/src/inchi/INCHI-1-SRC/INCHI_BASE/src/ichirvr4.c

Source
/*
 * International Chemical Identifier (InChI)
 * Version 1
 * Software version 1.07
 * April 30, 2024
 *
 * MIT License
 *
 * Copyright (c) 2024 IUPAC and InChI Trust
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
*
* 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.
 * Some portions of code were developed/changed by external contributors
 * (either contractor or volunteer) which are listed in the file
 * 'External-contributors' included in this distribution.
 *
 * info@inchi-trust.org
 *
*/

#include <string.h>

/*#define CHECK_WIN32_VC_HEAP*/

#include "mode.h"

#if ( READ_INCHI_STRING == 1 )
#include "ichitime.h"
#include "ichirvrs.h"
#include "ichicant.h"
#include "ichi_io.h"
#include "ichimake.h"

#include "bcf_s.h"

/****************************************************************************/
int ForbidCarbonChargeEdges(BN_STRUCT* pBNS,
    ALL_TC_GROUPS* pTCGroups,
    EDGE_LIST* pCarbonChargeEdges,
    int forbidden_edge_mask)
{
#define MAX_NUM_CARBON_CHARGE_EDGES 2
    int nType, i, k, ret;
    BNS_EDGE* pEdge;
    if ((ret = AllocEdgeList(pCarbonChargeEdges, MAX_NUM_CARBON_CHARGE_EDGES))) /* djb-rwth: addressing LLVM warning */
    {
        goto exit_function;
    }
    pCarbonChargeEdges->num_edges = 0;
    for (i = 0; i < MAX_NUM_CARBON_CHARGE_EDGES; i++)
    {
        switch (i)
        {
        case 0:
            nType = TCG_Plus_C0;
            break;
        case 1:
            nType = TCG_Minus_C0;
            break;
        default:
            ret = RI_ERR_PROGR;
            goto exit_function;
        }
        if ((k = pTCGroups->nGroup[nType]) >= 0)
        {
            k = pTCGroups->pTCG[k].nForwardEdge;
            if (k > 0)
            {
                pEdge = pBNS->edge + k;
                if (!(pEdge->forbidden & forbidden_edge_mask))
                {
                    pEdge->forbidden |= forbidden_edge_mask;
                    if ((ret = AddToEdgeList(pCarbonChargeEdges, k, 0))) /* djb-rwth: addressing LLVM warning */
                    {
                        goto exit_function;
                    }
                }
            }
            else
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
        }
    }
    ret = pCarbonChargeEdges->num_edges;

exit_function:

    return ret;
#undef MAX_NUM_CARBON_CHARGE_EDGES
}


/****************************************************************************/
int ForbidNintrogenPlus2BondsInSmallRings(BN_STRUCT* pBNS,
    inp_ATOM* at,
    int num_at,
    VAL_AT* pVA,
    int min_ring_size,
    ALL_TC_GROUPS* pTCGroups,
    EDGE_LIST* pNplus2BondsEdges,
    int forbidden_edge_mask)
{
    int i, j, ret;
    BNS_EDGE* e;

    /* djb-rwth: removing redundant code */
        /* --- forbid edges that allow to make =N(+)= or #N(+)- in small ring */
    for (i = 0; i < num_at; i++)
    {
        if (at[i].valence == 2 &&
            !at[i].num_H && !at[i].endpoint &&
            pVA[i].cNumValenceElectrons == 5 &&
            pVA[i].cPeriodicRowNumber == 1 &&
            !pVA[i].cMaxFlowToMetal && pVA[i].nCPlusGroupEdge > 0 &&
            pVA[i].cnListIndex > 0 && cnList[pVA[i].cnListIndex - 1].bits == cn_bits_MNP &&
            pVA[i].cMinRingSize && pVA[i].cMinRingSize <= min_ring_size)
        {

            e = pBNS->edge + (j = pVA[i].nCPlusGroupEdge - 1);
            if (!(e->forbidden & forbidden_edge_mask))
            {
                e->forbidden |= forbidden_edge_mask;
                if ((ret = AddToEdgeList(pNplus2BondsEdges, j, 128))) /* djb-rwth: addressing LLVM warning */
                {
                    goto exit_function;
                }
            }
        }
    }
    ret = 0;

exit_function:

    return ret;
}


/****************************************************************************
Problem: Formula in InChI from the reversed structure has
less H than in the input InChI
Solutions:

(a)   |                        |
     -B(-)-NH-=..-=N(+)<   => -B(-)-NH(+)=-..=-N<
      |                        |

                                (H is not removed from the ion pair)

                  |                      |
(b)  >N(+)=-=...-=N-NH     =>  >N-=-...=-N(+)-NH
                  |                      |

                                (charge from onium cannot be moved to remove H+)
****************************************************************************/
int FixLessHydrogenInFormula(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    inp_ATOM* atf,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    int* pnNumRunBNS,
    int* pnTotalDelta, int forbidden_edge_mask)
{
    int iBPlus = NO_VERTEX, iNV = NO_VERTEX, iNH = NO_VERTEX, neigh;
    EDGE_LIST NewlyFixedEdges;
    int ret, i, j;
    int num_at = pStruct->num_atoms;
    int inv_forbidden_edge_mask = ~forbidden_edge_mask;
    /* for RunBnsTestOnce */
    Vertex     vPathStart, vPathEnd;
    int        nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;

    AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_CLEAR);
    if ((ret = AllocEdgeList(&NewlyFixedEdges, 2 * num_at))) /* djb-rwth: addressing LLVM warning */
    {
        goto exit_function;
    }
    for (i = 0; i < num_at; i++)
    {
        if ((j = pVA[i].nCMinusGroupEdge - 1) >= 0)
        {
            if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
            pBNS->edge[j].forbidden |= forbidden_edge_mask;
        }
        if ((j = pVA[i].nCPlusGroupEdge - 1) >= 0)
        {
            if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
            pBNS->edge[j].forbidden |= forbidden_edge_mask;
        }
    }
    /* extra H has been removed; check non-tautomeric atoms */
    for (i = 0; i < num_at; i++)
    {
        if (!at2[i].endpoint && !pVA[i].cMetal &&
            pVA[i].cNumValenceElectrons == 5 && pVA[i].cPeriodicRowNumber == 1 &&
            at2[i].num_H == atf[i].num_H + 1)
        {
            /* H was removed from N */
            iNH = i;
            break;
        }
    }
    if (0 <= iNH && iNH < num_at)
    {
        /* check neighbors for  |                 |
                          (a)  -B(+)-  or  (b)   =N-
                                |                 |
        */
        for (j = 0; j < at2[i].valence; j++)
        {
            neigh = at2[iNH].neighbor[j];
            if (at2[neigh].valence == 4)
            {
                if (at2[neigh].charge == -1 && at2[neigh].chem_bonds_valence == 4 &&
                    !at2[neigh].radical && !at[neigh].num_H)
                {
                    iBPlus = neigh;
                }
            }
        }
    }
    if (0 <= iNH && iNH < num_at)
    {
        int bond_type_at2;
        int bond_type_atf;
        /* djb-rwth: removing redundant variables */
        int delta = -1, nxt = iNH, prv = NO_VERTEX, nxt_is_NPlus;
        /* the changed bond to the dehydrogenated atom H should have greater order */
        /* delta = (new bond order in atf[]) - (restored bond order in at2[]) */
        nxt_is_NPlus = 0;
        do
        {
            i = nxt;
            nxt = NO_VERTEX;
            delta = -delta;
            for (j = 0; j < at2[i].valence; j++)
            {
                bond_type_at2 = at2[i].bond_type[j] & BOND_TYPE_MASK; /* restored bond */
                bond_type_atf = atf[i].bond_type[j] & BOND_TYPE_MASK; /* normalized bond */
                nxt_is_NPlus = 0;
                if ((bond_type_atf - bond_type_at2 == delta || bond_type_atf == BOND_ALT12NS) &&
                    BOND_TYPE_SINGLE <= bond_type_at2 + delta && bond_type_at2 + delta <= BOND_TYPE_TRIPLE &&
                    !at2[(int)at2[i].neighbor[j]].cFlags)
                {
                    prv = i;
                    nxt = at2[i].neighbor[j];
                    nxt_is_NPlus = at2[nxt].charge == 1 && atf[nxt].charge == 0 &&
                        pVA[nxt].cNumValenceElectrons == 5 && pVA[nxt].cPeriodicRowNumber == 1;
                    at2[i].cFlags |= 1;  /* avoid cycling */
                    /* djb-rwth: removing redundant code */
                    if (delta == -1 && at2[prv].valence == 4 && at2[prv].chem_bonds_valence == 5 &&
                        !at2[prv].charge && !at2[prv].radical && pVA[prv].cNumValenceElectrons == 5 &&
                        pVA[prv].nCPlusGroupEdge > 0)
                    {
                        iNV = prv;
                    }
                    if (at2[nxt].charge != atf[nxt].charge)
                    {
                        if ((at2[nxt].charge == 1 || atf[nxt].charge == 1) &&
                            pVA[nxt].nCPlusGroupEdge > 0)
                        {
                            pBNS->edge[pVA[nxt].nCPlusGroupEdge - 1].forbidden &= inv_forbidden_edge_mask;
                        }
                        if ((at2[nxt].charge == -1 || atf[nxt].charge == -1) &&
                            pVA[nxt].nCMinusGroupEdge > 0)
                        {
                            pBNS->edge[pVA[nxt].nCMinusGroupEdge - 1].forbidden &= inv_forbidden_edge_mask;
                        }
                    }
                    break; /* found */
                }
            }
        } while (nxt >= 0 && !(nxt_is_NPlus && delta == -1));
        for (i = 0; i < num_at; i++)
        {
            at2[i].cFlags = 0;
        }
        if (nxt >= 0 && nxt_is_NPlus && delta == -1)
        {
            /* a simple alt path from NH-= to =N(+) has been found */
            if (iBPlus || iNV)
            {
                /* move (+) charge from N(+) to iNV or, if iBPlus, then to iNH */
                if ((iNV >= 0 && (j = pVA[iNV].nCPlusGroupEdge - 1) > 0 && pBNS->edge[j].flow > 0) ||
                    (iNH >= 0 && (j = pVA[iNH].nCPlusGroupEdge - 1) > 0 && pBNS->edge[j].flow > 0)) /* djb-rwth: addressing LLVM warnings */
                {
                    int          ieFlower;
                    BNS_EDGE* pe = pBNS->edge + j, * peFlower = NULL;
                    Vertex      v1 = pe->neighbor1;
                    Vertex      v2 = v1 ^ pe->neighbor12;
                    BNS_VERTEX* pv1 = pBNS->vert + v1;
                    BNS_VERTEX* pv2 = pBNS->vert + v2;

                    delta = 1;
                    /* prevent conversion of >N(+)= into N(V) neutral */
                    ieFlower = GetChargeFlowerUpperEdge(pBNS, pVA, pVA[nxt].nCPlusGroupEdge - 1);
                    if (ieFlower >= 0)
                    {
                        peFlower = pBNS->edge + ieFlower;
                        if (peFlower->flow == delta)
                        {
                            peFlower->forbidden |= forbidden_edge_mask;
                            if ((ret = AddToEdgeList(&NewlyFixedEdges, ieFlower, 0))) /* djb-rwth: addressing LLVM warning */
                            {
                                goto exit_function;
                            }
                        }
                    }
                    pe->forbidden |= forbidden_edge_mask;
                    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 < 0)
                    {
                        goto exit_function;
                    }
                    if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
                        (vPathEnd == v2 && vPathStart == v1)) &&
                        nDeltaCharge <= 0  /* charge moving to this atom disappers*/) /* djb-rwth: addressing LLVM warnings */
                    {
                        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
                        (*pnNumRunBNS)++;
                        if (ret < 0)
                        {
                            goto exit_function;
                        }
                        else
                            if (ret == 1)
                            {
                                *pnTotalDelta += ret;
                            }
                            else
                            {
                                ret = RI_ERR_PROGR;
                                goto exit_function;
                            }
                    }
                    else
                    {
                        ret = 0;
                        pe->flow += delta;
                        pv1->st_edge.flow += delta;
                        pv2->st_edge.flow += delta;
                        pBNS->tot_st_flow += 2 * delta;
                    }
                }
            }
        }
    }

exit_function:
    /* remove bond fixation */
    RemoveForbiddenEdgeMask(pBNS, &NewlyFixedEdges, forbidden_edge_mask);
    AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_FREE);

    return ret;
}


/****************************************************************************

    X=Y-O(-)  => X(-)-Y=O

****************************************************************************/
int FixMoreHydrogenInFormula(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    inp_ATOM* atf,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask)
{
    int iNH = NO_VERTEX, neigh, neigh2;
    EDGE_LIST NewlyFixedEdges;
    int ret, i, j, k, k2 = 0, delta;
    int num_at = pStruct->num_atoms;
    int inv_forbidden_edge_mask = ~forbidden_edge_mask;
    Vertex v1, v2;
    /* for RunBnsTestOnce */
    Vertex     vPathStart, vPathEnd;
    int        nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;
    BNS_EDGE* pe, * pe2;

    AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_CLEAR);
    if ((ret = AllocEdgeList(&NewlyFixedEdges, 2 * num_at))) /* djb-rwth: addressing LLVM warning */
    {
        goto exit_function;
    }
    /* fix all charges */
    for (i = 0; i < num_at; i++)
    {
        if ((j = pVA[i].nCMinusGroupEdge - 1) >= 0)
        {
            if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
            pBNS->edge[j].forbidden |= forbidden_edge_mask;
        }
        if ((j = pVA[i].nCPlusGroupEdge - 1) >= 0)
        {
            if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
            pBNS->edge[j].forbidden |= forbidden_edge_mask;
        }
    }

    /* H(+) has been added to -O(-); check non-tautomeric atoms */
    for (i = 0; i < num_at; i++)
    {
        neigh = at2[i].neighbor[0]; /* djb-rwth: avoiding unsequenced modification and access to neigh */
        if (!(pStruct->bMobileH ? at2[i].endpoint : pStruct->endpoint[i]) && !pVA[i].cMetal &&
            at2[i].num_H + 1 == atf[i].num_H &&      /* normalization added H ??? What would happen in Fixed-H case?*/
            (k = pVA[i].nCMinusGroupEdge - 1) >= 0 &&
            pBNS->edge[k].flow == 1 &&               /* atom had (-) charge before preprocessing */
            at2[i].charge == -1 && atf[i].charge == 0 && /* and has no charge after preprocessing */
            at2[i].valence == 1 && at2[i].chem_bonds_valence == 1 && /* connected by a single bond */
            pVA[i].cNumValenceElectrons == 6 &&     /* atom is O, S, Se, Te */
            at2[neigh].chem_bonds_valence > at2[neigh].valence
            /* atom's single neighbor has multiple bond(s)*/
            )
        {
            /* H(+) was added to O in Y=X-O(-), where X is the only neighbor of O, X=neigh, Y=neigh2 */
            iNH = i;
            for (j = 0; j < at2[neigh].valence; j++)
            {
                neigh2 = at2[neigh].neighbor[j];
                if (neigh2 != iNH && !at2[neigh2].endpoint &&
                    !pBNS->edge[(int)pBNS->vert[neigh].iedge[j]].forbidden &&
                    4 <= pVA[neigh2].cNumValenceElectrons &&
                    pVA[neigh2].cNumValenceElectrons <= 5 && /* neig2 is C or N */
                    (k2 = pVA[neigh2].nCMinusGroupEdge - 1) >= 0 &&
                    !pBNS->edge[k2].flow /* negative charge may be moved to neigh2 */)
                {
                    break;
                }
            }
            if (j < at2[neigh].valence)
            {
                delta = 1;
                pe = pBNS->edge + k;  /* -O(-) negative charge edge; flow = 1 */
                pe2 = pBNS->edge + k2; /* X charge edge; flow = 0 */
                v1 = pe->neighbor1;
                v2 = pe->neighbor12 ^ v1;
                pe->flow -= delta;
                pBNS->vert[v1].st_edge.flow -= delta;
                pBNS->vert[v2].st_edge.flow -= delta;
                pBNS->tot_st_flow -= 2 * delta;
                pe2->forbidden &= inv_forbidden_edge_mask; /* allow the charge to move */

                ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
                    &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
                if (ret < 0)
                {
                    goto exit_function;
                }
                if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
                    (vPathEnd == v2 && vPathStart == v1)) &&
                    nDeltaCharge <= 1) /* djb-rwth: addressing LLVM warnings */
                {
                    ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
                    (*pnNumRunBNS)++;
                    if (ret < 0)
                    {
                        goto exit_function;
                    }
                    else
                        if (ret)
                        {
                            *pnTotalDelta += ret;
                        }
                        else
                        {
                            ret = RI_ERR_PROGR;
                        }
                    break;
                }
                else
                {
                    /* the attempt has failed; restore the flow */
                    ret = 0;
                    pe->flow += delta;
                    pBNS->vert[v1].st_edge.flow += delta;
                    pBNS->vert[v2].st_edge.flow += delta;
                    pBNS->tot_st_flow += 2 * delta;
                }
            }
        }
    }

exit_function:
    /* remove bond fixation */
    RemoveForbiddenEdgeMask(pBNS, &NewlyFixedEdges, forbidden_edge_mask);
    AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_FREE);

    return ret;
}


#if ( FIX_ADD_PROTON_FOR_ADP == 1 )
/****************************************************************************/
int FixAddProtonForADP(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    inp_ATOM* atf,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    ICR* picr,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask)
{
    int iBPlus = NO_VERTEX, iNV = NO_VERTEX, iNH = NO_VERTEX, neigh, neigh2;
    EDGE_LIST NewlyFixedEdges;
    int ret, i, j, k, k2, delta;
    int num_at = pStruct->num_atoms;
    int inv_forbidden_edge_mask = ~forbidden_edge_mask;
    Vertex v1, v2;
    /* for RunBnsTestOnce */
    Vertex     vPathStart, vPathEnd;
    int        nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;
    BNS_EDGE* pe, * pe2;

    ret = 0;
    /*
    AllocEdgeList( &NewlyFixedEdges, EDGE_LIST_CLEAR );

    for ( i = 0; i < num_at; i ++ ) {
        if ( at2[i].radical == RADICAL_DOUBLET && at2[i].endpoint ) {
            pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;
            ret = 1;
            break;
        }
    }
    */
    return ret;
}
#endif


