BALL  1.5.0
smartsMatcher.h
Go to the documentation of this file.
1 // -*- Mode: C++; tab-width: 2; -*-
2 // vi: set ts=2:
3 //
4 
5 #ifndef BALL_STRUCTURE_SMARTSMATCHER_H
6 #define BALL_STRUCTURE_SMARTSMATCHER_H
7 
8 #ifndef BALL_STRUCTURE_SMARTSPARSER_H
10 #endif
11 
12 #include <vector>
13 #include <set>
14 #include <map>
15 
16 #include <boost/shared_ptr.hpp>
17 
18 namespace BALL
19 {
20  // forward declaration
21  class Molecule;
22 
45  {
46  public:
47 
51  typedef std::vector<std::set<const Atom*> > Match;
53 
54 
60 
62  virtual ~SmartsMatcher();
64 
65 
70  void match(Match& matches, Molecule& mol, const String& smarts);
71 
73  void match(Match& matches, Molecule& mol, const String& smarts, const std::set<const Atom*>& start_atoms);
74 
76  void match(std::vector<Match>& matches, Molecule& mol, const std::vector<String>& smarts);
77 
79  void match(std::vector<Match>& matches, Molecule& mol, const std::vector<String>& smarts, const std::set<const Atom*>& start_atoms);
80 
82  void setSSSR(const std::vector<std::vector<Atom*> >& sssr);
83 
85  void unsetSSSR();
87 
88 
89  private:
90 
92  SmartsMatcher(const SmartsMatcher& matcher);
93 
98  SmartsMatcher& operator = (const SmartsMatcher& matcher);
100 
101 
102  protected:
103 
112 
115  {
116  public:
117 
120 
123 
125  virtual ~RecStructCore_();
126 
128  RecStructCore_& operator = (const RecStructCore_&);
129 
131  void clear();
132 
134  std::vector<std::set<const Atom*> > matched_atoms;
135 
137  std::vector<std::map<const SPNode*, const Atom*> > mapped_atoms;
138 
140  std::vector<std::set<const Atom*> > visited_atoms;
141 
143  std::vector<std::set<const Bond*> > visited_bonds;
144 
146  std::vector<std::set<const SPEdge*> > visited_edges;
147 
149  std::vector<std::pair<const SPNode*, const Atom*> > first_matches;
150  };
151 
154  {
155  public:
156 
159 
161  virtual ~RecStructPool_();
162 
165 
168 
170  void destroy(Position pos);
171 
172  private:
173 
175  void resize_();
176 
179 
181  RecStructPool_& operator = (const RecStructPool_&);
182 
184  std::vector<RecStructCore_*> rec_struct_pool_;
185 
187  std::vector<Position> free_list_;
188 
190  Position last_position_;
191  };
192 
193 
196  {
197  private:
199  RecStructCore_* rec_struct_core_;
200 
201  public:
202 
205 
207  RecStruct_(const RecStruct_& rec_struct);
208 
210  virtual ~RecStruct_();
211 
213  RecStruct_& operator = (const RecStruct_&);
214 
216  std::vector<std::set<const Atom*> >& matched_atoms;
217 
219  std::vector<std::map<const SPNode*, const Atom*> >& mapped_atoms;
220 
222  std::vector<std::set<const Atom*> >& visited_atoms;
223 
225  std::vector<std::set<const Bond*> >& visited_bonds;
226 
228  std::vector<std::set<const SPEdge*> >& visited_edges;
229 
231  std::vector<std::pair<const SPNode*, const Atom*> >& first_matches;
232 
234  void add(const RecStruct_& rec_struct);
235 
237  void add(const RecStruct_& rec_struct, Size i);
238 
240  void clear();
241 
243  void dump(const String& name, Size depth_ = 0);
244 
245  private:
246 
248  Position pos_;
249  };
250 
252  static boost::shared_ptr<RecStructPool_> pool_;
253 
255  bool evaluateRingEdges_(const std::set<const Atom*>& matching, const std::map<const SPNode*, const Atom*>& mapping, const String& smarts);
256 
258  void evaluate_( RecStruct_& rs, SPNode* start_node, const Atom* start_atom);
259 
261  bool evaluate_node_(RecStruct_& rs, SPNode* start_node, const Atom* start_atom);
262 
264  bool evaluate_edge_(RecStruct_& rs, SPEdge* start_node, const Atom* start_atom, const Bond* start_bond);
265 
267  std::map<SPNode*, std::vector<std::set<const Atom*> > > rec_matches_;
268 
271 
273  std::vector<std::vector<Atom*> > sssr_;
274 
275  // debug output depth
277  };
278 
279 } // namespace BALL
280 
281 #endif // BALL_STRUCTURE_SMARTSMATCHER_H
282 
Definition: constants.h:13
SmartsParser::SPBond SPBond
std::vector< std::vector< Atom * > > sssr_
user sssr
bool evaluate_edge_(RecStruct_ &rs, SPEdge *start_node, const Atom *start_atom, const Bond *start_bond)
method for evaluating a edge of a pseudo-tree
void unsetSSSR()
this function is used to cause the matcher to do an ring perception if needed (do not use the set SSS...
SmartsParser::SPAtom SPAtom
void setSSSR(const std::vector< std::vector< Atom * > > &sssr)
sets an SSSR which is used instead of doing an ring perception
SmartsParser::SPNode SPNode
bool evaluate_node_(RecStruct_ &rs, SPNode *start_node, const Atom *start_atom)
method for evaluating a node of a pseudo-tree
SmartsParser::SPEdge SPEdge
std::map< SPNode *, std::vector< std::set< const Atom * > > > rec_matches_
matches from the recurive part
void match(std::vector< Match > &matches, Molecule &mol, const std::vector< String > &smarts, const std::set< const Atom * > &start_atoms)
method to match several Smarts patterns given as a vector of string. The atoms used for start matchin...
void evaluate_(RecStruct_ &rs, SPNode *start_node, const Atom *start_atom)
method for the evaluation of a pseudo-tree
virtual ~SmartsMatcher()
destructor
bool has_user_sssr_
user SSSR set?
static boost::shared_ptr< RecStructPool_ > pool_
the pool of rec struct objects
std::vector< std::set< const Atom * > > Match
Definition: smartsMatcher.h:51
void match(Match &matches, Molecule &mol, const String &smarts, const std::set< const Atom * > &start_atoms)
method to match a Smarts pattern given as a string to given molecule. The atoms which will be used fo...
bool evaluateRingEdges_(const std::set< const Atom * > &matching, const std::map< const SPNode *, const Atom * > &mapping, const String &smarts)
method for evaluation of ring edges, after the the smarts tree is matched to molcule
void match(Match &matches, Molecule &mol, const String &smarts)
method to match a Smarts pattern given as a string to given molecule
void match(std::vector< Match > &matches, Molecule &mol, const std::vector< String > &smarts)
method to match several Smarts patterns given as a vector of strings
SmartsMatcher()
default constructor
core structure of the recursive matching algorithm for the object pool
std::vector< std::set< const Atom * > > visited_atoms
contains vector of visited atoms of different matches
std::vector< std::set< const Bond * > > visited_bonds
contains vector of visited bonds of different matches
std::vector< std::set< const SPEdge * > > visited_edges
contains vector of visited edges of the Smarts tree of different matches
virtual ~RecStructCore_()
destructor
RecStructCore_(const RecStructCore_ &)
copy constructor
std::vector< std::map< const SPNode *, const Atom * > > mapped_atoms
container which contains a vector of mappings from different matches
void clear()
method that deletes all content from the containers
std::vector< std::pair< const SPNode *, const Atom * > > first_matches
contains the first matched atoms of different matches (needed for recursive Smarts)
RecStructCore_()
default constructor
std::vector< std::set< const Atom * > > matched_atoms
container which contains a vector of matched atoms from different matches
class which does the pool operations of the RecStructCore_ pool
void destroy(Position pos)
frees the structure at position pos
RecStructCore_ * getNextFree()
returns the a free RecStructCore_ of the pool (creates new ones if needed)
Position getLastPosition()
returns the position of the last RecStructCore_* from getNextFree()
virtual ~RecStructPool_()
destructor
RecStructPool_()
default constructors
a wrapper class which is used as an interface in the matching code to the pool
void dump(const String &name, Size depth_=0)
dumps the contents (for debugging)
virtual ~RecStruct_()
destructor
std::vector< std::set< const SPEdge * > > & visited_edges
reference to the visited edges in the core structure
RecStruct_(const RecStruct_ &rec_struct)
copy constructor
void clear()
deletes all contents
std::vector< std::map< const SPNode *, const Atom * > > & mapped_atoms
reference to the mapped SPNodes to Atoms in the core structure
std::vector< std::pair< const SPNode *, const Atom * > > & first_matches
reference to the first matches in the core structure
std::vector< std::set< const Atom * > > & visited_atoms
reference to the visited atoms in the core structure
std::vector< std::set< const Bond * > > & visited_bonds
reference to the visited bonds in the core structure
std::vector< std::set< const Atom * > > & matched_atoms
reference to the matched atoms in the core structure
void add(const RecStruct_ &rec_struct)
adds the content of the given struct
RecStruct_()
default constructor
void add(const RecStruct_ &rec_struct, Size i)
adds the the ith part of the content of the given struct
Bond representation of the smarts parser.
Definition: smartsParser.h:106
Smarts Parser Atom class.
Definition: smartsParser.h:189
Edge representation of the smarts parser graph.
Definition: smartsParser.h:386
Representation of a node in the smarts parser graph.
Definition: smartsParser.h:487
#define BALL_EXPORT
Definition: COMMON/global.h:50