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Reaction Class Reference

#include <Reaction.h>

Inheritance diagram for Reaction:

[legend]List of all members.

Public Methods
int	GetNumberChangedByReaction (int chemicalNumber)
void	DoReactionOnce ()
	Reaction ()
	Reaction (std::string reactionName)
virtual	~Reaction ()
std::vector< Chemical * > *	GetChemicals ()
virtual double	GetRate () const=0
virtual std::vector< JElement * > *	GetChemicalJacobian ()=0
virtual std::string	GetTeXForm () const
virtual void	SetTeXForm ()=0
std::string	GetName () const
Protected Attributes
std::vector< Chemical * >	chemicals
std::vector< int >	numberOfEachChemicalChangedByReaction
std::vector< RateConstant * >	rateConstants
std::vector< JElement * >	chemicalJacobian
std::string	reactionName
std::string	m_sTeXForm

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Constructor & Destructor Documentation

Reaction::Reaction (    )

Definition at line 15 of file Reaction.cpp.

Reaction::Reaction (  std::string    reactionName )

Definition at line 20 of file Reaction.cpp. References reactionName.

Reaction::~Reaction (    )  [virtual]

Definition at line 25 of file Reaction.cpp. References chemicalJacobian.

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Member Function Documentation

void Reaction::DoReactionOnce (    )

Definition at line 43 of file Reaction.cpp. References chemicals, and numberOfEachChemicalChangedByReaction. Referenced by CContinuousTimeMonteCarloMover::DoMove, and CMixedReactionMover::DoStochasticMove.

virtual std::vector<JElement *>* Reaction::GetChemicalJacobian (    )  [pure virtual]

Implemented in CTrimerDissociation.

std::vector< Chemical * > * Reaction::GetChemicals (    )

Definition at line 38 of file Reaction.cpp. References chemicals. Referenced by CMixedReactionMover::DoStochasticMove.

std::string Reaction::GetName (    )  const [inline]

Definition at line 60 of file Reaction.h. References reactionName.

int Reaction::GetNumberChangedByReaction (  int    chemicalNumber )

Definition at line 54 of file Reaction.cpp. References numberOfEachChemicalChangedByReaction. Referenced by CMixedReactionMover::DoStochasticMove.

virtual double Reaction::GetRate (    )  const [pure virtual]

Implemented in CTrimerDissociation. Referenced by CTauNetwork::GetReactionRates, CMixedReactionNetwork::GetReactionRates, CMixedReactionNetwork::GetTotalStochasticReactionProbability, and CMixedReactionMover::Move.

virtual std::string Reaction::GetTeXForm (    )  const [inline, virtual]

Definition at line 58 of file Reaction.h. References m_sTeXForm.

virtual void Reaction::SetTeXForm (    )  [pure virtual]

Implemented in CTrimerDissociation.

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Member Data Documentation

std::vector<JElement *> Reaction::chemicalJacobian [protected]

Definition at line 74 of file Reaction.h. Referenced by CatalyzedTranslationReaction::CatalyzedTranslationReaction, CChemicalSink::CChemicalSink, CChemicalSource::CChemicalSource, CConstantSinkReaction::CConstantSinkReaction, CConstantSourceReaction::CConstantSourceReaction, CFirstOrderDestructionReaction::CFirstOrderDestructionReaction, CMichaelisMentenHeterodimerizationReaction::CMichaelisMentenHeterodimerizationReaction, CNormalizedLinearAmplifier::CNormalizedLinearAmplifier, CNormalizedLinearAttenuator::CNormalizedLinearAttenuator, CPoolTransitionReaction::CPoolTransitionReaction, CTauReaction::CTauReaction, CTrimerDissociation::CTrimerDissociation, CTrimerFormation::CTrimerFormation, GenerationReaction::GenerationReaction, UnaryDegradationReaction::GetChemicalJacobian, CTrimerFormation::GetChemicalJacobian, CTrimerDissociation::GetChemicalJacobian, TransformationReaction::GetChemicalJacobian, TranscriptionReaction::GetChemicalJacobian, CTauReaction::GetChemicalJacobian, CPoolTransitionReaction::GetChemicalJacobian, PlasmidReplicationReaction::GetChemicalJacobian, CNormalizedLinearAttenuator::GetChemicalJacobian, CNormalizedLinearAmplifier::GetChemicalJacobian, MichaelisMentenReaction::GetChemicalJacobian, CMichaelisMentenHeterodimerizationReaction::GetChemicalJacobian, HomodimerizationReaction::GetChemicalJacobian, HomodimerDissociationReaction::GetChemicalJacobian, HeterodimerizationReaction::GetChemicalJacobian, HeterodimerDissociationReaction::GetChemicalJacobian, GenerationReaction::GetChemicalJacobian, CFirstOrderDestructionReaction::GetChemicalJacobian, CConstantSourceReaction::GetChemicalJacobian, CConstantSinkReaction::GetChemicalJacobian, CompetitiveDegradationReaction::GetChemicalJacobian, CChemicalSource::GetChemicalJacobian, CChemicalSink::GetChemicalJacobian, CatalyzedTranslationReaction::GetChemicalJacobian, HeterodimerDissociationReaction::HeterodimerDissociationReaction, HeterodimerizationReaction::HeterodimerizationReaction, HomodimerDissociationReaction::HomodimerDissociationReaction, HomodimerizationReaction::HomodimerizationReaction, MichaelisMentenReaction::MichaelisMentenReaction, PlasmidReplicationReaction::PlasmidReplicationReaction, TranscriptionReaction::TranscriptionReaction, TransformationReaction::TransformationReaction, UnaryDegradationReaction::UnaryDegradationReaction, and ~Reaction.

