iotbx - file readers and writers

The iotbx module contains most tools for reading and writing the standard formats used by both macromolecular and small-molecule crystallographers, including PDB, CIF, MTZ, and various other file types. For some formats the resulting data will be encapsulated in objects defined in cctbx and/or scitbx; others have custom classes, in particular PDB/mmCIF files which have their own complex internal representation independent of the X-ray scattering properties.

Subpackages

• iotbx.managers
  • Overview
  • API documentation
    • add_tuples_int()
    • dummy_map_manager()
    • get_indices_from_index()
    • get_sites_cart_from_index()
    • map_manager
      • map_manager.absolute_center_cart()
      • map_manager.add_label()
      • map_manager.add_limitation()
      • map_manager.apply_mask()
      • map_manager.apply_spectral_scaling()
      • map_manager.as_full_size_map()
      • map_manager.as_map_model_manager()
      • map_manager.binary_filter()
      • map_manager.cart_to_grid_units()
      • map_manager.cc_to_other_map_manager()
      • map_manager.create_mask_around_atoms()
      • map_manager.create_mask_around_density()
      • map_manager.create_mask_around_edges()
      • map_manager.create_mask_with_map_data()
      • map_manager.customized_copy()
      • map_manager.deep_copy()
      • map_manager.delete_mask()
      • map_manager.density_at_sites_cart()
      • map_manager.experiment_type()
      • map_manager.external_origin_as_grid_units()
      • map_manager.external_origin_is_compatible_with_gridding()
      • map_manager.find_map_symmetry()
      • map_manager.find_n_highest_grid_points_as_sites_cart()
      • map_manager.fourier_coefficients_as_map_manager()
      • map_manager.gaussian_filter()
      • map_manager.get_boxes_to_tile_map()
      • map_manager.get_density_along_line()
      • map_manager.get_mask_as_map_manager()
      • map_manager.get_n_real_for_grid_spacing()
      • map_manager.grid_units_to_cart()
      • map_manager.initialize_map_data()
      • map_manager.invert_hand()
      • map_manager.is_compatible_model()
      • map_manager.is_compatible_ncs_object()
      • map_manager.is_consistent_with_wrapping()
      • map_manager.is_dummy_map_manager()
      • map_manager.is_full_size()
      • map_manager.is_mask()
      • map_manager.is_similar()
      • map_manager.map_as_fourier_coefficients()
      • map_manager.map_map_cc()
      • map_manager.minimum_resolution()
      • map_manager.ncs_cc()
      • map_manager.ncs_object()
      • map_manager.origin_is_zero()
      • map_manager.randomize()
      • map_manager.remove_labels()
      • map_manager.resample_on_different_grid()
      • map_manager.resolution()
      • map_manager.resolution_filter()
      • map_manager.scattering_table()
      • map_manager.set_crystal_symmetry_to_p1()
      • map_manager.set_experiment_type()
      • map_manager.set_is_mask()
      • map_manager.set_log()
      • map_manager.set_map_data()
      • map_manager.set_mean_zero_sd_one()
      • map_manager.set_model_symmetries_and_shift_cart_to_match_map()
      • map_manager.set_ncs_object()
      • map_manager.set_ncs_object_shift_cart_to_match_map()
      • map_manager.set_original_origin_and_gridding()
      • map_manager.set_output_external_origin()
      • map_manager.set_program_name()
      • map_manager.set_resolution()
      • map_manager.set_scattering_table()
      • map_manager.set_unit_cell_crystal_symmetry()
      • map_manager.set_wrapping()
      • map_manager.shift_aware_rt()
      • map_manager.shift_cart()
      • map_manager.shift_model_to_match_map()
      • map_manager.shift_ncs_object_to_match_map_and_return_new_ncs_object()
      • map_manager.shift_origin()
      • map_manager.shift_origin_to_match_original()
      • map_manager.soft_mask()
      • map_manager.trace_atoms_in_map()
      • map_manager.warning_message()
      • map_manager.wrapping()
      • map_manager.write_map()
    • remove_site_with_most_neighbors()
    • select_n_in_biggest_cluster()
    • shift_aware_rt
      • shift_aware_rt.absolute_rt_info()
      • shift_aware_rt.apply_rt()
      • shift_aware_rt.get_absolute_rt_info()
      • shift_aware_rt.inverse()
      • shift_aware_rt.is_similar()
      • shift_aware_rt.working_rt_info()
    • subtract_tuples_int()
    • apply_aniso_b_cart_to_f_array_info()
    • apply_ncs_to_dv_results()
    • convert_tlso_group_info_to_lists()
    • create_fine_spacing_array()
    • create_map_manager_with_value_list()
    • cutoff_values()
    • get_average_scale_factors()
    • get_center_of_box_frac()
    • get_map_coeffs_as_fp_phi()
    • get_map_counts()
    • get_map_histograms()
