COPASI API
4.16.103
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This is the complete list of members for CReaction, including all inherited members.
add(CCopasiObject *pObject, const bool &adopt=true) | CCopasiContainer | virtual |
addDirectDependency(const CCopasiObject *pObject) | CCopasiObject | |
addMatrixReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
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) | CCopasiContainer | inlineprotected |
addParameterMapping(const size_t &index, const std::string &key) | CReaction | |
addParameterMapping(const std::string ¶meterName, 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) | CCopasiContainer | inlineprotected |
Array enum value | CCopasiObject | protected |
buildUpdateSequence(const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) | CCopasiObject | static |
calculate() | CReaction | private |
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) | CAnnotation | static |
castObject(const CCopasiObject *pObject) | CAnnotation | static |
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() | CCopasiObject | protected |
CCopasiObject(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | CCopasiObject | protected |
CCopasiObject(const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | CCopasiObject | |
cleanup() | CReaction | |
clearDirectDependencies() | CCopasiObject | |
clearParameterMapping(const std::string ¶meterName) | CReaction | |
clearParameterMapping(const size_t &index) | CReaction | |
clearRefresh() | CCopasiObject | |
CObjectInterface() | CObjectInterface | inline |
compile() | CReaction | |
Container enum value | CCopasiObject | protected |
CReaction(const std::string &name="NoName", const CCopasiContainer *pParent=NULL) | CReaction | |
CReaction(const CReaction &src, const CCopasiContainer *pParent=NULL) | CReaction | |
DataModel enum value | CCopasiObject | protected |
DataObjectSet typedef | CCopasiObject | |
DataUpdateSequence typedef | CCopasiObject | |
dependsOn(DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const | CCopasiObject | |
EmptyList | CCopasiContainer | static |
escapeId(const std::string &id) | CReaction | private |
Flag enum name | CCopasiObject | protected |
getAllDependencies(DataObjectSet &dependencies, const DataObjectSet &context) const | CCopasiObject | |
getCallParameters() const | CReaction | |
getChemEq() const | CReaction | |
getChemEq() | CReaction | |
getChildObjectUnits(const CCopasiObject *pObject) const | CReaction | virtual |
getCN() const | CCopasiObject | virtual |
getCompartmentNumber() const | CReaction | |
getDeletedObjects() const | CReaction | virtual |
getDirectDependencies(const DataObjectSet &context=DataObjectSet()) const | CCopasiObject | virtual |
getExpressionTree() | CReaction | |
getFlux() const | CReaction | |
getFluxReference() | CReaction | |
getFluxReference() const | CReaction | |
getFunction() const | CReaction | |
getFunctionParameters() const | CReaction | |
getKey() const | CReaction | virtual |
getLargestCompartment() const | CReaction | |
getMiriamAnnotation() const | CAnnotation | |
getNotes() const | CAnnotation | |
getObject(const CCopasiObjectName &cn) const | CReaction | virtual |
getObjectAncestor(const std::string &type) const | CCopasiObject | |
getObjectDataModel() | CCopasiObject | |
getObjectDataModel() const | CCopasiObject | |
getObjectDisplayName(bool regular=true, bool richtext=false) const | CReaction | virtual |
getObjectName() const | CCopasiObject | |
getObjectParent() const | CCopasiObject | |
getObjects() const | CCopasiContainer | virtual |
getObjectType() const | CCopasiObject | |
getParameterIndex(const std::string ¶meterName, CFunctionParameter::DataType *pType=NULL) const | CReaction | |
getParameterMapping(const size_t &index) const | CReaction | |
getParameterMapping(const std::string ¶meterName) const | CReaction | |
getParameterMappings() const | CReaction | inline |
getParameterMappings() | CReaction | inline |
getParameters() const | CReaction | |
getParameters() | CReaction | |
getParameterValue(const std::string ¶meterName) const | CReaction | |
getParticleFlux() const | CReaction | |
getParticleFluxReference() | CReaction | |
getParticleFluxReference() const | CReaction | |
getPrerequisites() const | CCopasiObject | virtual |
getPropensityReference() | CReaction | |
getPropensityReference() const | CReaction | |
getRefresh() const | CCopasiObject | virtual |
getSBMLId() const | CReaction | |
getUnits() const | CCopasiContainer | virtual |
getUnsupportedAnnotations() | CAnnotation | |
getUnsupportedAnnotations() const | CAnnotation | |
getUpdateMethod() const | CCopasiObject | |
getValueObject() const | CCopasiContainer | virtual |
getValuePointer() const | CCopasiObject | virtual |
Gui enum value | CCopasiObject | protected |
hasCircularDependencies(DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const | CCopasiObject | |
