rdkit.Chem.Fingerprints.MolSimilarity module — The RDKit 2025.09.6 documentation

# rdkit.Chem.Fingerprints.MolSimilarity module

utility functionality for molecular similarity

  includes a command line app for screening databases

Sample Usage:

> python MolSimilarity.py -d data.gdb -t daylight_sig –idName=”Mol_ID” –topN=100 –smiles=’c1(C=O)ccc(Oc2ccccc2)cc1’ –smilesTable=raw_dop_data –smilesName=”structure” -o results.csv

rdkit.Chem.Fingerprints.MolSimilarity.GetFingerprints(details)

  returns an iterable sequence of fingerprints each fingerprint will have a _fieldsFromDb member whose first entry is the id.

rdkit.Chem.Fingerprints.MolSimilarity.ScreenFingerprints(details, data, mol=None, probeFp=None)

  Returns a list of results

rdkit.Chem.Fingerprints.MolSimilarity.ScreenFromDetails(details, mol=None)

  Returns a list of results

rdkit.Chem.Fingerprints.MolSimilarity.ScreenInDb(details, mol)