RingPerceptionProcessor Class Reference

Processor, which marks all atoms and bonds in a ring structure with the Composite Property "InRing". More...

#include <ringPerceptionProcessor.h>

Inheritance diagram for RingPerceptionProcessor:

List of all members.

[NOHEADER]
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< MolecularGraph * > &bcc, MolecularGraph &graph)
void	DFSBCC_ (std::vector< MolecularGraph * > &bccs, Size dfbi, HashMap< NodeItem< Index, Index > *, Size > DFBIndex, NodeItem< Index, Index > *v)
Size	BalducciPearlmanAlgorithm_ (std::vector< std::vector< Atom * > > &sssr, MolecularGraph &graph)
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_
void	BalducciPearlmanRingSelector_ (BitVector bit_vector)
HashMap< TNode_ *, NodeItem< Index, Index > * >	tnode_to_atom_
	mapping for internal TNode structure and the nodes of the molecular graph
HashMap< NodeItem< Index, Index > *, TNode_ * >	atom_to_tnode_
HashMap< EdgeItem< Index, Index > *, Size >	bond_to_index_
	mapping for the path representation as bitvectors
HashMap< Size, EdgeItem< Index, Index > * >	index_to_bond_
std::vector< BitVector >	rings_
	the SSSR detected by the algorithm
std::vector< BitVector >	matrix_
	the matrix for the independency tests
std::vector< BitVector >	forwarded_rings_
	the rings of the ith phase, which are to be forwarded to the ring selector
std::vector< BitVector >	tested_beers_
	rings (beer) which have already been tested
std::vector< std::vector< Atom * > >	all_small_rings_
	contains all 3 to 6 membered rings after the procedure of the Balducci-Pearlman algorithm
std::vector< BitVector >	all_small_beers_
	contains all 3 to 6 membered rings as beers
Public Member Functions
const vector< vector< Atom * > > &	getAllSmallRings () const
	Getter which returns all the 3 - 6 membered rings, calculateSSSR with the Balducci-Pearlman Algorithm (defalt) is needed prior this call.
Size	findAllBCC (std::vector< MolecularGraph * > &bcc, MolecularGraph &graph)
	Method that finds all biconnected components, the algorithm is freely adapted from a standard bcc (binary connected components) algorithm.
void	setDefaultOptions ()
	sets the default options of this processor
Constrcutors and Destructors
	RingPerceptionProcessor ()
	Default constructor.
	RingPerceptionProcessor (const RingPerceptionProcessor &rp)
	Copy constructor.
virtual	~RingPerceptionProcessor ()
	Destructor.
Assignment
RingPerceptionProcessor &	operator= (const RingPerceptionProcessor &rp)
	Assignment operator.
Accessors
Size	calculateSSSR (vector< vector< Atom * > > &sssr, AtomContainer &ac)
	Method to get a smallest set of smallest rings (SSSR) from a molecule.
Processor-related methods
Processor::Result	operator() (AtomContainer &ac)
	operator ()
Public Attributes
Options	options

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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

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Member Function Documentation

Size 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

Size RingPerceptionProcessor::findAllBCC (  std::vector< MolecularGraph * > &  bcc, MolecularGraph &  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.

const vector<vector<Atom*> >& RingPerceptionProcessor::getAllSmallRings (   )  const

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