############# # some re-definitions from coot python functions ############ # sorted by header files: import coot # c-interface.h: chain_id = coot.chain_id_py remarks = coot.remarks_py residue_centre = coot.residue_centre_py coot_sys_build_type = coot.coot_sys_build_type_py accept_moving_atoms = coot.accept_moving_atoms_py molecule_name_stub = coot.molecule_name_stub_py run_clear_backups = coot.run_clear_backups_py het_group_residues = coot.het_group_residues_py replace_residues_from_mol = coot.replace_residues_from_mol_py test_internal = coot.test_internal_py test_internal_single = coot.test_internal_single_py select_atom_under_pointer = coot.select_atom_under_pointer_py get_map_colour = coot.get_map_colour_py average_map = coot.average_map_py refmac_parameters = coot.refmac_parameters_py map_parameters = coot.map_parameters_py cell = coot.cell_py map_cell = coot.cell_py get_refmac_sad_atom_info = coot.get_refmac_sad_atom_info_py origin_pre_shift = coot.origin_pre_shift_py save_coords_name_suggestion = coot.save_coords_name_suggestion_py save_state_file = coot.save_state_file_py save_state_file_name = coot.save_state_file_name_py run_state_file = coot.run_state_file_py go_to_ligand = coot.go_to_ligand_py centre_of_mass_string = coot.centre_of_mass_string_py set_atom_attributes = coot.set_atom_attributes_py test_function = coot.test_function_py glyco_tree = coot.glyco_tree_py glyco_tree_residues = coot.glyco_tree_residues_py glyco_tree_residue_id = coot.glyco_tree_residue_id_py glyco_tree_compare_trees = coot.glyco_tree_compare_trees_py glyco_tree_matched_residue_pairs = coot.glyco_tree_matched_residue_pairs_py display_maps = coot.display_maps_py space_group = coot.space_group_py symmetry_operators = coot.symmetry_operators_py symmetry_operators_to_xHM = coot.symmetry_operators_to_xHM_py merge_molecules = coot.merge_molecules_py set_merge_molecules_ligand_spec = coot.set_merge_molecules_ligand_spec_py alignment_results = coot.alignment_results_py nearest_residue_by_sequence = coot.nearest_residue_by_sequence_py change_chain_id_with_result = coot.change_chain_id_with_result_py probe_available_p = coot.probe_available_p_py # to be renamed later matching_compound_names_from_dictionary = coot.matching_compound_names_from_dictionary_py # keep for compatibility reasons comp_id_to_name = coot.comp_id_to_name_py refine_residues = coot.refine_residues_py refine_residues_with_modes_with_alt_conf = coot.refine_residues_with_modes_with_alt_conf_py refine_residues_with_alt_conf = coot.refine_residues_with_alt_conf_py regularize_residues = coot.regularize_residues_py regularize_residues_with_alt_conf = coot.regularize_residues_with_alt_conf_py refine_zone_with_score = coot.refine_zone_with_score_py regularize_zone_with_score = coot.regularize_zone_with_score_py chiral_volume_errors = coot.chiral_volume_errors_py add_extra_bond_restraints = coot.add_extra_bond_restraints_py delete_extra_restraints_for_residue_spec = coot.delete_extra_restraints_for_residue_spec_py generate_local_self_restraints_by_residues = coot.generate_local_self_restraints_by_residues_py delete_extra_restraint = coot.delete_extra_restraint_py list_extra_restraints = coot.list_extra_restraints_py add_atom_geometry_distance = coot.add_atom_geometry_distance_py get_pointer_position_frac = coot.get_pointer_position_frac_py non_standard_residue_names = coot.non_standard_residue_names_py chain_id_for_shelxl_residue_number = coot.chain_id_for_shelxl_residue_number_py gln_asn_b_factor_outliers = coot.gln_asn_b_factor_outliers_py map_peaks = coot.map_peaks_py map_peaks_near_point = coot.map_peaks_near_point_py map_peaks_near_point_from_list = coot.map_peaks_near_point_from_list_py map_peaks_around_molecule = coot.map_peaks_around_molecule_py screen_vectors = coot.screen_vectors_py get_torsion = coot.get_torsion_py set_torsion = coot.set_torsion_py multi_residue_torsion = coot.multi_residue_torsion_py view_name = coot.view_name_py view_description = coot.view_description_py go_to_view = coot.go_to_view_py movie_file_name_prefix = coot.movie_file_name_prefix_py execute_ligand_search = coot.execute_ligand_search_py