NFcore::TemplateMolecule Class Reference

#include <templateMolecule.hh>

List of all members.

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.

Michael Sneddon

Public Member Functions

 TemplateMolecule (MoleculeType *moleculeType)
 ~TemplateMolecule ()
MoleculeTypegetMoleculeType () 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

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
bool hasVisitedThis

Static Protected Attributes

static int TotalTemplateMoleculeCount = 0
static queue< TemplateMolecule * > q
static queue< int > d
static vector
< TemplateMolecule * >
static list< TemplateMolecule * >

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  ) 

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]

The documentation for this class was generated from the following files:
Generated on Thu Dec 9 11:02:48 2010 for NFsim by  doxygen 1.5.4