Utilities

• Assembly Utilities
  • build_assemblies_from_asym_unit()
• Bond Utilities
  • LongBondPolicyType
  • add_bonds_from_struct_conn()
  • build_bond_dict_for_atom_array()
  • correct_charged_amide_nitrogens()
  • correct_formal_charges_for_specified_atoms()
  • filter_bonds_by_distance()
  • generate_inter_level_bond_hash()
  • get_coarse_graph_as_nodes_and_edges()
  • get_connected_nodes()
  • get_inter_pn_unit_bond_mask()
  • get_struct_conn_bonds()
  • hash_atom_array()
  • hash_graph()
  • remap_intra_residue_coordination_bonds()
• CCD Utilities
  • aa_chem_comps()
  • add_annotations_from_ccd()
  • atom_array_from_ccd_code()
  • build_ccd_entries_from_cif_block()
  • check_ccd_codes_are_available()
  • chem_comp_to_one_letter()
  • clear_custom_ccd_registry()
  • custom_ccd_residues()
  • dna_chem_comps()
  • get_atom_names_for_residue()
  • get_available_ccd_codes()
  • get_available_ccd_codes_in_biotite()
  • get_available_ccd_codes_in_mirror()
  • get_ccd_component_from_biotite()
  • get_ccd_component_from_mirror()
  • get_ccd_descriptors()
  • get_chain_type_from_ccd_code()
  • get_chain_type_from_chem_comp_type()
  • get_chem_comp_type()
  • get_custom_ccd_entries()
  • get_parent_comp_id()
  • get_parent_template_atom_names()
  • get_polymerization_atoms()
  • get_standard_ccd_codes()
  • get_std_to_alt_atom_name_map()
  • get_unknown_ccd_code_for_chem_comp_type()
  • is_parent_strict_atom_subset()
  • na_chem_comps()
  • parse_ccd_cif()
  • register_custom_ccd_entries()
  • register_custom_ccd_entry()
  • register_custom_residues_from_atom_array()
  • rna_chem_comps()
  • snapshot_custom_ccd_registry()
  • unregister_custom_ccd_entry()
• Chain Utilities
  • create_chain_id_generator()
• I/O Utilities
  • CIFWriteConfig
  • apply_sharding_pattern()
  • build_sharding_pattern()
  • get_structure()
  • load_any()
  • parse_sharding_pattern()
  • read_any()
  • suppress_logging_messages()
  • to_cif_buffer()
  • to_cif_file()
  • to_cif_string()
• Non-RCSB Utilities
  • get_identity_assembly_gen_category()
  • get_identity_op_expr_category()
• Atom Selection Syntax
  • The path grammar
  • Interactive gallery
  • Combining path selection with the query language
  • Programmatic API
• Query & Selection
  • AtomSelection
  • AtomSelectionStack
  • QueryExpression
  • get_mask_from_atom_selection()
  • get_mask_from_selection_string()
  • idxs()
  • mask()
  • parse_pymol_string()
  • parse_selection_string()
  • query()
• Segment & Annotation Utilities
  • annot_start_stop_idxs()
  • get_annotation()
  • get_residue_starts()
• Sequence Utilities
  • get_1_from_3_letter_code()
  • get_3_from_1_letter_code()
• Testing Utilities
  • assert_same_annotation_cardinality()
  • assert_same_atom_array_or_stack()
  • get_pdb_path()
  • get_pdb_path_or_buffer()
  • has_ambiguous_annotation_set()
  • is_same_in_group()
  • is_same_in_segment()
  • verify_atom_array_chain_info_consistency()
• Visualization Utilities
  • view()