Index

_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W

_

__getitem__() (RoadRunner.ExecutableModel method)
__init__() (roadrunner.RoadRunner method)
__setitem__() (RoadRunner.ExecutableModel method)
_COMPARTMENT (roadrunner.SelectionRecord attribute)

A

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)

B

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

C

clearModel() (RoadRunner.RoadRunner method)
COMPARTMENT (roadrunner.SelectionRecord attribute)
Compiler (class in RoadRunner)
CONCENTRATION (roadrunner.SelectionRecord attribute)
conservedMoieties (RoadRunner.LoadSBMLOptions attribute)
conservedMoietyAnalysis (RoadRunner.RoadRunner attribute)
CONSREVED_MOIETY (roadrunner.SelectionRecord attribute)
CONTROL (roadrunner.SelectionRecord attribute)
createSelection() (roadrunner.RoadRunner method)
CURRENT (roadrunner.SelectionRecord attribute)

D

DEPENDENT (roadrunner.SelectionRecord attribute)
disableConsoleLogging() (RoadRunner.Logger static method)
disableFileLogging() (RoadRunner.Logger static method)
disableLogging() (RoadRunner.Logger static method)

E

EIGENVALUE (roadrunner.SelectionRecord attribute)
EIGENVALUE_COMPLEX (roadrunner.SelectionRecord attribute)
ELASTICITY (roadrunner.SelectionRecord attribute)
ELEMENT (roadrunner.SelectionRecord attribute)
enableConsoleLogging() (RoadRunner.Logger static method)
enableFileLogging() (RoadRunner.Logger static method)

