BALL 1.5.0
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#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 |
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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 | |
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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 |
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.
BALL::RingPerceptionProcessor::RingPerceptionProcessor | ( | ) |
Default constructor
BALL::RingPerceptionProcessor::RingPerceptionProcessor | ( | const RingPerceptionProcessor & | rp | ) |
Copy constructor
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virtual |
Destructor
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protected |
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staticprotected |
Size BALL::RingPerceptionProcessor::calculateSSSR | ( | vector< vector< Atom * > > & | sssr, |
AtomContainer & | ac | ||
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Method to get a smallest set of smallest rings (SSSR) from a molecule.
SSSR,vector | of rings, where the rings are stored in vector<Atom*> |
AtomContiner,from | which AtomContainer the rings are to be percepted |
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.
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virtual |
operator ()
Reimplemented from BALL::UnaryProcessor< AtomContainer >.
RingPerceptionProcessor & BALL::RingPerceptionProcessor::operator= | ( | const RingPerceptionProcessor & | rp | ) |
Assignment operator
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staticprotected |
contains all 3 to 6 membered rings as beers
Definition at line 161 of file ringPerceptionProcessor.h.
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staticprotected |
contains all 3 to 6 membered rings after the procedure of the Balducci-Pearlman algorithm
Definition at line 158 of file ringPerceptionProcessor.h.
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staticprotected |
Definition at line 139 of file ringPerceptionProcessor.h.
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staticprotected |
mapping for the path representation as bitvectors
Definition at line 142 of file ringPerceptionProcessor.h.
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staticprotected |
the rings of the ith phase, which are to be forwarded to the ring selector
Definition at line 152 of file ringPerceptionProcessor.h.
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staticprotected |
Definition at line 143 of file ringPerceptionProcessor.h.
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staticprotected |
the matrix for the independency tests
Definition at line 149 of file ringPerceptionProcessor.h.
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staticprotected |
the SSSR detected by the algorithm
Definition at line 146 of file ringPerceptionProcessor.h.
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staticprotected |
rings (beer) which have already been tested
Definition at line 155 of file ringPerceptionProcessor.h.