lm::cme::TwoStateHillSwitch Class Reference

#include <TwoStateHillSwitch.h>

Inheritance diagram for lm::cme::TwoStateHillSwitch:

Collaboration diagram for lm::cme::TwoStateHillSwitch:

Classes
struct	KHillPropensityArgs

Public Member Functions
	TwoStateHillSwitch ()
virtual	~TwoStateHillSwitch ()
virtual bool	needsReactionModel ()
	Tells whether the solver needs a reaction model.
virtual bool	needsDiffusionModel ()
	Tells whether the solver needs a reaction model.
virtual void	generateTrajectory ()
	Actually run the simulation.
virtual void	runConstantProtein ()
virtual void	runGeometricProtein ()
Public Member Functions inherited from lm::cme::GillespieDSolver
	GillespieDSolver ()
virtual	~GillespieDSolver ()
virtual void	buildModel (const uint numberSpecies, const uint numberReactions, const uint *initialSpeciesCounts, const uint *reactionType, const double *k, const int *S, const uint *D, const uint kCols=1)
Public Member Functions inherited from lm::cme::CMESolver
	CMESolver (RandomGenerator::Distributions neededDists)
virtual	~CMESolver ()
virtual void	initialize (unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)
	Initialize the simulation.
virtual void	setReactionModel (lm::io::ReactionModel *reactionModel)
virtual void	setModelPropensityFunction (uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg)
virtual void	setSpeciesUpperLimit (uint species, uint limit)
virtual void	setSpeciesLowerLimit (uint species, uint limit)
virtual void	setFptTrackingList (list< uint > speciesList)
virtual void	addToParameterTrackingList (pair< string, double * >parameter)
virtual void	setReactionRateCME (unsigned int reactionId, double rate)
virtual void	getSpeciesCountView (uint **counts, int *number)
virtual void	getReactionRateConstantsView (int reactionNumber, double **rates, int *rateConstantCount)
Public Member Functions inherited from lm::me::MESolver
	MESolver ()
	Create the MESolver.
virtual	~MESolver ()

Static Protected Member Functions
static double	kHillPropensity (double time, uint *speciesCounts, void *pargs)
static double	negativeKHillPropensity (double time, uint *speciesCounts, void *pargs)
Static Protected Member Functions inherited from lm::cme::CMESolver
static double	zerothOrderPropensity (double time, uint *speciesCounts, void *pargs)
static double	firstOrderPropensity (double time, uint *speciesCounts, void *pargs)
static double	secondOrderPropensity (double time, uint *speciesCounts, void *pargs)
static double	secondOrderSelfPropensity (double time, uint *speciesCounts, void *pargs)
static double	kHillPropensity (double time, uint *speciesCounts, void *pargs)
static double	kHillTransportPropensity (double time, uint *speciesCounts, void *pargs)
static double	zerothOrderHeavisidePropensity (double time, uint *speciesCounts, void *pargs)
static double	michaelisMentenPropensity (double time, uint *speciesCounts, void *pargs)
static double	competitiveMMPropensity (double time, uint *speciesCounts, void *pargs)
static double	uncompetitiveMMPropensity (double time, uint *speciesCounts, void *pargs)
static double	noncompetitiveMMPropensity (double time, uint *speciesCounts, void *pargs)

Additional Inherited Members
Protected Member Functions inherited from lm::cme::GillespieDSolver
virtual void	destroyModel ()
void	updateAllPropensities (double time)
void	updatePropensities (double time, uint r)
virtual int	hookSimulation (double time)
virtual int	onBeginTrajectory ()
virtual int	onEndTrajectory ()
Protected Member Functions inherited from lm::cme::CMESolver
virtual void	allocateModel (uint numberSpecies, uint numberReactions)
virtual double	recordParameters (double nextRecordTime, double recordInterval, double simulationTime)
virtual void	queueRecordedParameters (bool flush=false)
void	updateSpeciesCounts (uint r)
bool	reachedSpeciesLimit ()
Protected Attributes inherited from lm::cme::GillespieDSolver
double *	propensities
Protected Attributes inherited from lm::cme::CMESolver
RandomGenerator::Distributions	neededDists
unsigned int	replicate
map< string, string > *	parameters
ResourceAllocator::ComputeResources *	resources
RandomGenerator *	rng
uint	numberSpecies
uint	numberSpeciesToTrack
uint	numberReactions
uint *	initialSpeciesCounts
uint *	speciesCounts
uint *	reactionTypes
int *	S
uint *	D
void **	propensityFunctions
void **	propensityFunctionArgs
list< PropensityArgs * >	propensityArgs
uint	numberSpeciesLimits
SpeciesLimit *	speciesLimits
uint	numberFptTrackedSpecies
FPTTracking *	fptTrackedSpecies
list< TrackedParameter >	trackedParameters
uint *	numberDependentSpecies
uint **	dependentSpecies
int **	dependentSpeciesChange
uint *	numberDependentReactions
uint **	dependentReactions

Constructor & Destructor Documentation

TwoStateHillSwitch()

lm::cme::TwoStateHillSwitch::TwoStateHillSwitch

(

)

~TwoStateHillSwitch()

lm::cme::TwoStateHillSwitch::~TwoStateHillSwitch ( )

virtual

Member Function Documentation

generateTrajectory()

void lm::cme::TwoStateHillSwitch::generateTrajectory ( )

virtual

Actually run the simulation.

Reimplemented from lm::cme::GillespieDSolver.

Here is the call graph for this function:

kHillPropensity()

double lm::cme::TwoStateHillSwitch::kHillPropensity ( double time, uint * speciesCounts, void * pargs )

staticprotected

Here is the caller graph for this function:

needsDiffusionModel()

virtual bool lm::cme::TwoStateHillSwitch::needsDiffusionModel ( )

inlinevirtual

Tells whether the solver needs a reaction model.

Reimplemented from lm::cme::GillespieDSolver.

needsReactionModel()

virtual bool lm::cme::TwoStateHillSwitch::needsReactionModel ( )

inlinevirtual

Tells whether the solver needs a reaction model.

Reimplemented from lm::cme::GillespieDSolver.

negativeKHillPropensity()

double lm::cme::TwoStateHillSwitch::negativeKHillPropensity ( double time, uint * speciesCounts, void * pargs )

staticprotected

Here is the caller graph for this function:

runConstantProtein()

void lm::cme::TwoStateHillSwitch::runConstantProtein ( )

virtual

runGeometricProtein()

void lm::cme::TwoStateHillSwitch::runGeometricProtein ( )

virtual

---

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

• /data2/LM_zls_github/Lattice-Microbes/src/cme/TwoStateHillSwitch.h
• /data2/LM_zls_github/Lattice-Microbes/src/cme/TwoStateHillSwitch.cpp