#include <CReactionInterface.h>

Public Member Functions
void	clearChemEquation ()

	CReactionInterface ()

bool	createMetabolites ()

bool	createMetabolites (std::vector< std::string > &createdKeys)

bool	createOtherObjects () const

bool	createOtherObjects (std::vector< std::string > &createdKeys) const
	createOtherObjects More...

CUndoData	createUndoData (const CCore::Framework &framework) const

std::string	getAmountRateUnit () const

const CChemEqInterface &	getChemEqInterface () const

std::string	getChemEqString () const

std::string	getConcentrationRateUnit () const

std::string	getDefaultScalingCompartment () const

std::set< const CDataObject * >	getDeletedParameters () const

std::string	getEffectiveKineticLawUnit () const

CReaction::KineticLawUnit	getEffectiveKineticLawUnitType () const

const CFunction &	getFunction () const

std::string	getFunctionDescription () const

std::string	getFunctionName () const

const CReaction::KineticLawUnit &	getKineticLawUnitType () const

const std::vector< std::string > &	getListOfMetabs (CFunctionParameter::Role role) const

std::vector< std::string >	getListOfPossibleFunctions () const

const C_FLOAT64 &	getLocalValue (size_t index) const

const std::string &	getMapping (size_t index) const

const std::vector< std::string > &	getMappings (size_t index) const

const std::string &	getNoiseExpression () const

std::string	getParameterName (size_t index) const

const std::string &	getScalingCompartment () const

std::string	getUnit (size_t index) const

std::vector< std::string >	getUnitVector (size_t index) const

CFunctionParameter::Role	getUsage (size_t index) const

const bool &	hasNoise () const

void	init (const CReaction &reaction)

bool	isLocalValue (size_t index) const

bool	isLocked (CFunctionParameter::Role usage) const

bool	isLocked (size_t index) const

bool	isMulticompartment () const

bool	isReversible () const

bool	isValid () const

bool	isVector (size_t index) const

void	reverse (bool rev, const std::string &newFunction)

void	setChemEqString (const std::string &eq, const std::string &newFunction)

void	setFunctionAndDoMapping (const std::string &fn)

void	setFunctionWithEmptyMapping (const std::string &fn)

void	setHasNoise (const bool &hasNoise)

void	setKineticLawUnitType (const CReaction::KineticLawUnit &kineticLawUnitType)

void	setLocal (size_t index)

void	setLocalValue (size_t index, C_FLOAT64 value)

void	setMapping (size_t index, std::string mn)

bool	setNoiseExpression (const std::string &expression)

void	setReversibility (bool rev, const std::string &newFunction)

void	setScalingCompartment (const std::string &scalingCompartment)

size_t	size () const

bool	writeBackToReaction (CReaction *rea=NULL, bool compile=true)

	~CReactionInterface ()

Private Member Functions
void	connectFromScratch (CFunctionParameter::Role role)

void	connectNonMetabolites ()

void	copyMapping ()

void	findAndSetFunction (const std::string &newFunction)

std::vector< std::string >	getExpandedMetabList (CFunctionParameter::Role role) const

void	initMapping ()

bool	loadMappingAndValues ()

void	updateModifiersInChemEq ()

Private Attributes
CChemEqInterface	mChemEqI

bool	mHasNoise

std::vector< std::vector< std::string > * >	mIndexMap

std::vector< bool >	mIsLocal

CReaction::KineticLawUnit	mKineticLawUnitType

CCopasiParameterGroup	mLocalParameters

CFunction	mMassAction

std::map< std::string, std::vector< std::string > >	mNameMap

std::string	mNoiseExpression

const CFunction *	mpFunction

const CFunctionParameters *	mpFunctionParameters

const CModel *	mpModel

const CReaction *	mpReaction

std::string	mScalingCompartment

std::vector< C_FLOAT64 >	mValues

Detailed Description

This class provides an interface for dealing with reactions. For representing the parameter mappings it uses object names. A CReactionInterface allows editing a reaction while trying to keep everything consistent.

Note: Many of the methods need to be provided with a model. While handling of the metabolites is completely independent of the model (they are handled by name, and they don't need to exist), the mapping of Compartments and global parameters is done with the entities that exist in the model. This may seem inconsistent, but the idea is that metabolites can be created from the gui by entering them into the reaction equation. Compartments and global parameters can only be chosen from the list of existing objects.

