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1 : : /*
2 : : * International Chemical Identifier (InChI)
3 : : * Version 1
4 : : * Software version 1.07
5 : : * April 30, 2024
6 : : *
7 : : * MIT License
8 : : *
9 : : * Copyright (c) 2024 IUPAC and InChI Trust
10 : : *
11 : : * Permission is hereby granted, free of charge, to any person obtaining a copy
12 : : * of this software and associated documentation files (the "Software"), to deal
13 : : * in the Software without restriction, including without limitation the rights
14 : : * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
15 : : * copies of the Software, and to permit persons to whom the Software is
16 : : * furnished to do so, subject to the following conditions:
17 : : *
18 : : * The above copyright notice and this permission notice shall be included in all
19 : : * copies or substantial portions of the Software.
20 : : *
21 : : * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
22 : : * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
23 : : * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
24 : : * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
25 : : * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
26 : : * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
27 : : * SOFTWARE.
28 : : *
29 : : * The InChI library and programs are free software developed under the
30 : : * auspices of the International Union of Pure and Applied Chemistry (IUPAC).
31 : : * Originally developed at NIST.
32 : : * Modifications and additions by IUPAC and the InChI Trust.
33 : : * Some portions of code were developed/changed by external contributors
34 : : * (either contractor or volunteer) which are listed in the file
35 : : * 'External-contributors' included in this distribution.
36 : : *
37 : : * info@inchi-trust.org
38 : : *
39 : : */
40 : :
41 : : #include <string.h>
42 : :
43 : : /*#define CHECK_WIN32_VC_HEAP*/
44 : : #include "mode.h"
45 : : #include "ichicant.h"
46 : : #include "ichitime.h"
47 : : #include "ichirvrs.h"
48 : :
49 : : #include "bcf_s.h"
50 : :
51 : : #if ( READ_INCHI_STRING == 1 )
52 : :
53 : : #define INC_ADD_EDGE 64
54 : :
55 : : /* local types */
56 : :
57 : : /* types for TgDiffHChgFH */
58 : : #define fNumRPosChgH 0 /* number of positive charges on endpoints that have H in at2[] */
59 : : #define fNumRPosChgU 1 /* number of positive charges on endpoints that have no H in at2[] */
60 : : #define fNumRNegChgO 2 /* number of negative charges on O endpoints */
61 : : #define fNumRNegChgN 3 /* number of negative charges on N endpoints */
62 : : #define fNumRNeutrlH 4 /* number of neutral endp that have H in at2[] */
63 : :
64 : : #define fNumNPosChgH 5 /* number of positive charges on endpoints that have H in atf[] */
65 : : #define fNumNPosChgU 6 /* number of positive charges on endpoints that have no H in atf[] */
66 : : #define fNumNNegChgO 7 /* number of negative charges on O endpoints */
67 : : #define fNumNNegChgN 8 /* number of negative charges on N endpoints */
68 : : #define fNumNNeutrlH 9 /* number of neutral endp that have H in atf[] */
69 : :
70 : : #define fNumAllChgT 10 /* total number of fNum... */
71 : :
72 : : typedef struct tagTgDiffHChgFH {
73 : : short itg; /* t-group index; endpoint = itg+1 */
74 : : short nNumHInchi; /* number of H in t-group from orig. InChI */
75 : : short nNumHRevrs; /* number of H in at2[] */
76 : : short nNumHNorml; /* number of H in Normalized atfMobile_H_Revrs[] */
77 : : short nNumMInchi; /* number of (-) in InChI */
78 : : short nNumMRevrs; /* number of (-) in at2[] */
79 : : short nNumMNorml; /* number of (-) in atf[] */
80 : : short nNumPRevrs; /* number of (+) in at2[] */
81 : : short nNumPNorml; /* number of (+) in Normalized atfMobile_H_Revrs[] */
82 : : short n[fNumAllChgT]; /* all numbers */
83 : : short i[fNumAllChgT]; /* all indices */
84 : : } TgDiffHChgFH;
85 : :
86 : : /* local prototypes */
87 : : static int FillTgDiffHChgFH( TgDiffHChgFH tdhc[], int max_tdhc, inp_ATOM at2[], inp_ATOM atf[],
88 : : AT_NUMB *nCanon2AtnoRevrs, VAL_AT *pVA, T_GROUP_INFO *ti, EDGE_LIST *pAtomIndList );
89 : :
90 : :
91 : : /****************************************************************************/
92 : 0 : int bHas_N_V( inp_ATOM *at2, int num_atoms )
93 : : {
94 : 0 : int i, num_found = 0;
95 [ # # ]: 0 : for (i = 0; i < num_atoms; i++)
96 : : {
97 [ # # ]: 0 : if (at2[i].el_number == EL_NUMBER_N &&
98 [ # # ]: 0 : !at2[i].charge &&
99 [ # # ]: 0 : !at2[i].num_H &&
100 [ # # ]: 0 : !at2[i].radical &&
101 [ # # ]: 0 : at2[i].chem_bonds_valence == 5 &&
102 [ # # ]: 0 : ( at2[i].valence == 3 ))
103 : : {
104 : 0 : num_found++;
105 : : }
106 : : }
107 : :
108 : 0 : return num_found;
109 : : }
110 : :
111 : :
112 : : /****************************************************************************/
113 : 0 : int FillTgDiffHChgFH( TgDiffHChgFH tdhc[],
114 : : int max_tdhc,
115 : : inp_ATOM at2[],
116 : : inp_ATOM atf[],
117 : : AT_NUMB *nCanon2AtnoRevrs,
118 : : VAL_AT *pVA,
119 : : T_GROUP_INFO *ti,
120 : : EDGE_LIST *pAtomIndList )
121 : : {
122 : :
123 : : int i, j, iat, itg, num, itg_out; /* djb-rwth: removing redundant variables */
124 : : EDGE_LIST IndList; /* type, itg */
125 : : TgDiffHChgFH cur_tdhc;
126 : : AT_NUMB *pEndp0;
127 : : inp_ATOM *at2i, *atfi;
128 : 0 : int typeR, typeN, type, ret = 0, nCurIndListLen;
129 : :
130 : 0 : AllocEdgeList( &IndList, EDGE_LIST_CLEAR );
131 : 0 : pAtomIndList->num_edges = 0;
132 : 0 : itg_out = 0;
133 : : /* djb-rwth: removing redundant code */
134 : 0 : memset( tdhc, 0, max_tdhc ); /* djb-rwth: memset_s C11/Annex K variant? */
135 : :
136 [ # # ]: 0 : for (itg = 0; itg < ti->num_t_groups; itg++)
137 : : {
138 : 0 : memset( &cur_tdhc, 0, sizeof( cur_tdhc ) ); /* djb-rwth: memset_s C11/Annex K variant? */
139 : :
140 : 0 : cur_tdhc.itg = itg;
141 : 0 : cur_tdhc.nNumHInchi = ti->t_group[itg].num[0] - ti->t_group[itg].num[1];
142 : 0 : cur_tdhc.nNumMInchi = ti->t_group[itg].num[1];
143 : :
144 : 0 : pEndp0 = ti->nEndpointAtomNumber + ti->t_group[itg].nFirstEndpointAtNoPos;
145 : 0 : nCurIndListLen = IndList.num_edges;
146 [ # # ]: 0 : for (j = 0; j < ti->t_group[itg].nNumEndpoints; j++)
147 : : {
148 : 0 : i = pEndp0[j];
149 : 0 : iat = nCanon2AtnoRevrs[i];
150 : :
151 : 0 : at2i = at2 + iat;
152 : 0 : atfi = atf + iat;
153 : :
154 : 0 : typeR = typeN = -1;
155 [ # # ]: 0 : if (at2i->charge == 1)
156 : : {
157 [ # # ]: 0 : if (at2i->num_H)
158 : : {
159 : 0 : typeR = fNumRPosChgH;
160 : : }
161 : : else
162 : : {
163 : 0 : typeR = fNumRPosChgU;
164 : : }
165 : 0 : cur_tdhc.nNumPRevrs++;
166 : : }
167 : : else
168 : : {
169 [ # # ]: 0 : if (at2i->charge == -1)
170 : : {
171 [ # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 6)
172 : : {
173 : 0 : typeR = fNumRNegChgO;
174 : : }
175 : : else
176 : : {
177 [ # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 5)
178 : : {
179 : 0 : typeR = fNumRNegChgN;
180 : : }
181 : : }
182 : 0 : cur_tdhc.nNumMRevrs++;
183 : : }
184 : : else
185 : : {
186 [ # # # # ]: 0 : if (at2i->num_H && at2i->valence == at2i->chem_bonds_valence)
187 : : {
188 : 0 : typeR = fNumRNeutrlH;
189 : : }
190 : : }
191 : : }
192 : 0 : cur_tdhc.nNumHRevrs += at2i->num_H;
193 : :
194 [ # # ]: 0 : if (atfi->charge == 1)
195 : : {
196 [ # # ]: 0 : if (atfi->num_H)
197 : : {
198 : 0 : typeN = fNumNPosChgH;
199 : : }
200 : : else
201 : : {
202 : 0 : typeN = fNumNPosChgU;
203 : : }
204 : 0 : cur_tdhc.nNumPNorml++;
205 : : }
206 : : else
207 : : {
208 [ # # ]: 0 : if (atfi->charge == -1)
209 : : {
210 [ # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 6)
211 : : {
212 : 0 : typeN = fNumNNegChgO;
213 : : }
214 : : else
215 [ # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 5)
216 : : {
217 : 0 : typeN = fNumNNegChgN;
218 : : }
219 : 0 : cur_tdhc.nNumMNorml++;
220 : : }
221 : : else
222 : : {
223 [ # # # # ]: 0 : if (atfi->num_H && atfi->valence == atfi->chem_bonds_valence)
224 : : {
225 : 0 : typeN = fNumNNeutrlH;
226 : : }
227 : : }
228 : : }
229 : 0 : cur_tdhc.nNumHNorml += atfi->num_H;
230 [ # # # # ]: 0 : if (at2[iat].charge < 0 || 0 < pVA[iat].nCPlusGroupEdge)
231 : : {
232 [ # # # # ]: 0 : if (typeR >= 0 && (
233 [ # # ]: 0 : ( ret = AddToEdgeList( &IndList, typeR, INC_ADD_EDGE ) ) ||
234 [ # # ]: 0 : ( ret = AddToEdgeList( &IndList, itg, INC_ADD_EDGE ) ) ||
235 : 0 : ( ret = AddToEdgeList( &IndList, iat, INC_ADD_EDGE ) ) ))
236 : : {
237 : 0 : goto exit_function;
238 : : }
239 [ # # # # ]: 0 : if (typeN >= 0 && (
240 [ # # ]: 0 : ( ret = AddToEdgeList( &IndList, typeN, INC_ADD_EDGE ) ) ||
241 [ # # ]: 0 : ( ret = AddToEdgeList( &IndList, itg, INC_ADD_EDGE ) ) ||
242 : 0 : ( ret = AddToEdgeList( &IndList, iat, INC_ADD_EDGE ) ) ))
243 : : {
244 : 0 : goto exit_function;
245 : : }
246 : : }
247 : : }
248 [ # # ]: 0 : if (cur_tdhc.nNumHNorml == cur_tdhc.nNumHInchi &&
249 [ # # ]: 0 : cur_tdhc.nNumMNorml == cur_tdhc.nNumMInchi)
250 : : {
251 : 0 : IndList.num_edges = nCurIndListLen; /* t-group seems to be correct */
252 : 0 : continue;
253 : : }
254 [ # # ]: 0 : if (itg_out < max_tdhc)
255 : : {
256 : 0 : tdhc[itg_out++] = cur_tdhc;
257 : : }
258 : : else
259 : : {
260 : : /* djb-rwth: removing redundant code */
261 : 0 : IndList.num_edges = nCurIndListLen;
262 : 0 : break;
263 : : }
264 : : }
265 : :
266 : : /* fill out atom index list */
267 [ # # ]: 0 : if (itg_out)
268 : : {
269 : 0 : itg_out--; /* djb-rwth: fixing undefined index value / buffer overflow */
270 : : /* djb-rwth: removing redundant code */
271 [ # # ]: 0 : for (type = 0; type < fNumAllChgT; type++)
272 : : {
273 : 0 : j = 0;
274 [ # # ]: 0 : for (i = 0; i < itg_out; i++)
275 : : {
276 : 0 : num = 0;
277 : 0 : itg = tdhc[i].itg;
278 : 0 : tdhc[i].i[type] = -999; /* empty */
279 [ # # ]: 0 : while (IndList.pnEdges[j + 1] == itg)
280 : : {
281 [ # # ]: 0 : if (IndList.pnEdges[j] == type)
282 : : {
283 [ # # ]: 0 : if (!num++)
284 : : {
285 : 0 : tdhc[i].i[type] = pAtomIndList->num_edges;
286 : : }
287 [ # # ]: 0 : if ((ret = AddToEdgeList( pAtomIndList, IndList.pnEdges[j + 2], INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
288 : : {
289 : 0 : goto exit_function;
290 : : }
291 : : }
292 : 0 : j += 3;
293 : : }
294 : 0 : tdhc[i].n[type] = num;
295 : : }
296 : : }
297 : : }
298 : 0 : ret = itg_out;
299 : :
300 : 0 : exit_function:
301 : :
302 : 0 : AllocEdgeList( &IndList, EDGE_LIST_FREE );
303 : :
304 : 0 : return ret;
305 : : /*
306 : : #undef fNumRPosChgH
307 : : #undef fNumRPosChgU
308 : : #undef fNumRNegChgO
309 : : #undef fNumRNegChgN
310 : :
311 : : #undef fNumNPosChgH
312 : : #undef fNumNPosChgU
313 : : #undef fNumNNegChgO
314 : : #undef fNumNNegChgN
315 : :
316 : : #undef fNumAllChgT
317 : : */
318 : : }
319 : :
320 : :
321 : : /****************************************************************************/
322 : : /* djb-rwth: placed as global variables to avoid function buffer issues */
323 : : short iat_DB_O[MAX_DIFF_FIXH], iat_SB_O_Minus[MAX_DIFF_FIXH];
324 : : short iat_DB_O_Plus[MAX_DIFF_FIXH], iat_SB_NH[MAX_DIFF_FIXH];
325 : : short iat_SB_N_Minus[MAX_DIFF_FIXH], iat_DB_N[MAX_DIFF_FIXH];
326 : : short iat_SB_Neutr[MAX_DIFF_FIXH], iat_DB_Charged[MAX_DIFF_FIXH];
327 : : short iat_DB_NHn_Plus[MAX_DIFF_FIXH], iat_SB_NHm_Neutr[MAX_DIFF_FIXH];
328 : : short iat_DB_O_Neutr[MAX_DIFF_FIXH], iat_DB_N_Neutr[MAX_DIFF_FIXH];
329 : : short iat_SB_N_Neutr[MAX_DIFF_FIXH], iat_N_V_Array[MAX_DIFF_FIXH];
330 : : short iat_Central[MAX_DIFF_FIXH], iat_NO2[MAX_DIFF_FIXH];
331 : : TgDiffHChgFH tdhc[MAX_DIFF_FIXH];
332 : :
333 : 0 : int FixFixedHRestoredStructure( CANON_GLOBALS *pCG,
334 : : INCHI_CLOCK *ic,
335 : : ICHICONST INPUT_PARMS *ip,
336 : : STRUCT_DATA *sd,
337 : : BN_STRUCT *pBNS,
338 : : BN_DATA *pBD,
339 : : StrFromINChI *pStruct,
340 : : inp_ATOM *at,
341 : : inp_ATOM *at2,
342 : : inp_ATOM *at3,
343 : : VAL_AT *pVA,
344 : : ALL_TC_GROUPS *pTCGroups,
345 : : T_GROUP_INFO **ppt_group_info,
346 : : inp_ATOM **ppat_norm,
347 : : inp_ATOM **ppat_prep,
348 : : INChI *pInChI[],
349 : : long num_inp,
350 : : int bHasSomeFixedH,
351 : : int *pnNumRunBNS,
352 : : int *pnTotalDelta,
353 : : int forbidden_edge_mask,
354 : : int forbidden_stereo_edge_mask )
355 : : {
356 : : /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/
357 : : /* at2 should be the most recently restored atom, Fixed-H */
358 : 0 : int i, j, k, delta, num_try, tot_succes, cur_success, ret = 0, bAllowedNFlowerEdges = 0, num_zero_ret;
359 : : CMP2FHINCHI c2i;
360 : 0 : CMP2FHINCHI *pc2i = &c2i;
361 : :
362 : : EDGE_LIST AllChargeEdges, CurrEdges, SFlowerEdges, NFlowerEdges, OtherNFlowerEdges, FixedLargeRingStereoEdges;
363 : : EDGE_LIST AllBondEdges;
364 : :
365 : : EdgeIndex e;
366 : : BNS_EDGE *pe;
367 : : Vertex v1, v2;
368 : : BNS_VERTEX *pv1, *pv2;
369 : :
370 : : Vertex vPathStart, vPathEnd;
371 : : int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;
372 : :
373 : 0 : int nNumRunBNS = 0, forbidden_edge_mask_inv = ~forbidden_edge_mask; /* djb-rwth: ignoring LLVM warning: variable used */
374 : :
375 : : INCHI_HEAPCHK
376 : :
377 : 0 : AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR );
378 : 0 : AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR );
379 : 0 : AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR );
380 : 0 : AllocEdgeList( &SFlowerEdges, EDGE_LIST_CLEAR );
381 : 0 : AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR );
382 : 0 : AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR );
383 : 0 : AllocEdgeList( &AllBondEdges, EDGE_LIST_CLEAR );
384 : :
385 : 0 : tot_succes = 0;
386 : :
387 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
388 : : {
389 : 0 : goto exit_function; /* no fixed-H found */
390 : : }
391 : :
392 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
393 : : {
394 [ # # # # : 0 : if (( e = pVA[i].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden &&
# # ]
395 : 0 : ( ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ) ))
396 : : {
397 : 0 : goto exit_function;
398 : : }
399 [ # # # # ]: 0 : if (( e = pVA[i].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden)
400 : : {
401 [ # # ]: 0 : if ((ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
402 : : {
403 : 0 : goto exit_function;
404 : : }
405 : :
406 : : /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */
407 [ # # # # : 0 : if (pVA[i].cNumValenceElectrons == 5 && !pVA[i].cMetal && /* N, P, As */
# # ]
408 : 0 : NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ))
409 : : {
410 : :
411 [ # # ]: 0 : if (pBNS->edge[j].forbidden)
412 : : {
413 : 0 : continue;
414 : : }
415 : :
416 [ # # ]: 0 : if (pBNS->edge[j].flow)
417 : : {
418 [ # # ]: 0 : if ((ret = AddToEdgeList( &AllChargeEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
419 : : {
420 : 0 : goto exit_function;
421 : : }
422 [ # # ]: 0 : if ((ret = AddToEdgeList( &NFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
423 : : {
424 : 0 : goto exit_function;
425 : : }
426 : : }
427 : : else
428 : : {
429 [ # # ]: 0 : if ((ret = AddToEdgeList( &OtherNFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
430 : : {
431 : 0 : goto exit_function;
432 : : }
433 : : }
434 : : }
435 : : else
436 : : {
437 : : /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */
438 [ # # # # : 0 : if (pVA[i].cNumValenceElectrons == 6 && !pVA[i].cMetal && /* N, P, As */
# # ]
439 : 0 : NO_VERTEX != ( j = GetChargeFlowerUpperEdge( pBNS, pVA, e ) ))
440 : : {
441 : :
442 [ # # ]: 0 : if (pBNS->edge[j].forbidden)
443 : : {
444 : 0 : continue;
445 : : }
446 : :
447 [ # # ]: 0 : if (pBNS->edge[j].flow)
448 : : {
449 [ # # ]: 0 : if ((ret = AddToEdgeList( &SFlowerEdges, j, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
450 : : {
451 : 0 : goto exit_function;
452 : : }
453 : : }
454 : : }
455 : : }
456 : : }
457 [ # # ]: 0 : for (j = 0; j < at2[i].valence; j++)
458 : : {
459 : 0 : k = at2[i].neighbor[j];
460 [ # # # # ]: 0 : if (k < i && !pBNS->edge[e = pBNS->vert[i].iedge[j]].forbidden)
461 : : {
462 [ # # ]: 0 : if ((ret = AddToEdgeList( &AllBondEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
463 : : {
464 : 0 : goto exit_function;
465 : : }
466 : : }
467 : : }
468 : : }
469 [ # # ]: 0 : if (forbidden_stereo_edge_mask)
470 : : {
471 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
472 : : {
473 [ # # ]: 0 : for (j = 0; j < at2[i].valence; j++)
474 : : {
475 [ # # ]: 0 : if (pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask)
476 : : {
477 : 0 : int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q,
478 : 0 : pStruct->pbfsq->nAtomLevel,
479 : 0 : pStruct->pbfsq->cSource, 99 /* max ring size */ );
480 [ # # # # ]: 0 : if (0 < nMinRingSize && ( ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, INC_ADD_EDGE ) ))
481 : : {
482 : 0 : goto exit_function;
483 : : }
484 : : }
485 : : }
486 : : }
487 : : }
488 : :
489 : : INCHI_HEAPCHK
490 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
491 : : {
492 : 0 : goto exit_function;
493 : : }
494 : : INCHI_HEAPCHK
495 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
496 : : {
497 : 0 : goto exit_function;
498 : : }
499 : :
500 : : INCHI_HEAPCHK
501 : :
502 [ # # ]: 0 : if (!pc2i->bHasDifference ||
503 [ # # # # ]: 0 : (!pc2i->len_c2at && pc2i->nNumTgRevrs == pc2i->nNumTgInChI &&
504 [ # # ]: 0 : pc2i->nNumEndpRevrs == pc2i->nNumRemHInChI &&
505 [ # # ]: 0 : pc2i->nNumEndpRevrs == pc2i->nNumEndpInChI &&
506 [ # # # # ]: 0 : !pc2i->nNumTgDiffMinus && !pc2i->nNumTgDiffH)) /* djb-rwth: addressing LLVM warning */
507 : : {
508 : 0 : goto exit_function; /* nothing to do */
509 : : }
510 : :
511 : : /*goto exit_function;*/ /* debug only*/
512 : :
513 [ # # ]: 0 : if (pc2i->len_c2at >= 2)
514 : : {
515 : : /*----------------------------------------------------*/
516 : : /* case 01: restored: O=AB-O(-) original: (-)O-AB=O */
517 : : /* FixH: 0 -1 -1 0 */
518 : : /* MobH: 0 1 1 0 */
519 : : /* non-taut non-taut */
520 : : /* O = O, S, Se; charged atoms O are not tautomeric */
521 : : /* Solution: move (-) from B-O(-) to O=A */
522 : : /*----------------------------------------------------*/
523 : 0 : int num_DB_O = 0, num_SB_O_Minus = 0, iat;
524 : 0 : cur_success = 0;
525 : :
526 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
527 : : {
528 : 0 : iat = pc2i->c2at[i].atomNumber;
529 [ # # ]: 0 : if (pc2i->c2at[i].nValElectr == 6 /* && !pc2i->c2at[i].endptInChI -- mod#1*/ &&
530 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
531 : : {
532 [ # # ]: 0 : if ( /* orig. InChI info: */
533 : 0 : num_SB_O_Minus < MAX_DIFF_FIXH &&
534 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 &&
535 : : /* reversed structure info: */
536 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == -1 && pc2i->c2at[i].nMobHRevrs == 1 &&
537 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H && /* at2 is Fixed-H */
538 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1)
539 : : {
540 : 0 : iat_SB_O_Minus[num_SB_O_Minus++] = iat;
541 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
542 : : {
543 : 0 : goto exit_function;
544 : : }
545 : : }
546 : : else
547 : : {
548 [ # # ]: 0 : if ( /* orig. InChI info: */
549 : 0 : num_DB_O < MAX_DIFF_FIXH &&
550 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 &&
551 : : /* reversed structure info: */
552 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
553 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
554 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2)
555 : : {
556 : 0 : iat_DB_O[num_DB_O++] = iat;
557 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
558 : : {
559 : 0 : goto exit_function;
560 : : }
561 : : }
562 : : }
563 : : }
564 : : }
565 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */
566 : : {
567 : : /* detected; attempt to fix */
568 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
569 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
570 : 0 : delta = 1;
571 [ # # # # ]: 0 : for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++)
572 : : {
573 : 0 : iat = iat_SB_O_Minus[i];
574 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
575 [ # # ]: 0 : if (!pe->flow)
576 : 0 : continue;
577 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
578 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
579 : :
580 : 0 : pe->forbidden |= forbidden_edge_mask;
581 : 0 : pe->flow -= delta; /* remove (-) from AB-O(-) */
582 : 0 : pv1->st_edge.flow -= delta;
583 : 0 : pv2->st_edge.flow -= delta;
584 : 0 : pBNS->tot_st_flow -= 2 * delta;
585 : :
586 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
587 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
588 : :
589 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
590 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */
# # ]
591 : : {
592 : : /* Added (-)charge to O=AB => nDeltaCharge == -1 */
593 : : /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */
594 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
595 [ # # ]: 0 : if (ret > 0)
596 : : {
597 : 0 : nNumRunBNS++;
598 : 0 : cur_success++; /* 01 */
599 : : }
600 : : }
601 : : else
602 : : {
603 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
604 : 0 : pe->flow += delta;
605 : 0 : pv1->st_edge.flow += delta;
606 : 0 : pv2->st_edge.flow += delta;
607 : 0 : pBNS->tot_st_flow += 2 * delta;
608 : : }
609 : : INCHI_HEAPCHK
610 : : }
611 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
612 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
613 : : }
614 [ # # ]: 0 : if (cur_success)
615 : : {
616 : 0 : tot_succes += cur_success;
617 : : /* recalculate InChI from the structure */
618 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic,
619 : : ip, sd, pBNS, pStruct,
620 : : at, at2, at3, pVA,
621 : : pTCGroups,
622 : : ppt_group_info, ppat_norm,
623 : : ppat_prep)))
624 : : {
625 : 0 : goto exit_function;
626 : : }
627 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
628 : : {
629 : 0 : goto exit_function;
630 : : }
631 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
632 : : {
633 : 0 : goto exit_function; /* no fixed-H found */
634 : : }
635 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
636 : : {
637 : 0 : goto exit_function;
638 : : }
639 [ # # ]: 0 : if (!pc2i->bHasDifference)
640 : : {
641 : 0 : goto exit_function; /* nothing to do */
642 : : }
643 : : }
644 : : }
645 : :
646 [ # # ]: 0 : if (pc2i->len_c2at >= 1)
647 : : {
648 : : /*--------------------------------------------------------------*/
649 : : /* case 02: restored: -O(+)=AB-NH2 original: -O-AB=NH2(+) */
650 : : /* FixH: 0 0 0 1 */
651 : : /* MobH: 0 2 0 1 */
652 : : /* O = P, As, Sb, O, S, Se, F, Cl, Br, I; not taut. in InChI */
653 : : /* N = N, O, S, Se, Te; has H; tautomeric or not tautomeric */
654 : : /* Solution: move (+) from O(+) to NH2 */
655 : : /*--------------------------------------------------------------*/
656 : 0 : int num_DB_O_Plus = 0, num_SB_NH = 0, iat;
657 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
658 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
659 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : NULL;
660 : 0 : cur_success = 0;
661 : 0 : num_zero_ret = 0;
662 : :
663 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
664 : : {
665 : 0 : iat = pc2i->c2at[i].atomNumber;
666 [ # # ]: 0 : if ( /* orig. InChI info: =NH2(+), =OH(+) */
667 : 0 : num_SB_NH < MAX_DIFF_FIXH &&
668 [ # # # # ]: 0 : ((pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) ||
669 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6) /* N, O, S, Se, Te */ &&
670 : : /*!pc2i->c2at[i].endptInChI &&*/ /* <=== relaxation */
671 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
672 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI>0 /*== 1 --modification#2*/ && /*pc2i->c2at[i].nMobHInChI == 1 &&*/
673 : : /* reversed structure info: */
674 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && /* pc2i->c2at[i].nMobHRevrs == 0 &&*/
675 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H &&
676 [ # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence) /* djb-rwth: addressing LLVM warning */
677 : : {
678 : 0 : iat_SB_NH[num_SB_NH++] = iat;
679 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
680 : : {
681 : 0 : goto exit_function;
682 : : }
683 : : }
684 : : }
685 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
686 : : {
687 : : /* i = canonical number - 1 */
688 : 0 : iat = nCanon2AtnoRevrs[i];
689 [ # # ]: 0 : if ( /* in restored atom: charge=+1, no H, has double bond, P, As, O, S, Se, Te, F, Cl, Br, I */
690 : 0 : num_DB_O_Plus < MAX_DIFF_FIXH &&
691 [ # # # # ]: 0 : at2[iat].charge == 1 && !at2[iat].num_H &&
692 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
693 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cNumValenceElectrons == 7 ||
694 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber > 1)) &&
695 : : /* in orig.InChI: not an endpoint, has no H */
696 [ # # ]: 0 : !pStruct->endpoint[i] &&
697 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
698 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
699 : : /* has (+) edge */
700 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
701 : : {
702 : 0 : iat_DB_O_Plus[num_DB_O_Plus++] = iat;
703 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
704 : : {
705 : 0 : goto exit_function;
706 : : }
707 : : }
708 : : }
709 [ # # ]: 0 : if ((num_try = inchi_min(num_DB_O_Plus, num_SB_NH))) /* djb-rwth: addressing LLVM warning */
710 : : {
711 : : /* detected; attempt to fix */
712 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
713 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
714 : 0 : delta = 1;
715 : 0 : repeat_02_allow_NV:
716 [ # # # # ]: 0 : for (i = 0; i < num_SB_NH && cur_success < num_try; i++)
717 : : {
718 : 0 : iat = iat_SB_NH[i];
719 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
720 [ # # ]: 0 : if (!pe->flow)
721 : 0 : continue;
722 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
723 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
724 : :
725 : 0 : pe->forbidden |= forbidden_edge_mask;
726 : 0 : pe->flow -= delta;
727 : 0 : pv1->st_edge.flow -= delta;
728 : 0 : pv2->st_edge.flow -= delta;
729 : 0 : pBNS->tot_st_flow -= 2 * delta;
730 : :
731 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
732 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
733 : :
734 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
735 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warning */
# # ]
736 : : {
737 : : /* Removed charge from O(+) => nDeltaCharge == -1 */
738 : : /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */
739 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
740 [ # # ]: 0 : if (ret > 0)
741 : : {
742 : 0 : nNumRunBNS++;
743 : 0 : cur_success++; /* 02 */
744 : : }
745 : : }
746 : : else
747 : : {
748 : 0 : num_zero_ret += !ret;
749 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
750 : 0 : pe->flow += delta;
751 : 0 : pv1->st_edge.flow += delta;
752 : 0 : pv2->st_edge.flow += delta;
753 : 0 : pBNS->tot_st_flow += 2 * delta;
754 : : }
755 : : INCHI_HEAPCHK
756 : : }
757 [ # # # # : 0 : if (num_zero_ret == num_try && !bAllowedNFlowerEdges && NFlowerEdges.num_edges)
# # ]
758 : : {
759 : 0 : RemoveForbiddenEdgeMask(pBNS, &NFlowerEdges, forbidden_edge_mask);
760 : 0 : bAllowedNFlowerEdges = 1;
761 : 0 : goto repeat_02_allow_NV;
762 : : }
763 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
764 : : /* djb-rwth: removing redundant code */
765 : : }
766 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
767 [ # # ]: 0 : if (cur_success)
768 : : {
769 : 0 : tot_succes += cur_success;
770 : : /* recalculate InChI from the structure */
771 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
772 : : ppt_group_info, ppat_norm, ppat_prep)))
773 : : {
774 : 0 : goto exit_function;
775 : : }
776 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
777 : : {
778 : 0 : goto exit_function;
779 : : }
780 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
781 : : {
782 : 0 : goto exit_function; /* no fixed-H found */
783 : : }
784 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
785 : : {
786 : 0 : goto exit_function;
787 : : }
788 [ # # ]: 0 : if (!pc2i->bHasDifference)
789 : : {
790 : 0 : goto exit_function; /* nothing to do */
791 : : }
792 : : }
793 : : }
794 : :
795 [ # # # # ]: 0 : if (pc2i->len_c2at >= 1 && pc2i->nNumTgRevrs == 1 &&
796 [ # # # # ]: 0 : ( pc2i->nNumEndpRevrs > pc2i->nNumEndpInChI || pc2i->nNumTgInChI > 1 ) /* ADP in Revrs */)
797 : : {
798 : : /*--------------------------------------------------------------*/
799 : : /* case 03: restored: -N(-)-AB=O original: -N=AB-O(-) */
800 : : /* FixH: 0 0 0 -1 */
801 : : /* MobH: 0 0 0 1 */
802 : : /* O = O, S, Se; N = N; */
803 : : /* restored atoms are tautomeric; original atoms are not taut. */
804 : : /* restored struct has 1 t-group; original has less endpoints */
805 : : /* and possibly >1 t-groups */
806 : : /* Solution: move (-) from N(-) to =O */
807 : : /* these atoms are tautomeric in restored structure */
808 : : /*--------------------------------------------------------------*/
809 : 0 : int num_SB_N_Minus = 0, num_DB_O = 0, iat;
810 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
811 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
812 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
813 : : /*
814 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
815 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
816 : : */
817 : 0 : cur_success = 0;
818 : :
819 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
820 : : {
821 : 0 : iat = pc2i->c2at[i].atomNumber;
822 [ # # ]: 0 : if ( /* orig. InChI info: -O(-) */
823 : 0 : num_DB_O < MAX_DIFF_FIXH &&
824 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ &&
825 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
826 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
827 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 &&
828 : : /* reversed structure info: */
829 [ # # ]: 0 : pc2i->c2at[i].endptRevrs &&
830 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
831 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
832 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2)
833 : : {
834 : 0 : iat_DB_O[num_DB_O++] = iat;
835 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
836 : : {
837 : 0 : goto exit_function;
838 : : }
839 : : }
840 : : }
841 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
842 : : {
843 : : /* i = canonical number - 1 */
844 : 0 : iat = nCanon2AtnoRevrs[i];
845 [ # # ]: 0 : if ( /* in restored atom N: charge=-1, no H, has no double bond, endpoint */
846 : 0 : num_SB_N_Minus < MAX_DIFF_FIXH &&
847 [ # # ]: 0 : at2[iat].charge == -1 && /*!at2[iat].num_H &&*/
848 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
849 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
# # ]
850 [ # # ]: 0 : at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint &&
851 : : /* in orig.InChI: not an endpoint, has no H */
852 : : /* !pStruct->endpoint[i] && */
853 : : /*
854 : : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
855 : : !(nMobHInChI && nMobHInChI[i] ) &&
856 : : */
857 : : /* has (-) edge */
858 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
859 : : {
860 : 0 : iat_SB_N_Minus[num_SB_N_Minus++] = iat;
861 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
862 : : {
863 : 0 : goto exit_function;
864 : : }
865 : : }
866 : : }
867 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_N_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */
868 : : {
869 : : /* detected; attempt to fix */
870 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
871 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
872 : 0 : delta = 1;
873 [ # # # # ]: 0 : for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++)
874 : : {
875 : 0 : iat = iat_SB_N_Minus[i];
876 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1; /* 2006-03-03: changed from CPlusGroupEdge */
877 [ # # ]: 0 : if (!pe->flow)
878 : 0 : continue;
879 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
880 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
881 : :
882 : 0 : pe->forbidden |= forbidden_edge_mask;
883 : 0 : pe->flow -= delta;
884 : 0 : pv1->st_edge.flow -= delta;
885 : 0 : pv2->st_edge.flow -= delta;
886 : 0 : pBNS->tot_st_flow -= 2 * delta;
887 : :
888 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
889 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
890 : :
891 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
892 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */
# # ]
893 : : {
894 : : /* Added (-) charge to =O => nDeltaCharge == 1 */
895 : : /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */
896 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
897 [ # # ]: 0 : if (ret > 0)
898 : : {
899 : 0 : nNumRunBNS++;
900 : 0 : cur_success++; /* 03 */
901 : : }
902 : : }
903 : : else
904 : : {
905 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
906 : 0 : pe->flow += delta;
907 : 0 : pv1->st_edge.flow += delta;
908 : 0 : pv2->st_edge.flow += delta;
909 : 0 : pBNS->tot_st_flow += 2 * delta;
910 : : }
911 : : INCHI_HEAPCHK
912 : : }
913 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
914 : : }
915 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
916 [ # # ]: 0 : if (cur_success)
917 : : {
918 : 0 : tot_succes += cur_success;
919 : : /* recalculate InChI from the structure */
920 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
921 : : ppt_group_info, ppat_norm, ppat_prep)))
922 : : {
923 : 0 : goto exit_function;
924 : : }
925 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
926 : : {
927 : 0 : goto exit_function;
928 : : }
929 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
930 : : {
931 : 0 : goto exit_function; /* no fixed-H found */
932 : : }
933 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
934 : : {
935 : 0 : goto exit_function;
936 : : }
937 [ # # ]: 0 : if (!pc2i->bHasDifference)
938 : : {
939 : 0 : goto exit_function; /* nothing to do */
940 : : }
941 : : }
942 : : }
943 : :
944 [ # # ]: 0 : if (pc2i->nNumTgRevrs == 1 && /* pc2i->nNumRemHInChI < 0 &&*/
945 [ # # # # ]: 0 : ( pc2i->nNumEndpRevrs > pc2i->nNumEndpInChI || pc2i->nNumTgInChI > 1 ) /* ADP in Revrs */)
946 : : {
947 : : /*--------------------------------------------------------------*/
948 : : /* case 03a:restored: -N(-)-AB=O original: -N=AB-O(-) */
949 : : /* FixH: 0 0 0 0 */
950 : : /* MobH: 0 0 0 0 */
951 : : /* O = O, S, Se; N = N; taut */
952 : : /* restored atoms are tautomeric; original atom is; N may be. */
953 : : /* restored struct has 1 t-group; original has less endpoints */
954 : : /* and possibly >1 t-groups */
955 : : /* Solution: move (-) from N(-) to =O */
956 : : /* these atoms are tautomeric in restored structure */
957 : : /*--------------------------------------------------------------*/
958 : 0 : int num_SB_N_Minus = 0, num_DB_O = 0, iat;
959 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
