pdbeccdutils Logo
0.8.6
  • Introduction
    • Installation
  • Getting started
    • Reading CCD mmCIF files
    • Reading PRD mmCIF files
      • Component
    • Infer Covalently Linked Components (CLC) from PDB model files
    • Reading CLC mmCIF files
    • Writing CCD/PRD/CLC files
  • Depictions
  • Fragments
    • Identifying fragments of a chemical component
    • Identifying all chemical components with penicillin fragment
    • PDBe supplied fragments
  • Scaffolds
  • Similarity
  • Pipelines
    • Processing of CCD/PRD
      • Data enrichment process
    • Processing of boundmolecules from PDB model files
  • API documentation
    • computations
      • pdbeccdutils.computations.parity_method
        • compare_molecules()
    • core
      • pdbeccdutils.core.ccd_reader
      • pdbeccdutils.core.component
        • Component
      • 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
        • 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
        • DepictionValidator
      • pdbeccdutils.core.fragment_library
        • FragmentLibrary
      • pdbeccdutils.core.models
        • AssemblyResidue
        • CCDProperties
        • ConformerType
        • DepictionResult
        • DepictionSource
        • Descriptor
        • FragmentEntry
        • InChIFromRDKit
        • LogType
        • MolFromRDKit
        • ParityResult
        • ReleaseStatus
        • Residue
        • SanitisationResult
        • 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
        • change_bonds_type()
        • correct_atom_coords()
        • fix_conformer()
        • fix_molecule()
        • get_conformer()
        • inchi_from_mol()
        • inchikey_from_inchi()
        • is_degenerate_conformer()
        • mol_from_inchi()
        • rdkit_object_property()
        • sanitize()
    • utils
      • pubchem_downloader
        • PubChemDownloader
        • download_template()
        • rescale_molecule()
      • web_services
        • get_agreed_unichem_mapping()
        • get_all_unichem_mapping()
    • scripts
      • PDBeChem pipeline
        • PDBeChemManager
        • create_parser()
        • main()
      • Setup PubChem library
        • main()
pdbeccdutils
  • Search

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