/*
 * 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 <stdlib.h>
#include <string.h>

#include "mode.h"
#include "ichimain.h"
#include "ichi_io.h"

#include "bcf_s.h"

#include "logging.h"                   /*(@nnuk : Nauman Ullah Khan) :: Needed for logging functionality*/

/* Local */

int GetHillFormulaCounts( U_CHAR *nAtom,
                          S_CHAR *nNum_H,
                          int num_atoms,
                          AT_NUMB *nTautomer,
                          int lenTautomer,
                          int *pnum_C,
                          int *pnum_H,
                          int *pnLen,
                          int *pnNumNonHAtoms );
int MakeHillFormula( U_CHAR *nAtom,
                     int num_atoms,
                     char *szLinearCT,
                     int nLen_szLinearCT,
                     int num_C,
                     int num_H,
                     int *bOverflow );

#if ( FIX_DALKE_BUGS == 1 )
#else
char *AllocateAndFillHillFormula( INChI *pINChI );
#endif

int AddElementAndCount( const char *szElement,
                        int mult, char *szLinearCT,
                        int nLenLinearCT,
                        int *bOverflow );

int Copy2StereoBondOrAllene( INChI_Stereo *Stereo,
                             int *nNumberOfStereoCenters,
                             int *nNumberOfStereoBonds,
                             AT_STEREO_DBLE *LinearCTStereoDble,
                             AT_NUMB *pCanonOrd, AT_RANK *pCanonRank,
                             sp_ATOM *at,
                             int bIsotopic );

int CopyLinearCTStereoToINChIStereo( INChI_Stereo *Stereo,
                                     AT_STEREO_CARB *LinearCTStereoCarb,
                                     int nLenLinearCTStereoCarb,
                                     AT_STEREO_DBLE *LinearCTStereoDble,
                                     int nLenLinearCTStereoDble,
                                     AT_NUMB *pCanonOrd, AT_RANK *pCanonRank,
                                     sp_ATOM *at,
                                     int bIsotopic,
                                     AT_STEREO_CARB *LinearCTStereoCarbInv,
                                     AT_STEREO_DBLE *LinearCTStereoDbleInv,
                                     AT_NUMB *pCanonOrdInv,
                                     AT_RANK *pCanonRankInv );

int GetHillFormulaIndexLength( int count );

int MarkAmbiguousStereo( sp_ATOM *at,
                         inp_ATOM *norm_at,
                         int bIsotopic,
                         AT_NUMB *pCanonOrd,
                         AT_STEREO_CARB *LinearCTStereoCarb, int nLenLinearCTStereoCarb,
                         AT_STEREO_DBLE *LinearCTStereoDble, int nLenLinearCTStereoDble );

INCHI_MODE UnmarkAllUndefinedUnknownStereo( INChI_Stereo *Stereo, INCHI_MODE nUserMode );

int CleanCoord( MOL_COORD szCoord, int delim );



/****************************************************************************
    Print single-component Hill formula whole structure output.
****************************************************************************/
int MakeHillFormulaString( char *szHillFormula,
                           INCHI_IOS_STRING *strbuf,
                           int *bOverflow )
{
    int nUsedLength0 = strbuf->nUsedLength;
    if (szHillFormula && !*bOverflow)
    {
        if (-1 == inchi_strbuf_printf( strbuf, "%s", szHillFormula ))
        {
            *bOverflow |= 1;
            return  nUsedLength0 + 1;
        }
    }
    return ( strbuf->nUsedLength - nUsedLength0 );
}


/****************************************************************************
    MS Windows dependent: sprintf() is supposed to return the length
    of the output string.
    Carbon atoms are always first.
    Bridging hydrogen atoms are always last.
****************************************************************************/
int GetHillFormulaIndexLength( int count )
{
    char szCount[16];
    if (count > 1)
    {
        return sprintf(szCount, "%d", count);
    }

    return 0;
}


/****************************************************************************
    Estimate dimensions of Hill formula for single component
****************************************************************************/
int GetHillFormulaCounts( U_CHAR *nAtom,
                          S_CHAR *nNum_H,
                          int num_atoms,
                          AT_NUMB *nTautomer,
                          int lenTautomer,
                          int *pnum_C,
                          int *pnum_H,
                          int *pnLen,
                          int *pnNumNonHAtoms )
{
    char szElement[4];
    U_CHAR nPrevAtom = (U_CHAR) -2;
    int  bCarbon, bHydrogen, nElemLen, nFormLen, nNumNonHAtoms;
    int  mult, i, num_H, num_C;

    num_H = 0;
    num_C = 0;
    bCarbon = 0;
    bHydrogen = 0;
    nElemLen = 0;
    nFormLen = 0;
    mult = 0;
    nNumNonHAtoms = num_atoms;

    for (i = 0; i < num_atoms; i++)
    {
        if (nPrevAtom != nAtom[i])
        {
            if (mult)
            {
                if (bHydrogen)
                {
                    num_H += mult;
                }
                else if (bCarbon)
                {
                    num_C += mult;
                }
                else
                {
                    nFormLen += nElemLen;
                    nFormLen += GetHillFormulaIndexLength( mult );
                }
            }
            /*if (-1 == get_element_chemical_symbol( (int) nAtom[i], szElement ))*/
            if (-1 == get_element_or_pseudoelement_symbol( (int) nAtom[i], szElement ))
            {
                return -1;
            }
            mult = 1;
            nElemLen = (int) strlen( szElement );
            nPrevAtom = nAtom[i];
            bCarbon = !strcmp( szElement, "C" );
            bHydrogen = !strcmp( szElement, "H" );
            if (bHydrogen)
            {
                nNumNonHAtoms = i;
            }
        }
        else
        {
            mult++;
        }

        num_H += nNum_H[i];
    }

    /* NumGroups; ((NumAt+1, NumH, At1..AtNumAt),...) */

    if (nTautomer && lenTautomer > 0)
    {
        int num_groups = nTautomer[0];

        for (i = 1; i < lenTautomer && num_groups > 0; i += nTautomer[i] + 1, num_groups--)
        {
            num_H += nTautomer[i + 1];
        }
    }

    if (mult)
    {
        if (bHydrogen)
        {
            num_H += mult;
        }
        else if (bCarbon)
        {
            num_C += mult;
        }
        else
        {
            nFormLen += nElemLen;
            nFormLen += GetHillFormulaIndexLength( mult );
        }
    }

    if (num_C)
    {
        nFormLen += (int) strlen( "C" );
        nFormLen += GetHillFormulaIndexLength( num_C );
    }

    if (num_H)
    {
        nFormLen += (int) strlen( "H" );
        nFormLen += GetHillFormulaIndexLength( num_H );
    }

    *pnum_C = num_C;
    *pnum_H = num_H;
    *pnLen = nFormLen;
    *pnNumNonHAtoms = nNumNonHAtoms;

    return 0;
}


/****************************************************************************
 Add a portion to Hill formula for single component.
****************************************************************************/
int AddElementAndCount( const char *szElement, int mult, char *szLinearCT, int nLenLinearCT, int *bOverflow )
{
    char szMult[16];
    int len1, len2;
    if (mult > 0 && !*bOverflow && 0 < ( len1 = strlen( szElement ) ))
    {
        if (mult > 1)
        {
            len2 = sprintf(szMult, "%d", mult);
        }
        else
        {
            len2 = 0;
            szMult[0] = '\0';
        }
        if (len1 + len2 < nLenLinearCT)
        {
            memcpy(szLinearCT, szElement, len1);
            memcpy(szLinearCT + len1, szMult, (long long)len2 + 1); /*  adding zero termination */ /* djb-rwth: added cast operator */
            return len1 + len2;
        }
        else
        {
            ( *bOverflow )++;
        }
    }

    return 0;
}


/****************************************************************************
    Make Hill formula for single component.

