Uses of Class
ambit2.smarts.SMIRKSReaction

Packages that use SMIRKSReaction

Package	Description
ambit2.reactions
ambit2.reactions.rules
ambit2.sln.io
ambit2.smarts	SMARTS parser
ambit2.smarts.processors
ambit2.smarts.smirks

Uses of SMIRKSReaction in ambit2.reactions

Fields in ambit2.reactions declared as SMIRKSReaction

Modifier and Type	Field and Description
protected SMIRKSReaction	GenericReaction.smirksReaction

Methods in ambit2.reactions that return SMIRKSReaction

Modifier and Type	Method and Description
SMIRKSReaction	GenericReaction.getSmirksReaction()

Methods in ambit2.reactions with parameters of type SMIRKSReaction

Modifier and Type	Method and Description
void	GenericReaction.setSmirksReaction(SMIRKSReaction smirksReaction)

Uses of SMIRKSReaction in ambit2.reactions.rules

Fields in ambit2.reactions.rules declared as SMIRKSReaction

Modifier and Type	Field and Description
SMIRKSReaction	RetroSynthRule.reaction

Uses of SMIRKSReaction in ambit2.sln.io

Methods in ambit2.sln.io that return SMIRKSReaction

Modifier and Type	Method and Description
SMIRKSReaction	SLN2ChemObject.slnContainerToSMIRKSReaction(SLNContainer container)

Methods in ambit2.sln.io with parameters of type SMIRKSReaction

Modifier and Type	Method and Description
SLNContainer	SLN2ChemObject.SMIRKSReactionToSLNContainer(SMIRKSReaction reaction)

Uses of SMIRKSReaction in ambit2.smarts

Methods in ambit2.smarts that return SMIRKSReaction

Modifier and Type	Method and Description
SMIRKSReaction	SMIRKSManager.parse(String smirks)

Methods in ambit2.smarts with parameters of type SMIRKSReaction

Modifier and Type	Method and Description
void	SMIRKSManager.applyAromaticityTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, List<org.openscience.cdk.interfaces.IAtom> newProdAtoms, SMIRKSReaction reaction)
void	SMIRKSManager.applyHAtomTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, List<org.openscience.cdk.interfaces.IAtom> newProdAtoms, SMIRKSReaction reaction)
void	SMIRKSManager.applyStereoTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, List<org.openscience.cdk.interfaces.IAtom> newProdAtoms, SMIRKSReaction reaction)
boolean	SMIRKSManager.applyTransformation(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction)
boolean	SMIRKSManager.applyTransformation(org.openscience.cdk.interfaces.IAtomContainer target, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainer	SMIRKSManager.applyTransformationsAtLocationsWithCloning(org.openscience.cdk.interfaces.IAtomContainer target, List<List<org.openscience.cdk.interfaces.IAtom>> rMaps, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainerSet	SMIRKSManager.applyTransformationWithCombinedOverlappedPos(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainerSet	SMIRKSManager.applyTransformationWithSingleCopyForEachPos(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction)
org.openscience.cdk.interfaces.IAtomContainerSet	SMIRKSManager.applyTransformationWithSingleCopyForEachPos(org.openscience.cdk.interfaces.IAtomContainer target, IAcceptable selection, SMIRKSReaction reaction, SmartsConst.SSM_MODE SSMode)
void	SMIRKSManager.applyTransformAtLocation(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.interfaces.IAtom> rMap, SMIRKSReaction reaction)
boolean	SMIRKSManager.matchReaction(SMIRKSReaction reaction, org.openscience.cdk.interfaces.IAtomContainer targetReactants, org.openscience.cdk.interfaces.IAtomContainer targetProducts, org.openscience.cdk.interfaces.IAtomContainer targetAgents)
boolean	SMIRKSManager.matchReaction(SMIRKSReaction reaction, org.openscience.cdk.interfaces.IAtomContainerSet targetReactants, org.openscience.cdk.interfaces.IAtomContainerSet targetProducts, org.openscience.cdk.interfaces.IAtomContainerSet targetAgents)

Uses of SMIRKSReaction in ambit2.smarts.processors

Fields in ambit2.smarts.processors declared as SMIRKSReaction

Modifier and Type	Field and Description
protected SMIRKSReaction	SMIRKSTransformation.smirksReaction

Uses of SMIRKSReaction in ambit2.smarts.smirks

Methods in ambit2.smarts.smirks with parameters of type SMIRKSReaction

Modifier and Type	Method and Description
boolean	ReactionSearch.matchReaction(SMIRKSReaction targetReaction)