CMathReaction Class Reference

#include <CMathReaction.h>

Collaboration diagram for CMathReaction:

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

Detailed Description

Definition at line 18 of file CMathReaction.h.

Constructor & Destructor Documentation

CMathReaction::CMathReaction

(

)

Constructor

Definition at line 13 of file CMathReaction.cpp.

                            :
  mpReaction(NULL),
  mpParticleFlux(NULL),
  mpFlux(NULL),
  mpPropensity(NULL),
  mModifiedSpecies(),
  mStepUpdates()
{}

CMathReaction::~CMathReaction

(

)

Destructor

Definition at line 22 of file CMathReaction.cpp.

{}

Member Function Documentation

void CMathReaction::copy	(	const CMathReaction &	src,
		CMathContainer &	container,
		const size_t &	valueOffset,
		const size_t &	objectOffset
	)

Copy an existing object

Parameters

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().

{
  mpReaction = src.mpReaction;

  mpParticleFlux = src.mpParticleFlux + objectOffset;
  mpFlux = src.mpFlux + objectOffset;
  mpPropensity = src.mpPropensity + objectOffset;

  mStepUpdates.resize(src.mStepUpdates.size());
  std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdate = mStepUpdates.array();
  std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdateEnd = pStepUpdate + mStepUpdates.size();
  const std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdateSrc = src.mStepUpdates.array();

  for (; pStepUpdate != pStepUpdateEnd; ++pStepUpdate, ++pStepUpdateSrc)
    {
      pStepUpdate->first = pStepUpdateSrc->first;
      pStepUpdate->second = pStepUpdateSrc->second + valueOffset;
    }

  CObjectInterface::ObjectSet::const_iterator it = src.mModifiedSpecies.begin();
  CObjectInterface::ObjectSet::const_iterator end = src.mModifiedSpecies.end();

  for (; it != end; ++it)
    {
      mModifiedSpecies.insert(*it + objectOffset);
    }
}

void CMathReaction::fire

(

const C_FLOAT64 &

count

)

Fire the reaction count times. Note count must not necessarily be an integer

Parameters

const

C_FLOAT64 & count

Definition at line 81 of file CMathReaction.cpp.

References CVectorCore< CType >::array(), mStepUpdates, and CVectorCore< CType >::size().

{
  std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdate = mStepUpdates.array();
  std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdateEnd = pStepUpdate + mStepUpdates.size();

  for (; pStepUpdate != pStepUpdateEnd; ++pStepUpdate)
    {
      *pStepUpdate->second += pStepUpdate->first * count;
    }
}

const CMathObject * CMathReaction::getFluxObject

(

)

const

Retrieve a pointer to the mathematical object for the flux.

Returns

const CMathObject * pFluxObject

Definition at line 97 of file CMathReaction.cpp.

References mpFlux.

{
  return mpFlux;
}

const CReaction * CMathReaction::getModelReaction

(

)

const

Retrieve a pointer to the model reaction

Returns

const CReaction * pModelReaction

Definition at line 112 of file CMathReaction.cpp.

References mpReaction.

{
  return mpReaction;
}

const CObjectInterface::ObjectSet & CMathReaction::getModifiedSpecies

(

)

const

Retrieve the set of modified species

Returns

const CObjectInterface::ObjectSet & modifiedSpecies

Definition at line 107 of file CMathReaction.cpp.

References mModifiedSpecies.

{
  return mModifiedSpecies;
}

const CMathObject * CMathReaction::getParticleFluxObject

(

)

const

Retrieve a pointer to the mathematical object for the particle flux.

Returns

const CMathObject * pParticleFluxObject

Definition at line 92 of file CMathReaction.cpp.

References mpParticleFlux.

{
  return mpParticleFlux;
}

const CMathObject * CMathReaction::getPropensityObject

(

)

const

Retrieve a pointer to the mathematical object for the propensity.

Returns

const CMathObject * pPropensityObject

Definition at line 102 of file CMathReaction.cpp.

References mpPropensity.

{
  return mpPropensity;
}

void CMathReaction::initialize	(	const CReaction *	pReaction,
		CMathContainer &	container
	)

Initialize the reaction from the model reaction in the given container context

Parameters

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().

{
  mpReaction = pReaction;

  // Sanity Check
  if (mpReaction == NULL) return;

  mpParticleFlux = container.getMathObject(mpReaction->getParticleFluxReference());
  mpFlux = container.getMathObject(mpReaction->getFluxReference());
  mpPropensity = container.getMathObject(mpReaction->getPropensityReference());

  mStepUpdates.resize(mpReaction->getChemEq().getBalances().size());
  std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdate = mStepUpdates.array();
  std::pair< C_FLOAT64, C_FLOAT64 * > * pStepUpdateEnd = pStepUpdate + mStepUpdates.size();
  CCopasiVector < CChemEqElement >::const_iterator it = mpReaction->getChemEq().getBalances().begin();

  for (; pStepUpdate != pStepUpdateEnd; ++pStepUpdate, ++it)
    {
      CMathObject * pParticleNumber = container.getMathObject((*it)->getMetabolite()->getValueReference());
      mModifiedSpecies.insert(pParticleNumber);
      pStepUpdate->first = (*it)->getMultiplicity();
      pStepUpdate->second = (C_FLOAT64 *) pParticleNumber->getValuePointer();
    }
}

Member Data Documentation

CObjectInterface::ObjectSet CMathReaction::mModifiedSpecies

private

The set of modified species

Definition at line 107 of file CMathReaction.h.

Referenced by copy(), getModifiedSpecies(), and initialize().

CMathObject* CMathReaction::mpFlux

private

A pointer to the mathematical flux.

Definition at line 97 of file CMathReaction.h.

Referenced by copy(), getFluxObject(), and initialize().

CMathObject* CMathReaction::mpParticleFlux

private

A pointer to the mathematical particle flux.

Definition at line 92 of file CMathReaction.h.

Referenced by copy(), getParticleFluxObject(), and initialize().

CMathObject* CMathReaction::mpPropensity

private

A pointer to the mathematical propensity.

Definition at line 102 of file CMathReaction.h.

Referenced by copy(), getPropensityObject(), and initialize().

const CReaction* CMathReaction::mpReaction

private

A pointer to model reaction.

Definition at line 87 of file CMathReaction.h.

Referenced by copy(), getModelReaction(), and initialize().

CVector< std::pair< C_FLOAT64, C_FLOAT64 * > > CMathReaction::mStepUpdates

private

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().

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

• CMathReaction.h
• CMathReaction.cpp