overlap_ligands = coot.overlap_ligands_py analyse_ligand_differences = coot.analyse_ligand_differences_py # compare_ligand_atom_types = coot.compare_ligand_atom_types_py # comment out hack to load this smoothly. additional_representation_info = coot.additional_representation_info_py pepflip_using_difference_map = coot.pepflip_using_difference_map_py rigid_body_refine_by_residue_ranges = coot.rigid_body_refine_by_residue_ranges_py find_terminal_residue_type = coot.find_terminal_residue_type_py delete_residues = coot.delete_residues_py cis_peptides = coot.cis_peptides_py twisted_trans_peptides = coot.twisted_trans_peptides_py get_rotamer_name = coot.get_rotamer_name_py missing_atom_info = coot.missing_atom_info_py rotamer_graphs = coot.rotamer_graphs_py add_alt_conf = coot.add_alt_conf_py highly_coordinated_waters = coot.highly_coordinated_waters_py metal_coordination = coot.metal_coordination_py add_lsq_atom_pair = coot.add_lsq_atom_pair_py apply_lsq_matches = coot.apply_lsq_matches_py get_lsq_matrix = coot.get_lsq_matrix_py make_image_raster3d = coot.make_image_raster3d_py make_image_povray = coot.make_image_povray_py raster_screen_shot = coot.raster_screen_shot_py ncs_master_chains = coot.ncs_master_chains_py copy_residue_range_from_ncs_master_to_chains = coot.copy_residue_range_from_ncs_master_to_chains_py copy_from_ncs_master_to_chains = coot.copy_from_ncs_master_to_chains_py ncs_chain_differences = coot.ncs_chain_differences_py ncs_chain_ids = coot.ncs_chain_ids_py ncs_ghosts = coot.ncs_ghosts_py new_molecule_by_residue_specs = coot.new_molecule_by_residue_specs_py pucker_info = coot.pucker_info_py sequence_info = coot.sequence_info_py alignment_mismatches = coot.alignment_mismatches_py do_clipped_surface = coot.do_clipped_surface_py user_mods = coot.user_mods_py drag_intermediate_atom = coot.drag_intermediate_atom_py mark_atom_as_fixed = coot.mark_atom_as_fixed_py mark_multiple_atoms_as_fixed = coot.mark_multiple_atoms_as_fixed_py ccp4i_projects = coot.ccp4i_projects_py add_dipole = coot.add_dipole_py add_dipole_for_residues = coot.add_dipole_for_residues_py get_pkgdatadir = coot.get_pkgdatadir_py pkgdatadir = coot.get_pkgdatadir_py handle_pisa_interfaces = coot.handle_pisa_interfaces_py add_pisa_interface_bond = coot.add_pisa_interface_bond_py matching_compound_names_from_sbase = coot.matching_compound_names_from_sbase_py add_linked_residue = coot.add_linked_residue_py all_molecule_rotamer_score = coot.all_molecule_rotamer_score_py all_molecule_ramachandran_score = coot.all_molecule_ramachandran_score_py all_molecule_ramachandran_region = coot.all_molecule_ramachandran_region_py add_cablam_markup = coot.add_cablam_markup_py user_defined_click = coot.user_defined_click_py # graphics_info.h: #run_post_manipulation_hook = coot.run_post_manipulation_hook_py # c-interface-python.hh: make_atom_spec = coot.make_atom_spec_py # cc-interface.hh: goto_next_atom_maybe = coot.goto_next_atom_maybe_py goto_prev_atom_maybe = coot.goto_prev_atom_maybe_py set_go_to_atom_from_res_spec = coot.set_go_to_atom_from_res_spec_py set_go_to_atom_from_atom_spec = coot.set_go_to_atom_from_atom_spec_py active_atom_spec = coot.active_atom_spec_py get_symmetry = coot.get_symmetry_py map_colour_components = coot.map_colour_components_py multi_residue_torsion_fit = coot.multi_residue_torsion_fit_py dictionaries_read = coot.dictionaries_read_py cif_file_for_comp_id = coot.cif_file_for_comp_id_py dictionary_entries = coot.dictionary_entries_py SMILES_for_comp_id = coot.SMILES_for_comp_id_py monomer_restraints = coot.monomer_restraints_py monomer_restraints_for_molecule = coot.monomer_restraints_for_molecule_py set_monomer_restraints = coot.set_monomer_restraints_py list_nomenclature_errors = coot.list_nomenclature_errors_py residue_spec_make_triple = coot.residue_spec_make_triple_py get_residue_specs_in_mol = coot.get_residue_specs_in_mol_py get_residue_by_type = coot.get_residue_by_type_py atom_info_string = coot.atom_info_string_py residue_info = coot.residue_info_py residue_name = coot.residue_name_py all_residues_with_serial_numbers = coot.all_residues_with_serial_numbers_py