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

Class Reaction

java.lang.Object

de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule

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

All Implemented Interfaces:

Featureable, Module

Direct Known Subclasses:

DynamicReaction, EquilibriumReaction, MichaelisMentenReaction, NthOrderReaction

public abstract class Reaction
extends AbstractSectionSpecificModule
implements Featureable

A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. The ChemicalEntitys used in a Reaction are encapsulated to Reactants to define stoichiometry and ReactantRole. The implementations of Reaction have to specify how to calculate the actual acceleration of a reaction.

Field Summary

Fields

Modifier and Type	Field and Description
protected Set<Class<? extends Feature>>	availableFeatures

Fields inherited from class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule

halfTime

Constructor Summary

Constructors

Constructor and Description
Reaction()
Reaction(Simulation simulation)

Method Summary

Modifier and Type	Method and Description
List<Delta>	calculateDeltas(ConcentrationContainer concentrationContainer)
abstract double	calculateVelocity(ConcentrationContainer concentrationContainer)
protected double	determineConcentration(ConcentrationContainer concentrationContainer, ReactantRole role) Determines the concentration of reactants that influence the velocity of the reaction.
Set<Class<? extends Feature>>	getAvailableFeatures()
String	getDisplayString()
<FeatureType extends Feature> FeatureType	getFeature(Class<FeatureType> featureTypeClass)
Collection<Feature<?>>	getFeatures()
List<ChemicalEntity>	getProducts()
protected <FeatureContent> FeatureContent	getScaledFeature(Class<? extends ScalableFeature<FeatureContent>> featureClass)
List<StoichiometricReactant>	getStoichiometricReactants() Returns the list of reactants for this reaction.
List<ChemicalEntity>	getSubstrates()
<FeatureType extends Feature> boolean	hasFeature(Class<FeatureType> featureTypeClass)
boolean	isElementary() Returns true if this Reaction is considered elementary and false otherwise.
void	setElementary(boolean elementary) Sets this Reaction as elementary.
<FeatureType extends Feature> void	setFeature(Class<FeatureType> featureTypeClass)
<FeatureType extends Feature> void	setFeature(FeatureType feature)
void	setStoichiometricReactants(List<StoichiometricReactant> stoichiometricReactants) Sets the list of reactants for this reaction.

Methods inherited from class de.bioforscher.singa.simulation.modules.model.AbstractSectionSpecificModule

addDeltaFunction, applyAlways, determineAllDeltas, determineDeltas, determineDeltasForNode, getCurrentCellSection, getCurrentNode, getFeature, getLargestLocalError, getSimulation, onlyApplyIf, resetLargestLocalError, setSimulation

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.bioforscher.singa.features.model.Featureable

canBeFeaturedWith, scaleScalableFeatures

Field Detail

availableFeatures

protected final Set<Class<? extends Feature>> availableFeatures

Constructor Detail

Reaction

public Reaction(Simulation simulation)

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.

getSubstrates

public List<ChemicalEntity> getSubstrates()

getProducts

public List<ChemicalEntity> getProducts()

determineConcentration

protected double determineConcentration(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

public List<Delta> calculateDeltas(ConcentrationContainer concentrationContainer)

calculateVelocity

public abstract double calculateVelocity(ConcentrationContainer concentrationContainer)

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.

getDisplayString

public String getDisplayString()

getFeatures

public Collection<Feature<?>> getFeatures()

Specified by:

getFeatures in interface Featureable

getFeature

public <FeatureType extends Feature> FeatureType getFeature(Class<FeatureType> featureTypeClass)

Specified by:

getFeature in interface Featureable

getScaledFeature

protected <FeatureContent> FeatureContent getScaledFeature(Class<? extends ScalableFeature<FeatureContent>> featureClass)

setFeature

public <FeatureType extends Feature> void setFeature(Class<FeatureType> featureTypeClass)

Specified by:

setFeature in interface Featureable

setFeature

public <FeatureType extends Feature> void setFeature(FeatureType feature)

Specified by:

setFeature in interface Featureable

hasFeature

public <FeatureType extends Feature> boolean hasFeature(Class<FeatureType> featureTypeClass)

Specified by:

hasFeature in interface Featureable

getAvailableFeatures

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

Specified by:

getAvailableFeatures in interface Featureable