    • get_normalization_data_for_unit_binning()
    • get_pointer_to_old_dv_id_dict()
    • get_selection_inside_box()
    • get_selections_and_boxes_to_split_model()
    • get_selections_for_segments()
    • get_selections_from_boxes()
    • get_skip_waters_and_hetero_lines()
    • get_split_maps_and_models()
    • get_tlso_group_info_from_model()
    • get_tlso_resid()
    • get_weights_for_unit_binning()
    • is_inside_mask()
    • map_model_manager
      • map_model_manager.add_crystal_symmetry_to_model_if_necessary()
      • map_model_manager.add_map_from_fourier_coefficients()
      • map_model_manager.add_map_manager_by_id()
      • map_model_manager.add_model_by_id()
      • map_model_manager.add_to_info()
      • map_model_manager.apply_mask_to_map()
      • map_model_manager.apply_mask_to_maps()
      • map_model_manager.as_map_model_manager()
      • map_model_manager.as_map_model_manager_with_resampled_maps()
      • map_model_manager.as_match_map_model_ncs()
      • map_model_manager.box_all_maps_around_density_and_shift_origin()
      • map_model_manager.box_all_maps_around_mask_and_shift_origin()
      • map_model_manager.box_all_maps_around_model_and_shift_origin()
      • map_model_manager.box_all_maps_around_unique_and_shift_origin()
      • map_model_manager.box_all_maps_with_bounds_and_shift_origin()
      • map_model_manager.check_stop_file()
      • map_model_manager.choose_best_set()
      • map_model_manager.counts()
      • map_model_manager.create_mask_around_atoms()
      • map_model_manager.create_mask_around_density()
      • map_model_manager.create_mask_around_edges()
      • map_model_manager.create_masked_copies_of_maps()
      • map_model_manager.create_spherical_mask()
      • map_model_manager.crystal_symmetry()
      • map_model_manager.customized_copy()
      • map_model_manager.deep_copy()
      • map_model_manager.density_at_model_sites()
      • map_model_manager.duplicate_id()
      • map_model_manager.duplicate_map_manager()
      • map_model_manager.expand_mask()
      • map_model_manager.experiment_type()
      • map_model_manager.external_sharpen()
      • map_model_manager.extract_all_maps_around_density()
      • map_model_manager.extract_all_maps_around_mask()
      • map_model_manager.extract_all_maps_around_model()
      • map_model_manager.extract_all_maps_around_unique()
      • map_model_manager.extract_all_maps_with_bounds()
      • map_model_manager.find_k_sol_b_sol()
      • map_model_manager.generate_map()
      • map_model_manager.get_any_map_manager()
      • map_model_manager.get_cb_resseq_to_skip()
      • map_model_manager.get_counts_and_histograms()
      • map_model_manager.get_diffs_for_matching_target_and_model()
      • map_model_manager.get_info()
      • map_model_manager.get_map_data_by_id()
      • map_model_manager.get_map_manager_by_id()
      • map_model_manager.get_map_model_manager_with_selected()
      • map_model_manager.get_map_rmse()
      • map_model_manager.get_model_by_id()
      • map_model_manager.get_model_from_other()
      • map_model_manager.get_ncs_from_map()
      • map_model_manager.get_ncs_from_model()
      • map_model_manager.get_rms_f_list()
      • map_model_manager.get_selection_string_from_chain_dict()
      • map_model_manager.half_map_sharpen()
      • map_model_manager.hierarchy()
      • map_model_manager.histograms()
      • map_model_manager.info()
      • map_model_manager.initialize_maps()
      • map_model_manager.local_fsc()
      • map_model_manager.map_as_fourier_coefficients()
      • map_model_manager.map_data()
      • map_model_manager.map_data_1()
      • map_model_manager.map_data_2()
      • map_model_manager.map_data_list()
      • map_model_manager.map_dict()
      • map_model_manager.map_id_list()
      • map_model_manager.map_info()
      • map_model_manager.map_manager()
      • map_model_manager.map_manager_1()
      • map_model_manager.map_manager_2()
      • map_model_manager.map_manager_mask()
      • map_model_manager.map_managers()
      • map_model_manager.map_map_cc()
      • map_model_manager.map_map_fsc()
      • map_model_manager.map_model_cc()
      • map_model_manager.mask_all_maps_around_atoms()
      • map_model_manager.mask_all_maps_around_density()
      • map_model_manager.mask_all_maps_around_edges()
      • map_model_manager.mask_info()
      • map_model_manager.match_cb_to_ca()
      • map_model_manager.match_model_b_to_map()
      • map_model_manager.merge_split_maps_and_models()
      • map_model_manager.minimum_resolution()
      • map_model_manager.model()
      • map_model_manager.model_building()
      • map_model_manager.model_dict()
      • map_model_manager.model_from_hierarchy()
      • map_model_manager.model_from_sites_cart()
