fern.network

Interface PropensityCalculator

All Known Subinterfaces:

ComplexDependenciesPropensityCalculator, KineticConstantPropensityCalculator, PartialDerivativePropensityCalculator

All Known Implementing Classes:

AbstractKineticConstantPropensityCalculator, ArrayKineticConstantPropensityCalculator, SBMLPropensityCalculator

public interface PropensityCalculator

A PropensityCalculator is the way, a Network tells a Simulator how to calculate propensities for the reactions. Each Simulator calls the calculatePropensity method, when the amount of some reactants of a reactions has changed.

Author:

Florian Erhard

Method Summary

Modifier and Type	Method and Description
double	calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for a reaction given the amounts of the AmountManager.

Method Detail

calculatePropensity

double calculatePropensity(int reaction,
                           AmountManager amount,
                           Simulator sim)

Calculates the propensity for a reaction given the amounts of the AmountManager. If a positive value for volume is given, it is assumed that the constants are deterministic rate constants and are hence to be transformed to specific reaction rate constants.

Parameters:

reaction - index of the reaction

amount - AmountManager

sim - Simulator

Returns:

actual propensity of the reaction