Constructor & Destructor Documentation

◆ CReactionInterface()

CReactionInterface::CReactionInterface ( )

◆ ~CReactionInterface()

CReactionInterface::~CReactionInterface ( )

Member Function Documentation

◆ clearChemEquation()

void CReactionInterface::clearChemEquation ( )

internal function that temporarily removes the equation

References CChemEqInterface::clearAll(), mChemEqI, and setFunctionWithEmptyMapping().

◆ connectFromScratch()

void CReactionInterface::connectFromScratch ( CFunctionParameter::Role role )

private

guesses how to connect metabs with parameters for a specific usage

References fatalError, CFunctionParameter::FLOAT64, getExpandedMetabList(), CChemEqInterface::getListOfDisplayNames(), CFunctionParameters::getNumberOfParametersByUsage(), CDataObject::getObjectName(), CFunctionParameters::getParameterByUsage(), CFunctionParameter::getType(), mChemEqI, mNameMap, mpFunction, mpFunctionParameters, and CFunctionParameter::VFLOAT64.

Referenced by setFunctionAndDoMapping().

◆ connectNonMetabolites()

void CReactionInterface::connectNonMetabolites ( )

private

tries to determine the mapping for PARAMETER, VOLUME, TIME only if the current mapping is "unknown". Is typically called after initMapping() and copyMapping()

References CChemEqInterface::getCompartment(), CModel::getModelValues(), CDataObject::getObjectName(), getParameterName(), getUsage(), isLocalValue(), mChemEqI, mIndexMap, CFunctionParameter::MODIFIER, mpModel, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CDataVector< CType >::size(), size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, and CFunctionParameter::VOLUME.

Referenced by setFunctionAndDoMapping().

◆ copyMapping()

void CReactionInterface::copyMapping ( )

private

create new mapping, try to keep as much information from the current mapping. Calls initMapping().

References CFunctionParameters::findParameterByName(), getParameterName(), getUsage(), initMapping(), isVector(), mIsLocal, mNameMap, mpFunctionParameters, mValues, size(), and CFunctionParameter::VFLOAT64.

Referenced by setFunctionAndDoMapping().

◆ createMetabolites() [1/2]

bool CReactionInterface::createMetabolites ( )

create all metabolites that are needed by the reaction but do not exist in the model yet.

Referenced by CReaction::setReactionScheme().

◆ createMetabolites() [2/2]

bool CReactionInterface::createMetabolites ( std::vector< std::string > & createdKeys )

create all metabolites that are needed by the reaction but do not exist in the model yet.

Parameters

createdKeys vector, that will be filled with the keys of created elements

Returns: true in case elements were created, false otherwise

References CChemEqInterface::createNonExistingMetabs(), getFunctionName(), mChemEqI, and setFunctionAndDoMapping().

◆ createOtherObjects() [1/2]

bool CReactionInterface::createOtherObjects ( ) const

create all other objects that are needed by the reaction but do not exist in the model yet.

Referenced by CReaction::setReactionScheme().

◆ createOtherObjects() [2/2]

bool CReactionInterface::createOtherObjects ( std::vector< std::string > & createdKeys ) const

createOtherObjects

Parameters

createdKeys vector that will be filled with created keys

Returns: true, in case elements were created, false otherwise

References CModel::createCompartment(), CModel::createModelValue(), CModelEntity::getKey(), getUsage(), CDataContainer::insert(), isLocalValue(), mIndexMap, mpModel, CFunctionParameter::PARAMETER, size(), and CFunctionParameter::VOLUME.

◆ createUndoData()

CUndoData CReactionInterface::createUndoData ( const CCore::Framework & framework ) const

Create the undo data which represents the changes recording the differences between the provided oldData and the current data.

