40 #ifdef USE_MATH_CONTAINER
42 #endif // USE_MATH_CONTAINER
86 enum TimeUnit {
dimensionlessTime = 0,
d,
h,
min,
s,
ms,
micros,
ns,
ps,
fs,
OldMinute};
152 #ifdef WITH_PE_EVENT_CREATION
156 bool createEventsForTimeseries(
CExperiment* experiment = NULL);
376 const std::string &
getKey()
const;
453 size_t findMoiety(
const std::string &Target)
const;
801 const std::string & compartment,
807 const bool & recursive =
true);
809 const bool & recursive =
true);
811 const bool & recursive =
true);
825 std::set< const CCopasiObject * > & dependentReactions,
826 std::set< const CCopasiObject * > & dependentMetabolites,
827 std::set< const CCopasiObject * > & dependentCompartments,
828 std::set< const CCopasiObject * > & dependentModelValues,
829 std::set< const CCopasiObject * > & dependentEvents)
const;
839 std::set< const CCopasiObject * > & dependents)
const;
850 std::set< const CCopasiObject * > & dependents)
const;
860 std::set< const CCopasiObject * > & dependents)
const;
870 std::set< const CCopasiObject * > & dependents)
const;
880 std::set< const CCopasiObject * > & dependents)
const;
915 const bool & recursive =
true);
919 const bool & recursive =
true);
923 const bool & recursive =
true);
934 const bool & recursive =
true);
938 const bool & recursive =
true);
942 const bool & recursive =
true);
946 const bool & recursive =
true);
962 const bool & recursive =
true);
971 const bool & recursive =
true);
980 const bool & recursive =
true);
991 const bool & recursive =
true);
993 const bool & recursive =
true);
995 const bool & recursive =
true);
1534 #ifdef USE_MATH_CONTAINER
1536 #endif // USE_MATH_CONTAINER
1547 const bool & ignoreDiscrete);
1558 const bool & equality,
1571 const bool & equality,
1572 const bool & correct,
1602 #ifdef USE_MATH_CONTAINER
1614 #endif // USE_MATH_CONTAINER
static const char * LengthUnitNames[]
CArrayAnnotation * mpRedStoiAnnotation
CModel::AreaUnit getAreaUnitEnum() const
const C_FLOAT64 & getAvogadro() const
static const char * ModelTypeNames[]
const CModelParameterSet & getModelParameterSet() const
Header file of class CModelEntity and CModelValue.
bool setAreaUnit(const std::string &name)
CEvent * createEvent(const std::string &name)
CCopasiObject * getCorrespondingTransientObject(const CCopasiObject *pObject) const
bool setVolumeUnit(const std::string &name)
CCopasiVectorN< CEvent > & getEvents()
std::string getTimeUnitsDisplayString() const
CCopasiVectorN< CEvent > mEvents
const CLinkMatrixView & getL() const
const CCopasiVector< CMetab > & getMetabolites() const
std::string getConcentrationRateUnitsDisplayString() const
C_FLOAT64 calculateDivergence() const
std::string getFrequencyUnitsDisplayString() const
const CCopasiVectorN< CModelValue > & getModelValues() const
CModel::QuantityUnit getQuantityUnitEnum() const
size_t mNumMetabolitesReactionIndependent
std::string getQuantityUnitOldXMLName() const
const CVector< CMathTrigger::CRootFinder * > & getRootFinders() const
bool removeMetabolite(const std::string &key, const bool &recursive=true)
bool setLengthUnit(const std::string &name)
void evaluateRoots(CVectorCore< C_FLOAT64 > &rootValues, const bool &ignoreDiscrete)
void updateNonSimulatedValues(void)
CModelParameterSet mParameterSet
CMatrix< C_FLOAT64 > mElasticities
size_t getNumMetabs() const
const CVector< C_FLOAT64 > & getParticleFlux() const
const std::vector< Refresh * > & getListOfConstantRefreshes() const
void setInitialState(const CState &state)
bool setTimeUnit(const std::string &name)
void applyActiveParameterSet()
void updateSimulatedValues(const bool &updateMoieties)
void calculateJacobianX(CMatrix< C_FLOAT64 > &jacobianX, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)
bool removeCompartment(const size_t index, const bool &recursive=true)
std::string getTimeUnitName() const
bool buildNonSimulatedSequence()
std::string getQuantityRateUnitsDisplayString() const
CCopasiVectorNS< CCompartment > mCompartments
std::string printParameterOverview()
std::string getVolumeRateUnitsDisplayString() const
const CMathModel * getMathModel() const
const std::set< const CCopasiObject * > & getUptoDateObjects() const
void calculateJacobian(CMatrix< C_FLOAT64 > &jacobian, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)
CModelValue * createModelValue(const std::string &name, const C_FLOAT64 &value=0.0)
size_t getNumODEMetabs() const
CMatrix< C_FLOAT64 > mStoi
CMatrix< C_FLOAT64 > mRedStoi
bool buildStateTemplate()
void updateMoietyValues()
void applyInitialValues()
std::vector< Refresh * > mNonSimulatedRefreshes
CCopasiVectorN< CModelValue > mValues
const std::vector< Refresh * > & getListOfSimulatedRefreshes() const
std::vector< Refresh * > DataUpdateSequence
const CMatrix< C_FLOAT64 > & getRedStoi() const
const CCopasiVector< CMoiety > & getMoieties() const
void calculateRootDerivatives(CVector< C_FLOAT64 > &rootDerivatives)
size_t mNumMetabolitesUnused
size_t getTotSteps() const
bool hasReversibleReaction() const
void setInitialTime(const C_FLOAT64 &time)
CCopasiVector< CMetab > mMetabolites
bool removeModelValue(const CModelValue *pModelValue, const bool &recursive=true)
bool appendDependentReactions(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const
std::set< const CCopasiObject * > mSimulatedUpToDateObjects
std::vector< Refresh * > mApplyInitialValuesRefreshes
std::string getLengthUnitsDisplayString() const
CStateTemplate mStateTemplate
CArrayAnnotation * mpLinkMatrixAnnotation
bool getInitialUpdateSequence(const CMath::SimulationContextFlag &context, const CCopasiObject::DataObjectSet &changedObjects, const CCopasiObject::DataObjectSet &requestedObjects, CCopasiObject::DataUpdateSequence &updateSequence) const
const C_FLOAT64 & getQuantity2NumberFactor() const
bool 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
CVector< C_FLOAT64 > mParticleFluxes
C_FLOAT64 mNumber2QuantityFactor
const C_FLOAT64 & getNumber2QuantityFactor() const
size_t getNumVariableMetabs() const
const std::vector< Refresh * > & getListOfNonSimulatedRefreshes() const
size_t getNumDependentReactionMetabs() const
size_t findMetabByName(const std::string &Target) const
std::string getVolumeUnitsDisplayString() const
void setState(const CState &state)
void removeDependentModelObjects(const std::set< const CCopasiObject * > &deletedObjects)
bool buildDependencyGraphs()
void determineIsAutonomous()
size_t mNumMetabolitesAssignment
void processRoots(const C_FLOAT64 &time, const bool &equality, const bool &correct, const CVector< C_INT > &roots)
CReaction * createReaction(const std::string &name)
void refreshActiveParameterSet()
const bool & isAutonomous() const
CCopasiVector< CMetab > mMetabolitesX
const C_FLOAT64 & getInitialTime() const
std::vector< Refresh * > mInitialRefreshes
bool appendDependentCompartments(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const
void calculateElasticityMatrix(const C_FLOAT64 &factor, const C_FLOAT64 &resolution)
void initializeMetabolites()
std::string getLengthUnitName() const
QuantityUnit mQuantityUnit
CModel::LengthUnit getLengthUnitEnum() const
std::vector< Refresh * > mSimulatedRefreshes
bool handleUnusedMetabolites()
bool appendDependentMetabolites(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const
bool getTransientUpdateSequence(const CMath::SimulationContextFlag &context, const CCopasiObject::DataObjectSet &changedObjects, const CCopasiObject::DataObjectSet &requestedObjects, CCopasiObject::DataUpdateSequence &updateSequence) const
std::vector< const CEvaluationTree * > getTreesWithDiscontinuities() const
bool buildApplyInitialValuesSequence()
CCopasiVectorN< CModelParameterSet > mParameterSets
const CCopasiVectorN< CModelParameterSet > & getModelParameterSets() const
const std::string & getKey() const
size_t findMoiety(const std::string &Target) const
CMathDependencyGraph mTransientDependencies
Header file of class CCopasiContainer.
size_t getNumIndependentReactionMetabs() const
const C_FLOAT64 & getTime() const
void setCompileFlag(bool flag=true)
bool processQueue(const C_FLOAT64 &time, const bool &equality, CProcessQueue::resolveSimultaneousAssignments pResolveSimultaneousAssignments)
bool mBuildInitialSequence
CProcessReport * mpCompileHandler
static const char * AreaUnitNames[]
void setTime(const C_FLOAT64 &time)
void calculateDerivativesX(C_FLOAT64 *derivativesX)
std::string getAreaUnitName() const
std::string getConcentrationUnitsDisplayString() const
bool getUpdateSequence(CMathDependencyGraph &dependencyGraph, const CMath::SimulationContextFlag &context, const CCopasiObject::DataObjectSet &changedObjects, const CCopasiObject::DataObjectSet &requestedObjects, CCopasiObject::DataUpdateSequence &updateSequence) const
CCopasiVectorNS< CCompartment > & getCompartments()
std::string getQuantityUnitsDisplayString() const
void updateMatrixAnnotations()
CModel::TimeUnit getTimeUnitEnum() const
virtual std::string getChildObjectUnits(const CCopasiObject *pObject) const
iterator(* resolveSimultaneousAssignments)(const std::multimap< CKey, CAction > &, const C_FLOAT64 &, const bool &, const size_t &)
CMathDependencyGraph mInitialDependencies
size_t mNumMetabolitesReaction
std::string getQuantityUnitName() const
const CState & getInitialState() const
bool compileIfNecessary(CProcessReport *pProcessReport)
std::string mActiveParameterSetKey
CMatrix< C_FLOAT64 > mStoiInternal
size_t getNumAssignmentMetabs() const
CModel & operator=(const CModel &src)
const CStateTemplate & getStateTemplate() const
size_t getNumModelValues() const
CCopasiVectorNS< CReaction > mSteps
const ModelType & getModelType() const
CCopasiVectorNS< CReaction > & getReactions()
bool setQuantityUnit(const std::string &name)
bool appendDependentEvents(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const
const C_FLOAT64 & getProcessQueueExecutionTime() const
bool updateInitialValues()
void calculateDerivatives(C_FLOAT64 *derivatives)
const CLinkMatrix & getL0() const
std::string getAreaUnitsDisplayString() const
CVector< C_FLOAT64 > initializeAtolVector(const C_FLOAT64 &baseTolerance, const bool &reducedModel) const
Header file of class CEvent.
bool convert2NonReversible()
const std::vector< Refresh * > & getListOfInitialRefreshes() const
const CState & getState() const
void setAvogadro(const C_FLOAT64 &avogadro)
std::string getVolumeUnitName() const
const CCopasiVector< CMetab > & getMetabolitesX() const
CModel::VolumeUnit getVolumeUnitEnum() const
const CMatrix< C_FLOAT64 > & getStoi() const
static const char * TimeUnitNames[]
std::vector< Refresh * > buildInitialRefreshSequence(std::set< const CCopasiObject * > &changedObjects)
std::set< const CCopasiObject * > DataObjectSet
size_t mNumMetabolitesODE
void setModelType(const ModelType &modelType)
size_t getNumRoots() const
std::string suitableForStochasticSimulation() const
CArrayAnnotation * mpStoiAnnotation
static const char * QuantityUnitOldXMLNames[]
bool buildInitialSequence()
C_FLOAT64 mQuantity2NumberFactor
bool removeLocalReactionParameter(const std::string &key, const bool &recursive=true)
CCopasiVector< CMoiety > mMoieties
CVector< size_t > mJacobianPivot
bool isStateVariable(const CCopasiObject *pObject) const
bool appendDependentModelValues(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependents) const
CMathDependencyGraph mPhysicalDependencies
C_INT32 load(CReadConfig &configBuffer)
bool removeEvent(const size_t index, const bool &recursive=true)
bool removeReaction(const CReaction *pReaction, const bool &recursive=true)
CCompartment * createCompartment(const std::string &name, const C_FLOAT64 &volume=1.0)
static const char * QuantityUnitNames[]
static const char * VolumeUnitNames[]
bool forceCompile(CProcessReport *pProcessReport)
bool buildSimulatedSequence()
CMetab * createMetabolite(const std::string &name, const std::string &compartment, const C_FLOAT64 &iconc=1.0, const CModelEntity::Status &status=CModelEntity::REACTIONS)
CModel(const CModel &src)