API documentation

This part of the documentation is automatically generated from the pdbeccdutils source code and comments.

The pdbeccdutils package is made up of the following modules:

• computations
  • pdbeccdutils.computations.parity_method
    • compare_molecules()
• core
  • pdbeccdutils.core.ccd_reader
  • pdbeccdutils.core.component
    • Component
      • Component.atoms_ids
      • Component.compute_2d()
      • Component.compute_3d()
      • Component.descriptors
      • Component.export_2d_annotation()
      • Component.export_2d_svg()
      • Component.external_mappings
      • Component.fetch_external_mappings()
      • Component.formula
      • Component.fragments
      • Component.get_conformer()
      • Component.get_scaffolds()
      • Component.has_degenerated_conformer()
      • Component.id
      • Component.inchi
      • Component.inchi_from_rdkit
      • Component.inchikey
      • Component.inchikey_from_rdkit
      • Component.inchikey_from_rdkit_matches_ccd()
      • Component.library_search()
      • Component.locate_fragment()
      • Component.modified_date
      • Component.mol_no_h
      • Component.name
      • Component.number_atoms
      • Component.pdbx_release_status
      • Component.physchem_properties
      • Component.released
      • Component.scaffolds
  • pdbeccdutils.core.ccd_writer
    • to_cml_str()
    • to_json_dict()
    • to_json_str()
    • to_pdb_ccd_cif_file()
    • to_pdb_str()
    • to_sdf_str()
    • to_xml_str()
    • to_xml_xml()
    • to_xyz_str()
    • write_molecule()
  • pdbeccdutils.core.prd_reader
    • read_pdb_cif_file()
    • read_pdb_components_file()
  • pdbeccdutils.core.prd_writer
    • to_pdb_ccd_cif_file()
    • to_pdb_str()
    • write_molecule()
  • pdbeccdutils.core.clc_reader
    • CLCReaderResult
      • CLCReaderResult.bound_molecule
      • CLCReaderResult.component
      • CLCReaderResult.errors
      • CLCReaderResult.sanitized
      • CLCReaderResult.warnings
    • get_chem_comp_bonds()
    • infer_multiple_chem_comp()
    • read_clc_cif_file()
    • read_clc_components_file()
    • read_pdb_cif_file()
  • pdbeccdutils.core.clc_writer
    • to_cml_str()
    • to_pdb_clc_cif_file()
    • to_pdb_str()
    • to_xml_xml()
    • write_molecule()
  • pdbeccdutils.core.boundmolecule
    • find_pntr_entry()
    • infer_bound_molecules()
    • parse_bound_molecules()
    • parse_ligands_from_branch_scheme()
    • parse_ligands_from_nonpoly_scheme()
  • pdbeccdutils.core.depictions
    • DepictionManager
      • DepictionManager.depict_molecule()
    • DepictionValidator
      • DepictionValidator.count_bond_collisions()
      • DepictionValidator.count_suboptimal_atom_positions()
      • DepictionValidator.depiction_score()
      • DepictionValidator.has_bond_crossing()
      • DepictionValidator.has_degenerated_atom_positions()
  • pdbeccdutils.core.fragment_library
    • FragmentLibrary
      • FragmentLibrary.generate_conformers()
      • FragmentLibrary.to_image()
  • pdbeccdutils.core.models
    • AssemblyResidue
      • AssemblyResidue.to_dict()
    • CCDProperties
    • ConformerType
      • ConformerType.Ideal
      • ConformerType.Model
      • ConformerType.Depiction
      • ConformerType.Computed
      • ConformerType.AllConformers
    • DepictionResult
      • DepictionResult.mol
      • DepictionResult.score
      • DepictionResult.source
      • DepictionResult.template_name
    • DepictionSource
    • Descriptor
      • Descriptor.program
      • Descriptor.program_version
      • Descriptor.type
      • Descriptor.value
    • FragmentEntry
    • InChIFromRDKit
      • InChIFromRDKit.errors
      • InChIFromRDKit.inchi
      • InChIFromRDKit.warnings
    • LogType
      • LogType.ERROR
      • LogType.WARNING
      • LogType.DEPICTION_FAILED
      • LogType.DEPICTION_SCORE
    • MolFromRDKit
      • MolFromRDKit.errors
      • MolFromRDKit.mol
      • MolFromRDKit.warnings
    • ParityResult
      • ParityResult.similarity_score
    • ReleaseStatus
      • ReleaseStatus.from_str()
    • Residue
      • Residue.to_arpeggio()
      • Residue.to_dict()
    • SanitisationResult
      • SanitisationResult.mol
      • SanitisationResult.status
    • ScaffoldingMethod
    • Subcomponent
    • SubstructureMapping
  • pdbeccdutils.core.exceptions
    • CCDUtilsError
    • EntryFailedException
• helpers
  • pdbeccdutils.helpers.cif_tools
    • fix_updated_mmcif()
    • get_ccd_cif_enriched_dir()
    • get_prd_cif_enriched_dir()
    • get_prd_code()
    • get_prdcc_code()
    • preprocess_cif_category()
  • pdbeccdutils.helpers.drawing
    • convert_svg()
    • draw_molecule()
    • get_drawing_scale()
    • save_no_image()
  • pdbeccdutils.helpers.conversions
    • listit()
    • str_to_float()
    • str_to_int()
  • pdbeccdutils.helpers.helper
    • bond_pdb_order()
    • check_args()
    • get_additional_fields()
    • set_up_logger()
    • validate_path_exists()
  • pdbeccdutils.helpers.mol_tools
    • correct_atom_coords()
    • fix_conformer()
    • fix_molecule()
    • get_component_atom_id()
    • get_conformer()
    • inchi_from_mol()
    • inchikey_from_inchi()
    • is_degenerate_conformer()
    • mol_from_inchi()
    • sanitize()
• utils
  • pubchem_downloader
    • PubChemDownloader
      • PubChemDownloader.process_template()
      • PubChemDownloader.update_ccd_dir()
      • PubChemDownloader.update_ccd_file()
    • download_template()
    • rescale_molecule()
  • web_services
    • get_agreed_unichem_mapping()
    • get_all_unichem_mapping()
• scripts
  • PDBeChem pipeline
    • PDBeChemManager
      • PDBeChemManager.process_single_component()
      • PDBeChemManager.run()
    • create_parser()
    • main()
  • Setup PubChem library
    • main()