Parameters

const CCore::Framework & framework

Returns: CUndoData undoData

References CData::ADD_NOISE, CCopasiParameterGroup::addParameter(), CUndoData::addPreProcessData(), CUndoData::addProperty(), CData::addProperty(), C_FLOAT64, C_INVALID_INDEX, CUndoData::CHANGE, CData::CHEMICAL_EQUATION, CCore::Concentration, CChemEqInterface::displayNameToNamePair(), CCopasiParameter::DOUBLE, CCommonName::escape(), CDataObject::getCN(), CCopasiParameter::getCN(), CModel::getCompartments(), CDataVector< CType >::getIndex(), CDataVectorN< CType >::getIndex(), CModel::getMetabolites(), CModel::getMetabolitesX(), CModel::getModelValues(), CModel::getNumber2QuantityFactor(), CDataObject::getObjectName(), CCopasiParameterGroup::getParameter(), getParameterName(), CReaction::getParameters(), CData::getProperty(), CModel::getQuantity2NumberFactor(), getUsage(), CUndoData::INSERT, CData::KINETIC_LAW, CData::KINETIC_LAW_UNIT_TYPE, CData::KINETIC_LAW_VARIABLE_MAPPING, CReaction::KineticLawUnitTypeName, CChemEqInterface::listOfNonExistingMetabNames(), CData::LOCAL_REACTION_PARAMETERS, mChemEqI, mHasNoise, mIndexMap, mIsLocal, mKineticLawUnitType, mNoiseExpression, CFunctionParameter::MODIFIER, mpFunction, mpModel, mpReaction, mScalingCompartment, mValues, CData::NOISE_EXPRESSION, CData::OBJECT_NAME, CData::OBJECT_PARENT_CN, CData::OBJECT_REFERENCE_CN, CData::OBJECT_REFERENCE_INDEX, CData::OBJECT_REFERENCES, CFunctionParameter::PARAMETER, CData::PARAMETER_VALUE, CCore::ParticleNumbers, CFunctionParameter::PRODUCT, CData::SCALING_COMPARTMENT, CMetab::setInitialConcentration(), CModelEntity::setInitialValue(), size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, CReaction::toData(), CCopasiParameter::toData(), CChemEqInterface::toDataValue(), CDataValue::toDataVector(), and CFunctionParameter::VOLUME.

◆ findAndSetFunction()

void CReactionInterface::findAndSetFunction ( const std::string & newFunction )

private

checks if newFunction is an valid function for the reaction. If it is not or if newFunction="" another function is chosen.

References C_FLOAT64, fl(), getFunctionName(), CChemEqInterface::getListOfDisplayNames(), getListOfPossibleFunctions(), getLocalValue(), CChemEqInterface::getReversibility(), mChemEqI, CFunctionParameter::PRODUCT, setFunctionAndDoMapping(), and setLocalValue().

Referenced by reverse(), setChemEqString(), and setReversibility().

◆ getAmountRateUnit()

std::string CReactionInterface::getAmountRateUnit ( ) const

Returns: the amount rate unit display name

References CModel::getQuantityUnit(), CModel::getTimeUnit(), and mpModel.

Referenced by getEffectiveKineticLawUnit().

◆ getChemEqInterface()

const CChemEqInterface & CReactionInterface::getChemEqInterface ( ) const

References mChemEqI.

◆ getChemEqString()

std::string CReactionInterface::getChemEqString ( ) const

References CChemEqInterface::getChemEqString(), and mChemEqI.

Referenced by CReaction::getReactionScheme().

◆ getConcentrationRateUnit()

std::string CReactionInterface::getConcentrationRateUnit ( ) const

Returns: the concentration rate unit display name

References C_INVALID_INDEX, CModel::getCompartments(), getDefaultScalingCompartment(), CDataVectorN< CType >::getIndex(), CModel::getQuantityUnit(), CModel::getTimeUnit(), CCompartment::getUnits(), CModel::getVolumeUnit(), and mpModel.

Referenced by getEffectiveKineticLawUnit().

◆ getDefaultScalingCompartment()

std::string CReactionInterface::getDefaultScalingCompartment ( ) const

Returns: the default scaling compartment

References CReaction::Default, CChemEqInterface::getDefaultCompartment(), mChemEqI, mKineticLawUnitType, and mScalingCompartment.

Referenced by getConcentrationRateUnit().

◆ getDeletedParameters()

std::set< const CDataObject * > CReactionInterface::getDeletedParameters ( ) const

Retrieve the list of parameters which will be deleted

Returns: std::set< const CDataObject * > DeletedParameters

References CReaction::getFunction(), CDataObject::getObjectName(), CCopasiParameterGroup::getParameter(), getParameterName(), CReaction::getParameters(), CFunctionParameter::getUsage(), CFunction::getVariables(), CReaction::isLocalParameter(), mIsLocal, mpReaction, CFunctionParameter::PARAMETER, CFunctionParameters::size(), and size().

◆ getEffectiveKineticLawUnit()

std::string CReactionInterface::getEffectiveKineticLawUnit ( ) const

Returns: the effective kinetic law unit

References CReaction::AmountPerTime, CReaction::ConcentrationPerTime, getAmountRateUnit(), getConcentrationRateUnit(), and getEffectiveKineticLawUnitType().

◆ getEffectiveKineticLawUnitType()

CReaction::KineticLawUnit CReactionInterface::getEffectiveKineticLawUnitType ( ) const

Returns: the effective unit type in case the default is selected

References CReaction::AmountPerTime, CReaction::ConcentrationPerTime, CReaction::Default, isMulticompartment(), and mKineticLawUnitType.

