COPASI API
4.16.103
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#include <CMathReaction.h>
Public Member Functions | |
CMathReaction () | |
void | copy (const CMathReaction &src, CMathContainer &container, const size_t &valueOffset, const size_t &objectOffset) |
void | fire (const C_FLOAT64 &count) |
const CMathObject * | getFluxObject () const |
const CReaction * | getModelReaction () const |
const CObjectInterface::ObjectSet & | getModifiedSpecies () const |
const CMathObject * | getParticleFluxObject () const |
const CMathObject * | getPropensityObject () const |
void | initialize (const CReaction *pReaction, CMathContainer &container) |
~CMathReaction () | |
Private Attributes | |
CObjectInterface::ObjectSet | mModifiedSpecies |
CMathObject * | mpFlux |
CMathObject * | mpParticleFlux |
CMathObject * | mpPropensity |
const CReaction * | mpReaction |
CVector< std::pair< C_FLOAT64, C_FLOAT64 * > > | mStepUpdates |
Definition at line 18 of file CMathReaction.h.
CMathReaction::CMathReaction | ( | ) |
Constructor
Definition at line 13 of file CMathReaction.cpp.
CMathReaction::~CMathReaction | ( | ) |
void CMathReaction::copy | ( | const CMathReaction & | src, |
CMathContainer & | container, | ||
const size_t & | valueOffset, | ||
const size_t & | objectOffset | ||
) |
Copy an existing object
const | CMathReaction & src |
CMathContainer | & container |
const | size_t & valueOffset |
const | size_t & objectOffset |
Definition at line 50 of file CMathReaction.cpp.
References CVectorCore< CType >::array(), mModifiedSpecies, mpFlux, mpParticleFlux, mpPropensity, mpReaction, mStepUpdates, CVector< CType >::resize(), and CVectorCore< CType >::size().
Referenced by CMathContainer::CMathContainer().
Fire the reaction count times. Note count must not necessarily be an integer
const | C_FLOAT64 & count |
Definition at line 81 of file CMathReaction.cpp.
References CVectorCore< CType >::array(), mStepUpdates, and CVectorCore< CType >::size().
const CMathObject * CMathReaction::getFluxObject | ( | ) | const |
Retrieve a pointer to the mathematical object for the flux.
Definition at line 97 of file CMathReaction.cpp.
References mpFlux.
const CReaction * CMathReaction::getModelReaction | ( | ) | const |
Retrieve a pointer to the model reaction
Definition at line 112 of file CMathReaction.cpp.
References mpReaction.
const CObjectInterface::ObjectSet & CMathReaction::getModifiedSpecies | ( | ) | const |
Retrieve the set of modified species
Definition at line 107 of file CMathReaction.cpp.
References mModifiedSpecies.
const CMathObject * CMathReaction::getParticleFluxObject | ( | ) | const |
Retrieve a pointer to the mathematical object for the particle flux.
Definition at line 92 of file CMathReaction.cpp.
References mpParticleFlux.
const CMathObject * CMathReaction::getPropensityObject | ( | ) | const |
Retrieve a pointer to the mathematical object for the propensity.
Definition at line 102 of file CMathReaction.cpp.
References mpPropensity.
void CMathReaction::initialize | ( | const CReaction * | pReaction, |
CMathContainer & | container | ||
) |
Initialize the reaction from the model reaction in the given container context
const | CReaction * pReaction |
CMathContainer | & container |
Definition at line 25 of file CMathReaction.cpp.
References CVectorCore< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, CChemEq::getBalances(), CReaction::getChemEq(), CReaction::getFluxReference(), CMathContainer::getMathObject(), CReaction::getParticleFluxReference(), CReaction::getPropensityReference(), CMathObject::getValuePointer(), mModifiedSpecies, mpFlux, mpParticleFlux, mpPropensity, mpReaction, mStepUpdates, CVector< CType >::resize(), CVectorCore< CType >::size(), and CCopasiVector< T >::size().
Referenced by CMathContainer::init().
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The set of modified species
Definition at line 107 of file CMathReaction.h.
Referenced by copy(), getModifiedSpecies(), and initialize().
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A pointer to the mathematical flux.
Definition at line 97 of file CMathReaction.h.
Referenced by copy(), getFluxObject(), and initialize().
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A pointer to the mathematical particle flux.
Definition at line 92 of file CMathReaction.h.
Referenced by copy(), getParticleFluxObject(), and initialize().
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A pointer to the mathematical propensity.
Definition at line 102 of file CMathReaction.h.
Referenced by copy(), getPropensityObject(), and initialize().
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A pointer to model reaction.
Definition at line 87 of file CMathReaction.h.
Referenced by copy(), getModelReaction(), and initialize().
Information for updating the species particle numbers when the reaction fires.
Definition at line 113 of file CMathReaction.h.
Referenced by copy(), fire(), and initialize().