simulator.reaction.Reaction Class Reference

Class containing methods to create and query reactions that occur in the simulation. More...

Inheritance diagram for simulator.reaction.Reaction:

Public Member Functions
void	init (Simulator aSim, XMLParser aReactionRoot)
	Initialises a reaction object, giving the object the properties stated in the protocol file. More...
void	initFromAgent (ActiveAgent anAgent, Simulator aSim, XMLParser xmlRoot)
	Use the reaction class to fill the parameters fields of the agent. Populate only the yield vector, the kinetic vector will be filled by the subdefined method in the child classes. More...
void	register (String aReactionName, Simulator aSimulator)
	End of the initialization procedure. Store the name and simulation dictionary index for this reaction. More...
LinkedList< String >	declareSolutes ()
	Utilised by a solver instance to know the solutes affected by this reaction. More...
void	fillParameters (Simulator aSim, XMLParser xmlRoot)
	Reads the reaction information (name, solute yield, particle yield etc) from the XML file and initialises this reaction. More...
void	addAgent (ActiveAgent anAgent)
	Register an agent among the guild of this pathway. More...
void	removeAgent (ActiveAgent anAgent)
	Remove an agent among the guild of this pathway. More...
abstract double	computeMassGrowthRate (ActiveAgent anAgent)
	Compute the marginal growth rate (i.e the specific growth rate times the mass of the particle which is mediating this reaction) More...
abstract double	computeSpecGrowthRate (ActiveAgent anAgent)
	Compute the specific growth rate. More...
abstract void	computeSpecificGrowthRate (ActiveAgent anAgent)
	Return the specific reaction rate for a given agent. More...
abstract void	computeSpecificGrowthRate (double[] s, ActiveAgent anAgent)
	Compute specific growth rate in function to concentrations sent. More...
abstract void	computeSpecificGrowthRate (double[] s)
	Compute specific growth rate in function of concentrations sent Parameters used are those defined for the reaction. More...
abstract void	computeUptakeRate (double[] s, double mass, double t)
	Update the array of uptake rates and the array of its derivative. Based on default values of parameters. Unit is fg.h-1. More...
void	applyReaction (SpatialGrid[] concGrid, SpatialGrid[] reacGrid, SpatialGrid[] diffReacGrid, SpatialGrid biomassGrid)
	Compute reaction rate on each concerned solute grids Assumes same parameters for all the agents of a same guild. More...
void	fitAgentMassOnGrid (SpatialGrid aSpG)
	Add the mass of all the agents of the guild on a received grid. The stored value is a CONCENTRATION. More...
double[]	readConcentrationSeen (ActiveAgent anAgent, SoluteGrid[] concGrid)
	Return a double array with all concentration seen by an agent on the default solute grid. More...
void	writeReport (ResultFile bufferState, ResultFile bufferSum) throws Exception
	Write reaction information to the result file stream. More...
void	fitGuildOnGrid ()
	Build a grid with mass and mass-growth-rate of all agents of the guild. More...
double[]	getSoluteYield ()
	Return the solute yield. More...
int[]	getSoluteIndex ()
	Return the solute index. More...
double[]	getParticulateYield ()
	Return the particulate yield. More...
double[]	getKinetic ()
	Return the kinetic parameters used in this reaction. More...
LinkedList< ActiveAgent >	getGuild ()
	Return the guild of this pathway. More...
abstract Matrix	calcdMUdS (Matrix S, double biomass)
	Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix. More...
abstract Matrix	calcdMUdT (Matrix S, double biomass)
	Calculate the rate of change of each uptake rate with respect to time. More...
abstract void	updateMarginalMu (double[] s)
	Update the Marginal Mu data matrix. More...
abstract double	computeSpecRate (double[] s)
	Compute the specific growth rate. More...
abstract double[]	computeMarginalDiffMu (double[] s)
	Compute the marginal difference array. More...

Public Attributes
String	reactionName
int	reactionIndex
int	_catalystIndex
int[]	_mySoluteIndex
boolean	autocatalytic
double[]	totalUptake
double	Dil

Protected Attributes
LinkedList< ActiveAgent >	_guild = new LinkedList<ActiveAgent>()
SoluteGrid[]	_soluteList
SoluteGrid	_reacGrid
SoluteGrid	_guildGrid
double	_specRate
double[]	_diffUptakeRate
double[]	_uptakeRate
double[]	_soluteYield
double[]	_kineticParam
double[]	_particleYield
String[]	_particleNameYield

Detailed Description

Class containing methods to create and query reactions that occur in the simulation.

