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

Class Reaction

java.lang.Object

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

Direct Known Subclasses:

BiochemicalReaction, DynamicReaction, EquilibriumReaction, NthOrderReaction

public abstract class Reaction
extends Object

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.

Constructor Summary

Constructors

Constructor and Description
Reaction()

Method Summary

Modifier and Type	Method and Description
abstract javax.measure.Quantity<ReactionRate>	calculateAcceleration(BioNode node, CellSection section) Determines the actual acceleration of concentration that would result in a change in concentration if the reaction is occurring in the given BioNode.
abstract Set<ChemicalEntity<?>>	collectAllReferencedEntities()
protected javax.measure.Quantity<MolarConcentration>	determineConcentration(BioNode node, CellSection section, ReactantRole role) Determines the concentration of reactants that influence the velocity of the reaction.
String	getDisplayString()
List<ChemicalEntity>	getProducts()
List<StoichiometricReactant>	getStoichiometricReactants() Returns the list of reactants for this reaction.
List<ChemicalEntity>	getSubstrates()
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.

Methods inherited from class java.lang.Object

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

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.

getSubstrates

public List<ChemicalEntity> getSubstrates()

getProducts

public List<ChemicalEntity> getProducts()

determineConcentration

protected javax.measure.Quantity<MolarConcentration> determineConcentration(BioNode node,
                                                                            CellSection section,
                                                                            ReactantRole role)

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

Parameters:

node - The node, where the concentrations are collected.

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

section - The cell section.

Returns:

The total concentration.

calculateAcceleration

public abstract javax.measure.Quantity<ReactionRate> calculateAcceleration(BioNode node,
                                                                           CellSection section)

Determines the actual acceleration of concentration that would result in a change in concentration if the reaction is occurring in the given BioNode.

Parameters:

node - The node containing the concentrations of species subject to this reaction.

section - The cell section.

Returns:

The acceleration of concentration (change in reaction rate for the species of this reaction)

collectAllReferencedEntities

public abstract Set<ChemicalEntity<?>> collectAllReferencedEntities()

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()