CMESolver Member List

This is the complete list of members for CMESolver, including all inherited members.

addToParameterTrackingList(pair< string, double * >parameter)	CMESolver	virtual
allocateModel(uint numberSpecies, uint numberReactions)	CMESolver	protectedvirtual
buildModel(const uint numberSpecies, const uint numberReactions, const uint *initialSpeciesCounts, const uint *reactionTypesA, const double *k, const int *S, const uint *D, const uint kCols=1)	CMESolver	virtual
CMESolver(RandomGenerator::Distributions neededDists)	CMESolver
competitiveMMPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
D	CMESolver	protected
dependentReactions	CMESolver	protected
dependentSpecies	CMESolver	protected
dependentSpeciesChange	CMESolver	protected
destroyModel()	CMESolver	protectedvirtual
firstOrderPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
fptTrackedSpecies	CMESolver	protected
generateTrajectory()=0	CMESolver	pure virtual
getReactionRateConstantsView(int reactionNumber, double **rates, int *rateConstantCount)	CMESolver	virtual
getSpeciesCountView(uint **counts, int *number)	CMESolver	virtual
hookSimulation(double time)	CMESolver	protectedvirtual
initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)	CMESolver	virtual
initialSpeciesCounts	CMESolver	protected
kHillPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
kHillTransportPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
michaelisMentenPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
neededDists	CMESolver	protected
noncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
numberDependentReactions	CMESolver	protected
numberDependentSpecies	CMESolver	protected
numberFptTrackedSpecies	CMESolver	protected
numberReactions	CMESolver	protected
numberSpecies	CMESolver	protected
numberSpeciesLimits	CMESolver	protected
numberSpeciesToTrack	CMESolver	protected
onBeginTrajectory()	CMESolver	protectedvirtual
onEndTrajectory()	CMESolver	protectedvirtual
parameters	CMESolver	protected
propensityArgs	CMESolver	protected
propensityFunctionArgs	CMESolver	protected
propensityFunctions	CMESolver	protected
queueRecordedParameters(bool flush=false)	CMESolver	protectedvirtual
reachedSpeciesLimit()	CMESolver	inlineprotected
reactionTypes	CMESolver	protected
recordParameters(double nextRecordTime, double recordInterval, double simulationTime)	CMESolver	protectedvirtual
replicate	CMESolver	protected
resources	CMESolver	protected
rng	CMESolver	protected
S	CMESolver	protected
secondOrderPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
secondOrderSelfPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
setFptTrackingList(list< uint > speciesList)	CMESolver	virtual
setModelPropensityFunction(uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg)	CMESolver	virtual
setReactionModel(lm::io::ReactionModel *reactionModel)	CMESolver	virtual
setReactionRateCME(unsigned int reactionId, double rate)	CMESolver	virtual
setSpeciesLowerLimit(uint species, uint limit)	CMESolver	virtual
setSpeciesUpperLimit(uint species, uint limit)	CMESolver	virtual
speciesCounts	CMESolver	protected
speciesLimits	CMESolver	protected
trackedParameters	CMESolver	protected
uncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
updateSpeciesCounts(uint r)	CMESolver	inlineprotected
zerothOrderHeavisidePropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
zerothOrderPropensity(double time, uint *speciesCounts, void *pargs)	CMESolver	protectedstatic
~CMESolver()	CMESolver	virtual