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!
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) |
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.
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.
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.
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.
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.
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.
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.
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.