#include <CReaction.h>

Inheritance diagram for CReaction:

Public Member Functions
	CReaction (const std::string &name="NoName", const CCopasiContainer *pParent=NULL)
	CReaction (const CReaction &src, const CCopasiContainer *pParent=NULL)
	~CReaction ()
virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const
void	cleanup ()
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
C_INT32	load (CReadConfig &configbuffer)
virtual bool	setObjectParent (const CCopasiContainer *pParent)
virtual std::set< const CCopasiObject * >	getDeletedObjects () const
virtual const std::string &	getKey () const
const CChemEq &	getChemEq () const
CChemEq &	getChemEq ()
const CFunction *	getFunction () const
const C_FLOAT64 &	getFlux () const
const C_FLOAT64 &	getParticleFlux () const
bool	isReversible () const
bool	addSubstrate (const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
bool	addProduct (const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
bool	addModifier (const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
bool	setFunction (const std::string &functionName)
bool	setFunction (CFunction *pFunction)
void	setParameterValue (const std::string &parameterName, const C_FLOAT64 &value, const bool &updateStatus=true)
const C_FLOAT64 &	getParameterValue (const std::string &parameterName) const
void	setParameterMapping (const C_INT32 &index, const std::string &key)
void	addParameterMapping (const C_INT32 &index, const std::string &key)
void	setParameterMapping (const std::string &parameterName, const std::string &key)
void	addParameterMapping (const std::string &parameterName, const std::string &key)
void	setParameterMappingVector (const std::string &parameterName, const std::vector< std::string > &keys)
void	clearParameterMapping (const std::string &parameterName)
void	clearParameterMapping (const C_INT32 &index)
const std::vector< std::vector < std::string > > &	getParameterMappings () const
std::vector< std::vector < std::string > > &	getParameterMappings ()
const std::vector< std::string > &	getParameterMapping (const std::string &parameterName) const
const CCopasiParameterGroup &	getParameters () const
CCopasiParameterGroup &	getParameters ()
bool	isLocalParameter (const C_INT32 &index) const
bool	isLocalParameter (const std::string &parameterName) const
const CFunctionParameters &	getFunctionParameters () const
void	setReversible (bool reversible)
void	compile ()
const C_FLOAT64 &	calculateFlux ()
const C_FLOAT64 &	calculateParticleFlux ()
CCopasiObject *	getParticleFluxReference ()
C_FLOAT64	calculatePartialDerivative (C_FLOAT64 *pXi, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)
unsigned C_INT32	getCompartmentNumber () const
const CCompartment &	getLargestCompartment () const
bool	setFunctionFromExpressionTree (CEvaluationTree tree, std::map< CCopasiObject , SBase * > &copasi2sbmlmap, CFunctionDB *pFunctionDB)
CEvaluationNode *	getExpressionTree ()
void	setSBMLId (const std::string &id)
const std::string &	getSBMLId () const
void	printDebug () const
Friends
std::ostream &	operator<< (std::ostream &os, const CReaction &d)

Constructor & Destructor Documentation

CReaction::CReaction	(	const std::string &	name = `"NoName"`,
		const CCopasiContainer *	pParent = `NULL`
	)

Default constructor

Parameters:

const	std::string & name (default: "NoName")
const	CCopasiContainer * pParent (default: NULL)

CReaction::CReaction	(	const CReaction &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor

Parameters:

const CReaction &	src
const	CCopasiContainer * pParent (default: NULL)

CReaction::~CReaction ( )

Destructor

Member Function Documentation

bool CReaction::addModifier	(	const std::string &	metabKey,
		const C_FLOAT64 &	multiplicity = `1.0`
	)

Add a modifier to the reaction

Parameters:

std::string	& metabKey
const	C_FLOAT64 & multiplicity (Default 1.0)

Returns:: bool success

void CReaction::addParameterMapping	(	const C_INT32 &	index,
		const std::string &	key
	)

Add a parameter mapping for the indexed parameter.

Parameters:

const	C_INT32 & index
const	std::string & key

void CReaction::addParameterMapping	(	const std::string &	parameterName,
		const std::string &	key
	)

Add a parameter mapping for the named parameter.

