_t::set_map_colour_saturation (C++ function) coot::molecule_t::set_map_is_difference_map (C++ function) coot::molecule_t::set_molecule_name (C++ function) coot::molecule_t::set_other_map_for_colouring_invert_colour_ramp (C++ function) coot::molecule_t::set_other_map_for_colouring_min_max (C++ function) coot::molecule_t::set_really_do_backups (C++ function) coot::molecule_t::set_residue_to_rotamer_move_atoms (C++ function) coot::molecule_t::set_show_symmetry (C++ function) coot::molecule_t::set_updating_maps_diff_diff_map_peaks (C++ function) coot::molecule_t::set_use_bespoke_carbon_atom_colour (C++ function) coot::molecule_t::set_user_defined_atom_colour_by_selections (C++ function) coot::molecule_t::set_user_defined_bond_colours (C++ function) coot::molecule_t::setup_cylinder_clashes (C++ function) coot::molecule_t::setup_dots (C++ function) coot::molecule_t::sfcalc_genmap (C++ function) coot::molecule_t::sfcalc_genmaps_using_bulk_solvent (C++ function) coot::molecule_t::shelxins (C++ member) coot::molecule_t::shiftfield_b_factor_refinement (C++ function) coot::molecule_t::show_symmetry (C++ member) coot::molecule_t::side_chain_180 (C++ function) coot::molecule_t::simple_geometric_distortions_from_mol (C++ function) coot::molecule_t::store_user_defined_atom_colour_selections (C++ function) coot::molecule_t::suggest_new_chain_id (C++ function) coot::molecule_t::sum_density_for_atoms_in_residue (C++ function) coot::molecule_t::transform_by (C++ function), [1], [2] coot::molecule_t::trim_atom_label_table (C++ function) coot::molecule_t::try_add_by_consolidation (C++ function) coot::molecule_t::turn_off_when_close_target_position_restraint (C++ function) coot::molecule_t::undo (C++ function) coot::molecule_t::unused_chain_id (C++ function) coot::molecule_t::update_map_triangles (C++ function) coot::molecule_t::update_map_triangles_using_thread_pool (C++ function) coot::molecule_t::update_symmetry (C++ function) coot::molecule_t::updating_maps_diff_diff_map_peaks (C++ member) coot::molecule_t::updating_maps_previous_difference_map (C++ member) coot::molecule_t::use_bespoke_grey_colour_for_carbon_atoms (C++ member) coot::molecule_t::use_gemmi (C++ member) coot::molecule_t::user_defined_bond_colours (C++ member) coot::molecule_t::write_coordinates (C++ function) coot::molecule_t::write_map (C++ function) coot::molecule_t::write_shelx_ins_file (C++ function) coot::molecule_t::xmap (C++ member) coot::molecule_t::xmap_is_diff_map (C++ member) coot::operator<< (C++ function), [1], [2], [3], [4] coot::PhonyNameDueToError::RESIDUE_NUMBER_UNSET (C++ enumerator) coot::residue_spec_t (C++ class) coot::residue_spec_t::chain_id (C++ member) coot::residue_spec_t::empty (C++ function) coot::residue_spec_t::float_user_data (C++ member) coot::residue_spec_t::format (C++ function) coot::residue_spec_t::get_residue (C++ function) coot::residue_spec_t::ins_code (C++ member) coot::residue_spec_t::int_user_data (C++ member) coot::residue_spec_t::label (C++ function), [1] coot::residue_spec_t::model_number (C++ member) coot::residue_spec_t::next (C++ function) coot::residue_spec_t::previous (C++ function) coot::residue_spec_t::res_no (C++ member) coot::residue_spec_t::residue_spec_t (C++ function), [1], [2], [3], [4], [5], [6] coot::residue_spec_t::select_atoms (C++ function) coot::residue_spec_t::string_user_data (C++ member) coot::residue_spec_t::unset_p (C++ function) coot::residue_validation_information_t (C++ class) coot::residue_validation_information_t::atom_spec (C++ member) coot::residue_validation_information_t::function_value (C++ member) coot::residue_validation_information_t::label (C++ member) coot::residue_validation_information_t::residue_spec (C++ member) coot::residue_validation_information_t::residue_validation_information_t (C++ function), [1] coot::simple_mesh_t (C++ class) coot::simple_mesh_t::add_submesh (C++ function) coot::simple_mesh_t::change_colour (C++ function) coot::simple_mesh_t::clear (C++ function) coot::simple_mesh_t::colour_index_to_colour_map (C++ member) coot::simple_mesh_t::export_to_gltf (C++ function) coot::simple_mesh_t::fill_colour_map (C++ function) coot::simple_mesh_t::make_sphere (C++ function) coot::simple_mesh_t::name (C++ member) coot::simple_mesh_t::scale (C++ function) coot::simple_mesh_t::set_name (C++ function) coot::simple_mesh_t::simple_mesh_t (C++ function), [1], [2], [3] coot::simple_mesh_t::status (C++ member) coot::simple_mesh_t::translate (C++ function) coot::simple_mesh_t::triangles (C++ member) coot::simple_mesh_t::vandt (C++ function) coot::simple_mesh_t::vertices (C++ member) coot::stats (C++ type) coot::stats::get_kolmogorov_smirnov_vs_normal (C++ function) coot::stats::pnorm (C++ class) coot::stats::pnorm::erf (C++ function) coot::stats::pnorm::get (C++ function) coot::stats::pnorm::init (C++ function) coot::stats::pnorm::pnorm (C++ function) coot::stats::single (C++ class) coot::stats::single::add (C++ function), [1] coot::stats::single::empty (C++ function) coot::stats::single::get_ith_highest (C++ function) coot::stats::single::get_ith_lowest (C++ function) coot::stats::single::kurtosis (C++ function) coot::stats::single::mean (C++ function) coot::stats::single::median_and_iqr (C++ function) coot::stats::single::single (C++ function), [1] coot::stats::single::size (C++ function) coot::stats::single::skew (C++ function) coot::stats::single::v (C++ member) coot::stats::single::variance (C++ function) coot::trans_selection_t (C++ class) coot::trans_selection_t::back (C++ member) coot::trans_selection_t::bottom (C++ member) coot::trans_selection_t::front (C++ member) coot::trans_selection_t::left (C++ member) coot::trans_selection_t::point_is_in_box (C++ function) coot::trans_selection_t::right (C++ member) coot::trans_selection_t::top (C++ member) coot::util (C++ type), [1], [2] coot::util::amplitude_vs_resolution (C++ function) coot::util::analyse_map_point_density_change (C++ function) coot::util::average_map (C++ function) coot::util::average_of_sample_map_at_sphere_points (C++ function) coot::util::b_factor (C++ function) coot::util::backrub_residue_triple_t (C++ class) coot::util::backrub_residue_triple_t::backrub_residue_triple_t (C++ function) coot::util::backrub_residue_triple_t::trim_next_residue_atoms (C++ function) coot::util::backrub_residue_triple_t::trim_prev_residue_atoms (C++ function) coot::util::backrub_residue_triple_t::trim_residue_atoms_generic (C++ function) coot::util::backrub_residue_triple_t::trim_this_residue_atoms (C++ function) coot::util::calc_atom_map (C++ function) coot::util::compare_structure_factors (C++ function) coot::util::correlation_parts_t (C++ class) coot::util::correlation_parts_t::top (C++ member) coot::util::correlation_parts_t::var_x (C++ member) coot::util::correlation_parts_t::var_y (C++ member) coot::util::density_around_point (C++ function) coot::util::density_at_map_point (C++ function) coot::util::density_at_point (C++ function) coot::util::density_at_point_by_cubic_interp (C++ function) coot::util::density_at_point_by_linear_interpolation (C++ function) coot::util::density_at_point_by_nearest_grid (C++ function) coot::util::density_correlation_stats_info_t (C++ class) coot::util::density_correlation_stats_info_t::add (C++ function) coot::util::density_correlation_stats_info_t::correlation (C++ function) coot::util::density_correlation_stats_info_t::correlation_by_parts (C++ function) coot::util::density_correlation_stats_info_t::density_correlation_stats_info_t (C++ function), [1] coot::util::density_correlation_stats_info_t::density_values (C++ member) coot::util::density_correlation_stats_info_t::n (C++ member) coot::util::density_correlation_stats_info_t::operator< (C++ function) coot::util::density_correlation_stats_info_t::sum_sqrd_x (C++ member) coot::util::density_correlation_stats_info_t::sum_sqrd_y (C++ member) coot::util::density_correlation_stats_info_t::sum_x (C++ member) coot::util::density_correlation_stats_info_t::sum_xy (C++ member) coot::util::density_correlation_stats_info_t::sum_y (C++ member) coot::util::density_correlation_stats_info_t::var_x (C++ function) coot::util::density_correlation_stats_info_t::var_y (C++ function) coot::util::density_map_points_in_sphere (C++ function) coot::util::density_stats_info_t (C++ class) coot::util::density_stats_info_t::add (C++ function), [1] coot::util::density_stats_info_t::density_stats_info_t (C++ function) coot::util::density_stats_info_t::mean_and_variance (C++ function) coot::util::density_stats_info_t::n (C++ member) coot::util::density_stats_info_t::sum (C++ member) coot::util::density_stats_info_t::sum_sq (C++ member) coot::util::density_stats_info_t::sum_weight (C++ member) coot::util::difference_map (C++ function) coot::util::filter_by_resolution (C++ function) coot::util::find_struct_fragment_coord_fracs_v2 (C++ function) coot::util::flip_hand (C++ function) coot::util::fsc (C++ function) coot::util::gradient_at_point (C++ function) coot::util::is_EM_map (C++ function) coot::util::laplacian_transform (C++ function) coot::util::make_map_mask (C++ function) coot::util::make_phi_thetas (C++ function) coot::util::make_rtop_orth_from (C++ function) coot::util::map_fill_from_mtz (C++ function), [1] coot::util::map_fragment_info_t (C++ class) coot::util::map_fragment_info_t::box_radius_a_internal (C++ member) coot::util::map_fragment_info_t::box_radius_b_internal (C++ member) coot::util::map_fragment_info_t::box_radius_c_internal (C++ member) coot::util::map_fragment_info_t::init (C++ function) coot::util::map_fragment_info_t::init_making_map_centred_at_origin (C++ function) coot::util::map_fragment_info_t::make_grid_map (C++ function) coot::util::map_fragment_info_t::map_fragment_info_t (C++ function) coot::util::map_fragment_info_t::offset (C++ member) coot::util::map_fragment_info_t::simple_origin_shift (C++ function) coot::util::map_fragment_info_t::unshift (C++ function) coot::util::map_fragment_info_t::xmap (C++ member) coot::util::map_molecule_centre (C++ function) coot::util::map_molecule_centre_info_t (C++ class) coot::util::map_molecule_centre_info_t::map_molecule_centre_info_t (C++ function) coot::util::map_molecule_centre_info_t::success (C++ member) coot::util::map_molecule_centre_info_t::suggested_contour_level (C++ member) coot::util::map_molecule_centre_info_t::suggested_radius (C++ member) coot::util::map_molecule_centre_info_t::sum_of_densities (C++ member) coot::util::map_molecule_centre_info_t::updated_centre (C++ member) coot::util::map_molecule_recentre_from_position (C++ function) coot::util::map_ref_triple_t (C++ class) coot::util::map_ref_triple_t::density (C++ member) coot::util::map_ref_triple_t::dist_sq (C++ member) coot::util::map_ref_triple_t::iw (C++ member) coot::util::map_ref_triple_t::map_ref_triple_t (C++ function), [1] coot::util::map_ref_triple_t::operator< (C++ function) coot::util::map_score (C++ function), [1] coot::util::map_score_atom (C++ function) coot::util::map_score_by_residue_specs (C++ function) coot::util::map_stats_holder_helper_t (C++ class) coot::util::map_stats_holder_helper_t::add_xy (C++ function) coot::util::map_stats_holder_helper_t::map_stats_holder_helper_t (C++ function) coot::util::map_stats_holder_helper_t::n (C++ member) coot::util::map_stats_holder_helper_t::sum_x (C++ member) coot::util::map_stats_holder_helper_t::sum_x_squared (C++ member) coot::util::map_stats_holder_helper_t::sum_xy (C++ member) coot::util::map_stats_holder_helper_t::sum_y (C++ member) coot::util::map_stats_holder_helper_t::sum_y_squared (C++ member) coot::util::map_to_model_correlation (C++ function) coot::util::map_to_model_correlation_per_residue (C++ function) coot::util::map_to_model_correlation_stats (C++ function) coot::util::map_to_model_correlation_stats_per_residue (C++ function) coot::util::map_to_model_correlation_stats_per_residue_run (C++ function) coot::util::mask_map (C++ function) coot::util::max_gridding (C++ function) coot::util::mean_and_variance (C++ function) coot::util::multi_sharpen_blur_map (C++ function) coot::util::partition_map_by_chain (C++ function) coot::util::phitheta (C++ type) coot::util::power_scale (C++ function) coot::util::qq_plot_for_map_over_model (C++ function) coot::util::real_space_zero_dose_extrapolation (C++ function) coot::util::regen_weighted_map (C++ function) coot::util::reinterp_map (C++ function), [1] coot::util::reinterp_map_fine_gridding (C++ function) coot::util::residue_triple_t (C++ class) coot::util::residue_triple_t::alt_conf (C++ member) coot::util::residue_triple_t::deep_copy (C++ function) coot::util::residue_triple_t::next_residue (C++ member) coot::util::residue_triple_t::prev_residue (C++ member) coot::util::residue_triple_t::residue_triple_t (C++ function), [1] coot::util::residue_triple_t::this_residue (C++ member) coot::util::residue_triple_t::~residue_triple_t (C++ function) coot::util::reverse_map (C++ function) coot::util::segment_map (C++ class) coot::util::segment_map::compare_density_values_map_refs (C++ function) coot::util::segment_map::find_biggest_segment (C++ function) coot::util::segment_map::find_smallest_segment (C++ function) coot::util::segment_map::flood_fill_segmented_map (C++ function) coot::util::segment_map::path_to_peak (C++ function) coot::util::segment_map::PhonyNameDueToError::TOO_LOW (C++ enumerator) coot::util::segment_map::PhonyNameDueToError::UNASSIGNED (C++ enumerator) coot::util::segment_map::resegment_watershed_points (C++ function) coot::util::segment_map::segment (C++ function), [1] coot::util::segment_map::segment_emsley_flood (C++ function) coot::util::segment_map::segment_map (C++ function) coot::util::segment_map::sort_segment_vec (C++ function) coot::util::sfcalc_genmap (C++ function) coot::util::sfcalc_genmap_stats_t (C++ class) coot::util::sfcalc_genmap_stats_t::bulk_correction (C++ member) coot::util::sfcalc_genmap_stats_t::bulk_solvent_volume (C++ member) coot::util::sfcalc_genmap_stats_t::free_r_factor (C++ member) coot::util::sfcalc_genmap_stats_t::loc_table (C++ member) coot::util::sfcalc_genmap_stats_t::loc_table_t (C++ class) coot::util::sfcalc_genmap_stats_t::loc_table_t::add (C++ function) coot::util::sfcalc_genmap_stats_t::loc_table_t::items (C++ member) coot::util::sfcalc_genmap_stats_t::loc_table_t::loc_table_item_t (C++ class) coot::util::sfcalc_genmap_stats_t::loc_table_t::loc_table_item_t::invresolsq (C++ member) coot::util::sfcalc_genmap_stats_t::loc_table_t::loc_table_item_t::lack_of_closure (C++ member) coot::util::sfcalc_genmap_stats_t::loc_table_t::loc_table_item_t::loc_table_item_t (C++ function) coot::util::sfcalc_genmap_stats_t::loc_table_t::loc_table_item_t::scale (C++ member) coot::util::sfcalc_genmap_stats_t::loc_table_t::loc_table_t (C++ function) coot::util::sfcalc_genmap_stats_t::loc_table_t::size (C++ function) coot::util::sfcalc_genmap_stats_t::n_splines (C++ member) coot::util::sfcalc_genmap_stats_t::r_factor (C++ member) coot::util::sfcalc_genmap_stats_t::sfcalc_genmap_stats_t (C++ function), [1] coot::util::sfcalc_genmaps_using_bulk_solvent (C++ function) coot::util::sharpen_blur_map (C++ function), [1] coot::util::sharpen_blur_map_with_reduced_sampling (C++ function) coot::util::sharpen_blur_map_with_resample (C++ function) coot::util::sharpen_map (C++ function) coot::util::simple_residue_triple_t (C++ class) coot::util::simple_residue_triple_t::alt_conf (C++ member) coot::util::simple_residue_triple_t::next_residue (C++ member) coot::util::simple_residue_triple_t::prev_residue (C++ member) coot::util::simple_residue_triple_t::simple_residue_triple_t (C++ function), [1] coot::util::simple_residue_triple_t::this_residue (C++ member) coot::util::soi_variance (C++ class) coot::util::soi_variance::apply_variance_values (C++ function) coot::util::soi_variance::make_variance_map (C++ function) coot::util::soi_variance::mri_var_pair_sorter (C++ function) coot::util::soi_variance::proc (C++ function) coot::util::soi_variance::protein_treatment_map (C++ function) coot::util::soi_variance::soi_variance (C++ function) coot::util::soi_variance::solvent_treatment_map (C++ function) coot::util::soi_variance::xmap (C++ member) coot::util::spin_search (C++ function) coot::util::suggested_grid_sampling (C++ function) coot::util::transform_map (C++ function) coot::util::variance_map (C++ function) coot::util::zero_dose_extrapolation (C++ function) coot::validation_information_min_max_t (C++ class) coot::validation_information_min_max_t::is_set (C++ member) coot::validation_information_min_max_t::max (C++ member) coot::validation_information_min_max_t::min (C++ member) coot::validation_information_min_max_t::validation_information_min_max_t (C++ function), [1] coot::validation_information_t (C++ class) coot::validation_information_t::add (C++ function) coot::validation_information_t::add_residue_validation_information (C++ function) coot::validation_information_t::cviv (C++ member) coot::validation_information_t::empty (C++ function) coot::validation_information_t::get_index_for_chain (C++ function) coot::validation_information_t::get_stats (C++ function) coot::validation_information_t::min_max (C++ member) coot::validation_information_t::name (C++ member) coot::validation_information_t::set_min_max (C++ function) coot::validation_information_t::type (C++ member) coot::validation_information_t::validation_information_t (C++ function), [1]

G

g_triangle (C++ class) g_triangle::g_triangle (C++ function), [1] g_triangle::operator<< (C++ function) g_triangle::operator[] (C++ function), [1] g_triangle::point_id (C++ member) g_triangle::rebase (C++ function)