residue_centre_from_spec = coot.residue_centre_from_spec_py chain_fragments = coot.chain_fragments_py set_b_factor_residues = coot.set_b_factor_residues_py clear_and_update_molecule = coot.clear_and_update_molecule_py add_molecule = coot.add_molecule_py active_residue = coot.active_residue_py closest_atom_simple = coot.closest_atom_simple_py closest_atom = coot.closest_atom_py closest_atom_raw = coot.closest_atom_raw_py residues_near_residue = coot.residues_near_residue_py residues_near_residues = coot.residues_near_residues_py residues_near_position = coot.residues_near_position_py get_environment_distances_representation = coot.get_environment_distances_representation_py all_residues_with_serial_numbers = coot.all_residues_with_serial_numbers_py refine_zone_with_full_residue_spec = coot.refine_zone_with_full_residue_spec_py morph_fit_residues = coot.morph_fit_residues_py find_blobs = coot.find_blobs_py water_chain_from_shelx_ins = coot.water_chain_from_shelx_ins_py water_chain = coot.water_chain_py make_variance_map = coot.make_variance_map_py spin_search = coot.spin_search_py spin_N = coot.spin_N_py ligand_search_make_conformers = coot.ligand_search_make_conformers_py cootaneer = coot.cootaneer_py generic_string_vector_to_list_internal = coot.generic_string_vector_to_list_internal_py generic_list_to_string_vector_internal = coot.generic_list_to_string_vector_internal_py generic_int_vector_to_list_internal = coot.generic_int_vector_to_list_internal_py inverse_rtop = coot.inverse_rtop_py # curl and hence coot_get_url_as_string are conditionally compiled. try: coot_get_url_as_string = coot.coot_get_url_as_string_py curl_progress_info = coot.curl_progress_info_py except: pass # or print a message score_rotamers = coot.score_rotamers_py protein_db_loops = coot.protein_db_loops_py make_link = coot.make_link_py link_info = coot.link_info_py map_to_model_correlation = coot.map_to_model_correlation_py map_to_model_correlation_stats = coot.map_to_model_correlation_stats_py map_to_model_correlation_per_residue = coot.map_to_model_correlation_per_residue_py qq_plot_map_and_model = coot.qq_plot_map_and_model_py density_score_residue = coot.density_score_residue_py map_mean = coot.map_mean_py map_sigma = coot.map_sigma_py map_statistics = coot.map_statistics_py register_interesting_positions_list = coot.register_interesting_positions_list_py molecule_atom_overlaps = coot.molecule_atom_overlaps_py align_to_closest_chain = coot.align_to_closest_chain_py key_sym_code = coot.key_sym_code_py # c-interface-ligands-swig.hh: # new_molecule_sans_biggest_ligand = coot.new_molecule_sans_biggest_ligand_py # comment out hack to load this smoothly. # gui_ligand_metrics = coot.gui_ligand_metrics_py # comment out hack to load this smoothly. residues_torsions_match = coot.residues_torsions_match_py get_intermediate_atoms_distortions = coot.get_intermediate_atoms_distortions_py ligand_atom_overlaps = coot.ligand_atom_overlaps_py residues_torsions_match = coot.residues_torsions_match_py kolmogorov_smirnov = coot.kolmogorov_smirnov_py kolmogorov_smirnov_vs_normal = coot.kolmogorov_smirnov_vs_normal_py kullback_liebler = coot.kullback_liebler_py linked_residues = coot.linked_residues_py add_target_position_restraint_for_intermediate_atom = coot.add_target_position_restraint_for_intermediate_atom_py add_target_position_restraints_for_intermediate_atoms = coot.add_target_position_restraints_for_intermediate_atoms_py coot_contact_dots_for_ligand = coot.coot_contact_dots_for_ligand_py switch_HIS_protonation = coot.switch_HIS_protonation_py # probe-clash-score.hh probe_clash_score = coot.probe_clash_score_py # probe_clash_score_as = coot.probe_clash_score_as_py # comment out hack to load this smoothly. # c-interface-generic-objects.h generic_object_name = coot.generic_object_name_py # and some acronyms de_chainsaw = coot.fill_partial_residues # fix typo of set_find_hydrogen_torsions (for backwards compatibility?!) set_find_hydrogen_torsion = coot.set_find_hydrogen_torsions # redefine in case someone has old function toggle_idle_ligand_interactions = coot.toggle_flev_idle_ligand_interactions