#include <BALL/STRUCTURE/smartsMatcher.h>

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

Public Member Functions
Constructors and Destructors
	SmartsMatcher ()
	default constructor
virtual	~SmartsMatcher ()
	destructor

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
static boost::shared_ptr< RecStructPool_ >	pool_
	the pool of rec struct objects
std::map< SPNode , std::vector< std::set< const Atom > > >	rec_matches_
	matches from the recurive part
bool	has_user_sssr_
	user SSSR set?
std::vector< std::vector< Atom * > >	sssr_
	user sssr
Size	depth_
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
void	evaluate_ (RecStruct_ &rs, SPNode start_node, const Atom start_atom)
	method for the evaluation of a pseudo-tree
bool	evaluate_node_ (RecStruct_ &rs, SPNode start_node, const Atom start_atom)
	method for evaluating a node of a pseudo-tree
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

Accessors
void	match (Match &matches, Molecule &mol, const String &smarts)
	method to match a Smarts pattern given as a string to given molecule
void	match (Match &matches, Molecule &mol, const String &smarts, const std::set< const Atom * > &start_atoms)
	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	match (std::vector< Match > &matches, Molecule &mol, const std::vector< String > &smarts)
	method to match several Smarts patterns given as a vector of strings
void	match (std::vector< Match > &matches, Molecule &mol, const std::vector< String > &smarts, const std::set< const Atom * > &start_atoms)
	method to match several Smarts patterns given as a vector of string. The atoms used for start matchings are given in start_atoms
void	setSSSR (const std::vector< std::vector< Atom * > > &sssr)
	sets an SSSR which is used instead of doing an ring perception
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)

Detailed Description

Definition at line 44 of file smartsMatcher.h.

Member Typedef Documentation

◆ Match

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

Definition at line 51 of file smartsMatcher.h.

◆ SPAtom

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

protected

Definition at line 109 of file smartsMatcher.h.

◆ SPBond

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

protected

Definition at line 110 of file smartsMatcher.h.

◆ SPEdge

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

protected

Definition at line 108 of file smartsMatcher.h.

◆ SPNode

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

protected

Definition at line 107 of file smartsMatcher.h.

Constructor & Destructor Documentation

◆ SmartsMatcher()

BALL::SmartsMatcher::SmartsMatcher ( )

default constructor

◆ ~SmartsMatcher()

virtual BALL::SmartsMatcher::~SmartsMatcher ( )

virtual

destructor

Member Function Documentation

◆ evaluate_()

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

protected

method for the evaluation of a pseudo-tree

◆ evaluate_edge_()

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

◆ evaluate_node_()

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

protected

method for evaluating a node of a pseudo-tree

◆ evaluateRingEdges_()

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

◆ match() [1/4]

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

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

◆ match() [2/4]

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

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

◆ match() [3/4]

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

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

◆ match() [4/4]

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

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

◆ setSSSR()

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

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

◆ unsetSSSR()

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

◆ depth_

Size BALL::SmartsMatcher::depth_

protected

Definition at line 276 of file smartsMatcher.h.

◆ has_user_sssr_

bool BALL::SmartsMatcher::has_user_sssr_

protected

user SSSR set?

Definition at line 270 of file smartsMatcher.h.

◆ pool_

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

staticprotected

the pool of rec struct objects

Definition at line 252 of file smartsMatcher.h.

◆ rec_matches_

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

protected

matches from the recurive part

Definition at line 267 of file smartsMatcher.h.

◆ sssr_

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

protected

user sssr

Definition at line 273 of file smartsMatcher.h.

Classes

Public Member Functions

Typedefs

Accessors

Detailed Description

Member Typedef Documentation

◆ Match

◆ SPAtom

◆ SPBond

◆ SPEdge

◆ SPNode

Constructor & Destructor Documentation

◆ SmartsMatcher()

◆ ~SmartsMatcher()

Member Function Documentation

◆ evaluate_()

◆ evaluate_edge_()

◆ evaluate_node_()

◆ evaluateRingEdges_()

◆ match() [1/4]

◆ match() [2/4]

◆ match() [3/4]

◆ match() [4/4]

◆ setSSSR()

◆ unsetSSSR()

Member Data Documentation

◆ depth_

◆ has_user_sssr_

◆ pool_

◆ rec_matches_

◆ sssr_