960 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
961 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
962 [ # # # # ]: 0 : S_CHAR *pnMobHInChI = ( pInChI[1] && pInChI[1]->nNum_H ) ? pInChI[1]->nNum_H :
963 [ # # # # ]: 0 : ( pInChI[0] && pInChI[0]->nNum_H ) ? pInChI[0]->nNum_H : NULL;
964 : 0 : S_CHAR *pnFixHInChI = pStruct->fixed_H;
965 : :
966 : 0 : cur_success = 0;
967 : 0 : CurrEdges.num_edges = 0;
968 : :
969 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
970 : : { /* i = canonical number - 1 */
971 : 0 : iat = nCanon2AtnoRevrs[i];
972 [ # # ]: 0 : if ( /* in restored atom N: charge=-1, no H, has no double bond, endpoint */
973 : 0 : num_SB_N_Minus < MAX_DIFF_FIXH &&
974 [ # # ]: 0 : at2[iat].charge == -1 && /*!at2[iat].num_H &&*/
975 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
976 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
# # ]
977 [ # # ]: 0 : at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint &&
978 : : /* in orig.InChI: may be an endpoint, has no H */
979 : : /* has (-) edge */
980 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
981 : : {
982 : 0 : iat_SB_N_Minus[num_SB_N_Minus++] = iat;
983 : : }
984 : : else
985 [ # # ]: 0 : if (num_DB_O < MAX_DIFF_FIXH &&
986 [ # # ]: 0 : at2[iat].charge == 0 && /*!at2[iat].num_H &&*/
987 [ # # # # ]: 0 : at2[iat].valence + 1 == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
988 [ # # # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
989 [ # # ]: 0 : at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint && /* endpoint in Reconstructed */
990 [ # # # # ]: 0 : (pStruct->endpoint[i] || /* endpoint or H(+) acceptor in original */
991 [ # # # # : 0 : (pnMobHInChI && pnMobHInChI[i] == 1 && pnFixHInChI && pnFixHInChI[i] == -1)) &&
# # ]
992 : : /* has (-) edge */
993 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
994 : : {
995 : 0 : iat_DB_O[num_DB_O++] = iat;
996 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
997 : : {
998 : 0 : goto exit_function;
999 : : }
1000 : : }
1001 : : }
1002 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_N_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */
1003 : : {
1004 : : /* detected; attempt to fix */
1005 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1006 : : /* allow charge transfer to all found =O */
1007 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
1008 : 0 : delta = 1;
1009 [ # # # # ]: 0 : for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++)
1010 : : {
1011 : 0 : iat = iat_SB_N_Minus[i];
1012 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
1013 [ # # ]: 0 : if (!pe->flow)
1014 : 0 : continue;
1015 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
1016 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
1017 : :
1018 : 0 : pe->forbidden |= forbidden_edge_mask;
1019 : 0 : pe->flow -= delta;
1020 : 0 : pv1->st_edge.flow -= delta;
1021 : 0 : pv2->st_edge.flow -= delta;
1022 : 0 : pBNS->tot_st_flow -= 2 * delta;
1023 : :
1024 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1025 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
1026 : :
1027 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
1028 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */
# # ]
1029 : : {
1030 : : /* Added (-) charge to =O => nDeltaCharge == 1 */
1031 : : /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */
1032 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
1033 [ # # ]: 0 : if (ret > 0)
1034 : : {
1035 : 0 : nNumRunBNS++;
1036 : 0 : cur_success++; /* 03a */
1037 : : }
1038 : : }
1039 : : else
1040 : : {
1041 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
1042 : 0 : pe->flow += delta;
1043 : 0 : pv1->st_edge.flow += delta;
1044 : 0 : pv2->st_edge.flow += delta;
1045 : 0 : pBNS->tot_st_flow += 2 * delta;
1046 : : }
1047 : : INCHI_HEAPCHK
1048 : : }
1049 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1050 : : }
1051 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1052 [ # # ]: 0 : if (cur_success)
1053 : : {
1054 : 0 : tot_succes += cur_success;
1055 : : /* recalculate InChI from the structure */
1056 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1057 : : ppt_group_info, ppat_norm, ppat_prep)))
1058 : : {
1059 : 0 : goto exit_function;
1060 : : }
1061 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
1062 : : {
1063 : 0 : goto exit_function;
1064 : : }
1065 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1066 : : {
1067 : 0 : goto exit_function; /* no fixed-H found */
1068 : : }
1069 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
1070 : : {
1071 : 0 : goto exit_function;
1072 : : }
1073 [ # # ]: 0 : if (!pc2i->bHasDifference)
1074 : : {
1075 : 0 : goto exit_function; /* nothing to do */
1076 : : }
1077 : : }
1078 : : }
1079 : :
1080 [ # # # # ]: 0 : if (pc2i->len_c2at >= 1 && pc2i->nNumTgInChI == 1 && /* ADP in InChI */
1081 [ # # # # ]: 0 : ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ))
1082 : : {
1083 : : /*--------------------------------------------------------------*/
1084 : : /* case 04: restored: OH(+)=AB-O- OH- orig. HO-AB=O(+)- OH- */
1085 : : /* FixH: 1 0 0 1 0 1 */
1086 : : /* MobH: 0 0 1 0 0 0 */
1087 : : /* non-taut. taut taut */
1088 : : /* ADP: one t-group or more endpoints */
1089 : : /* O(+) = N, P, As, As, O, S, Se; OH = N, O, S, Se, Te */
1090 : : /* Solution: move (+) from O(+) to NH2 */
1091 : : /*--------------------------------------------------------------*/
1092 : 0 : int num_SB_Neutr = 0, num_DB_Charged = 0, iat;
1093 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
1094 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
1095 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
1096 : 0 : cur_success = 0;
1097 : :
1098 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
1099 : : { /* i = canonical number - 1 */
1100 : 0 : iat = nCanon2AtnoRevrs[i];
1101 [ # # ]: 0 : if ( /* in restored atom: charge=+1, has H, has double bond, N, O, S, Se, Te */
1102 : 0 : num_DB_Charged < MAX_DIFF_FIXH &&
1103 [ # # # # ]: 0 : at2[iat].charge == 1 && at2[iat].num_H &&
1104 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
1105 [ # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6 ||
1106 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1)) &&
1107 : : /* in orig.InChI: an endpoint, has fixed-H */
1108 [ # # ]: 0 : pStruct->endpoint[i] &&
1109 [ # # # # ]: 0 : (pStruct->fixed_H && pStruct->fixed_H[i]) &&
1110 : : /*!(nMobHInChI && nMobHInChI[i] ) &&*/
1111 : : /* has (+) edge */
1112 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
1113 : : {
1114 : :
1115 : 0 : iat_DB_Charged[num_DB_Charged++] = iat;
1116 : :
1117 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
1118 : : {
1119 : 0 : goto exit_function;
1120 : : }
1121 : : }
1122 : : else
1123 : : {
1124 [ # # ]: 0 : if ( /* in restored atom: charge=0, has no H, has no double bond, N, P, O, S, Se, Te */
1125 : 0 : num_SB_Neutr < MAX_DIFF_FIXH &&
1126 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
1127 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
1128 [ # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6 ||
1129 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 5) &&
1130 : : /* in orig.InChI: an endpoint, has fixed-H */
1131 : : /* pStruct->endpoint[i] && */
1132 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
1133 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
1134 : : /* has (+) edge */
1135 [ # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 &&
1136 [ # # ]: 0 : 0 == pBNS->edge[e].forbidden)
1137 : : {
1138 : :
1139 : 0 : iat_SB_Neutr[num_SB_Neutr++] = iat;
1140 : :
1141 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
1142 : : {
1143 : 0 : goto exit_function;
1144 : : }
1145 : : }
1146 : : }
1147 : : }
1148 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */
1149 : : {
1150 : : /* detected; attempt to fix */
1151 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1152 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
1153 : 0 : delta = 1;
1154 [ # # # # ]: 0 : for (i = 0; i < num_SB_Neutr && cur_success < num_try; i++)
1155 : : {
1156 : 0 : iat = iat_SB_Neutr[i];
1157 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
1158 [ # # ]: 0 : if (!pe->flow)
1159 : 0 : continue;
1160 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
1161 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
1162 : :
1163 : 0 : pe->forbidden |= forbidden_edge_mask;
1164 : 0 : pe->flow -= delta;
1165 : 0 : pv1->st_edge.flow -= delta;
1166 : 0 : pv2->st_edge.flow -= delta;
1167 : 0 : pBNS->tot_st_flow -= 2 * delta;
1168 : :
1169 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1170 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
1171 : :
1172 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
1173 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */
# # ]
1174 : : {
1175 : : /* Removed charge from O(+) => nDeltaCharge == -1 */
1176 : : /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */
1177 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
1178 [ # # ]: 0 : if (ret > 0)
1179 : : {
1180 : 0 : nNumRunBNS++;
1181 : 0 : cur_success++; /* 04 */
1182 : : }
1183 : : }
1184 : : else
1185 : : {
1186 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
1187 : 0 : pe->flow += delta;
1188 : 0 : pv1->st_edge.flow += delta;
1189 : 0 : pv2->st_edge.flow += delta;
1190 : 0 : pBNS->tot_st_flow += 2 * delta;
1191 : : }
1192 : : INCHI_HEAPCHK
1193 : : }
1194 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1195 : : }
1196 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1197 [ # # ]: 0 : if (cur_success)
1198 : : {
1199 : 0 : tot_succes += cur_success;
1200 : : /* recalculate InChI from the structure */
1201 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1202 : : ppt_group_info, ppat_norm, ppat_prep)))
1203 : : {
1204 : 0 : goto exit_function;
1205 : : }
1206 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
1207 : : {
1208 : 0 : goto exit_function;
1209 : : }
1210 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1211 : : {
1212 : 0 : goto exit_function; /* no fixed-H found */
1213 : : }
1214 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
1215 : : {
1216 : 0 : goto exit_function;
1217 : : }
1218 [ # # ]: 0 : if (!pc2i->bHasDifference)
1219 : : {
1220 : 0 : goto exit_function; /* nothing to do */
1221 : : }
1222 : : }
1223 : : }
1224 : :
1225 [ # # ]: 0 : if (pc2i->len_c2at > 1)
1226 : : {
1227 : : /*--------------------------------------------------------------*/
1228 : : /* case 05: restored: O=AB-NH original:(-)O-AB=NH(+) */
1229 : : /* FixH: 0 0 -1 1 */
1230 : : /* MobH: 0 1 1 0 */
1231 : : /* O = O, S, Se; N = N, O, S, Se, Te; all atoms not tautomeric */
1232 : : /* Solution: Separate charges */
1233 : : /*--------------------------------------------------------------*/
1234 : 0 : int num_DB_O = 0, num_SB_NH = 0, iat;
1235 : 0 : cur_success = 0;
1236 : :
1237 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
1238 : : {
1239 : 0 : iat = pc2i->c2at[i].atomNumber;
1240 [ # # ]: 0 : if ( /* orig. InChI info: =NH2(+), =OH(+) */
1241 : 0 : num_SB_NH < MAX_DIFF_FIXH &&
1242 [ # # # # ]: 0 : ((pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) ||
1243 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6) /* N, O, S, Se, Te */ &&
1244 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
1245 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
1246 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 1 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/
1247 : : /* reversed structure info: */
1248 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs &&
1249 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H &&
1250 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
1251 [ # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence)
1252 : : {
1253 : 0 : iat_SB_NH[num_SB_NH++] = iat;
1254 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
1255 : : {
1256 : 0 : goto exit_function;
1257 : : }
1258 : : }
1259 : : else
1260 : : {
1261 [ # # ]: 0 : if ( /* orig. InChI info: -O(-) */
1262 : 0 : num_DB_O < MAX_DIFF_FIXH &&
1263 [ # # ]: 0 : (pc2i->c2at[i].nValElectr == 6) /* O, S, Se, Te */ &&
1264 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
1265 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
1266 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 &&
1267 : : /* reversed structure info: */
1268 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
1269 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
1270 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
1271 [ # # ]: 0 : at2[iat].valence + 1 == at2[iat].chem_bonds_valence)
1272 : : {
1273 : 0 : iat_DB_O[num_DB_O++] = iat;
1274 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
1275 : : {
1276 : 0 : goto exit_function;
1277 : : }
1278 : : }
1279 : : }
1280 : : }
1281 [ # # ]: 0 : if ((num_try = inchi_min(num_DB_O, num_SB_NH))) /* djb-rwth: addressing LLVM warning */
1282 : : {
1283 : : /* detected; attempt to fix */
1284 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1285 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
1286 : 0 : delta = 1;
1287 [ # # # # ]: 0 : for (i = 0; i < num_SB_NH && cur_success < num_try; i++)
1288 : : {
1289 : 0 : iat = iat_SB_NH[i];
1290 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
1291 [ # # ]: 0 : if (!pe->flow)
1292 : 0 : continue;
1293 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
1294 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
1295 : :
1296 : 0 : pe->forbidden |= forbidden_edge_mask;
1297 : 0 : pe->flow -= delta;
1298 : 0 : pv1->st_edge.flow -= delta;
1299 : 0 : pv2->st_edge.flow -= delta;
1300 : 0 : pBNS->tot_st_flow -= 2 * delta;
1301 : :
1302 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1303 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
1304 : :
1305 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
1306 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */
# # ]
1307 : : {
1308 : : /* Added charge to =O => nDeltaCharge == 1 */
1309 : : /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */
1310 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
1311 [ # # ]: 0 : if (ret > 0)
1312 : : {
1313 : 0 : nNumRunBNS++;
1314 : 0 : cur_success++; /* 05 */
1315 : : }
1316 : : }
1317 : : else
1318 : : {
1319 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
1320 : 0 : pe->flow += delta;
1321 : 0 : pv1->st_edge.flow += delta;
1322 : 0 : pv2->st_edge.flow += delta;
1323 : 0 : pBNS->tot_st_flow += 2 * delta;
1324 : : }
1325 : : INCHI_HEAPCHK
1326 : : }
1327 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1328 : : }
1329 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1330 [ # # ]: 0 : if (cur_success)
1331 : : {
1332 : 0 : tot_succes += cur_success;
1333 : : /* recalculate InChI from the structure */
1334 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1335 : : ppt_group_info, ppat_norm, ppat_prep)))
1336 : : {
1337 : 0 : goto exit_function;
1338 : : }
1339 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
1340 : : {
1341 : 0 : goto exit_function;
1342 : : }
1343 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1344 : : {
1345 : 0 : goto exit_function; /* no fixed-H found */
1346 : : }
1347 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
1348 : : {
1349 : 0 : goto exit_function;
1350 : : }
1351 [ # # ]: 0 : if (!pc2i->bHasDifference)
1352 : : {
1353 : 0 : goto exit_function; /* nothing to do */
1354 : : }
1355 : : }
1356 : : }
1357 : :
1358 [ # # # # : 0 : if (pStruct->fixed_H && pStruct->endpoint && pc2i->nChargeFixHInChI > 0 && pc2i->nChargeFixHInChI > pc2i->nChargeMobHInChI)
# # # # ]
1359 : : {
1360 : : /*----------------------------------------------------------*/
1361 : : /* case 06c: restored -NH- or -NH(+) orig: -NH- */
1362 : : /* Fixed-H 1 1 0 */
1363 : : /* Mobile-H 0 0 1 */
1364 : : /* not tautomeric not tautomeric */
1365 : : /* has adjacent (+) */
1366 : : /* charges */
1367 : : /* Solution: move (+) charges to the -NH- unless it already*/
1368 : : /* N = N, O, S, Se, Te */
1369 : : /* has (+) charge blocked by adjacent (+) */
1370 : : /*----------------------------------------------------------*/
1371 : : int iat;
1372 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
1373 : : /*
1374 : : inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
1375 : : pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL;
1376 : : inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] &&
1377 : : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds?
1378 : : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL;
1379 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
1380 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : NULL;
1381 : : */
1382 : : EDGE_LIST CurChargeEdges;
1383 : : EdgeIndex e2;
1384 : 0 : cur_success = 0;
1385 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR );
1386 : 0 : CurrEdges.num_edges = 0;
1387 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
1388 : : {
1389 : : /* atoms -NH- from which H(+) were removed by the Normalization in orig. InChI */
1390 : 0 : iat = pc2i->c2at[i].atomNumber;
1391 [ # # ]: 0 : if (( pc2i->c2at[i].nValElectr == 6 ||
1392 [ # # # # ]: 0 : (pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) ) &&
1393 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
1394 [ # # # # ]: 0 : ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
1395 : : {
1396 : 0 : if ( /* orig. InChI info: -NH- */
1397 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 1 && pc2i->c2at[i].nMobHInChI == 0 &&
1398 : : /* reversed structure info: */
1399 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 1 && /* was not removed */
1400 [ # # ]: 0 : /*pc2i->c2at[i].nAtChargeRevrs == 0 &&*/ at2[iat].num_H && /* at2 is Fixed-H */
1401 [ # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence)
1402 : : {
1403 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
1404 : : {
1405 : 0 : goto exit_function;
1406 : : }
1407 : : }
1408 : : }
1409 : : }
1410 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
1411 : : {
1412 : : /* find adjacent charged atoms */
1413 : 0 : iat = nCanon2AtnoRevrs[i];
1414 [ # # # # : 0 : if (pStruct->endpoint[i] || at2[iat].charge != 1 || at2[iat].radical || pVA[iat].cMetal)
# # # # ]
1415 : : {
1416 : 0 : continue;
1417 : : }
1418 [ # # # # : 0 : if (0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow && pVA[iat].cNumValenceElectrons >= 5)
# # # # ]
1419 : : {
1420 : : /* positively charged atom */
1421 [ # # ]: 0 : for (j = 0; j < at2[iat].valence; j++)
1422 : : {
1423 [ # # # # ]: 0 : if (at2[k = (int) at2[iat].neighbor[j]].charge == 1 && !pVA[k].cMetal &&
1424 [ # # # # : 0 : 0 <= ( e2 = pVA[k].nCPlusGroupEdge - 1 ) && !pBNS->edge[e2].forbidden && !pBNS->edge[e2].flow)
# # ]
1425 : : {
1426 [ # # # # ]: 0 : if (0 > FindInEdgeList( &CurrEdges, e ) &&
1427 [ # # ]: 0 : 0 > FindInEdgeList( &CurChargeEdges, e ) &&
1428 : 0 : ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) ))
1429 : : {
1430 : 0 : goto exit_case_06c;
1431 : : }
1432 [ # # # # ]: 0 : if (0 > FindInEdgeList( &CurrEdges, e2 ) &&
1433 [ # # ]: 0 : 0 > FindInEdgeList( &CurChargeEdges, e2 ) &&
1434 : 0 : ( ret = AddToEdgeList( &CurChargeEdges, e2, INC_ADD_EDGE ) ))
1435 : : {
1436 : 0 : goto exit_case_06c;
1437 : : }
1438 : : }
1439 : : }
1440 : : }
1441 : : }
1442 [ # # ]: 0 : if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */
1443 : : {
1444 : : /* detected; attempt to fix */
1445 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
1446 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask );
1447 : 0 : delta = 1;
1448 [ # # # # ]: 0 : for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++)
1449 : : {
1450 : 0 : e = CurrEdges.pnEdges[i];
1451 : 0 : pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */
1452 [ # # ]: 0 : if (!pe->flow)
1453 : 0 : continue;
1454 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
1455 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
1456 : :
1457 : 0 : pe->flow -= delta; /* add (+) to -NHm */
1458 : 0 : pv1->st_edge.flow -= delta;
1459 : 0 : pv2->st_edge.flow -= delta;
1460 : 0 : pBNS->tot_st_flow -= 2 * delta;
1461 : :
1462 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1463 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
1464 : :
1465 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
1466 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warning */
# # ]
1467 : : {
1468 : : /* Removed (+)charge from -NH- => nDeltaCharge == -1 */
1469 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
1470 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
1471 [ # # ]: 0 : if (ret > 0)
1472 : : {
1473 : 0 : nNumRunBNS++;
1474 : 0 : cur_success++; /* 06c */
1475 : : }
1476 : : }
1477 : : else
1478 : : {
1479 : 0 : pe->flow += delta;
1480 : 0 : pv1->st_edge.flow += delta;
1481 : 0 : pv2->st_edge.flow += delta;
1482 : 0 : pBNS->tot_st_flow += 2 * delta;
1483 : : }
1484 : : INCHI_HEAPCHK
1485 : : }
1486 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
1487 : : }
1488 : 0 : exit_case_06c:
1489 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1490 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE );
1491 [ # # ]: 0 : if (ret < 0)
1492 : : {
1493 : 0 : goto exit_function;
1494 : : }
1495 [ # # ]: 0 : if (cur_success)
1496 : : {
1497 : 0 : tot_succes += cur_success;
1498 : : /* recalculate InChI from the structure */
1499 [ # # ]: 0 : if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1500 : : ppt_group_info, ppat_norm, ppat_prep ) ))
1501 : : {
1502 : 0 : goto exit_function;
1503 : : }
1504 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
1505 : : {
1506 : 0 : goto exit_function;
1507 : : }
1508 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1509 : : {
1510 : 0 : goto exit_function; /* no fixed-H found */
1511 : : }
1512 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
1513 : : {
1514 : 0 : goto exit_function;
1515 : : }
1516 [ # # ]: 0 : if (!pc2i->bHasDifference)
1517 : : {
1518 : 0 : goto exit_function; /* nothing to do */
1519 : : }
1520 : : }
1521 : : }
1522 : :
1523 [ # # ]: 0 : if (pc2i->len_c2at >= 2)
1524 : : {
1525 : : /*------------------------------------------------------------*/
1526 : : /* case 06d: restored: XH(+)=-AB-NH orig.: XH-=AB=NH(+) */
1527 : : /* FixH: 1 1 0 0 1 1 */
1528 : : /* MobH: 0 taut 1 1 taut 0 */
1529 : : /* */
1530 : : /* */
1531 : : /* N = N, O, S, Se; atoms N are not tautomeric in orig InChI */
1532 : : /* X = N, O, S, Se, Te, F, Cl, Br, I; atom X is non-taut */
1533 : : /* Solution: move (+) from X to NH */
1534 : : /*------------------------------------------------------------*/
1535 : : int iat;
1536 : : /*
1537 : : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
1538 : : inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
1539 : : pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL;
1540 : : inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] &&
1541 : : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds?
1542 : : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds :
1543 : : pStruct->pOne_norm_data[TAUT_NON]->at;
1544 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
1545 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
1546 : : */
1547 : : EDGE_LIST CurChargeEdges;
1548 : 0 : cur_success = 0;
1549 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR );
1550 : 0 : CurrEdges.num_edges = 0;
1551 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
1552 : : {
1553 : 0 : iat = pc2i->c2at[i].atomNumber;
1554 : : /* XH(+) */
1555 : 0 : if ( /* reconstructed: non-taut and (+) */
1556 [ # # ]: 0 : ( pc2i->c2at[i].nMobHRevrs + 1 == pc2i->c2at[i].nFixHRevrs &&
1557 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs > 0 && !pc2i->c2at[i].endptRevrs &&
1558 [ # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 1 &&
1559 : : /* original InChI: non-taut & has H or an endpoint, has Fixed H */
1560 [ # # # # ]: 0 : ( (!pc2i->c2at[i].nFixHInChI && pc2i->c2at[i].nMobHInChI == pc2i->c2at[i].nFixHRevrs) ||
1561 [ # # # # ]: 0 : (pc2i->c2at[i].nFixHInChI == pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].endptInChI) ) ) &&
1562 [ # # # # : 0 : 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow) /* djb-rwth: addressing LLVM warnings */
# # ]
1563 : : {
1564 : :
1565 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
1566 : : {
1567 : 0 : goto exit_case_06d;
1568 : : }
1569 : : }
1570 : : else
1571 : : {
1572 : : /* -NH- */
1573 : 0 : if ( /* original InChI: has H and is not an endpoint */
1574 [ # # ]: 0 : ( pc2i->c2at[i].nMobHInChI + 1 == pc2i->c2at[i].nFixHInChI &&
1575 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI > 0 && !pc2i->c2at[i].endptInChI &&
1576 [ # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 &&
1577 : : /* reconstructed InChI: non-taut & has H or an endpoint, has Fixed H */
1578 [ # # # # ]: 0 : ( (!pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].nMobHRevrs == pc2i->c2at[i].nFixHInChI) ||
1579 [ # # # # ]: 0 : (pc2i->c2at[i].nFixHRevrs == pc2i->c2at[i].nFixHInChI && pc2i->c2at[i].endptRevrs) ) ) &&
1580 [ # # # # ]: 0 : 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden &&
1581 [ # # ]: 0 : pBNS->edge[e].flow) /* djb-rwth: addressing LLVM warnings */
1582 : : {
1583 : :
1584 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
1585 : : {
1586 : 0 : goto exit_case_06d;
1587 : : }
1588 : : }
1589 : : }
1590 : : }
1591 [ # # ]: 0 : if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */
1592 : : {
1593 : : /* detected; attempt to fix */
1594 : 0 : int bSFlowerEdgesMayBeForbidden = ( SFlowerEdges.num_edges > 0 );
1595 : : int bSFlowerEdgesIsForbidden;
1596 : 0 : for (bSFlowerEdgesIsForbidden = bSFlowerEdgesMayBeForbidden;
1597 [ # # ]: 0 : 0 <= bSFlowerEdgesIsForbidden; bSFlowerEdgesIsForbidden--)
1598 : : {
1599 [ # # ]: 0 : if (bSFlowerEdgesIsForbidden)
1600 : : {
1601 : : /* on the 1st pass disallow -S(+)= => =S=, allow only -S(+)= => -S- */
1602 : 0 : SetForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask );
1603 : : }
1604 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
1605 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask );
1606 : 0 : delta = 1;
1607 [ # # # # ]: 0 : for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++)
1608 : : {
1609 : 0 : e = CurrEdges.pnEdges[i];
1610 : 0 : pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */
1611 [ # # ]: 0 : if (!pe->flow)
1612 : 0 : continue;
1613 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
1614 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
1615 : :
1616 : 0 : pe->flow -= delta; /* add (+) to -NHm */
1617 : 0 : pv1->st_edge.flow -= delta;
1618 : 0 : pv2->st_edge.flow -= delta;
1619 : 0 : pBNS->tot_st_flow -= 2 * delta;
1620 : :
1621 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1622 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
1623 : :
1624 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
1625 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */
# # ]
1626 : : {
1627 : : /* Removed (+)charge from -NH- => nDeltaCharge == -1 */
1628 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
1629 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
1630 [ # # ]: 0 : if (ret > 0)
1631 : : {
1632 : 0 : nNumRunBNS++;
1633 : 0 : cur_success++; /* 06d */
1634 : : }
1635 : : }
1636 : : else
1637 : : {
1638 : 0 : pe->flow += delta;
1639 : 0 : pv1->st_edge.flow += delta;
1640 : 0 : pv2->st_edge.flow += delta;
1641 : 0 : pBNS->tot_st_flow += 2 * delta;
1642 : : }
1643 : : INCHI_HEAPCHK
1644 : : }
1645 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
1646 : 0 : RemoveForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask );
1647 : : }
1648 : : }
1649 : 0 : exit_case_06d:
1650 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1651 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE );
1652 [ # # ]: 0 : if (cur_success)
1653 : : {
1654 : 0 : tot_succes += cur_success;
1655 : : /* recalculate InChI from the structure */
1656 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1657 : : ppt_group_info, ppat_norm, ppat_prep ) ))
1658 : : {
1659 : 0 : goto exit_function;
1660 : : }
1661 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
1662 : : {
1663 : 0 : goto exit_function;
1664 : : }
1665 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1666 : : {
1667 : 0 : goto exit_function; /* no fixed-H found */
1668 : : }
1669 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
1670 : : {
1671 : 0 : goto exit_function;
1672 : : }
1673 [ # # ]: 0 : if (!pc2i->bHasDifference)
1674 : : {
1675 : 0 : goto exit_function; /* nothing to do */
1676 : : }
1677 : : }
1678 : : }
1679 : :
1680 [ # # ]: 0 : if (pc2i->len_c2at >= 2)
1681 : : {
1682 : : /*--------------------------------------------------------*/
1683 : : /* case 06: restored: NHn(+)=AB-NHm orig.: NHn-AB=NHm(+) */
1684 : : /* FixH: 1 0 0 1 */
1685 : : /* MobH: n-1 m n m-1 */
1686 : : /* N = N, O, S, Se; atoms N are not tautomeric */
1687 : : /* Solution: move (+) from NHn(+) to NHn */
1688 : : /*--------------------------------------------------------*/
1689 : 0 : int num_DB_NHn_Plus = 0, num_SB_NHm_Neutr = 0, iat;
1690 : 0 : cur_success = 0;
1691 : :
1692 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
1693 : : {
1694 : 0 : iat = pc2i->c2at[i].atomNumber;
1695 [ # # ]: 0 : if ((pc2i->c2at[i].nValElectr == 6 ||
1696 [ # # # # ]: 0 : (pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1)) &&
1697 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
1698 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
1699 : : {
1700 [ # # ]: 0 : if ( /* orig. InChI info: NHm */
1701 : 0 : num_SB_NHm_Neutr < MAX_DIFF_FIXH &&
1702 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 1 && /*pc2i->c2at[i].nMobHInChI == 0 &&*/
1703 : : /* reversed structure info: */
1704 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && /*pc2i->c2at[i].nMobHRevrs == 1 &&*/
1705 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H && /* at2 is Fixed-H */
1706 [ # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence)
1707 : : {
1708 : 0 : iat_SB_NHm_Neutr[num_SB_NHm_Neutr++] = iat;
1709 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
1710 : : {
1711 : 0 : goto exit_function;
1712 : : }
1713 : : }
1714 : : else
1715 : : {
1716 [ # # ]: 0 : if ( /* orig. InChI info: */
1717 : 0 : num_DB_NHn_Plus < MAX_DIFF_FIXH &&
1718 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI &&*/
1719 : : /* reversed structure info: */
1720 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 1 && /*pc2i->c2at[i].nMobHRevrs == 0 &&*/
1721 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 1 && at2[iat].num_H &&
1722 [ # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence)
1723 : : {
1724 : 0 : iat_DB_NHn_Plus[num_DB_NHn_Plus++] = iat;
1725 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
1726 : : {
1727 : 0 : goto exit_function;
1728 : : }
1729 : : }
1730 : : }
1731 : : }
1732 : : }
1733 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_NHm_Neutr, num_DB_NHn_Plus))) /* djb-rwth: addressing LLVM warning */
1734 : : {
1735 : : /* detected; attempt to fix */
1736 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1737 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
1738 : 0 : delta = 1;
1739 [ # # # # ]: 0 : for (i = 0; i < num_SB_NHm_Neutr && cur_success < num_try; i++)
1740 : : {
1741 : 0 : iat = iat_SB_NHm_Neutr[i];
1742 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
1743 [ # # ]: 0 : if (!pe->flow)
1744 : 0 : continue;
1745 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
1746 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
1747 : :
1748 : 0 : pe->forbidden |= forbidden_edge_mask;
1749 : 0 : pe->flow -= delta; /* add (+) to -NHm */
1750 : 0 : pv1->st_edge.flow -= delta;
1751 : 0 : pv2->st_edge.flow -= delta;
1752 : 0 : pBNS->tot_st_flow -= 2 * delta;
1753 : :
1754 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1755 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
1756 : :
1757 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
1758 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */
# # ]
1759 : : {
1760 : : /* Removed (+)charge from -NHn => nDeltaCharge == -1 */
1761 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
1762 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
1763 [ # # ]: 0 : if (ret > 0)
1764 : : {
1765 : 0 : nNumRunBNS++;
1766 : 0 : cur_success++; /* 06 */
1767 : : }
1768 : : }
1769 : : else
1770 : : {
1771 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
1772 : 0 : pe->flow += delta;
1773 : 0 : pv1->st_edge.flow += delta;
1774 : 0 : pv2->st_edge.flow += delta;
1775 : 0 : pBNS->tot_st_flow += 2 * delta;
1776 : : }
1777 : : INCHI_HEAPCHK
1778 : : }
1779 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
1780 : : }
1781 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1782 [ # # ]: 0 : if (cur_success)
1783 : : {
1784 : 0 : tot_succes += cur_success;
1785 : : /* recalculate InChI from the structure */
1786 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1787 : : ppt_group_info, ppat_norm, ppat_prep)))
1788 : : {
1789 : 0 : goto exit_function;
1790 : : }
1791 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
1792 : : {
1793 : 0 : goto exit_function;
1794 : : }
1795 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1796 : : {
1797 : 0 : goto exit_function; /* no fixed-H found */
1798 : : }
1799 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
1800 : : {
1801 : 0 : goto exit_function;
1802 : : }
1803 [ # # ]: 0 : if (!pc2i->bHasDifference)
1804 : : {
1805 : 0 : goto exit_function; /* nothing to do */
1806 : : }
1807 : : }
1808 : : }
1809 : :
1810 [ # # # # ]: 0 : if (( (pc2i->nNumTgInChI > pc2i->nNumTgRevrs && pc2i->nNumTgRevrs == 1) ||
1811 [ # # ]: 0 : pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs ) &&
1812 [ # # ]: 0 : pStruct->nNumRemovedProtonsMobHInChI == pStruct->One_ti.tni.nNumRemovedProtons &&
1813 [ # # # # : 0 : pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */
# # # # ]
1814 : : {
1815 : : /*----------------------------------------------------------*/
1816 : : /* case 06a: restored: N'(+)=-AB-NH orig.: N'-=AB=NH(+) */
1817 : : /* FixH: 0 1 0 1 */
1818 : : /* MobH: 0 0 0 0 */
1819 : : /* single t-group multiple t-groups */
1820 : : /* N = N, O, S, Se; atoms N are not tautomeric */
1821 : : /* N' = N atom N' is not tautomeric */
1822 : : /* Solution: move (+) from N' to NH */
1823 : : /*----------------------------------------------------------*/
1824 : : int iat;
1825 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
1826 : : /*
1827 : : inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
1828 : : pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL;
1829 : : */
1830 : 0 : inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] &&
1831 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ?
1832 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL;
1833 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
1834 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
1835 : : EDGE_LIST CurChargeEdges;
1836 : 0 : cur_success = 0;
1837 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR );
1838 : 0 : CurrEdges.num_edges = 0;
1839 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
1840 : : {
1841 : 0 : iat = nCanon2AtnoRevrs[i];
1842 [ # # ]: 0 : if (pStruct->endpoint[i])
1843 : : {
1844 : 0 : continue;
1845 : : }
1846 : : /* -NH-, -OH */
1847 [ # # # # : 0 : if (pStruct->fixed_H[i] && nMobHInChI && !nMobHInChI[i] &&
# # ]
1848 [ # # # # ]: 0 : at2[iat].charge == 0 && at2[iat].radical == 0 &&
1849 [ # # # # : 0 : 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # # # ]
1850 : 0 : ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) )) /* djb-rwth: fixing a NULL pointer dereference */
1851 : : {
1852 : 0 : goto exit_case_06a;
1853 : : }
1854 : : else
1855 : : {
1856 : : /* >N(+)= */
1857 [ # # # # ]: 0 : if (at2[iat].charge == 1 && !at2[iat].num_H &&
1858 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
# # ]
1859 [ # # ]: 0 : atfMobile_H_Revrs && atfMobile_H_Revrs[iat].charge == 0 &&
1860 [ # # # # : 0 : 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow &&
# # # # ]
1861 : 0 : ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) ))
1862 : : {
1863 : 0 : goto exit_case_06a;
1864 : : }
1865 : : }
1866 : : }
1867 [ # # ]: 0 : if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */
1868 : : {
1869 : : /* detected; attempt to fix */
1870 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
1871 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask );
1872 : 0 : delta = 1;
1873 [ # # # # ]: 0 : for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++)
1874 : : {
1875 : 0 : e = CurrEdges.pnEdges[i];
1876 : 0 : pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */
1877 [ # # ]: 0 : if (!pe->flow)
1878 : 0 : continue;
1879 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
1880 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
1881 : :
1882 : 0 : pe->flow -= delta; /* add (+) to -NHm */
1883 : 0 : pv1->st_edge.flow -= delta;
1884 : 0 : pv2->st_edge.flow -= delta;
1885 : 0 : pBNS->tot_st_flow -= 2 * delta;
1886 : :
1887 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
1888 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
1889 : :
1890 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
1891 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */
# # ]
1892 : : {
1893 : : /* Removed (+)charge from -NH- => nDeltaCharge == -1 */
1894 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
1895 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
1896 [ # # ]: 0 : if (ret > 0)
1897 : : {
1898 : 0 : nNumRunBNS++;
1899 : 0 : cur_success++; /* 06a */
1900 : : }
1901 : : }
1902 : : else
1903 : : {
1904 : 0 : pe->flow += delta;
1905 : 0 : pv1->st_edge.flow += delta;
1906 : 0 : pv2->st_edge.flow += delta;
1907 : 0 : pBNS->tot_st_flow += 2 * delta;
1908 : : }
1909 : : INCHI_HEAPCHK
1910 : : }
1911 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
1912 : : }
1913 : 0 : exit_case_06a:
1914 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
1915 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE );
1916 [ # # ]: 0 : if (cur_success)
1917 : : {
1918 : 0 : tot_succes += cur_success;
1919 : : /* recalculate InChI from the structure */
1920 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
1921 : : ppt_group_info, ppat_norm, ppat_prep ) ))
1922 : : {
1923 : 0 : goto exit_function;
1924 : : }
1925 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
1926 : : {
1927 : 0 : goto exit_function;
1928 : : }
1929 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
1930 : : {
1931 : 0 : goto exit_function; /* no fixed-H found */
1932 : : }
1933 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
1934 : : {
1935 : 0 : goto exit_function;
1936 : : }
1937 [ # # ]: 0 : if (!pc2i->bHasDifference)
1938 : : {
1939 : 0 : goto exit_function; /* nothing to do */
1940 : : }
1941 : : }
1942 : : }
1943 [ # # # # ]: 0 : if (( (pc2i->nNumTgInChI > pc2i->nNumTgRevrs && pc2i->nNumTgRevrs == 1) ||
1944 [ # # ]: 0 : pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs ) &&
1945 [ # # ]: 0 : ( pStruct->nNumRemovedProtonsMobHInChI == pStruct->One_ti.tni.nNumRemovedProtons ||
1946 [ # # ]: 0 : pStruct->nNumRemovedProtonsMobHInChI > pStruct->One_ti.tni.nNumRemovedProtons ) &&
1947 [ # # # # : 0 : pStruct->fixed_H && pStruct->endpoint && pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */
# # # # ]
1948 : : {
1949 : : /*----------------------------------------------------------*/
1950 : : /* case 06b: restored: X(+)=-AB-NH orig.: X-=AB=NH(+) */
1951 : : /* FixH: 0 1 1 0 1 */
1952 : : /* MobH: 0 0 t 0 0 */
1953 : : /* single t-group multiple t-groups */
1954 : : /* or no t-groupd */
1955 : : /* N = N, O, S, Se; atoms N are not tautomeric */
1956 : : /* X = O, S, Se, Te, F, Cl, Br, I; atom X is not tautomeric*/
1957 : : /* Solution: move (+) from X to NH */
1958 : : /*----------------------------------------------------------*/
1959 : : int iat;
1960 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
1961 : : /*
1962 : : inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
1963 : : pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL;
1964 : : */
1965 : 0 : inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] &&
1966 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ?
1967 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds : NULL;
1968 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
1969 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
1970 : : EDGE_LIST CurChargeEdges;
1971 : 0 : cur_success = 0;
1972 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR );
1973 : 0 : CurrEdges.num_edges = 0;
1974 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
1975 : : {
1976 : 0 : iat = nCanon2AtnoRevrs[i];
1977 [ # # ]: 0 : if (pStruct->endpoint[i])
1978 : : {
1979 : 0 : continue;
1980 : : }
1981 : : /* -NH-, -OH */
1982 [ # # # # : 0 : if (pStruct->fixed_H[i] && nMobHInChI && !nMobHInChI[i] &&
# # ]
1983 [ # # # # ]: 0 : at2[iat].charge == 0 && at2[iat].radical == 0 &&
1984 [ # # # # : 0 : 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # # # ]
1985 : 0 : ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) )) /* djb-rwth: fixing a NULL pointer dereference */
1986 : : {
1987 : 0 : goto exit_case_06b;
1988 : : }
1989 : : else
1990 : : {
1991 : : /* X(+)= */
1992 [ # # # # ]: 0 : if (at2[iat].charge == 1 && !at2[iat].num_H &&
1993 [ # # # # : 0 : ( pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cPeriodicRowNumber == 7 ) &&
# # ]
1994 [ # # ]: 0 : atfMobile_H_Revrs && atfMobile_H_Revrs[iat].charge == 1 &&
1995 [ # # # # : 0 : 0 <= ( e = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && !pBNS->edge[e].flow &&
# # # # ]
1996 : 0 : ( ret = AddToEdgeList( &CurChargeEdges, e, INC_ADD_EDGE ) ))
1997 : : {
1998 : 0 : goto exit_case_06b;
1999 : : }
2000 : : }
2001 : : }
2002 [ # # ]: 0 : if ((num_try = inchi_min( CurrEdges.num_edges, CurChargeEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */
2003 : : {
2004 : : /* detected; attempt to fix */
2005 : 0 : int bSFlowerEdgesMayBeForbidden = ( SFlowerEdges.num_edges > 0 );
2006 : : int bSFlowerEdgesIsForbidden;
2007 : 0 : for (bSFlowerEdgesIsForbidden = bSFlowerEdgesMayBeForbidden;
2008 [ # # ]: 0 : 0 <= bSFlowerEdgesIsForbidden; bSFlowerEdgesIsForbidden--)
2009 : : {
2010 [ # # ]: 0 : if (bSFlowerEdgesIsForbidden)
2011 : : {
2012 : : /* on the 1st pass disallow -S(+)= => =S=, allow only -S(+)= => -S- */
2013 : 0 : SetForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask );
2014 : : }
2015 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
2016 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurChargeEdges, forbidden_edge_mask );
2017 : 0 : delta = 1;
2018 [ # # # # ]: 0 : for (i = 0; i < CurrEdges.num_edges && cur_success < num_try; i++)
2019 : : {
2020 : 0 : e = CurrEdges.pnEdges[i];
2021 : 0 : pe = pBNS->edge + e; /* (+)charge edge of -NH- or -OH */
2022 [ # # ]: 0 : if (!pe->flow)
2023 : 0 : continue;
2024 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
2025 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
2026 : :
2027 : 0 : pe->flow -= delta; /* add (+) to -NHm */
2028 : 0 : pv1->st_edge.flow -= delta;
2029 : 0 : pv2->st_edge.flow -= delta;
2030 : 0 : pBNS->tot_st_flow -= 2 * delta;
2031 : :
2032 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
2033 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
2034 : :
2035 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
2036 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */
# # ]
2037 : : {
2038 : : /* Removed (+)charge from -NH- => nDeltaCharge == -1 */
2039 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
2040 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
2041 [ # # ]: 0 : if (ret > 0)
2042 : : {
2043 : 0 : nNumRunBNS++;
2044 : 0 : cur_success++; /* 06b */
2045 : : }
2046 : : }
2047 : : else
2048 : : {
2049 : 0 : pe->flow += delta;
2050 : 0 : pv1->st_edge.flow += delta;
2051 : 0 : pv2->st_edge.flow += delta;
2052 : 0 : pBNS->tot_st_flow += 2 * delta;
2053 : : }
2054 : : INCHI_HEAPCHK
2055 : : }
2056 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
2057 : 0 : RemoveForbiddenEdgeMask( pBNS, &SFlowerEdges, forbidden_edge_mask );
2058 : : }
2059 : : }
2060 : 0 : exit_case_06b:
2061 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
2062 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_FREE );
2063 [ # # ]: 0 : if (cur_success)
2064 : : {
2065 : 0 : tot_succes += cur_success;
2066 : : /* recalculate InChI from the structure */
2067 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
2068 : : ppt_group_info, ppat_norm, ppat_prep ) ))
2069 : : {
2070 : 0 : goto exit_function;
2071 : : }
2072 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
2073 : : {
2074 : 0 : goto exit_function;
2075 : : }
2076 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
2077 : : {
2078 : 0 : goto exit_function; /* no fixed-H found */
2079 : : }
2080 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
2081 : : {
2082 : 0 : goto exit_function;
2083 : : }
2084 [ # # ]: 0 : if (!pc2i->bHasDifference)
2085 : : {
2086 : 0 : goto exit_function; /* nothing to do */
2087 : : }
2088 : : }
2089 : : }
2090 : :
2091 [ # # ]: 0 : if (pc2i->nNumTgInChI > 1 &&
2092 [ # # # # ]: 0 : ( pStruct->nNumRemovedProtonsMobHInChI > 0 || pStruct->ti.tni.nNumRemovedProtons > 0 ) &&
2093 [ # # # # ]: 0 : pStruct->fixed_H && pStruct->endpoint &&
2094 [ # # # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES] && pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds)
2095 : : {
2096 : : /*----------------------------------------------------------*/
2097 : : /* case 06e:restored: XHn(+)=-AB-YHm orig.: XHn-=AB=YHm(+) */
2098 : : /* FixH: 1 0 1 1 */
2099 : : /* MobH: 0 1 t t */
2100 : : /* non-taut atoms multiple t-groups */
2101 : : /* */
2102 : : /* 1. orig. t-group has more H on its endpoints counted */
2103 : : /* in atf and has no (+) on endpoint that has H */
2104 : : /* 2. orig. t-group has less H on its endpoints counted */
2105 : : /* in atf and has (+) on endpoint that has H */
2106 : : /* in reconstructed struct and less H in atf */
2107 : : /* Solution: move (+) from (2) to atom in (1) that has H */
2108 : : /* */
2109 : : /* tg1 reconstr: XHn and more H than in orig t-group */
2110 : : /* atf: XHn */
2111 : : /* tg2 reconstr: XHm(+) and less H than in */
2112 : : /* atf: XH(m-1) orig in t-group */
2113 : : /* */
2114 : : /* N = N, O, S, Se; atoms N are not tautomeric */
2115 : : /* X = O, S, Se, Te, F, Cl, Br, I; atom X is not tautomeric*/
2116 : : /* Solution: move (+) from X to NH */
2117 : : /*----------------------------------------------------------*/
2118 : :
2119 : : int iat, nNumWrongTg, jjoffs, jj, nNum2RemovePlus, nNum2AddPlus, nNum2MovePlus;
2120 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
2121 : : /*
2122 : : inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
2123 : : pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL;
2124 : : */
2125 : 0 : inp_ATOM *atfMobile_H_Revrs = pStruct->pOne_norm_data[TAUT_YES] &&
2126 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds ?
2127 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at_fixed_bonds :
2128 : 0 : pStruct->pOne_norm_data[TAUT_YES] &&
2129 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at ?
2130 [ # # ]: 0 : pStruct->pOne_norm_data[TAUT_YES]->at : NULL;
2131 : : /*
2132 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
2133 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
2134 : : */
2135 : : EDGE_LIST CurChargeEdges /* source of (+)*/, EndpList;
2136 : : BNS_VERTEX *pv1n, *pv2n;
2137 : : BNS_EDGE *pe1n, *pe2n;
2138 : : Vertex v1n, v2n;
2139 : :
2140 : 0 : cur_success = 0;
2141 : 0 : AllocEdgeList( &CurChargeEdges, EDGE_LIST_CLEAR );
2142 : 0 : AllocEdgeList( &EndpList, EDGE_LIST_CLEAR );
2143 : 0 : CurrEdges.num_edges = 0; /* receptors of (+) */
2144 : :
2145 [ # # ]: 0 : if (!atfMobile_H_Revrs)
2146 : : {
2147 : 0 : goto exit_case_06e;
2148 : : }
2149 : 0 : nNumWrongTg = FillTgDiffHChgFH(tdhc, MAX_DIFF_FIXH, at2, atfMobile_H_Revrs,
2150 : : nCanon2AtnoRevrs, pVA, &pStruct->ti, &EndpList);
2151 [ # # ]: 0 : if (nNumWrongTg < 1)
2152 : : {
2153 : 0 : goto exit_case_06e; /* for now only transfer (+) from one Mobile-H group to another */
2154 : : }
2155 : 0 : nNum2RemovePlus = nNum2AddPlus = 0; /* djb-rwth: removing redundant code */
2156 [ # # ]: 0 : for (i = 0; i < nNumWrongTg; i++)
2157 : : {
2158 : : /* detect t-group that has extra (+) on H */
2159 [ # # ]: 0 : if (tdhc[i].nNumHInchi > tdhc[i].nNumHNorml &&
2160 [ # # # # ]: 0 : tdhc[i].nNumPRevrs > tdhc[i].nNumPNorml && tdhc[i].n[fNumRPosChgH])
2161 : 0 : {
2162 : : /* count how many (+) to remove */
2163 : : /* store XH(+) atom numbers */
2164 : 0 : int nNumNeeded = inchi_min(tdhc[i].nNumHInchi - tdhc[i].nNumHNorml, tdhc[i].n[fNumRPosChgH]);
2165 : 0 : nNum2RemovePlus += nNumNeeded;
2166 : 0 : jjoffs = tdhc[i].i[fNumRPosChgH];
2167 [ # # ]: 0 : for (jj = 0; jj < tdhc[i].n[fNumRPosChgH]; jj++)
2168 : : {
2169 : 0 : iat = EndpList.pnEdges[jjoffs + jj];
2170 : 0 : e = pVA[iat].nCPlusGroupEdge - 1;
2171 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurChargeEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2172 : : {
2173 : 0 : goto exit_case_06e;
2174 : : }
2175 : : }
2176 : : }
2177 : : else
2178 : : {
2179 : : /* detect t-group that needs (+) on XH to reduce number of H */
2180 [ # # # # ]: 0 : if (tdhc[i].nNumHInchi < tdhc[i].nNumHNorml && tdhc[i].n[fNumRNeutrlH])
2181 : : {
2182 : : /* store XH atom numbers */
2183 : 0 : int nNumNeeded = inchi_min(tdhc[i].nNumHNorml - tdhc[i].nNumHInchi, tdhc[i].n[fNumRNeutrlH]);
2184 : 0 : nNum2AddPlus += nNumNeeded;
2185 : 0 : jjoffs = tdhc[i].i[fNumRNeutrlH];
2186 [ # # ]: 0 : for (jj = 0; jj < tdhc[i].n[fNumRNeutrlH]; jj++)
2187 : : {
2188 : 0 : iat = EndpList.pnEdges[jjoffs + jj];
2189 : 0 : e = pVA[iat].nCPlusGroupEdge - 1;
2190 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2191 : : {
2192 : 0 : goto exit_case_06e;
2193 : : }
2194 : : }
2195 : : }
2196 : : }
2197 : : }
2198 : 0 : nNum2MovePlus = inchi_min(nNum2RemovePlus, nNum2AddPlus);
2199 [ # # # # ]: 0 : if (CurrEdges.num_edges > 0 && CurChargeEdges.num_edges > 0)
2200 : : {
2201 [ # # # # ]: 0 : for (i = 0; 0 < nNum2MovePlus && i < nNumWrongTg; i++)
2202 : : {
2203 : : /* detect t-group that has extra (+) on H */
2204 [ # # ]: 0 : if (tdhc[i].nNumHInchi > tdhc[i].nNumHNorml &&
2205 [ # # # # ]: 0 : tdhc[i].nNumPRevrs > tdhc[i].nNumPNorml && tdhc[i].n[fNumRPosChgH])
2206 : : {
2207 : 0 : int nNum2Remove = tdhc[i].nNumHInchi - tdhc[i].nNumHNorml;
2208 [ # # ]: 0 : if (nNum2Remove < tdhc[i].n[fNumRPosChgH])
2209 : : {
2210 : 0 : nNum2Remove = tdhc[i].n[fNumRPosChgH];
2211 : : }
2212 : : /* store XH(+) atom numbers */
2213 : 0 : jjoffs = tdhc[i].i[fNumRPosChgH];
2214 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2215 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
2216 [ # # # # : 0 : for (jj = 0; 0 < nNum2MovePlus && 0 < nNum2Remove && jj < tdhc[i].n[fNumRPosChgH]; jj++)
# # ]
2217 : : {
2218 : 0 : iat = EndpList.pnEdges[jjoffs + jj];
2219 : 0 : e = pVA[iat].nCPlusGroupEdge - 1;
2220 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
2221 [ # # ]: 0 : if (pe->flow)
2222 : 0 : continue;
2223 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
2224 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
2225 : :
2226 [ # # ]: 0 : for (j = pv1->num_adj_edges - 1; 0 <= j; j--)
2227 : : {
2228 : 0 : pe1n = pBNS->edge + pv1->iedge[j];
2229 [ # # # # ]: 0 : if (pe1n->flow && !pe1n->forbidden)
2230 : : {
2231 : 0 : pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1);
2232 : 0 : break;
2233 : : }
2234 : : }
2235 [ # # ]: 0 : if (j < 0)
2236 : : {
2237 : 0 : continue; /* not found */
2238 : : }
2239 [ # # ]: 0 : for (j = pv2->num_adj_edges - 2; 0 <= j; j--)
2240 : : {
2241 : 0 : pe2n = pBNS->edge + pv2->iedge[j];
2242 [ # # # # ]: 0 : if (pe2n->flow && !pe2n->forbidden)
2243 : : {
2244 : 0 : pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2);
2245 : 0 : break;
2246 : : }
2247 : : }
2248 [ # # ]: 0 : if (j < 0)
2249 : : {
2250 : 0 : continue; /* not found */
2251 : : }
2252 : 0 : delta = 1;
2253 : 0 : pe->flow += delta;
2254 : 0 : pe1n->flow -= delta;
2255 : 0 : pe2n->flow -= delta;
2256 : 0 : pv1n->st_edge.flow -= delta;
2257 : 0 : pv2n->st_edge.flow -= delta;
2258 : 0 : pBNS->tot_st_flow -= 2 * delta;
2259 : :
2260 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
2261 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
2262 : :
2263 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) ||
# # ]
2264 [ # # # # ]: 0 : (vPathEnd == v2n && vPathStart == v1n)) &&
2265 [ # # # # ]: 0 : (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */
2266 : : {
2267 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
2268 [ # # ]: 0 : if (ret > 0)
2269 : : {
2270 : 0 : nNumRunBNS++;
2271 : 0 : nNum2Remove--;
2272 : 0 : nNum2MovePlus--;
2273 : 0 : cur_success++; /* 06e */
2274 : : }
2275 : : }
2276 : : else
2277 : : {
2278 : 0 : pe->flow -= delta;
2279 : 0 : pe1n->flow += delta;
2280 : 0 : pe2n->flow += delta;
2281 : 0 : pv1n->st_edge.flow += delta;
2282 : 0 : pv2n->st_edge.flow += delta;
2283 : 0 : pBNS->tot_st_flow += 2 * delta;
2284 : : }
2285 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE)))
2286 : : {
2287 : 0 : goto exit_case_06e;
2288 : : }
2289 : : }
2290 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2291 : : }
2292 : : }
2293 : : }
2294 : 0 : exit_case_06e:
2295 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
2296 : 0 : AllocEdgeList(&CurChargeEdges, EDGE_LIST_FREE);
2297 : 0 : AllocEdgeList(&EndpList, EDGE_LIST_FREE);
2298 [ # # ]: 0 : if (cur_success)
2299 : : {
2300 : 0 : tot_succes += cur_success;
2301 : : /* recalculate InChI from the structure */
2302 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
2303 : : ppt_group_info, ppat_norm, ppat_prep)))
2304 : : {
2305 : 0 : goto exit_function;
2306 : : }
2307 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
2308 : : {
2309 : 0 : goto exit_function;
2310 : : }
2311 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
2312 : : {
2313 : 0 : goto exit_function; /* no fixed-H found */
2314 : : }
2315 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
2316 : : {
2317 : 0 : goto exit_function;
2318 : : }
2319 [ # # ]: 0 : if (!pc2i->bHasDifference)
2320 : : {
2321 : 0 : goto exit_function; /* nothing to do */
2322 : : }
2323 : : }
2324 : : }
2325 : :
2326 [ # # ]: 0 : if (pc2i->len_c2at >= 1)
2327 : : {
2328 : : /*--------------------------------------------------------------*/
2329 : : /* case 07: restored: O(-)-AB=O original: O=AB-O(-) */
2330 : : /* FixH: 0 0 0 -1 */
2331 : : /* MobH: 0 0 0 1 */
2332 : : /* taut (non-taut) (taut) non-taut */
2333 : : /* taut (taut) (non-taut) non-taut */
2334 : : /* O = O, S, Se, Te */
2335 : : /* Solution: move (-) from O(-)-AB to AB=O */
2336 : : /*--------------------------------------------------------------*/
2337 : 0 : int num_SB_O_Minus = 0, num_DB_O_Neutr = 0, iat;
2338 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
2339 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
2340 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
2341 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
2342 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
2343 : 0 : cur_success = 0;
2344 : :
2345 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
2346 : : {
2347 : 0 : iat = pc2i->c2at[i].atomNumber;
2348 [ # # ]: 0 : if ( /* orig. InChI info: -O(-), non-taut */
2349 : 0 : num_DB_O_Neutr < MAX_DIFF_FIXH &&
2350 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ &&
2351 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
2352 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
2353 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 &&
2354 : : /* reversed structure info: */
2355 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
2356 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
2357 [ # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence)
2358 : : {
2359 : 0 : iat_DB_O_Neutr[num_DB_O_Neutr++] = iat;
2360 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2361 : : {
2362 : 0 : goto exit_function;
2363 : : }
2364 : : }
2365 : : }
2366 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
2367 : : {
2368 : : /* i = canonical number - 1 */
2369 : 0 : iat = nCanon2AtnoRevrs[i];
2370 [ # # ]: 0 : if ( /* in restored atom: charge=-1, no H, has single bond, O, S, Se, Te */
2371 : 0 : num_SB_O_Minus < MAX_DIFF_FIXH &&
2372 [ # # # # ]: 0 : at2[iat].charge == -1 && !at2[iat].num_H &&
2373 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
2374 [ # # # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
2375 [ # # ]: 0 : at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint &&
2376 : : /* in orig.InChI: not an endpoint, has no H */
2377 : : /*pStruct->endpoint[i] && -- modificatuion#1 */
2378 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
2379 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
2380 : : /* has (-) edge */
2381 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
2382 : : {
2383 : 0 : iat_SB_O_Minus[num_SB_O_Minus++] = iat;
2384 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2385 : : {
2386 : 0 : goto exit_function;
2387 : : }
2388 : : }
2389 : : }
2390 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O_Neutr))) /* djb-rwth: addressing LLVM warning */
2391 : : {
2392 : : /* detected; attempt to fix */
2393 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2394 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
2395 : 0 : delta = 1;
2396 [ # # # # ]: 0 : for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++)
2397 : : {
2398 : 0 : iat = iat_SB_O_Minus[i];
2399 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
2400 [ # # ]: 0 : if (!pe->flow)
2401 : 0 : continue;
2402 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
2403 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
2404 : :
2405 : 0 : pe->forbidden |= forbidden_edge_mask;
2406 : 0 : pe->flow -= delta;
2407 : 0 : pv1->st_edge.flow -= delta;
2408 : 0 : pv2->st_edge.flow -= delta;
2409 : 0 : pBNS->tot_st_flow -= 2 * delta;
2410 : :
2411 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
2412 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
2413 : :
2414 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
2415 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */
# # ]
2416 : : {
2417 : : /* Moved (-) charge to AB=O => nDeltaCharge == 1 */
2418 : : /* Flow change on pe (-)charge edge (O(-)-AB) is not known to RunBnsTestOnce()) */
2419 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
2420 [ # # ]: 0 : if (ret > 0)
2421 : : {
2422 : 0 : nNumRunBNS++;
2423 : 0 : cur_success++; /* 07 */
2424 : : }
2425 : : }
2426 : : else
2427 : : {
2428 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
2429 : 0 : pe->flow += delta;
2430 : 0 : pv1->st_edge.flow += delta;
2431 : 0 : pv2->st_edge.flow += delta;
2432 : 0 : pBNS->tot_st_flow += 2 * delta;
2433 : : }
2434 : : INCHI_HEAPCHK
2435 : : }
2436 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2437 : : }
2438 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
2439 [ # # ]: 0 : if (cur_success)
2440 : : {
2441 : 0 : tot_succes += cur_success;
2442 : : /* recalculate InChI from the structure */
2443 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
2444 : : ppt_group_info, ppat_norm, ppat_prep)))
2445 : : {
2446 : 0 : goto exit_function;
2447 : : }
2448 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
2449 : : {
2450 : 0 : goto exit_function;
2451 : : }
2452 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
2453 : : {
2454 : 0 : goto exit_function; /* no fixed-H found */
2455 : : }
2456 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
2457 : : {
2458 : 0 : goto exit_function;
2459 : : }
2460 [ # # ]: 0 : if (!pc2i->bHasDifference)
2461 : : {
2462 : 0 : goto exit_function; /* nothing to do */
2463 : : }
2464 : : }
2465 : : }
2466 : :
2467 [ # # ]: 0 : if (pc2i->len_c2at >= 1)
2468 : : {
2469 : : /*--------------------------------------------------------------*/
2470 : : /* case 07a: restored: O(-)-N(V)B=O original: O=N(V)B-O(-) */
2471 : : /* FixH: 0 0 0 -1 */
2472 : : /* MobH: 0 0 0 1 */
2473 : : /* non-taut (non-taut) non-taut non-taut */
2474 : : /* non-taut (taut) non-taut non-taut */
2475 : : /* O = O, S, Se, Te */
2476 : : /* Solution: move (-) from O(-)-AB to AB=O */
2477 : : /*--------------------------------------------------------------*/
2478 : 0 : int num_SB_O_Minus = 0, num_DB_O_Neutr = 0, iat, iN;
2479 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
2480 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
2481 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
2482 : 0 : cur_success = 0;
2483 : :
2484 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
2485 : : {
2486 : 0 : iat = pc2i->c2at[i].atomNumber;
2487 [ # # ]: 0 : if ( /* orig. InChI info: -O(-), non-taut */
2488 : 0 : num_DB_O_Neutr < MAX_DIFF_FIXH &&
2489 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ &&
2490 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
2491 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
2492 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == -1 && pc2i->c2at[i].nMobHInChI == 1 &&
2493 : : /* reversed structure info: */
2494 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
2495 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
2496 [ # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence)
2497 : : {
2498 : 0 : iat_DB_O_Neutr[num_DB_O_Neutr++] = iat;
2499 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2500 : : {
2501 : 0 : goto exit_function;
2502 : : }
2503 : : }
2504 : : }
2505 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
2506 : : {
2507 : : /* i = canonical number - 1 */
2508 : 0 : iat = nCanon2AtnoRevrs[i];
2509 [ # # ]: 0 : if ( /* in restored atom: charge=-1, no H, has single bond, O, S, Se, Te */
2510 : 0 : num_SB_O_Minus < MAX_DIFF_FIXH &&
2511 [ # # # # ]: 0 : at2[iat].charge == -1 && !at2[iat].num_H &&
2512 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
2513 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
2514 : : /*at_Mobile_H_Revrs && !at_Mobile_H_Revrs[iat].endpoint &&*/
2515 : : /* in orig.InChI: not an endpoint, has no H */
2516 [ # # ]: 0 : !pStruct->endpoint[i] &&
2517 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
2518 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
2519 : : /* has N(V) neighbor */
2520 [ # # # # ]: 0 : 1 == at2[iat].valence && at2[iN = at2[iat].neighbor[0]].chem_bonds_valence == 5 &&
2521 [ # # # # ]: 0 : !at2[iN].charge && pVA[iN].cNumValenceElectrons == 5 &&
2522 : : /* has (-) edge */
2523 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
2524 : : {
2525 : 0 : iat_SB_O_Minus[num_SB_O_Minus++] = iat;
2526 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2527 : : {
2528 : 0 : goto exit_function;
2529 : : }
2530 : : }
2531 : : }
2532 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O_Neutr))) /* djb-rwth: addressing LLVM warning */
2533 : : {
2534 : : /* detected; attempt to fix */
2535 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2536 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
2537 : 0 : delta = 1;
2538 [ # # # # ]: 0 : for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++)
2539 : : {
2540 : 0 : iat = iat_SB_O_Minus[i];
2541 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
2542 [ # # ]: 0 : if (!pe->flow)
2543 : 0 : continue;
2544 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
2545 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
2546 : :
2547 : 0 : pe->forbidden |= forbidden_edge_mask;
2548 : 0 : pe->flow -= delta;
2549 : 0 : pv1->st_edge.flow -= delta;
2550 : 0 : pv2->st_edge.flow -= delta;
2551 : 0 : pBNS->tot_st_flow -= 2 * delta;
2552 : :
2553 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
2554 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
2555 : :
2556 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
2557 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */
# # ]
2558 : : {
2559 : : /* Moved (-) charge to AB=O => nDeltaCharge == 1 */
2560 : : /* Flow change on pe (-)charge edge (O(-)-AB) is not known to RunBnsTestOnce()) */
2561 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
2562 [ # # ]: 0 : if (ret > 0)
2563 : : {
2564 : 0 : nNumRunBNS++;
2565 : 0 : cur_success++; /* 07 */
2566 : : }
2567 : : }
2568 : : else
2569 : : {
2570 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
2571 : 0 : pe->flow += delta;
2572 : 0 : pv1->st_edge.flow += delta;
2573 : 0 : pv2->st_edge.flow += delta;
2574 : 0 : pBNS->tot_st_flow += 2 * delta;
2575 : : }
2576 : : INCHI_HEAPCHK
2577 : : }
2578 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2579 : : }
2580 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
2581 [ # # ]: 0 : if (cur_success)
2582 : : {
2583 : 0 : tot_succes += cur_success;
2584 : : /* recalculate InChI from the structure */
2585 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
2586 : : ppt_group_info, ppat_norm, ppat_prep)))
2587 : : {
2588 : 0 : goto exit_function;
2589 : : }
2590 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
2591 : : {
2592 : 0 : goto exit_function;
2593 : : }
2594 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
2595 : : {
2596 : 0 : goto exit_function; /* no fixed-H found */
2597 : : }
2598 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
2599 : : {
2600 : 0 : goto exit_function;
2601 : : }
2602 [ # # ]: 0 : if (!pc2i->bHasDifference)
2603 : : {
2604 : 0 : goto exit_function; /* nothing to do */
2605 : : }
2606 : : }
2607 : : }
2608 : :
2609 [ # # ]: 0 : if ( /*(pc2i->len_c2at >= 1 || pc2i->nNumRemHRevrs) &&*/ pc2i->nNumTgInChI == 1 && /* ADP in InChI */
2610 [ # # # # ]: 0 : (pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1))
2611 : : {
2612 : : /*----------------------------------------------------------------*/
2613 : : /* case 08: restored: O(-)-AB=N- OH- orig. O=AB-N(-)- OH- */
2614 : : /* FixH: 1 0 0 0 0 1 */
2615 : : /* MobH: 0 0 1 0 0 0 */
2616 : : /* may be taut or not non-taut taut taut taut */
2617 : : /* ADP: one t-group or more endpoints */
2618 : : /* O(-) = S, Se, Te; N = N; */
2619 : : /* Solution: move (-) from O(-) to =N-; avoid stereogenic DB on N */
2620 : : /*----------------------------------------------------------------*/
2621 : 0 : int num_DB_N_Neutr = 0, num_SB_O_Minus = 0, iat;
2622 : :
2623 : 0 : AT_NUMB* nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
2624 [ # # # # ]: 0 : S_CHAR* nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
2625 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
2626 : 0 : cur_success = 0;
2627 : :
2628 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
2629 : : {
2630 : : /* i = canonical number - 1 */
2631 : 0 : iat = nCanon2AtnoRevrs[i];
2632 [ # # ]: 0 : if ( /* in restored atom: charge=-1, has no H, has single bond, O, S, Se, Te */
2633 : 0 : num_SB_O_Minus < MAX_DIFF_FIXH &&
2634 [ # # # # ]: 0 : at2[iat].charge == -1 && !at2[iat].num_H &&
2635 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
2636 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
2637 : : /* in orig.InChI: an endpoint, may have fixed-H */
2638 [ # # # # ]: 0 : pStruct->endpoint[i] &&
2639 : : /*!(pStruct->fixed_H && pStruct->fixed_H[i]) &&*/
2640 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
2641 : : /* has (-) edge */
2642 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
2643 : : {
2644 : :
2645 : 0 : iat_SB_O_Minus[num_SB_O_Minus++] = iat;
2646 : :
2647 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2648 : : {
2649 : 0 : goto exit_function;
2650 : : }
2651 : : }
2652 : : else
2653 : : {
2654 [ # # ]: 0 : if ( /* in restored atom: charge=0, has no H, has double non-stereogenic bond, N */
2655 : 0 : num_DB_N_Neutr < MAX_DIFF_FIXH &&
2656 [ # # # # : 0 : at2[iat].charge == 0 && !at2[iat].num_H && !at2[iat].sb_parity[0] &&
# # ]
2657 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
2658 [ # # # # ]: 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
2659 : : /* in orig.InChI: an endpoint, has no fixed-H */
2660 [ # # ]: 0 : pStruct->endpoint[i] &&
2661 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
2662 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
2663 : : /* has (-) edge */
2664 [ # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 &&
2665 [ # # ]: 0 : 0 == pBNS->edge[e].forbidden)
2666 : : {
2667 : :
2668 : 0 : iat_DB_N_Neutr[num_DB_N_Neutr++] = iat;
2669 : :
2670 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
2671 : : {
2672 : 0 : goto exit_function;
2673 : : }
2674 : : }
2675 : : }
2676 : : }
