rdkit.DataManip.Metric.rdMetricMatrixCalc module — The RDKit 2025.09.6 documentation

# rdkit.DataManip.Metric.rdMetricMatrixCalc module

Module containing the calculator for metric matrix calculation, e.g. similarity and distance matrices

rdkit.DataManip.Metric.rdMetricMatrixCalc.GetEuclideanDistMat((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)descripMat) → object :

  Compute the distance matrix from a descriptor matrix using the Euclidean distance metric

  > ARGUMENTS:

  > > descripMat - A python object of any one of the following types
  > >   1. A numeric array of dimensions n by m where n is the number of items in the data set

  > >        and m is the number of descriptors

  > >   2. A list of Numeric Vectors (or 1D arrays), each entry in the list corresponds

  > >        to descriptor vector for one item

  > >   3. A list (or tuple) of lists (or tuples) of values, where the values can be extracted to

  > >        double.

  > RETURNS:

  >   A numeric one-dimensional array containing the lower triangle elements of the symmetric distance matrix

  C++ signature :

    _object* GetEuclideanDistMat(boost::python::api::object)

rdkit.DataManip.Metric.rdMetricMatrixCalc.GetTanimotoDistMat((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bitVectList) → object :

  Compute the distance matrix from a list of BitVects using the Tanimoto distance metric

  > ARGUMENTS:

  > > bitVectList - a list of bit vectors. Currently this works only for a list of explicit bit vectors,

  > >   needs to be expanded to support a list of SparseBitVects

  > RETURNS:

  >   A numeric 1 dimensional array containing the lower triangle elements of the symmetric distance matrix

  C++ signature :

    _object* GetTanimotoDistMat(boost::python::api::object)

rdkit.DataManip.Metric.rdMetricMatrixCalc.GetTanimotoSimMat((rdkit.Chem.rdMolDescriptors.AtomPairsParameters)bitVectList) → object :

  Compute the similarity matrix from a list of BitVects

  > ARGUMENTS:

  > > bitVectList - a list of bit vectors. Currently this works only for a list of explicit bit vectors,

  > >   needs to be expanded to support a list of SparseBitVects

  > RETURNS:

  >   A numeric 1 dimensional array containing the lower triangle elements of the symmetric similarity matrix

  C++ signature :

    _object* GetTanimotoSimMat(boost::python::api::object)