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libcootapi
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libcootapi
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This is the complete list of members for coot::molecule_t, including all inherited members.
| add_alternative_conformation(const std::string &cid) | coot::molecule_t | |
| add_colour_rule(const std::string &selection, const std::string &colour_name) | coot::molecule_t | |
| add_compound(const dictionary_residue_restraints_t &monomer_restraints, const Cartesian &position, const clipper::Xmap< float > &xmap, float map_rmsd) (defined in coot::molecule_t) | coot::molecule_t | |
| add_hydrogen_atoms(protein_geometry *geom) | coot::molecule_t | |
| add_named_glyco_tree(const std::string &glycosylation_name, const std::string &chain_id, int res_no, const clipper::Xmap< float > &xmap, protein_geometry *geom) (defined in coot::molecule_t) | coot::molecule_t | |
| add_neighbor_residues_for_refinement_help(mmdb::Manager *mol) (defined in coot::molecule_t) | coot::molecule_t | |
| add_parallel_plane_restraint(coot::residue_spec_t spec_1, coot::residue_spec_t spec_2) (defined in coot::molecule_t) | coot::molecule_t | |
| add_target_position_restraint(const std::string &atom_cid, float pos_x, float pos_y, float pos_z) (defined in coot::molecule_t) | coot::molecule_t | |
| add_target_position_restraint_and_refine(const std::string &atom_cid, float pos_x, float pos_y, float pos_z, int n_cyles, coot::protein_geometry *geom_p) (defined in coot::molecule_t) | coot::molecule_t | |
| add_terminal_residue_directly(const residue_spec_t &spec, const std::string &new_res_type, const protein_geometry &geom, const clipper::Xmap< float > &xmap, mmdb::Manager *standard_residues_asc_mol, ctpl::thread_pool &static_thread_pool) (defined in coot::molecule_t) | coot::molecule_t | |
| add_to_non_drawn_bonds(const std::string &atom_selection_cid) (defined in coot::molecule_t) | coot::molecule_t | |
| all_molecule_contact_dots(const coot::protein_geometry &geom, unsigned int num_subdivisions) const | coot::molecule_t | |
| apply_transformation_to_atom_selection(const std::string &atom_selection_cid, int n_atoms_in_selection, clipper::Coord_orth &rotation_centre, clipper::RTop_orth &rtop) (defined in coot::molecule_t) | coot::molecule_t | |
| apply_user_defined_atom_colour_selections(const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also, mmdb::Manager *mol) (defined in coot::molecule_t) | coot::molecule_t | |
| assign_sequence(const clipper::Xmap< float > &xmap, const coot::protein_geometry &geom) | coot::molecule_t | |
| associate_data_mtz_file_with_map(const std::string &data_mtz_file_name, const std::string &f_col, const std::string &sigf_col, const std::string &r_free_col) (defined in coot::molecule_t) | coot::molecule_t | |
| associate_sequence_with_molecule(const std::string &chain_id, const std::string &sequence) (defined in coot::molecule_t) | coot::molecule_t | |
| atom_sel (defined in coot::molecule_t) | coot::molecule_t | |
| atoms_with_position_restraints (defined in coot::molecule_t) | coot::molecule_t | |
| auto_fit_rotamer(const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, const clipper::Xmap< float > &xmap, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| backrub_rotamer(mmdb::Residue *residue_p, const clipper::Xmap< float > &xmap, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| backrub_rotamer(const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, const clipper::Xmap< float > &xmap, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| base_colour_for_bonds (defined in coot::molecule_t) | coot::molecule_t | |
| blender_mesh (defined in coot::molecule_t) | coot::molecule_t | |
| chains_in_model() const (defined in coot::molecule_t) | coot::molecule_t | |
| change_alt_locs(const std::string &cid, const std::string &change_mode) (defined in coot::molecule_t) | coot::molecule_t | |
| change_chain_id(const std::string &from_chain_id, const std::string &to_chain_id, bool use_resno_range, int start_resno, int end_resno) (defined in coot::molecule_t) | coot::molecule_t | |
| change_chain_id_with_residue_range(const std::string &from_chain_id, const std::string &to_chain_id, int start_resno, int end_resno) (defined in coot::molecule_t) | coot::molecule_t | |
| change_chain_id_with_residue_range_helper_insert_or_add(mmdb::Chain *to_chain_p, mmdb::Residue *new_residue) (defined in coot::molecule_t) | coot::molecule_t | |
| change_rotamer_number(const coot::residue_spec_t &res_spec, const std::string &alt_conf, int rotamer_change_direction, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| change_to_first_rotamer(const coot::residue_spec_t &res_spec, const std::string &alt_conf, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| change_to_next_rotamer(const coot::residue_spec_t &res_spec, const std::string &alt_conf, const coot::protein_geometry &pg) | coot::molecule_t | |
| change_to_previous_rotamer(const coot::residue_spec_t &res_spec, const std::string &alt_conf, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| cid_to_atom(const std::string &cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| cid_to_atom_spec(const std::string &cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| cid_to_residue(const std::string &cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| cid_to_residue_spec(const std::string &cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| cid_to_residues(const std::string &cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| cis_trans_conversion(const std::string &atom_cid, mmdb::Manager *standard_residues_mol) (defined in coot::molecule_t) | coot::molecule_t | |
| clear_extra_restraints() (defined in coot::molecule_t) | coot::molecule_t | |
| clear_non_drawn_bonds() (defined in coot::molecule_t) | coot::molecule_t | inline |
| clear_refinement() | coot::molecule_t | |
| clear_target_position_restraint(const std::string &atom_cid) | coot::molecule_t | |
| clear_target_position_restraints() | coot::molecule_t | |
| close_yourself() (defined in coot::molecule_t) | coot::molecule_t | |
| colour_rules | coot::molecule_t | |
| contact_dots_for_ligand(const std::string &cid, const protein_geometry &geom, unsigned int num_subdivisions) const | coot::molecule_t | |
| copy_and_add_chain_residues_to_chain(mmdb::Chain *new_chain, mmdb::Chain *this_molecule_chain) (defined in coot::molecule_t) | coot::molecule_t | |
| copy_and_add_residue_to_chain(mmdb::Chain *this_model_chain, mmdb::Residue *add_model_residue, bool new_resno_by_hundreds_flag=true) (defined in coot::molecule_t) | coot::molecule_t | |
| copy_ncs_chain(const std::string &from_chain_id, const std::string &to_chain_id) | coot::molecule_t | |
| default_temperature_factor_for_new_atoms (defined in coot::molecule_t) | coot::molecule_t | |
| delete_all_carbohydrate() | coot::molecule_t | |
| delete_atom(atom_spec_t &atom_spec) (defined in coot::molecule_t) | coot::molecule_t | |
| delete_atoms(const std::vector< atom_spec_t > &atoms) (defined in coot::molecule_t) | coot::molecule_t | |
| delete_chain_using_atom_cid(const std::string &cid) (defined in coot::molecule_t) | coot::molecule_t | |
| delete_colour_rules() | coot::molecule_t | |
| delete_hydrogen_atoms() | coot::molecule_t | |
| delete_literal_using_cid(const std::string &cid) (defined in coot::molecule_t) | coot::molecule_t | |
| delete_residue(residue_spec_t &residue_spec) (defined in coot::molecule_t) | coot::molecule_t | |
| delete_residue_atoms_with_alt_conf(coot::residue_spec_t &residue_spec, const std::string &alt_conf) (defined in coot::molecule_t) | coot::molecule_t | |
| delete_side_chain(const residue_spec_t &residue_spec) (defined in coot::molecule_t) | coot::molecule_t | |
| difference_map_peaks(mmdb::Manager *mol, float n_rmsd) const (defined in coot::molecule_t) | coot::molecule_t | |
| draw_vector_sets_lock (defined in coot::molecule_t) | coot::molecule_t | static |
| eigen_flip_residue(const residue_spec_t &residue_spec) (defined in coot::molecule_t) | coot::molecule_t | |
| execute_simple_nucleotide_addition(const std::string &term_type, mmdb::Residue *res_p, const std::string &chain_id, mmdb::Manager *standard_residues_asc_mol) (defined in coot::molecule_t) | coot::molecule_t | |
| execute_simple_nucleotide_addition(mmdb::Residue *residue_p, mmdb::Manager *standard_residues_asc_mol) (defined in coot::molecule_t) | coot::molecule_t | |
| execute_simple_nucleotide_addition(const std::string &cid, mmdb::Manager *standard_residues_asc_mol) (defined in coot::molecule_t) | coot::molecule_t | |
| export_chemical_features_as_gltf(const std::string &cid, const protein_geometry &geom, const std::string &file_name) const (defined in coot::molecule_t) | coot::molecule_t | |
| export_map_molecule_as_gltf(clipper::Coord_orth &position, float radius, float contour_level, const std::string &file_name) | coot::molecule_t | |
