C API Documentation
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This is the complete list of members for rr::RoadRunner, including all inherited members.
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< string > reactants, std::vector< string > products, const std::string &kineticLaw, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
addSpecies(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 | |
addTrigger(const std::string &eid, const std::string &trigger, bool forceRegenerate=true) (defined in rr::RoadRunner) | rr::RoadRunner | |
changeInitialConditions(const std::vector< double > &ic) (defined in rr::RoadRunner) | rr::RoadRunner | |
clearModel() | rr::RoadRunner | |
createSelection(const std::string &str) | rr::RoadRunner | |
ensureSolversRegistered() | rr::RoadRunner | static |
evalModel() (defined in rr::RoadRunner) | rr::RoadRunner | |
getBoundarySpeciesAmountsNamedArray() | rr::RoadRunner | |
getBoundarySpeciesByIndex(const int &index) (defined in rr::RoadRunner) | rr::RoadRunner | |
getBoundarySpeciesConcentrationIds() | rr::RoadRunner | |
getBoundarySpeciesConcentrationsNamedArray() | rr::RoadRunner | |
getBoundarySpeciesIds() (defined in rr::RoadRunner) | rr::RoadRunner | |
getCC(const std::string &variableName, const std::string ¶meterName) | 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 | |
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() (defined in rr::RoadRunner) | rr::RoadRunner | |
getExtendedStoichiometryMatrix() (defined in rr::RoadRunner) | rr::RoadRunner | |
getExtendedVersionInfo() | rr::RoadRunner | static |
getFloatingSpeciesAmountsNamedArray() | rr::RoadRunner | |
getFloatingSpeciesConcentrationIds() | rr::RoadRunner | |
getFloatingSpeciesConcentrationsNamedArray() | rr::RoadRunner | |
getFloatingSpeciesInitialConcentrationIds() | 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 | |
getFullJacobian() | rr::RoadRunner | |
getFullReorderedJacobian() (defined in rr::RoadRunner) | rr::RoadRunner | |
getFullStoichiometryMatrix() | rr::RoadRunner | |
getGlobalParameterByIndex(const int &index) (defined in rr::RoadRunner) | rr::RoadRunner | |
getGlobalParameterByName(const std::string ¶m) | rr::RoadRunner | |
getGlobalParameterIds() (defined in rr::RoadRunner) | rr::RoadRunner | |
getIds(int types, std::list< std::string > &ids) | rr::RoadRunner | |
getIndependentFloatingSpeciesIds() | rr::RoadRunner | |
getIndependentRatesOfChange() | rr::RoadRunner | |
getIndependentRatesOfChangeNamedArray() | rr::RoadRunner | |
getInfo() | 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 | |
getModelName() | rr::RoadRunner | |
getNrMatrix() | rr::RoadRunner | |
getNumberOfIndependentSpecies() (defined in rr::RoadRunner) | rr::RoadRunner | |
getOptions() | rr::RoadRunner | |
getParamPromotedSBML(const std::string &sArg) | rr::RoadRunner | static |
getRatesOfChange() | rr::RoadRunner | |
getRatesOfChangeNamedArray() | rr::RoadRunner | |
getReducedEigenValues() | rr::RoadRunner | |
getReducedJacobian(double h=-1.0) | rr::RoadRunner | |
getReducedStoichiometryMatrix() | rr::RoadRunner | |
getRegisteredIntegratorNames() | 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 | |
getSelectedValues() | rr::RoadRunner | |
getSelections() | rr::RoadRunner | |
getSimulateOptions() | rr::RoadRunner | |
getSimulationData() const | rr::RoadRunner | |
getSteadyStateSelections() | rr::RoadRunner | |
getSteadyStateSelectionStrings() const | rr::RoadRunner | |
getSteadyStateSolver() | rr::RoadRunner | |
getSteadyStateThreshold() const | rr::RoadRunner | |
getSteadyStateValues() | rr::RoadRunner | |
getSteadyStateValuesNamedArray() | rr::RoadRunner | |
getSupportedIdTypes() | rr::RoadRunner | |
getTempDir() (defined in rr::RoadRunner) | 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 string &reactionName, const 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(std::string name) (defined in rr::RoadRunner) | 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(std::string filename) (defined in rr::RoadRunner) | rr::RoadRunner | |
makeIntegrator(std::string name) | rr::RoadRunner | |
mcaSteadyState() (defined in rr::RoadRunner) | rr::RoadRunner | |
oneStep(double currentTime, double stepSize, bool reset=true) | rr::RoadRunner | |
regenerate(bool forceRegenerate=true, bool reset=false) | rr::RoadRunner | |
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) | 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 | |
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 | |
RR_DEPRECATED(int getNumberOfReactions()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(double getReactionRate(const int &index)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(double getRateOfChange(const int &index)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< std::string > getRateOfChangeIds()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(int getNumberOfCompartments()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setCompartmentByIndex(const int &index, const double &value)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(double getCompartmentByIndex(const int &index)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< std::string > getCompartmentIds()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(int getNumberOfBoundarySpecies()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getBoundarySpeciesConcentrations()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setBoundarySpeciesConcentrations(const std::vector< double > &values)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(int getNumberOfFloatingSpecies()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(double getFloatingSpeciesByIndex(int index)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setFloatingSpeciesByIndex(int index, double value)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getFloatingSpeciesConcentrationsV()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getFloatingSpeciesAmountsV()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getBoundarySpeciesConcentrationsV()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getBoundarySpeciesAmountsV()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getFloatingSpeciesInitialConcentrations()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setFloatingSpeciesConcentrations(const std::vector< double > &values)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setFloatingSpeciesInitialConcentrationByIndex(const int &index, const double &value)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setFloatingSpeciesInitialConcentrations(const std::vector< double > &values)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< std::string > getFloatingSpeciesIds()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< std::string > getFloatingSpeciesInitialConditionIds()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(size_t getNumberOfGlobalParameters()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(void setGlobalParameterByIndex(const int index, const double value)) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getGlobalParameterValues()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(int getNumberOfDependentSpecies()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< double > getReactionRates()) (defined in rr::RoadRunner) | rr::RoadRunner | |
RR_DEPRECATED(std::vector< std::string > getReactionIds()) (defined in rr::RoadRunner) | rr::RoadRunner | |
saveState(std::string filename, char opt='b') (defined in rr::RoadRunner) | rr::RoadRunner | |
setBoundary(const std::string &sid, bool boundaryCondition, bool forceRegenerate=true) | rr::RoadRunner | |
setBoundarySpeciesByIndex(const int &index, const double &value) (defined in rr::RoadRunner) | 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 | |
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(std::string name) (defined in rr::RoadRunner) | rr::RoadRunner | |
setKineticLaw(const std::string &rid, const std::string &kineticLaw, bool forceRegenerate=true) (defined in rr::RoadRunner) | 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 | |
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 | |
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(std::string name) (defined in rr::RoadRunner) | rr::RoadRunner | |
setSteadyStateThreshold(double val) | rr::RoadRunner | |
setTempDir(const std::string &folder) (defined in rr::RoadRunner) | 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 Dictionary *options=0) | rr::RoadRunner | |
steadyState(const Dictionary *dict=0) | rr::RoadRunner | |
steadyStateApproximate(const Dictionary *dict=0) | rr::RoadRunner | |
steadyStateNamedArray(const Dictionary *dict=0) | rr::RoadRunner | |
steadyStateSolverExists(std::string name) (defined in rr::RoadRunner) | rr::RoadRunner | |
validateCurrentSBML() | rr::RoadRunner | |
~RoadRunner() | rr::RoadRunner | virtual |