Model a reaction using Haldane Kinetics. More...

Inheritance diagram for simulator.reaction.kinetic.HaldaneKinetic:

Public Member Functions
	HaldaneKinetic (double Ks, double Ki)
	Constructor to set kinetic parameters to the supplied values. More...

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...

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

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...

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

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

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

Additional Inherited Members
Public Attributes inherited from simulator.reaction.kinetic.IsKineticFactor
int	nParam

Detailed Description

Model a reaction using Haldane Kinetics.

Model a reaction using Haldane Kinetics. From Wikipedia: Haldane Kinetics was of the same algebraic form as Micahallis-Menten equation (Monod), but their derivation is based on the quasi steady state approximation, that is the concentration of intermediate complex (or complexes) does not change.

Constructor & Destructor Documentation

simulator.reaction.kinetic.HaldaneKinetic.HaldaneKinetic	(	double	Ks,
		double	Ki
	)

Constructor to set kinetic parameters to the supplied values.

Constructor to set kinetic parameters to the supplied values

Parameters

Ks	Half-Maximum concentration of the solute
Ki	Concentration of solute

Member Function Documentation

void simulator.reaction.kinetic.HaldaneKinetic.init ( Element defMarkUp )

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

Implements simulator.reaction.kinetic.IsKineticFactor.

void simulator.reaction.kinetic.HaldaneKinetic.initFromAgent	(	Element	defMarkUp,
		double[]	kineticParam,
		int	paramIndex
	)

virtual

Initialise the reaction from a parent of the agent.

Initialise the reaction from a parent of the agent

Parameters

defMarkUp	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

Implements simulator.reaction.kinetic.IsKineticFactor.

double simulator.reaction.kinetic.HaldaneKinetic.kineticDiff ( double solute )

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

Implements simulator.reaction.kinetic.IsKineticFactor.

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

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

Implements simulator.reaction.kinetic.IsKineticFactor.

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

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

Implements simulator.reaction.kinetic.IsKineticFactor.

double simulator.reaction.kinetic.HaldaneKinetic.kineticValue ( double solute )

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

Implements simulator.reaction.kinetic.IsKineticFactor.

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation