#include <BALL/STRUCTURE/smartsMatcher.h>

Classes
class	RecStruct_
	a wrapper class which is used as an interface in the matching code to the pool More...

class	RecStructCore_
	core structure of the recursive matching algorithm for the object pool More...

class	RecStructPool_
	class which does the pool operations of the RecStructCore_ pool More...

Public Member Functions
Constructors and Destructors
	SmartsMatcher ()
	default constructor More...

virtual	~SmartsMatcher ()
	destructor More...

Accessors
void	match (Match &matches, Molecule &mol, const String &smarts) throw (Exception::ParseError)
	method to match a Smarts pattern given as a string to given molecule More...

void	match (Match &matches, Molecule &mol, const String &smarts, const std::set< const Atom * > &start_atoms) throw (Exception::ParseError)
	method to match a Smarts pattern given as a string to given molecule. The atoms which will be used for starting matching are given in atoms More...

void	match (std::vector< Match > &matches, Molecule &mol, const std::vector< String > &smarts) throw (Exception::ParseError)
	method to match several Smarts patterns given as a vector of strings More...

void	match (std::vector< Match > &matches, Molecule &mol, const std::vector< String > &smarts, const std::set< const Atom * > &start_atoms) throw (Exception::ParseError)
	method to match several Smarts patterns given as a vector of string. The atoms used for start matchings are given in start_atoms More...

void	setSSSR (const std::vector< std::vector< Atom * > > &sssr)
	sets an SSSR which is used instead of doing an ring perception More...

void	unsetSSSR ()
	this function is used to cause the matcher to do an ring perception if needed (do not use the set SSSR any more) More...

Protected Member Functions
bool	evaluateRingEdges_ (const std::set< const Atom * > &matching, const std::map< const SPNode , const Atom > &mapping, const String &smarts)
	method for evaluation of ring edges, after the the smarts tree is matched to molcule More...

void	evaluate_ (RecStruct_ &rs, SPNode start_node, const Atom start_atom)
	method for the evaluation of a pseudo-tree More...

bool	evaluate_node_ (RecStruct_ &rs, SPNode start_node, const Atom start_atom)
	method for evaluating a node of a pseudo-tree More...

bool	evaluate_edge_ (RecStruct_ &rs, SPEdge start_node, const Atom start_atom, const Bond *start_bond)
	method for evaluating a edge of a pseudo-tree More...

Protected Attributes
std::map< SPNode , std::vector< std::set < const Atom > > >	rec_matches_
	matches from the recurive part More...

bool	has_user_sssr_
	user SSSR set? More...

std::vector< std::vector< Atom * > >	sssr_
	user sssr More...

Size	depth_

Static Protected Attributes
static boost::shared_ptr < RecStructPool_ >	pool_
	the pool of rec struct objects More...

Private Member Functions
	SmartsMatcher (const SmartsMatcher &matcher)
	copy constructor More...

Operators
SmartsMatcher &	operator= (const SmartsMatcher &matcher)
	assignment operator More...

Typedefs
typedef std::vector< std::set < const Atom * > >	Match

typedef SmartsParser::SPNode	SPNode

typedef SmartsParser::SPEdge	SPEdge

typedef SmartsParser::SPAtom	SPAtom

typedef SmartsParser::SPBond	SPBond

Detailed Description

Definition at line 44 of file smartsMatcher.h.

Member Typedef Documentation

typedef std::vector<std::set<const Atom*> > BALL::SmartsMatcher::Match

Definition at line 51 of file smartsMatcher.h.

typedef SmartsParser::SPAtom BALL::SmartsMatcher::SPAtom

protected

Definition at line 113 of file smartsMatcher.h.

typedef SmartsParser::SPBond BALL::SmartsMatcher::SPBond

protected

Definition at line 114 of file smartsMatcher.h.

typedef SmartsParser::SPEdge BALL::SmartsMatcher::SPEdge

protected

Definition at line 112 of file smartsMatcher.h.

typedef SmartsParser::SPNode BALL::SmartsMatcher::SPNode

protected

Definition at line 111 of file smartsMatcher.h.

Constructor & Destructor Documentation

BALL::SmartsMatcher::SmartsMatcher ( )

default constructor

virtual BALL::SmartsMatcher::~SmartsMatcher ( )

virtual

destructor

BALL::SmartsMatcher::SmartsMatcher ( const SmartsMatcher & matcher )

private

copy constructor

Member Function Documentation

void BALL::SmartsMatcher::evaluate_	(	RecStruct_ &	rs,
		SPNode *	start_node,
		const Atom *	start_atom
	)

protected

method for the evaluation of a pseudo-tree

bool BALL::SmartsMatcher::evaluate_edge_	(	RecStruct_ &	rs,
		SPEdge *	start_node,
		const Atom *	start_atom,
		const Bond *	start_bond
	)

protected

method for evaluating a edge of a pseudo-tree

bool BALL::SmartsMatcher::evaluate_node_	(	RecStruct_ &	rs,
		SPNode *	start_node,
		const Atom *	start_atom
	)

protected

method for evaluating a node of a pseudo-tree

bool BALL::SmartsMatcher::evaluateRingEdges_	(	const std::set< const Atom * > &	matching,
		const std::map< const SPNode , const Atom > &	mapping,
		const String &	smarts
	)

protected

method for evaluation of ring edges, after the the smarts tree is matched to molcule

void BALL::SmartsMatcher::match	(	Match &	matches,
		Molecule &	mol,
		const String &	smarts
	)		throw (Exception::ParseError)

method to match a Smarts pattern given as a string to given molecule

void BALL::SmartsMatcher::match	(	Match &	matches,
		Molecule &	mol,
		const String &	smarts,
		const std::set< const Atom * > &	start_atoms
	)		throw (Exception::ParseError)

method to match a Smarts pattern given as a string to given molecule. The atoms which will be used for starting matching are given in atoms

void BALL::SmartsMatcher::match	(	std::vector< Match > &	matches,
		Molecule &	mol,
		const std::vector< String > &	smarts
	)		throw (Exception::ParseError)

method to match several Smarts patterns given as a vector of strings

void BALL::SmartsMatcher::match	(	std::vector< Match > &	matches,
		Molecule &	mol,
		const std::vector< String > &	smarts,
		const std::set< const Atom * > &	start_atoms
	)		throw (Exception::ParseError)

method to match several Smarts patterns given as a vector of string. The atoms used for start matchings are given in start_atoms

SmartsMatcher& BALL::SmartsMatcher::operator= ( const SmartsMatcher & matcher )

private

assignment operator

void BALL::SmartsMatcher::setSSSR ( const std::vector< std::vector< Atom * > > & sssr )

sets an SSSR which is used instead of doing an ring perception

void BALL::SmartsMatcher::unsetSSSR ( )

this function is used to cause the matcher to do an ring perception if needed (do not use the set SSSR any more)

Member Data Documentation

Size BALL::SmartsMatcher::depth_

protected

Definition at line 280 of file smartsMatcher.h.

bool BALL::SmartsMatcher::has_user_sssr_

protected

user SSSR set?

Definition at line 274 of file smartsMatcher.h.

boost::shared_ptr<RecStructPool_> BALL::SmartsMatcher::pool_

staticprotected

the pool of rec struct objects

Definition at line 256 of file smartsMatcher.h.

std::map<SPNode*, std::vector<std::set<const Atom*> > > BALL::SmartsMatcher::rec_matches_

protected

matches from the recurive part

Definition at line 271 of file smartsMatcher.h.

std::vector<std::vector<Atom*> > BALL::SmartsMatcher::sssr_

protected

user sssr

Definition at line 277 of file smartsMatcher.h.

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Member Functions

Typedefs

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation