COPASI API  4.40.278
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Member Functions | Static Private Member Functions | Private Attributes | Friends | List of all members
CReaction Class Reference

#include <CReaction.h>

Inheritance diagram for CReaction:
[legend]

Public Types

enum class  KineticLawUnit { Default , AmountPerTime , ConcentrationPerTime , __SIZE }
 
- 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 Types inherited from CAnnotation
typedef std::map< std::string, std::string > UnsupportedAnnotation
 

Public Member Functions

bool addModifier (const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
 
bool addParameterObject (const size_t &index, const CDataObject *object)
 
bool addParameterObject (const std::string &name, const CDataObject *object)
 
bool addProduct (const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
 
bool addSubstrate (const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
 
virtual bool applyData (const CData &data, CUndoData::CChangeSet &changes)
 
CIssue compile ()
 
 CReaction (const CReaction &src, const CDataContainer *pParent)
 
 CReaction (const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT)
 
CFunction * createFunctionFromExpression (const std::string &infix)
 
virtual void createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
 
const CCallParameters< C_FLOAT64 > & getCallParameters () const
 
CChemEq & getChemEq ()
 
const CChemEq & getChemEq () const
 
virtual std::string getChildObjectUnits (const CDataObject *pObject) const
 
size_t getCompartmentNumber () const
 
std::string getDefaultNoiseExpression () const
 
KineticLawUnit getEffectiveKineticLawUnitType () const
 
CEvaluationNode * getExpressionTree ()
 
const C_FLOAT64 & getFlux () const
 
CDataObject * getFluxReference ()
 
const CDataObject * getFluxReference () const
 
const CFunction * getFunction () const
 
const CFunctionParameters & getFunctionParameters () const
 
virtual const std::string & getKey () const
 
std::string getKineticLawUnit () const
 
const KineticLawUnit & getKineticLawUnitType () const
 
const CCompartment * getLargestCompartment () const
 
const CFunctionParameterMap & getMap () const
 
std::string getNoiseExpression () const
 
CExpression * getNoiseExpressionPtr ()
 
const CExpression * getNoiseExpressionPtr () const
 
const CDataObject * getNoiseReference () const
 
virtual const CObjectInterface * getObject (const CCommonName &cn) const
 
virtual std::string getObjectDisplayName () const
 
const std::vector< std::vector< CRegisteredCommonName > > & getParameterCNs () const
 
const std::vector< CRegisteredCommonName > & getParameterCNs (const size_t &index) const
 
const std::vector< CRegisteredCommonName > & getParameterCNs (const std::string &name) const
 
size_t getParameterIndex (const std::string &parameterName, const CFunctionParameter **ppFunctionParameter=NULL) const
 
const std::vector< std::vector< const CDataObject * > > & getParameterObjects () const
 
const std::vector< const CDataObject * > & getParameterObjects (const size_t &index) const
 
const std::vector< const CDataObject * > & getParameterObjects (const std::string &name) const
 
CCopasiParameterGroup & getParameters ()
 
const CCopasiParameterGroup & getParameters () const
 
const C_FLOAT64 & getParameterValue (const std::string &parameterName) const
 
const C_FLOAT64 & getParticleFlux () const
 
CDataObject * getParticleFluxReference ()
 
const CDataObject * getParticleFluxReference () const
 
const CDataObject * getParticleNoiseReference () const
 
CDataObject * getPropensityReference ()
 
const CDataObject * getPropensityReference () const
 
std::string getReactionScheme () const
 
const std::string & getSBMLId () const
 
const CCompartment * getScalingCompartment () const
 
const CCommonName & getScalingCompartmentCN () const
 
const bool & hasNoise () const
 
const bool & isFast () const
 
bool isLocalParameter (const size_t &index) const
 
bool isLocalParameter (const std::string &parameterName) const
 
bool isReversible () const
 
C_INT32 load (CReadConfig &configbuffer)
 
void printDebug () const
 
void setFast (const bool &fast)
 
bool setFunction (CFunction *pFunction)
 
bool setFunction (const std::string &functionName)
 
CFunction * setFunctionFromExpressionTree (const CExpression &tree, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)
 
void setHasNoise (const bool &hasNoise)
 
void setKineticLawUnitType (const KineticLawUnit &kineticLawUnitType)
 
bool setNoiseExpression (const std::string &expression)
 
bool setNoiseExpressionPtr (CExpression *pExpression)
 
virtual bool setObjectParent (const CDataContainer *pParent)
 
bool setParameterCNs (const size_t &index, const std::vector< CRegisteredCommonName > &CNs)
 
bool setParameterCNs (const std::string &name, const std::vector< CRegisteredCommonName > &CNs)
 
bool setParameterObject (const size_t &index, const CDataObject *object)
 
bool setParameterObject (const std::string &name, const CDataObject *object)
 
bool setParameterObjects (const size_t &index, const std::vector< const CDataObject * > &objects)
 
bool setParameterObjects (const std::string &name, const std::vector< const CDataObject * > &objects)
 
void setParameterValue (const std::string &parameterName, const C_FLOAT64 &value)
 
bool setReactionScheme (const std::string &scheme, const std::string &newFunction="", bool createMetabolites=true, bool createOther=true)
 
void setReversible (bool reversible)
 
void setSBMLId (const std::string &id) const
 
void setScalingCompartment (const CCompartment *pCompartment)
 
void setScalingCompartmentCN (const std::string &compartmentCN)
 
virtual CData toData () const
 
virtual ~CReaction ()
 
- Public Member Functions inherited from CDataContainer
virtual bool add (CDataObject *pObject, const bool &adopt=true)
 
virtual bool appendDeletedDependentData (CUndoData &undoData) const
 
 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)
 
void getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const
 
virtual size_t getIndex (const CDataObject *pObject) const
 
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 ~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
 
CDataContainer * getObjectAncestor (const std::string &type) const
 
CDataModel * getObjectDataModel () const
 
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)
 
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 ()
 
- Public Member Functions inherited from CAnnotation
bool addUnsupportedAnnotation (const std::string &name, const std::string &xml)
 
bool applyData (const CData &data, CUndoData::CChangeSet &changes)
 
 CAnnotation ()
 
 CAnnotation (const CAnnotation &src)
 
void createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const
 
const std::string & getMiriamAnnotation () const
 
const std::string & getNotes () const
 
UnsupportedAnnotation & getUnsupportedAnnotations ()
 
const UnsupportedAnnotation & getUnsupportedAnnotations () const
 
void initMiriamAnnotation (const std::string &newId)
 
bool operator== (const CAnnotation &rhs) const
 
bool removeUnsupportedAnnotation (const std::string &name)
 
bool replaceUnsupportedAnnotation (const std::string &name, const std::string &xml)
 
void setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)
 
void setNotes (const std::string &notes)
 
CData toData () const
 
virtual ~CAnnotation ()
 

Static Public Member Functions

static CReaction * fromData (const CData &data, CUndoObjectInterface *pParent)
 
- 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 Member Functions inherited from CAnnotation
static CMIRIAMInfo * allocateMiriamInfo (CDataContainer *pParent)
 
static CAnnotation * castObject (CDataObject *pObject)
 
static const CAnnotation * castObject (const CDataObject *pObject)
 
static void freeMiriamInfo (CDataContainer *pParent)
 

Static Public Attributes

static CEnumAnnotation< std::string, KineticLawUnit > KineticLawUnitTypeName
 
- Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList EmptyList
 

Private Member Functions

void calculate ()
 
CIssue compileFunctionParameters (std::set< const CDataObject * > &Dependencies)
 
std::string escapeId (const std::string &id)
 
const CModel * getFirstCModelOrDefault (std::map< const CDataObject *, SBase * > &copasi2sbmlmap)
 
void initializeParameterMapping ()
 
void initializeParameters ()
 
void initObjects ()
 
C_INT32 loadOld (CReadConfig &configbuffer)
 
bool loadOneRole (CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix)
 
CEvaluationNodeVariable * object2variable (const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &replacementMap, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)
 
CEvaluationNode * objects2variables (const CEvaluationNode *expression, std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &replacementMap, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)
 
CReaction & operator= (const CReaction &)
 
CDataObject * resolveCN (const CModel *pModel, CCommonName cn)
 
void setScalingFactor ()
 
CEvaluationNodeObject * variable2object (CEvaluationNodeVariable *pVariableNode)
 
CEvaluationNode * variables2objects (CEvaluationNode *expression)
 

Static Private Member Functions

static std::string sanitizeSBMLId (const std::string &id)
 

Private Attributes

CChemEq mChemEq
 
bool mFast
 
C_FLOAT64 mFlux
 
bool mHasNoise
 
KineticLawUnit mKineticLawUnit
 
CFunctionParameterMap mMap
 
C_FLOAT64 mNoise
 
std::vector< std::vector< CRegisteredCommonName > > mParameterIndexToCNs
 
std::vector< std::vector< const CDataObject * > > mParameterIndexToObjects
 
std::map< std::string, size_t > mParameterNameToIndex
 
CCopasiParameterGroup mParameters
 
C_FLOAT64 mParticleFlux
 
C_FLOAT64 mParticleNoise
 
CDataObjectReference< C_FLOAT64 > * mpFluxReference
 
CFunction * mpFunction
 
CExpression * mpNoiseExpression
 
CDataObjectReference< C_FLOAT64 > * mpNoiseReference
 
CDataObjectReference< C_FLOAT64 > * mpParticleFluxReference
 
CDataObjectReference< C_FLOAT64 > * mpParticleNoiseReference
 
CDataObjectReference< C_FLOAT64 > * mpPropensityReference
 
C_FLOAT64 mPropensity
 
const CCompartment * mpScalingCompartment
 
std::string mSBMLId
 
CRegisteredCommonName mScalingCompartmentCN
 

Friends

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

Additional Inherited Members

- 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
 
- Protected Attributes inherited from CAnnotation
std::string mKey
 

Member Enumeration Documentation

◆ KineticLawUnit

enum CReaction::KineticLawUnit
strong
Enumerator
Default 
AmountPerTime 
ConcentrationPerTime 
__SIZE 

Constructor & Destructor Documentation

◆ CReaction() [1/2]

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

Default constructor

Parameters
conststd::string & name (default: "NoName")
constCDataContainer * pParent (default: NULL)

References CKeyFactory::add(), CONSTRUCTOR_TRACE, CRootContainer::getKeyFactory(), CDataObject::getObjectType(), CRootContainer::getUndefinedFunction(), CAnnotation::initMiriamAnnotation(), initObjects(), CAnnotation::mKey, and setFunction().

Referenced by fromData().

◆ CReaction() [2/2]

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

Copy constructor

Parameters
const CReaction &src
constCDataContainer * pParent (default: NULL)

References CKeyFactory::add(), CONSTRUCTOR_TRACE, CRootContainer::getKeyFactory(), CAnnotation::getMiriamAnnotation(), CDataObject::getObjectType(), initObjects(), CAnnotation::mKey, mpFunction, mScalingCompartmentCN, CAnnotation::setMiriamAnnotation(), and setScalingCompartmentCN().

◆ ~CReaction()

CReaction::~CReaction ( )
virtual

Destructor

References CRootContainer::getKeyFactory(), CDataObject::getObjectAncestor(), CAnnotation::mKey, CKeyFactory::remove(), and CModel::setCompileFlag().

Member Function Documentation

◆ addModifier()

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

Add a modifier to the reaction

Parameters
std::string& metabKey
constC_FLOAT64 & multiplicity (Default 1.0)
Returns
bool success

References CChemEq::addMetabolite(), mChemEq, and CChemEq::MODIFIER.

Referenced by CModelAdd::addReactions(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::duplicateReaction(), and ModifierHandler::processStart().

◆ addParameterObject() [1/2]

bool CReaction::addParameterObject ( const size_t &  index,
const CDataObject *  object 
)

References CDataObject::getCN(), CDataObject::getObjectAncestor(), mParameterIndexToCNs, mParameterIndexToObjects, and CModel::setCompileFlag().

Referenced by addParameterObject().

◆ addParameterObject() [2/2]

bool CReaction::addParameterObject ( const std::string &  name,
const CDataObject *  object 
)

References addParameterObject(), and mParameterNameToIndex.

◆ addProduct()

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

Add a product to the reaction

Parameters
std::string& metabKey
constC_FLOAT64 & multiplicity (Default 1.0)
Returns
bool success

References CChemEq::addMetabolite(), mChemEq, and CChemEq::PRODUCT.

Referenced by CModelAdd::addReactions(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::createDiffusionReaction(), CModelExpansion::duplicateReaction(), and ProductHandler::processStart().

◆ addSubstrate()

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

Add a substrate to the reaction

Parameters
std::string& metabKey
constC_FLOAT64 & multiplicity (Default 1.0)
Returns
bool success

References CChemEq::addMetabolite(), mChemEq, and CChemEq::SUBSTRATE.

Referenced by CModelAdd::addReactions(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::createDiffusionReaction(), CModelExpansion::duplicateReaction(), and SubstrateHandler::processStart().

◆ applyData()

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

Apply the provided data to the object

Parameters
constCData & data
Returns
bool success

Reimplemented from CDataContainer.

References CData::ADD_NOISE, CAnnotation::applyData(), CDataContainer::applyData(), CCopasiParameter::applyData(), CData::CHEMICAL_EQUATION, CChemEqInterface::fromDataValue(), CDataObject::getObjectAncestor(), CCopasiParameterGroup::getParameter(), CData::getProperty(), CChemEqInterface::init(), CData::isSetProperty(), CData::KINETIC_LAW, CData::KINETIC_LAW_UNIT_TYPE, CData::KINETIC_LAW_VARIABLE_MAPPING, KineticLawUnitTypeName, CData::LOCAL_REACTION_PARAMETERS, mChemEq, mHasNoise, mParameterNameToIndex, mParameters, CData::NOISE_EXPRESSION, CData::OBJECT_NAME, CData::PARAMETER_VALUE, CData::SCALING_COMPARTMENT, CModel::setCompileFlag(), setFunction(), setKineticLawUnitType(), setNoiseExpression(), setParameterCNs(), setScalingCompartmentCN(), CDataValue::toBool(), toData(), CDataValue::toDataVector(), toEnum(), CDataValue::toString(), and CChemEqInterface::writeToChemEq().

◆ calculate()

void CReaction::calculate ( )
private

Calculate the kinetic function

◆ compile()

CIssue 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).

Returns
bool success

References CValidity::add(), CFlags< Enum >::All, CDataVector< CType >::begin(), CExpression::compile(), compileFunctionParameters(), CDataVector< CType >::end(), CChemEq::getModifiers(), CDataObject::getObjectAncestor(), CDataObject::getObjectName(), CChemEq::getProducts(), CChemEq::getSubstrates(), CRootContainer::getUndefinedFunction(), CReactionInterface::init(), CIssue::KineticsUndefined, mChemEq, mFlux, mHasNoise, mParticleFlux, mpFunction, mpNoiseExpression, CDataObject::mPrerequisits, CObjectInterface::mValidity, CIssue::ObjectNotFound, CValidity::remove(), CReactionInterface::setFunctionAndDoMapping(), setScalingFactor(), CIssue::VariablesMismatch, CIssue::Warning, and CReactionInterface::writeBackToReaction().

Referenced by CModel::convert2NonReversible(), CModelExpansion::replaceInReaction(), and setNoiseExpressionPtr().

◆ compileFunctionParameters()

CIssue CReaction::compileFunctionParameters ( std::set< const CDataObject * > &  Dependencies)
private

References CValidity::add(), CFunctionParameterMap::addCallParameter(), CFlags< Enum >::All, CFunctionParameterMap::clearCallParameter(), CObjectInterface::DataObject(), CIssue::Error, CFunctionParameterMap::getFunctionParameters(), getFunctionParameters(), CDataObject::getObjectAncestor(), CDataObject::getObjectFromCN(), CDataObject::getObjectName(), CDataObject::getValueObject(), CUndoObjectInterface::insert(), mMap, mParameterIndexToCNs, mParameterIndexToObjects, CObjectInterface::mValidity, CIssue::ObjectNotFound, CFunctionParameterMap::pUnmappedObject, CValidity::remove(), resolveCN(), CFunctionParameterMap::setCallParameter(), CFunctionParameters::size(), CIssue::VariablesMismatch, and CFunctionParameter::VINT32.

Referenced by compile().

◆ createFunctionFromExpression()

CFunction * CReaction::createFunctionFromExpression ( const std::string &  infix)

Creates a kinetic function and sets it for the reaction

Parameters
conststring & infix
Returns
CFunction * pFunction

References CFunctionDB::addAndAdaptName(), CDataVector< CType >::begin(), CFunctionParameters::begin(), CDataVector< CType >::end(), CFunctionParameters::end(), CCopasiMessage::ERROR, CChemEq::getCompartments(), CRootContainer::getFunctionList(), CChemEq::getModifiers(), CMetab::getObjectDisplayName(), CDataObject::getObjectName(), CChemEq::getProducts(), CChemEq::getSubstrates(), CFunction::getVariables(), mChemEq, MCReaction, CFunctionParameter::MODIFIER, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CFunction::setInfix(), CDataObject::setObjectName(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, CFunctionParameter::VARIABLE, and CFunctionParameter::VOLUME.

◆ createUndoData()

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

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

Parameters
CUndoData& undoData
constCUndoData::Type & type
constCData & oldData (default: empty data)
constCCore::Framework & framework (default: CCore::Framework::ParticleNumbers)
Returns
CUndoData undoData

Reimplemented from CDataContainer.

References CData::ADD_NOISE, CUndoData::addProperty(), CData::addProperty(), CFunctionParameters::begin(), CCopasiParameterGroup::beginName(), C_FLOAT64, CUndoData::CHANGE, CData::CHEMICAL_EQUATION, CAnnotation::createUndoData(), CDataContainer::createUndoData(), CCopasiParameterGroup::endName(), CEvaluationTree::getInfix(), CDataObject::getObjectName(), CData::getProperty(), CFunction::getVariables(), CChemEqInterface::init(), CData::KINETIC_LAW, CData::KINETIC_LAW_UNIT_TYPE, CData::KINETIC_LAW_VARIABLE_MAPPING, KineticLawUnitTypeName, CData::LOCAL_REACTION_PARAMETERS, mChemEq, mHasNoise, mKineticLawUnit, mParameterIndexToCNs, mParameters, mpFunction, mpNoiseExpression, mScalingCompartmentCN, CData::NOISE_EXPRESSION, CData::OBJECT_NAME, CData::PARAMETER_VALUE, CData::SCALING_COMPARTMENT, CChemEqInterface::toDataValue(), and CDataValue::toDataVector().

◆ escapeId()

std::string CReaction::escapeId ( const std::string &  id)
private

Escapes double quotes and backslashes in a string and puts strings with tabs and spaces in double quotes.

Referenced by object2variable().

◆ fromData()

CReaction * CReaction::fromData ( const CData &  data,
CUndoObjectInterface *  pParent 
)
static

Static method to create a CDataObject based on the provided data

Parameters
constCData & data
Returns
CReaction * pDataObject

References CReaction(), CData::getProperty(), NO_PARENT, CData::OBJECT_NAME, and CDataValue::toString().

◆ getCallParameters()

const CCallParameters< C_FLOAT64 > & CReaction::getCallParameters ( ) const

Retrieve the call parameter given to the kinetic function.

Returns
const CCallParameters< C_FLOAT64 > & callParameters

References CFunctionParameterMap::getPointers(), and mMap.

Referenced by CMathObject::compileFlux().

◆ getChemEq() [1/2]

CChemEq & CReaction::getChemEq ( )

Retrieves the chemical equation of the reaction

Returns
CChemEq & chemEq

References mChemEq.

◆ getChemEq() [2/2]

const CChemEq & CReaction::getChemEq ( ) const

Retrieves the chemical equation of the reaction

Returns
const CChemEq & chemEq

References mChemEq.

Referenced by CModelAdd::addReactions(), CModelAnalyzer::checkReaction(), CMathObject::compilePropensity(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createKineticLaw(), CSBMLExporter::createReaction(), CLayoutInitializer::createReactionGlyph(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), SBMLImporter::findCorrespondingFunction(), CChemEqInterface::getChemEqString(), CEFMTask::getNetReactionData(), CEFMTask::getSpeciesChanges(), CReactionInterface::init(), CMathReaction::initialize(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), object2variable(), CModelAdd::reactionInvolvesCompartment(), CModelExpansion::replaceInReaction(), CCopasiXML::saveModel(), CChemEqInterface::setChemEqFromString(), SBMLImporter::setCorrectUsage(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), CLLayoutRenderer::update_associations(), CReactionInterface::writeBackToReaction(), and CMMLOutput::writeRHS().

◆ getChildObjectUnits()

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

Retrieve the units of the child object.

Returns
std::string units

Reimplemented from CDataContainer.

References CDataObject::getObjectAncestor(), CDataObject::getObjectName(), CModel::getQuantityUnit(), and CModel::getTimeUnit().

◆ getCompartmentNumber()

size_t CReaction::getCompartmentNumber ( ) const

Retrieves the number of compartments the reaction is acting in.

Returns
"size_t" the compartment number

References CChemEq::getCompartmentNumber(), and mChemEq.

◆ getDefaultNoiseExpression()

std::string CReaction::getDefaultNoiseExpression ( ) const

Retrieve the default expression for the noise.

Returns
std::string expression

References CDataObject::getCN(), and mpParticleFluxReference.

Referenced by CReactionInterface::setHasNoise().

◆ getEffectiveKineticLawUnitType()

CReaction::KineticLawUnit CReaction::getEffectiveKineticLawUnitType ( ) const

Retrieve the effective kinetic law unit type

Returns
KineticLawUnit kineticLawUnitType

References AmountPerTime, ConcentrationPerTime, Default, CChemEq::getCompartmentNumber(), mChemEq, and mKineticLawUnit.

Referenced by CMathObject::compileFlux(), CMathObject::compileReactionNoise(), CSBMLExporter::createKineticLaw(), CODEExporter::exportReacParamsAndFuncs(), getKineticLawUnit(), setScalingFactor(), and CMMLOutput::writeRHS().

◆ getExpressionTree()

CEvaluationNode * CReaction::getExpressionTree ( )

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

References getFunction(), and variables2objects().

◆ getFirstCModelOrDefault()

const CModel * CReaction::getFirstCModelOrDefault ( std::map< const CDataObject *, SBase * > &  copasi2sbmlmap)
private
Returns
the first non-null CModel from the map or the default one

References CDataObject::getObjectDataModel().

Referenced by object2variable().

◆ getFlux()

const C_FLOAT64 & CReaction::getFlux ( ) const

Retrieves the flux of the reaction

Returns
const C_FLOAT64 & flux

References mFlux.

◆ getFluxReference() [1/2]

CDataObject * CReaction::getFluxReference ( )

Retrieve object referencing the flux

Returns
CDataObject * fluxReference

References mpFluxReference.

Referenced by CMathObject::compileParticleFlux(), CModel::convert2NonReversible(), SBMLImporter::createCModelFromSBMLDocument(), CDataModel::findObjectByDisplayName(), CMathContainer::getMathReaction(), CModelParameterGroup::getObjectUnit(), and CMathReaction::initialize().

◆ getFluxReference() [2/2]

const CDataObject * CReaction::getFluxReference ( ) const

Retrieve const object referencing the flux

Returns
CDataObject * fluxReference

References mpFluxReference.

◆ getFunction()

const CFunction * CReaction::getFunction ( ) const

Retrieves the rate function of the reaction

Returns
"CBaseFunction &"

References mpFunction.

Referenced by CModelAdd::addReactions(), CSBMLExporter::checkForPiecewiseFunctions(), CModelAnalyzer::checkReaction(), CMathObject::compileFlux(), CModel::convert2NonReversible(), CSBMLExporter::createKineticLaw(), CMMLOutput::createParameterMapping(), CSBMLExporter::createReaction(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), CODEExporterC::exportKineticFunctionGroup(), CReactionInterface::getDeletedParameters(), getExpressionTree(), CReactionInterface::init(), CODEExporterC::KineticFunction2ODEmember(), CModel::prepareElasticity(), CCopasiXML::saveModel(), SBMLImporter::setCorrectUsage(), and CMMLOutput::writeRHS().

◆ getFunctionParameters()

const CFunctionParameters & CReaction::getFunctionParameters ( ) const

Gets the description of what parameters the function expects.

References fatalError, CFunctionParameterMap::getFunctionParameters(), mMap, and mpFunction.

Referenced by CModelAdd::addReactions(), CModelAnalyzer::checkReaction(), compileFunctionParameters(), CFunctionAnalyzer::constructCallParametersActualValues(), CModel::convert2NonReversible(), CSBMLExporter::createKineticLaw(), CMMLOutput::createParameterMapping(), CModelExpansion::duplicateReaction(), CODEExporterC::exportTitleData(), CODEExporterC::KineticFunction2ODEmember(), CModelMerging::mergeMetabolites(), CModelExpansion::replaceInReaction(), and CCopasiXML::saveModel().

◆ getKey()

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

Retrieves the key of the reaction

Returns
std::string key

Reimplemented from CAnnotation.

References CAnnotation::getKey().

Referenced by CLayoutInitializer::createReactionGlyph(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), CODEExporter::exportSingleFunction(), SBMLImporter::importMIRIAM(), CODEExporterBM::KineticFunction2ODEmember(), CODEExporterXPPAUT::KineticFunction2ODEmember(), ReactionHandler::processEnd(), ReactionGlyphHandler::processStart(), TextGlyphHandler::processStart(), and CCopasiXML::saveModel().

◆ getKineticLawUnit()

std::string CReaction::getKineticLawUnit ( ) const

Retrieve the effective kinetic law unit

Returns
std::string kineticLawUnit

References AmountPerTime, getEffectiveKineticLawUnitType(), CDataObject::getObjectAncestor(), CModel::getQuantityUnit(), CModel::getTimeUnit(), and CModel::getVolumeUnit().

Referenced by CModelParameter::getUnit().

◆ getKineticLawUnitType()

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

Retrieve the kinetic law unit type

Returns
const KineticLawUnit & kineticLawUnitType

References mKineticLawUnit.

Referenced by CModelExpansion::duplicateReaction(), CReactionInterface::init(), and CCopasiXML::saveModel().

◆ getLargestCompartment()

const CCompartment * CReaction::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 CChemEq::getLargestCompartment(), and mChemEq.

◆ getMap()

const CFunctionParameterMap & CReaction::getMap ( ) const

References mMap.

Referenced by CModel::prepareElasticity().

◆ getNoiseExpression()

std::string CReaction::getNoiseExpression ( ) const

Retrieve the expression for the noise.

Returns
std::string expression

References CEvaluationTree::getInfix(), mpNoiseExpression, and CExpression::updateInfix().

Referenced by CModelExpansion::duplicateReaction(), CReactionInterface::init(), and CCopasiXML::saveModel().

◆ getNoiseExpressionPtr() [1/2]

CExpression * CReaction::getNoiseExpressionPtr ( )

Retrieve the pointer to the expression for ODE model values.

Returns
CExpression*

References mpNoiseExpression, and CExpression::updateInfix().

◆ getNoiseExpressionPtr() [2/2]

const CExpression * CReaction::getNoiseExpressionPtr ( ) const

Retrieve the pointer to the expression for ODE model values.

Returns
CExpression*

References mpNoiseExpression, and CExpression::updateInfix().

Referenced by CMathObject::compileReactionParticleNoise(), and CModelExpansion::duplicateReaction().

◆ getNoiseReference()

const CDataObject * CReaction::getNoiseReference ( ) const

Retrieve object referencing the noise

Returns
const CDataObject * noiseReference

References mpNoiseReference.

◆ getObject()

const CObjectInterface * CReaction::getObject ( const CCommonName &  cn) const
virtual

We are hiding local reaction parameter which are covered by global quantities.

Parameters
constCCommonName & cn
Returns
const CObjectInterface * pObject

Reimplemented from CDataContainer.

References CDataContainer::getObject(), CDataObject::getObjectName(), CDataObject::getObjectParent(), CDataObject::hasFlag(), isLocalParameter(), mParameters, and CDataObject::StaticString.

Referenced by SBMLImporter::sbmlId2CopasiCN().

◆ getObjectDisplayName()

std::string CReaction::getObjectDisplayName ( ) const
virtual

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

Reimplemented from CDataObject.

References CDataObject::getObjectAncestor(), CDataObject::getObjectDisplayName(), and CDataObject::getObjectName().

◆ getParameterCNs() [1/3]

const std::vector< std::vector< CRegisteredCommonName > > & CReaction::getParameterCNs ( ) const

References mParameterIndexToCNs.

Referenced by getParameterCNs().

◆ getParameterCNs() [2/3]

const std::vector< CRegisteredCommonName > & CReaction::getParameterCNs ( const size_t &  index) const

References mParameterIndexToCNs.

Referenced by CModel::convert2NonReversible().

◆ getParameterCNs() [3/3]

const std::vector< CRegisteredCommonName > & CReaction::getParameterCNs ( const std::string &  name) const

References getParameterCNs(), and mParameterNameToIndex.

◆ getParameterIndex()

size_t CReaction::getParameterIndex ( const std::string &  parameterName,
const CFunctionParameter **  ppFunctionParameter = NULL 
) const

Retrieve the index of the given parameter name in the function call. If pType is not NULL the type of the parameter is returned

Parameters
conststd::string & parameterName
constCFunctionParameter ** ppFunctionParameter (default: NULL)
Returns
size_t index;

Retrieve the index of the given parameter name in the function call

Parameters
conststd::string & parameterName
Returns
size_t index;

References CFunctionParameterMap::findParameterByName(), and mMap.

Referenced by SBMLImporter::findCorrespondingFunction(), CDataModel::findObjectByDisplayName(), CModelParameterGroup::getObjectUnit(), initializeParameters(), and variable2object().

◆ getParameterObjects() [1/3]

const std::vector< std::vector< const CDataObject * > > & CReaction::getParameterObjects ( ) const

References mParameterIndexToObjects.

Referenced by getParameterObjects().

◆ getParameterObjects() [2/3]

const std::vector< const CDataObject * > & CReaction::getParameterObjects ( const size_t &  index) const

References mParameterIndexToObjects.

Referenced by CModelAnalyzer::checkReaction(), CFunctionAnalyzer::constructCallParametersActualValues(), CModel::convert2NonReversible(), CSBMLExporter::createKineticLaw(), CMMLOutput::createParameterMapping(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), CDataModel::findObjectByDisplayName(), CODEExporterC::KineticFunction2ODEmember(), CReactionInterface::loadMappingAndValues(), CModelExpansion::replaceInReaction(), and CCopasiXML::saveModel().

◆ getParameterObjects() [3/3]

const std::vector< const CDataObject * > & CReaction::getParameterObjects ( const std::string &  name) const

References C_INVALID_INDEX, getParameterObjects(), and mParameterNameToIndex.

◆ getParameters() [1/2]

CCopasiParameterGroup & CReaction::getParameters ( )

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

References mParameters.

◆ getParameters() [2/2]

const CCopasiParameterGroup & CReaction::getParameters ( ) const

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

References mParameters.

Referenced by CModelAnalyzer::checkReaction(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CReactionInterface::createUndoData(), CModelExpansion::duplicateReaction(), CODEExporter::exportReacParamsAndFuncs(), CReactionInterface::getDeletedParameters(), CReactionInterface::init(), CReactionInterface::loadMappingAndValues(), ConstantHandler::processStart(), CCopasiXML::saveModel(), and CReactionInterface::writeBackToReaction().