F

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

getAvailableIntegrators() (RoadRunner.RoadRunner method)
getBoundarySpeciesAmounts() (RoadRunner.ExecutableModel method)
getBoundarySpeciesConcentrations() (RoadRunner.ExecutableModel method)
getBoundarySpeciesIds() (RoadRunner.ExecutableModel method)
getCC() (RoadRunner.RoadRunner method)
getColoredOutput() (RoadRunner.Logger static method)
getCompartmentIds() (RoadRunner.ExecutableModel method)
getCompartmentVolumes() (RoadRunner.ExecutableModel method)
getCompiler() (RoadRunner.Compiler method)
(roadrunner.RoadRunner method)
getCompilerLocation() (RoadRunner.Compiler method)
getConfigFilePath() (RoadRunner.Config static method)
getConfigurationXML() (RoadRunner.RoadRunner method)
getConservationMatrix() (RoadRunner.RoadRunner method)
getConservedMoietyIds() (RoadRunner.ExecutableModel method)
getConservedMoietyValues() (RoadRunner.ExecutableModel method)
getCopyrightStr() (in module roadrunner)
getCurrentLevelAsString() (RoadRunner.Logger static method)
getCurrentSBML() (RoadRunner.RoadRunner method)
getDefaultTargetTriple() (RoadRunner.Compiler method)
getDependentFloatingSpeciesIds() (RoadRunner.ExecutableModel method)
getDescription() (roadrunner.Solver method)
getDiffStepSize() (RoadRunner.RoadRunner method)
getDisplayName() (roadrunner.Solver method)
getEE() (RoadRunner.RoadRunner method)
getEigenValueIds() (RoadRunner.RoadRunner method)
getExistingIntegratorNames() (RoadRunner.RoadRunner method)
getExtendedVersionInfo() (RoadRunner.RoadRunner method)
getFileName() (RoadRunner.Logger static method)
getFloatingSpeciesAmountRates() (RoadRunner.ExecutableModel method)
getFloatingSpeciesAmounts() (RoadRunner.ExecutableModel method)
getFloatingSpeciesConcentrations() (RoadRunner.ExecutableModel method)
getFloatingSpeciesIds() (RoadRunner.ExecutableModel method)
getFloatingSpeciesInitAmountIds() (RoadRunner.ExecutableModel method)
getFloatingSpeciesInitAmounts() (RoadRunner.ExecutableModel method)
getFloatingSpeciesInitConcentrationIds() (RoadRunner.ExecutableModel method)
getFloatingSpeciesInitConcentrations() (RoadRunner.ExecutableModel method)
getFormattingPattern() (RoadRunner.Logger static method)
getFrequencyResponse() (RoadRunner.RoadRunner method)
getFullEigenValues() (RoadRunner.RoadRunner method)
getFullJacobian() (RoadRunner.RoadRunner method)
getFullStoichiometryMatrix() (RoadRunner.RoadRunner method)
getGlobalParameterIds() (RoadRunner.ExecutableModel method)
getGlobalParameterValues() (RoadRunner.ExecutableModel method)
getHint() (roadrunner.Solver method)
getHostCPUName() (RoadRunner.Compiler method)
getIds() (roadrunner.RoadRunner method)
getIndependentFloatingSpeciesIds() (RoadRunner.ExecutableModel method)
getInfo() (RoadRunner.ExecutableModel method)
(RoadRunner.RoadRunner method)
getInstanceCount() (RoadRunner.RoadRunner method)
getInstanceID() (RoadRunner.RoadRunner method)
getIntegrator() (RoadRunner.RoadRunner method)
getIntegratorByName() (RoadRunner.RoadRunner method)
getKMatrix() (RoadRunner.RoadRunner method)
getL0Matrix() (RoadRunner.RoadRunner method)
getLevel() (RoadRunner.Logger static method)
getLinkMatrix() (RoadRunner.RoadRunner method)
getModel() (RoadRunner.RoadRunner method)
getModelName() (RoadRunner.ExecutableModel method)
getName() (roadrunner.Solver method)
getNrMatrix() (RoadRunner.RoadRunner method)
getNumBoundarySpecies() (RoadRunner.ExecutableModel method)
getNumCompartments() (RoadRunner.ExecutableModel method)
getNumConservedMoieties() (RoadRunner.ExecutableModel method)
getNumEvents() (RoadRunner.ExecutableModel method)
getNumFloatingSpecies() (RoadRunner.ExecutableModel method)
getNumGlobalParameters() (RoadRunner.ExecutableModel method)
getNumParams() (roadrunner.Solver method)
getNumRateRules() (RoadRunner.ExecutableModel method)
getNumReactions() (RoadRunner.ExecutableModel method)
getParamDesc() (roadrunner.Solver method)
getParamHint() (roadrunner.Solver method)
getParamName() (roadrunner.Solver method)
getParamPromotedSBML() (RoadRunner.RoadRunner method)
getProcessTriple() (RoadRunner.Compiler method)
getReactionIds() (RoadRunner.ExecutableModel method)
getReactionRates() (RoadRunner.ExecutableModel method)
getReducedEigenValues() (RoadRunner.RoadRunner method)
getReducedJacobian() (RoadRunner.RoadRunner method)
getReducedStoichiometryMatrix() (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)
getSettings() (roadrunner.Solver method)
getSettingsRepr() (roadrunner.Solver method)
getStateVector() (RoadRunner.ExecutableModel method)
getStateVectorId() (RoadRunner.ExecutableModel method)
getStateVectorIds() (RoadRunner.ExecutableModel method)
getStateVectorRate() (RoadRunner.ExecutableModel method)
getSteadyStateSolver() (RoadRunner.RoadRunner method)
getSteadyStateThreshold() (RoadRunner.RoadRunner method)
getSteadyStateValues() (RoadRunner.RoadRunner method)
getStoichiometry() (RoadRunner.ExecutableModel method)
getSupportCodeFolder() (RoadRunner.Compiler method)
getTime() (RoadRunner.ExecutableModel method)
getType() (roadrunner.Solver method)
getuCC() (RoadRunner.RoadRunner method)
getuEE() (RoadRunner.RoadRunner method)
getUnscaledConcentrationControlCoefficientMatrix() (RoadRunner.RoadRunner method)
getUnscaledElasticityMatrix() (RoadRunner.RoadRunner method)
getUnscaledFluxControlCoefficientMatrix() (RoadRunner.RoadRunner method)
getUnscaledParameterElasticity() (RoadRunner.RoadRunner method)
getUnscaledSpeciesElasticity() (RoadRunner.RoadRunner method)
getValue() (roadrunner.RoadRunner method)
(roadrunner.Solver method)
getValueAsBool() (roadrunner.Solver method)
getValueAsChar() (roadrunner.Solver method)
getValueAsDouble() (roadrunner.Solver method)
getValueAsFloat() (roadrunner.Solver method)
getValueAsInt() (roadrunner.Solver method)
getValueAsLong() (roadrunner.Solver method)
getValueAsString() (roadrunner.Solver method)
getValueAsUChar() (roadrunner.Solver method)
getValueAsUInt() (roadrunner.Solver method)
getValueAsULong() (roadrunner.Solver method)
getVersion() (RoadRunner:.Compiler method)
getVersionStr() (in module roadrunner)
gillespie() (RoadRunner.RoadRunner method)
GLOBAL_PARAMETER (roadrunner.SelectionRecord attribute)

H

hasValue() (roadrunner.Solver method)

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)
integrate() (RoadRunner.RoadRunner method)
isModelLoaded() (RoadRunner.RoadRunner method)
items() (RoadRunner.ExecutableModel method)

K

keys() (RoadRunner.ExecutableModel method)

