File: kekulize.cpp

package info (click to toggle)
openbabel 2.2.3-1
  • links: PTS, VCS
  • area: main
  • in suites: squeeze
  • size: 36,644 kB
  • ctags: 33,717
  • sloc: cpp: 242,528; ansic: 87,037; sh: 10,280; perl: 5,518; python: 5,156; pascal: 793; makefile: 747; cs: 392; xml: 97; ruby: 54; java: 23
file content (606 lines) | stat: -rw-r--r-- 22,346 bytes parent folder | download
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
/**********************************************************************
kekulize.cpp - Alternate algorithm to kekulize a molecule.

Copyright (C) 2004-2006 by Fabien Fontaine
Some portions Copyright (C) 2005-2009 by Geoffrey R. Hutchison
Some portions Copyright (C) 2009 by Craig A. James

This file is part of the Open Babel project.
For more information, see <http://openbabel.sourceforge.net/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#define DEBUG 0

#include <openbabel/babelconfig.h>

#include <openbabel/mol.h>
#include <openbabel/ring.h>
#include <openbabel/obiter.h>
// #include <openbabel/graphsym.h>

#include <sstream>

// Some names to make the code more readable
#define SINGLE 1
#define DOUBLE 2

#define NOT_IN_RINGS      -1
#define DOUBLE_ASSIGNED    0
#define DOUBLE_ALLOWED     1
#define DOUBLE_PROHIBITED  2

using namespace std;

namespace OpenBabel 
{

  // Modified internal-only versions
  int expand_cycle (OBMol *mol, OBAtom *atom, OBBitVec &avisit, OBBitVec &cvisit, 
                    int rootIdx, int prevAtomIdx = -1, int depth = 19);
  bool expandkekulize(OBMol *mol, int bond_idx,
                      std::vector<int> &atomState,
                      std::vector<int> &bondState);
  bool has_no_leftover_electrons(OBMol *mol, std::vector<int> &atomState);

  ///////////////////////////////////////////////////////////////////////////////
  //! \brief Kekulize aromatic rings without using implicit valence
  //!
  //! This new perceive kekule bonds function has been designed to 
  //! handle molecule files without explicit hydrogens such as pdb or xyz.
  //! (It can, of course, easily handle explicit hydrogens too.)
  //! The function does not rely on GetImplicitValence function
  //! The function looks for groups of aromatic cycle 
  //! For each group it tries to guess the number of electrons given by each atom
  //! in order to satisfy the huckel (4n+2) rule
  //! If the huckel rule cannot be satisfied the algorithm try with its best alternative guess
  //! Then it recursively walk on the atoms of the cycle and assign single and double bonds
  void OBMol::NewPerceiveKekuleBonds() 
  {

    if (HasKekulePerceived())  return;
    SetKekulePerceived();

    OBAtom *atom;
    int n, de, minde;
    std::vector<OBAtom*> cycle;
    OBBitVec avisit,cvisit;
    avisit.Resize(NumAtoms()+1);
    cvisit.Resize(NumAtoms()+1);
    OBBond *bond;
    std::vector<OBBond*>::iterator bi;
    std::vector<int> electron;
    int sume, orden;
    int bestatom = 1;
    int bestorden = 99;
    // Init the kekulized bonds
    unsigned i;
    FOR_BONDS_OF_MOL(b, *this)
      {
        switch (b->GetBO())
          {
          case 2: b->SetKDouble(); break;
          case 3: b->SetKTriple(); break;
          case 1: b->SetKSingle(); break;
          }
      }

    // Check if we should allow "fused ring" analysis -- we fall back to expanding as needed
    // We'll only do this if an atom is in 3 or more rings.
    bool fusedRings = false;
    OBSmartsPattern fused; fused.Init("[aR3]");  
    if (fused.Match(*this))
      fusedRings = true;

    // Find all the groups of aromatic cycle
    for(i=1; i<= NumAtoms(); i++ ) {
      atom = GetAtom(i);
      //      cout << "Checking for cycle at " << i << endl;
      if (atom->HasAromaticBond() && !cvisit[i]) { // is new aromatic atom of an aromatic cycle ?

        avisit.Clear();
        electron.clear();
        cycle.clear();

        avisit.SetBitOn(i);

        if (fusedRings)
          expandcycle(atom, avisit);
        else {
          int depth = expand_cycle(this, atom, avisit, cvisit, atom->GetIdx());
          if (depth <= 0)
            continue; // no valid cycle from this atom
        }

        // Check to see that at least 2 bonds are included
        // e.g.           __
        //           ____/  \   bad because, we should start at a ring atom
        //               \__/
        std::vector<OBBond*>::iterator b;
        OBAtom *nbr;

        unsigned int bondCount = 0;
        for (nbr = atom->BeginNbrAtom(b);nbr;nbr = atom->NextNbrAtom(b)) {
          if (avisit[nbr->GetIdx()])
            bondCount++;
        }
        if (bondCount < 2) {
          //          cout << "rejected cycle" << endl;
          continue; // this atom isn't a root for the cycle
        }

        //        cout << " depth: " << depth << endl;
        //store the atoms of the cycle(s)
        unsigned int j;
        //        cout << " cycle: " << NumAtoms() << " ";
        for(j=1; j<= NumAtoms(); ++j) {
          if ( avisit[j] ) {
            //            cout << "\t" << j;
            atom = GetAtom(j);
            cycle.push_back(atom);
          }
        }
        //        cout << endl;

        // This isn't a real aromatic cycle -- give up
        // Fixes PR#1965566
        // Fixes PR#1784204
        if (cycle.size() < 3)
          continue;

        // At the beginning each atom give one electron to the cycle
        for(j=0; j< cycle.size(); ++j) {
          electron.push_back(1);
        }

        // remove one electron if the atom make a double bond out of the cycle
        sume =0;
        for(j=0; j< cycle.size(); ++j) {
          atom = cycle[j];
          for(bond = atom->BeginBond(bi); bond; bond = atom->NextBond(bi)) {
            if ( bond->IsDouble() ) {
              OBAtom *atom2 = bond->GetNbrAtom(atom);
              int fcharge = atom->GetFormalCharge();
              int fcharge2 = atom2->GetFormalCharge();
              if(atom->IsNitrogen() && atom2->IsOxygen() 
                 && fcharge == 0 && fcharge2 == 0) { //n=O to [n+][O-]
                atom->SetFormalCharge(1);
                atom2->SetFormalCharge(-1);
                bond->SetKSingle();
                bond->SetBO(1);
              }
              else {
                electron[j] = 0;
              }
            }
          }
          // count the number of electrons
          sume += electron[j];
        }

        // Save the electron state in case huckel rule is not satisfied
        vector<int> previousElectron = electron;

        // find the ideal number of electrons according to the huckel 4n+2 rule
        minde=99;
        for (i=1; 1; ++i) {
          n = 4 *i +2;
          de = n - sume;
          if (  de < minde )
            minde=de;
          else if ( minde < 0 )
            minde=de;
          else
            break;
        }

        stringstream errorMsg;

        //        cout << "minde before:" << minde << endl;
        // if huckel rule not satisfied some atoms must give more electrons
        while ( minde != 0 ) {
          bestorden=99;
          for(j=0; j< cycle.size(); ++j) {
            if (electron[j] == 1) {
              orden = getorden(cycle[j]);
              if (orden < bestorden) {
                bestorden = orden;
                bestatom = j;
              }
            }
          }
          if (bestorden==99) {  // no electron giving atom found
            errorMsg << "Kekulize: Huckel rule not satisfied for molecule " << GetTitle() << endl;
            obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
            break;             // Huckel rule cannot be satisfied
          }                    // try to kekulize anyway
          else {
            electron[bestatom] += 1;
            minde--;
          }
        }

        if (bestorden == 99) { // Huckel rule not satisfied, just try to get an even number of electron before kekulizing

          electron = previousElectron; // restore electon's state

          int odd = sume % 2; 
          //cout << "odd:" << odd << endl;
          if(odd) { // odd number of electrons try to add an electron to the best possible atom
            for(j=0; j< cycle.size(); ++j) {
              if (electron[j] == 1) {
                orden = getorden(cycle[j]);
                if (orden < bestorden) {
                  bestorden = orden;
                  bestatom = j;
                }
              }
            }
            if (bestorden==99) {  // no electron giving atom found
              errorMsg << "Kekulize: Cannot get an even number of electron for molecule " << GetTitle() << "\n";
              obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
              break;             // impossible to choose an atom to obtain an even number of electron
            }                    // try to kekulize anyway
            else {
              electron[bestatom] += 1;
            }
          }
        }

        /*
          cout << "minde after:" << minde <<endl;
          cout << "atom: ";
          for(j=0; j < cycle.size(); ++j) {
          OBAtom *cycleAtom = cycle[j];
          cout << "\t" << cycleAtom->GetIdx();
          }
          cout << endl;

          cout << "atom: ";
          for(j=0; j < electron.size(); ++j) {
          cout << "\t" << electron[j];
          }
          cout << endl;
        */

        // kekulize the cycle(s)
        start_kekulize(cycle,electron);

        // Set the kekulized cycle(s) as visited
        for(j=1; j<= NumAtoms(); ++j) {
          if (avisit[j])
            cvisit.SetBitOn(j);
        }

      }
    }
    // Double bond have been assigned, set the remaining aromatic bonds to single
    //std::cout << "Set not assigned single bonds\n"; 
    FOR_BONDS_OF_MOL(b, *this)
      {
        //std::cout << "bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " ";   
        if (b->GetBO()==5 ) {
          b->SetKSingle();
          b->SetBO(1);
          //std::cout << "single\n";
        }
        //else
        //  std::cout << "double\n";
      }

    return;
  }

  ///////////////////////////////////////////////////////////////////////////////////////
  //! \brief Find a consistent assignment of single/double bonds to a
  //! Kekule' ring or a set of fused aromatic rings.
  //!
  //! The initial electronic state indicates whether each atom can make a
  //! double bond or not.  The function works recursively to "walk" around
  //! the ring or rings and try all possible arrangements of single and
  //! double bonds.

  void OBMol::start_kekulize( std::vector <OBAtom*> &cycle, std::vector<int> &electron) {

    std::vector<int> initAtomState;
    std::vector<int> atomState;
    std::vector<int> initBondState;
    std::vector<int> bondState;
    int Idx;
    OBAtom *atom, *atom2;
    OBBond *bond;

    // Initialize the atom and arrays
    initAtomState.resize(NumAtoms()+1);
    atomState.resize(NumAtoms()+1);
    for (int i = 0; i < NumAtoms()+1; ++i) {
      initAtomState[i] = NOT_IN_RINGS;
      atomState[i]     = NOT_IN_RINGS;
    }

    // Initialize the bond arrays with single bonds
    initBondState.resize(NumBonds());
    bondState.resize(NumBonds());
    for (int i = 0; i < NumBonds(); ++i) {
      initBondState[i] = SINGLE;
      bondState[i] = SINGLE;
    }

    // Figure out which atoms are in this ring system and whether or not each
    // atom can donate an electron.

    for (int i = 0; i < cycle.size(); ++i) {
      atom = cycle[i];
      Idx =  atom->GetIdx();
      if (electron[i] == 1) {
        initAtomState[Idx] = DOUBLE_ALLOWED;	// It has an electron it can donate
      } else {
        initAtomState[Idx] = DOUBLE_PROHIBITED;	// No electrons to contribute to aromatic system
      }
      atomState[Idx] = initAtomState[Idx];	// initialize atoms' current state too
    }

    // Do a recursive walk around the aromatic system, and see if we can find
    // an assignment of double/single bonds that works.
    atom = cycle[0];
    if (!expandkekulize(this, 0, atomState, bondState) ) {
      stringstream errorMsg;
      errorMsg << "Kekulize Error for molecule " << GetTitle() << endl;
      obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obInfo);
      return;
    }

    // We found a successful assignment, now actually change the bonds to double

    if (DEBUG) {std::cout << "Set double bonds\n";}
    for (int i = 0; i < NumBonds(); ++i) {
      bond = GetBond(i);    
      if (DEBUG) { std::cout << "  bond " << bond->GetBeginAtomIdx() << " " << bond->GetEndAtomIdx() << " ";}
      if (bond->GetBO()==5 && bondState[i] == DOUBLE) {
        if (   bond->GetBeginAtom()->IsSulfur()
               && bond->GetEndAtom()->IsSulfur()) {
          // no double bonds between aromatic sulfur atoms -- PR#1504089
          continue;
        }

        bond->SetKDouble();
        bond->SetBO(2);
        if (DEBUG) {std::cout << "double\n";}
      }
      else {
        if (DEBUG) {std::cout << "single\n";}
      }
    }

