COPASI API  4.16.103
CModel Member List

This is the complete list of members for CModel, 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
addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)CCopasiContainerinlineprotected
addUnsupportedAnnotation(const std::string &name, const std::string &xml)CAnnotation
addVectorReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)CCopasiContainerinlineprotected
appendDependentCompartments(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const CModelprivate
appendDependentEvents(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const CModelprivate
appendDependentMetabolites(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const CModelprivate
appendDependentModelObjects(const std::set< const CCopasiObject * > &candidates, std::set< const CCopasiObject * > &dependentReactions, std::set< const CCopasiObject * > &dependentMetabolites, std::set< const CCopasiObject * > &dependentCompartments, std::set< const CCopasiObject * > &dependentModelValues, std::set< const CCopasiObject * > &dependentEvents) const CModel
appendDependentModelValues(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const CModelprivate
appendDependentReactions(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const CModel
applyActiveParameterSet()CModel
applyInitialValues()CModel
AreaUnit enum nameCModel
AreaUnitNamesCModelstatic
Array enum valueCCopasiObjectprotected
ASSIGNMENT enum valueCModelEntity
buildApplyInitialValuesSequence()CModelprivate
buildDependencyGraphs()CModel
buildInitialRefreshSequence(std::set< const CCopasiObject * > &changedObjects)CModel
buildInitialSequence()CModelprivate
buildLinkZero()CModel
buildMoieties()CModel
buildNonSimulatedSequence()CModelprivate
buildRedStoi()CModel
buildSimulatedSequence()CModelprivate
buildStateTemplate()CModelprivate
buildStoi()CModel
buildUpdateSequence(const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())CCopasiObjectstatic
buildUserOrder()CModelprivate
calculate()CModelEntityvirtual
calculateDerivatives(C_FLOAT64 *derivatives)CModel
calculateDerivativesX(C_FLOAT64 *derivativesX)CModel
calculateDivergence() const CModel
calculateElasticityMatrix(const C_FLOAT64 &factor, const C_FLOAT64 &resolution)CModel
calculateJacobian(CMatrix< C_FLOAT64 > &jacobian, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)CModel
calculateJacobianX(CMatrix< C_FLOAT64 > &jacobianX, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)CModel
calculateRootDerivatives(CVector< C_FLOAT64 > &rootDerivatives)CModel
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
clearDirectDependencies()CCopasiObject
clearMoieties()CModelprivate
clearRefresh()CCopasiObject
cm enum valueCModel
cm2 enum valueCModel
CModel(const CModel &src)CModelprivate
CModel(CCopasiContainer *pParent)CModel
CModelEntity(const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="ModelEntity", const unsigned C_INT32 &flag=CCopasiObject::Container|CCopasiObject::ValueDbl)CModelEntity
CModelEntity(const CModelEntity &src, const CCopasiContainer *pParent=NULL)CModelEntity
CObjectInterface()CObjectInterfaceinline
compile()CModelprivatevirtual
compileEvents()CModelprivate
compileIfNecessary(CProcessReport *pProcessReport)CModel
Container enum valueCCopasiObjectprotected
convert2NonReversible()CModel
createCompartment(const std::string &name, const C_FLOAT64 &volume=1.0)CModel
createEvent(const std::string &name)CModel
createMetabolite(const std::string &name, const std::string &compartment, const C_FLOAT64 &iconc=1.0, const CModelEntity::Status &status=CModelEntity::REACTIONS)CModel
createModelValue(const std::string &name, const C_FLOAT64 &value=0.0)CModel
createReaction(const std::string &name)CModel
d enum valueCModel
DataModel enum valueCCopasiObjectprotected
DataObjectSet typedefCCopasiObject
DataUpdateSequence typedefCCopasiObject
DependencyType enum nameCModel
