Uses of Interface
bio.singa.simulation.entities.ChemicalEntity

Packages that use ChemicalEntity

Package	Description
bio.singa.simulation.entities
bio.singa.simulation.export.reactiongraph
bio.singa.simulation.features
bio.singa.simulation.features.model
bio.singa.simulation.model.concentrations
bio.singa.simulation.model.graphs
bio.singa.simulation.model.modules
bio.singa.simulation.model.modules.concentration
bio.singa.simulation.model.modules.concentration.imlementations.reactions
bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants
bio.singa.simulation.model.modules.concentration.imlementations.transport
bio.singa.simulation.model.modules.concentration.specifity
bio.singa.simulation.model.rules
bio.singa.simulation.model.sections
bio.singa.simulation.model.simulation
bio.singa.simulation.model.simulation.error
bio.singa.simulation.reactions
bio.singa.simulation.reactions.conditions
bio.singa.simulation.reactions.modifications
bio.singa.simulation.reactions.reactors
bio.singa.simulation.trajectories.nested

Uses of ChemicalEntity in bio.singa.simulation.entities

Classes in bio.singa.simulation.entities that implement ChemicalEntity

Modifier and Type	Class	Description
class	ComplexEntity
class	SimpleEntity

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

Modifier and Type	Method	Description
static ChemicalEntity	EntityRegistry.get(String referenceIdentifier)
ChemicalEntity	GraphComplexNode.getEntity()
static ChemicalEntity	EntityRegistry.matchExactly(String... containedIdentifiers)

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

Modifier and Type	Method	Description
static List<ChemicalEntity>	EntityRegistry.allWith(String... containedIdentifiers)
static Collection<ChemicalEntity>	EntityRegistry.getAll()
static List<ChemicalEntity>	ChemicalEntities.sortByComplexDependencies(List<ChemicalEntity> entities)

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

Modifier and Type	Method	Description
Optional<ComplexEntity>	ComplexEntity.add(ChemicalEntity otherEntity, BindingSite bindingSite)
void	ComplexEntity.addBindingSite(ChemicalEntity first, BindingSite bindingSite)
ComplexEntityBuilder.CombineStep	ComplexEntityBuilder.CombineStep.combine(ChemicalEntity first, ChemicalEntity second)
ComplexEntityBuilder.CombineStep	ComplexEntityBuilder.CombineStep.combine(ChemicalEntity first, ChemicalEntity second, BindingSite bindingSite)
ComplexEntityBuilder.CombineStep	ComplexEntityBuilder.ComplexEntityCombiner.combine(ChemicalEntity first, ChemicalEntity second)
ComplexEntityBuilder.CombineStep	ComplexEntityBuilder.ComplexEntityCombiner.combine(ChemicalEntity first, ChemicalEntity second, BindingSite bindingSite)
boolean	ComplexEntity.containsEntity(ChemicalEntity entity)
long	ComplexEntity.countParts(ChemicalEntity entity)
static BindingSite	BindingSite.forPair(ChemicalEntity first, ChemicalEntity second)
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)
boolean	GraphComplexNode.isEntity(ChemicalEntity entity)
static void	EntityRegistry.put(ChemicalEntity entity)
static void	EntityRegistry.put(String identifier, ChemicalEntity entity)
Optional<ComplexEntity>	ComplexEntity.remove(ChemicalEntity chemicalEntity, BindingSite bindingSite)
void	GraphComplexNode.setEntity(ChemicalEntity entity)
void	ComplexEntity.snapTo(ChemicalEntity chemicalEntity, Set<BindingSite> bindingSites)

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

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 BindingSite	BindingSite.forPair(bio.singa.core.utility.Pair<ChemicalEntity> pair)
static List<ChemicalEntity>	ChemicalEntities.sortByComplexDependencies(List<ChemicalEntity> entities)

Uses of ChemicalEntity in bio.singa.simulation.export.reactiongraph

Methods in bio.singa.simulation.export.reactiongraph that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	ReactionGraphNode.getEntity()

Methods in bio.singa.simulation.export.reactiongraph with parameters of type ChemicalEntity

Modifier and Type	Method	Description
ReactionGraphNode	ReactionGraph.addNode(ChemicalEntity entity)
Optional<ReactionGraphNode>	ReactionGraph.getNodeWithContent(ChemicalEntity content)
void	ReactionGraphNode.setEntity(ChemicalEntity entity)

Constructors in bio.singa.simulation.export.reactiongraph with parameters of type ChemicalEntity

Constructor	Description
ReactionGraphNode(Integer identifier, ChemicalEntity entity)

Uses of ChemicalEntity in bio.singa.simulation.features

Methods in bio.singa.simulation.features with parameters of type ChemicalEntity

Modifier and Type	Method	Description
protected AttachedMotor	AttachedMotor.Builder.createObject(ChemicalEntity quantity)
protected BoostMediatingEntity	BoostMediatingEntity.Builder.createObject(ChemicalEntity quantity)
protected Cargo	Cargo.Builder.createObject(ChemicalEntity quantity)
protected Transporter	Transporter.Builder.createObject(ChemicalEntity quantity)
static AttachedMotor.Builder	AttachedMotor.of(ChemicalEntity quantity)
static BoostMediatingEntity.Builder	BoostMediatingEntity.of(ChemicalEntity quantity)
static Cargo.Builder	Cargo.of(ChemicalEntity quantity)
static Cargoes.Builder	Cargoes.of(ChemicalEntity... entities)
static MatchingQSnares.Builder	MatchingQSnares.of(ChemicalEntity... entities)
static MatchingRSnares.Builder	MatchingRSnares.of(ChemicalEntity... entities)
static PrimaryCargoes.Builder	PrimaryCargoes.of(ChemicalEntity... entities)
static ScalingEntities.Builder	ScalingEntities.of(ChemicalEntity... entities)
static Solutes.Builder	Solutes.of(ChemicalEntity... entities)
static Transporter.Builder	Transporter.of(ChemicalEntity quantity)

Method parameters in bio.singa.simulation.features with type arguments of type ChemicalEntity

Modifier and Type	Method	Description
protected Cargoes	Cargoes.Builder.createObject(List<ChemicalEntity> quantity)
protected MatchingQSnares	MatchingQSnares.Builder.createObject(List<ChemicalEntity> quantity)
protected MatchingRSnares	MatchingRSnares.Builder.createObject(List<ChemicalEntity> quantity)
protected PrimaryCargoes	PrimaryCargoes.Builder.createObject(List<ChemicalEntity> quantity)
protected ScalingEntities	ScalingEntities.Builder.createObject(List<ChemicalEntity> quantity)
protected Solutes	Solutes.Builder.createObject(List<ChemicalEntity> quantity)
static Cargoes.Builder	Cargoes.of(Collection<ChemicalEntity> quantity)
static Cargoes.Builder	Cargoes.of(List<ChemicalEntity> quantity)
static MatchingQSnares.Builder	MatchingQSnares.of(List<ChemicalEntity> quantity)
static MatchingRSnares.Builder	MatchingRSnares.of(List<ChemicalEntity> quantity)
static PrimaryCargoes.Builder	PrimaryCargoes.of(List<ChemicalEntity> quantity)
static ScalingEntities.Builder	ScalingEntities.of(List<ChemicalEntity> quantity)
static Solutes.Builder	Solutes.of(List<ChemicalEntity> quantity)

Constructors in bio.singa.simulation.features with parameters of type ChemicalEntity

Constructor	Description
AttachedMotor(ChemicalEntity entity)
BoostMediatingEntity(ChemicalEntity entity)
Builder(ChemicalEntity quantity)
Builder(ChemicalEntity quantity)
Builder(ChemicalEntity quantity)
Builder(ChemicalEntity quantity)
Cargo(ChemicalEntity entity)
Transporter(ChemicalEntity entity)

Constructor parameters in bio.singa.simulation.features with type arguments of type ChemicalEntity

Constructor	Description
Builder(List<ChemicalEntity> quantity)
Builder(List<ChemicalEntity> quantity)
Builder(List<ChemicalEntity> quantity)
Builder(List<ChemicalEntity> quantity)
Builder(List<ChemicalEntity> quantity)
Builder(List<ChemicalEntity> quantity)
Cargoes(List<ChemicalEntity> chemicalEntities)
MatchingQSnares(List<ChemicalEntity> chemicalEntities)
MatchingRSnares(List<ChemicalEntity> chemicalEntities)
PrimaryCargoes(List<ChemicalEntity> chemicalEntities)
ScalingEntities(List<ChemicalEntity> chemicalEntities)
Solutes(List<ChemicalEntity> chemicalEntities)

Uses of ChemicalEntity in bio.singa.simulation.features.model

Constructors in bio.singa.simulation.features.model with parameters of type ChemicalEntity

Constructor	Description
EntityFeature(ChemicalEntity entity)
EntityFeature(ChemicalEntity entity, bio.singa.features.model.Evidence evidence)
EntityFeature(ChemicalEntity entity, List<bio.singa.features.model.Evidence> evidence)

Constructor parameters in bio.singa.simulation.features.model with type arguments of type ChemicalEntity

Constructor	Description
MultiEntityFeature(List<ChemicalEntity> chemicalEntities)
MultiEntityFeature(List<ChemicalEntity> chemicalEntities, bio.singa.features.model.Evidence evidence)
MultiEntityFeature(List<ChemicalEntity> chemicalEntities, List<bio.singa.features.model.Evidence> evidence)

Uses of ChemicalEntity in bio.singa.simulation.model.concentrations

Methods in bio.singa.simulation.model.concentrations that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	InitialConcentration.getEntity()

Methods in bio.singa.simulation.model.concentrations with parameters of type ChemicalEntity

Modifier and Type	Method	Description
ConcentrationBuilder.PoolStep	ConcentrationBuilder.ConcentrationBuilderImpl.entity(ChemicalEntity entity)
ConcentrationBuilder.PoolStep	ConcentrationBuilder.EntityStep.entity(ChemicalEntity entity)
void	InitialConcentration.setEntity(ChemicalEntity entity)

Uses of ChemicalEntity in bio.singa.simulation.model.graphs

Methods in bio.singa.simulation.model.graphs that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
static Map<String,ChemicalEntity>	AutomatonGraphs.generateMapOfEntities(AutomatonGraph graph)	Creates and returns a map that contains all chemical entities that are present in the given graph as values and with the name of the entity as key.

Uses of ChemicalEntity in bio.singa.simulation.model.modules

Methods in bio.singa.simulation.model.modules that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
Set<ChemicalEntity>	AbstractUpdateModule.getReferencedChemicalEntities()	Returns all chemical entities that might be accessed by this module.
Set<ChemicalEntity>	UpdateModule.getReferencedChemicalEntities()

Methods in bio.singa.simulation.model.modules with parameters of type ChemicalEntity

Modifier and Type	Method	Description
protected void	AbstractUpdateModule.addReferencedEntity(ChemicalEntity chemicalEntity)	Adds a referenced chemical entity.

Method parameters in bio.singa.simulation.model.modules with type arguments of type ChemicalEntity

Modifier and Type	Method	Description
protected void	AbstractUpdateModule.addReferencedEntities(Collection<? extends ChemicalEntity> chemicalEntities)	Adds multiple referenced chemical entities.

Uses of ChemicalEntity in bio.singa.simulation.model.modules.concentration

Methods in bio.singa.simulation.model.modules.concentration that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	ConcentrationDelta.getChemicalEntity()	Returns the chemical entity.
ChemicalEntity	FieldSupplier.getCurrentEntity()	Returns the current chemical entity.
ChemicalEntity	ConcentrationDeltaIdentifier.getEntity()	Returns the chemical entity the delta is assigned to.

Methods in bio.singa.simulation.model.modules.concentration that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
List<ChemicalEntity>	ConcentrationDeltaManager.getFixedEntities()

Methods in bio.singa.simulation.model.modules.concentration with parameters of type ChemicalEntity

Modifier and Type	Method	Description
void	ConcentrationDeltaManager.fix(ChemicalEntity chemicalEntity)
protected double	ConcentrationBasedModule.getScaledFeature(ChemicalEntity entity, Class<? extends bio.singa.features.model.AbstractScalableQuantitativeFeature<?>> featureClass)	Returns the requested feature of the given chemical entities, scaled according to the current time step and spatial scaling.
void	FieldSupplier.setCurrentEntity(ChemicalEntity entity)	Sets the current chemical entity.

Constructors in bio.singa.simulation.model.modules.concentration with parameters of type ChemicalEntity

Constructor	Description
ConcentrationDelta(UpdateModule module, CellSubsection cellSubsection, ChemicalEntity chemicalEntity, double value)	Creates a new concentration delta.
ConcentrationDeltaIdentifier(Updatable updatable, CellSubsection section, ChemicalEntity entity)	Creates a new DeltaIdentifier.
ConcentrationDeltaIdentifier(Updatable updatable, CellSubsection section, String reference, ChemicalEntity entity)

Uses of ChemicalEntity in bio.singa.simulation.model.modules.concentration.imlementations.reactions

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions with parameters of type ChemicalEntity

Modifier and Type	Method	Description
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addCatalyst(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addCatalyst(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addCatalyst(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addProduct(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticBuilder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, double stoichiometricNumber)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
ReactionBuilder.StaticReactantStep	ReactionBuilder.StaticReactantStep.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)

Uses of ChemicalEntity in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	Reactant.getEntity()	Gets the entity representing this reactant.

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
List<ChemicalEntity>	ReactantBehavior.getReferencedEntities()
List<ChemicalEntity>	RuleBasedReactantBehavior.getReferencedEntities()
List<ChemicalEntity>	StaticReactantBehavior.getReferencedEntities()

Methods in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants with parameters of type ChemicalEntity

Modifier and Type	Method	Description
void	Reactant.setEntity(ChemicalEntity entity)	Sets the entity representing this reactant.

Constructors in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.reactants with parameters of type ChemicalEntity

Constructor	Description
Reactant(ChemicalEntity entity, ReactantRole role)	Creates a new reactant.
Reactant(ChemicalEntity entity, ReactantRole role, double stoichiometricNumber)
Reactant(ChemicalEntity entity, ReactantRole role, double stoichiometricNumber, double reactionOrder)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology)
Reactant(ChemicalEntity chemicalEntity, ReactantRole role, CellTopology topology, double stoichiometricNumber)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology, double stoichiometricNumber, double reactionOrder)
Reactant(ChemicalEntity entity, ReactantRole role, CellTopology preferredTopology, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)
Reactant(ChemicalEntity entity, ReactantRole role, javax.measure.Unit<bio.singa.features.quantities.MolarConcentration> preferredConcentrationUnit)

Uses of ChemicalEntity in bio.singa.simulation.model.modules.concentration.imlementations.transport

Methods in bio.singa.simulation.model.modules.concentration.imlementations.transport with parameters of type ChemicalEntity