/****************************************************************************
      OH              OH
     /               /
  -NH      =>   -NH(+)        to eliminate false tautomerism.
     \\              \        S(IV) or N(V) or P(V) may be a centerpoint
      O               O(-)
****************************************************************************/
int FixRemoveExtraTautEndpoints(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    inp_ATOM* atf,
    inp_ATOM* atn,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups, ICR* picr,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask)
{
    EDGE_LIST NewlyFixedEdges;
    int ret, i, j, k, delta, centerpoint, endpoint1, endpoint2;
    int num_at = pStruct->num_atoms;
    int inv_forbidden_edge_mask = ~forbidden_edge_mask;
    Vertex v1, v2;
    /* for RunBnsTestOnce */
    Vertex     vPathStart, vPathEnd;
    int        nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;
    BNS_EDGE* pe, * pe2;

    ret = 0; /* djb-rwth: ignoring LLVM warning: value might be returned */

    AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_CLEAR);
    if ((ret = AllocEdgeList(&NewlyFixedEdges, 2 * num_at))) /* djb-rwth: addressing LLVM warning */
    {
        goto exit_function;
    }
    /* fix all charges */
    for (i = 0; i < num_at; i++)
    {
        if ((j = pVA[i].nCMinusGroupEdge - 1) >= 0)
        {
            if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
            pBNS->edge[j].forbidden |= forbidden_edge_mask;
        }
        if ((j = pVA[i].nCPlusGroupEdge - 1) >= 0)
        {
            if ((ret = AddToEdgeList(&NewlyFixedEdges, j, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
            pBNS->edge[j].forbidden |= forbidden_edge_mask;
        }
    }

    for (i = 0; i < picr->num_endp_in1_only; i++)
    {
        endpoint1 = picr->endp_in1_only[i] - 1;
        if (at2[endpoint1].valence == at2[endpoint1].chem_bonds_valence ||
            pVA[endpoint1].nCMinusGroupEdge <= 0)
        {
            continue;
        }
        /* find centerpoint */
        for (j = 0; j < at2[endpoint1].valence; j++)
        {
            if (BOND_TYPE_DOUBLE == (BOND_TYPE_MASK & at2[endpoint1].bond_type[j]))
            {
                centerpoint = at2[endpoint1].neighbor[j];
                if (at2[centerpoint].charge || pVA[centerpoint].nCPlusGroupEdge <= 0 ||
                    !is_centerpoint_elem(at2[centerpoint].el_number))
                {
                    continue;
                }
                /* -- the centerpoint as depicted has no ChargeStruct flower ---
                m = GetChargeFlowerUpperEdge( pBNS, pVA, pVA[centerpoint].nCPlusGroupEdge-1 );
                if ( m < 0 || pBNS->edge[m].flow ) {
                    continue;
                }
                */
                /* find 2nd endpoint */
                for (k = 0; k < at2[centerpoint].valence; k++)
                {
                    if (BOND_TYPE_SINGLE != (BOND_TYPE_MASK & at2[centerpoint].bond_type[k]))
                    {
                        continue;
                    }
                    endpoint2 = at2[centerpoint].neighbor[k];
                    if (!at2[endpoint2].endpoint && atn[endpoint2].endpoint)
                    {
                        break;
                    }
                }
                if (k == at2[centerpoint].valence)
                {
                    continue;
                }
                /* the centerpoint and two extra endpoints have been found */
                pe = pBNS->edge + pVA[centerpoint].nCPlusGroupEdge - 1;
                if (!pe->flow)
                {
                    continue;
                }
                pe2 = pBNS->edge + pVA[endpoint1].nCMinusGroupEdge - 1;
                if (pe2->flow)
                {
                    continue;
                }
                delta = 1;
                v1 = pe->neighbor1;
                v2 = pe->neighbor12 ^ v1;
                pe->flow -= delta;
                pBNS->vert[v1].st_edge.flow -= delta;
                pBNS->vert[v2].st_edge.flow -= delta;
                pBNS->tot_st_flow -= 2 * delta;
                pe2->forbidden &= inv_forbidden_edge_mask; /* allow the charge to move */

                ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
                    &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
                if (ret < 0)
                {
                    goto exit_function;
                }
                if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
                    (vPathEnd == v2 && vPathStart == v1)) &&
                    nDeltaCharge <= 1) /* djb-rwth: addressing LLVM warnings */
                {
                    ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
                    (*pnNumRunBNS)++;
                    if (ret < 0)
                    {
                        goto exit_function;
                    }
                    else
                    {
                        if (ret)
                        {
                            *pnTotalDelta += ret;
                        }
                        else
                        {
                            ret = RI_ERR_PROGR;
                        }
                    }
                    goto exit_function;
                }
                else
                {
                    ret = 0;
                    pe->flow += delta;
                    pBNS->vert[v1].st_edge.flow += delta;
                    pBNS->vert[v2].st_edge.flow += delta;
                    pBNS->tot_st_flow += 2 * delta;
                    pe2->forbidden |= forbidden_edge_mask;
                }
            }
        }
    }

exit_function:
    /* remove bond fixation */
    RemoveForbiddenEdgeMask(pBNS, &NewlyFixedEdges, forbidden_edge_mask);
    AllocEdgeList(&NewlyFixedEdges, EDGE_LIST_FREE);

    return ret;
}


/****************************************************************************/
int  FillOutExtraFixedHDataRestr(StrFromINChI* pStruct)
{
    int i, j, k, len, ret = 0;
    AT_NUMB* pNum;
    for (i = 0; i < TAUT_NUM; i++)
    {
        if (pStruct->pOneINChI_Aux[i])
        {
            pNum = (pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd &&
                pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd[0]) ?
                pStruct->pOneINChI_Aux[i]->nIsotopicOrigAtNosInCanonOrd :
                (pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd &&
                    pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd[0]) ?
                pStruct->pOneINChI_Aux[i]->nOrigAtNosInCanonOrd : NULL;
        }
        else
        {
            pNum = NULL;
        }
        if (pNum)
        {
            len = pStruct->num_atoms * sizeof(pStruct->nCanon2Atno[0][0]);
            if ((!pStruct->nCanon2Atno[i] &&
                !(pStruct->nCanon2Atno[i] = (AT_NUMB*)inchi_malloc(len))) ||
                (!pStruct->nAtno2Canon[i] &&
                    !(pStruct->nAtno2Canon[i] = (AT_NUMB*)inchi_malloc(len)))) /* djb-rwth: addressing LLVM warnings */
            {
                ret = RI_ERR_ALLOC;
                goto exit_function;
            }

            INCHI_HEAPCHK

                memcpy(pStruct->nCanon2Atno[i], pNum, len); /* ??? the next for(...) fills it out */

            INCHI_HEAPCHK

                for (j = 0; j < pStruct->num_atoms; j++)
                {
                    k = pNum[j] - 1; /* atom number */
                    pStruct->nCanon2Atno[i][j] = (AT_NUMB)k;
                    pStruct->nAtno2Canon[i][k] = (AT_NUMB)j;
                    INCHI_HEAPCHK
                }
        }
        else
        {
            if (!i)
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            else
            {
                if (pStruct->nCanon2Atno[i])
                {
                    inchi_free(pStruct->nCanon2Atno[i]);
                    pStruct->nCanon2Atno[i] = NULL;
                }
                INCHI_HEAPCHK
                    if (pStruct->nAtno2Canon[i])
                    {
                        inchi_free(pStruct->nAtno2Canon[i]);
                        pStruct->nAtno2Canon[i] = NULL;
                    }
                INCHI_HEAPCHK
            }
        }
    }

exit_function:

    return ret;
}


/****************************************************************************/
int  FillOutExtraFixedHDataInChI(StrFromINChI* pStruct, INChI* pInChI[])
{
    int ret = 0;
    /*--- allocate memory for Mobile/Fixed-H data from the input InChI ---*/
    if (NULL == pStruct->endpoint)
    {
        pStruct->endpoint = (AT_NUMB*)inchi_calloc(pStruct->num_atoms, sizeof(pStruct->endpoint[0]));
    }
    else
    {
        memset(pStruct->endpoint, 0, pStruct->num_atoms * sizeof(pStruct->endpoint[0])); /* djb-rwth: memset_s C11/Annex K variant? */
    }
    if (NULL == pStruct->fixed_H)
    {
        pStruct->fixed_H = (S_CHAR*)inchi_malloc(pStruct->num_atoms * sizeof(pStruct->fixed_H[0]));
    }
    if (!pStruct->endpoint || !pStruct->fixed_H)
    {
        ret = RI_ERR_ALLOC;
        goto exit_function;
    }
    /*--- fill out Mobile/Fixed-H data from the input InChI ---*/
    GetTgroupInfoFromInChI(&pStruct->ti, NULL, pStruct->endpoint, pInChI[1]);
    if (pInChI[0]->nNum_H_fixed)
    {
        memcpy(pStruct->fixed_H, pInChI[0]->nNum_H_fixed, pStruct->num_atoms * sizeof(pStruct->fixed_H[0]));
    }
    else
    {
        memset(pStruct->fixed_H, 0, pStruct->num_atoms * sizeof(pStruct->fixed_H[0])); /* djb-rwth: memset_s C11/Annex K variant? */
    }

exit_function:

    return ret;
}


/****************************************************************************/
int FillOutCMP2FHINCHI(StrFromINChI* pStruct,
    inp_ATOM* at2,
    VAL_AT* pVA,
    INChI* pInChI[],
    CMP2FHINCHI* pc2i)
{
    int       ret = 0, i, j;
    int       bFixHRevrsExists = pInChI[1] && pInChI[1]->nNumberOfAtoms > 0 && !pInChI[1]->bDeleted;
    inp_ATOM* at_Mobile_H_Revrs = (pStruct->pOne_norm_data[1] &&
        pStruct->pOne_norm_data[1]->at) ? pStruct->pOne_norm_data[1]->at : NULL;
    S_CHAR* num_Fixed_H_Revrs = pStruct->pOneINChI[0]->nNum_H_fixed ? pStruct->pOneINChI[0]->nNum_H_fixed : NULL;
    /* atom number in structure that produced original InChI is atom number in all inp_ATOM *atoms */
    /* atom number in structure that produced restored InChI is in nAtomRevrs[]: */
    AT_NUMB* nAtno2CanonRevrs = pStruct->nAtno2Canon[0];
    S_CHAR* pnMobHInChI = (pInChI[1] && pInChI[1]->nNum_H) ? pInChI[1]->nNum_H :
        (pInChI[0] && pInChI[0]->nNum_H) ? pInChI[0]->nNum_H : NULL;
    S_CHAR* pnMobHRevrs = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H) ?
        pStruct->pOneINChI[1]->nNum_H :
        (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ?
        pStruct->pOneINChI[0]->nNum_H : NULL;
    int     nNumTgHInChI, nNumTgMInChI, nNumTgHRevrs, nNumTgMRevrs;
    memset(pc2i, 0, sizeof(*pc2i)); /* djb-rwth: memset_s C11/Annex K variant? */
    pc2i->nNumTgInChI = pStruct->ti.num_t_groups;
    pc2i->nNumTgRevrs = pStruct->One_ti.num_t_groups;
    pc2i->bHasDifference |= pc2i->nNumTgInChI != pc2i->nNumTgRevrs;

    pc2i->nNumRemHInChI = pStruct->nNumRemovedProtonsMobHInChI;
    pc2i->nNumRemHRevrs = pStruct->One_ti.tni.nNumRemovedProtons;
    pc2i->bHasDifference |= pc2i->nNumRemHInChI != pc2i->nNumRemHRevrs;

    pc2i->bFixedHLayerExistsRevrs = bFixHRevrsExists;
    pc2i->bHasDifference |= !bFixHRevrsExists;

    for (i = 0; i < pStruct->ti.num_t_groups && i < pStruct->One_ti.num_t_groups; i++)
    {
        nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1];
        nNumTgMInChI = pStruct->ti.t_group[i].num[1];
        nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1];
        nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1];

        pc2i->bHasDifference |= nNumTgHInChI != nNumTgHRevrs;
        pc2i->bHasDifference |= nNumTgMInChI != nNumTgMRevrs;

        if (pStruct->ti.t_group[i].nNumEndpoints ==
            pStruct->One_ti.t_group[i].nNumEndpoints)
        {

            if (nNumTgHInChI != nNumTgHRevrs)
            {
                pc2i->nNumTgDiffH++;
            }
            if (nNumTgMInChI != nNumTgMRevrs)
            {
                pc2i->nNumTgDiffMinus++;
            }
        }
        pc2i->bHasDifference |= pStruct->ti.t_group[i].nNumEndpoints !=
            pStruct->One_ti.t_group[i].nNumEndpoints;

        pc2i->nNumTgHInChI += nNumTgHInChI;
        pc2i->nNumTgMInChI += nNumTgMInChI;
        pc2i->nNumTgHRevrs += nNumTgHRevrs;
        pc2i->nNumTgMRevrs += nNumTgMRevrs;
    }
    for (; i < pStruct->ti.num_t_groups; i++)
    {
        nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1];
        nNumTgMInChI = pStruct->ti.t_group[i].num[1];
        pc2i->nNumTgHInChI += nNumTgHInChI;
        pc2i->nNumTgMInChI += nNumTgMInChI;
        pc2i->bHasDifference |= 1;
    }
    for (; i < pStruct->One_ti.num_t_groups; i++)
    {
        nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1];
        nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1];
        pc2i->nNumTgHRevrs += nNumTgHRevrs;
        pc2i->nNumTgMRevrs += nNumTgMRevrs;
        pc2i->bHasDifference |= 1;
    }
    for (i = j = 0; i < pStruct->num_atoms; i++)
    {
        /* i = original InChI canonical number - 1 */
        /* k = atom number from InChI created out of restored Fixed-H structure */
        int iCanonRevrs = nAtno2CanonRevrs[i];
        int endptInChI = pStruct->endpoint[i]; /* endpoint in InChI */
        int endptRevrs = at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].endpoint : 0;
        int nFixHInChI = pStruct->fixed_H[i];
        int nFixHRevrs = num_Fixed_H_Revrs ? num_Fixed_H_Revrs[iCanonRevrs] : 0;
        int nMobHInChI = pnMobHInChI ? pnMobHInChI[i] : 0;
        int nMobHRevrs = pnMobHRevrs ? pnMobHRevrs[iCanonRevrs] : 0;
        if ( /*(!endptInChI || !endptRevrs) &&*/ (nFixHInChI != nFixHRevrs) ||
            (!endptInChI != !endptRevrs) || nMobHInChI != nMobHRevrs)
        {
            /* in InChI or reversed InChI atom[i] is not tautomeric */
            /* and number of fixed-H on the atom[i] differs */
            if (j >= MAX_DIFF_FIXH)
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            pc2i->c2at[j].endptInChI = endptInChI;
            pc2i->c2at[j].endptRevrs = endptRevrs;
            pc2i->bHasDifference |= !endptInChI != !endptRevrs;
            pc2i->c2at[j].atomNumber = i;
            pc2i->c2at[j].nValElectr = pVA[i].cNumValenceElectrons;
            pc2i->c2at[j].nPeriodNum = pVA[i].cPeriodicRowNumber;
            pc2i->c2at[j].nFixHInChI = nFixHInChI;
            pc2i->c2at[j].nFixHRevrs = nFixHRevrs;
            pc2i->bHasDifference |= nFixHInChI != nFixHRevrs;
            pc2i->c2at[j].nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H[i] :
                pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H[i] : 0;
            pc2i->c2at[j].nMobHRevrs = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H) ?
                pStruct->pOneINChI[1]->nNum_H[iCanonRevrs] :
                (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ?
                pStruct->pOneINChI[0]->nNum_H[iCanonRevrs] : 0;
            pc2i->nNumDiffMobH += (nMobHInChI != nMobHRevrs && !endptRevrs && !endptInChI);
            pc2i->bHasDifference |= nMobHInChI != nMobHRevrs;
            pc2i->c2at[j].nNumHRevrs = at2[i].num_H;
            pc2i->c2at[j].nAtChargeRevrs = at2[i].charge;
            j++;
        }
        pc2i->nNumEndpInChI += (endptInChI != 0);
        pc2i->nNumEndpRevrs += (endptRevrs != 0);

        if (!pVA[i].cMetal)
        {
            pc2i->nChargeFixHRevrsNonMetal += at2[i].charge;
            pc2i->nChargeMobHRevrsNonMetal += at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].charge : 0;
        }

        /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/
    }
    pc2i->nChargeFixHInChI = pInChI[0] ? pInChI[0]->nTotalCharge : 0;
    pc2i->nChargeMobHInChI = pInChI[1] ? pInChI[1]->nTotalCharge : 0;

    pc2i->nChargeMobHRevrs = pStruct->pOneINChI[1] ? pStruct->pOneINChI[1]->nTotalCharge :
        pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0;
    pc2i->nChargeFixHRevrs = pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0;

    pc2i->bHasDifference |= pc2i->nChargeFixHInChI != pc2i->nChargeFixHRevrs;
    pc2i->bHasDifference |= pc2i->nChargeMobHInChI != pc2i->nChargeMobHRevrs;

exit_function:
    pc2i->len_c2at = j;

    return ret;
}


/****************************************************************************/
int FillOutCMP2MHINCHI(StrFromINChI* pStruct,
    ALL_TC_GROUPS* pTCGroups,
    inp_ATOM* at2,
    VAL_AT* pVA,
    INChI* pInChI[],
    CMP2MHINCHI* pc2i)
{
    int       ret = 0, i, j, iat;
    int       bFixHRevrsExists = pInChI[1] && pInChI[1]->nNumberOfAtoms > 0 && !pInChI[1]->bDeleted;
    inp_ATOM* at_Mobile_H_Revrs = (pStruct->pOne_norm_data[0] &&
        pStruct->pOne_norm_data[0]->at) ? pStruct->pOne_norm_data[0]->at : NULL;
    /* atom number in structure that produced original InChI is atom number in all inp_ATOM *atoms */
    /* atom number in structure that produced restored InChI is in nAtomRevrs[]: */
    AT_NUMB* nCanon2AtnoRevrs = pStruct->nCanon2Atno[0];
    AT_NUMB* nAtno2CanonRevrs = pStruct->nAtno2Canon[0];
    S_CHAR* pnMobHInChI = (pInChI[0] && pInChI[0]->nNum_H) ? pInChI[0]->nNum_H : NULL;
    S_CHAR* pnMobHRevrs = (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ?
        pStruct->pOneINChI[0]->nNum_H : NULL;
    int     nNumTgHInChI, nNumTgMInChI, nNumTgHRevrs, nNumTgMRevrs;
    memset(pc2i, 0, sizeof(*pc2i)); /* djb-rwth: memset_s C11/Annex K variant? */
    pc2i->nNumTgInChI = pStruct->ti.num_t_groups;
    pc2i->nNumTgRevrs = pStruct->One_ti.num_t_groups;
    pc2i->bHasDifference |= pc2i->nNumTgInChI != pc2i->nNumTgRevrs;

    pc2i->nNumRemHInChI = pStruct->nNumRemovedProtonsMobHInChI;
    pc2i->nNumRemHRevrs = pStruct->One_ti.tni.nNumRemovedProtons;
    /*pc2i->bHasDifference |= pc2i->nNumRemHInChI != pc2i->nNumRemHRevrs;*/

    pc2i->bFixedHLayerExistsRevrs = bFixHRevrsExists;
    /*pc2i->bHasDifference |= !bFixHRevrsExists;*/

    for (i = 0; i < pStruct->ti.num_t_groups; i++)
    {
        int jFst = pStruct->ti.t_group[i].nFirstEndpointAtNoPos;
        int jNum = pStruct->ti.t_group[i].nNumEndpoints;
        int is_N, is_O;
        for (j = 0; j < jNum; j++)
        {
            iat = pStruct->ti.nEndpointAtomNumber[jFst + j];
            is_N = pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1;
            is_O = pVA[iat].cNumValenceElectrons == 6;
            if (is_N + is_O != 1)
            {
                return RI_ERR_SYNTAX;
            }
            pc2i->nNumTgNInChI += is_N;
            pc2i->nNumTgOInChI += is_O;
            if (at2[iat].chem_bonds_valence == at2[iat].valence)
            {
                /* donor */
                if (is_N)
                {
                    /* N */
                    pc2i->nNumTgNHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1;
                    pc2i->nNumTgNH2InChI += at2[iat].charge == 0 && at2[iat].num_H == 2;
                    pc2i->nNumTgNMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0;
                    pc2i->nNumTgNHMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 1;
                }
                else
                {
                    /* O, S, Se, Te */
                    pc2i->nNumTgOHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1;
                    pc2i->nNumTgOMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0;
                }
            }
            else
            {
                if (at2[iat].chem_bonds_valence == at2[iat].valence + 1)
                {
                    /* donor */
                    if (is_N)
                    {
                        /* N */
                        pc2i->nNumTgDBNHInChI += at2[iat].charge == 0 && at2[iat].num_H == 1;
                        pc2i->nNumTgDBNMinusInChI += at2[iat].charge == -1 && at2[iat].num_H == 0;
                        pc2i->nNumTgDBNInChI += at2[iat].charge == 0 && at2[iat].num_H == 0;
                    }
                    else
                    {
                        /* O, S, Se, Te */
                        pc2i->nNumTgDBOInChI += at2[iat].charge == 0 && at2[iat].num_H == 0;
                    }
                }
            }
        }
    }
    for (i = 0; i < pStruct->One_ti.num_t_groups; i++)
    {
        int jFst = pStruct->One_ti.t_group[i].nFirstEndpointAtNoPos;
        int jNum = pStruct->One_ti.t_group[i].nNumEndpoints;
        int is_N, is_O;
        for (j = 0; j < jNum; j++)
        {
            iat = nCanon2AtnoRevrs[(int)pStruct->One_ti.nEndpointAtomNumber[jFst + j]];
            is_N = pVA[iat].cNumValenceElectrons == 5 && pVA[iat].cPeriodicRowNumber == 1;
            is_O = pVA[iat].cNumValenceElectrons == 6;
            if (is_N + is_O != 1)
            {
                return RI_ERR_PROGR;
            }
            pc2i->nNumTgNRevrs += is_N;
            pc2i->nNumTgORevrs += is_O;
            if (at2[iat].chem_bonds_valence == at2[iat].valence)
            {
                /* donor */
                if (is_N)
                {
                    /* N */
                    pc2i->nNumTgNHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1;
                    pc2i->nNumTgNH2Revrs += at2[iat].charge == 0 && at2[iat].num_H == 2;
                    pc2i->nNumTgNMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0;
                    pc2i->nNumTgNHMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 1;
                }
                else
                {
                    /* O, S, Se, Te */
                    pc2i->nNumTgOHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1;
                    pc2i->nNumTgOMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0;
                }
            }
            else
            {
                if (at2[iat].chem_bonds_valence == at2[iat].valence + 1)
                {
                    /* donor */
                    if (is_N)
                    {
                        /* N */
                        pc2i->nNumTgDBNHRevrs += at2[iat].charge == 0 && at2[iat].num_H == 1;
                        pc2i->nNumTgDBNMinusRevrs += at2[iat].charge == -1 && at2[iat].num_H == 0;
                        pc2i->nNumTgDBNRevrs += at2[iat].charge == 0 && at2[iat].num_H == 0;
                    }
                    else
                    {
                        /* O, S, Se, Te */
                        pc2i->nNumTgDBORevrs += at2[iat].charge == 0 && at2[iat].num_H == 0;
                    }
                }
            }
        }
    }

    for (i = 0; i < pStruct->ti.num_t_groups && i < pStruct->One_ti.num_t_groups; i++)
    {
        nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1];
        nNumTgMInChI = pStruct->ti.t_group[i].num[1];
        nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1];
        nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1];

        pc2i->bHasDifference |= nNumTgHInChI != nNumTgHRevrs;
        pc2i->bHasDifference |= nNumTgMInChI != nNumTgMRevrs;

        if (pStruct->ti.t_group[i].nNumEndpoints ==
            pStruct->One_ti.t_group[i].nNumEndpoints)
        {

            if (nNumTgHInChI != nNumTgHRevrs)
            {
                pc2i->nNumTgDiffH++;
            }
            if (nNumTgMInChI != nNumTgMRevrs)
            {
                pc2i->nNumTgDiffMinus++;
            }
        }
        pc2i->bHasDifference |= pStruct->ti.t_group[i].nNumEndpoints !=
            pStruct->One_ti.t_group[i].nNumEndpoints;

        pc2i->nNumTgHInChI += nNumTgHInChI;
        pc2i->nNumTgMInChI += nNumTgMInChI;
        pc2i->nNumTgHRevrs += nNumTgHRevrs;
        pc2i->nNumTgMRevrs += nNumTgMRevrs;
    }
    for (; i < pStruct->ti.num_t_groups; i++)
    {
        nNumTgHInChI = pStruct->ti.t_group[i].num[0] - pStruct->ti.t_group[i].num[1];
        nNumTgMInChI = pStruct->ti.t_group[i].num[1];
        pc2i->nNumTgHInChI += nNumTgHInChI;
        pc2i->nNumTgMInChI += nNumTgMInChI;
        pc2i->bHasDifference |= 1;
    }
    for (; i < pStruct->One_ti.num_t_groups; i++)
    {
        nNumTgHRevrs = pStruct->One_ti.t_group[i].num[0] - pStruct->One_ti.t_group[i].num[1];
        nNumTgMRevrs = pStruct->One_ti.t_group[i].num[1];
        pc2i->nNumTgHRevrs += nNumTgHRevrs;
        pc2i->nNumTgMRevrs += nNumTgMRevrs;
        pc2i->bHasDifference |= 1;
    }
    for (i = j = 0; i < pStruct->num_atoms; i++)
    {
        /* i = original InChI canonical number - 1 */
        /* k = atom number from InChI created out of restored Fixed-H structure */
        int iCanonRevrs = nAtno2CanonRevrs[i];
        int endptInChI = at2[i].endpoint; /* endpoint in InChI */
        int endptRevrs = at_Mobile_H_Revrs ? at_Mobile_H_Revrs[i].endpoint : 0;
        int nMobHInChI = pnMobHInChI ? pnMobHInChI[i] : 0;
        int nMobHRevrs = pnMobHRevrs ? pnMobHRevrs[iCanonRevrs] : 0;
        if ((!endptInChI != !endptRevrs) || nMobHInChI != nMobHRevrs)
        {
            /* in InChI or reversed InChI atom[i] is not tautomeric */
            /* and number of fixed-H on the atom[i] differs */
            if (j >= MAX_DIFF_FIXH)
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            pc2i->c2at[j].endptInChI = endptInChI;
            pc2i->c2at[j].endptRevrs = endptRevrs;
            pc2i->bHasDifference |= !endptInChI != !endptRevrs;
            pc2i->c2at[j].atomNumber = i;
            pc2i->c2at[j].nValElectr = pVA[i].cNumValenceElectrons;
            pc2i->c2at[j].nPeriodNum = pVA[i].cPeriodicRowNumber;
            pc2i->c2at[j].nMobHInChI = pInChI[1] && pInChI[1]->nNum_H ? pInChI[1]->nNum_H[i] :
                pInChI[0] && pInChI[0]->nNum_H ? pInChI[0]->nNum_H[i] : 0;
            pc2i->c2at[j].nMobHRevrs = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNum_H) ?
                pStruct->pOneINChI[1]->nNum_H[iCanonRevrs] :
                (pStruct->pOneINChI[0] && pStruct->pOneINChI[0]->nNum_H) ?
                pStruct->pOneINChI[0]->nNum_H[iCanonRevrs] : 0;

            pc2i->nNumDiffMobH += (nMobHInChI != nMobHRevrs && !endptRevrs && !endptInChI);
            pc2i->bHasDifference |= (nMobHInChI != nMobHRevrs);
            pc2i->c2at[j].nNumHRevrs = at2[i].num_H;
            pc2i->c2at[j].nAtChargeRevrs = at2[i].charge;
            j++;
        }
        pc2i->nNumEndpInChI += (endptInChI != 0);
        pc2i->nNumEndpRevrs += (endptRevrs != 0);

        if (!pVA[i].cMetal)
        {
            pc2i->nChargeMobHRevrsNonMetal += (at_Mobile_H_Revrs && !at_Mobile_H_Revrs[i].endpoint) ? at_Mobile_H_Revrs[i].charge : 0;
        }


        /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/
    }
    pc2i->nChargeMobHRevrsNonMetal += pTCGroups->tgroup_charge;

    pc2i->nChargeMobHInChI = pInChI[0] ? pInChI[0]->nTotalCharge : 0;

    pc2i->nChargeMobHRevrs = pStruct->pOneINChI[0] ? pStruct->pOneINChI[0]->nTotalCharge : 0;

    pc2i->bHasDifference |= pc2i->nChargeMobHInChI != pc2i->nChargeMobHRevrs;

exit_function:
    pc2i->len_c2at = j;

    return ret;
}


/****************************************************************************/
int NormalizeAndCompare(CANON_GLOBALS* pCG,
    INCHI_CLOCK* ic,
    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,
    INChI* pInChI[],
    long num_inp,
    int bHasSomeFixedH,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask,
    int forbidden_stereo_edge_mask)
{
    int i;
    int err;
    ICR icr, icr2;
    int num_norm_endpoints, num_endpoints, num_norm_t_groups, ret = 0; /* djb-rwth: ignoring LLVM warning: variables used; removing redundant variables */
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
    const char* szCurHdr = (ip->pSdfValue && ip->pSdfValue[0]) ? ip->pSdfValue : "???";
    int         iComponent = pTCGroups->iComponent;
#endif
#endif
    T_GROUP_INFO* t_group_info = NULL;
    inp_ATOM* at_norm = NULL; /* normalized */
    inp_ATOM* at_prep = NULL; /* preprocessed */
    INCHI_MODE  cmpInChI, cmpInChI2;
    int         nDeltaPrev, nDeltaCur;
    int         iOrigInChI, iRevrInChI;


    /***********************************************************/
    /* normalize and create one component InChI                */
    /***********************************************************/
    ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
        &t_group_info, &at_norm, &at_prep);
    if (ret < 0)
    {
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
        fprintf(stdout, "\nERROR in MakeOneInchi-1: %ld %s Comp:%d %c%c Err:%d\n", num_inp,
            szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret);
#endif
#endif
        goto exit_function;
    }
    if (pStruct->bMobileH == TAUT_NON)
    {
        /* these indexes are used to compare Mobile-H InChI */
        iOrigInChI = (pInChI[1] && pInChI[1]->nNumberOfAtoms && !pInChI[1]->bDeleted) ? 1 : 0;
        iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0;
    }
    else
    {
        iOrigInChI = 0;
        iRevrInChI = 0;
    }

    /* Intercept and correct non-polymer Zz to Zy if applicable */
    if (pStruct->n_zy && pStruct->n_pzz)
    {
        if (pStruct->pOneINChI[iRevrInChI]->szHillFormula)
        {
            INCHI_IOS_STRING temp_string_container;
            INCHI_IOS_STRING* strbuf = &temp_string_container;
            int len0 = strlen(pStruct->pOneINChI[iRevrInChI]->szHillFormula);
            if (inchi_strbuf_init(strbuf, len0 + 1, len0 + 1) > 0)
            {
                inchi_strbuf_printf(strbuf, "%-s", pStruct->pOneINChI[iRevrInChI]->szHillFormula);
            }
            MergeZzInHillFormula(strbuf);
            if (strbuf->nUsedLength > len0 + 1)
            {
                char* ctmp; /* djb-rwth: supplementary variable */
                ctmp = (char*)inchi_realloc(pStruct->pOneINChI[iRevrInChI]->szHillFormula, (long long)strbuf->nUsedLength + 1); /* djb-rwth: cast operator added */
                if (ctmp != NULL) /* djb-rwth: NULL pointer must not be assigned to pStruct->pOneINChI[iRevrInChI]->szHillFormula */
                    pStruct->pOneINChI[iRevrInChI]->szHillFormula = ctmp;
            }
            strcpy(pStruct->pOneINChI[iRevrInChI]->szHillFormula, strbuf->pStr);
            inchi_strbuf_close(strbuf);
        }
    }


