############# # some re-definitions from coot python functions ############ # sorted by header files: # c-interface.h: chain_id = chain_id_py remarks = remarks_py residue_centre = residue_centre_py coot_sys_build_type = coot_sys_build_type_py run_clear_backups = run_clear_backups_py het_group_residues = het_group_residues_py test_internal = test_internal_py test_internal_single = test_internal_single_py get_map_colour = get_map_colour_py average_map = average_map_py refmac_parameters = refmac_parameters_py map_sigma = map_sigma_py map_parameters = map_parameters_py cell = cell_py map_cell = cell_py get_refmac_sad_atom_info = get_refmac_sad_atom_info_py origin_pre_shift = origin_pre_shift_py save_state_file = save_state_file_py save_state_file_name = save_state_file_name_py run_state_file = run_state_file_py wrapped_create_run_state_file_dialog = wrapped_create_run_state_file_dialog_py centre_of_mass_string = centre_of_mass_string_py set_atom_attributes = set_atom_attributes_py symmetry_operators = symmetry_operators_py symmetry_operators_to_xHM = symmetry_operators_to_xHM_py merge_molecules = merge_molecules_py alignment_results = alignment_results_py nearest_residue_by_sequence = nearest_residue_by_sequence_py refine_residues = refine_residues_py copy_residue_range_from_ncs_master_to_chains = copy_residue_range_from_ncs_master_to_chains_py copy_from_ncs_master_to_chains = copy_from_ncs_master_to_chains_py # to be renamed later matching_compound_names_from_dictionary = matching_compound_names_from_dictionary_py comp_id2name = comp_id_to_name_py refine_residues_with_alt_conf = refine_residues_with_alt_conf_py refine_zone_with_score = refine_zone_with_score_py regularize_residues = regularize_residues_py regularize_residues_with_alt_conf = regularize_residues_with_alt_conf_py refine_zone_with_score = refine_zone_with_score_py regularize_zone_with_score = regularize_zone_with_score_py change_chain_id_with_result = change_chain_id_with_result_py non_standard_residue_names = non_standard_residue_names_py chain_id_for_shelxl_residue_number = chain_id_for_shelxl_residue_number_py gln_asn_b_factor_outliers = gln_asn_b_factor_outliers_py map_peaks = map_peaks_py map_peaks_near_point = map_peaks_near_point_py view_name = view_name_py view_description = view_description_py go_to_view = go_to_view_py movie_file_name_prefix = movie_file_name_prefix_py execute_ligand_search = execute_ligand_search_py overlap_ligands = overlap_ligands_py analyse_ligand_differences = analyse_ligand_differences_py # compare_ligand_atom_types = compare_ligand_atom_types_py # comment out hack to load this smoothly. additional_representation_info = additional_representation_info_py rigid_body_refine_by_residue_ranges = rigid_body_refine_by_residue_ranges_py find_terminal_residue_type = find_terminal_residue_type_py cis_peptides = cis_peptides_py get_rotamer_name = get_rotamer_name_py missing_atom_info = missing_atom_info_py rotamer_graphs = rotamer_graphs_py add_alt_conf = add_alt_conf_py highly_coordinated_waters = highly_coordinated_waters_py add_lsq_atom_pair = add_lsq_atom_pair_py apply_lsq_matches = apply_lsq_matches_py get_lsq_matrix = get_lsq_matrix_py make_image_raster3d = make_image_raster3d_py make_image_povray = make_image_povray_py raster_screen_shot = raster_screen_shot_py ncs_master_chains = ncs_master_chains_py ncs_chain_differences = ncs_chain_differences_py ncs_chain_ids = ncs_chain_ids_py ncs_ghosts = ncs_ghosts_py pucker_info = pucker_info_py sequence_info = sequence_info_py alignment_mismatches = alignment_mismatches_py do_clipped_surface = do_clipped_surface_py generic_object_name = generic_object_name_py user_mods = user_mods_py probe_available_p = probe_available_p_py drag_intermediate_atom = drag_intermediate_atom_py mark_atom_as_fixed = mark_atom_as_fixed_py mark_multiple_atoms_as_fixed = mark_multiple_atoms_as_fixed_py ccp4i_projects = ccp4i_projects_py add_dipole = add_dipole_py add_dipole_for_residues = add_dipole_for_residues_py get_pkgdatadir = get_pkgdatadir_py handle_pisa_interfaces = handle_pisa_interfaces_py pkgdatadir = get_pkgdatadir_py