Main Page Namespace List Class Hierarchy Alphabetical List Compound List File List Compound Members File Members
Compound Members
_ | a | b | c | d | e | f | g | h | i | j | k | l | m | n | o | p | q | r | s | t | u | v | w | y | z | ~
Here is a list of all class members with links to the class documentation for each member:- _ -
- _commentChar
: ParameterReader
- _data
: Experiment
- _experimentList
: NetworkMinimizableDirector
- _experimentName
: Experiment
- _fileList
: Experiment
- _forcingData
: Experiment
- _forcingFileList
: Experiment
- _jValue
: Reaction::JElement
- _lineBuffer
: ParameterReader
- _minimizableList
: NetworkMinimizableDirector
- _moverList
: NetworkMinimizableDirector
- _networkList
: NetworkMinimizableDirector
- _observers
: Subject
- _parameterFileStream
: ParameterReader
- _plotterList
: CQuorumSensingNetworkMinimizableDirector, CPC12RapMinusMinimizableDirector, PC12EGFNGFMinimizableDirector, CPC12AlternateMinimizableDirector, CExampleNetworkMinimizableDirector, CForestNitrogenCyclingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector, CEGFRTraffickingMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector
- _reactionNetwork
: Experiment
- _withRespectTo
: Reaction::JElement
- a -
- b -
- c -
- c
: Rand
- C
: CTrimerFormation, CTrimerDissociation
- CA1
: CComponents
- CA2
: CComponents
- CA3
: CComponents
- CAcceptanceRatioFreeEnergyEstimator()
: CAcceptanceRatioFreeEnergyEstimator
- CalcWidth()
: CGeometry
- CAlgebraicChemical()
: CAlgebraicChemical
- CAlternateErkSubnetwork()
: CAlternateErkSubnetwork
- CAlternateOneGeneInhibitoryNetwork()
: CAlternateOneGeneInhibitoryNetwork
- CAlternateOneGeneInhibitoryNetworkMinimizableDirector()
: CAlternateOneGeneInhibitoryNetworkMinimizableDirector
- CashKarpStep()
: CQualityControlCashKarpMover
- catalyst
: CatalyzedTranslationReaction
- CatalyzedTranslationReaction()
: CatalyzedTranslationReaction
- CBasicQuenchMinimizer()
: CBasicQuenchMinimizer
- CBinaryNetworkDataRelation()
: CBinaryNetworkDataRelation
- CCell()
: CCell
- CChemicalSink()
: CChemicalSink
- CChemicalSource()
: CChemicalSource
- CClonalCommaES()
: CClonalCommaES
- CCombinatorialNetwork()
: CCombinatorialNetwork
- CCombinatorialNetworkMinimizableDirector()
: CCombinatorialNetworkMinimizableDirector
- CCombinatorialNetworksSloppyMinimizableDirector()
: CCombinatorialNetworksSloppyMinimizableDirector
- CCombinatorialRunDirector()
: CCombinatorialRunDirector
- CCommaStrategyOne()
: CCommaStrategyOne
- CComponents()
: CComponents
- CConjugateGradientMinimizer()
: CConjugateGradientMinimizer
- CConjugateGradientObserver()
: CConjugateGradientObserver
- CConstantSinkReaction()
: CConstantSinkReaction
- CConstantSourceReaction()
: CConstantSourceReaction
- CContinuousTimeMonteCarloMover()
: CContinuousTimeMonteCarloMover
- CConversionFactor()
: CConversionFactor
- CCoupledOneGeneNetworksMinimizableDirector()
: CCoupledOneGeneNetworksMinimizableDirector
- CCoupledPC12NetworksMinimizableDirector()
: CCoupledPC12NetworksMinimizableDirector
- CCoupledReplicasMinimizableDirector()
: CCoupledReplicasMinimizableDirector
- CCurrentToCurrentRatioChemical()
: CCurrentToCurrentRatioChemical
- CCurrentToInitialRatioChemical()
: CCurrentToInitialRatioChemical
- cd
: Rand
- CDifferentialEquationMover()
: CDifferentialEquationMover
- CDirector()
: CDirector
- CDisplay()
: CDisplay
- CDNA()
: CDNA
- CEGFRTraffickingCHOMinimizableDirector()
: CEGFRTraffickingCHOMinimizableDirector
- CEGFRTraffickingCoupledMinimizableDirector()
: CEGFRTraffickingCoupledMinimizableDirector
- CEGFRTraffickingEnsembleDirector()
: CEGFRTraffickingEnsembleDirector
- CEGFRTraffickingIdealCellMinimizableDirector()
: CEGFRTraffickingIdealCellMinimizableDirector
- CEGFRTraffickingMinimizableDirector()
: CEGFRTraffickingMinimizableDirector
- CEGFRTraffickingNetwork()
: CEGFRTraffickingNetwork
- CEGFRTraffickingNIH3T3MinimizableDirector()
: CEGFRTraffickingNIH3T3MinimizableDirector
- CEGFRTraffickingPredictionNetwork()
: CEGFRTraffickingPredictionNetwork
- CEGFRTraffickingRunDirector()
: CEGFRTraffickingRunDirector
- CellAverageObserver()
: CellAverageObserver
- cellObserver
: SingleNetworkMinimizable
- cellObservers
: SharedBFactorNetworkMinimizable
- CEnsembleCombinationDirector()
: CEnsembleCombinationDirector
- CEnsembleMember()
: CEnsembleMember
- CEnsembleRunDirector()
: CEnsembleRunDirector
- CEquations()
: CEquations
- CEvolutionStrategy()
: CEvolutionStrategy
- CEvolutionStrategyChromosome()
: CEvolutionStrategyChromosome
- CEvolutionStrategyChromosomeComparator()
: CEvolutionStrategyChromosome::CEvolutionStrategyChromosomeComparator
- CExampleNetwork()
: CExampleNetwork
- CExampleNetworkMinimizableDirector()
: CExampleNetworkMinimizableDirector
- CFirstOrderDestructionReaction()
: CFirstOrderDestructionReaction
- CForcesObserver()
: CForcesObserver
- CForceVectorPoint()
: CForceVectorPoint
- CForceVectorPointComparator()
: CForceVectorPoint::CForceVectorPointComparator
- CForcingData()
: CForcingData
- CForestNitrogenCycleNetwork()
: CForestNitrogenCycleNetwork
- CForestNitrogenCyclingMinimizableDirector()
: CForestNitrogenCyclingMinimizableDirector
- CGeometry()
: CGeometry
- ChangedChemical
: CConstantSourceReaction, CConstantSinkReaction, CChemicalSource, CChemicalSink
- CheckBounds()
: CPositiveDefiniteLevenbergMarquardtMinimizer, CLevenbergMarquardtMinimizer
- CheckFuncTol()
: CNelderMeadSimplexMinimizer, CConjugateGradientMinimizer
- CheckGradTol()
: CConjugateGradientMinimizer
- CheckNegConc()
: CComponents
- CheckTerm()
: CDNA
- CheckVolume()
: CGeometry
- chemData
: ChemicalTimeSeriesData
- Chemical()
: Chemical
- chemicalJacobian
: Reaction
- chemicalNumber
: Chemical
- ChemicalReset()
: ReactionNetwork, CMixedReactionNetwork
- chemicals
: ReactionNetwork, Reaction
- ChemicalTimeSeriesData()
: ChemicalTimeSeriesData
- ChemicalTransportReaction()
: ChemicalTransportReaction
- chemNumber
: TimeVectorPoint
- chemX
: GnuPlotterTrajectoryObserver
- chemY
: GnuPlotterTrajectoryObserver
- chemZ
: GnuPlotterTrajectoryObserver
- ChooseMove()
: CContinuousTimeMonteCarloMover
- CIdentityParameterFilter()
: CIdentityParameterFilter
- CImprovedLevenbergMarquardtMinimizer()
: CImprovedLevenbergMarquardtMinimizer
- CIntegration()
: CIntegration
- CL
: CGeometry
- CLaubLoomisDictyNetwork()
: CLaubLoomisDictyNetwork
- CLaubLoomisDictyNetworkEnsembleDirector()
: CLaubLoomisDictyNetworkEnsembleDirector
- CLaubLoomisDictyNetworkMinimizableDirector()
: CLaubLoomisDictyNetworkMinimizableDirector
- CLaubLoomisDictyRunDirector()
: CLaubLoomisDictyRunDirector
- CLeastSquaresADMinimizer()
: CLeastSquaresADMinimizer
- CLeastSquaresMinimizer()
: CLeastSquaresMinimizer
- CLeastSquaresObserver()
: CLeastSquaresObserver
- CLevenbergMarquardtMinimizer()
: CLevenbergMarquardtMinimizer
- CLogChemical()
: CLogChemical
- CLogParameterFilter()
: CLogParameterFilter
- CLowDimensionalCostFunctionMapper()
: CLowDimensionalCostFunctionMapper
- cm
: Rand
- CMartielGoldbeterDictyNetwork()
: CMartielGoldbeterDictyNetwork
- CMartielGoldbeterDictyNetworkMinimizableDirector()
: CMartielGoldbeterDictyNetworkMinimizableDirector
- CMatrixOperations()
: CMatrixOperations
- CMDOChemical()
: CMDOChemical
- CMichaelisMentenHeterodimerizationReaction()
: CMichaelisMentenHeterodimerizationReaction
- CMixedReactionMover()
: CMixedReactionMover
- CMixedReactionNetwork()
: CMixedReactionNetwork
- CNelderMeadSimplexMinimizer()
: CNelderMeadSimplexMinimizer
- CNormalizedLinearAmplifier()
: CNormalizedLinearAmplifier
- CNormalizedLinearAttenuator()
: CNormalizedLinearAttenuator
- code
: GeneticCode
- col
: RowColumnSparseMatrix::MatrixElement
- competitivebinder
: CompetitiveDegradationReaction
- CompetitiveDegradationReaction()
: CompetitiveDegradationReaction
- compute_current()
: TranslationModelMinimizable
- ComputeAmount()
: CCurrentToInitialRatioChemical, CCurrentToCurrentRatioChemical, CSumChemical, CLogChemical, CAlgebraicChemical, CMDOChemical
- ComputeApproximateHessian()
: CStochasticSensitivityAnalysis
- ComputeBoxes()
: CDNA
- ComputeChiSqTol()
: CLevenbergMarquardtMinimizer
- ComputeDerivativeInformation()
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- ComputeDerivatives()
: CDifferentialEquationMover
- ComputeErrorInInitialAmount()
: CCurrentToInitialRatioChemical, CCurrentToCurrentRatioChemical, CSumChemical, CLogChemical, CAlgebraicChemical, CMDOChemical
- ComputeES()
: SingleNetworkMinimizable, SharedBFactorNetworkMinimizable, NLLSMinimizable, NetworkMinimizableDirector, NetworkMinimizable, Minimizable
- ComputeGradient()
: CConjugateGradientMinimizer
- ComputeGradTol()
: CLevenbergMarquardtMinimizer
- ComputeHistograms()
: CAcceptanceRatioFreeEnergyEstimator
- ComputeInitialAmount()
: CCurrentToInitialRatioChemical, CCurrentToCurrentRatioChemical, CSumChemical, CLogChemical, CAlgebraicChemical, CMDOChemical
- ComputeJacobian()
: CDifferentialEquationMover
- ComputeParTol()
: CLevenbergMarquardtMinimizer
- ComputePointSum()
: CNelderMeadSimplexMinimizer
- ComputeResiduals()
: TranslationModelMinimizable, SingleNetworkMinimizable, CSharedParametersMinimizableDirector, SharedBFactorNetworkMinimizable, CReplicaMinimizableDirector, NLLSMinimizable, NetworkMinimizableDirector, NetworkMinimizable, CCoupledReplicasMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector, CEGFRTraffickingCHOMinimizableDirector
- ComputeTrueHessian()
: CStochasticSensitivityAnalysis
- ComputeVolume()
: CGeometry
- ConcentrationObserver()
: ConcentrationObserver
- COneGeneEnsembleDirector()
: COneGeneEnsembleDirector
- COneGeneEnsembleRunDirector()
: COneGeneEnsembleRunDirector
- COneGeneInhibitoryAveragingDirector()
: COneGeneInhibitoryAveragingDirector
- COneGeneInhibitoryNetworkMinimizableDirector()
: COneGeneInhibitoryNetworkMinimizableDirector
- COneGeneInhibitoryNetworkRunDirector()
: COneGeneInhibitoryNetworkRunDirector
- COneGeneReplicaMinimizableDirector()
: COneGeneReplicaMinimizableDirector
- COneGeneStochasticNetworkMinimizableDirector()
: COneGeneStochasticNetworkMinimizableDirector
- COneGeneStochasticNetworkRunDirector()
: COneGeneStochasticNetworkRunDirector
- ConstructTrialMove()
: CStochasticSensitivityAnalysis
- ConvertToStatistics()
: CEnsembleRunDirector, CEnsembleCombinationDirector
- Cool()
: CVariableStepsizeAnnealMinimizer, CSimulatedAnnealingStrategy, CBasicQuenchMinimizer
- CParameterFilter()
: CParameterFilter
- CParameterRandomizer()
: CParameterRandomizer
- CParameterTranslator()
: CParameterTranslator
- CPC12AlternateEnsembleDirector()
: CPC12AlternateEnsembleDirector
- CPC12AlternateMinimizableDirector()
: CPC12AlternateMinimizableDirector
- CPC12EGFNGFEnsembleDirector()
: CPC12EGFNGFEnsembleDirector
- CPC12EGFNGFRunDirector()
: CPC12EGFNGFRunDirector
- CPC12ParameterTranslator()
: CPC12ParameterTranslator
- CPC12RapMinusEnsembleDirector()
: CPC12RapMinusEnsembleDirector
- CPC12RapMinusMinimizableDirector()
: CPC12RapMinusMinimizableDirector
- CPC12RapMinusNetwork()
: CPC12RapMinusNetwork
- CPeriodicQuenchMinimizer()
: CPeriodicQuenchMinimizer
- CPoolTransitionReaction()
: CPoolTransitionReaction
- CPositiveDefiniteLevenbergMarquardtMinimizer()
: CPositiveDefiniteLevenbergMarquardtMinimizer
- CQualityControlCashKarpMover()
: CQualityControlCashKarpMover
- CQualityControlRK2TMover()
: CQualityControlRK2TMover
- CQualityControlRungeKuttaMover()
: CQualityControlRungeKuttaMover
- CQuorumSensingEnsembleDirector()
: CQuorumSensingEnsembleDirector
- CQuorumSensingNetwork()
: CQuorumSensingNetwork
- CQuorumSensingNetworkMinimizableDirector()
: CQuorumSensingNetworkMinimizableDirector
- CQuorumSensingRunDirector()
: CQuorumSensingRunDirector
- CReactionMover()
: CReactionMover
- CReplicaMinimizableDirector()
: CReplicaMinimizableDirector
- CRK2ExplicitEulerHybridMover()
: CRK2ExplicitEulerHybridMover
- CRK2TMover()
: CRK2TMover
- CRK4Mover()
: CRK4Mover
- CRobustLevenbergMarquardtMinimizer()
: CRobustLevenbergMarquardtMinimizer
- CRunDirector()
: CRunDirector
- CRungeKuttaMover()
: CRungeKuttaMover
- CRunnable()
: CRunnable
- CScaleInvariantMarquardtMinimizer()
: CScaleInvariantMarquardtMinimizer
- CSharedParametersMinimizableDirector()
: CSharedParametersMinimizableDirector
- CSharedPC12NetworksMinimizableDirector()
: CSharedPC12NetworksMinimizableDirector
- CSimulatedAnnealingStrategy()
: CSimulatedAnnealingStrategy
- CSL
: CGeometry
- CSloppyDataMinimizableDirector()
: CSloppyDataMinimizableDirector
- CSquareRootParameterFilter()
: CSquareRootParameterFilter
- CStiffBulirschStoerMover()
: CStiffBulirschStoerMover
- CStochasticSensitivityAnalysis()
: CStochasticSensitivityAnalysis
- CSumChemical()
: CSumChemical
- CSynchronizedCashKarpMover()
: CSynchronizedCashKarpMover
- CSynchronizedRungeKuttaMover()
: CSynchronizedRungeKuttaMover
- CTauNetwork()
: CTauNetwork
- CTauReaction()
: CTauReaction
- CTrimerDissociation()
: CTrimerDissociation
- CTrimerFormation()
: CTrimerFormation
- currentNetworkData
: SingleNetworkMinimizable, SharedBFactorNetworkMinimizable
- CVariableStepsizeAnnealMinimizer()
: CVariableStepsizeAnnealMinimizer
- CW
: CGeometry
- CXComparator()
: CXYPoint::CXComparator
- CXYPoint()
: CXYPoint
- CXYVector()
: CXYVector
- CYComparator()
: CXYPoint::CYComparator
- d -
- DataPoint()
: DataPoint
- DataPointComparator()
: DataPoint::DataPointComparator
- datum
: DataPoint
- DecideStepSize()
: CComponents
- DefineExperiments()
: CQuorumSensingNetworkMinimizableDirector, CQuorumSensingEnsembleDirector, CPC12RapMinusMinimizableDirector, CPC12RapMinusEnsembleDirector, PC12EGFNGFMinimizableDirector, CPC12EGFNGFEnsembleDirector, CPC12AlternateMinimizableDirector, CPC12AlternateEnsembleDirector, COneGeneStochasticNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector, COneGeneInhibitoryNetworkMinimizableDirector, COneGeneEnsembleDirector, CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CSharedParametersMinimizableDirector, CReplicaMinimizableDirector, NetworkMinimizableDirector, CExampleNetworkMinimizableDirector, CEnsembleCombinationDirector, CCoupledReplicasMinimizableDirector, CForestNitrogenCyclingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector, CEGFRTraffickingMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingEnsembleDirector, CEGFRTraffickingCHOMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector, CLaubLoomisDictyNetworkEnsembleDirector, CCombinatorialNetworkMinimizableDirector
- DefineRuns()
: CQuorumSensingRunDirector, CQuorumSensingEnsembleDirector, CPC12RapMinusEnsembleDirector, CPC12EGFNGFRunDirector, CPC12EGFNGFEnsembleDirector, CPC12AlternateEnsembleDirector, COneGeneStochasticNetworkRunDirector, COneGeneInhibitoryNetworkRunDirector, COneGeneEnsembleRunDirector, COneGeneEnsembleDirector, CSloppyDataMinimizableDirector, CRunDirector, CEnsembleCombinationDirector, CEGFRTraffickingRunDirector, CEGFRTraffickingEnsembleDirector, CLaubLoomisDictyRunDirector, CLaubLoomisDictyNetworkEnsembleDirector, CCombinatorialRunDirector, CCombinatorialNetworksSloppyMinimizableDirector
- DEN
: CGeometry
- DestroyingEnzyme
: CFirstOrderDestructionReaction
- Detach()
: Subject
- DEV
: CComponents
- directoryName
: LocateInputFileDirectory
- discrete()
: Rand
- Divide()
: CGeometry, CDNA, CComponents
- Division()
: CCell
- DivisionCheck()
: CCell
- DnaA
: CDNA
- DnaABoxes
: CDNA
- DoAnalysis()
: CStochasticSensitivityAnalysis
- DoMove()
: CContinuousTimeMonteCarloMover
- DoReactionOnce()
: Reaction
- DoStochasticMove()
: CMixedReactionMover
- DotProduct()
: CMatrixOperations
- DT
: CComponents
- DumpPetriNetDotFile()
: ReactionNetwork
- DumpResidualInfo()
: NetworkMinimizableDirector
- DumpTeXForm()
: ReactionNetwork
- DY6S
: CComponents
- DY8S
: CComponents
- DY9
: CComponents
- e -
- E2
: CGeometry
- E23
: CGeometry
- E3
: CGeometry
- E3Rate
: CComponents
- eatwhite()
: TranslationModelMinimizable
- EcoInit()
: CDNA
- efficiency
: TranslationModelMinimizable
- ElementCopy()
: CMatrixOperations
- EntropyShift()
: TranslationModelMinimizable, SingleNetworkMinimizable, NLLSMinimizable, NetworkMinimizableDirector, NetworkMinimizable, Minimizable
- Enzyme
: MichaelisMentenReaction, CMichaelisMentenHeterodimerizationReaction
- Equilibrated()
: CVariableStepsizeAnnealMinimizer, CSimulatedAnnealingStrategy, CBasicQuenchMinimizer
- Equilibrium()
: CDNA
- ErkSubnetwork()
: ErkSubnetwork
- error
: DataPoint
- errorInInitialAmount
: Chemical
- errorInInitialValue
: RateConstant
- ErrorMessage()
: CDisplay
- Evaluate()
: CBinaryNetworkDataRelation
- EvaluateOffspring()
: CEvolutionStrategy
- EvaluateSimplex()
: CNelderMeadSimplexMinimizer
- Execute()
: COneGeneInhibitoryAveragingDirector, CRunDirector, CEnsembleRunDirector, CEnsembleCombinationDirector, CDirector
- experiment
: SingleNetworkMinimizable
- Experiment()
: Experiment
- experiments
: SharedBFactorNetworkMinimizable
- f -
- F()
: TranslationModelMinimizable, SingleNetworkMinimizable, SharedBFactorNetworkMinimizable, NLLSMinimizable, NetworkMinimizableDirector, NetworkMinimizable, Minimizable
- F0()
: TranslationModelMinimizable, SingleNetworkMinimizable, SharedBFactorNetworkMinimizable, NLLSMinimizable, NetworkMinimizableDirector, NetworkMinimizable, Minimizable
- FirstInt()
: CComponents
- FixMinimizable()
: GnuPlotterEnsembleDataDirectorObserver
- FixRunnable()
: GnuPlotterEnsembleRunDirectorObserver
- FlushGnuPlotter()
: GnuPlotter
- Flux()
: CComponents
- fm
: TranslationModelMinimizable
- fmerr
: TranslationModelMinimizable
- ForkPos
: CDNA
- ForwardTransformation()
: CParameterFilter
- FourthOrderStep()
: CRK4Mover
- fp
: TranslationModelMinimizable
- fperr
: TranslationModelMinimizable
- freePromoter
: TranscriptionReaction
- g -
- gamma()
: CDNA
- gaussian()
: Rand
- GD
: CDNA
- GenerateMove()
: CVariableStepsizeAnnealMinimizer, CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer, CBasicQuenchMinimizer
- Generation()
: CCell
- GenerationReaction()
: GenerationReaction
- Generator
: GenerationReaction, PlasmidReplicationReaction
- GeneticCode()
: GeneticCode
- geneticcode
: TranslationModelMinimizable
- GenTime
: CCell
- Get()
: LocateInputFileDirectory
- get_anticodon()
: GeneticCode
- GetAcceptanceRatio()
: CSimulatedAnnealingStrategy
- GetAlgebraicIndices()
: ReactionNetwork
- GetAmount()
: Chemical
- GetAverageConcentration()
: CellAverageObserver
- GetAverages()
: CEnsembleRunDirector
- GetCellObserver()
: SingleNetworkMinimizable, SharedBFactorNetworkMinimizable, CRunnable
- GetChemical()
: CTauNetwork, ReactionNetwork, CMixedReactionNetwork
- GetChemicalJacobian()
: UnaryDegradationReaction, TransformationReaction, TranscriptionReaction, CTauReaction, MichaelisMentenReaction, HomodimerizationReaction, HomodimerDissociationReaction, HeterodimerizationReaction, HeterodimerDissociationReaction, GenerationReaction, CFirstOrderDestructionReaction, CompetitiveDegradationReaction, PlasmidReplicationReaction, CMichaelisMentenHeterodimerizationReaction, CatalyzedTranslationReaction, Reaction, CNormalizedLinearAttenuator, CNormalizedLinearAmplifier, CConstantSourceReaction, CConstantSinkReaction, CChemicalSource, CChemicalSink, CPoolTransitionReaction, CTrimerFormation, CTrimerDissociation
- GetChemicalNumber()
: Chemical
- GetChemicals()
: CTauNetwork, ReactionNetwork, Reaction, CMixedReactionNetwork
- GetChemicalTimeSeriesData()
: Experiment
- GetChemNumber()
: TimeVectorPoint, CForceVectorPoint
- GetCol()
: RowColumnSparseMatrix::MatrixElement
- GetComponents()
: CCell
- GetConversionFactor()
: SingleNetworkMinimizable, NetworkMinimizable
- GetCost()
: CEnsembleMember
- GetDataAverages()
: CEnsembleCombinationDirector
- GetDataStdDevs()
: CEnsembleCombinationDirector
- GetDatum()
: DataPoint
- GetDeterministicReaction()
: CMixedReactionNetwork
- GetDeterministicReactionRates()
: CMixedReactionNetwork
- GetDeterministicReactions()
: CMixedReactionNetwork
- GetDisplay()
: CCell
- GetDNA()
: CCell
- GetDY6S()
: CComponents
- GetDY8S()
: CComponents
- GetDY9()
: CComponents
- GetE2Bar()
: CSimulatedAnnealingStrategy
- GetEBar()
: CSimulatedAnnealingStrategy
- GetEigenvectorMatrix()
: CStochasticSensitivityAnalysis
- GetEMin()
: CSimulatedAnnealingStrategy
- GetEnergyLastComputed()
: Minimizable
- GetEnsemble()
: CStochasticSensitivityAnalysis
- GetEntropyLastComputed()
: Minimizable
- GetError()
: DataPoint
- GetErrorInInitialAmount()
: Chemical
- GetErrorInInitialValue()
: RateConstant
- GetExperiment()
: SingleNetworkMinimizable, SharedBFactorNetworkMinimizable, NetworkMinimizable
- GetExperimentName()
: Experiment
- GetFactorValue()
: CConversionFactor
- GetForceMatrix()
: CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- GetForceVector()
: CConjugateGradientMinimizer
- GetForcingData()
: Experiment
- GetForcingVector()
: CForcingData
- GetGeometry()
: CCell
- GetInitialAmount()
: Chemical
- GetInitialChemConcOptimizable()
: SingleNetworkMinimizable, NetworkMinimizable
- GetInitialChemConcWeight()
: SingleNetworkMinimizable, NetworkMinimizable
- GetInitialValue()
: RateConstant
- GetJValue()
: Reaction::JElement
- GetLatestDataTime()
: ChemicalTimeSeriesData
- GetLatestForcingTime()
: CForcingData
- GetLogsInObjectiveFunction()
: SingleNetworkMinimizable, NetworkMinimizable
- GetLRGraph()
: OneGeneInhibitoryNetwork, ReactionNetwork
- GetMaxStepSize()
: CReactionMover
- GetMinimizable()
: CEnsembleCombinationDirector
- GetMinStepSize()
: CReactionMover
- GetMover()
: NetworkMinimizableDirector, CEnsembleCombinationDirector
- GetName()
: Reaction, RateConstant, Chemical
- GetNBFactors()
: SingleNetworkMinimizable, NetworkMinimizable
- GetNCells()
: SingleNetworkMinimizable, NetworkMinimizable
- GetNChemicals()
: ChemicalTimeSeriesData
- GetNDataPoints()
: ChemicalTimeSeriesData
- GetNExp()
: SharedBFactorNetworkMinimizable
- GetNExperiments()
: NetworkMinimizableDirector, CEnsembleCombinationDirector
- GetNextDataTime()
: ChemicalTimeSeriesData
- GetNextForcingTime()
: CForcingData
- GetNObjectParameters()
: CEvolutionStrategyChromosome
- GetNoDataAverages()
: CEnsembleCombinationDirector
- GetNoDataStdDevs()
: CEnsembleCombinationDirector
- GetNParameters()
: TranslationModelMinimizable, CQuorumSensingNetworkMinimizableDirector, CPC12RapMinusMinimizableDirector, PC12EGFNGFMinimizableDirector, CPC12AlternateMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector, COneGeneInhibitoryNetworkMinimizableDirector, CAlternateOneGeneInhibitoryNetworkMinimizableDirector, CSloppyDataMinimizableDirector, SingleNetworkMinimizable, CSharedParametersMinimizableDirector, SharedBFactorNetworkMinimizable, CReplicaMinimizableDirector, NetworkMinimizableDirector, NetworkMinimizable, CNelderMeadSimplexMinimizer, CLeastSquaresMinimizer, CLeastSquaresADMinimizer, CConjugateGradientMinimizer, Minimizable, CExampleNetworkMinimizableDirector, CCoupledReplicasMinimizableDirector, CForestNitrogenCyclingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector, CEGFRTraffickingMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector, CCombinatorialNetworksSloppyMinimizableDirector, CCombinatorialNetworkMinimizableDirector
- GetNResiduals()
: NLLSMinimizable, CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- GetNStrategyParameters()
: CEvolutionStrategyChromosome
- GetNTermsPerLine()
: ReactionNetwork, CForestNitrogenCycleNetwork, CMartielGoldbeterDictyNetwork, CLaubLoomisDictyNetwork
- GetNTimeSeries()
: ChemicalTimeSeriesData
- GetNumAnticodons()
: GeneticCode
- GetNumberChangedByReaction()
: Reaction
- GetNumberOfAlgebraicChemicals()
: ReactionNetwork
- GetNumberOfCells()
: CellAverageObserver
- GetNumberOfChemicals()
: CTauNetwork, ReactionNetwork, CMixedReactionNetwork
- GetNumberOfDeterministicReactions()
: CMixedReactionNetwork
- GetNumberOfRateConstants()
: ReactionNetwork, CMixedReactionNetwork
- GetNumberOfReactions()
: CTauNetwork, ReactionNetwork, CMixedReactionNetwork
- GetNumberOfStochasticReactions()
: CMixedReactionNetwork
- GetNumberOfTimeSteps()
: CellAverageObserver
- GetNumCodons()
: GeneticCode
- GetObjectParameter()
: CEvolutionStrategyChromosome
- GetObjectParameters()
: CEvolutionStrategyChromosome
- GetObjFuncValue()
: CEvolutionStrategyChromosome
- GetParameter()
: CQuorumSensingNetworkMinimizableDirector, CPC12RapMinusMinimizableDirector, PC12EGFNGFMinimizableDirector, CPC12AlternateMinimizableDirector, COneGeneStochasticNetworkMinimizableDirector, COneGeneInhibitoryNetworkMinimizableDirector, CAlternateOneGeneInhibitoryNetworkMinimizableDirector, SingleNetworkMinimizable, CSharedParametersMinimizableDirector, SharedBFactorNetworkMinimizable, CReplicaMinimizableDirector, NetworkMinimizableDirector, NetworkMinimizable, CExampleNetworkMinimizableDirector, CEnsembleMember, CCoupledReplicasMinimizableDirector, CForestNitrogenCyclingMinimizableDirector, CEGFRTraffickingNIH3T3MinimizableDirector, CEGFRTraffickingMinimizableDirector, CEGFRTraffickingIdealCellMinimizableDirector, CEGFRTraffickingCHOMinimizableDirector, CMartielGoldbeterDictyNetworkMinimizableDirector, CLaubLoomisDictyNetworkMinimizableDirector, CCombinatorialNetworkMinimizableDirector
- GetParameterSize()
: CEnsembleMember
- GetQ1()
: CBinaryNetworkDataRelation
- GetQ2()
: CBinaryNetworkDataRelation
- GetQuadratic()
: CEnsembleMember
- GetR1()
: CBinaryNetworkDataRelation
- GetR2()
: CBinaryNetworkDataRelation
- GetRate()
: UnaryDegradationReaction, TransformationReaction, TranscriptionReaction, CTauReaction, MichaelisMentenReaction, HomodimerizationReaction, HomodimerDissociationReaction, HeterodimerizationReaction, HeterodimerDissociationReaction, GenerationReaction, CFirstOrderDestructionReaction, CompetitiveDegradationReaction, PlasmidReplicationReaction, CMichaelisMentenHeterodimerizationReaction, CatalyzedTranslationReaction, Reaction, CNormalizedLinearAttenuator, CNormalizedLinearAmplifier, CConstantSourceReaction, CConstantSinkReaction, CChemicalSource, CChemicalSink, CPoolTransitionReaction, CTrimerFormation, CTrimerDissociation
- GetRateConstant()
: ReactionNetwork, CMixedReactionNetwork
- GetRateConstants()
: ReactionNetwork, CMixedReactionNetwork
- GetRateConstantsOptimizable()
: SingleNetworkMinimizable, NetworkMinimizable
- GetRateConstantsWeight()
: SingleNetworkMinimizable, NetworkMinimizable
- GetReaction()
: ReactionNetwork, CMixedReactionNetwork
- GetReactionMover()
: CRunnable
- GetReactionNetwork()
: CRunnable, NetworkMinimizableDirector, CReactionMover, Experiment
- GetReactionRates()
: CTauNetwork, ReactionNetwork, CMixedReactionNetwork
- GetReactions()
: CTauNetwork, ReactionNetwork, CMixedReactionNetwork, Chemical
- GetRescale()
: CStochasticSensitivityAnalysis
- GetResidual()
: CEnsembleMember
- GetResiduals()
: NLLSMinimizable
- GetResidualsSize()
: CEnsembleMember
- GetRow()
