roadrunner  2.6.0
Fast simulator for SBML models
rrllvm::LLVMExecutableModel Member List

This is the complete list of members for rrllvm::LLVMExecutableModel, including all inherited members.

applyEvents(double timeEnd, const unsigned char *previousEventState, const double *initialState, double *finalState)rrllvm::LLVMExecutableModelvirtual
assignEvent(size_t eventId, double *data)rrllvm::LLVMExecutableModelinline
computeAllRatesOfChange()rr::ExecutableModelinline
copyCachedModel(a_type *src, b_type *dst)rrllvm::LLVMExecutableModelfriend
evalInitialConditions(uint32_t flags=0)rrllvm::LLVMExecutableModel
ExecutableModel()rr::ExecutableModel
ExecutableModelFlags enum namerr::ExecutableModel
getAssignmentRuleIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getBoundarySpeciesAmounts(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getBoundarySpeciesConcentrations(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getBoundarySpeciesId(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getBoundarySpeciesIndex(const std::string &) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getBoundarySpeciesInitAmounts(size_t size_t, const int *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getBoundarySpeciesInitConcentrations(size_t len, const int *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getCompartmentId(size_t) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getCompartmentIndex(const std::string &) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getCompartmentIndexForBoundarySpecies(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getCompartmentIndexForFloatingSpecies(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getCompartmentInitVolumes(size_t len, const int *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getCompartmentVolumes(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getConservedMoietyId(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getConservedMoietyIndex(const std::string &name) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getConservedMoietyValues(size_t len, int const *indx, double *values) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getEventBufferSize(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getEventData(size_t eventId, double *data) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getEventDelay(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getEventId(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getEventIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getEventIndex(const std::string &eid)rrllvm::LLVMExecutableModelvirtual
getEventInitialValue(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getEventListener(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getEventPersistent(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getEventPriority(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getEventRoots(double time, const double *y, double *gdot)rrllvm::LLVMExecutableModelvirtual
getEventTieBreak(size_t eventA, size_t eventB) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModel
getEventTrigger(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModel
getEventTriggers(size_t len, const int *indx, unsigned char *eventState)rrllvm::LLVMExecutableModelvirtual
getEventUseValuesFromTriggerTime(size_t event) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelinline
getExecutableModelDesc() constrrllvm::LLVMExecutableModelinlinevirtual
getFlags() constrrllvm::LLVMExecutableModelinlinevirtual
getFloatingSpeciesAmountRate(size_t index, const double *reactionRates)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesAmountRates(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesAmounts(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesConcentrationRates(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesConcentrations(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesId(size_t index) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesIndex(const std::string &) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesInitAmounts(size_t size_t, const int *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getFloatingSpeciesInitConcentrations(size_t len, const int *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getGlobalParameterId(size_t)rrllvm::LLVMExecutableModelvirtual
getGlobalParameterIndex(const std::string &)rrllvm::LLVMExecutableModelvirtual
getGlobalParameterInitValues(size_t len, const int *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getGlobalParameterValues(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getIds(int types, std::list< std::string > &ids)rrllvm::LLVMExecutableModelvirtual
getInfo() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getInitialAssignmentIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getModelName()rrllvm::LLVMExecutableModelvirtual
getNextPendingEventTime(bool pop) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getNumBoundarySpecies()rrllvm::LLVMExecutableModelvirtual
getNumCompartments() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getNumConservedMoieties() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getNumDepFloatingSpecies()rrllvm::LLVMExecutableModelvirtual
getNumEvents() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getNumFloatingSpecies()rrllvm::LLVMExecutableModelvirtual
getNumGlobalParameters()rrllvm::LLVMExecutableModelvirtual
