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

#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.
	SmartsParser (const SmartsParser &parser)
	Copy constructor.
virtual	~SmartsParser ()
	Destructor.
Parsing
void	parse (const String &s) throw (Exception::ParseError)
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

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).

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

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

enum BALL::SmartsParser::ZEIsomerType

Enumerator:

ANY_ZE
NONE
Z
E

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

void BALL::SmartsParser::addNode ( SPNode * node ) [inline]

adds a node to the tree

void BALL::SmartsParser::addRecursiveEdge ( SPEdge * edge ) [inline]

adds a recursive edge to the tree

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_	(	SPEdge *	edge,
		Size	depth
	)			`[protected]`

dump method for the tree

void BALL::SmartsParser::dumpTreeRecursive_	(	SPNode *	node,
		Size	depth
	)			`[protected]`

dump method for the tree

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

returns the edges stored in the tree

bool BALL::SmartsParser::getNeedsSSSR ( ) const [inline]

returns true if the SMARTS pattern contains ring related parts

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

returns the eodes stored in the tree

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

bool BALL::SmartsParser::hasComponentGrouping ( ) const [inline]

returns true if the component level grouping was enabled

bool BALL::SmartsParser::hasRecursiveEdge ( SPEdge * edge ) const [inline]

returns true if the tree has the given recursive edge

bool BALL::SmartsParser::isRecursive ( ) const [inline]

returns true if the tree represents a recursive SMARTS pattern

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

void BALL::SmartsParser::setNeedsSSSR ( bool needs_sssr ) [inline]

sets the sssr needed flag

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

void BALL::SmartsParser::setRoot ( SPNode * root ) [inline]

sets the root SPNode of the tree

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

int BALL::SmartsParser::component_no_ [protected]

the actual component number

SmartsParser* BALL::SmartsParser::current_parser_ [static, protected]

current instance

std::set<SPEdge*> BALL::SmartsParser::edges_ [protected]

the edges

bool BALL::SmartsParser::needs_SSSR_ [protected]

sssr needed flag

std::set<SPNode*> BALL::SmartsParser::nodes_ [protected]

the nodes

std::set<SPEdge*> BALL::SmartsParser::rec_edges_ [protected]

the recursive edges

bool BALL::SmartsParser::recursive_ [protected]

recursive flag

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

the ring connection sorted by index of the SMARTS pattern

SPNode* BALL::SmartsParser::root_ [protected]

the root node of the tree

vector<std::set<const Atom*> >* BALL::SmartsParser::sssr_ [static, protected]

the sssr

State BALL::SmartsParser::state [static]

static member for the parser itself

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

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

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