    /************************************************************/
    /* compare                                                  */
    /************************************************************/
    if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct)))
    {
        goto exit_function;
    }
    cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *a2*/, &icr, &err);
    if (cmpInChI & IDIF_PROBLEM)
    {
        ret = RI_ERR_PROGR; /* severe restore problem */
        goto exit_function;
    }
    if (err)
    {
        ret = RI_ERR_ALLOC;
        goto exit_function;
    }
    /********** InChI from restored structure has LESS hydrogen atoms ******************************/
    if ((cmpInChI & IDIF_LESS_H) && at_prep && 0 < (nDeltaCur = icr.tot_num_H2 - icr.tot_num_H1))
    {
        do
        {
            ret = FixLessHydrogenInFormula(pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups,
                pnNumRunBNS, pnTotalDelta, forbidden_edge_mask);
            if (ret < 0)
            {
                goto exit_function;
            }
            if (ret)
            {
                /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */
                ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
                    &t_group_info, &at_norm, &at_prep);
                if (ret < 0)
                {
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
                    fprintf(stdout, "\nERROR in MakeOneInchi-2: %ld %s Comp:%d %c%c Err:%d\n", num_inp,
                        szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret);
#endif
#endif
                    goto exit_function;
                }
                /* compare new InChI to the original InChI */
                if (pStruct->bMobileH == TAUT_NON)
                {
                    iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0;
                }
                else
                {
                    iRevrInChI = 0;
                }
                if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct)))
                {
                    goto exit_function;
                }
                cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err);
                nDeltaPrev = nDeltaCur;
                nDeltaCur = icr.tot_num_H2 - icr.tot_num_H1;
            }
            else
            {
                break;
            }
        } while ((cmpInChI & IDIF_LESS_H) && at_prep && nDeltaCur && nDeltaCur < nDeltaPrev);
    }
    /********** InChI from restored structure has MORE hydrogen atoms ******************************/
    if ((cmpInChI & IDIF_MORE_H) && at_prep && 0 < (nDeltaCur = icr.tot_num_H1 - icr.tot_num_H2))
    {
        do
        {
            ret = FixMoreHydrogenInFormula(pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups,
                pnNumRunBNS, pnTotalDelta, forbidden_edge_mask);
            if (ret < 0)
            {
                goto exit_function;
            }
            if (ret)
            {
                /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */
                ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
                    &t_group_info, &at_norm, &at_prep);
                if (ret < 0)
                {
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
                    fprintf(stdout, "\nERROR in MakeOneInchi-3: %ld %s Comp:%d %c%c Err:%d\n", num_inp,
                        szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret);
#endif
#endif
                    goto exit_function;
                }
                /* compare new InChI to the original InChI */
                if (pStruct->bMobileH == TAUT_NON)
                {
                    iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0;
                }
                else
                {
                    iRevrInChI = 0;
                }
                if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct)))
                {
                    goto exit_function;
                }
                cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err);
                nDeltaPrev = nDeltaCur;
                nDeltaCur = icr.tot_num_H1 - icr.tot_num_H2;
            }
            else
            {
                break;
            }
        } while ((cmpInChI & IDIF_MORE_H) && at_prep && nDeltaCur && nDeltaCur < nDeltaPrev);
    }
    /***************** Fix non-taut atoms normalized to tautomeric endpoints ***********************/
    if ((cmpInChI & IDIF_EXTRA_TG_ENDP) && at_norm && 0 < (nDeltaCur = icr.num_endp_in1_only))
    {
        do
        {
            ret = FixRemoveExtraTautEndpoints(pBNS, pBD, pStruct, at, at2, at_prep, at_norm, pVA, pTCGroups, &icr,
                pnNumRunBNS, pnTotalDelta, forbidden_edge_mask);
            if (ret < 0)
            {
                goto exit_function;
            }
            if (ret)
            {
                /* Probably success. The changes are in pBNS. Create new InChI out of the new restored structure */
                ret = MakeOneInChIOutOfStrFromINChI2(pCG, ic, ip, sd, pBNS, pStruct, at, at2, at3, pVA, pTCGroups,
                    &t_group_info, &at_norm, &at_prep);
                if (ret < 0)
                {
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
                    fprintf(stdout, "\nERROR in MakeOneInchi-4: %ld %s Comp:%d %c%c Err:%d\n", num_inp,
                        szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret);
#endif
#endif
                    goto exit_function;
                }
                /* compare new InChI to the original InChI */
                if (pStruct->bMobileH == TAUT_NON)
                {
                    iRevrInChI = (pStruct->pOneINChI[1] && pStruct->pOneINChI[1]->nNumberOfAtoms && !pStruct->pOneINChI[1]->bDeleted) ? 1 : 0;
                }
                else
                {
                    iRevrInChI = 0;
                }
                if (pStruct->iMobileH == TAUT_NON && (ret = FillOutExtraFixedHDataRestr(pStruct)))
                {
                    goto exit_function;
                }
                cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL, &icr, &err);
                nDeltaPrev = nDeltaCur;
                nDeltaCur = icr.num_endp_in1_only;
            }
            else
            {
                break;
            }
        } while ((cmpInChI & IDIF_EXTRA_TG_ENDP) && at_norm && nDeltaCur && nDeltaCur < nDeltaPrev);
    }
    /************************ case of Fixed-H ******************************************************/

    if (pStruct->bMobileH == TAUT_NON)
    {
        int num_tries = 0;
        do
        {
            if (0 > (ret = FixFixedHRestoredStructure(pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups,
                &t_group_info, &at_norm, &at_prep, pInChI,
                num_inp, bHasSomeFixedH, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask,
                forbidden_stereo_edge_mask)))
            {
                goto exit_function;
            }
        } while (num_tries++ < 2 && ret > 0);
    }
    /************************ case of Fixed-H ******************************************************/
    if (pStruct->bMobileH == TAUT_YES)
    {
        if (0 > (ret = FixMobileHRestoredStructure(pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups,
            &t_group_info, &at_norm, &at_prep, pInChI,
            num_inp, bHasSomeFixedH, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask,
            forbidden_stereo_edge_mask)))
        {
            goto exit_function;
        }
    }
    /**********************************************************************************************/
    /* stereo */
    cmpInChI = CompareReversedINChI2(pStruct->pOneINChI[0], pInChI[0], pStruct->pOneINChI_Aux[0], NULL /*INChI_Aux *a2*/, &icr, &err);
    if (cmpInChI & IDIF_PROBLEM)
    {
        ret = RI_ERR_PROGR; /* severe restore problem */
        goto exit_function;
    }
    if (err)
    {
        ret = RI_ERR_ALLOC;
        goto exit_function;
    }
    cmpInChI2 = 0;
    memset(&icr2, 0, sizeof(icr2)); /* djb-rwth: memset_s C11/Annex K variant? */
    if (iRevrInChI || iOrigInChI)
    {
        /* additional mobile-H compare in case of Fixed-H */
        cmpInChI2 = CompareReversedINChI2(pStruct->pOneINChI[iRevrInChI], pInChI[iOrigInChI], pStruct->pOneINChI_Aux[iRevrInChI], NULL /*INChI_Aux *a2*/, &icr2, &err);
        if (cmpInChI & IDIF_PROBLEM)
        {
            ret = RI_ERR_PROGR; /* severe restore problem */
            goto exit_function;
        }
        if (err)
        {
            ret = RI_ERR_ALLOC;
            goto exit_function;
        }
    }
    ret = FixRestoredStructureStereo(pCG, ic,
        cmpInChI, &icr, cmpInChI2, &icr2,
        ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups,
        &t_group_info, &at_norm, &at_prep, pInChI,
        num_inp, pnNumRunBNS, pnTotalDelta, forbidden_edge_mask,
        forbidden_stereo_edge_mask);

    if (ret < 0)
    {
        goto exit_function;
    }
#if ( FIX_ADD_PROTON_FOR_ADP == 1 )
    /************************ check and fix ADP by adding a proton (dummy) *************************/
    if (cmpInChI && pTCGroups->num_tgroups && pBNS->tot_st_cap > pBNS->tot_st_flow)
    {
        ret = FixAddProtonForADP(pBNS, pBD, pStruct, at, at2, at_prep, pVA, pTCGroups, &icr,
            pnNumRunBNS, pnTotalDelta, forbidden_edge_mask);
        if (ret < 0)
        {
            goto exit_function;
        }
    }
#endif
    /* moved to MakeOneInChIOutOfStrFromINChI():
      pStruct->nNumRemovedProtons = (pStruct->iMobileH == TAUT_YES)? pStruct->One_ti.tni.nNumRemovedProtons : 0;
    */

    /* count endpoints */
    num_endpoints = 0;
    num_norm_endpoints = 0;
    num_norm_t_groups = 0;
    /* djb-rwth: removing redundant code */
    at_norm = pStruct->pOne_norm_data[0]->at;
    for (i = 0; i < pTCGroups->num_tgroups; i++)
    {
        num_endpoints += pTCGroups->pTCG[i].num_edges;
        /* djb-rwth: removing redundant code */
    }

    if (t_group_info)
    {
        /* after canonicalization, t_group_info->t_group[i].num[0] = number of H   */
        /*                         t_group_info->t_group[i].num[1] = number of (-) */
        for (i = 0; i < t_group_info->num_t_groups; i++)
        {
            if (t_group_info->t_group[i].num[0])
            {
                num_norm_t_groups++;
                num_norm_endpoints += t_group_info->t_group[i].nNumEndpoints;
                /* djb-rwth: removing redundant code */
            }
        }
    }
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
    if (num_norm_t_groups != pTCGroups->num_tgroups || num_norm_endpoints != num_endpoints)
    {
        /* need aggressive (de)protonation */
        /* pStruct->bExtract |= EXTRACT_STRUCT_NUMBER; */
        fprintf(stdout, "NORMCOMP: %s comp=%d %c%c: InChI/NormRvrs NumTg=%d/%d NumEndp=%d/%d\n",
            (*ip).pSdfValue, (*pTCGroups).iComponent,
            pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F',
            pTCGroups->num_tgroups, num_norm_t_groups,
            num_endpoints, num_norm_endpoints);
    }
#endif
#endif

exit_function:

    for (i = 0; i < TAUT_NUM; i++)
    {
        Free_INChI(&pStruct->pOneINChI[i]);
        Free_INChI_Aux(&pStruct->pOneINChI_Aux[i]);
        FreeInpAtomData(pStruct->pOne_norm_data[i]);
        if (pStruct->pOne_norm_data[i])
        {
            inchi_free(pStruct->pOne_norm_data[i]);
            pStruct->pOne_norm_data[i] = NULL;
        }
    }

    free_t_group_info(&pStruct->One_ti);

    return ret;
}


/****************************************************************************
 Find A=X< where all bonds to X except A=X are marked as stereogenic;
 temporary allow stereobonds  change and make A=X bonds single                                                                   */
int CheckAndRefixStereobonds(BN_STRUCT* pBNS, BN_DATA* pBD, StrFromINChI* pStruct,
    inp_ATOM* at, inp_ATOM* at2, VAL_AT* pVA, ALL_TC_GROUPS* pTCGroups,
    int* pnNumRunBNS, int* pnTotalDelta, int forbidden_edge_mask)
{
    int forbidden_edge_stereo = BNS_EDGE_FORBIDDEN_MASK;
    int inv_forbidden_edge_stereo = ~forbidden_edge_stereo;

    int i, k, ne, j1, j2, num_wrong, num_fixed;
    int ret2, retBNS, ret;
    int num_at = pStruct->num_atoms;
    int num_deleted_H = pStruct->num_deleted_H;
    int len_at = num_at + num_deleted_H;
    EDGE_LIST FixedEdges, WrongEdges, CarbonChargeEdges;

    BNS_EDGE* pEdge;
    Vertex      v1, v2;
    BNS_VERTEX* pv1, * pv2;

    ret = 0;

    /* to simplify, prepare new at[] from pBNS */
    memcpy(at2, at, len_at * sizeof(at2[0]));
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
    if (ret2 < 0)
    {
        return ret;
    }

    num_wrong = 0;
    /* find wrong double bonds */
    for (i = 0; i < num_at; i++)
    {
        if (at2[i].valence == 3 &&
            at2[i].chem_bonds_valence - at2[i].valence == 1 &&
            at2[i].sb_parity[0] && at2[i].sb_parity[1] && !at2[i].sb_parity[2] &&
            (at2[i].bond_type[j1 = (int)at2[i].sb_ord[0]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE &&
            (at2[i].bond_type[j2 = (int)at2[i].sb_ord[1]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE &&
            j1 != j2)
        {

            num_wrong++;
        }
    }
    if (!num_wrong)
    {
        return 0;
    }
    num_fixed = 0;
    for (i = 0; i < pBNS->num_bonds; i++)
    {
        pEdge = pBNS->edge + i;
        if (pEdge->forbidden & forbidden_edge_stereo)
        {
            num_fixed++;
        }
    }

    /* there may be no fixed stereo bonds at all, see #87607 */
    AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_CLEAR);
    AllocEdgeList(&FixedEdges, EDGE_LIST_CLEAR);
    AllocEdgeList(&WrongEdges, EDGE_LIST_CLEAR);

    /* do not goto exit_function before reaching this point: EdgeLists have not been initiated */

    if (0 > (ret = ForbidCarbonChargeEdges(pBNS, pTCGroups, &CarbonChargeEdges, forbidden_edge_mask)))
    {
        goto exit_function;
    }
    if ((ret = AllocEdgeList(&FixedEdges, num_fixed)) ||
        (ret = AllocEdgeList(&WrongEdges, num_wrong)))
    {
        goto exit_function;
    }
    /* collect wrong double bonds and set flow=0 */
    for (i = 0; i < num_at && WrongEdges.num_edges < num_wrong; i++)
    {
        if (at2[i].valence == 3 &&
            at2[i].chem_bonds_valence - at2[i].valence == 1 &&
            at2[i].sb_parity[0] && at2[i].sb_parity[1] && !at2[i].sb_parity[2] &&
            (at2[i].bond_type[j1 = (int)at2[i].sb_ord[0]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE &&
            (at2[i].bond_type[j2 = (int)at2[i].sb_ord[1]] & BOND_TYPE_MASK) == BOND_TYPE_SINGLE &&
            j1 != j2)
        {
            switch (j1 + j2)
            {
            case 1: /* 0, 1 */
                k = 2;
                break;
            case 2: /* 0, 2 */
                k = 1;
                break;
            case 3: /* 1, 2 */
                k = 0;
                break;
            default:
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            ne = pBNS->vert[i].iedge[k];
            pEdge = pBNS->edge + ne;
            v1 = pEdge->neighbor1;
            v2 = pEdge->neighbor12 ^ v1;
            pv1 = pBNS->vert + v1;
            pv2 = pBNS->vert + v2;

            if (!pEdge->flow)
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            pEdge->flow--;
            pEdge->forbidden |= forbidden_edge_mask;
            pv1->st_edge.flow--;
            pv2->st_edge.flow--;
            pBNS->tot_st_flow -= 2;
            if ((ret = AddToEdgeList(&WrongEdges, ne, 0))) /* djb-rwth: addressing LLVM warning */
            {
                goto exit_function;
            }
        }
    }
    /* remove forbidden mark from stereo bonds (unfix stereo bonds) */
    for (i = 0; i < pBNS->num_bonds && FixedEdges.num_edges < num_fixed; i++)
    {
        pEdge = pBNS->edge + i;
        if (pEdge->forbidden & forbidden_edge_stereo)
        {
            pEdge->forbidden &= inv_forbidden_edge_stereo;
            FixedEdges.pnEdges[FixedEdges.num_edges++] = i;
        }
    }
    /* Run BNS to move charges and rearrange bond orders */
    retBNS = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
    (*pnNumRunBNS)++;
    if (retBNS < 0)
    {
        goto exit_function;
    }
    else
    {
        if (retBNS > 0)
        {
            *pnTotalDelta += retBNS;
        }
    }
    /* remove forbidden_edge_mask and set forbidden_edge_stereo */
    RemoveForbiddenEdgeMask(pBNS, &WrongEdges, forbidden_edge_mask);
    /* allow carbon charges to change */
    RemoveForbiddenEdgeMask(pBNS, &CarbonChargeEdges, forbidden_edge_mask);
    /* fix previously unfixed stereo bonds */
    SetForbiddenEdgeMask(pBNS, &FixedEdges, forbidden_edge_stereo);
    /* Run BNS again in case not all edge flows are maximal */
    ret2 = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
    (*pnNumRunBNS)++;
    if (ret2 < 0)
    {
        goto exit_function;
    }
    else
    {
        if (ret2 > 0)
        {
            *pnTotalDelta += retBNS;
        }
    }
    ret = retBNS;

exit_function:

    AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_FREE);
    AllocEdgeList(&FixedEdges, EDGE_LIST_FREE);
    AllocEdgeList(&WrongEdges, EDGE_LIST_FREE);

    return ret;
}


/****************************************************************************
 Find and eliminate false Mobile-H groups: Cl(=O)3(-O(-)) => Cl(-)(=O)4
****************************************************************************/
int MoveChargeToRemoveCenerpoints(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask)
{
    int i, j, neigh, num_success; /* djb-rwth: removing redundant variables */
    int num_donors, num_acceptors, bond_type, num_donors_O, num_acceptors_O, is_centerpoint_N, num_known_endpoints, num_wrong_neigh;
    int ret2, ret_forbid_edges, ret, delta;
    int num_at = pStruct->num_atoms;
    int num_deleted_H = pStruct->num_deleted_H;
    int len_at = num_at + num_deleted_H;
    int forbidden_edge_test = BNS_EDGE_FORBIDDEN_TEST;
    int bPossiblyIgnore = pStruct->charge >= 0 && (!pTCGroups->num_tgroups || (pStruct->iMobileH == TAUT_NON && pStruct->ti.num_t_groups)); /* djb-rwth: addressing LLVM warning */
    S_CHAR MobileChargeNeigh[MAXVAL], DoubleBondAcceptors[MAXVAL], DoubleBondNotONeigh[MAXVAL];
    int    numMobileChargeNeigh, numDoubleBondAcceptors, numDoubleBondNotONeigh; /* djb-rwth: removing redundant variables */
    EDGE_LIST ChargeListAllExcept_DB_O;


    BNS_EDGE* pEdgeMinus, * pe;
    Vertex      v1m, v2m;
    BNS_VERTEX* pv1m, * pv2m;
    /* djb-rwth: removing redundant code */
    num_success = 0;

    /* count O(+)H, N(+)H */

    /*
    if ( pStruct->charge >= 0 && (!pTCGroups->num_tgroups || pStruct->iMobileH == TAUT_NON && pStruct->ti.num_t_groups) ) {
        goto exit_function;
    }
    */
    if ((ret = AllocEdgeList(&ChargeListAllExcept_DB_O, EDGE_LIST_CLEAR))) /* djb-rwth: addressing LLVM warning */
    {
        goto exit_function;
    }


    /* to simplify, prepare new at[] from pBNS */
    memcpy(at2, at, len_at * sizeof(at2[0]));
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
    if (ret2 < 0)
    {
        ret = ret2;
        goto exit_function;
    }
#if ( FIND_RING_SYSTEMS == 1 )
    ret2 = MarkRingSystemsInp(at2, num_at, 0);
    if (ret2 < 0)
    {
        ret = ret2;
        goto exit_function;
    }
#endif
    /* mark bonds that cannot be tautomeric; do not forget to remove the marks later */
    ret_forbid_edges = SetForbiddenEdges(pBNS, at2, num_at, forbidden_edge_test, 0, NULL);
    if (ret_forbid_edges < 0)
    {
        ret = ret_forbid_edges;
        goto exit_function;
    }

    for (i = 0; i < num_at; i++)
    {
        if (pVA[i].cNumValenceElectrons != 4 && /* not C, Si, Ge */
            !(pVA[i].nTautGroupEdge || (pStruct->iMobileH == TAUT_NON && pStruct->endpoint && pStruct->endpoint[i])) &&
            !at2[i].num_H && !at2[i].charge && at2[i].valence >= 2 &&
            at2[i].valence < at2[i].chem_bonds_valence &&
            is_centerpoint_elem(at2[i].el_number)) /* djb-rwth: addressing LLVM warning */
        {

            is_centerpoint_N = (pVA[i].cNumValenceElectrons == 5 && (pVA[i].cPeriodicRowNumber == 1 || pVA[i].cMetal));
            /* look at the neighbors */
            numMobileChargeNeigh = numDoubleBondAcceptors = numDoubleBondNotONeigh = num_donors = num_acceptors = 0;
            num_donors_O = num_acceptors_O = 0;
            num_known_endpoints = num_wrong_neigh = 0;
            for (j = 0; j < at2[i].valence; j++) /* djb-rwth: removing redundant code */
            {
                neigh = at2[i].neighbor[j];
                if ((at2[neigh].endpoint || (pStruct->iMobileH == TAUT_NON && pStruct->endpoint && pStruct->endpoint[neigh])) || at2[neigh].charge > 0) /* djb-rwth: addressing LLVM warning */
                {
                    num_known_endpoints++;
                    continue;
                }
                if (pBNS->edge[pBNS->vert[i].iedge[j]].forbidden & forbidden_edge_test)
                {
                    continue;
                }
                bond_type = at2[i].bond_type[j] & BOND_TYPE_MASK;
                if (bond_type > BOND_TYPE_DOUBLE)
                {
                    num_wrong_neigh++;
                    continue;
                }
                if (at2[neigh].num_H && bond_type == BOND_TYPE_SINGLE)
                {
                    break;  /* not this case */
                }
                if (at2[neigh].chem_bonds_valence - at2[neigh].charge
                    != get_endpoint_valence(at2[neigh].el_number))
                {
                    if (bond_type == BOND_TYPE_DOUBLE && pVA[neigh].cNumValenceElectrons != 6)
                    {
                        DoubleBondNotONeigh[numDoubleBondNotONeigh++] = j;
                    }
                    continue;
                }
                if (at2[neigh].charge == -1 && bond_type == BOND_TYPE_SINGLE &&
                    (pVA[neigh].nCMinusGroupEdge < 1 || pBNS->edge[pVA[neigh].nCMinusGroupEdge - 1].flow != 1))
                {
                    break;
                }
                switch (bond_type)
                {
                case BOND_TYPE_SINGLE:
                    if (at2[neigh].charge != -1 || pVA[neigh].nCMinusGroupEdge <= 0)
                    {
                        num_wrong_neigh++;
                        continue;
                    }
                    num_donors++;
                    num_donors_O += (pVA[neigh].cNumValenceElectrons == 6 && pVA[neigh].cPeriodicRowNumber <= 4);
                    MobileChargeNeigh[numMobileChargeNeigh++] = j;
                    break;
                case BOND_TYPE_DOUBLE:
                    if (at2[neigh].charge)
                    {
                        num_wrong_neigh++;
                        continue;
                    }
                    DoubleBondAcceptors[numDoubleBondAcceptors++] = j;
                    num_acceptors++;
                    num_acceptors_O += (pVA[neigh].cNumValenceElectrons == 6 && pVA[neigh].cPeriodicRowNumber <= 4);
                }
            }
            if (j != at2[i].valence || !num_donors || !num_acceptors)
            {
                continue;
            }
            /* special case NOn(-) */
            if (is_centerpoint_N && (num_donors == num_donors_O) && (num_acceptors == num_acceptors_O))
            {
                continue;
            }
            if (pStruct->iMobileH == TAUT_NON && num_donors == numDoubleBondNotONeigh)
            {
                /* fix all charges except on =O */
                Vertex     vPathStart, vPathEnd;
                int        nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;
                int k, e, num_MovedCharges = 0;

                if (!ChargeListAllExcept_DB_O.num_edges)
                {
                    /* djb-rwth: removing redundant code */
                    for (k = 0; k < num_at; k++)
                    {
                        if (!((1 == at2[k].valence && pBNS->edge[pBNS->vert[k].iedge[0]].flow &&
                            !pBNS->edge[pBNS->vert[k].iedge[0]].forbidden &&
                            !((e = pVA[k].nCMinusGroupEdge - 1) >= 0 && pBNS->edge[e].flow) &&
                            !((e = pVA[k].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[e].flow) &&
                            /* 0 == at2[k].charge && */
                            pVA[k].cNumValenceElectrons == 6 && !pVA[k].cMetal &&
                            (pStruct->endpoint && pStruct->endpoint[k])) ||
                            (pStruct->fixed_H && pStruct->fixed_H[k]))) /* djb-rwth: addressing LLVM warnings */
                            /* djb-rwth: removing redundant code */
                            if ((e = pVA[k].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[e].flow &&
                                !pBNS->edge[e].forbidden &&
                                (ret = AddToEdgeList(&ChargeListAllExcept_DB_O, e, 64)))
                            {
                                goto exit_function;
                            }
                        if ((e = pVA[k].nCPlusGroupEdge - 1) >= 0 &&
                            !pBNS->edge[e].forbidden &&
                            (ret = AddToEdgeList(&ChargeListAllExcept_DB_O, e, 64)))
                        {
                            goto exit_function;
                        }
                    }
                }
                /* fix double bonds to non-O neighbors connected by double bonds;
                   we will try to make these bons single */
                for (k = 0; k < numDoubleBondNotONeigh; k++)
                {
                    e = pBNS->vert[i].iedge[(int)DoubleBondNotONeigh[k]];
                    if (!pBNS->edge[e].forbidden &&
                        (ret = AddToEdgeList(&ChargeListAllExcept_DB_O, e, 64)))
                    {
                        goto exit_function;
                    }
                }
                /* attempt to make DoubleBondNotONeigh[] single */
                SetForbiddenEdgeMask(pBNS, &ChargeListAllExcept_DB_O, forbidden_edge_mask);
                for (k = 0; k < numDoubleBondNotONeigh && num_MovedCharges < numMobileChargeNeigh; k++)
                {
                    pe = pBNS->edge + pBNS->vert[i].iedge[(int)DoubleBondNotONeigh[k]];
                    delta = 1;
                    if (pe->flow != delta)
                        continue;
                    pv1m = pBNS->vert + (v1m = pe->neighbor1);
                    pv2m = pBNS->vert + (v2m = pe->neighbor12 ^ v1m);
                    pv1m->st_edge.flow -= delta;
                    pv2m->st_edge.flow -= delta;
                    pe->flow -= delta;
                    pBNS->tot_st_flow -= 2 * delta;
                    ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
                        &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
                    if (ret < 0)
                    {
                        goto exit_function;
                    }
                    if (ret == 1 && ((vPathEnd == v1m && vPathStart == v2m) ||
                        (vPathEnd == v2m && vPathStart == v1m)) &&
                        nDeltaCharge == 0  /* (-) moving from one to another atom*/) /* djb-rwth: addressing LLVM warnings */
                    {
                        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
                        (*pnNumRunBNS)++;
                        if (ret < 0)
                        {
                            goto exit_function;
                        }
                        else
                        {
                            if (ret == 1)
                            {
                                *pnTotalDelta += ret;
                                num_MovedCharges++;
                            }
                            else
                            {
                                ret = RI_ERR_PROGR;
                                goto exit_function;
                            }
                        }
                    }
                    else
                    {
                        /* djb-rwth: removing redundant code */
                        pv1m->st_edge.flow += delta;
                        pv2m->st_edge.flow += delta;
                        pe->flow += delta;
                        pBNS->tot_st_flow += 2 * delta;
                    }
                }
                RemoveForbiddenEdgeMask(pBNS, &ChargeListAllExcept_DB_O, forbidden_edge_mask);
            }
            else
            {
                if (!bPossiblyIgnore || (!num_known_endpoints && !num_wrong_neigh && (num_acceptors_O + num_donors_O >= 3))) /* djb-rwth: addressing LLVM warning */
                {
                    /* remove negative charges from the neighbors */
                    pBNS->vert[i].st_edge.cap += num_donors; /* enough to make all bonds to donors double */
                    pBNS->tot_st_cap += num_donors;
                    pVA[i].cInitCharge -= num_donors; /* work no matter what are known charge/valence */
                    for (j = 0; j < numMobileChargeNeigh; j++)
                    {
                        neigh = at2[i].neighbor[(int)MobileChargeNeigh[j]];
                        pEdgeMinus = pBNS->edge + ((long long)pVA[neigh].nCMinusGroupEdge - 1); /* djb-rwth: cast operator added */
                        v1m = pEdgeMinus->neighbor1;
                        v2m = pEdgeMinus->neighbor12 ^ v1m;
                        pv1m = pBNS->vert + v1m;
                        pv2m = pBNS->vert + v2m;
                        delta = pEdgeMinus->flow;
                        pv1m->st_edge.flow -= delta;
                        pv2m->st_edge.flow -= delta;
                        if (IS_BNS_VT_C_GR(pv1m->type))
                        {
                            /* irreversible change to ChargeStruct */
                            pv1m->st_edge.cap -= delta;
                        }
                        else
                        {
                            if (IS_BNS_VT_C_GR(pv2m->type))
                            {
                                /* irreversible change to ChargeStruct */
                                pv2m->st_edge.cap -= delta;
                            }
                            else
                            {
                                ret = RI_ERR_PROGR;
                                goto exit_function;
                            }
                        }
                        pBNS->tot_st_cap -= delta;
                        pBNS->tot_st_flow -= 2 * delta;
                        pEdgeMinus->flow -= delta;
                    }
                    ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
                    (*pnNumRunBNS)++;
                    if (ret < 0)
                    {
                        goto exit_function;
                    }
                    else
                        if (ret == num_donors)
                        {
                            *pnTotalDelta += ret;
                            num_success++;
                            /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/
                        }
                        else
                        {
                            ret = RI_ERR_PROGR;
                            goto exit_function;
                        }
                }
            }
        }
    }
    if (ret_forbid_edges)
    {
        /* remove the marks */
        RemoveForbiddenBondFlowBits(pBNS, forbidden_edge_test);
    }
    ret = num_success;

exit_function:

    AllocEdgeList(&ChargeListAllExcept_DB_O, EDGE_LIST_FREE);

    return ret;
}


/****************************************************************************
 Find and eliminate cases when Mobile H endpoint has radical on it
 (typical for wrong P(VI)(=O)3OH
****************************************************************************/
int MakeSingleBondsMetal2ChargedHeteroat(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask)
{
    int i;

    int ret2, ret, pass;
    int num_at = pStruct->num_atoms;
    int num_deleted_H = pStruct->num_deleted_H;
    int len_at = num_at + num_deleted_H;
    int inv_forbidden_edge_mask = ~forbidden_edge_mask;

    int         j, k;
    int        cur_num_edges;
    BNS_EDGE* e;
    Vertex     v1, v2;

    EdgeIndex* pFixedEdges;
    int        nNumEdgesToFix;

    ret = 0;

    /* to simplify, prepare new at[] from pBNS */
    memcpy(at2, at, len_at * sizeof(at2[0]));
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
    if (ret2 < 0)
    {
        ret = ret2;
        goto exit_function;
    }

    pFixedEdges = NULL;

    nNumEdgesToFix = 0; /* cpunt nNumEdgesToFix only when pass==0 */
    cur_num_edges = 0; /* count cur_num_edges  only when pass==1; at the end they must be equal */
    for (pass = 0; pass < 2; pass++)
    {
        if (pass)
        {
            /* 2nd pass: allocate edge storage */
            if (!nNumEdgesToFix)
            {
                break; /* nothing to do */
            }
            pFixedEdges = (EdgeIndex*)inchi_malloc(nNumEdgesToFix * sizeof(pFixedEdges[0]));
            if (!pFixedEdges)
            {
                ret = RI_ERR_ALLOC;
                goto exit_function;
            }
        }
        for (i = 0; i < num_at; i++)
        {
            int neigh;
            if (pVA[i].cMetal)
            {
                for (j = 0; j < at2[i].valence; j++)
                {
                    neigh = at2[i].neighbor[j];
                    if (pVA[neigh].cNumValenceElectrons == 4 &&
                        pVA[neigh].cPeriodicRowNumber == 1)
                    {
                        continue; /* ignore carbon */
                    }
                    if (at2[i].bond_type[j] > BOND_TYPE_SINGLE && at2[neigh].charge &&
                        !pVA[neigh].cMetal && pVA[neigh].cnListIndex > 0)
                    {
                        int cnBits = at2[neigh].charge > 0 ? MAKE_CN_BITS(cn_bits_N, cn_bits_P, 0, 0) :
                            MAKE_CN_BITS(cn_bits_N, cn_bits_M, 0, 0);
                        int atBits = cnList[pVA[neigh].cnListIndex - 1].bits;
                        for (k = 0; k < MAX_NUM_CN_BITS - 1; k++, atBits >>= cn_bits_shift)
                        {
                            /* ??? */
                            if ((atBits & cnBits) == cnBits)
                            {
                                break;
                            }
                        }
                        if (k == MAX_NUM_CN_BITS - 1)
                        {
                            continue;
                        }
                        if (pass == 0)
                        {
                            nNumEdgesToFix++;
                        }
                        else
                        {
                            pFixedEdges[cur_num_edges++] = pBNS->vert[i].iedge[j];
                        }
                    }
                }
            }
        }
    }

    /* restore the initial structures */
    memcpy(at2, at, ((long long)num_at + (long long)num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */

    if (nNumEdgesToFix && pFixedEdges)
    {
        if (nNumEdgesToFix != cur_num_edges)
        {
            ret = RI_ERR_PROGR;
            goto pre_exit_function; /* djb-rwth: fixing coverity ID #499637 */
        }
        /* change edge flow, fix the edges, and run BNS */
        for (i = 0; i < nNumEdgesToFix; i++)
        {
            e = pBNS->edge + pFixedEdges[i];
            v1 = e->neighbor1;
            v2 = e->neighbor12 ^ v1;
            e->flow--;
            e->forbidden |= forbidden_edge_mask;
            pBNS->vert[v1].st_edge.flow--;
            pBNS->vert[v2].st_edge.flow--;
            pBNS->tot_st_flow -= 2;
            (*pnTotalDelta) -= 2;
        }
        /* Run BNS allowing to change any charges */
        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
        (*pnNumRunBNS)++;
        if (ret < 0)
        {
            goto pre_exit_function; /* djb-rwth: fixing coverity ID #499637 */
        }
        else
        {
            (*pnTotalDelta) += ret;
        }
        /* unfix the edges */
        for (i = 0; i < nNumEdgesToFix; i++)
        {
            e = pBNS->edge + pFixedEdges[i];
            e->forbidden &= inv_forbidden_edge_mask;
        }
        if (ret < 2 * nNumEdgesToFix)
        {
            /* not all fixes succeeded */
            ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
            (*pnNumRunBNS)++;
            if (ret < 0)
            {
                goto pre_exit_function; /* djb-rwth: fixing coverity ID #499637 */
            }
            else
            {
                (*pnTotalDelta) += ret;
            }
        }
    }

pre_exit_function:
    if (pFixedEdges)
    {
        inchi_free(pFixedEdges);
        pFixedEdges = NULL;
    }

exit_function:
    return ret;
}



/**************************************************************************/
/* In Reconnected structure change 'salt bonds' to 'coordination bonds    */
/* for example, M-O-C=  ->  M(+)-O(-)-C=                                  */
/* Defect: instead of NH2-C=O(+)-M it will restore NH2(+)=C-O(-)-M(+)     */
/* However, in this release metal-organic compounds do not get much care  */
int SaltBondsToCoordBonds(BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    inp_ATOM* at,
    inp_ATOM* at2,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    int* pnNumRunBNS,
    int* pnTotalDelta,
    int forbidden_edge_mask)
{
    int i;

    int ret2, ret, cur_success;
    int num_at = pStruct->num_atoms;
    int num_edges = pBNS->num_bonds + 2 * pBNS->num_atoms;
    int num_deleted_H = pStruct->num_deleted_H;
    int len_at = num_at + num_deleted_H;
    int inv_forbidden_edge_mask = ~forbidden_edge_mask;
    EDGE_LIST AllChargeEdges;

    int         j, k, n;
    BNS_EDGE* pe, * pePlusMetal, * peMinusO;
    BNS_VERTEX* pv1, * pv2, * pvO, * pvM;
    Vertex     v1, v2, vPlusMinus;

    EdgeIndex  ie, iePlusMetal, ieMinusO;

    Vertex     vPathStart, vPathEnd;
    int        delta, nPathLen, nDeltaH, nDeltaCharge, nNumVisitedAtoms;

    ret = 0;
    cur_success = 0;
    AllocEdgeList(&AllChargeEdges, EDGE_LIST_CLEAR);

    if (pStruct->iInchiRec == INCHI_BAS || !pStruct->pSrm->bMetalAddFlower || pStruct->pSrm->nMetalMinBondOrder)
    {
        goto exit_function;
    }

    /* to simplify, prepare new at[] from pBNS */
    memcpy(at2, at, len_at * sizeof(at2[0]));
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
    if (ret2 < 0)
    {
        ret = ret2;
        goto exit_function;
    }
    for (i = 0; i < num_at; i++)
    {
        if (bIsMetalSalt(at2, i))
        {
            if (!AllChargeEdges.num_edges)
            {
                /*--------- one-time action: fix all bonds, charges, taut. group edges ------------*/
                for (j = 0; j < num_at; j++)
                {
                    /* all bonds */
                    for (k = 0; k < at2[j].valence; k++)
                    {
                        n = at2[j].neighbor[k];
                        if (n < j && !pBNS->edge[ie = pBNS->vert[j].iedge[k]].forbidden &&
                            (ret = AddToEdgeList(&AllChargeEdges, ie, num_edges)))
                        {
                            goto exit_function;
                        }
                    }
                    /* charge edges */
                    if ((ie = pVA[j].nCMinusGroupEdge - 1) >= 0 && !pBNS->edge[ie].forbidden &&
                        (ret = AddToEdgeList(&AllChargeEdges, ie, num_edges)))
                    {
                        goto exit_function;
                    }
                    if ((ie = pVA[j].nCPlusGroupEdge - 1) >= 0 && !pBNS->edge[ie].forbidden &&
                        (ret = AddToEdgeList(&AllChargeEdges, ie, num_edges)))
                    {
                        goto exit_function;
                    }
                }
                /* taut group edges */
                for (j = 0; j < pTCGroups->num_tgroups; j++)
                {
                    pv1 = pBNS->vert + (v1 = pTCGroups->pTCG[j].nVertexNumber); /* t-group vertex */ /* djb-rwth: ignoring LLVM warning: see comment below */
                    for (k = 0; k < pv1->num_adj_edges; k++)
                    {
                        /* ie, 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 + (ie = pv1->iedge[k]))->neighbor1; /* djb-rwth: ignoring LLVM warning: see comment above */
                        if ((ret = AddToEdgeList(&AllChargeEdges, ie, num_edges))) /* djb-rwth: addressing LLVM warning */
                        {
                            goto exit_function;
                        }
                    }
                }
                /*---------------------------------------------------------------*/
            }
            /* replace all single bonds to neutral neighbors with zero-order bonds
               allow neighbor charge change to (-1) and metal atom charge increment +1 */
            for (k = 0; k < at2[i].valence; k++)
            {
                n = at2[i].neighbor[k];
                pe = pBNS->edge + pBNS->vert[i].iedge[k];
                if (at2[n].charge || at2[i].bond_type[k] != BOND_TYPE_SINGLE)
                {
                    continue;
                }
                iePlusMetal = pVA[i].nCPlusGroupEdge - 1;
                ieMinusO = pVA[n].nCMinusGroupEdge - 1;

                if (pe->flow != 1 || pe->forbidden || iePlusMetal < 0)
                {
                    continue;
                }
                pePlusMetal = pBNS->edge + iePlusMetal;
                if (pePlusMetal->flow <= 0)
                {
                    continue; /* to add (+) to metal this flow must be decremented */
                }
                if (ieMinusO >= 0)
                {
                    /* usually does not happen */
                    peMinusO = pBNS->edge + ieMinusO;

                    if (peMinusO->flow || pePlusMetal->forbidden || peMinusO->forbidden)
                    {
                        continue;
                    }

                    /* decrement bond order to 0 */
                    delta = 1;
                    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;

                    SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
                    pePlusMetal->forbidden &= inv_forbidden_edge_mask;
                    peMinusO->forbidden &= inv_forbidden_edge_mask;

                    ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
                        &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);

                    if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
                        (vPathEnd == v2 && vPathStart == v1)) /*&& nDeltaCharge > 0*/) /* djb-rwth: addressing LLVM warnings */
                    {
                        /* (+)charge was just moved, no change in number of charges */
                        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
                        if (ret > 0)
                        {
                            (*pnNumRunBNS)++;
                            cur_success++; /* 01 */
                        }
                    }
                    else
                    {
                        pe->flow += delta; /* roll back */
                        pv1->st_edge.flow += delta;
                        pv2->st_edge.flow += delta;
                        pBNS->tot_st_flow += 2 * delta;
                    }
                    RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
                }
                else
                {
                    if (NO_VERTEX != (vPlusMinus = GetPlusMinusVertex(pBNS, pTCGroups, 1, 1)))
                    {
                        /* manually add (-) charge to O and (+) charge to metal */
                        /* decrement bond order to 0 */
                        /*---------------------------------------------------------------------------*/
                        /*                                                                           */
                        /*      (+/-)*               (+/-)           Result:                         */
                        /*        |                    ||                                            */
                        /*        |                    ||            - Added (+) to M                */
                        /*       (+)super             (+)super       - Incremented bond M-O          */
                        /*        ||                   |                                             */
                        /*        ||          =>       |             To make this attachment H,      */
                        /*       (Y)                  (Y)            increment                       */
                        /*        |                    ||            pTCGroups->pTCG[itg].tg_num_H   */
                        /*        |                    ||                                            */
                        /*       (+)metal             (+)hetero      Technical details:              */
                        /*         \\                   \            increase capacities of          */
                        /*           M                    M(+)       edges to (+/-) otherwise        */
                        /*           |                    ||         flow may not be able to         */
                        /*          -O*                -O-O          increase                        */
                        /*                                                                           */
                        /*   After that change M=O bond order from 2 to 0                            */
                        /*---------------------------------------------------------------------------*/
                        int i1, j1, k1;
                        delta = 1;
                        pvO = pBNS->vert + n;
                        pvM = pBNS->vert + i;
                        /* Increment st_edge.cap on (+/-) vertex */
                        pBNS->vert[vPlusMinus].st_edge.cap += delta;
                        /* Increment st_edge.cap on O */
                        pvO->st_edge.cap += delta;
                        /* increment cap on M-O edge */
                        pe->cap += delta;
                        /* total cap count */
                        pBNS->tot_st_cap += 2 * delta;

                        v1 = vPlusMinus;
                        v2 = n; /* atom O */

                        /* increase capacities of edges to Y  */
                        for (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++)
                        {
                            j1 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus;
                            for (k1 = 0; k1 < pBNS->vert[j1].num_adj_edges; k1++)
                            {
                                pBNS->edge[pBNS->vert[j1].iedge[k1]].cap += delta;
                            }
                        }
                        SetForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
                        pePlusMetal->forbidden &= inv_forbidden_edge_mask;
                        pe->forbidden &= inv_forbidden_edge_mask;

                        ret = RunBnsTestOnce(pBNS, pBD, pVA, &vPathStart, &vPathEnd, &nPathLen,
                            &nDeltaH, &nDeltaCharge, &nNumVisitedAtoms);
                        cur_success = 0;
                        if (ret == 1 && ((vPathEnd == v1 && vPathStart == v2) ||
                            (vPathEnd == v2 && vPathStart == v1)) /*&& nDeltaCharge == 1*/) /* djb-rwth: addressing LLVM warnings */
                        {
                            /* 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)
                            {
                                (*pnNumRunBNS)++;
                                cur_success++; /* 01 */
                            }
                        }
                        if (cur_success)
                        {
                            /* set bond M=O order = 0 */
                            if (pe->flow != 2 * delta)
                            {
                                ret = RI_ERR_PROGR;
                                goto exit_function;
                            }
                            /* reduce pe bond order by 2*delta */
                            pe->flow -= 2 * delta;
                            pvO->st_edge.cap -= 2 * delta;
                            pvO->st_edge.flow -= 2 * delta;
                            pvM->st_edge.flow -= 2 * delta;
                            pvM->st_edge.cap -= 2 * delta;
                            pBNS->tot_st_cap -= 3 * delta;
                            pBNS->tot_st_flow -= 4 * delta;
                            /* fix M-O bond order to zero */
                            pe->cap -= 2 * delta;
                            /* add fixed (-) charge to O */
                            pVA[n].cInitCharge -= delta;
                        }
                        else
                        {
                            /* failed */
                            pBNS->vert[vPlusMinus].st_edge.cap -= delta;
                            pvO->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 (i1 = 0; i1 < pBNS->vert[vPlusMinus].num_adj_edges; i1++)
                            {
                                j1 = pBNS->edge[pBNS->vert[vPlusMinus].iedge[i1]].neighbor12 ^ vPlusMinus;
                                for (k1 = 0; k1 < pBNS->vert[j1].num_adj_edges; k1++)
                                {
                                    pBNS->edge[pBNS->vert[j1].iedge[k1]].cap -= delta;
                                }
                            }
                        }
                        RemoveForbiddenEdgeMask(pBNS, &AllChargeEdges, forbidden_edge_mask);
                    }
                }
            }
        }
    }

exit_function:

    AllocEdgeList(&AllChargeEdges, EDGE_LIST_FREE);

    return ret;
}


#if ( KEEP_METAL_EDGE_FLOW == 1 )


/****************************************************************************/
int ForbidMetalCarbonEdges(BN_STRUCT* pBNS,
    inp_ATOM* at,
    int num_at,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    EDGE_LIST* pMetalCarbonEdges,
    int forbidden_edge_mask)
{

    int i, j, neigh, nNumEdgeMetalCarbon = 0, pass = 0, ret = 0;
    BNS_VERTEX* pVert, * pNeigh;
    BNS_EDGE* pEdge;

    /* count carbon-metal edges */

    if (pTCGroups->num_metal_atoms)
    {
    fill_ForbiddenEdgesMetalCarbon:
        for (i = 0; i < num_at; i++)
        {
            if (pVA[i].cMetal && pVA[i].cNumBondsToMetal)
            {
                pVert = pBNS->vert + i;
                for (j = 0; j < pVert->num_adj_edges; j++)
                {
                    pEdge = pBNS->edge + pVert->iedge[j];
                    neigh = pEdge->neighbor12 ^ i;
                    pNeigh = pBNS->vert + neigh;
                    if (!IS_BNS_VT_ATOM(pNeigh->type))
                        continue;
                    if (at[neigh].endpoint)
                        continue;
                    if (pVA[neigh].cNumValenceElectrons == 4 && pVA[neigh].cPeriodicRowNumber == 1 &&
                        pNeigh->st_edge.cap >= at[neigh].valence + 1)
                    {
                        if (pass)
                        {
                            if (ret = AddToEdgeList(pMetalCarbonEdges, pVert->iedge[j], 0))
                            {
                                goto exit_function;
                            }
                            pEdge->forbidden |= forbidden_edge_mask;
                        }
                        else
                        {
                            nNumEdgeMetalCarbon++;
                        }
                    }
                }
            }
        }
        if (!pass && nNumEdgeMetalCarbon)
        {
            if (ret = AllocEdgeList(pMetalCarbonEdges, nNumEdgeMetalCarbon))
            {
                goto exit_function;
            }
            pass++;
            goto fill_ForbiddenEdgesMetalCarbon;
        }
    }

exit_function:

    return ret;
}


#endif


/****************************************************************************
 Restore bonds & charges
*****************************************************************************/
int RunBnsRestore1(CANON_GLOBALS* pCG,
    INCHI_CLOCK* ic,
    ICHICONST INPUT_PARMS* ip,
    STRUCT_DATA* sd,
    BN_STRUCT* pBNS,
    BN_DATA* pBD,
    StrFromINChI* pStruct,
    VAL_AT* pVA,
    ALL_TC_GROUPS* pTCGroups,
    INChI* pInChI[],
    long num_inp,
    int bHasSomeFixedH)
{
    int        nNumRunBNS = 0;

    EDGE_LIST CarbonChargeEdges, MetalCarbonEdges, Nplus2BondsEdges;

    int nTotalDelta = 0, ret = 0; /* djb-rwth: removing redundant variables */
    inp_ATOM* at = pStruct->at;
    inp_ATOM* at2 = NULL; /* restored structure */
    inp_ATOM* at3 = NULL; /* structure for calculating one InChI */
    int     num_at = pStruct->num_atoms;
    int     num_deleted_H = pStruct->num_deleted_H;
#ifdef _DEBUG
    int ret2;
#endif

#if ( KEEP_METAL_EDGE_FLOW == 1 )
    BNS_VERTEX* pVert, * pNeigh;
    int         j, neigh;
#endif

    /* Edge lists initialization */
    AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_CLEAR);
    AllocEdgeList(&MetalCarbonEdges, EDGE_LIST_CLEAR);
    AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_CLEAR);

    if (pStruct->iMobileH == TAUT_NON &&
        (ret = FillOutExtraFixedHDataInChI(pStruct, pInChI)))
    {
        goto exit_function;
    }

    if ((!at2 && !(at2 = (inp_ATOM*)inchi_malloc(((long long)num_at + (long long)num_deleted_H) * sizeof(at2[0])))) ||
        (!at3 && !(at3 = (inp_ATOM*)inchi_malloc(((long long)num_at + (long long)num_deleted_H) * sizeof(at3[0]))))) /* djb-rwth: cast operators added; addressing LLVM warning */
    {
        inchi_free(at2);
        inchi_free(at3);
        return RI_ERR_ALLOC;
    }

    if (0 > (ret = ForbidCarbonChargeEdges(pBNS, pTCGroups, &CarbonChargeEdges, BNS_EDGE_FORBIDDEN_TEMP)))
    {
        goto exit_function;
    }

#if ( KEEP_METAL_EDGE_FLOW == 1 )
    /* count edges of -C(IV)< carbons connected to metals */
    if (0 > (ret = ForbidMetalCarbonEdges(pBNS, at, num_at, pVA, pTCGroups, &MetalCarbonEdges, BNS_EDGE_FORBIDDEN_TEMP)))
    {
        goto exit_function;
    }
#endif
    if (0 > (ret = ForbidNintrogenPlus2BondsInSmallRings(pBNS, at, num_at, pVA, 6,
        pTCGroups, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP)))
    {
        goto exit_function;
    }

    /*********** Run BNS #1: no charge on carbons and =N= ***************/
    if (Nplus2BondsEdges.num_edges)
    {
        /* Run BNS leaving carbon charges unchanged */
        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
        nNumRunBNS++;
        if (ret < 0)
        {
            goto exit_function;
        }
        else
        {
            nTotalDelta += ret;
        }
        RemoveForbiddenEdgeMask(pBNS, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP);
        AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_FREE);
    }
#ifdef _DEBUG
    /* debug only */
    memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
#endif
    /*************************** extend min ring size to 8 ****************************/
    if (0 > (ret = ForbidNintrogenPlus2BondsInSmallRings(pBNS, at, num_at, pVA, 8,
        pTCGroups, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP)))
    {
        goto exit_function;
    }
    if (Nplus2BondsEdges.num_edges)
    {
        /* Run BNS leaving carbon charges unchanged */
        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
        nNumRunBNS++;
        if (ret < 0)
        {
            goto exit_function;
        }
        else
        {
            nTotalDelta += ret;
        }
        RemoveForbiddenEdgeMask(pBNS, &Nplus2BondsEdges, BNS_EDGE_FORBIDDEN_TEMP);
        AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_FREE);
    }
#ifdef _DEBUG
    /* debug only */
    memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
#endif
    /*******************************************************************/
    if (CarbonChargeEdges.num_edges > 0)
    {
        /* Run BNS leaving carbon charges unchanged */
        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
        nNumRunBNS++;
        if (ret < 0)
        {
            goto exit_function;
        }
        else
        {
            nTotalDelta += ret;
        }
        RemoveForbiddenEdgeMask(pBNS, &CarbonChargeEdges, BNS_EDGE_FORBIDDEN_TEMP);
        AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_FREE);
    }
#ifdef _DEBUG
    /* debug only */
    memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
#endif
    /*******************************************************************/
    if (MetalCarbonEdges.num_edges > 0)
    {
        /* Run BNS leaving carbon charges unchanged */
        ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
        nNumRunBNS++;
        if (ret < 0)
        {
            goto exit_function;
        }
        else
        {
            nTotalDelta += ret;
        }
        RemoveForbiddenEdgeMask(pBNS, &MetalCarbonEdges, BNS_EDGE_FORBIDDEN_TEMP);
        AllocEdgeList(&MetalCarbonEdges, EDGE_LIST_FREE);
    }
    /*******************************************************************/
    /* Run BNS allowing to change any charges */
    ret = RunBnsRestoreOnce(pBNS, pBD, pVA, pTCGroups);
    nNumRunBNS++;
    if (ret < 0)
    {
        goto exit_function;
    }
    else
    {
        nTotalDelta += ret;
    }
#ifdef _DEBUG
    /* debug only */
    memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
#endif

#if ( BNS_RAD_SEARCH == 1 )
    /****************************************************************************/
    /* move unfulfilled 'radicals' from ChargeStruct to atoms         */
    /* and set change charges of affected atoms to fit total charge   */
    ret = MoveRadToAtomsAddCharges(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
#endif
    /**************************************************************/
    /**************************************************************/
    /*****           fix restore inconsistencies              *****/
    /**************************************************************/
    /**************************************************************/
#ifdef _DEBUG
    /* debug only */
    memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
#endif

    /* rearrange (+) and (-) edges flow so that there is no (+)flow=0 and (-)flow=1 */
    ret = RearrangePlusMinusEdgesFlow(pBNS, pBD, pVA, pTCGroups, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }

    /*****************************************************************/
    /*       Increment zero order metal bonds to heteroatoms         */
    /*****************************************************************/
    ret = IncrementZeroOrderBondsToHeteroat(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }

#ifdef _DEBUG
    /* debug only */
    memcpy(at2, at, ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H) * sizeof(at2[0])); /* djb-rwth: cast operators added */
    pStruct->at = at2;
    ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
    pStruct->at = at;
#endif

