/*
 * International Chemical Identifier (InChI)
 * Version 1
 * Software version 1.04
 * September 9, 2011
 *
 * The InChI library and programs are free software developed under the
 * auspices of the International Union of Pure and Applied Chemistry (IUPAC).
 * Originally developed at NIST. Modifications and additions by IUPAC 
 * and the InChI Trust.
 *
 * IUPAC/InChI-Trust Licence for the International Chemical Identifier (InChI) 
 * Software version 1.0.
 * Copyright (C) IUPAC and InChI Trust Limited
 * 
 * This library is free software; you can redistribute it and/or modify it under the 
 * terms of the IUPAC/InChI Trust Licence for the International Chemical Identifier 
 * (InChI) Software version 1.0; either version 1.0 of the License, or 
 * (at your option) any later version.
 * 
 * This library is distributed in the hope that it will be useful, 
 * but WITHOUT ANY WARRANTY; without even the implied warranty of 
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
 * See the IUPAC/InChI Trust Licence for the International Chemical Identifier (InChI) 
 * Software version 1.0 for more details.
 * 
 * You should have received a copy of the IUPAC/InChI Trust Licence for the 
 * International Chemical Identifier (InChI) Software version 1.0 along with 
 * this library; if not, write to:
 * 
 * The InChI Trust
 * c/o FIZ CHEMIE Berlin
 * Franklinstrasse 11
 * 10587 Berlin
 * GERMANY
 * 
 */


#include <stdio.h>
#include <stdlib.h>
#include <string.h>


#include "mode.h"

#include "incomdef.h"
#include "extr_ct.h"
#include "ichitaut.h"
#include "ichicant.h"
#include "ichicomn.h"
#include "ichister.h"

#include "ichicomp.h"




typedef struct tagStereoBondNeighbor {  /*  *n = sort key */
    AT_RANK       nRank;       /*  *1 opposite atom rank; equal ranks mean constit. equivalence */
    AT_RANK       nNeighRank1; /*  rank of the neighbor in the direction to the opposite atom */
    AT_RANK       nNeighRank2; /*  rank of the opposite atom neighbor in the direction to the current atom */
    AT_RANK       num;       /*  number of same type bonds to constitutionally equivalent neighbors */
    AT_RANK       num_any_parity;     /*  at least one atom has parity in 1..4 range */
    AT_RANK       num_defined_parity; /*  number of neighbors with defined parity <= num */
    /* AT_RANK       num_undef_parity; */
    /* AT_RANK       num_unkn_parity; */
    AT_RANK       what2do;
    U_CHAR        cumulene_len; /*  high nimble bits: (cumulene length - 1) */
    U_CHAR        bond_type;   /*  *2 all same, not a real bond type */
} STEREO_BOND_NEIGH;

/* local prototypes */
int SetHalfStereoBondIllDefPariy( sp_ATOM *at, int jn, /* atom number*/ int k1 /* stereo bond number*/, int new_parity );
int RemoveHalfStereoBond( sp_ATOM *at, int jn, /* atom number*/ int k1 /* stereo bond number*/ );
int SetKnownStereoBondParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                const AT_RANK *nRank, const AT_RANK *nAtomNumber );
int MarkKnownEqualStereoBondParities( sp_ATOM *at, int num_atoms,
                                      const AT_RANK *nRank, const AT_RANK *nAtomNumber );
int GetNextNeighborAndRank( sp_ATOM *at, AT_RANK cur, AT_RANK prev, AT_RANK *n, AT_RANK *cr, const AT_RANK *nCanonRank );
int GetAndCheckNextNeighbors( sp_ATOM *at, AT_RANK cur1, AT_RANK prev1, AT_RANK cur2, AT_RANK prev2,
                              AT_RANK *n1, AT_RANK *n2, AT_RANK *nVisited1, AT_RANK *nVisited2,
                              const AT_RANK *nRank, const AT_RANK *nCanonRank );
AT_RANK PathsHaveIdenticalKnownParities( sp_ATOM *at, AT_RANK prev1, AT_RANK cur1, AT_RANK prev2, AT_RANK cur2,
                                         AT_RANK *nVisited1, AT_RANK *nVisited2,
                                         const AT_RANK *nRank, const AT_RANK *nCanonRank, AT_RANK nLength );
int RemoveKnownNonStereoBondParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                      const AT_RANK *nRank, CANON_STAT *pCS);
int SetKnownStereoCenterParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                  const AT_RANK *nRank, const AT_RANK *nAtomNumber );
int RemoveKnownNonStereoCenterParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                        const AT_RANK *nRank, CANON_STAT *pCS);
int MarkKnownEqualStereoCenterParities( sp_ATOM *at, int num_atoms,
                                        const AT_RANK *nRank, const AT_RANK *nAtomNumber );

/**********************************************************************************/
/*  Depth First Search for an atom with parity */
int find_atoms_with_parity( sp_ATOM *at, S_CHAR *visited, int from_atom, int cur_atom )
{
    int i, next_atom;
    if ( visited[cur_atom] )
        return 0;
    if ( at[cur_atom].parity )
        return 1;
    visited[cur_atom] = 1;
    for ( i = 0; i < at[cur_atom].valence; i ++ ) {
        next_atom = at[cur_atom].neighbor[i];
        if ( next_atom != from_atom && find_atoms_with_parity( at, visited, cur_atom, next_atom ) )
            return 1;
    }
    return 0;
}
/**********************************************************************************/
int SetHalfStereoBondIllDefPariy( sp_ATOM *at, int jn, /* atom number*/ int k1 /* stereo bond number*/, int new_parity )
{
    int parity;
    if ( k1 < MAX_NUM_STEREO_BOND_NEIGH && at[jn].stereo_bond_neighbor[k1] ) {
        parity = at[jn].stereo_bond_parity[k1] ^ PARITY_VAL(at[jn].stereo_bond_parity[k1]);
        at[jn].stereo_bond_parity[k1] = parity | PARITY_VAL(new_parity);
        at[jn].parity = PARITY_VAL(new_parity);
        return 1;  /*  success */
    }
    return 0; /*  failed             */
}