◆ getParameterValue()

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

Retrieves a parameter value

References C_FLOAT64, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), and mParameters.

Referenced by CModelAdd::addReactions(), CModel::convert2NonReversible(), CSBMLExporter::createKineticLaw(), CMMLOutput::createParameterMapping(), and CModelExpansion::duplicateReaction().

◆ getParticleFlux()

const C_FLOAT64 & CReaction::getParticleFlux ( ) const

Retrieves the scaled flux of the reaction

Returns
const C_FLOAT64 & scaledFlux

References mParticleFlux.

◆ getParticleFluxReference() [1/2]

CDataObject * CReaction::getParticleFluxReference ( )

Retrieve object referencing the particle flux

Returns
CDataObject * particleFluxReference

References mpParticleFluxReference.

Referenced by CMathObject::compilePropensity(), CModel::convert2NonReversible(), CDataModel::findObjectByDisplayName(), and CMathReaction::initialize().

◆ getParticleFluxReference() [2/2]

const CDataObject * CReaction::getParticleFluxReference ( ) const

Retrieve const object referencing the particle flux

Returns
CDataObject * particleFluxReference

References mpParticleFluxReference.

◆ getParticleNoiseReference()

const CDataObject * CReaction::getParticleNoiseReference ( ) const

Retrieve object referencing the particle noise

Returns
const CDataObject * particleNoiseReference

References mpParticleNoiseReference.

Referenced by CMathObject::compileReactionNoise().

◆ getPropensityReference() [1/2]

CDataObject * CReaction::getPropensityReference ( )

Retrieve object referencing the propensity

Returns
CDataObject * propensityReference

References mpPropensityReference.

Referenced by CMathReaction::initialize().

◆ getPropensityReference() [2/2]

const CDataObject * CReaction::getPropensityReference ( ) const

Retrieve object referencing the propensity

Returns
CDataObject * propensityReference

References mpPropensityReference.

◆ getReactionScheme()

std::string CReaction::getReactionScheme ( ) const
Returns
the reaction scheme of this reaction

References CReactionInterface::getChemEqString(), CDataObject::getObjectDataModel(), and CReactionInterface::init().

◆ getSBMLId()

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

Returns a reference to the SBML Id.

References mSBMLId.

Referenced by SBMLImporter::applyStoichiometricExpressions(), CSBMLExporter::collectIds(), SBMLImporter::createCModelFromSBMLDocument(), CSBMLExporter::createReaction(), SEDMLUtils::getXPathForObjectAndType(), object2variable(), SBMLImporter::replaceObjectNames(), CCopasiXML::saveModel(), CEvaluationNodeObject::toAST(), and VariableInfo::VariableInfo().

◆ getScalingCompartment()

const CCompartment * CReaction::getScalingCompartment ( ) const

Retrieve the compartment used for scaling the kinetic function

Returns
const CCompartment * scalingCompartment

References mpScalingCompartment.

Referenced by CMathObject::compile(), CMathObject::compileReactionNoise(), CSBMLExporter::createKineticLaw(), CModelExpansion::duplicateReaction(), CReactionInterface::init(), CCopasiXML::saveModel(), and CMMLOutput::writeRHS().

◆ getScalingCompartmentCN()

const CCommonName & CReaction::getScalingCompartmentCN ( ) const

Retrieve the CN of the scaling compartment.

Returns
const CCommonName & scalingCompartmentCN

References mScalingCompartmentCN.

◆ hasNoise()

const bool & CReaction::hasNoise ( ) const

Check whether noise is added to the reaction rate

Returns
const bool & hasNoise

References mHasNoise.

Referenced by CMathObject::compileReactionNoise(), CMathObject::compileReactionParticleNoise(), CModelExpansion::duplicateReaction(), CReactionInterface::init(), CCopasiXML::saveModel(), and setHasNoise().

◆ initializeParameterMapping()

void CReaction::initializeParameterMapping ( )
private

Initializes the mMetabNameMap vectors to the right size.

References fatalError, CFunctionParameterMap::getFunctionParameters(), CDataObject::getObjectName(), CFunctionParameter::getType(), mMap, mParameterIndexToCNs, mParameterIndexToObjects, mParameterNameToIndex, mpFunction, CFunctionParameters::size(), and CFunctionParameter::VINT32.

Referenced by setFunction().

◆ initializeParameters()

void CReaction::initializeParameters ( )
private

creates the mParamters List of CParameter objects. mMap needs to be initialized before.

References CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::beginIndex(), C_FLOAT64, C_INVALID_INDEX, CCopasiParameter::DOUBLE, CCopasiParameterGroup::endIndex(), fatalError, CCopasiParameter::getCN(), CFunctionParameterMap::getFunctionParameters(), CFunctionParameters::getNumberOfParametersByUsage(), CDataObject::getObjectName(), CCopasiParameterGroup::getParameter(), CFunctionParameters::getParameterByUsage(), getParameterIndex(), mMap, mParameterIndexToCNs, mParameterIndexToObjects, mParameterNameToIndex, mParameters, mpFunction, CFunctionParameter::PARAMETER, and CCopasiParameterGroup::removeParameter().

Referenced by setFunction().

◆ initObjects()

void CReaction::initObjects ( )
private

References CDataContainer::addObjectReference(), mFlux, mNoise, mParticleFlux, mParticleNoise, mpFluxReference, mpNoiseReference, mpParticleFluxReference, mpParticleNoiseReference, mpPropensityReference, mPropensity, and CDataObject::ValueDbl.

Referenced by CReaction().

◆ isFast()

const bool & CReaction::isFast ( ) const

Check whether the reaction needs to be treated as fast @ return const bool & fast

References mFast.

Referenced by CModelExpansion::duplicateReaction(), CMathReaction::isFast(), and CCopasiXML::saveModel().

◆ isLocalParameter() [1/2]

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

Check whether the indexed parameter is a local parameter.

Parameters
constsize_t & index
Returns
bool isLocal

References C_INVALID_INDEX, CDataObject::getObjectParent(), mParameterIndexToObjects, and mParameters.

Referenced by CModelAdd::addReactions(), CFixLocalReactionParameters::changeModel(), CModel::convert2NonReversible(), CSBMLExporter::createKineticLaw(), CMMLOutput::createParameterMapping(), CModelExpansion::duplicateReaction(), CODEExporter::exportKineticFunction(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CReactionInterface::getDeletedParameters(), getObject(), CModelParameterGroup::getObjectUnit(), isLocalParameter(), CODEExporterC::KineticFunction2ODEmember(), CReactionInterface::loadMappingAndValues(), and toData().

◆ isLocalParameter() [2/2]

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

Check whether the named parameter is a local parameter.

Parameters
conststd::string & parameterName
Returns
bool isLocal

References isLocalParameter(), and mParameterNameToIndex.

◆ isReversible()

bool CReaction::isReversible ( ) const

Retrieves whether the reaction is reversible

Returns
bool

References CChemEq::getReversibility(), and mChemEq.

Referenced by CModelAdd::addReactions(), CModelAnalyzer::checkReaction(), CMathObject::compilePropensity(), SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createReaction(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), SBMLImporter::findCorrespondingFunction(), CEFMTask::getReactionEquation(), CModel::prepareElasticity(), CCopasiXML::saveModel(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), and setFunctionFromExpressionTree().

◆ load()

C_INT32 CReaction::load ( CReadConfig &  configbuffer)

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

Parameters
pconfigbufferreference to a CReadConfig object.
Returns
mFail
See also
mFail

References C_INT32, CReadConfig::getVariable(), loadOld(), mChemEq, mpFunction, CReadConfig::SEARCH, CChemEqInterface::setChemEqFromString(), setFunction(), CDataObject::setObjectName(), and CChemEq::setReversibility().

◆ loadOld()

C_INT32 CReaction::loadOld ( CReadConfig &  configbuffer)
private

Loads a reaction from a Gepasi file

References C_FLOAT64, C_INT32, fatalError, CFunctionParameter::FLOAT64, CFunctionParameterMap::getFunctionParameters(), CFunctionParameters::getNumberOfParametersByUsage(), CDataObject::getObjectName(), CFunctionParameters::getParameterByUsage(), CFunctionParameter::getType(), CReadConfig::getVariable(), loadOneRole(), mMap, CFunctionParameter::MODIFIER, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, setParameterValue(), StringPrint(), and CFunctionParameter::SUBSTRATE.

Referenced by load().

◆ loadOneRole()

bool CReaction::loadOneRole ( CReadConfig &  configbuffer,
CFunctionParameter::Role  role,
C_INT32  n,
const std::string &  prefix 
)
private

Used for loading Gepasi files. Loads the mapping for one role

References CChemEq::addMetabolite(), C_INT32, fatalError, CModel::findMetabByName(), CDataObject::getCN(), CFunctionParameterMap::getFunctionParameters(), CModelEntity::getKey(), CFunctionParameters::getNumberOfParametersByUsage(), CDataObject::getObjectAncestor(), CDataObject::getObjectDataModel(), CDataObject::getObjectName(), CFunctionParameters::getParameterByUsage(), CFunctionParameter::getType(), CReadConfig::getVariable(), CFunctionParameters::isVector(), mChemEq, mMap, CFunctionParameter::MODIFIER, CChemEq::MODIFIER, mParameterIndexToCNs, mParameterIndexToObjects, mParameterNameToIndex, CDataModel::pOldMetabolites, StringPrint(), and CFunctionParameter::VINT32.

Referenced by loadOld().

◆ object2variable()

CEvaluationNodeVariable * CReaction::object2variable ( const CEvaluationNodeObject *  objectNode,
std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &  replacementMap,
std::map< const CDataObject *, SBase * > &  copasi2sbmlmap 
)
private

Converts a single object node to a variable node. The usage term of the variable nodes is recorded in terms of CFunctionParameters that are stored in the replacementMap. On failure a NULL pointer is returned.

References CEvaluationNode::DEFAULT, CCopasiMessage::ERROR, escapeId(), CCopasiMessage::EXCEPTION, CFunctionParameter::FLOAT64, getChemEq(), CEvaluationNodeObject::getData(), getFirstCModelOrDefault(), CChemEq::getModifiers(), CChemEq::getProducts(), getSBMLId(), CChemEq::getSubstrates(), MCReaction, MCSBML, CFunctionParameter::MODIFIER, CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, resolveCN(), sanitizeSBMLId(), CDataVector< CType >::size(), CFunctionParameter::SUBSTRATE, CFunctionParameter::TIME, and CFunctionParameter::VOLUME.

Referenced by objects2variables().

◆ objects2variables()

CEvaluationNode * CReaction::objects2variables ( const CEvaluationNode *  expression,
std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &  replacementMap,
std::map< const CDataObject *, SBase * > &  copasi2sbmlmap 
)
private

Replaces all object nodes in an expression tree by variable nodes. The usage term of the variable nodes is recorded in terms of CFunctionParameters that are stored in the replacementMap. On failure a NULL pointer is returned.

References CEvaluationNode::AVOGADRO, CNodeContextIterator< Node, Context >::context(), CNodeContextIterator< Node, Context >::end(), CCopasiMessage::ERROR, fatalError, CEvaluationNode::INVALID, MCReaction, CEvaluationNode::MV_FUNCTION, CNodeContextIterator< Node, Context >::next(), CEvaluationNode::OBJECT, object2variable(), CNodeContextIterator< Node, Context >::parentContextPtr(), CEvaluationNode::STRUCTURE, and CEvaluationNode::VARIABLE.

Referenced by setFunctionFromExpressionTree().

◆ operator=()

CReaction& CReaction::operator= ( const CReaction &  )
private

◆ printDebug()

void CReaction::printDebug ( ) const

◆ resolveCN()

CDataObject * CReaction::resolveCN ( const CModel *  pModel,
CCommonName  cn 
)
private
Parameters
pModelthe model in which to resolve the cn
cnthe common name, primary parts before model will be dropped
Returns
the data object for the given cn

References CObjectInterface::DataObject(), CDataContainer::getObject(), CCommonName::getObjectName(), CCommonName::getObjectType(), and CCommonName::getRemainder().

Referenced by compileFunctionParameters(), and object2variable().

◆ sanitizeSBMLId()

std::string CReaction::sanitizeSBMLId ( const std::string &  id)
staticprivate

Convert SBML to a valid COPASI infix identifier

Parameters
conststd::string & id
Returns
std::string

Referenced by object2variable().

◆ setFast()

void CReaction::setFast ( const bool &  fast)

Set whether the reaction is to be treated as fast

Parameters
constbool & fast

References mFast.

Referenced by CModelExpansion::duplicateReaction(), and ReactionHandler::processStart().

◆ setFunction() [1/2]

bool CReaction::setFunction ( CFunction *  pFunction)

Sets the rate function of the reaction

Parameters
CFunction* pFunction
Returns
bool success

References CRootContainer::getUndefinedFunction(), CFunction::getVariables(), CFunctionParameterMap::initializeFromFunctionParameters(), initializeParameterMapping(), initializeParameters(), mMap, mpFunction, and CDataObject::mPrerequisits.

◆ setFunction() [2/2]

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

Sets the rate function of the reaction

Parameters
conststring & functionName
Returns
bool success

References CCopasiMessage::ERROR, CFunctionDB::findLoadFunction(), CRootContainer::getFunctionList(), and MCReaction.

Referenced by CModelAdd::addReactions(), applyData(), CModel::convert2NonReversible(), CReaction(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::createDiffusionReaction(), CModelExpansion::duplicateReaction(), load(), KineticLawHandler::processEnd(), setFunctionFromExpressionTree(), and CReactionInterface::writeBackToReaction().

◆ setFunctionFromExpressionTree()

CFunction * CReaction::setFunctionFromExpressionTree ( const CExpression &  tree,
std::map< const CDataObject *, SBase * > &  copasi2sbmlmap 
)

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

References CDataContainer::add(), CFunction::addVariable(), SBMLImporter::areEqualFunctions(), CEvaluationTree::compile(), CEvaluationNode::copyBranch(), CCopasiMessage::ERROR_FILTERED, findFunction(), CRootContainer::getFunctionList(), CDataObject::getObjectName(), CEvaluationTree::getRoot(), CFunctionParameter::getType(), CFunctionParameter::getUsage(), CFunction::getVariables(), CFunction::isReversible(), isReversible(), mParameterIndexToCNs, mParameterIndexToObjects, mParameterNameToIndex, mpFunction, objects2variables(), pdelete, setFunction(), CDataObject::setObjectName(), CFunction::setReversible(), CEvaluationTree::setRoot(), TriFalse, and TriTrue.

Referenced by SBMLImporter::createCReactionFromReaction().

◆ setHasNoise()

void CReaction::setHasNoise ( const bool &  hasNoise)

Set whether to add noise to the reaction rate

Parameters
constbool & hasNoise

References CDataObject::getObjectAncestor(), hasNoise(), mHasNoise, and CModel::setCompileFlag().

Referenced by CModelExpansion::duplicateReaction(), ReactionHandler::processStart(), and CReactionInterface::writeBackToReaction().

◆ setKineticLawUnitType()

void CReaction::setKineticLawUnitType ( const KineticLawUnit &  kineticLawUnitType)

Set the kinetic law unit type;

Parameters
constKineticLawUnit & kineticLawUnit

References mKineticLawUnit.

Referenced by applyData(), CModelExpansion::duplicateReaction(), KineticLawHandler::processStart(), and CReactionInterface::writeBackToReaction().

◆ setNoiseExpression()

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

Set the expression expression for the noise

Parameters
conststd::string & expression
Returns
bool success

References CEvaluationTree::getInfix(), CDataObject::getObjectAncestor(), mpNoiseExpression, CModel::setCompileFlag(), and CExpression::setInfix().

Referenced by applyData(), CModelExpansion::duplicateReaction(), ReactionHandler::processEnd(), and CReactionInterface::writeBackToReaction().

◆ setNoiseExpressionPtr()

bool CReaction::setNoiseExpressionPtr ( CExpression *  pExpression)

Set the noise expression for ODE model values

Parameters
CExpression*
Returns
bool success

References CDataContainer::add(), compile(), CDataObject::getObjectAncestor(), mpNoiseExpression, pdelete, CDataContainer::remove(), CModel::setCompileFlag(), CDataObject::setObjectName(), and CDataObject::setObjectParent().

◆ setObjectParent()

bool CReaction::setObjectParent ( const CDataContainer *  pParent)
virtual

Sets the parent of the metabolite;

Parameters
constCDataContainer * pParent
Returns
bool success

Reimplemented from CDataObject.

References CDataObject::setObjectParent().

◆ setParameterCNs() [1/2]

bool CReaction::setParameterCNs ( const size_t &  index,
const std::vector< CRegisteredCommonName > &  CNs 
)

References CObjectInterface::DataObject(), CDataObject::getObjectFromCN(), mParameterIndexToCNs, mParameterIndexToObjects, and CFunctionParameterMap::pUnmappedObject.

Referenced by applyData(), CModel::convert2NonReversible(), and setParameterCNs().

◆ setParameterCNs() [2/2]

bool CReaction::setParameterCNs ( const std::string &  name,
const std::vector< CRegisteredCommonName > &  CNs 
)

References mParameterNameToIndex, and setParameterCNs().

◆ setParameterObject() [1/2]

bool CReaction::setParameterObject ( const size_t &  index,
const CDataObject *  object 
)

References setParameterObjects().

◆ setParameterObject() [2/2]

bool CReaction::setParameterObject ( const std::string &  name,
const CDataObject *  object 
)

References setParameterObjects().

◆ setParameterObjects() [1/2]

bool CReaction::setParameterObjects ( const size_t &  index,
const std::vector< const CDataObject * > &  objects 
)

References CDataObject::getObjectAncestor(), mParameterIndexToCNs, mParameterIndexToObjects, and CModel::setCompileFlag().

Referenced by CFixLocalReactionParameters::changeModel(), CModelExpansion::createDiffusionReaction(), SBMLImporter::doMapping(), CModelExpansion::duplicateReaction(), KineticLawHandler::processEnd(), CModelExpansion::replaceInReaction(), setParameterObject(), setParameterObjects(), CModelParameter::updateModel(), and CReactionInterface::writeBackToReaction().

◆ setParameterObjects() [2/2]

bool CReaction::setParameterObjects ( const std::string &  name,
const std::vector< const CDataObject * > &  objects 
)

References mParameterNameToIndex, and setParameterObjects().

◆ setParameterValue()

void CReaction::setParameterValue ( const std::string &  parameterName,
const C_FLOAT64 &  value 
)

Sets a parameter value

Parameters
conststd::string & parameterName
constC_FLOAT64 & value

References fatalError, CFunctionParameters::findParameterByName(), CFunctionParameter::FLOAT64, CCopasiParameter::getCN(), CCopasiParameterGroup::getParameter(), CFunctionParameter::getType(), CFunction::getVariables(), mParameterIndexToCNs, mParameterNameToIndex, mParameters, mpFunction, and CCopasiParameter::setValue().

Referenced by CModelAdd::addReactions(), CModel::convert2NonReversible(), CModelExpansion::duplicateReaction(), loadOld(), and CReactionInterface::writeBackToReaction().

◆ setReactionScheme()

bool CReaction::setReactionScheme ( const std::string &  scheme,
const std::string &  newFunction = "",
bool  createMetabolites = true,
bool  createOther = true 
)

Initializes this reaction from the specified reaction scheme

Parameters
schemethe new reaction scheme to be used
newFunctiona candidate function to be used
createMetabolietsif true, new metabolites will be created
createOtherif true, additional elements will be created as well
Returns
success / failure

Initializes this reaction from the specified reaction scheme

References CModel::compileIfNecessary(), CReactionInterface::createMetabolites(), CReactionInterface::createOtherObjects(), CDataModel::getModel(), CDataObject::getObjectDataModel(), CReactionInterface::init(), CReactionInterface::setChemEqString(), and CReactionInterface::writeBackToReaction().

◆ setReversible()

void CReaction::setReversible ( bool  reversible)

Sets whether the reaction is reversible

Parameters
boolreversible

References mChemEq, and CChemEq::setReversibility().

Referenced by CModelAdd::addReactions(), CModel::convert2NonReversible(), SBMLImporter::createCReactionFromReaction(), CModelExpansion::createDiffusionReaction(), CModelExpansion::duplicateReaction(), and ReactionHandler::processStart().

◆ setSBMLId()

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

Sets the SBMLId.

References mSBMLId.

Referenced by SBMLImporter::createCReactionFromReaction(), CSBMLExporter::createReaction(), ReactionHandler::processStart(), and SBMLMapHandler::processStart().

◆ setScalingCompartment()

void CReaction::setScalingCompartment ( const CCompartment *  pCompartment)

Set the compartment used for scaling the kinetic function

Parameters
constCCompartment * pCompartment

References CDataObject::getCN(), mpScalingCompartment, and mScalingCompartmentCN.

Referenced by CModelExpansion::duplicateReaction().

◆ setScalingCompartmentCN()

void CReaction::setScalingCompartmentCN ( const std::string &  compartmentCN)

Set the CN of the compartment used for scaling the kinetic function

Parameters
conststd::string & compartmentCN

References CDataObject::getObjectDataModel(), CObjectInterface::GetObjectFromCN(), mpScalingCompartment, and mScalingCompartmentCN.

Referenced by applyData(), CReaction(), KineticLawHandler::processStart(), and CReactionInterface::writeBackToReaction().

◆ setScalingFactor()

void CReaction::setScalingFactor ( )
private

Sets the scaling factor of the for the fluxes

References ConcentrationPerTime, Default, CDataObject::getCN(), CMetab::getCompartment(), getEffectiveKineticLawUnitType(), CDataObject::getObjectDataModel(), CObjectInterface::GetObjectFromCN(), CChemEq::getProducts(), CChemEq::getSubstrates(), mChemEq, mKineticLawUnit, mpScalingCompartment, mScalingCompartmentCN, and CDataVector< CType >::size().

Referenced by compile().

◆ toData()

CData CReaction::toData ( ) const
virtual

Retrieve the data describing the object

Returns
CData data

Reimplemented from CDataContainer.

References CData::ADD_NOISE, CData::addProperty(), CData::appendData(), CFunctionParameters::begin(), CCopasiParameterGroup::beginName(), CData::CHEMICAL_EQUATION, CCopasiParameterGroup::endName(), CEvaluationTree::getInfix(), CDataObject::getObjectName(), CFunction::getVariables(), CChemEqInterface::init(), isLocalParameter(), CData::KINETIC_LAW, CData::KINETIC_LAW_UNIT_TYPE, CData::KINETIC_LAW_VARIABLE_MAPPING, KineticLawUnitTypeName, CData::LOCAL_REACTION_PARAMETERS, mChemEq, mHasNoise, mKineticLawUnit, mParameterIndexToCNs, mParameters, mpFunction, mpNoiseExpression, mScalingCompartmentCN, CData::NOISE_EXPRESSION, CData::OBJECT_NAME, CData::PARAMETER_VALUE, CData::SCALING_COMPARTMENT, CAnnotation::toData(), CDataContainer::toData(), and CChemEqInterface::toDataValue().

Referenced by applyData(), and CReactionInterface::createUndoData().

◆ variable2object()

CEvaluationNodeObject * CReaction::variable2object ( CEvaluationNodeVariable *  pVariableNode)
private

Converts a single variable node to an object node. On failure a NULL pointer is returned.

