Package com.chemaxon.clustering.framework

Interface FrameworkClusteringResults

  • @Beta
@PublicAPI
public interface FrameworkClusteringResults
    Results of a framework based clustering. A framework based clustering result is a composition of a clustering hierarchy (represented by an IDBasedHierarchicClustering) and an association of cluster to structural framework. Leaf IDs (indices) of the hierarchy refer to the input structures while cluster IDs (indices) refer to the frameworks. The framework representation can be implementation dependent (like List of structural framework SMILES or Molecule objects).

    Note that this interface can represent the clustering results of Library MCS algorithm which: it is not a pure structural framework based clustering.

    Note that the retrieval of the input structures is not a responsibility of this interface. When needed the input structures must be stored independently. A typical clustering implementation might read input structures through a SmilesMemoizingMoleculeIterator instance (created by MoleculeIo#molImporterMemoizingIterator(com.chemaxon.calculations.io.CloseableIterator, com.chemaxon.calculations.io.Sink)) which provides explicit index mapping and structure retrieval

    Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

    • Method Detail

      • getFrameworkAsMolecule

        Molecule getFrameworkAsMolecule​(int clusterIndex)
        Get framework as Molecule.
        Parameters:
        clusterIndex - Cluster index
        Returns:
        Framework as Molecule object

      • getFrameworkAsSmiles

        String getFrameworkAsSmiles​(int clusterIndex)
        Get framework as SMILES.
        Parameters:
        clusterIndex - Cluster index
        Returns:
        Framework as SMILES

      • getFrameworksCount

        int getFrameworksCount()
        Total represented frameworks.
        Returns:
        framworks count.

      • getHierarchy

        IDBasedHierarchicClustering getHierarchy()
        Get clustering hierarchy. Cluster representants are set to an arbitrary structure from the cluster.
        Returns:
        Clustering hierarchy

      • getFrameworkAsSmilesFunction

        com.google.common.base.Function<Integer,​String> getFrameworkAsSmilesFunction()
        Delegate getFrameworkAsSmiles(int).
        Returns:
        Function to retrieve frameworks for clusterIds as SMILES Strings.