2677 [ # # ]: 0 : if ((num_try = inchi_min(num_DB_N_Neutr, num_SB_O_Minus))) /* djb-rwth: addressing LLVM warning */
2678 : : {
2679 : : /* detected; attempt to fix */
2680 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2681 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
2682 : : /* allow stereobonds in rings change */
2683 [ # # ]: 0 : if (forbidden_stereo_edge_mask)
2684 : 0 : RemoveForbiddenEdgeMask(pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask);
2685 : :
2686 : 0 : delta = 1;
2687 [ # # # # ]: 0 : for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++)
2688 : : {
2689 : 0 : iat = iat_SB_O_Minus[i];
2690 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
2691 [ # # ]: 0 : if (!pe->flow)
2692 : 0 : continue;
2693 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
2694 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
2695 : :
2696 : 0 : pe->forbidden |= forbidden_edge_mask;
2697 : 0 : pe->flow -= delta;
2698 : 0 : pv1->st_edge.flow -= delta;
2699 : 0 : pv2->st_edge.flow -= delta;
2700 : 0 : pBNS->tot_st_flow -= 2 * delta;
2701 : :
2702 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
2703 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
2704 : :
2705 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
2706 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */
# # ]
2707 : : {
2708 : : /* Moved (-) charge to =N- => nDeltaCharge == 1 */
2709 : : /* Flow change on pe (-)charge edge (atom (-)O-) is not known to RunBnsTestOnce()) */
2710 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
2711 [ # # ]: 0 : if (ret > 0)
2712 : : {
2713 : 0 : nNumRunBNS++;
2714 : 0 : cur_success++; /* 08 */
2715 : : }
2716 : : }
2717 : : else
2718 : : {
2719 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
2720 : 0 : pe->flow += delta;
2721 : 0 : pv1->st_edge.flow += delta;
2722 : 0 : pv2->st_edge.flow += delta;
2723 : 0 : pBNS->tot_st_flow += 2 * delta;
2724 : : }
2725 : : INCHI_HEAPCHK
2726 : : }
2727 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
2728 [ # # ]: 0 : if (forbidden_stereo_edge_mask)
2729 : 0 : SetForbiddenEdgeMask(pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask);
2730 : : }
2731 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
2732 [ # # ]: 0 : if (cur_success)
2733 : : {
2734 : 0 : tot_succes += cur_success;
2735 : : /* recalculate InChI from the structure */
2736 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
2737 : : ppt_group_info, ppat_norm, ppat_prep)))
2738 : : {
2739 : 0 : goto exit_function;
2740 : : }
2741 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
2742 : : {
2743 : 0 : goto exit_function;
2744 : : }
2745 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
2746 : : {
2747 : 0 : goto exit_function; /* no fixed-H found */
2748 : : }
2749 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
2750 : : {
2751 : 0 : goto exit_function;
2752 : : }
2753 [ # # ]: 0 : if (!pc2i->bHasDifference)
2754 : : {
2755 : 0 : goto exit_function; /* nothing to do */
2756 : : }
2757 : : }
2758 : : }
2759 : :
2760 [ # # ]: 0 : if (pc2i->len_c2at >= 2)
2761 : : {
2762 : : /*--------------------------------------------------------*/
2763 : : /* case 09: restored: NH2(+)=C--NH2 orig.: NH2-C(+)-NH2 */
2764 : : /* FixH: 2 | 2 0 | 0 */
2765 : : /* MobH: 0 0 2 2 */
2766 : : /* N = N, taut taut non-taut non-taut*/
2767 : : /* Solution: move (+) from NH2(+) to C */
2768 : : /*--------------------------------------------------------*/
2769 : : int iat;
2770 : 0 : cur_success = 0;
2771 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
2772 : : {
2773 : 0 : iat = pc2i->c2at[i].atomNumber;
2774 [ # # # # ]: 0 : if (( pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1 ) &&
2775 : : /* orig. InChI info: */
2776 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
2777 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI &&
2778 : : /* reversed structure info: */
2779 [ # # ]: 0 : pc2i->c2at[i].endptRevrs &&
2780 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs && !pc2i->c2at[i].nMobHRevrs &&
2781 [ # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 1 &&
2782 [ # # ]: 0 : at2[iat].valence + 1 == at2[iat].chem_bonds_valence &&
2783 [ # # # # ]: 0 : ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden)
2784 : : {
2785 : 0 : EdgeIndex eNC = NO_VERTEX, eCPlusC;
2786 : : int iNH2, iatC, iatNH2; /* djb-rwth: removing redundant variables */
2787 : : /* found NH2(+)=; locate =C< and find whether it has -NH2 neighbor */
2788 [ # # ]: 0 : for (j = 0; j < at2[iat].valence; j++)
2789 : : {
2790 [ # # ]: 0 : if (at2[iat].bond_type[j] == BOND_TYPE_DOUBLE)
2791 : 0 : break;
2792 : : }
2793 [ # # ]: 0 : if (j == at2[iat].valence)
2794 : : {
2795 : 0 : continue;
2796 : : }
2797 : 0 : eNC = pBNS->vert[iat].iedge[j]; /* edge NH2(+)=C */
2798 : 0 : iatC = at2[iat].neighbor[j];
2799 [ # # # # : 0 : if (pVA[iatC].cNumValenceElectrons != 4 || pVA[iatC].cMetal || at2[iatC].charge ||
# # ]
2800 [ # # # # ]: 0 : at2[iatC].valence != 3 || at2[iatC].valence + 1 != at2[iatC].chem_bonds_valence ||
2801 [ # # # # ]: 0 : ( eCPlusC = pVA[iatC].nCPlusGroupEdge - 1 ) < 0 || pBNS->edge[eCPlusC].forbidden)
2802 : : {
2803 : 0 : continue;
2804 : : }
2805 [ # # ]: 0 : for (j = 0; j < at2[iatC].valence; j++)
2806 : : {
2807 : 0 : iatNH2 = at2[iatC].neighbor[j];
2808 [ # # # # ]: 0 : if (iatNH2 == iat || pVA[iatNH2].cNumValenceElectrons != 5 ||
2809 [ # # # # : 0 : pVA[iatNH2].cPeriodicRowNumber != 1 || !at2[iatNH2].num_H || at2[iatNH2].charge)
# # ]
2810 : 0 : continue;
2811 : : /* djb-rwth: removing redundant code */
2812 [ # # ]: 0 : for (iNH2 = 0; iNH2 < pc2i->len_c2at; iNH2++)
2813 : : {
2814 [ # # ]: 0 : if (iatNH2 == pc2i->c2at[iNH2].atomNumber)
2815 : 0 : break;
2816 : : }
2817 [ # # ]: 0 : if (iNH2 == pc2i->len_c2at)
2818 : : {
2819 : 0 : continue;
2820 : : }
2821 : :
2822 [ # # # # ]: 0 : if (( pc2i->c2at[iNH2].nValElectr == 5 && pc2i->c2at[iNH2].nPeriodNum == 1 ) &&
2823 : : /* orig. InChI info: */
2824 [ # # ]: 0 : !pc2i->c2at[iNH2].endptInChI &&
2825 [ # # # # ]: 0 : pc2i->c2at[iNH2].nFixHInChI == 0 && pc2i->c2at[iNH2].nMobHInChI &&
2826 : : /* reversed structure info: */
2827 [ # # ]: 0 : pc2i->c2at[iNH2].endptRevrs &&
2828 [ # # # # ]: 0 : pc2i->c2at[iNH2].nFixHRevrs && !pc2i->c2at[iNH2].nMobHRevrs &&
2829 [ # # ]: 0 : pc2i->c2at[iNH2].nAtChargeRevrs == 0 &&
2830 [ # # ]: 0 : at2[iatNH2].valence == at2[iatNH2].chem_bonds_valence)
2831 : : {
2832 : : /* we have found NH2(+)=, =C<, and bond between them */
2833 : :
2834 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
2835 : : {
2836 : 0 : goto exit_function;
2837 : : }
2838 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, eCPlusC, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
2839 : : {
2840 : 0 : goto exit_function;
2841 : : }
2842 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
2843 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask );
2844 : 0 : delta = 1;
2845 : :
2846 : 0 : pe = pBNS->edge + eNC;
2847 [ # # ]: 0 : if (!pe->flow)
2848 : 0 : continue;
2849 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
2850 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
2851 : :
2852 : 0 : pe->forbidden |= forbidden_edge_mask;
2853 : 0 : pe->flow -= delta; /* add (+) to -NHm */
2854 : 0 : pv1->st_edge.flow -= delta;
2855 : 0 : pv2->st_edge.flow -= delta;
2856 : 0 : pBNS->tot_st_flow -= 2 * delta;
2857 : :
2858 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
2859 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
2860 : :
2861 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
2862 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */
# # ]
2863 : : {
2864 : : /* Removed (+)charge from -NHn => nDeltaCharge == -1 */
2865 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
2866 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
2867 [ # # ]: 0 : if (ret > 0)
2868 : : {
2869 : 0 : nNumRunBNS++;
2870 : 0 : cur_success++; /* 09 */
2871 : : }
2872 : : }
2873 : : else
2874 : : {
2875 : 0 : pe->flow += delta;
2876 : 0 : pv1->st_edge.flow += delta;
2877 : 0 : pv2->st_edge.flow += delta;
2878 : 0 : pBNS->tot_st_flow += 2 * delta;
2879 : : }
2880 : : INCHI_HEAPCHK
2881 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
2882 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
2883 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
2884 : 0 : break;
2885 : : }
2886 : : }
2887 : : }
2888 : : }
2889 [ # # ]: 0 : if (cur_success)
2890 : : {
2891 : 0 : tot_succes += cur_success;
2892 : : /* recalculate InChI from the structure */
2893 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
2894 : : ppt_group_info, ppat_norm, ppat_prep ) ))
2895 : : {
2896 : 0 : goto exit_function;
2897 : : }
2898 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
2899 : : {
2900 : 0 : goto exit_function;
2901 : : }
2902 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
2903 : : {
2904 : 0 : goto exit_function; /* no fixed-H found */
2905 : : }
2906 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
2907 : : {
2908 : 0 : goto exit_function;
2909 : : }
2910 [ # # ]: 0 : if (!pc2i->bHasDifference)
2911 : : {
2912 : 0 : goto exit_function; /* nothing to do */
2913 : : }
2914 : : }
2915 : : }
2916 : :
2917 [ # # ]: 0 : if (pc2i->len_c2at >= 2)
2918 : : {
2919 : : /*--------------------------------------------------------*/
2920 : : /* case 10: restored: NH2-X(+)-NH- orig.: NH2(+)=X-NH- */
2921 : : /* FixH: 0 0 2 1 */
2922 : : /* MobH: 2 1 0 0 */
2923 : : /* N = N,O,S,Se,Te non-taut non-taut taut taut */
2924 : : /* Solution: move (+) from X(+) to NH2 or NH */
2925 : : /*--------------------------------------------------------*/
2926 : : int iat;
2927 : 0 : cur_success = 0;
2928 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
2929 : : {
2930 [ # # ]: 0 : if (pc2i->c2at[i].nValue)
2931 : 0 : continue;
2932 : 0 : iat = pc2i->c2at[i].atomNumber;
2933 [ # # ]: 0 : if (( pc2i->c2at[i].nValElectr == 6 ||
2934 [ # # # # ]: 0 : (pc2i->c2at[i].nValElectr == 5 && pc2i->c2at[i].nPeriodNum == 1) ) &&
2935 : : /* orig. InChI info: */
2936 [ # # ]: 0 : pc2i->c2at[i].endptInChI &&
2937 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI && !pc2i->c2at[i].nMobHInChI &&
2938 : : /* reversed structure info: */
2939 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
2940 [ # # # # ]: 0 : !pc2i->c2at[i].nFixHRevrs && pc2i->c2at[i].nMobHRevrs &&
2941 [ # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 &&
2942 [ # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence &&
2943 [ # # # # ]: 0 : ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
2944 : : {
2945 : :
2946 : 0 : EdgeIndex eCPlusC, eCPlusNH2, bContinue = 1;
2947 : : int iNH2, iatC, iatNH2, j1, j2; /* djb-rwth: removing redundant variables */
2948 : : BNS_EDGE *pe_iat, *pe_iNH2;
2949 : : /* found NH2- locate -X(+) and find whether it has another -NH2 neighbor */
2950 [ # # # # ]: 0 : for (j1 = 0; j1 < at2[iat].valence && bContinue; j1++)
2951 : : {
2952 [ # # ]: 0 : if (at2[iat].bond_type[j1] == BOND_TYPE_SINGLE &&
2953 [ # # ]: 0 : at2[iatC = at2[iat].neighbor[j1]].charge == 1 &&
2954 [ # # # # ]: 0 : ( 4 <= pVA[iatC].cNumValenceElectrons && pVA[iatC].cNumValenceElectrons <= 6 ) &&
2955 [ # # ]: 0 : at2[iatC].valence == at2[iatC].chem_bonds_valence &&
2956 [ # # # # ]: 0 : ( eCPlusC = pVA[iatC].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eCPlusC].forbidden)
2957 : : {
2958 : : /* found a candidate for X; find another NH2 */
2959 [ # # # # ]: 0 : for (j2 = 0; j2 < at2[iatC].valence && bContinue; j2++)
2960 : : {
2961 [ # # ]: 0 : if (at2[iatC].bond_type[j2] == BOND_TYPE_SINGLE &&
2962 [ # # ]: 0 : iat != ( iatNH2 = at2[iatC].neighbor[j2] ) &&
2963 [ # # # # ]: 0 : at2[iatNH2].charge == 0 && at2[iatNH2].num_H &&
2964 [ # # # # ]: 0 : ( pVA[iatNH2].cNumValenceElectrons == 5 || pVA[iatNH2].cNumValenceElectrons == 6 ) &&
2965 [ # # ]: 0 : at2[iatNH2].valence == at2[iatNH2].chem_bonds_valence &&
2966 [ # # # # ]: 0 : ( eCPlusNH2 = pVA[iatNH2].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eCPlusNH2].forbidden)
2967 : : {
2968 [ # # ]: 0 : for (iNH2 = 0; iNH2 < pc2i->len_c2at; iNH2++)
2969 : : {
2970 [ # # # # ]: 0 : if (iatNH2 != pc2i->c2at[iNH2].atomNumber || pc2i->c2at[iNH2].nValue)
2971 : 0 : continue;
2972 : : /* check the second -NH */
2973 : : /* djb-rwth: removing redundant code */
2974 : 0 : if ( /* orig. InChI info: */
2975 [ # # ]: 0 : pc2i->c2at[iNH2].endptInChI &&
2976 [ # # # # ]: 0 : pc2i->c2at[iNH2].nFixHInChI && !pc2i->c2at[iNH2].nMobHInChI &&
2977 : : /* reversed structure info: */
2978 [ # # ]: 0 : !pc2i->c2at[iNH2].endptRevrs &&
2979 [ # # # # ]: 0 : !pc2i->c2at[iNH2].nFixHRevrs && pc2i->c2at[iNH2].nMobHRevrs &&
2980 [ # # ]: 0 : pc2i->c2at[iNH2].nAtChargeRevrs == 0)
2981 : : {
2982 : : /* we have found NH-X(+)-NH; remove charge from X(+) */
2983 : 0 : pe_iat = pBNS->edge + pBNS->vert[iat].iedge[j1];
2984 : 0 : pe_iNH2 = pBNS->edge + pBNS->vert[iatC].iedge[j2];
2985 : : /* pick up one of -NH to move (+) to it */
2986 [ # # # # ]: 0 : if (!pe_iat->forbidden && pBNS->edge[e].flow)
2987 : : {
2988 : 0 : pe = pBNS->edge + e;
2989 : : }
2990 : : else
2991 [ # # # # ]: 0 : if (!pe_iNH2->forbidden && pBNS->edge[eCPlusNH2].flow)
2992 : : {
2993 : 0 : pe = pBNS->edge + eCPlusNH2;
2994 : : }
2995 : : else
2996 : : {
2997 : 0 : continue; /* none of the two -X(+)- bonds may be changed */
2998 : : }
2999 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, eCPlusC, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
3000 : : {
3001 : 0 : goto exit_function;
3002 : : }
3003 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
3004 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask );
3005 : 0 : delta = 1;
3006 : :
3007 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
3008 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
3009 : :
3010 : : /*pe->forbidden |= forbidden_edge_mask;*/
3011 : 0 : pe->flow -= delta; /* add (+) to -NHm */
3012 : 0 : pv1->st_edge.flow -= delta;
3013 : 0 : pv2->st_edge.flow -= delta;
3014 : 0 : pBNS->tot_st_flow -= 2 * delta;
3015 : :
3016 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
3017 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
3018 : :
3019 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
3020 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == -1) /* djb-rwth: addressing LLVM warnings */
# # ]
3021 : : {
3022 : : /* Removed (+)charge from -NHn => nDeltaCharge == -1 */
3023 : : /* Flow change on pe (+)charge edge (atom NHm(+)) is not known to RunBnsTestOnce()) */
3024 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
3025 [ # # ]: 0 : if (ret > 0)
3026 : : {
3027 : 0 : nNumRunBNS++;
3028 : 0 : cur_success++; /* 10 */
3029 : 0 : bContinue = 0;
3030 : 0 : pc2i->c2at[i].nValue = 1; /* mark as used */
3031 : 0 : pc2i->c2at[iNH2].nValue = 1; /* mark as used */
3032 : : }
3033 : : }
3034 : : else
3035 : : {
3036 : 0 : pe->flow += delta;
3037 : 0 : pv1->st_edge.flow += delta;
3038 : 0 : pv2->st_edge.flow += delta;
3039 : 0 : pBNS->tot_st_flow += 2 * delta;
3040 : : }
3041 : : INCHI_HEAPCHK
3042 : :
3043 : : /*pe->forbidden &= forbidden_edge_mask_inv;*/
3044 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
3045 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
3046 : 0 : break;
3047 : : }
3048 : : } /* iNH2: pc2i->c2at[iNH2] cycle */
3049 : : }
3050 : : } /* j2: iatC neighbors cycle */
3051 : : }
3052 : : } /* j1: iat neighbors cycle */
3053 : : }
3054 : : } /* i: pc2i->c2at[i] cycle */
3055 : :
3056 [ # # ]: 0 : if (cur_success)
3057 : : {
3058 : : /*
3059 : : for ( i = 0; i < pc2i->len_c2at; i ++ ) {
3060 : : pc2i->c2at[i].nValue = 0;
3061 : : }
3062 : : */
3063 : 0 : tot_succes += cur_success;
3064 : : /* recalculate InChI from the structure */
3065 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
3066 : : ppt_group_info, ppat_norm, ppat_prep ) ))
3067 : : {
3068 : 0 : goto exit_function;
3069 : : }
3070 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
3071 : : {
3072 : 0 : goto exit_function;
3073 : : }
3074 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
3075 : : {
3076 : 0 : goto exit_function; /* no fixed-H found */
3077 : : }
3078 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
3079 : : {
3080 : 0 : goto exit_function;
3081 : : }
3082 [ # # ]: 0 : if (!pc2i->bHasDifference)
3083 : : {
3084 : 0 : goto exit_function; /* nothing to do */
3085 : : }
3086 : : }
3087 : : }
3088 : :
3089 [ # # ]: 0 : if ( /*pc2i->len_c2at >= 1 &&*/ pc2i->nNumTgInChI == 1 && /* ADP in InChI */
3090 [ # # # # ]: 0 : ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ))
3091 : : {
3092 : : /*--------------------------------------------------------------*/
3093 : : /* case 11: restored: NH(+)=AB-N< OH- orig. NH-AB=N(+)< OH- */
3094 : : /* FixH: 0 0 0 1 0 1 */
3095 : : /* MobH: 1 0 1 0 0 0 */
3096 : : /* non-taut. taut taut */
3097 : : /* ADP: one t-group or more endpoints */
3098 : : /* NH(+)= => N, O, S, Se; -N< => N */
3099 : : /* Solution: move (+) from NH(+) to -N< */
3100 : : /*--------------------------------------------------------------*/
3101 : 0 : int num_SB_Neutr = 0, num_DB_Charged = 0, iat;
3102 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
3103 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
3104 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
3105 : 0 : cur_success = 0;
3106 : :
3107 : : /* search for NH(+)= */
3108 : : /* search for -N< */
3109 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
3110 : : { /* i = canonical number - 1 */
3111 : 0 : iat = nCanon2AtnoRevrs[i];
3112 [ # # ]: 0 : if ( /* in restored atom: charge=0, has no H, has no double bond, N only */
3113 : 0 : num_DB_Charged < MAX_DIFF_FIXH &&
3114 [ # # # # ]: 0 : at2[iat].charge == 1 && at2[iat].num_H &&
3115 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
3116 [ # # # # ]: 0 : ((pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1) ||
3117 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 6) &&
3118 : : /* in orig.InChI: an endpoint, has fixed-H */
3119 : : /*pStruct->endpoint[i] &&*/
3120 [ # # # # ]: 0 : (pStruct->fixed_H && pStruct->fixed_H[i]) &&
3121 : : /*!(nMobHInChI && nMobHInChI[i] ) &&*/
3122 : : /* has (+) edge */
3123 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
3124 : : {
3125 : :
3126 : 0 : iat_DB_Charged[num_DB_Charged++] = iat;
3127 : : /*
3128 : : if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) {
3129 : : goto exit_function;
3130 : : }
3131 : : */
3132 : : }
3133 : : else
3134 : : {
3135 [ # # ]: 0 : if ( /* in restored atom: charge=0, has no H, has no double bond, N only */
3136 : 0 : num_SB_Neutr < MAX_DIFF_FIXH &&
3137 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
3138 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
3139 [ # # ]: 0 : (pVA[iat].cNumValenceElectrons == 5 &&
3140 [ # # ]: 0 : pVA[iat].cPeriodicRowNumber == 1) &&
3141 : : /* in orig.InChI: an endpoint, has fixed-H */
3142 : : /*pStruct->endpoint[i] &&*/
3143 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
3144 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
3145 : : /* has (+) edge */
3146 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden)
3147 : : {
3148 : :
3149 : 0 : iat_SB_Neutr[num_SB_Neutr++] = iat;
3150 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
3151 : : {
3152 : 0 : goto exit_function;
3153 : : }
3154 : : }
3155 : : }
3156 : : }
3157 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */
3158 : : {
3159 : : /* detected; attempt to fix */
3160 : : BNS_VERTEX* pv1n, * pv2n;
3161 : : BNS_EDGE* pe1n, * pe2n;
3162 : : Vertex v1n, v2n;
3163 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3164 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
3165 : 0 : delta = 1;
3166 [ # # # # ]: 0 : for (i = 0; i < num_DB_Charged && cur_success < num_try; i++)
3167 : : {
3168 : 0 : iat = iat_DB_Charged[i];
3169 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
3170 [ # # ]: 0 : if (pe->flow)
3171 : 0 : continue;
3172 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
3173 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
3174 : :
3175 [ # # ]: 0 : for (j = pv1->num_adj_edges - 1; 0 <= j; j--)
3176 : : {
3177 : 0 : pe1n = pBNS->edge + pv1->iedge[j];
3178 [ # # # # ]: 0 : if (pe1n->flow && !pe1n->forbidden)
3179 : : {
3180 : 0 : pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1);
3181 : 0 : break;
3182 : : }
3183 : : }
3184 [ # # ]: 0 : if (j < 0)
3185 : : {
3186 : 0 : continue; /* not found */
3187 : : }
3188 : :
3189 [ # # ]: 0 : for (j = pv2->num_adj_edges - 2; 0 <= j; j--)
3190 : : {
3191 : 0 : pe2n = pBNS->edge + pv2->iedge[j];
3192 [ # # # # ]: 0 : if (pe2n->flow && !pe2n->forbidden)
3193 : : {
3194 : 0 : pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2);
3195 : 0 : break;
3196 : : }
3197 : : }
3198 [ # # ]: 0 : if (j < 0)
3199 : : {
3200 : 0 : continue; /* not found */
3201 : : }
3202 : :
3203 : 0 : pe->flow += delta;
3204 : 0 : pe1n->flow -= delta;
3205 : 0 : pe2n->flow -= delta;
3206 : 0 : pv1n->st_edge.flow -= delta;
3207 : 0 : pv2n->st_edge.flow -= delta;
3208 : 0 : pBNS->tot_st_flow -= 2 * delta;
3209 : :
3210 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
3211 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
3212 : :
3213 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) ||
# # ]
3214 [ # # # # ]: 0 : (vPathEnd == v2n && vPathStart == v1n)) &&
3215 [ # # # # ]: 0 : (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */
3216 : : {
3217 : : /* before setting flows the structure could be:
3218 : : [NH+ neigh, v1n]=e1n=[NH+,v1]-pe-[+,v2]=e2n=[another at or its chargeStruct]
3219 : : or
3220 : :
3221 : : [NH+ or ChStr, v1n]=pe1n=[NH+ or ChStr, v1]-pe-[+,v2]=pe2n=[at2 or ChStr, v2n]
3222 : : ^ ^ ^
3223 : : NH+(+)edge | N (+) edge: only
3224 : : | these are not forbidden
3225 : : |
3226 : : hetero (+) vertex
3227 : :
3228 : : After setting flows (* mark radicals, =pe= is forbidden):
3229 : :
3230 : : *[NH+ or ChStr, v1n]-pe1n-[NH+ or ChStr, v1]=pe=[+,v2]-pe2n-[at2 or ChStr, v2n]*
3231 : : ^ ^ ^
3232 : : NH+(+)edge | N (+) edge: only
3233 : : | these are not forbidden
3234 : : |
3235 : : hetero (+) vertex
3236 : :
3237 : : Flow in
3238 : : pe1n and pe2n will or will not change, depending on the structure.
3239 : :
3240 : : Consider what happens if pe2n changes. It may only increment.
3241 : : If pe2n flow increments then another (+)edge flow dectrements. If
3242 : : [at2 or ChStr, v2n] is at2 then at2 charge would change from (+) to 0,
3243 : : and another N charge would change from 0 to (+), giving tot. change of
3244 : : number of charges (-1)+(+1)=0. However, if [at2 or ChStr, v2n] is
3245 : : ChargeStruct then at2 will not be on the alt path and only the creation
3246 : : of another (+) will be detected.
3247 : : */
3248 : : /* Removed charge from O(+) => nDeltaCharge == -1 */
3249 : : /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */
3250 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
3251 [ # # ]: 0 : if (ret > 0)
3252 : : {
3253 : 0 : nNumRunBNS++;
3254 : 0 : cur_success++; /* 11 */
3255 : : }
3256 : : }
3257 : : else
3258 : : {
3259 : 0 : pe->flow -= delta;
3260 : 0 : pe1n->flow += delta;
3261 : 0 : pe2n->flow += delta;
3262 : 0 : pv1n->st_edge.flow += delta;
3263 : 0 : pv2n->st_edge.flow += delta;
3264 : 0 : pBNS->tot_st_flow += 2 * delta;
3265 : : }
3266 : : INCHI_HEAPCHK
3267 : : }
3268 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3269 : : }
3270 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
3271 [ # # ]: 0 : if (cur_success)
3272 : : {
3273 : 0 : tot_succes += cur_success;
3274 : : /* recalculate InChI from the structure */
3275 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
3276 : : ppt_group_info, ppat_norm, ppat_prep)))
3277 : : {
3278 : 0 : goto exit_function;
3279 : : }
3280 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
3281 : : {
3282 : 0 : goto exit_function;
3283 : : }
3284 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
3285 : : {
3286 : 0 : goto exit_function; /* no fixed-H found */
3287 : : }
3288 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
3289 : : {
3290 : 0 : goto exit_function;
3291 : : }
3292 [ # # ]: 0 : if (!pc2i->bHasDifference)
3293 : : {
3294 : 0 : goto exit_function; /* nothing to do */
3295 : : }
3296 : : }
3297 : : }
3298 : :
3299 [ # # # # ]: 0 : if (pc2i->len_c2at >= 1 && pc2i->nNumTgInChI == 1 &&
3300 [ # # ]: 0 : pc2i->nNumRemHInChI >= -1 && /* 2006-03-03 */
3301 [ # # # # ]: 0 : ( pc2i->nNumEndpInChI > pc2i->nNumEndpRevrs || pc2i->nNumTgRevrs > 1 ) /* ADP in InChI */)
3302 : : {
3303 : : /*--------------------------------------------------------------*/
3304 : : /* case 12: restored: O=AB-N< original: (-)O-AB=N(+)< */
3305 : : /* FixH: 0 0 0 0 */
3306 : : /* MobH: 0 0 0 0 */
3307 : : /* non-taut taut */
3308 : : /* O = O, S, Se, N; N = N; */
3309 : : /* restored atom O is not tautomeric; original atom O is taut. */
3310 : : /* original struct has 1 t-group; restored has less endpoints */
3311 : : /* and/or possibly >1 t-groups */
3312 : : /* Solution: separate charges between O= and -N< */
3313 : : /* allow moving charge to N(V) to make it N(IV)(+) */
3314 : : /*--------------------------------------------------------------*/
3315 : 0 : int bOnly_N_V = 1;
3316 : : /* djb-rwth: removing redundant code */
3317 : : while (1)
3318 : 0 : {
3319 : 0 : int num_SB_N_Neutr = 0, num_DB_O = 0, iat, num_N_V = 0, bN_V;
3320 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
3321 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
3322 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
3323 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
3324 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
3325 : 0 : cur_success = 0;
3326 : :
3327 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
3328 : : {
3329 : 0 : iat = pc2i->c2at[i].atomNumber;
3330 [ # # ]: 0 : if ( /* orig. InChI info: -O(-) */
3331 : 0 : num_DB_O < MAX_DIFF_FIXH &&
3332 [ # # ]: 0 : (pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ ||
3333 [ # # ]: 0 : (pc2i->c2at[i].nValElectr == 5 &&
3334 [ # # ]: 0 : pc2i->c2at[i].nPeriodNum == 1) /* N */) && /* djb-rwth: addressing LLVM warning */
3335 [ # # ]: 0 : pc2i->c2at[i].endptInChI &&
3336 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
3337 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 &&
3338 : : /* reversed structure info: */
3339 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
3340 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
3341 [ # # # # : 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
# # ]
3342 [ # # ]: 0 : ((pc2i->c2at[i].nValElectr == 6) ?
3343 [ # # # # ]: 0 : (at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2) :
3344 [ # # ]: 0 : (pc2i->c2at[i].nValElectr == 5) ?
3345 [ # # # # ]: 0 : (at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3) :
3346 : : 0))
3347 : : {
3348 : :
3349 : 0 : iat_DB_O[num_DB_O++] = iat;
3350 : : /*
3351 : : if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) {
3352 : : goto exit_function;
3353 : : }
3354 : : */
3355 : : }
3356 : : }
3357 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
3358 : : {
3359 : : /* i = canonical number - 1 */
3360 : 0 : iat = nCanon2AtnoRevrs[i];
3361 : 0 : bN_V = 0;
3362 [ # # ]: 0 : if ( /* in restored atom N: charge=0, no H, has no double bond, not an endpoint */
3363 : 0 : num_SB_N_Neutr < MAX_DIFF_FIXH &&
3364 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
3365 [ # # ]: 0 : (at2[iat].valence == at2[iat].chem_bonds_valence ||
3366 [ # # ]: 0 : (bN_V = at2[iat].valence + 2 == at2[iat].chem_bonds_valence)) &&
3367 [ # # ]: 0 : !pVA[iat].cMetal &&
3368 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
# # ]
3369 [ # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) &&
3370 : : /* in orig.InChI: not an endpoint, has no H */
3371 [ # # ]: 0 : !pStruct->endpoint[i] &&
3372 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
3373 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
3374 : : /* has (+) edge */
3375 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
3376 : : {
3377 : :
3378 [ # # # # : 0 : if (bOnly_N_V && bN_V &&
# # ]
3379 : 0 : NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) &&
3380 [ # # # # ]: 0 : !pBNS->edge[j].forbidden && !pBNS->edge[j].flow)
3381 : : {
3382 [ # # ]: 0 : if (!num_N_V)
3383 : : {
3384 : : /* switch to N(V) only mode */
3385 : 0 : CurrEdges.num_edges = 0;
3386 : 0 : num_SB_N_Neutr = 0;
3387 : : }
3388 : 0 : iat_SB_N_Neutr[num_SB_N_Neutr++] = iat;
3389 : 0 : num_N_V++;
3390 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
3391 : : {
3392 : 0 : goto exit_function;
3393 : : }
3394 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, j, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
3395 : : {
3396 : 0 : goto exit_function;
3397 : : }
3398 : : }
3399 : : else
3400 : : {
3401 [ # # ]: 0 : if (!num_N_V)
3402 : : {
3403 : 0 : iat_SB_N_Neutr[num_SB_N_Neutr++] = iat;
3404 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
3405 : : {
3406 : 0 : goto exit_function;
3407 : : }
3408 : : /* in addition, permit N(V)=>N(IV)(+) change by allowing charge flower edge change flow */
3409 [ # # # # ]: 0 : if (bN_V && NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) &&
3410 [ # # # # ]: 0 : !pBNS->edge[j].forbidden && !pBNS->edge[j].flow)
3411 : : {
3412 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, j, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
3413 : : {
3414 : 0 : goto exit_function;
3415 : : }
3416 : : }
3417 : : }
3418 : : }
3419 : : }
3420 : : }
3421 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_N_Neutr, num_DB_O))) /* djb-rwth: addressing LLVM warning */
3422 : : {
3423 : : /* detected; attempt to fix */
3424 : : BNS_EDGE* pe_CMinus;
3425 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3426 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
3427 : 0 : delta = 1;
3428 [ # # # # ]: 0 : for (i = 0; i < num_DB_O && cur_success < num_try; i++)
3429 : : {
3430 : 0 : iat = iat_DB_O[i];
3431 : 0 : pe_CMinus = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
3432 : 0 : pe_CMinus->forbidden &= forbidden_edge_mask_inv;
3433 : :
3434 : 0 : pe = pBNS->edge + pBNS->vert[iat].iedge[0]; /* double bond O=...*/
3435 [ # # ]: 0 : if (!pe->flow)
3436 : 0 : continue;
3437 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
3438 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
3439 : :
3440 : 0 : pe->forbidden |= forbidden_edge_mask; /* change bond O=X to O(rad)-X(rad) */
3441 : 0 : pe->flow -= delta;
3442 : 0 : pv1->st_edge.flow -= delta;
3443 : 0 : pv2->st_edge.flow -= delta;
3444 : 0 : pBNS->tot_st_flow -= 2 * delta;
3445 : :
3446 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
3447 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
3448 : :
3449 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
3450 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 2) /* djb-rwth: addressing LLVM warnings */
# # ]
3451 : : {
3452 : : /* Added (-) charge to =O and (+) charge to N => nDeltaCharge == 2 */
3453 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
3454 [ # # ]: 0 : if (ret > 0)
3455 : : {
3456 : 0 : nNumRunBNS++;
3457 : 0 : cur_success++; /* 12 */
3458 : : }
3459 : : }
3460 : : else
3461 : : {
3462 : 0 : pe->flow += delta;
3463 : 0 : pv1->st_edge.flow += delta;
3464 : 0 : pv2->st_edge.flow += delta;
3465 : 0 : pBNS->tot_st_flow += 2 * delta;
3466 : : }
3467 : 0 : pe->forbidden &= forbidden_edge_mask_inv; /* allow changes to O=X bond */
3468 : : INCHI_HEAPCHK
3469 : : }
3470 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3471 : : }
3472 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
3473 [ # # ]: 0 : if (cur_success)
3474 : : {
3475 : 0 : tot_succes += cur_success;
3476 : : /* recalculate InChI from the structure */
3477 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
3478 : : ppt_group_info, ppat_norm, ppat_prep)))
3479 : : {
3480 : 0 : goto exit_function;
3481 : : }
3482 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
3483 : : {
3484 : 0 : goto exit_function;
3485 : : }
3486 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
3487 : : {
3488 : 0 : goto exit_function; /* no fixed-H found */
3489 : : }
3490 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
3491 : : {
3492 : 0 : goto exit_function;
3493 : : }
3494 [ # # ]: 0 : if (!pc2i->bHasDifference)
3495 : : {
3496 : 0 : goto exit_function; /* nothing to do */
3497 : : }
3498 : 0 : break;
3499 : : }
3500 : : else
3501 : : {
3502 [ # # ]: 0 : if (bOnly_N_V)
3503 : : {
3504 : 0 : bOnly_N_V = 0;
3505 : : }
3506 : : else
3507 : : {
3508 : 0 : break;
3509 : : }
3510 : : }
3511 : : }
3512 : : }
3513 : :
3514 : :
3515 [ # # ]: 0 : if (pc2i->nNumTgDiffMinus /*|| pc2i->nNumTgDiffH */ /* no ADP in InChI needed */)
3516 : : {
3517 : : /*--------------------------------------------------------------*/
3518 : : /* | | */
3519 : : /* case 13: restored: O=AB=N= original: (-)O-AB-N(+)= */
3520 : : /* FixH: 0 0 0 0 */
3521 : : /* MobH: 0 0 0 0 */
3522 : : /* non-taut taut non-taut */
3523 : : /* O = O, S, Se, N; N = N, P, ... */
3524 : : /* t-group in original has same num. endpoints */
3525 : : /* same num_H and less (-) than in the restored structure */
3526 : : /* original atom O is tautomeric, N is not taut in both */
3527 : : /* original struct has 1 t-group; restored has less endpoints */
3528 : : /* and/or possibly >1 t-groups */
3529 : : /* Solution: separate charges between O= and -N< */
3530 : : /* allow moving charge to N(V) to make it N(IV)(+) */
3531 : : /*--------------------------------------------------------------*/
3532 : : int itg;
3533 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
3534 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
3535 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
3536 : :
3537 : 0 : S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL;
3538 [ # # ]: 0 : S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ?