#if (MOVE_CHARGES_FROM_HETEREO_TO_METAL == 1 )
    /*****************************************************************/
    /* move charges from heteroatoms to metal atoms                  */
    /*****************************************************************/
    ret = MoveChargeFromHeteroatomsToMetals(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
#endif
    /***********************************************************************
            NH2                NH2
               \                  \
                C==S(+)-   =>      C(+)-S-   where NH2 are not tautomeric
               /                  /
            NH2                NH2
    ************************************************************************/
    ret = MovePlusFromS2DiaminoCarbon(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /*****************************************************************/
    /*       Avoid charge separation on heteroatoms                  */
    /*****************************************************************/
    ret = EliminateChargeSeparationOnHeteroatoms(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, 0);
    if (ret < 0)
    {
        goto exit_function;
    }
    if (ret)
    {
        /*charge separation remains; allow changes of stereobonds in a ring and try again */
        ret = EliminateChargeSeparationOnHeteroatoms(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
            &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP,
            BNS_EDGE_FORBIDDEN_MASK);
        if (ret < 0)
        {
            goto exit_function;
        }
    }
    /*****************************************************************/
    /*         convert N#N(+)-N= into N(-)=N(+)=N-                   */
    /*****************************************************************/
    ret = RestoreNNNgroup(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /*****************************************************************/
    /*     convert Metal(q)-N(-)-O(-) Metal(q-2)-N=O (local change)  */
    /*****************************************************************/
    ret = FixMetal_Nminus_Ominus(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /*****************************************************************/
    /*         convert N(-)=C= into N#C-         -                   */
    /*****************************************************************/
    ret = RestoreCyanoGroup(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /*****************************************************************/
    /*         convert C(+)#N(+)- into C(-)#N(+)-                    */
    /*****************************************************************/
    ret = RestoreIsoCyanoGroup(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /*****************************************************************/
    /*         eliminate =N(V)= if possible                          */
    /*                    |                                          */
    /*****************************************************************/
    ret = EliminateNitrogen5Val3Bonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }

    /*****************************************************************/
    /*                    |      |                                   */
    /*         convert   -S- to =S= if possible                      */
    /*                    |      |                                   */
    /*****************************************************************/
    ret = Convert_SIV_to_SVI(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }

    /*****************************************************************/
    /*                  =N(+)=O     =N-O(-)                          */
    /*         convert           => if possible                      */
    /*                  Metal(q)    Metal(q+2)                       */
    /*****************************************************************/
    ret = PlusFromDB_N_DB_O_to_Metal(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }

    /*****************************************************************/
    /*  forbidden edges prevents required in InChI tautomerism       */
    /*  incorrectly restored mobile H mix separate tautomeric groups */
    /*  because an edge may not become forbidden                     */
    /* note: removes this 'forbidden_edge' bit from ALL edges        */
    /*****************************************************************/
    ret = MoveMobileHToAvoidFixedBonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);

    if (ret < 0)
    {
        goto exit_function;
    }
    /**************************************************************************/
    /* 2. Mobile H endpoint has radical on it (typical for wrong P(VI)(=O)3OH */
    /* djb-rwth: removing redundant code */
    if (pStruct->iMobileH == TAUT_NON)
    {
        ret = RemoveRadFromMobileHEndpointFixH(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
            &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    }
    else
    {
        ret = RemoveRadFromMobileHEndpoint(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
            &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    }
    if (ret < 0)
    {
        goto exit_function;
    }
    /* djb-rwth: removing redundant code */
    /**************************************************************/
    /* make bonds between a charged heteroatom and a metal single */
    ret = MakeSingleBondsMetal2ChargedHeteroat(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /**************************************************************/
    /* move (+) charges to >N- and other centerpoints             */
    ret = MoveChargeToMakeCenerpoints(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }

    /**************************************************************************/
    /* Find and eliminate false Mobile-H groups: Cl(=O)3(-O(-)) => Cl(-)(=O)4 */
    ret = MoveChargeToRemoveCenerpoints(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /**************************************************************************/
    /* Find A=X< where all bonds to X except A=X are marked as stereogenic    */
    /* make bonds A=X single                                                  */
    ret = CheckAndRefixStereobonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /**************************************************************************/
    /* In Reconnected structure change 'salt bonds' to 'coordination bonds    */
    /* for example, M-O-C=  ->  M(+)-O(-)-C=                                  */
    /* Defect: instead of NH2-C=O(+)-M it will restore NH2(+)=C-O(-)-M(+)     */
    /* However, in this release metal-organic compounds do not get much care  */
    ret = SaltBondsToCoordBonds(pBNS, pBD, pStruct, at, at2, pVA, pTCGroups,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP);
    if (ret < 0)
    {
        goto exit_function;
    }
    /**************************************************************************/
    /* Normalize the structure and compare t-groups and stereobonds           */
    ret = NormalizeAndCompare(pCG, ic, ip, sd, pBNS, pBD, pStruct, at, at2, at3, pVA, pTCGroups, pInChI, num_inp, bHasSomeFixedH,
        &nNumRunBNS, &nTotalDelta, BNS_EDGE_FORBIDDEN_TEMP, BNS_EDGE_FORBIDDEN_MASK);
    if (ret < 0)
    {
        goto exit_function;
    }
    /**************************************************************************/
    /* Create InChI out of the restored structure                             */


    /*ret = nTotalDelta;*/

exit_function:

    pStruct->at = at;
    pStruct->at2 = at2;
    at2 = NULL;
    AllocEdgeList(&CarbonChargeEdges, EDGE_LIST_FREE);
    AllocEdgeList(&MetalCarbonEdges, EDGE_LIST_FREE);
    AllocEdgeList(&Nplus2BondsEdges, EDGE_LIST_FREE);
    if (at2)
    {
        inchi_free(at2);
    }
    if (at3)
    {
        inchi_free(at3);
    }

    return ret;
}


/****************************************************************************/
int RestoreAtomMakeBNS(INCHI_CLOCK* ic, CANON_GLOBALS* pCG,
    ICHICONST INPUT_PARMS* ip,
    STRUCT_DATA* sd,
    StrFromINChI* pStruct,
    int iComponent,
    int iAtNoOffset,
    INChI* pInChI[],
    const char* szCurHdr,
    long num_inp,
    int bHasSomeFixedH)
{
    int i, j, ret = 0, ret2;
    /*int nDelta, nTotalDelta;*/
    VAL_AT* pVA = NULL;
    VAL_AT    va1;
    int    num_at = pStruct->num_atoms;
    inp_ATOM* at = pStruct->at;
    ALL_TC_GROUPS   TCGroups;
    ALL_TC_GROUPS* pTCGroups = &TCGroups;
    int            nAddEdges2eachAtom = 2, nAddVertices = 0;

    BFS_Q bfsq;

    /* BNS creation */
    BN_STRUCT* pBNS = NULL;
    BN_DATA* pBD = NULL;
    int            nNum_changed_bonds = 0;
    int            bTreatMoreAtomsAsMetals = 0, bSecondPassNewMetals = 0;
    int            nMaxAddAtoms = 2, nMaxAddEdges = 2, max_altp = BN_MAX_ALTP;

    memset(pTCGroups, 0, sizeof(pTCGroups[0])); /* djb-rwth: memset_s C11/Annex K variant? */
    for (i = 0; i < NUM_TCGROUP_TYPES; i++)
    {
        pTCGroups->nGroup[i] = TCG_None; /* unassigned */
    }
    pTCGroups->iComponent = iComponent;
    pTCGroups->iAtNoOffset = iAtNoOffset;

    if (num_at == 1)
    {
        /* single atom -- no bonds to restore */
        inp_ATOM* at2 = (inp_ATOM*)inchi_malloc(sizeof(at2[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */
        inp_ATOM* at3 = (inp_ATOM*)inchi_malloc(sizeof(at3[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */
        pStruct->at2 = at2;
        at[0].charge = pInChI[0]->nTotalCharge;
        if (at2)
        {
            memcpy(at2, at, sizeof(at2[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */
        }
        if (!at2 || !at3)
        {
            if (at3) inchi_free(at3);
            return RI_ERR_ALLOC;
        }
        ret = MakeOneInChIOutOfStrFromINChI(pCG, ic, ip, sd, pStruct, pStruct->at2, at3, pTCGroups);
        /* clean up */
        for (i = 0; i < TAUT_NUM; i++)
        {
            Free_INChI(&pStruct->pOneINChI[i]);
            Free_INChI_Aux(&pStruct->pOneINChI_Aux[i]);
            FreeInpAtomData(pStruct->pOne_norm_data[i]);
            if (pStruct->pOne_norm_data[i])
            {
                inchi_free(pStruct->pOne_norm_data[i]);
                pStruct->pOne_norm_data[i] = NULL;
            }
        }
        /* djb-rwth: fixing oss-fuzz issue #69602 */
        /* free_t_group_info(&pStruct->One_ti); */
        inchi_free(at3);

        return ret;
    }

    AllocBfsQueue(&bfsq, BFS_Q_CLEAR, 0);
    if (!(pVA = (VAL_AT*)inchi_calloc(num_at, sizeof(pVA[0]))))
    {
        ret = RI_ERR_ALLOC;
        goto exit_function;
    }
    pStruct->pVA = pVA;
    memset(&va1, 0, sizeof(va1)); /* djb-rwth: memset_s C11/Annex K variant? */
    pTCGroups->total_charge = pInChI[0]->nTotalCharge;
    if (0 > (ret = AllocBfsQueue(&bfsq, num_at, 0 /* min ring size undefined */)))
    {
        goto exit_function;
    }
    pStruct->pbfsq = &bfsq;

    if (pStruct->iMobileH == TAUT_NON && pInChI[1] && pInChI[1]->nNumberOfAtoms > 1 &&
        (ret = FillOutpStructEndpointFromInChI(pInChI[1], &pStruct->endpoint)))
    {
        goto exit_function;
    }

    /* mark metal atoms; find min ring sizes for atoms that have 2 bonds */
    for (i = 0; i < num_at; i++)
    {
        pVA[i].cNumValenceElectrons = get_sp_element_type(at[i].el_number, &j);
        pVA[i].cPeriodicRowNumber = j;
        pVA[i].cPeriodicNumber = at[i].el_number;
        pVA[i].cNumValenceElectrons--; /* = -1 d- and f- metals, 0 for H, 1 for Na, 2 for Mg,.. = (ATYPE_Xx-1)  */

        if (is_el_a_metal(at[i].el_number))
        {
            if (pStruct->pSrm->bStereoRemovesMetalFlag)
            {
                /* treat metal as non-metal if it is stereogenic or has a stereobond */
                pVA[i].cMetal = !(at[i].p_parity || at[i].sb_parity[0]);
            }
            else
            {
                pVA[i].cMetal = 1;
            }
        }
        if (at[i].valence == 2 && !at[i].num_H)
        {
            pVA[i].cMinRingSize = is_bond_in_Nmax_memb_ring(at, i, 0, bfsq.q, bfsq.nAtomLevel,
                bfsq.cSource, 99 /* max ring size */);
        }
        else
        {
            pVA[i].cMinRingSize = 0;
        }
    }
    /* AllocBfsQueue( &bfsq, BFS_Q_FREE, 0 ); */

repeat_for_new_metals:
    /* set valences for the first time; find ChargeValence structures for each atom */
    for (i = 0; i < num_at; i++)
    {
        /* get additional fictitious atoms information */
        pVA[i].cInitFreeValences = 0;

        ret = GetAtomRestoreInfo(pCG, at, i, pVA, pStruct->pSrm, pStruct->bMobileH, pStruct->endpoint);

        if (ret < 0)
        {
            goto exit_function;
        }
        if (ret == TREAT_ATOM_AS_METAL && !bSecondPassNewMetals && !pVA[i].cMetal)
        {
            if (pStruct->pSrm->bStereoRemovesMetalFlag)
            {
                /* treat metal as non-metal if it is stereogenic or has a stereobond */
                pVA[i].cMetal = !(at[i].p_parity || at[i].sb_parity[0]);
            }
            else
            {
                pVA[i].cMetal = 1;
            }
            if (pVA[i].cMetal)
            {
                bTreatMoreAtomsAsMetals++;
            }
        }
        pTCGroups->charge_on_atoms += pVA[i].cInitCharge;
    }
    if (bTreatMoreAtomsAsMetals && !bSecondPassNewMetals)
    {
        for (i = 0; i < num_at; i++)
        {
            /* clear all members of pVA[i] except two */
            pTCGroups->charge_on_atoms -= pVA[i].cInitCharge;
            va1.cMetal = pVA[i].cMetal;
            va1.cMinRingSize = pVA[i].cMinRingSize;
            va1.cNumValenceElectrons = pVA[i].cNumValenceElectrons;
            va1.cPeriodicRowNumber = pVA[i].cPeriodicRowNumber;
            va1.cPeriodicNumber = pVA[i].cPeriodicNumber;
            pVA[i] = va1;
        }
        bSecondPassNewMetals = 1;
        goto repeat_for_new_metals;
    }

    /* count atoms, bonds, additional edges and vertices in ChargeValence structures and t-groups */
    ret = nCountBnsSizes(at, num_at, nAddEdges2eachAtom, nAddVertices, &pStruct->ti,
        pVA, pStruct->pSrm, pTCGroups);
    if (ret < 0)
    {
        goto exit_function;
    }

    /* find and count groups; add counts of all other vertices to be created */
    ret = nAddSuperCGroups(pTCGroups);
    if (ret < 0)
    {
        goto exit_function;
    }

    /* create the BNS and fill it with all real atoms */
    pBNS = AllocateAndInitTCGBnStruct(pStruct, pVA, pTCGroups,
        nMaxAddAtoms, nMaxAddEdges, max_altp, &nNum_changed_bonds);
    if (!pBNS)
    {
        ret = BNS_OUT_OF_RAM;
        goto exit_function;
    }
    /* add t-groups to the BNS */
    ret = AddTGroups2TCGBnStruct(pBNS, pStruct, pVA, pTCGroups, nMaxAddEdges);
    if (ret < 0)
    {
        goto exit_function;
    }

    /* add c-groups to the BNS; adjust charges */
    ret = AddCGroups2TCGBnStruct(pBNS, pStruct, pVA, pTCGroups, nMaxAddEdges);
    if (ret < 0)
    {
        goto exit_function;
    }

    pBNS->ulTimeOutTime = NULL;             /* v. 1.05 */
    pBNS->ic = ic;                          /* v. 1.05 */

    /* allocate BNData */
    pBD = AllocateAndInitBnData(pBNS->max_vertices + pBNS->max_vertices / 2);
    if (!pBD)
    {
        ret = BNS_OUT_OF_RAM;
        goto exit_function;
    }
    CheckBnsConsistency(pStruct, pBNS, pVA, pTCGroups, 0);

    /* restore bonds & charges */
    ret = RunBnsRestore1(pCG, ic, ip, sd, pBNS, pBD, pStruct, pVA, pTCGroups, pInChI, num_inp, bHasSomeFixedH);
    if (ret < 0)
    {
        goto exit_function;
    }

    ret = CheckBnsConsistency(pStruct, pBNS, pVA, pTCGroups, 1);
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
    if (ret)
    {
        fprintf(stdout, "Msg for: %ld %s comp=%d %c%c\n", num_inp, (szCurHdr && szCurHdr[0]) ? szCurHdr : "", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F');
    }
    if (pStruct->iMobileH == TAUT_YES && pStruct->nNumRemovedProtons)
    {
        fprintf(stdout, "REMOVED_PROTONS%+d %ld %s\n", pStruct->nNumRemovedProtons, num_inp, (szCurHdr && szCurHdr[0]) ? szCurHdr : "");
        /*pStruct->bExtract |= EXTRACT_STRUCT_NUMBER;*/
    }
    if (pStruct->bExtract & EXTRACT_STRUCT_NUMBER)
    {
        fprintf(stdout, "EXTRACT: %ld: %s\n", num_inp, (szCurHdr && szCurHdr[0]) ? szCurHdr : "");
    }
#endif
#endif
    {  /* create the final structure in pStruct->at2 */
        inp_ATOM* at_tmp = pStruct->at;
        pStruct->at = pStruct->at2;
        memcpy(pStruct->at, at_tmp, sizeof(pStruct->at[0]) * ((long long)pStruct->num_atoms + (long long)pStruct->num_deleted_H)); /* djb-rwth: cast operators added */
        ret2 = CopyBnsToAtom(pStruct, pBNS, pVA, pTCGroups, 1);
        pStruct->at2 = pStruct->at;
        pStruct->at = at_tmp;
        if (ret2 < 0)
        {
            ret = ret2;
        }
    }

exit_function:

    pStruct->pbfsq = NULL;
    AllocBfsQueue(&bfsq, BFS_Q_FREE, 0);

    pBD = DeAllocateBnData(pBD); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */
    pBNS = DeAllocateBnStruct(pBNS); /* djb-rwth: ignoring LLVM warning: variable used to store function return value */
    /*
    if ( pVA ) inchi_free( pVA );
    */
    if (pTCGroups->pTCG) inchi_free(pTCGroups->pTCG);

    return ret;
}


/****************************************************************************/
int OneInChI2Atom(INCHI_CLOCK* ic,
    CANON_GLOBALS* pCG,
    ICHICONST INPUT_PARMS* ip_inp,
    STRUCT_DATA* sd,
    const char* szCurHdr,
    long num_inp,
    StrFromINChI* pStruct,
    int iComponent,
    int iAtNoOffset,
    int bHasSomeFixedH,
    INChI* pInChI[])
{
    int ret;
    INPUT_PARMS* ip, ip_loc;

    ip_loc = *ip_inp;
    ip = &ip_loc;

    sd->pStrErrStruct[0] = '\0';
    ret = RestoreAtomConnectionsSetStereo(pStruct, iComponent, iAtNoOffset, pInChI[0], pInChI[1]);
    if (ret < 0)
    {
        goto exit_function;
    }
    ret = SetStereoBondTypesFrom0DStereo(pStruct, pInChI[0]);
    if (ret < 0)
    {
        goto exit_function;
    }
    ret = ReconcileAllCmlBondParities(pStruct->at, pStruct->num_atoms, 0);
    if (ret < 0)
    {
        goto exit_function;
    }

    /* main InChI restore function */
    ret = RestoreAtomMakeBNS(ic, pCG, ip, sd, pStruct, iComponent, iAtNoOffset, pInChI, szCurHdr, num_inp, bHasSomeFixedH);