hasUpdateMethod() const | CCopasiObject | |
initializeMetaboliteKeyMap() | CReaction | private |
initializeParameters() | CReaction | private |
initObjects() | CReaction | private |
isArray() const | CCopasiObject | |
isContainer() const | CCopasiObject | |
isDataModel() const | CCopasiObject | |
isFast() const | CReaction | |
isLocalParameter(const size_t &index) const | CReaction | |
isLocalParameter(const std::string ¶meterName) const | CReaction | |
isMatrix() const | CCopasiObject | |
isNameVector() const | CCopasiObject | |
isNonUniqueName() const | CCopasiObject | |
isPrerequisiteForContext(const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const | CCopasiObject | virtual |
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) | CReaction | private |
loadOneRole(CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix) | CReaction | private |
Matrix enum value | CCopasiObject | protected |
mChemEq | CReaction | private |
mDefaultScalingFactor | CReaction | privatestatic |
mFast | CReaction | private |
mFlux | CReaction | private |
mKey | CAnnotation | protected |
mMap | CReaction | private |
mMetabKeyMap | CReaction | private |
mObjects | CCopasiContainer | protected |
ModelEntity enum value | CCopasiObject | protected |
mParameters | CReaction | private |
mParticleFlux | CReaction | private |
mpFluxReference | CReaction | private |
mpFunction | CReaction | private |
mpParticleFluxReference | CReaction | private |
mpPropensityReference | CReaction | private |
mPropensity | CReaction | private |
mSBMLId | CReaction | private |
mScalingFactor | CReaction | private |
mUnitScalingFactor | CReaction | private |
mustBeDeleted(const DataObjectSet &deletedObjects) const | CReaction | virtual |
NameVector enum value | CCopasiObject | protected |
NonUniqueName enum value | CCopasiObject | protected |
object2variable(const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap) | CReaction | private |
objectMap typedef | CCopasiContainer | |
objects2variables(const CEvaluationNode *expression, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap) | CReaction | private |
ObjectSet typedef | CObjectInterface | |
operator<<(std::ostream &os, const CReaction &d) | CReaction | friend |
operator=(const CReaction &) | CReaction | private |
operator==(const CAnnotation &rhs) const | CAnnotation | |
print(std::ostream *ostream) const | CCopasiObject | virtual |
printDebug() const | CReaction | |
Reference enum value | CCopasiObject | protected |
remove(CCopasiObject *pObject) | CCopasiContainer | virtual |
removeDirectDependency(const CCopasiObject *pObject) | CCopasiObject | |
removeUnsupportedAnnotation(const std::string &name) | CAnnotation | |
replaceUnsupportedAnnotation(const std::string &name, const std::string &xml) | CAnnotation | |
Root enum value | CCopasiObject | protected |
Separator enum value | CCopasiObject | protected |
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 ¬es) | CAnnotation | |
setObjectName(const std::string &name) | CCopasiObject | |
setObjectParent(const CCopasiContainer *pParent) | CReaction | virtual |
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 ¶meterName, const std::string &key) | CReaction | |
setParameterMappingVector(const std::string ¶meterName, const std::vector< std::string > &keys) | CReaction | |
setParameterValue(const std::string ¶meterName, const C_FLOAT64 &value, const bool &updateStatus=true) | CReaction | |
setRefresh(CType *pType, void(CType::*method)(void)) | CCopasiObject | inline |
setRenameHandler(CRenameHandler *rh) | CCopasiObject | inlinestatic |
setReversible(bool reversible) | CReaction | |
setSBMLId(const std::string &id) | CReaction | |
setScalingFactor() | CReaction | private |
setUpdateMethod(CType *pType, void(CType::*method)(const C_FLOAT64 &)) | CCopasiObject | inline |
setUpdateMethod(CType *pType, void(CType::*method)(const C_INT32 &)) | CCopasiObject | inline |
setUpdateMethod(CType *pType, void(CType::*method)(const bool &)) | CCopasiObject | inline |
smpRenameHandler | CCopasiObject | protectedstatic |
StaticString enum value | CCopasiObject | protected |
UnsupportedAnnotation typedef | CAnnotation | |
UpdateSequence typedef | CObjectInterface | |
ValueBool enum value | CCopasiObject | protected |
ValueDbl enum value | CCopasiObject | protected |
ValueInt enum value | CCopasiObject | protected |
ValueInt64 enum value | CCopasiObject | protected |
ValueString enum value | CCopasiObject | protected |
variable2object(CEvaluationNodeVariable *pVariableNode) | CReaction | private |
variables2objects(CEvaluationNode *expression) | CReaction | private |
Vector enum value | CCopasiObject | protected |
~CAnnotation() | CAnnotation | virtual |
~CCopasiContainer() | CCopasiContainer | virtual |
~CCopasiObject() | CCopasiObject | virtual |
~CObjectInterface() | CObjectInterface | inlinevirtual |
~CReaction() | CReaction | virtual |