      • map_model_manager.model_from_text()
      • map_model_manager.model_id_list()
      • map_model_manager.model_sharpen()
      • map_model_manager.models()
      • map_model_manager.ncs_cc()
      • map_model_manager.ncs_object()
      • map_model_manager.nproc()
      • map_model_manager.propagate_model_from_other()
      • map_model_manager.remove_anisotropy()
      • map_model_manager.remove_map_manager_by_id()
      • map_model_manager.remove_model_by_id()
      • map_model_manager.remove_model_outside_map()
      • map_model_manager.remove_origin_shift_and_unit_cell_crystal_symmetry()
      • map_model_manager.resolution()
      • map_model_manager.resolution_filter()
      • map_model_manager.rmsd_of_matching_residues()
      • map_model_manager.scattering_table()
      • map_model_manager.select_matching_segments()
      • map_model_manager.sequence()
      • map_model_manager.set_experiment_type()
      • map_model_manager.set_info()
      • map_model_manager.set_log()
      • map_model_manager.set_map_id_lists()
      • map_model_manager.set_map_manager()
      • map_model_manager.set_minimum_resolution()
      • map_model_manager.set_model()
      • map_model_manager.set_model_symmetries_and_shift_cart_to_match_map()
      • map_model_manager.set_multiprocessing()
      • map_model_manager.set_name()
      • map_model_manager.set_ncs_object()
      • map_model_manager.set_original_origin_grid_units()
      • map_model_manager.set_resolution()
      • map_model_manager.set_scattering_table()
      • map_model_manager.set_stop_file()
      • map_model_manager.set_up_map_dict()
      • map_model_manager.set_up_model_dict()
      • map_model_manager.set_verbose()
      • map_model_manager.shift_any_model_to_match()
      • map_model_manager.shift_aware_rt()
      • map_model_manager.shift_aware_rt_to_superpose_other()
      • map_model_manager.shift_cart()
      • map_model_manager.shift_origin_to_match_original()
      • map_model_manager.show_summary()
      • map_model_manager.split_up_map_and_model_by_boxes()
      • map_model_manager.split_up_map_and_model_by_chain()
      • map_model_manager.split_up_map_and_model_by_ncs_groups()
      • map_model_manager.split_up_map_and_model_by_segment()
      • map_model_manager.split_up_map_and_model_by_supplied_selections()
      • map_model_manager.superposed_map_manager_from_other()
      • map_model_manager.tls_from_map()
      • map_model_manager.unit_cell_crystal_symmetry()
      • map_model_manager.warning_message()
      • map_model_manager.write_map()
      • map_model_manager.write_model()
      • map_model_manager.xray_structure()
    • match_map_model_ncs
      • match_map_model_ncs.add_map_manager()
      • match_map_model_ncs.add_model()
      • match_map_model_ncs.add_ncs_object()
      • match_map_model_ncs.as_map_model_manager()
      • match_map_model_ncs.check_model_and_set_to_match_map_if_necessary()
      • match_map_model_ncs.crystal_symmetry()
      • match_map_model_ncs.deep_copy()
      • match_map_model_ncs.get_coordinate_shift()
      • match_map_model_ncs.map_manager()
      • match_map_model_ncs.model()
      • match_map_model_ncs.ncs_object()
      • match_map_model_ncs.read_map()
      • match_map_model_ncs.read_model()
      • match_map_model_ncs.read_ncs_file()
      • match_map_model_ncs.set_log()
      • match_map_model_ncs.set_original_origin_and_gridding()
      • match_map_model_ncs.shift_model_to_match_original_map()
      • match_map_model_ncs.shift_model_to_match_working_map()
      • match_map_model_ncs.shift_ncs_to_match_original_map()
      • match_map_model_ncs.shift_ncs_to_match_working_map()
      • match_map_model_ncs.shift_origin()
      • match_map_model_ncs.show_summary()
      • match_map_model_ncs.unit_cell_crystal_symmetry()
      • match_map_model_ncs.write_map()
      • match_map_model_ncs.write_model()
    • residue_group_is_linked_to_previous()
    • run_anisotropic_scaling_as_class
    • run_fsc_as_class
    • set_nearby_empty_values()
• iotbx.file_reader - generic file input
  • API documentation
    • FormatError
    • any_file()
    • any_file_fast()
    • any_file_fast_input
    • any_file_input
      • any_file_input.assert_file_type()
      • any_file_input.check_file_type()
      • any_file_input.crystal_symmetry()
      • any_file_input.file_content
      • any_file_input.file_info()
      • any_file_input.file_name
      • any_file_input.file_object
      • any_file_input.file_server
      • any_file_input.file_type
      • any_file_input.set_file_type()
      • any_file_input.show_summary()
      • any_file_input.try_all_types()
    • directory_input
      • directory_input.file_info()
    • find_closest_base_name()
    • get_wildcard_string()
    • get_wildcard_strings()
    • group_files
    • guess_file_type()
    • sort_by_file_type()
    • splitext()
    • strip_shelx_format_extension()
• iotbx.cif
  • Overview
    • Reading a CIF file
    • Python representation of a CIF file
    • Dictionary validation
    • Creating a standalone C++ CIF parser
  • API documentation
    • iotbx.cif objects
      • reader
        • reader.as_miller_arrays()
        • reader.as_original_arrays()
        • reader.build_crystal_structures()
        • reader.build_miller_arrays()
        • reader.error_count()
        • reader.model()
        • reader.show_errors()
      • cif
        • cif.copy()
        • cif.deepcopy()
        • cif.get()
        • cif.get_errors()
        • cif.keys()
        • cif.show()
        • cif.sort()
        • cif.validate()
      • save
        • save.show()
      • block
        • block.keys()
        • block.show()
        • block.sort()
        • block.update()
      • loop
        • loop.add_column()
        • loop.add_columns()
        • loop.add_row()
        • loop.check_key_is_unique()
        • loop.copy()
        • loop.deepcopy()
        • loop.delete_row()
        • loop.find_row()
        • loop.iterrows()
        • loop.keys()
        • loop.n_columns()
        • loop.n_rows()
        • loop.name()
        • loop.order()
        • loop.show()
        • loop.size()
        • loop.sort()
        • loop.update_column()
      • miller_arrays_as_cif_block
        • miller_arrays_as_cif_block.add_miller_array()
    • Accessory classes and functions
• iotbx.pdb
  • API documentation
    • Input methods and objects
      • input()
      • input
        • input.as_pdb_string()
        • input.atoms()
        • input.atoms_with_labels()
        • input.bookkeeping_section()
        • input.break_indices()
        • input.chain_indices()
        • input.connectivity_annotation_section()
        • input.connectivity_section()
        • input.construct_hierarchy()
        • input.construct_hierarchy_BIOMT_expanded()
        • input.construct_hierarchy_MTRIX_expanded()
        • input.crystal_symmetry()
        • input.crystal_symmetry_from_cryst1()
        • input.crystallographic_section()
        • input.deposition_date()
        • input.extract_LINK_records()
        • input.extract_authors()
        • input.extract_connectivity()
        • input.extract_cryst1_z_columns()
        • input.extract_f_model_core_constants()
        • input.extract_header_year()
        • input.extract_remark_iii_records()
        • input.extract_secondary_structure()
        • input.extract_tls_params()
        • input.extract_wavelength()
        • input.file_type()
        • input.get_experiment_type()
        • input.get_link_records()
        • input.get_matthews_coeff()
        • input.get_program_name()
        • input.get_r_rfree_sigma()
        • input.get_restraints_used()
        • input.get_solvent_content()
        • input.heterogen_section()
        • input.miscellaneous_features_section()
        • input.model_atom_counts()
        • input.model_ids()
        • input.model_indices()
        • input.primary_structure_section()
        • input.process_BIOMT_records()
        • input.process_MTRIX_records()
        • input.record_type_counts()
        • input.remark_section()
        • input.resolution()
        • input.scale_matrix()
        • input.secondary_structure_section()
        • input.sequence_from_SEQRES()
        • input.source_info()
        • input.special_position_settings()
        • input.ter_indices()
        • input.title_section()
        • input.unknown_section()
        • input.used_amber_restraints()
        • input.used_cdl_restraints()
        • input.used_omega_cdl_restraints()
        • input.write_pdb_file()
        • input.xray_structure_simple()
        • input.xray_structures_simple()
      • cif_input
        • cif_input.atoms()
        • cif_input.atoms_with_labels()
        • cif_input.connectivity_annotation_section()
        • cif_input.connectivity_section()
        • cif_input.construct_hierarchy()
        • cif_input.crystal_symmetry()
        • cif_input.crystal_symmetry_from_cryst1()
        • cif_input.crystallographic_section()
        • cif_input.deposition_date()
        • cif_input.extract_cryst1_z_columns()
        • cif_input.extract_f_model_core_constants()
        • cif_input.extract_header_year()
        • cif_input.extract_secondary_structure()
        • cif_input.extract_tls_params()
        • cif_input.extract_wavelength()
        • cif_input.file_type()
        • cif_input.get_experiment_type()
        • cif_input.get_matthews_coeff()
        • cif_input.get_program_name()
