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ReactionNetwork Class Reference

#include <ReactionNetwork.h>

Inheritance diagram for ReactionNetwork:

[legend]List of all members.

Public Methods
	ReactionNetwork ()
virtual	~ReactionNetwork ()
virtual Chemical *	GetChemical (int chemicalNumber)
virtual RateConstant *	GetRateConstant (int rateConstantNumber)
virtual Reaction *	GetReaction (int reactionNumber)
virtual int	GetNumberOfRateConstants () const
virtual int	GetNumberOfReactions () const
virtual int	GetNumberOfChemicals () const
virtual int	GetNumberOfAlgebraicChemicals () const
virtual void	SetAmount (int chemicalNumber, double amount)
virtual void	AddAlgebraicIndex (Chemical *chemical)
virtual void	ChemicalReset ()
virtual void	RateConstantReset ()
virtual std::vector< int > *	GetAlgebraicIndices ()
virtual std::vector< Reaction * > *	GetReactions ()
virtual std::vector< Chemical * > *	GetChemicals ()
virtual std::vector< RateConstant * > *	GetRateConstants ()
virtual std::vector< double > *	GetReactionRates ()
virtual void	RemoveReaction (int rxnNumber)
virtual void	DumpTeXForm (std::string fileName)
virtual void	DumpPetriNetDotFile (std::string fileName)
virtual int	GetNTermsPerLine ()
virtual bool	GetLRGraph ()
Protected Attributes
std::vector< Chemical * >	chemicals
std::vector< Reaction * >	reactions
std::vector< RateConstant * >	rateConstants
std::vector< double >	reactionRates
std::vector< int >	algebraicIndices

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Constructor & Destructor Documentation

ReactionNetwork::ReactionNetwork (    )

Definition at line 16 of file ReactionNetwork.cpp. References algebraicIndices.

ReactionNetwork::~ReactionNetwork (    )  [virtual]

Definition at line 23 of file ReactionNetwork.cpp. References algebraicIndices, chemicals, rateConstants, and reactions.

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Member Function Documentation

void ReactionNetwork::AddAlgebraicIndex (  Chemical *    chemical )  [virtual]

Definition at line 136 of file ReactionNetwork.cpp. References algebraicIndices, and Chemical::GetChemicalNumber. Referenced by CEGFRTraffickingNetwork::CEGFRTraffickingNetwork, CEGFRTraffickingPredictionNetwork::CEGFRTraffickingPredictionNetwork, and CQuorumSensingNetwork::CQuorumSensingNetwork.

void ReactionNetwork::ChemicalReset (    )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 55 of file ReactionNetwork.cpp. References GetChemical, GetNumberOfChemicals, and Chemical::Reset. Referenced by SingleNetworkMinimizable::ComputeResiduals, and CRunnable::Run.

void ReactionNetwork::DumpPetriNetDotFile (  std::string    fileName )  [virtual]

Definition at line 276 of file ReactionNetwork.cpp. References chemicals, GetLRGraph, and reactions.

void ReactionNetwork::DumpTeXForm (  std::string    fileName )  [virtual]

Definition at line 150 of file ReactionNetwork.cpp. References algebraicIndices, chemicals, GetNTermsPerLine, and reactions.

std::vector< int > * ReactionNetwork::GetAlgebraicIndices (    )  [virtual]

Definition at line 86 of file ReactionNetwork.cpp. References algebraicIndices.

Chemical * ReactionNetwork::GetChemical (  int    chemicalNumber )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 71 of file ReactionNetwork.cpp. References chemicals. Referenced by CForcingData::AttachNewForcingData, ChemicalTimeSeriesData::AttachNewTimeSeries, ChemicalReset, CMixedReactionNetwork::ChemicalReset, ChemicalTimeSeriesData::ChemicalTimeSeriesData, SingleNetworkMinimizable::ComputeResiduals, CMixedReactionNetwork::GetChemical, SingleNetworkMinimizable::Initialize, CSynchronizedRungeKuttaMover::Move, CSynchronizedCashKarpMover::Move, CStiffBulirschStoerMover::Move, CRungeKuttaMover::Move, CRK4Mover::Move, CRK2ExplicitEulerHybridMover::Move, CQualityControlRungeKuttaMover::Move, CQualityControlRK2TMover::Move, CQualityControlCashKarpMover::Move, CMixedReactionMover::Move, SetAmount, CMixedReactionNetwork::SetAmount, GnuPlotterTrajectoryObserver::Update, GnuPlotterTimeSeriesSharedBFactorObserver::Update, GnuPlotterTimeSeriesObserver::Update, GnuPlotterRunnableObserver::Update, GnuPlotterEnsembleRunDirectorObserver::Update, GnuPlotterEnsembleDataDirectorObserver::Update, ConcentrationObserver::Update, and CellAverageObserver::Update.

std::vector< Chemical * > * ReactionNetwork::GetChemicals (    )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 96 of file ReactionNetwork.cpp. References chemicals. Referenced by CDifferentialEquationMover::ComputeDerivatives, CDifferentialEquationMover::ComputeJacobian, and CMixedReactionNetwork::GetChemicals.