| export_model_molecule_as_gltf(const std::string &mode, const std::string &selection_cid, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops, const std::string &file_name) | coot::molecule_t | |
| export_molecular_representation_as_gltf(const std::string &atom_selection_cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag, const std::string &file_name) (defined in coot::molecule_t) | coot::molecule_t | |
| extra_restraints (defined in coot::molecule_t) | coot::molecule_t | |
| fill_default_colour_rules() (defined in coot::molecule_t) | coot::molecule_t | |
| fill_fobs_sigfobs() (defined in coot::molecule_t) | coot::molecule_t | |
| fill_partial_residue(const residue_spec_t &res_spec, const std::string &alt_conf, const clipper::Xmap< float > &xmap, const protein_geometry &geom) | coot::molecule_t | |
| fill_partial_residues(const clipper::Xmap< float > &xmap, protein_geometry *geom) | coot::molecule_t | |
| fit_to_map_by_random_jiggle(const residue_spec_t &res_spec, const clipper::Xmap< float > &xmap, float map_rmsd, int n_trials, float translation_scale_factor) (defined in coot::molecule_t) | coot::molecule_t | |
| fit_to_map_by_random_jiggle_using_atom_selection(const std::string &cid, const clipper::Xmap< float > &xmap, float map_rmsd, int n_trials, float translation_scale_factor) | coot::molecule_t | |
| fix_atom_selection_during_refinement(const std::string &atom_selection_cid) (defined in coot::molecule_t) | coot::molecule_t | |
| flip_peptide(const atom_spec_t &rs, const std::string &alt_conf) (defined in coot::molecule_t) | coot::molecule_t | |
| generate_chain_self_restraints(float local_dist_max, const std::string &chain_id, const coot::protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| generate_local_self_restraints(float local_dist_max, const std::vector< coot::residue_spec_t > &residue_specs, const coot::protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| generate_local_self_restraints(float local_dist_max, const std::string &multi_selection_cid, const coot::protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| generate_local_self_restraints(int selHnd, float local_dist_max, const coot::protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| generate_self_restraints(float local_dist_max, const coot::protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| geometric_distortions_for_one_residue_from_mol(const std::string &ligand_cid, bool with_nbcs, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool) | coot::molecule_t | |
| geometric_distortions_for_selection_from_mol(const std::string &selection_cid, bool with_nbcs, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool) | coot::molecule_t | |
| get_atom(const atom_spec_t &atom_spec) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_atom_overlap_score(protein_geometry *geom_p) const | coot::molecule_t | |
| get_atom_overlaps(protein_geometry *geom_p) | coot::molecule_t | |
| get_bonds_mesh(const std::string &mode, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops) (defined in coot::molecule_t) | coot::molecule_t | |
| get_bonds_mesh_for_selection_instanced(const std::string &mode, const std::string &selection_cid, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, bool render_atoms_as_aniso, bool render_aniso_atoms_as_ortep, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops) (defined in coot::molecule_t) | coot::molecule_t | |
| get_bonds_mesh_instanced(const std::string &mode, protein_geometry *geom, bool against_a_dark_background, float bonds_width, float atom_radius_to_bond_width_ratio, bool render_atoms_as_aniso, float aniso_probability, bool render_aniso_atoms_as_ortep, int smoothness_factor, bool draw_hydrogen_atoms_flag, bool draw_missing_residue_loops) (defined in coot::molecule_t) | coot::molecule_t | |
| get_chain_ids() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_chemical_features_mesh(const std::string &cid, const protein_geometry &geom) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_colour_rules() const | coot::molecule_t | |
| get_colour_table_for_blender() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_density_at_position(const clipper::Coord_orth &pos) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_distances_between_atoms_of_residues(const std::string &cid_res_1, const std::string &cid_res_2, float dist_max) const | coot::molecule_t | |
| get_extra_restraints_mesh(int mode) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_fixed_atoms() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_gaussian_surface(float sigma, float contour_level, float box_radius, float grid_scale, float fft_b_factor) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_goodsell_style_mesh(protein_geometry *geom_p, float colour_wheel_rotation_step, float saturation, float goodselliness) (defined in coot::molecule_t) | coot::molecule_t | |
| get_goodsell_style_mesh_instanced(protein_geometry *geom_p, float colour_wheel_rotation_step, float saturation, float goodselliness) (defined in coot::molecule_t) | coot::molecule_t | |
| get_HOLE(const clipper::Coord_orth &start_pos, const clipper::Coord_orth &end_pos, const protein_geometry &geom) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_last_restraints() (defined in coot::molecule_t) | coot::molecule_t | inline |
| get_map_contours_mesh(clipper::Coord_orth position, float radius, float contour_level, bool use_thread_pool, ctpl::thread_pool *thread_pool_p) (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_contours_mesh_using_other_map_for_colours(const clipper::Coord_orth &position, float radius, float contour_level, const clipper::Xmap< float > &xmap) (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_contours_mesh_using_other_map_for_colours(const clipper::Coord_orth &position, float radius, float contour_level, const user_defined_colour_table_t &udct, const clipper::Xmap< float > &xmap) (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_histogram(unsigned int n_bins, float zoom_factor) const | coot::molecule_t | |
| get_map_mean() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_molecule_centre() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_rmsd_approx() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_section_texture(int section_index, int axis, float data_value_for_bottom, float data_value_for_top) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_map_vertices_histogram(const clipper::Xmap< float > &other_xmap, const clipper::Coord_orth &pt, float radius, float contour_level, bool use_thread_pool, ctpl::thread_pool *thread_pool_p, unsigned int n_bins) (defined in coot::molecule_t) | coot::molecule_t | |
| get_median_temperature_factor() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_mesh_for_ligand_validation_vs_dictionary(const std::string &ligand_cid, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool) | coot::molecule_t | |
| get_missing_residue_ranges() const | coot::molecule_t | |
| get_molecular_representation_mesh(const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondaryStructureUsageFlag) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_molecule_centre() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_molecule_diameter() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_molecule_index() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| get_molecule_selection_as_json(const std::string &cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_mutation_info() const | coot::molecule_t | |
| get_name() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| get_ncs_related_chains() const | coot::molecule_t | |
| get_non_standard_residues_in_molecule() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_number_of_atoms() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_number_of_hydrogen_atoms() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_number_of_map_sections(int axis_id) const | coot::molecule_t | |
| get_original_fobs_sigfobs() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| get_original_rfree_flags() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| get_overlap_dots(protein_geometry *geom_p) | coot::molecule_t | |
| get_overlap_dots_for_ligand(const std::string &cid_ligand, protein_geometry *geom_p) | coot::molecule_t | |
| get_overlaps_for_ligand(const std::string &cid_ligand, protein_geometry *geom_p) | coot::molecule_t | |
| get_pucker_analysis_info() const | coot::molecule_t | |
| get_radius_of_gyration() const | coot::molecule_t | |
| get_residue(const residue_spec_t &residue_spec) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_residue(const std::string &residue_cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_residue_average_position(const std::string &cid) const | coot::molecule_t | |
| get_residue_CA_position(const std::string &cid) const | coot::molecule_t | |
| get_residue_closest_to(mmdb::Manager *mol, const clipper::Coord_orth &co) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_residue_name(const residue_spec_t &residue_spec) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_residue_names_with_no_dictionary(const protein_geometry &geom) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_residue_sidechain_average_position(const std::string &cid) const | coot::molecule_t | |
| get_residue_types_without_dictionaries(const protein_geometry &geom) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_rotamer_dodecs(protein_geometry *geom_p, rotamer_probability_tables *rpt) (defined in coot::molecule_t) | coot::molecule_t | |
| get_rotamer_dodecs_instanced(protein_geometry *geom_p, rotamer_probability_tables *rpt) (defined in coot::molecule_t) | coot::molecule_t | |
| get_sequence_info() const | coot::molecule_t | |
| get_show_symmetry() (defined in coot::molecule_t) | coot::molecule_t | inline |
| get_simple_molecule(int imol, const std::string &residue_cid, const bool draw_hydrogen_atoms_flag, coot::protein_geometry *geom_p) | coot::molecule_t | |
| get_simple_molecule(int imol, mmdb::Residue *residue_p, bool draw_hydrogen_atoms_flag, coot::protein_geometry *geom_p) (defined in coot::molecule_t) | coot::molecule_t | |
| get_single_letter_codes_for_chain(const std::string &chain_id) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_suggested_initial_contour_level() const | coot::molecule_t | |
| get_svg_for_2d_ligand_environment_view(const std::string &residue_cid, protein_geometry *geom, bool add_key) const | coot::molecule_t | |
| get_symmetry(float symmetry_search_radius, const Cartesian &symm_centre) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_temperature_factor_of_atom(const std::string &atom_cid) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_torsion(const std::string &cid, const std::vector< std::string > &atom_names) const (defined in coot::molecule_t) | coot::molecule_t | |
| get_triangles_for_blender() const (defined in coot::molecule_t) | coot::molecule_t | |
| get_types_in_molecule() const | coot::molecule_t | |
| get_updating_maps_diff_diff_map_peaks(const clipper::Coord_orth &screen_centre) const | coot::molecule_t | |
| get_vertices_for_blender() const (defined in coot::molecule_t) | coot::molecule_t | |
| gltf_pbr_metalicity (defined in coot::molecule_t) | coot::molecule_t | |
| gltf_pbr_roughness (defined in coot::molecule_t) | coot::molecule_t | |
| have_unsaved_changes() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| hydrogen_atom_should_be_drawn() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| indexed_user_defined_colour_selection_cids (defined in coot::molecule_t) | coot::molecule_t | |
| indexed_user_defined_colour_selection_cids_apply_to_non_carbon_atoms_also (defined in coot::molecule_t) | coot::molecule_t | |
| init_all_molecule_refinement(int imol_ref_mol, coot::protein_geometry &geom, const clipper::Xmap< float > &xmap, float map_weight, ctpl::thread_pool *thread_pool) (defined in coot::molecule_t) | coot::molecule_t | |
| insert_waters_into_molecule(const minimol::molecule &water_mol, const std::string &res_name) (defined in coot::molecule_t) | coot::molecule_t | |
| is_closed() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| is_difference_map_p() const (defined in coot::molecule_t) | coot::molecule_t | |
| is_EM_map() const (defined in coot::molecule_t) | coot::molecule_t | |
| is_het_residue(mmdb::Residue *residue_p) const (defined in coot::molecule_t) | coot::molecule_t | |
| is_valid_map_molecule() const (defined in coot::molecule_t) | coot::molecule_t | |
| is_valid_model_molecule() const (defined in coot::molecule_t) | coot::molecule_t | |
| jed_flip(coot::residue_spec_t &spec, const std::string &atom_name, const std::string &alt_conf, bool invert_selection, protein_geometry *geom) (defined in coot::molecule_t) | coot::molecule_t | |
| jed_flip_internal(coot::atom_tree_t &tree, const std::vector< coot::dict_torsion_restraint_t > &interesting_torsions, const std::string &atom_name, bool invert_selection) (defined in coot::molecule_t) | coot::molecule_t | |
| jed_flip_internal(coot::atom_tree_t &tree, const dict_torsion_restraint_t &torsion, const std::string &atom_name, bool invert_selection) (defined in coot::molecule_t) | coot::molecule_t | |
| M2T_float_params (defined in coot::molecule_t) | coot::molecule_t | |
| M2T_int_params (defined in coot::molecule_t) | coot::molecule_t | |
| M2T_updateFloatParameter(const std::string ¶m_name, float value) | coot::molecule_t | |
