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 |