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

Definition at line 68 of file Reaction.h. Referenced by CatalyzedTranslationReaction::CatalyzedTranslationReaction, CChemicalSink::CChemicalSink, CChemicalSource::CChemicalSource, CConstantSinkReaction::CConstantSinkReaction, CConstantSourceReaction::CConstantSourceReaction, CFirstOrderDestructionReaction::CFirstOrderDestructionReaction, CMichaelisMentenHeterodimerizationReaction::CMichaelisMentenHeterodimerizationReaction, CNormalizedLinearAmplifier::CNormalizedLinearAmplifier, CNormalizedLinearAttenuator::CNormalizedLinearAttenuator, CompetitiveDegradationReaction::CompetitiveDegradationReaction, CPoolTransitionReaction::CPoolTransitionReaction, CTauReaction::CTauReaction, CTrimerDissociation::CTrimerDissociation, CTrimerFormation::CTrimerFormation, DoReactionOnce, GenerationReaction::GenerationReaction, UnaryDegradationReaction::GetChemicalJacobian, CTrimerFormation::GetChemicalJacobian, CTrimerDissociation::GetChemicalJacobian, TransformationReaction::GetChemicalJacobian, CTauReaction::GetChemicalJacobian, CPoolTransitionReaction::GetChemicalJacobian, PlasmidReplicationReaction::GetChemicalJacobian, CNormalizedLinearAttenuator::GetChemicalJacobian, CNormalizedLinearAmplifier::GetChemicalJacobian, MichaelisMentenReaction::GetChemicalJacobian, CMichaelisMentenHeterodimerizationReaction::GetChemicalJacobian, HomodimerizationReaction::GetChemicalJacobian, HomodimerDissociationReaction::GetChemicalJacobian, HeterodimerizationReaction::GetChemicalJacobian, HeterodimerDissociationReaction::GetChemicalJacobian, GenerationReaction::GetChemicalJacobian, CFirstOrderDestructionReaction::GetChemicalJacobian, CConstantSourceReaction::GetChemicalJacobian, CConstantSinkReaction::GetChemicalJacobian, CChemicalSource::GetChemicalJacobian, CChemicalSink::GetChemicalJacobian, CatalyzedTranslationReaction::GetChemicalJacobian, GetChemicals, UnaryDegradationReaction::GetRate, CTrimerFormation::GetRate, CTrimerDissociation::GetRate, TransformationReaction::GetRate, TranscriptionReaction::GetRate, CTauReaction::GetRate, CPoolTransitionReaction::GetRate, PlasmidReplicationReaction::GetRate, CNormalizedLinearAttenuator::GetRate, CNormalizedLinearAmplifier::GetRate, MichaelisMentenReaction::GetRate, CMichaelisMentenHeterodimerizationReaction::GetRate, HomodimerizationReaction::GetRate, HomodimerDissociationReaction::GetRate, HeterodimerizationReaction::GetRate, HeterodimerDissociationReaction::GetRate, GenerationReaction::GetRate, CFirstOrderDestructionReaction::GetRate, CompetitiveDegradationReaction::GetRate, CChemicalSource::GetRate, CChemicalSink::GetRate, CatalyzedTranslationReaction::GetRate, HeterodimerDissociationReaction::HeterodimerDissociationReaction, HeterodimerizationReaction::HeterodimerizationReaction, HomodimerDissociationReaction::HomodimerDissociationReaction, HomodimerizationReaction::HomodimerizationReaction, MichaelisMentenReaction::MichaelisMentenReaction, PlasmidReplicationReaction::PlasmidReplicationReaction, UnaryDegradationReaction::SetTeXForm, CTrimerFormation::SetTeXForm, CTrimerDissociation::SetTeXForm, TransformationReaction::SetTeXForm, TranscriptionReaction::SetTeXForm, CTauReaction::SetTeXForm, CPoolTransitionReaction::SetTeXForm, PlasmidReplicationReaction::SetTeXForm, CNormalizedLinearAttenuator::SetTeXForm, CNormalizedLinearAmplifier::SetTeXForm, MichaelisMentenReaction::SetTeXForm, CMichaelisMentenHeterodimerizationReaction::SetTeXForm, HomodimerizationReaction::SetTeXForm, HomodimerDissociationReaction::SetTeXForm, HeterodimerizationReaction::SetTeXForm, HeterodimerDissociationReaction::SetTeXForm, GenerationReaction::SetTeXForm, CFirstOrderDestructionReaction::SetTeXForm, CChemicalSource::SetTeXForm, CChemicalSink::SetTeXForm, CatalyzedTranslationReaction::SetTeXForm, TranscriptionReaction::TranscriptionReaction, TransformationReaction::TransformationReaction, and UnaryDegradationReaction::UnaryDegradationReaction.

std::string Reaction::m_sTeXForm [protected]

Definition at line 78 of file Reaction.h. Referenced by GetTeXForm, UnaryDegradationReaction::SetTeXForm, CTrimerFormation::SetTeXForm, CTrimerDissociation::SetTeXForm, TransformationReaction::SetTeXForm, TranscriptionReaction::SetTeXForm, CTauReaction::SetTeXForm, CPoolTransitionReaction::SetTeXForm, PlasmidReplicationReaction::SetTeXForm, CNormalizedLinearAttenuator::SetTeXForm, CNormalizedLinearAmplifier::SetTeXForm, MichaelisMentenReaction::SetTeXForm, CMichaelisMentenHeterodimerizationReaction::SetTeXForm, HomodimerizationReaction::SetTeXForm, HomodimerDissociationReaction::SetTeXForm, HeterodimerizationReaction::SetTeXForm, HeterodimerDissociationReaction::SetTeXForm, GenerationReaction::SetTeXForm, CFirstOrderDestructionReaction::SetTeXForm, CConstantSourceReaction::SetTeXForm, CConstantSinkReaction::SetTeXForm, CChemicalSource::SetTeXForm, CChemicalSink::SetTeXForm, and CatalyzedTranslationReaction::SetTeXForm.

std::vector<int> Reaction::numberOfEachChemicalChangedByReaction [protected]

Definition at line 70 of file Reaction.h. Referenced by CatalyzedTranslationReaction::CatalyzedTranslationReaction, CChemicalSink::CChemicalSink, CChemicalSource::CChemicalSource, CConstantSinkReaction::CConstantSinkReaction, CConstantSourceReaction::CConstantSourceReaction, CFirstOrderDestructionReaction::CFirstOrderDestructionReaction, CMichaelisMentenHeterodimerizationReaction::CMichaelisMentenHeterodimerizationReaction, CNormalizedLinearAmplifier::CNormalizedLinearAmplifier, CNormalizedLinearAttenuator::CNormalizedLinearAttenuator, CompetitiveDegradationReaction::CompetitiveDegradationReaction, CPoolTransitionReaction::CPoolTransitionReaction, CTauReaction::CTauReaction, CTrimerDissociation::CTrimerDissociation, CTrimerFormation::CTrimerFormation, DoReactionOnce, GenerationReaction::GenerationReaction, GetNumberChangedByReaction, HeterodimerDissociationReaction::HeterodimerDissociationReaction, HeterodimerizationReaction::HeterodimerizationReaction, HomodimerDissociationReaction::HomodimerDissociationReaction, HomodimerizationReaction::HomodimerizationReaction, MichaelisMentenReaction::MichaelisMentenReaction, PlasmidReplicationReaction::PlasmidReplicationReaction, TranscriptionReaction::TranscriptionReaction, TransformationReaction::TransformationReaction, and UnaryDegradationReaction::UnaryDegradationReaction.

