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

Class ReversibleReaction

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.ReversibleReaction

All Implemented Interfaces:

UpdateModule

public class ReversibleReaction
extends Reaction

Reversible reactions are Reactions where the substrates form products, and products can also from substrates.

  A <-> B

The corresponding rate law is as follows:

  v = kfwd * cA - kbwd * cB

where v is the velocity of the reaction, kfwd is any ForwardsRateConstant, kbwd is any BackwardsRateConstant, cA is the concentration of the substrate, and cB is the concentration of the product. Reversible reactions are SectionSpecific and supply IndependentUpdates.

  // setup kfwd
  RateConstant forwardsRate = RateConstant.create(10)
         .forward().firstOrder()
         .timeUnit(SECOND)
         .build();

  // setup kbwd
  RateConstant backwardsRate = RateConstant.create(10)
         .backward().firstOrder()
         .timeUnit(SECOND)
         .build();

  // set up species
  SmallMolecule speciesA = new SmallMolecule.Builder("A")
         .build();

  SmallMolecule speciesB = new SmallMolecule.Builder("A")
         .build();

  // create reaction
  ReversibleReaction.inSimulation(simulation)
         .addSubstrate(speciesA)
         .addProduct(speciesB)
         .forwardsRateConstant(forwardsRate)
         .backwardsRateConstant(backwardsRate)
         .build();

Author:

cl

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ReversibleReaction.ReversibleReactionBuilder

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
ReversibleReaction()

Method Summary

Modifier and Type	Method and Description
double	calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the reaction velocity, depending on the kinetic law.
void	checkFeatures()
static ModuleBuilder	getBuilder(Simulation simulation)
String	getReactionString() Returns a nicely formatted string representation of the reaction.
void	initialize()
static ReversibleReaction.ReversibleReactionBuilder	inSimulation(Simulation simulation)

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

addStochiometricReactant, calculateDeltas, collectProductsString, collectSubstrateString, getProductEntities, getProducts, 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

ReversibleReaction

public ReversibleReaction()

Method Detail

inSimulation

public static ReversibleReaction.ReversibleReactionBuilder inSimulation(Simulation simulation)

initialize

public void initialize()

Specified by:

initialize in class Reaction

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.

getReactionString

public String getReactionString()

Description copied from class: Reaction

Returns a nicely formatted string representation of the reaction.

Overrides:

getReactionString in class Reaction

Returns:

A nicely formatted string representation of the reaction.

checkFeatures

public void checkFeatures()

Specified by:

checkFeatures in interface UpdateModule

Overrides:

checkFeatures in class ConcentrationBasedModule<SectionDeltaFunction>

getBuilder

public static ModuleBuilder getBuilder(Simulation simulation)