NFcore::TemplateMolecule Class Reference

#include <templateMolecule.hh>

List of all members.

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Detailed Description

Used for matching Molecule objects to the given pattern.

TemplateMolecules are regular expression like objects needed to identify specific configurations of connected Molecules. Individual TemplateMolecules are derived from a particular MoleculeType and inherit their set of components from their parent MoleculeType. TemplateMolecules can be connected to other TemplateMolecules through component bonds forming the regular expression pattern. An individual Molecule matches an individual TemplateMolecule if they are of the same MoleculeType and their component bonds and state values match. Any component state not explicitly specified in a TemplateMolecule is treated as a wild-card and will always match the corresponding component of a Molecule. For more complex patterns, an entire connected set of Molecules is matched to a connected set of TemplateMolecules through a recursive algorithm that checks for graph isomorphism between the two sets. The worst case performance of the recursive matching algorithm is proportional to the number of connected TemplateMolecules in the pattern. However, the average performance is much better because a match is rejected as soon as a single difference in component states or molecule connectivity is found.

Author:

Michael Sneddon

Public Member Functions
	TemplateMolecule (MoleculeType *moleculeType)
	~TemplateMolecule ()
MoleculeType *	getMoleculeType () const
string	getMoleculeTypeName () const
int	getN_symComps () const
int	getN_symCompBonds () const
int	getN_mapGenerators () const
int	getN_connectedTo () const
void	addEmptyComponent (string cName)
void	addBoundComponent (string cName)
void	addComponentConstraint (string cName, string stateName)
void	addComponentConstraint (string cName, int stateValue)
void	addComponentExclusion (string cName, string stateName)
void	addComponentExclusion (string cName, int stateValue)
void	addBond (string thisBsiteName, TemplateMolecule *t2, string bSiteName2)
void	addConnectedTo (TemplateMolecule *t2, int otherConToIndex)
void	addConnectedTo (TemplateMolecule *t2, int otherConToIndex, bool otherHasRxnCenter)
void	clearConnectedTo ()
void	addSymCompConstraint (string cName, string uniqueId, int bondState, int stateConstraint)
void	addSymBond (string thisBsiteName, string thisCompId, TemplateMolecule *t2, string bSiteName2)
void	addMapGenerator (MapGenerator *mg)
bool	contains (TemplateMolecule *tempMol)
bool	compare (Molecule *m)
bool	compare (Molecule *m, ReactantContainer *rc, MappingSet *ms, bool holdMolClearToEnd=false)
void	clear ()
void	clearTemplateOnly ()
bool	tryToMap (Molecule *toMap, string toMapComponent, Molecule *mappedFrom, string mappedFromComponent)
bool	isSymMapValid ()
void	printErrorAndExit (string message)
void	printDetails ()
void	printDetails (ostream &o)
string	getPatternString ()
void	printPattern ()
void	printPattern (ostream &o)
Static Public Member Functions
static void	bind (TemplateMolecule *t1, string bSiteName1, string compId1, TemplateMolecule *t2, string bSiteName2, string compId2)
static void	traverse (TemplateMolecule *tempMol, vector< TemplateMolecule * > &tmList, bool skipConnectedTo)
static int	getNumDisjointSets (vector< TemplateMolecule * > &tMolecules, vector< vector< TemplateMolecule * > > &sets, vector< int > &uniqueSetId)
static bool	checkSymmetry (TemplateMolecule *tm1, TemplateMolecule *tm2, string bSite1, string bSite2)
static bool	checkSymmetryAroundBond (TemplateMolecule *tm1, TemplateMolecule *tm2, string bSite1, string bSite2)
Static Public Attributes
static const int	EMPTY = 0
static const int	OCCUPIED = 1
static const int	NO_CONSTRAINT = -1
static const bool	FIND_ALL = false
static const bool	SKIP_CONNECTED_TO = true
Protected Attributes
MoleculeType *	moleculeType
int	uniqueTemplateID
int	n_mapGenerators
MapGenerator **	mapGenerators
int	n_emptyComps
int *	emptyComps
int	n_occupiedComps
int *	occupiedComps
int	n_compStateConstraint
int *	compStateConstraint_Comp
int *	compStateConstraint_Constraint
int	n_compStateExclusion
int *	compStateExclusion_Comp
int *	compStateExclusion_Exclusion
int	n_bonds
int *	bondComp
string *	bondCompName
TemplateMolecule **	bondPartner
string *	bondPartnerCompName
int *	bondPartnerCompIndex
bool *	hasVisitedBond
int	n_connectedTo
TemplateMolecule **	connectedTo
bool *	hasTraversedDownConnectedTo
int *	otherTemplateConnectedToIndex
bool *	connectedToHasRxnCenter
int	n_symComps
string *	symCompName
string *	symCompUniqueId
int *	symCompStateConstraint
int *	symCompBoundState
TemplateMolecule **	symBondPartner
string *	symBondPartnerCompName
int *	symBondPartnerCompIndex
vector< vector< int > >	canBeMappedTo
bool *	hasTraversedDownSym
int	n_totalComps
bool *	isSymCompMapped
bool *	compIsAlwaysMapped
Molecule *	matchMolecule
bool	hasVisitedThis
Static Protected Attributes
static int	TotalTemplateMoleculeCount = 0
static queue< TemplateMolecule * >	q
static queue< int >	d
static vector < TemplateMolecule * > ::iterator	tmVecIter
static list< TemplateMolecule * > ::iterator	tmIter