dependsOn(DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const CCopasiObject
determineIsAutonomous()CModelprivate
deterministic enum valueCModel
dimensionlessArea enum valueCModel
dimensionlessLength enum valueCModel
dimensionlessQuantity enum valueCModel
dimensionlessTime enum valueCModel
dimensionlessVolume enum valueCModel
dm enum valueCModel
dm2 enum valueCModel
EmptyListCCopasiContainerstatic
evaluateRoots(CVectorCore< C_FLOAT64 > &rootValues, const bool &ignoreDiscrete)CModel
findMetabByName(const std::string &Target) const CModel
findMoiety(const std::string &Target) const CModel
FIXED enum valueCModelEntity
fl enum valueCModel
Flag enum nameCCopasiObjectprotected
fm enum valueCModel
fm2 enum valueCModel
fMol enum valueCModel
forceCompile(CProcessReport *pProcessReport)CModel
fs enum valueCModel
getAllDependencies(DataObjectSet &dependencies, const DataObjectSet &context) const CCopasiObject
getAreaUnitEnum() const CModel
getAreaUnitName() const CModel
getAreaUnitsDisplayString() const CModel
getAvogadro() const CModel
getChildObjectUnits(const CCopasiObject *pObject) const CModelvirtual
getCN() const CCopasiObjectvirtual
getCompartments()CModel
getCompartments() const CModel
getConcentrationRateUnitsDisplayString() const CModel
getConcentrationUnitsDisplayString() const CModel
getCorrespondingTransientObject(const CCopasiObject *pObject) const CModel
getDeletedObjects() const CModelEntityvirtual
getDirectDependencies(const DataObjectSet &context=DataObjectSet()) const CCopasiObjectvirtual
getEvents()CModel
getEvents() const CModel
getExpression() const CModelEntity
getExpressionPtr() const CModelEntity
getExpressionPtr()CModelEntity
getFrequencyUnitsDisplayString() const CModel
getInitialExpression() const CModelEntity
getInitialExpressionPtr() const CModelEntity
getInitialExpressionPtr()CModelEntity
getInitialState() const CModel
getInitialTime() const CModel
getInitialUpdateSequence(const CMath::SimulationContextFlag &context, const CCopasiObject::DataObjectSet &changedObjects, const CCopasiObject::DataObjectSet &requestedObjects, CCopasiObject::DataUpdateSequence &updateSequence) const CModel
getInitialValue() const CModelEntity
getInitialValueReference() const CModelEntity
getKey() const CModelvirtual
getL() const CModel
getL0() const CModel
getLengthUnitEnum() const CModel
getLengthUnitName() const CModel
getLengthUnitsDisplayString() const CModel
getListOfConstantRefreshes() const CModel
getListOfInitialRefreshes() const CModel
getListOfNonSimulatedRefreshes() const CModel
getListOfSimulatedRefreshes() const CModel
getMathModel() const CModel
getMathModel()CModel
getMetabolites() const CModel
getMetabolites()CModel
getMetabolitesX() const CModel
getMetabolitesX()CModel
getMiriamAnnotation() const CAnnotation
getModelParameterSet() const CModel
getModelParameterSet()CModel
getModelParameterSets() const CModel
getModelParameterSets()CModel
getModelType() const CModel
getModelValues() const CModel
getModelValues()CModel
getMoieties() const CModel
getNotes() const CAnnotation
getNumAssignmentMetabs() const CModel
getNumber2QuantityFactor() const CModel
getNumDependentReactionMetabs() const CModel
getNumIndependentReactionMetabs() const CModel
getNumMetabs() const CModel
getNumModelValues() const CModel
getNumODEMetabs() const CModel
getNumRoots() const CModel
getNumVariableMetabs() const CModel
getObject(const CCopasiObjectName &cn) const CCopasiContainervirtual
getObjectAncestor(const std::string &type) const CCopasiObject
getObjectDataModel()CCopasiObject
getObjectDataModel() const CCopasiObject
getObjectDisplayName(bool regular=true, bool richtext=false) const CCopasiObjectvirtual
getObjectName() const CCopasiObject
getObjectParent() const CCopasiObject
getObjects() const CCopasiContainervirtual
getObjectType() const CCopasiObject
getParticleFlux() const CModel
getPrerequisites() const CCopasiObjectvirtual
getProcessQueueExecutionTime() const CModel