matching_compound_names_from_sbase = matching_compound_names_from_sbase_py add_linked_residue = add_linked_residue_py all_molecule_rotamer_score = all_molecule_rotamer_score_py all_molecule_ramachandran_score = all_molecule_ramachandran_score_py all_molecule_ramachandran_region = all_molecule_ramachandran_region_py user_defined_click = user_defined_click_py get_torsion = get_torsion_py set_torsion = set_torsion_py multi_residue_torsion = multi_residue_torsion_py multi_residue_torsion_fit = multi_residue_torsion_fit_py test_function = test_function_py display_maps = display_maps_py space_group = space_group_py molecule_name_stub = molecule_name_stub_py # graphics_info.h: #run_post_manipulation_hook = run_post_manipulation_hook_py # c-interface-python.hh: make_atom_spec = make_atom_spec_py # cc-interface.hh: goto_next_atom_maybe = goto_next_atom_maybe_py goto_prev_atom_maybe = goto_prev_atom_maybe_py set_go_to_atom_from_res_spec = set_go_to_atom_from_res_spec_py get_symmetry = get_symmetry_py map_colour_components = map_colour_components_py dictionaries_read = dictionaries_read_py cif_file_for_comp_id = cif_file_for_comp_id_py dictionary_entries = dictionary_entries_py SMILES_for_comp_id = SMILES_for_comp_id_py monomer_restraints = monomer_restraints_py set_monomer_restraints = set_monomer_restraints_py list_nomenclature_errors = list_nomenclature_errors_py atom_info_string = atom_info_string_py residue_info = residue_info_py residue_name = residue_name_py clear_and_update_molecule = clear_and_update_molecule_py add_molecule = add_molecule_py active_residue = active_residue_py closest_atom = closest_atom_py residues_near_residue = residues_near_residue_py residues_near_position = residues_near_position_py refine_zone_with_full_residue_spec = refine_zone_with_full_residue_spec_py list_extra_restraints = list_extra_restraints_py delete_extra_restraint = delete_extra_restraint_py water_chain_from_shelx_ins = water_chain_from_shelx_ins_py water_chain = water_chain_py make_variance_map = make_variance_map_py spin_search = spin_search_py cootaneer = cootaneer_py generic_string_vector_to_list_internal = generic_string_vector_to_list_internal_py generic_list_to_string_vector_internal = generic_list_to_string_vector_internal_py generic_int_vector_to_list_internal = generic_int_vector_to_list_internal_py inverse_rtop = inverse_rtop_py protein_db_loops = protein_db_loops_py make_link = make_link_py link_info = link_info_py map_to_model_correlation = map_to_model_correlation_py map_to_model_correlation_per_residue = map_to_model_correlation_per_residue_py # qq_plot_map_and_model = qq_plot_map_and_model_py # comment out hack to load this smoothly. align_to_closest_chain = align_to_closest_chain_py key_sym_code = key_sym_code_py screen_vectors = screen_vectors_py get_residue_by_type = get_residue_by_type_py score_rotamers = score_rotamers_py # c-interface-ligands-swig.hh: # new_molecule_sans_biggest_ligand = new_molecule_sans_biggest_ligand_py # comment out hack to load this smoothly. # gui_ligand_metrics = gui_ligand_metrics_py # comment out hack to load this smoothly. residues_torsions_match = residues_torsions_match_py kolmogorov_smirnov = kolmogorov_smirnov_py kullback_liebler = kullback_liebler_py chain_fragments = chain_fragments_py find_blobs = find_blobs_py morph_fit_residues = morph_fit_residues_py density_score_residue = density_score_residue_py align_to_closest_chain = align_to_closest_chain_py active_atom_spec = active_atom_spec_py # probe-clash-score.hh probe_clash_score = probe_clash_score_py # probe_clash_score_as = probe_clash_score_as_py # comment out hack to load this smoothly. # curl and hence coot_get_url_as_string are conditionally compiled. try: coot_get_url_as_string = coot_get_url_as_string_py curl_progress_info = curl_progress_info_py except: pass # or print a message # and some acronyms de_chainsaw = fill_partial_residues # fix typo of set_find_hydrogen_torsions (for backwards compatibility?!) set_find_hydrogen_torsion = set_find_hydrogen_torsions # redefine in case someone has old function toggle_idle_ligand_interactions = toggle_flev_idle_ligand_interactions