#ifndef COMPILE_ANSI_ONLY
    if ((pStruct->num_inp_actual > 0 ? pStruct->num_inp_actual : num_inp) >= ip->first_struct_number &&
        ((/*ret > 0 &&*/ ip->bDisplayIfRestoreWarnings) && pStruct->pXYZ))
    {
        inchiTime     ulTStart;
        InchiTimeGet(&ulTStart);
        DisplayRestoredComponent(pCG, pStruct, iComponent, iAtNoOffset, pInChI[0], szCurHdr);
        sd->ulStructTime -= InchiTimeElapsed(ic, &ulTStart); /* subtract display time */
    }
#endif

    if (ret < 0)
    {
        goto exit_function;
    }
    if ((pStruct->num_inp_actual ? pStruct->num_inp_actual : num_inp) >= ip->first_struct_number && ret >= 0)
    {
        /* remove t-group markings and increment zero-order bonds,
           otherwise MakeInChIOutOfStrFromINChI2() woild fail */
           /* --- moved to MakeInChIOutOfStrFromINChI2 ---
           IncrZeroBondsAndClearEndpts(pStruct->at2, pStruct->num_atoms, iComponent+1);
           CopySt2At( pStruct->at2, pStruct->st, pStruct->num_atoms );
           */
           /* include all restored structure features in pStruct->at2 */
           /* make full InChI out of pStruct->at2, pStruct->num_atoms */
           /***************************************************************************************/
           /* !!! pStruct->One_InChI etc. were removed at the exit from NormalizeAndCompare() !!! */
           /***************************************************************************************/
        if (bHasSomeFixedH && pStruct->iInchiRec == INCHI_REC && pStruct->iMobileH == TAUT_YES &&
            !pStruct->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC))
        {
            /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */
            ip->nMode |= REQ_MODE_BASIC;
        }

        ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct, iComponent, iAtNoOffset, num_inp);

        if (ret >= 0)
        {
            ;
        }
#if ( bRELEASE_VERSION == 0 )
#ifndef TARGET_API_LIB
        else
        {
            fprintf(stdout, "\nERROR in MakeInChI-1: %ld %s Comp:%d %c%c Err:%d\n", num_inp,
                szCurHdr ? szCurHdr : "???", iComponent, pStruct->iInchiRec ? 'R' : 'D', pStruct->iMobileH ? 'M' : 'F', ret);
        }
#endif
#endif
    }

exit_function:

    return ret;
}


/****************************************************************************/
int MakeProtonComponent(StrFromINChI* pStruct, int iComponent, int num_prot)
{
    inp_ATOM* at = NULL;
    int        i;

    if (num_prot <= 0)
    {
        return 0;
    }
    /* allocate */
    pStruct->at = (inp_ATOM*)inchi_calloc(num_prot, sizeof(pStruct->at[0]));
    pStruct->at2 = (inp_ATOM*)inchi_calloc(num_prot, sizeof(pStruct->at2[0]));
    if (!pStruct->at || !pStruct->at2)
    {
        return 0;
    }
    /* create protons */
    at = pStruct->at;
    /* fill out proton atom info */
    for (i = 0; i < num_prot; i++)
    {
        strcpy(at[i].elname, "H");
        at[i].el_number = EL_NUMBER_H;
        at[i].orig_at_number = i + 1;
        /*
        at[i].orig_compt_at_numb = i + 1;
        at[i].component = i + 1;
        */
        at[i].charge = 1;
    }
    memcpy(pStruct->at2, at, num_prot * sizeof(pStruct->at2[0]));
    pStruct->bDeleted = 0;
    pStruct->num_atoms = num_prot;
    pStruct->bMobileH = TAUT_YES;
    pStruct->iMobileH = TAUT_YES;

    return num_prot;
}


/****************************************************************************/
int AddRemProtonsInRestrStruct(INCHI_CLOCK* ic,
    CANON_GLOBALS* pCG,
    ICHICONST INPUT_PARMS* ip_inp,
    STRUCT_DATA* sd, long num_inp,
    int bHasSomeFixedH,
    StrFromINChI* pStruct,
    int num_components,
    StrFromINChI* pStructR,
    int num_componentsR,
    NUM_H* nProtonsToBeRemovedByNormFromRevrs,
    int* recmet_change_balance)
{
    /* on entry and exit, all at[i].num_H do not include isotopic H  and explicit terminal H are connected */
    int  iComp, q, ret = 0;
    int      num_atoms, num_deleted_H, num_tg, num_changed, num_deleted_components; /* djb-rwth: removing redundant variables */
    inp_ATOM* at;
    INPUT_PARMS* ip, ip_loc;
    int      num_prot = *nProtonsToBeRemovedByNormFromRevrs;
    int      delta_recmet_prot, num_prot_prev, bAccumulateChanges = 0, nNumProtAddedByRevrs;
    INChI_Aux* pINChI_Aux;
    INCHI_MODE bNormalizationFlags;
    int        nChargeRevrs, nChargeInChI;

    if (!num_prot)
    {
        return 0;
    }
    delta_recmet_prot = 0;
    num_changed = 0;
    num_deleted_components = 0;
    ip_loc = *ip_inp;
    ip = &ip_loc;
    /*----------------------------------------------------------------------------------
    nLink < 0 && num_componentsR > 0 => This is a Disconnected structure component; it is
                                        same as already processed reconnected one
                                        Do no preicess it

    nLink > 0 && num_componentsR > 0 => This is a Disconnected structure component;
    (should not happen)                 It it is a result of (nLink-1)th Reconeected
                                        component disconnection (NOT IMPLEMENTED YET)

    nLink = 0                        => Process this component. It is either a reconnected
                                        component, or a result of a disconnection (for now)

    nLink > 0 && num_componentsR = 0 => This is a Reconnected component that is same as
                                        a disconnected one that will not be processed.
                                        Process and save charge delta.
    -----------------------------------------------------------------------------------*/

    for (iComp = 0; iComp < num_components && num_prot; iComp++)
    {
        bAccumulateChanges = 0;
        if (pStruct[iComp].nLink < 0 && num_componentsR > 0)
        {
            /* check */
            q = -(pStruct[iComp].nLink + 1);
            if (!pStructR || !num_componentsR || q >= num_componentsR || pStructR[q].nLink != (iComp + 1))
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            continue; /* Disconnected structure component has already been processed as a Reconnected one */
        }

        at = pStruct[iComp].at2;
        num_atoms = pStruct[iComp].num_atoms;
        num_deleted_H = pStruct[iComp].num_deleted_H; /* djb-rwth: removing redundant code */
        bAccumulateChanges = (pStruct[iComp].nLink > 0 && !num_componentsR);
        nChargeRevrs = pStruct[iComp].nChargeRevrs;
        nChargeInChI = pStruct[iComp].nChargeInChI;
        num_deleted_components += (0 != pStruct[iComp].bDeleted);
        if (!at || !num_atoms)
        {
            continue;
        }
        /* find whether it is a reconnected structure */
        q = bRevInchiComponentExists(pStruct + iComp, INCHI_REC, TAUT_YES, 0) ? INCHI_REC : INCHI_BAS;
        /*
        q = pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC] &&
            pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] &&
            pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms? INCHI_REC : INCHI_BAS;
        */
        pINChI_Aux = pStruct[iComp].RevInChI.pINChI_Aux[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */
        /*nNumProtAddedByRevrs = pINChI_Aux->nNumRemovedProtons;*/
        nNumProtAddedByRevrs = -pStruct[iComp].nNumRemovedProtonsByRevrs;
        bNormalizationFlags = pINChI_Aux->bNormalizationFlags;
        num_tg = pINChI_Aux->nNumberOfTGroups;


        /* disconnect all explicit H and add the number of implicit iso H and all explicit terminal H to the number of implicit H */
        if (0 > (ret = DisconnectedConnectedH(at, num_atoms, num_deleted_H)))
        {
            goto exit_function;
        }
        num_prot_prev = num_prot;
        ret = AddRemoveProtonsRestr(at, num_atoms, &num_prot, nNumProtAddedByRevrs,
            bNormalizationFlags, num_tg, nChargeRevrs, nChargeInChI);

        pStruct[iComp].bPostProcessed = ret;
        num_changed += (ret > 0);
        if (ret < 0)
        {
            goto exit_function;
        }
        if (ret > 0)
        {
            /* recalculate InChI; it will reconnect at */
            StrFromINChI* pStruct1 = pStruct + iComp;
            INCHI_MODE    nMode = ip->nMode;
            FreeAllINChIArrays(pStruct1->RevInChI.pINChI,
                pStruct1->RevInChI.pINChI_Aux,
                pStruct1->RevInChI.num_components);

            if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES &&
                !pStruct1->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC))
            {
                /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */
                ip->nMode |= REQ_MODE_BASIC;
            }
            /* calls ConnectDisconnectedH(...): subtracts number of implicit iso H from implicit H */

            ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct1, 0, 0, num_inp);

            ip->nMode = nMode;
            if (ret < 0)
            {
                goto exit_function;
            }
        }
        else
        {
            /* reconnect disconnected terminal H and subtracts number of implicit iso H from implicit H */
            if (0 > (ret = ConnectDisconnectedH(at, num_atoms, num_deleted_H)))
            {
                goto exit_function;
            }
        }
        if (bAccumulateChanges && recmet_change_balance)
        {
            /* processed Reconnected layer component that is also present in Disconnected layer */
            delta_recmet_prot += num_prot - num_prot_prev;
        }
    }

    iComp = num_components - 1;
    if (!bHasSomeFixedH && num_prot > 0 && 1 == num_deleted_components && iComp >= 0 && pStruct[iComp].bDeleted)
    {
        /* add bare protons to the deleted Mobile-H component; undelete the component */
        num_prot_prev = num_prot;
        if (!MakeProtonComponent(pStruct + iComp, iComp, num_prot))
        {
            goto exit_function;
        }
        else
        {
            /* recalculate InChI; it will reconnect at */
            StrFromINChI* pStruct1 = pStruct + iComp;
            INCHI_MODE    nMode = ip->nMode;
            num_changed++;
            num_prot = 0;
            FreeAllINChIArrays(pStruct1->RevInChI.pINChI,
                pStruct1->RevInChI.pINChI_Aux,
                pStruct1->RevInChI.num_components);

            if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES &&
                !pStruct1->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC))
            {
                /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */
                ip->nMode |= REQ_MODE_BASIC;
            }
            /* Although MakeInChIOutOfStrFromINChI2() calls ConnectDisconnectedH(...) */
            /* to subtracts number of implicit iso H from implicit H */
            /* this CANNOT have any effect on the deleted H component */

            ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct1, 0, 0, num_inp);

            ip->nMode = nMode;
            if (ret < 0)
            {
                goto exit_function;
            }
            if (bAccumulateChanges && recmet_change_balance)
            {
                /* processed Reconnected layer component that is also present in Disconnected layer */
                delta_recmet_prot += num_prot - num_prot_prev;
            }
        }
    }
    *nProtonsToBeRemovedByNormFromRevrs = num_prot;
    if (recmet_change_balance)
    {
        *recmet_change_balance = delta_recmet_prot;
    }

exit_function:

    return ret < 0 ? ret : num_changed;
}


/****************************************************************************/
int AddRemIsoProtonsInRestrStruct(INCHI_CLOCK* ic,
    CANON_GLOBALS* pCG,
    ICHICONST INPUT_PARMS* ip_inp,
    STRUCT_DATA* sd,
    long num_inp,
    int bHasSomeFixedH,
    StrFromINChI* pStruct,
    int num_components,
    StrFromINChI* pStructR,
    int num_componentsR,
    NUM_H pProtonBalance[],
    NUM_H recmet_change_balance[])
{
    /* on entry and exit, all at[i].num_H do not include isotopic H and explicit terminal H are connected */
    int  iComp, q, k, ret = 0, bNotEmpty;
    int      num_atoms, num_deleted_H, num_tg, num_changed; /* djb-rwth: removing redundant variables */
    inp_ATOM* at;
    NUM_H    num_prot[NUM_H_ISOTOPES], delta_recmet_prot[NUM_H_ISOTOPES], num_prot_prev[NUM_H_ISOTOPES];
    int      bAccumulateChanges;
    INChI_Aux* pINChI_Aux;
    /* djb-rwth: removing redundant variables */
    INPUT_PARMS* ip, ip_loc;

    ip_loc = *ip_inp;
    ip = &ip_loc;

    memcpy(num_prot, pProtonBalance, sizeof(num_prot));
    for (bNotEmpty = 0, k = 0; k < NUM_H_ISOTOPES; k++)
    {
        bNotEmpty |= num_prot[k];
    }
    if (!bNotEmpty)
    {
        return 0;
    }
    memset(delta_recmet_prot, 0, sizeof(delta_recmet_prot)); /* djb-rwth: memset_s C11/Annex K variant? */
    num_changed = 0;
    /*----------------------------------------------------------------------------------
    nLink < 0 && num_componentsR > 0 => This is a Disconnected structure component; it is
                                        same as already processed reconnected one
                                        Do no process it

    nLink > 0 && num_componentsR > 0 => This is a Disconnected structure component;
    (should not happen)                 It it is a result of (nLink-1)th Reconeected
                                        component disconnection (NOT IMPLEMENTED YET)

    nLink = 0                        => Process this component. It is either a reconnected
                                        component, or a result of a disconnection (for now)

    nLink > 0 && num_componentsR = 0 => This is a Reconnected component that is same as
                                        a disconnected one that will not be processed.
                                        Process and save charge delta.
    -----------------------------------------------------------------------------------*/

    for (iComp = 0; iComp < num_components && num_prot; iComp++) /* djb-rwth: the condition will always evaluate to true only if pProtonBalance is not NULL */
    {
        /* djb-rwth: removing redundant code */
        if (pStruct[iComp].nLink < 0 && num_componentsR > 0)
        {
            /* check */
            q = -(pStruct[iComp].nLink + 1);
            if (!pStructR || !num_componentsR || q >= num_componentsR || pStructR[q].nLink != (iComp + 1))
            {
                ret = RI_ERR_PROGR;
                goto exit_function;
            }
            continue; /* Disconnected structure component has already been processed as a Reconnected one */
        }

        at = pStruct[iComp].at2;
        num_atoms = pStruct[iComp].num_atoms;
        num_deleted_H = pStruct[iComp].num_deleted_H; /* djb-rwth: removing redundant code */
        bAccumulateChanges = (pStruct[iComp].nLink > 0 && !num_componentsR);

        if (!at || !num_atoms)
        {
            continue;
        }
        /* find whether it is a reconnected structure */
        q = pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC] &&
            pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES] &&
            pStruct[iComp].RevInChI.pINChI_Aux[INCHI_REC][0][TAUT_YES]->nNumberOfAtoms ? INCHI_REC : INCHI_BAS;

        pINChI_Aux = pStruct[iComp].RevInChI.pINChI_Aux[q][0][TAUT_YES]; /* 0 = 1st component in RevInChI */
        /* djb-rwth: removing redundant code */
        num_tg = pINChI_Aux->nNumberOfTGroups;
        memcpy(num_prot_prev, num_prot, sizeof(num_prot_prev));

        /* pass CONNECTED explicit H to AddRemoveIsoProtonsRestr() for isotopic H addition */
        ret = AddRemoveIsoProtonsRestr(at, num_atoms, num_prot, num_tg);

        pStruct[iComp].bPostProcessed |= ret;
        num_changed += (ret > 0);
        if (ret < 0)
        {
            goto exit_function;
        }
        if (ret > 0)
        {
            StrFromINChI* pStruct1 = pStruct + iComp;
            INCHI_MODE    nMode = ip->nMode;
            /* recalculate InChI; MakeInChIOutOfStrFromINChI2() will reconnect explicit H */
            /* disconnect all explicit H and add the number of implicit iso H and all explicit terminal H to the number of implicit H */
            if (0 > (ret = DisconnectedConnectedH(at, num_atoms, num_deleted_H)))
            {
                goto exit_function;
            }
            FreeAllINChIArrays(pStruct1->RevInChI.pINChI,
                pStruct1->RevInChI.pINChI_Aux,
                pStruct1->RevInChI.num_components);
            if (bHasSomeFixedH && pStruct1->iInchiRec == INCHI_REC && pStruct1->iMobileH == TAUT_YES &&
                !pStruct1->bFixedHExists && !(ip->nMode & REQ_MODE_BASIC))
            {
                /* reconnected components without Fixed-H layer may produce 'tautomeric' fragments like Cl(-) */
                ip->nMode |= REQ_MODE_BASIC;
            }
            /* input: disconnected explicit H, output: connected explicit H */
            ret = MakeInChIOutOfStrFromINChI2(ic, pCG, ip, sd, pStruct1, 0, 0, num_inp);
            ip->nMode = nMode;
            if (ret < 0)
            {
                goto exit_function;
            }
        }
        /* the following was commented out 2007-08-28 by DT. Reason: it's a bug since H must be already connected */
        /* else {
            if ( 0 > ( ret = ConnectDisconnectedH( at, num_atoms, num_deleted_H ) ) ) {
                goto exit_function;
            }
        } */
        if (bAccumulateChanges)
        {
            /* processed Reconnected layer component that is also present in Disconnected layer */
            for (k = 0; k < NUM_H_ISOTOPES; k++)
            {
                delta_recmet_prot[k] += num_prot[k] - num_prot_prev[k];
            }
        }
    }

    memcpy(pProtonBalance, num_prot, sizeof(num_prot));
    if (recmet_change_balance)
    {
        memcpy(recmet_change_balance, delta_recmet_prot, sizeof(delta_recmet_prot));
    }

exit_function:

    return ret < 0 ? ret : num_changed;
}

#endif

Coverage Report

Created: 2026-05-30 06:15