getNumIndFloatingSpecies()rrllvm::LLVMExecutableModelvirtual
getNumPiecewiseTriggers()rrllvm::LLVMExecutableModelvirtual
getNumRateRules() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getNumReactions()rrllvm::LLVMExecutableModelvirtual
getPendingEventSize() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getPiecewiseTriggerRoots(double time, const double *y, double *gdot) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getRandom()rrllvm::LLVMExecutableModelvirtual
getRandomSeed()rrllvm::LLVMExecutableModelvirtual
getRateRuleIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getRateRuleRates(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getRateRuleSymbols() constrrllvm::LLVMExecutableModelvirtual
getRateRuleValues(double *rateRuleValues)rrllvm::LLVMExecutableModelvirtual
getReactionId(size_t)rrllvm::LLVMExecutableModelvirtual
getReactionIndex(const std::string &)rrllvm::LLVMExecutableModelvirtual
getReactionRates(size_t len, int const *indx, double *values)rrllvm::LLVMExecutableModelvirtual
getStateVector(double *stateVector)rrllvm::LLVMExecutableModelvirtual
getStateVectorId(size_t index)rrllvm::LLVMExecutableModelvirtual
getStateVectorRate(double time, const double *y, double *dydt=0)rrllvm::LLVMExecutableModelvirtual
getStoichiometry(int index)rrllvm::LLVMExecutableModelvirtual
getStoichiometry(int speciesIndex, int reactionIndex)rrllvm::LLVMExecutableModelvirtual
getStoichiometryId(size_t)rrllvm::LLVMExecutableModelvirtual
getStoichiometryIndex(const std::string &)rrllvm::LLVMExecutableModelvirtual
getStoichiometryIndex(const std::string &speciesId, const std::string &reactionId)rrllvm::LLVMExecutableModelvirtual
getSupportedIdTypes()rrllvm::LLVMExecutableModelvirtual
getTime() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
getValue(const std::string &id)rrllvm::LLVMExecutableModelvirtual
INTEGRATION enum valuerr::ExecutableModel
LLVMExecutableModel()rrllvm::LLVMExecutableModel
LLVMExecutableModel(const std::shared_ptr< ModelResources > &resources, LLVMModelData *modelData)rrllvm::LLVMExecutableModel
LLVMExecutableModel(std::istream &in, uint modelGeneratorOpt) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModel
LLVMModelGenerator (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelfriend
mIntegrationStartTime (defined in rr::ExecutableModel)rr::ExecutableModelprotected
OPTIMIZE_REACTION_RATE_SELECTION enum valuerr::ExecutableModel
print(std::ostream &stream) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
reset()rrllvm::LLVMExecutableModelvirtual
reset(int options)rrllvm::LLVMExecutableModelvirtual
resetEvents() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
saveState(std::ostream &out) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values, bool strict) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setBoundarySpeciesConcentrations(size_t len, int const *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setBoundarySpeciesInitAmounts(size_t len, const int *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setBoundarySpeciesInitConcentrations(size_t len, const int *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setCompartmentInitVolumes(size_t len, const int *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setCompartmentVolumes(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setCompartmentVolumes(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setConservedMoietyValues(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setEventListener(size_t index, rr::EventListenerPtr eventHandler) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setFlags(uint32_t val)rrllvm::LLVMExecutableModelinlinevirtual
setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setFloatingSpeciesConcentrations(size_t len, int const *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setFloatingSpeciesInitAmounts(size_t len, const int *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setFloatingSpeciesInitConcentrations(size_t len, const int *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setGlobalParameterInitValues(size_t len, const int *indx, double const *values)rrllvm::LLVMExecutableModelvirtual
setGlobalParameterValues(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setGlobalParameterValues(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setIntegration(bool value)rr::ExecutableModelinlineprotected
setIntegrationStartTime(double time) (defined in rr::ExecutableModel)rr::ExecutableModelvirtual
setRandomSeed(int64_t)rrllvm::LLVMExecutableModelvirtual
setStateVector(const double *stateVector)rrllvm::LLVMExecutableModelvirtual
setStoichiometries(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setStoichiometries(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setStoichiometry(int index, double value) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setStoichiometry(int speciesIndex, int reactionIndex, double value) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setTime(double _time) (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
setValue(const std::string &id, double value)rrllvm::LLVMExecutableModelvirtual
testConstraints() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual
~ExecutableModel()rr::ExecutableModelinlinevirtual
~LLVMExecutableModel() (defined in rrllvm::LLVMExecutableModel)rrllvm::LLVMExecutableModelvirtual