ambit2.smarts.groups

Class GroupMatch

java.lang.Object

ambit2.smarts.groups.GroupMatch

public class GroupMatch
extends Object

Constructor Summary

Constructors

Constructor and Description
GroupMatch(String smarts, SmartsParser parser, IsomorphismTester isoTester)

Method Summary

Modifier and Type	Method and Description
void	configure()
String	getError()
SmartsConst.SSM_MODE	getFlagSSMode()
IsomorphismTester	getIsoTester()
List<List<org.openscience.cdk.interfaces.IAtom>>	getMappings(org.openscience.cdk.interfaces.IAtomContainer target)
SmartsParser	getParser()
List<SmartsAtomExpression>	getRecursiveAtoms(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
List<QuerySequenceElement>	getSequence()
String	getSmarts()
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	getSmartsQuery()
boolean	isFlagPrepareTarget()
void	mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression> recursiveAtoms, org.openscience.cdk.interfaces.IAtomContainer target)
boolean	match(org.openscience.cdk.interfaces.IAtomContainer target)
boolean	matchAtPosition(org.openscience.cdk.interfaces.IAtomContainer target, int atomNum)
int	matchCount(org.openscience.cdk.interfaces.IAtomContainer target)
void	setFlagPrepareTarget(boolean flagPrepareTarget)
void	setFlagSSMode(SmartsConst.SSM_MODE flagSSMode)

Methods inherited from class java.lang.Object

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

Constructor Detail

GroupMatch

public GroupMatch(String smarts,
                  SmartsParser parser,
                  IsomorphismTester isoTester)
           throws EmptyMoleculeException

Throws:

EmptyMoleculeException

Method Detail

configure

public void configure()
               throws EmptyMoleculeException

Throws:

EmptyMoleculeException

getRecursiveAtoms

public List<SmartsAtomExpression> getRecursiveAtoms(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

match

public boolean match(org.openscience.cdk.interfaces.IAtomContainer target)
              throws EmptyMoleculeException

Throws:

EmptyMoleculeException

matchAtPosition

public boolean matchAtPosition(org.openscience.cdk.interfaces.IAtomContainer target,
                               int atomNum)
                        throws EmptyMoleculeException

Throws:

EmptyMoleculeException

getMappings

public List<List<org.openscience.cdk.interfaces.IAtom>> getMappings(org.openscience.cdk.interfaces.IAtomContainer target)
                                                             throws EmptyMoleculeException

Throws:

EmptyMoleculeException

matchCount

public int matchCount(org.openscience.cdk.interfaces.IAtomContainer target)
               throws EmptyMoleculeException

Throws:

EmptyMoleculeException

mapRecursiveAtomsAgainstTarget

public void mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression> recursiveAtoms,
                                           org.openscience.cdk.interfaces.IAtomContainer target)
                                    throws EmptyMoleculeException

Throws:

EmptyMoleculeException

getFlagSSMode

public SmartsConst.SSM_MODE getFlagSSMode()

setFlagSSMode

public void setFlagSSMode(SmartsConst.SSM_MODE flagSSMode)

isFlagPrepareTarget

public boolean isFlagPrepareTarget()

setFlagPrepareTarget

public void setFlagPrepareTarget(boolean flagPrepareTarget)

getIsoTester

public IsomorphismTester getIsoTester()

getParser

public SmartsParser getParser()

getSmarts

public String getSmarts()

getSmartsQuery

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer getSmartsQuery()

getSequence

public List<QuerySequenceElement> getSequence()

getError

public String getError()