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

Packages that use IReaction

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.depict
org.openscience.cdk.geometry
org.openscience.cdk.interfaces
org.openscience.cdk.io.cml
org.openscience.cdk.isomorphism
org.openscience.cdk.layout
org.openscience.cdk.libio.cml
org.openscience.cdk.reaction
org.openscience.cdk.reaction.mechanism
org.openscience.cdk.renderer
org.openscience.cdk.renderer.generators
org.openscience.cdk.silent
org.openscience.cdk.smiles
org.openscience.cdk.smsd.labelling
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IReaction in org.openscience.cdk

Classes in org.openscience.cdk that implement IReaction

Modifier and Type	Class and Description
class	Reaction Represents the idea of a chemical reaction.

Methods in org.openscience.cdk that return IReaction

Modifier and Type	Method and Description
IReaction	ReactionSet.getReaction(int number) Returns the Reaction at position number in the container.

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

Modifier and Type	Method and Description
Iterable<IReaction>	ReactionSet.reactions() Get an iterator for this reaction set.

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

Modifier and Type	Method and Description
void	ReactionSet.addReaction(IReaction reaction) Adds an reaction to this container.
void	ReactionSet.removeReaction(IReaction relevantReaction)

Uses of IReaction in org.openscience.cdk.debug

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

Modifier and Type	Class and Description
class	DebugReaction Debugging data class.

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

Modifier and Type	Method and Description
IReaction	DebugReactionSet.getReaction(int number) Returns the Reaction at position number in the container.

Methods in org.openscience.cdk.debug that return types with arguments of type IReaction

Modifier and Type	Method and Description
Iterable<IReaction>	DebugReactionSet.reactions() Get an iterator for this reaction set.

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

Modifier and Type	Method and Description
void	DebugReactionSet.addReaction(IReaction reaction) Adds an reaction to this container.
void	DebugReactionSet.removeReaction(IReaction reaction) Removes all instances of a reaction from this IReactionSet.

Uses of IReaction in org.openscience.cdk.depict

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

Modifier and Type	Method and Description
Depiction	DepictionGenerator.depict(IReaction rxn) Depict a reaction.

Uses of IReaction in org.openscience.cdk.geometry

Methods in org.openscience.cdk.geometry with parameters of type IReaction

Modifier and Type	Method and Description
static double	GeometryTools.getBondLengthAverage(IReaction reaction)
static double	GeometryUtil.getBondLengthAverage(IReaction reaction)
static double[]	GeometryUtil.shiftReactionVertical(IReaction reaction, double[] bounds, double[] last, double gap) Shift the containers in a reaction vertically upwards to not overlap with the reference rectangle.
static Rectangle2D	GeometryTools.shiftReactionVertical(IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap) Shift the containers in a reaction vertically upwards to not overlap with the reference Rectangle2D.

Uses of IReaction in org.openscience.cdk.interfaces

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

Modifier and Type	Method and Description
IReaction	IReactionSet.getReaction(int number) Returns the Reaction at position number in the container.

Methods in org.openscience.cdk.interfaces that return types with arguments of type IReaction

Modifier and Type	Method and Description
Iterable<IReaction>	IReactionSet.reactions() Returns the Iterable over Reactions of this container.

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

Modifier and Type	Method and Description
void	IReactionSet.addReaction(IReaction reaction) Adds an reaction to this container.
void	IReactionSet.removeReaction(IReaction relevantReaction) Removes all instances of a reaction from this IReactionSet.

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

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

Modifier and Type	Field and Description
protected IReaction	CMLCoreModule.currentReaction

Uses of IReaction in org.openscience.cdk.isomorphism

Methods in org.openscience.cdk.isomorphism with parameters of type IReaction

Modifier and Type	Method and Description
Mappings	Pattern.matchAll(IReaction target) Find all mappings of this pattern in the target reaction.
boolean	Pattern.matches(IReaction target) Determine if there is a mapping of this pattern in the target reaction.

Uses of IReaction in org.openscience.cdk.layout

Methods in org.openscience.cdk.layout with parameters of type IReaction

Modifier and Type	Method and Description
void	StructureDiagramGenerator.generateCoordinates(IReaction reaction) Convenience method to generate 2D coordinates for a reaction.

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

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

Modifier and Type	Method and Description
org.xmlcml.cml.element.CMLReaction	Convertor.cdkReactionToCMLReaction(IReaction reaction)
org.xmlcml.cml.element.CMLReactionStep	Convertor.cdkReactionToCMLReactionStep(IReaction reaction)

Uses of IReaction in org.openscience.cdk.reaction

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

Modifier and Type	Method and Description
IReaction	ReactionChain.getReaction(int position) Get the reaction of this chain reaction object at the position.
IReaction	IReactionMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.