/**********************************************************************************/
int RemoveHalfStereoBond( sp_ATOM *at, int jn, /* atom number*/ int k1 /* stereo bond number*/ )
{
    int k2;    
    if ( k1 < MAX_NUM_STEREO_BOND_NEIGH && at[jn].stereo_bond_neighbor[k1] ) {
        for ( k2 = k1; k2+1 < MAX_NUM_STEREO_BOND_NEIGH; k2++ ) {
            at[jn].stereo_bond_neighbor[k2] = at[jn].stereo_bond_neighbor[k2+1];
            at[jn].stereo_bond_ord[k2]      = at[jn].stereo_bond_ord[k2+1];
            at[jn].stereo_bond_z_prod[k2]   = at[jn].stereo_bond_z_prod[k2+1];
            at[jn].stereo_bond_parity[k2]   = at[jn].stereo_bond_parity[k2+1];
        }
        at[jn].stereo_bond_neighbor[k2] = 0;
        at[jn].stereo_bond_ord[k2]      = 0;
        at[jn].stereo_bond_z_prod[k2]   = 0;
        at[jn].stereo_bond_parity[k2]   = 0;

        if ( !at[jn].stereo_bond_neighbor[0] ) {  /*  curled braces added 6-6-2002 */
            at[jn].parity                  = 0;
            at[jn].stereo_atom_parity      = 0;
            at[jn].final_parity            = 0;
            /* at[jn].bHasStereoOrEquToStereo = 0; */
        }
        return 1; /*  success            */
    }
    return 0; /*  failed             */
}

/**********************************************************************************/
int SetOneStereoBondIllDefParity( sp_ATOM *at, int jc, /* atom number*/ int k /* stereo bond ord. number*/, int new_parity )
{
    int k1, ret=0, kn, jn = (int)at[jc].stereo_bond_neighbor[k]-1;

    /*  opposite end */
    for ( k1 = kn = ret = 0; k1 < MAX_NUM_STEREO_BOND_NEIGH && (kn=at[jn].stereo_bond_neighbor[k1]); k1++ ) {
        if ( kn - 1 == jc ) {
            ret = SetHalfStereoBondIllDefPariy( at, jn, /* atom number*/ k1 /* stereo bond number*/, new_parity );
            break;
        }
    }
    if ( ret ) {
        ret = SetHalfStereoBondIllDefPariy( at, jc, k, new_parity );
    }     
    return ret;
}

/**********************************************************************************/
int RemoveOneStereoBond( sp_ATOM *at, int jc, /* atom number*/ int k /* stereo bond number*/ )
{
    int k1, ret=0, kn, jn = (int)at[jc].stereo_bond_neighbor[k]-1;

    /*  opposite end */
    for ( k1 = kn = ret = 0; k1 < MAX_NUM_STEREO_BOND_NEIGH && (kn=at[jn].stereo_bond_neighbor[k1]); k1++ ) {
        if ( kn - 1 == jc ) {
            ret = RemoveHalfStereoBond( at, jn, k1 );
            break;
        }
    }
    if ( ret ) {
        ret = RemoveHalfStereoBond( at, jc, k );
    }     
    return ret;
}
/**********************************************************************************/
int RemoveOneStereoCenter( sp_ATOM *at, int jc /* atom number*/ )
{
    if ( at[jc].parity ) {
        at[jc].parity             = 0; /*  remove parity */
        at[jc].stereo_atom_parity = 0;
        at[jc].final_parity       = 0;
        /*  at[jc].bHasStereoOrEquToStereo = 0; */
        return 1;
    }
    return 0; /*  failed: not a stereo center */
}
/**********************************************************************************/
/*  Remove stereo parity from centers having constitutionally equivalent */
/*  cut-vertex neighbors whose attachments do not have stereogenic elements. */
/*  Currently checks ALL constitutionally equivalent neighbors. */
/*  To optimize, check only one. */
int UnmarkNonStereo( sp_ATOM *at, int num_atoms, const AT_RANK *nRank, const AT_RANK *nAtomNumber, int bIsotopic )
{
    int i, i1, i2, j, k, k1, k2, kn /* neigh*/, val, ic/* center*/, jc, num_implicit_H;
    int num_neighbors_with_parity, num_no_parity_atoms, num_removed_parities=-1, num_removed_parities0;
    AT_RANK nNeighborNumber[MAX_NUM_STEREO_ATOM_NEIGH];
    AT_RANK nPrevAtomRank, nPrevNeighRank;
    S_CHAR *visited = (S_CHAR *) inchi_malloc(num_atoms * sizeof(visited[0]));
    if ( !visited )
        goto exit_function;
    num_removed_parities = 0;
    num_no_parity_atoms  = 0;

    do {
        num_removed_parities0 = num_removed_parities;
        for ( i = i1 = 0, nPrevAtomRank = 0; i <= num_atoms; i++ ) {
            /*  bounds violation check (i!=num_atoms) added 6-21-2002 */
            if ( i == num_atoms || nPrevAtomRank != nRank[j = nAtomNumber[i]]
                 /* at[j].parity && 1 < at[j].valence && at[j].valence < MAX_NUM_STEREO_ATOM_NEIGH*/ ) {
                