    If num_C > 0 then nAtom does not contain C or H
    otherwise all elements are in alphabetic order
****************************************************************************/
int MakeHillFormula( U_CHAR *nAtom,
                     int num_atoms,
                     char *szLinearCT,
                     int nLen_szLinearCT,
                     int num_C,
                     int num_H,
                     int *bOverflow )
{
    char szElement[4];
    int  mult, compare2H;
    int  i, nLen, bOvfl;
    U_CHAR nPrevAtom;

    nLen = 0;
    mult = 0;
    bOvfl = 0;
    nPrevAtom = (U_CHAR) -2; /*  non-existent number */

    if (num_C)
    {
        nLen += AddElementAndCount( "C", num_C, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl );
        if (num_H)
        {
            nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl );
            num_H = 0;
        }
    }

    for (i = 0; i < num_atoms; i++)
    {

        if (nPrevAtom != nAtom[i])
        {
            if (mult)
            {
                nLen += AddElementAndCount( szElement, mult, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl );
            }
            mult = 1;
            /*if (-1 == get_element_chemical_symbol( (int) nAtom[i], szElement ))*/
            if (-1 == get_element_or_pseudoelement_symbol( (int) nAtom[i], szElement ))
            {
                return -1; /*  wrong element */
            }

            nPrevAtom = nAtom[i];
            if (!strcmp( "C", szElement ))
            {
                return -1;
            }
            compare2H = strcmp( "H", szElement );
            if (!compare2H)
            {
                return -1;
            }
            if (compare2H < 0 && num_H)
            {
                /*   H-atom should be located in front of szElement */
                nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl );
                num_H = 0;
            }
        }
        else
        {
            mult++;
        }
    }
    if (mult)
    {
        /*  the last element if any */
        nLen += AddElementAndCount( szElement, mult, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl );
    }
    if (num_H)
    {
        /*  if H has not been output... */
        nLen += AddElementAndCount( "H", num_H, szLinearCT + nLen, nLen_szLinearCT - nLen, &bOvfl );
    }
    *bOverflow |= ( 0 != bOvfl );

    return bOvfl ? nLen_szLinearCT + 1 : nLen;
}


/****************************************************************************
    Allocate space and produce Hill formula for single component
****************************************************************************/
char *AllocateAndFillHillFormula( INChI *pINChI )
{
    int num_C, num_H, nLen, nNumNonHAtoms, ret, bOverflow;
    char *pHillFormula = NULL;

    bOverflow = 0;

    if (!GetHillFormulaCounts( pINChI->nAtom,
        pINChI->nNum_H,
        pINChI->nNumberOfAtoms,
        pINChI->nTautomer,
        pINChI->lenTautomer,
        &num_C, &num_H,
        &nLen,
        &nNumNonHAtoms ))
    {

#if ( FIX_GAF_2019_2==1 )
        pHillFormula = (char*)inchi_calloc((long long )nLen + 1, sizeof(char)); /* djb-rwth: cast operator added */
#else
        pHillFormula = (char*)inchi_malloc(nLen + 1);
#endif

        if (pHillFormula)
        {

            ret = MakeHillFormula( pINChI->nAtom + num_C,
                                   nNumNonHAtoms - num_C,
                                   pHillFormula,
                                   nLen + 1,
                                   num_C, num_H,
                                   &bOverflow );

            if (ret != nLen || bOverflow)
            {
                inchi_free( pHillFormula );
                pHillFormula = NULL;
            }
        }
    }

    return pHillFormula;
}


/************************************************************************************/
/* Return value: 0 => copied to stereo bonds; 1=> Allene copied to stereocenters    */
/* on input nNumberOfStereoBonds==NULL means second call, use Stereo->...Inv        */
/************************************************************************************/
int Copy2StereoBondOrAllene( INChI_Stereo *Stereo,
                             int *nNumberOfStereoCenters,
                             int *nNumberOfStereoBonds,
                             AT_STEREO_DBLE *LinearCTStereoDble,
                             AT_NUMB *pCanonOrd,
                             AT_RANK *pCanonRank,
                             sp_ATOM *at,
                             int bIsotopic )
{
    int cumulene_len,
        j,
        next_j = 0 /* ordering number of the central allene atom */,
        next_neigh;
    AT_RANK
        at_num;
    int parity;

    if (pCanonOrd && pCanonRank)
    {
        j = pCanonOrd[(int) LinearCTStereoDble->at_num1 - 1];

        /* if allene then find the central atom, at[next_j] */

        if (bIsotopic)
        {
            cumulene_len = BOND_CHAIN_LEN( at[j].stereo_bond_parity2[0] );

            if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS || !at[j].stereo_bond_neighbor2[1] ))
            {
                next_j = at[j].neighbor[(int) at[j].stereo_bond_ord2[0]];

                for (cumulene_len = ( cumulene_len - 1 ) / 2; cumulene_len && 2 == at[next_j].valence; cumulene_len--)
                {
                    next_neigh = ( j == at[next_j].neighbor[0] );
                    j = next_j;
                    next_j = at[next_j].neighbor[next_neigh];
                }
                /* next_j is the central atom */
            }
            else
            {
                cumulene_len = -1; /* not an allene */
            }
        }
        else
        {
            cumulene_len = BOND_CHAIN_LEN( at[j].stereo_bond_parity[0] );

            if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS || !at[j].stereo_bond_neighbor[1] ))
            {
                next_j = at[j].neighbor[(int) at[j].stereo_bond_ord[0]];

                for (cumulene_len = ( cumulene_len - 1 ) / 2; cumulene_len && 2 == at[next_j].valence; cumulene_len--)
                {
                    next_neigh = ( j == at[next_j].neighbor[0] );
                    j = next_j;
                    next_j = at[next_j].neighbor[next_neigh];
                }
            }
            else
            {
                cumulene_len = -1; /* not an allene */
            }
        }

        if (!cumulene_len)
        {
            /* allene has been found; insert new stereocenter and parity */

            AT_NUMB *nNumber;
            S_CHAR  *t_parity;

            nNumber = nNumberOfStereoBonds ? Stereo->nNumber : Stereo->nNumberInv;
            t_parity = nNumberOfStereoBonds ? Stereo->t_parity : Stereo->t_parityInv;

            at_num = pCanonRank[next_j];
            parity = LinearCTStereoDble->parity;

            /* free room for the new stereocenter */
            for (j = 0; j < *nNumberOfStereoCenters && Stereo->nNumber[j] < at_num; j++)
            {
                ;
            }

            if (j < *nNumberOfStereoCenters)
            {
                memmove(nNumber + j + 1, nNumber + j, (*nNumberOfStereoCenters - (long long)j) * sizeof(nNumber[0])); /* djb-rwth: cast operator added */
                memmove(t_parity + j + 1, t_parity + j, (*nNumberOfStereoCenters - (long long)j) * sizeof(t_parity[0])); /* djb-rwth: cast operator added */
            }

            /* fill the new stereo center info */

            nNumber[j] = at_num;
            t_parity[j] = parity;
            ( *nNumberOfStereoCenters )++;
            return 1;
        }
    }

    /* Save the stereo bond info */

    if (nNumberOfStereoBonds)
    {
        j = *nNumberOfStereoBonds;
        Stereo->b_parity[j] = LinearCTStereoDble->parity;
        Stereo->nBondAtom1[j] = LinearCTStereoDble->at_num1;
        Stereo->nBondAtom2[j] = LinearCTStereoDble->at_num2;
        ( *nNumberOfStereoBonds )++;
    }

    return 0;
}


/***************************************************************************/
int CopyLinearCTStereoToINChIStereo( INChI_Stereo *Stereo,
                                     AT_STEREO_CARB *LinearCTStereoCarb,
                                     int nLenLinearCTStereoCarb,
                                     AT_STEREO_DBLE *LinearCTStereoDble,
                                     int nLenLinearCTStereoDble,
                                     AT_NUMB *pCanonOrd, AT_RANK *pCanonRank,
                                     sp_ATOM *at,
                                     int bIsotopic,
                                     AT_STEREO_CARB *LinearCTStereoCarbInv,
                                     AT_STEREO_DBLE *LinearCTStereoDbleInv,
                                     AT_NUMB *pCanonOrdInv, AT_RANK *pCanonRankInv )
{
    int n, i, nErrorCode = 0, len;
    int bAllene;
    int diff;
    int lenInv, bAlleneInv;

    /* Stereo centers */

    /* djb-rwth: fixing oss-fuzz issue #68271 */
    if (Stereo)
    {
        n = Stereo->nNumberOfStereoCenters = nLenLinearCTStereoCarb;

        for (i = 0; i < n; i++)
        {
            if (LinearCTStereoCarb) /* djb-rwth: fixing a NULL pointer dereference */
            {
                Stereo->nNumber[i] = LinearCTStereoCarb[i].at_num;
                Stereo->t_parity[i] = LinearCTStereoCarb[i].parity;
            }
            if (LinearCTStereoCarbInv) /* djb-rwth: fixing a NULL pointer dereference */
            {
                Stereo->nNumberInv[i] = LinearCTStereoCarbInv[i].at_num;
                Stereo->t_parityInv[i] = LinearCTStereoCarbInv[i].parity;
            }
        }

        /* Stereo bonds */

        n = nLenLinearCTStereoDble;
        lenInv = Stereo->nNumberOfStereoCenters;

        for (i = len = 0; i < n; i++)
        {
            bAllene =
                Copy2StereoBondOrAllene(Stereo,
                    &Stereo->nNumberOfStereoCenters,
                    &len,
                    LinearCTStereoDble + i,
                    pCanonOrd, pCanonRank,
                    at,
                    bIsotopic);

            bAlleneInv =
                Copy2StereoBondOrAllene(Stereo,
                    &lenInv,
                    NULL,
                    LinearCTStereoDbleInv + i,
                    pCanonOrdInv, pCanonRankInv,
                    at,
                    bIsotopic);

            /* make sure double bond stereo is identical in original and inverted geometry */
            /* Note: all allenes are AFTER double bonds in LinearCTStereoDble... */
            if (bAllene != bAlleneInv || (!bAllene &&
                CompareLinCtStereoDble(LinearCTStereoDble + i, 1,
                    LinearCTStereoDbleInv + i, 1))) /* djb-rwth: addressing LLVM warning */
            {
                /* double bond stereo Inv is NOT identical to Abs */
                nErrorCode = -4;
                goto exit_function;
            }
        }

        Stereo->nNumberOfStereoBonds = len;

        if (lenInv != Stereo->nNumberOfStereoCenters)
        {
            nErrorCode = -5; /* different number of stereo centers in Abs and Inv */
            goto exit_function;
        }


        /* compare inverted stereocenters to absolute */

        n = Stereo->nNumberOfStereoCenters;
        /* djb-rwth: removing redundant code */

        for (i = 0, diff = 0; i < n; i++)
        {
            if (Stereo->nNumberInv[i] != Stereo->nNumber[i])
            {
                diff = (Stereo->nNumberInv[i] > Stereo->nNumber[i]) ? 2 : -2;
                break; /* Abs != Inv */
            }
            if (Stereo->t_parityInv[i] != Stereo->t_parity[i])
            {
                diff = (Stereo->t_parityInv[i] > Stereo->t_parity[i]) ? 1 : -1;
                break; /* Abs != Inv */
            }
        }

        Stereo->nCompInv2Abs =
            (diff > 0) ? 1 : (diff < 0) ? -1 : 0;

        if (diff == -1 || diff == 1)
        {
            /* The first found difference was in parities */
            for (i = 0, diff = 0; i < n; i++)
            {
                if (Stereo->nNumberInv[i] != Stereo->nNumber[i])
                {
                    diff = 2; /* difference in stereo center numbering */
                    break;
                }

                /*  Parities can be only 1, 2, 3, 4. Therefore only mutually inverted pairs
                 *  (t_parityInv, t_parity) = (1,2) or (2,1) statisfy conditions
                 *  (t_parityInv != t_parity) && (t_parityInv + t_parity == 3)
                 */

                if (Stereo->t_parityInv[i] == Stereo->t_parity[i] ||
                    Stereo->t_parityInv[i] + Stereo->t_parity[i] != 3)
                {
                    diff = 1; /* parities are same or different and cannot be obtained by simple inversion */
                    break;
                }
            }
            Stereo->bTrivialInv = !diff;
        }
        else
        {
            Stereo->bTrivialInv = 0;
        }
    }
    else
    {
        nErrorCode = 1;
    }

exit_function:
    return nErrorCode;
}


/****************************************************************************/
int MarkAmbiguousStereo( sp_ATOM *at,
                         inp_ATOM *norm_at,
                         int bIsotopic,
                         AT_NUMB *pCanonOrd,
                         AT_STEREO_CARB *LinearCTStereoCarb,
                         int nLenLinearCTStereoCarb,
                         AT_STEREO_DBLE *LinearCTStereoDble,
                         int nLenLinearCTStereoDble )
{
    int n, i, j1, j2, num, mark_atom, mark_bond;

    if (!pCanonOrd)
    {
        return -1;
    }

    num = 0;

    n = nLenLinearCTStereoCarb;

    mark_atom = bIsotopic ? AMBIGUOUS_STEREO_ATOM_ISO : AMBIGUOUS_STEREO_ATOM;

    for (i = 0; i < n; i++)
    {
        /*  Mark ambiguous stereo centers (for displaying and "Ambiguous stereo" message) */
        if (ATOM_PARITY_NOT_UNKN( LinearCTStereoCarb[i].parity ) &&
             at[j1 = pCanonOrd[(int) LinearCTStereoCarb[i].at_num - 1]].bAmbiguousStereo)
        {
            at[j1].bAmbiguousStereo |= mark_atom;
            norm_at[j1].bAmbiguousStereo |= mark_atom;
            num++;
        }
    }

    n = nLenLinearCTStereoDble;

    mark_bond = bIsotopic ? AMBIGUOUS_STEREO_BOND_ISO : AMBIGUOUS_STEREO_BOND;

    for (i = 0; i < n; i++)
    {
        /*  Mark ambiguous stereo bonds or allenes (for displaying and "Ambiguous stereo" message) */

        if (ATOM_PARITY_WELL_DEF( LinearCTStereoDble[i].parity ))
        {
            j1 = pCanonOrd[(int) LinearCTStereoDble[i].at_num1 - 1];
            j2 = pCanonOrd[(int) LinearCTStereoDble[i].at_num2 - 1];

            if (at[j1].bAmbiguousStereo || at[j2].bAmbiguousStereo)
            {
                /* If it is an allene then mark the central atom only
                   because the bonds should not be marked to avoid misleading
                   message "Ambiguous stereo: bond(s)": Allene makes a stereocenter
                */

                int j1_parity = bIsotopic ? at[j1].stereo_bond_parity2[0] : at[j1].stereo_bond_parity[0];

                int cumulene_len = BOND_CHAIN_LEN( j1_parity ); /* 0 => double bond, 1 => allene, 2 => cumulene,..*/

                if (cumulene_len % 2 && ( 1 >= MAX_NUM_STEREO_BONDS ||
                    !( bIsotopic ? at[j1].stereo_bond_neighbor2[1] : at[j1].stereo_bond_neighbor[1] ) )
                    )
                {
                    /*  found an allene; locate its central atom */

                    int next_j, next_neigh;
                    int j = j1;

                    next_j = at[j].neighbor[bIsotopic ? at[j].stereo_bond_ord2[0] : at[j].stereo_bond_ord[0]];

                    for (cumulene_len = ( cumulene_len - 1 ) / 2;
                         cumulene_len && 2 == at[next_j].valence;
                         cumulene_len--)
                    {
                        next_neigh = ( j == at[next_j].neighbor[0] );
                        j = next_j;
                        next_j = at[next_j].neighbor[next_neigh];
                    }
                    /* next_j is the central atom */
                    if (2 == at[next_j].valence)
                    {
                        at[next_j].bAmbiguousStereo |= mark_atom;
                        norm_at[next_j].bAmbiguousStereo |= mark_atom;
                        num++;
                        continue; /* do not mark the cumulene "bond" endpoints */
                    }
                }

