Uses of Class
bio.singa.simulation.entities.BindingSite

Packages that use BindingSite

Package	Description
bio.singa.simulation.entities
bio.singa.simulation.reactions
bio.singa.simulation.reactions.conditions
bio.singa.simulation.reactions.modifications
bio.singa.simulation.reactions.reactors

Uses of BindingSite in bio.singa.simulation.entities

Methods in bio.singa.simulation.entities that return BindingSite

Modifier and Type	Method	Description
static BindingSite	BindingSite.createNamed(String bindingSiteName)
static BindingSite	BindingSite.forPair(bio.singa.core.utility.Pair<ChemicalEntity> pair)
static BindingSite	BindingSite.forPair(ChemicalEntity first, ChemicalEntity second)
BindingSite	GraphComplexEdge.getConnectedSite()

Methods in bio.singa.simulation.entities that return types with arguments of type BindingSite

Modifier and Type	Method	Description
List<BindingSite>	GraphComplexNode.getBindingSites()

Methods in bio.singa.simulation.entities with parameters of type BindingSite

Modifier and Type	Method	Description
Optional<ComplexEntity>	ComplexEntity.add(ChemicalEntity otherEntity, BindingSite bindingSite)
void	ComplexEntity.addBindingSite(ChemicalEntity first, BindingSite bindingSite)
void	GraphComplexNode.addBindingSite(BindingSite bindingSite)
int	ComplexEntity.addEdgeBetween(GraphComplexNode source, GraphComplexNode target, BindingSite bindingSite)
Optional<ComplexEntity>	ComplexEntity.bind(ComplexEntity otherComplex, BindingSite bindingSite)
void	ComplexEntity.combine(GraphComplexNode first, GraphComplexNode second, ComplexEntity secondGraph, BindingSite bindingSite)
ComplexEntityBuilder.CombineStep	ComplexEntityBuilder.CombineStep.combine(ChemicalEntity first, ChemicalEntity second, BindingSite bindingSite)
ComplexEntityBuilder.CombineStep	ComplexEntityBuilder.ComplexEntityCombiner.combine(ChemicalEntity first, ChemicalEntity second, BindingSite bindingSite)
static ComplexEntity	ComplexEntity.from(ChemicalEntity chemicalEntity, BindingSite bindingSite)
List<GraphComplexNode>	ComplexEntity.getNodesWithUnoccupiedBindingSite(BindingSite bindingSite)
Optional<GraphComplexNode>	ComplexEntity.getNodeWithUnoccupiedBindingSite(BindingSite bindingSite)
boolean	GraphComplexNode.hasBindingSite(BindingSite bindingSite)
Optional<ComplexEntity>	ComplexEntity.remove(ChemicalEntity chemicalEntity, BindingSite bindingSite)
void	GraphComplexEdge.setConnectedSite(BindingSite connectedSite)
Optional<List<ComplexEntity>>	ComplexEntity.unbind(BindingSite bindingSite)

Method parameters in bio.singa.simulation.entities with type arguments of type BindingSite

Modifier and Type	Method	Description
static void	ComplexEntityBuilder.attachBindingSites(Map<ChemicalEntity,Set<BindingSite>> bindingSiteMapping, Map.Entry<BindingSite,bio.singa.core.utility.Pair<ChemicalEntity>> entry)
static void	ComplexEntityBuilder.attachBindingSites(Map<ChemicalEntity,Set<BindingSite>> bindingSiteMapping, Map.Entry<BindingSite,bio.singa.core.utility.Pair<ChemicalEntity>> entry)
static ComplexEntity	ComplexEntity.from(ChemicalEntity chemicalEntity, Collection<BindingSite> bindingSites)
void	GraphComplexNode.setBindingSites(List<BindingSite> bindingSites)
void	ComplexEntity.snapTo(ChemicalEntity chemicalEntity, Set<BindingSite> bindingSites)

Uses of BindingSite in bio.singa.simulation.reactions

Methods in bio.singa.simulation.reactions that return types with arguments of type BindingSite

Modifier and Type	Method	Description
Map<ChemicalEntity,Set<BindingSite>>	ReactionNetworkGenerator.determineBindingSites()

Method parameters in bio.singa.simulation.reactions with type arguments of type BindingSite

Modifier and Type	Method	Description
Set<ComplexEntity>	ReactionNetworkGenerator.createInitialEntities(Map<ChemicalEntity,Set<BindingSite>> bindingSiteMapping)

Uses of BindingSite in bio.singa.simulation.reactions.conditions

Methods in bio.singa.simulation.reactions.conditions with parameters of type BindingSite

Modifier and Type	Method	Description
boolean	CandidateCondition.concerns(BindingSite bindingSite)
boolean	HasAnyNumberOfEntities.concerns(BindingSite bindingSite)
boolean	HasNoMoreThanNumberOfPartners.concerns(BindingSite bindingSite)
boolean	HasNumberOfEntities.concerns(BindingSite bindingSite)
boolean	HasOccupiedBindingSite.concerns(BindingSite bindingSite)
boolean	HasUnoccupiedBindingSite.concerns(BindingSite bindingSite)
boolean	IsOnlyBoundAt.concerns(BindingSite bindingSite)
static CandidateCondition	CandidateConditionBuilder.hasOccupiedBindingSite(BindingSite bindingSite)
static CandidateCondition	CandidateConditionBuilder.hasUnoccupiedBindingSite(BindingSite bindingSite)
static CandidateCondition	CandidateConditionBuilder.isOnlyBoundAt(BindingSite bindingSite)

Constructors in bio.singa.simulation.reactions.conditions with parameters of type BindingSite

Constructor	Description
HasOccupiedBindingSite(BindingSite bindingSite)
HasUnoccupiedBindingSite(BindingSite bindingSite)
IsOnlyBoundAt(BindingSite bindingSite)

Uses of BindingSite in bio.singa.simulation.reactions.modifications

Methods in bio.singa.simulation.reactions.modifications that return BindingSite

Modifier and Type	Method	Description
BindingSite	AbstractComplexEntityModification.getBindingSite()
BindingSite	ComplexEntityModification.getBindingSite()

Methods in bio.singa.simulation.reactions.modifications with parameters of type BindingSite

Modifier and Type	Method	Description
static ComplexEntityModification	ComplexEntityModificationBuilder.add(BindingSite bindingSite, ChemicalEntity complex)
static ComplexEntityModification	ComplexEntityModificationBuilder.bind(BindingSite bindingSite)
static ComplexEntityModification	ComplexEntityModificationBuilder.release(BindingSite bindingSite)
static ComplexEntityModification	ComplexEntityModificationBuilder.remove(BindingSite bindingSite, ChemicalEntity entityToRemove)
void	AbstractComplexEntityModification.setBindingSite(BindingSite bindingSite)

Constructors in bio.singa.simulation.reactions.modifications with parameters of type BindingSite

Constructor	Description
AbstractComplexEntityModification(BindingSite bindingSite)
AddModification(BindingSite bindingSite, ChemicalEntity complexToAdd)
BindModification(BindingSite bindingSite)
ReleaseModification(BindingSite bindingSite)
RemoveModification(BindingSite bindingSite, ChemicalEntity entityToRemove)

Uses of BindingSite in bio.singa.simulation.reactions.reactors

Fields in bio.singa.simulation.reactions.reactors declared as BindingSite

Modifier and Type	Field	Description
protected BindingSite	ReactionChainBuilder.AbstractReactorBuilder.bindingSite

Methods in bio.singa.simulation.reactions.reactors that return types with arguments of type BindingSite

Modifier and Type	Method	Description
Map.Entry<BindingSite,bio.singa.core.utility.Pair<ChemicalEntity>>	AbstractGraphComplexReactor.getBindingSite()
Map.Entry<BindingSite,bio.singa.core.utility.Pair<ChemicalEntity>>	ComplexReactor.getBindingSite()

Methods in bio.singa.simulation.reactions.reactors with parameters of type BindingSite

Modifier and Type	Method	Description
ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.AbstractReactorBuilder.bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.ReactorChoiceStep.bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.ReleaseReactorPrimaryConditionStep	ReactionChainBuilder.release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)

Constructors in bio.singa.simulation.reactions.reactors with parameters of type BindingSite

Constructor	Description
AddReactionChainBuilder(BindingSite bindingSite, ChemicalEntity secondaryEntity)
BindReactionChainBuilder(BindingSite bindingSite, ChemicalEntity primaryEntity)
ReleaseReactionChainBuilder(BindingSite bindingSite, ChemicalEntity primaryEntity)
RemoveReactionChainBuilder(BindingSite bindingSite, ChemicalEntity secondaryEntity)