getQuantity2NumberFactor() const CModel
getQuantityRateUnitsDisplayString() const CModel
getQuantityUnitEnum() const CModel
getQuantityUnitName() const CModel
getQuantityUnitOldXMLName() const CModel
getQuantityUnitsDisplayString() const CModel
getRate() const CModelEntity
getRateReference() const CModelEntity
getReactions()CModel
getReactions() const CModel
getRedStoi() const CModel
getRefresh() const CCopasiObjectvirtual
getRootFinders() const CModel
getSBMLId() const CModelEntity
getState() const CModel
getStateTemplate() const CModel
getStateTemplate()CModel
getStatus() const CModelEntity
getStoi() const CModel
getTime() const CModel
getTimeUnitEnum() const CModel
getTimeUnitName() const CModel
getTimeUnitsDisplayString() const CModel
getTotSteps() const CModel
getTransientUpdateSequence(const CMath::SimulationContextFlag &context, const CCopasiObject::DataObjectSet &changedObjects, const CCopasiObject::DataObjectSet &requestedObjects, CCopasiObject::DataUpdateSequence &updateSequence) const CModel
getTreesWithDiscontinuities() const CModel
getUnits() const CCopasiContainervirtual
getUnsupportedAnnotations()CAnnotation
getUnsupportedAnnotations() const CAnnotation
getUpdateMethod() const CCopasiObject
getUpdateSequence(CMathDependencyGraph &dependencyGraph, const CMath::SimulationContextFlag &context, const CCopasiObject::DataObjectSet &changedObjects, const CCopasiObject::DataObjectSet &requestedObjects, CCopasiObject::DataUpdateSequence &updateSequence) const CModelprivate
getUptoDateObjects() const CModel
getValue() const CModelEntity
getValueObject() const CModelEntityvirtual
getValuePointer() const CModelEntityvirtual
getValueReference() const CModelEntity
getVolumeRateUnitsDisplayString() const CModel
getVolumeUnitEnum() const CModel
getVolumeUnitName() const CModel
getVolumeUnitsDisplayString() const CModel
Gui enum valueCCopasiObjectprotected
h enum valueCModel
handleUnusedMetabolites()CModelprivate
hasCircularDependencies(DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const CCopasiObject
hasReversibleReaction() const CModel
hasUpdateMethod() const CCopasiObject
initial enum valueCModel
initializeAtolVector(const C_FLOAT64 &baseTolerance, const bool &reducedModel) const CModel
initializeMetabolites()CModel
initObjects()CModelprivate
isArray() const CCopasiObject
isAutonomous() const CModel
isContainer() const CCopasiObject
isDataModel() const CCopasiObject
isFixed() const CModelEntityinline
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
isRoot() const CCopasiObject
isSeparator() const CCopasiObject
isStateVariable(const CCopasiObject *pObject) const CModel
isStaticString() const CCopasiObject
isUsed() const CModelEntity
isValueBool() const CCopasiObject
isValueDbl() const CCopasiObject
isValueInt() const CCopasiObject
isValueInt64() const CCopasiObject
isValueString() const CCopasiObject
isVector() const CCopasiObject
l enum valueCModel
LengthUnit enum nameCModel
LengthUnitNamesCModelstatic
load(CReadConfig &configBuffer)CModel
m enum valueCModel
m2 enum valueCModel
m3 enum valueCModel
mActiveParameterSetKeyCModelprivate
mApplyInitialValuesRefreshesCModelprivate
mAreaUnitCModelprivate
Matrix enum valueCCopasiObjectprotected
mAvogadroCModelprivate
mBuildInitialSequenceCModelprivate
mCompartmentsCModelprivate
mCompileIsNecessaryCModelprivate
mCurrentStateCModelprivate
mElasticitiesCModelprivate
mEventsCModelprivate
microl enum valueCModel
microm enum valueCModel
microm2 enum valueCModel
microMol enum valueCModel
micros enum valueCModel
min enum valueCModel
mInitialDependenciesCModelmutableprivate
mInitialRefreshesCModelprivate
mInitialStateCModelprivate
mIsAutonomousCModelprivate
mJacobianPivotCModelprivate
mKeyCAnnotationprotected
ml enum valueCModel
mLCModelprivate
mLengthUnitCModelprivate
mLViewCModelprivate
mm enum valueCModel
mm2 enum valueCModel
mMetabolitesCModelprivate