        • cif_input.get_r_rfree_sigma()
        • cif_input.get_restraints_used()
        • cif_input.get_solvent_content()
        • cif_input.heterogen_section()
        • cif_input.model_ids()
        • cif_input.model_indices()
        • cif_input.process_BIOMT_records()
        • cif_input.process_MTRIX_records()
        • cif_input.remark_section()
        • cif_input.resolution()
        • cif_input.scale_matrix()
        • cif_input.source_info()
        • cif_input.ter_indices()
        • cif_input.title_section()
        • cif_input.used_amber_restraints()
        • cif_input.used_cdl_restraints()
        • cif_input.used_omega_cdl_restraints()
    • PDB hierarchy objects
      • root
        • root.adopt_xray_structure()
        • root.altloc_indices()
        • root.altlocs_present()
        • root.append_model()
        • root.apply_atom_selection()
        • root.apply_rotation_translation()
        • root.as_cif_block()
        • root.as_dict_of_chain_id_resseq_as_int_residue_names()
        • root.as_forward_compatible_hierarchy()
        • root.as_forward_compatible_string()
        • root.as_list_of_residue_names()
        • root.as_mmcif_string()
        • root.as_model_manager()
        • root.as_pdb_input()
        • root.as_pdb_or_mmcif_string()
        • root.as_pdb_string()
        • root.as_sequence()
        • root.as_str()
        • root.atom_groups()
        • root.atom_selection_cache()
        • root.atoms()
        • root.atoms_reset_serial()
        • root.atoms_size()
        • root.atoms_with_i_seq_mismatch()
        • root.atoms_with_labels()
        • root.chain_ids()
        • root.chain_type()
        • root.chain_types()
        • root.chains()
        • root.chunk_selections()
        • root.clear_label_asym_id_lookups()
        • root.composition()
        • root.contains_break_records()
        • root.contains_dna()
        • root.contains_hetero()
        • root.contains_nucleic_acid()
        • root.contains_protein()
        • root.contains_rna()
        • root.conversion_info()
        • root.convert_met_to_semet()
        • root.convert_multi_word_text_to_forward_compatible()
        • root.convert_semet_to_met()
        • root.de_deuterate()
        • root.deep_copy()
        • root.distance_based_simple_two_way_bond_sets()
        • root.exchangeable_hd_selections()
        • root.expand_to_p1()
        • root.extract_xray_structure()
        • root.find_model_index()
        • root.first_chain_id()
        • root.first_resseq_as_int()
        • root.fits_in_pdb_format()
        • root.flip_symmetric_amino_acids()
        • root.format_correction_for_H()
        • root.format_fasta()
        • root.forward_compatible_hierarchy_as_standard()
        • root.get_atom_selection_cache()
        • root.get_auth_asym_id()
        • root.get_auth_asym_id_iseq()
        • root.get_auth_seq_id()
        • root.get_auth_seq_id_iseq()
        • root.get_conformer_indices()
        • root.get_label_alt_id_atom()
        • root.get_label_alt_id_iseq()
        • root.get_label_asym_id()
        • root.get_label_asym_id_iseq()
        • root.get_label_seq_id()
        • root.get_label_seq_id_iseq()
        • root.get_overall_counts()
        • root.get_peptide_c_alpha_selection()
        • root.guess_chemical_elements()
        • root.has_icodes()
        • root.info
        • root.insert_model()
        • root.is_ca_only()
        • root.is_forward_compatible_hierarchy()
        • root.is_hierarchy_altloc_consistent()
        • root.is_similar_hierarchy()
        • root.last_resseq_as_int()
        • root.memory_id()
        • root.merge_atoms_at_end_to_residues()
        • root.models()
        • root.models_size()
        • root.occupancy_counts()
        • root.occupancy_groups_simple()
        • root.only_atom()
        • root.only_atom_group()
        • root.only_chain()
        • root.only_conformer()
        • root.only_model()
        • root.only_residue()
        • root.only_residue_group()
        • root.overall_counts()
        • root.pdb_or_mmcif_string_info()
        • root.pre_allocate_models()
        • root.remove_alt_confs()
        • root.remove_atoms()
        • root.remove_hd()
        • root.remove_hetero()
        • root.remove_incomplete_main_chain_protein()
        • root.remove_model()
        • root.remove_residue_groups_with_atoms_on_special_positions_selective()
        • root.remove_ter_or_break()
        • root.rename_chain_id()
        • root.reset_atom_i_seqs()
        • root.reset_i_seq_if_necessary()
        • root.residue_groups()
        • root.round_occupancies_in_place()
        • root.select()
        • root.set_atomic_charge()
        • root.shift_to_origin()
