#include <BALL/QSAR/ringPerceptionProcessor.h>
Classes | |
| struct | PathMessage_ |
| struct | TNode_ |
Public Member Functions | |
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) |
| const vector< vector< Atom * > > & | getAllSmallRings () const |
 Public Member Functions inherited from BALL::UnaryProcessor< AtomContainer > | |
| UnaryProcessor () | |
| UnaryProcessor (const UnaryProcessor &) | |
| virtual | ~UnaryProcessor () |
| virtual bool | start () |
| virtual bool | finish () |
Processor-related methods | |
| 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... | |
| Processor::Result | operator() (AtomContainer &ac) |
| static void | BalducciPearlmanRingSelector_ (BitVector bit_vector) |
| Size | BalducciPearlmanAlgorithm_ (std::vector< std::vector< Atom * > > &sssr, SimpleMolecularGraph &graph) |
Additional Inherited Members | |
| Public Types inherited from BALL::UnaryFunctor< ArgumentType, ResultType > | |
| typedef ResultType | result_type |
| typedef ArgumentType | argument_type |
| typedef ArgumentType & | argument_reference |
| typedef const ArgumentType & | const_argument_reference |
| typedef ArgumentType * | argument_pointer |
| typedef const ArgumentType * | 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 the Balducci Pearlman algorithm described in: Renzo Balducci, Robert S. Pearlman, J. Chem. Inf. Comput. Sci., 34:822-831, 1994
Definition at line 36 of file ringPerceptionProcessor.h.
Constructor & Destructor Documentation
◆ RingPerceptionProcessor() [1/2]
| BALL::RingPerceptionProcessor::RingPerceptionProcessor | ( | ) |
Default constructor
◆ RingPerceptionProcessor() [2/2]
| BALL::RingPerceptionProcessor::RingPerceptionProcessor | ( | const RingPerceptionProcessor & | rp | ) |
Copy constructor
◆ ~RingPerceptionProcessor()
|
virtual |
Destructor
Member Function Documentation
◆ BalducciPearlmanAlgorithm_()
|
protected |
◆ BalducciPearlmanRingSelector_()
|
staticprotected |
◆ calculateSSSR()
| 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
◆ getAllSmallRings()
| 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.
◆ operator()()
|
virtual |
operator ()
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
◆ operator=()
| RingPerceptionProcessor& BALL::RingPerceptionProcessor::operator= | ( | const RingPerceptionProcessor & | rp | ) |
Assignment operator
Member Data Documentation
◆ all_small_beers_
|
staticprotected |
contains all 3 to 6 membered rings as beers
Definition at line 161 of file ringPerceptionProcessor.h.
◆ all_small_rings_
|
staticprotected |
contains all 3 to 6 membered rings after the procedure of the Balducci-Pearlman algorithm
Definition at line 158 of file ringPerceptionProcessor.h.
◆ atom_to_tnode_
|
staticprotected |
Definition at line 139 of file ringPerceptionProcessor.h.
◆ bond_to_index_
|
staticprotected |
mapping for the path representation as bitvectors
Definition at line 142 of file ringPerceptionProcessor.h.
◆ forwarded_rings_
|
staticprotected |
the rings of the ith phase, which are to be forwarded to the ring selector
Definition at line 152 of file ringPerceptionProcessor.h.
◆ index_to_bond_
|
staticprotected |
Definition at line 143 of file ringPerceptionProcessor.h.
◆ matrix_
|
staticprotected |
the matrix for the independency tests
Definition at line 149 of file ringPerceptionProcessor.h.
◆ rings_
|
staticprotected |
the SSSR detected by the algorithm
Definition at line 146 of file ringPerceptionProcessor.h.
◆ tested_beers_
|
staticprotected |
rings (beer) which have already been tested
Definition at line 155 of file ringPerceptionProcessor.h.
