--- name: smartclass description: > Classify chemical structures using SMARTS patterns against Wikidata-sourced chemical classes. Use when writing Python code that uses the smartclass package. license: MIT compatibility: Requires Python >=3.12. --- # smartclass Classify chemical structures using SMARTS patterns against Wikidata-sourced chemical classes ## Installation ```bash pip install smartclass ``` ## API overview ### Classes Main classes provided by the package - `exceptions.ChemicalConversionError` - `exceptions.ClassificationError` - `exceptions.ConfigurationError` - `exceptions.DataExportError` - `exceptions.DataLoadingError` - `exceptions.InChIError` - `exceptions.InvalidInputError` - `exceptions.MoleculeParsingError` - `exceptions.NetworkError` - `exceptions.SMARTSError` - `exceptions.SMILESError` ### Exceptions Exception classes - `SmartclassError`: Base exception for all smartclass errors ### Functions Utility functions - `bfs_search_classes_generator.tqdm_bfs_search_classes_generator` - `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` - `resources.get_chebi` - `sample_list`: Randomly sample items from a list - `search_class.build_filter_catalog` - `search_classes.tqdm_bfs_search_classes_generator` - `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` - `get_class_structures`: Build a mapping from class IDs to their SMARTS structures - `io`: Smartclass classifies structures using SMARTS.io - `schema` - `testing` - `wikidata`: Smartclass classifies structures using SMARTS.resources.wikidata ## Resources - [llms.txt](llms.txt) — Indexed API reference for LLMs - [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs