OBSmartsPattern Class Reference

#include <openbabel/parsmart.h>

Public Types
enum	MatchType { All, Single, AllUnique }

Public Member Functions
	OBSmartsPattern ()
virtual	~OBSmartsPattern ()
	OBSmartsPattern (const OBSmartsPattern &cp)
OBSmartsPattern &	operator= (const OBSmartsPattern &cp)
void	WriteMapList (std::ostream &)
Initialization Methods
bool	Init (const char *pattern)
bool	Init (const std::string &pattern)
Pattern Properties
const std::string &	GetSMARTS () const
std::string &	GetSMARTS ()
bool	Empty () const
bool	IsValid () const
unsigned int	NumAtoms () const
unsigned int	NumBonds () const
void	GetBond (int &src, int &dst, int &ord, int idx)
int	GetAtomicNum (int idx)
int	GetCharge (int idx)
int	GetVectorBinding (int idx) const
Matching methods (SMARTS on a specific OBMol)
bool	Match (OBMol &mol, bool single=false)
bool	Match (OBMol &mol, std::vector< std::vector< int > > &mlist, MatchType mtype=All) const
bool	HasMatch (OBMol &mol) const
bool	RestrictedMatch (OBMol &mol, std::vector< std::pair< int, int > > &pairs, bool single=false)
bool	RestrictedMatch (OBMol &mol, OBBitVec &bv, bool single=false)
unsigned int	NumMatches () const
std::vector< std::vector< int > > &	GetMapList ()
std::vector< std::vector< int > >::iterator	BeginMList ()
std::vector< std::vector< int > >::iterator	EndMList ()
std::vector< std::vector< int > > &	GetUMapList ()

Protected Member Functions
Pattern *	ParseSMARTSPattern (void)
Pattern *	ParseSMARTSPart (Pattern *, int)
Pattern *	SMARTSError (Pattern *pat)
Pattern *	ParseSMARTSError (Pattern *pat, BondExpr *expr)
AtomExpr *	ParseSimpleAtomPrimitive (void)
AtomExpr *	ParseComplexAtomPrimitive (void)
AtomExpr *	ParseAtomExpr (int level)
BondExpr *	ParseBondPrimitive (void)
BondExpr *	ParseBondExpr (int level)
Pattern *	ParseSMARTSString (char *ptr)
Pattern *	ParseSMARTSRecord (char *ptr)
int	GetVectorBinding ()
Pattern *	SMARTSParser (Pattern *pat, ParseState *stat, int prev, int part)

Protected Attributes
OBSmartsPrivate *	_d
std::vector< bool >	_growbond
std::vector< std::vector< int > >	_mlist
Pattern *	_pat
std::string	_str
char *	_buffer
char *	LexPtr
char *	MainPtr

Detailed Description

SMARTS (SMiles ARbitrary Target Specification) substructure searching.

Substructure search is an incredibly useful tool in the context of a small molecule programming library. Having an efficient substructure search engine reduces the amount of hard code needed for molecule perception, as well as increases the flexibility of certain operations. For instance, atom typing can be easily performed based on hard coded rules of element type and bond orders (or hybridization). Alternatively, atom typing can also be done by matching a set of substructure rules read at run time. In the latter case customization based on application (such as changing the pH) becomes a facile operation. Fortunately for Open Babel and its users, Roger Sayle donated a SMARTS parser which became the basis for SMARTS matching in Open Babel.

For more information on the SMARTS support in Open Babel, see the wiki page: http://openbabel.org/wiki/SMARTS

The SMARTS matcher, or OBSmartsPattern, is a separate object which can match patterns in the OBMol class. The following code demonstrates how to use the OBSmartsPattern class:

OBMol mol;
...
OBSmartsPattern sp;
sp.Init("CC");
sp.Match(mol);
vector<vector<int> > maplist;
maplist = sp.GetMapList();
//or maplist = sp.GetUMapList();
//print out the results
vector<vector<int> >::iterator i;
vector<int>::iterator j;
for (i = maplist.begin();i != maplist.end();++i)
{
for (j = i->begin();j != i->end();++j)
cout << j << ' `;
cout << endl;
}