Parameters:

const	std::string & parameterName
const	std::string & key

bool CReaction::addProduct	(	const std::string &	metabKey,
		const C_FLOAT64 &	multiplicity = `1.0`
	)

Add a product to the reaction

Parameters:

std::string	& metabKey
const	C_FLOAT64 & multiplicity (Default 1.0)

Returns:: bool success

bool CReaction::addSubstrate	(	const std::string &	metabKey,
		const C_FLOAT64 &	multiplicity = `1.0`
	)

Add a substrate to the reaction

Parameters:

std::string	& metabKey
const	C_FLOAT64 & multiplicity (Default 1.0)

Returns:: bool success

const C_FLOAT64 & CReaction::calculateFlux ( )

Calculate the kinetic function and returns the flux

Returns:: const C_FLOAT64 & Flux

C_FLOAT64 CReaction::calculatePartialDerivative	(	C_FLOAT64 *	pXi,
		const C_FLOAT64 &	derivationFactor,
		const C_FLOAT64 &	resolution
	)

Calculate partial derivative of the flux

Parameters:

C_FLOAT64	* pXi
const	C_FLOAT64 & derivationFactor
const	C_FLOAT64 & resolution (unscaled resolution)

Returns:: C_FLOAT64 partial

const C_FLOAT64 & CReaction::calculateParticleFlux ( )

Calculates the kinetic function and returns the particle flux

Returns:: const C_FLOAT64 & ParticleFlux

void CReaction::cleanup ( )

Delete

void CReaction::clearParameterMapping ( const std::string & parameterName )

Clear the parameter mapping for the named parameter.

Parameters:

const C_INT32 & index

void CReaction::clearParameterMapping ( const C_INT32 & index )

Clear the parameter mapping for the indexed parameter.

Parameters:

const C_INT32 & index

void CReaction::compile ( )

Compile the reaction, i.e., links the metabolites and parameters with the rate function. The connection of the reaction and the function parameter mapping to the actual metabolites is established (before compile() the chemical equation and the reaction only hold the names of the metabolites).

Parameters:

CCopasiVectorNS < CCompartment > & compartments

const CChemEq & CReaction::getChemEq ( ) const

Retrieves the chemical equation of the reaction

Returns:: const CChemEq & chemEq

CChemEq & CReaction::getChemEq ( )

Retrieves the chemical equation of the reaction

Returns:: CChemEq & chemEq

std::string CReaction::getChildObjectUnits ( const CCopasiObject * pObject ) const [virtual]

Retrieve the units of the child object.

Returns:: std::string units

Reimplemented from CCopasiContainer.

unsigned C_INT32 CReaction::getCompartmentNumber ( ) const

Retrieves the number of compartments the reaction is acting in.

Returns:: "unsigned C_INT32" the compartment number

std::set< const CCopasiObject * > CReaction::getDeletedObjects ( ) const [virtual]

Retrieve the list of deleted numeric child objects;

Returns:: std::set< const CCopasiObject * > deletedObjects

CEvaluationNode * CReaction::getExpressionTree ( )

Converts the function tree into the corresponding expression tree. All variable nodes are replaced by object nodes.

const C_FLOAT64 & CReaction::getFlux ( ) const

Retrieves the flux of the reaction

Returns:: const C_FLOAT64 & flux

const CFunction * CReaction::getFunction ( ) const

Retrieves the rate function of the reaction

Returns:: "CBaseFunction &"

const CFunctionParameters & CReaction::getFunctionParameters ( ) const

Gets the description of what parameters the function expects.

const std::string & CReaction::getKey ( ) const [virtual]

Retrieves the key of the reaction

Returns:: std::string key

Reimplemented from CCopasiObject.

const CCompartment & CReaction::getLargestCompartment ( ) const

get the largest (smallest) compartment that the reaction touches.

std::string CReaction::getObjectDisplayName	(	bool	regular = `true`,
		bool	richtext = `false`
	)		const `[virtual]`

Overload display name. Special treatment for reaction to provide a shorter display

Reimplemented from CCopasiObject.

const std::vector< std::string > & CReaction::getParameterMapping ( const std::string & parameterName ) const

const std::vector< std::vector<std::string> >& CReaction::getParameterMappings ( ) const [inline]

Retrieve the mappings of kinetic function parameters.

std::vector< std::vector<std::string> >& CReaction::getParameterMappings ( ) [inline]

const CCopasiParameterGroup & CReaction::getParameters ( ) const

Gets the list of kinetic parameter objects of the reaction/function

CCopasiParameterGroup & CReaction::getParameters ( )

Gets the list of kinetic parameter objects of the reaction/function

const C_FLOAT64 & CReaction::getParameterValue ( const std::string & parameterName ) const

Retrieves a parameter value

const C_FLOAT64 & CReaction::getParticleFlux ( ) const

Retrieves the scaled flux of the reaction

Returns:: const C_FLOAT64 & scaledFlux

CCopasiObject * CReaction::getParticleFluxReference ( )

Retrieve object referencing the particle flux

Returns:: CCopasiObject * particleFluxReference

const std::string & CReaction::getSBMLId ( ) const

Returns a reference to the SBML Id.

bool CReaction::isLocalParameter ( const C_INT32 & index ) const

Check whether the indexed parameter is a local parameter.

Parameters:

const C_INT32 & index

Returns:: bool isLocal

bool CReaction::isLocalParameter ( const std::string & parameterName ) const

Check whether the named parameter is a local parameter.

Parameters:

const std::string & parameterName

Returns:: bool isLocal

bool CReaction::isReversible ( ) const

Retrieves whether the reaction is reversible

Returns:: bool

C_INT32 CReaction::load ( CReadConfig & configbuffer )

Loads an object with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters:

pconfigbuffer reference to a CReadConfig object.

Returns:: mFail

See also:: mFail

void CReaction::printDebug ( ) const

bool CReaction::setFunction ( const std::string & functionName )

Sets the rate function of the reaction

Parameters:

const string & functionName

Returns:: bool success

bool CReaction::setFunction ( CFunction * pFunction )

Sets the rate function of the reaction

Parameters:

CFunction * pFunction

Returns:: bool success

bool CReaction::setFunctionFromExpressionTree	(	CEvaluationTree *	tree,
		std::map< CCopasiObject , SBase > &	copasi2sbmlmap,
		CFunctionDB *	pFunctionDB
	)

Converts an expression tree into a CFunction object and sets the mapping for the reaction.

bool CReaction::setObjectParent ( const CCopasiContainer * pParent ) [virtual]

Sets the parent of the metabolite;

Parameters:

const CCopasiContainer * pParent

Returns:: bool success

Reimplemented from CCopasiObject.

void CReaction::setParameterMapping	(	const C_INT32 &	index,
		const std::string &	key
	)

Sets a parameter mapping for the indexed parameter.

Parameters:

const	C_INT32 & index
const	std::string & key

void CReaction::setParameterMapping	(	const std::string &	parameterName,
		const std::string &	key
	)

Sets a parameter mapping for the named parameter.

Parameters:

const	std::string & parameterName
const	std::string & key

void CReaction::setParameterMappingVector	(	const std::string &	parameterName,
		const std::vector< std::string > &	keys
	)

Set the mapping for the name parameter which must be of type vector

Parameters:

const	std::string & parameterName
const	std::vector<std::string> & keys

void CReaction::setParameterValue	(	const std::string &	parameterName,
		const C_FLOAT64 &	value,
		const bool &	updateStatus = `true`
	)

Sets a parameter value if updateStatus==true the status is also updated to make sure the value is actually used (instead of a global value that may have been used before). if updateStatus==false only the value of the local parameter is set, even if it is not used

Parameters:

const	std::string & parameterName
const	C_FLOAT64 & value
const	bool & updateStatus (default: true(

void CReaction::setReversible ( bool reversible )

Sets whether the reaction is reversible

Parameters:

bool	reversible

void CReaction::setSBMLId ( const std::string & id )

Sets the SBMLId.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const CReaction &	d
	)		`[friend]`

Friend declaration for ostream operator

Parameters:

std::ostream	& os
const	CReaction & d

Returns:: std::ostream & os

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

copasi/model/CReaction.h
copasi/model/CReaction.cpp

Public Member Functions

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation