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molecules_container_t Member List

This is the complete list of members for molecules_container_t, including all inherited members.

accept_rotamer_probability_tables_compressed_data(const std::string &data_stream)molecules_container_t
add_alternative_conformation(int imol_model, const std::string &cid)molecules_container_t
add_colour_rule(int imol, const std::string &selection_cid, const std::string &colour)molecules_container_t
add_colour_rules_multi(int imol, const std::string &selections_and_colours_combo_string)molecules_container_t
add_compound(int imol, const std::string &tlc, int imol_dict, int imol_map, float x, float y, float z)molecules_container_t
add_hydrogen_atoms(int imol_model)molecules_container_t
add_lsq_superpose_atom_match(const std::string &chain_id_ref, int res_no_ref, const std::string &atom_name_ref, const std::string &chain_id_mov, int res_no_mov, const std::string &atom_name_mov)molecules_container_t
add_lsq_superpose_match(const std::string &chain_id_ref, int res_no_ref_start, int res_no_ref_end, const std::string &chain_id_mov, int res_no_mov_start, int res_no_mov_end, int match_type)molecules_container_t
add_named_glyco_tree(int imol_model, int imol_map, const std::string &glycosylation_name, const std::string &asn_chain_id, int asn_res_no)molecules_container_t
add_parallel_plane_restraint(int imol, const std::string &residue_cid_1, const std::string &residue_cid_2)molecules_container_t
add_target_position_restraint(int imol, const std::string &atom_cid, float pos_x, float pos_y, float pos_z)molecules_container_t
add_target_position_restraint_and_refine(int imol, const std::string &atom_cid, float pos_x, float pos_y, float pos_z, int n_cycles)molecules_container_t
add_terminal_residue_directly(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)molecules_container_t
add_terminal_residue_directly_using_bucca_ml_growing(int imol, const coot::residue_spec_t &spec)molecules_container_t
add_terminal_residue_directly_using_bucca_ml_growing_using_cid(int imol, const std::string &cid)molecules_container_t
add_terminal_residue_directly_using_cid(int imol, const std::string &cid)molecules_container_t
add_to_non_drawn_bonds(int imol, const std::string &atom_selection_cid)molecules_container_t
add_waters(int imol_model, int imol_map)molecules_container_t
all_molecule_contact_dots(int imol, unsigned int smoothness_factor) constmolecules_container_t
apply_transformation_to_atom_selection(int imol, const std::string &atoms_selection_cid, int n_atoms, float m00, float m01, float m02, float m10, float m11, float m12, float m20, float m21, float m22, float c0, float c1, float c2, float t0, float t1, float t2)molecules_container_t
assign_sequence(int imol_model, int imol_map)molecules_container_t
associate_data_mtz_file_with_map(int imol, const std::string &data_mtz_file_name, const std::string &f_col, const std::string &sigf_col, const std::string &free_r_col)molecules_container_t
associate_sequence(int imol, const std::string &name_or_chain_id, const std::string &sequence)molecules_container_t
atom_cid_to_atom_spec(int imol, const std::string &cid) constmolecules_container_t
auto_fit_rotamer(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, int imol_map)molecules_container_t
auto_read_mtz(const std::string &file_name)molecules_container_t
average_map(const std::string &imol_maps, std::vector< float > &scales)molecules_container_t
calculate_new_rail_points()molecules_container_t
change_alt_locs(int imol, const std::string &cid, const std::string &change_mode)molecules_container_t
change_chain_id(int imol, const std::string &from_chain_id, const std::string &to_chain_id, bool use_resno_range, int start_resno, int end_resno)molecules_container_t
change_to_first_rotamer(int imol, const std::string &residue_cid, const std::string &alt_conf)molecules_container_t
change_to_next_rotamer(int imol, const std::string &residue_cid, const std::string &alt_conf)molecules_container_t
change_to_previous_rotamer(int imol, const std::string &residue_cid, const std::string &alt_conf)molecules_container_t
cis_trans_convert(int imol, const std::string &atom_cid)molecules_container_t
clear()molecules_container_t
clear_extra_restraints(int imol)molecules_container_t
clear_lsq_matches()molecules_container_t
clear_non_drawn_bonds(int imol)molecules_container_t
clear_refinement(int imol)molecules_container_t
clear_target_position_restraint(int imol, const std::string &atom_cid)molecules_container_t
clear_target_position_restraints(int imol)molecules_container_t
close_molecule(int imol)molecules_container_t
colour_map_by_other_map_user_defined_table (defined in molecules_container_t)molecules_container_t
connect_updating_maps(int imol_model, int imol_with_data_info_attached, int imol_map_2fofc, int imol_map_fofc)molecules_container_t
contact_dots_for_ligand(int imol, const std::string &cid, unsigned int smoothness_factor) constmolecules_container_t
contains_unsaved_models() constmolecules_container_t
copy_dictionary(const std::string &monomer_name, int imol_current, int imol_new)molecules_container_t
copy_fragment_for_refinement_using_cid(int imol, const std::string &multi_cid)molecules_container_t
copy_fragment_using_cid(int imol, const std::string &multi_cid)molecules_container_t
copy_fragment_using_residue_range(int imol, const std::string &chain_id, int res_no_start, int res_no_end)molecules_container_t
copy_molecule(int imol)molecules_container_t
create_empty_molecules(unsigned int n_empty)molecules_container_t
dedust_map(int imol)molecules_container_t
delete_all_carbohydrate(int imol)molecules_container_t
delete_atom(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &atom_name, const std::string &alt_conf)molecules_container_t
delete_atom_using_cid(int imol, const std::string &cid)molecules_container_t
delete_chain_using_cid(int imol, const std::string &cid)molecules_container_t
delete_colour_rules(int imol)molecules_container_t
delete_hydrogen_atoms(int imol_model)molecules_container_t
delete_literal_using_cid(int imol, const std::string &cid)molecules_container_t
delete_residue(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)molecules_container_t
delete_residue_atoms_using_cid(int imol, const std::string &cid)molecules_container_t
delete_residue_atoms_with_alt_conf(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf)molecules_container_t
delete_residue_using_cid(int imol, const std::string &cid)molecules_container_t
delete_side_chain(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)molecules_container_t
delete_side_chain_using_cid(int imol, const std::string &cid)molecules_container_t
delete_using_cid(int imol, const std::string &cid, const std::string &scope)molecules_container_t
density_correlation_analysis(int imol_model, int imol_map) constmolecules_container_t
density_fit_analysis(int imol_model, int imol_map) constmolecules_container_t
dictionary_atom_name_map(const std::string &comp_id_1, int imol_1, const std::string &comp_id_2, int imol_2)molecules_container_t
difference_map_peaks(int imol_map, int imol_protein, float n_rmsd) constmolecules_container_t
display_molecule_names_table() constmolecules_container_t
eigen_flip_ligand(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)molecules_container_t
eigen_flip_ligand_using_cid(int imol, const std::string &residue_cid)molecules_container_t
end_delete_closed_molecules()molecules_container_t
export_chemical_features_as_gltf(int imol, const std::string &cid, const std::string &file_name) constmolecules_container_t
export_map_molecule_as_gltf(int imol, float pos_x, float pos_y, float pos_z, float radius, float contour_level, const std::string &file_name)molecules_container_t
export_model_molecule_as_gltf(int imol, const std::string &selection_cid, const std::string &mode, 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)molecules_container_t
export_molecular_representation_as_gltf(int imol, 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)molecules_container_t
file_name_to_string(const std::string &file_name) constmolecules_container_t
fill_partial_residue(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)molecules_container_t
fill_partial_residue_using_cid(int imol, const std::string &cid)molecules_container_t
fill_partial_residues(int imol)molecules_container_t
fill_rotamer_probability_tables()molecules_container_t
find_water_baddies(int imol_model, int imol_map, float b_factor_lim, float outlier_sigma_level, float min_dist, float max_dist, bool ignore_part_occ_contact_flag, bool ignore_zero_occ_flag)molecules_container_t
fit_ligand(int imol_protein, int imol_map, int imol_ligand, float n_rmsd, bool use_conformers, unsigned int n_conformers)molecules_container_t
fit_ligand_multi_ligand(int imol_protein, int imol_map, const std::string &multi_ligand_molecule_number_list, float n_rmsd, bool use_conformers, unsigned int n_conformers)molecules_container_t
fit_ligand_right_here(int imol_protein, int imol_map, int imol_ligand, float x, float y, float z, float n_rmsd, bool use_conformers, unsigned int n_conformers)molecules_container_t
fit_to_map_by_random_jiggle(int imol, const coot::residue_spec_t &res_spec, int n_trials, float translation_scale_factor)molecules_container_t
fit_to_map_by_random_jiggle_using_cid(int imol, const std::string &cid, int n_trials, float translation_scale_factor)molecules_container_t
fit_to_map_by_random_jiggle_with_blur_using_cid(int imol, int imol_map, const std::string &cid, float b_factor, int n_trials, float translation_scale_factor)molecules_container_t
fix_atom_selection_during_refinement(int imol, const std::string &atom_selection_cid)molecules_container_t
flip_hand(int imol_map)molecules_container_t
flip_peptide_using_cid(int imol, const std::string &atom_cid, const std::string &alt_conf)molecules_container_t
flood(int imol_model, int imol_map, float n_rmsd)molecules_container_t
fourier_shell_correlation(int imol_map_1, int imol_map_2) constmolecules_container_t
generate_chain_self_restraints(int imol, float local_dist_max, const std::string &chain_id)molecules_container_t
generate_local_self_restraints(int imol, float local_dist_max, const std::string &residue_cids)molecules_container_t
generate_self_restraints(int imol, float local_dist_max)molecules_container_t
geometry_init_standard()molecules_container_t
get_acedrg_atom_types(const std::string &compound_id, int imol_enc) constmolecules_container_t
get_acedrg_atom_types_for_ligand(int imol, const std::string &residue_cid) constmolecules_container_t
get_active_atom(float x, float y, float z, const std::string &displayed_model_molecules_list) constmolecules_container_t
get_atom_differences(int imol1, int imol2)molecules_container_t
get_atom_overlap_score(int imol)molecules_container_t
get_atom_overlaps(int imol)molecules_container_t
get_atom_using_cid(int imol, const std::string &cid) constmolecules_container_t
get_bonds_mesh(int imol, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor)molecules_container_t
get_bonds_mesh_for_selection_instanced(int imol, const std::string &atom_selection_cid, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, bool show_atoms_as_aniso_flag, bool show_aniso_atoms_as_ortep_flag, bool draw_hydrogen_atoms_flag, int smoothness_factor)molecules_container_t
get_bonds_mesh_instanced(int imol, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, bool show_atoms_as_aniso_flag, bool show_aniso_atoms_as_ortep_flag, bool draw_hydrogen_atoms_flag, int smoothness_factor)molecules_container_t
get_cell(int imol) constmolecules_container_t
get_chains_in_model(int imol) constmolecules_container_t
get_chemical_features_mesh(int imol, const std::string &cid) constmolecules_container_t
get_cif_file_name(const std::string &comp_id, int imol_enc) constmolecules_container_t
get_cif_restraints_as_string(const std::string &comp_id, int imol_enc) constmolecules_container_t
get_colour_rules(int imol) constmolecules_container_t
get_colour_table(int imol, bool against_a_dark_background) constmolecules_container_t
get_colour_table_for_blender(int imol)molecules_container_t
get_contouring_time() constmolecules_container_tinline
get_data_set_file_name(int imol) constmolecules_container_t
get_density_at_position(int imol_map, float x, float y, float z) constmolecules_container_t
get_dictionary_conformers(const std::string &comp_id, int imol_enc, bool remove_internal_clash_conformers)molecules_container_t
get_diff_diff_map_peaks(int imol_diff_map, float screen_centre_x, float screen_centre_y, float screen_centre_z) constmolecules_container_t
get_distances_between_atoms_of_residues(int imol, const std::string &cid_res_1, const std::string &cid_res_2, float dist_max) constmolecules_container_t
get_eigenvalues(int imol, const std::string &chain_id, int res_no, const std::string &ins_code)molecules_container_t
get_extra_restraints_mesh(int imol, int mode)molecules_container_t
get_gaussian_surface(int imol, float sigma, float contour_level, float box_radius, float grid_scale, float b_factor) constmolecules_container_t