References C_INVALID_INDEX, CEvaluationNode::CN, CObjectInterface::DataObject(), CCopasiMessage::EXCEPTION, CDataObject::getCN(), CCopasiNode< _Data >::getData(), CDataObject::getObjectFromCN(), getParameterIndex(), CFunctionParameter::getType(), MCReaction, mParameterIndexToCNs, CFunctionParameter::VFLOAT64, and CFunctionParameter::VINT32.

Referenced by variables2objects().

◆ variables2objects()

CEvaluationNode * CReaction::variables2objects ( CEvaluationNode *  expression)
private

Replaces all variable nodes in a function tree by object nodes. On failure a NULL pointer is returned.

References CCopasiNode< _Data >::addChild(), CEvaluationNode::CALL, CEvaluationNode::CHOICE, CEvaluationNode::CONSTANT, CCopasiMessage::ERROR, CEvaluationNode::FUNCTION, CCopasiNode< _Data >::getChild(), CCopasiNode< _Data >::getData(), CCopasiNode< _Data >::getSibling(), CEvaluationNode::INVALID, CEvaluationNode::LOGICAL, CEvaluationNode::mainType(), MCReaction, CEvaluationNode::MV_FUNCTION, CEvaluationNode::NUMBER, CEvaluationNode::OBJECT, CEvaluationNode::OPERATOR, CEvaluationNode::STRUCTURE, CEvaluationNode::subType(), CEvaluationNode::VARIABLE, variable2object(), and CEvaluationNode::WHITESPACE.

Referenced by getExpressionTree().

Friends And Related Function Documentation

◆ operator<<

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

Friend declaration for ostream operator

Parameters
std::ostream& os
constCReaction & d
Returns
std::ostream & os

Member Data Documentation

◆ KineticLawUnitTypeName

CEnumAnnotation< std::string, CReaction::KineticLawUnit > CReaction::KineticLawUnitTypeName
static

Referenced by applyData(), CReactionInterface::createUndoData(), createUndoData(), KineticLawHandler::processStart(), CCopasiXML::saveModel(), and toData().

◆ mChemEq

CChemEq CReaction::mChemEq
private

The chemical equation

Referenced by addModifier(), addProduct(), addSubstrate(), applyData(), compile(), createFunctionFromExpression(), createUndoData(), getChemEq(), getCompartmentNumber(), getEffectiveKineticLawUnitType(), getLargestCompartment(), isReversible(), load(), loadOneRole(), setReversible(), setScalingFactor(), and toData().

◆ mFast

bool CReaction::mFast
private

This flag indicates whether the reaction is treated as fast. The interpretation of fast is up to to the integration algorithm.

Referenced by isFast(), and setFast().

◆ mFlux

C_FLOAT64 CReaction::mFlux
private

The flux of the reaction, as amount of substance/time

Referenced by compile(), getFlux(), and initObjects().

◆ mHasNoise

bool CReaction::mHasNoise
private

A Boolean flag indicating whether to add noise to the reaction

Referenced by applyData(), compile(), createUndoData(), hasNoise(), setHasNoise(), and toData().

◆ mKineticLawUnit

KineticLawUnit CReaction::mKineticLawUnit
private

This indicates what the units of the kinetic law are

Referenced by createUndoData(), getEffectiveKineticLawUnitType(), getKineticLawUnitType(), setKineticLawUnitType(), setScalingFactor(), and toData().

◆ mMap

CFunctionParameterMap CReaction::mMap
private

This describes the mapping of the species and parameters to the function parameters. Here are the pointers to the actual objects and values.

Referenced by compileFunctionParameters(), getCallParameters(), getFunctionParameters(), getMap(), getParameterIndex(), initializeParameterMapping(), initializeParameters(), loadOld(), loadOneRole(), and setFunction().

◆ mNoise

C_FLOAT64 CReaction::mNoise
private

The noise of the reaction

Referenced by initObjects().

◆ mParameterIndexToCNs

std::vector< std::vector< CRegisteredCommonName > > CReaction::mParameterIndexToCNs
private

Referenced by addParameterObject(), compileFunctionParameters(), createUndoData(), getParameterCNs(), initializeParameterMapping(), initializeParameters(), loadOneRole(), setFunctionFromExpressionTree(), setParameterCNs(), setParameterObjects(), setParameterValue(), toData(), and variable2object().

◆ mParameterIndexToObjects

std::vector< std::vector< const CDataObject * > > CReaction::mParameterIndexToObjects
private

Referenced by addParameterObject(), compileFunctionParameters(), getParameterObjects(), initializeParameterMapping(), initializeParameters(), isLocalParameter(), loadOneRole(), setFunctionFromExpressionTree(), setParameterCNs(), and setParameterObjects().

◆ mParameterNameToIndex

std::map< std::string, size_t > CReaction::mParameterNameToIndex
private

This describes the mapping of the species to the function parameters. Here the keys of the metabolites (as in the chemical equation) are stored.

Referenced by addParameterObject(), applyData(), getParameterCNs(), getParameterObjects(), initializeParameterMapping(), initializeParameters(), isLocalParameter(), loadOneRole(), setFunctionFromExpressionTree(), setParameterCNs(), setParameterObjects(), and setParameterValue().

◆ mParameters

CCopasiParameterGroup CReaction::mParameters
private

This is a list of parameter objects.

Referenced by applyData(), createUndoData(), getObject(), getParameters(), getParameterValue(), initializeParameters(), isLocalParameter(), setParameterValue(), and toData().

◆ mParticleFlux

C_FLOAT64 CReaction::mParticleFlux
private

The scaled flux of the reaction, as particle number/time

Referenced by compile(), getParticleFlux(), and initObjects().

◆ mParticleNoise

C_FLOAT64 CReaction::mParticleNoise
private

The particle noise

Referenced by initObjects().

◆ mpFluxReference

CDataObjectReference<C_FLOAT64>* CReaction::mpFluxReference
private

Referenced by getFluxReference(), and initObjects().

◆ mpFunction

CFunction* CReaction::mpFunction
private

A pointer to the rate function of the reaction

Referenced by compile(), CReaction(), createUndoData(), getFunction(), getFunctionParameters(), initializeParameterMapping(), initializeParameters(), load(), setFunction(), setFunctionFromExpressionTree(), setParameterValue(), and toData().

◆ mpNoiseExpression

CExpression* CReaction::mpNoiseExpression
private

Optional noise term

Referenced by compile(), createUndoData(), getNoiseExpression(), getNoiseExpressionPtr(), setNoiseExpression(), setNoiseExpressionPtr(), and toData().

◆ mpNoiseReference

CDataObjectReference<C_FLOAT64>* CReaction::mpNoiseReference
private

Referenced by getNoiseReference(), and initObjects().

◆ mpParticleFluxReference

CDataObjectReference<C_FLOAT64>* CReaction::mpParticleFluxReference
private

Referenced by getDefaultNoiseExpression(), getParticleFluxReference(), and initObjects().

◆ mpParticleNoiseReference

CDataObjectReference<C_FLOAT64>* CReaction::mpParticleNoiseReference
private

Referenced by getParticleNoiseReference(), and initObjects().

◆ mpPropensityReference

CDataObjectReference<C_FLOAT64>* CReaction::mpPropensityReference
private

Referenced by getPropensityReference(), and initObjects().

◆ mPropensity

C_FLOAT64 CReaction::mPropensity
private

The propensity of the reaction

Referenced by initObjects().

◆ mpScalingCompartment

const CCompartment* CReaction::mpScalingCompartment
private

Referenced by getScalingCompartment(), setScalingCompartment(), setScalingCompartmentCN(), and setScalingFactor().

◆ mSBMLId

std::string CReaction::mSBMLId
mutableprivate

The id of the corresponding reaction in an SBML file. This value is either set upon importing an SBML file, or when the object is first exported to an SBML file.

Referenced by getSBMLId(), and setSBMLId().

◆ mScalingCompartmentCN

CRegisteredCommonName CReaction::mScalingCompartmentCN
private

Referenced by CReaction(), createUndoData(), getScalingCompartmentCN(), setScalingCompartment(), setScalingCompartmentCN(), setScalingFactor(), and toData().

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