#include <CChemEq.h>

Inheritance diagram for CChemEq:

Public Types
enum	MetaboliteRole { PRODUCT = 0 , SUBSTRATE , MODIFIER , NOROLE }

Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Public Member Functions
bool	addMetabolite (const std::string &key, const C_FLOAT64 multiplicity, const MetaboliteRole &role)

	CChemEq (const CChemEq &src, const CDataContainer *pParent)

	CChemEq (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT)

void	cleanup ()

const CDataVector< CChemEqElement > &	getBalances () const

size_t	getCompartmentNumber () const

std::set< const CCompartment * >	getCompartments () const

const CCompartment *	getLargestCompartment () const

const CDataVector< CChemEqElement > &	getModifiers () const

size_t	getMolecularity (const MetaboliteRole role) const

const CDataVector< CChemEqElement > &	getProducts () const

const bool &	getReversibility () const

const CDataVector< CChemEqElement > &	getSubstrates () const

bool	setMultiplicity (const CMetab *pMetab, C_FLOAT64 newMult, MetaboliteRole role)

void	setReversibility (const bool &reversible)

virtual	~CChemEq ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes) override

	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const override

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual size_t	getIndex (const CDataObject *pObject) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const override

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual bool	remove (CDataObject *pObject)

virtual CData	toData () const override

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

virtual const std::string &	getKey () const

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

virtual void *	getValuePointer () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

virtual void	print (std::ostream *ostream) const override

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CDataContainer *pParent)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CUndoObjectInterface ()

Private Member Functions
void	addElement (CDataVector< CChemEqElement > &structure, const CChemEqElement &element, CChemEq::MetaboliteRole role=CChemEq::PRODUCT)

Private Attributes
CDataVector< CChemEqElement >	mBalances

CDataVector< CChemEqElement >	mModifiers

CDataVector< CChemEqElement >	mProducts

bool	mReversible

CDataVector< CChemEqElement >	mSubstrates

Friends
std::ostream &	operator<< (std::ostream &os, const CChemEq &d)

Additional Inherited Members
Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Member Enumeration Documentation

◆ MetaboliteRole

enum CChemEq::MetaboliteRole

Enumerator
PRODUCT
SUBSTRATE
MODIFIER
NOROLE

Constructor & Destructor Documentation

◆ CChemEq() [1/2]

CChemEq::CChemEq	(	const std::string &	name = `"NoName"`,
		const CDataContainer *	pParent = `NO_PARENT`
	)

Default constructor

Parameters

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

References CONSTRUCTOR_TRACE.

◆ CChemEq() [2/2]

CChemEq::CChemEq	(	const CChemEq &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const CChemEq &	src
const	CDataContainer * pParent (default: NULL)

References CONSTRUCTOR_TRACE.

◆ ~CChemEq()

CChemEq::~CChemEq ( )

virtual

Destructor

References cleanup(), and DESTRUCTOR_TRACE.

Member Function Documentation

◆ addElement()

void CChemEq::addElement	(	CDataVector< CChemEqElement > &	structure,
		const CChemEqElement &	element,
		CChemEq::MetaboliteRole	role = `CChemEq::PRODUCT`
	)

private

Adds an element to the vector given by structure. The element is either SUBSTRATE or PRODUCT.

Parameters

CDataVector < CChemEqElement > &	structure
const CChemEqElement &	element
CChemEq::MetaboliteRole	role (

References CDataVector< CType >::add(), CChemEqElement::getMetaboliteKey(), CChemEqElement::getMultiplicity(), NO_PARENT, CChemEqElement::setMultiplicity(), CDataVector< CType >::size(), and SUBSTRATE.

Referenced by addMetabolite(), and setMultiplicity().

◆ addMetabolite()

bool CChemEq::addMetabolite	(	const std::string &	key,
		const C_FLOAT64	multiplicity,
		const MetaboliteRole &	role
	)

Add a species to the equation

Parameters

const	std::string & speciesKey
const	C_FLOAT64 & multiplicity
const	MetaboliteRole & role

Returns: bool success

References addElement(), fatalError, mBalances, mModifiers, MODIFIER, mProducts, mSubstrates, PRODUCT, CChemEqElement::setMetabolite(), CChemEqElement::setMultiplicity(), and SUBSTRATE.

Referenced by CReaction::addModifier(), CReaction::addProduct(), CReaction::addSubstrate(), SBMLImporter::applyStoichiometricExpressions(), SBMLImporter::isMassActionExpression(), CReaction::loadOneRole(), and CChemEqInterface::writeToChemEq().

◆ cleanup()

void CChemEq::cleanup ( )

Cleanup

References CDataVector< CType >::cleanup(), mBalances, mModifiers, mProducts, and mSubstrates.

Referenced by CChemEqInterface::writeToChemEq(), and ~CChemEq().

◆ getBalances()

const CDataVector< CChemEqElement > & CChemEq::getBalances ( ) const

Retrieves the vector of metabolites and their total balance in the chemical reaction.

Returns: "vector < CChemEqElement * > &" balances

References mBalances.

Referenced by CModel::appendAllDependents(), CMathReaction::initialize(), CModelExpansion::replaceInReaction(), and CMMLOutput::writeRHS().

◆ getCompartmentNumber()

size_t CChemEq::getCompartmentNumber ( ) const

Returns the number of compartments the chemical equation is associated with.

References getCompartments().

Referenced by CReaction::getCompartmentNumber(), and CReaction::getEffectiveKineticLawUnitType().

◆ getCompartments()

std::set< const CCompartment * > CChemEq::getCompartments ( ) const

Retrieves a set of the compartments.

References CDataVector< CType >::begin(), CDataVector< CType >::end(), mModifiers, mProducts, and mSubstrates.

Referenced by CReaction::createFunctionFromExpression(), and getCompartmentNumber().

◆ getLargestCompartment()

const CCompartment * CChemEq::getLargestCompartment ( ) const

Retrieve the largest compartment that the reaction touches. This is time dependent it can only be called after update initial values has been called. Note for an empty reaction a NULL pointer is returned.

Returns: const CCompartment * pCompartment

References C_FLOAT64, C_INVALID_INDEX, mProducts, mSubstrates, and CDataVector< CType >::size().

Referenced by CReaction::getLargestCompartment().

◆ getModifiers()

const CDataVector< CChemEqElement > & CChemEq::getModifiers ( ) const

Retrieves the vector of Modifiers and their multiplicity

References mModifiers.

Referenced by CModelAdd::addReactions(), CModelAnalyzer::checkReaction(), CReaction::compile(), SBMLImporter::createCReactionFromReaction(), CReaction::createFunctionFromExpression(), CSBMLExporter::createReaction(), CLayoutInitializer::createReactionGlyph(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), CChemEqInterface::init(), CModelMerging::mergeMetabolites(), CReaction::object2variable(), CModelAdd::reactionInvolvesCompartment(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), SBMLImporter::setCorrectUsage(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), and CLLayoutRenderer::update_associations().

◆ getMolecularity()

size_t CChemEq::getMolecularity ( const MetaboliteRole role ) const

Checks if it is possible to figure out a compartment from the information in the chemical equation. If there are substrates and if all the substrates are in the same compartment this compartment will be returned. If there are no substrates and there are Products and all Products are in the same compartment this compartment will be returned, else an exception will be thrown. This returns the sum of the multiplicities

References fatalError, mModifiers, MODIFIER, mProducts, mSubstrates, PRODUCT, CDataVector< CType >::size(), and SUBSTRATE.

◆ getProducts()

const CDataVector< CChemEqElement > & CChemEq::getProducts ( ) const

Retrieves the vector of products and their multiplicity in the chemical reaction.

Returns: "vector < CChemEqElement * > &" products

References mProducts.

Referenced by CModelAdd::addReactions(), CModelAnalyzer::checkReaction(), CReaction::compile(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CReaction::createFunctionFromExpression(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createReaction(), CLayoutInitializer::createReactionGlyph(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), SBMLImporter::findCorrespondingFunction(), CChemEqInterface::getCompartment(), CEFMTask::getNetReactionData(), CEFMTask::getSpeciesChanges(), CChemEqInterface::init(), SBMLImporter::isMassActionExpression(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), CReaction::object2variable(), CModelAdd::reactionInvolvesCompartment(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), SBMLImporter::setCorrectUsage(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), CReaction::setScalingFactor(), and CLLayoutRenderer::update_associations().

◆ getReversibility()

const bool & CChemEq::getReversibility ( ) const

Retrieve the reversibility of the equation

Returns: const bool & reversible

References mReversible.

Referenced by SBMLImporter::doMapping(), CChemEqInterface::init(), SBMLImporter::isMassActionExpression(), and CReaction::isReversible().

◆ getSubstrates()

const CDataVector< CChemEqElement > & CChemEq::getSubstrates ( ) const

Retrieves the vector of substrates and their multiplicity in the chemical reaction.

Returns: "vector < CChemEqElement * > &" substrates

References mSubstrates.

Referenced by CModelAdd::addReactions(), SBMLImporter::applyStoichiometricExpressions(), CModelAnalyzer::checkReaction(), CReaction::compile(), CMathObject::compilePropensity(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CReaction::createFunctionFromExpression(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createReaction(), CLayoutInitializer::createReactionGlyph(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), SBMLImporter::findCorrespondingFunction(), CChemEqInterface::getCompartment(), CEFMTask::getNetReactionData(), CEFMTask::getSpeciesChanges(), CChemEqInterface::init(), SBMLImporter::isMassActionExpression(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), CReaction::object2variable(), CModelAdd::reactionInvolvesCompartment(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), SBMLImporter::setCorrectUsage(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), CReaction::setScalingFactor(), and CLLayoutRenderer::update_associations().

◆ setMultiplicity()

bool CChemEq::setMultiplicity	(	const CMetab *	pMetab,
		C_FLOAT64	newMult,
		MetaboliteRole	role
	)

Sets the stoichiometry of the chemical element that corresponds to the given metabolite and role to the new value. The role has to be either CChemEqElement::SUBSTRATE or CChemEqElement::PRODUCT. If the role is invalid, the multiplicity is negative or zero or if the element for the metabolite and role can not be found in the chemical equation, false is returned and nothing is changed.

Sets the stoichiometry of the chemical element that corresponds to the given metabolite and role to the new value. The role has to be either CChemEqElement::SUBSTRATE or CChemEqElement::PRODUCT. If the role is invalid, the multiplicity if negative or if the element for the metabolite and role can not be found in the chemical equation, false is returned and nothing is changed.

References addElement(), CDataVector< CType >::begin(), C_FLOAT64, CDataVector< CType >::end(), CModelEntity::getKey(), mBalances, mProducts, mSubstrates, NO_PARENT, PRODUCT, CChemEqElement::setMultiplicity(), and SUBSTRATE.