BALL::SmartsParser Class Reference
[Matching of submolecular structures]

SMARTS Parser. More...

#include <smartsParser.h>

List of all members.

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
enum	LogicalOperator { AND, OR, AND_LOW, NOOP }
	The logical operator supported by SMARTS-pattern '&' -> and ',' -> or ';' -> low precedence and . More...
Public Member Functions
Constructors and Destructors
	SmartsParser ()
	Default constructor.
	SmartsParser (const SmartsParser &parser)
	Copy constructor.
virtual	~SmartsParser ()
	Destructor.
Parsing
void	parse (const String &s) throw (Exception::ParseError)
	Parse a SMARTS string.
Protected Member Functions
void	dumpTreeRecursive_ (SPNode *node, Size depth)
	dump method for the tree
void	dumpTreeRecursive_ (SPEdge *edge, Size depth)
	dump method for the tree
Protected Attributes
bool	needs_SSSR_
	sssr needed flag
bool	recursive_
	recursive flag
bool	component_grouping_
	component level grouping flag
std::map< Size, std::vector < SPNode * > >	ring_connections_
	the ring connection sorted by index of the SMARTS pattern
std::set< SPEdge * >	edges_
	the edges
std::set< SPNode * >	nodes_
	the nodes
std::set< SPEdge * >	rec_edges_
	the recursive edges
SPNode *	root_
	the root node of the tree
int	component_no_
	the actual component number
Static Protected Attributes
static vector< std::set< const Atom * > > *	sssr_
	the sssr
static SmartsParser *	current_parser_
	current instance
Accessors
static State	state
	static member for the parser itself
SPAtom *	createAtom (const String &symbol, bool in_bracket=false)
	creates a new atom of symbol
void	setRoot (SPNode *root)
	sets the root SPNode of the tree
SPNode *	getRoot () const
	returns the root SPNode of the tree
void	dumpTree ()
	dumps the tree to cerr
void	clear ()
	clear the tree
void	addRingConnection (SPNode *spnode, Size index)
	adds a ring connection, SPNode with an index used in the SMARTS pattern
std::map< Size, std::vector < SPNode * > >	getRingConnections () const
	returns the ring connections sorted by index from SMARTS pattern
void	setSSSR (const std::vector< std::vector< Atom * > > &sssr)
	sets the SSSR
void	setNeedsSSSR (bool needs_sssr)
	sets the sssr needed flag
bool	getNeedsSSSR () const
	returns true if the SMARTS pattern contains ring related parts
void	setRecursive (bool recursive)
	sets the recursive flag
bool	isRecursive () const
	returns true if the tree represents a recursive SMARTS pattern
void	setComponentGrouping (bool component_grouping)
	sets the component level flag
bool	hasComponentGrouping () const
	returns true if the component level grouping was enabled
const std::set< SPNode * > &	getNodes () const
	returns the eodes stored in the tree
const std::set< SPEdge * > &	getEdges () const
	returns the edges stored in the tree
void	addEdge (SPEdge *edge)
	adds an edge to the tree
void	addNode (SPNode *node)
	adds a node to the tree
bool	hasRecursiveEdge (SPEdge *edge) const
	returns true if the tree has the given recursive edge
void	addRecursiveEdge (SPEdge *edge)
	adds a recursive edge to the tree
void	setNextComponentNumberToSubTree (SPNode *spnode)
	gets the next component no and assigns it to the subtree

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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).

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Member Enumeration Documentation

enum BALL::SmartsParser::LogicalOperator

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

NOOP is just provided for convenience.