: RowColumnSparseMatrix::MatrixElement
- GetRunnable()
: CRunDirector
- GetRunnableName()
: CRunnable
- GetRWValue()
: CStochasticSensitivityAnalysis
- GetSeed()
: CReactionMover
- GetSepf()
: CGeometry
- GetSingularValues()
: CStochasticSensitivityAnalysis
- GetStdDevs()
: CEnsembleRunDirector
- GetStepSize()
: CQualityControlRungeKuttaMover, CDifferentialEquationMover
- GetStochasticReaction()
: CMixedReactionNetwork
- GetStochasticReactionRates()
: CMixedReactionNetwork
- GetStochasticReactions()
: CMixedReactionNetwork
- GetStrategyParameter()
: CEvolutionStrategyChromosome
- GetStrategyParameters()
: CEvolutionStrategyChromosome
- GetSummedConcentration()
: ConcentrationObserver
- GetSurface()
: CGeometry
- Gett1()
: CBinaryNetworkDataRelation
- Gett2()
: CBinaryNetworkDataRelation
- GetTemperature()
: CSimulatedAnnealingStrategy
- GetTeXForm()
: Reaction
- GetTeXName()
: RateConstant, Chemical
- GetTime()
: TimeVectorPoint, CForceVectorPoint, DataPoint
- GetTimeCount()
: CReactionMover
- GetTimeSeries()
: ChemicalTimeSeriesData
- GetTimeSeriesWeight()
: SingleNetworkMinimizable, NetworkMinimizable
- GetTimeVector()
: ChemicalTimeSeriesData
- GetTOfTau()
: CTauNetwork
- GetTotalStepsTaken()
: CReactionMover
- GetTotalStochasticReactionProbability()
: CMixedReactionNetwork
- GetType()
: CBinaryNetworkDataRelation
- GetValue()
: RowColumnSparseMatrix::MatrixElement, RateConstant, CForceVectorPoint
- GetVectorIndex()
: TimeVectorPoint
- GetVolume()
: CGeometry
- GetWidth()
: CGeometry
- GetWithRespectTo()
: Reaction::JElement
- GetX()
: CXYPoint
- GetXYVector()
: CXYVector
- GetY()
: CComponents, CXYPoint
- gnuplot_pipe
: GnuPlotter
- GnuPlotter()
: GnuPlotter
- GnuPlotterCostObserver()
: GnuPlotterCostObserver
- GnuPlotterDirectorObserver()
: GnuPlotterDirectorObserver
- GnuPlotterEnsembleDataDirectorObserver()
: GnuPlotterEnsembleDataDirectorObserver
- GnuPlotterEnsembleRunDirectorObserver()
: GnuPlotterEnsembleRunDirectorObserver
- GnuPlotterParameterScatterPlot()
: GnuPlotterParameterScatterPlot
- GnuPlotterResidualScatterPlot()
: GnuPlotterResidualScatterPlot
- GnuPlotterRunnableObserver()
: GnuPlotterRunnableObserver
- GnuPlotterSimulatedAnnealingObserver()
: GnuPlotterSimulatedAnnealingObserver
- GnuPlotterSingleRun()
: GnuPlotterSingleRun
- GnuPlotterTimeSeriesObserver()
: GnuPlotterTimeSeriesObserver
- GnuPlotterTimeSeriesSharedBFactorObserver()
: GnuPlotterTimeSeriesSharedBFactorObserver
- GnuPlotterTrajectoryObserver()
: GnuPlotterTrajectoryObserver
- gotFileName
: LocateInputFileDirectory
- Gradient()
: Minimizable
- h -
- i -
- i97
: Rand
- IncrementAmount()
: Chemical, CAlgebraicChemical
- IncrementTotalSteps()
: CReactionMover
- initialAmount
: Chemical
- initialChemConcOptimizable
: SingleNetworkMinimizable, NetworkMinimizable
- initialChemConcWeight
: SingleNetworkMinimizable, NetworkMinimizable
- Initialize()
: CComponents, SingleNetworkMinimizable, SharedBFactorNetworkMinimizable, NetworkMinimizable
- InitializePopulation()
: CEvolutionStrategy, CCommaStrategyOne, CClonalCommaES
- InitializeSimplex()
: CNelderMeadSimplexMinimizer
- InitializeTemperature()
: CVariableStepsizeAnnealMinimizer, CSimulatedAnnealingStrategy, CBasicQuenchMinimizer
- initialNetworkData
: SingleNetworkMinimizable, SharedBFactorNetworkMinimizable
- initialValue
: RateConstant
- InitialValues
: CComponents
- InputChemical
: CNormalizedLinearAttenuator, CNormalizedLinearAmplifier
- Integrate()
: CComponents
- IsFactorFixed()
: CConversionFactor
- IsFactorNeeded()
: CConversionFactor
- IsFileGood()
: ParameterReader
- ITN
: CComponents
- j -
- k -
- l -
- m -
- m_bBreakFlag
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer
- m_bCheckChi
: CLevenbergMarquardtMinimizer
- m_bCheckGrad
: CLevenbergMarquardtMinimizer
- m_bCheckPar
: CLevenbergMarquardtMinimizer
- m_bChiSqFlag
: CScaleInvariantMarquardtMinimizer, CImprovedLevenbergMarquardtMinimizer
- m_bFactorFixed
: CConversionFactor
- m_bFactorNeeded
: CConversionFactor
- m_bGradFlag
: CScaleInvariantMarquardtMinimizer, CImprovedLevenbergMarquardtMinimizer
- m_bHessianFlag
: CStochasticSensitivityAnalysis
- m_bParFlag
: CScaleInvariantMarquardtMinimizer, CImprovedLevenbergMarquardtMinimizer
- m_bPositiveSemiDef
: CLevenbergMarquardtMinimizer
- m_bReadFlag
: CStochasticSensitivityAnalysis
- m_bReconditionFlag
: CPositiveDefiniteLevenbergMarquardtMinimizer
- m_bSearchFlag
: CConjugateGradientMinimizer
- m_bSVDFlag
: CStochasticSensitivityAnalysis
- m_bSyncFlag
: CSynchronizedRungeKuttaMover, CSynchronizedCashKarpMover
- m_cType
: CBinaryNetworkDataRelation
- m_dAbsTol
: CMixedReactionMover
- m_dAcceptanceRatio
: CStochasticSensitivityAnalysis, CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer
- m_dAvgCost
: CEvolutionStrategy
- m_dC
: CVariableStepsizeAnnealMinimizer, CPeriodicQuenchMinimizer
- m_dChannelChosen
: CContinuousTimeMonteCarloMover
- m_dChiSqTol
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CLevenbergMarquardtMinimizer
- m_dCost
: CEnsembleMember
- m_dDefaultStepSize
: CDifferentialEquationMover
- m_dDeltaSquared
: CReplicaMinimizableDirector, CCoupledReplicasMinimizableDirector
- m_dDeltaX
: CVariableStepsizeAnnealMinimizer, CPeriodicQuenchMinimizer
- m_dDeterministicReactionRates
: CMixedReactionNetwork
- m_dE2Bar
: CSimulatedAnnealingStrategy
- m_dEBar
: CSimulatedAnnealingStrategy
- m_dEBest
: CSimulatedAnnealingStrategy
- m_dECurrent
: CVariableStepsizeAnnealMinimizer, CPeriodicQuenchMinimizer
- m_dEnergyLastComputed
: Minimizable
- m_dEntropyLastComputed
: Minimizable
- m_dEps
: CStiffBulirschStoerMover, CRK2ExplicitEulerHybridMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_dEpsSquared
: CReplicaMinimizableDirector, CCoupledReplicasMinimizableDirector
- m_dFactorValue
: CConversionFactor
- m_dFrequency
: CReactionMover
- m_dFuncAccuracy
: CStochasticSensitivityAnalysis, CLeastSquaresMinimizer, CLeastSquaresADMinimizer, CConjugateGradientMinimizer
- m_dFuncTol
: CConjugateGradientMinimizer
- m_dGammaSquared
: CSloppyDataMinimizableDirector, NetworkMinimizableDirector
- m_dGOLD
: CConjugateGradientMinimizer
- m_dGradTol
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CLevenbergMarquardtMinimizer, CConjugateGradientMinimizer
- m_dInitialSigma
: CCommaStrategyOne, CClonalCommaES
- m_dInitialStepScale
: CBasicQuenchMinimizer
- m_dInitialStepSize
: CStiffBulirschStoerMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_dLambda
: CVariableStepsizeAnnealMinimizer, CNelderMeadSimplexMinimizer, CLevenbergMarquardtMinimizer
- m_dLastStep
: CStiffBulirschStoerMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_dMarquardt
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer
- m_dMaxStepSize
: CReactionMover
- m_dMinStepSize
: CReactionMover
- m_dMinTol
: CConjugateGradientMinimizer
- m_dMNormSquared
: CStochasticSensitivityAnalysis
- m_dNextStep
: CStiffBulirschStoerMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_dNu
: CLevenbergMarquardtMinimizer
- m_dObjFuncValue
: CEvolutionStrategyChromosome
- m_dParTol
: CLevenbergMarquardtMinimizer
- m_dQuadratic
: CEnsembleMember
- m_dRescale
: CStochasticSensitivityAnalysis
- m_dRWValue
: CStochasticSensitivityAnalysis
- m_dSqrLogParDiff
: CVariableStepsizeAnnealMinimizer, CPeriodicQuenchMinimizer
- m_dStepScale
: CBasicQuenchMinimizer
- m_dStepSize
: CDifferentialEquationMover
- m_dStochasticReactionRates
: CMixedReactionNetwork
- m_dTau
: CLevenbergMarquardtMinimizer, CCommaStrategyOne, CClonalCommaES
- m_dTauPrime
: CCommaStrategyOne, CClonalCommaES
- m_dTemperature
: CStochasticSensitivityAnalysis, CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer
- m_dTime
: CReactionMover, CForceVectorPoint
- m_dTol
: CNelderMeadSimplexMinimizer
- m_dValue
: CForceVectorPoint
- m_dX
: CXYPoint
- m_dY
: CXYPoint
- m_iChemNumber
: CForceVectorPoint
- m_iCount
: CReactionMover
- m_iEnsembleSize
: CEnsembleRunDirector, CEnsembleCombinationDirector
- m_iHi
: CNelderMeadSimplexMinimizer
- m_iLambda
: CEvolutionStrategy
- m_iLo
: CNelderMeadSimplexMinimizer
- m_iMu
: CEvolutionStrategy
- m_iN0
: CAcceptanceRatioFreeEnergyEstimator
- m_iN1
: CAcceptanceRatioFreeEnergyEstimator
- m_iNBFactors
: SingleNetworkMinimizable, NetworkMinimizable
- m_iNCycles
: CBasicQuenchMinimizer
- m_iNEnsembleSize
: CStochasticSensitivityAnalysis
- m_iNextHi
: CNelderMeadSimplexMinimizer
- m_iNGenerations
: CEvolutionStrategy
- m_iNIterations
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CNelderMeadSimplexMinimizer, CLevenbergMarquardtMinimizer, CConjugateGradientMinimizer
- m_iNMCSteps
: CVariableStepsizeAnnealMinimizer, CPeriodicQuenchMinimizer
- m_iNObjectParameters
: CEvolutionStrategyChromosome
- m_iNParameters
: CStochasticSensitivityAnalysis
- m_iNQuenches
: CPeriodicQuenchMinimizer
- m_iNResiduals
: CStochasticSensitivityAnalysis, CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- m_iNRestarts
: CConjugateGradientMinimizer
- m_iNStrategyParameters
: CEvolutionStrategyChromosome, CEvolutionStrategy
- m_iNTrialSteps
: CBasicQuenchMinimizer
- m_iPriorList
: NetworkMinimizableDirector
- m_iPSize
: CEnsembleMember
- m_iQ1
: CBinaryNetworkDataRelation
- m_iQ2
: CBinaryNetworkDataRelation
- m_iR1
: CBinaryNetworkDataRelation
- m_iR2
: CBinaryNetworkDataRelation
- m_iRho
: CEvolutionStrategy
- m_iRNGSeed
: CStochasticSensitivityAnalysis, CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer
- m_iRSize
: CEnsembleMember
- m_iSeed
: CParameterRandomizer, CReactionMover
- m_it1
: CBinaryNetworkDataRelation
- m_it2
: CBinaryNetworkDataRelation
- m_iTotalStepsTaken
: CReactionMover
- m_iTrialCount
: CSimulatedAnnealingStrategy
- m_iWhichMinimizable
: GnuPlotterEnsembleDataDirectorObserver
- m_iWhichRunnable
: GnuPlotterEnsembleRunDirectorObserver
- m_pCell
: CGeometry, CDNA, CDisplay, CComponents
- m_pCellObserver
: CRunnable
- m_pChemTau
: CTauNetwork
- m_pComponents
: CCell
- m_pConversionFactors
: SingleNetworkMinimizable, NetworkMinimizable
- m_pdAlpha
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- m_pdBeta
: CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer
- m_pdCurrentParameters
: CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer, CConjugateGradientMinimizer
- m_pdCurrentResiduals
: CRobustLevenbergMarquardtMinimizer
- m_pdDiagonal
: CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- m_pdError
: CStiffBulirschStoerMover, CQualityControlCashKarpMover
- m_pdForceMatrix
: CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- m_pdForceVector
: CConjugateGradientMinimizer
- m_pdGrad
: CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- m_pdGradient
: CConjugateGradientMinimizer
- m_pdHessian
: CStochasticSensitivityAnalysis
- m_pDisplay
: CCell
- m_pdJacobian
: CStochasticSensitivityAnalysis, CRobustLevenbergMarquardtMinimizer
- m_pdLocalError
: CRK2ExplicitEulerHybridMover
- m_pdLowerBounds
: CPositiveDefiniteLevenbergMarquardtMinimizer
- m_pdMatrixV
: CStochasticSensitivityAnalysis
- m_pDNA
: CCell
- m_pdObjectParameters
: CEvolutionStrategyChromosome
- m_pdParameters
: CEnsembleMember
- m_pdPointSum
: CNelderMeadSimplexMinimizer
- m_pdResiduals
: CEnsembleMember
- m_pdSamplingMatrix
: CStochasticSensitivityAnalysis
- m_pdScale
: CStiffBulirschStoerMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_pdScalingMatrix
: CRobustLevenbergMarquardtMinimizer
- m_pdSearchDirection
: CConjugateGradientMinimizer
- m_pdSimplexCosts
: CNelderMeadSimplexMinimizer
- m_pdSingularValues
: CStochasticSensitivityAnalysis
- m_pdStrategyParameters
: CEvolutionStrategyChromosome
- m_pdTrialParameters
: CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer
- m_pdUpperBounds
: CPositiveDefiniteLevenbergMarquardtMinimizer
- m_pEqns
: CIntegration
- m_pFilter
: CStochasticSensitivityAnalysis, CSimulatedAnnealingStrategy, CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CPeriodicQuenchMinimizer, CNelderMeadSimplexMinimizer, CLeastSquaresMinimizer, CLeastSquaresADMinimizer, CEvolutionStrategy, CConjugateGradientMinimizer
- m_pGeometry
: CCell
- m_pMinimizable
: CNelderMeadSimplexMinimizer, CConjugateGradientMinimizer
- m_pMixedNetwork
: CTauNetwork
- m_pMixedReactionNetwork
: CMixedReactionMover
- m_pMO
: CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer, CNelderMeadSimplexMinimizer, CConjugateGradientMinimizer, CLowDimensionalCostFunctionMapper
- m_pODEMover
: CMixedReactionMover
- m_pQuencher
: CPeriodicQuenchMinimizer
- m_pReactionNetwork
: CReactionMover, CMixedReactionNetwork
- m_pReplicaOne
: CSharedParametersMinimizableDirector, CCoupledReplicasMinimizableDirector
- m_pReplicaTwo
: CSharedParametersMinimizableDirector, CCoupledReplicasMinimizableDirector
- m_pRNG
: CStochasticSensitivityAnalysis, CParameterRandomizer, CMixedReactionMover, CContinuousTimeMonteCarloMover, CSimulatedAnnealingStrategy, CPeriodicQuenchMinimizer, CEvolutionStrategy
- m_pRxnMover
: CRunnable
- m_pRxnNetwork
: CRunnable
- m_pRxnTauReaction
: CTauNetwork
- m_pSystem0
: CAcceptanceRatioFreeEnergyEstimator
- m_pSystem1
: CAcceptanceRatioFreeEnergyEstimator
- m_pTauNetwork
: CMixedReactionMover
- m_pTranslator
: CAcceptanceRatioFreeEnergyEstimator
- m_scdA
: CQualityControlCashKarpMover
- m_scdAlpha
: CRK2ExplicitEulerHybridMover
- m_scdB
: CQualityControlCashKarpMover
- m_scdC
: CQualityControlCashKarpMover
- m_scdCStar
: CQualityControlCashKarpMover
- m_scdERRCON
: CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_scdFCOR
: CQualityControlRungeKuttaMover, CQualityControlRK2TMover
- m_scdPGROW
: CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_scdPSHRINK
: CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_scdREDMAX
: CStiffBulirschStoerMover
- m_scdREDMIN
: CStiffBulirschStoerMover
- m_scdSAFE1
: CStiffBulirschStoerMover
- m_scdSAFE2
: CStiffBulirschStoerMover
- m_scdSAFETY
: CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_scdSCALMX
: CStiffBulirschStoerMover
- m_scdTINY
: CStiffBulirschStoerMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- m_sciIMAXX
: CStiffBulirschStoerMover
- m_sciKMAXX
: CStiffBulirschStoerMover
- m_sRunnableName
: CRunnable
- m_sTeXForm
: Reaction
- m_sTeXName
: RateConstant, Chemical
- m_sUnits
: ChemicalTimeSeriesData
- m_vdHistogram0
: CAcceptanceRatioFreeEnergyEstimator
- m_vdHistogram1
: CAcceptanceRatioFreeEnergyEstimator
- m_vdSteps
: CSynchronizedRungeKuttaMover, CSynchronizedCashKarpMover
- m_viChemNumbers
: GnuPlotterRunnableObserver
- m_viIntersectOne
: CSharedParametersMinimizableDirector, CReplicaMinimizableDirector, CCoupledReplicasMinimizableDirector
- m_viIntersectTwo
: CSharedParametersMinimizableDirector, CReplicaMinimizableDirector, CCoupledReplicasMinimizableDirector
- m_viParents
: CEvolutionStrategy
- m_viStochasticList
: CMixedReactionNetwork
- m_viWhichChemicals
: GnuPlotterEnsembleRunDirectorObserver
- m_vpCellObservers
: CDirector
- m_vpChemRefVector
: CAlgebraicChemical
- m_vpdDataSumC
: CEnsembleCombinationDirector
- m_vpdDataSumCSqr
: CEnsembleCombinationDirector
- m_vpdEnsemble0
: CAcceptanceRatioFreeEnergyEstimator
- m_vpdEnsemble1
: CAcceptanceRatioFreeEnergyEstimator
- m_vpdEnsembleParameters
: CEnsembleRunDirector, CEnsembleCombinationDirector
- m_vpDeterministicReactions
: CMixedReactionNetwork
- m_vpdNoDataSumC
: CEnsembleCombinationDirector
- m_vpdNoDataSumCSqr
: CEnsembleCombinationDirector
- m_vpdSimplex
: CNelderMeadSimplexMinimizer
- m_vpdSumC
: CEnsembleRunDirector
- m_vpdSumCSqr
: CEnsembleRunDirector
- m_vpEnsemble
: CStochasticSensitivityAnalysis
- m_vpEnsembleDataPlotters
: CEnsembleCombinationDirector
- m_vpEnsemblePlotters
: CEnsembleRunDirector
- m_vpEnsembleRunPlotters
: CEnsembleCombinationDirector
- m_vpExperiments
: CEnsembleCombinationDirector
- m_vpForcingVector
: CForcingData
- m_vpGnuPlotters
: CRunDirector
- m_vpMinimizables
: CEnsembleCombinationDirector
- m_vpMovers
: CEnsembleCombinationDirector
- m_vpNetworks
: CEnsembleCombinationDirector
- m_vpOffspring
: CEvolutionStrategy
- m_vpPlotterList
: COneGeneStochasticNetworkMinimizableDirector, COneGeneReplicaMinimizableDirector, COneGeneInhibitoryNetworkMinimizableDirector, CAlternateOneGeneInhibitoryNetworkMinimizableDirector
- m_vpPopulation
: CEvolutionStrategy
- m_vpRateRefVector
: CAlgebraicChemical
- m_vpRelationList
: CSloppyDataMinimizableDirector
- m_vpRunnables
: CRunDirector
- m_vpRxnMovers
: CDirector
- m_vpRxnNetworks
: CDirector
- m_vpStochasticReactions
: CMixedReactionNetwork
- m_vpXYVector
: CXYVector
- Map()
: CLowDimensionalCostFunctionMapper
- matrix
: RowColumnSparseMatrix
- MatrixElement()
: RowColumnSparseMatrix::MatrixElement
- MatrixElementComparator()
: RowColumnSparseMatrix::MatrixElement::MatrixElementComparator
- MAX_RNA_LENGTH
: TranslationModelMinimizable
- MAX_RNA_MOLS
: TranslationModelMinimizable
- MAX_STRING_LENGTH
: TranslationModelMinimizable
- MichaelisMentenDephosphorylationReaction()
: MichaelisMentenDephosphorylationReaction
- MichaelisMentenGProteinActivationReaction()
: MichaelisMentenGProteinActivationReaction
- MichaelisMentenGProteinDeactivationReaction()
: MichaelisMentenGProteinDeactivationReaction
- MichaelisMentenPhosphorylationReaction()
: MichaelisMentenPhosphorylationReaction
- MichaelisMentenProteinProteinActivationReaction()
: MichaelisMentenProteinProteinActivationReaction
- MichaelisMentenProteinProteinDeactivationReaction()
: MichaelisMentenProteinProteinDeactivationReaction
- MichaelisMentenReaction()
: MichaelisMentenReaction
- MichaelisMentenTransformationReaction()
: MichaelisMentenTransformationReaction
- MidBound
: CDNA
- Minimize()
: ZeroTAnnealMinimizer, CSimulatedAnnealingStrategy, CScaleInvariantMarquardtMinimizer, CRobustLevenbergMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CPeriodicQuenchMinimizer, CNelderMeadSimplexMinimizer, Minimizer, CImprovedLevenbergMarquardtMinimizer, CEvolutionStrategy, CConjugateGradientMinimizer
- Minimizer()
: Minimizer
- monitorChem
: GnuPlotterDirectorObserver
- Monomer
: HomodimerizationReaction, HomodimerDissociationReaction
- Move()
: CSynchronizedRungeKuttaMover, CSynchronizedCashKarpMover, CStiffBulirschStoerMover, CRungeKuttaMover, CRK4Mover, CRK2ExplicitEulerHybridMover, CReactionMover, CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover, CMixedReactionMover, CDifferentialEquationMover, CContinuousTimeMonteCarloMover
- MoveTimeIsZero()
: CReactionMover
- mRNA
: TranscriptionReaction, CatalyzedTranslationReaction
- Mutation()
: CEvolutionStrategy, CCommaStrategyOne, CClonalCommaES
- n -
- o -
- ObjectiveFunction()
: CSloppyDataMinimizableDirector, NLLSMinimizable, NetworkMinimizableDirector, Minimizable
- Observer()
: Observer
- ObtainTrialParameters()
: CLevenbergMarquardtMinimizer
- OddGD()
: CDNA
- OldForm
: TransformationReaction
- OldInit()
: CDNA
- OldPoolForm
: CPoolTransitionReaction
- OneGeneInhibitoryNetwork()
: OneGeneInhibitoryNetwork
- OneToZero()
: CPC12ParameterTranslator, CParameterTranslator
- Operator()
: CSquareRootParameterFilter, CParameterFilter, CLogParameterFilter, CIdentityParameterFilter
- operator()()
: CXYPoint::CYComparator, CXYPoint::CXComparator, TimeVectorPoint::TimeVectorPointComparator, RowColumnSparseMatrix::MatrixElement::MatrixElementComparator, CEvolutionStrategyChromosome::CEvolutionStrategyChromosomeComparator, CForceVectorPoint::CForceVectorPointComparator, DataPoint::DataPointComparator
- operator=()
: CComponents, CCell
- OperatorInverse()
: CSquareRootParameterFilter, CParameterFilter, CLogParameterFilter, CIdentityParameterFilter
- OrderElements()
: SparseMatrix, RowColumnSparseMatrix
- otherChem
: GnuPlotterTrajectoryObserver
- output
: Rand
- OutputChemical
: CNormalizedLinearAttenuator, CNormalizedLinearAmplifier
- outputReady
: Rand
- p -
- q -
- r -
- Rand()
: Rand
- Randomize()
: CParameterRandomizer
- ranmarin()
: Rand
- RateConstant()
: RateConstant
- rateConstantNumber
: RateConstant
- RateConstantReset()
: ReactionNetwork, CMixedReactionNetwork
- rateConstants
: ReactionNetwork, Reaction
- rateConstantsOptimizable
: SingleNetworkMinimizable, NetworkMinimizable
- rateConstantsWeight
: SingleNetworkMinimizable, NetworkMinimizable
- ReactantA
: HeterodimerizationReaction, HeterodimerDissociationReaction
- ReactantB
: HeterodimerizationReaction, HeterodimerDissociationReaction
- Reaction()
: Reaction
- reactionMover
: SingleNetworkMinimizable
- reactionMovers
: SharedBFactorNetworkMinimizable
- reactionName
: Reaction
- ReactionNetwork()
: ReactionNetwork
- reactionRates
: ReactionNetwork
- reactions
: ReactionNetwork, Chemical
- read_seq()
: GeneticCode
- ReadData()
: Experiment
- ReadForcingData()
: Experiment
- ReadHessian()
: CStochasticSensitivityAnalysis
- ReadParameter()
: ParameterReader
- ReceptorBindingReaction()
: ReceptorBindingReaction
- ReceptorUnbindingReaction()
: ReceptorUnbindingReaction
- Recombination()
: CEvolutionStrategy, CCommaStrategyOne, CClonalCommaES
- RemoveReaction()
: ReactionNetwork
- RescaleDatum()
: DataPoint
- RescaleDiagonal()
: CLevenbergMarquardtMinimizer
- RescaleError()
: DataPoint
- RescaleTime()
: DataPoint
- RescaleVector()
: CMatrixOperations
- Reset()
: RateConstant, ParameterReader, Chemical, CAlgebraicChemical
- ResetStepSize()
: CQualityControlRungeKuttaMover, CDifferentialEquationMover
- ResetStepStatistics()
: CReactionMover
- ResetY()
: CComponents
- residuals
: NLLSMinimizable
- RestoreDiagonal()
: CLevenbergMarquardtMinimizer
- rib_size
: TranslationModelMinimizable
- RightVectorMultiply()
: SparseMatrix, RowColumnSparseMatrix
- RNADegradationReaction()
: RNADegradationReaction
- RNAseq
: TranslationModelMinimizable
- row
: RowColumnSparseMatrix::MatrixElement
- RowColumnSparseMatrix()
: RowColumnSparseMatrix
- Run()
: CCell, CRunnable
- RungeKuttaStep()
: CRungeKuttaMover, CRK2TMover
- s -
- S
: CGeometry
- SampleGaussian()
: CStochasticSensitivityAnalysis
- SampleWithoutExplicitHessian()
: CStochasticSensitivityAnalysis
- SaveDiagonal()
: CLeastSquaresMinimizer, CLeastSquaresADMinimizer
- seed
: Rand, ZeroTAnnealMinimizer
- Select()
: CEvolutionStrategy, CCommaStrategyOne, CClonalCommaES
- SelectParents()
: CEvolutionStrategy, CCommaStrategyOne, CClonalCommaES
- SemiImplicitMidpoint()
: CStiffBulirschStoerMover
- SendPlotCommand()
: GnuPlotter
- SEPF
: CGeometry
- SetAll()
: CAlgebraicChemical
- SetAmount()
: ReactionNetwork, CMixedReactionNetwork, Chemical, CAlgebraicChemical
- SetBounds()
: CPositiveDefiniteLevenbergMarquardtMinimizer
- SetChemNumber()
: TimeVectorPoint, CForceVectorPoint
- SetComponents()
: CRunnable
- SetDatum()
: DataPoint
- SetError()
: DataPoint
- SetErrorInInitialAmount()
: Chemical, CAlgebraicChemical
- SetErrorInInitialValue()
: RateConstant
- SetFactorFixed()
: CConversionFactor
- SetFactorNeeded()
: CConversionFactor
- SetFactorValue()
: CConversionFactor
- SetInitialAmount()
: Chemical, CAlgebraicChemical
- SetInitialChemConcWeight()
: SingleNetworkMinimizable, NetworkMinimizable
- SetIntersectionLists()
: CSharedParametersMinimizableDirector, CReplicaMinimizableDirector, CCoupledReplicasMinimizableDirector
- SetJValue()
: Reaction::JElement
- SetMaxStepSize()
: CReactionMover
- SetMinStepSize()
: CReactionMover
- SetNResiduals()
: NLLSMinimizable
- SetObjectParameters()
: CEvolutionStrategyChromosome
- SetObjFuncValue()
: CEvolutionStrategyChromosome
- SetPlotAttributes()
: GnuPlotterSingleRun
- SetRateConstant()
: RateConstant
- SetRateConstantsWeight()
: SingleNetworkMinimizable, NetworkMinimizable
- SetRunnableName()
: CRunnable
- SetStepScale()
: CRK2ExplicitEulerHybridMover
- SetStepSize()
: CQualityControlRungeKuttaMover, CDifferentialEquationMover
- SetStrategyParameters()
: CEvolutionStrategyChromosome
- SetTeXForm()
: UnaryDegradationReaction, TransformationReaction, TranscriptionReaction, CTauReaction, MichaelisMentenReaction, HomodimerizationReaction, HomodimerDissociationReaction, HeterodimerizationReaction, HeterodimerDissociationReaction, GenerationReaction, CFirstOrderDestructionReaction, CompetitiveDegradationReaction, PlasmidReplicationReaction, CMichaelisMentenHeterodimerizationReaction, CatalyzedTranslationReaction, Reaction, CNormalizedLinearAttenuator, CNormalizedLinearAmplifier, CConstantSourceReaction, CConstantSinkReaction, CChemicalSource, CChemicalSink, CPoolTransitionReaction, CTrimerFormation, CTrimerDissociation
- SetTeXName()
: RateConstant, Chemical
- SetTime()
: TimeVectorPoint, CForceVectorPoint, DataPoint
- SetTimeSeriesWeight()
: SingleNetworkMinimizable, NetworkMinimizable
- SetTitle()
: GnuPlotter
- SetValue()
: CForceVectorPoint
- SetVectorIndex()
: TimeVectorPoint
- SetWithRespectTo()
: Reaction::JElement
- SetX()
: CXYPoint
- SetXYPair()
: CXYVector
- SetY()
: CXYPoint
- SgnProduct()
: CConjugateGradientMinimizer
- SharedBFactorNetworkMinimizable()
: SharedBFactorNetworkMinimizable
- SingleNetworkMinimizable()
: SingleNetworkMinimizable
- SinkChemical
: CChemicalSink
- SL
: CGeometry
- SmallErkSubnetwork()
: SmallErkSubnetwork
- SortChemTimeSeriesData()
: ChemicalTimeSeriesData
- SortForcingVector()
: CForcingData
- SortOnX()
: CXYVector
- SortOnY()
: CXYVector
- SortTimeVector()
: ChemicalTimeSeriesData
- SourceChemical
: CChemicalSource
- SparseMatrix()
: SparseMatrix
- StartAverages()
: CComponents
- Stepper()
: CQualityControlRungeKuttaMover, CQualityControlRK2TMover, CQualityControlCashKarpMover
- StiffBSStep()
: CStiffBulirschStoerMover
- Subject()
: Subject
- Substrate
: MichaelisMentenReaction, CFirstOrderDestructionReaction, CMichaelisMentenHeterodimerizationReaction
- SumAllocate()
: CEnsembleRunDirector, CEnsembleCombinationDirector
- summedConcentration
: ConcentrationObserver
- SumOfSquares()
: NLLSMinimizable
- SVDSolveMarquardtSystem()
: CScaleInvariantMarquardtMinimizer, CPositiveDefiniteLevenbergMarquardtMinimizer, CImprovedLevenbergMarquardtMinimizer
- t -
- u -
- u
: Rand
- UnaryDegradationReaction()
: UnaryDegradationReaction
- uniform()
: Rand
- UnstableChemical
: UnaryDegradationReaction
- UnstableProteinDegradationReaction()
: UnstableProteinDegradationReaction
- Update()
: Observer, CLeastSquaresObserver, GnuPlotterTrajectoryObserver, GnuPlotterTimeSeriesSharedBFactorObserver, GnuPlotterTimeSeriesObserver, GnuPlotterSingleRun, GnuPlotterSimulatedAnnealingObserver, GnuPlotterRunnableObserver, GnuPlotterResidualScatterPlot, GnuPlotterParameterScatterPlot, GnuPlotterEnsembleRunDirectorObserver, GnuPlotterEnsembleDataDirectorObserver, GnuPlotterDirectorObserver, GnuPlotterCostObserver, GnuPlotter, CForcesObserver, CConjugateGradientObserver, ConcentrationObserver, CellAverageObserver
- update_dens()
: TranslationModelMinimizable
- UpdateShape()
: CGeometry
- v -
- w -
- y -
- z -
- ~ -
Generated on Mon Nov 3 10:00:45 2003 by
1.2.14 written by Dimitri van Heesch,
© 1997-2002