3539 [ # # ]: 0 : pStruct->pOneINChI[1]->nNum_H :
3540 [ # # ]: 0 : ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ?
3541 [ # # ]: 0 : pStruct->pOneINChI[0]->nNum_H : NULL;
3542 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
3543 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
3544 : : /* djb-rwth: removing redundant code */
3545 : : /* find whether this may help */
3546 [ # # # # ]: 0 : for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++)
3547 : : {
3548 [ # # ]: 0 : if (pStruct->ti.t_group[itg].nNumEndpoints == pStruct->One_ti.t_group[itg].nNumEndpoints &&
3549 : 0 : pStruct->ti.t_group[itg].num[0] - pStruct->ti.t_group[itg].num[1] ==
3550 [ # # ]: 0 : pStruct->One_ti.t_group[itg].num[0] - pStruct->One_ti.t_group[itg].num[1] &&
3551 [ # # ]: 0 : pStruct->ti.t_group[itg].num[1] > pStruct->One_ti.t_group[itg].num[1])
3552 : : {
3553 : : /* restored InChI t-group has more (-) and same number of H */
3554 : 0 : int num_SB_N_Neutr = 0, num_DB_O = 0, iat;
3555 : 0 : cur_success = 0;
3556 : :
3557 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
3558 : : { /* i = canonical number - 1 */
3559 : 0 : iat = nCanon2AtnoRevrs[i];
3560 [ # # ]: 0 : if ( /* orig. InChI info: -O(-) */
3561 : 0 : num_DB_O < MAX_DIFF_FIXH &&
3562 [ # # ]: 0 : (pVA[i].cNumValenceElectrons == 6 /* O, S, Se, Te */) &&
3563 [ # # ]: 0 : pStruct->endpoint[i] == itg + 1 &&
3564 [ # # # # ]: 0 : (e = pVA[i].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
3565 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
3566 [ # # # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
3567 : : /* reversed structure info: */
3568 : : /*!pc2i->c2at[i].endptRevrs &&*/
3569 [ # # # # ]: 0 : !(num_Fixed_H_Revrs && num_Fixed_H_Revrs[iat]) &&
3570 [ # # ]: 0 : !(pnMobHRevrs && pnMobHRevrs[iat]) &&
3571 [ # # # # ]: 0 : at2[iat].charge == 0 && at2[iat].num_H == 0 &&
3572 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2)
3573 : : {
3574 : :
3575 : 0 : iat_DB_O[num_DB_O++] = iat;
3576 : : /*
3577 : : if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) {
3578 : : goto exit_function;
3579 : : }
3580 : : */
3581 : : }
3582 : : else
3583 : : {
3584 [ # # ]: 0 : if ( /* in restored atom N: charge=0, no H, has no double bond, not an endpoint */
3585 : 0 : num_SB_N_Neutr < MAX_DIFF_FIXH &&
3586 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
3587 : : /*at2[iat].valence == at2[iat].chem_bonds_valence ||*/
3588 [ # # # # ]: 0 : (at2[iat].valence == 4 && at2[iat].chem_bonds_valence == 5) &&
3589 [ # # ]: 0 : !pVA[iat].cMetal &&
3590 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber >= 1 &&
# # ]
3591 [ # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) &&
3592 : : /* in orig.InChI: not an endpoint, has no H */
3593 [ # # ]: 0 : !pStruct->endpoint[i] &&
3594 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
3595 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
3596 : : /* has (+) edge */
3597 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
3598 : : {
3599 : :
3600 : 0 : iat_SB_N_Neutr[num_SB_N_Neutr++] = iat;
3601 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
3602 : : {
3603 : 0 : goto exit_function;
3604 : : }
3605 : : }
3606 : : }
3607 : : }
3608 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_N_Neutr, num_DB_O))) /* djb-rwth: addressing LLVM warning */
3609 : : {
3610 : : /* detected; attempt to fix */
3611 : : BNS_EDGE* pe_CMinus;
3612 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3613 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
3614 : 0 : delta = 1;
3615 [ # # # # ]: 0 : for (i = 0; i < num_DB_O && cur_success < num_try; i++)
3616 : : {
3617 : 0 : iat = iat_DB_O[i];
3618 : 0 : pe_CMinus = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
3619 : 0 : pe_CMinus->forbidden &= forbidden_edge_mask_inv;
3620 : :
3621 : 0 : pe = pBNS->edge + pBNS->vert[iat].iedge[0]; /* double bond O=...*/
3622 [ # # ]: 0 : if (!pe->flow)
3623 : 0 : continue;
3624 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
3625 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
3626 : :
3627 : 0 : pe->forbidden |= forbidden_edge_mask; /* change bond O=X to O(rad)-X(rad) */
3628 : 0 : pe->flow -= delta;
3629 : 0 : pv1->st_edge.flow -= delta;
3630 : 0 : pv2->st_edge.flow -= delta;
3631 : 0 : pBNS->tot_st_flow -= 2 * delta;
3632 : :
3633 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
3634 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
3635 : :
3636 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
3637 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 2) /* djb-rwth: addressing LLVM warning */
# # ]
3638 : : {
3639 : : /* Added (-) charge to =O and (+) charge to N => nDeltaCharge == 2 */
3640 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
3641 [ # # ]: 0 : if (ret > 0)
3642 : : {
3643 : 0 : nNumRunBNS++;
3644 : 0 : cur_success++; /* 13 */
3645 : : }
3646 : : }
3647 : : else
3648 : : {
3649 : 0 : pe->flow += delta;
3650 : 0 : pv1->st_edge.flow += delta;
3651 : 0 : pv2->st_edge.flow += delta;
3652 : 0 : pBNS->tot_st_flow += 2 * delta;
3653 : : }
3654 : 0 : pe->forbidden &= forbidden_edge_mask_inv; /* allow changes to O=X bond */
3655 : : INCHI_HEAPCHK
3656 : : }
3657 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3658 : : }
3659 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
3660 [ # # ]: 0 : if (cur_success)
3661 : : {
3662 : 0 : tot_succes += cur_success;
3663 : : /* recalculate InChI from the structure */
3664 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
3665 : : ppt_group_info, ppat_norm, ppat_prep)))
3666 : : {
3667 : 0 : goto exit_function;
3668 : : }
3669 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
3670 : : {
3671 : 0 : goto exit_function;
3672 : : }
3673 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
3674 : : {
3675 : 0 : goto exit_function; /* no fixed-H found */
3676 : : }
3677 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
3678 : : {
3679 : 0 : goto exit_function;
3680 : : }
3681 [ # # ]: 0 : if (!pc2i->bHasDifference)
3682 : : {
3683 : 0 : goto exit_function; /* nothing to do */
3684 : : }
3685 : 0 : break;
3686 : : }/* else
3687 : : if ( bOnly_N_V ) {
3688 : : bOnly_N_V = 0;
3689 : : }
3690 : : */
3691 : : }
3692 : : }
3693 : : }
3694 : :
3695 [ # # ]: 0 : if (( (pc2i->nNumTgInChI <= 1 &&
3696 [ # # # # : 0 : pc2i->nNumRemHInChI > pc2i->nNumRemHRevrs) || pc2i->len_c2at ) &&
# # ]
3697 : 0 : bHas_N_V( at2, pStruct->num_atoms )) /* djb-rwth: addressing LLVM warnings */
3698 : : {
3699 : : /*-----------------------------------------------------------------*/
3700 : : /* | | */
3701 : : /* case 14: restored:-N=AB=N=CD-XH original: (-)N-AB-N(+)=CD-XH */
3702 : : /* FixH: 0 0 0/1 0 1 */
3703 : : /* MobH: 0 0 1/0 0 0 */
3704 : : /* non-taut n/t any non any */
3705 : : /* taut */
3706 : : /* X = O, S, Se, N; N = N */
3707 : : /* t-group in original may have more (-) than in restored */
3708 : : /* same num_H and less (-) than in the restored structure */
3709 : : /* atom N(V)/N(IV)(+) is not taut in both */
3710 : : /* The following transformation should be possible: */
3711 : : /* | | */
3712 : : /* N=AB=N=CD-XH -> (-)N-AB-N-CD=XH(+) */
3713 : : /* This allows ADP to remove H(+) from -XH */
3714 : : /* As the result, the original structure has 0 or 1 t-group */
3715 : : /* Solution: separate charges between -N(III)= and N(V) */
3716 : : /*-----------------------------------------------------------------*/
3717 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
3718 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
3719 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
3720 : :
3721 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
3722 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
3723 : 0 : int num_N_V = 0, iat, i1, i2, i3, e1Flower, e1Plus, e2Plus, e2Minus, e3Plus;
3724 : 0 : int max_success = pc2i->nNumRemHInChI - pc2i->nNumRemHRevrs;
3725 : : EDGE_LIST iat_X_List, iat_N_III_List;
3726 : 0 : AllocEdgeList( &iat_X_List, EDGE_LIST_CLEAR );
3727 : 0 : AllocEdgeList( &iat_N_III_List, EDGE_LIST_CLEAR );
3728 : 0 : cur_success = 0;
3729 : 0 : ret = 0;
3730 : :
3731 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
3732 : : {
3733 : 0 : iat = nCanon2AtnoRevrs[i];
3734 : : /* search for N(V), 3 bonds */
3735 [ # # ]: 0 : if ( /* restored structure */
3736 : 0 : num_N_V < MAX_DIFF_FIXH &&
3737 [ # # # # ]: 0 : at2[iat].chem_bonds_valence == 5 && at2[iat].valence == 3 &&
3738 [ # # # # ]: 0 : !at2[iat].charge && !at2[iat].radical &&
3739 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
# # ]
3740 [ # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) &&
3741 [ # # ]: 0 : !at2[iat].num_H &&
3742 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
3743 [ # # # # ]: 0 : pBNS->edge[e].flow /* no charge */ &&
3744 [ # # ]: 0 : NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) && !pBNS->edge[j].forbidden &&
3745 [ # # ]: 0 : !pBNS->edge[j].flow /* neutral, valence=5 */ &&
3746 : : /* orig. InChI */
3747 [ # # # # ]: 0 : !pStruct->endpoint[i] &&
3748 [ # # # # : 0 : !(nMobHInChI && nMobHInChI[i]) && pStruct->fixed_H && !pStruct->fixed_H[i]) /* djb-rwth: fixing a NULL pointer dereference */
# # ]
3749 : : {
3750 : 0 : iat_N_V_Array[num_N_V++] = iat;
3751 : : }
3752 : : else
3753 : : {
3754 : : /* search for -N= */
3755 : 0 : if ( /* restored structure */
3756 [ # # # # ]: 0 : at2[iat].chem_bonds_valence == 3 && at2[iat].valence == 2 &&
3757 [ # # # # ]: 0 : !at2[iat].charge && !at2[iat].radical &&
3758 [ # # # # : 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
# # ]
3759 [ # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) &&
3760 [ # # ]: 0 : !at2[iat].num_H &&
3761 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
3762 [ # # # # ]: 0 : !pBNS->edge[e].flow /* no charge */ &&
3763 : : /* orig. InChI */
3764 : : /*!pStruct->endpoint[i] &&*/
3765 [ # # # # : 0 : !(nMobHInChI && nMobHInChI[i]) && pStruct->fixed_H && !pStruct->fixed_H[i]) /* djb-rwth: fixing a NULL pointer dereference */
# # ]
3766 : : {
3767 : :
3768 [ # # ]: 0 : if ((ret = AddToEdgeList(&iat_N_III_List, iat, 32))) /* djb-rwth: addressing LLVM warning */
3769 : : {
3770 : 0 : goto exit_case_14;
3771 : : }
3772 : : }
3773 : : else
3774 : : {
3775 : : /* search for -OH -NH-, -NH2 */
3776 : 0 : if ( /* restored structure */
3777 [ # # ]: 0 : at2[iat].chem_bonds_valence == at2[iat].valence &&
3778 [ # # # # ]: 0 : !at2[iat].charge && !at2[iat].radical &&
3779 [ # # # # ]: 0 : ((pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1) ||
3780 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 6) &&
3781 [ # # ]: 0 : at2[iat].num_H &&
3782 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
3783 [ # # # # ]: 0 : pBNS->edge[e].flow /* no charge */ &&
3784 : : /* orig. InChI */
3785 [ # # # # : 0 : !(nMobHInChI && nMobHInChI[i]) && pStruct->fixed_H && pStruct->fixed_H[i]) /* djb-rwth: addressing LLVM warning; fixing a NULL pointer dereference */
# # ]
3786 : : {
3787 : :
3788 [ # # ]: 0 : if ((ret = AddToEdgeList(&iat_X_List, iat, 32))) /* djb-rwth: addressing LLVM warning */
3789 : : {
3790 : 0 : goto exit_case_14;
3791 : : }
3792 : : }
3793 : : }
3794 : : }
3795 : : }
3796 [ # # ]: 0 : if (!max_success)
3797 : : {
3798 : 0 : max_success = inchi_min(num_N_V, iat_N_III_List.num_edges);
3799 : 0 : max_success = inchi_min(max_success, iat_X_List.num_edges);
3800 : : }
3801 [ # # # # : 0 : if (num_N_V && iat_N_III_List.num_edges && iat_X_List.num_edges)
# # ]
3802 : : {
3803 [ # # # # ]: 0 : for (i1 = 0; i1 < num_N_V && cur_success < max_success; i1++)
3804 : : {
3805 : 0 : int iat_N_V = iat_N_V_Array[i1];
3806 [ # # ]: 0 : if (NO_VERTEX == iat_N_V ||
3807 [ # # # # ]: 0 : 0 >= (e1Plus = pVA[iat_N_V].nCPlusGroupEdge - 1) ||
3808 : 0 : NO_VERTEX == (e1Flower = GetChargeFlowerUpperEdge(pBNS, pVA, e1Plus)) ||
3809 [ # # ]: 0 : 1 != pBNS->edge[e1Plus].flow ||
3810 [ # # ]: 0 : 0 != pBNS->edge[e1Flower].flow)
3811 : : {
3812 : 0 : continue;
3813 : : }
3814 [ # # # # ]: 0 : for (i2 = iat_N_III_List.num_edges - 1; 0 <= i2 && cur_success < max_success; i2--)
3815 : : {
3816 : 0 : int iat_N_III = iat_N_III_List.pnEdges[i2];
3817 [ # # ]: 0 : if (NO_VERTEX == iat_N_III ||
3818 [ # # ]: 0 : 0 >= (e2Minus = pVA[iat_N_III].nCMinusGroupEdge - 1) ||
3819 [ # # ]: 0 : 0 >= (e2Plus = pVA[iat_N_III].nCPlusGroupEdge - 1) ||
3820 [ # # ]: 0 : 0 != pBNS->edge[e2Minus].flow ||
3821 [ # # ]: 0 : 1 != pBNS->edge[e2Plus].flow)
3822 : : {
3823 : : /* do not consider this atom anymore */
3824 : 0 : iat_N_III_List.pnEdges[i2] = NO_VERTEX;
3825 : 0 : continue;
3826 : : }
3827 [ # # # # ]: 0 : for (i3 = iat_X_List.num_edges - 1; 0 <= i3 && cur_success < max_success; i3--)
3828 : : {
3829 : 0 : int iat_X = iat_X_List.pnEdges[i3];
3830 : : BNS_VERTEX* pv1n, * pv2n;
3831 : : BNS_EDGE* pe1n, * pe2n, * pe1Plus, * pe2Minus, * pe3Plus;
3832 : : Vertex v1n, v2n;
3833 : 0 : ret = 0;
3834 [ # # ]: 0 : if (NO_VERTEX == iat_X ||
3835 [ # # ]: 0 : 0 >= (e3Plus = pVA[iat_X].nCPlusGroupEdge - 1) ||
3836 [ # # ]: 0 : 1 != pBNS->edge[e3Plus].flow)
3837 : : {
3838 : : /* do not consider this atom anymore */
3839 : 0 : iat_X_List.pnEdges[i3] = NO_VERTEX;
3840 : 0 : continue;
3841 : : }
3842 : : /* all is ready to check whether the following applies:
3843 : : forbid changes of all charges and N,P,... flowers
3844 : : allow to change edges: e2Minus, e3Plus
3845 : : Increment flow in e1Flower
3846 : : The result should be: increase in number of charges by 2
3847 : : */
3848 : 0 : pe1Plus = pBNS->edge + e1Plus; /* N(V) positive charge edge */
3849 : 0 : pe2Minus = pBNS->edge + e2Minus; /* =N- negative charge edge */
3850 : 0 : pe3Plus = pBNS->edge + e3Plus; /* -XH positive charge edge */
3851 : 0 : pe = pBNS->edge + e1Flower; /* N(V) flower edge */
3852 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
3853 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
3854 [ # # ]: 0 : for (j = pv1->num_adj_edges - 1; 0 <= j; j--)
3855 : : {
3856 : 0 : pe1n = pBNS->edge + pv1->iedge[j];
3857 [ # # # # : 0 : if (pe1n->flow && !pe1n->forbidden && pe1n != pe1Plus)
# # ]
3858 : : {
3859 : 0 : pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1);
3860 : 0 : break;
3861 : : }
3862 : : }
3863 [ # # ]: 0 : if (j < 0)
3864 : : {
3865 : 0 : continue; /* not found -- should not happen */
3866 : : }
3867 [ # # ]: 0 : for (j = pv2->num_adj_edges - 1; 0 <= j; j--)
3868 : : { /* was -2; changed 2006-2-28 12:35pm*/
3869 : 0 : pe2n = pBNS->edge + pv2->iedge[j];
3870 [ # # # # : 0 : if (pe2n->flow && !pe2n->forbidden && pe2n != pe1Plus)
# # ]
3871 : : {
3872 : 0 : pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2);
3873 : 0 : break;
3874 : : }
3875 : : }
3876 [ # # ]: 0 : if (j < 0)
3877 : : {
3878 : 0 : continue; /* not found -- should not happen */
3879 : : }
3880 : 0 : delta = 1;
3881 : 0 : pe->flow += delta;
3882 : 0 : pe1n->flow -= delta;
3883 : 0 : pe2n->flow -= delta;
3884 : 0 : pv1n->st_edge.flow -= delta;
3885 : 0 : pv2n->st_edge.flow -= delta;
3886 : 0 : pBNS->tot_st_flow -= 2 * delta;
3887 : :
3888 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3889 : 0 : SetForbiddenEdgeMask(pBNS, &OtherNFlowerEdges, forbidden_edge_mask);
3890 : :
3891 : : /* allow two charges to change */
3892 : 0 : pe2Minus->forbidden &= forbidden_edge_mask_inv;
3893 : 0 : pe3Plus->forbidden &= forbidden_edge_mask_inv;
3894 : : /* test #1 */
3895 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
3896 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
3897 : : INCHI_HEAPCHK
3898 [ # # ]: 0 : if (ret < 0)
3899 : : {
3900 : 0 : goto exit_case_14;
3901 : : }
3902 : : else
3903 : : {
3904 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) ||
# # ]
3905 [ # # # # ]: 0 : (vPathEnd == v2n && vPathStart == v1n)) &&
3906 [ # # ]: 0 : nDeltaCharge == 2) /* djb-rwth: addressing LLVM warning */
3907 : : {
3908 : : ; /* success */
3909 : : }
3910 : : else
3911 : : {
3912 : 0 : ret = 0;
3913 : : }
3914 : : }
3915 : : /* restore BNS */
3916 : 0 : pe2Minus->forbidden |= forbidden_edge_mask;
3917 : 0 : pe3Plus->forbidden |= forbidden_edge_mask;
3918 : 0 : pe->flow -= delta;
3919 : 0 : pe1n->flow += delta;
3920 : 0 : pe2n->flow += delta;
3921 : 0 : pv1n->st_edge.flow += delta;
3922 : 0 : pv2n->st_edge.flow += delta;
3923 : 0 : pBNS->tot_st_flow += 2 * delta;
3924 [ # # ]: 0 : if (ret == 1)
3925 : : {
3926 : : /* test #2: check if charge separation is possible */
3927 : 0 : pe->flow += delta;
3928 : 0 : pe1n->flow -= delta;
3929 : 0 : pe2n->flow -= delta;
3930 : 0 : pv1n->st_edge.flow -= delta;
3931 : 0 : pv2n->st_edge.flow -= delta;
3932 : 0 : pBNS->tot_st_flow -= 2 * delta;
3933 : :
3934 : : /* allow two charges (N(V) and N(III)) to change */
3935 : 0 : pe2Minus->forbidden &= forbidden_edge_mask_inv;
3936 : 0 : pe1Plus->forbidden &= forbidden_edge_mask_inv;
3937 : : /* test #2 */
3938 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
3939 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
3940 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) ||
# # ]
3941 [ # # # # ]: 0 : (vPathEnd == v2n && vPathStart == v1n)) &&
3942 [ # # ]: 0 : nDeltaCharge == 2) /* djb-rwth: addressing LLVM warnings */
3943 : : {
3944 : : /* success; actually change charges */
3945 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
3946 [ # # ]: 0 : if (ret > 0)
3947 : : {
3948 : 0 : nNumRunBNS++;
3949 : 0 : cur_success++; /* 14 */
3950 : : }
3951 : : }
3952 [ # # ]: 0 : if (ret <= 0)
3953 : : {
3954 : : /* failed: restore BNS flow */
3955 : 0 : pe->flow -= delta;
3956 : 0 : pe1n->flow += delta;
3957 : 0 : pe2n->flow += delta;
3958 : 0 : pv1n->st_edge.flow += delta;
3959 : 0 : pv2n->st_edge.flow += delta;
3960 : 0 : pBNS->tot_st_flow += 2 * delta;
3961 : : }
3962 : : INCHI_HEAPCHK
3963 : : }
3964 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3965 : 0 : RemoveForbiddenEdgeMask(pBNS, &OtherNFlowerEdges, forbidden_edge_mask);
3966 [ # # ]: 0 : if (ret > 0)
3967 : : {
3968 : : /* do not repeat for the same atoms */
3969 : 0 : iat_N_V_Array[i1] = NO_VERTEX;
3970 : 0 : iat_N_III_List.pnEdges[i2] = NO_VERTEX;
3971 : 0 : iat_X_List.pnEdges[i3] = NO_VERTEX;
3972 : : }
3973 [ # # ]: 0 : if (ret < 0)
3974 : : {
3975 : 0 : goto exit_case_14;
3976 : : }
3977 [ # # ]: 0 : if (ret > 0)
3978 : : {
3979 : 0 : break;
3980 : : }
3981 : : } /* i3 cycle */
3982 [ # # ]: 0 : if (ret > 0)
3983 : : {
3984 : 0 : break;
3985 : : }
3986 : : } /* i2 cycle */
3987 : : }
3988 : : }
3989 : 0 : exit_case_14:
3990 : 0 : AllocEdgeList(&iat_X_List, EDGE_LIST_FREE);
3991 : 0 : AllocEdgeList(&iat_N_III_List, EDGE_LIST_FREE);
3992 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
3993 : 0 : RemoveForbiddenEdgeMask(pBNS, &OtherNFlowerEdges, forbidden_edge_mask);
3994 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
3995 [ # # ]: 0 : if (ret < 0)
3996 : : {
3997 : 0 : goto exit_function;
3998 : : }
3999 [ # # ]: 0 : if (cur_success)
4000 : : {
4001 : 0 : tot_succes += cur_success;
4002 : : /* recalculate InChI from the structure */
4003 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4004 : : ppt_group_info, ppat_norm, ppat_prep)))
4005 : : {
4006 : 0 : goto exit_function;
4007 : : }
4008 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
4009 : : {
4010 : 0 : goto exit_function;
4011 : : }
4012 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4013 : : {
4014 : 0 : goto exit_function; /* no fixed-H found */
4015 : : }
4016 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
4017 : : {
4018 : 0 : goto exit_function;
4019 : : }
4020 [ # # ]: 0 : if (!pc2i->bHasDifference)
4021 : : {
4022 : 0 : goto exit_function; /* nothing to do */
4023 : : }
4024 : : }
4025 : : }
4026 : :
4027 [ # # ]: 0 : if (pc2i->nNumTgMRevrs > pc2i->nNumTgMInChI ||
4028 [ # # ]: 0 : pc2i->nNumRemHRevrs < pc2i->nNumRemHInChI ||
4029 [ # # ]: 0 : pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI ||
4030 [ # # # # ]: 0 : (pc2i->nNumTgInChI <= 1 && pc2i->nNumTgRevrs > pc2i->nNumTgInChI)) /* djb-rwth: addressing LLVM warning */
4031 : : {
4032 : : /*--------------------------------------------------------------*/
4033 : : /* case 15: restored: -(+)O=AB-N< orig: -O-AB=N(+)< */
4034 : : /* (a) restored t-groups have more (-) than in original InChI */
4035 : : /* (b) Mobile-H charge: restored > original InChI *and* */
4036 : : /* removed H: restored < original InChI */
4037 : : /* (c) restored t-groups have less endpnoits than in orig InChI */
4038 : : /* O = O, S, Se, Te; N = N */
4039 : : /* Solution: move (+) from -O(+)= to -N< */
4040 : : /*--------------------------------------------------------------*/
4041 : 0 : int num_SB_Neutr = 0, num_DB_Charged = 0, iat;
4042 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
4043 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
4044 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
4045 : 0 : cur_success = 0;
4046 : :
4047 : : /* search for -O(+)= */
4048 : : /* search for -N< */
4049 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
4050 : : { /* i = canonical number - 1 */
4051 : 0 : iat = nCanon2AtnoRevrs[i];
4052 [ # # ]: 0 : if ( /* -O(+)= in restored atom: charge=1, has no H, a double bond */
4053 : 0 : num_DB_Charged < MAX_DIFF_FIXH &&
4054 [ # # # # ]: 0 : at2[iat].charge == 1 && !at2[iat].num_H &&
4055 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4056 [ # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6) &&
4057 : : /* in orig.InChI: an endpoint, has fixed-H */
4058 : : /*pStruct->endpoint[i] &&*/
4059 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
4060 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
4061 : : /* has (+) edge */
4062 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden)
4063 : : {
4064 : :
4065 : 0 : iat_DB_Charged[num_DB_Charged++] = iat;
4066 : : /*
4067 : : if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) {
4068 : : goto exit_function;
4069 : : }
4070 : : */
4071 : : }
4072 : : else
4073 : : {
4074 [ # # ]: 0 : if ( /* -N< in restored atom: charge=0, has no H, has no double bond, N only */
4075 : 0 : num_SB_Neutr < MAX_DIFF_FIXH &&
4076 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
4077 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4078 [ # # ]: 0 : (pVA[iat].cNumValenceElectrons == 5 &&
4079 [ # # ]: 0 : pVA[iat].cPeriodicRowNumber == 1) &&
4080 : : /* in orig.InChI: an endpoint, has fixed-H */
4081 : : /*pStruct->endpoint[i] &&*/
4082 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
4083 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
4084 : : /* has (+) edge */
4085 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && 0 == pBNS->edge[e].forbidden)
4086 : : {
4087 : :
4088 : 0 : iat_SB_Neutr[num_SB_Neutr++] = iat;
4089 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
4090 : : {
4091 : 0 : goto exit_function;
4092 : : }
4093 : : }
4094 : : }
4095 : : }
4096 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */
4097 : : {
4098 : : /* detected; attempt to fix */
4099 : : BNS_VERTEX* pv1n, * pv2n;
4100 : : BNS_EDGE* pe1n, * pe2n;
4101 : : Vertex v1n, v2n;
4102 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4103 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
4104 : 0 : delta = 1;
4105 [ # # # # ]: 0 : for (i = 0; i < num_DB_Charged && cur_success < num_try; i++)
4106 : : {
4107 : 0 : iat = iat_DB_Charged[i];
4108 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
4109 [ # # ]: 0 : if (pe->flow)
4110 : 0 : continue;
4111 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
4112 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
4113 : :
4114 [ # # ]: 0 : for (j = pv1->num_adj_edges - 1; 0 <= j; j--)
4115 : : {
4116 : 0 : pe1n = pBNS->edge + pv1->iedge[j];
4117 [ # # # # ]: 0 : if (pe1n->flow && !pe1n->forbidden)
4118 : : {
4119 : 0 : pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1);
4120 : 0 : break;
4121 : : }
4122 : : }
4123 [ # # ]: 0 : if (j < 0)
4124 : : {
4125 : 0 : continue; /* not found */
4126 : : }
4127 : :
4128 [ # # ]: 0 : for (j = pv2->num_adj_edges - 1; 0 <= j; j--)
4129 : : { /* was -2; changed 2006-2-28 12:35pm*/
4130 : 0 : pe2n = pBNS->edge + pv2->iedge[j];
4131 [ # # # # ]: 0 : if (pe2n->flow && !pe2n->forbidden)
4132 : : {
4133 : 0 : pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2);
4134 : 0 : break;
4135 : : }
4136 : : }
4137 [ # # ]: 0 : if (j < 0)
4138 : : {
4139 : 0 : continue; /* not found */
4140 : : }
4141 : :
4142 : 0 : pe->flow += delta;
4143 : 0 : pe1n->flow -= delta;
4144 : 0 : pe2n->flow -= delta;
4145 : 0 : pv1n->st_edge.flow -= delta;
4146 : 0 : pv2n->st_edge.flow -= delta;
4147 : 0 : pBNS->tot_st_flow -= 2 * delta;
4148 : :
4149 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
4150 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
4151 : :
4152 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) ||
# # ]
4153 [ # # # # ]: 0 : (vPathEnd == v2n && vPathStart == v1n)) &&
4154 [ # # # # ]: 0 : (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */
4155 : : {
4156 : : /* Moved charge from O(+) to -N< => nDeltaCharge == 1 or 0 if pe2n = -N< charge edge */
4157 : : /* Flow change on pe (+)charge edge (atom NH2) is not known to RunBnsTestOnce()) */
4158 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
4159 [ # # ]: 0 : if (ret > 0)
4160 : : {
4161 : 0 : nNumRunBNS++;
4162 : 0 : cur_success++; /* 15 */
4163 : : }
4164 : : }
4165 : : else
4166 : : {
4167 : 0 : pe->flow -= delta;
4168 : 0 : pe1n->flow += delta;
4169 : 0 : pe2n->flow += delta;
4170 : 0 : pv1n->st_edge.flow += delta;
4171 : 0 : pv2n->st_edge.flow += delta;
4172 : 0 : pBNS->tot_st_flow += 2 * delta;
4173 : : }
4174 : : INCHI_HEAPCHK
4175 : : }
4176 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4177 : : }
4178 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4179 [ # # ]: 0 : if (cur_success)
4180 : : {
4181 : 0 : tot_succes += cur_success;
4182 : : /* recalculate InChI from the structure */
4183 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4184 : : ppt_group_info, ppat_norm, ppat_prep)))
4185 : : {
4186 : 0 : goto exit_function;
4187 : : }
4188 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
4189 : : {
4190 : 0 : goto exit_function;
4191 : : }
4192 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4193 : : {
4194 : 0 : goto exit_function; /* no fixed-H found */
4195 : : }
4196 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
4197 : : {
4198 : 0 : goto exit_function;
4199 : : }
4200 [ # # ]: 0 : if (!pc2i->bHasDifference)
4201 : : {
4202 : 0 : goto exit_function; /* nothing to do */
4203 : : }
4204 : : }
4205 : : }
4206 : :
4207 [ # # ]: 0 : if (pc2i->nNumTgDiffMinus)
4208 : : {
4209 : : /*----------------------------------------------------------------*/
4210 : : /* case 16: restored: O=X-NH(-) orig.: O(-)-X=NH */
4211 : : /* t-group: (H,-) (2H) */
4212 : : /* O(-) = S, Se, Te; N = N; */
4213 : : /* Solution: move (-) from O(-) to -NH(-) */
4214 : : /*----------------------------------------------------------------*/
4215 : 0 : int num_SB_N_Minus = 0, num_DB_O_Neutr = 0, iat, itg;
4216 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
4217 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
4218 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
4219 : 0 : cur_success = 0; /* djb-rwth: ignoring LLVM warning: variable used */
4220 : :
4221 [ # # # # ]: 0 : for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++)
4222 : : {
4223 [ # # ]: 0 : if (pStruct->ti.t_group[itg].nNumEndpoints != pStruct->One_ti.t_group[itg].nNumEndpoints ||
4224 [ # # ]: 0 : pStruct->ti.t_group[itg].num[1] >= pStruct->One_ti.t_group[itg].num[1])
4225 : : {
4226 : 0 : continue;
4227 : : }
4228 : 0 : CurrEdges.num_edges = num_SB_N_Minus = num_DB_O_Neutr = 0;
4229 : 0 : cur_success = 0;
4230 : 0 : for (j = 0, k = pStruct->One_ti.t_group[itg].nFirstEndpointAtNoPos;
4231 [ # # ]: 0 : j < pStruct->One_ti.t_group[itg].nNumEndpoints; j++)
4232 : : {
4233 : 0 : i = pStruct->One_ti.nEndpointAtomNumber[k + j]; /* canonical number in restored struct. */
4234 : 0 : iat = nCanon2AtnoRevrs[i];
4235 [ # # ]: 0 : if ( /* in restored atom: charge=0, has no H, has double bond, O, S, Se, Te */
4236 : 0 : num_DB_O_Neutr < MAX_DIFF_FIXH &&
4237 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
4238 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4239 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
4240 : : /* in orig.InChI: an endpoint, may have fixed-H */
4241 [ # # # # ]: 0 : pStruct->endpoint[i] &&
4242 : : /*!(pStruct->fixed_H && pStruct->fixed_H[i]) &&*/
4243 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
4244 : : /* has (-) edge */
4245 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden)
4246 : : {
4247 : :
4248 : 0 : iat_DB_O_Neutr[num_DB_O_Neutr++] = iat;
4249 : :
4250 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
4251 : : {
4252 : 0 : goto exit_function;
4253 : : }
4254 : : }
4255 : : else
4256 : : {
4257 [ # # ]: 0 : if ( /* in restored atom: charge=-1, has H, has double bond, N */
4258 : 0 : num_SB_N_Minus < MAX_DIFF_FIXH &&
4259 [ # # # # ]: 0 : at2[iat].charge == -1 && at2[iat].num_H &&
4260 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4261 [ # # # # ]: 0 : pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1 &&
4262 : : /* in orig.InChI: an endpoint, has no fixed-H */
4263 [ # # ]: 0 : pStruct->endpoint[i] &&
4264 [ # # # # : 0 : (pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
4265 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
4266 : : /* has (-) edge */
4267 [ # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 &&
4268 [ # # ]: 0 : 0 == pBNS->edge[e].forbidden)
4269 : : {
4270 : :
4271 : 0 : iat_SB_N_Minus[num_SB_N_Minus++] = iat;
4272 : : /*
4273 : : if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) {
4274 : : goto exit_function;
4275 : : }
4276 : : */
4277 : : }
4278 : : }
4279 : : }
4280 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_N_Minus, num_DB_O_Neutr))) /* djb-rwth: addressing LLVM warning */
4281 : : {
4282 : : /* detected; attempt to fix */
4283 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4284 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
4285 : : /* allow stereobonds in rings change */
4286 : : /*
4287 : : if ( forbidden_stereo_edge_mask )
4288 : : RemoveForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask );
4289 : : */
4290 : 0 : delta = 1;
4291 [ # # # # ]: 0 : for (i = 0; i < num_SB_N_Minus && cur_success < num_try; i++)
4292 : : {
4293 : 0 : iat = iat_SB_N_Minus[i];
4294 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
4295 [ # # ]: 0 : if (!pe->flow)
4296 : 0 : continue;
4297 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
4298 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
4299 : :
4300 : : /*pe->forbidden |= forbidden_edge_mask;*/
4301 : 0 : pe->flow -= delta;
4302 : 0 : pv1->st_edge.flow -= delta;
4303 : 0 : pv2->st_edge.flow -= delta;
4304 : 0 : pBNS->tot_st_flow -= 2 * delta;
4305 : :
4306 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
4307 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
4308 : :
4309 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
4310 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */
# # ]
4311 : : {
4312 : : /* Moved (-) charge to =O => nDeltaCharge == 1 */
4313 : : /* Flow change on pe (-)charge edge (atom -NH(-)) is not known to RunBnsTestOnce()) */
4314 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
4315 [ # # ]: 0 : if (ret > 0)
4316 : : {
4317 : 0 : nNumRunBNS++;
4318 : 0 : cur_success++; /* 16 */
4319 : : }
4320 : : }
4321 : : else
4322 : : {
4323 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
4324 : 0 : pe->flow += delta;
4325 : 0 : pv1->st_edge.flow += delta;
4326 : 0 : pv2->st_edge.flow += delta;
4327 : 0 : pBNS->tot_st_flow += 2 * delta;
4328 : : }
4329 : : INCHI_HEAPCHK
4330 : : }
4331 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4332 : : /*
4333 : : if ( forbidden_stereo_edge_mask )
4334 : : SetForbiddenEdgeMask( pBNS, &FixedLargeRingStereoEdges, forbidden_stereo_edge_mask );
4335 : : */
4336 : : }
4337 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4338 [ # # ]: 0 : if (cur_success)
4339 : : {
4340 : 0 : tot_succes += cur_success;
4341 : : /* recalculate InChI from the structure */
4342 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4343 : : ppt_group_info, ppat_norm, ppat_prep)))
4344 : : {
4345 : 0 : goto exit_function;
4346 : : }
4347 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
4348 : : {
4349 : 0 : goto exit_function;
4350 : : }
4351 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4352 : : {
4353 : 0 : goto exit_function; /* no fixed-H found */
4354 : : }
4355 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
4356 : : {
4357 : 0 : goto exit_function;
4358 : : }
4359 [ # # ]: 0 : if (!pc2i->bHasDifference)
4360 : : {
4361 : 0 : goto exit_function; /* nothing to do */
4362 : : }
4363 : : }
4364 : : }
4365 : : }
4366 : :
4367 [ # # ]: 0 : if (pc2i->nNumRemHInChI < pc2i->nNumRemHRevrs)
4368 : : {
4369 : : /*--------------------------------------------------------------*/
4370 : : /* case 17: restored: OH(+)=AB-O- orig. HO-AB=O(+)- */
4371 : : /* number of removed H: n+m n */
4372 : : /* OH(+) = N, O, S, Se; -O- = P,As,O,S,Se,Te,F,Cl,Br,I */
4373 : : /* Solution: move (+) from OH(+) to -O- */
4374 : : /*--------------------------------------------------------------*/
4375 : 0 : int num_SB_Neutr = 0, num_DB_Charged = 0, iat;
4376 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
4377 [ # # # # ]: 0 : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H :
4378 [ # # # # ]: 0 : pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H : 0;
4379 : 0 : cur_success = 0;
4380 : :
4381 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
4382 : : { /* i = canonical number - 1 */
4383 : 0 : iat = nCanon2AtnoRevrs[i];
4384 [ # # ]: 0 : if ( /* in restored atom: charge=+1, has H, has double bond, N, O, S, Se, Te */
4385 : 0 : num_DB_Charged < MAX_DIFF_FIXH &&
4386 [ # # # # ]: 0 : at2[iat].charge == 1 && at2[iat].num_H &&
4387 [ # # # # ]: 0 : at2[iat].valence < at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4388 [ # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6 ||
4389 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1)) &&
4390 : : /* has (+) edge */
4391 [ # # # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warnings */
4392 : : {
4393 : :
4394 : 0 : iat_DB_Charged[num_DB_Charged++] = iat;
4395 : : /*
4396 : : if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) {
4397 : : goto exit_function;
4398 : : }
4399 : : */
4400 : : }
4401 : : else
4402 : : {
4403 [ # # ]: 0 : if ( /* in restored atom: charge=0, has no H, has no double bond, N, P, O, S, Se, Te */
4404 : 0 : num_SB_Neutr < MAX_DIFF_FIXH &&
4405 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
4406 [ # # # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4407 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6 || pVA[iat].cNumValenceElectrons == 7 ||
4408 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber > 1)) &&
4409 : : /* in orig.InChI: not an endpoint */
4410 [ # # ]: 0 : !pStruct->endpoint[i] &&
4411 [ # # # # : 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
# # ]
4412 [ # # ]: 0 : !(nMobHInChI && nMobHInChI[i]) &&
4413 : : /* has (+) edge */
4414 [ # # ]: 0 : (e = pVA[iat].nCPlusGroupEdge - 1) >= 0 &&
4415 [ # # ]: 0 : 0 == pBNS->edge[e].forbidden) /* djb-rwth: addressing LLVM warning */
4416 : : {
4417 : :
4418 : 0 : iat_SB_Neutr[num_SB_Neutr++] = iat;
4419 : :
4420 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
4421 : : {
4422 : 0 : goto exit_function;
4423 : : }
4424 : : }
4425 : : }
4426 : : }
4427 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_Neutr, num_DB_Charged))) /* djb-rwth: addressing LLVM warning */
4428 : : {
4429 : : BNS_VERTEX* pv1n, * pv2n;
4430 : : BNS_EDGE* pe1n, * pe2n;
4431 : : Vertex v1n, v2n;
4432 : :
4433 : 0 : num_try = inchi_min(num_try, pc2i->nNumRemHRevrs - pc2i->nNumRemHInChI);
4434 : : /* detected; attempt to fix */
4435 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4436 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
4437 : 0 : delta = 1;
4438 [ # # # # ]: 0 : for (i = 0; i < num_DB_Charged && cur_success < num_try; i++)
4439 : : {
4440 : 0 : iat = iat_DB_Charged[i];
4441 : 0 : pe = pBNS->edge + pVA[iat].nCPlusGroupEdge - 1;
4442 [ # # ]: 0 : if (pe->flow)
4443 : : {
4444 : 0 : continue;
4445 : : }
4446 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
4447 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
4448 : :
4449 [ # # ]: 0 : for (j = pv1->num_adj_edges - 1; 0 <= j; j--)
4450 : : {
4451 : 0 : pe1n = pBNS->edge + pv1->iedge[j];
4452 [ # # # # ]: 0 : if (pe1n->flow && !pe1n->forbidden)
4453 : : {
4454 : 0 : pv1n = pBNS->vert + (v1n = pe1n->neighbor12 ^ v1);
4455 : 0 : break;
4456 : : }
4457 : : }
4458 [ # # ]: 0 : if (j < 0)
4459 : : {
4460 : 0 : continue; /* not found */
4461 : : }
4462 : :
4463 [ # # ]: 0 : for (j = pv2->num_adj_edges - 1; 0 <= j; j--)
4464 : : { /* was -2; changed 2006-2-28 12:35pm*/
4465 : 0 : pe2n = pBNS->edge + pv2->iedge[j];
4466 [ # # # # ]: 0 : if (pe2n->flow && !pe2n->forbidden)
4467 : : {
4468 : 0 : pv2n = pBNS->vert + (v2n = pe2n->neighbor12 ^ v2);
4469 : 0 : break;
4470 : : }
4471 : : }
4472 [ # # ]: 0 : if (j < 0)
4473 : 0 : continue; /* not found */
4474 : :
4475 : 0 : pe->flow += delta;
4476 : 0 : pe1n->flow -= delta;
4477 : 0 : pe2n->flow -= delta;
4478 : 0 : pv1n->st_edge.flow -= delta;
4479 : 0 : pv2n->st_edge.flow -= delta;
4480 : 0 : pBNS->tot_st_flow -= 2 * delta;
4481 : :
4482 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
4483 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
4484 : :
4485 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1n && vPathStart == v2n) ||
# # ]
4486 [ # # # # ]: 0 : (vPathEnd == v2n && vPathStart == v1n)) &&
4487 [ # # # # ]: 0 : (nDeltaCharge == 0 || nDeltaCharge == 1)) /* djb-rwth: addressing LLVM warnings */
4488 : : {
4489 : : /* Moved charge from OH(+) to -O- => nDeltaCharge == 1 or 0 if pe2n = -O- charge edge */
4490 : : /* Flow change on pe (+)charge edge (atom OH(+)) is not known to RunBnsTestOnce()) */
4491 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
4492 [ # # ]: 0 : if (ret > 0)
4493 : : {
4494 : 0 : nNumRunBNS++;
4495 : 0 : cur_success++; /* 17 */
4496 : : }
4497 : : }
4498 : : else
4499 : : {
4500 : 0 : pe->flow -= delta;
4501 : 0 : pe1n->flow += delta;
4502 : 0 : pe2n->flow += delta;
4503 : 0 : pv1n->st_edge.flow += delta;
4504 : 0 : pv2n->st_edge.flow += delta;
4505 : 0 : pBNS->tot_st_flow += 2 * delta;
4506 : : }
4507 : : INCHI_HEAPCHK
4508 : : }
4509 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4510 : : }
4511 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4512 [ # # ]: 0 : if (cur_success)
4513 : : {
4514 : 0 : tot_succes += cur_success;
4515 : : /* recalculate InChI from the structure */
4516 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4517 : : ppt_group_info, ppat_norm, ppat_prep)))
4518 : : {
4519 : 0 : goto exit_function;
4520 : : }
4521 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
4522 : : {
4523 : 0 : goto exit_function;
4524 : : }
4525 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4526 : : {
4527 : 0 : goto exit_function; /* no fixed-H found */
4528 : : }
4529 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
4530 : : {
4531 : 0 : goto exit_function;
4532 : : }
4533 [ # # ]: 0 : if (!pc2i->bHasDifference)
4534 : : {
4535 : 0 : goto exit_function; /* nothing to do */
4536 : : }
4537 : : }
4538 : : }
4539 : :
4540 [ # # # # ]: 0 : if (( pc2i->nNumTgInChI && pStruct->endpoint &&
4541 [ # # # # ]: 0 : pc2i->nNumTgMInChI > pc2i->nNumTgMRevrs && pc2i->nNumEndpInChI > pc2i->nNumEndpRevrs ))
4542 : : {
4543 : : /*-----------------------------------------------------------------*/
4544 : : /* */
4545 : : /* case 18: restored:-N=AB-X -(-)N-AB-X(+) */
4546 : : /* FixH: 0 0 0 0 */
4547 : : /* MobH: 0 0 0 0 */
4548 : : /* non non taut non */
4549 : : /* taut taut taut */
4550 : : /* X = any heteroatom N=N */
4551 : : /* t-group in original has (Hn,-m) in the restored: (Hn,-m+1) */
4552 : : /* same num_H and more (-) than in the restored structure */
4553 : : /* atom X is not taut in both */
4554 : : /* Solution: separate charges between -N(III)= and X */
4555 : : /*-----------------------------------------------------------------*/
4556 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
4557 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
4558 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
4559 : : int iat, e1, itg, max_success;
4560 : 0 : CurrEdges.num_edges = 0;
4561 : 0 : cur_success = 0;
4562 : 0 : ret = 0;
4563 : : /* search for -N= */
4564 [ # # # # ]: 0 : for (itg = 0; itg < pStruct->ti.num_t_groups && itg < pStruct->One_ti.num_t_groups; itg++)
4565 : : {
4566 [ # # ]: 0 : if (pStruct->ti.t_group[itg].nNumEndpoints <= pStruct->One_ti.t_group[itg].nNumEndpoints ||
4567 [ # # ]: 0 : pStruct->ti.t_group[itg].num[1] <= pStruct->One_ti.t_group[itg].num[1])
4568 : : {
4569 : 0 : continue;
4570 : : }
4571 : 0 : CurrEdges.num_edges = 0;
4572 : 0 : cur_success = 0;
4573 : 0 : for (j = 0, k = pStruct->ti.t_group[itg].nFirstEndpointAtNoPos;
4574 [ # # ]: 0 : j < pStruct->ti.t_group[itg].nNumEndpoints; j++)
4575 : : {
4576 : 0 : i = pStruct->ti.nEndpointAtomNumber[k + j]; /* canonical number in restored struct. */
4577 : 0 : iat = nCanon2AtnoRevrs[i];
4578 [ # # # # : 0 : if (!pStruct->endpoint[i] || !at_Mobile_H_Revrs || at_Mobile_H_Revrs[iat].endpoint ||
# # ]
4579 [ # # # # ]: 0 : pVA[i].cNumValenceElectrons != 5 || pVA[i].cPeriodicRowNumber != 1 ||
4580 [ # # # # : 0 : 2 != at2[iat].valence || at2[iat].num_H || at2[iat].radical ||
# # ]
4581 [ # # # # ]: 0 : (0 <= ( e1 = pVA[iat].nCPlusGroupEdge - 1 ) && !pBNS->edge[e1].flow) ||
4582 [ # # # # : 0 : 0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow) /* djb-rwth: addressing LLVM warning */
# # ]
4583 : : {
4584 : 0 : continue;
4585 : : }
4586 : : /* found -N= */
4587 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
4588 : : {
4589 : 0 : goto exit_function;
4590 : : }
4591 : : }
4592 : : }
4593 [ # # ]: 0 : if (!( max_success = CurrEdges.num_edges ))
4594 : : {
4595 : 0 : goto exit_case_18;
4596 : : }
4597 : : /* search for X */
4598 [ # # # # ]: 0 : for (i = 0; i < pStruct->num_atoms && cur_success < max_success; i++)
4599 : : {
4600 : 0 : iat = nCanon2AtnoRevrs[i];
4601 [ # # # # : 0 : if (pStruct->endpoint[i] || !pVA[i].cNumValenceElectrons || pVA[i].cNumValenceElectrons == 4 ||
# # ]
4602 [ # # # # ]: 0 : at2[iat].num_H || at2[iat].radical ||
4603 [ # # # # ]: 0 : (0 <= ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e1].flow) ||
4604 [ # # # # : 0 : 0 >( e = pVA[iat].nCPlusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow != 1) /* djb-rwth: addressing LLVM warnings */
# # ]
4605 : : {
4606 : 0 : continue;
4607 : : }
4608 : : /* try to move the charge */
4609 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
4610 : 0 : SetForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask );
4611 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask );
4612 : :
4613 : 0 : pe = pBNS->edge + e;
4614 [ # # ]: 0 : if (!pe->flow)
4615 : 0 : continue;
4616 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
4617 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
4618 : :
4619 : 0 : delta = 1;
4620 : 0 : pe->flow -= delta;
4621 : 0 : pv1->st_edge.flow -= delta;
4622 : 0 : pv2->st_edge.flow -= delta;
4623 : 0 : pBNS->tot_st_flow -= 2 * delta;
4624 : :
4625 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
4626 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
4627 : :
4628 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
4629 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */
# # ]
4630 : : {
4631 : : /* Created (-) charge on -N= => nDeltaCharge == 1 */
4632 : : /* Flow change on pe (+)charge edge (atom X) is not known to RunBnsTestOnce()) */
4633 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
4634 [ # # ]: 0 : if (ret > 0)
4635 : : {
4636 : 0 : nNumRunBNS++;
4637 : 0 : cur_success++; /* 18 */
4638 : : }
4639 : : }
4640 : : else
4641 : : {
4642 : 0 : pe->flow += delta;
4643 : 0 : pv1->st_edge.flow += delta;
4644 : 0 : pv2->st_edge.flow += delta;
4645 : 0 : pBNS->tot_st_flow += 2 * delta;
4646 : : }
4647 : : INCHI_HEAPCHK
4648 : : }
4649 : 0 : exit_case_18:
4650 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
4651 : 0 : RemoveForbiddenEdgeMask( pBNS, &OtherNFlowerEdges, forbidden_edge_mask );
4652 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4653 [ # # ]: 0 : if (ret < 0)
4654 : : {
4655 : 0 : goto exit_function;
4656 : : }
4657 [ # # ]: 0 : if (cur_success)
4658 : : {
4659 : 0 : tot_succes += cur_success;
4660 : : /* recalculate InChI from the structure */
4661 [ # # ]: 0 : if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4662 : : ppt_group_info, ppat_norm, ppat_prep ) ))
4663 : : {
4664 : 0 : goto exit_function;
4665 : : }
4666 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
4667 : : {
4668 : 0 : goto exit_function;
4669 : : }
4670 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4671 : : {
4672 : 0 : goto exit_function; /* no fixed-H found */
4673 : : }
4674 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
4675 : : {
4676 : 0 : goto exit_function;
4677 : : }
4678 [ # # ]: 0 : if (!pc2i->bHasDifference)
4679 : : {
4680 : 0 : goto exit_function; /* nothing to do */
4681 : : }
4682 : : }
4683 : : }
4684 : :
4685 [ # # ]: 0 : if (pc2i->len_c2at >= 1)
4686 : : {
4687 : : /*--------------------------------------------------------------*/
4688 : : /* case 19 restored: M--OH original: M(-)==OH(+) */
4689 : : /* FixH: metal 0 1 */
4690 : : /* MobH: 1 0 */
4691 : : /* O = O, S, Se, Te; not taut. in InChI */
4692 : : /* In restored structure has H; tautomeric or not tautomeric */
4693 : : /* Solution: move (+) from -OH to M; charhe on M may vary */
4694 : : /*--------------------------------------------------------------*/
4695 : : int iat;
4696 : : EdgeIndex eMPlus, eMMinus; /* djb-rwth: removing redundant variables/code */
4697 : : BNS_EDGE *peOHPlus, *peMPlus, *peMMinus, *peOMBond;
4698 : : int iatMetal, ChargeOnMetal, DeltaChargeExpected;
4699 : 0 : cur_success = 0;
4700 : : /* djb-rwth: removing redundant code */
4701 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
4702 : : {
4703 : 0 : iat = pc2i->c2at[i].atomNumber;
4704 : 0 : if ( /* orig. InChI info: =NH2(+), =OH(+) */
4705 [ # # ]: 0 : ( pc2i->c2at[i].nValElectr == 6 ) /* N, O, S, Se, Te */ &&
4706 : : /*!pc2i->c2at[i].endptInChI &&*/ /* <=== relaxation */
4707 [ # # # # : 0 : ( e = pVA[iat].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # ]
4708 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 1 && pc2i->c2at[i].nMobHInChI == 0 &&
4709 : : /* reversed structure info: */
4710 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 1 &&
4711 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && at2[iat].num_H &&
4712 [ # # ]: 0 : at2[iat].valence == 1 &&
4713 [ # # ]: 0 : at2[iat].valence == at2[iat].chem_bonds_valence &&
4714 : : /* metal atom */
4715 [ # # ]: 0 : pVA[iatMetal = at2[iat].neighbor[0]].cMetal &&
4716 [ # # # # ]: 0 : ( eMPlus = pVA[iatMetal].nCPlusGroupEdge - 1 ) >= 0 && !pBNS->edge[eMPlus].forbidden &&
4717 [ # # # # ]: 0 : ( eMMinus = pVA[iatMetal].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[eMMinus].forbidden &&
4718 [ # # ]: 0 : !pBNS->edge[pBNS->vert[iat].iedge[0]].forbidden
4719 : : ) /* djb-rwth: removing redundant code */
4720 : : {
4721 : : /* -OH charge edges */
4722 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, iat, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
4723 : : {
4724 : 0 : goto exit_function;
4725 : : }
4726 : : }
4727 : : }
4728 [ # # ]: 0 : if (CurrEdges.num_edges)
4729 : : {
4730 : : /* detected; fix */
4731 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
4732 : 0 : SetForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask );
4733 : 0 : SetForbiddenEdgeMask( pBNS, &AllBondEdges, forbidden_edge_mask );
4734 [ # # ]: 0 : for (i = 0; i < CurrEdges.num_edges; i++)
4735 : : {
4736 : : /* v1 is -OH, v2 is adjacent to it Metal */
4737 : 0 : iat = CurrEdges.pnEdges[i];
4738 : 0 : iatMetal = at2[iat].neighbor[0];
4739 : 0 : peOHPlus = pBNS->edge + ( (long long)pVA[iat].nCPlusGroupEdge - 1 ); /* djb-rwth: removing redundant variables/code */
4740 : 0 : peMPlus = pBNS->edge + ( (long long)pVA[iatMetal].nCPlusGroupEdge - 1 ); /* djb-rwth: removing redundant variables/code */
4741 : 0 : peMMinus = pBNS->edge + ( (long long)pVA[iatMetal].nCMinusGroupEdge - 1 ); /* djb-rwth: removing redundant variables/code */
4742 : 0 : peOMBond = pBNS->edge + ( pBNS->vert[iat].iedge[0] ); /* djb-rwth: removing redundant variables/code */
4743 : : /* remove forbidden edge masks */
4744 : 0 : peMPlus->forbidden &= forbidden_edge_mask_inv;
4745 : 0 : peMMinus->forbidden &= forbidden_edge_mask_inv;
4746 : 0 : peOMBond->forbidden &= forbidden_edge_mask_inv;
4747 : :
4748 : 0 : ChargeOnMetal = ( peMPlus->cap - peMPlus->flow ) - peMMinus->flow;
4749 [ # # ]: 0 : if (1 == ChargeOnMetal)
4750 : : {
4751 : : /* We are going to subtract 1 from the charge on Metal */
4752 : : /* Added (+)charge to -OH is not known to RunBnsTestOnce() */
4753 : 0 : DeltaChargeExpected = -1; /* charge will become = 0 */
4754 : : }
4755 : : else
4756 : : {
4757 [ # # ]: 0 : if (0 == ChargeOnMetal)
4758 : : {
4759 : 0 : DeltaChargeExpected = 1; /* charge on Metal will be created */
4760 : : }
4761 : : else
4762 : : {
4763 : 0 : DeltaChargeExpected = 0;
4764 : : }
4765 : : }
4766 : :
4767 : 0 : delta = 1;
4768 : 0 : pe = peOHPlus;
4769 [ # # ]: 0 : if (!pe->flow)
4770 : 0 : continue;
4771 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
4772 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
4773 : :
4774 : 0 : pe->flow -= delta; /* remove (-) from AB-O(-) */
4775 : 0 : pv1->st_edge.flow -= delta;
4776 : 0 : pv2->st_edge.flow -= delta;
4777 : 0 : pBNS->tot_st_flow -= 2 * delta;
4778 : :
4779 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
4780 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
4781 : :
4782 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
4783 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == DeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */
# # ]
4784 : : {
4785 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
4786 [ # # ]: 0 : if (ret > 0)
4787 : : {
4788 : 0 : nNumRunBNS++;
4789 : 0 : cur_success++; /* 19 */
4790 : : }
4791 : : }
4792 : : else
4793 : : {
4794 : 0 : pe->flow += delta;
4795 : 0 : pv1->st_edge.flow += delta;
4796 : 0 : pv2->st_edge.flow += delta;
4797 : 0 : pBNS->tot_st_flow += 2 * delta;
4798 : : }
4799 : : INCHI_HEAPCHK
4800 : : /* set forbidden edge masks back */
4801 : 0 : peMPlus->forbidden |= forbidden_edge_mask;
4802 : 0 : peMMinus->forbidden |= forbidden_edge_mask;
4803 : 0 : peOMBond->forbidden |= forbidden_edge_mask;
4804 : : }
4805 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
4806 : 0 : RemoveForbiddenEdgeMask( pBNS, &NFlowerEdges, forbidden_edge_mask );
4807 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllBondEdges, forbidden_edge_mask );
4808 : :
4809 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4810 [ # # ]: 0 : if (cur_success)
4811 : : {
4812 : 0 : tot_succes += cur_success;
4813 : : /* recalculate InChI from the structure */
4814 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4815 : : ppt_group_info, ppat_norm, ppat_prep ) ))
4816 : : {
4817 : 0 : goto exit_function;
4818 : : }
4819 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
4820 : : {
4821 : 0 : goto exit_function;
4822 : : }
4823 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4824 : : {
4825 : 0 : goto exit_function; /* no fixed-H found */
4826 : : }
4827 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
4828 : : {
4829 : 0 : goto exit_function;
4830 : : }
4831 [ # # ]: 0 : if (!pc2i->bHasDifference)
4832 : : {
4833 : 0 : goto exit_function; /* nothing to do */
4834 : : }
4835 : : }
4836 : : }
4837 : : }
4838 : :
4839 [ # # # # : 0 : if (pc2i->len_c2at > 1 && pc2i->nNumTgRevrs && pc2i->nNumTgInChI)
# # ]
4840 : : {
4841 : : /*--------------------------------------------------------------*/
4842 : : /* case 20: restored: O(-)-AB=N- original: O=AB-N(-)- */
4843 : : /* FixH: 0 0 0 -1 */
4844 : : /* MobH: 0 0 0 1 */
4845 : : /* taut non-taut non-taut taut */
4846 : : /* or taut no H */
4847 : : /* no H */
4848 : : /* O = O, S, Se; N = N, O, S, Se, Te; */
4849 : : /* restored atoms are taut/non-taut; original are opposite. */
4850 : : /* Solution: move (-) from O(-) to =N- */
4851 : : /*--------------------------------------------------------------*/
4852 : 0 : int num_SB_O_Minus = 0, num_DB_N = 0, iat;
4853 : :
4854 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
4855 : : /*
4856 : : inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
4857 : : pStruct->pOne_norm_data[1]->at)? pStruct->pOne_norm_data[1]->at : NULL;
4858 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
4859 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
4860 : : */
4861 : 0 : cur_success = 0;
4862 : :
4863 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4864 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
4865 : : {
4866 : 0 : iat = pc2i->c2at[i].atomNumber;
4867 [ # # ]: 0 : if ( /* orig. InChI info: =O or -N= */
4868 : 0 : num_DB_N < MAX_DIFF_FIXH &&
4869 [ # # ]: 0 : pc2i->c2at[i].endptInChI &&
4870 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
4871 [ # # ]: 0 : pBNS->edge[e].flow == 0 &&
4872 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 &&
4873 : : /* if more than 1 t-group are in orig. InChI then do not move (-) to N */
4874 [ # # # # ]: 0 : (pc2i->nNumTgInChI == 1 || pc2i->c2at[i].nValElectr == 6) &&
4875 : : /* reversed structure info: */
4876 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
4877 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && /*pc2i->c2at[i].nMobHRevrs == 0 &&*/
4878 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
4879 [ # # ]: 0 : at2[iat].valence + 1 == at2[iat].chem_bonds_valence)
4880 : : {
4881 : 0 : iat_DB_N[num_DB_N++] = iat;
4882 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
4883 : : {
4884 : 0 : goto exit_function;
4885 : : }
4886 : : }
4887 : : else
4888 : : {
4889 [ # # ]: 0 : if ( /* orig. InChI info: -O(-) */
4890 : 0 : num_SB_O_Minus < MAX_DIFF_FIXH &&
4891 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
4892 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
4893 [ # # ]: 0 : pBNS->edge[e].flow == 1 &&
4894 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 &&
4895 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 &&
4896 : : /* reversed structure info: */
4897 [ # # ]: 0 : pc2i->c2at[i].endptRevrs &&
4898 [ # # # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 && pc2i->c2at[i].nMobHRevrs == 0 &&
4899 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H &&
4900 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1)
4901 : : {
4902 : 0 : iat_SB_O_Minus[num_SB_O_Minus++] = iat;
4903 : : }
4904 : : }
4905 : : }
4906 [ # # ]: 0 : if (!num_DB_N)
4907 : : {
4908 : : /* search among N that are tautomeric in both cases */
4909 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
4910 : : { /* i = canonical number - 1 */
4911 [ # # ]: 0 : if (!pStruct->endpoint[i])
4912 : : {
4913 : 0 : continue;
4914 : : }
4915 : 0 : iat = nCanon2AtnoRevrs[i];
4916 [ # # ]: 0 : if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */
4917 : 0 : num_DB_N < MAX_DIFF_FIXH &&
4918 [ # # # # ]: 0 : at2[iat].charge == 0 && !at2[iat].num_H &&
4919 [ # # # # ]: 0 : at2[iat].valence + 1 == at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
4920 : : /* in orig.InChI: an endpoint, has no H */
4921 [ # # # # ]: 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
4922 : : /*!(nMobHInChI && nMobHInChI[i] ) &&*/
4923 : : /* has (-) edge */
4924 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
4925 [ # # ]: 0 : !pBNS->edge[e].flow)
4926 : : {
4927 : :
4928 : 0 : iat_DB_N[num_DB_N++] = iat;
4929 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
4930 : : {
4931 : 0 : goto exit_function;
4932 : : }
4933 : : }
4934 : : }
4935 : : }
4936 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_O_Minus, num_DB_N))) /* djb-rwth: addressing LLVM warning */
4937 : : {
4938 : : /* detected; attempt to fix */
4939 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4940 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
4941 : 0 : delta = 1;
4942 [ # # # # ]: 0 : for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++)
4943 : : {
4944 : 0 : iat = iat_SB_O_Minus[i];
4945 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
4946 [ # # ]: 0 : if (!pe->flow)
4947 : 0 : continue;
4948 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
4949 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
4950 : :
4951 : 0 : pe->flow -= delta;
4952 : 0 : pv1->st_edge.flow -= delta;
4953 : 0 : pv2->st_edge.flow -= delta;
4954 : 0 : pBNS->tot_st_flow -= 2 * delta;
4955 : :
4956 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
4957 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
4958 : :
4959 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
4960 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */
# # ]
4961 : : {
4962 : : /* Added (-) charge to =N- => nDeltaCharge == 1 */
4963 : : /* Flow change on pe (-)charge edge (atom -O(-)) is not known to RunBnsTestOnce()) */
4964 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
4965 [ # # ]: 0 : if (ret > 0)
4966 : : {
4967 : 0 : nNumRunBNS++;
4968 : 0 : cur_success++; /* 20 */
4969 : : }
4970 : : }
4971 : : else
4972 : : {
4973 : 0 : pe->flow += delta;
4974 : 0 : pv1->st_edge.flow += delta;
4975 : 0 : pv2->st_edge.flow += delta;
4976 : 0 : pBNS->tot_st_flow += 2 * delta;
4977 : : }
4978 : : INCHI_HEAPCHK
4979 : : }
4980 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
4981 : : }
4982 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
4983 [ # # ]: 0 : if (cur_success)
4984 : : {
4985 : 0 : tot_succes += cur_success;
4986 : : /* recalculate InChI from the structure */
4987 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
4988 : : ppt_group_info, ppat_norm, ppat_prep)))
4989 : : {
4990 : 0 : goto exit_function;
4991 : : }
4992 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
4993 : : {
4994 : 0 : goto exit_function;
4995 : : }
4996 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
4997 : : {
4998 : 0 : goto exit_function; /* no fixed-H found */
4999 : : }
5000 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
5001 : : {
5002 : 0 : goto exit_function;
5003 : : }
5004 [ # # ]: 0 : if (!pc2i->bHasDifference)
5005 : : {
5006 : 0 : goto exit_function; /* nothing to do */
5007 : : }
5008 : : }
5009 : : }
5010 : :
5011 [ # # # # : 0 : if (pc2i->len_c2at && pc2i->nNumTgRevrs && pc2i->nNumTgHInChI && pStruct->endpoint)
# # # # ]
5012 : : {
5013 : : /*--------------------------------------------------------------*/
5014 : : /* O(-) O */
5015 : : /* | || */
5016 : : /* case 21: restored: R=S=O original: R-S=O */
5017 : : /* | | */
5018 : : /* O(-) O(-) */
5019 : : /* All O are taut R is not taut */
5020 : : /* */
5021 : : /* In addition, another atom O that should have been tautomeric */
5022 : : /* or has H(+) added in Mobile-H layer is not like that */
5023 : : /* O = O, S, Se; S=S, Se, Te */
5024 : : /* Solution: move (-) from O(-) to =O */
5025 : : /* these atoms are tautomeric in restored structure */
5026 : : /*--------------------------------------------------------------*/
5027 : 0 : int num_SB_O_Minus = 0, num_DB_O = 0, iat, iS;
5028 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
5029 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
5030 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
5031 : : /*
5032 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
5033 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
5034 : : */
5035 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5036 : 0 : cur_success = 0;
5037 : :
5038 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
5039 : : {
5040 : 0 : iat = pc2i->c2at[i].atomNumber;
5041 [ # # ]: 0 : if ( /* orig. InChI info: =O */
5042 : 0 : num_DB_O < MAX_DIFF_FIXH &&
5043 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ &&
5044 [ # # # # ]: 0 : (pc2i->c2at[i].endptInChI || pc2i->c2at[i].nMobHInChI) &&
5045 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
5046 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/
5047 : : /* reversed structure info: */
5048 [ # # # # ]: 0 : !(pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs) &&
5049 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 &&
5050 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
5051 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2)
5052 : : {
5053 : 0 : iat_DB_O[num_DB_O++] = iat;
5054 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
5055 : : {
5056 : 0 : goto exit_function;
5057 : : }
5058 : : }
5059 : : }
5060 [ # # # # ]: 0 : for (i = 0; num_DB_O && i < pStruct->num_atoms; i++)
5061 : : {
5062 : : /* i = canonical number - 1 */
5063 [ # # ]: 0 : if (!pStruct->endpoint[i])
5064 : : {
5065 : 0 : continue;
5066 : : }
5067 : 0 : iat = nCanon2AtnoRevrs[i];
5068 [ # # ]: 0 : if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */
5069 : 0 : num_SB_O_Minus < MAX_DIFF_FIXH &&
5070 [ # # # # ]: 0 : at2[iat].charge == -1 && !at2[iat].num_H &&
5071 [ # # # # : 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence && !pVA[iat].cMetal &&
# # ]
5072 [ # # # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
5073 [ # # ]: 0 : (at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) &&
5074 : : /* in orig.InChI: an endpoint, has no H */
5075 [ # # # # ]: 0 : !(pStruct->fixed_H && pStruct->fixed_H[i]) &&
5076 : : /*!(nMobHInChI && nMobHInChI[i] ) &&*/
5077 : : /* has (-) edge */
5078 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
5079 [ # # ]: 0 : pBNS->edge[e].flow)
5080 : : {
5081 : 0 : int nNumTautSB = 0, nNumTautDB = 0, nNumOtherDB = 0, nNumOtherSB = 0, nNumOthers = 0, nNumNegEndp = 0; /* djb-rwth: ignoring LLVM warning: variables used */
5082 : : /* traverse neighbors of the centerpoint iS */
5083 : 0 : iS = at2[i].neighbor[0];
5084 [ # # ]: 0 : for (j = 0; j < num_SB_O_Minus; j++)
5085 : : {
5086 [ # # ]: 0 : if (iat_Central[j] == iS)
5087 : 0 : break;
5088 : : }
5089 [ # # ]: 0 : if (j < num_SB_O_Minus)
5090 : : {
5091 : 0 : continue; /* have already been there */
5092 : : }
5093 [ # # ]: 0 : for (j = 0; j < at[iS].valence; j++)
5094 : : {
5095 : 0 : int bond_type = at2[iS].bond_type[j];
5096 : 0 : k = at2[iS].neighbor[j];
5097 [ # # ]: 0 : if (k == i)
5098 : : {
5099 : 0 : continue;
5100 : : }
5101 [ # # ]: 0 : if (pStruct->endpoint[k] == pStruct->endpoint[i])
5102 : : {
5103 : 0 : nNumTautSB += (bond_type == BOND_TYPE_SINGLE);
5104 : 0 : nNumTautDB += (bond_type == BOND_TYPE_DOUBLE);
5105 : : }
5106 : : else
5107 : : {
5108 [ # # ]: 0 : if (bond_type == BOND_TYPE_DOUBLE)
5109 : : {
5110 : 0 : nNumOtherDB++;
5111 : : }
5112 : : else
5113 : : {
5114 [ # # ]: 0 : if (bond_type == BOND_TYPE_SINGLE)
5115 : : {
5116 : 0 : nNumOtherSB++;
5117 : : }
5118 : : else
5119 : : {
5120 : 0 : nNumOthers++;
5121 : : }
5122 : : }
5123 : : }
5124 [ # # # # ]: 0 : if (at2[k].endpoint == at2[i].endpoint && at2[k].valence == 1 &&
5125 [ # # # # ]: 0 : at2[k].charge == -1 && pVA[k].cNumValenceElectrons == 6)
5126 : : {
5127 : 0 : nNumNegEndp++;
5128 : : }
5129 : : }
5130 [ # # ]: 0 : if (!nNumTautSB)
5131 : : {
5132 : 0 : continue;
5133 : : }
5134 [ # # # # ]: 0 : if (!(nNumOtherDB && nNumTautDB))
5135 : : {
5136 : 0 : continue; /* ignore */
5137 : : }
5138 : :
5139 : 0 : iat_SB_O_Minus[num_SB_O_Minus] = iat;
5140 : 0 : iat_Central[num_SB_O_Minus++] = iS;
5141 : : }
5142 : : }
5143 [ # # ]: 0 : if ((num_try = inchi_min(num_SB_O_Minus, num_DB_O))) /* djb-rwth: addressing LLVM warning */
5144 : : {
5145 : : /* detected; attempt to fix */
5146 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
5147 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
5148 : 0 : delta = 1;
5149 [ # # # # ]: 0 : for (i = 0; i < num_SB_O_Minus && cur_success < num_try; i++)
5150 : : {
5151 : 0 : iat = iat_SB_O_Minus[i];
5152 : 0 : pe = pBNS->edge + pVA[iat].nCMinusGroupEdge - 1;
5153 [ # # ]: 0 : if (!pe->flow)
5154 : 0 : continue;
5155 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
5156 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
5157 : :
5158 : 0 : pe->forbidden |= forbidden_edge_mask;
5159 : 0 : pe->flow -= delta;
5160 : 0 : pv1->st_edge.flow -= delta;
5161 : 0 : pv2->st_edge.flow -= delta;
5162 : 0 : pBNS->tot_st_flow -= 2 * delta;
5163 : :
5164 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
5165 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
5166 : :
5167 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
5168 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warning */
# # ]
5169 : : {
5170 : : /* Added (-) charge to =O => nDeltaCharge == 1 */
5171 : : /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */
5172 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
5173 [ # # ]: 0 : if (ret > 0)
5174 : : {
5175 : 0 : nNumRunBNS++;
5176 : 0 : cur_success++; /* 21 */
5177 : : }
5178 : : }
5179 : : else
5180 : : {
5181 : 0 : pe->flow += delta;
5182 : 0 : pv1->st_edge.flow += delta;
5183 : 0 : pv2->st_edge.flow += delta;
5184 : 0 : pBNS->tot_st_flow += 2 * delta;
5185 : : }
5186 : : INCHI_HEAPCHK
5187 : : }
5188 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
5189 : : }
5190 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5191 [ # # ]: 0 : if (cur_success)
5192 : : {
5193 : 0 : tot_succes += cur_success;
5194 : : /* recalculate InChI from the structure */
5195 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
5196 : : ppt_group_info, ppat_norm, ppat_prep)))
5197 : : {
5198 : 0 : goto exit_function;
5199 : : }
5200 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
5201 : : {
5202 : 0 : goto exit_function;
5203 : : }
5204 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
5205 : : {
5206 : 0 : goto exit_function; /* no fixed-H found */
5207 : : }
5208 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
5209 : : {
5210 : 0 : goto exit_function;
5211 : : }
5212 [ # # ]: 0 : if (!pc2i->bHasDifference)
5213 : : {
5214 : 0 : goto exit_function; /* nothing to do */
5215 : : }
5216 : : }
5217 : : }
5218 : :
5219 [ # # # # : 0 : if (pc2i->len_c2at && pc2i->nNumTgRevrs && pc2i->nNumEndpInChI < pc2i->nNumEndpRevrs)
# # ]
5220 : : {
5221 : : /*--------------------------------------------------------------*/
5222 : : /* O O */
5223 : : /* || || */
5224 : : /* case 21a:restored: R=S-R' =X original: R-S-R' -X(-) */
5225 : : /* | || */
5226 : : /* O(-) O(-) */
5227 : : /* All O and X are taut O and X are not taut */
5228 : : /* it is possible that X is R */
5229 : : /* */
5230 : : /* O = O, S, Se; S=S, Se, Te; X = N, O, S, Se, Te */
5231 : : /* Solution: move (-) from O(-) to =X */
5232 : : /* these atoms are tautomeric in restored structure */
5233 : : /*--------------------------------------------------------------*/
5234 : : int iat, iS;
5235 : : /*
5236 : : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
5237 : : */
5238 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
5239 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
5240 : : /*
5241 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
5242 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
5243 : : */
5244 : : EDGE_LIST OtherSO, CentralS, SOMinus, MinusAcceptord;
5245 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5246 : 0 : AllocEdgeList( &OtherSO, EDGE_LIST_CLEAR );
5247 : 0 : AllocEdgeList( &CentralS, EDGE_LIST_CLEAR );
5248 : 0 : AllocEdgeList( &SOMinus, EDGE_LIST_CLEAR );
5249 : 0 : AllocEdgeList( &MinusAcceptord, EDGE_LIST_CLEAR );
5250 : 0 : cur_success = 0;
5251 [ # # ]: 0 : if (!at_Mobile_H_Revrs)
5252 : : {
5253 : 0 : goto exit_case_21a;
5254 : : }
5255 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
5256 : : {
5257 : 0 : iat = pc2i->c2at[i].atomNumber;
5258 : 0 : if ( /* orig. InChI info: -X(-) */
5259 : : /*num_DB_O < MAX_DIFF_FIXH &&*/
5260 : : /*pc2i->c2at[i].nValElectr == 6 */ /* O, S, Se, Te */
5261 [ # # ]: 0 : !pc2i->c2at[i].endptInChI &&
5262 [ # # # # ]: 0 : ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden &&
5263 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/
5264 : : /* reversed structure info: */
5265 [ # # # # ]: 0 : ( pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs ) &&
5266 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 &&
5267 [ # # ]: 0 : /*pc2i->c2at[i].nAtChargeRevrs == 0 &&*/ !at2[iat].num_H)
5268 : : {
5269 [ # # # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 6 && at2[iat].charge == -1 &&
5270 [ # # ]: 0 : pBNS->edge[e].flow &&
5271 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 1 &&
5272 [ # # # # ]: 0 : pVA[iS = (int) at2[iat].neighbor[0]].cNumValenceElectrons == 6 && pVA[iS].cPeriodicRowNumber > 1 &&
5273 [ # # ]: 0 : at2[iS].valence >= 4)
5274 : 0 : {
5275 : : /* a candidate for S in -SO2- */
5276 : 0 : int nNumTautSB = 0, nNumTautDB = 0, nNumOtherDB = 0, nNumOtherSB = 0; /* djb-rwth: ignoring LLVM warning: variables used */
5277 : 0 : int nNumOthers = 0, nNumNegEndp = 0, nNumEndpO = 0;
5278 : : /* check whether we have already found it */
5279 [ # # ]: 0 : if (0 <= FindInEdgeList( &CentralS, iS ))
5280 : : {
5281 : 0 : continue;
5282 : : }
5283 [ # # ]: 0 : for (j = 0; j < at[iS].valence; j++)
5284 : : {
5285 : 0 : int bond_type = at2[iS].bond_type[j];
5286 : 0 : k = at2[iS].neighbor[j];
5287 [ # # ]: 0 : if (k == iat)
5288 : : {
5289 : 0 : continue;
5290 : : }
5291 [ # # # # ]: 0 : if (pc2i->c2at[i].endptRevrs == at_Mobile_H_Revrs[k].endpoint && !at2[k].endpoint)
5292 : : {
5293 : 0 : nNumTautSB += ( bond_type == BOND_TYPE_SINGLE );
5294 : 0 : nNumTautDB += ( bond_type == BOND_TYPE_DOUBLE );
5295 [ # # # # ]: 0 : nNumEndpO += ( pVA[k].cNumValenceElectrons == 6 && at2[k].valence == 1 );
5296 : : }
5297 : : else
5298 : : {
5299 [ # # ]: 0 : if (bond_type == BOND_TYPE_DOUBLE)
5300 : : {
5301 : 0 : nNumOtherDB++;
5302 : : }
5303 : : else
5304 : : {
5305 [ # # ]: 0 : if (bond_type == BOND_TYPE_SINGLE)
5306 : : {
5307 : 0 : nNumOtherSB++;
5308 : : }
5309 : : else
5310 : : {
5311 : 0 : nNumOthers++;
5312 : : }
5313 : : }
5314 : : }
5315 [ # # # # ]: 0 : if (at2[k].endpoint == at2[i].endpoint && at2[k].valence == 1 &&
5316 [ # # # # ]: 0 : at2[k].charge == -1 && pVA[k].cNumValenceElectrons == 6)
5317 : : {
5318 : 0 : nNumNegEndp++;
5319 : : }
5320 : : }
5321 [ # # ]: 0 : if (!nNumEndpO)
5322 : : {
5323 : 0 : continue;
5324 : : }
5325 [ # # ]: 0 : if (nNumTautSB + nNumTautDB + nNumOtherDB <= nNumEndpO)
5326 : : {
5327 : 0 : continue; /* ignore */
5328 : : }
5329 : : /* collect double bond taut =O */
5330 [ # # ]: 0 : for (j = 0; j < at[iS].valence; j++)
5331 : : {
5332 : 0 : int bond_type = at2[iS].bond_type[j];
5333 : 0 : k = at2[iS].neighbor[j];
5334 [ # # ]: 0 : if (pc2i->c2at[i].endptRevrs == at_Mobile_H_Revrs[k].endpoint &&
5335 [ # # # # : 0 : !at2[k].endpoint && pVA[k].cNumValenceElectrons == 6 && at2[k].valence == 1 &&
# # ]
5336 [ # # # # ]: 0 : 0 <= ( e = pVA[k].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden)
5337 : : {
5338 [ # # # # : 0 : if (bond_type == BOND_TYPE_DOUBLE && !at2[k].charge && !pBNS->edge[e].flow)
# # ]
5339 : : {
5340 : : /* charges to be unchanged */
5341 [ # # ]: 0 : if ((ret = AddToEdgeList( &OtherSO, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
5342 : : {
5343 : 0 : goto exit_case_21a;
5344 : : }
5345 : : }
5346 : : else
5347 : : {
5348 [ # # # # : 0 : if (bond_type == BOND_TYPE_SINGLE && at2[k].charge == -1 && pBNS->edge[e].flow)
# # ]
5349 : : {
5350 : : /* charges to be removed */
5351 [ # # ]: 0 : if ((ret = AddToEdgeList( &SOMinus, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
5352 : : {
5353 : 0 : goto exit_case_21a;
5354 : : }
5355 : : }
5356 : : }
5357 : : }
5358 : : }
5359 [ # # ]: 0 : if ((ret = AddToEdgeList( &CentralS, iS, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
5360 : : {
5361 : 0 : goto exit_case_21a;
5362 : : }
5363 : : }
5364 : : else
5365 [ # # # # ]: 0 : if (at2[iat].charge == 0 && !pBNS->edge[e].flow &&
5366 [ # # ]: 0 : at2[iat].valence + 1 == at2[iat].chem_bonds_valence)
5367 : : {
5368 : : /* changeable charges */
5369 [ # # ]: 0 : if ((ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
5370 : : {
5371 : 0 : goto exit_function;
5372 : : }
5373 : : }
5374 : : }
5375 : : }
5376 : : /* remove unchangeable from changeable */
5377 [ # # ]: 0 : for (i = 0; i < OtherSO.num_edges; i++)
5378 : : {
5379 : 0 : RemoveFromEdgeListByValue( &CurrEdges, OtherSO.pnEdges[i] );
5380 : : }
5381 : :
5382 [ # # ]: 0 : if ((num_try = inchi_min( SOMinus.num_edges, CurrEdges.num_edges ))) /* djb-rwth: addressing LLVM warning */
5383 : : {
5384 : : /* detected; attempt to fix */
5385 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
5386 : 0 : RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask );
5387 : 0 : delta = 1;
5388 [ # # # # ]: 0 : for (i = 0; i < SOMinus.num_edges && cur_success < num_try; i++)
5389 : : {
5390 : 0 : pe = pBNS->edge + SOMinus.pnEdges[i];
5391 [ # # ]: 0 : if (!pe->flow)
5392 : 0 : continue;
5393 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
5394 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
5395 : :
5396 : : /*pe->forbidden |= forbidden_edge_mask;*/
5397 : 0 : pe->flow -= delta;
5398 : 0 : pv1->st_edge.flow -= delta;
5399 : 0 : pv2->st_edge.flow -= delta;
5400 : 0 : pBNS->tot_st_flow -= 2 * delta;
5401 : :
5402 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
5403 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
5404 : :
5405 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
5406 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1) ) && nDeltaCharge == 1) /* djb-rwth: addressing LLVM warnings */
# # ]
5407 : : {
5408 : : /* Added (-) charge to =O => nDeltaCharge == 1 */
5409 : : /* Flow change on pe (-)charge edge (atom -N(-)-) is not known to RunBnsTestOnce()) */
5410 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
5411 [ # # ]: 0 : if (ret > 0)
5412 : : {
5413 : 0 : nNumRunBNS++;
5414 : 0 : cur_success++; /* 21a */
5415 : : }
5416 : : }
5417 : : else
5418 : : {
5419 : 0 : pe->flow += delta;
5420 : 0 : pv1->st_edge.flow += delta;
5421 : 0 : pv2->st_edge.flow += delta;
5422 : 0 : pBNS->tot_st_flow += 2 * delta;
5423 : : }
5424 : : INCHI_HEAPCHK
5425 : : }
5426 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
5427 : : }
5428 : 0 : exit_case_21a:
5429 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5430 : 0 : AllocEdgeList( &OtherSO, EDGE_LIST_FREE );
5431 : 0 : AllocEdgeList( &CentralS, EDGE_LIST_FREE );
5432 : 0 : AllocEdgeList( &SOMinus, EDGE_LIST_FREE );
5433 : 0 : AllocEdgeList( &MinusAcceptord, EDGE_LIST_FREE );
5434 [ # # ]: 0 : if (cur_success)
5435 : : {
5436 : 0 : tot_succes += cur_success;
5437 : : /* recalculate InChI from the structure */
5438 [ # # ]: 0 : if (0 > ( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
5439 : : ppt_group_info, ppat_norm, ppat_prep ) ))
5440 : : {
5441 : 0 : goto exit_function;
5442 : : }
5443 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
5444 : : {
5445 : 0 : goto exit_function;
5446 : : }
5447 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
5448 : : {
5449 : 0 : goto exit_function; /* no fixed-H found */
5450 : : }
5451 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
5452 : : {
5453 : 0 : goto exit_function;
5454 : : }
5455 [ # # ]: 0 : if (!pc2i->bHasDifference)
5456 : : {
5457 : 0 : goto exit_function; /* nothing to do */
5458 : : }
5459 : : }
5460 : : }
5461 : :
5462 [ # # ]: 0 : if (pc2i->len_c2at)
5463 : : {
5464 : : /*------------------------------------------------------------------*/
5465 : : /* case 22: restored: N(-)=N(+)=C...=O orig: N#N-N=...-O(-) */
5466 : : /* im InChI -O(-) may have H(+) added by Normalization */
5467 : : /* or may be tautomeric */
5468 : : /* Solution: move (-) from N(-) to =O */
5469 : : /* */
5470 : : /*------------------------------------------------------------------*/
5471 : 0 : int num_DB_O = 0, iat;
5472 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
5473 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
5474 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
5475 : : int iN2, iC;
5476 : : BNS_EDGE *peDB_O_Minus;
5477 : : /*
5478 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
5479 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
5480 : : */
5481 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5482 : 0 : cur_success = 0;
5483 : :
5484 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
5485 : : {
5486 : 0 : iat = pc2i->c2at[i].atomNumber;
5487 [ # # ]: 0 : if ( /* orig. InChI info: =O */
5488 : 0 : num_DB_O < MAX_DIFF_FIXH &&
5489 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ &&
5490 [ # # # # ]: 0 : (pc2i->c2at[i].endptInChI || pc2i->c2at[i].nMobHInChI) &&
5491 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
5492 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/
5493 : : /* reversed structure info: */
5494 [ # # # # ]: 0 : !(pc2i->c2at[i].endptRevrs || pc2i->c2at[i].nMobHRevrs) &&
5495 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 &&
5496 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
5497 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2)
5498 : : {
5499 : 0 : iat_DB_O[num_DB_O++] = iat;
5500 : : }
5501 : : }
5502 [ # # # # ]: 0 : for (i = 0; num_DB_O && i < pStruct->num_atoms; i++)
5503 : : {
5504 : : /* i = canonical number - 1 */
5505 : 0 : iat = nCanon2AtnoRevrs[i];
5506 : 0 : if ( /* in restored atom O: charge=-1, no H, has no double bond, endpoint */
5507 [ # # # # ]: 0 : at2[iat].charge == -1 && !at2[iat].num_H &&
5508 [ # # # # : 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && !pVA[iat].cMetal &&
# # ]
5509 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 5 &&
5510 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
5511 [ # # # # ]: 0 : pBNS->edge[e].flow &&
5512 [ # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) &&
5513 [ # # ]: 0 : pVA[iN2 = at2[iat].neighbor[0]].cNumValenceElectrons == 5 &&
5514 [ # # ]: 0 : at2[iat].bond_type[0] == BOND_TYPE_DOUBLE &&
5515 [ # # # # : 0 : at2[iN2].charge == 1 && at2[iN2].valence == 2 && at2[iN2].chem_bonds_valence == 4 &&
# # ]
5516 [ # # ]: 0 : pVA[iC = at2[iN2].neighbor[at2[iN2].neighbor[0] == iN2]].cNumValenceElectrons == 4) /* djb-rwth: ignoring LLVM warning: variable used */
5517 : : {
5518 : :
5519 [ # # ]: 0 : if ((ret = AddToEdgeList(&CurrEdges, e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
5520 : : {
5521 : 0 : goto exit_function;
5522 : : }
5523 : : }
5524 : : }
5525 [ # # ]: 0 : if ((num_try = inchi_min(CurrEdges.num_edges, num_DB_O))) /* djb-rwth: addressing LLVM warning */
5526 : : {
5527 : : /* detected; attempt to fix */
5528 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
5529 : 0 : RemoveForbiddenEdgeMask(pBNS, &CurrEdges, forbidden_edge_mask);
5530 : 0 : delta = 1;
5531 [ # # # # ]: 0 : for (i = 0; i < num_DB_O && cur_success < num_try; i++)
5532 : : {
5533 : 0 : iat = iat_DB_O[i];
5534 : :
5535 : 0 : peDB_O_Minus = pBNS->edge + ((long long)pVA[iat].nCMinusGroupEdge - 1); /* djb-rwth: cast operator added */
5536 : 0 : pe = pBNS->edge + pBNS->vert[iat].iedge[0];
5537 [ # # ]: 0 : if (!pe->flow)
5538 : 0 : continue;
5539 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
5540 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
5541 : :
5542 : 0 : pe->forbidden |= forbidden_edge_mask;
5543 : 0 : peDB_O_Minus->forbidden &= forbidden_edge_mask_inv;
5544 : :
5545 : 0 : pe->flow -= delta;
5546 : 0 : pv1->st_edge.flow -= delta;
5547 : 0 : pv2->st_edge.flow -= delta;
5548 : 0 : pBNS->tot_st_flow -= 2 * delta;
5549 : :
5550 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
5551 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
5552 : :
5553 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
5554 [ # # # # : 0 : (vPathEnd == v2 && vPathStart == v1)) && nDeltaCharge == 0) /* djb-rwth: addressing LLVM warnings */
# # ]
5555 : : {
5556 : : /* Added (-) charge to =O and removed from =N(-) => nDeltaCharge == 0 */
5557 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
5558 [ # # ]: 0 : if (ret > 0)
5559 : : {
5560 : 0 : nNumRunBNS++;
5561 : 0 : cur_success++; /* 22 */
5562 : : }
5563 : : }
5564 : : else
5565 : : {
5566 : 0 : pe->flow += delta;
5567 : 0 : pv1->st_edge.flow += delta;
5568 : 0 : pv2->st_edge.flow += delta;
5569 : 0 : pBNS->tot_st_flow += 2 * delta;
5570 : : }
5571 : : INCHI_HEAPCHK
5572 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
5573 : 0 : peDB_O_Minus->forbidden |= forbidden_edge_mask;
5574 : : }
5575 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
5576 : : }
5577 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5578 [ # # ]: 0 : if (cur_success)
5579 : : {
5580 : 0 : tot_succes += cur_success;
5581 : : /* recalculate InChI from the structure */
5582 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
5583 : : ppt_group_info, ppat_norm, ppat_prep)))
5584 : : {
5585 : 0 : goto exit_function;
5586 : : }
5587 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct))) /* djb-rwth: addressing LLVM warning */
5588 : : {
5589 : 0 : goto exit_function;
5590 : : }
5591 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
5592 : : {
5593 : 0 : goto exit_function; /* no fixed-H found */
5594 : : }
5595 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
5596 : : {
5597 : 0 : goto exit_function;
5598 : : }
5599 [ # # ]: 0 : if (!pc2i->bHasDifference)
5600 : : {
5601 : 0 : goto exit_function; /* nothing to do */
5602 : : }
5603 : : }
5604 : : }
5605 : :
5606 [ # # # # ]: 0 : if (pc2i->len_c2at && pc2i->nNumTgInChI == 1)
5607 : : {
5608 : : /*------------------------------------------------------------------*/
5609 : : /* case 23: -NO2 are to be tautomeric but they are not AND */
5610 : : /* InChI has a SINGLE tautomeric group */
5611 : : /* */
5612 : : /* (-)O (-)O */
5613 : : /* Solution: convert \ \ */
5614 : : /* N-X=...-Z(-) => N(+)=X- ...=Z */
5615 : : /* // / */
5616 : : /* O (-)O */
5617 : : /* */
5618 : : /* O O */
5619 : : /* or \\ \\ */
5620 : : /* N-X=...-Z(-) => N=X- ...=Z */
5621 : : /* // / */
5622 : : /* O (-)O */
5623 : : /* */
5624 : : /* */
5625 : : /* (a) move (-) from other tautomeric atom to O in O=N-X */
5626 : : /* or from other atom that has to be tautomeric */
5627 : : /* but is not */
5628 : : /* (b) create (+) [ion pair creation] on N as in */
5629 : : /* */
5630 : : /* OH OH */
5631 : : /* / / */
5632 : : /* -C=N => =C-N(+) */
5633 : : /* \\ \\ */
5634 : : /* O O */
5635 : : /* */
5636 : : /*------------------------------------------------------------------*/
5637 : 0 : int num_DB_O = 0, iat;
5638 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
5639 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
5640 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
5641 : : /*
5642 : : inp_ATOM *atfMobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
5643 : : pStruct->pOne_norm_data[1]->at_fixed_bonds)?
5644 : : pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL;
5645 : : */
5646 : 0 : S_CHAR *num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL;
5647 [ # # ]: 0 : S_CHAR *pnMobHRevrs = ( pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H ) ?
5648 [ # # ]: 0 : pStruct->pOneINChI[1]->nNum_H :
5649 [ # # ]: 0 : ( pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H ) ?
5650 [ # # ]: 0 : pStruct->pOneINChI[0]->nNum_H : NULL;
5651 : : int iN, one_success;
5652 : : BNS_EDGE *peDB_O_Minus;
5653 : : int neigh, nNumO, nNumOthers;
5654 : : #define CHG_SET_NOOH 0
5655 : : #define CHG_SET_WRONG_TAUT 1
5656 : : #define CHG_SET_TAUT 2
5657 : : #define CHG_LAST_SET 2 /* the last index in trying */
5658 : : #define CHG_SET_O_FIXED 3
5659 : : #define CHG_SET_NUM 4
5660 : : EDGE_LIST ChangeableEdges[CHG_SET_NUM];
5661 : 0 : memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */
5662 : : /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */
5663 : : /*
5664 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
5665 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
5666 : : */
5667 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5668 : 0 : cur_success = 0;
5669 : :
5670 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
5671 : : {
5672 : 0 : iat = pc2i->c2at[i].atomNumber;
5673 [ # # ]: 0 : if ( /* orig. InChI info: taut in orig. InChI =O located in -NO2 that is not taut in Reconstructed InChI */
5674 : 0 : num_DB_O < MAX_DIFF_FIXH &&
5675 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 6 /* O, S, Se, Te */ &&
5676 [ # # ]: 0 : (pc2i->c2at[i].endptInChI /*|| pc2i->c2at[i].nMobHInChI*/) &&
5677 [ # # # # ]: 0 : (e = pVA[iat].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].forbidden &&
5678 [ # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/
5679 : : /* reversed structure info: */
5680 [ # # ]: 0 : !(pc2i->c2at[i].endptRevrs /*|| pc2i->c2at[i].nMobHRevrs*/) &&
5681 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 &&
5682 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
5683 [ # # # # ]: 0 : at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 &&
5684 : : /* find whether it belongs to NO2 */
5685 [ # # ]: 0 : pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 &&
5686 [ # # # # : 0 : at2[iN].valence == 3 && (at2[iN].charge == 0 || at2[iN].charge == 1) &&
# # ]
5687 [ # # ]: 0 : at2[iN].chem_bonds_valence == 5 - at2[iN].charge)
5688 : : {
5689 : : /* find the second O */
5690 : 0 : nNumO = nNumOthers = 0;
5691 [ # # ]: 0 : for (k = 0; k < at2[iN].valence; k++)
5692 : : {
5693 : 0 : neigh = at2[iN].neighbor[k];
5694 [ # # ]: 0 : if (neigh == iat)
5695 : : {
5696 : 0 : continue;
5697 : : }
5698 [ # # ]: 0 : if (pVA[neigh].cNumValenceElectrons == 6 &&
5699 [ # # # # ]: 0 : pStruct->endpoint[neigh] &&
5700 [ # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[neigh].endpoint) &&
5701 [ # # # # ]: 0 : at2[neigh].valence == 1 && at2[neigh].num_H == 0 &&
5702 [ # # # # : 0 : at2[neigh].radical == 0 && (at2[neigh].charge == 0 || at2[neigh].charge == -1) &&
# # ]
5703 [ # # ]: 0 : at2[neigh].chem_bonds_valence - at2[neigh].charge == 2)
5704 : : {
5705 : 0 : nNumO++;
5706 : : }
5707 : : else
5708 : : {
5709 [ # # ]: 0 : if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE &&
5710 [ # # ]: 0 : at2[neigh].valence > 1 &&
5711 [ # # ]: 0 : at2[neigh].valence < at2[neigh].chem_bonds_valence)
5712 : : {
5713 : 0 : nNumOthers++;
5714 : : }
5715 : : }
5716 : : }
5717 [ # # # # ]: 0 : if (nNumO != 1 || nNumOthers != 1)
5718 : : {
5719 : 0 : continue;
5720 : : }
5721 [ # # ]: 0 : for (k = 0; k < num_DB_O; k++)
5722 : : {
5723 [ # # ]: 0 : if (iat_NO2[k] == iN)
5724 : : {
5725 : 0 : break;
5726 : : }
5727 : : }
5728 [ # # ]: 0 : if (k == num_DB_O)
5729 : : {
5730 : 0 : iat_NO2[num_DB_O] = iN;
5731 : 0 : iat_DB_O[num_DB_O++] = iat;
5732 : : }
5733 : : /* save the edge to avoid interference */
5734 [ # # ]: 0 : if ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))) /* djb-rwth: addressing LLVM warning */
5735 : : {
5736 : 0 : goto exit_case_23;
5737 : : }
5738 : : }
5739 : : }
5740 [ # # ]: 0 : if (num_DB_O)
5741 : : {
5742 : : /* 1. search for =N(=O)-OH; assume =N(+)(-O(-))(-OH) does not happen */
5743 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
5744 : : {
5745 : : /* i = canonical number - 1 */
5746 : : /* find O=N(V) */
5747 : 0 : iat = nCanon2AtnoRevrs[i];
5748 [ # # # # ]: 0 : if (!pStruct->endpoint[i] || pVA[i].cNumValenceElectrons != 6 ||
5749 [ # # # # ]: 0 : at2[iat].valence != 1 || at2[iat].charge ||
5750 [ # # ]: 0 : 0 > (e = pVA[iat].nCMinusGroupEdge - 1) ||
5751 [ # # ]: 0 : at2[iat].num_H + at2[iat].chem_bonds_valence != 2 ||
5752 [ # # ]: 0 : pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons != 5 ||
5753 [ # # ]: 0 : 0 > (e = pVA[iN].nCPlusGroupEdge - 1) ||
5754 [ # # # # ]: 0 : pBNS->edge[e].forbidden || !pBNS->edge[e].flow ||
5755 [ # # # # : 0 : at2[iN].charge || at2[iN].valence != 3 || at2[iN].chem_bonds_valence != 5) /* djb-rwth: ignoring LLVM warning: variable used */
# # ]
5756 : : {
5757 : 0 : continue;
5758 : : }
5759 : : /* find the second O, -OH */
5760 : 0 : nNumO = nNumOthers = 0;
5761 [ # # ]: 0 : for (k = 0; k < at2[iN].valence; k++)
5762 : : {
5763 : 0 : neigh = at2[iN].neighbor[k];
5764 [ # # ]: 0 : if (neigh == iat)
5765 : : {
5766 : 0 : continue;
5767 : : }
5768 [ # # ]: 0 : if (pVA[neigh].cNumValenceElectrons == 6 &&
5769 [ # # ]: 0 : pStruct->endpoint[neigh] &&
5770 [ # # # # ]: 0 : at2[neigh].valence == 1 && at2[neigh].num_H == 1 &&
5771 [ # # # # ]: 0 : at2[neigh].radical == 0 && (at2[neigh].charge == 0))
5772 : : {
5773 : 0 : nNumO++;
5774 : : }
5775 : : else
5776 [ # # ]: 0 : if (at2[iN].bond_type[k] == BOND_TYPE_DOUBLE &&
5777 [ # # ]: 0 : at2[neigh].valence >= 2 &&
5778 [ # # ]: 0 : at2[neigh].valence < at2[neigh].chem_bonds_valence)
5779 : : {
5780 : 0 : nNumOthers++;
5781 : : }
5782 : : }
5783 [ # # # # ]: 0 : if (nNumO != 1 || nNumOthers != 1)
5784 : : {
5785 : 0 : continue;
5786 : : }
5787 : : /* save edges to be changed */
5788 [ # # # # ]: 0 : if ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_NOOH], e, INC_ADD_EDGE)) ||
5789 : 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE)))
5790 : : {
5791 : 0 : goto exit_case_23;
5792 : : }
5793 [ # # # # ]: 0 : if (NO_VERTEX != (j = GetChargeFlowerUpperEdge(pBNS, pVA, e)) &&
5794 [ # # ]: 0 : ((ret = AddToEdgeList(&ChangeableEdges[CHG_SET_NOOH], j, INC_ADD_EDGE)) ||
5795 : 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))))
5796 : : {
5797 : 0 : goto exit_case_23;
5798 : : }
5799 : : }
5800 : : /* 2. search for (-) atoms that are tautomeric but should not be */
5801 : : /* or that got H from Normalization but they shouldn't */
5802 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
5803 : : { /* i = canonical number - 1 */
5804 : 0 : iat = nCanon2AtnoRevrs[i];
5805 [ # # ]: 0 : if (at2[iat].charge == -1 &&
5806 [ # # # # ]: 0 : !pStruct->endpoint[i] &&
5807 : 0 : (at_Mobile_H_Revrs &&
5808 [ # # # # ]: 0 : (at_Mobile_H_Revrs[i].endpoint || at2[iat].num_H < at_Mobile_H_Revrs[i].num_H)))
5809 : : {
5810 : :
5811 [ # # # # ]: 0 : if (0 <= (e = pVA[iat].nCMinusGroupEdge - 1) &&
5812 : 0 : 0 > FindInEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e) &&
5813 [ # # # # : 0 : !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # ]
5814 : : (
5815 [ # # ]: 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE)) ||
5816 : 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))
5817 : : ))
5818 : : {
5819 : 0 : goto exit_case_23;
5820 : : }
5821 : : }
5822 : : else
5823 : : {
5824 : : /* negatively charged atom in Reconstructed structure got H(+) from Normalization */
5825 : : /* and is not tautomeric; in the original structure it is tautomeric */
5826 [ # # ]: 0 : if (at2[iat].charge == -1 &&
5827 [ # # # # ]: 0 : pStruct->endpoint[i] &&
5828 [ # # # # ]: 0 : !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) &&
5829 [ # # # # ]: 0 : (num_Fixed_H_Revrs && num_Fixed_H_Revrs[i] == -1) &&
5830 [ # # ]: 0 : (pnMobHRevrs && pnMobHRevrs[i] == 1) &&
5831 [ # # ]: 0 : pStruct->fixed_H[i] == 0)
5832 : : {
5833 : :
5834 [ # # # # ]: 0 : if (0 <= (e = pVA[iat].nCMinusGroupEdge - 1) &&
5835 : 0 : 0 > FindInEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e) &&
5836 [ # # # # : 0 : !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # ]
5837 : : (
5838 [ # # ]: 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_WRONG_TAUT], e, INC_ADD_EDGE)) ||
5839 : 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE))
5840 : : ))
5841 : : {
5842 : 0 : goto exit_case_23;
5843 : : }
5844 : : }
5845 : : }
5846 : : }
5847 : : /* 3. Search for (-) atoms that are tautomeric */
5848 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
5849 : : {
5850 : : /* i = canonical number - 1 */
5851 : 0 : iat = nCanon2AtnoRevrs[i];
5852 [ # # # # ]: 0 : if (pStruct->endpoint[i] &&
5853 [ # # ]: 0 : (at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint) &&
5854 [ # # ]: 0 : at2[iat].charge == -1
5855 : : /*&& pVA[i].cNumValenceElectrons == 6*/)
5856 : : {
5857 [ # # ]: 0 : if (0 <= (e = pVA[iat].nCMinusGroupEdge - 1) &&
5858 [ # # # # : 0 : !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # ]
5859 [ # # ]: 0 : 0 > FindInEdgeList(&ChangeableEdges[CHG_SET_O_FIXED], e) &&
5860 : 0 : (ret = AddToEdgeList(&ChangeableEdges[CHG_SET_TAUT], e, INC_ADD_EDGE)))
5861 : : {
5862 : 0 : goto exit_case_23;
5863 : : }
5864 : : }
5865 : : }
5866 : :
5867 : : /* ------- finally, try to move charges from O=N --------------*/
5868 [ # # ]: 0 : for (i = 0; i < num_DB_O; i++)
5869 : : {
5870 : : int nDeltaChargeExpected;
5871 : 0 : one_success = 0;
5872 : 0 : delta = 1;
5873 : 0 : iat = iat_DB_O[i];
5874 : 0 : peDB_O_Minus = pBNS->edge + ((long long)pVA[iat].nCMinusGroupEdge - 1);/* djb-rwth: cast operator added */
5875 : 0 : pe = pBNS->edge + pBNS->vert[iat].iedge[0];
5876 : :
5877 [ # # ]: 0 : if (!pe->flow)
5878 : 0 : continue;
5879 : 0 : pv1 = pBNS->vert + (v1 = pe->neighbor1);
5880 : 0 : pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1);
5881 : :
5882 : 0 : pe->forbidden |= forbidden_edge_mask;
5883 : :
5884 : 0 : pe->flow -= delta;
5885 : 0 : pv1->st_edge.flow -= delta;
5886 : 0 : pv2->st_edge.flow -= delta;
5887 : 0 : pBNS->tot_st_flow -= 2 * delta;
5888 : :
5889 [ # # # # ]: 0 : for (k = 0; !one_success && k <= CHG_LAST_SET; k++)
5890 : : {
5891 [ # # ]: 0 : if (!ChangeableEdges[k].num_edges)
5892 : : {
5893 : 0 : continue;
5894 : : }
5895 [ # # ]: 0 : nDeltaChargeExpected = (k == CHG_SET_NOOH) ? 2 : 0;
5896 : :
5897 : 0 : SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
5898 : 0 : RemoveForbiddenEdgeMask(pBNS, &ChangeableEdges[k], forbidden_edge_mask);
5899 : : /* allow (-) charge to move to N=O */
5900 : 0 : peDB_O_Minus->forbidden &= forbidden_edge_mask_inv;
5901 : :
5902 : 0 : ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
5903 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
5904 : :
5905 [ # # # # : 0 : if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
# # ]
5906 [ # # # # ]: 0 : (vPathEnd == v2 && vPathStart == v1)) &&
5907 [ # # ]: 0 : nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */
5908 : : {
5909 : : /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */
5910 : 0 : ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
5911 [ # # ]: 0 : if (ret > 0)
5912 : : {
5913 : 0 : nNumRunBNS++;
5914 : 0 : one_success++; /* 23 */
5915 : : }
5916 : : }
5917 : : INCHI_HEAPCHK
5918 : : }
5919 : 0 : cur_success += one_success;
5920 : :
5921 : 0 : RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
5922 : 0 : pe->forbidden &= forbidden_edge_mask_inv;
5923 : :
5924 [ # # ]: 0 : if (!one_success)
5925 : : {
5926 : 0 : pe->flow += delta;
5927 : 0 : pv1->st_edge.flow += delta;
5928 : 0 : pv2->st_edge.flow += delta;
5929 : 0 : pBNS->tot_st_flow += 2 * delta;
5930 : : }
5931 : : }
5932 : : }
5933 : 0 : exit_case_23:
5934 [ # # ]: 0 : for (i = 0; i < CHG_SET_NUM; i++)
5935 : : {
5936 : 0 : AllocEdgeList(&ChangeableEdges[i], EDGE_LIST_FREE);
5937 : : }
5938 : :
5939 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
5940 [ # # ]: 0 : if (cur_success)
5941 : : {
5942 : 0 : tot_succes += cur_success;
5943 : : /* recalculate InChI from the structure */
5944 [ # # ]: 0 : if (0 > (ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
5945 : : ppt_group_info, ppat_norm, ppat_prep)))
5946 : : {
5947 : 0 : goto exit_function;
5948 : : }
5949 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr(pStruct)))/* djb-rwth: addressing LLVM warning */
5950 : : {
5951 : 0 : goto exit_function;
5952 : : }
5953 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
5954 : : {
5955 : 0 : goto exit_function; /* no fixed-H found */
5956 : : }
5957 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI(pStruct, at2, pVA, pInChI, pc2i))) /* djb-rwth: addressing LLVM warning */
5958 : : {
5959 : 0 : goto exit_function;
5960 : : }
5961 [ # # ]: 0 : if (!pc2i->bHasDifference)
5962 : : {
5963 : 0 : goto exit_function; /* nothing to do */
5964 : : }
5965 : : }
5966 : :
5967 : : #undef CHG_SET_NOOH
5968 : : #undef CHG_SET_WRONG_TAUT
5969 : : #undef CHG_SET_TAUT
5970 : : #undef CHG_LAST_SET
5971 : : #undef CHG_SET_O_FIXED
5972 : : #undef CHG_SET_NUM
5973 : : }
5974 : :
5975 [ # # # # ]: 0 : if (pc2i->len_c2at && pc2i->nNumTgInChI == 1)
5976 : : {
5977 : : /*------------------------------------------------------------------*/
5978 : : /* case 24: InChI norm. -N(-)-N(+)(IV) => -N=N(V) prevents tauto- */
5979 : : /* merism on -N(-)- in case of ADP */
5980 : : /* */
5981 : : /* Solution: convert N(V)=N- ...=X -> N(IV)(+)-N=...-X(-)*/
5982 : : /* N(IV)(+)-N(-)-...=X */
5983 : : /* */
5984 : : /* Orig InChI taut taut, 1 t-group only(ADP?) */
5985 : : /* Reconstructed struct non-taut possibly not taut */
5986 : : /* */
5987 : : /* Details: 1a. store next to N(V) (+)edge its flower edge */
5988 : : /* 1b. store next to N(-) edge NO_VERTEX */
5989 : : /* 2. Release (-) edges of other missing endpoints or */
5990 : : /* all endpoints if no other is missing */
5991 : : /* 3. Decrement flow on (+) edge */
5992 : : /* if flower edge is stored then expect DeltaCharge=2*/
5993 : : /* otherwise DeltaCharge = 0 */
5994 : : /*------------------------------------------------------------------*/
5995 : : int iat;
5996 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
5997 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
5998 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
5999 [ # # ]: 0 : inp_ATOM *atf = ( pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->at_fixed_bonds ) ?
6000 [ # # ]: 0 : pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL;
6001 : : int iN, one_success;
6002 : : EdgeIndex ef, e1;
6003 : : BNS_EDGE *pef;
6004 : : #define CHG_SET_MISSED_TAUT 0
6005 : : #define CHG_SET_OTHER_TAUT_O 1
6006 : : #define CHG_SET_OTHER_TAUT_N 2
6007 : : #define CHG_LAST_SET 2 /* the last index in trying */
6008 : : #define CHG_SET_NN 3
6009 : : #define CHG_SET_AVOID 4
6010 : : #define CHG_SET_NUM 5
6011 : : EDGE_LIST ChangeableEdges[CHG_SET_NUM];
6012 : 0 : memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */
6013 : : /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */
6014 : : /*
6015 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
6016 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
6017 : : */
6018 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
6019 : 0 : cur_success = 0;
6020 [ # # ]: 0 : for (i = 0; i < pc2i->len_c2at; i++)
6021 : : {
6022 : 0 : iat = pc2i->c2at[i].atomNumber;
6023 : 0 : if ( /* orig. InChI info: -N=N(V) */
6024 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 5 /* N or P */ &&
6025 [ # # ]: 0 : ( pc2i->c2at[i].endptInChI /* only N */ ) &&
6026 [ # # # # ]: 0 : ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e1].forbidden &&
6027 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 &&
6028 : : /* reversed structure info: */
6029 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
6030 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 &&
6031 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == 0 && !at2[iat].num_H &&
6032 [ # # # # ]: 0 : at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3 &&
6033 : : /* find whether -N= has =N(V) neighbor; Note: operator comma: (A,B) returns B */
6034 : 0 : ( iN = at2[iat].neighbor[at2[iat].bond_type[0] != BOND_TYPE_DOUBLE],
6035 [ # # ]: 0 : pVA[iN].cNumValenceElectrons == 5 ) &&
6036 [ # # ]: 0 : at2[iN].chem_bonds_valence == 5 &&
6037 [ # # # # : 0 : at2[iN].charge == 0 && !at2[iN].num_H && !at2[iN].radical &&
# # ]
6038 [ # # # # : 0 : 0 <= ( e = pVA[iN].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # # # ]
6039 : 0 : 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ))
6040 : : {
6041 : :
6042 : 0 : ef = GetChargeFlowerUpperEdge( pBNS, pVA, e ); /* == NO_VERTEX if N(V) has 4 bonds */
6043 [ # # # # ]: 0 : if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) ||
6044 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], ef, INC_ADD_EDGE ) ) ||
6045 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */
6046 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) ) ||
6047 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) ||
6048 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], ef, INC_ADD_EDGE ) ))
6049 : : {
6050 : 0 : goto exit_case_24;
6051 : : }
6052 : : /* mark -N= so that (-) will not be moved to it */
6053 [ # # # # : 0 : if (0 <= ( e = pVA[iat].nCMinusGroupEdge ) && !pBNS->edge[e].forbidden &&
# # ]
6054 [ # # ]: 0 : 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) &&
6055 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ))
6056 : : {
6057 : 0 : goto exit_case_24;
6058 : : }
6059 : : }
6060 : : else
6061 : : {
6062 [ # # ]: 0 : if ( /* orig. InChI info: -N(-)N(IV)(+) */
6063 : 0 : atf &&
6064 [ # # ]: 0 : pc2i->c2at[i].nValElectr == 5 /* N or P */ &&
6065 [ # # ]: 0 : pc2i->c2at[i].endptInChI /* only N */ &&
6066 [ # # # # ]: 0 : ( e = pVA[iat].nCMinusGroupEdge - 1 ) >= 0 && !pBNS->edge[e].forbidden &&
6067 [ # # # # ]: 0 : pc2i->c2at[i].nFixHInChI == 0 && pc2i->c2at[i].nMobHInChI == 0 &&
6068 : : /* reversed structure info: */
6069 [ # # ]: 0 : !pc2i->c2at[i].endptRevrs &&
6070 [ # # ]: 0 : pc2i->c2at[i].nFixHRevrs == 0 &&
6071 [ # # # # ]: 0 : pc2i->c2at[i].nAtChargeRevrs == -1 && !at2[iat].num_H &&
6072 [ # # # # ]: 0 : at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 2 &&
6073 [ # # # # ]: 0 : atf[iat].valence == 2 && atf[iat].chem_bonds_valence == 3 &&
6074 : : /* find whether -N= has =N(V) neighbor; Note: operator comma: (A,B) returns B */
6075 : 0 : ( iN = atf[iat].neighbor[atf[iat].bond_type[0] != BOND_TYPE_DOUBLE],
6076 [ # # ]: 0 : pVA[iN].cNumValenceElectrons == 5 ) &&
6077 [ # # ]: 0 : at2[iN].charge == 1 && /* double bond neighbor */
6078 [ # # ]: 0 : at2[iN].chem_bonds_valence == 4 &&
6079 [ # # ]: 0 : atf[iN].charge == 0 &&
6080 [ # # ]: 0 : atf[iN].chem_bonds_valence == 5 && /* InChI normalization created N(V)=N- out of N(IV)(+)-N(-)- */
6081 [ # # # # ]: 0 : !at2[iN].num_H && !at2[iN].radical &&
6082 [ # # # # : 0 : 0 <= ( e = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow &&
# # # # ]
6083 : 0 : 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ))
6084 : : {
6085 : : /* save (-) edge */
6086 [ # # # # ]: 0 : if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], e, INC_ADD_EDGE ) ) ||
6087 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], NO_VERTEX, INC_ADD_EDGE ) ) ||
6088 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NN], 1, INC_ADD_EDGE ) ) || /* expected nDeltaCharge */
6089 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ))
6090 : : {
6091 : 0 : goto exit_case_24;
6092 : : }
6093 : : }
6094 : : }
6095 : : }
6096 [ # # ]: 0 : if (!ChangeableEdges[CHG_SET_NN].num_edges)
6097 : : {
6098 : 0 : goto exit_case_24;
6099 : : }
6100 : : /* Collect all relevant tautomeric atoms */
6101 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
6102 : : {
6103 : : /* i = canonical number - 1 */
6104 [ # # ]: 0 : if (!pStruct->endpoint[i])
6105 : : {
6106 : 0 : continue;
6107 : : }
6108 : 0 : iat = nCanon2AtnoRevrs[i];
6109 [ # # # # : 0 : if (at2[iat].charge || at2[iat].radical || at2[iat].valence == at2[iat].chem_bonds_valence)
# # ]
6110 : : {
6111 : 0 : continue; /* cannot be an acceptor of (-) */
6112 : : }
6113 [ # # # # : 0 : if (0 > ( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden || pBNS->edge[e].flow)
# # ]
6114 : : {
6115 : 0 : continue;
6116 : : }
6117 [ # # ]: 0 : if (0 <= FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ))
6118 : : {
6119 : 0 : continue; /* has already been used */
6120 : : }
6121 : : /* missing endpoint */
6122 [ # # # # ]: 0 : if (!( at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint ))
6123 : : {
6124 [ # # # # ]: 0 : if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && (
6125 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT], e, INC_ADD_EDGE ) ) ||
6126 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) ))
6127 : : {
6128 : 0 : goto exit_case_24;
6129 : : }
6130 : : }
6131 : : else
6132 : : {
6133 : : /* endpoint O */
6134 [ # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 6)
6135 : : {
6136 [ # # # # ]: 0 : if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && (
6137 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_O], e, INC_ADD_EDGE ) ) ||
6138 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) ))
6139 : : {
6140 : 0 : goto exit_case_24;
6141 : : }
6142 : : }
6143 : : else
6144 : : {
6145 : : /* endpoint N */
6146 [ # # ]: 0 : if (pVA[iat].cNumValenceElectrons == 5)
6147 : : {
6148 [ # # # # ]: 0 : if (0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) && (
6149 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_N], e, INC_ADD_EDGE ) ) ||
6150 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) ))
6151 : : {
6152 : 0 : goto exit_case_24;
6153 : : }
6154 : : }
6155 : : }
6156 : : }
6157 : : }
6158 : : /* ------- finally, try to move charges from -N(-)-N(+) or to N(V) --------------*/
6159 [ # # ]: 0 : for (i = 0; i < ChangeableEdges[CHG_SET_NN].num_edges; i += 3)
6160 : : {
6161 : : int nDeltaChargeExpected;
6162 : 0 : one_success = 0;
6163 : 0 : delta = 1;
6164 : 0 : pe = pBNS->edge + ChangeableEdges[CHG_SET_NN].pnEdges[i];
6165 : 0 : pef = ( NO_VERTEX != ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] ) ?
6166 [ # # ]: 0 : pBNS->edge + ChangeableEdges[CHG_SET_NN].pnEdges[i + 1] : NULL;
6167 : 0 : nDeltaChargeExpected = ChangeableEdges[CHG_SET_NN].pnEdges[i + 2];
6168 : :
6169 [ # # ]: 0 : if (!pe->flow)
6170 : 0 : continue;
6171 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
6172 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
6173 : :
6174 : 0 : pe->flow -= delta;
6175 : 0 : pv1->st_edge.flow -= delta;
6176 : 0 : pv2->st_edge.flow -= delta;
6177 : 0 : pBNS->tot_st_flow -= 2 * delta;
6178 : :
6179 [ # # # # ]: 0 : for (k = 0; !one_success && k <= CHG_LAST_SET; k++)
6180 : : {
6181 [ # # ]: 0 : if (!ChangeableEdges[k].num_edges)
6182 : : {
6183 : 0 : continue;
6184 : : }
6185 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
6186 : 0 : RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask );
6187 : : /* allow change of N(V) flower edge */
6188 [ # # ]: 0 : if (pef)
6189 : : {
6190 : 0 : pef->forbidden &= forbidden_edge_mask_inv;
6191 : : }
6192 : :
6193 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
6194 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
6195 : :
6196 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
6197 [ # # # # ]: 0 : (vPathEnd == v2 && vPathStart == v1) ) &&
6198 [ # # ]: 0 : nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */
6199 : : {
6200 : : /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */
6201 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
6202 [ # # ]: 0 : if (ret > 0)
6203 : : {
6204 : 0 : nNumRunBNS++;
6205 : 0 : one_success++; /* 24 */
6206 : : }
6207 : : }
6208 : : INCHI_HEAPCHK
6209 : : }
6210 : 0 : cur_success += one_success;
6211 : :
6212 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
6213 : :
6214 [ # # ]: 0 : if (!one_success)
6215 : : {
6216 : 0 : pe->flow += delta;
6217 : 0 : pv1->st_edge.flow += delta;
6218 : 0 : pv2->st_edge.flow += delta;
6219 : 0 : pBNS->tot_st_flow += 2 * delta;
6220 : : }
6221 : : }
6222 : 0 : exit_case_24:
6223 [ # # ]: 0 : for (i = 0; i < CHG_SET_NUM; i++)
6224 : : {
6225 : 0 : AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE );
6226 : : }
6227 : :
6228 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
6229 [ # # ]: 0 : if (cur_success)
6230 : : {
6231 : 0 : tot_succes += cur_success;
6232 : : /* recalculate InChI from the structure */
6233 [ # # ]: 0 : if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
6234 : : ppt_group_info, ppat_norm, ppat_prep ) ))
6235 : : {
6236 : 0 : goto exit_function;
6237 : : }
6238 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
6239 : : {
6240 : 0 : goto exit_function;
6241 : : }
6242 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
6243 : : {
6244 : 0 : goto exit_function; /* no fixed-H found */
6245 : : }
6246 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
6247 : : {
6248 : 0 : goto exit_function;
6249 : : }
6250 [ # # ]: 0 : if (!pc2i->bHasDifference)
6251 : : {
6252 : 0 : goto exit_function; /* nothing to do */
6253 : : }
6254 : : }
6255 : : #undef CHG_SET_NN
6256 : : #undef CHG_SET_MISSED_TAUT
6257 : : #undef CHG_SET_OTHER_TAUT_O
6258 : : #undef CHG_SET_OTHER_TAUT_N
6259 : : #undef CHG_LAST_SET
6260 : : #undef CHG_SET_AVOID
6261 : : #undef CHG_SET_NUM
6262 : : }
6263 : :
6264 : : /* pStruct->nNumRemovedProtonsMobHInChI == pc2i->nNumRemHInChI */
6265 : :
6266 [ # # # # ]: 0 : if (pc2i->len_c2at && pc2i->nNumTgInChI == 1 &&
6267 [ # # # # ]: 0 : pc2i->nNumRemHRevrs > pc2i->nNumRemHInChI && 0 > pc2i->nNumRemHInChI &&
6268 [ # # ]: 0 : ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI ||
6269 [ # # ]: 0 : pc2i->nNumTgRevrs > pc2i->nNumTgInChI ))
6270 : : {
6271 : : /*------------------------------------------------------------------*/
6272 : : /* case 25: Restored InChI does not have 2 or more added protons */
6273 : : /* possibly taut. endpoints are missing */
6274 : : /* has -N(-O(-))-O(-) group(s) */
6275 : : /* Original InChI has only one t-group */
6276 : : /* */
6277 : : /* Solution: convert -N(-O(-))-O(-) -> -N(+)(=O)-O(-) */
6278 : : /* and direct 2(-) to the missing taut atoms*/
6279 : : /* at first attempt try to move (-) to N only */
6280 : : /* */
6281 : : /*------------------------------------------------------------------*/
6282 : : int iat;
6283 : 0 : AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
6284 : 0 : AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0];
6285 : 0 : inp_ATOM *at_Mobile_H_Revrs = ( pStruct->pOne_norm_data[1] &&
6286 [ # # # # ]: 0 : pStruct->pOne_norm_data[1]->at ) ? pStruct->pOne_norm_data[1]->at : NULL;
6287 : : /*
6288 : : inp_ATOM *atf = (pStruct->pOne_norm_data[1] && pStruct->pOne_norm_data[1]->at_fixed_bonds)?
6289 : : pStruct->pOne_norm_data[1]->at_fixed_bonds : NULL;
6290 : : */
6291 : : int iN, neigh, one_success;
6292 : : EdgeIndex e1, bFirst;
6293 : : BNS_EDGE *pef;
6294 : : #define CHG_SET_MISSED_TAUT_1 0
6295 : : #define CHG_SET_MISSED_TAUT_ALL 1
6296 : : #define CHG_SET_OTHER_TAUT_1 2
6297 : : #define CHG_SET_OTHER_TAUT_ALL 3
6298 : : #define CHG_LAST_SET 3 /* the last index in trying */
6299 : : #define CHG_SET_NO_IN_NO2M2 4
6300 : : #define CHG_SET_AVOID 5
6301 : : #define CHG_SET_NUM 6
6302 : : EDGE_LIST ChangeableEdges[CHG_SET_NUM];
6303 : 0 : memset( ChangeableEdges, 0, sizeof( ChangeableEdges ) ); /* djb-rwth: memset_s C11/Annex K variant? */
6304 : : /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */
6305 : : /*
6306 : : S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H :
6307 : : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0;
6308 : : */
6309 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
6310 : 0 : cur_success = 0;
6311 : : /* find all -N(-O(-))-O(-) */
6312 [ # # ]: 0 : for (i = 0; i < pStruct->num_atoms; i++)
6313 : : {
6314 : 0 : iat = nCanon2AtnoRevrs[i];
6315 [ # # ]: 0 : if (pStruct->endpoint[i])
6316 : : {
6317 [ # # # # : 0 : if (0 >( e = pVA[iat].nCMinusGroupEdge - 1 ) || pBNS->edge[e].forbidden ||
# # ]
6318 : 0 : 0 <= FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ))
6319 : : {
6320 : 0 : continue;
6321 : : }
6322 [ # # # # ]: 0 : bFirst = ( (pVA[iat].cNumValenceElectrons == 5 && pc2i->nNumTgInChI == 1) ||
6323 [ # # # # ]: 0 : (pVA[iat].cNumValenceElectrons == 6 && pc2i->nNumTgInChI != 1) ); /* djb-rwth: addressing LLVM warnings */
6324 : : /* many or no t-groups -> try O only first */
6325 : : /* single t-group -> try only N first */
6326 [ # # # # ]: 0 : if (!( at_Mobile_H_Revrs && at_Mobile_H_Revrs[i].endpoint ))
6327 : : {
6328 : : /* missed tautomeric endpoint */
6329 [ # # # # ]: 0 : if (bFirst &&
6330 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_1], e, INC_ADD_EDGE ) ))
6331 : : {
6332 : 0 : goto exit_case_25;
6333 : : }
6334 [ # # ]: 0 : if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_MISSED_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
6335 : : {
6336 : 0 : goto exit_case_25;
6337 : : }
6338 : : }
6339 [ # # # # ]: 0 : if (bFirst &&
6340 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_1], e, INC_ADD_EDGE ) ))
6341 : : {
6342 : 0 : goto exit_case_25;
6343 : : }
6344 [ # # ]: 0 : if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_OTHER_TAUT_ALL], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
6345 : : {
6346 : 0 : goto exit_case_25;
6347 : : }
6348 [ # # ]: 0 : if ((ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ))) /* djb-rwth: addressing LLVM warning */
6349 : : {
6350 : 0 : goto exit_case_25;
6351 : : }
6352 : : }
6353 : : else
6354 : : {
6355 [ # # # # ]: 0 : if (at2[iat].valence == 1 && at2[iat].charge == -1 &&
6356 [ # # ]: 0 : pVA[iat].cNumValenceElectrons == 6 &&
6357 [ # # ]: 0 : pVA[iN = at2[iat].neighbor[0]].cNumValenceElectrons == 5 && /* -O(-) */
6358 [ # # ]: 0 : !pStruct->endpoint[nAtno2CanonRevrs[iN]] &&
6359 [ # # # # ]: 0 : at2[iN].valence == 3 && at2[iN].chem_bonds_valence == 3 &&
6360 [ # # # # ]: 0 : !at2[iN].charge && !at2[iN].radical &&
6361 [ # # # # ]: 0 : 0 <= ( e = pVA[iN].nCPlusGroupEdge - 1 ) && !pBNS->edge[e].forbidden &&
6362 [ # # ]: 0 : pBNS->edge[e].flow && /* NPlus edge */
6363 [ # # # # ]: 0 : 0 <= ( e1 = pVA[iat].nCMinusGroupEdge - 1 ) && !pBNS->edge[e1].forbidden &&
6364 [ # # # # ]: 0 : pBNS->edge[e1].flow && /* OMinus edge */
6365 [ # # ]: 0 : 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e ) &&
6366 : 0 : 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1 ))
6367 : : {
6368 : : /* found >N-O(-) */
6369 : 0 : int nNumO = 0, nNumOthers = 0;
6370 [ # # ]: 0 : for (k = 0; k < at2[iN].valence; k++)
6371 : : {
6372 : 0 : neigh = at2[iN].neighbor[k];
6373 [ # # ]: 0 : if (neigh == iat)
6374 : : {
6375 : 0 : continue;
6376 : : }
6377 [ # # ]: 0 : if (pVA[neigh].cNumValenceElectrons == 6 &&
6378 [ # # ]: 0 : !pStruct->endpoint[neigh] &&
6379 [ # # # # ]: 0 : at2[neigh].valence == 1 && at2[neigh].num_H == 0 &&
6380 [ # # # # ]: 0 : at2[neigh].radical == 0 && at2[neigh].charge == -1 &&
6381 [ # # ]: 0 : at2[neigh].chem_bonds_valence == 1)
6382 : : {
6383 : 0 : nNumO++;
6384 : : }
6385 : : else
6386 : : {
6387 [ # # ]: 0 : if (at2[iN].bond_type[k] == BOND_TYPE_SINGLE &&
6388 [ # # ]: 0 : at2[neigh].valence > 1 &&
6389 [ # # ]: 0 : at2[neigh].valence < at2[neigh].chem_bonds_valence)
6390 : : {
6391 : 0 : nNumOthers++;
6392 : : }
6393 : : }
6394 : : }
6395 [ # # # # ]: 0 : if (nNumO != 1 && nNumOthers != 1)
6396 : : {
6397 : 0 : continue;
6398 : : }
6399 : : /* save charge edges: NPlus first, OMinus second */
6400 [ # # # # ]: 0 : if (( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e, INC_ADD_EDGE ) ) ||
6401 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_NO_IN_NO2M2], e1, INC_ADD_EDGE ) ) ||
6402 [ # # ]: 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e, INC_ADD_EDGE ) ) ||
6403 : 0 : ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_AVOID], e1, INC_ADD_EDGE ) ))
6404 : : {
6405 : 0 : goto exit_case_25;
6406 : : }
6407 : : }
6408 : : }
6409 : : }
6410 [ # # ]: 0 : if (!ChangeableEdges[CHG_SET_NO_IN_NO2M2].num_edges ||
6411 [ # # ]: 0 : !ChangeableEdges[CHG_SET_OTHER_TAUT_ALL].num_edges)
6412 : : {
6413 : 0 : goto exit_case_25;
6414 : : }
6415 : : /* ------- finally, try to move charges from -NO2(2-) or to tautomeric endpoints ----*/
6416 [ # # ]: 0 : for (i = 0; i < ChangeableEdges[CHG_SET_NO_IN_NO2M2].num_edges; i += 2)
6417 : : {
6418 : 0 : int nDeltaChargeExpected = 3;
6419 : : /* change flow on O(-) to make it neutral; 3 new charges will be created:
6420 : : N(+), and two (-) on InChI endpoints
6421 : : alternatively, if we change flow on N to make N(+) then O(-) will
6422 : : be nutralized (-1 charge) and two (-) charges on taut. endpoints will be
6423 : : created (+2); the total change in this case would be (-1)+(+2) = +1
6424 : : */
6425 : 0 : one_success = 0;
6426 : 0 : delta = 1;
6427 : 0 : pe = pBNS->edge + ChangeableEdges[CHG_SET_NO_IN_NO2M2].pnEdges[i + 1]; /* O(-) edge */
6428 : 0 : pef = pBNS->edge + ChangeableEdges[CHG_SET_NO_IN_NO2M2].pnEdges[i]; /* >N- (+) edge */
6429 : :
6430 [ # # ]: 0 : if (!pe->flow)
6431 : 0 : continue;
6432 : 0 : pv1 = pBNS->vert + ( v1 = pe->neighbor1 );
6433 : 0 : pv2 = pBNS->vert + ( v2 = pe->neighbor12 ^ v1 );
6434 : :
6435 : 0 : pe->flow -= delta;
6436 : 0 : pv1->st_edge.flow -= delta;
6437 : 0 : pv2->st_edge.flow -= delta;
6438 : 0 : pBNS->tot_st_flow -= 2 * delta;
6439 : :
6440 [ # # # # ]: 0 : for (k = 0; !one_success && k <= CHG_LAST_SET; k++)
6441 : : {
6442 [ # # ]: 0 : if (!ChangeableEdges[k].num_edges)
6443 : : {
6444 : 0 : continue;
6445 : : }
6446 : 0 : SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
6447 : 0 : RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask );
6448 : : /* allow change of N(V) flower edge */
6449 : 0 : pef->forbidden &= forbidden_edge_mask_inv;
6450 : :
6451 : 0 : ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
6452 : : &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms );
6453 : :
6454 [ # # # # : 0 : if (ret == 1 && ( (vPathEnd == v1 && vPathStart == v2) ||
# # ]
6455 [ # # # # ]: 0 : (vPathEnd == v2 && vPathStart == v1) ) &&
6456 [ # # ]: 0 : nDeltaCharge == nDeltaChargeExpected) /* djb-rwth: addressing LLVM warnings */
6457 : : {
6458 : : /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */
6459 : 0 : ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups );
6460 [ # # ]: 0 : if (ret > 0)
6461 : : {
6462 : 0 : nNumRunBNS++;
6463 : 0 : one_success++; /* 24 */
6464 : : }
6465 : : }
6466 : : INCHI_HEAPCHK
6467 : : }
6468 : 0 : cur_success += one_success;
6469 : :
6470 : 0 : RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask );
6471 : :
6472 [ # # ]: 0 : if (!one_success)
6473 : : {
6474 : 0 : pe->flow += delta;
6475 : 0 : pv1->st_edge.flow += delta;
6476 : 0 : pv2->st_edge.flow += delta;
6477 : 0 : pBNS->tot_st_flow += 2 * delta;
6478 : : }
6479 : : }
6480 : 0 : exit_case_25:
6481 [ # # ]: 0 : for (i = 0; i < CHG_SET_NUM; i++)
6482 : : {
6483 : 0 : AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE );
6484 : : }
6485 : :
6486 : 0 : CurrEdges.num_edges = 0; /* clear current edge list */
6487 [ # # ]: 0 : if (cur_success)
6488 : : {
6489 : 0 : tot_succes += cur_success;
6490 : : /* recalculate InChI from the structure */
6491 [ # # ]: 0 : if (0 >( ret = MakeOneInChIOutOfStrFromINChI2( pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
6492 : : ppt_group_info, ppat_norm, ppat_prep ) ))
6493 : : {
6494 : 0 : goto exit_function;
6495 : : }
6496 [ # # ]: 0 : if ((ret = FillOutExtraFixedHDataRestr( pStruct ))) /* djb-rwth: addressing LLVM warning */
6497 : : {
6498 : 0 : goto exit_function;
6499 : : }
6500 [ # # # # ]: 0 : if (!pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed)
6501 : : {
6502 : 0 : goto exit_function; /* no fixed-H found */
6503 : : }
6504 [ # # ]: 0 : if ((ret = FillOutCMP2FHINCHI( pStruct, at2, pVA, pInChI, pc2i ))) /* djb-rwth: addressing LLVM warning */
6505 : : {
6506 : 0 : goto exit_function;
6507 : : }
6508 [ # # ]: 0 : if (!pc2i->bHasDifference)
6509 : : {
6510 : 0 : goto exit_function; /* nothing to do */
6511 : : }
6512 : : }
6513 : : #undef CHG_SET_NN
6514 : : #undef CHG_SET_MISSED_TAUT
6515 : : #undef CHG_SET_OTHER_TAUT_O
6516 : : #undef CHG_SET_OTHER_TAUT_N
6517 : : #undef CHG_LAST_SET
6518 : : #undef CHG_SET_AVOID
6519 : : #undef CHG_SET_NUM
6520 : : }
6521 : :
6522 : :
6523 : 0 : exit_function:
6524 : :
6525 : 0 : AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE );
6526 : 0 : AllocEdgeList( &CurrEdges, EDGE_LIST_FREE );
6527 : 0 : AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE );
6528 : 0 : AllocEdgeList( &SFlowerEdges, EDGE_LIST_FREE );
6529 : 0 : AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE );
6530 : 0 : AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE );
6531 : 0 : AllocEdgeList( &AllBondEdges, EDGE_LIST_FREE );
6532 : :
6533 [ # # # # : 0 : return ret < 0 ? ret : ( tot_succes && pc2i->bHasDifference );
# # ]
6534 : : }
6535 : :
6536 : : #endif
|