get_geman_mcclure_alpha() constmolecules_container_tinline
get_goodsell_style_mesh_instanced(int imol, float colour_wheel_rotation_step, float saturation, float goodselliness)molecules_container_t
get_gphl_chem_comp_info(const std::string &compound_id, int imol_enc)molecules_container_t
get_group_for_monomer(const std::string &residue_name) constmolecules_container_t
get_groups_for_monomers(const std::vector< std::string > &residue_names) constmolecules_container_t
get_h_bonds(int imol, const std::string &cid_str, bool mcdonald_and_thornton_mode) constmolecules_container_t
get_hb_type(const std::string &compound_id, int imol_enc, const std::string &atom_name) constmolecules_container_t
get_header_info(int imol) constmolecules_container_t
get_HOLE(int imol, float start_pos_x, float start_pos_y, float start_pos_z, float end_pos_x, float end_pos_y, float end_pos_z) constmolecules_container_t
get_imol_enc_any() constmolecules_container_t
get_interesting_places(int imol, const std::string &mode) constmolecules_container_t
get_latest_sfcalc_stats() constmolecules_container_tinline
get_ligand_distortion(int imol, const std::string &ligand_cid, bool include_non_bonded_contacts)molecules_container_t
get_ligand_validation_vs_dictionary(int imol, const std::string &ligand_cid, bool include_non_bonded_contacts)molecules_container_t
get_lsq_matrix(int imol_ref, int imol_mov, bool summary_to_screen) constmolecules_container_t
get_make_backups() constmolecules_container_tinline
get_map_contours_mesh(int imol, double position_x, double position_y, double position_z, float radius, float contour_level)molecules_container_t
get_map_contours_mesh_using_other_map_for_colours(int imol_ref, int imol_map_for_colouring, double position_x, double position_y, double position_z, float radius, float contour_level, float other_map_for_colouring_min_value, float other_map_for_colouring_max_value, bool invert_colour_ramp)molecules_container_t
get_map_histogram(int imol, unsigned int n_bins, float zoom_factor) constmolecules_container_t
get_map_mean(int imol) constmolecules_container_t
get_map_molecule_centre(int imol) constmolecules_container_t
get_map_rmsd_approx(int imol_map) constmolecules_container_t
get_map_sampling_rate()molecules_container_tinline
get_map_section_texture(int imol, int section_id, int axis, float data_value_for_bottom, float data_value_for_top) constmolecules_container_t
get_map_vertices_histogram(int imol, int imol_map_for_sampling, double position_x, double position_y, double position_z, float radius, float contour_level, unsigned int n_bins)molecules_container_t
get_map_weight() constmolecules_container_tinline
get_max_number_of_simple_mesh_vertices() const (defined in molecules_container_t)molecules_container_t
get_mean_and_variance_of_density_for_non_water_atoms(int imol_coords, int imol_map) constmolecules_container_t
get_median_temperature_factor(int imol) constmolecules_container_t
get_mesh_for_ligand_validation_vs_dictionary(int imol, const std::string &ligand_cid)molecules_container_t
get_missing_residue_ranges(int imol) constmolecules_container_t
get_mmrrcc(int imol, const std::string &chain_id, unsigned int n_residue_per_residue_range, int imol_map) constmolecules_container_t
get_molecular_representation_mesh(int imol, const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag)molecules_container_t
get_molecule_centre(int imol) constmolecules_container_t
get_molecule_diameter(int imol) constmolecules_container_t
get_molecule_name(int imol) constmolecules_container_t
get_molecule_selection_as_json(int imol, const std::string &cid) constmolecules_container_t
get_monomer(const std::string &monomer_name)molecules_container_t
get_monomer_and_position_at(const std::string &comp_id, int imol, float x, float y, float z)molecules_container_t
get_monomer_from_dictionary(const std::string &comp_id, int imol, bool idealised_flag)molecules_container_t
get_mutation_info(int imol) constmolecules_container_t
get_ncs_related_chains(int imol) constmolecules_container_t
get_non_standard_residues_in_molecule(int imol) constmolecules_container_t
get_number_of_atoms(int imol) constmolecules_container_t
get_number_of_atoms_in_residue(int imol, const std::string &residue_cid) constmolecules_container_t
get_number_of_hydrogen_atoms(int imol) constmolecules_container_t
get_number_of_map_sections(int imol_map, int axis_id) constmolecules_container_t
