Package org.openscience.cdk.smsd.algorithm.rgraph

Class CDKMCSHandler

java.lang.Object

org.openscience.cdk.smsd.interfaces.AbstractMCSAlgorithm

org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSHandler

All Implemented Interfaces:

IMCSBase

@Deprecated
public class CDKMCSHandler
extends AbstractMCSAlgorithm
implements IMCSBase

Deprecated.

This class is part of SMSD and either duplicates functionality elsewhere in the CDK or provides public access to internal implementation details. SMSD has been deprecated from the CDK with a newer, more recent version of SMSD is available at http://github.com/asad/smsd.

This class acts as a handler class for CDKMCS algorithm.

Author:

Syed Asad Rahman <asad@ebi.ac.uk>

Source code:

main

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor	Description
CDKMCSHandler()	Deprecated.

Method Summary

Modifier and Type	Method	Description
List<Map<IAtom,IAtom>>	getAllAtomMapping()	Deprecated. Returns all plausible mappings between query and target molecules.
List<Map<Integer,Integer>>	getAllMapping()	Deprecated. Returns all plausible mappings between query and target molecules.
Map<IAtom,IAtom>	getFirstAtomMapping()	Deprecated. Returns one of the best matches with atoms mapped.
Map<Integer,Integer>	getFirstMapping()	Deprecated. Returns one of the best matches with atom indexes mapped.
protected IAtomContainerSet	getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)	Deprecated.
void	searchMCS(boolean shouldMatchBonds)	Deprecated. Initialise the MCS search algorithm.
void	set(IQueryAtomContainer source, IAtomContainer target)	Deprecated. Initialise the query and target molecule.
void	set(MolHandler source, MolHandler target)	Deprecated. Initialise the query and target molecule.

Methods inherited from class java.lang.Object

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

Constructor Detail

CDKMCSHandler

public CDKMCSHandler()

Deprecated.

Method Detail

set

public void set(MolHandler source,
                MolHandler target)

Deprecated.

Initialise the query and target molecule.

Specified by:

set in interface IMCSBase

Parameters:

source -

target -

set

public void set(IQueryAtomContainer source,
                IAtomContainer target)

Deprecated.

Initialise the query and target molecule.

Specified by:

set in interface IMCSBase

Parameters:

source -

target -

searchMCS

public void searchMCS(boolean shouldMatchBonds)

Deprecated.

Initialise the MCS search algorithm. Each MCS algorithm should contain this method.

Specified by:

searchMCS in class AbstractMCSAlgorithm

Parameters:

shouldMatchBonds -

getUncommon

protected IAtomContainerSet getUncommon(IAtomContainer mol,
                                        IAtomContainer mcss,
                                        boolean shouldMatchBonds)
                                 throws CDKException

Deprecated.

Parameters:

mol -

mcss -

shouldMatchBonds -

Returns:

IMolecule Set

Throws:

CDKException

getAllMapping

public List<Map<Integer,Integer>> getAllMapping()

Deprecated.

Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence index of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule

Specified by:

getAllMapping in interface IMCSBase

Returns:

All possible MCS Mapping Index

getFirstMapping

public Map<Integer,Integer> getFirstMapping()

Deprecated.

Returns one of the best matches with atom indexes mapped.

Specified by:

getFirstMapping in interface IMCSBase

Returns:

Best Mapping Index

getAllAtomMapping

public List<Map<IAtom,IAtom>> getAllAtomMapping()

Deprecated.

Returns all plausible mappings between query and target molecules. Each map in the list has atom-atom equivalence of the mappings between query and target molecule i.e. map.getKey() for the query and map.getValue() for the target molecule

Specified by:

getAllAtomMapping in interface IMCSBase

Returns:

All possible MCS atom Mappings

getFirstAtomMapping

public Map<IAtom,IAtom> getFirstAtomMapping()

Deprecated.

Returns one of the best matches with atoms mapped.

Specified by:

getFirstAtomMapping in interface IMCSBase

Returns:

Best Atom Mapping