Lattice Microbes 2.5
This is for whole cell modeling
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lm::cme::LacHillSwitch Member List

This is the complete list of members for lm::cme::LacHillSwitch, including all inherited members.

addToParameterTrackingList(pair< string, double * >parameter)lm::cme::CMESolvervirtual
allocateModel(uint numberSpecies, uint numberReactions)lm::cme::CMESolverprotectedvirtual
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)lm::cme::FluctuatingNRSolvervirtual
buildModel(const uint numberSpecies, const uint numberReactions, const uint *initialSpeciesCounts, const uint *reactionType, const double *K, const int *S, const uint *D, const double *nvar, const double *ntau, const double noiseRecalcFraction, const uint kCols=1)lm::cme::FluctuatingNRSolvervirtual
CMESolver(RandomGenerator::Distributions neededDists)lm::cme::CMESolver
competitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
Dlm::cme::CMESolverprotected
dependentReactionslm::cme::CMESolverprotected
dependentSpecieslm::cme::CMESolverprotected
dependentSpeciesChangelm::cme::CMESolverprotected
destroyModel()lm::cme::FluctuatingNRSolverprotectedvirtual
firstOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
FluctuatingNRSolver()lm::cme::FluctuatingNRSolver
fptTrackedSpecieslm::cme::CMESolverprotected
generateTrajectory()lm::cme::NextReactionSolvervirtual
getReactionRateConstantsView(int reactionNumber, double **rates, int *rateConstantCount)lm::cme::CMESolvervirtual
getSpeciesCountView(uint **counts, int *number)lm::cme::CMESolvervirtual
hookSimulation(double time)lm::cme::NextReactionSolverprotectedvirtual
initialize(unsigned int replicate, map< string, string > *parameters, ResourceAllocator::ComputeResources *resources)lm::cme::CMESolvervirtual
initialSpeciesCountslm::cme::CMESolverprotected
kHillPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
kHillTransportPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
LacHillSwitch()lm::cme::LacHillSwitch
MESolver()lm::me::MESolver
michaelisMentenPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
neededDistslm::cme::CMESolverprotected
needsDiffusionModel()lm::cme::NextReactionSolverinlinevirtual
needsReactionModel()lm::cme::NextReactionSolverinlinevirtual
NextReactionSolver()lm::cme::NextReactionSolver
NextReactionSolver(RandomGenerator::Distributions neededDists)lm::cme::NextReactionSolver
noncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
numberDependentReactionslm::cme::CMESolverprotected
numberDependentSpecieslm::cme::CMESolverprotected
numberFptTrackedSpecieslm::cme::CMESolverprotected
numberReactionslm::cme::CMESolverprotected
numberSpecieslm::cme::CMESolverprotected
numberSpeciesLimitslm::cme::CMESolverprotected
numberSpeciesToTracklm::cme::CMESolverprotected
onBeginTrajectory()lm::cme::CMESolverprotectedvirtual
onEndTrajectory()lm::cme::CMESolverprotectedvirtual
ouPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::FluctuatingNRSolverprotectedstatic
parameterslm::cme::CMESolverprotected
propensityArgslm::cme::CMESolverprotected
propensityFunctionArgslm::cme::CMESolverprotected
propensityFunctionslm::cme::CMESolverprotected
queueRecordedParameters(bool flush=false)lm::cme::CMESolverprotectedvirtual
reachedSpeciesLimit()lm::cme::CMESolverinlineprotected
reactionQueuelm::cme::NextReactionSolverprotected
reactionTypeslm::cme::CMESolverprotected
recordParameters(double nextRecordTime, double recordInterval, double simulationTime)lm::cme::CMESolverprotectedvirtual
replicatelm::cme::CMESolverprotected
resourceslm::cme::CMESolverprotected
rnglm::cme::CMESolverprotected
Slm::cme::CMESolverprotected
secondOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
secondOrderSelfPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
setFptTrackingList(list< uint > speciesList)lm::cme::CMESolvervirtual
setModelPropensityFunction(uint reaction, double(*propensityFunction)(double time, uint *speciesCounts, void *args), void *propensityFunctionArg)lm::cme::CMESolvervirtual
setReactionModel(lm::io::ReactionModel *rm)lm::cme::LacHillSwitchvirtual
setReactionRateCME(unsigned int reactionId, double rate)lm::cme::CMESolvervirtual
setSpeciesLowerLimit(uint species, uint limit)lm::cme::CMESolvervirtual
setSpeciesUpperLimit(uint species, uint limit)lm::cme::CMESolvervirtual
speciesCountslm::cme::CMESolverprotected
speciesLimitslm::cme::CMESolverprotected
trackedParameterslm::cme::CMESolverprotected
uncompetitiveMMPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
updateAllReactionEvents(double time, int rngNext, double *expRngValues)lm::cme::NextReactionSolverinlineprotected
updateReactionEvents(uint sourceReaction, double time, int rngNext, double *expRngValues)lm::cme::NextReactionSolverinlineprotected
updateSpeciesCounts(uint r)lm::cme::CMESolverinlineprotected
zerothOrderHeavisidePropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
zerothOrderPropensity(double time, uint *speciesCounts, void *pargs)lm::cme::CMESolverprotectedstatic
~CMESolver()lm::cme::CMESolvervirtual
~FluctuatingNRSolver()lm::cme::FluctuatingNRSolvervirtual
~LacHillSwitch()lm::cme::LacHillSwitchvirtual
~MESolver()lm::me::MESolvervirtual
~NextReactionSolver()lm::cme::NextReactionSolvervirtual