22 #ifndef COPASI_CReaction
23 #define COPASI_CReaction
52 CReaction(
const std::string & name =
"NoName",
123 virtual const std::string &
getKey()
const;
193 bool setFunction(
const std::string & functionName);
226 const bool & updateStatus =
true);
268 const std::vector<std::string> & keys);
293 const std::vector<std::string> &
getParameterMapping(
const std::string & parameterName)
const;
437 std::map<CCopasiObject*, SBase*> & copasi2sbmlmap,
470 void setFast(
const bool & fast);
476 const bool &
isFast()
const;
490 const std::string & prefix);
517 std::map<std::string, std::pair<CCopasiObject*, CFunctionParameter*> >& replacementMap,
518 std::map<CCopasiObject*, SBase*>& copasi2sbmlmap);
527 std::map<std::string, std::pair<CCopasiObject*, CFunctionParameter*> >& replacementMap,
528 std::map<CCopasiObject*, SBase*>& copasi2sbmlmap);
546 std::string
escapeId(
const std::string&
id);
626 #endif // COPASI_CReaction
CCopasiParameterGroup mParameters
void setReversible(bool reversible)
CCopasiObjectReference< C_FLOAT64 > * mpFluxReference
CCopasiObject * getParticleFluxReference()
CCopasiObjectReference< C_FLOAT64 > * mpPropensityReference
CFunction * setFunctionFromExpressionTree(const CExpression &tree, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CFunctionDB *pFunctionDB)
C_INT32 loadOld(CReadConfig &configbuffer)
const C_FLOAT64 & getParticleFlux() const
bool addSubstrate(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
virtual std::string getChildObjectUnits(const CCopasiObject *pObject) const
virtual const std::string & getKey() const
void setParameterValue(const std::string ¶meterName, const C_FLOAT64 &value, const bool &updateStatus=true)
friend std::ostream & operator<<(std::ostream &os, const CReaction &d)
virtual std::string getObjectDisplayName(bool regular=true, bool richtext=false) const
const CCallParameters< C_FLOAT64 > & getCallParameters() const
bool addProduct(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
bool isLocalParameter(const size_t &index) const
C_FLOAT64 calculatePartialDerivative(C_FLOAT64 *pXi, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)
CEvaluationNode * objects2variables(const CEvaluationNode *expression, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)
void clearParameterMapping(const std::string ¶meterName)
const C_FLOAT64 & calculateFlux()
const C_FLOAT64 & getFlux() const
CCopasiObject * getPropensityReference()
virtual const CObjectInterface * getObject(const CCopasiObjectName &cn) const
void setParameterMappingVector(const std::string ¶meterName, const std::vector< std::string > &keys)
virtual std::set< const CCopasiObject * > getDeletedObjects() const
CEvaluationNodeVariable * object2variable(const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)
const C_FLOAT64 * mUnitScalingFactor
const std::string & getSBMLId() const
const CFunction * getFunction() const
CEvaluationNode * variables2objects(CEvaluationNode *expression)
virtual bool mustBeDeleted(const DataObjectSet &deletedObjects) const
const CFunctionParameters & getFunctionParameters() const
CReaction(const std::string &name="NoName", const CCopasiContainer *pParent=NULL)
size_t getParameterIndex(const std::string ¶meterName, CFunctionParameter::DataType *pType=NULL) const
bool addModifier(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)
CFunctionParameterMap mMap
bool setFunction(const std::string &functionName)
void setSBMLId(const std::string &id)
C_INT32 load(CReadConfig &configbuffer)
std::vector< std::vector< std::string > > & getParameterMappings()
const C_FLOAT64 & calculateParticleFlux()
bool isReversible() const
const bool & isFast() const
const C_FLOAT64 * mScalingFactor
const CCopasiParameterGroup & getParameters() const
const CCompartment * getLargestCompartment() const
void setParameterMapping(const size_t &index, const std::string &key)
size_t getCompartmentNumber() const
bool loadOneRole(CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix)
The class for handling a chemical kinetic function.
void setFast(const bool &fast)
std::string escapeId(const std::string &id)
CEvaluationNodeObject * variable2object(CEvaluationNodeVariable *pVariableNode)
virtual bool setObjectParent(const CCopasiContainer *pParent)
std::vector< std::vector< std::string > > mMetabKeyMap
CEvaluationNode * getExpressionTree()
const std::vector< std::vector< std::string > > & getParameterMappings() const
static C_FLOAT64 mDefaultScalingFactor
CReaction & operator=(const CReaction &)
void initializeParameters()
std::set< const CCopasiObject * > DataObjectSet
CCopasiObjectReference< C_FLOAT64 > * mpParticleFluxReference
const CChemEq & getChemEq() const
const C_FLOAT64 & getParameterValue(const std::string ¶meterName) const
void addParameterMapping(const size_t &index, const std::string &key)
void initializeMetaboliteKeyMap()
const std::vector< std::string > & getParameterMapping(const size_t &index) const
CCopasiObject * getFluxReference()