ambit2.smarts

Class SMIRKSManager

java.lang.Object

ambit2.smarts.SMIRKSManager

public class SMIRKSManager
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
protected EquivalenceTester	eqTester
protected boolean	FlagAddImplicitHAtomsOnResultProcess
protected boolean	FlagApplyStereoTransformation
protected boolean	FlagAromaticityTransformation
protected boolean	FlagCheckAromaticityOnResultProcess
protected boolean	FlagCheckResultStereo
protected boolean	FlagClearAromaticityBeforeResultProcess
protected boolean	FlagClearExcplicitHAtomsBeforeResultProcess
protected boolean	FlagClearHybridizationBeforeResultProcess
protected boolean	FlagClearImplicitHAtomsBeforeResultProcess
protected boolean	FlagConvertAddedImplicitHToExplicitOnResultProcess
protected boolean	FlagConvertExplicitHToImplicitOnResultProcess
protected boolean	FlagFilterEquivalentMappings
protected boolean	FlagHAtomsTransformation
protected SmartsConst.HandleHAtoms	FlagHAtomsTransformationMode
protected boolean	FlagProcessResultStructures
protected SmartsConst.SSM_MODE	FlagSSMode
protected IsomorphismTester	isoTester
protected SmartsParser	parser
protected List<String>	parserErrors
protected SmartsToChemObject	stco