                /*  end of constitutionally equivalent atoms sequence */
                
                /* nPrevRank = nRank[j]; */
                i2 = i;
                if ( i2 - i1 > num_no_parity_atoms /*&& at[jc = nAtomNumber[i1]].parity*/ ) {
                    /*  at[nAtomNumber[i1]]..at[nAtomNumber[i2-1]] are constitutionally equivalent and some of them have parity */
                    jc = nAtomNumber[i1];
                    num_no_parity_atoms = 0;
                    val = at[jc].valence; /*  all equivalent atoms have equal valences, etc. (except parities) */
                    num_implicit_H = at[jc].endpoint? 0 : at[jc].num_H;
                    /*  Only atoms with valence <= MAX_NUM_STEREO_ATOM_NEIGH may have parity. However, check: */
                    if ( val + num_implicit_H > MAX_NUM_STEREO_ATOM_NEIGH ) {
                        continue;  /*  program error ??? */ /*   <BRKPT> */
                    }
                    for ( k = 0; k < val; k ++ ) {
                        nNeighborNumber[k] = k; /*  initialize an array of indexes for sorting */
                    }
                    /*  check parities */
                    for ( ic = i1; ic < i2; ic ++ ) {
                        jc = nAtomNumber[ic];
                        /*  sort neighbors according to their canon. equivalence ranks */
                        pNeighborsForSort = at[jc].neighbor;
                        pn_RankForSort    = nRank;
                        insertions_sort( nNeighborNumber, val, sizeof(nNeighborNumber[0]), CompNeighborsAT_NUMBER );
                        num_neighbors_with_parity = -1; /*  non-zero */
                        for ( k = k1 = 0, nPrevNeighRank = 0; k <= val; k ++ ) {
                            if ( k == val || nPrevNeighRank != nRank[at[jc].neighbor[nNeighborNumber[k]]] ) {
                                k2 = k;
                                if ( k2 - k1 > 1 ) {
                                    /*  found 2 or more constitutionally equivalent neighbors */
                                    /*  Check if they have only non-stereogenic neighbors */
                                    for ( kn = k1, num_neighbors_with_parity = 0; kn < k2; kn ++ ) {
                                        memset( visited, 0, num_atoms * sizeof(visited[0]));
                                        visited[jc] = 1; /*  starting point; the only atom with parity */
                                        num_neighbors_with_parity +=
                                        find_atoms_with_parity( at, visited, jc, (int)at[jc].neighbor[nNeighborNumber[kn]] );
                                    }
                                }
                                if ( !num_neighbors_with_parity ) {
                                    break; /*  at[jc] cannot have defined parity */
                                }
                                if ( k + 1 < val ) {
                                    k1 = k; /*  at least 2 more neighbors left */
                                    nPrevNeighRank = nRank[at[jc].neighbor[nNeighborNumber[k]]];
                                } else {
                                    break;
                                }
                            }
                        }
                        if ( num_implicit_H > 1 ) {
                            if ( ((bIsotopic && (at[jc].num_iso_H[0] > 1)) ||
                                               at[jc].num_iso_H[1] > 1 ||
                                               at[jc].num_iso_H[2] > 1 ) ||
                                  num_implicit_H > NUM_H_ISOTOPES        ||
                                  !bIsotopic 
                                ) {
                                num_neighbors_with_parity = 0;
                            }
                        }
                        /*  increment if: */
                        /*  (a) constitutionally equivalent neighbors do exist, and */
                        /*  (b) all constitutionally equivalent neighbors do not have parity, and */
                        /*  (c) all constitutionally equivalent neighbors are not connected to atoms with parity */
                        num_no_parity_atoms += !num_neighbors_with_parity;
                    }
                    if ( num_no_parity_atoms == i2 - i1 ) {
                        /*  all atoms at[nAtomNumber[i1]]..at[nAtomNumber[i2-1]] cannot be */
                        /*  stereo centers or belong to stereo bonds */
                        for ( ic = i1; ic < i2; ic ++ ) {
                            int jn;
                            jc = nAtomNumber[ic];
                            at[jc].parity             = 0; /*  remove parity */
                            at[jc].stereo_atom_parity = 0;
                            at[jc].final_parity       = 0;
                            at[jc].bHasStereoOrEquToStereo = 0;
                            /*  remove stereo bonds */
                            for ( k = 0; k < MAX_NUM_STEREO_BOND_NEIGH && (jn=at[jc].stereo_bond_neighbor[k]); k++ ) {
                                jn--; /*  stereo bond neighbor */
                                /*  opposite end */
                                for ( k1 = 0; k1 < MAX_NUM_STEREO_BOND_NEIGH && (kn=at[jn].stereo_bond_neighbor[k1]); k1++ ) {
                                    if ( kn - 1 == jc ) {
                                        RemoveHalfStereoBond( at, jn, k1 );
                                        break;
                                    }
                                }
                                /*  at at[jc] stereo bond end; since references to all at[jc] */
                                /*  stereo bond neighbors are to be removed, do not shift them */
                                at[jc].stereo_bond_neighbor[k] = 0;
                                at[jc].stereo_bond_ord[k]      = 0;
                                at[jc].stereo_bond_z_prod[k]   = 0;
                                at[jc].stereo_bond_parity[k]   = 0;
                            
                            }

                        }
                        num_removed_parities += num_no_parity_atoms;
                    }

                }
                if ( i < num_atoms ) {
                    nPrevAtomRank = nRank[j];
                    i1 = i;
                }
                num_no_parity_atoms = 0;
            }
            num_no_parity_atoms += (i < num_atoms && !at[j].parity);
        }
    } while ( num_removed_parities != num_removed_parities0 );

exit_function:
    if ( visited )
        inchi_free( visited );
    return num_removed_parities;
}
/**********************************************************************************
 *
 *  Add stereo descriptor(s) for atom #i
 *
 **********************************************************************************/
int FillSingleStereoDescriptors(sp_ATOM *at, int i, int num_trans, const AT_RANK *nRank
                          , AT_STEREO_CARB *LinearCTStereoCarb, int *nStereoCarbLen, int nMaxStereoCarbLen
                          , AT_STEREO_DBLE *LinearCTStereoDble, int *nStereoDbleLen, int nMaxStereoDbleLen
                          , int bAllene )
{
    if ( !LinearCTStereoDble && !LinearCTStereoCarb ) {
            return 0; /*  return immediately if no stereo have been requested */
    }

        /***************************************************
           add stereo centers and stereo bonds to the CT
         ***************************************************/
        if ( at[i].parity || at[i].stereo_bond_neighbor[0] ) {
            AT_RANK r_neigh, rank = nRank[i];
            AT_NUMB nNeighborNumber2[MAXVAL];
            unsigned parity;
            int      k;
            int num_allene = 0;
            if ( ATOM_PARITY_WELL_DEF(at[i].parity) && num_trans < 0 ) {
                /*  number of neighbors transpositions to the sorted order is unknown. Find it. */
                /*  If parity is not well-defined then doing this is a waste of time */
                int num_neigh = at[i].valence;
                for ( k = 0; k < num_neigh; k ++) {
                    nNeighborNumber2[k] = k;
                }
                pNeighborsForSort = at[i].neighbor;
                pn_RankForSort    = nRank;
                num_trans=insertions_sort( nNeighborNumber2, num_neigh, sizeof(nNeighborNumber2[0]), CompNeighborsAT_NUMBER );
#ifndef CT_NEIGH_INCREASE
                num_trans += ((num_neigh*(num_neigh-1))/2)%2;  /*  get correct parity for ascending order */
#endif
            }

            /*  stereo bonds */
            if ( LinearCTStereoDble && at[i].stereo_bond_neighbor[0] ) {

                /* HalfStereoBondParity( sp_ATOM *at, int at_no1, int i_sb_neigh, AT_RANK *nRank ) */
                AT_NUMB nStereoNeighNumber[MAX_NUM_STEREO_BONDS], nStereoNeigh[MAX_NUM_STEREO_BONDS], n;
                int       num_stereo, stereo_neigh, stereo_neigh_ord, stereo_bond_parity;
                for ( num_stereo = 0;
                      num_stereo < MAX_NUM_STEREO_BONDS &&
                      (n=at[i].stereo_bond_neighbor[num_stereo]); num_stereo ++ ) {
                    nStereoNeighNumber[num_stereo] = num_stereo;
                    nStereoNeigh[num_stereo] = n-1;
                    num_allene += IS_ALLENE_CHAIN(at[i].stereo_bond_parity[num_stereo]);
                }
                if ( (bAllene > 0 && !num_allene) || (bAllene == 0 && num_allene) ) {
                    return 0;
                }
                /*  sort stereo bonds according to the ranks of the neighbors */
                pNeighborsForSort = nStereoNeigh;
                pn_RankForSort    = nRank;
                insertions_sort( nStereoNeighNumber, num_stereo, sizeof(nStereoNeighNumber[0]), CompNeighborsAT_NUMBER );

                /*  process stereo bonds one by one */
                for ( k = 0; k < num_stereo; k ++ ) {
                    stereo_neigh = nStereoNeigh[stereo_neigh_ord=(int)nStereoNeighNumber[k]];
                    if ( (r_neigh = (AT_NUMB)nRank[stereo_neigh]) CT_NEIGH_SMALLER_THAN rank ) {
                        /* accept only neighbors that have smaller ranks */
                        stereo_bond_parity = PARITY_VAL(at[i].stereo_bond_parity[stereo_neigh_ord]);
                        if ( stereo_bond_parity == AB_PARITY_NONE )
                            continue;

                        /* stereo_neigh      = at[i].stereo_bond_neighbor[nStereoNeighNumber[k]]-1; */
                        if ( ATOM_PARITY_KNOWN(stereo_bond_parity) ) {
                            parity = stereo_bond_parity;
                        } else
                        if ( ATOM_PARITY_WELL_DEF(at[i].parity) &&
                             ATOM_PARITY_WELL_DEF(at[stereo_neigh].parity) &&
                             MIN_DOT_PROD <= abs(at[i].stereo_bond_z_prod[stereo_neigh_ord]) ) {
                            /*  bond parity can be calculated */
                            int half_parity1, half_parity2, j, nn, stereo_neigh_ord2;
                            stereo_neigh_ord2 = -1;
                            for ( j = 0; j < MAX_NUM_STEREO_BONDS &&
                                         (nn=(int)at[stereo_neigh].stereo_bond_neighbor[j]); j++ ) {
                                if ( i+1 == nn ) {
                                    /* found the opposite end of the stereo bond */
                                    stereo_neigh_ord2 = j;
                                    break;
                                }
                            }
                            if ( stereo_neigh_ord2 >= 0 ) {
                                half_parity1 = HalfStereoBondParity( at, i, stereo_neigh_ord, nRank );
                                half_parity2 = HalfStereoBondParity( at, stereo_neigh, stereo_neigh_ord2, nRank );
                                if ( ATOM_PARITY_WELL_DEF(half_parity1) &&
                                     ATOM_PARITY_WELL_DEF(half_parity2)  ) {
                                    parity = 2 - ( half_parity1 + half_parity2
                                             + (at[i].stereo_bond_z_prod[stereo_neigh_ord] < 0))%2; 
                                } else {
                                    return CT_STEREOBOND_ERROR;  /*   <BRKPT> */
                                }
                            } else {
                                return CT_STEREOBOND_ERROR;  /*   <BRKPT> */
                            }
                        } else {
                            /*  parity cannot be calculated: not enough info or 'unknown' */
                            if ( AB_PARITY_NONE == (parity = inchi_max(at[i].parity, at[stereo_neigh].parity)) )
                                continue;
                            if ( ATOM_PARITY_WELL_DEF(parity) )
                                parity = AB_PARITY_UNDF; /*  should not happen */
                        }
                        if ( CHECK_OVERFLOW(*nStereoDbleLen, nMaxStereoDbleLen) )
                            return CT_OVERFLOW;  /*   <BRKPT> */
                        /*  first stereo bond atom */
                        LinearCTStereoDble[*nStereoDbleLen].at_num1 = rank;
                        /*  second stereo bond atom (opposite end) */
                        LinearCTStereoDble[*nStereoDbleLen].at_num2 = r_neigh;
                        /*  bond parity */
                        LinearCTStereoDble[*nStereoDbleLen].parity = parity;
                        (*nStereoDbleLen) ++;
                    }
                }
            }


            /*  stereo carbon */
            if ( bAllene > 0 ) {
                return 0;
            }
            if ( LinearCTStereoCarb && !at[i].stereo_bond_neighbor[0] ) {
                if ( CHECK_OVERFLOW(*nStereoCarbLen, nMaxStereoCarbLen) )
                    return CT_OVERFLOW;  /*   <BRKPT> */
                /*  stereo atom rank */
                LinearCTStereoCarb[*nStereoCarbLen].at_num = rank;
                /*  stereo atom parity */
                parity = ATOM_PARITY_WELL_DEF(at[i].parity)? (2 - (at[i].parity + num_trans)%2) : at[i].parity;
                LinearCTStereoCarb[*nStereoCarbLen].parity = parity;
                (*nStereoCarbLen) ++;
            }

        }

        return 0;
}
/**********************************************************************************/
void SwitchAtomStereoAndIsotopicStereo( sp_ATOM *at, int num_atoms, int *bSwitched )
{
    int i;
    /*  switch atom stereo data */
    for ( i = 0; i < num_atoms; i ++ ) {
        inchi_swap( (char*)&at[i].parity, (char*)&at[i].parity2, sizeof( at[i].parity ) );
        inchi_swap( (char*)&at[i].final_parity, (char*)&at[i].final_parity2, sizeof( at[i].final_parity ) );
        inchi_swap( (char*)&at[i].stereo_atom_parity, (char*)&at[i].stereo_atom_parity2, sizeof( at[i].stereo_atom_parity ) );
        inchi_swap( (char*)&at[i].bHasStereoOrEquToStereo, (char*)&at[i].bHasStereoOrEquToStereo2, sizeof( at[i].bHasStereoOrEquToStereo ) );

        inchi_swap( (char*)at[i].stereo_bond_neighbor, (char*)at[i].stereo_bond_neighbor2, sizeof( at[i].stereo_bond_neighbor ) );
        inchi_swap( (char*)at[i].stereo_bond_ord, (char*)at[i].stereo_bond_ord2, sizeof( at[i].stereo_bond_ord ) );
        inchi_swap( (char*)at[i].stereo_bond_z_prod, (char*)at[i].stereo_bond_z_prod2, sizeof( at[i].stereo_bond_z_prod ) );
        inchi_swap( (char*)at[i].stereo_bond_parity, (char*)at[i].stereo_bond_parity2, sizeof( at[i].stereo_bond_parity ) );
    }
    *bSwitched = !*bSwitched;
}
/**********************************************************************************/
void SetCtToIsotopicStereo( CANON_STAT *pCS, CANON_STAT *pCS2 )
{
    pCS->LinearCTStereoDble  = pCS2->LinearCTIsotopicStereoDble; /*  enable stereo */
    pCS->LinearCTStereoCarb  = pCS2->LinearCTIsotopicStereoCarb;

