Uses of Interface
org.openscience.cdk.interfaces.IReactionSet
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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)
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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
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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)
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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 aList
ofIGenerator
s 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 aIChemObject
, 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)
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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)
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