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Chemical Class Reference

#include <Chemical.h>

Inheritance diagram for Chemical:

[legend]List of all members.

Public Methods
std::string	GetName () const
std::string	GetTeXName () const
	Chemical ()
	Chemical (int chemicalNumber, double amount=0, std::string name="")
	Chemical (int chemicalNumber, double amount, double errorInInitialAmount, std::string name)
virtual	~Chemical ()
double	GetAmount () const
double	GetInitialAmount () const
double	GetErrorInInitialAmount () const
virtual void	SetErrorInInitialAmount (double errorInInitialAmount)
virtual void	SetAmount (double amount)
virtual void	SetInitialAmount (double initialAmount)
virtual void	IncrementAmount (double change)
virtual void	Reset ()
const std::vector< Reaction * > *	GetReactions () const
int	GetChemicalNumber ()
void	SetTeXName ()
Protected Attributes
int	chemicalNumber
std::vector< Reaction * >	reactions
double	amount
double	initialAmount
double	errorInInitialAmount
std::string	name
std::string	m_sTeXName

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Constructor & Destructor Documentation

Chemical::Chemical (    )

Definition at line 43 of file Chemical.cpp.

Chemical::Chemical (  int    chemicalNumber, double    amount = 0, std::string    name = "" )

Definition at line 16 of file Chemical.cpp. References amount, chemicalNumber, errorInInitialAmount, initialAmount, name, SetAmount, and SetTeXName.

Chemical::Chemical (  int    chemicalNumber, double    amount, double    errorInInitialAmount, std::string    name )

Definition at line 33 of file Chemical.cpp. References amount, chemicalNumber, errorInInitialAmount, initialAmount, name, SetAmount, and SetTeXName.

Chemical::~Chemical (    )  [virtual]

Definition at line 48 of file Chemical.cpp.

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Member Function Documentation

double Chemical::GetAmount (    )  const

Definition at line 53 of file Chemical.cpp. References amount. Referenced by CTauNetwork::GetTOfTau, CSynchronizedRungeKuttaMover::Move, CSynchronizedCashKarpMover::Move, CStiffBulirschStoerMover::Move, CRungeKuttaMover::Move, CRK4Mover::Move, CRK2ExplicitEulerHybridMover::Move, CQualityControlRungeKuttaMover::Move, CQualityControlRK2TMover::Move, CQualityControlCashKarpMover::Move, CMixedReactionMover::Move, ConcentrationObserver::Update, and CellAverageObserver::Update.

int Chemical::GetChemicalNumber (    )

Definition at line 103 of file Chemical.cpp. References chemicalNumber. Referenced by ReactionNetwork::AddAlgebraicIndex, and CTauNetwork::GetChemical.

double Chemical::GetErrorInInitialAmount (    )  const

Definition at line 63 of file Chemical.cpp. References errorInInitialAmount. Referenced by SingleNetworkMinimizable::ComputeResiduals.

double Chemical::GetInitialAmount (    )  const

Definition at line 58 of file Chemical.cpp. References initialAmount. Referenced by SingleNetworkMinimizable::Initialize.

std::string Chemical::GetName (    )  const

Definition at line 98 of file Chemical.cpp. References name. Referenced by CForcingData::AttachNewForcingData, ChemicalTimeSeriesData::AttachNewTimeSeries, ChemicalTimeSeriesData::ChemicalTimeSeriesData, GnuPlotterTrajectoryObserver::Update, GnuPlotterTimeSeriesSharedBFactorObserver::Update, GnuPlotterTimeSeriesObserver::Update, GnuPlotterRunnableObserver::Update, GnuPlotterEnsembleRunDirectorObserver::Update, and GnuPlotterEnsembleDataDirectorObserver::Update.

const std::vector< Reaction * > * Chemical::GetReactions (    )  const

Definition at line 78 of file Chemical.cpp. References reactions.

std::string Chemical::GetTeXName (    )  const [inline]

Definition at line 30 of file Chemical.h. References m_sTeXName.

void Chemical::IncrementAmount (  double    change )  [virtual]

Reimplemented in CAlgebraicChemical. Definition at line 83 of file Chemical.cpp. References amount.

void Chemical::Reset (    )  [virtual]

Reimplemented in CAlgebraicChemical. Definition at line 93 of file Chemical.cpp. References initialAmount, and SetAmount. Referenced by ReactionNetwork::ChemicalReset, and CMixedReactionNetwork::ChemicalReset.

void Chemical::SetAmount (  double    amount )  [virtual]

Reimplemented in CAlgebraicChemical. Definition at line 88 of file Chemical.cpp. References amount. Referenced by Chemical, CDifferentialEquationMover::ComputeDerivatives, CDifferentialEquationMover::ComputeJacobian, SingleNetworkMinimizable::ComputeResiduals, CSynchronizedRungeKuttaMover::Move, CSynchronizedCashKarpMover::Move, CStiffBulirschStoerMover::Move, CRungeKuttaMover::Move, CRK4Mover::Move, CRK2ExplicitEulerHybridMover::Move, CQualityControlRungeKuttaMover::Move, CQualityControlRK2TMover::Move, CQualityControlCashKarpMover::Move, CMixedReactionMover::Move, Reset, ReactionNetwork::SetAmount, and CMixedReactionNetwork::SetAmount.

void Chemical::SetErrorInInitialAmount (  double    errorInInitialAmount )  [virtual]

Reimplemented in CAlgebraicChemical. Definition at line 73 of file Chemical.cpp. References errorInInitialAmount.

void Chemical::SetInitialAmount (  double    initialAmount )  [virtual]

Reimplemented in CAlgebraicChemical. Definition at line 68 of file Chemical.cpp. References initialAmount.

void Chemical::SetTeXName (    )

Definition at line 108 of file Chemical.cpp. References m_sTeXName, and name. Referenced by CAlgebraicChemical::CAlgebraicChemical, and Chemical.

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Member Data Documentation

double Chemical::amount [protected]

Definition at line 49 of file Chemical.h. Referenced by Chemical, CSumChemical::ComputeAmount, CMDOChemical::ComputeAmount, CLogChemical::ComputeAmount, CCurrentToInitialRatioChemical::ComputeAmount, CCurrentToCurrentRatioChemical::ComputeAmount, GetAmount, IncrementAmount, CAlgebraicChemical::Reset, and SetAmount.

int Chemical::chemicalNumber [protected]

Definition at line 47 of file Chemical.h. Referenced by CAlgebraicChemical::CAlgebraicChemical, Chemical, and GetChemicalNumber.

double Chemical::errorInInitialAmount [protected]

Definition at line 51 of file Chemical.h. Referenced by Chemical, CSumChemical::ComputeErrorInInitialAmount, CMDOChemical::ComputeErrorInInitialAmount, CLogChemical::ComputeErrorInInitialAmount, CCurrentToInitialRatioChemical::ComputeErrorInInitialAmount, CCurrentToCurrentRatioChemical::ComputeErrorInInitialAmount, GetErrorInInitialAmount, and SetErrorInInitialAmount.

double Chemical::initialAmount [protected]

Definition at line 50 of file Chemical.h. Referenced by Chemical, CSumChemical::ComputeInitialAmount, CMDOChemical::ComputeInitialAmount, CLogChemical::ComputeInitialAmount, CCurrentToInitialRatioChemical::ComputeInitialAmount, CCurrentToCurrentRatioChemical::ComputeInitialAmount, GetInitialAmount, Reset, CAlgebraicChemical::Reset, and SetInitialAmount.

std::string Chemical::m_sTeXName [protected]

Definition at line 53 of file Chemical.h. Referenced by GetTeXName, and SetTeXName.

std::string Chemical::name [protected]

Definition at line 52 of file Chemical.h. Referenced by CAlgebraicChemical::CAlgebraicChemical, Chemical, GetName, and SetTeXName.

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

Definition at line 48 of file Chemical.h. Referenced by GetReactions.

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

• Chemical.h
• Chemical.cpp

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