Extends SpeciesParam, adding parameters used to simulate an agents involvement in a reaction. More...

Inheritance diagram for simulator.agent.ActiveParam:

Public Member Functions
void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction. More...

Public Member Functions inherited from simulator.agent.SpeciesParam
void	init (Simulator aSim, XMLParser aSpeciesRoot)
	Read in specific parameters for this species, changing the default if required. More...

Public Attributes
double[]	particleDensity

double[][]	soluteYield

double[][]	particleYield

double[][]	reactionKinetic

double[]	lysisYield

Public Attributes inherited from simulator.agent.SpeciesParam
double	initialMassCV = .1

Detailed Description

Extends SpeciesParam, adding parameters used to simulate an agents involvement in a reaction.

Extends SpeciesParam, adding parameters used to simulate an agents involvement in a reaction

Author: Andreas Dötsch (andre.nosp@m.as.d.nosp@m.oetsc.nosp@m.h@he.nosp@m.lmhol.nosp@m.tz-h.nosp@m.zi.de), Helmholtz Centre for Infection Research (Germany); Laurent Lardon (lardo.nosp@m.nl@s.nosp@m.upagr.nosp@m.o.in.nosp@m.ra.fr), INRA, France; Brian Merkey (brim@.nosp@m.env..nosp@m.dtu.d.nosp@m.k, bvm@n.nosp@m.orth.nosp@m.weste.nosp@m.rn.e.nosp@m.du), Department of Engineering Sciences and Applied Mathematics, Northwestern University (USA)

Member Function Documentation

void simulator.agent.ActiveParam.init	(	Simulator	aSim,
		XMLParser	aSpeciesRoot
	)

Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction.

Stores the reaction parameters for an active species and calculates the particle density of compounds involved in the reaction

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
aSpeciesRoot	A Species mark-up within the specified protocol file

double [] simulator.agent.ActiveParam.lysisYield

For each defined solute the contribution of a cell when it dies

double [] simulator.agent.ActiveParam.particleDensity

Density of different cell compartments ; by convention the first one is the cell, the last one is the extracellular eps

double [][] simulator.agent.ActiveParam.particleYield

Particle yield from the reaction

double [][] simulator.agent.ActiveParam.reactionKinetic

Kinetic information for this reaction

double [][] simulator.agent.ActiveParam.soluteYield

Solute yield from the reaction

The documentation for this class was generated from the following file: