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

Class BiochemicalReaction

java.lang.Object

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

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

public class BiochemicalReaction
extends Reaction

Author:

cl

Constructor Summary

Constructors

Constructor and Description
BiochemicalReaction(Enzyme enzyme)
BiochemicalReaction(KineticLaw 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()

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

BiochemicalReaction

public BiochemicalReaction(KineticLaw kineticLaw)

BiochemicalReaction

public BiochemicalReaction(Enzyme enzyme)

Method Detail

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