#include <BALL/STRUCTURE/smartsParser.h>

Classes
class	SPAtom
	Smarts Parser Atom class. More...

class	SPBond
	Bond representation of the smarts parser. More...

class	SPEdge
	Edge representation of the smarts parser graph. More...

class	SPNode
	Representation of a node in the smarts parser graph. More...

struct	State
	Parser state (used by the parser itself) More...

Public Types
enum	ZEIsomerType { ANY_ZE = 1, NONE, Z, E }

enum	ChiralClass { CHIRAL_CLASS_UNSPECIFIED = 1, NONCHIRAL, NONCHIRAL_OR_UNSPECIFIED, CW_DEFAULT, CW_DEFAULT_OR_UNSPECIFIED, CCW_DEFAULT, CCW_DEFAULT_OR_UNSPECIFIED, CW_TH, CW_TH_OR_UNSPECIFIED, CCW_TH, CCW_TH_OR_UNSPECIFIED, CW_AL, CW_AL_OR_UNSPECIFIED, CCW_AL, CCW_AL_OR_UNSPECIFIED, CW_SP, CW_SP_OR_UNSPECIFIED, CCW_SP, CCW_SP_OR_UNSPECIFIED, CW_TB, CW_TB_OR_UNSPECIFIED, CCW_TB, CCW_TB_OR_UNSPECIFIED, CW_OH, CW_OH_OR_UNSPECIFIED, CCW_OH, CCW_OH_OR_UNSPECIFIED }
	chiral class definitions CW = clock wise, CCW = counter clock wise More...

enum	LogicalOperator { AND, OR, AND_LOW, NOOP }

Public Member Functions
Constructors and Destructors
	SmartsParser ()
	Default constructor. More...

	SmartsParser (const SmartsParser &parser)
	Copy constructor. More...

virtual	~SmartsParser ()
	Destructor. More...

Parsing
void	parse (const String &s) throw (Exception::ParseError)

Protected Member Functions
void	dumpTreeRecursive_ (SPNode *node, Size depth)
	dump method for the tree More...

void	dumpTreeRecursive_ (SPEdge *edge, Size depth)
	dump method for the tree More...

Protected Attributes
bool	needs_SSSR_
	sssr needed flag More...

bool	recursive_
	recursive flag More...

bool	component_grouping_
	component level grouping flag More...

std::map< Size, std::vector < SPNode * > >	ring_connections_
	the ring connection sorted by index of the SMARTS pattern More...

std::set< SPEdge * >	edges_
	the edges More...

std::set< SPNode * >	nodes_
	the nodes More...

std::set< SPEdge * >	rec_edges_
	the recursive edges More...

SPNode *	root_
	the root node of the tree More...

int	component_no_
	the actual component number More...

Static Protected Attributes
static vector< std::set< const Atom * > > *	sssr_
	the sssr More...

static SmartsParser *	current_parser_
	current instance More...

Accessors
static State	state
	static member for the parser itself More...

SPAtom *	createAtom (const String &symbol, bool in_bracket=false)
	creates a new atom of symbol More...

void	setRoot (SPNode *root)
	sets the root SPNode of the tree More...

SPNode *	getRoot () const
	returns the root SPNode of the tree More...

void	dumpTree ()
	dumps the tree to cerr More...

void	clear ()
	clear the tree More...

void	addRingConnection (SPNode *spnode, Size index)
	adds a ring connection, SPNode with an index used in the SMARTS pattern More...

std::map< Size, std::vector < SPNode * > >	getRingConnections () const
	returns the ring connections sorted by index from SMARTS pattern More...

void	setSSSR (const std::vector< std::vector< Atom * > > &sssr)
	sets the SSSR More...

void	setNeedsSSSR (bool needs_sssr)
	sets the sssr needed flag More...

bool	getNeedsSSSR () const
	returns true if the SMARTS pattern contains ring related parts More...

void	setRecursive (bool recursive)
	sets the recursive flag More...

bool	isRecursive () const
	returns true if the tree represents a recursive SMARTS pattern More...

void	setComponentGrouping (bool component_grouping)
	sets the component level flag More...

