#include <Goldbeter1991SrnModel.hpp>

Inheritance diagram for Goldbeter1991SrnModel:

Collaboration diagram for Goldbeter1991SrnModel:

Public Member Functions
	Goldbeter1991SrnModel (boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

AbstractSrnModel *	CreateSrnModel ()

void	Initialise ()

void	SimulateToCurrentTime ()

void	OutputSrnModelParameters (out_stream &rParamsFile)

double	GetC ()

double	GetM ()

double	GetX ()

Public Member Functions inherited from AbstractOdeSrnModel
	AbstractOdeSrnModel (unsigned stateSize, boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~AbstractOdeSrnModel ()

virtual void	ResetForDivision ()

void	SetInitialConditions (std::vector< double > initialConditions)

virtual void	ScaleSrnVariables (const double theta)

Public Member Functions inherited from AbstractSrnModel
	AbstractSrnModel ()

virtual	~AbstractSrnModel ()

virtual void	SetCell (CellPtr pCell)

virtual void	InitialiseDaughterCell ()

CellPtr	GetCell ()

void	SetSimulatedToTime (double simulatedToTime)

double	GetSimulatedToTime () const

void	OutputSrnModelInfo (out_stream &rParamsFile)

void	SetEdgeLocalIndex (unsigned index)

unsigned	GetEdgeLocalIndex ()

bool	HasEdgeModel () const

void	SetEdgeModelIndicator (const bool isEdgeModel)

virtual void	AddSrnQuantities (AbstractSrnModel *pOtherSrn, const double scale=1.0)

virtual void	AddShrunkEdgeSrn (AbstractSrnModel *pShrunkEdgeSrn)

virtual void	AddMergedEdgeSrn (AbstractSrnModel *pMergedEdgeSrn)

virtual void	AddShrunkEdgeToInterior (AbstractSrnModel *pShrunkEdgeSrn)

virtual void	SplitEdgeSrn (const double relativePosition)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Public Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (double lastTime=SimulationTime::Instance() ->GetTime(), boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver=boost::shared_ptr< AbstractCellCycleModelOdeSolver >())

virtual	~CellCycleModelOdeHandler ()

AbstractOdeSystem *	GetOdeSystem () const

void	SetOdeSystem (AbstractOdeSystem *pOdeSystem)

const boost::shared_ptr< AbstractCellCycleModelOdeSolver >	GetOdeSolver () const

void	SetLastTime (double lastTime)

double	GetDt ()

void	SetDt (double timeStep)

void	SetStateVariables (const std::vector< double > &rStateVariables)

std::vector< double >	GetProteinConcentrations () const

void	SetProteinConcentrationsForTestsOnly (double lastTime, std::vector< double > proteinConcentrations)

Protected Member Functions
	Goldbeter1991SrnModel (const Goldbeter1991SrnModel &rModel)

Protected Member Functions inherited from AbstractOdeSrnModel
void	Initialise (AbstractOdeSystem *pOdeSystem)

	AbstractOdeSrnModel (const AbstractOdeSrnModel &rModel)

Protected Member Functions inherited from AbstractSrnModel
	AbstractSrnModel (const AbstractSrnModel &rModel)

Protected Member Functions inherited from CellCycleModelOdeHandler
	CellCycleModelOdeHandler (const CellCycleModelOdeHandler &rHandler)

bool	SolveOdeToTime (double currentTime)

virtual void	AdjustOdeParameters (double currentTime)

Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractOdeSrnModel
std::vector< double >	mInitialConditions

unsigned	mStateSize

Protected Attributes inherited from AbstractSrnModel
CellPtr	mpCell

double	mSimulatedToTime

unsigned	mEdgeLocalIndex = UNSIGNED_UNSET

bool	mIsEdgeBasedModel = false

Protected Attributes inherited from CellCycleModelOdeHandler
double	mDt

AbstractOdeSystem *	mpOdeSystem

boost::shared_ptr< AbstractCellCycleModelOdeSolver >	mpOdeSolver

double	mLastTime

bool	mFinishedRunningOdes

Detailed Description

A Subcellular Reaction Network Model that includes a Goldbeter1991 ODE system in the sub-cellular reaction network.

Todo:: #2752 give reference for this ODE system

Definition at line 51 of file Goldbeter1991SrnModel.hpp.

Constructor & Destructor Documentation

◆ Goldbeter1991SrnModel() [1/2]

Goldbeter1991SrnModel::Goldbeter1991SrnModel ( const Goldbeter1991SrnModel & rModel )

protected

Protected copy-constructor for use by CreateSrnModel(). The only way for external code to create a copy of a SRN model is by calling that method, to ensure that a model of the correct subclass is created.

This copy-constructor helps subclasses to ensure that all member variables are correctly copied when this happens.

This method is called by child classes to set member variables for a daughter cell upon cell division. Note that the parent SRN model will have had ResetForDivision() called just before CreateSrnModel() is called, so performing an exact copy of the parent is suitable behaviour. Any daughter-cell-specific initialisation can be done in InitialiseDaughterCell().

Parameters

rModel the SRN model to copy.

Definition at line 51 of file Goldbeter1991SrnModel.cpp.

References CellCycleModelOdeHandler::GetOdeSystem(), AbstractParameterisedSystem< VECTOR >::rGetStateVariables(), and CellCycleModelOdeHandler::SetOdeSystem().

◆ Goldbeter1991SrnModel() [2/2]

Goldbeter1991SrnModel::Goldbeter1991SrnModel ( boost::shared_ptr< AbstractCellCycleModelOdeSolver > pOdeSolver = boost::shared_ptr<AbstractCellCycleModelOdeSolver>() )

Default constructor calls base class.

Parameters

pOdeSolver An optional pointer to a cell-cycle model ODE solver object (allows the use of different ODE solvers)

Definition at line 38 of file Goldbeter1991SrnModel.cpp.

References CellCycleModelOdeSolver< CELL_CYCLE_MODEL, ODE_SOLVER >::Instance(), CellCycleModelOdeHandler::mpOdeSolver, and CellCycleModelOdeHandler::SetDt().

Member Function Documentation

◆ CreateSrnModel()

AbstractSrnModel * Goldbeter1991SrnModel::CreateSrnModel ( )

virtual

Overridden builder method to create new copies of this SRN model.

Returns: Returns a copy of the current SRN model.

Implements AbstractSrnModel.

Definition at line 73 of file Goldbeter1991SrnModel.cpp.

◆ GetC()

double Goldbeter1991SrnModel::GetC ( )

Returns: the value of the state variable C in the ODE system.

Definition at line 95 of file Goldbeter1991SrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

◆ GetM()

double Goldbeter1991SrnModel::GetM ( )

Returns: the value of the state variable M in the ODE system.

Definition at line 102 of file Goldbeter1991SrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

◆ GetX()

double Goldbeter1991SrnModel::GetX ( )

Returns: the value of the state variable X in the ODE system.

Definition at line 109 of file Goldbeter1991SrnModel.cpp.

References CellCycleModelOdeHandler::mpOdeSystem, and AbstractParameterisedSystem< VECTOR >::rGetStateVariables().

◆ Initialise()

void Goldbeter1991SrnModel::Initialise ( )

virtual

Initialise the SRN model at the start of a simulation.

This overridden method sets up a new Delta-Notch ODE system.

Reimplemented from AbstractOdeSrnModel.

Definition at line 84 of file Goldbeter1991SrnModel.cpp.

References AbstractOdeSrnModel::Initialise().

◆ OutputSrnModelParameters()

void Goldbeter1991SrnModel::OutputSrnModelParameters ( out_stream & rParamsFile )

virtual

Output SRN model parameters to file.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractOdeSrnModel.

Definition at line 89 of file Goldbeter1991SrnModel.cpp.

References AbstractOdeSrnModel::OutputSrnModelParameters().

◆ serialize()

template<class Archive >

void Goldbeter1991SrnModel::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the SRN model and member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 64 of file Goldbeter1991SrnModel.hpp.

◆ SimulateToCurrentTime()

void Goldbeter1991SrnModel::SimulateToCurrentTime ( )

virtual

Overridden SimulateToTime() method for custom behaviour.

Todo:: #2752 say what it does in this class

Reimplemented from AbstractOdeSrnModel.

Definition at line 78 of file Goldbeter1991SrnModel.cpp.

References AbstractOdeSrnModel::SimulateToCurrentTime().

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 56 of file Goldbeter1991SrnModel.hpp.

The documentation for this class was generated from the following files:

cell_based/src/cell/srn/Goldbeter1991SrnModel.hpp
cell_based/src/cell/srn/Goldbeter1991SrnModel.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Goldbeter1991SrnModel() [1/2]

◆ Goldbeter1991SrnModel() [2/2]

Member Function Documentation

◆ CreateSrnModel()

◆ GetC()

◆ GetM()

◆ GetX()

◆ Initialise()

◆ OutputSrnModelParameters()

◆ serialize()

◆ SimulateToCurrentTime()

Friends And Related Symbol Documentation

◆ boost::serialization::access