Reference

This page includes the reference documentation for all user-facing code from the Smartclass Python package.

Functions

`bfs_search_classes_generator`(classes, ...[, ...])	Perform substructure search using Breadth-First Search traversal.
`calculate_mcs`(mols[, threshold, ...])	Calculate Maximum Common Substructure (MCS) for a list of molecules.
`check_missing_stereochemistry`(smiles[, ...])	Check stereochemistry.
`check_smiles_contains_no_dot`(smiles)	Checks if SMILES contains no dot.
`check_smiles_contains_no_isotope`(smiles)	Checks if SMILES contains no isotope.
`check_smiles_isomeric`(smiles_isomeric[, ...])	Check isomeric smiles.
`combine_csv_files`(input_files, output_file)	Combine multiple CSV files into a single CSV file.
`configure_logging`([level, format_string, ...])	Configure logging for the smartclass package.
`convert_chemical_formula`(text)	Convert chemical formula.
`convert_classyfire_dict`([classyfire_json, ...])	Converts the classyfire json into a CHEMONTID dictionary.
`convert_inchi_to_inchikey`(inchi)	Convert a structure InChI to InChIKey.
`convert_inchi_to_mass`(inchi)	Convert a structure InChI to mass.
`convert_inchi_to_mol`(inchi)	Convert a structure InChI to MOL.
`convert_inchi_to_smiles`(inchi)	Convert a structure InChI to SMILES.
`convert_list_of_dict`(list_of_dict, key, value)	Convert a list of dictionaries to a dictionary with possible inversion.
`convert_mol_to_cxsmiles`(mol)	Convert a structure MOL to CXSMILES.
`convert_mol_to_inchi`(mol)	Convert a structure MOL to InChI.
`convert_mol_to_inchikey`(mol)	Convert an RDKit Mol object to an InChIKey.
`convert_mol_to_smarts`(mol)	Convert a structure MOL to SMARTS.
`convert_mol_to_smiles`(mol)	Convert a structure MOL to SMILES.
`convert_molblock_to_mol`(molblock)	Convert a structure MOLBlock to MOL.
`convert_smarts_to_mol`(smarts)	Convert a structure SMARTS to MOL.
`convert_smiles_to_canonical_smiles`(smiles)	Convert a structure SMILES to canonical SMILES.
`convert_smiles_to_formula`(smiles)	Convert a structure SMILES to a molecular formula.
`convert_smiles_to_inchi`(smiles)	Convert a structure SMILES to InChI.
`convert_smiles_to_mass`(smiles)	Convert a structure SMILES to an exact mass.
`convert_smiles_to_mol`(smiles[, sanitize])	Convert a SMILES string to an RDKit Mol object.
`download_file_if_not_exists`(url, output)	Downloads a file from the specified URL if it does not exist.
`enumerate_structures`(mol)	Enumerate structural variants of a molecule.
`export_dict_to_json`(dic, output)	Export dict to json.
`export_results`(output, results)	Export a list of dictionaries to a CSV or TSV file.
`fix_inchi_tautomerization`(smiles)	Fix InChI tautomerization.
`get_class_structures`(classes)	Build a mapping from class IDs to their SMARTS structures.
`get_config`()	Get the global configuration instance.
`get_logger`(name)	Get a logger for the given module name.
`get_num_atoms_bonds`(mol)	Get number of atoms and bonds.
`get_num_matched_atoms_bonds`(mol_1, mol_2)	Get number of matched atoms and bonds.
`get_request`(url, query[, max_retries, ...])	Send a GET request to a SPARQL endpoint and retrieve JSON data.
`load_csv_from_path`(path)	Load csv from path.
`load_external_classes_file`(file[, id_name, ...])	Load a Polars DataFrame from an external tsv file with chemical classes.
`load_json_from_path`(path)	Load json from path.
`load_json_from_url`(url)	Load JSON from URL.
`load_json_from_url_or_path`(url, name)	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`([file_path])	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`(file[, directory])	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`(input[, column, limit])	Load unique SMILES strings from a CSV or TSV file.
`load_tsv_from_path`(path)	Load tsv from path.
`read_query`(query)	Read a SPARQL query from a file path or URL.
`sample_list`(items[, max_samples])	Randomly sample items from a list.
`search_class`(class_dict, structures[, params])	Search for a single class and return results as dictionaries.
`search_classes`([classes_file, ...])	Perform substructure search to classify chemical structures.
`split_csv`(input_file, output_dir[, ...])	Split a CSV file into multiple smaller CSV files.
`standardize`(smiles)	Standardize.

Classes

SmartclassError(message, *args, **kwargs)

Base exception for all smartclass errors.