virtual bool ReactionNetwork::GetLRGraph (    )  [inline, virtual]

Reimplemented in OneGeneInhibitoryNetwork. Definition at line 59 of file ReactionNetwork.h. Referenced by DumpPetriNetDotFile.

virtual int ReactionNetwork::GetNTermsPerLine (    )  [inline, virtual]

Reimplemented in CLaubLoomisDictyNetwork. Definition at line 58 of file ReactionNetwork.h. Referenced by DumpTeXForm.

int ReactionNetwork::GetNumberOfAlgebraicChemicals (    )  const [virtual]

Definition at line 40 of file ReactionNetwork.cpp. References algebraicIndices.

int ReactionNetwork::GetNumberOfChemicals (    )  const [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 35 of file ReactionNetwork.cpp. References chemicals. Referenced by CForcingData::AttachNewForcingData, ChemicalTimeSeriesData::AttachNewTimeSeries, ChemicalReset, ChemicalTimeSeriesData::ChemicalTimeSeriesData, CDifferentialEquationMover::ComputeDerivatives, CDifferentialEquationMover::ComputeJacobian, SingleNetworkMinimizable::ComputeResiduals, SingleNetworkMinimizable::GetNParameters, CMixedReactionNetwork::GetNumberOfChemicals, SingleNetworkMinimizable::Initialize, CSynchronizedRungeKuttaMover::Move, CSynchronizedCashKarpMover::Move, CStiffBulirschStoerMover::Move, CRungeKuttaMover::Move, CRK4Mover::Move, CRK2ExplicitEulerHybridMover::Move, CQualityControlRungeKuttaMover::Move, CQualityControlRK2TMover::Move, CQualityControlCashKarpMover::Move, ConcentrationObserver::Update, and CellAverageObserver::Update.

int ReactionNetwork::GetNumberOfRateConstants (    )  const [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 50 of file ReactionNetwork.cpp. References rateConstants. Referenced by SingleNetworkMinimizable::ComputeResiduals, SingleNetworkMinimizable::GetNParameters, CMixedReactionNetwork::GetNumberOfRateConstants, SingleNetworkMinimizable::Initialize, RateConstantReset, CSharedParametersMinimizableDirector::SetIntersectionLists, and CCoupledReplicasMinimizableDirector::SetIntersectionLists.

int ReactionNetwork::GetNumberOfReactions (    )  const [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 45 of file ReactionNetwork.cpp. References reactions. Referenced by CContinuousTimeMonteCarloMover::ChooseMove, CMixedReactionNetwork::CMixedReactionNetwork, CDifferentialEquationMover::ComputeDerivatives, CDifferentialEquationMover::ComputeJacobian, CMixedReactionNetwork::GetNumberOfReactions, GetReactionRates, and CMixedReactionNetwork::GetReactionRates.

RateConstant * ReactionNetwork::GetRateConstant (  int    rateConstantNumber )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 76 of file ReactionNetwork.cpp. References rateConstants. Referenced by SingleNetworkMinimizable::ComputeResiduals, CMixedReactionNetwork::GetRateConstant, SingleNetworkMinimizable::Initialize, RateConstantReset, CMixedReactionNetwork::RateConstantReset, CSharedParametersMinimizableDirector::SetIntersectionLists, and CCoupledReplicasMinimizableDirector::SetIntersectionLists.

std::vector< RateConstant * > * ReactionNetwork::GetRateConstants (    )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 101 of file ReactionNetwork.cpp. References rateConstants. Referenced by CMixedReactionNetwork::GetRateConstants.

Reaction * ReactionNetwork::GetReaction (  int    reactionNumber )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 81 of file ReactionNetwork.cpp. References reactions. Referenced by CContinuousTimeMonteCarloMover::DoMove, CMixedReactionNetwork::GetReaction, and CMixedReactionNetwork::GetReactionRates.

std::vector< double > * ReactionNetwork::GetReactionRates (    )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 106 of file ReactionNetwork.cpp. References GetNumberOfReactions, reactionRates, and reactions. Referenced by CContinuousTimeMonteCarloMover::ChooseMove, and CDifferentialEquationMover::ComputeDerivatives.

std::vector< Reaction * > * ReactionNetwork::GetReactions (    )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 91 of file ReactionNetwork.cpp. References reactions. Referenced by CMixedReactionNetwork::CMixedReactionNetwork, CDifferentialEquationMover::ComputeDerivatives, CDifferentialEquationMover::ComputeJacobian, and CMixedReactionNetwork::GetReactions.

void ReactionNetwork::RateConstantReset (    )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 63 of file ReactionNetwork.cpp. References GetNumberOfRateConstants, GetRateConstant, and RateConstant::Reset. Referenced by SingleNetworkMinimizable::ComputeResiduals.

void ReactionNetwork::RemoveReaction (  int    rxnNumber )  [virtual]

Definition at line 142 of file ReactionNetwork.cpp. References reactions.

void ReactionNetwork::SetAmount (  int    chemicalNumber, double    amount )  [virtual]

Reimplemented in CMixedReactionNetwork. Definition at line 131 of file ReactionNetwork.cpp. References GetChemical, and Chemical::SetAmount.

