NFcore::MoleculeType Class Reference

#include <NFcore.hh>

List of all members.

---

Detailed Description

Keeps track of the types of molecules that can exist.

This class maintains information about a "type" of molecule in the System. It keeps track of all reactions that this "type" of molecule can possibly be a part of and a list of the default binding sites and states. It also keeps track and updates all Observables that pertain to this MoleculeType. And perhaps most importantly, it keeps track of all Molecules that exist in the simulation of this molecule "type." It has functions which allow it also to populate itself with a number of default molecules, making initializations of the simulation easier.

Author:

Michael Sneddon

Public Member Functions
	MoleculeType (string name, vector< string > &compName, System *s)
	MoleculeType (string name, vector< string > &compName, vector< string > &defaultCompState, System *s)
	MoleculeType (string name, vector< string > &compName, vector< string > &defaultCompState, vector< vector< string > > &possibleCompStates, System *system)
	MoleculeType (string name, vector< string > &compName, vector< string > &defaultCompState, vector< vector< string > > &possibleCompStates, vector< bool > isIntegerComponent, System *system)
	~MoleculeType ()
string	getName () const
int	getTypeID () const
System *	getSystem () const
int	getNumOfComponents () const
string	getComponentName (int cIndex) const
void	getPossibleComponentStates (int cIndex, list< string > &nameList)
int	getDefaultComponentState (int cIndex) const
int	getCompIndexFromName (string cName) const
string	getComponentStateName (int cIndex, int cValue)
int	getStateValueFromName (int cIndex, string stateName) const
int	getNumOfEquivalencyClasses () const
string *	getEquivalencyClassCompNames () const
void	addEquivalentComponents (vector< vector< string > > &identicalComponents)
bool	isEquivalentComponent (string cName) const
bool	isEquivalentComponent (int cIndex) const
void	getEquivalencyClass (int *&components, int &n_components, string cName) const
int	getEquivalencyClassNumber (string cName) const
bool	isIntegerComponent (string cName) const
bool	isIntegerComponent (int cIndex) const
int	getNumOfMolObs () const
string	getMolObsName (int obsIndex) const
MoleculesObservable *	getMolObs (int obsIndex) const
int	getMolObsCount (int obsIndex) const
void	removeFromObservables (Molecule *m)
void	addToObservables (Molecule *m)
void	outputMolObsNames (NFstream &fout)
void	outputMolObsCounts (NFstream &fout)
void	printMolObsNames ()
void	printMolObsCounts ()
void	addAllToObservables ()
Molecule *	getMolecule (int ID_molecule) const
int	getMoleculeCount () const
int	getReactionCount () const
int	getRxnIndex (ReactionClass *rxn, int rxnPosition)
Molecule *	genDefaultMolecule ()
void	addMoleculeToRunningSystem (Molecule *&mol)
void	removeMoleculeFromRunningSystem (Molecule *&m)
void	removeFromRxns (Molecule *m)
void	addReactionClass (ReactionClass *r, int rPosition)
void	addMolObs (MoleculesObservable *mo)
int	createComplex (Molecule *m)
void	addTemplateMolecule (TemplateMolecule *t)
void	updateRxnMembership (Molecule *m)
void	populateWithDefaultMolecules (int moleculeCount)
void	prepareForSimulation ()
void	printDetails () const
void	printAllMolecules ()
int	addLocalFunc_TypeI (LocalFunction *lf)
int	addLocalFunc_TypeII (LocalFunction *lf)
int	getNumOfTypeIFunctions () const
LocalFunction *	getTypeILocalFunction (int index)
int	getNumOfTypeIIFunctions () const
LocalFunction *	getTypeIILocalFunction (int index)
int	getNumOfDORrxns () const
ReactionClass *	getDORrxn (int dorRxnIndex) const
int	getDORrxnIndex (int dorRxnIndex) const
int	getDORrxnPosition (int dorRxnIndex) const
void	setUpLocalFunctionListForMolecules ()
Public Attributes
vector< LocalFunction * >	locFuncs_typeI
vector< LocalFunction * >	locFuncs_typeII
Protected Member Functions
void	init (string name, vector< string > &compName, vector< string > &defaultCompState, vector< vector< string > > &possibleCompStates, vector< bool > isIntegerComponent, System *system)
Protected Attributes
System *	system
string	name
int	type_id
int	numOfComponents
string *	compName
vector< vector< string > >	possibleCompStates
int *	defaultCompState
bool *	isIntegerCompState
int	n_eqComp
string *	eqCompOriginalName
int *	eqCompSizes
string **	eqCompName
int **	eqCompIndex
MoleculeList *	mList
vector< ReactionClass * >	reactions
vector< int >	reactionPositions
vector< int >	indexOfDORrxns
vector< MoleculesObservable * >	molObs
vector< TemplateMolecule * >	allTemplates
ReactionClass *	rxn