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Constructor & Destructor Documentation

TemplateMolecule::TemplateMolecule

(

MoleculeType *

moleculeType

)

Only constructor for TemplateMolecules

TemplateMolecule::~TemplateMolecule

(

)

---

Member Function Documentation

MoleculeType* NFcore::TemplateMolecule::getMoleculeType

(

)

const [inline]

string TemplateMolecule::getMoleculeTypeName

(

)

const

int NFcore::TemplateMolecule::getN_symComps

(

)

const [inline]

int NFcore::TemplateMolecule::getN_symCompBonds

(

)

const [inline]

int NFcore::TemplateMolecule::getN_mapGenerators

(

)

const [inline]

int NFcore::TemplateMolecule::getN_connectedTo

(

)

const [inline]

void TemplateMolecule::addEmptyComponent

(

string

cName

)

void TemplateMolecule::addBoundComponent

(

string

cName

)

void TemplateMolecule::addComponentConstraint	(	string	cName,
		string	stateName
	)

void TemplateMolecule::addComponentConstraint	(	string	cName,
		int	stateValue
	)

void TemplateMolecule::addComponentExclusion	(	string	cName,
		string	stateName
	)

void TemplateMolecule::addComponentExclusion	(	string	cName,
		int	stateValue
	)

void TemplateMolecule::addBond	(	string	thisBsiteName,
		TemplateMolecule *	t2,
		string	bSiteName2
	)

void TemplateMolecule::addConnectedTo	(	TemplateMolecule *	t2,
		int	otherConToIndex
	)

void TemplateMolecule::addConnectedTo	(	TemplateMolecule *	t2,
		int	otherConToIndex,
		bool	otherHasRxnCenter
	)

void TemplateMolecule::clearConnectedTo

(

)

void TemplateMolecule::addSymCompConstraint	(	string	cName,
		string	uniqueId,
		int	bondState,
		int	stateConstraint
	)

void TemplateMolecule::addSymBond	(	string	thisBsiteName,
		string	thisCompId,
		TemplateMolecule *	t2,
		string	bSiteName2
	)

void TemplateMolecule::bind	(	TemplateMolecule *	t1,
		string	bSiteName1,
		string	compId1,
		TemplateMolecule *	t2,
		string	bSiteName2,
		string	compId2
	)			[static]

void TemplateMolecule::addMapGenerator

(

MapGenerator *

mg

)

bool TemplateMolecule::contains

(

TemplateMolecule *

tempMol

)

void TemplateMolecule::traverse	(	TemplateMolecule *	tempMol,
		vector< TemplateMolecule * > &	tmList,
		bool	skipConnectedTo
	)			[static]

int TemplateMolecule::getNumDisjointSets	(	vector< TemplateMolecule * > &	tMolecules,
		vector< vector< TemplateMolecule * > > &	sets,
		vector< int > &	uniqueSetId
	)			[static]

bool TemplateMolecule::compare

(

Molecule *

m

)

bool TemplateMolecule::compare	(	Molecule *	m,
		ReactantContainer *	rc,
		MappingSet *	ms,
		bool	holdMolClearToEnd = false
	)

