Uses of Class
ambit2.base.exceptions.EmptyMoleculeException

Packages that use EmptyMoleculeException

Package	Description
ambit2.groupcontribution.nmr
ambit2.groupcontribution.nmr.nmr_1h
ambit2.reactions
ambit2.reactions.retrosynth
ambit2.reactions.rules.conditions
ambit2.smarts	SMARTS parser
ambit2.smarts.groups
ambit2.smarts.processors

Uses of EmptyMoleculeException in ambit2.groupcontribution.nmr

Methods in ambit2.groupcontribution.nmr that throw EmptyMoleculeException

Modifier and Type	Method and Description
void	HNMRShifts.calculateHShifts()
void	HNMRShifts.findAllGroupMappings()

Uses of EmptyMoleculeException in ambit2.groupcontribution.nmr.nmr_1h

Methods in ambit2.groupcontribution.nmr.nmr_1h that throw EmptyMoleculeException

Modifier and Type	Method and Description
void	HNMRKnowledgeBase.configure()
protected void	HNMRKnowledgeBase.configure(HAtomEnvironment hae, int num)

Uses of EmptyMoleculeException in ambit2.reactions

Methods in ambit2.reactions that throw EmptyMoleculeException

Modifier and Type	Method and Description
List<List<org.openscience.cdk.interfaces.IAtom>>	GenericReaction.findReactionInstances(org.openscience.cdk.interfaces.IAtomContainer target, SMIRKSManager smrkMan)
List<List<org.openscience.cdk.interfaces.IAtom>>	GenericReaction.findReactionInstances(org.openscience.cdk.interfaces.IAtomContainer target, SMIRKSManager smrkMan, SmartsConst.SSM_MODE SSMode)

Uses of EmptyMoleculeException in ambit2.reactions.retrosynth

Methods in ambit2.reactions.retrosynth that throw EmptyMoleculeException

Modifier and Type	Method and Description
Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>>	ReactionSequence.generateAllReactionInstances(org.openscience.cdk.interfaces.IAtomContainer mol)
Map<GenericReaction,List<List<org.openscience.cdk.interfaces.IAtom>>>	ReactionSequence.generateAllReactionInstances(org.openscience.cdk.interfaces.IAtomContainer mol, List<GenericReaction> reactions)
ArrayList<RetroSynthNode>	RetroSynthesis.generateChildrenNodes(RetroSynthNode node)
RetroSynthesisResult	RetroSynthesis.run()

Uses of EmptyMoleculeException in ambit2.reactions.rules.conditions

Constructors in ambit2.reactions.rules.conditions that throw EmptyMoleculeException

Constructor and Description
ReactionGroupCondition(ReactionGroupCondition.RGConditionType conditionType, String smarts, SmartsParser parser, IsomorphismTester isoTester)

Uses of EmptyMoleculeException in ambit2.smarts

Methods in ambit2.smarts that throw EmptyMoleculeException

Modifier and Type	Method and Description
void	SmartsManager.handleGroupRecursiveAtoms(org.openscience.cdk.interfaces.IAtomContainer target, org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer groupQuery)
void	SMIRKSManager.mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression> recursiveAtoms, org.openscience.cdk.interfaces.IAtomContainer target)
void	SmartsManager.markAtomGroups(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> groupQueries) Calculates for each atom a bit set which describes the participation of this atom in each of the predefined groups.
void	SmartsManager.markAtomGroups(org.openscience.cdk.interfaces.IAtomContainer target, List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> groupQueries, SmartsConst.SSM_MODE FlagSSMode)
protected boolean	SMIRKSManager.matchCLG(List<org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer> queryFragments, List<Integer> queryCLG, org.openscience.cdk.interfaces.IAtomContainerSet targetComponents)
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)
void	IsomorphismTester.setQuery(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer container)

Constructors in ambit2.smarts that throw EmptyMoleculeException

Constructor and Description
Screening(List<String> externalSmartsKeys) structural keys by external file

Uses of EmptyMoleculeException in ambit2.smarts.groups

Methods in ambit2.smarts.groups that throw EmptyMoleculeException

Modifier and Type	Method and Description
void	GroupMatch.configure()
List<List<org.openscience.cdk.interfaces.IAtom>>	GroupMatch.getMappings(org.openscience.cdk.interfaces.IAtomContainer target)
void	GroupMatch.mapRecursiveAtomsAgainstTarget(List<SmartsAtomExpression> recursiveAtoms, org.openscience.cdk.interfaces.IAtomContainer target)
boolean	GroupMatch.match(org.openscience.cdk.interfaces.IAtomContainer target)
boolean	GroupMatch.matchAtPosition(org.openscience.cdk.interfaces.IAtomContainer target, int atomNum)
int	GroupMatch.matchCount(org.openscience.cdk.interfaces.IAtomContainer target)

Constructors in ambit2.smarts.groups that throw EmptyMoleculeException

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

Uses of EmptyMoleculeException in ambit2.smarts.processors

Methods in ambit2.smarts.processors that throw EmptyMoleculeException

Modifier and Type	Method and Description
protected void	StructureKeysBitSetGenerator.prepareKeySequences(List<String> keys, int nKeys)
void	StructureKeysBitSetGenerator.setSmartsKeys(List<String> smartsKeys)