com.chemaxon.clustering.framework

Class MoleculeFrameworks

java.lang.Object

com.chemaxon.clustering.framework.MoleculeFrameworks

@Beta
public final class MoleculeFrameworks
extends Object

Molecule transformations used in Bemis-Murcko clustering. Functionality is loosely based on the implementation in jklustor. Transformation steps are implemented as StandardizerWrapper instances. Note that license JKLUSTOR needed to use this class.

Constructor Summary

Constructors

Constructor and Description
MoleculeFrameworks() Construct.

Method Summary

Modifier and Type	Method and Description
StandardizerWrapper	aromatizeBasic()
StandardizerWrapper	aromatizeGeneral()
StandardizerWrapper	aromatizeLoose()
Function<Molecule,Iterator<String>>	bemisMurckoFrameworkAssociation()
Function<Molecule,String>	canonicalSmiles()
<T> Function<Molecule,Iterator<T>>	canonicalSmilesBasedFrameworks(Function<Molecule,T> canonicalSmilesExporter, StandardizerWrapper... wrappers)
StandardizerWrapper	clearMoleculeProperties()
StandardizerWrapper	generalize(boolean keepAtomTypes, boolean keepBondTypes)
StandardizerWrapper	reduceGraph()
StandardizerWrapper	removeAllExplicitH()
StandardizerWrapper	removeSidechains()
StandardizerWrapper	removeSmallFragments()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MoleculeFrameworks

public MoleculeFrameworks()

Construct.

Throws:

LicenseException - when appropriate license is not available

Method Detail

generalize

public StandardizerWrapper generalize(boolean keepAtomTypes,
                                      boolean keepBondTypes)

reduceGraph

public StandardizerWrapper reduceGraph()

removeSidechains

public StandardizerWrapper removeSidechains()

removeSmallFragments

public StandardizerWrapper removeSmallFragments()

removeAllExplicitH

public StandardizerWrapper removeAllExplicitH()

aromatizeBasic

public StandardizerWrapper aromatizeBasic()

aromatizeGeneral

public StandardizerWrapper aromatizeGeneral()

aromatizeLoose

public StandardizerWrapper aromatizeLoose()

clearMoleculeProperties

public StandardizerWrapper clearMoleculeProperties()

canonicalSmiles

public Function<Molecule,String> canonicalSmiles()

canonicalSmilesBasedFrameworks

public <T> Function<Molecule,Iterator<T>> canonicalSmilesBasedFrameworks(Function<Molecule,T> canonicalSmilesExporter,
                                                                         StandardizerWrapper... wrappers)

bemisMurckoFrameworkAssociation

public Function<Molecule,Iterator<String>> bemisMurckoFrameworkAssociation()