Referenced by getEffectiveKineticLawUnit().

◆ getExpandedMetabList()

std::vector< std::string > CReactionInterface::getExpandedMetabList ( CFunctionParameter::Role role ) const

private

returns a list of metabolites (from the chemical equation). Species can occur several times according to the multiplicity

References C_FLOAT64, CChemEqInterface::getListOfDisplayNames(), CChemEqInterface::getListOfMultiplicities(), mChemEqI, and CFunctionParameter::MODIFIER.

Referenced by connectFromScratch().

◆ getFunction()

const CFunction & CReactionInterface::getFunction ( ) const

Returns: the function

References CChemEqInterface::getMolecularity(), CDataObject::getObjectName(), CEvaluationTree::getType(), CRootContainer::getUndefinedFunction(), CFunction::isReversible(), mChemEqI, mMassAction, mpFunction, CFunctionParameter::PRODUCT, CFunction::setInfix(), CDataObject::setObjectName(), CFunctionParameter::SUBSTRATE, and TriTrue.

◆ getFunctionDescription()

std::string CReactionInterface::getFunctionDescription ( ) const

Returns: the function description

References CEvaluationTree::getInfix(), and mpFunction.

◆ getFunctionName()

std::string CReactionInterface::getFunctionName ( ) const

Returns: the function name

References CDataObject::getObjectName(), and mpFunction.

Referenced by createMetabolites(), and findAndSetFunction().

◆ getKineticLawUnitType()

const CReaction::KineticLawUnit & CReactionInterface::getKineticLawUnitType ( ) const

Returns: the currently set unit type

References mKineticLawUnitType.

◆ getListOfMetabs()

const std::vector< std::string > & CReactionInterface::getListOfMetabs ( CFunctionParameter::Role role ) const

This produces a list of metabolite names (from the chem eq) for use in the combo boxes. The role must be given like a usage, e.g. "SUBSTRATE".

References CChemEqInterface::getListOfDisplayNames(), and mChemEqI.

Referenced by setMapping().

◆ getListOfPossibleFunctions()

std::vector< std::string > CReactionInterface::getListOfPossibleFunctions ( ) const

Returns: a vector of possible functions for the specified number substrates / products and reversibility

References CRootContainer::getFunctionList(), CChemEqInterface::getMolecularity(), isReversible(), mChemEqI, CFunctionParameter::PRODUCT, CFunctionParameter::SUBSTRATE, CFunctionDB::suitableFunctions(), TriFalse, and TriTrue.

Referenced by findAndSetFunction().

◆ getLocalValue()

const double & CReactionInterface::getLocalValue ( size_t index ) const

Return the local parameter value of the parameter with given index

Parameters

index the index of the parameter

Returns: the value of the parameter with given index

References mValues.

Referenced by findAndSetFunction().

◆ getMapping()

const std::string & CReactionInterface::getMapping ( size_t index ) const

return the first mapping for the given index

Parameters

index the index

Returns: the first mapping for the given index

References mIndexMap.

Referenced by updateModifiersInChemEq().

◆ getMappings()

const std::vector< std::string > & CReactionInterface::getMappings ( size_t index ) const

returns all mappings for the given index

Parameters

index the index

Returns: the string vector of all mappings for the given index

References mIndexMap.

◆ getNoiseExpression()

const std::string & CReactionInterface::getNoiseExpression ( ) const

Retrieve the expression for non FIXED model values.

Returns: const std::string & expression

References mNoiseExpression.

◆ getParameterName()

std::string CReactionInterface::getParameterName ( size_t index ) const

Returns the name of the parameter with given index

Parameters

index the index

Returns: the name of the parameter if found, or an empty string

References mpFunctionParameters, and size().

Referenced by connectNonMetabolites(), copyMapping(), createUndoData(), getDeletedParameters(), initMapping(), loadMappingAndValues(), setMapping(), and writeBackToReaction().

◆ getScalingCompartment()

const std::string & CReactionInterface::getScalingCompartment ( ) const

Returns: the specified scaling compartment

References mScalingCompartment.

◆ getUnit()

std::string CReactionInterface::getUnit ( size_t index ) const

◆ getUnitVector()

std::vector< std::string > CReactionInterface::getUnitVector ( size_t index ) const

◆ getUsage()

CFunctionParameter::Role CReactionInterface::getUsage ( size_t index ) const

returns the function parameter role for the parameter with given index

Parameters

index the index

Returns: the role of that function parameter

References mpFunctionParameters, size(), and CFunctionParameter::VARIABLE.

