Uses of Interface
org.openscience.cdk.interfaces.IReactionSet

Packages that use IReactionSet

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.depict
org.openscience.cdk.interfaces
org.openscience.cdk.io.cml
org.openscience.cdk.libio.cml
org.openscience.cdk.reaction
org.openscience.cdk.reaction.type
org.openscience.cdk.renderer
org.openscience.cdk.silent
org.openscience.cdk.smiles
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IReactionSet in org.openscience.cdk

Classes in org.openscience.cdk that implement IReactionSet

Modifier and Type	Class	Description
class	ReactionScheme	Classes that extends the definition of reaction to a scheme.
class	ReactionSet	A set of reactions, for example those taking part in a reaction.

Fields in org.openscience.cdk declared as IReactionSet

Modifier and Type	Field	Description
protected IReactionSet	ChemModel.setOfReactions	A ReactionSet.

Methods in org.openscience.cdk that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	ChemModel.getReactionSet()	Gets the ReactionSet contained in this ChemModel.

Methods in org.openscience.cdk with parameters of type IReactionSet

Modifier and Type	Method	Description
void	ChemModel.setReactionSet(IReactionSet sor)	Sets the ReactionSet contained in this ChemModel.

Uses of IReactionSet in org.openscience.cdk.debug

Classes in org.openscience.cdk.debug that implement IReactionSet

Modifier and Type	Class	Description
class	DebugReactionScheme	Debugging data class.
class	DebugReactionSet	Debugging data class.

Methods in org.openscience.cdk.debug that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	DebugChemModel.getReactionSet()	Gets the ReactionSet contained in this ChemModel.

Methods in org.openscience.cdk.debug with parameters of type IReactionSet

Modifier and Type	Method	Description
void	DebugChemModel.setReactionSet(IReactionSet sor)	Sets the ReactionSet contained in this ChemModel.

Uses of IReactionSet in org.openscience.cdk.depict

Methods in org.openscience.cdk.depict with parameters of type IReactionSet

Modifier and Type	Method	Description
Depiction	DepictionGenerator.depict(IReactionSet rxns)

Uses of IReactionSet in org.openscience.cdk.interfaces

Subinterfaces of IReactionSet in org.openscience.cdk.interfaces

Modifier and Type	Interface	Description
interface	IReactionScheme	Classes that implement this interface of a scheme.

Methods in org.openscience.cdk.interfaces that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	IChemModel.getReactionSet()	Gets the ReactionSet contained in this ChemModel.

Methods in org.openscience.cdk.interfaces with parameters of type IReactionSet

Modifier and Type	Method	Description
void	IChemModel.setReactionSet(IReactionSet sor)	Sets the ReactionSet contained in this ChemModel.

Uses of IReactionSet in org.openscience.cdk.io.cml

Fields in org.openscience.cdk.io.cml declared as IReactionSet

Modifier and Type	Field	Description
protected IReactionSet	CMLCoreModule.currentReactionSet

Uses of IReactionSet in org.openscience.cdk.libio.cml

Methods in org.openscience.cdk.libio.cml with parameters of type IReactionSet

Modifier and Type	Method	Description
org.xmlcml.cml.element.CMLReactionList	Convertor.cdkReactionSetToCMLReactionList(IReactionSet reactionSet)

Uses of IReactionSet in org.openscience.cdk.reaction

Classes in org.openscience.cdk.reaction that implement IReactionSet

Modifier and Type	Class	Description
class	ReactionChain	Classes that extends the definition of reaction to a chain reaction.

Methods in org.openscience.cdk.reaction that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	IReactionProcess.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiates the process for the given Reaction.

Uses of IReactionSet in org.openscience.cdk.reaction.type

Methods in org.openscience.cdk.reaction.type that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	AdductionProtonLPReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	AdductionProtonPBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	AdductionSodiumLPReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	CarbonylEliminationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	ElectronImpactNBEReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	ElectronImpactPDBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	ElectronImpactSDBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HeterolyticCleavagePBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HeterolyticCleavageSBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HomolyticCleavageReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HyperconjugationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	PiBondingMovementReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalChargeSiteInitiationHReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalChargeSiteInitiationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrAlphaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrBetaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrDeltaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrGammaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteInitiationHReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteInitiationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrAlphaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrBetaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrDeltaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrGammaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementAnionReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementCationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementLonePairReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementRadicalReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingAnionReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingChargeDBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingChargeSBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingLonePairReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	TautomerizationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.

Uses of IReactionSet in org.openscience.cdk.renderer

Methods in org.openscience.cdk.renderer that return types with arguments of type IReactionSet

Modifier and Type	Method	Description
List<IGenerator<IReactionSet>>	ReactionSetRenderer.getGenerators()	Returns a List of IGenerators for this renderer.

Methods in org.openscience.cdk.renderer with parameters of type IReactionSet

Modifier and Type	Method	Description
static double	AverageBondLengthCalculator.calculateAverageBondLength(IReactionSet reactionSet)	Calculate the average bond length for the bonds in a reaction set.
static Rectangle2D	BoundsCalculator.calculateBounds(IReactionSet reactionSet)	Calculate the bounding rectangle for a reaction set.
Rectangle	ReactionSetRenderer.calculateDiagramBounds(IReactionSet reactionSet)	Given a IChemObject, calculates the bounding rectangle in screen space.
Rectangle	ReactionSetRenderer.paint(IReactionSet reactionSet, IDrawVisitor drawVisitor)	Paint an IChemObject.
void	ReactionSetRenderer.paint(IReactionSet reactionSet, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter)	Paint a set of reactions.
void	ReactionSetRenderer.setScale(IReactionSet reactionSet)	Set the scale for an IReactionSet.
void	ReactionSetRenderer.setup(IReactionSet reactionSet, Rectangle screen)	Setup the transformations necessary to draw this Reaction Set.