Reactions in which solutes or biomass are produced or consumed mediate the dynamics of the entire iDynoMiCS simulation. The REACTION markup in the XML file specifies the reactions that occur. These may be defined via both stoichiometric and kinetic forms, and both of these representations are used in definining reactions in the protocol file.

Version

1.2

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

Kieran Alden (k.j.a.nosp@m.lden.nosp@m.@bham.nosp@m..ac..nosp@m.uk), Centre for Systems Biology, University of Birmingham, UK

Member Function Documentation

void simulator.reaction.Reaction.addAgent

(

ActiveAgent

anAgent

)

Register an agent among the guild of this pathway.

Register an agent among the guild of this pathway

Parameters

anAgent

ActiveAgent to register

void simulator.reaction.Reaction.applyReaction	(	SpatialGrid[]	concGrid,
		SpatialGrid[]	reacGrid,
		SpatialGrid[]	diffReacGrid,
		SpatialGrid	biomassGrid
	)

Compute reaction rate on each concerned solute grids Assumes same parameters for all the agents of a same guild.

Compute reaction rate on each concerned solute grids Assumes same parameters for all the agents of a same guild

Parameters

concGrid	Solute concentration
reacGrid	Contribution of the reaction to the solute concentration dynamics
diffReacGrid	Derivative of the previous grid
biomassGrid	CONCENTRATION of the catalyst

See Also

multigrid solver

abstract Matrix simulator.reaction.Reaction.calcdMUdS ( Matrix  S, double  biomass  )

pure virtual

Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix.

Calculate the rate of change of each uptake rate with respect to each solute. Returned as a matrix

Parameters

S	Temporary container for solute concentration
biomass	Total particle mass in the system which catalyses this reaction

Returns

Matrix containing rate of change of each uptake rate with respect to each solute

Implemented in simulator.reaction.ReactionFactor, simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionGrowthFitness, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

abstract Matrix simulator.reaction.Reaction.calcdMUdT ( Matrix  S, double  biomass  )

pure virtual

Calculate the rate of change of each uptake rate with respect to time.

Calculate the rate of change of each uptake rate with respect to time. dMUdT = catalyticBiomass*specificGrowthRate*soluteYield. Returned as a matrix

Parameters

S	Temporary container for solute concentration
biomass	Total particle mass in the system which catalyses this reaction

Returns

Matrix containing rate of change of each uptake rate with respect to time

Implemented in simulator.reaction.ReactionFactor, simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionGrowthFitness, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

abstract double [] simulator.reaction.Reaction.computeMarginalDiffMu ( double[]  s )

pure virtual

Compute the marginal difference array.

Compute the marginal difference array. Don't forget to update marginalMu before calling this!

Parameters

s	Temporary container for solute concentration

Returns

Marginal diff array

Implemented in simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionGrowthFitness, simulator.reaction.ReactionFactor, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

abstract double simulator.reaction.Reaction.computeMassGrowthRate ( ActiveAgent  anAgent )

pure virtual

Compute the marginal growth rate (i.e the specific growth rate times the mass of the particle which is mediating this reaction)

Compute the marginal growth rate (i.e the specific growth rate times the mass of the particle which is mediating this reaction)

Parameters

anAgent

Specific growth rate for this ActiveAgent

Returns

The marginal growth rate

Implemented in simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.ReactionGrowthFitness, simulator.reaction.FirstOrder, and simulator.reaction.SingleMonod.

abstract double simulator.reaction.Reaction.computeSpecGrowthRate ( ActiveAgent  anAgent )

pure virtual

Compute the specific growth rate.

Compute the specific growth rate

Parameters

anAgent

Specific growth rate for this ActiveAgent

Returns

The specific growth rate

Implemented in simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.ReactionGrowthFitness, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

abstract void simulator.reaction.Reaction.computeSpecificGrowthRate ( ActiveAgent  anAgent )

pure virtual

Return the specific reaction rate for a given agent.

Return the specific reaction rate for a given agent

Parameters

anAgent

Agent to use to determine solute concentration and calculate reaction rate

See Also

ActiveAgent.grow()

Episome.computeRate(EpiBac)

Implemented in simulator.reaction.ReactionGrowthFitness, simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.FirstOrder, and simulator.reaction.SingleMonod.

abstract void simulator.reaction.Reaction.computeSpecificGrowthRate ( double[]  s, ActiveAgent  anAgent  )

pure virtual

Compute specific growth rate in function to concentrations sent.

Compute specific growth rate in function to concentrations sent

Parameters

s	Array of solute concentration
anAgent	Parameters used are those defined for THIS agent

Implemented in simulator.reaction.ReactionGrowthFitness, simulator.reaction.ReactionFactor, simulator.reaction.ReactionFactorWithConstant, simulator.reaction.FirstOrder, and simulator.reaction.SingleMonod.

abstract void simulator.reaction.Reaction.computeSpecificGrowthRate ( double[]  s )

pure virtual

Compute specific growth rate in function of concentrations sent Parameters used are those defined for the reaction.

Compute specific growth rate in function of concentrations sent Parameters used are those defined for the reaction.

Parameters

s	Array of solute concentration

Implemented in simulator.reaction.ReactionGrowthFitness, simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

abstract double simulator.reaction.Reaction.computeSpecRate ( double[]  s )

pure virtual

Compute the specific growth rate.

Compute the specific growth rate. Don't forget to update marginalMu before calling this!

Parameters

s	Temporary container for solute concentration

Returns

The specific growth rate

Implemented in simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.ReactionGrowthFitness, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

abstract void simulator.reaction.Reaction.computeUptakeRate ( double[]  s, double  mass, double  t  )

pure virtual

Update the array of uptake rates and the array of its derivative. Based on default values of parameters. Unit is fg.h-1.

Update the array of uptake rates and the array of its derivative. Based on default values of parameters. Unit is fg.h-1

Parameters

s	The concentration of solute locally observed
mass	Mass of the catalyst (cell...)
t	Time

Implemented in simulator.reaction.ReactionGrowthFitness, simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.SingleMonod, and simulator.reaction.FirstOrder.

LinkedList<String> simulator.reaction.Reaction.declareSolutes

(

)

Utilised by a solver instance to know the solutes affected by this reaction.

Utility method called by a solver instance to know the solutes affected by this reaction

Returns

a list of solutes affected by this reaction

See Also

DiffusionSolver.addReaction()

void simulator.reaction.Reaction.fillParameters	(	Simulator	aSim,
		XMLParser	xmlRoot
	)

Reads the reaction information (name, solute yield, particle yield etc) from the XML file and initialises this reaction.

This method takes one reaction from the XML file and initialises a Reaction object with the properties stated in the protocol file. This includes reaction name, what the reaction is catalysed by, reaction kinetics, and solute and particle yields

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
xmlRoot	The XML object containing the definition of one reaction in the protocol file

void simulator.reaction.Reaction.fitAgentMassOnGrid

(

SpatialGrid

aSpG

)

Add the mass of all the agents of the guild on a received grid. The stored value is a CONCENTRATION.

Add the mass of all the agents of the guild on a received grid. The stored value is a CONCENTRATION

Parameters

aSpG	Spatial grid of reactive biomass

void simulator.reaction.Reaction.fitGuildOnGrid

(

)

Build a grid with mass and mass-growth-rate of all agents of the guild.

Build a grid with mass and mass-growth-rate of all agents of the guild. Used when outputting simulation state to file

LinkedList<ActiveAgent> simulator.reaction.Reaction.getGuild

(

)

Return the guild of this pathway.

Return the guild of this pathway

Returns

LinkedList containing all agents in the guild

double [] simulator.reaction.Reaction.getKinetic

(

)

Return the kinetic parameters used in this reaction.

Return the kinetic parameters used in this reaction

Returns

Double array containing kinetic parameters

double [] simulator.reaction.Reaction.getParticulateYield

(

)

Return the particulate yield.

Return the particulate yield

Returns

Double array of particulate yield

int [] simulator.reaction.Reaction.getSoluteIndex

(

)

Return the solute index.

Return the solute index

Returns

Integer array of solute index

double [] simulator.reaction.Reaction.getSoluteYield

(

)

Return the solute yield.

Return the solute yield

Returns

Double array of solute yield

void simulator.reaction.Reaction.init	(	Simulator	aSim,
		XMLParser	aReactionRoot
	)

Initialises a reaction object, giving the object the properties stated in the protocol file.

Reactions in which solutes or biomass are produced or consumed mediate the dynamics of iDynoMiCS. This constructor initialises a particular reaction that is stated in the protocol file. Kinetic parameters are managed by the subdefined method in the children class

Parameters

aSim	The simulation object used to simulate the conditions specified in the protocol file
aReactionRoot	The XML object containing the definition of one reaction in the protocol file

See Also

Simulator.createReaction()

void simulator.reaction.Reaction.initFromAgent	(	ActiveAgent	anAgent,
		Simulator	aSim,
		XMLParser	xmlRoot
	)

Use the reaction class to fill the parameters fields of the agent. Populate only the yield vector, the kinetic vector will be filled by the subdefined method in the child classes.

Use the reaction class to fill the parameters fields of the agent. Populate only the yield vector, the kinetic vector will be filled by the subdefined method in the child classes

Parameters

anAgent	The ActiveAgent which parameters are being populated
aSim	The simulation object used to simulate the conditions specified in the protocol file
xmlRoot	The XML object containing the definition of one reaction in the protocol file

See Also

Simulator.createReaction()

double [] simulator.reaction.Reaction.readConcentrationSeen	(	ActiveAgent	anAgent,
		SoluteGrid[]	concGrid
	)

Return a double array with all concentration seen by an agent on the default solute grid.

Return a double array with all concentration seen by an agent on the default solute grid

Parameters

anAgent	ActiveAgent responding to solute levels
concGrid	Solute concentration grid

Returns

all the concentration seen by an agent on the default solute grid

void simulator.reaction.Reaction.register	(	String	aReactionName,
		Simulator	aSimulator
	)

End of the initialization procedure. Store the name and simulation dictionary index for this reaction.

End of the initialization procedure. Store the name and simulation dictionary index for this reaction

Parameters

aReactionName	Name of this reaction
aSimulator	Integer reference to the readcion simulation dictionary

See Also

Simulator.addReaction()

void simulator.reaction.Reaction.removeAgent

(

ActiveAgent

anAgent

)

Remove an agent among the guild of this pathway.

Remove an agent among the guild of this pathway

Parameters

anAgent

ActiveAgent to remove

abstract void simulator.reaction.Reaction.updateMarginalMu ( double[]  s )

pure virtual

Update the Marginal Mu data matrix.

Update the Marginal Mu data matrix

Parameters

s	Temporary container for solute concentration

Implemented in simulator.reaction.ReactionFactorWithConstant, simulator.reaction.ReactionFactor, simulator.reaction.SingleMonod, simulator.reaction.ReactionGrowthFitness, and simulator.reaction.FirstOrder.

void simulator.reaction.Reaction.writeReport	(	ResultFile	bufferState,
		ResultFile	bufferSum
	)		throws Exception

Write reaction information to the result file stream.

Write reaction information to the result file stream

Parameters

bufferState	Buffer for state result files
bufferSum	Buffer for sum result files

Exceptions

Exception

Exception thrown if these files cannot be opened

Member Data Documentation

int simulator.reaction.Reaction._catalystIndex

Holds an integer that references the simulation particle dictionary - notes the particle that catalyses this reaction

double [] simulator.reaction.Reaction._diffUptakeRate

protected

Buffer vector used to communicate diffision uptake rate to the solver, for each solute

LinkedList<ActiveAgent> simulator.reaction.Reaction._guild = new LinkedList<ActiveAgent>()

protected

Agents hosting this process

SoluteGrid simulator.reaction.Reaction._guildGrid

protected

Grid concerning the biomass that catalyses this reaction

double [] simulator.reaction.Reaction._kineticParam

protected

Array to store the kinetic factors involved in this reaction

int [] simulator.reaction.Reaction._mySoluteIndex

A list of solute indices: if that solute's yield in this reaction is non-zero then it is on this list. Hence, this is the list of solutes which are affected by this reaction.

String [] simulator.reaction.Reaction._particleNameYield

protected

Array to store the names of the particles yielded in this reaction (sonia: 21-05-09)

double [] simulator.reaction.Reaction._particleYield

protected

Array to store the particle yield from this reaction. If a solute is not concerned by the current reaction, the yield will be zero

SoluteGrid simulator.reaction.Reaction._reacGrid

protected

Solute grid that stores reaction rate for this reaction

SoluteGrid [] simulator.reaction.Reaction._soluteList

protected

Local copy of the solute grids used in this simulation. Used for efficiency purposes

double [] simulator.reaction.Reaction._soluteYield

protected

Array to store the solute yield from this reaction. If a solute is not concerned by the current reaction, the yield will be zero

double simulator.reaction.Reaction._specRate

protected

Temporary storage used during computation of reaction rates

double [] simulator.reaction.Reaction._uptakeRate

protected

Buffer vector used to communicate uptake rate to the solver, for each solute

boolean simulator.reaction.Reaction.autocatalytic

Boolean noting whether or not the catalytic particle is affected by the reaction

double simulator.reaction.Reaction.Dil

dilution rate from associated bulk (sonia 21-04-10)

int simulator.reaction.Reaction.reactionIndex

Index to this reaction in the simulation dictionary

String simulator.reaction.Reaction.reactionName

Name of this reaction. Set from the relevant tag in the protocol file

double [] simulator.reaction.Reaction.totalUptake

Buffer vector used to communicate uptake rate to the solver, for each solute

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

• /home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/reaction/Reaction.java