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Constructor & Destructor Documentation

MoleculeType::MoleculeType	(	string	name,
		vector< string > &	compName,
		System *	s
	)

MoleculeType::MoleculeType	(	string	name,
		vector< string > &	compName,
		vector< string > &	defaultCompState,
		System *	s
	)

MoleculeType::MoleculeType	(	string	name,
		vector< string > &	compName,
		vector< string > &	defaultCompState,
		vector< vector< string > > &	possibleCompStates,
		System *	system
	)

MoleculeType::MoleculeType	(	string	name,
		vector< string > &	compName,
		vector< string > &	defaultCompState,
		vector< vector< string > > &	possibleCompStates,
		vector< bool >	isIntegerComponent,
		System *	system
	)

MoleculeType::~MoleculeType

(

)

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Member Function Documentation

string NFcore::MoleculeType::getName

(

)

const [inline]

int NFcore::MoleculeType::getTypeID

(

)

const [inline]

System* NFcore::MoleculeType::getSystem

(

)

const [inline]

int NFcore::MoleculeType::getNumOfComponents

(

)

const [inline]

string MoleculeType::getComponentName

(

int

cIndex

)

const

void NFcore::MoleculeType::getPossibleComponentStates	(	int	cIndex,
		list< string > &	nameList
	)

int NFcore::MoleculeType::getDefaultComponentState

(

int

cIndex

)

const [inline]

int MoleculeType::getCompIndexFromName

(

string

cName

)

const

string MoleculeType::getComponentStateName	(	int	cIndex,
		int	cValue
	)

int MoleculeType::getStateValueFromName	(	int	cIndex,
		string	stateName
	)			const

int NFcore::MoleculeType::getNumOfEquivalencyClasses

(

)

const [inline]

string* NFcore::MoleculeType::getEquivalencyClassCompNames

(

)

const [inline]

void MoleculeType::addEquivalentComponents

(

vector< vector< string > > &

identicalComponents

)

bool MoleculeType::isEquivalentComponent

(

string

cName

)

const

bool MoleculeType::isEquivalentComponent

(

int

cIndex

)

const

void MoleculeType::getEquivalencyClass	(	int *&	components,
		int &	n_components,
		string	cName
	)			const

int MoleculeType::getEquivalencyClassNumber

(

string

cName

)

const

bool MoleculeType::isIntegerComponent

(

string

cName

)

const

bool MoleculeType::isIntegerComponent

(

int

cIndex

)

const

int NFcore::MoleculeType::getNumOfMolObs

(

)

const [inline]

string MoleculeType::getMolObsName

(

int

obsIndex

)

const

MoleculesObservable* NFcore::MoleculeType::getMolObs

(

int

obsIndex

)

const [inline]

int MoleculeType::getMolObsCount

(

int

obsIndex

)

const

void MoleculeType::removeFromObservables

(

Molecule *

m

)

void MoleculeType::addToObservables

(

Molecule *

m

)

void MoleculeType::outputMolObsNames

(

NFstream &

fout

)

void MoleculeType::outputMolObsCounts

(

NFstream &

fout

)

void MoleculeType::printMolObsNames

(

)

void MoleculeType::printMolObsCounts

(

)

void MoleculeType::addAllToObservables

(

)

Molecule * MoleculeType::getMolecule

(

int

ID_molecule

)

const

int MoleculeType::getMoleculeCount

(

)

const

int NFcore::MoleculeType::getReactionCount

(

)

const [inline]

int MoleculeType::getRxnIndex	(	ReactionClass *	rxn,
		int	rxnPosition
	)

Molecule * MoleculeType::genDefaultMolecule

(

)

void MoleculeType::addMoleculeToRunningSystem

(

Molecule *&

mol

)

void MoleculeType::removeMoleculeFromRunningSystem

(

Molecule *&

m

)

void MoleculeType::removeFromRxns

(

Molecule *

m

)

void MoleculeType::addReactionClass	(	ReactionClass *	r,
		int	rPosition
	)

void NFcore::MoleculeType::addMolObs

(

MoleculesObservable *

mo

)

[inline]

int NFcore::MoleculeType::createComplex

(

Molecule *

m

)

[inline]

void MoleculeType::addTemplateMolecule

(

TemplateMolecule *

t

)

void MoleculeType::updateRxnMembership

(

Molecule *

m

)

void MoleculeType::populateWithDefaultMolecules

(

int

moleculeCount

)

void MoleculeType::prepareForSimulation

(

)

void MoleculeType::printDetails

(

)

const

void MoleculeType::printAllMolecules

(

)

int MoleculeType::addLocalFunc_TypeI

(

LocalFunction *

lf

)

int MoleculeType::addLocalFunc_TypeII

(

LocalFunction *

lf

)

int NFcore::MoleculeType::getNumOfTypeIFunctions

(

)

const [inline]

LocalFunction* NFcore::MoleculeType::getTypeILocalFunction

(

int

index

)

[inline]

int NFcore::MoleculeType::getNumOfTypeIIFunctions

(

)

const [inline]

LocalFunction* NFcore::MoleculeType::getTypeIILocalFunction

(

int

index

)

[inline]

int NFcore::MoleculeType::getNumOfDORrxns

(

)

const [inline]

ReactionClass* NFcore::MoleculeType::getDORrxn

(

int

dorRxnIndex

)

const [inline]

int NFcore::MoleculeType::getDORrxnIndex

(

int

dorRxnIndex

)

const [inline]

int NFcore::MoleculeType::getDORrxnPosition

(

int

dorRxnIndex

)

const [inline]

void MoleculeType::setUpLocalFunctionListForMolecules

(

)

void MoleculeType::init	(	string	name,
		vector< string > &	compName,
		vector< string > &	defaultCompState,
		vector< vector< string > > &	possibleCompStates,
		vector< bool >	isIntegerComponent,
		System *	system
	)			[protected]

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Member Data Documentation

vector<LocalFunction *> NFcore::MoleculeType::locFuncs_typeI

vector<LocalFunction *> NFcore::MoleculeType::locFuncs_typeII

System* NFcore::MoleculeType::system [protected]

string NFcore::MoleculeType::name [protected]

int NFcore::MoleculeType::type_id [protected]

int NFcore::MoleculeType::numOfComponents [protected]

string* NFcore::MoleculeType::compName [protected]

vector< vector < string > > NFcore::MoleculeType::possibleCompStates [protected]

int* NFcore::MoleculeType::defaultCompState [protected]

bool* NFcore::MoleculeType::isIntegerCompState [protected]

int NFcore::MoleculeType::n_eqComp [protected]

string* NFcore::MoleculeType::eqCompOriginalName [protected]

int* NFcore::MoleculeType::eqCompSizes [protected]

string** NFcore::MoleculeType::eqCompName [protected]

int** NFcore::MoleculeType::eqCompIndex [protected]

MoleculeList* NFcore::MoleculeType::mList [protected]

vector<ReactionClass *> NFcore::MoleculeType::reactions [protected]

vector<int> NFcore::MoleculeType::reactionPositions [protected]

vector<int> NFcore::MoleculeType::indexOfDORrxns [protected]

vector<MoleculesObservable *> NFcore::MoleculeType::molObs [protected]

vector<TemplateMolecule *> NFcore::MoleculeType::allTemplates [protected]

ReactionClass* NFcore::MoleculeType::rxn [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/moleculeType.cpp

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