bool	hasComponentGrouping () const
	returns true if the component level grouping was enabled More...

const std::set< SPNode * > &	getNodes () const
	returns the eodes stored in the tree More...

const std::set< SPEdge * > &	getEdges () const
	returns the edges stored in the tree More...

void	addEdge (SPEdge *edge)
	adds an edge to the tree More...

void	addNode (SPNode *node)
	adds a node to the tree More...

bool	hasRecursiveEdge (SPEdge *edge) const
	returns true if the tree has the given recursive edge More...

void	addRecursiveEdge (SPEdge *edge)
	adds a recursive edge to the tree More...

void	setNextComponentNumberToSubTree (SPNode *spnode)
	gets the next component no and assigns it to the subtree More...

Detailed Description

SMARTS Parser.

This class implements the parser for SMARTS patterns. The SMARTS string is converted into a tree, which is used for matching it to molecules. The tree has also some additional features, i.e. additional edges which allows also for graph features (kind of cyclic structure).

Definition at line 35 of file smartsParser.h.

Member Enumeration Documentation

enum BALL::SmartsParser::ChiralClass

chiral class definitions CW = clock wise, CCW = counter clock wise

Enumerator
CHIRAL_CLASS_UNSPECIFIED
NONCHIRAL
NONCHIRAL_OR_UNSPECIFIED
CW_DEFAULT
CW_DEFAULT_OR_UNSPECIFIED
CCW_DEFAULT
CCW_DEFAULT_OR_UNSPECIFIED
CW_TH
CW_TH_OR_UNSPECIFIED
CCW_TH
CCW_TH_OR_UNSPECIFIED
CW_AL
CW_AL_OR_UNSPECIFIED
CCW_AL
CCW_AL_OR_UNSPECIFIED
CW_SP
CW_SP_OR_UNSPECIFIED
CCW_SP
CCW_SP_OR_UNSPECIFIED
CW_TB
CW_TB_OR_UNSPECIFIED
CCW_TB
CCW_TB_OR_UNSPECIFIED
CW_OH
CW_OH_OR_UNSPECIFIED
CCW_OH
CCW_OH_OR_UNSPECIFIED

Definition at line 48 of file smartsParser.h.

enum BALL::SmartsParser::LogicalOperator

The logical operator supported by SMARTS-pattern
'&' -> and
',' -> or
';' -> low precedence and

NOOP is just provided for convenience.

Enumerator
AND
OR
AND_LOW
NOOP

Definition at line 86 of file smartsParser.h.

enum BALL::SmartsParser::ZEIsomerType

Enumerator
ANY_ZE
NONE
Z
E

Definition at line 39 of file smartsParser.h.

Constructor & Destructor Documentation

BALL::SmartsParser::SmartsParser ( )

Default constructor.

BALL::SmartsParser::SmartsParser ( const SmartsParser & parser )

Copy constructor.

virtual BALL::SmartsParser::~SmartsParser ( )

virtual

Destructor.

Member Function Documentation

void BALL::SmartsParser::addEdge ( SPEdge * edge )

inline

adds an edge to the tree

Definition at line 717 of file smartsParser.h.

void BALL::SmartsParser::addNode ( SPNode * node )

inline

adds a node to the tree

Definition at line 720 of file smartsParser.h.

void BALL::SmartsParser::addRecursiveEdge ( SPEdge * edge )

inline

adds a recursive edge to the tree

Definition at line 726 of file smartsParser.h.

void BALL::SmartsParser::addRingConnection	(	SPNode *	spnode,
		Size	index
	)

adds a ring connection, SPNode with an index used in the SMARTS pattern

void BALL::SmartsParser::clear ( )

clear the tree

SPAtom* BALL::SmartsParser::createAtom	(	const String &	symbol,
		bool	in_bracket = `false`
	)

creates a new atom of symbol

void BALL::SmartsParser::dumpTree ( )

dumps the tree to cerr

void BALL::SmartsParser::dumpTreeRecursive_	(	SPNode *	node,
		Size	depth
	)

protected

dump method for the tree

void BALL::SmartsParser::dumpTreeRecursive_	(	SPEdge *	edge,
		Size	depth
	)

protected

dump method for the tree

const std::set<SPEdge*>& BALL::SmartsParser::getEdges ( ) const

inline

returns the edges stored in the tree

Definition at line 714 of file smartsParser.h.