mMetabolitesXCModelprivate
mMoietiesCModelprivate
mMol enum valueCModel
mNonSimulatedRefreshesCModelprivate
mNumber2QuantityFactorCModelprivate
mNumMetabolitesAssignmentCModelprivate
mNumMetabolitesODECModelprivate
mNumMetabolitesReactionCModelprivate
mNumMetabolitesReactionIndependentCModelprivate
mNumMetabolitesUnusedCModelprivate
mObjectsCCopasiContainerprotected
ModelEntity enum valueCCopasiObjectprotected
ModelType enum nameCModel
ModelTypeNamesCModelstatic
Mol enum valueCModel
mParameterSetCModelprivate
mParameterSetsCModelprivate
mParticleFluxesCModelprivate
mpCompileHandlerCModelprivate
mpExpressionCModelEntityprotected
mPhysicalDependenciesCModelprivate
mpInitialExpressionCModelEntityprotected
mpIValueCModelEntityprotected
mpIValueReferenceCModelEntityprotected
mpLinkMatrixAnnotationCModelprivate
mpMathModelCModelprivate
mpModelCModelEntityprotected
mpRateReferenceCModelEntityprotected
mpRedStoiAnnotationCModelprivate
mpStoiAnnotationCModelprivate
mpValueCModelEntityprotected
mpValueReferenceCModelEntityprotected
mQuantity2NumberFactorCModelprivate
mQuantityUnitCModelprivate
mRateCModelEntityprotected
mRedStoiCModelprivate
mReorderNeededCModelprivate
ms enum valueCModel
mSBMLIdCModelEntityprotected
mSimulatedRefreshesCModelprivate
mSimulatedUpToDateObjectsCModelprivate
mStateTemplateCModelprivate
mStepsCModelprivate
mStoiCModelprivate
mStoiInternalCModelprivate
mTimeUnitCModelprivate
mTransientDependenciesCModelmutableprivate
mTypeCModelprivate
mustBeDeleted(const DataObjectSet &deletedObjects) const CModelEntityvirtual
mValuesCModelprivate
mVolumeUnitCModelprivate
NameVector enum valueCCopasiObjectprotected
nl enum valueCModel
nm enum valueCModel
nm2 enum valueCModel
nMol enum valueCModel
NonUniqueName enum valueCCopasiObjectprotected
ns enum valueCModel
number enum valueCModel
objectMap typedefCCopasiContainer
ObjectSet typedefCObjectInterface
ODE enum valueCModelEntity
OldMinute enum valueCModel
OldXML enum valueCModel
operator=(const CModel &src)CModelprivate
operator==(const CAnnotation &rhs) const CAnnotation
physical enum valueCModel
pl enum valueCModel
pm enum valueCModel
pm2 enum valueCModel
pMol enum valueCModel
print(std::ostream *ostream) const CCopasiObjectvirtual
printParameterOverview()CModel
processQueue(const C_FLOAT64 &time, const bool &equality, CProcessQueue::resolveSimultaneousAssignments pResolveSimultaneousAssignments)CModel
processRoots(const C_FLOAT64 &time, const bool &equality, const bool &correct, const CVector< C_INT > &roots)CModel
ps enum valueCModel
QuantityUnit enum nameCModel
QuantityUnitNamesCModelstatic
QuantityUnitOldXMLNamesCModelstatic
REACTIONS enum valueCModelEntity
Reference enum valueCCopasiObjectprotected
refreshActiveParameterSet()CModel
refreshInitialValue()CModelEntityvirtual
remove(CCopasiObject *pObject)CCopasiContainervirtual
removeCompartment(const size_t index, const bool &recursive=true)CModel
removeCompartment(const std::string &key, const bool &recursive=true)CModel
removeCompartment(const CCompartment *pCompartment, const bool &recursive=true)CModel
removeDependentModelObjects(const std::set< const CCopasiObject * > &deletedObjects)CModel
removeDirectDependency(const CCopasiObject *pObject)CCopasiObject
removeEvent(const size_t index, const bool &recursive=true)CModel
removeEvent(const std::string &key, const bool &recursive=true)CModel
removeEvent(const CEvent *pEvent, const bool &recursive=true)CModel
removeLocalReactionParameter(const std::string &key, const bool &recursive=true)CModel
removeMetabolite(const std::string &key, const bool &recursive=true)CModel
removeMetabolite(const size_t index, const bool &recursive=true)CModel
removeMetabolite(const CMetab *pMetabolite, const bool &recursive=true)CModel
removeModelValue(const CModelValue *pModelValue, const bool &recursive=true)CModel
removeModelValue(const std::string &key, const bool &recursive=true)CModel