        • root.show()
        • root.sort_atoms_in_place()
        • root.sort_chains_by_id()
        • root.transfer_chains_from_other()
        • root.truncate_to_poly()
        • root.truncate_to_poly_ala()
        • root.truncate_to_poly_gly()
        • root.write_mmcif_file()
        • root.write_pdb_file()
        • root.write_pdb_or_mmcif_file()
      • model
        • model.append_chain()
        • model.atom_groups()
        • model.atoms()
        • model.atoms_size()
        • model.chains()
        • model.chains_size()
        • model.detached_copy()
        • model.find_chain_index()
        • model.id
        • model.insert_chain()
        • model.is_ca_only()
        • model.is_identical_hierarchy()
        • model.is_similar_hierarchy()
        • model.memory_id()
        • model.only_atom()
        • model.only_atom_group()
        • model.only_chain()
        • model.only_conformer()
        • model.only_residue()
        • model.only_residue_group()
        • model.parent()
        • model.pre_allocate_chains()
        • model.remove_chain()
        • model.residue_groups()
        • model.transfer_chains_from_other()
      • chain
        • chain.append_residue_group()
        • chain.as_dict_of_resseq_as_int_residue_names()
        • chain.as_dict_of_resseq_residue_names()
        • chain.as_list_of_residue_names()
        • chain.as_new_hierarchy()
        • chain.as_padded_sequence()
        • chain.as_sequence()
        • chain.atom_groups()
        • chain.atoms()
        • chain.atoms_size()
        • chain.conformers()
        • chain.detached_copy()
        • chain.find_pure_altloc_ranges()
        • chain.find_residue_group_index()
        • chain.format_fasta()
        • chain.get_residue_ids()
        • chain.get_residue_names_and_classes()
        • chain.get_residue_names_padded()
        • chain.id
        • chain.insert_residue_group()
        • chain.is_ca_only()
        • chain.is_identical_hierarchy()
        • chain.is_na()
        • chain.is_protein()
        • chain.is_similar_hierarchy()
        • chain.memory_id()
        • chain.merge_disconnected_residue_groups_with_pure_altloc()
        • chain.merge_residue_groups()
        • chain.occupancy_groups_simple()
        • chain.only_atom()
        • chain.only_atom_group()
        • chain.only_conformer()
        • chain.only_residue()
        • chain.only_residue_group()
        • chain.parent()
        • chain.pre_allocate_residue_groups()
        • chain.remove_residue_group()
        • chain.residue_groups()
        • chain.residue_groups_size()
        • chain.residues()
      • residue_group
        • residue_group.append_atom_group()
        • residue_group.atom_groups()
        • residue_group.atom_groups_size()
        • residue_group.atoms()
        • residue_group.atoms_size()
        • residue_group.conformers()
        • residue_group.detached_copy()
        • residue_group.edit_blank_altloc()
        • residue_group.find_atom_group_index()
        • residue_group.have_conformers()
        • residue_group.icode
        • residue_group.id_str()
        • residue_group.insert_atom_group()
        • residue_group.is_identical_hierarchy()
        • residue_group.is_similar_hierarchy()
        • residue_group.link_to_previous
        • residue_group.memory_id()
        • residue_group.merge_atom_groups()
        • residue_group.move_blank_altloc_atom_groups_to_front()
        • residue_group.only_atom()
        • residue_group.only_atom_group()
        • residue_group.parent()
        • residue_group.pre_allocate_atom_groups()
        • residue_group.remove_atom_group()
        • residue_group.resid()
        • residue_group.resseq
        • residue_group.resseq_as_int()
        • residue_group.unique_resnames()
      • atom_group
        • atom_group.altloc
        • atom_group.append_atom()
        • atom_group.append_atom_with_other_parent()
        • atom_group.atoms()
        • atom_group.atoms_size()
        • atom_group.confid()
        • atom_group.detached_copy()
        • atom_group.find_atom_index()
        • atom_group.get_atom()
        • atom_group.id_str()
        • atom_group.insert_atom()
        • atom_group.memory_id()
        • atom_group.occupancy()
        • atom_group.only_atom()
        • atom_group.parent()
        • atom_group.pre_allocate_atoms()
        • atom_group.remove_atom()
        • atom_group.resname
        • atom_group.sort_atoms_in_place()
      • atom
        • atom.angle()
        • atom.b
        • atom.chain()
        • atom.charge
        • atom.charge_as_int()
        • atom.charge_tidy()
        • atom.data_offsets()
        • atom.detached_copy()
        • atom.determine_chemical_element_simple()