    pCS->LinearCTStereoDbleInv  = pCS2->LinearCTIsotopicStereoDbleInv; /*  enable inv. stereo */
    pCS->LinearCTStereoCarbInv  = pCS2->LinearCTIsotopicStereoCarbInv;
    pCS->nMaxLenLinearCTStereoDble = pCS2->nMaxLenLinearCTIsotopicStereoDble;
    pCS->nMaxLenLinearCTStereoCarb = pCS2->nMaxLenLinearCTIsotopicStereoCarb;

    pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTIsotopicStereoDble;
    pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb;
}
/**********************************************************************************/
void SetCtToNonIsotopicStereo( CANON_STAT *pCS, CANON_STAT *pCS2 )
{
    pCS->LinearCTStereoDble  = pCS2->LinearCTStereoDble; /*  enable stereo */
    pCS->LinearCTStereoCarb  = pCS2->LinearCTStereoCarb;

    pCS->LinearCTStereoDbleInv  = pCS2->LinearCTStereoDbleInv; /*  enable inv. stereo */
    pCS->LinearCTStereoCarbInv  = pCS2->LinearCTStereoCarbInv;
    pCS->nMaxLenLinearCTStereoDble = pCS2->nMaxLenLinearCTStereoDble;
    pCS->nMaxLenLinearCTStereoCarb = pCS2->nMaxLenLinearCTStereoCarb;

    pCS->nLenLinearCTStereoDble = pCS2->nLenLinearCTStereoDble;
    pCS->nLenLinearCTStereoCarb = pCS2->nLenLinearCTStereoCarb;

    pCS->nLenLinearCTIsotopicStereoDble = pCS2->nLenLinearCTIsotopicStereoDble;
    pCS->nLenLinearCTIsotopicStereoCarb = pCS2->nLenLinearCTIsotopicStereoCarb;
}

/**********************************************************************************/
int FillAllStereoDescriptors( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank, const AT_RANK *nAtomNumberCanon, CANON_STAT *pCS )
{
    int ret=0, i;
    /*  initialize zero lengths */
    pCS->nLenLinearCTStereoCarb = 0;
    pCS->nLenLinearCTStereoDble = 0;

    /*  fill atom by atom */
    for ( i = 0; !ret && i < num_atoms; i ++ ) {
        ret = FillSingleStereoDescriptors( at, (int)nAtomNumberCanon[i], -1, nCanonRank
                          , pCS->LinearCTStereoCarb, &pCS->nLenLinearCTStereoCarb, pCS->nMaxLenLinearCTStereoCarb
                          , pCS->LinearCTStereoDble, &pCS->nLenLinearCTStereoDble, pCS->nMaxLenLinearCTStereoDble
                          , 0 /* bAllene */ );
    }
    for ( i = 0; !ret && i < num_atoms; i ++ ) {
        ret = FillSingleStereoDescriptors( at, (int)nAtomNumberCanon[i], -1, nCanonRank
                          , pCS->LinearCTStereoCarb, &pCS->nLenLinearCTStereoCarb, pCS->nMaxLenLinearCTStereoCarb
                          , pCS->LinearCTStereoDble, &pCS->nLenLinearCTStereoDble, pCS->nMaxLenLinearCTStereoDble
                          , 1 /* bAllene */);
    }

    return ret;
}
/**********************************************************************************/
/*  Find stereo bond parities known in advance */
int SetKnownStereoBondParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                const AT_RANK *nRank, const AT_RANK *nAtomNumber )
{
    int i, j, n, m, j1, k, num_neigh1, num_neigh2, iMax1, parity;
    int trans_i1, trans_i2, trans_k1, trans_k2, prev_trans, trans_k, num_set;
    int i1, i2, k1, k2, n1, n2, m1, m2, /*stereo_bond_parity,*/ cumulene_len;
    AT_RANK nAtomRank1, nAtomRank2, nAtom1NeighRank;
    AT_RANK nNeighRank1[MAX_NUM_STEREO_BONDS], nNeighRank2[MAX_NUM_STEREO_BONDS];
    AT_RANK nNeighCanonRank1[MAX_NUM_STEREO_BONDS], nNeighCanonRank2[MAX_NUM_STEREO_BONDS];
    for ( i1 = 0, num_set = 0; i1 < num_atoms; i1 ++ ) {
        if ( !at[i1].parity || !at[i1].stereo_bond_neighbor[0] ) {
            continue;
        }

        if ( !PARITY_WELL_DEF(at[i1].parity) ) {
            continue;
        }
        nAtomRank1  = nRank[i1];
        iMax1       = (int)nAtomRank1-1;
        num_neigh1  = at[i1].valence;
        for ( n1 = 0; n1 < MAX_NUM_STEREO_BONDS && (i2=(int)at[i1].stereo_bond_neighbor[n1]); n1++ ) {
            i2 --;
            /*  found a stereo bond at[i1]-at[i2] adjacent to at[i1] */
            for ( n2 = 0, m=0; n2 < MAX_NUM_STEREO_BONDS && (m=(int)at[i2].stereo_bond_neighbor[n2]) && m-1 != i1; n2++ )
                ; /* locate stereo bond (#n2) at the opposite atom at[i2] */
            if ( m-1 != i1 || at[i1].stereo_bond_parity[n1] != at[i2].stereo_bond_parity[n2] ) {
                return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
            }
            if ( i1 < i2 ) {
                continue; /* do not process same bond 2 times */
            }

            if ( PARITY_KNOWN(at[i1].stereo_bond_parity[n1]) || !PARITY_VAL(at[i1].stereo_bond_parity[n1]) ) {
                continue;
            }
            if ( !PARITY_WELL_DEF(at[i1].parity) || !PARITY_WELL_DEF(at[i2].parity) ) {
                continue;
            }
            if ( PARITY_VAL(at[i1].stereo_bond_parity[n1]) != AB_PARITY_CALC ) {
                continue;  /*  ?? program error ?? should not happen */ /*   <BRKPT> */
            }
            /*stereo_bond_parity = PARITY_VAL(at[i1].stereo_bond_parity[n1]);*/
            cumulene_len       = BOND_CHAIN_LEN(at[i1].stereo_bond_parity[n1]);
            nAtomRank2         = nRank[i2];
            nAtom1NeighRank    = nRank[(int)at[i1].neighbor[(int)at[i1].stereo_bond_ord[n1]]];
            num_neigh2  = at[i2].valence;
            /*  store ranks of at[i1] stereo bond neighbors except one connected by a stereo bond */
            k = (int)at[i1].stereo_bond_ord[n1];
            trans_i1 = 0;
            for ( i = j = 0; i < num_neigh1; i ++ ) {
                if ( i != k ) {
                    nNeighRank1[j] = nRank[(int)at[i1].neighbor[i]];
                    j ++;
                }
            }
            if ( j == 2 ) {
                if ( nNeighRank1[0] == nNeighRank1[1] ) {
                    /*  neighbors are constitutionally identical, can't find bond parity */
                    continue;
                }
                trans_i1 = insertions_sort(nNeighRank1, j, sizeof(nNeighRank1[0]), comp_AT_RANK);
            }
            /*  store ranks of at[i2] stereo bond neighbors except one connected by a stereo bond */
            k = (int)at[i2].stereo_bond_ord[n2];
            trans_i2 = 0;
            for ( i = j = 0; i < num_neigh2; i ++ ) {
                if ( i != k ) {
                    nNeighRank2[j] = nRank[(int)at[i2].neighbor[i]];
                    j ++;
                }
            }
            if ( j == 2 ) {
                if ( nNeighRank2[0] == nNeighRank2[1] ) {
                    /*  neighbors are constitutionally identical, can't find bond parity */
                    continue;
                }
                trans_i2 = insertions_sort(nNeighRank2, j, sizeof(nNeighRank2[0]), comp_AT_RANK);
            }
            prev_trans = -1;
            trans_k1   = -2;
            trans_k    = -4; /* 2004-04-28 */
            /*  find all pairs of atoms that can be mapped on at[i1], at[i2] pair */
            for ( j1 = 0; j1 <= iMax1 && nAtomRank1==nRank[k1=(int)nAtomNumber[iMax1-j1]]; j1 ++ ) {
                /*  at[k1] is constitutionally equivalent to at[i1] */
                /*  find all at[k1] neighbors that have rank nAtomRank2; */
                /*  then find at[k2] constitutionally equivalent at at[i2] */
                if ( at[k1].valence != num_neigh1 ) {
                    return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
                }
                for ( m1 = 0; m1 < num_neigh1; m1 ++ ) {
                    int prev, next, len;
                    if ( nAtom1NeighRank != nRank[k2=(int)at[k1].neighbor[m1]] ) {
                        continue;
                    }
                    m2 = -1; /*  undefined yet */
                    prev = k1;
                    len  = 0;
                    if ( cumulene_len ) {
                        for ( len=0, next = (int)at[k1].neighbor[m1]; len < cumulene_len; len ++ ) {
                            if ( at[next].valence == 2 && !at[next].num_H ) {
                                j = ((int)at[next].neighbor[0] == prev);
                                prev = next;
                                next = at[next].neighbor[j];
                            } else {
                                break; /*  cannot continue */
                            }
                        }
                        if ( len != cumulene_len || nAtomRank2 != nRank[next] ) {
                            continue;  /*  not found */
                        }
                        k2 = next;
                    }
                    if ( at[k2].valence != num_neigh2 ) {
                        return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
                    }
                    /*  store canon. ranks of at[k1] neighbors */ /*  use i,j,k,m,n */
                    for ( n = j = 0; n < num_neigh1; n ++ ) {
                        if ( n != m1 ) {
                            i=(int)at[k1].neighbor[n];
                            for ( m = 0; m < num_neigh1-1; m ++ ) {
                                if ( nRank[i] == nNeighRank1[m] ) {
                                    nNeighCanonRank1[m] = nCanonRank[i];
                                    j ++;
                                    break;
                                }
                            }
                        }
                    }
                    if ( j != num_neigh1-1 ) {
                        return CT_STEREOCOUNT_ERR;  /*   <BRKPT> */
                    }
                    if ( j == 2 ) {
                        trans_k1 = insertions_sort(nNeighCanonRank1, j, sizeof(nNeighCanonRank1[0]), comp_AT_RANK);
                    } else {
                        trans_k1 = 0;
                    }
                    /*  store canon. ranks of at[k2] neighbors */ /*  use i,j,k,m,n */
                    for ( n = j = 0; n < num_neigh2; n ++ ) {
                        i=(int)at[k2].neighbor[n];
                        if ( i == prev ) { /* neighbor belongs to the stereobond */
                            m2 = n;
                        } else {
                            for ( m = 0; m < num_neigh2-1; m ++ ) {
                                if ( nRank[i] == nNeighRank2[m] ) {
                                    nNeighCanonRank2[m] = nCanonRank[i];
                                    j ++;
                                    break;
                                }
                            }
                        }
                    }
                    if ( j != num_neigh2-1 || m2 < 0 ) {
                        return CT_STEREOCOUNT_ERR;  /*   <BRKPT> */
                    }
                    if ( j == 2 ) {
                        trans_k2 = insertions_sort(nNeighCanonRank2, j, sizeof(nNeighCanonRank2[0]), comp_AT_RANK);
                    } else {
                        trans_k2 = 0;
                    }
                    trans_k = (trans_k1 + trans_k2)%2;
                    if ( prev_trans < 0 ) {
                        prev_trans = trans_k;
                    } else
                    if ( prev_trans != trans_k ) { /* was != trans_k1, changed 9-23-2003 */
                        break; /*  different number of transpositions */
                    }
                } /* end of the second atom mapping cycle */
                if ( prev_trans >= 0 && prev_trans != trans_k ) { /* was != trans_k1, changed 9-23-2003 */
                    break;
                }
            } /* end of the first atom mapping cycle */
            if ( prev_trans == trans_k ) { /* was == trans_k1, changed 9-23-2003 */
                int z_prod;
                /*  all mappings of canonical numbers on the */
                /*  stereo bond at[i1]-at[i2] produce equivalent numberings. */
                /*  Therefore the stereo bond parity is known at this time. */
                /*  parity_1 = at[i1].parity + (trans_i1 + trans_k1 + num_neigh1 - 1) + (int)at[i1].stereo_bond_ord[n1] */
                /*  expression in parentheses is equivalent to rank[first neigh] > rank[second neigh] */
                /*  same for parity_2. */
                /*  parity_2 = at[i2].parity + (trans_i2 + trans_k2 + num_neigh2 - 1) + (int)at[i2].stereo_bond_ord[n2] */
                /*  Sum of the two parities (without stereo_bond_z_prod) is: */
                parity = (at[i1].parity + at[i2].parity + prev_trans + trans_i1 + trans_i2
                              + num_neigh1 + num_neigh2
                              + (int)at[i1].stereo_bond_ord[n1] + (int)at[i2].stereo_bond_ord[n2] ) %2;
                z_prod = at[i1].stereo_bond_z_prod[n1];
                if ( MIN_DOT_PROD > abs(z_prod)) {
                    parity = AB_PARITY_UNDF; /*  undefined because of geometry */
                } else {
                    parity = (z_prod > 0)? 2 - parity : 1 + parity;
                }
                at[i1].stereo_bond_parity[n1] = ALL_BUT_PARITY(at[i1].stereo_bond_parity[n1]) | parity;
                at[i2].stereo_bond_parity[n2] = ALL_BUT_PARITY(at[i2].stereo_bond_parity[n2]) | parity;
                num_set ++;
            }
        }
    }
    return num_set;
}
/**********************************************************************************/
/*  Find stereo center parities known in advance */
int MarkKnownEqualStereoBondParities( sp_ATOM *at, int num_atoms,
                                      const AT_RANK *nRank, const AT_RANK *nAtomNumber )
{
    int j, n, m, j1, num_neigh1, num_neigh2, iMax1;
    int num_set, /*num_sb1, num_sb2,*/ bDifferentParities;
    int i1, i2, k1, k2, n1, n2, m1, m2, s1, s2, stereo_bond_parity, stereo_bond_parity2, cumulene_len;
    AT_RANK nAtomRank1, nAtomRank2, nAtom1NeighRank, nAtom2NeighRank;
    num_set = 0;
    for ( i1 = 0, num_set = 0; i1 < num_atoms; i1 ++ ) {
        if ( !at[i1].parity || !at[i1].stereo_bond_neighbor[0] ) {
            continue;
        }
        nAtomRank1  = nRank[i1];
        iMax1       = (int)nAtomRank1-1;
        num_neigh1  = at[i1].valence;
        /*  count stereogenic bonds adjacent to at[i1] */
        for ( n1 = 0; n1 < MAX_NUM_STEREO_BONDS && at[i1].stereo_bond_neighbor[n1]; n1++ )
            ;
        /*num_sb1 = n1;*/
        /*  search for bonds possibly constitutionally equivalent to each of the adjacent bonds */
        /*  and find if all of them have same already known parity */
        for ( n1 = 0, i2 = 0; n1 < MAX_NUM_STEREO_BONDS && (i2=(int)at[i1].stereo_bond_neighbor[n1]); n1++ ) {
            i2 --;
            nAtomRank2         = nRank[i2];
            if ( nAtomRank2 < nAtomRank1 || (nAtomRank2 == nAtomRank1 && i1 < i2) ) {
                /*  An attempt to reduce unnecessary repetitions. */
                /*  We still have repetitions because we do not accumulate a list of */
                /*  processed (nAtomRank2, nAtomRank1) pairs. */
                continue;
            }
            bDifferentParities = -1;   /*  parities have not been compared yet */
            /*  found a stereo bond at[i1]-at[i2] (adjacent to at[i1]) */
            /*
            if ( !PARITY_KNOWN(at[i1].stereo_bond_parity[n1]) || (at[i1].stereo_bond_parity[n1] & KNOWN_PARITIES_EQL) ) {
                continue;
            }
            */
            if ( at[i1].stereo_bond_parity[n1] & KNOWN_PARITIES_EQL ) {
                continue;
            }
            /*  stereo bond has known or unknown parity; we have not checked it yet */
            for ( n2 = 0; n2 < MAX_NUM_STEREO_BONDS && at[i2].stereo_bond_neighbor[n2]; n2++ )
                ;
            /*num_sb2 = n2;*/
            for ( n2 = 0, m = 0; n2 < MAX_NUM_STEREO_BONDS && (m=(int)at[i2].stereo_bond_neighbor[n2]) && m-1 != i1; n2++ )
                ;
            if ( m-1 != i1 || at[i1].stereo_bond_parity[n1] != at[i2].stereo_bond_parity[n2] ) {
                return CT_STEREOCOUNT_ERR; /*  program error: stereo bonds data in two directions are different */ /*   <BRKPT> */
            }
            stereo_bond_parity = PARITY_VAL(at[i1].stereo_bond_parity[n1]);
            cumulene_len       = BOND_CHAIN_LEN(at[i1].stereo_bond_parity[n1]);
            nAtom1NeighRank    = nRank[(int)at[i1].neighbor[(int)at[i1].stereo_bond_ord[n1]]];
            nAtom2NeighRank    = nRank[(int)at[i2].neighbor[(int)at[i2].stereo_bond_ord[n2]]];
            num_neigh2  = at[i2].valence;
            /*  find all pairs of atoms that possibly can be mapped on at[i1], at[i2] pair */
            /*  (we may also find pairs that cannot be mapped, but we cannot miss any pair */
            /*  that can be mapped) */
            for ( j1 = 0; j1 <= iMax1 && nAtomRank1==nRank[k1=(int)nAtomNumber[iMax1-j1]]; j1 ++ ) {
                /*  at[k1] is constitutionally equivalent to at[i1] */
                /*  find all at[k1] stereo bond neighbors at[k2] that have rank nAtomRank2; */
                /*  then find at[k2] constitutionally equivalent at at[i2] */
                if ( at[k1].valence != num_neigh1 ) {
                    return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
                }
                if ( !at[k1].bHasStereoOrEquToStereo ) {
                    at[k1].bHasStereoOrEquToStereo = 1;
                }
                /* -- do not check number of stereo bonds, check bonds themselves --
                for ( s1 = 0; s1 < MAX_NUM_STEREO_BONDS && at[k1].stereo_bond_neighbor[s1]; s1++ )
                    ;
                if ( num_sb1 != s1 ) {
                    bDifferentParities = 1;
                }
                */
                for ( m1 = 0; m1 < num_neigh1; m1 ++ ) {
                    /*  Looking for at[k1] neighbor with nRank=nAtom1NeighRank. */
                    /*  This neighbor may be on the bond constit. equivalent to at[i1]-at[i2] stereo bond */
                    /*  (or may be constit. equivalent an adjacent to at[i1] atom in a stereogenic cumulene chain) */
                    int prev, next, len;
                    if ( nAtom1NeighRank != nRank[k2=(int)at[k1].neighbor[m1]] ) {
                        continue;
                    }
                    /*  found at[k1] neighbor with nRank=nAtom1NeighRank */
                    m2 = -1; /*  undefined yet */
                    prev = k1;
                    len  = 0;
                    /*  if cumulene then bypass the cumulene chain */
                    if ( cumulene_len ) {
                        for ( len=0, next = (int)at[k1].neighbor[m1]; len < cumulene_len; len ++ ) {
                            if ( at[next].valence == 2 && !at[next].num_H ) {
                                j = ((int)at[next].neighbor[0] == prev);
                                prev = next;
                                next = at[next].neighbor[j];
                            } else {
                                break; /*  cannot continue: end of cumulene chain */
                            }
                        }
                        if ( len != cumulene_len || nAtomRank2 != nRank[next] ) {
                            continue;  /*  cumulene chain not found at this neighbor */
                        }
                        if ( nAtom2NeighRank != nRank[prev] ) {
                            /* continue; */ /*  ??? program error ??? If not, must be a very rare event */
                            return CT_STEREOCOUNT_ERR;  /*   <BRKPT> */
                        }
                        k2 = next;
                    }
                    