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

Definition at line 72 of file Reaction.h. Referenced by CatalyzedTranslationReaction::CatalyzedTranslationReaction, CConstantSinkReaction::CConstantSinkReaction, CConstantSourceReaction::CConstantSourceReaction, CFirstOrderDestructionReaction::CFirstOrderDestructionReaction, CMichaelisMentenHeterodimerizationReaction::CMichaelisMentenHeterodimerizationReaction, CNormalizedLinearAmplifier::CNormalizedLinearAmplifier, CNormalizedLinearAttenuator::CNormalizedLinearAttenuator, CompetitiveDegradationReaction::CompetitiveDegradationReaction, CPoolTransitionReaction::CPoolTransitionReaction, CTrimerDissociation::CTrimerDissociation, CTrimerFormation::CTrimerFormation, GenerationReaction::GenerationReaction, UnaryDegradationReaction::GetChemicalJacobian, CTrimerFormation::GetChemicalJacobian, CTrimerDissociation::GetChemicalJacobian, TransformationReaction::GetChemicalJacobian, CPoolTransitionReaction::GetChemicalJacobian, PlasmidReplicationReaction::GetChemicalJacobian, CNormalizedLinearAttenuator::GetChemicalJacobian, CNormalizedLinearAmplifier::GetChemicalJacobian, MichaelisMentenReaction::GetChemicalJacobian, CMichaelisMentenHeterodimerizationReaction::GetChemicalJacobian, HomodimerizationReaction::GetChemicalJacobian, HomodimerDissociationReaction::GetChemicalJacobian, HeterodimerizationReaction::GetChemicalJacobian, HeterodimerDissociationReaction::GetChemicalJacobian, GenerationReaction::GetChemicalJacobian, CFirstOrderDestructionReaction::GetChemicalJacobian, CatalyzedTranslationReaction::GetChemicalJacobian, UnaryDegradationReaction::GetRate, CTrimerFormation::GetRate, CTrimerDissociation::GetRate, TransformationReaction::GetRate, TranscriptionReaction::GetRate, CPoolTransitionReaction::GetRate, PlasmidReplicationReaction::GetRate, CNormalizedLinearAttenuator::GetRate, CNormalizedLinearAmplifier::GetRate, MichaelisMentenReaction::GetRate, CMichaelisMentenHeterodimerizationReaction::GetRate, HomodimerizationReaction::GetRate, HomodimerDissociationReaction::GetRate, HeterodimerizationReaction::GetRate, HeterodimerDissociationReaction::GetRate, GenerationReaction::GetRate, CFirstOrderDestructionReaction::GetRate, CConstantSourceReaction::GetRate, CConstantSinkReaction::GetRate, CompetitiveDegradationReaction::GetRate, CatalyzedTranslationReaction::GetRate, HeterodimerDissociationReaction::HeterodimerDissociationReaction, HeterodimerizationReaction::HeterodimerizationReaction, HomodimerDissociationReaction::HomodimerDissociationReaction, HomodimerizationReaction::HomodimerizationReaction, MichaelisMentenReaction::MichaelisMentenReaction, PlasmidReplicationReaction::PlasmidReplicationReaction, UnaryDegradationReaction::SetTeXForm, CTrimerFormation::SetTeXForm, CTrimerDissociation::SetTeXForm, TransformationReaction::SetTeXForm, TranscriptionReaction::SetTeXForm, CPoolTransitionReaction::SetTeXForm, PlasmidReplicationReaction::SetTeXForm, CNormalizedLinearAttenuator::SetTeXForm, CNormalizedLinearAmplifier::SetTeXForm, MichaelisMentenReaction::SetTeXForm, CMichaelisMentenHeterodimerizationReaction::SetTeXForm, HomodimerizationReaction::SetTeXForm, HomodimerDissociationReaction::SetTeXForm, HeterodimerizationReaction::SetTeXForm, HeterodimerDissociationReaction::SetTeXForm, GenerationReaction::SetTeXForm, CFirstOrderDestructionReaction::SetTeXForm, CConstantSourceReaction::SetTeXForm, CConstantSinkReaction::SetTeXForm, CatalyzedTranslationReaction::SetTeXForm, TranscriptionReaction::TranscriptionReaction, TransformationReaction::TransformationReaction, and UnaryDegradationReaction::UnaryDegradationReaction.

std::string Reaction::reactionName [protected]

Definition at line 76 of file Reaction.h. Referenced by GetName, and Reaction.

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

• Reaction.h
• Reaction.cpp

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