get_number_of_molecules() constmolecules_container_tinline
get_octahemisphere(unsigned int n_divisions) constmolecules_container_t
get_overlap_dots(int imol)molecules_container_t
get_overlap_dots_for_ligand(int imol, const std::string &cid_ligand)molecules_container_t
get_overlaps_for_ligand(int imol, const std::string &cid_ligand)molecules_container_t
get_pucker_analysis_info(int imol) constmolecules_container_t
get_q_score(int imol_model, int imol_map) constmolecules_container_t
get_q_score_for_cid(int imol_model, const std::string &cid, int imol_map) constmolecules_container_t
get_r_factor_stats()molecules_container_t
get_radius_of_gyration(int imol) constmolecules_container_t
get_rama_plot_restraints_weight() constmolecules_container_tinline
get_ramachandran_validation_markup_mesh(int imol) constmolecules_container_t
get_rdkit_mol_pickle_base64(const std::string &residue_name, int imol_enc)molecules_container_t
get_residue_average_position(int imol, const std::string &cid) constmolecules_container_t
get_residue_CA_position(int imol, const std::string &cid) constmolecules_container_t
get_residue_name(int imol, const std::string &chain_id, int res_no, const std::string &ins_code) constmolecules_container_t
get_residue_names_with_no_dictionary(int imol) constmolecules_container_t
get_residue_sidechain_average_position(int imol, const std::string &cid) constmolecules_container_t
get_residue_type(int imol, const std::string &cid) constmolecules_container_t
get_residue_using_cid(int imol, const std::string &cid) constmolecules_container_t
get_residues_near_residue(int imol, const std::string &residue_cid, float dist) constmolecules_container_t
get_rotamer_dodecs(int imol)molecules_container_t
get_rotamer_dodecs_instanced(int imol)molecules_container_t
get_sequence_info(int imol) constmolecules_container_t
get_simple_molecule(int imol, const std::string &residue_cid, bool draw_hydrogen_atoms_flag)molecules_container_t
get_single_letter_codes_for_chain(int imol, const std::string &chain_id) constmolecules_container_t
get_SMILES_for_residue_type(const std::string &residue_name, int imol_enc) constmolecules_container_t
get_spherical_variance(int imol_map, int imol_model, const std::string &atom_cid, float mean_density_other_atoms) constmolecules_container_t
get_suggested_initial_contour_level(int imol) constmolecules_container_t
get_sum_density_for_atoms_in_residue(int imol, const std::string &cid, const std::vector< std::string > &atom_names, int imol_map)molecules_container_t
get_svg_for_2d_ligand_environment_view(int imol, const std::string &residue_cid, bool add_key)molecules_container_t
get_svg_for_residue_type(int imol, const std::string &comp_id, bool use_rdkit_svg, const std::string &background_type)molecules_container_t
get_symmetry(int imol, float symmetry_search_radius, float centre_x, float centre_y, float centre_z) constmolecules_container_t
get_temperature_factor_of_atom(int imol, const std::string &atom_cid) constmolecules_container_t
get_torsion(int imol, const std::string &cid, const std::vector< std::string > &atom_names)molecules_container_t
get_torsion_restraints_weight() constmolecules_container_tinline
get_triangles_for_blender(int imol)molecules_container_t
get_types_in_molecule(int imol) constmolecules_container_t
get_use_gemmi()molecules_container_tinline
get_use_rama_plot_restraints() constmolecules_container_tinline
get_use_torsion_restraints() constmolecules_container_tinline
get_validation_vs_dictionary_for_selection(int imol, const std::string &selection_cid, bool include_non_bonded_contacts)molecules_container_t
get_vertices_for_blender(int imol)molecules_container_t
go_to_blob(float x1, float y1, float z1, float x2, float y2, float z2, float contour_level)molecules_container_t
imol_difference_mapmolecules_container_t
imol_refinement_mapmolecules_container_t
import_cif_dictionary(const std::string &cif_file_name, int imol_enc)molecules_container_t
init_refinement_of_molecule_as_fragment_based_on_reference(int imol_frag, int imol_ref, int imol_map)molecules_container_t
interrupt_long_term_job (defined in molecules_container_t)molecules_container_t
is_a_difference_map(int imol_map) constmolecules_container_t
is_EM_map(int imol) constmolecules_container_t
is_valid_map_molecule(int imol_map) constmolecules_container_t
is_valid_model_molecule(int imol) constmolecules_container_t
