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

# rdkit.Chem.Fingerprints.ClusterMols module

utility functionality for clustering molecules using fingerprints

  includes a command line app for clustering

Sample Usage:

  python ClusterMols.py -d data.gdb -t daylight_sig –idName=”CAS_TF” -o clust1.pkl –actTable=”dop_test” –actName=”moa_quant”

rdkit.Chem.Fingerprints.ClusterMols.ClusterFromDetails(details)

  Returns the cluster tree

rdkit.Chem.Fingerprints.ClusterMols.ClusterPoints(data, metric, algorithmId, haveLabels=False, haveActs=True, returnDistances=False)

rdkit.Chem.Fingerprints.ClusterMols.GetDistanceMatrix(data, metric, isSimilarity=1)

  data should be a list of tuples with fingerprints in position 1 (the rest of the elements of the tuple are not important)

  > Returns the symmetric distance matrix (see ML.Cluster.Resemblance for layout documentation)