bio.singa.simulation.model.modules.concentration.reactants

Class KineticLaw

java.lang.Object

bio.singa.simulation.model.modules.concentration.reactants.KineticLaw

public class KineticLaw
extends Object

Dynamic kinetic laws allow for the definition of reaction kinetics based on equations. Equations are supplied to the Kinetic law as AppliedExpressions.

Author:

cl

Constructor Summary

Constructors

Constructor and Description
KineticLaw(AppliedExpression expression) Creates a new dynamic kinetic law with the applied expression.

Method Summary

Modifier and Type	Method and Description
double	calculateVelocity(ConcentrationContainer concentrationContainer) Calculates the velocity of the reaction based on the entities in the concentration container.
CellSubsection	getCurrentCellSection() Returns the current cell section the kinetic law is applied to.
AppliedExpression	getExpression() Returns the actual expression use to calculate this kinetic law.
void	referenceChemicalEntityToParameter(String parameterIdentifier, ChemicalEntity entity) Assigns a parameter of the expression to the concentration of a chemical species.
void	setAppliedScale(Double appliedScale) Sets the scaling factor that is applied to account for changes in the time step size.
void	setCurrentCellSection(CellSubsection currentCellSection) Sets the current cell section the kinetic law is applied to.

Methods inherited from class java.lang.Object

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

Constructor Detail

KineticLaw

public KineticLaw(AppliedExpression expression)

Creates a new dynamic kinetic law with the applied expression.

Parameters:

expression - The expression.

Method Detail

getExpression

public AppliedExpression getExpression()

Returns the actual expression use to calculate this kinetic law.

Returns:

The actual expression use to calculate this kinetic law.

referenceChemicalEntityToParameter

public void referenceChemicalEntityToParameter(String parameterIdentifier,
                                               ChemicalEntity entity)

Assigns a parameter of the expression to the concentration of a chemical species.

Parameters:

parameterIdentifier - The identifier of the parameter.

entity - The entity to be referenced.

setAppliedScale

public void setAppliedScale(Double appliedScale)

Sets the scaling factor that is applied to account for changes in the time step size.

Parameters:

appliedScale - The scaling factor.

getCurrentCellSection

public CellSubsection getCurrentCellSection()

Returns the current cell section the kinetic law is applied to.

Returns:

The current cell section the kinetic law is applied to.

setCurrentCellSection

public void setCurrentCellSection(CellSubsection currentCellSection)

Sets the current cell section the kinetic law is applied to.

Parameters:

currentCellSection - The current cell section the kinetic law is applied to.

calculateVelocity

public double calculateVelocity(ConcentrationContainer concentrationContainer)

Calculates the velocity of the reaction based on the entities in the concentration container.

Parameters:

concentrationContainer - The concentration container.

Returns:

The velocity.