    return;
  }


  /////////////////////////////////////////////////////////////////////////////////////////
  //! \brief Recursively assign single and double bonds according to the electronical state
  //! of the atoms.
  //
  // This can be thought of as a large boolean equation, with each bond of
  // the molecule a "boolean variable".  The bond can be double or single,
  // sort of like true/false, and the "boolean equation" is whether the
  // particular combination of single/double values results in a correct
  // electronic configuration.  This algorithm is pretty much a brute-force
  // test of every combination of single/double that is electronically
  // reasonable.
  //
  // The recursion is called with bond N.  It tries to make bond N double,
  // if that works, it recurses to bond N+1, and if that works, we're done.
  // Otherwise, it reverts to a single bond at N, and recurses to bond N+1.
  // If that works, we return success, if it fails, return failure.
  //
  // This recursive algorithm guarantees that if it succeeds (finds bond
  // assignments and returns true), then atomState[] will have the double
  // bonds marked, but if it fails, (returns false), then the atomState[]
  // and bondState[] will be unaltered.
  //
  // Note that the time to run this test grows as O(2^N), where N is the
  // number of double bonds that are needed to make the Kekule bonds.  It
  // will be very slow for large systems such as fullerenes.  The way to
  // make it more efficient would be to include a symmetry analysis and
  // divide the bonds into symmetrically-equivalent classes, and only try
  // combinations of single/double bonds that differ when symmetry is taken
  // into account.

  bool expandkekulize(OBMol *mol, int bond_idx,
                       std::vector<int> &atomState,
                       std::vector<int> &bondState)
  {
    // If all bonds are assigned, check that this is a sensible combination.
    // This is the "end of the line" for the recursion: Did this bond assignment
    // work or not?
    if (bond_idx >= bondState.size())
      return has_no_leftover_electrons(mol, atomState);

    // Get the bond and its atoms
    OBBond *bond = mol->GetBond(bond_idx);
    OBAtom *atom1 = bond->GetBeginAtom();
    OBAtom *atom2 = bond->GetEndAtom();
    int idx1 = atom1->GetIdx();
    int idx2 = atom2->GetIdx();

    // If this bond isn't part of the aromatic system, move on to the next bond.
    if (atomState[idx1] == NOT_IN_RINGS || atomState[idx2] == NOT_IN_RINGS)
      return expandkekulize(mol, bond_idx + 1, atomState, bondState);

    // Remember the current state so that we can backtrack if the attempt fails
    vector<int> previousState         = atomState;	// Backup the atom states
    vector<int> previousBondState     = bondState;	// ... and the bond states

    // Is a double bond allowed here?  Both atoms have to have an extra electron,
    // and not have been assigned a double bond from a previous step in recursion.

    if (atomState[idx1] == DOUBLE_ALLOWED && atomState[idx2] == DOUBLE_ALLOWED) {

      // Assign a double bond.
      atomState[idx1]  = DOUBLE_ASSIGNED;
      atomState[idx2]  = DOUBLE_ASSIGNED;
      bondState[bond_idx] = DOUBLE;        // set bond to double
      if (DEBUG) {std::cout << "bond " << bond_idx << " double\n";}

      // Recursively try the next bond
      if (expandkekulize(mol, bond_idx + 1, atomState, bondState))
        return true;

      // If the double bond didn't work, roll back the changes and try a single bond.
      atomState = previousState;
      bondState = previousBondState;
      if (DEBUG) {cout << "  double on bond " << bond_idx << " failed." << endl;}
    }

    // Double bond not allowed here, or double bond failed, just recurse with a single bond.
    if (DEBUG) {cout << "bond " << bond_idx << " single" << endl;}
    if (expandkekulize(mol, bond_idx + 1, atomState, bondState))
      return true;

    // If it didn't work, roll back the changes we made and return failure.
    if (DEBUG) {cout << "bond " << bond_idx << " single failed, rolling back changes" << endl;}
    atomState = previousState;
    bondState = previousBondState;
    return false;
  }

  // Check for leftover electrons.  This is used during expandkekulize() above
  // to make sure all of the 4n+2 electrons that were available for bonding in the
  // aromatic ring system were actually used during the assignment of single
  // and double bonds.
  bool has_no_leftover_electrons(OBMol *mol, std::vector<int> &atomState)
  {
    FOR_ATOMS_OF_MOL(a, mol) {
      int idx = a->GetIdx();
      if (atomState[idx] == DOUBLE_ALLOWED) {
        if (DEBUG) {cout << "  failure, extra electron on atom " << a->GetIdx() << endl;}
        return false;
      }
    }
    return true;	// no extra electrons found
  }

  int OBMol::expand_kekulize(OBAtom *atom1, OBAtom *atom2, std::vector<int> &currentState,
                             std::vector<int> &initState, std::vector<int> &bcurrentState,
                             std::vector<int> &binitState, std::vector<bool> &mark)
  {
    return 0; // deprecated over expandkekulize above
  }

  //! \brief Give the priority to give two electrons instead of 1
  //!
  //! Higher numbers will have the precedence to give two electrons (and get a double bond)
  //! instead of one
  int OBMol::getorden( OBAtom *atom) 
  {
    if ( atom->IsSulfur() && atom->GetFormalCharge() == 0) return 0;
    if ( atom->IsOxygen() ) return 2;
    if ( atom->GetAtomicNum() == 34 || atom->GetAtomicNum() == 52 ) return 3;
    if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->GetValence() == 3) return 4;
    if ( atom->IsAmideNitrogen() ) return 5;
    if ( atom->IsNitrogen() && atom->GetFormalCharge() == -1) return 6;
    if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 && atom->IsInRingSize(5) ) return 7;
    if ( atom->IsNitrogen() && atom->GetFormalCharge() == 0 ) return 8;
    if ( atom->IsCarbon() && atom->GetFormalCharge() == -1) return 9;
    //if ( atom->IsCarbon() ) return 9;

    return (100); //no atom found
  }

  //! Recursively find the aromatic atoms with an aromatic bond to the current atom
  bool OBMol::expandcycle (OBAtom *atom, OBBitVec &avisit, OBAtom *, int)
  {
    OBAtom *nbr;
    //  OBBond *bond;
    std::vector<OBBond*>::iterator i;
    int natom;
    //for each neighbour atom test if it is in the aromatic ring
    for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
      {
        natom = nbr->GetIdx();
        // if (!avisit[natom] && nbr->IsAromatic() && ((OBBond*) *i)->IsAromatic()) {
        if (!avisit[natom] && ((OBBond*) *i)->GetBO()==5 
            && ((OBBond*) *i)->IsInRing()) {
          avisit.SetBitOn(natom);
          expandcycle(nbr, avisit);
        }
      }

    return true;
  }

  // Keep track of which rings contain *all* atoms in the cycle
  // This method essentially does a modified depth-first search to find
  //  large aromatic cycles
  //! Recursively find the aromatic atoms with an aromatic bond to the current atom
  int expand_cycle (OBMol *mol, OBAtom *atom, OBBitVec &avisit, OBBitVec &cvisit, 
                    int rootIdx, int prevAtomIdx, int depth)
  {
    // early termination
    if (depth < 0)
      return depth;

    //    cout << " expand_cycle: " << atom->GetIdx() << " depth " << depth << endl;

    OBAtom *nbr;
    std::vector<OBBond*>::iterator i;
    int natom;

    // OK, here's the plan:
    // - If a neighboring atom is non-aromatic, we ignore it
    // - If the atom is in cvisit, it's already be assigned. Ignore it.
    // - If the atom is the previous step in the path, ignore it.
    // Otherwise recurse: look for a large cycle back to the root
    int trialScore, bestScore = 1000;
    OBBitVec trialMatch, bestMatch; // the best path we've found so far
    for (nbr = atom->BeginNbrAtom(i);nbr;nbr = atom->NextNbrAtom(i))
      {
        natom = nbr->GetIdx();
        //        cout << " checking: " << natom << " bo: " << (*i)->GetBO() << endl;
        if ((*i)->GetBO() != 5)
          continue; // this is a non-aromatic bond, skip it
        if (natom == prevAtomIdx) {
          // the previous step in our path
          continue;
        }

        if (avisit[natom] && natom != rootIdx) {
          continue; // skip this path, we should try to get to the root again
        }

        if (natom == rootIdx) {
          bestMatch = avisit;
          bestMatch.SetBitOn(natom);
          bestScore = depth;
          continue; // don't recurse further
        }

        trialMatch = avisit;
        trialMatch.SetBitOn(natom);
        trialScore = expand_cycle(mol, nbr, trialMatch, cvisit, rootIdx, atom->GetIdx(), depth - 1);
        if (trialScore > 0 && trialScore < bestScore) { // we found a larger, valid cycle
          //          cout << " score: " << trialScore << endl;
          bestMatch = trialMatch;
          bestScore = trialScore;
        }
      } // check all neighbors

    if (bestScore <= 0 || bestScore == 1000)
      return -1; // e.g., we have no valid choices

    avisit = bestMatch; // remember our path
    return bestScore;
  }

} // end namespace OpenBabel

//! \file kekulize.cpp
//! \brief Alternate algorithm to kekulize a molecule (OBMol::NewPerceiveKekuleBonds()).