| M2T_updateFloatParameter(const std::string ¶m_name, int value) | coot::molecule_t | |
| M2T_updateIntParameter(const std::string ¶m_name, int value) | coot::molecule_t | |
| make_bonds(protein_geometry *geom, rotamer_probability_tables *rot_prob_tables_p, bool draw_hydrogen_atoms_flag, bool draw_missing_loops_flag) (defined in coot::molecule_t) | coot::molecule_t | |
| make_colour_table(bool against_a_dark_background) const | coot::molecule_t | |
| make_colour_table_for_goodsell_style(float colour_wheel_rotation_step, float saturation, float goodselliness) const (defined in coot::molecule_t) | coot::molecule_t | |
| make_exportable_environment_bond_box(coot::residue_spec_t &spec, float max_dist, coot::protein_geometry &geom) const (defined in coot::molecule_t) | coot::molecule_t | |
| make_import_datanames(const std::string &fcol, const std::string &phi_col, const std::string &weight_col, int use_weights) const (defined in coot::molecule_t) | coot::molecule_t | |
| make_mesh_for_bonds_for_blender(const std::string &mode, protein_geometry *geom, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor) (defined in coot::molecule_t) | coot::molecule_t | |
| make_mesh_for_gaussian_surface_for_blender(float sigma, float contour_level, float box_radius, float grid_scale, float b_factor) (defined in coot::molecule_t) | coot::molecule_t | |
| make_mesh_for_goodsell_style_for_blender(protein_geometry *geom_p, float colour_wheel_rotation_step, float saturation, float goodselliness) (defined in coot::molecule_t) | coot::molecule_t | |
| make_mesh_for_map_contours_for_blender(Cartesian position, float contour_level, float radius) (defined in coot::molecule_t) | coot::molecule_t | |
| make_mesh_for_molecular_representation_for_blender(const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag) | coot::molecule_t | |
| map_chains_to_new_chains(const std::vector< std::string > &adding_model_chains, const std::vector< std::string > &this_model_chains) const (defined in coot::molecule_t) | coot::molecule_t | |
| match_torsions(mmdb::Residue *res_ref, const std::vector< coot::dict_torsion_restraint_t > &tr_ligand, const coot::protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| merge_ligand_to_near_chain(mmdb::Manager *mol) (defined in coot::molecule_t) | coot::molecule_t | |
| merge_molecules(const std::vector< mmdb::Manager * > &mols) | coot::molecule_t | |
| merge_molecules(const std::vector< atom_selection_container_t > &add_molecules) (defined in coot::molecule_t) | coot::molecule_t | |
| merge_molecules_just_one_residue_at_given_spec(atom_selection_container_t molecule_to_add, residue_spec_t target_spec) (defined in coot::molecule_t) | coot::molecule_t | |
| merge_molecules_just_one_residue_homogeneous(atom_selection_container_t molecule_to_add) (defined in coot::molecule_t) | coot::molecule_t | |
| minimize(const std::string &atom_selection_cid, int n_cycles, bool do_rama_plot_restraints, float rama_plot_weight, bool do_torsion_restraints, float torsion_weight, bool refinement_is_quiet, coot::protein_geometry *geom_p) (defined in coot::molecule_t) | coot::molecule_t | |
| molecule_t(const std::string &name_in, int mol_no_in) | coot::molecule_t | inline |
| molecule_t(const std::string &name_in, int mol_no_in, short int is_em_map) | coot::molecule_t | inline |
| molecule_t(const std::string &name_in, int mol_no_in, const clipper::Xmap< float > &xmap_in, bool is_em_map_flag) | coot::molecule_t | inline |
| molecule_t(atom_selection_container_t asc, int imol_no_in, const std::string &name_in) | coot::molecule_t | inlineexplicit |
| molecule_to_mmCIF_string() const | coot::molecule_t | |
| molecule_to_PDB_string() const | coot::molecule_t | |
| move_molecule_to_new_centre(const coot::Cartesian &new_centre) (defined in coot::molecule_t) | coot::molecule_t | |
| multiply_residue_temperature_factors(const std::string &cid, float factor) | coot::molecule_t | |
| mutate(const residue_spec_t &spec, const std::string &new_res_type) (defined in coot::molecule_t) | coot::molecule_t | |
| mutate_by_overlap(mmdb::Residue *residue_p, const dictionary_residue_restraints_t &restraints) (defined in coot::molecule_t) | coot::molecule_t | |
| neighbouring_residues (defined in coot::molecule_t) | coot::molecule_t | |
| new_positions_for_atoms_in_residues(const std::vector< api::moved_residue_t > &moved_residues) | coot::molecule_t | |
| new_positions_for_residue_atoms(const std::string &residue_cid, const std::vector< api::moved_atom_t > &moved_atoms) | coot::molecule_t | |
| new_positions_for_residue_atoms(mmdb::Residue *residue_p, const std::vector< api::moved_atom_t > &moved_atoms, bool do_backup) | coot::molecule_t | |
| next_residue_number_in_chain(mmdb::Chain *w, bool new_res_no_by_hundreds=false) const (defined in coot::molecule_t) | coot::molecule_t | |
| no_bonds_to_these_atom_indices (defined in coot::molecule_t) | coot::molecule_t | |
| non_standard_residue_types_in_model() const (defined in coot::molecule_t) | coot::molecule_t | |
| nucelotide_residue_name_to_base_atom_names(const std::string &rn) const (defined in coot::molecule_t) | coot::molecule_t | |
| peptide_omega_analysis(const protein_geometry &geom, const std::string &chain_id, bool mark_cis_peptides_as_bad_flag) const (defined in coot::molecule_t) | coot::molecule_t | |
| print_colour_rules() const (defined in coot::molecule_t) | coot::molecule_t | |
| print_colour_table(const std::string &debugging_label) const (defined in coot::molecule_t) | coot::molecule_t | |
| print_M2T_FloatParameters() const (defined in coot::molecule_t) | coot::molecule_t | |
| print_M2T_IntParameters() const (defined in coot::molecule_t) | coot::molecule_t | |
| print_non_drawn_bonds() const (defined in coot::molecule_t) | coot::molecule_t | |
| print_secondary_structure_info() const (defined in coot::molecule_t) | coot::molecule_t | |
| ramachandran_validation(const ramachandrans_container_t &rc) const (defined in coot::molecule_t) | coot::molecule_t | |
| rdkit_mol(const std::string &ligand_cid) | coot::molecule_t | |
| read_extra_restraints(const std::string &file_name) | coot::molecule_t | |
| redo() (defined in coot::molecule_t) | coot::molecule_t | |
| refine_direct(std::vector< mmdb::Residue * > rv, const std::string &alt_loc, const clipper::Xmap< float > &xmap, unsigned int max_number_of_threads, float map_weight, int n_cycles, const coot::protein_geometry &geom, bool do_rama_plot_restraints, float rama_plot_weight, bool do_torsion_restraints, float torsion_weight, bool refinement_is_quiet) | coot::molecule_t | |
| refine_using_last_restraints(int n_steps) | coot::molecule_t | |
| Refmac_fobs_col() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| refmac_fobs_col (defined in coot::molecule_t) | coot::molecule_t | |
| Refmac_mtz_filename() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| refmac_mtz_filename (defined in coot::molecule_t) | coot::molecule_t | |
| refmac_r_free_col (defined in coot::molecule_t) | coot::molecule_t | |
| refmac_r_free_flag_sensible (defined in coot::molecule_t) | coot::molecule_t | |
| Refmac_sigfobs_col() const (defined in coot::molecule_t) | coot::molecule_t | inline |
| refmac_sigfobs_col (defined in coot::molecule_t) | coot::molecule_t | |
| replace_fragment(atom_selection_container_t asc) | coot::molecule_t | |
| replace_fragment(mmdb::Manager *mol_ref, int old_atom_index_handle, int SelHnd) (defined in coot::molecule_t) | coot::molecule_t | |
| replace_molecule_by_model_from_file(const std::string &pdb_file_name) (defined in coot::molecule_t) | coot::molecule_t | |
| replace_residue(const std::string &residue_cid, const std::string &new_residue_type, int imol_enc, const protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| residue_is_nucleic_acid(const std::string &cid) const | coot::molecule_t | |
| residue_name_to_plane_atom_names(const std::string &rn) const (defined in coot::molecule_t) | coot::molecule_t | |
| residues_near_residue(const std::string &residue_cid, float dist) const | coot::molecule_t | |
| rigid_body_fit(const std::string &mult_cids, const clipper::Xmap< float > &xmap) (defined in coot::molecule_t) | coot::molecule_t | |
| rotate_around_bond(const std::string &residue_cid, const std::string &alt_conf, coot::atom_name_quad quad, double torsion_angle, protein_geometry &geom) (defined in coot::molecule_t) | coot::molecule_t | |
| scale_map(float scale_factor) (defined in coot::molecule_t) | coot::molecule_t | |
| select_residues(const residue_spec_t &spec, const std::string &mode) const | coot::molecule_t | |
| select_residues(const std::string &chain_id, int resno_start, int resno_end) const | coot::molecule_t | |
| select_residues(const std::string &multi_cid, const std::string &mode) const | coot::molecule_t | |
| set_base_colour_for_bonds(float r, float g, float b) | coot::molecule_t | |
