rdkit.ML.Cluster.Murtagh module

Interface to the C++ Murtagh hierarchic clustering code

rdkit.ML.Cluster.Murtagh.ClusterData(data, nPts, method, isDistData=0)

clusters the data points passed in and returns the cluster tree

Arguments

• data: a list of lists (or array, or whatever) with the input data (see discussion of _isDistData_ argument for the exception)

• nPts: the number of points to be used

• method: determines which clustering algorithm should be used.

  The defined constants for these are: ‘WARDS, SLINK, CLINK, UPGMA’

• isDistData: set this toggle when the data passed in is a

  distance matrix. The distance matrix should be stored symmetrically so that _LookupDist (above) can retrieve the results:

  for i<j: d_ij = dists[j*(j-1)//2 + i]

Returns

• a single entry list with the cluster tree