Index

_

__init__() (roadrunner.RoadRunner method)

__version__() (roadrunner.RoadRunner static method)

A

absolute (roadrunner.SimulateOptions attribute) ALL (roadrunner.SelectionRecord attribute) ALL_DEPENDENT (roadrunner.SelectionRecord attribute) ALL_DEPENDENT_AMOUNT (roadrunner.SelectionRecord attribute) ALL_DEPENDENT_CONCENTRATION (roadrunner.SelectionRecord attribute)

ALL_INDEPENDENT (roadrunner.SelectionRecord attribute) ALL_INDEPENDENT_AMOUNT (roadrunner.SelectionRecord attribute) ALL_INDEPENDENT_CONCENTRATION (roadrunner.SelectionRecord attribute) AMOUNT (roadrunner.SelectionRecord attribute) amounts (roadrunner.SimulateOptions attribute)

B

BOUNDARY (roadrunner.SelectionRecord attribute) BOUNDARY_AMOUNT (roadrunner.SelectionRecord attribute)

BOUNDARY_CONCENTRATION (roadrunner.SelectionRecord attribute)

C

COMPARTMENT (roadrunner.SelectionRecord attribute) CONCENTRATION (roadrunner.SelectionRecord attribute) concentrations (roadrunner.SimulateOptions attribute) conservedMoietyAnalysis (roadrunner.RoadRunner attribute)

CONSREVED_MOIETY (roadrunner.SelectionRecord attribute) CONTROL (roadrunner.SelectionRecord attribute) createSelection() (roadrunner.RoadRunner method), [1] CURRENT (roadrunner.SelectionRecord attribute)

D

DEPENDENT (roadrunner.SelectionRecord attribute)

duration (roadrunner.SimulateOptions attribute)

E

EIGENVALUE (roadrunner.SelectionRecord attribute) ELASTICITY (roadrunner.SelectionRecord attribute) ELEMENT (roadrunner.SelectionRecord attribute) end (roadrunner.SimulateOptions attribute)

evalInitialConditions() (roadrunner.ExecutableModel method) evalModel() (roadrunner.RoadRunner method) ExecutableModel (class in roadrunner)

F

flags (roadrunner.SimulateOptions attribute) FLOATING (roadrunner.SelectionRecord attribute) FLOATING_AMOUNT (roadrunner.SelectionRecord attribute)

FLOATING_AMOUNT_RATE (roadrunner.SelectionRecord attribute) FLOATING_CONCENTRATION (roadrunner.SelectionRecord attribute) FLOATING_CONCENTRATION_RATE (roadrunner.SelectionRecord attribute)

G

getBoundarySpeciesAmounts() (roadrunner.ExecutableModel method) getBoundarySpeciesConcentrations() (roadrunner.ExecutableModel method) getBoundarySpeciesIds() (roadrunner.ExecutableModel method) getCC() (roadrunner.RoadRunner method) getCompartmentIds() (roadrunner.ExecutableModel method) getCompartmentVolumes() (roadrunner.ExecutableModel method) getCompiler() (roadrunner.RoadRunner method) getConfigurationXML() (roadrunner.RoadRunner method) getConservationMatrix() (roadrunner.RoadRunner method) getConservedMoietyIds() (roadrunner.ExecutableModel method) getConservedMoietyValues() (roadrunner.ExecutableModel method) getCopyright() (roadrunner.RoadRunner static method) getCurrentSBML() (roadrunner.RoadRunner method) getEE() (roadrunner.RoadRunner method) getEigenvalueIds() (roadrunner.RoadRunner method) getEigenvalues() (roadrunner.RoadRunner method) getExtendedVersionInfo() (roadrunner.RoadRunner static method) getFloatingSpeciesAmountIds() (roadrunner.RoadRunner method) getFloatingSpeciesAmountRates() (roadrunner.ExecutableModel method) getFloatingSpeciesAmounts() (roadrunner.ExecutableModel method) getFloatingSpeciesConcentrations() (roadrunner.ExecutableModel method) getFloatingSpeciesIds() (roadrunner.ExecutableModel method) getFullJacobian() (roadrunner.RoadRunner method) getFullyReorderedStoichiometryMatrix() (roadrunner.RoadRunner method) getGlobalParameterValues() (roadrunner.ExecutableModel method) getInfo() (roadrunner.ExecutableModel method) (roadrunner.RoadRunner method) getInstanceCount() (roadrunner.RoadRunner method) getInstanceID() (roadrunner.RoadRunner method) getIntegrator() (roadrunner.RoadRunner method) getL0Matrix() (roadrunner.RoadRunner method) getlibSBMLVersion() (roadrunner.RoadRunner static method) getLinkMatrix() (roadrunner.RoadRunner method) getModelName() (roadrunner.ExecutableModel method) getNrMatrix() (roadrunner.RoadRunner method)