Methods in org.openscience.cdk.reaction with parameters of type IReaction

Modifier and Type	Method and Description
void	ReactionChain.addReaction(IReaction reaction, int position) Added a IReaction for this chain in position.
int	ReactionChain.getReactionStep(IReaction reaction) Get the position of the reaction into this chain reaction object.

Uses of IReaction in org.openscience.cdk.reaction.mechanism

Methods in org.openscience.cdk.reaction.mechanism that return IReaction

Modifier and Type	Method and Description
IReaction	TautomerizationMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	SharingElectronMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RemovingSEofNBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RemovingSEofBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RearrangementChargeMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RadicalSiteRearrangementMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	RadicalSiteIonizationMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	HomolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	HeterolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	AdductionPBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.
IReaction	AdductionLPMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList) Initiates the process for the given mechanism.

Uses of IReaction in org.openscience.cdk.renderer

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

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

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

Modifier and Type	Method and Description
static double	AverageBondLengthCalculator.calculateAverageBondLength(IReaction reaction) Calculate the average bond length for the bonds in a reaction.
static Rectangle2D	BoundsCalculator.calculateBounds(IReaction reaction) Calculate the bounding rectangle for a reaction.
Rectangle	ReactionRenderer.calculateDiagramBounds(IReaction reaction) Given a IChemObject, calculates the bounding rectangle in screen space.
IRenderingElement	ReactionRenderer.generateDiagram(IReaction reaction) The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
Rectangle	ReactionRenderer.paint(IReaction reaction, IDrawVisitor drawVisitor) Paint an IChemObject.
void	ReactionRenderer.paint(IReaction reaction, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter) Paint a reaction.
void	ReactionRenderer.setScale(IReaction reaction) Set the scale for an IReaction.
void	ReactionRenderer.setup(IReaction reaction, Rectangle screen) Setup the transformations necessary to draw this Reaction.

Constructor parameters in org.openscience.cdk.renderer with type arguments of type IReaction

Constructor and Description
ChemModelRenderer(List<IGenerator<IAtomContainer>> generators, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager)
ReactionRenderer(List<IGenerator<IAtomContainer>> generators, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager) A renderer that draws IReactions with the passed IGenerator for both IAtomContainer and IReaction content.
ReactionSetRenderer(List<IGenerator<IAtomContainer>> generators, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager) A renderer that generates diagrams using the specified generators for IAtomContainers and IReactionSets and manages fonts with the supplied font manager.
ReactionSetRenderer(RendererModel rendererModel, List<IGenerator<IAtomContainer>> generators, List<IGenerator<IReaction>> reactionGenerators, IFontManager fontManager)

Uses of IReaction in org.openscience.cdk.renderer.generators

Methods in org.openscience.cdk.renderer.generators with parameters of type IReaction

Modifier and Type	Method and Description
IRenderingElement	ReactionSceneGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	ReactionPlusGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	ReactionBoxGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	ReactionArrowGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	ReactantsBoxGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	ProductsBoxGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	MappingGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.
IRenderingElement	BoundsGenerator.generate(IReaction reaction, RendererModel model) Converts a IChemObject from the chemical data model into something that can be drawn in the chemical drawing.

Uses of IReaction in org.openscience.cdk.silent

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

Modifier and Type	Method and Description
IReaction	ReactionSet.getReaction(int number) Returns the Reaction at position number in the container.

Methods in org.openscience.cdk.silent that return types with arguments of type IReaction

Modifier and Type	Method and Description
Iterable<IReaction>	ReactionSet.reactions() Get an iterator for this reaction set.

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

Modifier and Type	Method and Description
void	ReactionSet.addReaction(IReaction reaction) Adds an reaction to this container.
void	ReactionSet.removeReaction(IReaction relevantReaction)

Uses of IReaction in org.openscience.cdk.smiles

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

Modifier and Type	Method and Description
IReaction	SmilesParser.parseReactionSmiles(String smiles) Parse a reaction SMILES.

Methods in org.openscience.cdk.smiles with parameters of type IReaction

Modifier and Type	Method and Description
String	SmilesGenerator.create(IReaction reaction) Create a SMILES for a reaction of the flavour specified in the constructor.
String	SmilesGenerator.create(IReaction reaction, int[] ordering) Create a SMILES for a reaction of the flavour specified in the constructor and write the output order to the provided array.
String	SmilesGenerator.createReactionSMILES(IReaction reaction) Deprecated. use SmilesGenerator.create(IAtomContainer)
String	SmilesGenerator.createSMILES(IReaction reaction) Deprecated. use #createReactionSMILES

Uses of IReaction in org.openscience.cdk.smsd.labelling

Methods in org.openscience.cdk.smsd.labelling that return IReaction

Modifier and Type	Method and Description
IReaction	SmilesReactionCanoniser.getCanonicalReaction(IReaction reaction) Deprecated. Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
IReaction	SignatureReactionCanoniser.getCanonicalReaction(IReaction reaction) Deprecated. Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
IReaction	ICanonicalReactionLabeller.getCanonicalReaction(IReaction reaction) Deprecated. Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
IReaction	AbstractReactionLabeller.labelReaction(IReaction reaction, ICanonicalMoleculeLabeller labeller) Deprecated.

Methods in org.openscience.cdk.smsd.labelling with parameters of type IReaction

Modifier and Type	Method and Description
IReaction	SmilesReactionCanoniser.getCanonicalReaction(IReaction reaction) Deprecated. Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
IReaction	SignatureReactionCanoniser.getCanonicalReaction(IReaction reaction) Deprecated. Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
IReaction	ICanonicalReactionLabeller.getCanonicalReaction(IReaction reaction) Deprecated. Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.
IReaction	AbstractReactionLabeller.labelReaction(IReaction reaction, ICanonicalMoleculeLabeller labeller) Deprecated.

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

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

Modifier and Type	Method and Description
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 IReaction	ChemModelManipulator.getRelevantReaction(IChemModel chemModel, IAtom atom) Retrieves the first IReaction containing a given IAtom from an IChemModel.
static IReaction	ReactionSetManipulator.getRelevantReaction(IReactionSet set, IAtom atom)
static IReaction	ReactionSetManipulator.getRelevantReaction(IReactionSet set, IBond bond)
static IReaction	ReactionManipulator.reverse(IReaction reaction) Returns a new Reaction object which is the reverse of the given Reaction.
static IReaction	ReactionManipulator.toReaction(IAtomContainer mol) Converts an 'inlined' reaction stored in a molecule back to a reaction.

Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IReaction

Modifier and Type	Method and Description
static List<IReaction>	ChemFileManipulator.getAllReactions(IChemFile file) Get a list of all IReaction inside an IChemFile.

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

Modifier and Type	Method and Description
static Set<IBond>	ReactionManipulator.findMappedBonds(IReaction reaction) Collect the set of bonds that mapped in both a reactant and a product.
static IAtomContainerSet	ReactionManipulator.getAllAgents(IReaction reaction)
static List<IAtomContainer>	ReactionManipulator.getAllAtomContainers(IReaction reaction) Returns all the AtomContainer's of a Reaction.
static List<IChemObject>	ReactionManipulator.getAllChemObjects(IReaction reaction)
static List<String>	ReactionManipulator.getAllIDs(IReaction reaction)
static IAtomContainerSet	ReactionManipulator.getAllMolecules(IReaction reaction) Get all molecule of a IReaction: reactants + products.
static IAtomContainerSet	ReactionManipulator.getAllProducts(IReaction reaction) get all products of a IReaction
static IAtomContainerSet	ReactionManipulator.getAllReactants(IReaction reaction) get all reactants of a IReaction
static int	ReactionManipulator.getAtomCount(IReaction reaction)
static int	ReactionManipulator.getBondCount(IReaction reaction)
static IChemObject	ReactionManipulator.getMappedChemObject(IReaction reaction, IChemObject chemObject) get the IAtom which is mapped
static IAtomContainer	ReactionManipulator.getRelevantAtomContainer(IReaction reaction, IAtom atom)
static IAtomContainer	ReactionManipulator.getRelevantAtomContainer(IReaction reaction, IBond bond)
static void	ReactionManipulator.removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
static void	ReactionManipulator.removeElectronContainer(IReaction reaction, IElectronContainer electrons)
static IReaction	ReactionManipulator.reverse(IReaction reaction) Returns a new Reaction object which is the reverse of the given Reaction.
static void	ReactionManipulator.setAtomProperties(IReaction reaction, Object propKey, Object propVal)
static IAtomContainer	ReactionManipulator.toMolecule(IReaction rxn) Converts a reaction to an 'inlined' reaction stored as a molecule.

Uses of IReaction in org.openscience.cdk.validate

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

Modifier and Type	Method and Description
ValidationReport	ValidatorEngine.validateReaction(IReaction subject)
ValidationReport	IValidator.validateReaction(IReaction subject)
ValidationReport	BasicValidator.validateReaction(IReaction subject)
ValidationReport	AbstractValidator.validateReaction(IReaction subject)