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

Class DynamicReaction

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.DynamicReaction

All Implemented Interfaces:

UpdateModule

public class DynamicReaction
extends Reaction

Author:

cl

Nested Class Summary

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.imlementations.Reaction

stoichiometricReactants

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

supplier

Constructor Summary

Constructors

Constructor and Description
DynamicReaction()

Method Summary

Modifier and Type	Method and Description
double	calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the reaction velocity, depending on the kinetic law.
List<CatalyticReactant>	getCatalyticReactants() Returns the catalytic reactants.
KineticLaw	getKineticLaw() Returns the kinetic law.
Set<Class<? extends Feature>>	getRequiredFeatures()
void	initialize()
void	setCatalyticReactants(List<CatalyticReactant> catalyticReactants) Sets the catalytic reactants.
void	setKineticLaw(KineticLaw kineticLaw) Sets the kinetic law.

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

addStochiometricReactant, calculateDeltas, collectProductsString, collectSubstrateString, determineEffectiveConcentration, getProducts, getReactionString, getStoichiometricReactants, getStringForProtocol, getSubstrates, isElementary, setElementary, setStoichiometricReactants, substratesAvailable, toString

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

addDeltaFunction, addModuleToSimulation, addReferencedEntities, addReferencedEntity, calculateUpdates, checkFeatures, deltaIsValid, determineLargestLocalError, getApplicationCondition, getDeltaCutoff, getErrorCutoff, getFeature, getFeatures, getIdentifier, getReferencedEntities, getScaledFeature, getScaledFeature, getScope, getSimulation, getSpecificity, getState, getSupplier, handleDelta, listFeatures, 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

DynamicReaction

public DynamicReaction()

Method Detail

initialize

public void initialize()

Specified by:

initialize in class Reaction

getKineticLaw

public KineticLaw getKineticLaw()

Returns the kinetic law.

Returns:

The kinetic law.

setKineticLaw

public void setKineticLaw(KineticLaw kineticLaw)

Sets the kinetic law.

Parameters:

kineticLaw - The kinetic law.

getCatalyticReactants

public List<CatalyticReactant> getCatalyticReactants()

Returns the catalytic reactants.

Returns:

The catalytic reactants.

setCatalyticReactants

public void setCatalyticReactants(List<CatalyticReactant> catalyticReactants)

Sets the catalytic reactants.

Parameters:

catalyticReactants - The catalytic reactants.

getRequiredFeatures

public Set<Class<? extends Feature>> getRequiredFeatures()

Specified by:

getRequiredFeatures in interface UpdateModule

Overrides:

getRequiredFeatures in class ConcentrationBasedModule<SectionDeltaFunction>

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.