| addAssignmentRule(const std::string &vid, const std::string &formula, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addCompartment(const std::string &cid, double initVolume, bool forceRegenerate=true) | rr::RoadRunner | |
| addDelay(const std::string &eid, const std::string &delay, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addEvent(const std::string &eid, bool useValuesFromTriggerTime, const std::string &trigger, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addEventAssignment(const std::string &eid, const std::string &vid, const std::string &formula, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addInitialAssignment(const std::string &vid, const std::string &formula, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addParameter(const std::string &pid, double value, bool forceRegenerate=true) | rr::RoadRunner | |
| addPriority(const std::string &eid, const std::string &priority, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addRateRule(const std::string &vid, const std::string &formula, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addReaction(const std::string &sbmlRep, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addReaction(const std::string &rid, std::vector< std::string > reactants, std::vector< std::string > products, const std::string &kineticLaw, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| addSpeciesAmount(const std::string &sid, const std::string &compartment, double initAmount=0, bool hasOnlySubstanceUnits=false, bool boundaryCondition=false, const std::string &substanceUnits="", bool forceRegenerate=true) | rr::RoadRunner | |
| addSpeciesConcentration(const std::string &sid, const std::string &compartment, double initConcentration, bool hasOnlySubstanceUnits=false, bool boundaryCondition=false, const std::string &substanceUnits="", bool forceRegenerate=true) | rr::RoadRunner | |
| addTrigger(const std::string &eid, const std::string &trigger, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| changeInitialConditions(const std::vector< double > &ic) | rr::RoadRunner | |
| clearModel() | rr::RoadRunner | |
| createSelection(const std::string &str) | rr::RoadRunner | |
| evalModel() | rr::RoadRunner | |
| getAssignmentRuleIds() | rr::RoadRunner | |
| getBoundarySpeciesAmountsNamedArray() | rr::RoadRunner | |
| getBoundarySpeciesAmountsV() | rr::RoadRunner | |
| getBoundarySpeciesByIndex(const int &index) | rr::RoadRunner | |
| getBoundarySpeciesConcentrationIds() | rr::RoadRunner | |
| getBoundarySpeciesConcentrationsNamedArray() | rr::RoadRunner | |
| getBoundarySpeciesConcentrationsV() | rr::RoadRunner | |
| getBoundarySpeciesIds() | rr::RoadRunner | |
| getCC(const std::string &variableName, const std::string ¶meterName) | rr::RoadRunner | |
| getCompartmentByIndex(const int &index) | rr::RoadRunner | |
| getCompartmentIds() | rr::RoadRunner | |
| getCompiler() | rr::RoadRunner | |
| getConservationMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getConservedMoietyAnalysis() | rr::RoadRunner | |
| getConservedMoietyIds() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getConservedMoietyValues() | rr::RoadRunner | |
| getCurrentSBML(int level=0, int version=0) | rr::RoadRunner | |
| getCurrentTime() | rr::RoadRunner | |
| getDependentFloatingSpeciesAmountsNamedArray() | rr::RoadRunner | |
| getDependentFloatingSpeciesAmountsV() | rr::RoadRunner | |
| getDependentFloatingSpeciesConcentrationsNamedArray() | rr::RoadRunner | |
| getDependentFloatingSpeciesConcentrationsV() | rr::RoadRunner | |
| getDependentFloatingSpeciesIds() | rr::RoadRunner | |
| getDependentRatesOfChange() | rr::RoadRunner | |
| getDependentRatesOfChangeNamedArray() | rr::RoadRunner | |
| getDiffStepSize() const | rr::RoadRunner | |
| getEE(const std::string &reactionName, const std::string ¶meterName) | rr::RoadRunner | |
| getEE(const std::string &reactionName, const std::string ¶meterName, bool computeSteadyState) | rr::RoadRunner | |
| getEigenValueIds() | rr::RoadRunner | |
| getExistingIntegratorNames() | rr::RoadRunner | |
| getExistingSensitivitySolverNames() | rr::RoadRunner | |
| getExistingSteadyStateSolverNames() | rr::RoadRunner | |
| getExtendedStoichiometryMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getExtendedVersionInfo() | rr::RoadRunner | static |
| getFloatingSpeciesAmountsNamedArray() | rr::RoadRunner | |
| getFloatingSpeciesAmountsV() | rr::RoadRunner | |
| getFloatingSpeciesByIndex(int index) | rr::RoadRunner | |
| getFloatingSpeciesConcentrationIds() | rr::RoadRunner | |
| getFloatingSpeciesConcentrationsNamedArray() | rr::RoadRunner | |
| getFloatingSpeciesConcentrationsV() | rr::RoadRunner | |
| getFloatingSpeciesIds() | rr::RoadRunner | |
| getFloatingSpeciesInitialConcentrationIds() | rr::RoadRunner | |
| getFloatingSpeciesInitialConcentrations() | rr::RoadRunner | |
| getFloatingSpeciesInitialConditionIds() | rr::RoadRunner | |
| getFluxThreshold() const | rr::RoadRunner | |
| getFrequencyResponse(double startFrequency, int numberOfDecades, int numberOfPoints, const std::string ¶meterName, const std::string &variableName, bool useDB, bool useHz) (defined in rr::RoadRunner) | rr::RoadRunner | |
| getFullEigenValues() | rr::RoadRunner | |
| getFullEigenValuesNamedArray() | rr::RoadRunner | |
| getFullJacobian() | rr::RoadRunner | |
| getFullReorderedJacobian() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getFullStoichiometryMatrix() | rr::RoadRunner | |
| getGlobalParameterByIndex(const int &index) | rr::RoadRunner | |
| getGlobalParameterByName(const std::string ¶m) | rr::RoadRunner | |
| getGlobalParameterIds() | rr::RoadRunner | |
| getGlobalParameterValues() | rr::RoadRunner | |
| getHasOnlySubstanceUnits(const std::string &sid) | rr::RoadRunner | |
| getIds(int types, std::list< std::string > &ids) | rr::RoadRunner | |
| getIndependentFloatingSpeciesAmountsNamedArray() | rr::RoadRunner | |
| getIndependentFloatingSpeciesAmountsV() | rr::RoadRunner | |
| getIndependentFloatingSpeciesConcentrationsNamedArray() | rr::RoadRunner | |
| getIndependentFloatingSpeciesConcentrationsV() | rr::RoadRunner | |
| getIndependentFloatingSpeciesIds() | rr::RoadRunner | |
| getIndependentRatesOfChange() | rr::RoadRunner | |
| getIndependentRatesOfChangeNamedArray() | rr::RoadRunner | |
| getInfo() | rr::RoadRunner | |
| getInitialAssignmentIds() | rr::RoadRunner | |
| getInstanceCount() | rr::RoadRunner | |
| getInstanceID() | rr::RoadRunner | |
| getIntegrator() | rr::RoadRunner | |
| getIntegratorByName(const std::string &name) | rr::RoadRunner | |
| getKineticLaw(const std::string &rid) | rr::RoadRunner | |
| getKMatrix() | rr::RoadRunner | |
| getL0Matrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getLinkMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getModel() | rr::RoadRunner | |
| getModelId() | rr::RoadRunner | |
| getModelName() | rr::RoadRunner | |
| getNrMatrix() | rr::RoadRunner | |
| getNumberOfBoundarySpecies() | rr::RoadRunner | |
| getNumberOfCompartments() | rr::RoadRunner | |
| getNumberOfDependentSpecies() | rr::RoadRunner | |
| getNumberOfFloatingSpecies() | rr::RoadRunner | |
| getNumberOfGlobalParameters() | rr::RoadRunner | |
| getNumberOfIndependentSpecies() | rr::RoadRunner | |
| getNumberOfReactions() | rr::RoadRunner | |
| getOptions() | rr::RoadRunner | |
| getParamPromotedSBML(const std::string &sArg) | rr::RoadRunner | static |
| getRateOfChange(const int &index) | rr::RoadRunner | |
| getRateOfChangeIds() | rr::RoadRunner | |
| getRateRuleIds() | rr::RoadRunner | |
| getRatesOfChange() | rr::RoadRunner | |
| getRatesOfChangeNamedArray() | rr::RoadRunner | |
| getReactionIds() | rr::RoadRunner | |
| getReactionRate(const int &index) | rr::RoadRunner | |
| getReactionRates() | rr::RoadRunner | |
| getReducedEigenValues() | rr::RoadRunner | |
| getReducedEigenValuesNamedArray() | rr::RoadRunner | |
| getReducedJacobian(double h=-1.0) | rr::RoadRunner | |
| getReducedStoichiometryMatrix() | rr::RoadRunner | |
| getRegisteredIntegratorNames() | rr::RoadRunner | static |
| getRegisteredSensitivitySolverNames() | rr::RoadRunner | static |
| getRegisteredSteadyStateSolverNames() | rr::RoadRunner | static |
| getSBML(int level=0, int version=0) | rr::RoadRunner | |
| getScaledConcentrationControlCoefficientMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getScaledElasticityMatrix() | rr::RoadRunner | |
