de.bioforscher.singa.simulation.modules.reactions.implementations

Class DynamicReaction

java.lang.Object

de.bioforscher.singa.simulation.modules.reactions.model.Reaction

de.bioforscher.singa.simulation.modules.reactions.implementations.DynamicReaction

public class DynamicReaction
extends Reaction

Author:

cl

Constructor Summary

Constructors

Constructor and Description
DynamicReaction(DynamicKineticLaw kineticLaw)

Method Summary

Modifier and Type	Method and Description
javax.measure.Quantity<ReactionRate>	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.
Set<ChemicalEntity<?>>	collectAllReferencedEntities()
List<CatalyticReactant>	getCatalyticReactants()
DynamicKineticLaw	getKineticLaw()
void	setCatalyticReactants(List<CatalyticReactant> catalyticReactants)
void	setKineticLaw(DynamicKineticLaw kineticLaw)

Methods inherited from class de.bioforscher.singa.simulation.modules.reactions.model.Reaction

determineConcentration, getDisplayString, getProducts, getStoichiometricReactants, getSubstrates, isElementary, setElementary, setStoichiometricReactants

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DynamicReaction

public DynamicReaction(DynamicKineticLaw kineticLaw)

Method Detail

getKineticLaw

public DynamicKineticLaw getKineticLaw()

setKineticLaw

public void setKineticLaw(DynamicKineticLaw kineticLaw)

getCatalyticReactants

public List<CatalyticReactant> getCatalyticReactants()

setCatalyticReactants

public void setCatalyticReactants(List<CatalyticReactant> catalyticReactants)

calculateAcceleration

public javax.measure.Quantity<ReactionRate> calculateAcceleration(BioNode node,
                                                                  CellSection section)

Description copied from class: Reaction

Determines the actual acceleration of concentration that would result in a change in concentration if the reaction is occurring in the given BioNode.

Specified by:

calculateAcceleration in class Reaction

Parameters:

node - The node containing the concentrations of species subject to this reaction.

section - The cell section.

Returns:

The acceleration of concentration (change in reaction rate for the species of this reaction)

collectAllReferencedEntities

public Set<ChemicalEntity<?>> collectAllReferencedEntities()

Specified by:

collectAllReferencedEntities in class Reaction