        • atom.distance()
        • atom.element
        • atom.element_is_hydrogen()
        • atom.element_is_ion()
        • atom.element_is_negative_ion()
        • atom.element_is_positive_ion()
        • atom.fdp
        • atom.fetch_labels()
        • atom.format_anisou_record()
        • atom.format_atom_record()
        • atom.format_atom_record_group()
        • atom.format_sigatm_record()
        • atom.format_siguij_record()
        • atom.fp
        • atom.has_siguij()
        • atom.hetero
        • atom.i_seq
        • atom.id_str()
        • atom.is_in_same_conformer_as()
        • atom.memory_id()
        • atom.name
        • atom.occ
        • atom.parent()
        • atom.pdb_element_charge_columns()
        • atom.pdb_label_columns()
        • atom.quote()
        • atom.segid
        • atom.serial
        • atom.serial_as_int()
        • atom.set_b()
        • atom.set_charge()
        • atom.set_chemical_element_simple_if_necessary()
        • atom.set_element()
        • atom.set_element_and_charge_from_scattering_type_if_necessary()
        • atom.set_fdp()
        • atom.set_fp()
        • atom.set_hetero()
        • atom.set_name()
        • atom.set_occ()
        • atom.set_segid()
        • atom.set_serial()
        • atom.set_sigb()
        • atom.set_sigocc()
        • atom.set_sigxyz()
        • atom.set_uij()
        • atom.set_xyz()
        • atom.sigb
        • atom.sigocc
        • atom.siguij_erase()
        • atom.siguij_is_defined()
        • atom.sigxyz
        • atom.sizeof_data()
        • atom.tmp
        • atom.uij
        • atom.uij_erase()
        • atom.uij_is_defined()
        • atom.xyz
      • atom_with_labels
        • atom_with_labels.altloc
        • atom_with_labels.chain_id
        • atom_with_labels.detached_copy()
        • atom_with_labels.fetch_labels()
        • atom_with_labels.format_anisou_record()
        • atom_with_labels.format_atom_record()
        • atom_with_labels.format_atom_record_group()
        • atom_with_labels.format_sigatm_record()
        • atom_with_labels.format_siguij_record()
        • atom_with_labels.icode
        • atom_with_labels.id_str()
        • atom_with_labels.is_first_after_break
        • atom_with_labels.is_first_in_chain
        • atom_with_labels.model_id
        • atom_with_labels.quote()
        • atom_with_labels.resid()
        • atom_with_labels.resname
        • atom_with_labels.resseq
        • atom_with_labels.resseq_as_int()
        • atom_with_labels.serial_as_int()
      • conformer
        • conformer.altloc
        • conformer.as_padded_sequence()
        • conformer.as_sec_str_sequence()
        • conformer.as_sequence()
        • conformer.atoms()
        • conformer.atoms_size()
        • conformer.format_fasta()
        • conformer.get_residue_ids()
        • conformer.get_residue_names_and_classes()
        • conformer.get_residue_names_padded()
        • conformer.is_na()
        • conformer.is_protein()
        • conformer.memory_id()
        • conformer.only_atom()
        • conformer.only_residue()
        • conformer.parent()
        • conformer.residues()
        • conformer.residues_size()
      • residue
        • residue.atoms()
        • residue.atoms_size()
        • residue.find_atom_by()
        • residue.icode
        • residue.id_str()
        • residue.is_pure_main_conf
        • residue.link_to_previous
        • residue.memory_id()
        • residue.only_atom()
        • residue.parent()
        • residue.resid()
        • residue.residue_name_plus_atom_names_interpreter()
        • residue.resname
        • residue.resseq
        • residue.resseq_as_int()
        • residue.root()
        • residue.standalone_copy()
      • af_shared_atom
        • af_shared_atom.append()
        • af_shared_atom.build_dict()
        • af_shared_atom.clear()
        • af_shared_atom.deep_copy()
        • af_shared_atom.extend()
        • af_shared_atom.extract_b()
        • af_shared_atom.extract_element()
        • af_shared_atom.extract_fdp()
        • af_shared_atom.extract_fp()
        • af_shared_atom.extract_hetero()
        • af_shared_atom.extract_i_seq()
        • af_shared_atom.extract_name()
        • af_shared_atom.extract_occ()
        • af_shared_atom.extract_segid()
        • af_shared_atom.extract_serial()
        • af_shared_atom.extract_sigb()
        • af_shared_atom.extract_sigocc()
        • af_shared_atom.extract_sigxyz()
        • af_shared_atom.extract_tmp_as_size_t()
        • af_shared_atom.extract_uij()
        • af_shared_atom.extract_xyz()
        • af_shared_atom.insert()
        • af_shared_atom.reserve()
        • af_shared_atom.reset_i_seq()
        • af_shared_atom.reset_serial()