removeModelValue(const size_t index, const bool &recursive=true)CModel
removeReaction(const CReaction *pReaction, const bool &recursive=true)CModel
removeReaction(const std::string &key, const bool &recursive=true)CModel
removeReaction(const size_t index, const bool &recursive=true)CModel
removeUnsupportedAnnotation(const std::string &name)CAnnotation
replaceUnsupportedAnnotation(const std::string &name, const std::string &xml)CAnnotation
Root enum valueCCopasiObjectprotected
s enum valueCModel
Separator enum valueCCopasiObjectprotected
setAreaUnit(const std::string &name)CModel
setAreaUnit(const CModel::AreaUnit &unit)CModel
setAvogadro(const C_FLOAT64 &avogadro)CModel
setCompileFlag(bool flag=true)CModel
setDirectDependencies(const DataObjectSet &directDependencies)CCopasiObject
setExpression(const std::string &expression)CModelEntity
setExpressionPtr(CExpression *pExpression)CModelEntity
setInitialExpression(const std::string &expression)CModelEntity
setInitialExpressionPtr(CExpression *pExpression)CModelEntity
setInitialState(const CState &state)CModel
setInitialTime(const C_FLOAT64 &time)CModel
setInitialValue(const C_FLOAT64 &initialValue)CModelEntityvirtual
setInitialValuePtr(C_FLOAT64 *pInitialValue)CModelEntity
setLengthUnit(const std::string &name)CModel
setLengthUnit(const CModel::LengthUnit &unit)CModel
setMiriamAnnotation(const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)CAnnotation
setModelType(const ModelType &modelType)CModel
setNotes(const std::string &notes)CAnnotation
setObjectName(const std::string &name)CCopasiObject
setObjectParent(const CCopasiContainer *pParent)CModelEntityvirtual
setObjectValue(const C_FLOAT64 &value)CCopasiObject
setObjectValue(const C_INT32 &value)CCopasiObject
setObjectValue(const bool &value)CCopasiObject
setQuantityUnit(const std::string &name)CModel
setQuantityUnit(const CModel::QuantityUnit &unit)CModel
setRate(const C_FLOAT64 &rate)CModelEntity
setRefresh(CType *pType, void(CType::*method)(void))CCopasiObjectinline
setRenameHandler(CRenameHandler *rh)CCopasiObjectinlinestatic
setSBMLId(const std::string &id)CModelEntity
setState(const CState &state)CModel
setStatus(const CModelEntity::Status &status)CModelEntityvirtual
setTime(const C_FLOAT64 &time)CModel
setTimeUnit(const std::string &name)CModel
setTimeUnit(const CModel::TimeUnit &unit)CModel
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
setUsed(const bool &used)CModelEntity
setValue(const C_FLOAT64 &value)CModelEntityvirtual
setValuePtr(C_FLOAT64 *pValue)CModelEntity
setVolumeUnit(const std::string &name)CModel
setVolumeUnit(const CModel::VolumeUnit &unit)CModel
smpRenameHandlerCCopasiObjectprotectedstatic
StaticString enum valueCCopasiObjectprotected
Status enum nameCModelEntity
StatusNameCModelEntitystatic
stochastic enum valueCModel
suitableForStochasticSimulation() const CModel
TIME enum valueCModelEntity
TimeUnit enum nameCModel
TimeUnitNamesCModelstatic
transient enum valueCModel
UnsupportedAnnotation typedefCAnnotation
updateInitialValues()CModel
updateInitialValues(std::set< const CCopasiObject * > &changedObjects)CModel
updateInitialValues(const CCopasiObject *changedObject)CModel
updateMatrixAnnotations()CModelprivate
updateMoietyValues()CModelprivate
updateNonSimulatedValues(void)CModel
UpdateSequence typedefCObjectInterface
updateSimulatedValues(const bool &updateMoieties)CModel
ValueBool enum valueCCopasiObjectprotected
ValueDbl enum valueCCopasiObjectprotected
ValueInt enum valueCCopasiObjectprotected
ValueInt64 enum valueCCopasiObjectprotected
ValueString enum valueCCopasiObjectprotected
Vector enum valueCCopasiObjectprotected
VolumeUnit enum nameCModel
VolumeUnitNamesCModelstatic
XMLStatusCModelEntitystatic
~CAnnotation()CAnnotationvirtual
~CCopasiContainer()CCopasiContainervirtual
~CCopasiObject()CCopasiObjectvirtual
~CModel()CModel
~CModelEntity()CModelEntity
~CObjectInterface()CObjectInterfaceinlinevirtual