BALL::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 BALL::RingPerceptionProcessor:
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Classes |
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| struct | Default |
| default options for the ring
perception
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| struct | Option |
| Option names.
More... |
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Public Member Functions |
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| 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. |
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| 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. |
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| void | setDefaultOptions () |
| sets the default options of this
processor |
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Constrcutors and Destructors
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| RingPerceptionProcessor () | |
| Default
constructor. |
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| RingPerceptionProcessor (const RingPerceptionProcessor &rp) | |
| Copy constructor. |
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| virtual | ~RingPerceptionProcessor () |
| Destructor. |
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Assignment
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| RingPerceptionProcessor & | operator= (const RingPerceptionProcessor &rp) |
| Assignment operator. |
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Accessors
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| Size | calculateSSSR (vector< vector< Atom * > > &sssr, AtomContainer &ac) |
| Method to get a smallest set of
smallest rings (SSSR) from a molecule. |
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Processor-related methods
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| Processor::Result | operator() (AtomContainer &ac) |
| operator () |
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Public Attributes |
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| Options | options |
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HashSet< NodeItem<
Index, Index > * > |
visited_ |
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HashSet< EdgeItem<
Index, Index > * > |
visited_bonds_ |
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HashMap< NodeItem<
Index, Index > *, Size > |
P_ |
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HashMap< NodeItem<
Index, Index > *, NodeItem< Index, Index > * > |
parents_ |
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std::stack< EdgeItem< Index, Index > * > |
BCC_ |
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static HashMap<
TNode_ *, NodeItem< Index, Index > * > |
tnode_to_atom_ |
| mapping for internal TNode structure
and the nodes of the molecular graph |
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static HashMap< NodeItem < Index, Index > *, TNode_ * > |
atom_to_tnode_ |
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static HashMap<
EdgeItem < Index, Index > *, Size > |
bond_to_index_ |
| mapping for the path representation
as bitvectors |
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static HashMap< Size,
EdgeItem < Index, Index > * > |
index_to_bond_ |
| static std::vector< BitVector > | rings_ |
| the SSSR detected by the
algorithm |
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| static std::vector< BitVector > | matrix_ |
| the matrix for the independency
tests |
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| static std::vector< BitVector > | forwarded_rings_ |
| the rings of the ith phase, which
are to be forwarded to the ring selector |
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| static std::vector< BitVector > | tested_beers_ |
| rings (beer) which have already been
tested |
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static std::vector < std::vector< Atom * > > |
all_small_rings_ |
| contains all 3 to 6 membered rings
after the procedure of the Balducci-Pearlman
algorithm |
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| static std::vector< BitVector > | all_small_beers_ |
| contains all 3 to 6 membered rings
as beers |
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| 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) |
| static void | BalducciPearlmanRingSelector_ (BitVector bit_vector) |
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
Member Function Documentation
| 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
| Size BALL::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.