        • af_shared_atom.reset_tmp()
        • af_shared_atom.reset_tmp_for_occupancy_groups_simple()
        • af_shared_atom.select()
        • af_shared_atom.set_adps_from_scatterers()
        • af_shared_atom.set_b()
        • af_shared_atom.set_chemical_element_simple_if_necessary()
        • af_shared_atom.set_fdp()
        • af_shared_atom.set_fp()
        • af_shared_atom.set_occ()
        • af_shared_atom.set_sigb()
        • af_shared_atom.set_sigocc()
        • af_shared_atom.set_sigxyz()
        • af_shared_atom.set_uij()
        • af_shared_atom.set_xyz()
        • af_shared_atom.size()
    • Accessory classes and functions
      • overall_counts
        • overall_counts.as_str()
        • overall_counts.errors()
        • overall_counts.errors_and_warnings()
        • overall_counts.get_n_residues_of_classes()
        • overall_counts.raise_chains_with_mix_of_proper_and_improper_alt_conf_if_necessary()
        • overall_counts.raise_duplicate_atom_labels_if_necessary()
        • overall_counts.raise_improper_alt_conf_if_necessary()
        • overall_counts.raise_residue_groups_with_multiple_resnames_using_same_altloc_if_necessary()
        • overall_counts.show()
        • overall_counts.show_chains_with_mix_of_proper_and_improper_alt_conf()
        • overall_counts.show_consecutive_residue_groups_with_same_resid()
        • overall_counts.show_duplicate_atom_labels()
        • overall_counts.show_improper_alt_conf()
        • overall_counts.show_residue_groups_with_multiple_resnames_using_same_altloc()
        • overall_counts.warnings()
    • Submodules
    • iotbx.pdb.multimer_reconstruction module
• iotbx.shelx
  • Overview
  • API documentation
    • parse_smtbx_refinement_model()
    • extract_from()
    • miller_array_export_as_shelx_hklf()
    • reader
      • reader.alphas()
      • reader.as_miller_arrays()
      • reader.batch_numbers()
      • reader.wavelengths()
    • atomname_token
      • atomname_token.name
      • atomname_token.plus_minus
      • atomname_token.residue_number
      • atomname_token.symmetry
    • element_token
      • element_token.element
      • element_token.plus_minus
      • element_token.residue_number
    • residue_token
      • residue_token.class_
      • residue_token.number
    • command_stream
      • command_stream.commands_allowing_atom_names
      • command_stream.shelx_commands
      • command_stream.symm_space
    • afix_parser
      • afix_parser.constraints
      • afix_parser.filtered_commands()
    • atom_parser
      • atom_parser.filtered_commands()
      • atom_parser.lex_scatterer()
      • atom_parser.process_occupancies_depending_on_free_variable()
      • atom_parser.process_possible_constrained_occupancy()
      • atom_parser.process_possible_u_iso_constraints()
    • crystal_symmetry_parser
      • crystal_symmetry_parser.filtered_commands()
      • crystal_symmetry_parser.parse()
    • decode_variables()
    • instruction_parser
      • instruction_parser.filtered_commands()
      • instruction_parser.issue_merohedral_twinning()
    • parser
      • parser.parse()
    • restraint_parser
      • restraint_parser.cache_restraint()
      • restraint_parser.filtered_commands()
      • restraint_parser.i_seqs_from_atoms()
      • restraint_parser.parse_restraints()
      • restraint_parser.restraint_types
    • variable_decoder
      • variable_decoder.decode_one_variable()
      • variable_decoder.decode_variables()
    • wavelength_parser
      • wavelength_parser.filtered_commands()
    • generator()
    • LATT_SYMM()
    • shelxd()
• iotbx.xds
  • Overview
  • API documentation
    • reader
      • reader.is_xds_inp_file()
      • reader.parse_lines()
      • reader.read_file()
    • reader
      • reader.find_version()
      • reader.is_xparm_file()
      • reader.parse_version_1_tokens()
      • reader.parse_version_2_tokens()
      • reader.read_file()
    • write()
    • writer
      • writer.show()
      • writer.write_file()
    • get_rhs()
    • reader
      • reader.as_miller_array()
      • reader.as_miller_arrays()
      • reader.batch_as_miller_array()
      • reader.column_index()
      • reader.crystal_symmetry()
      • reader.miller_set()
    • reader
      • reader.read_file()
    • writer
      • writer.write_file()
    • reader
      • reader.as_miller_arrays()
      • reader.is_integrate_hkl_file()
      • reader.read_file()
• iotbx.reflection_file_reader - generic reflection file input
  • any_reflection_file
    • any_reflection_file.as_miller_arrays()
    • any_reflection_file.file_content()
    • any_reflection_file.file_name()
    • any_reflection_file.file_type()
  • collect_arrays()
  • run()
  • try_all_readers()
  • unpickle_miller_arrays()