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

# rdkit.Chem.Fingerprints.FingerprintMols module

utility functionality for fingerprinting sets of molecules

  includes a command line app for working with fingerprints and databases

Sample Usage:

> python FingerprintMols.py -d data.gdb -t ‘raw_dop_data’ –smilesName=”Structure” –idName=”Mol_ID” –outTable=”daylight_sig”

rdkit.Chem.Fingerprints.FingerprintMols.FingerprintMol(mol, fingerprinter=<Boost.Python.function object>, **fpArgs)

class rdkit.Chem.Fingerprints.FingerprintMols.FingerprinterDetails

  Bases: `object`

  class for storing the details of a fingerprinting run, generates sensible defaults on construction

  GetMetricName()
  SetMetricFromName(name)

rdkit.Chem.Fingerprints.FingerprintMols.FingerprintsFromDetails(details, reportFreq=10)

rdkit.Chem.Fingerprints.FingerprintMols.FingerprintsFromMols(mols, fingerprinter=<Boost.Python.function object>, reportFreq=10, maxMols=-1, **fpArgs)

  fpArgs are passed as keyword arguments to the fingerprinter

  Returns a list of 2-tuples: (ID,fp)

rdkit.Chem.Fingerprints.FingerprintMols.FingerprintsFromPickles(dataSource, idCol, pklCol, fingerprinter=<Boost.Python.function object>, reportFreq=10, maxMols=-1, **fpArgs)

  fpArgs are passed as keyword arguments to the fingerprinter

  Returns a list of 2-tuples: (ID,fp)

rdkit.Chem.Fingerprints.FingerprintMols.FingerprintsFromSmiles(dataSource, idCol, smiCol, fingerprinter=<Boost.Python.function object>, reportFreq=10, maxMols=-1, **fpArgs)

  fpArgs are passed as keyword arguments to the fingerprinter

  Returns a list of 2-tuples: (ID,fp)

rdkit.Chem.Fingerprints.FingerprintMols.FoldFingerprintToTargetDensity(fp, **fpArgs)

rdkit.Chem.Fingerprints.FingerprintMols.GetRDKFingerprint(mol)

  uses default parameters

rdkit.Chem.Fingerprints.FingerprintMols.ParseArgs(details=None)

  parses the command line arguments and returns a _FingerprinterDetails_ instance with the results.

  Note:

  > - If you make modifications here, please update the global _usageDoc string so the Usage message is up to date.

  > - This routine is used by both the fingerprinter, the clusterer and the screener; not all arguments make sense for all applications.

rdkit.Chem.Fingerprints.FingerprintMols.Usage()

  prints a usage string and exits

rdkit.Chem.Fingerprints.FingerprintMols.error(msg)

rdkit.Chem.Fingerprints.FingerprintMols.message(msg)