COPASI API  4.16.103
Public Member Functions | Public Attributes | List of all members
CTrajectoryMethodDsaLsodar::CReactionDependencies Class Reference
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Public Member Functions

 CReactionDependencies ()
 
 CReactionDependencies (const CReactionDependencies &src)
 
CReactionDependenciesoperator= (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_FLOAT64mpParticleFlux
 
CVector< size_t > mSpeciesIndex
 
CVector< C_FLOAT64mSpeciesMultiplier
 
CVector< C_FLOAT64mSubstrateMultiplier
 

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.

42  :
44  mMethodSpecies(0),
45  mModelSpecies(0),
46  mCalculations(),
51  mpParticleFlux(NULL),
52  mSpeciesIndex(0)
53 {}
CTrajectoryMethodDsaLsodar::CReactionDependencies::CReactionDependencies ( const CReactionDependencies src)

Copy constructor

Parameters
constCReactionDependencies & src

Definition at line 55 of file CTrajectoryMethodDsaLsodar.cpp.

55  :
56  mSpeciesMultiplier(src.mSpeciesMultiplier),
57  mMethodSpecies(src.mMethodSpecies),
58  mModelSpecies(src.mModelSpecies),
59  mCalculations(src.mCalculations),
60  mDependentReactions(src.mDependentReactions),
61  mSubstrateMultiplier(src.mSubstrateMultiplier),
62  mMethodSubstrates(src.mMethodSubstrates),
63  mModelSubstrates(src.mModelSubstrates),
64  mpParticleFlux(src.mpParticleFlux),
65  mSpeciesIndex(src.mSpeciesIndex)
66 {}
CTrajectoryMethodDsaLsodar::CReactionDependencies::~CReactionDependencies ( )

Destructor

Definition at line 68 of file CTrajectoryMethodDsaLsodar.cpp.

69 {}

Member Function Documentation

CTrajectoryMethodDsaLsodar::CReactionDependencies & CTrajectoryMethodDsaLsodar::CReactionDependencies::operator= ( const CReactionDependencies rhs)

Assignment operator

Parameters
constCReactionDependencies & rhs
Returns
CReactionDependencies &

Definition at line 71 of file CTrajectoryMethodDsaLsodar.cpp.

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

72 {
73  mSpeciesMultiplier = rhs.mSpeciesMultiplier;
74  mMethodSpecies = rhs.mMethodSpecies;
75  mModelSpecies = rhs.mModelSpecies;
76  mCalculations = rhs.mCalculations;
77  mDependentReactions = rhs.mDependentReactions;
78  mSubstrateMultiplier = rhs.mSubstrateMultiplier;
79  mMethodSubstrates = rhs.mMethodSubstrates;
80  mModelSubstrates = rhs.mModelSubstrates;
81  mpParticleFlux = rhs.mpParticleFlux;
82  mSpeciesIndex = rhs.mSpeciesIndex;
83 
84  return * this;
85 }

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=().


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