roadrunner  2.6.0
Fast simulator for SBML models
rr::RoadRunner Member List

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< 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 &parameterName)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() constrr::RoadRunner
getEE(const std::string &reactionName, const std::string &parameterName)rr::RoadRunner
getEE(const std::string &reactionName, const std::string &parameterName, 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::RoadRunnerstatic
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() constrr::RoadRunner
getFrequencyResponse(double startFrequency, int numberOfDecades, int numberOfPoints, const std::string &parameterName, 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 &param)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::RoadRunnerstatic
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::RoadRunnerstatic
getRegisteredSensitivitySolverNames()rr::RoadRunnerstatic
getRegisteredSteadyStateSolverNames()rr::RoadRunnerstatic
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() constrr::RoadRunner
getSteadyStateSelections()rr::RoadRunner
getSteadyStateSelectionStrings() constrr::RoadRunner
getSteadyStateSolver()rr::RoadRunner
getSteadyStateSolverByName(const std::string &name)rr::RoadRunner
getSteadyStateThreshold() constrr::RoadRunner
getSteadyStateValues()rr::RoadRunner
getSteadyStateValuesNamedArray()rr::RoadRunner
getSupportedIdTypes()rr::RoadRunner
getuCC(const std::string &variableName, const std::string &parameterName)rr::RoadRunner
getuEE(const std::string &reactionName, const std::string &parameterName)rr::RoadRunner
getuEE(const std::string &reactionName, const std::string &parameterName, 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 &parameterName)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::RoadRunnerstatic
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 &param, 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 > &times)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::RoadRunnervirtual