The preceding code reads in a molecule, initializes a SMARTS pattern of two single-bonded carbons, and locates all instances of the pattern in the molecule. Note that calling the Match() function does not return the results of the substructure match. The results from a match are stored in the OBSmartsPattern, and a call to GetMapList() or GetUMapList() must be made to extract the results. The function GetMapList() returns all matches of a particular pattern while GetUMapList() returns only the unique matches. For instance, the pattern [OD1]~C~[OD1] describes a carboxylate group. This pattern will match both atom number permutations of the carboxylate, and if GetMapList() is called, both matches will be returned. If GetUMapList() is called only unique matches of the pattern will be returned. A unique match is defined as one which does not cover the identical atoms that a previous match has covered.

Member Enumeration Documentation

MatchType

enum MatchType

Enumerator
All
Single
AllUnique

Constructor & Destructor Documentation

OBSmartsPattern() [1/2]

OBSmartsPattern ( )

inline

~OBSmartsPattern()

~OBSmartsPattern ( )

virtual

OBSmartsPattern() [2/2]

OBSmartsPattern ( const OBSmartsPattern &  cp )

inline

Member Function Documentation

ParseSMARTSPattern()

Pattern * ParseSMARTSPattern ( void  )

protected

ParseSMARTSPart()

Pattern * ParseSMARTSPart ( Pattern *  result, int  part  )

protected

SMARTSError()

Pattern * SMARTSError ( Pattern *  pat )

protected

ParseSMARTSError()

Pattern * ParseSMARTSError ( Pattern *  pat, BondExpr *  expr  )

protected

ParseSimpleAtomPrimitive()

AtomExpr * ParseSimpleAtomPrimitive ( void  )

protected

ParseComplexAtomPrimitive()

AtomExpr * ParseComplexAtomPrimitive ( void  )

protected

ParseAtomExpr()

AtomExpr * ParseAtomExpr ( int  level )

protected

ParseBondPrimitive()

BondExpr * ParseBondPrimitive ( void  )

protected

ParseBondExpr()

BondExpr * ParseBondExpr ( int  level )

protected

ParseSMARTSString()

Pattern * ParseSMARTSString ( char *  ptr )

protected

ParseSMARTSRecord()

Pattern * ParseSMARTSRecord ( char *  ptr )

protected

GetVectorBinding() [1/2]

int GetVectorBinding ( )

protected

SMARTSParser()

Pattern * SMARTSParser ( Pattern *  pat, ParseState *  stat, int  prev, int  part  )

protected

operator=()

OBSmartsPattern& operator= ( const OBSmartsPattern &  cp )

inline

Init() [1/2]

bool Init

(

const char *

pattern

)

Parse the pattern SMARTS string.

Returns

Whether the pattern is a valid SMARTS expression

Referenced by patty::assign_rules(), OBBondTyper::AssignFunctionalGroupBonds(), OBBuilder::Build(), OBMol::DoTransformations(), OBBuilder::LoadFragments(), OBAtom::MatchesSMARTS(), OBRotorRule::OBRotorRule(), OBBondTyper::ParseLine(), OBAtomTyper::ParseLine(), OBRingTyper::ParseLine(), OBPhModel::ParseLine(), and patty::read_rules().

Init() [2/2]

bool Init

(

const std::string &

pattern

)

Parse the pattern SMARTS string.

Returns

Whether the pattern is a valid SMARTS expression

GetSMARTS() [1/2]

const std::string& GetSMARTS ( ) const

inline

Returns

the SMARTS string which is currently used

GetSMARTS() [2/2]

std::string& GetSMARTS ( )

inline

Returns

the SMARTS string which is currently used

Empty()

bool Empty ( ) const

inline

Returns

If the SMARTS pattern is an empty expression (e.g., invalid)

IsValid()

bool IsValid ( ) const

inline

Returns

If the SMARTS pattern is a valid expression

Referenced by OBRotorRule::IsValid().

NumAtoms()

unsigned int NumAtoms ( ) const

inline

Returns

the number of atoms in the SMARTS pattern

Referenced by OBPhModel::ParseLine().