                /* Not an allene, mark double bond or cumulene end atoms */
                if (at[j1].bAmbiguousStereo)
                {
                    at[j1].bAmbiguousStereo |= mark_bond; /*  ??? */
                    norm_at[j1].bAmbiguousStereo |= mark_bond;
                    num++;
                }

                if (at[j2].bAmbiguousStereo)
                {
                    at[j2].bAmbiguousStereo |= mark_bond; /*  ??? */
                    norm_at[j2].bAmbiguousStereo |= mark_bond;
                    num++;
                }
            }
        }
    }

    return num;
}


/****************************************************************************/
INCHI_MODE UnmarkAllUndefinedUnknownStereo( INChI_Stereo *Stereo,
                                            INCHI_MODE nUserMode )
{
    INCHI_MODE nRet = 0;
    int   i, n;

    if (!Stereo || (Stereo && !Stereo->nNumberOfStereoCenters && !Stereo->nNumberOfStereoBonds)) /* djb-rwth: addressing LLVM warning */
    {
        return nRet;
    }

    /* Stereocenters */
    if (!Stereo->nCompInv2Abs &&
        ( n = Stereo->nNumberOfStereoCenters ) > 0 && ( nUserMode & REQ_MODE_SC_IGN_ALL_UU ))
    {

        for (i = 0; i < n && !ATOM_PARITY_WELL_DEF( Stereo->t_parity[i] ); i++)
        {
            ;
        }

        if (i == n)
        {
            Stereo->nNumberOfStereoCenters = 0;

            for (i = 0; i < n; i++)
            {
                Stereo->t_parity[i] = 0;
                Stereo->nNumber[i] = 0;
                Stereo->t_parityInv[i] = 0;
                Stereo->nNumberInv[i] = 0;
            }

            nRet |= REQ_MODE_SC_IGN_ALL_UU;
        }
    }

    /* Stereobonds */

    if (( n = Stereo->nNumberOfStereoBonds ) > 0 && ( nUserMode & REQ_MODE_SB_IGN_ALL_UU ))
    {
        for (i = 0; i < n && !ATOM_PARITY_WELL_DEF( Stereo->b_parity[i] ); i++)
        {
            ;
        }

        if (i == n)
        {
            Stereo->nNumberOfStereoBonds = 0;
            for (i = 0; i < n; i++)
            {
                Stereo->b_parity[i] = 0;
                Stereo->nBondAtom1[i] = 0;
                Stereo->nBondAtom2[i] = 0;
            }
            nRet |= REQ_MODE_SB_IGN_ALL_UU;
        }
    }

    return nRet;
}


#if ( defined(TARGET_API_LIB) )


/****************************************************************************/
void WriteCoord( char *str, double x )
{
    if (x < -9999999.9)
    {
        sprintf( str, "%10.2e", x );
    }
    else
    {
        if (x < -999999.99)
        {
            sprintf( str, "%10.2f", x );
        }
        else
        {
            if (x < -99999.999)
            {
                sprintf( str, "%10.3f", x );
            }
            else
            {
                if (x < 99999.9999)
                {
                    sprintf( str, "%10.4f", x );
                }
                else
                {
                    if (x < 999999.999)
                    {
                        sprintf( str, "%10.3f", x );
                    }
                    else
                    {
                        if (x < 9999999.99)
                        {
                            sprintf( str, "%10.2f", x );
                        }
                        else
                        {
                            if (x < 99999999.9)
                            {
                                sprintf( str, "%10.1f", x );
                            }
                            else
                            {
                                sprintf( str, "%10.3e", x );
                            }
                        }
                    }
                }
            }
        }
    }
}
#endif



/* used CANON_STAT members

    pCS->LinearCT
    pCS->LinearCTIsotopic
    pCS->LinearCTIsotopicStereoCarb
    pCS->LinearCTIsotopicStereoCarbInv
    pCS->LinearCTIsotopicStereoDble
    pCS->LinearCTIsotopicStereoDbleInv
    pCS->LinearCTIsotopicTautomer
    pCS->LinearCTStereoCarb
    pCS->LinearCTStereoCarbInv
    pCS->LinearCTStereoDble
    pCS->LinearCTStereoDbleInv
    pCS->nCanonOrd
    pCS->nCanonOrdIsotopic
    pCS->nCanonOrdIsotopicStereo
    pCS->nCanonOrdIsotopicStereoInv
    pCS->nCanonOrdIsotopicStereoTaut
    pCS->nCanonOrdIsotopicTaut
    pCS->nCanonOrdStereo
    pCS->nCanonOrdStereoInv
    pCS->nCanonOrdStereoTaut
    pCS->nCanonOrdTaut
    pCS->nLenCanonOrd
    pCS->nLenCanonOrdIsotopic
    pCS->nLenCanonOrdIsotopicStereo
    pCS->nLenCanonOrdIsotopicStereoTaut
    pCS->nLenCanonOrdIsotopicTaut
    pCS->nLenCanonOrdStereo
    pCS->nLenCanonOrdStereoTaut
    pCS->nLenCanonOrdTaut
    pCS->nLenLinearCTAtOnly
    pCS->nLenLinearCTIsotopic
    pCS->nLenLinearCTIsotopicStereoCarb
    pCS->nLenLinearCTIsotopicStereoDble
    pCS->nLenLinearCTIsotopicTautomer
    pCS->nLenLinearCTStereoCarb
    pCS->nLenLinearCTStereoDble
    pCS->nNum_H
    pCS->nNum_H_fixed
    pCS->nSymmRank
    pCS->nSymmRankIsotopic
    pCS->nSymmRankIsotopicTaut
    pCS->nSymmRankTaut
    pCS->t_group_info
    pCS->t_group_info->num_t_groups

*/


/****************************************************************************
    Serialization: one-component InChI
****************************************************************************/
int FillOutINChI( INChI *pINChI,
                  INChI_Aux *pINChI_Aux,
                  int num_atoms,
                  int num_at_tg,
                  int num_removed_H,
                  sp_ATOM *at,
                  inp_ATOM *norm_at,
                  CANON_STAT *pCS,
                  CANON_GLOBALS *pCG,
                  int bTautomeric,
                  INCHI_MODE nUserMode,
                  char *pStrErrStruct,
                  int bNoWarnings )
{
    int i, j, m, n, g, len, ii, ret = 0;

    AT_NUMB   *pSymmRank, *pOrigNosInCanonOrd, *pConstitEquNumb, *pCanonOrd = NULL, *pCanonOrdInv = NULL, *pCanonOrdTaut;
    T_GROUP_INFO     *t_group_info = pCS->t_group_info;
    T_GROUP *t_group;

    int nErrorCode = 0;
    AT_NUMB *pCanonRank, *pCanonRankInv; /* canonical ranks of the atoms or tautomeric groups */
    AT_NUMB *pCanonRankAtoms = NULL, *pSortOrd = NULL;
    AT_RANK nMinOrd;

    INChI_Stereo *Stereo;
    int          bUseNumberingInv = 0, bUseIsotopicNumberingInv = 0;

    INCHI_MODE    nStereoUnmarkMode;

    /*AT_NUMB  *pCanonOrdNonIso = NULL, *pCanonOrdIso = NULL;*/
    /*AT_NUMB  *nOrigAtNosInCanonOrdNonIso = NULL, *nOrigAtNosInCanonOrdIso = NULL;*/


    /*  Check for warnings */
    if (pCS->nLenLinearCTStereoCarb < 0 || pCS->nLenLinearCTStereoDble < 0 ||
         pCS->nLenCanonOrdStereo < 0 || pCS->nLenCanonOrdStereoTaut < 0)
    {
        nErrorCode |= WARN_FAILED_STEREO;
    }
    if (pCS->nLenLinearCTIsotopic < 0 || pCS->nLenLinearCTIsotopicTautomer < 0 ||
         pCS->nLenCanonOrdIsotopic < 0 || pCS->nLenCanonOrdIsotopicTaut < 0)
    {
        nErrorCode |= WARN_FAILED_ISOTOPIC;
    }
    if (pCS->nLenLinearCTIsotopicStereoCarb < 0 || pCS->nLenLinearCTIsotopicStereoDble < 0 ||
         pCS->nLenCanonOrdIsotopicStereo < 0 || pCS->nLenCanonOrdIsotopicStereoTaut < 0)
    {
        nErrorCode |= WARN_FAILED_ISOTOPIC_STEREO;
    }

    pCanonRankAtoms = (AT_NUMB *) inchi_calloc( (long long)num_at_tg + 1, sizeof( pCanonRankAtoms[0] ) ); /* djb-rwth: cast operator added */

    pSortOrd = (AT_NUMB *) inchi_calloc( (long long)num_at_tg + 1, sizeof( pSortOrd[0] ) ); /*  must have more than num_atoms */ /* djb-rwth: cast operator added */

    if (!pCanonRankAtoms || !pSortOrd)
    {
        nErrorCode = 0;
        ret = CT_OUT_OF_RAM;  /*   <BRKPT> */
        pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM;
        goto exit_function;
    }

    /*  Total charge */
    /* djb-rwth: fixing oss-fuzz issue #69656 */
    for (i = 0, n = 0; i < num_atoms + num_removed_H; i++)
    {
        n += at[i].charge;
    }
    pINChI->nTotalCharge = n;

    /*  Number of atoms */
    pINChI->nNumberOfAtoms = num_atoms;
    pINChI_Aux->nNumberOfAtoms = num_atoms;

    /* Removed protons and detachable isotopic H */
    if (bTautomeric && t_group_info)
    {
        pINChI_Aux->nNumRemovedProtons = t_group_info->tni.nNumRemovedProtons;

        for (i = 0; i < NUM_H_ISOTOPES; i++)
        {
            pINChI_Aux->nNumRemovedIsotopicH[i] = t_group_info->num_iso_H[i]
                + t_group_info->tni.nNumRemovedProtonsIsotopic[i];
        }

        if (pINChI_Aux->bNormalizationFlags & FLAG_FORCE_SALT_TAUT)
        {
            pINChI->nFlags |= INCHI_FLAG_HARD_ADD_REM_PROTON;
        }
        if (pINChI_Aux->bNormalizationFlags & ( FLAG_NORM_CONSIDER_TAUT &~FLAG_PROTON_CHARGE_CANCEL ))
        {
            if (!bNoWarnings)
            {
                WarningMessage( pStrErrStruct, "Proton(s) added/removed" );
            }
        }
        if (pINChI_Aux->bNormalizationFlags & FLAG_PROTON_CHARGE_CANCEL)
        {
            if (!bNoWarnings)
            {
                WarningMessage( pStrErrStruct, "Charges neutralized" );
            }
        }
    }

    /* Abs or rel stereo may establish one of two canonical numberings */
    if (( pCS->nLenLinearCTStereoCarb > 0 || pCS->nLenLinearCTStereoDble > 0 ) &&
          pCS->nLenCanonOrdStereo > 0 &&
          ( (pCS->LinearCTStereoCarb && pCS->LinearCTStereoCarbInv) ||
              (pCS->LinearCTStereoDble && pCS->LinearCTStereoDbleInv) ) &&
          pCS->nCanonOrdStereo && pCS->nCanonOrdStereoInv
       ) /* djb-rwth: addressing LLVM warning */
    {
        pCanonRank = pCanonRankAtoms;
        pCanonOrd = pCS->nCanonOrdStereo;
        pCanonRankInv = pSortOrd;
        pCanonOrdInv = pCS->nCanonOrdStereoInv;
        Stereo = pINChI->Stereo;

        for (i = 0; i < num_at_tg; i++)
        {
            pCanonRankInv[pCanonOrdInv[i]] =
                pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 );
        }

        /********************************************************************/
        /* Copy stereo bonds and stereo centers; compare Inv and Abs stereo */
        /********************************************************************/

        nErrorCode = CopyLinearCTStereoToINChIStereo( Stereo,
                                                      pCS->LinearCTStereoCarb,
                                                      pCS->nLenLinearCTStereoCarb,
                                                      pCS->LinearCTStereoDble,
                                                      pCS->nLenLinearCTStereoDble,
                                                      pCanonOrd, pCanonRank,
                                                      at, 0 /* non-isotopic */,
                                                      pCS->LinearCTStereoCarbInv,
                                                      pCS->LinearCTStereoDbleInv,
                                                      pCanonOrdInv, pCanonRankInv );

        /* djb-rwth: fixing oss-fuzz issue #68271 */
        if (nErrorCode == 1)
        {
            nErrorCode = 0;
            ret = CT_OUT_OF_RAM;  /*   <BRKPT> */
            pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM;
            goto exit_function;
        }

        if (Stereo->t_parityInv && Stereo->nNumberInv)
        {
            if (nUserMode & REQ_MODE_RELATIVE_STEREO)
            {
                pINChI->nFlags |= INCHI_FLAG_REL_STEREO;
            }
            if (nUserMode & REQ_MODE_RACEMIC_STEREO)
            {
                pINChI->nFlags |= INCHI_FLAG_RAC_STEREO;
            }
            if (Stereo->nCompInv2Abs)
            {
                if (Stereo->nCompInv2Abs == -1)
                {
                    /* switch pointers in Stereo so that the stereo becomes the smallest (relative)  */
                    /* flag Stereo->nCompInv2Abs == -1 will keep track of this exchange */
                    AT_NUMB    *nNumberInv = Stereo->nNumberInv;
                    S_CHAR     *t_parityInv = Stereo->t_parityInv;
                    Stereo->nNumberInv = Stereo->nNumber;
                    Stereo->t_parityInv = Stereo->t_parity;
                    Stereo->nNumber = nNumberInv;
                    Stereo->t_parity = t_parityInv;
                    /* switch pointers to set rel. stereo to pINChI_Aux->nOrigAtNosInCanonOrd
                                       and inv. stereo to pINChI_Aux->nOrigAtNosInCanonOrdInv */
                    switch_ptrs( &pCanonRank, &pCanonRankInv );
                    switch_ptrs( &pCanonOrd, &pCanonOrdInv );
                    bUseNumberingInv = 1; /* use inverted stereo numbering instead of normal */
                }
            }
        }

        LOG_NO_ARGS("************************** Canonical Ordering with Stereo (L1183:ichimak2.c) ***************************\n");
        for (i = 0; i < num_atoms; i++)
        {
            pINChI_Aux->nOrigAtNosInCanonOrdInv[i] = at[pCanonOrdInv[i]].orig_at_number;
            pINChI_Aux->nOrigAtNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number;
            LOG_MULT_ARGS("Atom Nr: %d, Canonical Numbering Normal: %d, Element Name: %s\n", i + 1, at[pCanonOrd[i]].orig_at_number, at[i].elname);
        }

        LOG_NO_ARGS("\n******************************************************************************************************\n");

        if (bUseNumberingInv)
        {
            /* switch ptrs back to avoid confusion */
            switch_ptrs( &pCanonRank, &pCanonRankInv );
            switch_ptrs( &pCanonOrd, &pCanonOrdInv );
            /* save inverted stereo ranks & order because it represents the smallest (relative) */
            memcpy(pCanonRank, pCanonRankInv, num_at_tg * sizeof(pCanonRank[0]));
            /* change pCS->nCanonOrdStereo[] to inverted: */
            memcpy(pCanonOrd, pCanonOrdInv, num_at_tg * sizeof(pCanonOrd[0]));
        }

        pCanonRankInv = NULL;
        pCanonOrdInv = NULL;
        pOrigNosInCanonOrd = NULL;
    }
    else
    {
        /*------------------------------ no stereo */
        pCanonOrd = pCS->nLenCanonOrdStereo > 0 ? pCS->nCanonOrdStereo
                                                : pCS->nLenCanonOrd > 0  ? pCS->nCanonOrd
                                                                         : NULL;
        pCanonRank = pCanonRankAtoms;
        pOrigNosInCanonOrd = pINChI_Aux->nOrigAtNosInCanonOrd;

        if (pCanonOrd && pCanonRank)
        {
            for (i = 0; i < num_atoms; i++)
            {
                pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 );
                pOrigNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number;
            }
            for (; i < num_at_tg; i++)
            {
                pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 );
            }
        }
    }
    /*pCanonOrdNonIso = pCanonOrd;*/  /* save for aux info */


    if (pINChI_Aux->OrigInfo)
    {
        /* charges, radicals, valences */
        for (i = 0; i < num_atoms; i++)
        {
            if (pCanonOrd) /* djb-rwth: fixing a NULL pointer dereference */
            {
                ii = pCanonOrd[i]; 
                if (norm_at[ii].valence || norm_at[ii].num_H)
                {
                    pINChI_Aux->OrigInfo[i].cCharge = norm_at[ii].charge;

                    pINChI_Aux->OrigInfo[i].cRadical = (norm_at[ii].radical == RADICAL_SINGLET) ? 0 :
                        (norm_at[ii].radical == RADICAL_DOUBLET) ? 1 :
                        (norm_at[ii].radical == RADICAL_TRIPLET) ? 2 :
                        norm_at[ii].radical ? 3 : 0;

                    pINChI_Aux->OrigInfo[i].cUnusualValence =
                        get_unusual_el_valence(norm_at[ii].el_number, norm_at[ii].charge, norm_at[ii].radical,
                            norm_at[ii].chem_bonds_valence, norm_at[ii].num_H, norm_at[ii].valence);
                }
                else
                {
                    /* charge of a single atom component is in the INChI; valence = 0 is standard */
                    pINChI_Aux->OrigInfo[i].cRadical = (norm_at[ii].radical == RADICAL_SINGLET) ? 0 :
                        (norm_at[ii].radical == RADICAL_DOUBLET) ? 1 :
                        (norm_at[ii].radical == RADICAL_TRIPLET) ? 2 :
                        norm_at[ii].radical ? 3 : 0;
                }
            }
        }
    }

    /* Non-isotopic canonical numbers and equivalence of atoms (Aux) */
    pConstitEquNumb = pINChI_Aux->nConstitEquNumbers;  /*  contitutional equivalence */
    pSymmRank = pCS->nSymmRank;

    if (pCanonOrd && pCanonRank && pSymmRank && pConstitEquNumb)
    {
        for (i = 0; i < num_atoms; i++)
        {
            pConstitEquNumb[i] = pSymmRank[pCanonOrd[i]]; /*  constit. equ. ranks in order of canonical numbers */
            pSortOrd[i] = i;
        }
        for (; i < num_at_tg; i++)
        {
            pSortOrd[i] = MAX_ATOMS; /* for debugging only */
        }

        pCG->m_pn_RankForSort = pConstitEquNumb;
        inchi_qsort( pCG, pSortOrd, num_atoms, sizeof( pSortOrd[0] ), CompRanksOrd );

        for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= num_atoms; j++)
        {
            if (j == num_atoms || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]])
            {
                nMinOrd++;
                if (j - i > 1)
                {
                    /*  found a sequence of equivalent atoms: i..j-1 */
                    while (i < j)
                    {
                        pConstitEquNumb[pSortOrd[i++]] = nMinOrd; /*  = min. canon. rank in the group of equ. atoms */
                    }
                    /*  at this point j == i */
                }
                else
                {
                    pConstitEquNumb[pSortOrd[i++]] = 0; /*  means the atom is not equivalent to any other */
                }
                nMinOrd = pSortOrd[j]; /*  at the end j = num_atoms */
            }
        }
    }

    else
    {
        nErrorCode |= ERR_NO_CANON_RESULTS;
        ret = -1;  /*  program error; no breakpoint here */
        goto exit_function;
    }


    /*  Atomic numbers from the Periodic Table */
    for (i = 0; i < num_atoms; i++)
    {
        pINChI->nAtom[i] = (int) at[pCanonOrd[i]].el_number;
    }


    /*  Connection table: atoms only (before 7-29-2003 pCS->LinearCT2 contained non-isotopic CT) */
    if (pCS->nLenLinearCTAtOnly <= 0 || !pCS->LinearCT || !pINChI->nConnTable)
    {
        nErrorCode |= ERR_NO_CANON_RESULTS;
        ret = -2;
        goto exit_function;
    }

    memcpy(pINChI->nConnTable, pCS->LinearCT, sizeof(pINChI->nConnTable[0]) * pCS->nLenLinearCTAtOnly);

    pINChI->lenConnTable = pCS->nLenLinearCTAtOnly;

    /*  Tautomeric group(s) canonical representation */
    len = 0;
    if (bTautomeric && 0 < ( n = SortTautomerGroupsAndEndpoints(
        pCG, t_group_info,
        num_atoms, num_at_tg, pCanonRank ) ))
    {
        /* SortTautomerGroupsAndEndpoints() produces canonically ordered t-groups */
        pINChI->nFlags |=
            ( t_group_info->bTautFlagsDone & TG_FLAG_ALL_SALT_DONE ) ? INCHI_FLAG_ACID_TAUT
            : 0;

        /*  number of tautomeric groups */
        pINChI->nTautomer[len++] = (AT_NUMB) n;

        /* store each tautomeric group, one by one */
        for (i = 0; i < n; i++)
        {
            g = (int) t_group_info->tGroupNumber[i]; /* original group numbers in sorted order */
            t_group = t_group_info->t_group + g;    /* pointer to the tautomeric group */

            /*  NumAt+INCHI_T_NUM_MOVABLE (group length excluding this number) */

            pINChI->nTautomer[len++] = t_group->nNumEndpoints + INCHI_T_NUM_MOVABLE;

            /*  Num(H), Num(-) */

            for (j = 0; j < INCHI_T_NUM_MOVABLE; j++) /* djb-rwth: redundant condition; && j < T_NUM_NO_ISOTOPIC part should be checked; can INCHI_T_NUM_MOVABLE and T_NUM_NO_ISOTOPIC change values from 2? */
            {
                pINChI->nTautomer[len++] = t_group->num[j];
            }
            
            
            /* djb-rwth: erroneous loop execution condition
            
            for (j = T_NUM_NO_ISOTOPIC; j < INCHI_T_NUM_MOVABLE; j++)
            {
                pINChI->nTautomer[len++] = 0; // should not happen 
            }
            
            */

            /* tautomeric group endpoint canonical numbers, pre-sorted in ascending order */

            for (j = (int) t_group->nFirstEndpointAtNoPos,
                  m = j + (int) t_group->nNumEndpoints; j < m; j++)
            {
                pINChI->nTautomer[len++] = pCanonRank[(int) t_group_info->nEndpointAtomNumber[j]]; /*  At[j] */
            }
        }

        pINChI->lenTautomer = len;
        pINChI_Aux->nNumberOfTGroups = n;
    }
    else
    {
        pINChI->lenTautomer = 0;
        pINChI_Aux->nNumberOfTGroups = 0;

        if (t_group_info && ( ( t_group_info->tni.bNormalizationFlags & FLAG_NORM_CONSIDER_TAUT ) ||
            (t_group_info->nNumIsotopicEndpoints > 1 &&
            ( t_group_info->bTautFlagsDone & ( TG_FLAG_FOUND_ISOTOPIC_H_DONE | TG_FLAG_FOUND_ISOTOPIC_ATOM_DONE ) )) )
           ) /* djb-rwth: addressing LLVM warning */
        {
            /* only protons (re)moved or added */
            pINChI->lenTautomer = 1;
            pINChI->nTautomer[0] = 0;
        }
    }

    /*  Number of H (excluding tautomeric) */
    if (pCS->nNum_H)
    {
        for (i = 0; i < num_atoms; i++)
        {
            pINChI->nNum_H[i] = pCS->nNum_H[i];
        }
    }


    /*  Number of fixed H (tautomeric H in non-tautomeric representation) */
    if (pCS->nNum_H_fixed && !pINChI->lenTautomer)
    {
        for (i = 0; i < num_atoms; i++)
        {
            pINChI->nNum_H_fixed[i] = pCS->nNum_H_fixed[i];
            pINChI->nNum_H[i] += pCS->nNum_H_fixed[i];
        }
    }


    /***********************************************************
     *  Tautomeric group(s) numbering and symmetry;
     *  should not depend on switching to rel. stereo numbering
     */
    if (pINChI->lenTautomer && ( n = pINChI_Aux->nNumberOfTGroups ))
    {
        pCanonOrdTaut = pCS->nLenCanonOrdStereoTaut > 0 ? pCS->nCanonOrdStereoTaut :
            pCS->nLenCanonOrdTaut > 0 ? pCS->nCanonOrdTaut : NULL;
        pConstitEquNumb = pINChI_Aux->nConstitEquTGroupNumbers;
        pSymmRank = pCS->nSymmRankTaut;

        if (pCanonOrdTaut && pSymmRank && pConstitEquNumb)
        {
            for (i = 0; i < n; i++)
            {
                pConstitEquNumb[i] = pSymmRank[pCanonOrdTaut[i]];
                pSortOrd[i] = i;
            }
            pCG->m_pn_RankForSort = pConstitEquNumb;
            inchi_qsort( pCG, pSortOrd, n, sizeof( pSortOrd[0] ), CompRanksOrd );
            for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= n; j++)
            {
                if (j == n || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]])
                {
                    nMinOrd++; /* make is start from 1, not from zero */
                    if (j - i > 1)
                    {
                        /*  found a sequence of more than one equivalent t-groups: i..j-1 */
                        while (i < j)
                        {
                            pConstitEquNumb[pSortOrd[i++]] = nMinOrd;
                        }
                    }
                    else
                    {
                        pConstitEquNumb[pSortOrd[i++]] = 0;
                    }
                    nMinOrd = pSortOrd[j]; /*  at the end j == n */
                }
            }
        }
    }


    /*  Allocate and fill Hill formula */

    pINChI->szHillFormula = AllocateAndFillHillFormula( pINChI );

    if (!pINChI->szHillFormula)
    {
        nErrorCode = 0;
        ret = CT_WRONG_FORMULA; /* CT_OUT_OF_RAM;*/  /*   <BRKPT> */
        pINChI->nErrorCode = pINChI_Aux->nErrorCode = ret;
        goto exit_function;
    }

    nStereoUnmarkMode = UnmarkAllUndefinedUnknownStereo( pINChI->Stereo, nUserMode );

    if (nStereoUnmarkMode)
    {
        pINChI->nFlags |=
            ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_UU
            : 0;
        pINChI->nFlags |=
            ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SB_IGN_ALL_UU
            : 0;

        if (( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ||
            ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ))
        {
            if (!bNoWarnings)
            {
                WarningMessage( pStrErrStruct, "Omitted undefined stereo" );
            }
        }
    }

    /*************************/
    /* Mark ambiguous stereo */
    /*************************/

    MarkAmbiguousStereo( at, norm_at, 0 /* non-isotopic */, pCanonOrd,
                         pCS->LinearCTStereoCarb, pCS->nLenLinearCTStereoCarb,
                         pCS->LinearCTStereoDble, pCS->nLenLinearCTStereoDble );


    /************************************************************************
     *
     *  Isotopic part
     */

    /* abs or rel stereo may establish one of two canonical numberings */

    if (( pCS->nLenLinearCTIsotopicStereoCarb > 0 || pCS->nLenLinearCTIsotopicStereoDble > 0 ) &&
          pCS->nLenCanonOrdIsotopicStereo > 0 &&
          ( (pCS->LinearCTIsotopicStereoCarb && pCS->LinearCTIsotopicStereoCarbInv) ||
              (pCS->LinearCTIsotopicStereoDble && pCS->LinearCTIsotopicStereoDbleInv) ) &&
          pCS->nCanonOrdIsotopicStereo && pCS->nCanonOrdIsotopicStereoInv
          ) /* djb-rwth: addressing LLVM warning */
    {
        /* found isotopic stereo */

        pCanonRank = pCanonRankAtoms;
        pCanonOrd = pCS->nCanonOrdIsotopicStereo;
        pCanonRankInv = pSortOrd;
        pCanonOrdInv = pCS->nCanonOrdIsotopicStereoInv;
        Stereo = pINChI->StereoIsotopic;

        for (i = 0; i < num_at_tg; i++)
        {
            pCanonRankInv[pCanonOrdInv[i]] =
                pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 );
        }


        /********************************************************************/
        /* copy stereo bonds and stereo centers; compare Inv and Abs stereo */
        /********************************************************************/

        nErrorCode = CopyLinearCTStereoToINChIStereo( Stereo,
                                                      pCS->LinearCTIsotopicStereoCarb,
                                                      pCS->nLenLinearCTIsotopicStereoCarb,
                                                      pCS->LinearCTIsotopicStereoDble,
                                                      pCS->nLenLinearCTIsotopicStereoDble,
                                                      pCanonOrd, pCanonRank, at, 1 /* isotopic */,
                                                      pCS->LinearCTIsotopicStereoCarbInv,
                                                      pCS->LinearCTIsotopicStereoDbleInv,
                                                      pCanonOrdInv, pCanonRankInv );

        /* djb-rwth: fixing oss-fuzz issue #68271 */
        if (nErrorCode == 1)
        {
            nErrorCode = 0;
            ret = CT_OUT_OF_RAM;  /*   <BRKPT> */
            pINChI->nErrorCode = pINChI_Aux->nErrorCode = CT_OUT_OF_RAM;
            goto exit_function;
        }
        
        if (Stereo->t_parityInv && Stereo->nNumberInv)
        {
            if (nUserMode & REQ_MODE_RELATIVE_STEREO)
            {
                pINChI->nFlags |= INCHI_FLAG_REL_STEREO;
            }

            if (nUserMode & REQ_MODE_RACEMIC_STEREO)
            {
                pINChI->nFlags |= INCHI_FLAG_RAC_STEREO;
            }

            if (Stereo->nCompInv2Abs)
            {
                if (Stereo->nCompInv2Abs == -1)
                {
                    /* switch pointers so that the stereo becomes the smallest (relative)  */
                    /* flag Stereo->nCompInv2Abs == -1 will keep track of this exchange */
                    AT_NUMB    *nNumberInv = Stereo->nNumberInv;
                    S_CHAR     *t_parityInv = Stereo->t_parityInv;
                    Stereo->nNumberInv = Stereo->nNumber;
                    Stereo->t_parityInv = Stereo->t_parity;
                    Stereo->nNumber = nNumberInv;
                    Stereo->t_parity = t_parityInv;
                    switch_ptrs( &pCanonRank, &pCanonRankInv );
                    switch_ptrs( &pCanonOrd, &pCanonOrdInv );
                    bUseIsotopicNumberingInv = 1;
                }
            }
        }

        for (i = 0; i < num_atoms; i++)
        {
            pINChI_Aux->nIsotopicOrigAtNosInCanonOrdInv[i] = at[pCanonOrdInv[i]].orig_at_number;
            pINChI_Aux->nIsotopicOrigAtNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number;
        }

        if (bUseIsotopicNumberingInv)
        {
            switch_ptrs( &pCanonRank, &pCanonRankInv );
            switch_ptrs( &pCanonOrd, &pCanonOrdInv );
            memcpy(pCanonRank, pCanonRankInv, num_at_tg * sizeof(pCanonRank[0]));
            memcpy(pCanonOrd, pCanonOrdInv, num_at_tg * sizeof(pCanonOrd[0]));
        }

        pCanonRankInv = NULL;
        pCanonOrdInv = NULL;
        pOrigNosInCanonOrd = NULL;
    }
    else
    {
        /* no isotopic stereo */

        pCanonOrd = pCS->nLenCanonOrdIsotopicStereo > 0 ? pCS->nCanonOrdIsotopicStereo
            : pCS->nLenCanonOrdIsotopic > 0 ? pCS->nCanonOrdIsotopic
            : NULL;
        pCanonRank = pCanonRankAtoms;
        pOrigNosInCanonOrd = pINChI_Aux->nIsotopicOrigAtNosInCanonOrd;

        /* djb-rwth: fixing oss-fuzz issue #30496 */
        if (pCanonOrd && pCanonRank && pOrigNosInCanonOrd)
        {
            for (i = 0; i < num_atoms; i++)
            {
                /* Fix13 -- out of bounds */
                pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 );
                pOrigNosInCanonOrd[i] = at[pCanonOrd[i]].orig_at_number;
            }
            for (; i < num_at_tg; i++)
            {
                /* Fix13 -- out of bounds */
                pCanonRank[pCanonOrd[i]] = (AT_NUMB) ( i + 1 );
            }
        }
    }
    /*pCanonOrdIso = pCanonOrd;*/


    pConstitEquNumb = pINChI_Aux->nConstitEquIsotopicNumbers;
    pSymmRank = pCS->nSymmRankIsotopic;

    if (pCanonOrd && pCanonRank && pConstitEquNumb && pSymmRank)
    {
        for (i = 0; i < num_atoms; i++)
        {
            pConstitEquNumb[i] = pSymmRank[pCanonOrd[i]];
            pSortOrd[i] = i;
        }

        for (; i < num_at_tg; i++)
        {
            pSortOrd[i] = i;
        }

        pCG->m_pn_RankForSort = pConstitEquNumb;
        inchi_qsort( pCG, pSortOrd, num_atoms, sizeof( pSortOrd[0] ), CompRanksOrd );

        for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= num_atoms; j++)
        {
            if (j == num_atoms || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]])
            {
                nMinOrd++;

                if (j - i > 1)
                {
                    /*  found a sequence of equivalent atoms: i..j-1 */
                    while (i < j)
                    {
                        pConstitEquNumb[pSortOrd[i++]] = nMinOrd;
                    }
                }
                else
                {
                    pConstitEquNumb[pSortOrd[i++]] = 0; /* nMinOrd; */
                }
                nMinOrd = pSortOrd[j];
            }
        }
    }
    else
    {
        goto exit_function; /*  no isotopic info available */
    }


    /*  Isotopic atoms */

    n = pINChI->nNumberOfIsotopicAtoms = pCS->nLenLinearCTIsotopic;

    for (i = 0; i < n; i++)
    {
        pINChI->IsotopicAtom[i].nAtomNumber = pCS->LinearCTIsotopic[i].at_num;
        pINChI->IsotopicAtom[i].nIsoDifference = pCS->LinearCTIsotopic[i].iso_atw_diff;
        pINChI->IsotopicAtom[i].nNum_H = pCS->LinearCTIsotopic[i].num_1H;
        pINChI->IsotopicAtom[i].nNum_D = pCS->LinearCTIsotopic[i].num_D;
        pINChI->IsotopicAtom[i].nNum_T = pCS->LinearCTIsotopic[i].num_T;
    }

    /*  Isotopic tautomeric groups */

    n = pINChI->nNumberOfIsotopicTGroups = pCS->nLenLinearCTIsotopicTautomer;

    for (i = 0; i < n; i++)
    {
        pINChI->IsotopicTGroup[i].nTGroupNumber = pCS->LinearCTIsotopicTautomer[i].tgroup_num;
        pINChI->IsotopicTGroup[i].nNum_H = pCS->LinearCTIsotopicTautomer[i].num[2];
        pINChI->IsotopicTGroup[i].nNum_D = pCS->LinearCTIsotopicTautomer[i].num[1];
        pINChI->IsotopicTGroup[i].nNum_T = pCS->LinearCTIsotopicTautomer[i].num[0];
    }

    /* Atoms that may exchange isotopic H-atoms */

    if (pCS->nExchgIsoH && pINChI->nPossibleLocationsOfIsotopicH)
    {
        for (i = 0, j = 1; i < num_atoms; i++)
        {
            if (pCS->nExchgIsoH[i])
            {
                pINChI->nPossibleLocationsOfIsotopicH[j++] = (AT_NUMB) ( i + 1 ); /* canonical number */
            }
        }
        pINChI->nPossibleLocationsOfIsotopicH[0] = (AT_NUMB) j; /* length including the 0th element */
    }

    if ((nStereoUnmarkMode = UnmarkAllUndefinedUnknownStereo( pINChI->StereoIsotopic, nUserMode ))) /* djb-rwth: addressing LLVM warning */
    {
        pINChI->nFlags |=
            ( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU
            : 0;
        pINChI->nFlags |=
            ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ) ? INCHI_FLAG_SC_IGN_ALL_ISO_UU
            : 0;
        if (( nStereoUnmarkMode & REQ_MODE_SC_IGN_ALL_UU ) ||
            ( nStereoUnmarkMode & REQ_MODE_SB_IGN_ALL_UU ))
        {
            if (!bNoWarnings)
            {
                WarningMessage( pStrErrStruct, "Omitted undefined stereo" );
            }
        }
    }

    /* Mark ambiguous stereo */

    MarkAmbiguousStereo( at, norm_at, 1 /* isotopic */, pCanonOrd,
                         pCS->LinearCTIsotopicStereoCarb, pCS->nLenLinearCTIsotopicStereoCarb,
                         pCS->LinearCTIsotopicStereoDble, pCS->nLenLinearCTIsotopicStereoDble );


    /***********************************************************
     *  Isotopic tautomeric group(s) numbering and symmetry;
     *  should not depend on switching to rel. stereo numbering
     */

    if (pINChI->lenTautomer &&
         pINChI_Aux->nConstitEquIsotopicTGroupNumbers &&
         pCS->nSymmRankIsotopicTaut &&
         ( pCS->nLenLinearCTIsotopic || pCS->nLenLinearCTIsotopicTautomer ) &&
         t_group_info && t_group_info->num_t_groups > 0)
    {

        /* djb-rwth: removing redundant code */

        pCanonOrdTaut =
            pCS->nLenCanonOrdIsotopicStereoTaut > 0 ? ( n = pCS->nLenCanonOrdIsotopicStereoTaut, pCS->nCanonOrdIsotopicStereoTaut )
            : pCS->nLenCanonOrdIsotopicTaut > 0 ? ( n = pCS->nLenCanonOrdIsotopicTaut, pCS->nCanonOrdIsotopicTaut )
            : ( n = 0, (AT_RANK*) NULL );

        pConstitEquNumb = pINChI_Aux->nConstitEquIsotopicTGroupNumbers;

        pSymmRank = pCS->nSymmRankIsotopicTaut;

        if (pCanonOrdTaut && pSymmRank && pConstitEquNumb && n > 0)
        {
            for (i = 0; i < n; i++)
            {
                pConstitEquNumb[i] = pSymmRank[pCanonOrdTaut[i]];
                pSortOrd[i] = i;
            }

            pCG->m_pn_RankForSort = pConstitEquNumb;
            inchi_qsort( pCG, pSortOrd, n, sizeof( pSortOrd[0] ), CompRanksOrd );
            for (i = 0, nMinOrd = pSortOrd[0], j = 1; j <= n; j++)
            {
                if (j == n || pConstitEquNumb[pSortOrd[i]] != pConstitEquNumb[pSortOrd[j]])
                {
                    nMinOrd++;
                    if (j - i > 1)
                    {
                        /*  found a sequence of equivalent t-groups: i..j-1 */
                        while (i < j)
                        {
                            pConstitEquNumb[pSortOrd[i++]] = nMinOrd;
                        }
                    }
                    else
                    {
                        pConstitEquNumb[pSortOrd[i++]] = 0; /*  nMinOrd; */
                    }
                    nMinOrd = pSortOrd[j]; /*  at the end j = n */
                }
            }
        }
    }


exit_function:

    if (pCanonRankAtoms)
    {
        inchi_free( pCanonRankAtoms );
    }
    if (pSortOrd)
    {
        inchi_free( pSortOrd );
    }

    pINChI->nErrorCode |= nErrorCode;
    pINChI_Aux->nErrorCode |= nErrorCode;

    return ret;
}
