/* * International Chemical Identifier (InChI) * Version 1 * Software version 1.04 * September 9, 2011 * * The InChI library and programs are free software developed under the * auspices of the International Union of Pure and Applied Chemistry (IUPAC). * Originally developed at NIST. Modifications and additions by IUPAC * and the InChI Trust. * * IUPAC/InChI-Trust Licence No.1.0 for the * International Chemical Identifier (InChI) Software version 1.04 * Copyright (C) IUPAC and InChI Trust Limited * * This library is free software; you can redistribute it and/or modify it * under the terms of the IUPAC/InChI Trust InChI Licence No.1.0, * or any later version. * * Please note that this library is distributed WITHOUT ANY WARRANTIES * whatsoever, whether expressed or implied. See the IUPAC/InChI Trust * Licence for the International Chemical Identifier (InChI) Software * version 1.04, October 2011 ("IUPAC/InChI-Trust InChI Licence No.1.0") * for more details. * * You should have received a copy of the IUPAC/InChI Trust InChI * Licence No. 1.0 with this library; if not, please write to: * * The InChI Trust * c/o FIZ CHEMIE Berlin * * Franklinstrasse 11 * 10587 Berlin * GERMANY * * or email to: ulrich@inchi-trust.org. * */ #include #include #include /*#define CHECK_WIN32_VC_HEAP*/ #include "mode.h" #if ( READ_INCHI_STRING == 1 ) #include "ichi.h" #include "ichitime.h" #include "inpdef.h" #include "ichimain.h" #include "ichierr.h" #include "incomdef.h" #include "ichiring.h" #include "extr_ct.h" #include "ichitaut.h" #include "ichinorm.h" #include "util.h" #include "ichicomp.h" #include "ichister.h" #include "ichi_bns.h" #include "strutil.h" #include "ichirvrs.h" #define INC_ADD_EDGE 64 /***********************************************************************************************/ int GetPlusMinusVertex( BN_STRUCT *pBNS, ALL_TC_GROUPS *pTCGroups, int bCheckForbiddenPlus, int bCheckForbiddenMinus ) { int k, ePlusSuper, eMinusSuper, vPlusSuper, vMinusSuper, vPlusMinus1 = NO_VERTEX, vPlusMinus2 = NO_VERTEX; BNS_EDGE *pEdge; if ( (k = pTCGroups->nGroup[TCG_Plus]) >= 0 && (ePlusSuper = pTCGroups->pTCG[k].nForwardEdge) > 0 && (vPlusSuper = pTCGroups->pTCG[k].nVertexNumber) >= pBNS->num_atoms && !((pEdge=pBNS->edge + ePlusSuper)->forbidden && bCheckForbiddenPlus) ) { vPlusMinus1 = pEdge->neighbor12 ^ vPlusSuper; } if ( (k = pTCGroups->nGroup[TCG_Minus]) >= 0 && (eMinusSuper = pTCGroups->pTCG[k].nForwardEdge) > 0 && (vMinusSuper = pTCGroups->pTCG[k].nVertexNumber) >= pBNS->num_atoms && !((pEdge=pBNS->edge + eMinusSuper)->forbidden && bCheckForbiddenMinus) ) { vPlusMinus2 = pEdge->neighbor12 ^ eMinusSuper; } if ( bCheckForbiddenPlus && NO_VERTEX == vPlusMinus1 || bCheckForbiddenMinus && NO_VERTEX == vPlusMinus2 ) { return NO_VERTEX; } return (NO_VERTEX != vPlusMinus1)? vPlusMinus1 : vPlusMinus2; } /***********************************************************************************************/ int bIsUnsatCarbonInASmallRing( inp_ATOM *at2, VAL_AT *pVA, int iat, BFS_Q *pbfsq, int min_ring_size ) { int j, nCurRingSize, nMinRingSize; if ( min_ring_size < 5 ) { /* =C= in a small ring */ if ( at2[iat].valence == 2 && pVA[iat].cMinRingSize <= 5 && at2[iat].chem_bonds_valence == 4 ) { return 1; } } else { if ( at2[iat].valence == 2 && pVA[iat].cMinRingSize && pVA[iat].cMinRingSize <= min_ring_size && at2[iat].chem_bonds_valence == 3 ) { return 1; } nCurRingSize = nMinRingSize = min_ring_size+1; if ( (at2[iat].valence == 2 || at2[iat].valence == 3) && at2[iat].chem_bonds_valence == at2[iat].valence+1 ) { for ( j = 0; j < at2[iat].valence; j ++ ) { nCurRingSize = is_bond_in_Nmax_memb_ring( at2, iat, j, pbfsq->q, pbfsq->nAtomLevel, pbfsq->cSource, (AT_RANK)nMinRingSize /* max ring size */ ); if ( 0 < nCurRingSize && nCurRingSize < nMinRingSize ) { nMinRingSize = nCurRingSize; } } return (0 <= nCurRingSize)? (nMinRingSize <= min_ring_size) : nCurRingSize; } } return 0; } /***********************************************************************************************/ int FixMobileHRestoredStructure(ICHICONST INPUT_PARMS *ip, STRUCT_DATA *sd, BN_STRUCT *pBNS, BN_DATA *pBD, StrFromINChI *pStruct, inp_ATOM *at, inp_ATOM *at2, inp_ATOM *at3, VAL_AT *pVA, ALL_TC_GROUPS *pTCGroups, T_GROUP_INFO **ppt_group_info, inp_ATOM **ppat_norm, inp_ATOM **ppat_prep, INChI *pInChI[], long num_inp, int bHasSomeFixedH, int *pnNumRunBNS, int *pnTotalDelta, int forbidden_edge_mask, int forbidden_stereo_edge_mask) { /*--------- process extra or missing Fixed-H on non-tautomeric atoms ------*/ /* at2 should be the most recently restored atom, Fixed-H */ int i, j, k, iat, delta, tot_succes, cur_success, ret = 0; CMP2MHINCHI c2i; CMP2MHINCHI *pc2i = &c2i; EDGE_LIST AllChargeEdges, CurrEdges, CurrEdges2, CurrEdges3, TautEdges, NFlowerEdges, OtherNFlowerEdges, FixedLargeRingStereoEdges; EDGE_LIST *pEdgeList = NULL; EdgeIndex e; BNS_EDGE *pe; Vertex v1, v2, vPlusMinus; BNS_VERTEX *pv1, *pv2; Vertex vPathStart, vPathEnd; int nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms; int nNumRunBNS = 0, forbidden_edge_mask_inv = ~forbidden_edge_mask; INCHI_HEAPCHK AllocEdgeList( &AllChargeEdges, EDGE_LIST_CLEAR ); AllocEdgeList( &CurrEdges, EDGE_LIST_CLEAR ); AllocEdgeList( &NFlowerEdges, EDGE_LIST_CLEAR ); AllocEdgeList( &CurrEdges2, EDGE_LIST_CLEAR ); AllocEdgeList( &CurrEdges3, EDGE_LIST_CLEAR ); AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_CLEAR ); AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_CLEAR ); AllocEdgeList( &TautEdges, EDGE_LIST_CLEAR ); tot_succes = 0; if ( !pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed ) { goto exit_function; /* no fixed-H found */ } /* taut group edges */ for ( i = 0; i < pTCGroups->num_tgroups; i ++ ) { pv1 = pBNS->vert + (v1=pTCGroups->pTCG[i].nVertexNumber); /* t-group vertex */ for ( j = 0; j < pv1->num_adj_edges; j ++ ) { /* e, pe - tautomeric atom edge; pv2 - endpoint vertex */ /* Note: pe, pv2, v1 are not used here; they are to show how to traverse t-group */ pv2 = pBNS->vert + (pe = pBNS->edge + (e=pv1->iedge[j]))->neighbor1; if ( ret = AddToEdgeList( &TautEdges, e, INC_ADD_EDGE ) ) { goto exit_function; } } } /* charge and flower edges */ for ( i = 0; i < pStruct->num_atoms; i ++ ) { if ( (e=pVA[i].nCMinusGroupEdge-1) >= 0 && !pBNS->edge[e].forbidden && (ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE )) ) { goto exit_function; } if ( (e=pVA[i].nCPlusGroupEdge-1) >= 0 && !pBNS->edge[e].forbidden ) { if ( ret = AddToEdgeList( &AllChargeEdges, e, INC_ADD_EDGE ) ) { goto exit_function; } /* in addition, disallow N(V) creation by forbidding charge flower edge that has flow=1 */ if ( pVA[i].cNumValenceElectrons == 5 && !pVA[i].cMetal && /* N, P, As */ NO_VERTEX != (j = GetChargeFlowerUpperEdge( pBNS, pVA, e ))) { if ( !pBNS->edge[j].forbidden && pBNS->edge[j].flow ) { if ( ret = AddToEdgeList( &AllChargeEdges, j, INC_ADD_EDGE ) ) { goto exit_function; } if ( ret = AddToEdgeList( &NFlowerEdges, j, INC_ADD_EDGE ) ) { goto exit_function; } } else { if ( ret = AddToEdgeList( &OtherNFlowerEdges, j, INC_ADD_EDGE ) ) { goto exit_function; } } } } } if ( forbidden_stereo_edge_mask ) { for ( i = 0; i < pStruct->num_atoms; i ++ ) { for ( j = 0; j < at2[i].valence; j ++ ) { if ( pBNS->edge[k = pBNS->vert[i].iedge[j]].forbidden == forbidden_stereo_edge_mask ) { int nMinRingSize = is_bond_in_Nmax_memb_ring( at2, i, j, pStruct->pbfsq->q, pStruct->pbfsq->nAtomLevel, pStruct->pbfsq->cSource, 99 /* max ring size */ ); if ( 0 < nMinRingSize && (ret = AddToEdgeList( &FixedLargeRingStereoEdges, k, INC_ADD_EDGE ))) { goto exit_function; } } } } } INCHI_HEAPCHK if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } INCHI_HEAPCHK if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } INCHI_HEAPCHK if ( pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && pc2i->nNumTgDBNMinusRevrs + pc2i->nNumTgNHMinusRevrs == 0 && pc2i->nNumTgOMinusInChI && !(pTCGroups->pTCG[0].tg_RestoreFlags & TGRF_MINUS_FIRST) ) { /*----------------------------------------------------*/ /* case 01: restored has -O(-) and does not have N(-) */ /* endpoints defined by the original InChI */ /* restored has single taut. group or more */ /* tautomeric endpoints. */ /* Solution: move (-) from endp. -O(-) to endpoints N */ /*----------------------------------------------------*/ pTCGroups->pTCG[0].tg_RestoreFlags |= TGRF_MINUS_FIRST; /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( !pInChI[0]->nNum_H_fixed && !pStruct->pOneINChI[0]->nNum_H_fixed ) { goto exit_function; /* no fixed-H found */ } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } if ( !pc2i->bHasDifference ) { goto exit_function; /* nothing to do */ } } if ( pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && pc2i->nNumTgDBNMinusRevrs + pc2i->nNumTgNHMinusRevrs == 0 && pc2i->nNumTgOMinusInChI == 0 ) { /*-------------------------------------------------------*/ /* case 02: restored has no -O(-) and does not have N(-) */ /* restored has single taut. group or more */ /* tautomeric endpoints. */ /* Solution: >N-AB=N- => >N(+)=AB-NH- (add H(+)) */ /* Solution: >N-AB=NH => >N(+)=AB-NH2 (add H(+)) */ /* SB_N_III DB_N_III */ /*-------------------------------------------------------*/ int iat_SB_N_III[MAX_DIFF_MOBH], iat_DB_N_III[MAX_DIFF_MOBH]; int num_SB_N_III = 0, num_DB_N_III = 0, k1, k2; CurrEdges.num_edges = 0; cur_success = 0; for ( i = 0; i < pStruct->num_atoms; i ++ ) { iat = i; if ( pVA[iat].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && !at2[iat].endpoint && !at2[iat].charge && !at2[iat].radical ) { if ( num_DB_N_III < MAX_DIFF_MOBH && !at2[iat].num_H && at2[iat].valence == 2 && at2[iat].chem_bonds_valence == 3 && !at2[iat].sb_parity[0] && /* do not eliminate stereobonds */ (e=pVA[iat].nCMinusGroupEdge-1) >= 0 && !pBNS->edge[e].forbidden && pBNS->edge[e].cap && !pBNS->edge[e].flow ) { /* -N= */ iat_DB_N_III[ num_DB_N_III ++ ] = iat; } else if ( num_DB_N_III < MAX_DIFF_MOBH && 1 == at2[iat].num_H && at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && !at2[iat].sb_parity[0] && /* do not eliminate stereobonds */ (e=pVA[iat].nCMinusGroupEdge-1) >= 0 && !pBNS->edge[e].forbidden && pBNS->edge[e].cap && !pBNS->edge[e].flow ) { /* -N= */ iat_DB_N_III[ num_DB_N_III ++ ] = iat; } else if ( num_SB_N_III < MAX_DIFF_MOBH && !at2[iat].num_H && at2[iat].valence == 3 && at2[iat].chem_bonds_valence == 3 && (e=pVA[iat].nCPlusGroupEdge-1) >= 0 && !pBNS->edge[e].forbidden && pBNS->edge[e].cap && pBNS->edge[e].flow) { /* -N< */ iat_SB_N_III[ num_SB_N_III ++ ] = iat; if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { goto exit_function; } } } } if ( num_DB_N_III && num_SB_N_III ) { EdgeIndex ieMinus; BNS_EDGE *peMinus; SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); for ( i = 0; i < num_DB_N_III && !cur_success; i ++ ) { iat = iat_DB_N_III[ i ]; e = pBNS->edge[k1=pBNS->vert[iat].iedge[0]].flow? k1 : pBNS->edge[k2=pBNS->vert[iat].iedge[1]].flow? k2 : NO_VERTEX; if ( e == NO_VERTEX ) { continue; /* should not happen */ } ieMinus = pVA[iat].nCMinusGroupEdge-1; peMinus = pBNS->edge + ieMinus; pe = pBNS->edge + e; if ( !pe->flow ) continue; pv1 = pBNS->vert + (v1 = pe->neighbor1); pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); pe->forbidden |= forbidden_edge_mask; /* fix double bond */ peMinus->forbidden &= forbidden_edge_mask_inv; /* allow negative charge */ delta = 1; pe->flow -= delta; /* remove (-) from AB-O(-) */ pv1->st_edge.flow -= delta; pv2->st_edge.flow -= delta; pBNS->tot_st_flow -= 2*delta; ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); if ( ret == 1 && (vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1) && nDeltaCharge == 2 ) { /* Added (-)charge -N= and (+) to -N< => nDeltaCharge == 2 */ ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); if ( ret > 0 ) { nNumRunBNS ++; cur_success ++; /* 01 */ /* eliminate (-) charge and add H */ pv1 = pBNS->vert + (v1 = peMinus->neighbor1); /* atom */ pv2 = pBNS->vert + (v2 = peMinus->neighbor12 ^ v1);/* (=) vertex */ /* effectively eliminate (-) edge by setting its cap=flow= 0 */ peMinus->cap --; peMinus->flow --; pv1->st_edge.cap --; pv1->st_edge.flow --; pv2->st_edge.cap --; pv2->st_edge.flow --; pBNS->tot_st_flow -= 2; pBNS->tot_st_cap -= 2; /* add H */ pStruct->at[iat].num_H ++; /* register total charge increase */ pTCGroups->total_charge ++; pStruct->nNumRemovedProtonsByRevrs -= 1; } } else { pe->forbidden &= forbidden_edge_mask_inv; peMinus->forbidden |= forbidden_edge_mask; pe->flow += delta; pv1->st_edge.flow += delta; pv2->st_edge.flow += delta; pBNS->tot_st_flow += 2*delta; } } RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); CurrEdges.num_edges = 0; /* clear current edge list */ if ( cur_success ) { tot_succes += cur_success; /* recalculate InChI from the structure */ /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } if ( !pc2i->bHasDifference ) { goto exit_function; /* nothing to do */ } } } } if ( pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && /* ADP */ pc2i->nNumTgMInChI == 0 && pc2i->nNumTgNInChI && pc2i->nNumTgOInChI ) { /*-------------------------------------------------------*/ /* case 03: restored has N and O endpoints, no (-) endp */ /* case 04: original has single taut. group or more */ /* tautomeric endpoints. */ /* Solution: 1. Move taut attachment from O to N */ /* Solution: 2. Replace the attachment with (-) */ /* SB_N_III DB_N_III */ /*-------------------------------------------------------*/ /* int iat_SB_N_III[MAX_DIFF_MOBH], iat_DB_N_III[MAX_DIFF_MOBH]; int num_SB_N_III = 0, num_DB_N_III = 0, k1, k2, */ int itg, j1, j2, bAction = 0; BNS_VERTEX *pTg, *pvEndp, *pvEndp2, *pvCent; Vertex vEndp, vEndp2, vCent; BNS_EDGE *peTg, *peTg2, *peCent1, *peCent2; EdgeIndex eTg, eTg2; CurrEdges.num_edges = 0; CurrEdges2.num_edges = 0; cur_success = 0; /* 1st attempt: -NH-=O => -N(-)-=O or -N=-OH => -N(-)-=O */ for ( itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg ++ ) { pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; for ( i = 0; i < pTg->num_adj_edges && !cur_success; i ++ ) { pvEndp = pBNS->vert + (vEndp = (peTg = pBNS->edge + (eTg=pTg->iedge[i]))->neighbor1); eTg2 = -1; if ( pVA[vEndp].cNumValenceElectrons == 6 && peTg->cap ) { /* endpoint -OH or =O found; search for a possible centerpoint */ for ( j1 = 0; j1 < at2[vEndp].valence && eTg2 < 0; j1 ++ ) { peCent1 = pBNS->edge + pvEndp->iedge[j1]; /* edge from O to a centerpoint */ pvCent = pBNS->vert + (vCent = peCent1->neighbor12 ^ vEndp); /* centerpoint */ if ( at2[vCent].endpoint || !peCent1->cap || peCent1->flow + (peTg->cap == peTg->flow) != 1 ) { continue; } /* search for another endpoint, N, around vCent */ for ( j2 = 0; j2 < at2[vCent].valence; j2 ++ ) { peCent2 = pBNS->edge + pvCent->iedge[j2]; pvEndp2 = pBNS->vert + (vEndp2 = peCent2->neighbor12 ^ vCent); if ( !peCent2->cap || peCent2->flow+peCent1->flow != 1 || at2[vEndp2].endpoint != itg+1 || pVA[vEndp2].cNumValenceElectrons != 5 || 0 > (j=pVA[vEndp2].nTautGroupEdge-1) || (peTg2 = pBNS->edge + j)->forbidden || peCent2->flow + (peTg2->cap == peTg2->flow) != 1 ) { continue; } eTg2 = j; break; /* found OH-C=N- or O=C-NH- */ } } } if ( eTg2 >= 0 ) { /*-------------------------------------------- tg tg eTg //\ eTg2 eTg / \\eTg2 // \ / \\ vEndp HO--C==N vEndp2 --> vEndp O==C--NH vEndp2 ^ ^ ^ ^ ^ ^ eCent1 | eCent2 eCent1 | eCent2 vCent vCent additional action: -OH-C=N- => O=C-NH- -------------------------------------------*/ if ( 0 == peTg->cap - peTg->flow && 1 == peTg2->cap - peTg2->flow && 0 == peCent1->flow && 1 == peCent2->flow ) { peTg->flow --; /* 03 prepare */ peTg2->flow ++; peCent2->flow --; peCent1->flow ++; bAction |= 1; /* switched H position */ } if ( 1 == peTg->cap - peTg->flow && 0 == peTg2->cap - peTg2->flow && 1 == peCent1->flow && 0 == peCent2->flow ) { /* replace -NH- with -N(-)- */ pTCGroups->pTCG[itg].tg_num_H --; pTCGroups->pTCG[itg].tg_num_Minus ++; pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; pTCGroups->pTCG[itg].tg_set_Minus = vEndp2+1; pStruct->ti.t_group[itg].num[1] ++; /* increment number of (-), keep number of taut attachments */ pTCGroups->total_charge --; pTCGroups->tgroup_charge --; pStruct->nNumRemovedProtonsByRevrs += 1; bAction |= 2; /* single NH (at2[vEndp2]) replaced with N(-) */ cur_success ++; /* 03/04 */ } } } } if ( 0 == pc2i->nNumTgNHInChI+ pc2i->nNumTgNH2InChI && pc2i->nNumTgOHInChI && !cur_success ) { /* transfer an attachement to N */ for ( itg = 0; itg < pTCGroups->num_tgroups; itg ++ ) { pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; for ( i = 0; i < pTg->num_adj_edges; i ++ ) { pvEndp = pBNS->vert + (vEndp = (peTg = pBNS->edge + (eTg=pTg->iedge[i]))->neighbor1); if ( pVA[vEndp].cNumValenceElectrons == 6 && at2[vEndp].valence == at2[vEndp].chem_bonds_valence && peTg->flow && peTg->flow == peTg->cap ) { /* endpoint -OH found; save the tautomeric group edge */ if ( ret = AddToEdgeList( &CurrEdges, eTg, INC_ADD_EDGE ) ) { goto exit_function; } } else if ( pVA[vEndp].cNumValenceElectrons == 5 && pVA[vEndp].cPeriodicRowNumber == 1 && at2[vEndp].valence + 1 == at2[vEndp].chem_bonds_valence && peTg->cap && peTg->flow + 1 == peTg->cap ) { /* endpoint -N= or =NH found, check for -N=-OH */ e = -1; for ( j1 = 0; j1 < at2[vEndp].valence && e < 0; j1 ++ ) { peCent1 = pBNS->edge + pvEndp->iedge[j1]; if ( peCent1->flow == 1 ) { /* double bond */ pvCent = pBNS->vert + (vCent = peCent1->neighbor12 ^ vEndp); if ( at2[vCent].endpoint ) continue; for ( j2 = 0; j2 < at2[vCent].valence; j2 ++ ) { peCent2 = pBNS->edge + pvCent->iedge[j2]; pvEndp2 = pBNS->vert + (vEndp2 = peCent2->neighbor12 ^ vCent); if ( peCent2->flow || at2[vEndp2].endpoint != itg+1 || pVA[vEndp2].cNumValenceElectrons != 6 || 0 >= (e=pVA[vEndp2].nTautGroupEdge-1) || pBNS->edge[e].forbidden || !pBNS->edge[e].flow ) { e = -1; continue; } /*********************/ /* found -N=X-OH */ /* vEndp ^ vEndp2 */ /* vCent */ /*********************/ /* save this -OH taut edge */ if ( ret = AddToEdgeList( &CurrEdges2, e, INC_ADD_EDGE ) ) { goto exit_function; } break; } } } if ( e < 0 && (ret = AddToEdgeList( &CurrEdges, eTg, INC_ADD_EDGE )) ) { goto exit_function; } } } } /* rearrange the flows */ SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); SetForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); SetForbiddenEdgeMask( pBNS, &CurrEdges2, forbidden_edge_mask ); pEdgeList = CurrEdges2.num_edges? &CurrEdges2 : CurrEdges.num_edges? &CurrEdges : NULL; for ( i = 0; pEdgeList && i < pEdgeList->num_edges && !cur_success; i ++ ) { pe = pBNS->edge + pEdgeList->pnEdges[i]; /* pe->flow = 1 <=> -OH */ if ( !pe->flow ) continue; pv1 = pBNS->vert + (v1 = pe->neighbor1); /* -OH atom */ pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); /* t-group vertex */ /* locate the t-group */ for ( itg = 0; itg < pTCGroups->num_tgroups; itg ++ ) { if ( v2 == pTCGroups->pTCG[itg].nVertexNumber ) { break; } } if ( itg == pTCGroups->num_tgroups ) { /* tgroup not found -- should not happen */ continue; } delta = 1; pe->flow -= delta; /* add one attachment to */ pv1->st_edge.flow -= delta; pv2->st_edge.flow -= delta; pBNS->tot_st_flow -= 2*delta; ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); if ( ret == 1 && (vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1) && nDeltaCharge == 2 ) { /* Added (-)charge -N= and (+) to -N< => nDeltaCharge == 2 */ ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); if ( ret > 0 ) { nNumRunBNS ++; cur_success ++; /* 03 */ /* replace -NH- with -N(-)- */ pTCGroups->pTCG[itg].tg_num_H --; pTCGroups->pTCG[itg].tg_num_Minus ++; pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; pStruct->ti.t_group[itg].num[1] ++; pTCGroups->total_charge --; pTCGroups->tgroup_charge --; pStruct->nNumRemovedProtonsByRevrs += 1; bAction |= 4; /* H in the 1st available NH was replaced with (-) */ } } else { pe->flow += delta; pv1->st_edge.flow += delta; pv2->st_edge.flow += delta; pBNS->tot_st_flow += 2*delta; } } RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); } else if ( pc2i->nNumTgNHInChI+ pc2i->nNumTgNH2InChI && pc2i->nNumTgOInChI && !cur_success ) { /* change an attachement to N from H to (-) */ for ( itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg ++ ) { pTg = pBNS->vert + pTCGroups->pTCG[itg].nVertexNumber; for ( i = 0; i < pTg->num_adj_edges && !cur_success; i ++ ) { pvEndp2 = pBNS->vert + (vEndp2 = (peTg = pBNS->edge + pTg->iedge[i])->neighbor1); if ( pVA[vEndp2].cNumValenceElectrons == 5 && pVA[vEndp2].cPeriodicRowNumber == 1 && at2[vEndp2].valence == at2[vEndp2].chem_bonds_valence && peTg->flow && peTg->flow == peTg->cap ) { /* endpoint -NHn found; change its charge */ cur_success ++; /* 04 */ /* replace -NH- with -N(-)- */ pTCGroups->pTCG[itg].tg_num_H --; pTCGroups->pTCG[itg].tg_num_Minus ++; pTCGroups->pTCG[itg].tg_RestoreFlags |= TGRF_MINUS_FIRST; pTCGroups->pTCG[itg].tg_set_Minus = vEndp2 + 1; pStruct->ti.t_group[itg].num[1] ++; pTCGroups->total_charge --; pTCGroups->tgroup_charge --; pStruct->nNumRemovedProtonsByRevrs += 1; bAction |= 8; /* manually set (-) charge to NH atom, vEndp2 */ } } } } if ( cur_success ) { tot_succes += cur_success; /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } if ( pStruct->One_ti.num_t_groups == 1 && pStruct->One_ti.t_group[0].num[1] ) { /* this method did not work: no alt path from N(-) to =O */ itg = 0; if ( bAction & (8 | 2 ) ) { /* roll back NH -> N(-) replacement; H move from OH to N is not undone */ pTCGroups->pTCG[itg].tg_num_H ++; pTCGroups->pTCG[itg].tg_num_Minus --; pTCGroups->pTCG[itg].tg_RestoreFlags &= ~TGRF_MINUS_FIRST; pTCGroups->pTCG[itg].tg_set_Minus = 0; pStruct->ti.t_group[itg].num[1] --; pTCGroups->total_charge ++; pTCGroups->tgroup_charge ++; pStruct->nNumRemovedProtonsByRevrs -= 1; cur_success --; } else if ( bAction & 4 ) { pTCGroups->pTCG[itg].tg_num_H ++; pTCGroups->pTCG[itg].tg_num_Minus --; pTCGroups->pTCG[itg].tg_RestoreFlags &= ~TGRF_MINUS_FIRST; pStruct->ti.t_group[itg].num[1] --; pTCGroups->total_charge ++; pTCGroups->tgroup_charge ++; pStruct->nNumRemovedProtonsByRevrs -= 1; cur_success --; } else { ret = RI_ERR_PROGR; goto exit_function; } /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } } if ( !pc2i->bHasDifference ) { goto exit_function; /* nothing to do */ } } } if ( pc2i->nNumTgInChI == 1 && ( pc2i->nNumEndpRevrs < pc2i->nNumEndpInChI || pc2i->nNumTgRevrs > 1 ) && /* ADP */ pc2i->nNumTgMInChI == 0 && (pc2i->nNumTgNInChI || pc2i->nNumTgOInChI) && NO_VERTEX != (vPlusMinus = GetPlusMinusVertex( pBNS, pTCGroups, 1, 1 )) ) { /*---------------------------------------------------------------------------*/ /* case 05: restored has N endpoints, no (-) endpoints */ /* original has single taut. group or more */ /* tautomeric endpoints. */ /* Solution: Find -N< and allow (+) charge change */ /* Fix all charges and taut attachments exept */ /* =N- and =O (taut. endpoints) */ /* Increment st_edge.cap on (+/-) vertex => add (+) charge to -N< */ /* Increment tot. charge in other places */ /* Increment t-group st_edge.cap */ /* Run BNS */ /* */ /* (+/-)* (+/-) Result: */ /* | || */ /* | || - Added (+) to -N< */ /* (+)super (+)super - Added attachment point to O */ /* || | */ /* || => | To make this attachment H, */ /* (Y) (Y) increment */ /* | || pTCGroups->pTCG[itg].tg_num_H */ /* | || */ /* (+)hetero (+)hetero Technical details: */ /* \\ \ increase capacities of */ /* N N(+) edges to (+/-) otherwise */ /* | || flow may not be able to */ /* *(t)--O=R. (t)==O-R. increase */ /* */ /* */ /*---------------------------------------------------------------------------*/ int itg; BNS_VERTEX *pTg, *pvEndp; Vertex vEndp, vTg; BNS_EDGE *peTg; EdgeIndex eTg; AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; CurrEdges.num_edges = 0; CurrEdges2.num_edges = 0; cur_success = 0; /* find -N< and non-taut =N- or =O */ for ( i = 0; i < pStruct->num_atoms; i ++ ) { iat = nCanon2AtnoRevrs[i]; /* -N< */ if ( !at2[iat].endpoint && !at2[iat].charge && !at2[iat].radical && !at2[iat].num_H && pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 && 0 <= (e=pVA[iat].nCPlusGroupEdge-1) && pBNS->edge[e].flow && !pBNS->edge[e].forbidden) { if ( ret = AddToEdgeList( &CurrEdges, e, INC_ADD_EDGE ) ) { goto exit_function; } } } if ( !CurrEdges.num_edges ) { goto exit_case_05; } /* find taut -N= and =O */ for ( itg = 0; itg < pTCGroups->num_tgroups && !cur_success; itg ++ ) { CurrEdges2.num_edges = 0; pTg = pBNS->vert + (vTg = pTCGroups->pTCG[itg].nVertexNumber); for ( i = 0; i < pTg->num_adj_edges; i ++ ) { pvEndp = pBNS->vert + (vEndp = (peTg = pBNS->edge + (eTg=pTg->iedge[i]))->neighbor1); if ( at2[vEndp].charge || at2[vEndp].radical || peTg->cap - peTg->flow != 1 ) { continue; } /* t-group edges to -N= and =O */ if ( ret = AddToEdgeList( &CurrEdges2, eTg, INC_ADD_EDGE ) ) { goto exit_function; } } if ( !CurrEdges2.num_edges ) { goto exit_case_05; } /* fix all charge edges except -N< and all taut. edges except =O and =N- */ SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); SetForbiddenEdgeMask( pBNS, &TautEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &CurrEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &CurrEdges2, forbidden_edge_mask ); delta = 1; /* Increment st_edge.cap on (+/-) vertex */ pBNS->vert[vPlusMinus].st_edge.cap += delta; /* Increment st_edge.cap on t-group */ pTg->st_edge.cap += delta; /* total cap count */ pBNS->tot_st_cap += 2*delta; v1 = vPlusMinus; v2 = vTg; /* increase capacities of edges to Y */ for ( i = 0; i < pBNS->vert[vPlusMinus].num_adj_edges; i ++ ) { j = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i]].neighbor12 ^ vPlusMinus; for ( k = 0; k < pBNS->vert[j].num_adj_edges; k ++ ) { pBNS->edge[pBNS->vert[j].iedge[k]].cap += delta; } } ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); if ( ret == 1 && (vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1) && nDeltaCharge == 1 ) { /* Added (+)charge to -N< => nDeltaCharge == 1 */ /* Flow change on pe (-)charge edge (atom B-O(-)) is not known to RunBnsTestOnce()) */ ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); if ( ret > 0 ) { nNumRunBNS ++; cur_success ++; /* 01 */ /* update bookkeeping */ pTCGroups->total_charge += delta; pTCGroups->pTCG[itg].edges_cap += delta; pTCGroups->pTCG[itg].tg_num_H += delta; pStruct->nNumRemovedProtonsByRevrs -= delta; } } else { pBNS->vert[vPlusMinus].st_edge.cap -= delta; pTg->st_edge.cap -= delta; /*pTCGroups->pTCG[itg].edges_cap -= delta;*/ /* ???bug??? - commented out 2006-03-22 */ pBNS->tot_st_cap -= 2*delta; /* decrease capacities of edges to Y */ for ( i = 0; i < pBNS->vert[vPlusMinus].num_adj_edges; i ++ ) { j = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i]].neighbor12 ^ vPlusMinus; for ( k = 0; k < pBNS->vert[j].num_adj_edges; k ++ ) { pBNS->edge[pBNS->vert[j].iedge[k]].cap -= delta; } } } RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &TautEdges, forbidden_edge_mask ); } if ( cur_success ) { tot_succes += cur_success; /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } if ( !pc2i->bHasDifference ) { goto exit_function; /* nothing to do */ } } exit_case_05:; } while ( pc2i->nNumDiffMobH && pc2i->nChargeMobHRevrs > pc2i->nChargeMobHInChI ) { /*----------------------------------------------------*/ /* case 06: restored has extra H attached to -O(-) */ /* while the chrge should be on C, most pro- */ /* bably in a small ring.ut. group or more */ /* tautomeric endpoints. */ /* Solution: move (-) from O to C */ /*----------------------------------------------------*/ int iO, mode; EdgeIndex e2; BNS_EDGE *pe2; cur_success = 0; for ( i = 0; !cur_success && i < pc2i->len_c2at; i ++ ) { if ( pc2i->c2at[i].nMobHRevrs == pc2i->c2at[i].nMobHInChI + 1 && pc2i->c2at[i].nNumHRevrs == pc2i->c2at[i].nMobHInChI && !pc2i->c2at[i].endptInChI && !pc2i->c2at[i].endptRevrs && at2[iO = pc2i->c2at[i].atomNumber].charge == -1 && 0 <= (e=pVA[iO].nCMinusGroupEdge-1) && (pe=pBNS->edge+e)->flow ) { /* try suitable atoms C */ /* first look for =C= in a small ring */ for( mode = 4; !cur_success && mode <= 8; mode ++ ) { if ( mode == 8 ) mode = 99; for ( iat = 0; !cur_success && iat < pStruct->num_atoms; iat ++ ) { if ( !at2[iat].charge && !at2[iat].radical && pVA[iat].cNumValenceElectrons == 4 && 0 <= (e2=pVA[iat].nCMinusGroupEdge-1) && !(pe2=pBNS->edge+e2)->flow && 0 < bIsUnsatCarbonInASmallRing( at2, pVA, iat, pStruct->pbfsq, mode ) ) { SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); /* allow negative charge on the chosen carbon */ pe2->forbidden &= forbidden_edge_mask_inv; delta = 1; if ( !pe->flow ) continue; pv1 = pBNS->vert + (v1 = pe->neighbor1); pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); pe->flow -= delta; pv1->st_edge.flow -= delta; pv2->st_edge.flow -= delta; pBNS->tot_st_flow -= 2*delta; ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); if ( ret == 1 && (vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1) && nDeltaCharge == 1 ) { /* Added (-)charge to unsaturated C => nDeltaCharge == 2 */ ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); if ( ret > 0 ) { nNumRunBNS ++; cur_success ++; /* 01 */ tot_succes += cur_success; } } else { pe->forbidden |= forbidden_edge_mask; pe->flow += delta; pv1->st_edge.flow += delta; pv2->st_edge.flow += delta; pBNS->tot_st_flow += 2*delta; } SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); } } } } } if ( cur_success ) { /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } if ( !pc2i->bHasDifference ) { goto exit_function; /* nothing to do */ } } else { break; } } if ( pc2i->len_c2at && pc2i->nChargeMobHRevrs > pc2i->nChargeMobHInChI ) { /*------------------------------------------------------------------*/ /* case 07: -NO2 are to be tautomeric but they are not AND */ /* InChI has a SINGLE tautomeric group */ /* */ /* (-)O (-)O */ /* Solution: convert \ \ */ /* N-X=...-Z(-) => N(+)=X- ...=Z */ /* // / */ /* O (-)O */ /* */ /* O O */ /* or \\ \\ */ /* N-X=...-Z(-) => N=X- ...=Z */ /* // / */ /* O (-)O */ /* */ /* */ /* (a) move (-) from other tautomeric atom to O in O=N-X */ /* or from other atom that has to be tautomeric */ /* but is not */ /* (b) create (+) [ion pair creation] on N as in */ /* */ /* OH OH */ /* / / */ /* -C=N => =C-N(+) */ /* \\ \\ */ /* O O */ /* */ /*------------------------------------------------------------------*/ int num_DB_O = 0; short iat_DB_O[MAX_DIFF_FIXH], iat_NO2[MAX_DIFF_FIXH]; AT_NUMB *nCanon2AtnoRevrs = pStruct->nCanon2Atno[0]; /* AT_NUMB *nAtno2CanonRevrs = pStruct->nAtno2Canon[0]; */ inp_ATOM *at_Mobile_H_Revrs = (pStruct->pOne_norm_data[0] && pStruct->pOne_norm_data[0]->at)? pStruct->pOne_norm_data[0]->at : NULL; int iN, one_success; BNS_EDGE *peDB_O_Minus; int neigh, nNumO, nNumOthers; #define CHG_SET_WRONG_TAUT_N 0 #define CHG_SET_WRONG_TAUT_O 1 #define CHG_SET_WRONG_TAUT_ALL 2 #define CHG_LAST_SET 2 /* the last index in trying */ #define CHG_SET_O_FIXED 3 #define CHG_SET_NUM 4 EDGE_LIST ChangeableEdges[CHG_SET_NUM]; memset( ChangeableEdges, 0, sizeof(ChangeableEdges) ); /* equivalent to AllocEdgeList( &EdgeList, EDGE_LIST_CLEAR ); */ /* S_CHAR *nMobHInChI = pInChI[1] && pInChI[1]->nNum_H? pInChI[1]->nNum_H : pInChI[0] && pInChI[0]->nNum_H? pInChI[0]->nNum_H : 0; */ CurrEdges.num_edges = 0; /* clear current edge list */ cur_success = 0; for ( i = 0; i < pStruct->num_atoms; i ++ ) { iat = nCanon2AtnoRevrs[i]; if ( /* orig. InChI info: taut in orig. InChI =O located in -NO2 that is not taut in Reconstructed InChI */ num_DB_O < MAX_DIFF_FIXH && pVA[iat].cNumValenceElectrons == 6 /* O, S, Se, Te */ && (!at2[iat].endpoint /*|| pc2i->c2at[i].nMobHInChI*/) && (e=pVA[iat].nCMinusGroupEdge-1) >= 0 && !pBNS->edge[e].forbidden && at2[iat].num_H == 0 && /*pc2i->c2at[i].nMobHInChI == 1 &&*/ /* reversed structure info: */ !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[iat].endpoint) /*|| pc2i->c2at[i].nMobHRevrs*/ && !at2[iat].charge && at2[iat].valence == 1 && at2[iat].chem_bonds_valence == 2 && /* find whether it belongs to NO2 */ pVA[iN=at2[iat].neighbor[0]].cNumValenceElectrons == 5 && at2[iN].valence == 3 && (at2[iN].charge == 0 || at2[iN].charge == 1) && at2[iN].chem_bonds_valence == 5 - at2[iN].charge ) { /* find the second O */ nNumO = nNumOthers = 0; for ( k = 0; k < at2[iN].valence; k ++ ) { neigh = at2[iN].neighbor[k]; if ( neigh == iat ) { continue; } if ( pVA[neigh].cNumValenceElectrons == 6 && !at2[neigh].endpoint && !(at_Mobile_H_Revrs && at_Mobile_H_Revrs[neigh].endpoint) && at2[neigh].valence == 1 && at2[neigh].num_H == 0 && at2[neigh].radical == 0 && (at2[neigh].charge == 0 || at2[neigh].charge == -1) && at2[neigh].chem_bonds_valence - at2[neigh].charge == 2) { nNumO ++; } else if ( at2[iN].bond_type[k] == BOND_TYPE_SINGLE && at2[neigh].valence > 1 && at2[neigh].valence < at2[neigh].chem_bonds_valence ) { nNumOthers ++; } } if ( nNumO != 1 || nNumOthers != 1 ) { continue; } for ( k = 0; k < num_DB_O; k ++ ) { if ( iat_NO2[k] == iN ) { break; } } if ( k == num_DB_O ) { iat_NO2[num_DB_O] = iN; iat_DB_O[num_DB_O ++] = iat; } /* save the =O (-)-edge to avoid interference */ if ( ret = AddToEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e, INC_ADD_EDGE ) ) { goto exit_case_07; } } } if ( num_DB_O ) { /* search for falsely tautomeric negatively charged atoms N and O */ for ( i = 0; i < pc2i->len_c2at; i ++ ) { iat = pc2i->c2at[i].atomNumber; if ( pc2i->c2at[i].endptRevrs && !pc2i->c2at[i].endptInChI && pc2i->c2at[i].nAtChargeRevrs == - 1 && 0 <= (e=pVA[iat].nCMinusGroupEdge-1) && !pBNS->edge[e].forbidden && pBNS->edge[e].flow && 0 > FindInEdgeList( &ChangeableEdges[CHG_SET_O_FIXED], e ) ) { if ( pc2i->c2at[i].nValElectr == 6 ) { if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_O], e, INC_ADD_EDGE ) ) { goto exit_case_07; } } else if ( pc2i->c2at[i].nValElectr == 5 ) { if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_N], e, INC_ADD_EDGE ) ) { goto exit_case_07; } } if (ret = AddToEdgeList( &ChangeableEdges[CHG_SET_WRONG_TAUT_ALL], e, INC_ADD_EDGE ) ) { goto exit_case_07; } } } /* ------- finally, try to move charges from O=N --------------*/ for ( i = 0; i < num_DB_O; i ++ ) { int nDeltaChargeExpected; one_success = 0; delta = 1; iat = iat_DB_O[i]; peDB_O_Minus = pBNS->edge + (pVA[iat].nCMinusGroupEdge-1); pe = pBNS->edge + pBNS->vert[iat].iedge[0]; if ( !pe->flow ) continue; pv1 = pBNS->vert + (v1 = pe->neighbor1); pv2 = pBNS->vert + (v2 = pe->neighbor12 ^ v1); pe->forbidden |= forbidden_edge_mask; pe->flow -= delta; pv1->st_edge.flow -= delta; pv2->st_edge.flow -= delta; pBNS->tot_st_flow -= 2*delta; for ( k = 0; !one_success && k <= CHG_LAST_SET; k ++ ) { if ( !ChangeableEdges[k].num_edges ) { continue; } nDeltaChargeExpected = 0; SetForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); RemoveForbiddenEdgeMask( pBNS, &ChangeableEdges[k], forbidden_edge_mask ); /* allow (-) charge to move to N=O */ peDB_O_Minus->forbidden &= forbidden_edge_mask_inv; ret = RunBnsTestOnce( pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen, &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms ); if ( ret == 1 && (vPathEnd == v1 && vPathStart == v2 || vPathEnd == v2 && vPathStart == v1) && nDeltaCharge == nDeltaChargeExpected ) { /* Move (-) charge to =O and remove it an endpoint => nDeltaCharge == 0 */ ret = RunBnsRestoreOnce( pBNS, pBD, pVA, pTCGroups ); if ( ret > 0 ) { nNumRunBNS ++; one_success ++; /* 07 */ } } INCHI_HEAPCHK } cur_success += one_success; RemoveForbiddenEdgeMask( pBNS, &AllChargeEdges, forbidden_edge_mask ); pe->forbidden &= forbidden_edge_mask_inv; if ( !one_success ) { pe->flow += delta; pv1->st_edge.flow += delta; pv2->st_edge.flow += delta; pBNS->tot_st_flow += 2*delta; } } } exit_case_07: for ( i = 0; i < CHG_SET_NUM; i ++ ) { AllocEdgeList( &ChangeableEdges[i], EDGE_LIST_FREE ); } CurrEdges.num_edges = 0; /* clear current edge list */ if ( cur_success ) { tot_succes += cur_success; /* recalculate InChI from the structure */ if ( 0 > (ret = MakeOneInChIOutOfStrFromINChI2( ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups, ppt_group_info, ppat_norm, ppat_prep ) ) ) { goto exit_function; } if ( ret = FillOutExtraFixedHDataRestr( pStruct ) ) { goto exit_function; } if ( ret = FillOutCMP2MHINCHI( pStruct, pTCGroups, at2, pVA, pInChI, pc2i ) ) { goto exit_function; } if ( !pc2i->bHasDifference ) { goto exit_function; /* nothing to do */ } } #undef CHG_SET_NOOH #undef CHG_SET_WRONG_TAUT #undef CHG_SET_TAUT #undef CHG_LAST_SET #undef CHG_SET_O_FIXED #undef CHG_SET_NUM } exit_function: AllocEdgeList( &AllChargeEdges, EDGE_LIST_FREE ); AllocEdgeList( &CurrEdges, EDGE_LIST_FREE ); AllocEdgeList( &CurrEdges2, EDGE_LIST_FREE ); AllocEdgeList( &CurrEdges3, EDGE_LIST_FREE ); AllocEdgeList( &NFlowerEdges, EDGE_LIST_FREE ); AllocEdgeList( &OtherNFlowerEdges, EDGE_LIST_FREE ); AllocEdgeList( &FixedLargeRingStereoEdges, EDGE_LIST_FREE ); AllocEdgeList( &TautEdges, EDGE_LIST_FREE ); return ret; } #endif