CTrajectoryMethodDsaLsodar::CReactionDependencies Class Reference

Collaboration diagram for CTrajectoryMethodDsaLsodar::CReactionDependencies:

Public Member Functions
	CReactionDependencies ()
	CReactionDependencies (const CReactionDependencies &src)
CReactionDependencies &	operator= (const CReactionDependencies &rhs)
	~CReactionDependencies ()

Public Attributes
std::vector< Refresh * >	mCalculations
CVector< size_t >	mDependentReactions
CVector< C_FLOAT64 * >	mMethodSpecies
CVector< C_FLOAT64 * >	mMethodSubstrates
CVector< C_FLOAT64 * >	mModelSpecies
CVector< C_FLOAT64 * >	mModelSubstrates
C_FLOAT64 *	mpParticleFlux
CVector< size_t >	mSpeciesIndex
CVector< C_FLOAT64 >	mSpeciesMultiplier
CVector< C_FLOAT64 >	mSubstrateMultiplier

Detailed Description

Definition at line 58 of file CTrajectoryMethodDsaLsodar.h.

Constructor & Destructor Documentation

CTrajectoryMethodDsaLsodar::CReactionDependencies::CReactionDependencies

(

)

Default constructor

CTrajectoryMethodDsaLsodar

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

Definition at line 42 of file CTrajectoryMethodDsaLsodar.cpp.

                                                                      :
  mSpeciesMultiplier(0),
  mMethodSpecies(0),
  mModelSpecies(0),
  mCalculations(),
  mDependentReactions(0),
  mSubstrateMultiplier(0),
  mMethodSubstrates(0),
  mModelSubstrates(0),
  mpParticleFlux(NULL),
  mSpeciesIndex(0)
{}

CTrajectoryMethodDsaLsodar::CReactionDependencies::CReactionDependencies

(

const CReactionDependencies &

src

)

Copy constructor

Parameters

const

CReactionDependencies & src

Definition at line 55 of file CTrajectoryMethodDsaLsodar.cpp.

                                                                                                       :
  mSpeciesMultiplier(src.mSpeciesMultiplier),
  mMethodSpecies(src.mMethodSpecies),
  mModelSpecies(src.mModelSpecies),
  mCalculations(src.mCalculations),
  mDependentReactions(src.mDependentReactions),
  mSubstrateMultiplier(src.mSubstrateMultiplier),
  mMethodSubstrates(src.mMethodSubstrates),
  mModelSubstrates(src.mModelSubstrates),
  mpParticleFlux(src.mpParticleFlux),
  mSpeciesIndex(src.mSpeciesIndex)
{}

CTrajectoryMethodDsaLsodar::CReactionDependencies::~CReactionDependencies

(

)

Destructor

Definition at line 68 of file CTrajectoryMethodDsaLsodar.cpp.

{}

Member Function Documentation

CTrajectoryMethodDsaLsodar::CReactionDependencies & CTrajectoryMethodDsaLsodar::CReactionDependencies::operator=

(

const CReactionDependencies &

rhs

)

Assignment operator

Parameters

const

CReactionDependencies & rhs

Returns

CReactionDependencies &

Definition at line 71 of file CTrajectoryMethodDsaLsodar.cpp.

References mCalculations, mDependentReactions, mMethodSpecies, mMethodSubstrates, mModelSpecies, mModelSubstrates, mpParticleFlux, mSpeciesIndex, mSpeciesMultiplier, and mSubstrateMultiplier.

{
  mSpeciesMultiplier = rhs.mSpeciesMultiplier;
  mMethodSpecies = rhs.mMethodSpecies;
  mModelSpecies = rhs.mModelSpecies;
  mCalculations = rhs.mCalculations;
  mDependentReactions = rhs.mDependentReactions;
  mSubstrateMultiplier = rhs.mSubstrateMultiplier;
  mMethodSubstrates = rhs.mMethodSubstrates;
  mModelSubstrates = rhs.mModelSubstrates;
  mpParticleFlux = rhs.mpParticleFlux;
  mSpeciesIndex = rhs.mSpeciesIndex;

  return * this;
}

Member Data Documentation

std::vector< Refresh * > CTrajectoryMethodDsaLsodar::CReactionDependencies::mCalculations

Vector of refresh methods which need to be executed to update all values required for simulation

Definition at line 105 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::fireReaction(), and operator=().

CVector< size_t > CTrajectoryMethodDsaLsodar::CReactionDependencies::mDependentReactions

A vector of indexes of reaction which propensities have to be recalculated.

Definition at line 110 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::fireReaction(), and operator=().

CVector< C_FLOAT64 * > CTrajectoryMethodDsaLsodar::CReactionDependencies::mMethodSpecies

Vector of pointers to method internal species values to calculate the new state.

Definition at line 95 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::fireReaction(), and operator=().

CVector< C_FLOAT64 * > CTrajectoryMethodDsaLsodar::CReactionDependencies::mMethodSubstrates

Vector of pointers to method internal species values to calculate the new propensity.

Definition at line 120 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::calculateAmu(), and operator=().

CVector< C_FLOAT64 * > CTrajectoryMethodDsaLsodar::CReactionDependencies::mModelSpecies

Vector of pointers to model species values to calculate the new state.

Definition at line 100 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::fireReaction(), and operator=().

CVector< C_FLOAT64 * > CTrajectoryMethodDsaLsodar::CReactionDependencies::mModelSubstrates

Vector of pointers to model species values to calculate the new propensity.

Definition at line 125 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::calculateAmu(), and operator=().

C_FLOAT64* CTrajectoryMethodDsaLsodar::CReactionDependencies::mpParticleFlux

A pointer to the particle flux of the reaction.

Definition at line 130 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::calculateAmu(), and operator=().

CVector< size_t > CTrajectoryMethodDsaLsodar::CReactionDependencies::mSpeciesIndex

A vector containing the index of each species participating in the reaction as a substrate and/or product.

Definition at line 136 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::CPartition::determineStochasticSpecies(), and operator=().

CVector< C_FLOAT64 > CTrajectoryMethodDsaLsodar::CReactionDependencies::mSpeciesMultiplier

Vector of multiplier to calculate the new state

Definition at line 90 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::fireReaction(), and operator=().

CVector< C_FLOAT64 > CTrajectoryMethodDsaLsodar::CReactionDependencies::mSubstrateMultiplier

Vector of multiplier to calculate the new propensity.

Definition at line 115 of file CTrajectoryMethodDsaLsodar.h.

Referenced by CTrajectoryMethodDsaLsodar::calculateAmu(), and operator=().

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

• CTrajectoryMethodDsaLsodar.h
• CTrajectoryMethodDsaLsodar.cpp