NFcore::Molecule Class Reference

#include <NFcore.hh>

List of all members.

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Detailed Description

Each molecule in the system is represented by an instance of this.

The base unit of the NFsim program, this class maintains instances of individual objects that exist in the simulation. Molecules are able to interact with their MoleculeType so that they also 'know' about the reactions and observables they need to keep updated as they react and change states. There are also two static functions which are used to create and delete bonds (bind and unbind).

Author:

Michael Sneddon

Public Member Functions
	Molecule (MoleculeType *parentMoleculeType, int listId)
	~Molecule ()
int	getMolListId () const
string	getMoleculeTypeName () const
MoleculeType *	getMoleculeType () const
int	getUniqueID () const
bool	isAlive () const
void	setAlive (bool isAlive)
void	setComplexID (int currentComplex)
int	getComplexID () const
Complex *	getComplex () const
int	getDegree ()
int	getComponentState (int cIndex) const
int	getComponentIndexOfBond (int cIndex) const
void	setComponentState (int cIndex, int newValue)
void	setComponentState (string cName, int newValue)
void	setLocalFunctionValue (double newValue, int localFunctionIndex)
double	getLocalFunctionValue (int localFunctionIndex)
LocalFunction *	getLocalFunction (int localFunctionIndex)
void	setUpLocalFunctionList ()
bool	isBindingSiteOpen (int bIndex) const
bool	isBindingSiteBonded (int bIndex) const
Molecule *	getBondedMolecule (int bSiteIndex) const
int	getBondedMoleculeBindingSiteIndex (int cIndex) const
int	getRxnListMappingId (int rxnIndex) const
void	setRxnListMappingId (int rxnIndex, int rxnListMappingId)
void	setBondTo (Molecule *m2, int bindingSiteIndex)
void	moveToNewComplex (int newComplexID)
void	traverseBondedNeighborhood (list< Molecule * > &members, int traversalLimit)
void	depthFirstSearch (list< Molecule * > &members)
void	prepareForSimulation ()
void	updateRxnMembership ()
void	removeFromObservables ()
void	addToObservables ()
void	updateTypeIIFunctions ()
void	updateDORRxnValues ()
void	printDetails ()
void	printDetails (ostream &o)
int	isObs (int oIndex) const
void	setIsObs (int oIndex, int isObs)
Static Public Member Functions
static void	bind (Molecule *m1, int cIndex1, Molecule *m2, int cIndex2)
static void	bind (Molecule *m1, string compName1, Molecule *m2, string compName2)
static void	unbind (Molecule *m1, int bSiteIndex)
static void	unbind (Molecule *m1, char *bSiteName)
static void	breadthFirstSearch (list< Molecule * > &members, Molecule *m, int depth)
static void	printMoleculeList (list< Molecule * > &members)
static int	getUniqueIdCount ()
Public Attributes
bool	hasVisitedMolecule
bool *	hasVisitedBond
TemplateMolecule *	isMatchedTo
bool	hasEvaluatedMolecule
Static Public Attributes
static const int	NOT_IN_RXN = -1
static const int	NOSTATE = -1
static const int	NOBOND = 0
static const int	NOINDEX = -1
Protected Attributes
bool	isPrepared
bool	isAliveInSim
int	ID_complex
int	ID_type
int	ID_unique
int	listId
MoleculeType *	parentMoleculeType
bool	useComplex
int *	component
int	numOfComponents
Molecule **	bond
int *	indexOfBond
double *	localFunctionValues
int *	isObservable
int *	rxnListMappingId
int	nReactions
Static Protected Attributes
static int	uniqueIdCount = 0

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Constructor & Destructor Documentation

Molecule::Molecule	(	MoleculeType *	parentMoleculeType,
		int	listId
	)

Molecule::~Molecule

(

)

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Member Function Documentation

int NFcore::Molecule::getMolListId

(

)

const [inline]

string NFcore::Molecule::getMoleculeTypeName

(

)

const [inline]

MoleculeType* NFcore::Molecule::getMoleculeType

(

)

const [inline]

int NFcore::Molecule::getUniqueID

(

)

const [inline]

bool NFcore::Molecule::isAlive

(

)

const [inline]

void NFcore::Molecule::setAlive

(

bool

isAlive

)

[inline]

void NFcore::Molecule::setComplexID

(

int

currentComplex

)

[inline]

int NFcore::Molecule::getComplexID

(

)

const [inline]

