com.chemaxon.clustering.framework

Interface FrameworkClusteringResults

All Known Implementing Classes:

FrameworkClusteringResultsMolImpl, FrameworkClusteringResultsSmiImpl

@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 Summary

Modifier and Type	Method and Description
Molecule	getFrameworkAsMolecule(int clusterIndex) Get framework as Molecule.
Function<Integer,Molecule>	getFrameworkAsMoleculeFunction() Delegate getFrameworkAsMolecule(int).
String	getFrameworkAsSmiles(int clusterIndex) Get framework as SMILES.
Function<Integer,String>	getFrameworkAsSmilesFunction() Delegate getFrameworkAsSmiles(int).
int	getFrameworksCount() Total represented frameworks.
IDBasedHierarchicClustering	getHierarchy() Get clustering hierarchy.

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

Function<Integer,String> getFrameworkAsSmilesFunction()

Delegate getFrameworkAsSmiles(int).

Returns:

Function to retrieve frameworks for clusterIds as SMILES Strings.

getFrameworkAsMoleculeFunction

Function<Integer,Molecule> getFrameworkAsMoleculeFunction()

Delegate getFrameworkAsMolecule(int).

Returns:

Function to retrieve frameworks for clusterIds as Molecule objects..