RDKit Cluster Matrix






Generates a clustered distance matrix from a dataset of molecules using Butina clustering from RDKit. Is usefully combined with the Heatmap cell for displaying the distance matrix


A dataset of molecules


A dataset of basic objects containing the similarity scores for each cell in the matrix


ThresholdThe similarity threshold for clustering
Matrix thresholdThe similarity threshold for including the comparison in the output. If the similarity is less than the specified value it is excluded. Useful for reducing the size of the output by removing low similarities
DescriptorFingerprint type. Options are: maccs, morgan2, morgan3, rdkit (default
MetricSimilarity comparison metric. Options are: asymmetric, braunblanquet, cosine, dice, kulczynski, mcconnaughey, rogotgoldberg, russel, sokal, tanimoto (default)


Note: this cell is subject to change

The cell outputs a similarity matrix for a set of structures, and includes IDs that reflect the cluster that structure corresponds to. The Similarity threshold, Descriptor and metric determines the clustering. The Matrix threshold determines which scores are output.

Note: this cell does NOT output structures, only the pairwise similarity scores. If you just want the molecules clustering use the RDKit Butina Clustering cell.

A common use for this cell is to display the similarities amongst a set of structures using the Heatmap cell.