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

Packages that use ComplexEntity

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 ComplexEntity in bio.singa.simulation.entities

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

Modifier and Type	Method	Description
ComplexEntity	ComplexEntityBuilder.CombineStep.build()
ComplexEntity	ComplexEntityBuilder.ComplexEntityCombiner.build()
static ComplexEntity	ComplexEntity.from(ChemicalEntity chemicalEntity)
static ComplexEntity	ComplexEntity.from(ChemicalEntity chemicalEntity, BindingSite bindingSite)
static ComplexEntity	ComplexEntity.from(ChemicalEntity first, ChemicalEntity second)
static ComplexEntity	ComplexEntity.from(ChemicalEntity chemicalEntity, Collection<BindingSite> bindingSites)
ComplexEntity	ComplexEntity.getCopy()

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

Modifier and Type	Method	Description
Optional<ComplexEntity>	ComplexEntity.add(ChemicalEntity otherEntity, BindingSite bindingSite)
Optional<ComplexEntity>	ComplexEntity.bind(ComplexEntity otherComplex, BindingSite bindingSite)
Optional<ComplexEntity>	ComplexEntity.remove(ChemicalEntity chemicalEntity, BindingSite bindingSite)
Optional<List<ComplexEntity>>	ComplexEntity.unbind(BindingSite bindingSite)

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

Modifier and Type	Method	Description
Optional<ComplexEntity>	ComplexEntity.bind(ComplexEntity otherComplex, BindingSite bindingSite)
void	ComplexEntity.combine(GraphComplexNode first, GraphComplexNode second, ComplexEntity secondGraph, BindingSite bindingSite)

Uses of ComplexEntity in bio.singa.simulation.reactions

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

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

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

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

Modifier and Type	Method	Description
boolean	CandidateCondition.test(ComplexEntity graphComplex)
boolean	HasAnyNumberOfEntities.test(ComplexEntity graphComplex)
boolean	HasNoMoreThanNumberOfPartners.test(ComplexEntity graphComplex)
boolean	HasNumberOfEntities.test(ComplexEntity graphComplex)
boolean	HasOccupiedBindingSite.test(ComplexEntity graphComplex)
boolean	HasUnoccupiedBindingSite.test(ComplexEntity graphComplex)
boolean	IsOnlyBoundAt.test(ComplexEntity graphComplex)

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

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

Modifier and Type	Method	Description
List<ComplexEntity>	AbstractComplexEntityModification.getCandidates()
List<ComplexEntity>	AbstractComplexEntityModification.getResults()
List<ComplexEntity>	ComplexEntityModification.getResults()

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

Modifier and Type	Method	Description
void	AbstractComplexEntityModification.addCandidate(ComplexEntity candidate)
void	ComplexEntityModification.addCandidate(ComplexEntity candidate)
void	AddModification.apply(ComplexEntity complex)
void	BindModification.apply(ComplexEntity first, ComplexEntity second)
void	ReleaseModification.apply(ComplexEntity complex)
void	RemoveModification.apply(ComplexEntity complex)

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

Modifier and Type	Method	Description
void	AbstractComplexEntityModification.setCandidates(List<ComplexEntity> candidates)
void	AbstractComplexEntityModification.setResults(List<ComplexEntity> results)

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

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

Modifier and Type	Method	Description
protected List<ComplexEntity>	AbstractGraphComplexReactor.filterCandidates(List<ComplexEntity> complexes, List<CandidateCondition> conditions)
List<ComplexEntity>	ReactionTrack.getFirst()
List<ComplexEntity>	ReactionTrack.getLast()
List<ComplexEntity>	AbstractGraphComplexReactor.getPrimaryProducts()
List<ComplexEntity>	AbstractGraphComplexReactor.getPrimarySubstrates()
List<ComplexEntity>	ReactionElement.getProducts()
List<ComplexEntity>	OneToTwoReactor.getSecondaryProducts()
List<ComplexEntity>	TwoToOneReactor.getSecondarySubstrates()
List<ComplexEntity>	ReactionElement.getSubstrates()
Deque<List<ComplexEntity>>	ReactionTrack.getTrack()

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

Modifier and Type	Method	Description
static ReactionElement	ReactionElement.createOneToOne(ComplexEntity substrate, ComplexEntity product)
static ReactionElement	ReactionElement.createOneToTwo(ComplexEntity substrate, ComplexEntity primaryProduct, ComplexEntity secondaryProduct)
static ReactionElement	ReactionElement.createTwoToOne(ComplexEntity primarySubstrate, ComplexEntity secondarySubstrate, ComplexEntity product)

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

Modifier and Type	Method	Description
void	ReactionTrack.append(List<ComplexEntity> step)
void	ComplexReactor.collectCandidates(List<ComplexEntity> substrateCandidates)
void	OneToOneReactor.collectCandidates(List<ComplexEntity> substrateCandidates)
void	OneToTwoReactor.collectCandidates(List<ComplexEntity> substrateCandidates)
void	TwoToOneReactor.collectCandidates(List<ComplexEntity> substrateCandidates)
protected List<ComplexEntity>	AbstractGraphComplexReactor.filterCandidates(List<ComplexEntity> complexes, List<CandidateCondition> conditions)
void	ReactionChain.process(Collection<ComplexEntity> availableEntities)
void	AbstractGraphComplexReactor.setPrimaryProducts(List<ComplexEntity> primaryProducts)
void	AbstractGraphComplexReactor.setPrimarySubstrates(List<ComplexEntity> primarySubstrates)
void	ReactionElement.setProducts(List<ComplexEntity> products)
void	OneToTwoReactor.setSecondaryProducts(List<ComplexEntity> secondaryProducts)
void	TwoToOneReactor.setSecondarySubstrates(List<ComplexEntity> secondarySubstrates)
void	ReactionElement.setSubstrates(List<ComplexEntity> substrates)
void	ReactionTrack.setTrack(Deque<List<ComplexEntity>> track)

Constructor parameters in bio.singa.simulation.reactions.reactors with type arguments of type ComplexEntity

Constructor	Description
ReactionElement(List<ComplexEntity> substrates, List<ComplexEntity> products)