Uses of Class
de.bioforscher.singa.simulation.model.compartments.CellSection

Packages that use CellSection

Package	Description
de.bioforscher.singa.simulation.model.compartments
de.bioforscher.singa.simulation.model.graphs
de.bioforscher.singa.simulation.modules.model.updates
de.bioforscher.singa.simulation.modules.reactions.implementations
de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations
de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model
de.bioforscher.singa.simulation.modules.reactions.model

Uses of CellSection in de.bioforscher.singa.simulation.model.compartments

Subclasses of CellSection in de.bioforscher.singa.simulation.model.compartments

Modifier and Type	Class and Description
class	EnclosedCompartment An EnclosedCompartment is a CellSection that is bordered or enclosed by a Membrane.
class	Membrane

Uses of CellSection in de.bioforscher.singa.simulation.model.graphs

Methods in de.bioforscher.singa.simulation.model.graphs that return CellSection

Modifier and Type	Method and Description
CellSection	BioNode.getCellSection()
CellSection	AutomatonGraph.getSection(String identifier)

Methods in de.bioforscher.singa.simulation.model.graphs that return types with arguments of type CellSection

Modifier and Type	Method and Description
Set<CellSection>	SimpleConcentrationContainer.getAllReferencedSections()
Set<CellSection>	MultiConcentrationContainer.getAllReferencedSections()
Set<CellSection>	MembraneContainer.getAllReferencedSections()
Set<CellSection>	ConcentrationContainer.getAllReferencedSections() Returns all Compartments that are referenced in this container.
Set<CellSection>	BioNode.getAllReferencedSections()
Set<CellSection>	AutomatonGraph.getSections()

Methods in de.bioforscher.singa.simulation.model.graphs with parameters of type CellSection

Modifier and Type	Method and Description
void	AutomatonGraph.addSection(CellSection cellSection)
javax.measure.Quantity<MolarConcentration>	SimpleConcentrationContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	MultiConcentrationContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	MembraneContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity)
javax.measure.Quantity<MolarConcentration>	ConcentrationContainer.getAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity) Returns the available concentration based on the given compartment.
javax.measure.Quantity<MolarConcentration>	BioNode.getAvailableConcentration(ChemicalEntity entity, CellSection cellSection)
void	SimpleConcentrationContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration)
void	MultiConcentrationContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration)
void	MembraneContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration)
void	ConcentrationContainer.setAvailableConcentration(CellSection cellSection, ChemicalEntity chemicalEntity, javax.measure.Quantity<MolarConcentration> concentration) Sets the available concentration based on the given compartment.
void	BioNode.setAvailableConcentration(ChemicalEntity entity, CellSection cellSection, javax.measure.Quantity<MolarConcentration> quantity)
void	BioNode.setCellSection(CellSection cellSection)
static void	AutomatonGraphs.splitRectangularGraphWithMembrane(AutomatonGraph graph, GridCoordinateConverter converter, EnclosedCompartment innerSection, CellSection outerSection)

Constructors in de.bioforscher.singa.simulation.model.graphs with parameters of type CellSection

Constructor and Description
MembraneContainer(CellSection outerSection, CellSection innerSection, Membrane membrane)
MultiConcentrationContainer(CellSection cellSection)
SimpleConcentrationContainer(CellSection cellSection)

Constructor parameters in de.bioforscher.singa.simulation.model.graphs with type arguments of type CellSection

Constructor and Description
MultiConcentrationContainer(Set<CellSection> cellSections)

Uses of CellSection in de.bioforscher.singa.simulation.modules.model.updates

Methods in de.bioforscher.singa.simulation.modules.model.updates that return CellSection

Modifier and Type	Method and Description
CellSection	PotentialUpdate.getCellSection()

Constructors in de.bioforscher.singa.simulation.modules.model.updates with parameters of type CellSection

Constructor and Description
PotentialUpdate(BioNode node, CellSection cellSection, ChemicalEntity entity, javax.measure.Quantity<MolarConcentration> quantity)

Uses of CellSection in de.bioforscher.singa.simulation.modules.reactions.implementations

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations with parameters of type CellSection

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	NthOrderReaction.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	EquilibriumReaction.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	DynamicReaction.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	BiochemicalReaction.calculateAcceleration(BioNode node, CellSection section)

Uses of CellSection in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.implementations with parameters of type CellSection

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	MichaelsMentenWithKM.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	MichaelisMentenWithKCat.calculateAcceleration(BioNode node, CellSection section)
javax.measure.Quantity<ReactionRate>	DynamicKineticLaw.calculateAcceleration(BioNode node, CellSection section)

Uses of CellSection in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model

Methods in de.bioforscher.singa.simulation.modules.reactions.implementations.kineticLaws.model with parameters of type CellSection

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	KineticLaw.calculateAcceleration(BioNode node, CellSection section)

Uses of CellSection in de.bioforscher.singa.simulation.modules.reactions.model

Methods in de.bioforscher.singa.simulation.modules.reactions.model with parameters of type CellSection

Modifier and Type	Method and Description
abstract javax.measure.Quantity<ReactionRate>	Reaction.calculateAcceleration(BioNode node, CellSection section) Determines the actual acceleration of concentration that would result in a change in concentration if the reaction is occurring in the given BioNode.
PotentialUpdate	Reactions.calculateUpdate(BioNode node, CellSection section, ChemicalEntity entity)
protected javax.measure.Quantity<MolarConcentration>	Reaction.determineConcentration(BioNode node, CellSection section, ReactantRole role) Determines the concentration of reactants that influence the velocity of the reaction.