Standardization

chemFilters provides molecular standardization through ChemStandardizer and identifier conversion through InchiHandling.

ChemStandardizer

ChemStandardizer supports several standardization pipelines:

Method	Description	Extra required
"chembl"	ChEMBL structure pipeline	(base install)
"canon"	RDKit canonical SMILES	(base install)
"papyrus"	Papyrus structure pipeline	standardizers
"molvs"	MolVS standardizer	standardizers
callable	Any function taking rdkit.Mol	(depends on func)

from chemFilters.chem.standardizers import ChemStandardizer

standardizer = ChemStandardizer(method="chembl", from_smi=True)
standardized = standardizer(["CC(=O)Oc1ccccc1C(=O)O", "c1ccccc1"])

Using papyrus or molvs

Note

Requires the standardizers extra: pip install 'chem-filters[standardizers]'

standardizer = ChemStandardizer(method="papyrus", from_smi=True)

Custom standardizer

You can pass any callable that accepts rdkit.Chem.Mol objects:

def my_standardizer(mol):
    # your logic here
    return mol

standardizer = ChemStandardizer(method=my_standardizer, from_smi=False)

InchiHandling

Convert molecules to InChI, InChIKey, or connectivity layers:

from chemFilters.chem.standardizers import InchiHandling

converter = InchiHandling(convert_to="inchikey", from_smi=True)
keys = converter(["CC(=O)Oc1ccccc1C(=O)O", "c1ccccc1"])

The convert_to parameter accepts "inchi", "inchikey", or "connectivity".