BALL::RingPerceptionProcessor Class Reference

#include <BALL/QSAR/ringPerceptionProcessor.h>

Inheritance diagram for BALL::RingPerceptionProcessor:

Classes
struct	Default
	default options for the ring perception More...
struct	Option
	Option names. More...
struct	PathMessage_
struct	TNode_

Public Member Functions
const vector< vector< Atom * > > &	getAllSmallRings () const
Size	findAllBCC (std::vector< SimpleMolecularGraph * > &bcc, SimpleMolecularGraph &graph)
void	setDefaultOptions ()
Constrcutors and Destructors
	RingPerceptionProcessor ()
	RingPerceptionProcessor (const RingPerceptionProcessor &rp)
virtual	~RingPerceptionProcessor ()
Assignment
RingPerceptionProcessor &	operator= (const RingPerceptionProcessor &rp)
Accessors
Size	calculateSSSR (vector< vector< Atom * > > &sssr, AtomContainer &ac)
Processor-related methods
Processor::Result	operator() (AtomContainer &ac)
Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer >
	UnaryProcessor ()
	UnaryProcessor (const UnaryProcessor &)
virtual	~UnaryProcessor ()
virtual bool	start ()
virtual bool	finish ()

Public Attributes
Options	options
HashSet< NodeItem< Index, Index > * >	visited_
HashSet< EdgeItem< Index, Index > * >	visited_bonds_
HashMap< NodeItem< Index, Index > *, Size >	P_
HashMap< NodeItem< Index, Index > *, NodeItem< Index, Index > * >	parents_
std::stack< EdgeItem< Index, Index > * >	BCC_
static HashMap< TNode_ *, NodeItem< Index, Index > * >	tnode_to_atom_
	mapping for internal TNode structure and the nodes of the molecular graph More...
static HashMap< NodeItem < Index, Index > *, TNode_ * >	atom_to_tnode_
static HashMap< EdgeItem < Index, Index > *, Size >	bond_to_index_
	mapping for the path representation as bitvectors More...
static HashMap< Size, EdgeItem < Index, Index > * >	index_to_bond_
static std::vector< BitVector >	rings_
	the SSSR detected by the algorithm More...
static std::vector< BitVector >	matrix_
	the matrix for the independency tests More...
static std::vector< BitVector >	forwarded_rings_
	the rings of the ith phase, which are to be forwarded to the ring selector More...
static std::vector< BitVector >	tested_beers_
	rings (beer) which have already been tested More...
static std::vector < std::vector< Atom * > >	all_small_rings_
	contains all 3 to 6 membered rings after the procedure of the Balducci-Pearlman algorithm More...
static std::vector< BitVector >	all_small_beers_
	contains all 3 to 6 membered rings as beers More...
Size	FiguerasAlgorithm_ (vector< vector< Atom * > > &sssr, AtomContainer &ac)
Size	getRing_ (Atom *n, HashSet< Atom * > &ring_set)
void	checkEdges_ (HashSet< Atom * > &ring_set, AtomContainer &ac)
Size	findAllBCC_ (std::vector< SimpleMolecularGraph * > &bcc, SimpleMolecularGraph &graph)
void	DFSBCC_ (std::vector< SimpleMolecularGraph * > &bccs, Size dfbi, HashMap< NodeItem< Index, Index > *, Size > DFBIndex, NodeItem< Index, Index > *v)
Size	BalducciPearlmanAlgorithm_ (std::vector< std::vector< Atom * > > &sssr, SimpleMolecularGraph &graph)
static void	BalducciPearlmanRingSelector_ (BitVector bit_vector)

Additional Inherited Members
Public Types inherited from BALL::UnaryFunctor< AtomContainer, Processor::Result >
typedef Processor::Result	result_type
typedef AtomContainer	argument_type
typedef AtomContainer &	argument_reference
typedef const AtomContainer &	const_argument_reference
typedef AtomContainer *	argument_pointer
typedef const AtomContainer *	const_argument_pointer

Detailed Description

Processor, which marks all atoms and bonds in a ring structure with the Composite Property "InRing". calculateSSSR() can also compute the number of rings found.

The processor is an implementation of Figueras algorithm, described in: J. Figueras, J. Chem. Inf. Comput. Sci., 1996, 36(5), 986-991

and the Balducci Pearlman algorithm described in: Renzo Balducci, Robert S. Pearlman, J. Chem. Inf. Comput. Sci., 34:822-831, 1994

Definition at line 37 of file ringPerceptionProcessor.h.

Constructor & Destructor Documentation

BALL::RingPerceptionProcessor::RingPerceptionProcessor

(

)

Default constructor

BALL::RingPerceptionProcessor::RingPerceptionProcessor

(

const RingPerceptionProcessor &

rp

)

Copy constructor

virtual BALL::RingPerceptionProcessor::~RingPerceptionProcessor ( )

virtual

Destructor

Member Function Documentation

Size BALL::RingPerceptionProcessor::BalducciPearlmanAlgorithm_ ( std::vector< std::vector< Atom * > > &  sssr, SimpleMolecularGraph &  graph  )

protected

static void BALL::RingPerceptionProcessor::BalducciPearlmanRingSelector_ ( BitVector  bit_vector )

staticprotected

Size BALL::RingPerceptionProcessor::calculateSSSR	(	vector< vector< Atom * > > &	sssr,
		AtomContainer &	ac
	)

Method to get a smallest set of smallest rings (SSSR) from a molecule.

Parameters

SSSR,vector	of rings, where the rings are stored in vector<Atom*>
AtomContiner,from	which AtomContainer the rings are to be percepted

void BALL::RingPerceptionProcessor::checkEdges_ ( HashSet< Atom * > &  ring_set, AtomContainer &  ac  )

protected

void BALL::RingPerceptionProcessor::DFSBCC_ ( std::vector< SimpleMolecularGraph * > &  bccs, Size  dfbi, HashMap< NodeItem< Index, Index > *, Size >  DFBIndex, NodeItem< Index, Index > *  v  )

protected

Size BALL::RingPerceptionProcessor::FiguerasAlgorithm_ ( vector< vector< Atom * > > &  sssr, AtomContainer &  ac  )

protected

Size BALL::RingPerceptionProcessor::findAllBCC	(	std::vector< SimpleMolecularGraph * > &	bcc,
		SimpleMolecularGraph &	graph
	)

Method that finds all biconnected components, the algorithm is freely adapted from a standard bcc (binary connected components) algorithm. Returns the number of bccs found.

Size BALL::RingPerceptionProcessor::findAllBCC_ ( std::vector< SimpleMolecularGraph * > &  bcc, SimpleMolecularGraph &  graph  )

protected

const vector<vector<Atom*> >& BALL::RingPerceptionProcessor::getAllSmallRings

(

)

const

Getter which returns all the 3 - 6 membered rings, calculateSSSR with the Balducci-Pearlman Algorithm (defalt) is needed prior this call.

Size BALL::RingPerceptionProcessor::getRing_ ( Atom *  n, HashSet< Atom * > &  ring_set  )

protected

Processor::Result BALL::RingPerceptionProcessor::operator() ( AtomContainer &  )

virtual

operator ()

Reimplemented from BALL::UnaryProcessor< AtomContainer >.

RingPerceptionProcessor& BALL::RingPerceptionProcessor::operator=

(

const RingPerceptionProcessor &

rp

)

Assignment operator

void BALL::RingPerceptionProcessor::setDefaultOptions

(

)

sets the default options of this processor

Member Data Documentation

std::vector<BitVector> BALL::RingPerceptionProcessor::all_small_beers_

staticprotected

contains all 3 to 6 membered rings as beers

Definition at line 237 of file ringPerceptionProcessor.h.

std::vector<std::vector<Atom*> > BALL::RingPerceptionProcessor::all_small_rings_

staticprotected

contains all 3 to 6 membered rings after the procedure of the Balducci-Pearlman algorithm

Definition at line 234 of file ringPerceptionProcessor.h.

HashMap<NodeItem<Index, Index>* , TNode_*> BALL::RingPerceptionProcessor::atom_to_tnode_

staticprotected

Definition at line 215 of file ringPerceptionProcessor.h.

std::stack<EdgeItem<Index, Index>* > BALL::RingPerceptionProcessor::BCC_

protected

Definition at line 171 of file ringPerceptionProcessor.h.

HashMap<EdgeItem<Index, Index>*, Size> BALL::RingPerceptionProcessor::bond_to_index_

staticprotected

mapping for the path representation as bitvectors

Definition at line 218 of file ringPerceptionProcessor.h.

std::vector<BitVector> BALL::RingPerceptionProcessor::forwarded_rings_

staticprotected

the rings of the ith phase, which are to be forwarded to the ring selector

Definition at line 228 of file ringPerceptionProcessor.h.

HashMap<Size, EdgeItem<Index, Index>*> BALL::RingPerceptionProcessor::index_to_bond_

staticprotected

Definition at line 219 of file ringPerceptionProcessor.h.

std::vector<BitVector> BALL::RingPerceptionProcessor::matrix_

staticprotected

the matrix for the independency tests

Definition at line 225 of file ringPerceptionProcessor.h.

Options BALL::RingPerceptionProcessor::options

Definition at line 126 of file ringPerceptionProcessor.h.

HashMap<NodeItem<Index, Index>* , Size> BALL::RingPerceptionProcessor::P_

protected

Definition at line 169 of file ringPerceptionProcessor.h.

HashMap<NodeItem<Index, Index>*, NodeItem<Index, Index>* > BALL::RingPerceptionProcessor::parents_

protected

Definition at line 170 of file ringPerceptionProcessor.h.

std::vector<BitVector> BALL::RingPerceptionProcessor::rings_

staticprotected

the SSSR detected by the algorithm

Definition at line 222 of file ringPerceptionProcessor.h.

std::vector<BitVector> BALL::RingPerceptionProcessor::tested_beers_

staticprotected

rings (beer) which have already been tested

Definition at line 231 of file ringPerceptionProcessor.h.

HashMap<TNode_*, NodeItem<Index, Index>* > BALL::RingPerceptionProcessor::tnode_to_atom_

staticprotected

mapping for internal TNode structure and the nodes of the molecular graph

Definition at line 214 of file ringPerceptionProcessor.h.

HashSet<NodeItem<Index, Index>* > BALL::RingPerceptionProcessor::visited_

protected

Definition at line 167 of file ringPerceptionProcessor.h.

HashSet<EdgeItem<Index, Index>* > BALL::RingPerceptionProcessor::visited_bonds_

protected

Definition at line 168 of file ringPerceptionProcessor.h.