Complex* NFcore::Molecule::getComplex

(

)

const [inline]

int Molecule::getDegree

(

)

int NFcore::Molecule::getComponentState

(

int

cIndex

)

const [inline]

int NFcore::Molecule::getComponentIndexOfBond

(

int

cIndex

)

const [inline]

void Molecule::setComponentState	(	int	cIndex,
		int	newValue
	)

void Molecule::setComponentState	(	string	cName,
		int	newValue
	)

void Molecule::setLocalFunctionValue	(	double	newValue,
		int	localFunctionIndex
	)

double Molecule::getLocalFunctionValue

(

int

localFunctionIndex

)

LocalFunction * Molecule::getLocalFunction

(

int

localFunctionIndex

)

void Molecule::setUpLocalFunctionList

(

)

bool Molecule::isBindingSiteOpen

(

int

bIndex

)

const

bool Molecule::isBindingSiteBonded

(

int

bIndex

)

const

Molecule * Molecule::getBondedMolecule

(

int

bSiteIndex

)

const

int Molecule::getBondedMoleculeBindingSiteIndex

(

int

cIndex

)

const

int NFcore::Molecule::getRxnListMappingId

(

int

rxnIndex

)

const [inline]

void NFcore::Molecule::setRxnListMappingId	(	int	rxnIndex,
		int	rxnListMappingId
	)			[inline]

void NFcore::Molecule::setBondTo	(	Molecule *	m2,
		int	bindingSiteIndex
	)

void NFcore::Molecule::moveToNewComplex

(

int

newComplexID

)

[inline]

void Molecule::bind	(	Molecule *	m1,
		int	cIndex1,
		Molecule *	m2,
		int	cIndex2
	)			[static]

void Molecule::bind	(	Molecule *	m1,
		string	compName1,
		Molecule *	m2,
		string	compName2
	)			[static]

void Molecule::unbind	(	Molecule *	m1,
		int	bSiteIndex
	)			[static]

void Molecule::unbind	(	Molecule *	m1,
		char *	bSiteName
	)			[static]

void Molecule::traverseBondedNeighborhood	(	list< Molecule * > &	members,
		int	traversalLimit
	)

void Molecule::breadthFirstSearch	(	list< Molecule * > &	members,
		Molecule *	m,
		int	depth
	)			[static]

void Molecule::depthFirstSearch

(

list< Molecule * > &

members

)

void Molecule::prepareForSimulation

(

)

void Molecule::updateRxnMembership

(

)

void Molecule::removeFromObservables

(

)

void Molecule::addToObservables

(

)

void Molecule::updateTypeIIFunctions

(

)

void Molecule::updateDORRxnValues

(

)

void Molecule::printDetails

(

)

void Molecule::printDetails

(

ostream &

o

)

void Molecule::printMoleculeList

(

list< Molecule * > &

members

)

[static]

static int NFcore::Molecule::getUniqueIdCount

(

)

[inline, static]

int NFcore::Molecule::isObs

(

int

oIndex

)

const [inline]

void NFcore::Molecule::setIsObs	(	int	oIndex,
		int	isObs
	)			[inline]

---

Member Data Documentation

const int NFcore::Molecule::NOT_IN_RXN = -1 [static]

bool NFcore::Molecule::hasVisitedMolecule

bool* NFcore::Molecule::hasVisitedBond

TemplateMolecule* NFcore::Molecule::isMatchedTo

bool NFcore::Molecule::hasEvaluatedMolecule

const int NFcore::Molecule::NOSTATE = -1 [static]

const int NFcore::Molecule::NOBOND = 0 [static]

const int NFcore::Molecule::NOINDEX = -1 [static]

bool NFcore::Molecule::isPrepared [protected]

bool NFcore::Molecule::isAliveInSim [protected]

int NFcore::Molecule::ID_complex [protected]

int NFcore::Molecule::ID_type [protected]

int NFcore::Molecule::ID_unique [protected]

int NFcore::Molecule::listId [protected]

int Molecule::uniqueIdCount = 0 [static, protected]

MoleculeType* NFcore::Molecule::parentMoleculeType [protected]

bool NFcore::Molecule::useComplex [protected]

int* NFcore::Molecule::component [protected]

int NFcore::Molecule::numOfComponents [protected]

Molecule** NFcore::Molecule::bond [protected]

int* NFcore::Molecule::indexOfBond [protected]

double* NFcore::Molecule::localFunctionValues [protected]

int* NFcore::Molecule::isObservable [protected]

int* NFcore::Molecule::rxnListMappingId [protected]

int NFcore::Molecule::nReactions [protected]

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

• /home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFcore/NFcore.hh
• /home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFcore/molecule.cpp

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