This file is indexed.

/usr/include/rdkit/GraphMol/QueryOps.h is in librdkit-dev 201503-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
//
//  Copyright (C) 2003-2010 Greg Landrum and Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//

//! \file QueryOps.h
/*!
    \brief Includes a bunch of functionality for handling Atom and Bond queries.
*/
#ifndef _RD_QUERY_OPS_H
#define _RD_QUERY_OPS_H

#include <GraphMol/RDKitBase.h>
#include <Query/QueryObjects.h>
#include <Query/Query.h>

#ifdef RDK_THREADSAFE_SSS
#include <boost/thread/mutex.hpp>
#endif

namespace RDKit{
  typedef Queries::Query<bool,Atom const *,true> ATOM_BOOL_QUERY;
  typedef Queries::Query<bool,Bond const *,true> BOND_BOOL_QUERY;

  typedef Queries::AndQuery<int,Atom const *,true> ATOM_AND_QUERY;
  typedef Queries::AndQuery<int,Bond const *,true> BOND_AND_QUERY;

  typedef Queries::OrQuery<int,Atom const *,true> ATOM_OR_QUERY;
  typedef Queries::OrQuery<int,Bond const *,true> BOND_OR_QUERY;

  typedef Queries::XOrQuery<int,Atom const *,true> ATOM_XOR_QUERY;
  typedef Queries::XOrQuery<int,Bond const *,true> BOND_XOR_QUERY;

  typedef Queries::EqualityQuery<int,Atom const *,true> ATOM_EQUALS_QUERY;
  typedef Queries::EqualityQuery<int,Bond const *,true> BOND_EQUALS_QUERY;

  typedef Queries::GreaterQuery<int,Atom const *,true> ATOM_GREATER_QUERY;
  typedef Queries::GreaterQuery<int,Bond const *,true> BOND_GREATER_QUERY;

  typedef Queries::GreaterEqualQuery<int,Atom const *,true> ATOM_GREATEREQUAL_QUERY;
  typedef Queries::GreaterEqualQuery<int,Bond const *,true> BOND_GREATEREQUAL_QUERY;

  typedef Queries::LessQuery<int,Atom const *,true> ATOM_LESS_QUERY;
  typedef Queries::LessQuery<int,Bond const *,true> BOND_LESS_QUERY;

  typedef Queries::LessEqualQuery<int,Atom const *,true> ATOM_LESSEQUAL_QUERY;
  typedef Queries::LessEqualQuery<int,Bond const *,true> BOND_LESSEQUAL_QUERY;

  typedef Queries::RangeQuery<int,Atom const *,true> ATOM_RANGE_QUERY;
  typedef Queries::RangeQuery<int,Bond const *,true> BOND_RANGE_QUERY;

  typedef Queries::SetQuery<int,Atom const *,true> ATOM_SET_QUERY;
  typedef Queries::SetQuery<int,Bond const *,true> BOND_SET_QUERY;

  typedef Queries::Query<int,Bond const *,true> BOND_NULL_QUERY;
  typedef Queries::Query<int,Atom const *,true> ATOM_NULL_QUERY;

  // -------------------------------------------------
  // common atom queries

  static int queryAtomAromatic(Atom const * at) { return at->getIsAromatic(); };
  static int queryAtomAliphatic(Atom const * at) { return !(at->getIsAromatic()); };
  static int queryAtomExplicitDegree(Atom const * at) { return at->getDegree(); };
  static int queryAtomTotalDegree(Atom const * at) { return at->getTotalDegree(); };
  static int queryAtomHeavyAtomDegree(Atom const * at) { return at->getTotalDegree()-at->getTotalNumHs(true); };
  static int queryAtomHCount(Atom const * at) { return at->getTotalNumHs(true); };
  static int queryAtomImplicitHCount(Atom const * at) { return at->getTotalNumHs(false); };
  static int queryAtomHasImplicitH(Atom const * at) { return int(at->getTotalNumHs(false)>0); };
  static int queryAtomImplicitValence(Atom const * at) { return at->getImplicitValence(); };
  static int queryAtomExplicitValence(Atom const * at) { return at->getExplicitValence() - at->getNumExplicitHs(); };
  static int queryAtomTotalValence(Atom const * at) { return at->getExplicitValence()+at->getImplicitValence(); };
  static int queryAtomUnsaturated(Atom const * at) { return static_cast<int>(at->getDegree())<at->getExplicitValence(); };
  static int queryAtomNum(Atom const * at) { return at->getAtomicNum(); };
  static int massIntegerConversionFactor=1000;
  static int queryAtomMass(Atom const * at) {
    return static_cast<int>(round(massIntegerConversionFactor*at->getMass()));
  };
  static int queryAtomIsotope(Atom const * at) {
    return static_cast<int>(at->getIsotope());
  };
  static int queryAtomFormalCharge(Atom const * at) { 
      return static_cast<int>(at->getFormalCharge()); 
  };
  static int queryAtomHybridization(Atom const * at) { return at->getHybridization(); };
  unsigned int queryAtomBondProduct(Atom const * at);
  unsigned int queryAtomAllBondProduct(Atom const * at);
    
    
  // -------------------------------------------------
  // common bond queries

  static int queryBondOrder(Bond const * bond) { return static_cast<int>(bond->getBondType()); };
  static int queryBondDir(Bond const * bond) { return static_cast<int>(bond->getBondDir()); };
  static int queryIsBondInNRings(Bond const * at) {
    return at->getOwningMol().getRingInfo()->numBondRings(at->getIdx());
  };

  // -------------------------------------------------
  // ring queries 

  static int queryIsAtomInNRings(Atom const * at) {
    return at->getOwningMol().getRingInfo()->numAtomRings(at->getIdx());
  };
  static int queryIsAtomInRing(Atom const * at) {
    return at->getOwningMol().getRingInfo()->numAtomRings(at->getIdx())!=0;
  };
  static int queryAtomHasRingBond(Atom const * at) {
    ROMol::OBOND_ITER_PAIR atomBonds=at->getOwningMol().getAtomBonds(at);
    while(atomBonds.first != atomBonds.second){
      unsigned int bondIdx=at->getOwningMol().getTopology()[*atomBonds.first]->getIdx();
      if(at->getOwningMol().getRingInfo()->numBondRings(bondIdx)) {
        return 1;
      }
      ++atomBonds.first;  
    }
    return 0;
  };
  static int queryIsBondInRing(Bond const * bond) {
    return bond->getOwningMol().getRingInfo()->numBondRings(bond->getIdx())!=0;
  };
  static int queryAtomMinRingSize(Atom const *at){
    return at->getOwningMol().getRingInfo()->minAtomRingSize(at->getIdx());
  };
  static int queryBondMinRingSize(Bond const *bond){
    return bond->getOwningMol().getRingInfo()->minBondRingSize(bond->getIdx());
  };

  static int queryAtomRingBondCount(Atom const *at) {
    // EFF: cache this result
    int res=0;
    ROMol::OBOND_ITER_PAIR atomBonds=at->getOwningMol().getAtomBonds(at);
    while(atomBonds.first != atomBonds.second){
      unsigned int bondIdx=at->getOwningMol().getTopology()[*atomBonds.first]->getIdx();
      if(at->getOwningMol().getRingInfo()->numBondRings(bondIdx)) {
        res++;
      }
      ++atomBonds.first;  
    }
    return res;
  }

  template <int tgt>
  int queryAtomIsInRingOfSize(Atom const *at) {
    if(at->getOwningMol().getRingInfo()->isAtomInRingOfSize(at->getIdx(),tgt)){
      return tgt;
    } else {
      return 0;
    }
  };
  template <int tgt>
  int queryBondIsInRingOfSize(Bond const *bond) {
    if(bond->getOwningMol().getRingInfo()->isBondInRingOfSize(bond->getIdx(),tgt)){
      return tgt;
    } else {
      return 0;
    }
  };


  template <class T>
  T *makeAtomSimpleQuery(int what,int func(Atom const *),const std::string &description="Atom Simple"){
    T *res = new T;
    res->setVal(what);
    res->setDataFunc(func);
    res->setDescription(description);
    return res;
  }


  //! returns a Query for matching atomic number
  template <class T>
  T *makeAtomNumQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomNum,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomNumQuery(int what);

  //! returns a Query for matching implicit valence
  template <class T>
  T *makeAtomImplicitValenceQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomImplicitValence,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomImplicitValenceQuery(int what);

  //! returns a Query for matching explicit valence
  template <class T>
  T *makeAtomExplicitValenceQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomExplicitValence,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomExplicitValenceQuery(int what);

  //! returns a Query for matching total valence
  template <class T>
  T *makeAtomTotalValenceQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomTotalValence,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomTotalValenceQuery(int what);

  //! returns a Query for matching explicit degree
  template <class T>
  T *makeAtomExplicitDegreeQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomExplicitDegree,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomExplicitDegreeQuery(int what);

  //! returns a Query for matching atomic degree
  template <class T>
  T *makeAtomTotalDegreeQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomTotalDegree,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomTotalDegreeQuery(int what);

  //! returns a Query for matching hydrogen count
  template <class T>
  T *makeAtomHCountQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomHCount,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomHCountQuery(int what);

  //! returns a Query for matching ring atoms
  template <class T>
  T *makeAtomHasImplicitHQuery(const std::string &descr){
    return makeAtomSimpleQuery<T>(true,queryAtomHasImplicitH,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomHasImplicitHQuery();


  //! returns a Query for matching implicit hydrogen count
  template <class T>
  T *makeAtomImplicitHCountQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomImplicitHCount,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomImplicitHCountQuery(int what);

  //! returns a Query for matching the \c isAromatic flag
  template <class T>
  T *makeAtomAromaticQuery(const std::string &descr){
    return makeAtomSimpleQuery<T>(true,queryAtomAromatic,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomAromaticQuery();

  //! returns a Query for matching aliphatic atoms
  template <class T>
  T *makeAtomAliphaticQuery(const std::string &descr){
    return makeAtomSimpleQuery<T>(true,queryAtomAliphatic,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomAliphaticQuery();

  //! returns a Query for matching atoms with a particular mass
  template <class T>
  T *makeAtomMassQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(massIntegerConversionFactor*what,queryAtomMass,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomMassQuery(int what);

  //! returns a Query for matching atoms with a particular isotope
  template <class T>
  T *makeAtomIsotopeQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomIsotope,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomIsotopeQuery(int what);

  //! returns a Query for matching formal charge
  template <class T>
  T *makeAtomFormalChargeQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomFormalCharge,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomFormalChargeQuery(int what);

  //! returns a Query for matching hybridization
  template <class T>
  T *makeAtomHybridizationQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomHybridization,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomHybridizationQuery(int what);

  //! returns a Query for matching atoms with unsaturation:
  template <class T>
  T *makeAtomUnsaturatedQuery(const std::string &descr){
    return makeAtomSimpleQuery<T>(true,queryAtomUnsaturated,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomUnsaturatedQuery();


  //! returns a Query for matching ring atoms
  template <class T>
  T *makeAtomInRingQuery(const std::string &descr){
    return makeAtomSimpleQuery<T>(true,queryIsAtomInRing,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomInRingQuery();

  //! returns a Query for matching atoms in a particular number of rings
  template <class T>
  T *makeAtomInNRingsQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryIsAtomInNRings,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomInNRingsQuery(int what);

  //! returns a Query for matching atoms in rings of a particular size
  ATOM_EQUALS_QUERY *makeAtomInRingOfSizeQuery(int tgt);

  //! returns a Query for matching an atom's minimum ring size
  template <class T>
  T *makeAtomMinRingSizeQuery(int tgt,const std::string &descr){
    return makeAtomSimpleQuery<T>(tgt,queryAtomMinRingSize,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomMinRingSizeQuery(int tgt);

  //! returns a Query for matching atoms with a particular number of ring bonds
  template <class T>
  T *makeAtomRingBondCountQuery(int what,const std::string &descr){
    return makeAtomSimpleQuery<T>(what,queryAtomRingBondCount,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomRingBondCountQuery(int what);

  //! returns a Query for matching atoms with a particular number of ring bonds
  template <class T>
  T *makeAtomHasRingBondQuery(const std::string &descr){
    return makeAtomSimpleQuery<T>(1,queryAtomHasRingBond,descr);
  }
  //! \overload
  ATOM_EQUALS_QUERY *makeAtomHasRingBondQuery();

  //! returns a Query for matching bond orders
  BOND_EQUALS_QUERY *makeBondOrderEqualsQuery(Bond::BondType what);
  //! returns a Query for matching bond directions
  BOND_EQUALS_QUERY *makeBondDirEqualsQuery(Bond::BondDir what);
  //! returns a Query for matching ring bonds
  BOND_EQUALS_QUERY *makeBondIsInRingQuery();
  //! returns a Query for matching bonds in rings of a particular size
  BOND_EQUALS_QUERY *makeBondInRingOfSizeQuery(int what);
  //! returns a Query for matching a bond's minimum ring size
  BOND_EQUALS_QUERY *makeBondMinRingSizeQuery(int what);
  //! returns a Query for matching bonds in a particular number of rings
  BOND_EQUALS_QUERY *makeBondInNRingsQuery(int tgt);

  //! returns a Query for matching any bond
  BOND_NULL_QUERY *makeBondNullQuery();
  //! returns a Query for matching any atom
  ATOM_NULL_QUERY *makeAtomNullQuery();

  static int queryAtomRingMembership(Atom const *at) {
    return static_cast<int>(at->getOwningMol().getRingInfo()->numAtomRings(at->getIdx()));
  }
  // I'm pretty sure that this typedef shouldn't be necessary,
  // but VC++ generates a warning about const Atom const * in
  // the definition of Match, then complains about an override
  // that differs only by const/volatile (c4301), then generates
  // incorrect code if we don't do this... so let's do it.
  typedef Atom const *ConstAtomPtr;
  
  class AtomRingQuery : public Queries::EqualityQuery<int, ConstAtomPtr,true> {
  public:
    AtomRingQuery() : Queries::EqualityQuery<int,ConstAtomPtr,true>(-1) {
      // default is to just do a number of rings query:
      this->setDescription("AtomInNRings");
      this->setDataFunc(queryAtomRingMembership);
    };
    explicit AtomRingQuery(int v) : Queries::EqualityQuery<int,ConstAtomPtr,true>(v) {
      // default is to just do a number of rings query:
      this->setDescription("AtomInNRings");
      this->setDataFunc(queryAtomRingMembership);
    };

    virtual bool Match(const ConstAtomPtr what) const {
      int v = this->TypeConvert(what,Queries::Int2Type<true>());
      bool res;
      if(this->d_val<0){
        res = v!=0;
      } else {
        res=!Queries::queryCmp(v,this->d_val,this->d_tol);
      }
      if(this->getNegation()){
        res=!res;
      }
      return res;
    }

    //! returns a copy of this query
    Queries::Query<int,ConstAtomPtr,true> *
    copy() const {
      AtomRingQuery *res = new AtomRingQuery(this->d_val);
      res->setNegation(getNegation());
      res->setTol(this->getTol());
      res->d_description = this->d_description;
      res->d_dataFunc = this->d_dataFunc;
      return res;
    }
  };
  
  //! allows use of recursive structure queries (e.g. recursive SMARTS)
  class RecursiveStructureQuery : public Queries::SetQuery<int,Atom const *,true> {
  public:
    RecursiveStructureQuery() :
      Queries::SetQuery<int,Atom const *,true>(),
      d_serialNumber(0)
    {
      setDataFunc(getAtIdx);
      setDescription("RecursiveStructure");
    };
    //! initialize from an ROMol pointer
    /*!
      <b>Notes</b>
        - this takes over ownership of the pointer
    */
    RecursiveStructureQuery(ROMol const *query,unsigned int serialNumber=0) :
      Queries::SetQuery<int,Atom const *,true>(),
      d_serialNumber(serialNumber)
    {
      setQueryMol(query);
      setDataFunc(getAtIdx);
      setDescription("RecursiveStructure");
    };
    //! returns the index of an atom
    static int getAtIdx(Atom const *at) {
      PRECONDITION(at,"bad atom argument");
      return at->getIdx();
    };

    //! sets the molecule we'll use recursively
    /*!
      <b>Notes</b>
        - this takes over ownership of the pointer
    */
    void setQueryMol(ROMol const *query) {
      dp_queryMol.reset(query);
    }
    //! returns a pointer to our query molecule
    ROMol const * getQueryMol() const { return dp_queryMol.get(); };

    //! returns a copy of this query
    Queries::Query<int,Atom const *,true> *
    copy() const {
      RecursiveStructureQuery *res =
	new RecursiveStructureQuery();
      res->dp_queryMol.reset(new ROMol(*dp_queryMol,true));

      std::set<int>::const_iterator i;
      for(i=d_set.begin();i!=d_set.end();i++){
	res->insert(*i);
      }
      res->setNegation(getNegation());
      res->d_description = d_description;
      res->d_serialNumber=d_serialNumber;
      return res;
    }
    unsigned int getSerialNumber() const { return d_serialNumber; };
  
#ifdef RDK_THREADSAFE_SSS
    boost::mutex d_mutex;
#endif
  private:
    boost::shared_ptr<const ROMol>dp_queryMol;
    unsigned int d_serialNumber;
  };

  template <typename T>
  int nullDataFun(T arg) { return 1; }
  template <typename T>
  bool nullQueryFun(T arg) { return true; } 

  typedef Bond const *ConstBondPtr;

  // ! Query whether an atom has a property
  template<class TargetPtr>
  class HasPropQuery : public Queries::EqualityQuery<
    int, TargetPtr, true> {

    std::string propname;
  public:
    HasPropQuery():
    Queries::EqualityQuery<int,TargetPtr,true>(),
      propname() {
      // default is to just do a number of rings query:
      this->setDescription("AtomHasProp");
      this->setDataFunc(0);
    };
  explicit HasPropQuery(const std::string & v) :
    Queries::EqualityQuery<int,TargetPtr,true>(),
      propname(v) {
      // default is to just do a number of rings query:
      this->setDescription("AtomHasProp");
      this->setDataFunc(0);
    };

    virtual bool Match(const TargetPtr what) const {
      bool res = what->hasProp(propname);
      if(this->getNegation()){
        res=!res;
      }
      return res;
    }

    //! returns a copy of this query
    Queries::Query<int,TargetPtr,true> *
    copy() const {
      HasPropQuery *res = new HasPropQuery(this->propname);
      res->setNegation(this->getNegation());
      res->d_description = this->d_description;
      return res;
    }
  };

  typedef Queries::EqualityQuery<
    int,Atom const *,true> ATOM_PROP_QUERY;
  typedef Queries::EqualityQuery<
    int,Bond const *,true> BOND_PROP_QUERY;

  //! returns a Query for matching atoms that have a particular property
  template<class Target>
  Queries::EqualityQuery<int,const Target *,true> *makeHasPropQuery(
        const std::string &property)
  {
      return new HasPropQuery<const Target *>(property);
  }

  // ! Query whether an atom has a property with a value
  template<class TargetPtr, class T>
  class HasPropWithValueQuery : public Queries::EqualityQuery<
    int, TargetPtr, true> {
    std::string propname;
    T val;
    T tolerance;
  public:
    HasPropWithValueQuery():
    Queries::EqualityQuery<int,TargetPtr,true>(),
      propname(), val() {
      // default is to just do a number of rings query:
      this->setDescription("HasPropWithValue");
      this->setDataFunc(0);
    };
    explicit HasPropWithValueQuery(const std::string & prop, const T&v,
                                       const T&tol=0.0) :
    Queries::EqualityQuery<int,TargetPtr,true>(),
      propname(prop),
      val(v),
      tolerance(tol) {
      // default is to just do a number of rings query:
      this->setDescription("HasPropWithValue");
      this->setDataFunc(0);
    };

    virtual bool Match(const TargetPtr what) const {
      bool res = what->hasProp(propname);
      if (res)
      {
        try {
          T atom_val = what->template getProp<T>(propname);
          res = Queries::queryCmp(atom_val, this->val, this->tolerance) == 0;
        }
        catch (KeyErrorException e) {
          res = false;
        }
        catch (boost::bad_any_cast)
        {
          res = false;
        }

      }
      if(this->getNegation()){
        res=!res;
      }
      return res;
    }

    //! returns a copy of this query
    Queries::Query<int,TargetPtr,true> *
    copy() const {
      HasPropWithValueQuery *res = new HasPropWithValueQuery(
         this->propname, this->val, this->tolerance);
      res->setNegation(this->getNegation());
      res->d_description = this->d_description;
      return res;
    }
  };

  template<class TargetPtr>
    class HasPropWithValueQuery<TargetPtr, std::string> :
        public Queries::EqualityQuery<int, TargetPtr, true> {
    std::string propname;
    std::string val;
  public:
    HasPropWithValueQuery():
    Queries::EqualityQuery<int,TargetPtr,true>(),
      propname(), val() {
      // default is to just do a number of rings query:
      this->setDescription("HasPropWithValue");
      this->setDataFunc(0);
    };
    explicit HasPropWithValueQuery(const std::string & prop,
                                       const std::string &v,
                                       const std::string &tol="") :
    Queries::EqualityQuery<int,TargetPtr,true>(),
      propname(prop),
      val(v) {
      // default is to just do a number of rings query:
      this->setDescription("HasPropWithValue");
      this->setDataFunc(0);
    };

    virtual bool Match(const TargetPtr what) const {
      bool res = what->hasProp(propname);
      if (res)
      {
        try {
          std::string atom_val = what->template getProp<std::string>(propname);
          res = atom_val == this->val;
        }
        catch (KeyErrorException) {
          res = false;
        }
        catch (boost::bad_any_cast)
        {
          res = false;
        }
      }
      if(this->getNegation()){
        res=!res;
      }
      return res;
    }

    //! returns a copy of this query
    Queries::Query<int,TargetPtr,true> *
    copy() const {
      HasPropWithValueQuery<TargetPtr,std::string> *res =
        new HasPropWithValueQuery<TargetPtr, std::string>(
          this->propname, this->val);
      res->setNegation(this->getNegation());
      res->d_description = this->d_description;
      return res;
    }
  };
  
  
  template<class Target, class T>
    Queries::EqualityQuery<int, const Target *, true> *makePropQuery(
        const std::string &propname,
        const T&val,
        const T&tolerance=T())
    {
      return new HasPropWithValueQuery<const Target *, T>(
         propname, val, tolerance);
    }
};


#endif