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roadrunner
2.6.0
Fast simulator for SBML models
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This is the complete list of members for rr::ExecutableModel, including all inherited members.
| applyEvents(double timeEnd, const unsigned char *previousEventStatus, const double *initialState, double *finalState)=0 | rr::ExecutableModel | pure virtual |
| computeAllRatesOfChange() | rr::ExecutableModel | inline |
| ExecutableModel() | rr::ExecutableModel | |
| ExecutableModelFlags enum name | rr::ExecutableModel | |
| getAssignmentRuleIds(std::list< std::string > &)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getBoundarySpeciesAmounts(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getBoundarySpeciesConcentrations(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getBoundarySpeciesId(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getBoundarySpeciesIndex(const std::string &eid)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getBoundarySpeciesInitAmounts(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getBoundarySpeciesInitConcentrations(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getCompartmentId(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getCompartmentIndex(const std::string &eid)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getCompartmentIndexForBoundarySpecies(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getCompartmentIndexForFloatingSpecies(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getCompartmentInitVolumes(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getCompartmentVolumes(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getConservedMoietyId(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getConservedMoietyIndex(const std::string &eid)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getConservedMoietyValues(size_t len, int const *indx, double *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getEventId(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getEventIds(std::list< std::string > &)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getEventIndex(const std::string &eid)=0 | rr::ExecutableModel | pure virtual |
| getEventListener(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getEventRoots(double time, const double *y, double *gdot)=0 | rr::ExecutableModel | pure virtual |
| getEventTriggers(size_t len, const int *indx, unsigned char *values)=0 | rr::ExecutableModel | pure virtual |
| getExecutableModelDesc() const =0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getFlags() const =0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesAmountRate(size_t index, const double *reactionRates)=0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesAmountRates(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesAmounts(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesConcentrationRates(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesConcentrations(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesId(size_t index)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesIndex(const std::string &eid)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesInitAmounts(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getFloatingSpeciesInitConcentrations(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getGlobalParameterId(size_t index)=0 | rr::ExecutableModel | pure virtual |
| getGlobalParameterIndex(const std::string &eid)=0 | rr::ExecutableModel | pure virtual |
| getGlobalParameterInitValues(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getGlobalParameterValues(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getIds(int types, std::list< std::string > &ids)=0 | rr::ExecutableModel | pure virtual |
| getInfo()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getInitialAssignmentIds(std::list< std::string > &)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getModelName()=0 | rr::ExecutableModel | pure virtual |
| getNextPendingEventTime(bool pop)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getNumBoundarySpecies()=0 | rr::ExecutableModel | pure virtual |
| getNumCompartments()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getNumConservedMoieties()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getNumDepFloatingSpecies()=0 | rr::ExecutableModel | pure virtual |
| getNumEvents()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getNumFloatingSpecies()=0 | rr::ExecutableModel | pure virtual |
| getNumGlobalParameters()=0 | rr::ExecutableModel | pure virtual |
| getNumIndFloatingSpecies()=0 | rr::ExecutableModel | pure virtual |
| getNumPiecewiseTriggers()=0 | rr::ExecutableModel | pure virtual |
| getNumRateRules()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getNumReactions()=0 | rr::ExecutableModel | pure virtual |
| getPendingEventSize()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getPiecewiseTriggerRoots(double time, const double *y, double *gdot)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getRandom()=0 | rr::ExecutableModel | pure virtual |
| getRandomSeed()=0 | rr::ExecutableModel | pure virtual |
| getRateRuleIds(std::list< std::string > &)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getRateRuleRates(size_t len, int const *indx, double *values) | rr::ExecutableModel | virtual |
| getRateRuleSymbols() const =0 | rr::ExecutableModel | pure virtual |
| getRateRuleValues(double *rateRuleValues)=0 | rr::ExecutableModel | pure virtual |
| getReactionId(size_t index)=0 | rr::ExecutableModel | pure virtual |
| getReactionIndex(const std::string &eid)=0 | rr::ExecutableModel | pure virtual |
| getReactionRates(size_t len, int const *indx, double *values)=0 | rr::ExecutableModel | pure virtual |
| getStateVector(double *stateVector)=0 | rr::ExecutableModel | pure virtual |
| getStateVectorId(size_t index)=0 | rr::ExecutableModel | pure virtual |
| getStateVectorRate(double time, const double *y, double *dydt=0)=0 | rr::ExecutableModel | pure virtual |
| getStoichiometry(int index)=0 | rr::ExecutableModel | pure virtual |
| getStoichiometry(int speciesIndex, int reactionIndex)=0 | rr::ExecutableModel | pure virtual |
| getStoichiometryId(size_t index)=0 | rr::ExecutableModel | pure virtual |
| getStoichiometryIndex(const std::string &)=0 | rr::ExecutableModel | pure virtual |
| getStoichiometryIndex(const std::string &, const std::string &)=0 | rr::ExecutableModel | pure virtual |
| getSupportedIdTypes()=0 | rr::ExecutableModel | pure virtual |
| getTime()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| getValue(const std::string &id)=0 | rr::ExecutableModel | pure virtual |
| INTEGRATION enum value | rr::ExecutableModel | |
| mIntegrationStartTime (defined in rr::ExecutableModel) | rr::ExecutableModel | protected |
| OPTIMIZE_REACTION_RATE_SELECTION enum value | rr::ExecutableModel | |
| print(std::ostream &stream)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| reset()=0 | rr::ExecutableModel | pure virtual |
| reset(int options)=0 | rr::ExecutableModel | pure virtual |
| resetEvents()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| RoadRunner (defined in rr::ExecutableModel) | rr::ExecutableModel | friend |
| saveState(std::ostream &out) (defined in rr::ExecutableModel) | rr::ExecutableModel | inlinevirtual |
| setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values, bool strict)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setBoundarySpeciesConcentrations(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setBoundarySpeciesInitAmounts(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setBoundarySpeciesInitConcentrations(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setCompartmentInitVolumes(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setCompartmentVolumes(size_t len, int const *indx, const double *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setCompartmentVolumes(size_t len, int const *indx, const double *values, bool strict)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setConservedMoietyValues(size_t len, int const *indx, const double *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setEventListener(size_t index, EventListenerPtr eventHandler)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setFlags(uint32_t)=0 | rr::ExecutableModel | pure virtual |
| setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values, bool strict)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setFloatingSpeciesConcentrations(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setFloatingSpeciesInitAmounts(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setFloatingSpeciesInitConcentrations(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setGlobalParameterInitValues(size_t len, int const *indx, double const *values)=0 | rr::ExecutableModel | pure virtual |
| setGlobalParameterValues(size_t len, int const *indx, const double *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setGlobalParameterValues(size_t len, int const *indx, const double *values, bool strict)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setIntegration(bool value) | rr::ExecutableModel | inlineprotected |
| setIntegrationStartTime(double time) (defined in rr::ExecutableModel) | rr::ExecutableModel | virtual |
| setRandomSeed(int64_t)=0 | rr::ExecutableModel | pure virtual |
| setStateVector(const double *stateVector)=0 | rr::ExecutableModel | pure virtual |
| setStoichiometries(size_t len, int const *indx, const double *values)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setStoichiometries(size_t len, int const *indx, const double *values, bool strict)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setStoichiometry(int index, double value)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setStoichiometry(int speciesIndex, int reactionIndex, double value)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setTime(double _time)=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| setValue(const std::string &id, double value)=0 | rr::ExecutableModel | pure virtual |
| testConstraints()=0 (defined in rr::ExecutableModel) | rr::ExecutableModel | pure virtual |
| ~ExecutableModel() | rr::ExecutableModel | inlinevirtual |
1.9.1