Uses of Class
bio.singa.simulation.model.sections.CellTopology

Packages that use CellTopology

Package	Description
bio.singa.simulation.model.modules.concentration.imlementations
bio.singa.simulation.model.modules.concentration.reactants
bio.singa.simulation.model.sections

Uses of CellTopology in bio.singa.simulation.model.modules.concentration.imlementations

Methods in bio.singa.simulation.model.modules.concentration.imlementations that return CellTopology

Modifier and Type	Method and Description
CellTopology	ComplexBuildingReaction.getBindeeTopology()
CellTopology	ComplexBuildingReaction.getBinderTopology()

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

Modifier and Type	Method and Description
BuilderType	Reaction.Builder.addProduct(ChemicalEntity chemicalEntity, CellTopology topology)
BuilderType	Reaction.Builder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology)
BuilderType	Reaction.Builder.addSubstrate(ChemicalEntity chemicalEntity, CellTopology topology, double stoichiometricNumber)
ComplexBuildingReaction.BinderSelection	ComplexBuildingReaction.BindeeSectionSelection.in(CellTopology bindeeTopology)
ComplexBuildingReaction.BinderSelection	ComplexBuildingReaction.ComplexBuildingReactionBuilder.in(CellTopology binderTopology)
void	ComplexBuildingReaction.setBindeeTopology(CellTopology bindeeTopology)
void	ComplexBuildingReaction.setBinderTopology(CellTopology binderTopology)
ComplexBuildingReaction.BuilderStep	ComplexBuildingReaction.BinderSectionSelection.to(CellTopology binderTopology)
ComplexBuildingReaction.BuilderStep	ComplexBuildingReaction.ComplexBuildingReactionBuilder.to(CellTopology binderTopology)

Uses of CellTopology in bio.singa.simulation.model.modules.concentration.reactants

Methods in bio.singa.simulation.model.modules.concentration.reactants that return CellTopology

Modifier and Type	Method and Description
CellTopology	Reactant.getPreferredTopology()

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

Modifier and Type	Method and Description
void	Reactant.setPreferredTopology(CellTopology preferredTopology)

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

Constructor and Description
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)

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

Methods in bio.singa.simulation.model.sections that return CellTopology

Modifier and Type	Method and Description
static CellTopology	CellTopology.valueOf(String name) Returns the enum constant of this type with the specified name.
static CellTopology[]	CellTopology.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

Modifier and Type	Method and Description
Map.Entry<CellTopology,ConcentrationPool>	ConcentrationContainer.getPool(CellSubsection subsection) Returns the topology and concentration pool for the subsection.

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

Modifier and Type	Method and Description
void	CellRegion.addSubSection(CellTopology topology, CellSubsection subsection)
Optional<ChemicalEntity>	ConcentrationContainer.containsEntity(CellTopology topology, ChemicalEntity entity)
javax.measure.Quantity<MolarConcentration>	ConcentrationContainer.get(CellTopology topology, ChemicalEntity entity) Returns the concentration of the entity in the corresponding topology.
Map.Entry<CellSubsection,ConcentrationPool>	ConcentrationContainer.getPool(CellTopology topology) Returns the subsection and concentration pool for the topology.
CellSubsection	ConcentrationContainer.getSubsection(CellTopology topology) Returns the subsection corresponding to the topology.
void	ConcentrationContainer.initialize(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration)
void	ConcentrationContainer.initializeSubsection(CellSubsection subsection, CellTopology topology) Initializes a new concentration pool for the corresponding subsection and topology.
void	ConcentrationContainer.putSubsectionPool(CellSubsection subsection, CellTopology topology, ConcentrationPool concentrationPool) Adds a concentration pool, referenced to the subsection and topology.
void	ConcentrationContainer.removeSubsection(CellTopology topology) Removes a subsection, the given topology and concentration pool from the container.
void	ConcentrationContainer.set(CellTopology topology, ChemicalEntity entity, double concentration) Sets the concentration of the given entity in the subsection corresponding to the topological descriptor.
void	ConcentrationContainer.set(CellTopology topology, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> concentration) Sets the concentration of the given entity in the given topology.