getNumBoundarySpecies() (roadrunner.ExecutableModel method) getNumCompartments() (roadrunner.ExecutableModel method) getNumConservedMoieties() (roadrunner.ExecutableModel method) getNumDependentSpecies() (roadrunner.ExecutableModel method) getNumFloatingSpecies() (roadrunner.ExecutableModel method) getNumGlobalParameters() (roadrunner.ExecutableModel method) getNumIndependentSpecies() (roadrunner.ExecutableModel method) getNumReactions() (roadrunner.ExecutableModel method) getNumRules() (roadrunner.ExecutableModel method) getParamPromotedSBML() (roadrunner.RoadRunner static method) getReactionIds() (roadrunner.ExecutableModel method) getReactionRates() (roadrunner.ExecutableModel method) getReducedJacobian() (roadrunner.RoadRunner method) getReorderedStoichiometryMatrix() (roadrunner.RoadRunner method) getSBML() (roadrunner.RoadRunner method) getScaledConcentrationControlCoefficientMatrix() (roadrunner.RoadRunner method) getScaledElasticityMatrix() (roadrunner.RoadRunner method) getScaledFloatingSpeciesElasticity() (roadrunner.RoadRunner method) getScaledFluxControlCoefficientMatrix() (roadrunner.RoadRunner method) getSelectedValues() (roadrunner.RoadRunner method) getSimulationResult() (roadrunner.RoadRunner method) getSteadyStateValues() (roadrunner.RoadRunner method), [1] getStoichiometry() (roadrunner.ExecutableModel method) getStoichiometryMatrix() (roadrunner.ExecutableModel method) getTime() (roadrunner.ExecutableModel method) getuCC() (roadrunner.RoadRunner method) getuEE() (roadrunner.RoadRunner method) getUnscaledConcentrationControlCoefficientMatrix() (roadrunner.RoadRunner method) getUnscaledElasticityMatrix() (roadrunner.RoadRunner method) getUnscaledFluxControlCoefficientMatrix() (roadrunner.RoadRunner method) getUnscaledSpeciesElasticity() (roadrunner.RoadRunner method) getValue() (roadrunner.RoadRunner method) GLOBAL_PARAMETER (roadrunner.SelectionRecord attribute)

I

INDEPENDENT (roadrunner.SelectionRecord attribute) index (roadrunner.SelectionRecord attribute) INITIAL (roadrunner.SelectionRecord attribute)

INITIAL_FLOATING_AMOUNT (roadrunner.SelectionRecord attribute) INITIAL_FLOATING_CONCENTRATION (roadrunner.SelectionRecord attribute) isModelLoaded() (roadrunner.RoadRunner method)

L

load() (roadrunner.RoadRunner method)

M

model (roadrunner.RoadRunner attribute)

O

oneStep() (roadrunner.RoadRunner method)

P

p1 (roadrunner.SelectionRecord attribute)

p2 (roadrunner.SelectionRecord attribute)

R

RATE (roadrunner.SelectionRecord attribute) REACTION (roadrunner.SelectionRecord attribute) REACTION_RATE (roadrunner.SelectionRecord attribute) relative (roadrunner.SimulateOptions attribute) reset() (roadrunner.ExecutableModel method) (roadrunner.RoadRunner method) resetModel (roadrunner.SimulateOptions attribute)

RoadRunner (class in roadrunner) roadrunner (module) RoadRunner_getCopyright() (in module roadrunner) RoadRunner_getExtendedVersionInfo() (in module roadrunner) RoadRunner_getParamPromotedSBML() (in module roadrunner)

S

SelectionRecord (class in roadrunner) selections (roadrunner.RoadRunner attribute) selectionType (roadrunner.SelectionRecord attribute) setBoundarySpeciesConcentrations() (roadrunner.ExecutableModel method) setCompartmentVolumes() (roadrunner.ExecutableModel method) setConfigurationXML() (roadrunner.RoadRunner method) setConservedMoietyValues() (roadrunner.ExecutableModel method) setFloatingSpeciesAmounts() (roadrunner.ExecutableModel method) setFloatingSpeciesConcentrations() (roadrunner.ExecutableModel method) setGlobalParameterValues() (roadrunner.ExecutableModel method)

setTime() (roadrunner.ExecutableModel method) simulate() (roadrunner.RoadRunner method) SimulateOptions (class in roadrunner) simulateOptions (roadrunner.RoadRunner attribute) start (roadrunner.SimulateOptions attribute) steadyState() (roadrunner.RoadRunner method) steadyStateSelections (roadrunner.RoadRunner attribute) steps (roadrunner.SimulateOptions attribute) stiff (roadrunner.SimulateOptions attribute) STOICHIOMETRY (roadrunner.SelectionRecord attribute)

T

TIME (roadrunner.SelectionRecord attribute)

U

UNKNOWN (roadrunner.SelectionRecord attribute) UNKNOWN_CONCENTRATION (roadrunner.SelectionRecord attribute) UNKNOWN_ELEMENT (roadrunner.SelectionRecord attribute)

UNSCALED (roadrunner.SelectionRecord attribute) UNSCALED_CONTROL (roadrunner.SelectionRecord attribute) UNSCALED_ELASTICITY (roadrunner.SelectionRecord attribute)

V

variables (roadrunner.SimulateOptions attribute)