NFtest_ss Namespace Reference

---

Detailed Description

Namespace for the Simple System (abreviated ss) example.

This namespace maintains functions that create, run, and output a simple enzymatic reaction type system. If you want to learn the details of NFsim, this is the place to start looking. Be sure to look at these files: simple_system.hh and simple_system.cpp . Start with the run function in the cpp file, and follow the documentation to see how everything works. Have fun!

Author:

Michael Sneddon

Functions
void	run ()
	Runs the simple enzymatic type reaction system as an example system.
MoleculeType *	createX (System *s)
MoleculeType *	createY (System *s)
ReactionClass *	createReactionXDephos (MoleculeType *molX, double rate)
ReactionClass *	createReactionXYbind (MoleculeType *molX, MoleculeType *molY, double rate)
ReactionClass *	createReactionXYunbind (MoleculeType *molX, MoleculeType *molY, double rate)
ReactionClass *	createReactionYphosX (MoleculeType *molX, MoleculeType *molY, double rate)
void	addObs (System *s, MoleculeType *molX, MoleculeType *molY)

---

Function Documentation

void NFtest_ss::addObs	(	System *	s,
		MoleculeType *	molX,
		MoleculeType *	molY
	)

Creates the observables used in the Simple System. Look at this function to learn how basic observables can be created and added to the system.

Author:

Michael Sneddon

ReactionClass * NFtest_ss::createReactionXDephos	(	MoleculeType *	molX,
		double	rate
	)

Creates a simple dephosphorlyation reaction consisting of a single state change. Look here first to get the basic idea of how reactions are defined and in particular, how simple unimolecular reactions are created.

Author:

Michael Sneddon

ReactionClass * NFtest_ss::createReactionXYbind	(	MoleculeType *	molX,
		MoleculeType *	molY,
		double	rate
	)

Creates the binding reaction between X and Y. Look here to see how bimolecular reactions such as binding reactions can be defined.

Author:

Michael Sneddon

ReactionClass * NFtest_ss::createReactionXYunbind	(	MoleculeType *	molX,
		MoleculeType *	molY,
		double	rate
	)

Creates an unbinding reaction between X and Y. Look here to see how unbinding reactions can be defined.

Author:

Michael Sneddon

ReactionClass * NFtest_ss::createReactionYphosX	(	MoleculeType *	molX,
		MoleculeType *	molY,
		double	rate
	)

Creates the catalytic step of the enzymatic reaction in this simple system. Look here to learn how to create reactions that include multiple transformations of the reactants.

Author:

Michael Sneddon

MoleculeType * NFtest_ss::createX

(

System *

s

)

Creates Molecule of type X for the simple system. In this system, X is the molecule that gets modified (in this case phosphorylated) by the enzyme.

Author:

Michael Sneddon

MoleculeType * NFtest_ss::createY

(

System *

s

)

Creates Molecule of type Y for the simple system. In this system, Y is the enzyme that phosphorylates X.

Author:

Michael Sneddon

void NFtest_ss::run

(

)

Runs the simple enzymatic type reaction system as an example system.

Start here in simple_system.cpp to see how a simulation is created and run in the NFsim world.

Author:

Michael Sneddon

---