rdkit.ML.Cluster.ClusterUtils module

utility functions for clustering

rdkit.ML.Cluster.ClusterUtils.FindClusterCentroidFromDists(cluster, dists)

find the point in a cluster which has the smallest summed

Euclidean distance to all others

Arguments

• cluster: the cluster to work with
• dists: the distance matrix to use for the points

Returns

• the index of the centroid point

rdkit.ML.Cluster.ClusterUtils.GetNodeList(cluster)

returns an ordered list of all nodes below cluster

the ordering is done using the lengths of the child nodes

Arguments

• cluster: the cluster in question

Returns

• a list of the leaves below this cluster

rdkit.ML.Cluster.ClusterUtils.GetNodesDownToCentroids(cluster, above=1)

returns an ordered list of all nodes below cluster

rdkit.ML.Cluster.ClusterUtils.SplitIntoNClusters(cluster, n, breadthFirst=True)

splits a cluster tree into a set of branches

Arguments

• cluster: the root of the cluster tree
• n: the number of clusters to include in the split
• breadthFirst: toggles breadth first (vs depth first) cleavage of the cluster tree.

Returns

• a list of sub clusters