CTrajectoryMethodDsaLsodar::CPartition Class Reference

Public Types
typedef std::multimap< size_t, size_t * >	speciesToReactionsMap

Public Member Functions
	CPartition ()
	CPartition (const CPartition &src)
void	intialize (const CMathContainer *pContainer, const C_FLOAT64 &lowerThreshold, const C_FLOAT64 &upperThreshold)
bool	rePartition (const CVectorCore< C_FLOAT64 > &state)
	~CPartition ()

Public Attributes
CVector< const CMathReaction * >	mDeterministicReactions
size_t	mFirstReactionSpeciesIndex
bool	mHasDeterministic
bool	mHasStochastic
C_FLOAT64	mLowerThreshold
CVector< size_t >	mNumLowSpecies
size_t	mNumReactionSpecies
const CMathContainer *	mpContainer
const C_FLOAT64 *	mpFirstReactionValue
speciesToReactionsMap	mSpeciesToReactions
CVector< const CMathReaction * >	mStochasticReactions
CVector< bool >	mStochasticSpecies
C_FLOAT64	mUpperThreshold

Member Typedef Documentation

speciesToReactionsMap

typedef std::multimap< size_t, size_t * > CTrajectoryMethodDsaLsodar::CPartition::speciesToReactionsMap

Constructor & Destructor Documentation

CPartition() [1/2]

CTrajectoryMethodDsaLsodar::CPartition::CPartition

(

)

Default constructor

CTrajectoryMethodDsaLsodar

This class implements an hybrid algorithm for the simulation of a biochemical system over time.

CPartition() [2/2]

CTrajectoryMethodDsaLsodar::CPartition::CPartition

(

const CPartition &

src

)

Copy constructor

Parameters

const

CPartition & src

~CPartition()

CTrajectoryMethodDsaLsodar::CPartition::~CPartition

(

)

Destructor

Member Function Documentation

intialize()

void CTrajectoryMethodDsaLsodar::CPartition::intialize	(	const CMathContainer *	pContainer,
		const C_FLOAT64 &	lowerThreshold,
		const C_FLOAT64 &	upperThreshold
	)

References CVectorCore< CType >::array(), C_FLOAT64, CMathContainer::getCountDependentSpecies(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getCountIndependentSpecies(), CMathContainer::getCountODEs(), CMathReaction::getNumberBalance(), CMathContainer::getReactions(), CMathContainer::getState(), CTrajectoryMethodDsaLsodar::mFirstReactionSpeciesIndex, CCopasiMethod::mpContainer, and CVectorCore< CType >::size().

Referenced by CTrajectoryMethodDsaLsodar::start().

rePartition()

bool CTrajectoryMethodDsaLsodar::CPartition::rePartition

(

const CVectorCore< C_FLOAT64 > &

state

)

References CVectorCore< CType >::array(), C_FLOAT64, and CTrajectoryMethodDsaLsodar::mFirstReactionSpeciesIndex.

Referenced by CTrajectoryMethodDsaLsodar::doSingleStep().

Member Data Documentation

mDeterministicReactions

CVector< const CMathReaction * > CTrajectoryMethodDsaLsodar::CPartition::mDeterministicReactions

A vector containing pointers to stochastic reaction dependencies

Referenced by CTrajectoryMethodDsaLsodar::evalF().

mFirstReactionSpeciesIndex

size_t CTrajectoryMethodDsaLsodar::CPartition::mFirstReactionSpeciesIndex

The index of the first species determined by reactions in the state

Referenced by CTrajectoryMethodDsaLsodar::evalF().

mHasDeterministic

bool CTrajectoryMethodDsaLsodar::CPartition::mHasDeterministic

A Boolean flag indicating whether the system has deterministic reactions

mHasStochastic

bool CTrajectoryMethodDsaLsodar::CPartition::mHasStochastic

A Boolean flag indicating whether the system has stochastic reactions

Referenced by CTrajectoryMethodDsaLsodar::doSingleStep().

mLowerThreshold

C_FLOAT64 CTrajectoryMethodDsaLsodar::CPartition::mLowerThreshold

The threshold for switching to stochastic treatment

mNumLowSpecies

CVector< size_t > CTrajectoryMethodDsaLsodar::CPartition::mNumLowSpecies

A vector containing the number of low species for each reaction

mNumReactionSpecies

size_t CTrajectoryMethodDsaLsodar::CPartition::mNumReactionSpecies

The number of species determined by reactions

Referenced by CTrajectoryMethodDsaLsodar::evalF().

mpContainer

const CMathContainer* CTrajectoryMethodDsaLsodar::CPartition::mpContainer

A pointer to the math container;

mpFirstReactionValue

const C_FLOAT64* CTrajectoryMethodDsaLsodar::CPartition::mpFirstReactionValue

A pointer to the first species determined by reactions

Referenced by CTrajectoryMethodDsaLsodar::evalF().

mSpeciesToReactions

speciesToReactionsMap CTrajectoryMethodDsaLsodar::CPartition::mSpeciesToReactions

A map from a species index to the indexes of the reactions it participates in

mStochasticReactions

CVector< const CMathReaction * > CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions

A vector containing pointers to stochastic reaction dependencies

Referenced by CTrajectoryMethodDsaLsodar::calculatePropensities(), CTrajectoryMethodDsaLsodar::calculateTotalPropensity(), and CTrajectoryMethodDsaLsodar::doSingleStep().

mStochasticSpecies

CVector< bool > CTrajectoryMethodDsaLsodar::CPartition::mStochasticSpecies

A vector indicating whether a species is treated stochastically or not.

mUpperThreshold

C_FLOAT64 CTrajectoryMethodDsaLsodar::CPartition::mUpperThreshold

The threshold for switching to deterministic treatment

---

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

• CTrajectoryMethodDsaLsodar.h
• CTrajectoryMethodDsaLsodar.cpp