g_triangle::reverse_winding (C++ function) g_triangle_with_colour_index (C++ class) g_triangle_with_colour_index::colour_index (C++ member) g_triangle_with_colour_index::g_triangle_with_colour_index (C++ function) generic_3d_lines_bonds_box_t (C++ class) generic_3d_lines_bonds_box_t::generic_3d_lines_bonds_box_t (C++ function), [1] generic_3d_lines_bonds_box_t::line_segments (C++ member)

M

molecule_extents_t (C++ class) molecule_extents_t::atom_sel_cell_trans (C++ member) molecule_extents_t::back (C++ member) molecule_extents_t::bottom (C++ member) molecule_extents_t::centre (C++ member) molecule_extents_t::coord_to_unit_cell_translations (C++ function) molecule_extents_t::expansion_size_ (C++ member) molecule_extents_t::extents_selection (C++ member) molecule_extents_t::front (C++ member) molecule_extents_t::get_back (C++ function) molecule_extents_t::get_bottom (C++ function) molecule_extents_t::get_front (C++ function) molecule_extents_t::get_left (C++ function) molecule_extents_t::get_right (C++ function) molecule_extents_t::get_top (C++ function) molecule_extents_t::left (C++ member) molecule_extents_t::molecule_extents_t (C++ function) molecule_extents_t::operator<< (C++ function) molecule_extents_t::point_is_in_box (C++ function) molecule_extents_t::right (C++ member) molecule_extents_t::shift_matrix (C++ function) molecule_extents_t::top (C++ member) molecule_extents_t::trans_sel (C++ function), [1], [2] molecule_extents_t::trans_sel_o (C++ function) molecule_extents_t::which_boxes (C++ function) molecule_extents_t::which_strict_ncs (C++ function) molecule_extents_t::~molecule_extents_t (C++ function) molecules_container_t (C++ class) molecules_container_t::accept_rotamer_probability_tables_compressed_data (C++ function) molecules_container_t::add_alternative_conformation (C++ function) molecules_container_t::add_colour_rule (C++ function) molecules_container_t::add_colour_rules_multi (C++ function) molecules_container_t::add_compound (C++ function) molecules_container_t::add_hydrogen_atoms (C++ function) molecules_container_t::add_lsq_superpose_atom_match (C++ function) molecules_container_t::add_lsq_superpose_match (C++ function) molecules_container_t::add_parallel_plane_restraint (C++ function) molecules_container_t::add_target_position_restraint (C++ function) molecules_container_t::add_target_position_restraint_and_refine (C++ function) molecules_container_t::add_terminal_residue_directly (C++ function) molecules_container_t::add_terminal_residue_directly_using_bucca_ml_growing (C++ function) molecules_container_t::add_terminal_residue_directly_using_bucca_ml_growing_using_cid (C++ function) molecules_container_t::add_terminal_residue_directly_using_cid (C++ function) molecules_container_t::add_to_non_drawn_bonds (C++ function) molecules_container_t::add_waters (C++ function) molecules_container_t::adjust_refinement_residue_name (C++ function) molecules_container_t::all_molecule_contact_dots (C++ function) molecules_container_t::apply_transformation_to_atom_selection (C++ function) molecules_container_t::assign_sequence (C++ function) molecules_container_t::associate_data_mtz_file_with_map (C++ function) molecules_container_t::associate_sequence (C++ function) molecules_container_t::atom_cid_to_atom_spec (C++ function) molecules_container_t::auto_fit_rotamer (C++ function) molecules_container_t::auto_read_mtz (C++ function) molecules_container_t::auto_read_mtz_info_t (C++ class) molecules_container_t::auto_read_mtz_info_t::auto_read_mtz_info_t (C++ function), [1] molecules_container_t::auto_read_mtz_info_t::F (C++ member) molecules_container_t::auto_read_mtz_info_t::F_obs (C++ member) molecules_container_t::auto_read_mtz_info_t::idx (C++ member) molecules_container_t::auto_read_mtz_info_t::phi (C++ member) molecules_container_t::auto_read_mtz_info_t::Rfree (C++ member) molecules_container_t::auto_read_mtz_info_t::set_fobs_sigfobs (C++ function) molecules_container_t::auto_read_mtz_info_t::sigF_obs (C++ member) molecules_container_t::auto_read_mtz_info_t::w (C++ member) molecules_container_t::auto_read_mtz_info_t::weights_used (C++ member) molecules_container_t::average_map (C++ function) molecules_container_t::calculate_new_rail_points (C++ function) molecules_container_t::change_chain_id (C++ function) molecules_container_t::change_to_first_rotamer (C++ function) molecules_container_t::change_to_next_rotamer (C++ function) molecules_container_t::change_to_previous_rotamer (C++ function) molecules_container_t::cif_dictionary_read_number (C++ member) molecules_container_t::cis_trans_convert (C++ function) molecules_container_t::clear (C++ function) molecules_container_t::clear_extra_restraints (C++ function) molecules_container_t::clear_lsq_matches (C++ function) molecules_container_t::clear_non_drawn_bonds (C++ function) molecules_container_t::clear_refinement (C++ function) molecules_container_t::clear_target_position_restraint (C++ function) molecules_container_t::clear_target_position_restraints (C++ function) molecules_container_t::close_molecule (C++ function) molecules_container_t::connect_updating_maps (C++ function) molecules_container_t::contact_dots_for_ligand (C++ function) molecules_container_t::contains_unsaved_models (C++ function) molecules_container_t::continue_threaded_refinement_loop (C++ member) molecules_container_t::copy_dictionary (C++ function) molecules_container_t::copy_fragment_for_refinement_using_cid (C++ function) molecules_container_t::copy_fragment_using_cid (C++ function) molecules_container_t::copy_fragment_using_residue_range (C++ function) molecules_container_t::create_empty_molecules (C++ function) molecules_container_t::delete_atom (C++ function) molecules_container_t::delete_atom_using_cid (C++ function) molecules_container_t::delete_chain_using_cid (C++ function) molecules_container_t::delete_colour_rules (C++ function) molecules_container_t::delete_hydrogen_atoms (C++ function) molecules_container_t::delete_literal_using_cid (C++ function) molecules_container_t::delete_residue (C++ function) molecules_container_t::delete_residue_atoms_using_cid (C++ function) molecules_container_t::delete_residue_atoms_with_alt_conf (C++ function) molecules_container_t::delete_residue_using_cid (C++ function) molecules_container_t::delete_side_chain (C++ function) molecules_container_t::delete_side_chain_using_cid (C++ function) molecules_container_t::delete_using_cid (C++ function) molecules_container_t::density_correlation_analysis (C++ function) molecules_container_t::density_fit_analysis (C++ function) molecules_container_t::dictionary_atom_name_map (C++ function) molecules_container_t::difference_map_peaks (C++ function) molecules_container_t::display_molecule_names_table (C++ function) molecules_container_t::draw_missing_residue_loops_flag (C++ member) molecules_container_t::dummy_xmap (C++ member) molecules_container_t::eigen_flip_ligand (C++ function) molecules_container_t::eigen_flip_ligand_using_cid (C++ function) molecules_container_t::end_delete_closed_molecules (C++ function) molecules_container_t::export_chemical_features_as_gltf (C++ function) molecules_container_t::export_map_molecule_as_gltf (C++ function) molecules_container_t::export_model_molecule_as_gltf (C++ function) molecules_container_t::export_molecular_representation_as_gltf (C++ function) molecules_container_t::file_name_to_string (C++ function) molecules_container_t::fill_partial_residue (C++ function) molecules_container_t::fill_partial_residue_using_cid (C++ function) molecules_container_t::fill_partial_residues (C++ function) molecules_container_t::fill_rotamer_probability_tables (C++ function) molecules_container_t::find_water_baddies (C++ function) molecules_container_t::fit_ligand (C++ function) molecules_container_t::fit_ligand_info_t (C++ class) molecules_container_t::fit_ligand_info_t::cluster_idx (C++ member) molecules_container_t::fit_ligand_info_t::cluster_volume (C++ member) molecules_container_t::fit_ligand_info_t::fit_ligand_info_t (C++ function), [1] molecules_container_t::fit_ligand_info_t::fitting_score (C++ member) molecules_container_t::fit_ligand_info_t::get_cluster_volume (C++ function) molecules_container_t::fit_ligand_info_t::get_fitting_score (C++ function) molecules_container_t::fit_ligand_info_t::imol (C++ member) molecules_container_t::fit_ligand_info_t::ligand_idx (C++ member) molecules_container_t::fit_ligand_multi_ligand (C++ function) molecules_container_t::fit_ligand_right_here (C++ function) molecules_container_t::fit_to_map_by_random_jiggle (C++ function) molecules_container_t::fit_to_map_by_random_jiggle_using_cid (C++ function) molecules_container_t::fit_to_map_by_random_jiggle_with_blur_using_cid (C++ function) molecules_container_t::fix_atom_selection_during_refinement (C++ function) molecules_container_t::flip_hand (C++ function) molecules_container_t::flip_peptide (C++ function) molecules_container_t::flip_peptide_using_cid (C++ function) molecules_container_t::fourier_shell_correlation (C++ function) molecules_container_t::geman_mcclure_alpha (C++ member) molecules_container_t::generate_chain_self_restraints (C++ function) molecules_container_t::generate_local_self_restraints (C++ function) molecules_container_t::generate_self_restraints (C++ function) molecules_container_t::geom (C++ member) molecules_container_t::geometry_init_standard (C++ function) molecules_container_t::get_acedrg_atom_types (C++ function) molecules_container_t::get_acedrg_atom_types_for_ligand (C++ function) molecules_container_t::get_active_atom (C++ function) molecules_container_t::get_bonds_mesh (C++ function) molecules_container_t::get_bonds_mesh_for_selection_instanced (C++ function) molecules_container_t::get_bonds_mesh_instanced (C++ function) molecules_container_t::get_cell (C++ function) molecules_container_t::get_chains_in_model (C++ function) molecules_container_t::get_chemical_features_mesh (C++ function) molecules_container_t::get_cif_file_name (C++ function) molecules_container_t::get_cif_restraints_as_string (C++ function) molecules_container_t::get_colour_rules (C++ function) molecules_container_t::get_colour_table (C++ function) molecules_container_t::get_colour_table_for_blender (C++ function) molecules_container_t::get_contouring_time (C++ function) molecules_container_t::get_data_set_file_name (C++ function) molecules_container_t::get_density_at_position (C++ function) molecules_container_t::get_dictionary_conformers (C++ function) molecules_container_t::get_diff_diff_map_peaks (C++ function) molecules_container_t::get_eigenvalues (C++ function) molecules_container_t::get_extra_restraints_mesh (C++ function) molecules_container_t::get_gaussian_surface (C++ function) molecules_container_t::get_geman_mcclure_alpha (C++ function) molecules_container_t::get_goodsell_style_mesh_instanced (C++ function) molecules_container_t::get_gphl_chem_comp_info (C++ function) molecules_container_t::get_group_for_monomer (C++ function) molecules_container_t::get_groups_for_monomers (C++ function) molecules_container_t::get_h_bonds (C++ function) molecules_container_t::get_hb_type (C++ function) molecules_container_t::get_header_info (C++ function) molecules_container_t::get_imol_enc_any (C++ function) molecules_container_t::get_interesting_places (C++ function) molecules_container_t::get_latest_sfcalc_stats (C++ function) molecules_container_t::get_ligand_distortion (C++ function) molecules_container_t::get_ligand_validation_vs_dictionary (C++ function) molecules_container_t::get_lsq_matrix (C++ function) molecules_container_t::get_make_backups (C++ function) molecules_container_t::get_map_contours_mesh (C++ function) molecules_container_t::get_map_contours_mesh_using_other_map_for_colours (C++ function) molecules_container_t::get_map_histogram (C++ function) molecules_container_t::get_map_mean (C++ function) molecules_container_t::get_map_molecule_centre (C++ function) molecules_container_t::get_map_rmsd_approx (C++ function) molecules_container_t::get_map_sampling_rate (C++ function) molecules_container_t::get_map_section_texture (C++ function) molecules_container_t::get_map_weight (C++ function) molecules_container_t::get_median_temperature_factor (C++ function) molecules_container_t::get_mesh_for_ligand_validation_vs_dictionary (C++ function) molecules_container_t::get_molecular_representation_mesh (C++ function) molecules_container_t::get_molecule_centre (C++ function) molecules_container_t::get_molecule_diameter (C++ function) molecules_container_t::get_molecule_name (C++ function) molecules_container_t::get_monomer (C++ function) molecules_container_t::get_monomer_and_position_at (C++ function) molecules_container_t::get_monomer_from_dictionary (C++ function) molecules_container_t::get_ncs_related_chains (C++ function) molecules_container_t::get_non_standard_residues_in_molecule (C++ function) molecules_container_t::get_number_of_atoms (C++ function) molecules_container_t::get_number_of_hydrogen_atoms (C++ function) molecules_container_t::get_number_of_map_sections (C++ function) molecules_container_t::get_number_of_molecules (C++ function) molecules_container_t::get_octahemisphere (C++ function) molecules_container_t::get_overlap_dots (C++ function) molecules_container_t::get_overlap_dots_for_ligand (C++ function) molecules_container_t::get_overlaps (C++ function) molecules_container_t::get_overlaps_for_ligand (C++ function) molecules_container_t::get_q_score (C++ function) molecules_container_t::get_q_score_for_cid (C++ function) molecules_container_t::get_r_factor_stats (C++ function) molecules_container_t::get_rama_plot_restraints_weight (C++ function) molecules_container_t::get_ramachandran_validation_markup_mesh (C++ function) molecules_container_t::get_residue_average_position (C++ function) molecules_container_t::get_residue_CA_position (C++ function) molecules_container_t::get_residue_name (C++ function) molecules_container_t::get_residue_names_with_no_dictionary (C++ function) molecules_container_t::get_residue_sidechain_average_position (C++ function) molecules_container_t::get_residues_near_residue (C++ function) molecules_container_t::get_rotamer_dodecs (C++ function) molecules_container_t::get_rotamer_dodecs_instanced (C++ function) molecules_container_t::get_simple_molecule (C++ function)

molecules_container_t::get_single_letter_codes_for_chain (C++ function) molecules_container_t::get_suggested_initial_contour_level (C++ function) molecules_container_t::get_sum_density_for_atoms_in_residue (C++ function) molecules_container_t::get_svg_for_residue_type (C++ function) molecules_container_t::get_symmetry (C++ function) molecules_container_t::get_torsion (C++ function) molecules_container_t::get_torsion_restraints_weight (C++ function) molecules_container_t::get_triangles_for_blender (C++ function) molecules_container_t::get_use_gemmi (C++ function) molecules_container_t::get_use_rama_plot_restraints (C++ function) molecules_container_t::get_use_torsion_restraints (C++ function) molecules_container_t::get_vertices_for_blender (C++ function) molecules_container_t::go_to_blob (C++ function) molecules_container_t::imol_difference_map (C++ member) molecules_container_t::imol_moving_atoms (C++ member) molecules_container_t::imol_refinement_map (C++ member) molecules_container_t::import_cif_dictionary (C++ function) molecules_container_t::init_refinement_of_molecule_as_fragment_based_on_reference (C++ function) molecules_container_t::interrupt_long_term_job (C++ member) molecules_container_t::is_a_difference_map (C++ function) molecules_container_t::is_EM_map (C++ function) molecules_container_t::is_valid_map_molecule (C++ function) molecules_container_t::is_valid_model_molecule (C++ function) molecules_container_t::jed_flip (C++ function) molecules_container_t::last_restraints (C++ member) molecules_container_t::long_term_job_stats (C++ member) molecules_container_t::lsq_matchers (C++ member) molecules_container_t::lsq_superpose (C++ function) molecules_container_t::ltj_stats_t (C++ class) molecules_container_t::ltj_stats_t::count (C++ member) molecules_container_t::ltj_stats_t::function_value (C++ member) molecules_container_t::ltj_stats_t::ltj_stats_t (C++ function) molecules_container_t::ltj_stats_t::time_difference (C++ function) molecules_container_t::ltj_stats_t::timer (C++ member) molecules_container_t::ltj_stats_t::timer_start (C++ member) molecules_container_t::ltj_stats_t::update_timer (C++ function) molecules_container_t::M2T_updateFloatParameter (C++ function) molecules_container_t::M2T_updateIntParameter (C++ function) molecules_container_t::make_backups_flag (C++ member) molecules_container_t::make_ensemble (C++ function) molecules_container_t::make_exportable_environment_bond_box (C++ function) molecules_container_t::make_mask (C++ function) molecules_container_t::make_masked_maps_split_by_chain (C++ function) molecules_container_t::make_mesh_for_bonds_for_blender (C++ function) molecules_container_t::make_mesh_for_gaussian_surface_for_blender (C++ function) molecules_container_t::make_mesh_for_goodsell_style_for_blender (C++ function) molecules_container_t::make_mesh_for_map_contours_for_blender (C++ function) molecules_container_t::make_mesh_for_molecular_representation_for_blender (C++ function) molecules_container_t::make_mesh_from_gltf_file (C++ function) molecules_container_t::make_power_scaled_map (C++ function) molecules_container_t::map_weight (C++ member) molecules_container_t::mask_map_by_atom_selection (C++ function) molecules_container_t::match_ligand_position (C++ function) molecules_container_t::match_ligand_torsions (C++ function) molecules_container_t::match_ligand_torsions_and_position (C++ function) molecules_container_t::match_ligand_torsions_and_position_using_cid (C++ function) molecules_container_t::merge_molecules (C++ function) molecules_container_t::minimize (C++ function) molecules_container_t::minimize_energy (C++ function) molecules_container_t::mmcif_tests (C++ function) molecules_container_t::molecule_to_mmCIF_string (C++ function) molecules_container_t::molecule_to_PDB_string (C++ function) molecules_container_t::molecules (C++ member) molecules_container_t::molecules_container_t (C++ function) molecules_container_t::move_molecule_to_new_centre (C++ function) molecules_container_t::moving_atoms_asc_t (C++ enum) molecules_container_t::moving_atoms_asc_t::NEW_COORDS_ADD (C++ enumerator) molecules_container_t::moving_atoms_asc_t::NEW_COORDS_INSERT (C++ enumerator) molecules_container_t::moving_atoms_asc_t::NEW_COORDS_INSERT_CHANGE_ALTCONF (C++ enumerator) molecules_container_t::moving_atoms_asc_t::NEW_COORDS_REPLACE (C++ enumerator) molecules_container_t::moving_atoms_asc_t::NEW_COORDS_REPLACE_CHANGE_ALTCONF (C++ enumerator) molecules_container_t::moving_atoms_asc_t::NEW_COORDS_UNSET (C++ enumerator) molecules_container_t::moving_atoms_asc_type (C++ member) molecules_container_t::multiply_residue_temperature_factors (C++ function) molecules_container_t::mutate (C++ function) molecules_container_t::new_molecule (C++ function) molecules_container_t::new_positions_for_atoms_in_residues (C++ function) molecules_container_t::new_positions_for_residue_atoms (C++ function) molecules_container_t::non_standard_residue_types_in_model (C++ function) molecules_container_t::on_going_updating_map_lock (C++ member) molecules_container_t::pae_png (C++ function) molecules_container_t::partition_map_by_chain (C++ function) molecules_container_t::pepflips_using_difference_map (C++ function) molecules_container_t::peptide_omega_analysis (C++ function) molecules_container_t::pop_back (C++ function) molecules_container_t::print_colour_rules (C++ function) molecules_container_t::print_non_drawn_bonds (C++ function) molecules_container_t::print_secondary_structure_info (C++ function) molecules_container_t::r_factor_stats (C++ class) molecules_container_t::r_factor_stats::free_r_factor (C++ member) molecules_container_t::r_factor_stats::r_factor (C++ member) molecules_container_t::r_factor_stats::rail_points_new (C++ member) molecules_container_t::r_factor_stats::rail_points_total (C++ member) molecules_container_t::r_factor_stats_as_string (C++ function) molecules_container_t::rail_point_history (C++ member) molecules_container_t::rail_points_t (C++ class) molecules_container_t::rail_points_t::map_rail_points_delta (C++ member) molecules_container_t::rail_points_t::model_rail_points_delta (C++ member) molecules_container_t::rail_points_t::rail_points_delta (C++ function) molecules_container_t::rail_points_t::rail_points_t (C++ function), [1] molecules_container_t::rail_points_t::rmsd_of_difference_map (C++ member) molecules_container_t::rail_points_t::total (C++ function) molecules_container_t::rail_points_total (C++ function) molecules_container_t::rama_plot_restraints_weight (C++ member) molecules_container_t::ramachandran_analysis (C++ function) molecules_container_t::ramachandran_analysis_for_chain (C++ function) molecules_container_t::ramachandran_validation (C++ function) molecules_container_t::ramachandrans_container (C++ member) molecules_container_t::read_ccp4_map (C++ function) molecules_container_t::read_coordinates (C++ function) molecules_container_t::read_extra_restraints (C++ function) molecules_container_t::read_mtz (C++ function) molecules_container_t::read_pdb (C++ function) molecules_container_t::read_small_molecule_cif (C++ function) molecules_container_t::redo (C++ function) molecules_container_t::refine (C++ function) molecules_container_t::refine_residue_range (C++ function) molecules_container_t::refine_residues (C++ function) molecules_container_t::refine_residues_using_atom_cid (C++ function) molecules_container_t::refinement_immediate_replacement_flag (C++ member) molecules_container_t::refinement_is_quiet (C++ member) molecules_container_t::regen_map (C++ function) molecules_container_t::replace_fragment (C++ function) molecules_container_t::replace_map_by_mtz_from_file (C++ function) molecules_container_t::replace_molecule_by_model_from_file (C++ function) molecules_container_t::replace_residue (C++ function) molecules_container_t::residue_cid_to_residue_spec (C++ function) molecules_container_t::residues_with_missing_atoms (C++ function) molecules_container_t::rigid_body_fit (C++ function) molecules_container_t::rot_prob_tables (C++ member) molecules_container_t::rotamer_analysis (C++ function) molecules_container_t::rotate_around_bond (C++ function) molecules_container_t::save_unsaved_model_changes (C++ function) molecules_container_t::set_add_waters_sigma_cutoff (C++ function) molecules_container_t::set_add_waters_variance_limit (C++ function) molecules_container_t::set_add_waters_water_to_protein_distance_lim_max (C++ function) molecules_container_t::set_add_waters_water_to_protein_distance_lim_min (C++ function) molecules_container_t::set_base_colour_for_bonds (C++ function) molecules_container_t::set_bespoke_carbon_atom_colour (C++ function) molecules_container_t::set_colour_wheel_rotation_base (C++ function) molecules_container_t::set_draw_missing_residue_loops (C++ function) molecules_container_t::set_imol_refinement_map (C++ function) molecules_container_t::set_make_backups (C++ function) molecules_container_t::set_map_colour (C++ function) molecules_container_t::set_map_colour_saturation (C++ function) molecules_container_t::set_map_is_contoured_with_thread_pool (C++ function) molecules_container_t::set_map_sampling_rate (C++ function) molecules_container_t::set_map_weight (C++ function) molecules_container_t::set_max_number_of_threads (C++ function) molecules_container_t::set_max_number_of_threads_in_thread_pool (C++ function) molecules_container_t::set_molecule_name (C++ function) molecules_container_t::set_rama_plot_restraints_weight (C++ function) molecules_container_t::set_refinement_geman_mcclure_alpha (C++ function) molecules_container_t::set_refinement_is_verbose (C++ function) molecules_container_t::set_show_timings (C++ function) molecules_container_t::set_torsion_restraints_weight (C++ function) molecules_container_t::set_use_bespoke_carbon_atom_colour (C++ function) molecules_container_t::set_use_gemmi (C++ function) molecules_container_t::set_use_rama_plot_restraints (C++ function) molecules_container_t::set_use_torsion_restraints (C++ function) molecules_container_t::set_user_defined_atom_colour_by_selection (C++ function) molecules_container_t::set_user_defined_bond_colours (C++ function) molecules_container_t::sfcalc_genmap (C++ function) molecules_container_t::sfcalc_genmaps_using_bulk_solvent (C++ function) molecules_container_t::sharpen_blur_map (C++ function) molecules_container_t::sharpen_blur_map_with_resample (C++ function) molecules_container_t::shift_field_b_factor_refinement (C++ function) molecules_container_t::show_timings (C++ member) molecules_container_t::side_chain_180 (C++ function) molecules_container_t::split_multi_model_molecule (C++ function) molecules_container_t::SSM_superpose (C++ function) molecules_container_t::test_launching_threads (C++ function) molecules_container_t::test_origin_cube (C++ function) molecules_container_t::test_the_threading (C++ function) molecules_container_t::test_thread_pool_threads (C++ function) molecules_container_t::testing_interrogate_long_term_job (C++ function) molecules_container_t::testing_start_long_term_job (C++ function) molecules_container_t::testing_stop_long_term_job (C++ function) molecules_container_t::thread_pool (C++ member) molecules_container_t::torsion_restraints_weight (C++ member) molecules_container_t::transform_map_using_lsq_matrix (C++ function) molecules_container_t::turn_off_when_close_target_position_restraint (C++ function) molecules_container_t::undo (C++ function) molecules_container_t::unmodelled_blobs (C++ function) molecules_container_t::updating_maps_info_f (C++ class) molecules_container_t::updating_maps_info_f::imol_2fofc (C++ member) molecules_container_t::updating_maps_info_f::imol_fofc (C++ member) molecules_container_t::updating_maps_info_f::imol_model (C++ member) molecules_container_t::updating_maps_info_f::imol_with_data_info_attached (C++ member) molecules_container_t::updating_maps_info_f::maps_need_an_update (C++ member) molecules_container_t::updating_maps_info_f::updating_maps_info_f (C++ function) molecules_container_t::use_gemmi (C++ member) molecules_container_t::use_rama_plot_restraints (C++ member) molecules_container_t::use_torsion_restraints (C++ member) molecules_container_t::write_coordinates (C++ function) molecules_container_t::write_map (C++ function) molecules_container_t::write_png (C++ function) molecules_container_t::~molecules_container_t (C++ function) moorhen (C++ type) moorhen::h_bond (C++ class) moorhen::h_bond::acceptor (C++ member) moorhen::h_bond::acceptor_neigh (C++ member) moorhen::h_bond::angle_1 (C++ member) moorhen::h_bond::angle_2 (C++ member) moorhen::h_bond::angle_3 (C++ member) moorhen::h_bond::bond_has_hydrogen_flag (C++ member) moorhen::h_bond::dist (C++ member) moorhen::h_bond::donor (C++ member) moorhen::h_bond::donor_neigh (C++ member) moorhen::h_bond::h_bond (C++ function) moorhen::h_bond::hb_hydrogen (C++ member) moorhen::h_bond::hydrogen_is_ligand_atom (C++ member) moorhen::h_bond::ligand_atom_is_donor (C++ member) moorhen::h_bond_atom (C++ class) moorhen::h_bond_atom::altLoc (C++ member) moorhen::h_bond_atom::b_iso (C++ member) moorhen::h_bond_atom::chain (C++ member) moorhen::h_bond_atom::charge (C++ member) moorhen::h_bond_atom::element (C++ member) moorhen::h_bond_atom::h_bond_atom (C++ function) moorhen::h_bond_atom::model (C++ member) moorhen::h_bond_atom::name (C++ member) moorhen::h_bond_atom::occ (C++ member) moorhen::h_bond_atom::res_no (C++ member) moorhen::h_bond_atom::residue_name (C++ member) moorhen::h_bond_atom::serial (C++ member) moorhen::h_bond_atom::x (C++ member) moorhen::h_bond_atom::y (C++ member) moorhen::h_bond_atom::z (C++ member)

O

operator<< (C++ function), [1]

S

set_mmdb_cell_and_symm (C++ function) superpose_results_t (C++ class) superpose_results_t::aligned_pairs (C++ member) superpose_results_t::alignment (C++ member) superpose_results_t::alignment_info_vec (C++ member) superpose_results_t::superpose_info (C++ member) surface_face_data (C++ enum) surface_face_data::NO_FACE (C++ enumerator) surface_face_data::X_FACE (C++ enumerator) surface_face_data::Y_FACE (C++ enumerator) surface_face_data::Z_FACE (C++ enumerator) symm_trans_t (C++ class) symm_trans_t::add_shift (C++ function) symm_trans_t::as_mat44 (C++ function) symm_trans_t::fill_mat (C++ function) symm_trans_t::is_identity (C++ function) symm_trans_t::isym (C++ function)

symm_trans_t::mat (C++ member) symm_trans_t::operator<< (C++ function) symm_trans_t::str (C++ function) symm_trans_t::symm_as_string (C++ member) symm_trans_t::symm_no (C++ member) symm_trans_t::symm_trans_t (C++ function), [1], [2] symm_trans_t::x (C++ function) symm_trans_t::x_shift_ (C++ member) symm_trans_t::y (C++ function) symm_trans_t::y_shift_ (C++ member) symm_trans_t::z (C++ function) symm_trans_t::z_shift_ (C++ member) SymmMatrix (C++ class) SymmMatrix::add_unit_shift (C++ function) SymmMatrix::getMat (C++ function) SymmMatrix::mat (C++ member) SymmMatrix::operator<< (C++ function) SymmMatrix::SymmMatrix (C++ function), [1]

T

to_string (C++ function) translate_atom (C++ function)

translate_atom_with_pre_shift (C++ function) translated_atoms (C++ function)