| getScaledFloatingSpeciesElasticity(const std::string &reactionName, const std::string &speciesName) | rr::RoadRunner | |
| getScaledFluxControlCoefficientMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getSeed(const std::string &integratorName="") | rr::RoadRunner | |
| getSelectedValues() | rr::RoadRunner | |
| getSelections() | rr::RoadRunner | |
| getSensitivitySolver() | rr::RoadRunner | |
| getSensitivitySolverByName(const std::string &name) | rr::RoadRunner | |
| getSimulateOptions() | rr::RoadRunner | |
| getSimulationData() const | rr::RoadRunner | |
| getSteadyStateSelections() | rr::RoadRunner | |
| getSteadyStateSelectionStrings() const | rr::RoadRunner | |
| getSteadyStateSolver() | rr::RoadRunner | |
| getSteadyStateSolverByName(const std::string &name) | rr::RoadRunner | |
| getSteadyStateThreshold() const | rr::RoadRunner | |
| getSteadyStateValues() | rr::RoadRunner | |
| getSteadyStateValuesNamedArray() | rr::RoadRunner | |
| getSupportedIdTypes() | rr::RoadRunner | |
| getuCC(const std::string &variableName, const std::string ¶meterName) | rr::RoadRunner | |
| getuEE(const std::string &reactionName, const std::string ¶meterName) | rr::RoadRunner | |
| getuEE(const std::string &reactionName, const std::string ¶meterName, bool computeSteadystate) | rr::RoadRunner | |
| getUnscaledConcentrationControlCoefficientMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getUnscaledElasticityMatrix() | rr::RoadRunner | |
| getUnscaledFluxControlCoefficientMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
| getUnscaledParameterElasticity(const std::string &reactionName, const std::string ¶meterName) | rr::RoadRunner | |
| getUnscaledSpeciesElasticity(int reactionId, int speciesIndex) | rr::RoadRunner | |
| getValue(const std::string &sel) | rr::RoadRunner | |
| getValue(const SelectionRecord &record) (defined in rr::RoadRunner) | rr::RoadRunner | |
| integratorExists(const std::string &name) | rr::RoadRunner | |
| internalOneStep(double currentTime, double stepSize, bool reset=true) | rr::RoadRunner | |
| isModelLoaded() (defined in rr::RoadRunner) | rr::RoadRunner | |
| load(const std::string &uriOrSBML, const Dictionary *options=0) | rr::RoadRunner | |
| loadState(const std::string &filename) | rr::RoadRunner | |
| loadStateS(std::stringstream *state) | rr::RoadRunner | |
| makeIntegrator(const std::string &name) | rr::RoadRunner | |
| makeSensitivitySolver(const std::string &name) | rr::RoadRunner | |
| makeSteadyStateSolver(const std::string &name) | rr::RoadRunner | |
| mcaSteadyState() (defined in rr::RoadRunner) | rr::RoadRunner | |
| oneStep(double currentTime, double stepSize, bool reset=true) | rr::RoadRunner | |
| operator=(const RoadRunner &rr) | rr::RoadRunner | |
| regenerateModel(bool forceRegenerate=true, bool reset=false) | rr::RoadRunner | |
| registerSolvers() | rr::RoadRunner | static |
| removeCompartment(const std::string &cid, bool forceRegenerate=true) | rr::RoadRunner | |
| removeEvent(const std::string &eid, bool forceRegenerate=true) | rr::RoadRunner | |
| removeEventAssignments(const std::string &eid, const std::string &vid, bool forceRegenerate=true) | rr::RoadRunner | |
| removeInitialAssignment(const std::string &vid, bool forceRegenerate=true, bool errIfNotExist=true) | rr::RoadRunner | |
| removeParameter(const std::string &pid, bool forceRegenerate=true) | rr::RoadRunner | |
| removeReaction(const std::string &rid, bool deleteUnusedParameters=false, bool forceRegenerate=true) | rr::RoadRunner | |
| removeRules(const std::string &vid, bool useInitialValue=false, bool forceRegenerate=true) | rr::RoadRunner | |
| removeSpecies(const std::string &sid, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| reset() | rr::RoadRunner | |
| reset(int options) | rr::RoadRunner | |
| resetSeed() | rr::RoadRunner | |
| resetSelectionLists() | rr::RoadRunner | |
| RoadRunner(unsigned int level=3, unsigned int version=2) | rr::RoadRunner | |
| RoadRunner(const std::string &uriOrSBML, const Dictionary *options=0) | rr::RoadRunner | |
| RoadRunner(const std::string &compiler, const std::string &tempDir, const std::string &supportCodeDir) | rr::RoadRunner | |
| RoadRunner(const RoadRunner &rr) | rr::RoadRunner | |