Modifier and Type	Method	Description
EndocytoticPitAbsorption.InhibitionStep	EndocytoticPitAbsorption.AccelerationStep.acceleratingEntity(ChemicalEntity entity)
EndocytoticPitAbsorption.InhibitionStep	EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder.acceleratingEntity(ChemicalEntity acceleratingEntity)
MembraneDiffusion.BuildStep	MembraneDiffusion.CargoStep.cargo(ChemicalEntity cargo)
MembraneDiffusion.BuildStep	MembraneDiffusion.MembraneDiffusionBuilder.cargo(ChemicalEntity cargo)
SingleFileChannelMembraneTransport.SolutesStep	SingleFileChannelMembraneTransport.CargoStep.cargo(ChemicalEntity cargo)
SingleFileChannelMembraneTransport.SolutesStep	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.cargo(ChemicalEntity cargo)
Diffusion.SectionLimitationStep	Diffusion.DiffusionBuilder.forAllEntities(ChemicalEntity... chemicalEntities)
Diffusion.SectionLimitationStep	Diffusion.EntityLimitationStep.forAllEntities(ChemicalEntity... chemicalEntities)
EndocytoticPitAbsorption.AccelerationStep	EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder.forAllEntities(ChemicalEntity... chemicalEntities)
EndocytoticPitAbsorption.AccelerationStep	EndocytoticPitAbsorption.EntityStep.forAllEntities(ChemicalEntity... chemicalEntities)
LateralMembraneDiffusion.SectionLimitationStep	LateralMembraneDiffusion.EntityLimitationStep.forAllEntities(ChemicalEntity... chemicalEntities)
LateralMembraneDiffusion.SectionLimitationStep	LateralMembraneDiffusion.LateralMembraneDiffusionBuilder.forAllEntities(ChemicalEntity... chemicalEntities)
Diffusion.SectionLimitationStep	Diffusion.DiffusionBuilder.forEntity(ChemicalEntity chemicalEntity)
Diffusion.SectionLimitationStep	Diffusion.EntityLimitationStep.forEntity(ChemicalEntity chemicalEntity)
EndocytoticPitAbsorption.AccelerationStep	EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder.forEntity(ChemicalEntity chemicalEntity)
EndocytoticPitAbsorption.AccelerationStep	EndocytoticPitAbsorption.EntityStep.forEntity(ChemicalEntity chemicalEntity)
LateralMembraneDiffusion.SectionLimitationStep	LateralMembraneDiffusion.EntityLimitationStep.forEntity(ChemicalEntity chemicalEntity)
LateralMembraneDiffusion.SectionLimitationStep	LateralMembraneDiffusion.LateralMembraneDiffusionBuilder.forEntity(ChemicalEntity chemicalEntity)
SingleFileChannelMembraneTransport.BuildStep	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.forSolute(ChemicalEntity solute)
SingleFileChannelMembraneTransport.BuildStep	SingleFileChannelMembraneTransport.SolutesStep.forSolute(ChemicalEntity chemicalEntity)
SingleFileChannelMembraneTransport.BuildStep	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.forSolutes(ChemicalEntity... solutes)
SingleFileChannelMembraneTransport.BuildStep	SingleFileChannelMembraneTransport.SolutesStep.forSolutes(ChemicalEntity... chemicalEntities)
EndocytoticPitAbsorption.RateStep	EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder.inhibitingEntity(ChemicalEntity inhibitingEntity)
EndocytoticPitAbsorption.RateStep	EndocytoticPitAbsorption.InhibitionStep.inhibitingEntity(ChemicalEntity entity)
SingleFileChannelMembraneTransport.CargoStep	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.transporter(ChemicalEntity transporter)
SingleFileChannelMembraneTransport.CargoStep	SingleFileChannelMembraneTransport.TransporterStep.transporter(ChemicalEntity transporter)

Method parameters in bio.singa.simulation.model.modules.concentration.imlementations.transport with type arguments of type ChemicalEntity

Modifier and Type	Method	Description
Diffusion.SectionLimitationStep	Diffusion.DiffusionBuilder.forAllEntities(Collection<ChemicalEntity> chemicalEntities)
Diffusion.SectionLimitationStep	Diffusion.EntityLimitationStep.forAllEntities(Collection<ChemicalEntity> chemicalEntities)
EndocytoticPitAbsorption.AccelerationStep	EndocytoticPitAbsorption.EndocytoticPitAbsorptionBuilder.forAllEntities(Collection<ChemicalEntity> chemicalEntities)
EndocytoticPitAbsorption.AccelerationStep	EndocytoticPitAbsorption.EntityStep.forAllEntities(Collection<ChemicalEntity> chemicalEntities)
LateralMembraneDiffusion.SectionLimitationStep	LateralMembraneDiffusion.EntityLimitationStep.forAllEntities(Collection<ChemicalEntity> chemicalEntities)
LateralMembraneDiffusion.SectionLimitationStep	LateralMembraneDiffusion.LateralMembraneDiffusionBuilder.forAllEntities(Collection<ChemicalEntity> chemicalEntities)
SingleFileChannelMembraneTransport.BuildStep	SingleFileChannelMembraneTransport.SingleFileChannelMembraneTransportBuilder.forSolutes(List<ChemicalEntity> solutes)
SingleFileChannelMembraneTransport.BuildStep	SingleFileChannelMembraneTransport.SolutesStep.forSolutes(List<ChemicalEntity> chemicalEntities)

Uses of ChemicalEntity in bio.singa.simulation.model.modules.concentration.specifity

Methods in bio.singa.simulation.model.modules.concentration.specifity with parameters of type ChemicalEntity

Modifier and Type	Method	Description
void	EntitySpecific.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)
void	SectionSpecific.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)
void	UpdatableSpecific.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)
void	UpdateSpecificity.processContainer(ConcentrationContainer container, CellSubsection subsection, ChemicalEntity chemicalEntity)

Uses of ChemicalEntity in bio.singa.simulation.model.rules

Methods in bio.singa.simulation.model.rules that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	AssignmentRule.getTargetEntity()

Methods in bio.singa.simulation.model.rules that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
Map<ChemicalEntity,String>	AssignmentRule.getEntityReference()

Methods in bio.singa.simulation.model.rules with parameters of type ChemicalEntity

Modifier and Type	Method	Description
void	AssignmentRule.referenceChemicalEntityToParameter(String parameterIdentifier, ChemicalEntity entity)
void	AssignmentRule.setTargetEntity(ChemicalEntity targetEntity)

Method parameters in bio.singa.simulation.model.rules with type arguments of type ChemicalEntity

Modifier and Type	Method	Description
void	AssignmentRule.setEntityReference(Map<ChemicalEntity,String> entityReference)

Constructors in bio.singa.simulation.model.rules with parameters of type ChemicalEntity

Constructor	Description
AssignmentRule(ChemicalEntity targetEntity)

Uses of ChemicalEntity in bio.singa.simulation.model.sections

Methods in bio.singa.simulation.model.sections that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
Optional<ChemicalEntity>	ConcentrationContainer.containsHiddenEntity(CellTopology topology, ChemicalEntity query)
Map<ChemicalEntity,Double>	ConcentrationPool.getConcentrations()
Set<ChemicalEntity>	ConcentrationContainer.getReferencedEntities()	Returns all entities referenced in any concentration pool.
Set<ChemicalEntity>	ConcentrationPool.getReferencedEntities()	Returns all entities referenced in this map.

Methods in bio.singa.simulation.model.sections with parameters of type ChemicalEntity

Modifier and Type	Method	Description
boolean	ConcentrationContainer.containsEntity(CellSubsection subsection, ChemicalEntity entity)
boolean	ConcentrationContainer.containsEntity(CellTopology topology, ChemicalEntity entity)
Optional<ChemicalEntity>	ConcentrationContainer.containsHiddenEntity(CellTopology topology, ChemicalEntity query)
double	ConcentrationContainer.get(CellSubsection subsection, ChemicalEntity entity)	Returns the concentration of the entity in the corresponding subsection.
double	ConcentrationContainer.get(CellTopology topology, ChemicalEntity entity)	Returns the concentration of the entity in the corresponding topology.
double	ConcentrationPool.get(ChemicalEntity entity)	Returns the concentration of a entity.
void	ConcentrationContainer.initialize(CellSubsection subsection, ChemicalEntity entity, javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)
void	ConcentrationContainer.initialize(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<bio.singa.features.quantities.MolarConcentration> concentration)
void	ConcentrationContainer.set(CellSubsection subsection, ChemicalEntity entity, double concentration)	Sets the concentration of the given entity in the given subsection.
void	ConcentrationContainer.set(CellTopology topology, ChemicalEntity entity, double concentration)	Sets the concentration of the given entity in the given topology.
void	ConcentrationPool.set(ChemicalEntity entity, double concentration)	Sets the concentration of a entity.

Uses of ChemicalEntity in bio.singa.simulation.model.simulation

Methods in bio.singa.simulation.model.simulation that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	Simulation.getChemicalEntity(String primaryIdentifier)

Methods in bio.singa.simulation.model.simulation that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
Collection<ChemicalEntity>	Simulation.getChemicalEntities()	Returns the chemical entities.

Methods in bio.singa.simulation.model.simulation with parameters of type ChemicalEntity

Modifier and Type	Method	Description
void	Simulation.addReferencedEntity(ChemicalEntity chemicalEntity)

Uses of ChemicalEntity in bio.singa.simulation.model.simulation.error

Methods in bio.singa.simulation.model.simulation.error that return ChemicalEntity

Modifier and Type	Method	Description
ChemicalEntity	NumericalError.getChemicalEntity()	Returns the chemical entity where the error occurred.

Constructors in bio.singa.simulation.model.simulation.error with parameters of type ChemicalEntity

Constructor	Description
NumericalError(Updatable updatable, ChemicalEntity entity, double value)	Creates a new LocalError.

Uses of ChemicalEntity in bio.singa.simulation.reactions

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

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

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

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

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

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

Modifier and Type	Method	Description
boolean	CandidateCondition.concerns(ChemicalEntity chemicalEntity)
boolean	HasAnyNumberOfEntities.concerns(ChemicalEntity chemicalEntity)
boolean	HasNoMoreThanNumberOfPartners.concerns(ChemicalEntity chemicalEntity)
boolean	HasNumberOfEntities.concerns(ChemicalEntity chemicalEntity)
boolean	HasOccupiedBindingSite.concerns(ChemicalEntity chemicalEntity)
boolean	HasUnoccupiedBindingSite.concerns(ChemicalEntity chemicalEntity)
boolean	IsOnlyBoundAt.concerns(ChemicalEntity chemicalEntity)
static CandidateCondition	CandidateConditionBuilder.hasAnyOfEntity(ChemicalEntity entity)
static CandidateCondition	CandidateConditionBuilder.hasNoMoreThanNumberOfPartners(ChemicalEntity entity, int number)
static CandidateCondition	CandidateConditionBuilder.hasNoneOfEntity(ChemicalEntity entity)
static CandidateCondition	CandidateConditionBuilder.hasNotNumberOfEntity(ChemicalEntity entity, int number)
static CandidateCondition	CandidateConditionBuilder.hasNumberOfEntity(ChemicalEntity entity, int number)
static CandidateCondition	CandidateConditionBuilder.hasOneOfEntity(ChemicalEntity entity)

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

Constructor	Description
HasAnyNumberOfEntities(ChemicalEntity chemicalEntity)
HasNoMoreThanNumberOfPartners(ChemicalEntity chemicalEntity, int numberOfPartners)
HasNumberOfEntities(ChemicalEntity chemicalEntity, int numberOfParts)

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

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

Modifier and Type	Method	Description
ChemicalEntity	AbstractComplexEntityModification.getPrimaryEntity()
ChemicalEntity	ComplexEntityModification.getPrimaryEntity()
ChemicalEntity	AbstractComplexEntityModification.getSecondaryEntity()
ChemicalEntity	ComplexEntityModification.getSecondaryEntity()

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

Modifier and Type	Method	Description
static ComplexEntityModification	ComplexEntityModificationBuilder.add(BindingSite bindingSite, ChemicalEntity complex)
static ComplexEntityModification	ComplexEntityModificationBuilder.remove(BindingSite bindingSite, ChemicalEntity entityToRemove)
void	AbstractComplexEntityModification.setPrimaryEntity(ChemicalEntity primaryEntity)
void	ComplexEntityModification.setPrimaryEntity(ChemicalEntity chemicalEntity)
void	AbstractComplexEntityModification.setSecondaryEntity(ChemicalEntity secondaryEntity)
void	ComplexEntityModification.setSecondaryEntity(ChemicalEntity chemicalEntity)