Referenced by connectNonMetabolites(), copyMapping(), createOtherObjects(), createUndoData(), getUnit(), getUnitVector(), initMapping(), isLocked(), loadMappingAndValues(), setMapping(), updateModifiersInChemEq(), and writeBackToReaction().

◆ hasNoise()

const bool & CReactionInterface::hasNoise ( ) const

Check whether noise is added to the reaction rate

Returns: const bool & hasNoise

References mHasNoise.

Referenced by setHasNoise().

◆ init()

◆ initMapping()

void CReactionInterface::initMapping ( )

private

initialize mapping (resize vectors and set names to "unknown"). Also initializes mpParameters but doesn't delete the old mpParameters.

References getParameterName(), getUsage(), CFunction::getVariables(), isVector(), mIndexMap, mIsLocal, mNameMap, mpFunction, mpFunctionParameters, mValues, CFunctionParameter::PARAMETER, and size().

Referenced by copyMapping(), init(), and setFunctionWithEmptyMapping().

◆ isLocalValue()

bool CReactionInterface::isLocalValue ( size_t index ) const

tests whether the parameter with given index is a local parameter

Parameters

index the index

Returns: true, if the parameter with given index is local, false otherwise

References mIsLocal.

Referenced by connectNonMetabolites(), createOtherObjects(), and getUnit().

◆ isLocked() [1/2]

bool CReactionInterface::isLocked ( CFunctionParameter::Role usage ) const

Is the mapping of this parameter locked? The behavior of this method is different for different roles: SUBSTRATE, PRODUCT: according to the chemical equation MODIFIER: always unlocked TIME: always locked VOLUME, PARAMETER: according to the model

The idea is that in the reaction GUI new species can be entered in the chemical equation that are then created automatically. Compartments and global parameters can only be chosen from those existing in the model.

Parameters

usage the usage of the parameter

Returns: boolean indicating whether the parameter with given usage should be locked

References CModel::getCompartments(), CChemEqInterface::getListOfDisplayNames(), CModel::getModelValues(), CFunctionParameters::getNumberOfParametersByUsage(), CFunctionParameters::getParameterByUsage(), isVector(), mChemEqI, CFunctionParameter::MODIFIER, mpFunctionParameters, mpModel, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CDataVector< CType >::size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, and CFunctionParameter::VOLUME.

◆ isLocked() [2/2]

bool CReactionInterface::isLocked ( size_t index ) const

Is the mapping of this parameter locked? The behavior of this method is different for different roles: SUBSTRATE, PRODUCT: according to the chemical equation MODIFIER: always unlocked TIME: always locked VOLUME, PARAMETER: according to the model

The idea is that in the reaction GUI new species can be entered in the chemical equation that are then created automatically. Compartments and global parameters can only be chosen from those existing in the model.

Parameters

index the index of the parameter

Returns: boolean indicating whether the parameter is locked or not

References getUsage().

◆ isMulticompartment()

bool CReactionInterface::isMulticompartment ( ) const

this method tries to find out if the REACTION involves several compartments It only takes into account the metabolites that actually exist in the model. A non existing metabolite is assumed not to be in a different compartment

References CChemEqInterface::isMulticompartment(), and mChemEqI.

Referenced by getEffectiveKineticLawUnitType().

◆ isReversible()

bool CReactionInterface::isReversible ( ) const

References CChemEqInterface::getReversibility(), and mChemEqI.

Referenced by getListOfPossibleFunctions().

◆ isValid()

bool CReactionInterface::isValid ( ) const

Returns: boolean indicating whether this reaction is valid

References mIndexMap, mIsLocal, and size().

Referenced by writeBackToReaction().

◆ isVector()

bool CReactionInterface::isVector ( size_t index ) const

Tests whether the parameter at the given index is of type vector

Parameters

index the index

Returns: true, if the function parameter at the given index is a vector false otherwise

References mpFunctionParameters, size(), and CFunctionParameter::VFLOAT64.

Referenced by copyMapping(), getUnit(), initMapping(), isLocked(), loadMappingAndValues(), and setMapping().

