Interface for all kinetic reactions that can be defined in iDynoMiCS. More...

Inheritance diagram for simulator.reaction.kinetic.IsKineticFactor:

Public Member Functions
abstract void	init (Element defMarkUp)
	Initialise the kinetic, reading in kinetic parameter information from the protocol file and calculating any auxillaries needed for easing the kinetic calculation. More...

abstract void	initFromAgent (Element aReactionRoot, double[] kineticParam, int paramIndex)
	Initialise the reaction from a parent of the agent. More...

abstract double	kineticValue (double solute)
	Calculate the value of the kinetic for a given level of solute. More...

abstract double	kineticDiff (double solute)
	Used to compute marginal difference kinetic values for a given solute level. More...

abstract double	kineticValue (double solute, double[] paramTable, int index)
	Calculate the value of the kinetic from a given level of solute, an array containing parameters relating to the reaction, and an index to this array. More...

abstract double	kineticDiff (double solute, double[] paramTable, int index)
	Used to compute marginal difference kinetic values for a given solute level. More...

Public Attributes
int	nParam

Detailed Description

Interface for all kinetic reactions that can be defined in iDynoMiCS.

Kinetic factor mark-ups comprise the multiplicative terms that make up the entire reaction kinetic. iDynoMiCS includes a suite of kinetic factor terms. This interface defines the parameters and methods that are common for them all

Author: kieran

Member Function Documentation

abstract void simulator.reaction.kinetic.IsKineticFactor.init ( Element defMarkUp )

pure virtual

Initialise the kinetic, reading in kinetic parameter information from the protocol file and calculating any auxillaries needed for easing the kinetic calculation.

Initialise the kinetic, reading in kinetic parameter information from the protocol file and calculating any auxillaries needed for easing the kinetic calculation

Parameters

defMarkUp XML tags that define this kinetic in the protocol file

Implemented in simulator.reaction.kinetic.HillKinetic, simulator.reaction.kinetic.HaldaneKinetic, simulator.reaction.kinetic.SimpleInhibition, simulator.reaction.kinetic.MonodKinetic, simulator.reaction.kinetic.LinearKinetic, and simulator.reaction.kinetic.FirstOrderKinetic.

abstract void simulator.reaction.kinetic.IsKineticFactor.initFromAgent	(	Element	aReactionRoot,
		double[]	kineticParam,
		int	paramIndex
	)

pure virtual

Initialise the reaction from a parent of the agent.

Initialise the reaction from a parent of the agent

Parameters

aReactionRoot	XML tags that define this kinetic in the protocol file
kineticParam	Array of parameters associated with this reaction
paramIndex	An index to the parameter array

Implemented in simulator.reaction.kinetic.HillKinetic, simulator.reaction.kinetic.HaldaneKinetic, simulator.reaction.kinetic.SimpleInhibition, simulator.reaction.kinetic.MonodKinetic, simulator.reaction.kinetic.LinearKinetic, and simulator.reaction.kinetic.FirstOrderKinetic.

abstract double simulator.reaction.kinetic.IsKineticFactor.kineticDiff ( double solute )

pure virtual

Used to compute marginal difference kinetic values for a given solute level.

Used to compute marginal difference kinetic values for a given solute level

Parameters

solute Solute level

Returns: Level of the reaction kinetic

Implemented in simulator.reaction.kinetic.HillKinetic, simulator.reaction.kinetic.SimpleInhibition, simulator.reaction.kinetic.HaldaneKinetic, simulator.reaction.kinetic.MonodKinetic, simulator.reaction.kinetic.LinearKinetic, and simulator.reaction.kinetic.FirstOrderKinetic.

abstract double simulator.reaction.kinetic.IsKineticFactor.kineticDiff	(	double	solute,
		double[]	paramTable,
		int	index
	)

pure virtual

Used to compute marginal difference kinetic values for a given solute level.

Used to compute marginal difference kinetic values for a given solute level

Parameters

solute	Solute level
paramTable	Array of parameters relating to this reaction
index	An index to the parameter array

Returns: Level of the reaction kinetic

Implemented in simulator.reaction.kinetic.HillKinetic, simulator.reaction.kinetic.HaldaneKinetic, simulator.reaction.kinetic.SimpleInhibition, simulator.reaction.kinetic.MonodKinetic, simulator.reaction.kinetic.LinearKinetic, and simulator.reaction.kinetic.FirstOrderKinetic.

abstract double simulator.reaction.kinetic.IsKineticFactor.kineticValue ( double solute )

pure virtual

Calculate the value of the kinetic for a given level of solute.

Calculate the value of the kinetic for a given level of solute

Parameters

solute Double stating the level of that solute

Returns: Double value stating the value of the kinetic for this level of solute

Implemented in simulator.reaction.kinetic.HillKinetic, simulator.reaction.kinetic.HaldaneKinetic, simulator.reaction.kinetic.SimpleInhibition, simulator.reaction.kinetic.MonodKinetic, simulator.reaction.kinetic.LinearKinetic, and simulator.reaction.kinetic.FirstOrderKinetic.

abstract double simulator.reaction.kinetic.IsKineticFactor.kineticValue	(	double	solute,
		double[]	paramTable,
		int	index
	)

pure virtual

Calculate the value of the kinetic from a given level of solute, an array containing parameters relating to the reaction, and an index to this array.

Calculate the value of the kinetic from a given level of solute, an array containing parameters relating to the reaction, and an index to this array

Parameters

solute	Double stating the level of that solute
paramTable	Array of parameters relating to this reaction
index	An index to the parameter array

Returns: Double value stating the value of the kinetic for this level of solute

Implemented in simulator.reaction.kinetic.HillKinetic, simulator.reaction.kinetic.HaldaneKinetic, simulator.reaction.kinetic.SimpleInhibition, simulator.reaction.kinetic.MonodKinetic, simulator.reaction.kinetic.LinearKinetic, and simulator.reaction.kinetic.FirstOrderKinetic.

Member Data Documentation

int simulator.reaction.kinetic.IsKineticFactor.nParam

Number of parameters that are specified as part of this reaction

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

/home/kieran/Dropbox/workspace/iDynoMiCS/src/simulator/reaction/kinetic/IsKineticFactor.java

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

Member Data Documentation