Reference

Classes

Main classes provided by the package

exceptions.ChemicalConversionError: Error during chemical format conversion.
exceptions.ClassificationError: Error during chemical classification.
exceptions.ConfigurationError: Error in configuration settings.
exceptions.DataExportError: Error exporting data to a file.
exceptions.DataLoadingError: Error loading data from a file or URL.
exceptions.InChIError: Error parsing an InChI string.
exceptions.InvalidInputError: Error for invalid user input.
exceptions.MoleculeParsingError: Error parsing a molecule representation.
exceptions.NetworkError: Error during network operations.
exceptions.SMARTSError: Error parsing a SMARTS pattern.
exceptions.SMILESError: Error parsing a SMILES string.

Exceptions

Exception classes

SmartclassError: Base exception for all smartclass errors.

Functions

Utility functions

bfs_search_classes_generator.tqdm_bfs_search_classes_generator(): BFS search with tqdm progress bar.
calculate_mcs(): Calculate Maximum Common Substructure (MCS) for a list of molecules.
check_missing_stereochemistry(): Check stereochemistry.
check_smiles_contains_no_dot(): Checks if SMILES contains no dot.
check_smiles_contains_no_isotope(): Checks if SMILES contains no isotope.
check_smiles_isomeric(): Check isomeric smiles.
combine_csv_files(): Combine multiple CSV files into a single CSV file.
configure_logging(): Configure logging for the smartclass package.
convert_chemical_formula(): Convert chemical formula.
convert_classyfire_dict(): Converts the classyfire json into a CHEMONTID dictionary.
convert_inchi_to_inchikey(): Convert a structure InChI to InChIKey.
convert_inchi_to_mass(): Convert a structure InChI to mass.
convert_inchi_to_mol(): Convert a structure InChI to MOL.
convert_inchi_to_smiles(): Convert a structure InChI to SMILES.
convert_list_of_dict(): Convert a list of dictionaries to a dictionary with possible inversion.
convert_mol_to_cxsmiles(): Convert a structure MOL to CXSMILES.
convert_mol_to_inchi(): Convert a structure MOL to InChI.
convert_mol_to_inchikey(): Convert an RDKit Mol object to an InChIKey.
convert_mol_to_smarts(): Convert a structure MOL to SMARTS.
convert_mol_to_smiles(): Convert a structure MOL to SMILES.
convert_molblock_to_mol(): Convert a structure MOLBlock to MOL.
convert_smarts_to_mol(): Convert a structure SMARTS to MOL.
convert_smiles_to_canonical_smiles(): Convert a structure SMILES to canonical SMILES.
convert_smiles_to_formula(): Convert a structure SMILES to a molecular formula.
convert_smiles_to_inchi(): Convert a structure SMILES to InChI.
convert_smiles_to_mass(): Convert a structure SMILES to an exact mass.
convert_smiles_to_mol(): Convert a SMILES string to an RDKit Mol object.
download_file_if_not_exists(): Downloads a file from the specified URL if it does not exist.
enumerate_structures(): Enumerate structural variants of a molecule.
export_dict_to_json(): Export dict to json.
export_results(): Export a list of dictionaries to a CSV or TSV file.
fix_inchi_tautomerization(): Fix InChI tautomerization.
get_config(): Get the global configuration instance.
get_logger(): Get a logger for the given module name.
get_num_atoms_bonds(): Get number of atoms and bonds.
get_num_matched_atoms_bonds(): Get number of matched atoms and bonds.
get_request(): Send a GET request to a SPARQL endpoint and retrieve JSON data.
load_csv_from_path(): Load csv from path.
load_external_classes_file(): Load a Polars DataFrame from an external tsv file with chemical classes.
load_json_from_path(): Load json from path.
load_json_from_url(): Load JSON from URL.
load_json_from_url_or_path(): Load json from URL or path.
load_pkg_bitter_smiles(): Load bitter SMILES data from the package file into a Polars DataFrame.
load_pkg_chemical_hierarchy(): Load chemical class hierarchy from a TSV file.
load_pkg_classes(): Load chemical classes data from the package file into a Polars DataFrame.
load_pkg_data(): Load the package data.
load_pkg_file(): Load data from a package-bundled file into a Polars DataFrame.
load_pkg_mappings(): Load chemont__wd mappings data from the package file into a Polars DataFrame.
load_pkg_mia(): Load Mono Indole Alkaloids (MIA) data from the package file into a Polars DataFrame.
load_smiles(): Load unique SMILES strings from a CSV or TSV file.
load_tsv_from_path(): Load tsv from path.
read_query(): Read a SPARQL query from a file path or URL.
resources.extract_chebi(): Extract CHEBI.
resources.get_chebi(): Get CHEBI.
sample_list(): Randomly sample items from a list.
search_class.build_filter_catalog(): Build a FilterCatalog from SMARTS patterns.
search_classes.tqdm_bfs_search_classes_generator(): BFS search with tqdm progress bar.
split_csv(): Split a CSV file into multiple smaller CSV files.
standardize(): Standardize.

Constants

Module-level constants and data

bfs_search_classes_generator.ClassDict
bfs_search_classes_generator.ClassHierarchy
bfs_search_classes_generator.MatchResult
bfs_search_classes_generator.c
bfs_search_classes_generator.class_hierarchy
bfs_search_classes_generator.classes
bfs_search_classes_generator.logger
bfs_search_classes_generator.params
bfs_search_classes_generator.results_bfs
bfs_search_classes_generator.structures
search_class.logger
search_classes.RESULT_FIELDS
search_classes.logger

Other

Additional exports

api: SMARTCLASS API TODO.
chebi: Smartclass classifies structures using SMARTS.resources.chebi.
chem: Smartclass classifies structures using SMARTS.chem.
chembl: Smartclass classifies structures using SMARTS.resources.chembl.
chemont: Smartclass classifies structures using SMARTS.resources.chemont.
examples: Smartclass classifies structures using SMARTS.examples.
get_class_structures: Build class_id to class_structure mapping from a classes list.
io: Smartclass classifies structures using SMARTS.io.
schema: Smartclass classifies structures using SMARTS.schema.
testing: Smartclass classifies structures using SMARTS.testing.
wikidata: Smartclass classifies structures using SMARTS.resources.wikidata.