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Member Data Documentation

std::vector<int> ReactionNetwork::algebraicIndices [protected]

Definition at line 65 of file ReactionNetwork.h. Referenced by AddAlgebraicIndex, DumpTeXForm, GetAlgebraicIndices, GetNumberOfAlgebraicChemicals, ReactionNetwork, and ~ReactionNetwork.

std::vector<Chemical*> ReactionNetwork::chemicals [protected]

Definition at line 61 of file ReactionNetwork.h. Referenced by CAlternateErkSubnetwork::CAlternateErkSubnetwork, CAlternateOneGeneInhibitoryNetwork::CAlternateOneGeneInhibitoryNetwork, CCombinatorialNetwork::CCombinatorialNetwork, CEGFRTraffickingNetwork::CEGFRTraffickingNetwork, CEGFRTraffickingPredictionNetwork::CEGFRTraffickingPredictionNetwork, CExampleNetwork::CExampleNetwork, CForestNitrogenCycleNetwork::CForestNitrogenCycleNetwork, CLaubLoomisDictyNetwork::CLaubLoomisDictyNetwork, CMartielGoldbeterDictyNetwork::CMartielGoldbeterDictyNetwork, CPC12RapMinusNetwork::CPC12RapMinusNetwork, CQuorumSensingNetwork::CQuorumSensingNetwork, DumpPetriNetDotFile, DumpTeXForm, ErkSubnetwork::ErkSubnetwork, GetChemical, CTauNetwork::GetChemicals, GetChemicals, GetNumberOfChemicals, OneGeneInhibitoryNetwork::OneGeneInhibitoryNetwork, SmallErkSubnetwork::SmallErkSubnetwork, and ~ReactionNetwork.

std::vector<RateConstant*> ReactionNetwork::rateConstants [protected]

Definition at line 63 of file ReactionNetwork.h. Referenced by CAlternateErkSubnetwork::CAlternateErkSubnetwork, CAlternateOneGeneInhibitoryNetwork::CAlternateOneGeneInhibitoryNetwork, CCombinatorialNetwork::CCombinatorialNetwork, CEGFRTraffickingNetwork::CEGFRTraffickingNetwork, CEGFRTraffickingPredictionNetwork::CEGFRTraffickingPredictionNetwork, CExampleNetwork::CExampleNetwork, CForestNitrogenCycleNetwork::CForestNitrogenCycleNetwork, CLaubLoomisDictyNetwork::CLaubLoomisDictyNetwork, CMartielGoldbeterDictyNetwork::CMartielGoldbeterDictyNetwork, CPC12RapMinusNetwork::CPC12RapMinusNetwork, CQuorumSensingNetwork::CQuorumSensingNetwork, ErkSubnetwork::ErkSubnetwork, GetNumberOfRateConstants, GetRateConstant, GetRateConstants, OneGeneInhibitoryNetwork::OneGeneInhibitoryNetwork, SmallErkSubnetwork::SmallErkSubnetwork, and ~ReactionNetwork.

std::vector<double> ReactionNetwork::reactionRates [protected]

Definition at line 64 of file ReactionNetwork.h. Referenced by CTauNetwork::GetReactionRates, GetReactionRates, and CMixedReactionNetwork::GetReactionRates.

std::vector<Reaction*> ReactionNetwork::reactions [protected]

Definition at line 62 of file ReactionNetwork.h. Referenced by CAlternateErkSubnetwork::CAlternateErkSubnetwork, CAlternateOneGeneInhibitoryNetwork::CAlternateOneGeneInhibitoryNetwork, CCombinatorialNetwork::CCombinatorialNetwork, CEGFRTraffickingNetwork::CEGFRTraffickingNetwork, CEGFRTraffickingPredictionNetwork::CEGFRTraffickingPredictionNetwork, CExampleNetwork::CExampleNetwork, CForestNitrogenCycleNetwork::CForestNitrogenCycleNetwork, CLaubLoomisDictyNetwork::CLaubLoomisDictyNetwork, CMartielGoldbeterDictyNetwork::CMartielGoldbeterDictyNetwork, CPC12RapMinusNetwork::CPC12RapMinusNetwork, CQuorumSensingNetwork::CQuorumSensingNetwork, DumpPetriNetDotFile, DumpTeXForm, ErkSubnetwork::ErkSubnetwork, GetNumberOfReactions, GetReaction, GetReactionRates, CTauNetwork::GetReactions, GetReactions, OneGeneInhibitoryNetwork::OneGeneInhibitoryNetwork, RemoveReaction, SmallErkSubnetwork::SmallErkSubnetwork, and ~ReactionNetwork.

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The documentation for this class was generated from the following files:

• ReactionNetwork.h
• ReactionNetwork.cpp

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