bool BALL::SmartsParser::getNeedsSSSR ( ) const

inline

returns true if the SMARTS pattern contains ring related parts

Definition at line 685 of file smartsParser.h.

const std::set<SPNode*>& BALL::SmartsParser::getNodes ( ) const

inline

returns the eodes stored in the tree

Definition at line 711 of file smartsParser.h.

std::map<Size, std::vector<SPNode*> > BALL::SmartsParser::getRingConnections ( ) const

returns the ring connections sorted by index from SMARTS pattern

SPNode* BALL::SmartsParser::getRoot ( ) const

inline

returns the root SPNode of the tree

Definition at line 664 of file smartsParser.h.

bool BALL::SmartsParser::hasComponentGrouping ( ) const

inline

returns true if the component level grouping was enabled

Definition at line 697 of file smartsParser.h.

bool BALL::SmartsParser::hasRecursiveEdge ( SPEdge * edge ) const

inline

returns true if the tree has the given recursive edge

Definition at line 723 of file smartsParser.h.

bool BALL::SmartsParser::isRecursive ( ) const

inline

returns true if the tree represents a recursive SMARTS pattern

Definition at line 691 of file smartsParser.h.

void BALL::SmartsParser::parse ( const String & s ) throw (Exception::ParseError)

Parse a SMARTS string.

void BALL::SmartsParser::setComponentGrouping ( bool component_grouping )

inline

sets the component level flag

Definition at line 694 of file smartsParser.h.

void BALL::SmartsParser::setNeedsSSSR ( bool needs_sssr )

inline

sets the sssr needed flag

Definition at line 682 of file smartsParser.h.

void BALL::SmartsParser::setNextComponentNumberToSubTree ( SPNode * spnode )

gets the next component no and assigns it to the subtree

void BALL::SmartsParser::setRecursive ( bool recursive )

inline

sets the recursive flag

Definition at line 688 of file smartsParser.h.

void BALL::SmartsParser::setRoot ( SPNode * root )

inline

sets the root SPNode of the tree

Definition at line 661 of file smartsParser.h.

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

sets the SSSR

Member Data Documentation

bool BALL::SmartsParser::component_grouping_

protected

component level grouping flag

Definition at line 741 of file smartsParser.h.

int BALL::SmartsParser::component_no_

protected

the actual component number

Definition at line 771 of file smartsParser.h.

SmartsParser* BALL::SmartsParser::current_parser_

staticprotected

current instance

Definition at line 756 of file smartsParser.h.

std::set<SPEdge*> BALL::SmartsParser::edges_

protected

the edges

Definition at line 759 of file smartsParser.h.

bool BALL::SmartsParser::needs_SSSR_

protected

sssr needed flag

Definition at line 735 of file smartsParser.h.

std::set<SPNode*> BALL::SmartsParser::nodes_

protected

the nodes

Definition at line 762 of file smartsParser.h.

std::set<SPEdge*> BALL::SmartsParser::rec_edges_

protected

the recursive edges

Definition at line 765 of file smartsParser.h.

bool BALL::SmartsParser::recursive_

protected

recursive flag

Definition at line 738 of file smartsParser.h.

std::map<Size, std::vector<SPNode*> > BALL::SmartsParser::ring_connections_

protected

the ring connection sorted by index of the SMARTS pattern

Definition at line 753 of file smartsParser.h.

SPNode* BALL::SmartsParser::root_

protected

the root node of the tree

Definition at line 768 of file smartsParser.h.

vector<std::set<const Atom*> >* BALL::SmartsParser::sssr_

staticprotected

the sssr

Definition at line 744 of file smartsParser.h.

State BALL::SmartsParser::state

static

static member for the parser itself

Definition at line 708 of file smartsParser.h.

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Accessors

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation