bio.singa.simulation.model.modules.concentration.imlementations

Class MichaelisMentenReaction

java.lang.Object

bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule<SectionDeltaFunction>

bio.singa.simulation.model.modules.concentration.imlementations.Reaction

bio.singa.simulation.model.modules.concentration.imlementations.MichaelisMentenReaction

All Implemented Interfaces:

UpdateModule

public class MichaelisMentenReaction
extends Reaction

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MichaelisMentenReaction.MichaelisMentenReactionBuilder

Nested classes/interfaces inherited from class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

Reaction.Builder<TopLevelType extends Reaction,BuilderType extends Reaction.Builder>

Field Summary

Fields inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

supplier

Constructor Summary

Constructors

Constructor and Description
MichaelisMentenReaction()

Method Summary

Modifier and Type	Method and Description
protected List<ConcentrationDelta>	calculateDeltas(ConcentrationContainer concentrationContainer) Calculates all deltas for all reactants for the reaction.
double	calculateMembraneBasedVelocity(ConcentrationContainer concentrationContainer)
double	calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the reaction velocity, depending on the kinetic law.
void	checkFeatures()
static ModuleBuilder	getBuilder(Simulation simulation)
void	initialize()
static MichaelisMentenReaction.MichaelisMentenReactionBuilder	inSimulation(Simulation simulation)

Methods inherited from class bio.singa.simulation.model.modules.concentration.imlementations.Reaction

addStochiometricReactant, collectProductsString, collectSubstrateString, getProductEntities, getProducts, getReactionString, getStoichiometricReactants, getSubstrateEntities, getSubstrates, isElementary, setElementary, substratesAvailable, toString

Methods inherited from class bio.singa.simulation.model.modules.concentration.ConcentrationBasedModule

addDeltaFunction, addModuleToSimulation, addReferencedEntities, addReferencedEntity, calculateUpdates, deltaIsValid, determineLargestLocalError, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getRequiredFeatures, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getSupplier, handleDelta, onCompletion, onReset, optimizeTimeStep, resetState, scaleScalableFeatures, setApplicationCondition, setDeltaCutoff, setErrorCutoff, setFeature, setIdentifier, setSimulation

Methods inherited from class java.lang.Object

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

Constructor Detail

MichaelisMentenReaction

public MichaelisMentenReaction()

Method Detail

inSimulation

public static MichaelisMentenReaction.MichaelisMentenReactionBuilder inSimulation(Simulation simulation)

initialize

public void initialize()

Specified by:

initialize in class Reaction

calculateDeltas

protected List<ConcentrationDelta> calculateDeltas(ConcentrationContainer concentrationContainer)

Description copied from class: Reaction

Calculates all deltas for all reactants for the reaction.

Overrides:

calculateDeltas in class Reaction

Parameters:

concentrationContainer - The concentration container to calculate the deltas for.

Returns:

The calculated deltas.

calculateVelocity

public double calculateVelocity(ConcentrationContainer concentrationContainer)

Description copied from class: Reaction

Calculates the reaction velocity, depending on the kinetic law.

Specified by:

calculateVelocity in class Reaction

Parameters:

concentrationContainer - The concentration container to calculate the deltas for.

Returns:

The reaction velocity.

calculateMembraneBasedVelocity

public double calculateMembraneBasedVelocity(ConcentrationContainer concentrationContainer)

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

Overrides:

checkFeatures in class ConcentrationBasedModule<SectionDeltaFunction>

getBuilder

public static ModuleBuilder getBuilder(Simulation simulation)