| saveState(std::string filename, char opt='b') | rr::RoadRunner | |
| saveStateS(char opt='b') | rr::RoadRunner | |
| sensitivitySolverExists(const std::string &name) | rr::RoadRunner | |
| setBoundary(const std::string &sid, bool boundaryCondition, bool forceRegenerate=true) | rr::RoadRunner | |
| setBoundarySpeciesAmounts(const std::vector< double > &values) | rr::RoadRunner | |
| setBoundarySpeciesByIndex(const int &index, const double &value) | rr::RoadRunner | |
| setBoundarySpeciesConcentrations(const std::vector< double > &values) | rr::RoadRunner | |
| setCompartmentByIndex(const int &index, const double &value) | rr::RoadRunner | |
| setCompiler(const std::string &compiler) | rr::RoadRunner | |
| setConservedMoietyAnalysis(bool value) | rr::RoadRunner | |
| setConstant(const std::string &sid, bool constant, bool forceRegenerate=true) | rr::RoadRunner | |
| setDiffStepSize(double val) | rr::RoadRunner | |
| setFloatingSpeciesByIndex(int index, double value) | rr::RoadRunner | |
| setFloatingSpeciesConcentrations(const std::vector< double > &values) | rr::RoadRunner | |
| setFloatingSpeciesInitialConcentrationByIndex(const int &index, const double &value) | rr::RoadRunner | |
| setFloatingSpeciesInitialConcentrations(const std::vector< double > &values) | rr::RoadRunner | |
| setFluxThreshold(double val) | rr::RoadRunner | |
| setGlobalParameterByIndex(const int index, const double value) | rr::RoadRunner | |
| setGlobalParameterByName(const std::string ¶m, double value) | rr::RoadRunner | |
| setHasOnlySubstanceUnits(const std::string &sid, bool hasOnlySubstanceUnits, bool forceRegenerate=true) | rr::RoadRunner | |
| setInitAmount(const std::string &sid, double initAmount, bool forceRegenerate=true) | rr::RoadRunner | |
| setInitConcentration(const std::string &sid, double initConcentration, bool forceRegenerate=true) | rr::RoadRunner | |
| setIntegrator(const std::string &name) | rr::RoadRunner | |
| setKineticLaw(const std::string &rid, const std::string &kineticLaw, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setModelId(const std::string &id) | rr::RoadRunner | |
| setModelName(const std::string &name) | rr::RoadRunner | |
| setOptions(const RoadRunnerOptions &) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setPersistent(const std::string &eid, bool persistent, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setReversible(const std::string &rid, bool reversible, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setSeed(long int seed, bool resetModel=true) | rr::RoadRunner | |
| setSelections(const std::vector< std::string > &selections) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setSelections(const std::vector< rr::SelectionRecord > &selections) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setSensitivitySolver(const std::string &name) | rr::RoadRunner | |
| setSimulateOptions(const SimulateOptions &settings) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setSteadyStateSelections(const std::vector< std::string > &steadyStateSelections) | rr::RoadRunner | |
| setSteadyStateSelections(const std::vector< rr::SelectionRecord > &steadyStateSelections) | rr::RoadRunner | |
| setSteadyStateSolver(const std::string &name) | rr::RoadRunner | |
| setSteadyStateThreshold(double val) | rr::RoadRunner | |
| setTriggerInitialValue(const std::string &eid, bool initValue, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
| setValue(const std::string &id, double value) | rr::RoadRunner | |
| simulate(const SimulateOptions *options=0) | rr::RoadRunner | |
| simulate(double start, double stop, int points) | rr::RoadRunner | |
| simulate(const std::vector< double > ×) | rr::RoadRunner | |
| steadyState(Dictionary *dict=0) | rr::RoadRunner | |
| steadyStateNamedArray(const Dictionary *dict=0) | rr::RoadRunner | |
| steadyStateSolverExists(const std::string &name) | rr::RoadRunner | |
| timeSeriesSensitivities(double start, double stop, int num, std::vector< std::string > params=std::vector< std::string >(), std::vector< std::string > species=std::vector< std::string >(), int k=0) | rr::RoadRunner | |
| validateCurrentSBML() | rr::RoadRunner | |
| ~RoadRunner() | rr::RoadRunner | virtual |