jed_flip(int imol, const std::string &atom_cid, bool invert_selection)molecules_container_t
long_term_job_statsmolecules_container_t
lsq_matchers (defined in molecules_container_t)molecules_container_t
lsq_superpose(int imol_ref, int imol_mov)molecules_container_t
M2T_updateFloatParameter(int imol, const std::string &param_name, float value)molecules_container_t
M2T_updateIntParameter(int imol, const std::string &param_name, int value)molecules_container_t
make_backups_flagmolecules_container_t
make_ensemble(const std::string &model_molecules_list)molecules_container_t
make_exportable_environment_bond_box(int imol, coot::residue_spec_t &spec, float max_dist)molecules_container_t
make_mask(int imol_map_ref, int imol_model, const std::string &atom_selection_cid, float radius)molecules_container_t
make_masked_maps_split_by_chain(int imol, int imol_map)molecules_container_t
make_mesh_for_bonds_for_blender(int imol, const std::string &mode, bool against_a_dark_background, float bond_width, float atom_radius_to_bond_width_ratio, int smoothness_factor)molecules_container_t
make_mesh_for_gaussian_surface_for_blender(int imol, float sigma, float contour_level, float box_radius, float grid_scale, float b_factor)molecules_container_t
make_mesh_for_goodsell_style_for_blender(int imol, float colour_wheel_rotation_step, float saturation, float goodselliness)molecules_container_t
make_mesh_for_map_contours_for_blender(int imol, float x, float y, float z, float level, float radius)molecules_container_t
make_mesh_for_molecular_representation_for_blender(int imol, const std::string &cid, const std::string &colour_scheme, const std::string &style, int secondary_structure_usage_flag)molecules_container_t
make_mesh_from_gltf_file(const std::string &file_name)molecules_container_t
make_power_scaled_map(int imol_ref, int imol_map_for_scaling)molecules_container_t
mask_map_by_atom_selection(int imol_coords, int imol_map, const std::string &cid, float atom_radius, bool invert_flag)molecules_container_t
match_ligand_position(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref)molecules_container_t
match_ligand_torsions(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref)molecules_container_t
match_ligand_torsions_and_position(int imol_ligand, int imol_ref, const std::string &chain_id_ref, int resno_ref)molecules_container_t
match_ligand_torsions_and_position_using_cid(int imol_ligand, int imol_ref, const std::string &cid)molecules_container_t
merge_molecules(int imol, const std::string &list_of_other_molecules)molecules_container_t
minimize(int imol, 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)molecules_container_t
minimize_energy(int imol, 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)molecules_container_t
mmcif_tests(bool last_test_only)molecules_container_t
mmrrcc(int imol, const std::string &chain_id, int imol_map) constmolecules_container_t
mmrrcc_internal(const atom_selection_container_t &asc, const std::string &chain_id, unsigned int n_residue_per_residue_range, const clipper::Xmap< float > &xmap) const (defined in molecules_container_t)molecules_container_t
molecule_to_mmCIF_string(int imol) constmolecules_container_t
molecule_to_PDB_string(int imol) constmolecules_container_t
molecules_container_t(bool verbose=true)molecules_container_texplicit
move_molecule_to_new_centre(int imol, float x, float y, float z)molecules_container_t
multiply_residue_temperature_factors(int imol, const std::string &cid, float factor)molecules_container_t
mutate(int imol, const std::string &cid, const std::string &new_residue_type)molecules_container_t
new_molecule(const std::string &name)molecules_container_t
new_positions_for_atoms_in_residues(int imol, const std::vector< coot::api::moved_residue_t > &moved_residues)molecules_container_t
new_positions_for_residue_atoms(int imol, const std::string &residue_cid, std::vector< coot::api::moved_atom_t > &moved_atoms)molecules_container_t
non_standard_residue_types_in_model(int imol) constmolecules_container_t
package_version() constmolecules_container_t
pae_png(const std::string &pae_file_name) constmolecules_container_t
partition_map_by_chain(int imol_map, int imol_model)molecules_container_t
pepflips_using_difference_map(int imol_coords, int imol_difference_map, float n_sigma) constmolecules_container_t
peptide_omega_analysis(int imol_model) constmolecules_container_t
pop_back()molecules_container_t
print_colour_rules(int imol) constmolecules_container_t
print_non_drawn_bonds(int imol) constmolecules_container_t
print_secondary_structure_info(int imol) constmolecules_container_t
r_factor_stats_as_string(const r_factor_stats &rfs) constmolecules_container_t
rail_points_total() constmolecules_container_t
ramachandran_analysis(int imol_model) constmolecules_container_t
ramachandran_analysis_for_chain(int imol_model, const std::string &chain_id) constmolecules_container_t
ramachandran_validation(int imol) constmolecules_container_t
read_ccp4_map(const std::string &file_name, bool is_a_difference_map)molecules_container_t
read_coordinates(const std::string &file_name)molecules_container_t
read_extra_restraints(int imol, const std::string &file_name)molecules_container_t
read_mtz(const std::string &file_name, const std::string &f, const std::string &phi, const std::string &weight, bool use_weight, bool is_a_difference_map)molecules_container_t
read_pdb(const std::string &file_name)molecules_container_t
read_small_molecule_cif(const std::string &file_name)molecules_container_t
redo(int imol)molecules_container_t
refine(int imol, int n_cycles)molecules_container_t
refine_residue_range(int imol, const std::string &chain_id, int res_no_start, int res_no_end, int n_cycles)molecules_container_t
refine_residues(int imol, const std::string &chain_id, int res_no, const std::string &ins_code, const std::string &alt_conf, const std::string &mode, int n_cycles)molecules_container_t
refine_residues_using_atom_cid(int imol, const std::string &cid, const std::string &mode, int n_cycles)molecules_container_t
regen_map(int imol_map, const std::string &imol_maps, const std::vector< float > &scales)molecules_container_t
replace_fragment(int imol_base, int imol_reference, const std::string &atom_selection)molecules_container_t
replace_map_by_mtz_from_file(int imol, const std::string &file_name, const std::string &f, const std::string &phi, const std::string &weight, bool use_weight)molecules_container_t
replace_molecule_by_model_from_file(int imol, const std::string &pdb_file_name)molecules_container_t
replace_residue(int imol, const std::string &residue_cid, const std::string &new_residue_type, int imol_enc)molecules_container_t
residue_cid_to_residue_spec(int imol, const std::string &cid) constmolecules_container_t
residue_is_nucleic_acid(int imol, const std::string &cid) constmolecules_container_t
residues_with_missing_atoms(int imol)molecules_container_t
rigid_body_fit(int imol, const std::string &multi_cid, int imol_map)molecules_container_t
rotamer_analysis(int imol_model) constmolecules_container_t
rotate_around_bond(int imol, const std::string &residue_cid, const std::string &atom_name_1, const std::string &atom_name_2, const std::string &atom_name_3, const std::string &atom_name_4, double torsion_angle)molecules_container_t
save_unsaved_model_changes()molecules_container_t
scale_map(int imol_map, float scale_factor)molecules_container_t
servalcat_refine_xray(int imol, int imol_map, const std::string &output_prefix)molecules_container_t
servalcat_refine_xray_with_keywords(int imol, int imol_map, const std::string &output_prefix, const nanobind::dict &key_value_pairs)molecules_container_t
set_add_waters_sigma_cutoff(float d)molecules_container_tinline
set_add_waters_variance_limit(float d)molecules_container_tinline
set_add_waters_water_to_protein_distance_lim_max(float d)molecules_container_tinline
set_add_waters_water_to_protein_distance_lim_min(float d)molecules_container_tinline
set_base_colour_for_bonds(int imol, float r, float g, float b)molecules_container_t
set_bespoke_carbon_atom_colour(int imol, const coot::colour_t &col)molecules_container_t
set_colour_map_for_map_coloured_by_other_map(std::vector< std::pair< double, std::vector< double > > > colour_table) (defined in molecules_container_t)molecules_container_t
set_colour_wheel_rotation_base(int imol, float r)molecules_container_t
set_draw_missing_residue_loops(bool state)molecules_container_t
set_gltf_pbr_metalicity_factor(int imol, float metalicity)molecules_container_t
set_gltf_pbr_roughness_factor(int imol, float roughness_factor)molecules_container_t
set_imol_refinement_map(int i)molecules_container_tinline
set_logging_file(const std::string &file_name)molecules_container_t
set_logging_level(const std::string &level)molecules_container_t
set_make_backups(bool state)molecules_container_tinline
set_map_colour(int imol, float r, float g, float b)molecules_container_t
set_map_colour_saturation(int imol, float s)molecules_container_t
set_map_is_contoured_with_thread_pool(bool state)molecules_container_t
set_map_sampling_rate(float msr)molecules_container_tinline
set_map_weight(float w)molecules_container_tinline
set_max_number_of_simple_mesh_vertices(unsigned int n) (defined in molecules_container_t)molecules_container_t
set_max_number_of_threads(unsigned int n_threads)molecules_container_t
set_max_number_of_threads_in_thread_pool(unsigned int n_threads)molecules_container_t
set_molecule_name(int imol, const std::string &new_name)molecules_container_t
set_occupancy(int imol, const std::string &cid, float occ_new)molecules_container_t
set_rama_plot_restraints_weight(float f)molecules_container_tinline
set_refinement_geman_mcclure_alpha(float a)molecules_container_tinline
set_refinement_is_verbose(bool state)molecules_container_tinline
set_residue_to_rotamer_number(int imol, const std::string &residue_cid, const std::string &alt_conf, int rotamer_number)molecules_container_t
set_show_timings(bool s)molecules_container_tinline
set_temperature_factors_using_cid(int imol, const std::string &cid, float temp_fact)molecules_container_t
set_torsion_restraints_weight(float f)molecules_container_tinline
set_use_bespoke_carbon_atom_colour(int imol, bool state)molecules_container_t
set_use_gemmi(bool state)molecules_container_tinline
set_use_rama_plot_restraints(bool state)molecules_container_tinline
set_use_torsion_restraints(bool state)molecules_container_tinline
set_user_defined_atom_colour_by_selection(int imol, const std::vector< std::pair< std::string, unsigned int > > &indexed_residues_cids, bool colour_applies_to_non_carbon_atoms_also)molecules_container_t
set_user_defined_bond_colours(int imol, const std::map< unsigned int, std::array< float, 4 > > &colour_map)molecules_container_t
sfcalc_genmap(int imol_model, int imol_map_with_data_attached, int imol_updating_difference_map)molecules_container_t
sfcalc_genmaps_using_bulk_solvent(int imol_model, int imol_2fofc_map, int imol_updating_difference_map, int imol_map_with_data_attached)molecules_container_t
sharpen_blur_map(int imol_map, float b_factor, bool in_place_flag)molecules_container_t
sharpen_blur_map_with_resample(int imol_map, float b_factor, float resample_factor, bool in_place_flag)molecules_container_t
shift_field_b_factor_refinement(int imol, int imol_with_data_attached)molecules_container_t
side_chain_180(int imol, const std::string &atom_cid)molecules_container_t
split_multi_model_molecule(int imol)molecules_container_t
split_residue_using_map(int imol, const std::string &residue_cid, int imol_diff_map)molecules_container_t
SSM_superpose(int imol_ref, const std::string &chain_id_ref, int imol_mov, const std::string &chain_id_mov)molecules_container_t
test_function(const std::string &s) (defined in molecules_container_t)molecules_container_t
test_launching_threads(unsigned int n_threads_per_batch, unsigned int n_batches) constmolecules_container_t
test_origin_cube() constmolecules_container_t
test_the_threading(int n_threads)molecules_container_t
test_thread_pool_threads(unsigned int n_threads)molecules_container_t
testing_interrogate_long_term_job()molecules_container_tinline
testing_start_long_term_job(unsigned int n_seconds)molecules_container_t
testing_stop_long_term_job()molecules_container_t
transform_map_using_lsq_matrix(int imol_map, lsq_results_t lsq_matrix, float x, float y, float z, float radius)molecules_container_t
try_read_dictionaries_for_new_residue_types(int imol)molecules_container_t
turn_off_when_close_target_position_restraint(int imol)molecules_container_t
undo(int imol)molecules_container_t
unmodelled_blobs(int imol_model, int imol_map, float rmsd_cut_off) constmolecules_container_t
use_gemmi (defined in molecules_container_t)molecules_container_t
write_coordinates(int imol, const std::string &file_name) constmolecules_container_t
write_map(int imol, const std::string &file_name) constmolecules_container_t
write_png(const std::string &compound_id, int imol, const std::string &file_name) constmolecules_container_t
~molecules_container_t() (defined in molecules_container_t)molecules_container_t