Constructor Summary

Constructors

Constructor and Description
SMIRKSManager(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
void	applyAromaticityTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, List<org.openscience.cdk.interfaces.IAtom> newProdAtoms, SMIRKSReaction reaction)
void	applyHAtomTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, List<org.openscience.cdk.interfaces.IAtom> newProdAtoms, SMIRKSReaction reaction)
void	applyStereoTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, List<org.openscience.cdk.interfaces.IAtom> newProdAtoms, SMIRKSReaction reaction)
boolean	applyTransformation(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction)
boolean	applyTransformation(org.openscience.cdk.interfaces.IAtomContainer target, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainer	applyTransformationsAtLocationsWithCloning(org.openscience.cdk.interfaces.IAtomContainer target, List<List<org.openscience.cdk.interfaces.IAtom>> rMaps, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainerSet	applyTransformationWithCombinedOverlappedPos(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainerSet	applyTransformationWithSingleCopyForEachPos(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainerSet	applyTransformationWithSingleCopyForEachPos(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction, SmartsConst.SSM_MODE SSMode)
void	applyTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, SMIRKSReaction reaction)
void	checkInvalidatedDBStereo(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IStereoElement> invalidatedStereoElements, Map<org.openscience.cdk.interfaces.IStereoElement,StereoChange> stereoChanges)
List<List<org.openscience.cdk.interfaces.IAtom>>	getAllMappings(org.openscience.cdk.interfaces.IAtomContainer target)
static SMIRKSManager	getDefaultSMIRKSManager()
String	getErrors()
SmartsConst.HandleHAtoms	getFlagHAtomsTransformationMode()
SmartsConst.SSM_MODE	getFlagSSMode()
IsomorphismTester	getIsomorphismTester()
List<List<org.openscience.cdk.interfaces.IAtom>>	getNonIdenticalMappings(org.openscience.cdk.interfaces.IAtomContainer target)
List<List<org.openscience.cdk.interfaces.IAtom>>	getNonOverlappingMappings(org.openscience.cdk.interfaces.IAtomContainer target)
List<SmartsAtomExpression>	getRecursiveAtoms(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
SmartsParser	getSmartsParser()
boolean	hasErrors()
boolean	isFlagAddImplicitHAtomsOnResultProcess()
boolean	isFlagApplyStereoTransformation()
boolean	isFlagAromaticityTransformation()
boolean	isFlagCheckAromaticityOnResultProcess()
boolean	isFlagCheckResultStereo()
boolean	isFlagClearAromaticityBeforeResultProcess()
boolean	isFlagClearExcplicitHAtomsBeforeResultProcess()
boolean	isFlagClearHybridizationBeforeResultProcess()
boolean	isFlagClearImplicitHAtomsBeforeResultProcess()
boolean	isFlagConvertAddedImplicitHToExplicitOnResultProcess()
boolean	isFlagConvertExplicitHToImplicitOnResultProcess()
boolean	isFlagFilterEquivalentMappings()
boolean	isFlagHAtomsTransformation()
boolean	isFlagProcessResultStructures()
void	mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression> recursiveAtoms, org.openscience.cdk.interfaces.IAtomContainer target)
protected boolean	matchCLG(List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> queryFragments, List<Integer> queryCLG, org.openscience.cdk.interfaces.IAtomContainerSet targetComponents)
boolean	matchReaction(SMIRKSReaction reaction, org.openscience.cdk.interfaces.IAtomContainer targetReactants, org.openscience.cdk.interfaces.IAtomContainer targetProducts, org.openscience.cdk.interfaces.IAtomContainer targetAgents)
boolean	matchReaction(SMIRKSReaction reaction, org.openscience.cdk.interfaces.IAtomContainerSet targetReactants, org.openscience.cdk.interfaces.IAtomContainerSet targetProducts, org.openscience.cdk.interfaces.IAtomContainerSet targetAgents)
SMIRKSReaction	parse(String smirks)
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	parseComponent(String smarts, String compType, SmartsFlags flags, List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> fragments, List<Integer> CLG)
void	printMappingClusters(List<List<Integer>> clusterIndexes, org.openscience.cdk.interfaces.IAtomContainer target)
void	printSSMap(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap)
void	processProduct(org.openscience.cdk.interfaces.IAtomContainer mol)
void	setFlagAddImplicitHAtomsOnResultProcess(boolean flagAddImplicitHAtomsOnResultProcess)
void	setFlagApplyStereoTransformation(boolean flagApplyStereoTransformation)
void	setFlagAromaticityTransformation(boolean flagAromaticityTransformation)
void	setFlagCheckAromaticityOnResultProcess(boolean flagCheckAromaticityOnResultProcess)
void	setFlagCheckResultStereo(boolean flagCheckResultStereo)
void	setFlagClearAromaticityBeforeResultProcess(boolean flagClearAromaticityBeforeResultProcess) Typically this flag should be true since some aromatic atoms may have lost their aromaticity
void	setFlagClearExcplicitHAtomsBeforeResultProcess(boolean flagClearExcplicitHAtomsBeforeResultProcess)
void	setFlagClearHybridizationBeforeResultProcess(boolean flagClearHybridizationBeforeResultProcess) Typically this flag should be true in order to correctly detect the new atom types of the transformed molecules
void	setFlagClearImplicitHAtomsBeforeResultProcess(boolean flagClearImplicitHAtomsBeforeResultProcess) Typically this flag should be true in order to correctly detect the new atom types of the transformed molecules
void	setFlagConvertAddedImplicitHToExplicitOnResultProcess(boolean flagConvertAddedImplicitHToExplicitOnResultProcess) Typically if this flag is true it is expected that FlagAddImplicitHAtomsOnResultProcess = false
void	setFlagConvertExplicitHToImplicitOnResultProcess(boolean flagConvertExplicitHToImplicitOnResultProcess) Typically if this flag is true it is expected that FlagAddImlicitHAtomsOnResultProcess= false
void	setFlagFilterEquivalentMappings(boolean flagFilterEquivalentMappings)
void	setFlagHAtomsTransformation(boolean flagHAtomsTransformation)
void	setFlagHAtomsTransformationMode(SmartsConst.HandleHAtoms flagHAtomsTransformationMode)
void	setFlagProcessResultStructures(boolean flagProcessResultStructures) Triggers an optional (pre)processing for further use of reaction result
void	setFlagSSMode(SmartsConst.SSM_MODE flagSSMode)
void	setSSMode(SmartsConst.SSM_MODE mode)

Methods inherited from class java.lang.Object

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

Field Detail

parser

protected SmartsParser parser

isoTester

protected IsomorphismTester isoTester

stco

protected SmartsToChemObject stco

eqTester

protected EquivalenceTester eqTester

parserErrors

protected List<String> parserErrors

FlagSSMode

protected SmartsConst.SSM_MODE FlagSSMode

FlagFilterEquivalentMappings

protected boolean FlagFilterEquivalentMappings

FlagProcessResultStructures

protected boolean FlagProcessResultStructures

FlagClearHybridizationBeforeResultProcess

protected boolean FlagClearHybridizationBeforeResultProcess

FlagClearAromaticityBeforeResultProcess

protected boolean FlagClearAromaticityBeforeResultProcess

FlagClearImplicitHAtomsBeforeResultProcess

protected boolean FlagClearImplicitHAtomsBeforeResultProcess

FlagClearExcplicitHAtomsBeforeResultProcess

protected boolean FlagClearExcplicitHAtomsBeforeResultProcess

FlagAddImplicitHAtomsOnResultProcess

protected boolean FlagAddImplicitHAtomsOnResultProcess

FlagConvertAddedImplicitHToExplicitOnResultProcess

protected boolean FlagConvertAddedImplicitHToExplicitOnResultProcess

FlagCheckAromaticityOnResultProcess

protected boolean FlagCheckAromaticityOnResultProcess

FlagConvertExplicitHToImplicitOnResultProcess

protected boolean FlagConvertExplicitHToImplicitOnResultProcess

FlagCheckResultStereo

protected boolean FlagCheckResultStereo

FlagApplyStereoTransformation

protected boolean FlagApplyStereoTransformation

FlagHAtomsTransformation

protected boolean FlagHAtomsTransformation

FlagHAtomsTransformationMode

protected SmartsConst.HandleHAtoms FlagHAtomsTransformationMode

FlagAromaticityTransformation

protected boolean FlagAromaticityTransformation

Constructor Detail

SMIRKSManager

public SMIRKSManager(org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

getFlagSSMode

public SmartsConst.SSM_MODE getFlagSSMode()

isFlagCheckResultStereo

public boolean isFlagCheckResultStereo()

setFlagCheckResultStereo

public void setFlagCheckResultStereo(boolean flagCheckResultStereo)

setFlagSSMode

public void setFlagSSMode(SmartsConst.SSM_MODE flagSSMode)

isFlagFilterEquivalentMappings

public boolean isFlagFilterEquivalentMappings()

setFlagFilterEquivalentMappings

public void setFlagFilterEquivalentMappings(boolean flagFilterEquivalentMappings)

isFlagProcessResultStructures

public boolean isFlagProcessResultStructures()

setFlagProcessResultStructures

public void setFlagProcessResultStructures(boolean flagProcessResultStructures)

Triggers an optional (pre)processing for further use of reaction result

Parameters:

flagProcessResultStructures -

isFlagClearHybridizationBeforeResultProcess

public boolean isFlagClearHybridizationBeforeResultProcess()

setFlagClearHybridizationBeforeResultProcess

public void setFlagClearHybridizationBeforeResultProcess(boolean flagClearHybridizationBeforeResultProcess)

Typically this flag should be true in order to correctly detect the new atom types of the transformed molecules

Parameters:

flagClearHybridizationBeforeResultProcess -

isFlagClearAromaticityBeforeResultProcess

public boolean isFlagClearAromaticityBeforeResultProcess()

setFlagClearAromaticityBeforeResultProcess

public void setFlagClearAromaticityBeforeResultProcess(boolean flagClearAromaticityBeforeResultProcess)

Typically this flag should be true since some aromatic atoms may have lost their aromaticity

Parameters:

flagClearAromaticityBeforeResultProcess -

isFlagClearImplicitHAtomsBeforeResultProcess

public boolean isFlagClearImplicitHAtomsBeforeResultProcess()

setFlagClearImplicitHAtomsBeforeResultProcess

public void setFlagClearImplicitHAtomsBeforeResultProcess(boolean flagClearImplicitHAtomsBeforeResultProcess)

Typically this flag should be true in order to correctly detect the new atom types of the transformed molecules

Parameters:

flagClearImplicitHAtomsBeforeResultProcess -

isFlagAddImplicitHAtomsOnResultProcess

public boolean isFlagAddImplicitHAtomsOnResultProcess()

setFlagAddImplicitHAtomsOnResultProcess

public void setFlagAddImplicitHAtomsOnResultProcess(boolean flagAddImplicitHAtomsOnResultProcess)

isFlagConvertAddedImplicitHToExplicitOnResultProcess

public boolean isFlagConvertAddedImplicitHToExplicitOnResultProcess()

setFlagConvertAddedImplicitHToExplicitOnResultProcess

public void setFlagConvertAddedImplicitHToExplicitOnResultProcess(boolean flagConvertAddedImplicitHToExplicitOnResultProcess)

Typically if this flag is true it is expected that FlagAddImplicitHAtomsOnResultProcess = false

Parameters:

flagConvertAddedImlicitHToExplicitOnResultProcess -

isFlagCheckAromaticityOnResultProcess

public boolean isFlagCheckAromaticityOnResultProcess()

setFlagCheckAromaticityOnResultProcess

public void setFlagCheckAromaticityOnResultProcess(boolean flagCheckAromaticityOnResultProcess)

isFlagConvertExplicitHToImplicitOnResultProcess

public boolean isFlagConvertExplicitHToImplicitOnResultProcess()

setFlagConvertExplicitHToImplicitOnResultProcess

public void setFlagConvertExplicitHToImplicitOnResultProcess(boolean flagConvertExplicitHToImplicitOnResultProcess)

Typically if this flag is true it is expected that FlagAddImlicitHAtomsOnResultProcess= false

Parameters:

flagConvertExplicitHToImplicitOnResultProcess -

isFlagClearExcplicitHAtomsBeforeResultProcess

public boolean isFlagClearExcplicitHAtomsBeforeResultProcess()

setFlagClearExcplicitHAtomsBeforeResultProcess

public void setFlagClearExcplicitHAtomsBeforeResultProcess(boolean flagClearExcplicitHAtomsBeforeResultProcess)

isFlagApplyStereoTransformation

public boolean isFlagApplyStereoTransformation()

setFlagApplyStereoTransformation

public void setFlagApplyStereoTransformation(boolean flagApplyStereoTransformation)

isFlagHAtomsTransformation

public boolean isFlagHAtomsTransformation()

setFlagHAtomsTransformation

public void setFlagHAtomsTransformation(boolean flagHAtomsTransformation)

getFlagHAtomsTransformationMode

public SmartsConst.HandleHAtoms getFlagHAtomsTransformationMode()

setFlagHAtomsTransformationMode

public void setFlagHAtomsTransformationMode(SmartsConst.HandleHAtoms flagHAtomsTransformationMode)

isFlagAromaticityTransformation

public boolean isFlagAromaticityTransformation()

setFlagAromaticityTransformation

public void setFlagAromaticityTransformation(boolean flagAromaticityTransformation)

getDefaultSMIRKSManager

public static SMIRKSManager getDefaultSMIRKSManager()

getIsomorphismTester

public IsomorphismTester getIsomorphismTester()

getSmartsParser

public SmartsParser getSmartsParser()

setSSMode

public void setSSMode(SmartsConst.SSM_MODE mode)

hasErrors

public boolean hasErrors()

getErrors

public String getErrors()

parse

public SMIRKSReaction parse(String smirks)

parseComponent

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer parseComponent(String smarts,
                                                                                   String compType,
                                                                                   SmartsFlags flags,
                                                                                   List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> fragments,
                                                                                   List<Integer> CLG)

matchReaction

public boolean matchReaction(SMIRKSReaction reaction,
                             org.openscience.cdk.interfaces.IAtomContainer targetReactants,
                             org.openscience.cdk.interfaces.IAtomContainer targetProducts,
                             org.openscience.cdk.interfaces.IAtomContainer targetAgents)
                      throws EmptyMoleculeException

Parameters:

reaction - - this must be a valid SMIRKSReaction object created by parsing a valid SMIRKS expression

targetReactants - - the target reactants represented as a single atom container

targetProducts - - the target products represented as a single atom container

tagetAgents - - the target agents may null (not specified)- in this case the agents are not matched if

Returns:

true if reaction is matched against the targets All targets (reactants, products, agents) may be fragmented e.g. to represent several molecules/fragments This function check component level grouping if specified within the SMIRKS definition

Throws:

EmptyMoleculeException

matchReaction

public boolean matchReaction(SMIRKSReaction reaction,
                             org.openscience.cdk.interfaces.IAtomContainerSet targetReactants,
                             org.openscience.cdk.interfaces.IAtomContainerSet targetProducts,
                             org.openscience.cdk.interfaces.IAtomContainerSet targetAgents)
                      throws EmptyMoleculeException

Parameters:

reaction -

targetReactants -

targetProducts -

tagetAgents -

Returns:

true if reaction is matched against the targets This function check component level grouping if specified within the SMIRKS definition