Uses of IReactionSet in org.openscience.cdk.silent

Classes in org.openscience.cdk.silent that implement IReactionSet

Modifier and Type	Class	Description
class	ReactionScheme	Classes that extends the definition of reaction to a scheme.
class	ReactionSet	A set of reactions, for example those taking part in a reaction.

Fields in org.openscience.cdk.silent declared as IReactionSet

Modifier and Type	Field	Description
protected IReactionSet	ChemModel.setOfReactions	A ReactionSet.

Methods in org.openscience.cdk.silent that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	ChemModel.getReactionSet()	Gets the ReactionSet contained in this ChemModel.

Methods in org.openscience.cdk.silent with parameters of type IReactionSet

Modifier and Type	Method	Description
void	ChemModel.setReactionSet(IReactionSet sor)	Sets the ReactionSet contained in this ChemModel.

Uses of IReactionSet in org.openscience.cdk.smiles

Methods in org.openscience.cdk.smiles that return IReactionSet

Modifier and Type	Method	Description
IReactionSet	SmilesParser.parseReactionSetSmiles(String smiles)	Parse a SMILES that describes a set of reactions representing multiple synthesis steps or a metabolic pathway.

Uses of IReactionSet in org.openscience.cdk.tools.manipulator

Methods in org.openscience.cdk.tools.manipulator that return IReactionSet

Modifier and Type	Method	Description
static IReactionSet	ReactionSchemeManipulator.extractTopReactions(IReactionScheme reactionScheme)	Extract a set of Reactions which are in top of a IReactionScheme.
static IReactionSet	ReactionSchemeManipulator.getAllReactions(IReactionScheme scheme)	Get all IReaction's object from a given IReactionScheme.
static IReactionSet	ReactionSetManipulator.getRelevantReactions(IReactionSet reactSet, IAtomContainer molecule)	Get all Reactions object containing a Molecule from a set of Reactions.
static IReactionSet	ReactionSetManipulator.getRelevantReactionsAsProduct(IReactionSet reactSet, IAtomContainer molecule)	Get all Reactions object containing a Molecule as a Product from a set of Reactions.
static IReactionSet	ReactionSetManipulator.getRelevantReactionsAsReactant(IReactionSet reactSet, IAtomContainer molecule)	Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.

Methods in org.openscience.cdk.tools.manipulator with parameters of type IReactionSet

Modifier and Type	Method	Description
static IReactionScheme	ReactionSchemeManipulator.createReactionScheme(IReactionSet reactionSet)	Create a IReactionScheme give a IReactionSet object.
static List<IAtomContainer>	ReactionSetManipulator.getAllAtomContainers(IReactionSet set)	Returns all the AtomContainer's of a Reaction.
static List<IChemObject>	ReactionSetManipulator.getAllChemObjects(IReactionSet set)
static List<String>	ReactionSetManipulator.getAllIDs(IReactionSet set)
static IAtomContainerSet	ReactionSetManipulator.getAllMolecules(IReactionSet set)	get all Molecules object from a set of Reactions.
static int	ReactionSetManipulator.getAtomCount(IReactionSet set)
static int	ReactionSetManipulator.getBondCount(IReactionSet set)
static IReaction	ReactionSetManipulator.getReactionByAtomContainerID(IReactionSet reactionSet, String id)	Gets a reaction from a ReactionSet by ID of any product or reactant.
static IReaction	ReactionSetManipulator.getReactionByReactionID(IReactionSet reactionSet, String id)	Gets a reaction from a ReactionSet by ID.
static IAtomContainer	ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set, IAtom atom)
static IAtomContainer	ReactionSetManipulator.getRelevantAtomContainer(IReactionSet set, IBond bond)
static IReaction	ReactionSetManipulator.getRelevantReaction(IReactionSet set, IAtom atom)
static IReaction	ReactionSetManipulator.getRelevantReaction(IReactionSet set, IBond bond)
static IReactionSet	ReactionSetManipulator.getRelevantReactions(IReactionSet reactSet, IAtomContainer molecule)	Get all Reactions object containing a Molecule from a set of Reactions.
static IReactionSet	ReactionSetManipulator.getRelevantReactionsAsProduct(IReactionSet reactSet, IAtomContainer molecule)	Get all Reactions object containing a Molecule as a Product from a set of Reactions.
static IReactionSet	ReactionSetManipulator.getRelevantReactionsAsReactant(IReactionSet reactSet, IAtomContainer molecule)	Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.
static void	ReactionSetManipulator.removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom)
static void	ReactionSetManipulator.removeElectronContainer(IReactionSet set, IElectronContainer electrons)
static void	ReactionSetManipulator.setAtomProperties(IReactionSet set, Object propKey, Object propVal)

Uses of IReactionSet in org.openscience.cdk.validate

Methods in org.openscience.cdk.validate with parameters of type IReactionSet

Modifier and Type	Method	Description
ValidationReport	AbstractValidator.validateReactionSet(IReactionSet subject)
ValidationReport	IValidator.validateReactionSet(IReactionSet subject)
ValidationReport	ValidatorEngine.validateReactionSet(IReactionSet subject)