Uses of Interface
org.openscience.cdk.interfaces.IReaction
-
-
Uses of IReaction in org.openscience.cdk
Classes in org.openscience.cdk that implement IReaction Modifier and Type Class Description class
Reaction
Represents the idea of a chemical reaction.Methods in org.openscience.cdk that return IReaction Modifier and Type Method Description IReaction
ReactionSet. getReaction(int number)
Returns the Reaction at positionnumber
in the container.IReaction
DefaultChemObjectBuilder. newReaction()
Create a new reaction using the default constructor.Methods in org.openscience.cdk that return types with arguments of type IReaction Modifier and Type Method 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 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 Description class
DebugReaction
Debugging data class.Methods in org.openscience.cdk.debug that return IReaction Modifier and Type Method Description IReaction
DebugReactionSet. getReaction(int number)
Returns the Reaction at positionnumber
in the container.IReaction
DebugChemObjectBuilder. newReaction()
Create a new reaction using the default constructor.Methods in org.openscience.cdk.debug that return types with arguments of type IReaction Modifier and Type Method 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 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 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 Description static double
GeometryTools. getBondLengthAverage(IReaction reaction)
Deprecated.static double
GeometryUtil. getBondLengthAverage(IReaction reaction)
static boolean
GeometryUtil. has2DCoordinates(IReaction reaction)
Determine if all parts of a reaction have coodinatesstatic Rectangle2D
GeometryTools. shiftReactionVertical(IReaction reaction, Rectangle2D bounds, Rectangle2D last, double gap)
Deprecated.Shift the containers in a reaction vertically upwards to not overlap with the reference Rectangle2D.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. -
Uses of IReaction in org.openscience.cdk.interfaces
Methods in org.openscience.cdk.interfaces that return IReaction Modifier and Type Method Description IReaction
IReactionSet. getReaction(int number)
Returns the Reaction at positionnumber
in the container.IReaction
IChemObjectBuilder. newReaction()
Create a new reaction using the default constructor.Methods in org.openscience.cdk.interfaces that return types with arguments of type IReaction Modifier and Type Method Description Iterable<IReaction>
IReactionSet. reactions()
Returns theIterable
over Reactions of this container.Methods in org.openscience.cdk.interfaces with parameters of type IReaction Modifier and Type Method 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 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 Description Mappings
Pattern. matchAll(IReaction target)
Find all mappings of this pattern in thetarget
reaction.boolean
Pattern. matches(IReaction target)
Determine if there is a mapping of this pattern in thetarget
reaction. -
Uses of IReaction in org.openscience.cdk.layout
Methods in org.openscience.cdk.layout with parameters of type IReaction Modifier and Type Method 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 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 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 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 Description IReaction
AdductionLPMechanism. 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
HeterolyticCleavageMechanism. 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
RadicalSiteIonizationMechanism. 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
RearrangementChargeMechanism. 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
RemovingSEofNBMechanism. 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
TautomerizationMechanism. 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 Description List<IGenerator<IReaction>>
ReactionRenderer. getGenerators()
Returns aList
ofIGenerator
s for this renderer.Methods in org.openscience.cdk.renderer with parameters of type IReaction Modifier and Type Method 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 aIChemObject
, 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 ofIRenderingElement
s 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. -
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 Description IRenderingElement
BoundsGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
MappingGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ProductsBoxGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ReactantsBoxGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ReactionArrowGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ReactionBoxGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ReactionPlusGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing.IRenderingElement
ReactionSceneGenerator. generate(IReaction reaction, RendererModel model)
Converts aIChemObject
from the chemical data model into something that can be drawn in the chemical drawing. -
Uses of IReaction in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IReaction Modifier and Type Class Description class
Reaction
Represents the idea of a chemical reaction.Methods in org.openscience.cdk.silent that return IReaction Modifier and Type Method Description IReaction
ReactionSet. getReaction(int number)
Returns the Reaction at positionnumber
in the container.IReaction
SilentChemObjectBuilder. newReaction()
Create a new reaction using the default constructor.Methods in org.openscience.cdk.silent that return types with arguments of type IReaction Modifier and Type Method 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 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 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 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.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 Description 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
SignatureReactionCanoniser. getCanonicalReaction(IReaction reaction)
Deprecated.Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.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
AbstractReactionLabeller. labelReaction(IReaction reaction, ICanonicalMoleculeLabeller labeller)
Deprecated.Methods in org.openscience.cdk.smsd.labelling with parameters of type IReaction Modifier and Type Method Description 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
SignatureReactionCanoniser. getCanonicalReaction(IReaction reaction)
Deprecated.Convert a reaction into a canonical form by canonizing each of the structures in the reaction in turn.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
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 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 newIReaction
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 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 Description static void
ReactionManipulator. clearAtomConfigurations(IReaction reaction)
This method will reset all atom properties related to atom configuration to the valueCDKConstants.UNSET
.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)
Returns all agents of anIReaction
.static List<IAtomContainer>
ReactionManipulator. getAllAtomContainers(IReaction reaction)
Returns allIAtomContainers
of the given reaction.static List<IChemObject>
ReactionManipulator. getAllChemObjects(IReaction reaction)
static List<String>
ReactionManipulator. getAllIDs(IReaction reaction)
static IAtomContainerSet
ReactionManipulator. getAllMolecules(IReaction reaction)
Returns all components of anIReaction
, that is, reactants, agents and products.static IAtomContainerSet
ReactionManipulator. getAllProducts(IReaction reaction)
Returns all products of anIReaction
.static IAtomContainerSet
ReactionManipulator. getAllReactants(IReaction reaction)
Returns all reactants of anIReaction
.static int
ReactionManipulator. getAtomCount(IReaction reaction)
Returns the total number of atoms for all components of the givenreaction
.static int
ReactionManipulator. getBondCount(IReaction reaction)
Returns the total number of atoms for all components of the givenreaction
.static IChemObject
ReactionManipulator. getMappedChemObject(IReaction reaction, IChemObject chemObject)
Returns theIAtom
that is mapped.static IAtomContainer
ReactionManipulator. getRelevantAtomContainer(IReaction reaction, IAtom atom)
static IAtomContainer
ReactionManipulator. getRelevantAtomContainer(IReaction reaction, IBond bond)
static void
ReactionManipulator. perceiveAtomTypesAndConfigureAtoms(IReaction reaction)
static void
ReactionManipulator. perceiveAtomTypesAndConfigureUnsetProperties(IReaction reaction)
static void
ReactionManipulator. removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
Removes the providedatom
and its connected electron containers from the reaction.static void
ReactionManipulator. removeElectronContainer(IReaction reaction, IElectronContainer electrons)
Removes the providedelectrons
from the reaction.static IReaction
ReactionManipulator. reverse(IReaction reaction)
Returns a newIReaction
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 Description ValidationReport
AbstractValidator. validateReaction(IReaction subject)
ValidationReport
BasicValidator. validateReaction(IReaction subject)
ValidationReport
IValidator. validateReaction(IReaction subject)
ValidationReport
ValidatorEngine. validateReaction(IReaction subject)
-