Throws:

EmptyMoleculeException

applyTransformation

public boolean applyTransformation(org.openscience.cdk.interfaces.IAtomContainer target,
                                   SMIRKSReaction reaction)
                            throws Exception

Throws:

Exception

applyTransformation

public boolean applyTransformation(org.openscience.cdk.interfaces.IAtomContainer target,
                                   IAcceptable selection,
                                   SMIRKSReaction reaction)
                            throws Exception

Throws:

Exception

applyTransformationWithCombinedOverlappedPos

public org.openscience.cdk.interfaces.IAtomContainerSet applyTransformationWithCombinedOverlappedPos(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                                     IAcceptable selection,
                                                                                                     SMIRKSReaction reaction)
                                                                                              throws Exception

Throws:

Exception

applyTransformationWithSingleCopyForEachPos

public org.openscience.cdk.interfaces.IAtomContainerSet applyTransformationWithSingleCopyForEachPos(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                                    IAcceptable selection,
                                                                                                    SMIRKSReaction reaction)
                                                                                             throws Exception

Throws:

Exception

applyTransformationWithSingleCopyForEachPos

public org.openscience.cdk.interfaces.IAtomContainerSet applyTransformationWithSingleCopyForEachPos(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                                    IAcceptable selection,
                                                                                                    SMIRKSReaction reaction,
                                                                                                    SmartsConst.SSM_MODE SSMode)
                                                                                             throws Exception

Throws:

Exception

getNonOverlappingMappings

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

getNonIdenticalMappings

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

getAllMappings

public List<List<org.openscience.cdk.interfaces.IAtom>> getAllMappings(org.openscience.cdk.interfaces.IAtomContainer target)

applyTransformAtLocation

public void applyTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target,
                                     List<org.openscience.cdk.interfaces.IAtom> rMap,
                                     SMIRKSReaction reaction)

applyTransformationsAtLocationsWithCloning

public org.openscience.cdk.interfaces.IAtomContainer applyTransformationsAtLocationsWithCloning(org.openscience.cdk.interfaces.IAtomContainer target,
                                                                                                List<List<org.openscience.cdk.interfaces.IAtom>> rMaps,
                                                                                                SMIRKSReaction reaction)
                                                                                         throws Exception

Throws:

Exception

getRecursiveAtoms

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

mapRecursiveAtomsAgainstTarget

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

Throws:

EmptyMoleculeException

matchCLG

protected boolean matchCLG(List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> queryFragments,
                           List<Integer> queryCLG,
                           org.openscience.cdk.interfaces.IAtomContainerSet targetComponents)
                    throws EmptyMoleculeException

Throws:

EmptyMoleculeException

printSSMap

public void printSSMap(org.openscience.cdk.interfaces.IAtomContainer target,
                       List<org.openscience.cdk.interfaces.IAtom> rMap)

printMappingClusters

public void printMappingClusters(List<List<Integer>> clusterIndexes,
                                 org.openscience.cdk.interfaces.IAtomContainer target)

processProduct

public void processProduct(org.openscience.cdk.interfaces.IAtomContainer mol)
                    throws Exception

Throws:

Exception

checkInvalidatedDBStereo

public void checkInvalidatedDBStereo(org.openscience.cdk.interfaces.IAtomContainer target,
                                     List<org.openscience.cdk.interfaces.IStereoElement> invalidatedStereoElements,
                                     Map<org.openscience.cdk.interfaces.IStereoElement,StereoChange> stereoChanges)

applyStereoTransformAtLocation

public void applyStereoTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target,
                                           List<org.openscience.cdk.interfaces.IAtom> rMap,
                                           List<org.openscience.cdk.interfaces.IAtom> newProdAtoms,
                                           SMIRKSReaction reaction)

applyHAtomTransformAtLocation

public void applyHAtomTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target,
                                          List<org.openscience.cdk.interfaces.IAtom> rMap,
                                          List<org.openscience.cdk.interfaces.IAtom> newProdAtoms,
                                          SMIRKSReaction reaction)

applyAromaticityTransformAtLocation

public void applyAromaticityTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target,
                                                List<org.openscience.cdk.interfaces.IAtom> rMap,
                                                List<org.openscience.cdk.interfaces.IAtom> newProdAtoms,
                                                SMIRKSReaction reaction)