| set_bespoke_carbon_atom_colour(const colour_t &col) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_colour_wheel_rotation_base(float r) | coot::molecule_t | |
| set_map_colour(colour_holder holder) (defined in coot::molecule_t) | coot::molecule_t | |
| set_map_colour_saturation(float s) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_map_is_difference_map(bool flag) (defined in coot::molecule_t) | coot::molecule_t | |
| set_molecule_name(const std::string &n) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_occupancy(const std::string &cid, float occ_new) | coot::molecule_t | |
| set_other_map_for_colouring_invert_colour_ramp(bool state) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_other_map_for_colouring_min_max(float min_v, float max_v) | coot::molecule_t | |
| set_really_do_backups(bool state) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_residue_to_rotamer_number(coot::residue_spec_t res_spec, const std::string &alt_conf_in, int rotamer_number, const coot::protein_geometry &pg) (defined in coot::molecule_t) | coot::molecule_t | |
| set_show_symmetry(bool f) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_temperature_factors_using_cid(const std::string &cid, float temp_fact) (defined in coot::molecule_t) | coot::molecule_t | |
| set_updating_maps_diff_diff_map_peaks(const std::vector< std::pair< clipper::Coord_orth, float > > &v) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_use_bespoke_carbon_atom_colour(bool state) (defined in coot::molecule_t) | coot::molecule_t | inline |
| set_user_defined_atom_colour_by_selections(const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also, mmdb::Manager *mol) | coot::molecule_t | |
| set_user_defined_bond_colours(const std::map< unsigned int, std::array< float, 4 > > &colour_map) | coot::molecule_t | |
| sfcalc_genmap(const clipper::HKL_data< clipper::data32::F_sigF > &fobs, const clipper::HKL_data< clipper::data32::Flag > &free, clipper::Xmap< float > *xmap_p) (defined in coot::molecule_t) | coot::molecule_t | |
| sfcalc_genmaps_using_bulk_solvent(const clipper::HKL_data< clipper::data32::F_sigF > &fobs, const clipper::HKL_data< clipper::data32::Flag > &free, clipper::Xmap< float > *xmap_2fofc_p, clipper::Xmap< float > *xmap_fofc_p) (defined in coot::molecule_t) | coot::molecule_t | |
| shiftfield_b_factor_refinement(const clipper::HKL_data< clipper::data32::F_sigF > &F_sigF, const clipper::HKL_data< clipper::data32::Flag > &free_flag) (defined in coot::molecule_t) | coot::molecule_t | |
| side_chain_180(const residue_spec_t &residue_spec, const std::string &alt_conf, coot::protein_geometry *geom_p) (defined in coot::molecule_t) | coot::molecule_t | |
| simple_geometric_distortions_from_mol(const std::string &ligand_cid, bool with_nbcs, coot::protein_geometry &geom, ctpl::thread_pool &static_thread_pool) (defined in coot::molecule_t) | coot::molecule_t | |
| store_user_defined_atom_colour_selections(const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also) (defined in coot::molecule_t) | coot::molecule_t | |
| suggest_new_chain_id(const std::string ¤t_chain_id) const (defined in coot::molecule_t) | coot::molecule_t | |
| sum_density_for_atoms_in_residue(const std::string &cid, const std::vector< std::string > &atom_names, const clipper::Xmap< float > &xmap) const (defined in coot::molecule_t) | coot::molecule_t | |
| transform_by(mmdb::mat44 SSMAlign_TMatrix) (defined in coot::molecule_t) | coot::molecule_t | |
| transform_by(const clipper::RTop_orth &rtop, mmdb::Residue *res) (defined in coot::molecule_t) | coot::molecule_t | |
| transform_by(const clipper::RTop_orth &rtop) (defined in coot::molecule_t) | coot::molecule_t | |
| try_add_by_consolidation(mmdb::Manager *adding_mol) (defined in coot::molecule_t) | coot::molecule_t | |
| turn_off_when_close_target_position_restraint() (defined in coot::molecule_t) | coot::molecule_t | |
| undo() (defined in coot::molecule_t) | coot::molecule_t | |
| updating_maps_diff_diff_map_peaks (defined in coot::molecule_t) | coot::molecule_t | |
| updating_maps_previous_difference_map (defined in coot::molecule_t) | coot::molecule_t | |
| user_defined_bond_colours (defined in coot::molecule_t) | coot::molecule_t | |
| write_coordinates(const std::string &file_name) const (defined in coot::molecule_t) | coot::molecule_t | |
| write_map(const std::string &file_name) const (defined in coot::molecule_t) | coot::molecule_t | |
| xmap (defined in coot::molecule_t) | coot::molecule_t |
1.13.2