NumBonds()

unsigned int NumBonds ( ) const

inline

Returns

the number of bonds in the SMARTS pattern

GetBond()

void GetBond	(	int &	src,
		int &	dst,
		int &	ord,
		int	idx
	)

Access the bond idx in the internal pattern

Parameters

src	The index of the beginning atom
dst	The index of the end atom
ord	The bond order of this bond
idx	The index of the bond in the SMARTS pattern

GetAtomicNum()

int GetAtomicNum

(

int

idx

)

Returns

the atomic number of the atom idx in the internal pattern

GetCharge()

int GetCharge

(

int

idx

)

Returns

the formal charge of the atom idx in the internal pattern

GetVectorBinding() [2/2]

int GetVectorBinding ( int  idx ) const

inline

Returns

the vector binding of the atom idx in the internal pattern

Match() [1/2]

bool Match	(	OBMol &	mol,
		bool	single = false
	)

Perform SMARTS matching for the pattern specified using Init().

Parameters

mol	The molecule to use for matching
single	Whether only a single match is required (faster). Default is false.

Returns

Whether matches occurred

Referenced by OBBondTyper::AssignFunctionalGroupBonds(), OBBuilder::Build(), OBMol::DoTransformations(), and OBAtom::MatchesSMARTS().

Match() [2/2]

bool Match	(	OBMol &	mol,
		std::vector< std::vector< int > > &	mlist,
		MatchType	mtype = All
	)		const

Perform SMARTS matching for the pattern specified using Init(). This version is (more) thread safe.

Parameters

mol	The molecule to use for matching
mlist	The resulting match list
mtype	The match type to use. Default is All.

Returns

Whether matches occurred

HasMatch()

bool HasMatch

(

OBMol &

mol

)

const

Thread safe check for any SMARTS match

Parameters

mol	The molecule to use for matching

Returns

Whether there exists any match

RestrictedMatch() [1/2]

bool RestrictedMatch	(	OBMol &	mol,
		std::vector< std::pair< int, int > > &	pairs,
		bool	single = false
	)

Referenced by OBRotorRules::GetRotorIncrements().

RestrictedMatch() [2/2]

bool RestrictedMatch	(	OBMol &	mol,
		OBBitVec &	bv,
		bool	single = false
	)

NumMatches()

unsigned int NumMatches ( ) const

inline

Returns

the number of non-unique SMARTS matches To get the number of unique SMARTS matches, query GetUMapList()->size()

GetMapList()

std::vector<std::vector<int> >& GetMapList ( )

inline

Returns

the entire list of non-unique matches for this pattern

See also

GetUMapList()

Referenced by OBRotorRules::GetRotorIncrements().

BeginMList()

std::vector<std::vector<int> >::iterator BeginMList ( )

inline

Returns

An iterator over the (non-unique) match list, starting at the beginning

EndMList()

std::vector<std::vector<int> >::iterator EndMList ( )

inline

Returns

An iterator over the non-unique match list, set to the end

GetUMapList()

std::vector< std::vector< int > > & GetUMapList

(

)

Returns

the entire list of unique matches for this pattern A unique match is defined as one which does not cover the identical atoms that a previous match has covered.

For instance, the pattern [OD1]~C~[OD1] describes a carboxylate group. This pattern will match both atom number permutations of the carboxylate, and if GetMapList() is called, both matches will be returned. If GetUMapList() is called only unique matches of the pattern will be returned.

Referenced by OBBondTyper::AssignFunctionalGroupBonds(), OBBuilder::Build(), and OBAtom::MatchesSMARTS().

WriteMapList()

void WriteMapList

(

std::ostream &

ofs

)

Debugging – write a list of matches to the output stream.

Member Data Documentation

_d

OBSmartsPrivate* _d

protected

Internal data storage for future expansion.

_growbond

std::vector<bool> _growbond

protected

Deprecated:

(Not used)

_mlist

std::vector<std::vector<int> > _mlist

protected

The list of matches.

_pat

Pattern* _pat

protected

The parsed SMARTS pattern.

_str

std::string _str

protected

The string of the SMARTS expression.

Referenced by OBSmartsPattern::operator=().

_buffer

char* _buffer

protected

LexPtr

char* LexPtr

protected

MainPtr

char* MainPtr

protected

---

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

• parsmart.h
• parsmart.cpp