org.openscience.cdk.smsd.algorithm.rgraph

Class CDKRMapHandler

java.lang.Object

org.openscience.cdk.smsd.algorithm.rgraph.CDKRMapHandler

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.

@Deprecated
public class CDKRMapHandler
extends Object

This algorithm derives from the algorithm described in [Tonnelier, C. and Jauffret, Ph. and Hanser, Th. and Jauffret, Ph. and Kaufmann, G., Machine Learning of generic reactions: 3. An efficient algorithm for maximal common substructure determination, Tetrahedron Comput. Methodol., 1990, 3:351-358] and modified in the thesis of T. Hanser [Unknown BibTeXML type: HAN93].

Author:

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

Source code:

master

Belongs to CDK module:

smsd

Constructor Summary

Constructors

Constructor and Description
CDKRMapHandler() Deprecated.

Method Summary

Methods

Modifier and Type	Method and Description
void	calculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) Deprecated. This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
void	calculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) Deprecated. This function calculates all the possible combinations of MCS
void	calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) Deprecated. This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
void	calculateSubGraphs(IAtomContainer molecule1, IAtomContainer molecule2, boolean shouldMatchBonds) Deprecated. This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint
protected Stack<List<CDKRMap>>	getAllMaximum(List<List<CDKRMap>> overlaps) Deprecated.
List<Map<Integer,Integer>>	getMappings() Deprecated. Returns mapping solutions
protected List	getMaximum(List overlaps) Deprecated.
IAtomContainer	getSource() Deprecated. Returns source molecule
IAtomContainer	getTarget() Deprecated. Returns target molecule
protected void	identifyMatchedParts(List<List<CDKRMap>> list, IAtomContainer source, IAtomContainer target) Deprecated.
protected void	identifySingleAtomsMatchedParts(List<CDKRMap> list, IAtomContainer source, IAtomContainer target) Deprecated.
protected boolean	isSameRMap(CDKRMap sourceRMap, CDKRMap targetRMap) Deprecated.
protected boolean	isSubgraph(List<CDKRMap> rmaps1, List<CDKRMap> rmaps2) Deprecated.
boolean	isTimeoutFlag() Deprecated. Returns true if a time out occurred else false
protected List<CDKRMap>	removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps) Deprecated.
protected List<List<CDKRMap>>	removeSubGraph(List<List<CDKRMap>> overlaps) Deprecated.
void	setMappings(List<Map<Integer,Integer>> mappings) Deprecated. Set mapping solutions
void	setSource(IAtomContainer aSource) Deprecated. Set source molecule
void	setTarget(IAtomContainer aTarget) Deprecated. Set target molecule
void	setTimeoutFlag(boolean timeoutFlag) Deprecated. Set time out flag

Methods inherited from class java.lang.Object

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

Constructor Detail

CDKRMapHandler

public CDKRMapHandler()

Deprecated.

Method Detail

getSource

public IAtomContainer getSource()

Deprecated.

Returns source molecule

Returns:

the source

setSource

public void setSource(IAtomContainer aSource)

Deprecated.

Set source molecule

Parameters:

aSource - the source to set

getTarget

public IAtomContainer getTarget()

Deprecated.

Returns target molecule

Returns:

the target

setTarget

public void setTarget(IAtomContainer aTarget)

Deprecated.

Set target molecule

Parameters:

aTarget - the target to set

calculateOverlapsAndReduce

public void calculateOverlapsAndReduce(IAtomContainer molecule1,
                              IAtomContainer molecule2,
                              boolean shouldMatchBonds)
                                throws CDKException

Deprecated.

This function calculates all the possible combinations of MCS

Parameters:

molecule1 -

molecule2 -

shouldMatchBonds -

Throws:

CDKException

calculateOverlapsAndReduceExactMatch

public void calculateOverlapsAndReduceExactMatch(IAtomContainer molecule1,
                                        IAtomContainer molecule2,
                                        boolean shouldMatchBonds)
                                          throws CDKException

Deprecated.

This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint

Parameters:

molecule1 -

molecule2 -

shouldMatchBonds -

Throws:

CDKException

calculateSubGraphs

public void calculateSubGraphs(IAtomContainer molecule1,
                      IAtomContainer molecule2,
                      boolean shouldMatchBonds)
                        throws CDKException

Deprecated.

This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint

Parameters:

molecule1 -

molecule2 -

shouldMatchBonds -

Throws:

CDKException

calculateIsomorphs

public void calculateIsomorphs(IAtomContainer molecule1,
                      IAtomContainer molecule2,
                      boolean shouldMatchBonds)
                        throws CDKException

Deprecated.

This function calculates only one solution (exact) because we are looking at the molecules which are exactly same in terms of the bonds and atoms determined by the Fingerprint

Parameters:

molecule1 -

molecule2 -

shouldMatchBonds -

Throws:

CDKException

removeSubGraph

protected List<List<CDKRMap>> removeSubGraph(List<List<CDKRMap>> overlaps)

Deprecated.

Parameters:

overlaps -

Returns:

removeRedundantMappingsForSingleAtomCase

protected List<CDKRMap> removeRedundantMappingsForSingleAtomCase(List<CDKRMap> overlaps)

Deprecated.

Parameters:

overlaps -

Returns:

getMaximum

protected List getMaximum(List overlaps)

Deprecated.

Parameters:

overlaps -

Returns:

getAllMaximum

protected Stack<List<CDKRMap>> getAllMaximum(List<List<CDKRMap>> overlaps)

Deprecated.

Parameters:

overlaps -

Returns:

identifyMatchedParts

protected void identifyMatchedParts(List<List<CDKRMap>> list,
                        IAtomContainer source,
                        IAtomContainer target)

Deprecated.

Parameters:

list -

source -

target -

identifySingleAtomsMatchedParts

protected void identifySingleAtomsMatchedParts(List<CDKRMap> list,
                                   IAtomContainer source,
                                   IAtomContainer target)

Deprecated.

Parameters:

list -

source -

target -

isSubgraph

protected boolean isSubgraph(List<CDKRMap> rmaps1,
                 List<CDKRMap> rmaps2)

Deprecated.

Parameters:

rmaps1 -

rmaps2 -

Returns:

isSameRMap

protected boolean isSameRMap(CDKRMap sourceRMap,
                 CDKRMap targetRMap)

Deprecated.

Parameters:

sourceRMap - sourceAtom

targetRMap - targetAtom

Returns:

getMappings

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

Deprecated.

Returns mapping solutions

Returns:

the mappings

setMappings

public void setMappings(List<Map<Integer,Integer>> mappings)

Deprecated.

Set mapping solutions

Parameters:

mappings - the mappings to set

isTimeoutFlag

public boolean isTimeoutFlag()

Deprecated.

Returns true if a time out occurred else false

Returns:

the timeoutFlag

setTimeoutFlag

public void setTimeoutFlag(boolean timeoutFlag)

Deprecated.

Set time out flag

Parameters:

timeoutFlag - the timeoutFlag to set