End handle connected-to

void TemplateMolecule::clear

(

)

void TemplateMolecule::clearTemplateOnly

(

)

bool TemplateMolecule::tryToMap	(	Molecule *	toMap,
		string	toMapComponent,
		Molecule *	mappedFrom,
		string	mappedFromComponent
	)

bool TemplateMolecule::isSymMapValid

(

)

bool TemplateMolecule::checkSymmetry	(	TemplateMolecule *	tm1,
		TemplateMolecule *	tm2,
		string	bSite1,
		string	bSite2
	)			[static]

bool TemplateMolecule::checkSymmetryAroundBond	(	TemplateMolecule *	tm1,
		TemplateMolecule *	tm2,
		string	bSite1,
		string	bSite2
	)			[static]

void TemplateMolecule::printErrorAndExit

(

string

message

)

void TemplateMolecule::printDetails

(

)

void TemplateMolecule::printDetails

(

ostream &

o

)

string TemplateMolecule::getPatternString

(

)

void TemplateMolecule::printPattern

(

)

void TemplateMolecule::printPattern

(

ostream &

o

)

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Member Data Documentation

const int NFcore::TemplateMolecule::EMPTY = 0 [static]

const int NFcore::TemplateMolecule::OCCUPIED = 1 [static]

const int NFcore::TemplateMolecule::NO_CONSTRAINT = -1 [static]

const bool NFcore::TemplateMolecule::FIND_ALL = false [static]

const bool NFcore::TemplateMolecule::SKIP_CONNECTED_TO = true [static]

int TemplateMolecule::TotalTemplateMoleculeCount = 0 [static, protected]

MoleculeType* NFcore::TemplateMolecule::moleculeType [protected]

int NFcore::TemplateMolecule::uniqueTemplateID [protected]

int NFcore::TemplateMolecule::n_mapGenerators [protected]

MapGenerator** NFcore::TemplateMolecule::mapGenerators [protected]

int NFcore::TemplateMolecule::n_emptyComps [protected]

int* NFcore::TemplateMolecule::emptyComps [protected]

int NFcore::TemplateMolecule::n_occupiedComps [protected]

int* NFcore::TemplateMolecule::occupiedComps [protected]

int NFcore::TemplateMolecule::n_compStateConstraint [protected]

int* NFcore::TemplateMolecule::compStateConstraint_Comp [protected]

int* NFcore::TemplateMolecule::compStateConstraint_Constraint [protected]

int NFcore::TemplateMolecule::n_compStateExclusion [protected]

int* NFcore::TemplateMolecule::compStateExclusion_Comp [protected]

int* NFcore::TemplateMolecule::compStateExclusion_Exclusion [protected]

int NFcore::TemplateMolecule::n_bonds [protected]

int* NFcore::TemplateMolecule::bondComp [protected]

string* NFcore::TemplateMolecule::bondCompName [protected]

TemplateMolecule** NFcore::TemplateMolecule::bondPartner [protected]

string* NFcore::TemplateMolecule::bondPartnerCompName [protected]

int* NFcore::TemplateMolecule::bondPartnerCompIndex [protected]

bool* NFcore::TemplateMolecule::hasVisitedBond [protected]

int NFcore::TemplateMolecule::n_connectedTo [protected]

TemplateMolecule** NFcore::TemplateMolecule::connectedTo [protected]

bool* NFcore::TemplateMolecule::hasTraversedDownConnectedTo [protected]

int* NFcore::TemplateMolecule::otherTemplateConnectedToIndex [protected]

bool* NFcore::TemplateMolecule::connectedToHasRxnCenter [protected]

int NFcore::TemplateMolecule::n_symComps [protected]

string* NFcore::TemplateMolecule::symCompName [protected]

string* NFcore::TemplateMolecule::symCompUniqueId [protected]

int* NFcore::TemplateMolecule::symCompStateConstraint [protected]

int* NFcore::TemplateMolecule::symCompBoundState [protected]

TemplateMolecule** NFcore::TemplateMolecule::symBondPartner [protected]

string* NFcore::TemplateMolecule::symBondPartnerCompName [protected]

int* NFcore::TemplateMolecule::symBondPartnerCompIndex [protected]

vector< vector <int> > NFcore::TemplateMolecule::canBeMappedTo [protected]

bool* NFcore::TemplateMolecule::hasTraversedDownSym [protected]

int NFcore::TemplateMolecule::n_totalComps [protected]

bool* NFcore::TemplateMolecule::isSymCompMapped [protected]

bool* NFcore::TemplateMolecule::compIsAlwaysMapped [protected]

Molecule* NFcore::TemplateMolecule::matchMolecule [protected]

bool NFcore::TemplateMolecule::hasVisitedThis [protected]

queue< TemplateMolecule * > TemplateMolecule::q [static, protected]

queue< int > TemplateMolecule::d [static, protected]

vector< TemplateMolecule * >::iterator TemplateMolecule::tmVecIter [static, protected]

list< TemplateMolecule * >::iterator TemplateMolecule::tmIter [static, 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/templateMolecule.hh
• /home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFcore/templateMolecule.cpp

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