◆ loadMappingAndValues()

bool CReactionInterface::loadMappingAndValues ( )

private

Loads mapping and values from the specified reaction

Returns: true if successful, false otherwise

References C_FLOAT64, CMetabNameInterface::getDisplayName(), CModelEntity::getInitialValue(), CDataObject::getObjectName(), CCopasiParameterGroup::getParameter(), getParameterName(), CReaction::getParameterObjects(), CReaction::getParameters(), getUsage(), CCopasiParameter::getValue(), CReaction::isLocalParameter(), isVector(), mIndexMap, mIsLocal, mNameMap, CFunctionParameter::MODIFIER, mpModel, mpReaction, mValues, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, and CFunctionParameter::VOLUME.

Referenced by init().

◆ reverse()

void CReactionInterface::reverse	(	bool	rev,
		const std::string &	newFunction
	)

reverse the reaction and set the reversibility. newFunction suggests a new kinetic function which is only used if adequate.

References findAndSetFunction(), mChemEqI, CChemEqInterface::reverse(), and CChemEqInterface::setReversibility().

◆ setChemEqString()

void CReactionInterface::setChemEqString	(	const std::string &	eq,
		const std::string &	newFunction
	)

set a new chemical equation. newFunction suggests a new kinetic function which is only used if adequate.

References findAndSetFunction(), mChemEqI, and CChemEqInterface::setChemEqString().

Referenced by CReaction::setReactionScheme().

◆ setFunctionAndDoMapping()

void CReactionInterface::setFunctionAndDoMapping ( const std::string & fn )

set the function. a new mapping is created that tries to preserve as much information as possible from the old mapping. Then a default mapping is set from the chemical equation and the model (if possible).

References connectFromScratch(), connectNonMetabolites(), copyMapping(), CFunctionDB::findLoadFunction(), CRootContainer::getFunctionList(), CRootContainer::getUndefinedFunction(), CFunctionParameter::MODIFIER, mpFunction, CFunctionParameter::PRODUCT, and CFunctionParameter::SUBSTRATE.

Referenced by CReaction::compile(), createMetabolites(), findAndSetFunction(), and init().

◆ setFunctionWithEmptyMapping()

void CReactionInterface::setFunctionWithEmptyMapping ( const std::string & fn )

set the function. an empty mapping is created

References CFunctionDB::findLoadFunction(), CRootContainer::getFunctionList(), CRootContainer::getUndefinedFunction(), initMapping(), mpFunction, and mpFunctionParameters.

Referenced by clearChemEquation(), and init().

◆ setHasNoise()

void CReactionInterface::setHasNoise ( const bool & hasNoise )

Set whether to add noise to the reaction rate

Parameters

const bool & hasNoise

References CReaction::getDefaultNoiseExpression(), hasNoise(), mHasNoise, mNoiseExpression, and mpReaction.

◆ setKineticLawUnitType()

void CReactionInterface::setKineticLawUnitType ( const CReaction::KineticLawUnit & kineticLawUnitType )

Sets the kinetic law unit type

Parameters

kineticLawUnitType the type to set

References mKineticLawUnitType.

◆ setLocal()

void CReactionInterface::setLocal ( size_t index )

Specified that the parameter with given index should be a local parameter

Parameters

index the index

References mIsLocal.

◆ setLocalValue()

void CReactionInterface::setLocalValue	(	size_t	index,
		C_FLOAT64	value
	)

Specifies that the parameter with given index should be a local parameter and specifies the value

Parameters

index	the index of the parameter
value	the new value of the parameter

References mIsLocal, and mValues.

Referenced by findAndSetFunction().

◆ setMapping()

void CReactionInterface::setMapping	(	size_t	index,
		std::string	mn
	)

Sets the mapping of the parameter with given index

Parameters

index	the index
mn	the mapping

References CChemEqInterface::getListOfDisplayNames(), getListOfMetabs(), CFunctionParameters::getNumberOfParametersByUsage(), CFunctionParameters::getParameterByUsage(), getParameterName(), getUsage(), isVector(), mChemEqI, mIsLocal, mNameMap, CFunctionParameter::MODIFIER, mpFunctionParameters, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, updateModifiersInChemEq(), and CFunctionParameter::VOLUME.

◆ setNoiseExpression()

bool CReactionInterface::setNoiseExpression ( const std::string & expression )

Set the expression for non FIXED model values

Parameters

const std::string & expression

Returns: bool success

References mNoiseExpression.

◆ setReversibility()

void CReactionInterface::setReversibility	(	bool	rev,
		const std::string &	newFunction
	)

set the reversibility. newFunction suggests a new kinetic function which is only used if adequate.

References findAndSetFunction(), mChemEqI, and CChemEqInterface::setReversibility().

◆ setScalingCompartment()

void CReactionInterface::setScalingCompartment ( const std::string & scalingCompartment )

Sets the scaling compartment to be used for this reaction

Parameters

scalingCompartment

References mScalingCompartment.

◆ size()

size_t CReactionInterface::size ( ) const

Returns: number of function parameter

References mpFunctionParameters, and CFunctionParameters::size().

Referenced by connectNonMetabolites(), copyMapping(), createOtherObjects(), createUndoData(), getDeletedParameters(), getParameterName(), getUsage(), initMapping(), isValid(), isVector(), loadMappingAndValues(), updateModifiersInChemEq(), and writeBackToReaction().

◆ updateModifiersInChemEq()

void CReactionInterface::updateModifiersInChemEq ( )

private

updates the modifiers in the chemical equation according to the parameter mapping

References CChemEqInterface::addModifier(), CChemEqInterface::clearModifiers(), getMapping(), getUsage(), mChemEqI, CFunctionParameter::MODIFIER, and size().

Referenced by setMapping().

◆ writeBackToReaction()

bool CReactionInterface::writeBackToReaction	(	CReaction *	rea = `NULL`,
		bool	compile = `true`
	)

writes the information back to a CReaction. createMetabolites() and createOtherObjects() should be called before.

Parameters

bool	compile (default: true)

References C_INVALID_INDEX, CReaction::getChemEq(), CDataObject::getCN(), CModel::getCompartments(), CDataVectorN< CType >::getIndex(), CMetabNameInterface::getMetabolite(), CModel::getModelValues(), CDataObject::getObjectAncestor(), CDataObject::getObjectName(), CCopasiParameterGroup::getParameter(), getParameterName(), CReaction::getParameters(), getUsage(), CFunction::getVariables(), isValid(), mChemEqI, mHasNoise, mIndexMap, mIsLocal, mKineticLawUnitType, mNoiseExpression, CFunctionParameter::MODIFIER, mpFunction, mpFunctionParameters, mpModel, mpReaction, mScalingCompartment, mValues, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CReaction::setFunction(), CReaction::setHasNoise(), CReaction::setKineticLawUnitType(), CReaction::setNoiseExpression(), CReaction::setParameterObjects(), CReaction::setParameterValue(), CReaction::setScalingCompartmentCN(), size(), CMetabNameInterface::splitDisplayName(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, CFunctionParameter::VOLUME, and CChemEqInterface::writeToChemEq().

Referenced by CReaction::compile(), and CReaction::setReactionScheme().

Member Data Documentation

◆ mChemEqI

CChemEqInterface CReactionInterface::mChemEqI

private

A copy of the chemical equation of the reaction

Referenced by clearChemEquation(), connectFromScratch(), connectNonMetabolites(), createMetabolites(), createUndoData(), findAndSetFunction(), getChemEqInterface(), getChemEqString(), getDefaultScalingCompartment(), getExpandedMetabList(), getFunction(), getListOfMetabs(), getListOfPossibleFunctions(), init(), isLocked(), isMulticompartment(), isReversible(), reverse(), setChemEqString(), setMapping(), setReversibility(), updateModifiersInChemEq(), and writeBackToReaction().

◆ mHasNoise

bool CReactionInterface::mHasNoise

private

Referenced by createUndoData(), hasNoise(), init(), setHasNoise(), and writeBackToReaction().

◆ mIndexMap

std::vector< std::vector< std::string > * > CReactionInterface::mIndexMap

private

Referenced by connectNonMetabolites(), createOtherObjects(), createUndoData(), getMapping(), getMappings(), getUnit(), getUnitVector(), initMapping(), isValid(), loadMappingAndValues(), and writeBackToReaction().

◆ mIsLocal

std::vector<bool> CReactionInterface::mIsLocal

private

values of the kinetic parameters

Referenced by copyMapping(), createUndoData(), getDeletedParameters(), initMapping(), isLocalValue(), isValid(), loadMappingAndValues(), setLocal(), setLocalValue(), setMapping(), and writeBackToReaction().

◆ mKineticLawUnitType

CReaction::KineticLawUnit CReactionInterface::mKineticLawUnitType

private

Referenced by createUndoData(), getDefaultScalingCompartment(), getEffectiveKineticLawUnitType(), getKineticLawUnitType(), init(), setKineticLawUnitType(), and writeBackToReaction().

◆ mLocalParameters

CCopasiParameterGroup CReactionInterface::mLocalParameters

private

Referenced by init().

◆ mMassAction

CFunction CReactionInterface::mMassAction

mutableprivate

Referenced by getFunction().

◆ mNameMap

std::map< std::string, std::vector< std::string > > CReactionInterface::mNameMap

private

what metabolite for what function parameter

Referenced by connectFromScratch(), copyMapping(), initMapping(), loadMappingAndValues(), and setMapping().

◆ mNoiseExpression

std::string CReactionInterface::mNoiseExpression

private

Referenced by createUndoData(), getNoiseExpression(), init(), setHasNoise(), setNoiseExpression(), and writeBackToReaction().

◆ mpFunction

const CFunction* CReactionInterface::mpFunction

private

A pointer to the kinetic function of the reaction

Referenced by connectFromScratch(), createUndoData(), getFunction(), getFunctionDescription(), getFunctionName(), init(), initMapping(), setFunctionAndDoMapping(), setFunctionWithEmptyMapping(), and writeBackToReaction().

◆ mpFunctionParameters

const CFunctionParameters* CReactionInterface::mpFunctionParameters

private

A pointer of the function parameters

Referenced by connectFromScratch(), copyMapping(), getParameterName(), getUsage(), initMapping(), isLocked(), isVector(), setFunctionWithEmptyMapping(), setMapping(), size(), and writeBackToReaction().

◆ mpModel

const CModel* CReactionInterface::mpModel

mutableprivate

Referenced by connectNonMetabolites(), createOtherObjects(), createUndoData(), getAmountRateUnit(), getConcentrationRateUnit(), getUnit(), getUnitVector(), init(), isLocked(), loadMappingAndValues(), and writeBackToReaction().

◆ mpReaction

const CReaction* CReactionInterface::mpReaction

private

Referenced by createUndoData(), getDeletedParameters(), init(), loadMappingAndValues(), setHasNoise(), and writeBackToReaction().

◆ mScalingCompartment

std::string CReactionInterface::mScalingCompartment

private

Referenced by createUndoData(), getDefaultScalingCompartment(), getScalingCompartment(), init(), setScalingCompartment(), and writeBackToReaction().

◆ mValues

std::vector< C_FLOAT64 > CReactionInterface::mValues

private

values of the kinetic parameters

Referenced by copyMapping(), createUndoData(), getLocalValue(), initMapping(), loadMappingAndValues(), setLocalValue(), and writeBackToReaction().

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ CReactionInterface()

◆ ~CReactionInterface()

Member Function Documentation

◆ clearChemEquation()

◆ connectFromScratch()

◆ connectNonMetabolites()

◆ copyMapping()

◆ createMetabolites() [1/2]

◆ createMetabolites() [2/2]

◆ createOtherObjects() [1/2]

◆ createOtherObjects() [2/2]

◆ createUndoData()

◆ findAndSetFunction()

◆ getAmountRateUnit()

◆ getChemEqInterface()

◆ getChemEqString()

◆ getConcentrationRateUnit()

◆ getDefaultScalingCompartment()

◆ getDeletedParameters()

◆ getEffectiveKineticLawUnit()

◆ getEffectiveKineticLawUnitType()

◆ getExpandedMetabList()

◆ getFunction()

◆ getFunctionDescription()

◆ getFunctionName()

◆ getKineticLawUnitType()

◆ getListOfMetabs()

◆ getListOfPossibleFunctions()

◆ getLocalValue()

◆ getMapping()

◆ getMappings()

◆ getNoiseExpression()

◆ getParameterName()

◆ getScalingCompartment()

◆ getUnit()

◆ getUnitVector()

◆ getUsage()

◆ hasNoise()

◆ init()

◆ initMapping()

◆ isLocalValue()

◆ isLocked() [1/2]

◆ isLocked() [2/2]

◆ isMulticompartment()

◆ isReversible()

◆ isValid()

◆ isVector()

◆ loadMappingAndValues()

◆ reverse()

◆ setChemEqString()

◆ setFunctionAndDoMapping()

◆ setFunctionWithEmptyMapping()

◆ setHasNoise()

◆ setKineticLawUnitType()

◆ setLocal()

◆ setLocalValue()

◆ setMapping()

◆ setNoiseExpression()

◆ setReversibility()

◆ setScalingCompartment()

◆ size()

◆ updateModifiersInChemEq()

◆ writeBackToReaction()

Member Data Documentation

◆ mChemEqI

◆ mHasNoise

◆ mIndexMap

◆ mIsLocal

◆ mKineticLawUnitType

◆ mLocalParameters

◆ mMassAction

◆ mNameMap

◆ mNoiseExpression

◆ mpFunction

◆ mpFunctionParameters