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

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

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

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

Modifier and Type	Field	Description
protected ChemicalEntity	ReactionChainBuilder.AbstractReactorBuilder.primaryEntity
protected ChemicalEntity	ReactionChainBuilder.AbstractReactorBuilder.secondaryEntity

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

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 ChemicalEntity

Modifier and Type	Method	Description
ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.add(ChemicalEntity chemicalEntity)
static ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.add(ChemicalEntity chemicalEntity)
ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.add(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.AddReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.add(ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.AbstractReactorBuilder.bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.AbstractReactorBuilder.bind(ChemicalEntity chemicalEntity)
static ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.bind(ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.ReactorChoiceStep.bind(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorPrimaryConditionStep	ReactionChainBuilder.ReactorChoiceStep.bind(ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorPrimaryConditionStep	ReactionChainBuilder.ReleaseReactionChainBuilder.from(ChemicalEntity secondaryEntity)
ReactionChainBuilder.ReleaseReactorPrimaryConditionStep	ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep.from(ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorPrimaryConditionStep	ReactionChainBuilder.RemoveReactionChainBuilder.from(ChemicalEntity primaryEntity)
ReactionChainBuilder.RemoveReactorPrimaryConditionStep	ReactionChainBuilder.RemoveReactorSecondarySubstrateStep.from(ChemicalEntity chemicalEntity)
protected void	ReactionChainBuilder.AbstractReactorBuilder.oneToOneAssignment(ChemicalEntity primaryEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.release(ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.release(ChemicalEntity chemicalEntity)
static ReactionChainBuilder.ReleaseReactorPrimaryConditionStep	ReactionChainBuilder.release(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.ReleaseReactorSecondarySubstrateStep	ReactionChainBuilder.release(ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.AbstractReactorBuilder.remove(ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)
ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.ReactorChoiceStep.remove(ChemicalEntity chemicalEntity)
static ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.remove(BindingSite bindingSite, ChemicalEntity chemicalEntity)
static ReactionChainBuilder.RemoveReactorSecondarySubstrateStep	ReactionChainBuilder.remove(ChemicalEntity chemicalEntity)
ReactionChainBuilder.AddReactorPrimaryConditionStep	ReactionChainBuilder.AddReactionChainBuilder.to(ChemicalEntity primaryEntity)
ReactionChainBuilder.AddReactorPrimaryConditionStep	ReactionChainBuilder.AddReactorSecondarySubstrateStep.to(ChemicalEntity chemicalEntity)
ReactionChainBuilder.BindReactorSecondaryConditionStep	ReactionChainBuilder.BindReactionChainBuilder.to(ChemicalEntity secondaryEntity)
ReactionChainBuilder.BindReactorSecondaryConditionStep	ReactionChainBuilder.BindReactorSecondarySubstrateStep.to(ChemicalEntity chemicalEntity)

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

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

Uses of ChemicalEntity in bio.singa.simulation.trajectories.nested

Methods in bio.singa.simulation.trajectories.nested that return types with arguments of type ChemicalEntity

Modifier and Type	Method	Description
Map<ChemicalEntity,Double>	TrajectoryDataPoint.SubsectionDataPoint.getConcentrations()

Methods in bio.singa.simulation.trajectories.nested with parameters of type ChemicalEntity

Modifier and Type	Method	Description
void	TrajectoryDataPoint.SubsectionDataPoint.addConcentration(ChemicalEntity entity, double concentration)

Constructor parameters in bio.singa.simulation.trajectories.nested with type arguments of type ChemicalEntity

Constructor	Description
SubsectionDataPoint(Map<ChemicalEntity,Double> concentrations, List<bio.singa.mathematics.vectors.Vector2D> positions)