ambit2.smarts

Class IsomorphismTester

java.lang.Object

ambit2.smarts.IsomorphismTester

public class IsomorphismTester
extends Object

Author:

Nikolay Kochev nick@uni-plovdiv.bg

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	FlagCheckStereoElements
protected boolean	FlagStoreIsomorphismNode
protected boolean	isomorphismFound
protected List<Node>	isomorphismNodes
protected org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	query
protected List<QuerySequenceElement>	sequence
protected List<org.openscience.cdk.isomorphism.matchers.IQueryAtom>	sequencedAtoms
protected List<org.openscience.cdk.isomorphism.matchers.IQueryAtom>	sequencedBondAt1
protected List<org.openscience.cdk.isomorphism.matchers.IQueryAtom>	sequencedBondAt2
protected Stack<Node>	stack
protected org.openscience.cdk.interfaces.IAtomContainer	target
protected List<org.openscience.cdk.interfaces.IAtom>	targetAt

Constructor Summary

Constructors

Constructor and Description
IsomorphismTester()

Method Summary

Modifier and Type	Method and Description
boolean	checkIsomorphismAtPosition(org.openscience.cdk.interfaces.IAtomContainer container, int atomNum)
List<org.openscience.cdk.interfaces.IBond>	generateBondMapping(org.openscience.cdk.interfaces.IAtomContainer container, List<org.openscience.cdk.interfaces.IAtom> atomMapping)
List<List<org.openscience.cdk.interfaces.IAtom>>	getAllIsomorphismMappings(org.openscience.cdk.interfaces.IAtomContainer container) If no isomorphism is found the result is empty vector
List<org.openscience.cdk.interfaces.IAtom>	getIsomorphismMapping(org.openscience.cdk.interfaces.IAtomContainer container) This function returns null if no isomorphism is found
List<Integer>	getIsomorphismPositions(org.openscience.cdk.interfaces.IAtomContainer container)
List<List<org.openscience.cdk.interfaces.IAtom>>	getNonIdenticalMappings(org.openscience.cdk.interfaces.IAtomContainer container)
List<List<org.openscience.cdk.interfaces.IAtom>>	getNonOverlappingMappings(org.openscience.cdk.interfaces.IAtomContainer container)
List<List<Integer>>	getOverlappedMappingClusters(List<List<org.openscience.cdk.interfaces.IAtom>> maps)
List<QuerySequenceElement>	getSequence()
boolean	hasIsomorphism(org.openscience.cdk.interfaces.IAtomContainer container)
boolean	isFlagCheckStereoElements()
void	printDebugInfo()
void	setFlagCheckStereoElements(boolean flagCheckStereoElements)
void	setQuery(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer container)
void	setSequence(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer queryContainer, List<QuerySequenceElement> externalSequence)
List<QuerySequenceElement>	transferSequenceToOwner()

Methods inherited from class java.lang.Object

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

Field Detail

FlagCheckStereoElements

protected boolean FlagCheckStereoElements

query

protected org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query

target

protected org.openscience.cdk.interfaces.IAtomContainer target

isomorphismFound

protected boolean isomorphismFound

FlagStoreIsomorphismNode

protected boolean FlagStoreIsomorphismNode

isomorphismNodes

protected List<Node> isomorphismNodes

stack

protected Stack<Node> stack

targetAt

protected List<org.openscience.cdk.interfaces.IAtom> targetAt

sequence

protected List<QuerySequenceElement> sequence

sequencedAtoms

protected List<org.openscience.cdk.isomorphism.matchers.IQueryAtom> sequencedAtoms

sequencedBondAt1

protected List<org.openscience.cdk.isomorphism.matchers.IQueryAtom> sequencedBondAt1

sequencedBondAt2

protected List<org.openscience.cdk.isomorphism.matchers.IQueryAtom> sequencedBondAt2

Constructor Detail

IsomorphismTester

public IsomorphismTester()

Method Detail

isFlagCheckStereoElements

public boolean isFlagCheckStereoElements()

setFlagCheckStereoElements

public void setFlagCheckStereoElements(boolean flagCheckStereoElements)

setQuery

public void setQuery(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer container)
              throws EmptyMoleculeException

Throws:

EmptyMoleculeException

getSequence

public List<QuerySequenceElement> getSequence()

setSequence

public void setSequence(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer queryContainer,
                        List<QuerySequenceElement> externalSequence)

transferSequenceToOwner

public List<QuerySequenceElement> transferSequenceToOwner()

hasIsomorphism

public boolean hasIsomorphism(org.openscience.cdk.interfaces.IAtomContainer container)

getIsomorphismPositions

public List<Integer> getIsomorphismPositions(org.openscience.cdk.interfaces.IAtomContainer container)

checkIsomorphismAtPosition

public boolean checkIsomorphismAtPosition(org.openscience.cdk.interfaces.IAtomContainer container,
                                          int atomNum)

getIsomorphismMapping

public List<org.openscience.cdk.interfaces.IAtom> getIsomorphismMapping(org.openscience.cdk.interfaces.IAtomContainer container)

This function returns null if no isomorphism is found

Parameters:

container -

Returns:

generateBondMapping

public List<org.openscience.cdk.interfaces.IBond> generateBondMapping(org.openscience.cdk.interfaces.IAtomContainer container,
                                                                      List<org.openscience.cdk.interfaces.IAtom> atomMapping)

getAllIsomorphismMappings

public List<List<org.openscience.cdk.interfaces.IAtom>> getAllIsomorphismMappings(org.openscience.cdk.interfaces.IAtomContainer container)

If no isomorphism is found the result is empty vector

Parameters:

container -

Returns:

getNonIdenticalMappings

public List<List<org.openscience.cdk.interfaces.IAtom>> getNonIdenticalMappings(org.openscience.cdk.interfaces.IAtomContainer container)

getNonOverlappingMappings

public List<List<org.openscience.cdk.interfaces.IAtom>> getNonOverlappingMappings(org.openscience.cdk.interfaces.IAtomContainer container)

getOverlappedMappingClusters

public List<List<Integer>> getOverlappedMappingClusters(List<List<org.openscience.cdk.interfaces.IAtom>> maps)

printDebugInfo

public void printDebugInfo()