COPASI API  4.16.103
CReaction Member List

This is the complete list of members for CReaction, including all inherited members.

add(CCopasiObject *pObject, const bool &adopt=true)CCopasiContainervirtual
addDirectDependency(const CCopasiObject *pObject)CCopasiObject
addMatrixReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)CCopasiContainerinlineprotected
addModifier(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)CReaction
addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)CCopasiContainerinlineprotected
addParameterMapping(const size_t &index, const std::string &key)CReaction
addParameterMapping(const std::string &parameterName, const std::string &key)CReaction
addProduct(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)CReaction
addSubstrate(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)CReaction
addUnsupportedAnnotation(const std::string &name, const std::string &xml)CAnnotation
addVectorReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)CCopasiContainerinlineprotected
Array enum valueCCopasiObjectprotected
buildUpdateSequence(const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())CCopasiObjectstatic
calculate()CReactionprivate
calculateFlux()CReaction
calculatePartialDerivative(C_FLOAT64 *pXi, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)CReaction
calculateParticleFlux()CReaction
CAnnotation()CAnnotation
CAnnotation(const CAnnotation &src)CAnnotation
castObject(CCopasiObject *pObject)CAnnotationstatic
castObject(const CCopasiObject *pObject)CAnnotationstatic
CCopasiContainer(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)CCopasiContainer
CCopasiContainer(const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)CCopasiContainer
CCopasiObject()CCopasiObjectprotected
CCopasiObject(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)CCopasiObjectprotected
CCopasiObject(const CCopasiObject &src, const CCopasiContainer *pParent=NULL)CCopasiObject
cleanup()CReaction
clearDirectDependencies()CCopasiObject
clearParameterMapping(const std::string &parameterName)CReaction
clearParameterMapping(const size_t &index)CReaction
clearRefresh()CCopasiObject
CObjectInterface()CObjectInterfaceinline
compile()CReaction
Container enum valueCCopasiObjectprotected
CReaction(const std::string &name="NoName", const CCopasiContainer *pParent=NULL)CReaction
CReaction(const CReaction &src, const CCopasiContainer *pParent=NULL)CReaction
DataModel enum valueCCopasiObjectprotected
DataObjectSet typedefCCopasiObject
DataUpdateSequence typedefCCopasiObject
dependsOn(DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const CCopasiObject
EmptyListCCopasiContainerstatic
escapeId(const std::string &id)CReactionprivate
Flag enum nameCCopasiObjectprotected
getAllDependencies(DataObjectSet &dependencies, const DataObjectSet &context) const CCopasiObject
getCallParameters() const CReaction
getChemEq() const CReaction
getChemEq()CReaction
getChildObjectUnits(const CCopasiObject *pObject) const CReactionvirtual
getCN() const CCopasiObjectvirtual
getCompartmentNumber() const CReaction
getDeletedObjects() const CReactionvirtual
getDirectDependencies(const DataObjectSet &context=DataObjectSet()) const CCopasiObjectvirtual
getExpressionTree()CReaction
getFlux() const CReaction
getFluxReference()CReaction
getFluxReference() const CReaction
getFunction() const CReaction
getFunctionParameters() const CReaction
getKey() const CReactionvirtual
getLargestCompartment() const CReaction
getMiriamAnnotation() const CAnnotation
getNotes() const CAnnotation
getObject(const CCopasiObjectName &cn) const CReactionvirtual
getObjectAncestor(const std::string &type) const CCopasiObject
getObjectDataModel()CCopasiObject
getObjectDataModel() const CCopasiObject
getObjectDisplayName(bool regular=true, bool richtext=false) const CReactionvirtual
getObjectName() const CCopasiObject
getObjectParent() const CCopasiObject
getObjects() const CCopasiContainervirtual
getObjectType() const CCopasiObject
getParameterIndex(const std::string &parameterName, CFunctionParameter::DataType *pType=NULL) const CReaction
getParameterMapping(const size_t &index) const CReaction
getParameterMapping(const std::string &parameterName) const CReaction
getParameterMappings() const CReactioninline
getParameterMappings()CReactioninline
getParameters() const CReaction
getParameters()CReaction
getParameterValue(const std::string &parameterName) const CReaction
getParticleFlux() const CReaction
getParticleFluxReference()CReaction
getParticleFluxReference() const CReaction
getPrerequisites() const CCopasiObjectvirtual
getPropensityReference()CReaction
getPropensityReference() const CReaction
getRefresh() const CCopasiObjectvirtual
getSBMLId() const CReaction
getUnits() const CCopasiContainervirtual
getUnsupportedAnnotations()CAnnotation
getUnsupportedAnnotations() const CAnnotation
getUpdateMethod() const CCopasiObject
getValueObject() const CCopasiContainervirtual
getValuePointer() const CCopasiObjectvirtual
Gui enum valueCCopasiObjectprotected
hasCircularDependencies(DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const CCopasiObject
hasUpdateMethod() const CCopasiObject
initializeMetaboliteKeyMap()CReactionprivate
initializeParameters()CReactionprivate
initObjects()CReactionprivate
isArray() const CCopasiObject
isContainer() const CCopasiObject
isDataModel() const CCopasiObject
isFast() const CReaction
isLocalParameter(const size_t &index) const CReaction
isLocalParameter(const std::string &parameterName) const CReaction
isMatrix() const CCopasiObject
isNameVector() const CCopasiObject
isNonUniqueName() const CCopasiObject
isPrerequisiteForContext(const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const CCopasiObjectvirtual
isReference() const CCopasiObject
isReversible() const CReaction
isRoot() const CCopasiObject
isSeparator() const CCopasiObject
isStaticString() const CCopasiObject
isValueBool() const CCopasiObject
isValueDbl() const CCopasiObject
isValueInt() const CCopasiObject
isValueInt64() const CCopasiObject
isValueString() const CCopasiObject
isVector() const CCopasiObject
load(CReadConfig &configbuffer)CReaction
loadOld(CReadConfig &configbuffer)CReactionprivate
loadOneRole(CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix)CReactionprivate
Matrix enum valueCCopasiObjectprotected
mChemEqCReactionprivate
mDefaultScalingFactorCReactionprivatestatic
mFastCReactionprivate
mFluxCReactionprivate
mKeyCAnnotationprotected
mMapCReactionprivate
mMetabKeyMapCReactionprivate
mObjectsCCopasiContainerprotected
ModelEntity enum valueCCopasiObjectprotected
mParametersCReactionprivate
mParticleFluxCReactionprivate
mpFluxReferenceCReactionprivate
mpFunctionCReactionprivate
mpParticleFluxReferenceCReactionprivate
mpPropensityReferenceCReactionprivate
mPropensityCReactionprivate
mSBMLIdCReactionprivate
mScalingFactorCReactionprivate
mUnitScalingFactorCReactionprivate
mustBeDeleted(const DataObjectSet &deletedObjects) const CReactionvirtual
NameVector enum valueCCopasiObjectprotected
NonUniqueName enum valueCCopasiObjectprotected
object2variable(const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)CReactionprivate
objectMap typedefCCopasiContainer
objects2variables(const CEvaluationNode *expression, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)CReactionprivate
ObjectSet typedefCObjectInterface
operator<<(std::ostream &os, const CReaction &d)CReactionfriend
operator=(const CReaction &)CReactionprivate
operator==(const CAnnotation &rhs) const CAnnotation
print(std::ostream *ostream) const CCopasiObjectvirtual
printDebug() const CReaction
Reference enum valueCCopasiObjectprotected
remove(CCopasiObject *pObject)CCopasiContainervirtual
removeDirectDependency(const CCopasiObject *pObject)CCopasiObject
removeUnsupportedAnnotation(const std::string &name)CAnnotation
replaceUnsupportedAnnotation(const std::string &name, const std::string &xml)CAnnotation
Root enum valueCCopasiObjectprotected
Separator enum valueCCopasiObjectprotected
setDirectDependencies(const DataObjectSet &directDependencies)CCopasiObject
setFast(const bool &fast)CReaction
setFunction(const std::string &functionName)CReaction
setFunction(CFunction *pFunction)CReaction
setFunctionFromExpressionTree(const CExpression &tree, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CFunctionDB *pFunctionDB)CReaction
setMiriamAnnotation(const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)CAnnotation
setNotes(const std::string &notes)CAnnotation
setObjectName(const std::string &name)CCopasiObject
setObjectParent(const CCopasiContainer *pParent)CReactionvirtual
setObjectValue(const C_FLOAT64 &value)CCopasiObject
setObjectValue(const C_INT32 &value)CCopasiObject
setObjectValue(const bool &value)CCopasiObject
setParameterMapping(const size_t &index, const std::string &key)CReaction
setParameterMapping(const std::string &parameterName, const std::string &key)CReaction
setParameterMappingVector(const std::string &parameterName, const std::vector< std::string > &keys)CReaction
setParameterValue(const std::string &parameterName, const C_FLOAT64 &value, const bool &updateStatus=true)CReaction
setRefresh(CType *pType, void(CType::*method)(void))CCopasiObjectinline
setRenameHandler(CRenameHandler *rh)CCopasiObjectinlinestatic
setReversible(bool reversible)CReaction
setSBMLId(const std::string &id)CReaction
setScalingFactor()CReactionprivate
setUpdateMethod(CType *pType, void(CType::*method)(const C_FLOAT64 &))CCopasiObjectinline
setUpdateMethod(CType *pType, void(CType::*method)(const C_INT32 &))CCopasiObjectinline
setUpdateMethod(CType *pType, void(CType::*method)(const bool &))CCopasiObjectinline
smpRenameHandlerCCopasiObjectprotectedstatic
StaticString enum valueCCopasiObjectprotected
UnsupportedAnnotation typedefCAnnotation
UpdateSequence typedefCObjectInterface
ValueBool enum valueCCopasiObjectprotected
ValueDbl enum valueCCopasiObjectprotected
ValueInt enum valueCCopasiObjectprotected
ValueInt64 enum valueCCopasiObjectprotected
ValueString enum valueCCopasiObjectprotected
variable2object(CEvaluationNodeVariable *pVariableNode)CReactionprivate
variables2objects(CEvaluationNode *expression)CReactionprivate
Vector enum valueCCopasiObjectprotected
~CAnnotation()CAnnotationvirtual
~CCopasiContainer()CCopasiContainervirtual
~CCopasiObject()CCopasiObjectvirtual
~CObjectInterface()CObjectInterfaceinlinevirtual
~CReaction()CReactionvirtual