L

levelToString() (RoadRunner.Logger static method)
listTestModels() (in module roadrunner)
load() (RoadRunner.RoadRunner method)
LoadSBMLOptions (class in RoadRunner)
LOADSBMLOPTIONS_CONSERVED_MOIETIES (RoadRunner.Config attribute)
LOADSBMLOPTIONS_MUTABLE_INITIAL_CONDITIONS (RoadRunner.Config attribute)
LOADSBMLOPTIONS_OPTIMIZE_CFG_SIMPLIFICATION (RoadRunner.Config attribute)
LOADSBMLOPTIONS_OPTIMIZE_DEAD_CODE_ELIMINATION (RoadRunner.Config attribute)
LOADSBMLOPTIONS_OPTIMIZE_DEAD_INST_ELIMINATION (RoadRunner.Config attribute)
LOADSBMLOPTIONS_OPTIMIZE_GVN (RoadRunner.Config attribute)
LOADSBMLOPTIONS_OPTIMIZE_INSTRUCTION_COMBINING (RoadRunner.Config attribute)
LOADSBMLOPTIONS_OPTIMIZE_INSTRUCTION_SIMPLIFIER (RoadRunner.Config attribute)
LOADSBMLOPTIONS_PERMISSIVE (RoadRunner.Config attribute)
LOADSBMLOPTIONS_READ_ONLY (RoadRunner.Config attribute)
LOADSBMLOPTIONS_RECOMPILE (RoadRunner.Config attribute)
LOADSBMLOPTIONS_USE_MCJIT (RoadRunner.Config attribute)
loadTestModel() (in module roadrunner)
log() (RoadRunner.Logger static method)
LOG_CRITICAL (RoadRunner.Logger attribute)
LOG_CURRENT (RoadRunner.Logger attribute)
LOG_DEBUG (RoadRunner.Logger attribute)
LOG_ERROR (RoadRunner.Logger attribute)
LOG_FATAL (RoadRunner.Logger attribute)
LOG_INFORMATION (RoadRunner.Logger attribute)
LOG_NOTICE (RoadRunner.Logger attribute)
LOG_TRACE (RoadRunner.Logger attribute)
LOG_WARNING (RoadRunner.Logger attribute)

M

MAX_OUTPUT_ROWS (RoadRunner.Config attribute)
model (RoadRunner.RoadRunner attribute)
mutableInitialConditions (RoadRunner.LoadSBMLOptions attribute)

N

noDefaultSelections (RoadRunner.LoadSBMLOptions 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)
readConfigFile() (RoadRunner.Config static method)
readOnly (RoadRunner.LoadSBMLOptions attribute)
recompile (RoadRunner.LoadSBMLOptions attribute)
reset() (RoadRunner.ExecutableModel method)
(RoadRunner.RoadRunner method)
resetAll() (RoadRunner.ExecutableModel method)
(RoadRunner.RoadRunner method)
resetSettings() (roadrunner.Solver method)
resetToOrigin() (RoadRunner.ExecutableModel method)
(RoadRunner.RoadRunner method)
RoadRunner (class in roadrunner)
roadrunner (module)
Roadrunner.getSimulationData() (in module RoadRunner)
RoadRunner.plot() (in module RoadRunner)
roadrunner.Solver (class in roadrunner)
RoadRunner.steadyStateSolver (class in RoadRunner)
ROADRUNNER_DISABLE_PYTHON_DYNAMIC_PROPERTIES (RoadRunner.Config attribute)
ROADRUNNER_DISABLE_WARNINGS (RoadRunner.Config attribute)
RoadRunner_getExtendedVersionInfo() (in module roadrunner)
RoadRunner_getParamPromotedSBML() (in module roadrunner)

S

SelectionRecord (class in roadrunner)
selectionType (RoadRunner.SelectionRecord attribute)
setBoundarySpeciesConcentrations() (RoadRunner.ExecutableModel method)
setColoredOutput() (RoadRunner.Logger static method)
setCompartmentVolumes() (RoadRunner.ExecutableModel method)
setCompiler() (RoadRunner.Compiler method)
setCompilerLocation() (RoadRunner.Compiler method)
setConfigurationXML() (RoadRunner.RoadRunner method)
setConservedMoietyValues() (RoadRunner.ExecutableModel method)
setDiffStepSize() (RoadRunner.RoadRunner method)
setFloatingSpeciesAmounts() (RoadRunner.ExecutableModel method)
setFloatingSpeciesConcentrations() (RoadRunner.ExecutableModel method)
setFloatingSpeciesInitAmounts() (RoadRunner.ExecutableModel method)
setFloatingSpeciesInitConcentrations() (RoadRunner.ExecutableModel method)
setFormattingPattern() (RoadRunner.Logger static method)
setGlobalParameterValues() (RoadRunner.ExecutableModel method)
setIntegrator() (RoadRunner.RoadRunner method)
setIntegratorSetting() (RoadRunner.RoadRunner method)
setLevel() (RoadRunner.Logger static method)
setProperty() (RoadRunner.Logger static method)
setSteadyStateThreshold() (RoadRunner.RoadRunner method)
setSupportCodeFolder() (RoadRunner.Compiler method)
setTime() (RoadRunner.ExecutableModel method)
settingsPyDictRepr() (roadrunner.Solver method)
setValue() (RoadRunner.Config static method)
(roadrunner.Solver method)
simulate() (RoadRunner.RoadRunner method)
steadyState() (RoadRunner.RoadRunner method)
steadyStateSelections (RoadRunner.RoadRunner attribute)
steadyStateSolverExists() (RoadRunner.RoadRunner method)
STOICHIOMETRY (roadrunner.SelectionRecord attribute)
stringToLevel() (RoadRunner.Logger static method)

T

TIME (roadrunner.SelectionRecord attribute)
timeCourseSelections (RoadRunner.RoadRunner attribute)
toRepr() (roadrunner.Solver method)
toString() (roadrunner.Solver method)

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

validateSBML() (in module roadrunner)

W

writeConfigFile() (RoadRunner.Config static method)