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

Class Reaction

java.lang.Object

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

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

All Implemented Interfaces:

UpdateModule

Direct Known Subclasses:

DynamicReaction, MichaelisMentenReaction, NthOrderReaction, ReversibleReaction

public abstract class Reaction
extends ConcentrationBasedModule<SectionDeltaFunction>

Reactions in general are ConcentrationBasedModules following the laws of chemical kinetics. The calculation of the velocity is defined by the concrete implementation of this module. In general Reactant are defined as StoichiometricReactant that are consumed or produced during the reaction or CatalyticReactant that are used to modify the reaction speed but whose concentration is not altered.

Author:

cl

See Also:

ReversibleReaction, MichaelisMentenReaction, NthOrderReaction

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Reaction.Builder<TopLevelType extends Reaction,BuilderType extends Reaction.Builder>

Field Summary

Fields

Modifier and Type	Field and Description
protected List<StoichiometricReactant>	stoichiometricReactants The stoichiometric reactants.

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

supplier

Constructor Summary

Constructors

Constructor and Description
Reaction()

Method Summary

Modifier and Type	Method and Description
void	addStochiometricReactant(StoichiometricReactant stoichiometricReactant)
protected List<ConcentrationDelta>	calculateDeltas(ConcentrationContainer concentrationContainer) Calculates all deltas for all reactants for the reaction.
abstract double	calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the reaction velocity, depending on the kinetic law.
protected String	collectProductsString()
protected String	collectSubstrateString()
protected double	determineEffectiveConcentration(ConcentrationContainer concentrationContainer, ReactantRole role) Determines the concentration of reactants that influence the velocity of the reaction.
List<ChemicalEntity>	getProducts() Returns all products of this reaction.
String	getReactionString() Returns a nicely formatted string representation of the reaction.
List<StoichiometricReactant>	getStoichiometricReactants() Returns the list of reactants for this reaction.
String	getStringForProtocol()
List<ChemicalEntity>	getSubstrates() Returns all substrates of this reaction.
abstract void	initialize()
boolean	isElementary() Returns true if this Reaction is considered elementary and false otherwise.
void	setElementary(boolean elementary) Sets this Reaction as elementary.
void	setStoichiometricReactants(List<StoichiometricReactant> stoichiometricReactants) Sets the list of reactants for this reaction.
boolean	substratesAvailable(Updatable updatable)
String	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, getRequiredFeatures, 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

Field Detail

stoichiometricReactants

protected List<StoichiometricReactant> stoichiometricReactants

The stoichiometric reactants.

Constructor Detail

Reaction

public Reaction()

Method Detail

getStoichiometricReactants

public List<StoichiometricReactant> getStoichiometricReactants()

Returns the list of reactants for this reaction.

Returns:

The list of reactants for this reaction.

setStoichiometricReactants

public void setStoichiometricReactants(List<StoichiometricReactant> stoichiometricReactants)

Sets the list of reactants for this reaction.

Parameters:

stoichiometricReactants - The list of reactants for this reaction.

addStochiometricReactant

public void addStochiometricReactant(StoichiometricReactant stoichiometricReactant)

substratesAvailable

public boolean substratesAvailable(Updatable updatable)

getSubstrates

public List<ChemicalEntity> getSubstrates()

Returns all substrates of this reaction.

Returns:

All substrates of this reaction.

getProducts

public List<ChemicalEntity> getProducts()

Returns all products of this reaction.

Returns:

All products of this reaction.

determineEffectiveConcentration

protected double determineEffectiveConcentration(ConcentrationContainer concentrationContainer,
                                                 ReactantRole role)

Determines the concentration of reactants that influence the velocity of the reaction.

Parameters:

concentrationContainer - The container, where the concentrations are collected.

role - The role that is to be summarized (ReactantRole.INCREASING for Products and ReactantRole.DECREASING for Substrates).

Returns:

The total concentration.

calculateDeltas

protected List<ConcentrationDelta> calculateDeltas(ConcentrationContainer concentrationContainer)

Calculates all deltas for all reactants for the reaction.

Parameters:

concentrationContainer - The concentration container to calculate the deltas for.

Returns:

The calculated deltas.

calculateVelocity

public abstract double calculateVelocity(ConcentrationContainer concentrationContainer)

Calculates the reaction velocity, depending on the kinetic law.

Parameters:

concentrationContainer - The concentration container to calculate the deltas for.

Returns:

The reaction velocity.

initialize

public abstract void initialize()

isElementary

public boolean isElementary()

Returns true if this Reaction is considered elementary and false otherwise.

Returns:

true if this Reaction is considered elementary and false otherwise.

setElementary

public void setElementary(boolean elementary)

Sets this Reaction as elementary.

Parameters:

elementary - true if this Reaction is elementary and false otherwise.

getReactionString

public String getReactionString()

Returns a nicely formatted string representation of the reaction.

Returns:

A nicely formatted string representation of the reaction.

collectSubstrateString

protected String collectSubstrateString()

collectProductsString

protected String collectProductsString()

getStringForProtocol

public String getStringForProtocol()

Specified by:

getStringForProtocol in interface UpdateModule

Overrides:

getStringForProtocol in class ConcentrationBasedModule<SectionDeltaFunction>

toString

public String toString()

Overrides:

toString in class ConcentrationBasedModule<SectionDeltaFunction>