                    /*  a connected pair of constit. equivalent atoms found */
                    if ( at[k2].valence != num_neigh2 ) {
                        return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
                    }
                    for ( n = 0; n < num_neigh2; n ++ ) {
                        if ( prev == (int)at[k2].neighbor[n] ) {
                            m2 = n; /*  found bond from the opposite end of a possibly stereogenic bond */
                            break;
                        }
                    }
                    if ( m2 < 0 ) {
                        return CT_STEREOCOUNT_ERR; /*  program error: opposite direction bond not found */ /*   <BRKPT> */
                    }
                    if ( !at[k2].bHasStereoOrEquToStereo ) {
                        at[k2].bHasStereoOrEquToStereo = 1;
                    }

                    /*  check if atoms at[k1] and at[k2] are connected by a stereo bond */
                    for ( s1 = 0, m = 0; s1 < MAX_NUM_STEREO_BONDS && (m=(int)at[k1].stereo_bond_neighbor[s1]) && m-1 != k2; s1++ )
                        ;
                    if ( m-1 != k2 ) {
                        bDifferentParities = 1; /*  cannot find the stereo bond */
                        at[k1].bHasStereoOrEquToStereo =
                        at[k2].bHasStereoOrEquToStereo = 2;
                        continue;
                    }
                    /*  -- do not check number of stereo bonds, check bonds themselves --
                    for ( s2 = 0; s2 < MAX_NUM_STEREO_BONDS && at[k2].stereo_bond_neighbor[s2]; s2++ )
                        ;
                    if ( num_sb2 != s2 ) {
                        bDifferentParities = 1;
                        continue;
                    }
                    */
                    for ( s2 = 0, m = 0; s2 < MAX_NUM_STEREO_BONDS && (m=(int)at[k2].stereo_bond_neighbor[s2]) && m-1 != k1; s2++ )
                        ;
                    if ( m-1 != k1 ) {
                        /*
                        bDifferentParities = 1; // cannot find the stereo bond
                        continue;
                        */
                        return CT_STEREOCOUNT_ERR; /*  program error: opposite direction bond not found */ /*   <BRKPT> */
                    }
                    if ( at[k1].stereo_bond_parity[s1] != at[k2].stereo_bond_parity[s2] ) {
                        bDifferentParities = 1;
                        continue;
                    }
                    stereo_bond_parity2 = PARITY_VAL(at[k1].stereo_bond_parity[s1]);
                    if ( stereo_bond_parity2 != stereo_bond_parity ) {
                        bDifferentParities = 1;
                        continue;
                    }
                    if ( stereo_bond_parity2 == stereo_bond_parity && bDifferentParities < 0 ) {
                        bDifferentParities = 0;
                    }
                }
            }
            /*  mark equal parities */
            if ( 0 == bDifferentParities && PARITY_KNOWN( stereo_bond_parity ) ) {
                for ( j1 = 0; j1 <= iMax1 && nAtomRank1==nRank[k1=(int)nAtomNumber[iMax1-j1]]; j1 ++ ) {
                    /*  at[k1] is constitutionally equivalent to at[i1] */
                    for ( s1 = 0, k2 = 0; s1 < MAX_NUM_STEREO_BONDS && (k2=(int)at[k1].stereo_bond_neighbor[s1]); s1++ ) {
                        k2--;
                        if ( nRank[k2] == nAtomRank2 ) {
                            int b1, b2;
                            for ( s2 = 0, m = 0; s2 < MAX_NUM_STEREO_BONDS && (m=(int)at[k2].stereo_bond_neighbor[s2])
                                  && m-1 != k1; s2++ )
                                ;
                            if ( m-1 != k1 ) {
                                return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
                            }
                            /*  mark the stereo bonds */
                            b1 = !(at[k1].stereo_bond_parity[s1] & KNOWN_PARITIES_EQL);
                            b2 = !(at[k2].stereo_bond_parity[s2] & KNOWN_PARITIES_EQL);
                            if ( 2 == b1 + b2 ) {
                                at[k1].stereo_bond_parity[s1] |= KNOWN_PARITIES_EQL;
                                at[k2].stereo_bond_parity[s2] |= KNOWN_PARITIES_EQL;
                                num_set ++;
                            } else
                            if ( b1 || b2 ) {
                                return CT_STEREOCOUNT_ERR; /*  program error */ /*   <BRKPT> */
                            }
                        }
                    }
                }
            }
        }
    }
    return num_set;
}
#if ( REMOVE_KNOWN_NONSTEREO == 1 ) /* { */
/**********************************************************************************/
/*   Return next atom number (and its canon. rank) on the path prev->cur->next */
/*   in order of ascending canonical ranks of the next atoms:  *cr(output) >  *cr(input) */
/*   To start the sequence let *cr=0 */
/*   If no more neighbors available the return value = 0; if successgul then the return value = 1. */
int GetNextNeighborAndRank( sp_ATOM *at, AT_RANK cur, AT_RANK prev, AT_RANK *n, AT_RANK *cr, const AT_RANK *nCanonRank )
{
    int i, val;
    AT_RANK cr1 = MAX_ATOMS+1, j, j1=MAX_ATOMS+1, crj;

    for ( i = 0, val = at[(int)cur].valence; i < val; i ++ ) {
        if ( (j=at[cur].neighbor[i]) != prev && 
             cr1 > (crj=nCanonRank[(int)j]) && crj > *cr ) {
            cr1 = crj;
            j1  = j;
        }
    }
    if ( cr1 <= MAX_ATOMS ) {
        *cr = cr1;
        *n  = (AT_RANK)j1;
        return 1;
    }
    return 0;  /*  program error */ /*   <BRKPT> */
}

/**********************************************************************************/
/*  Find next pair of neighbors having the next greater canon. rank */
/*  The neighbors should be constitutionally identical and traversed simultaneouly or not traversed at all */
/*  If a bond cur1-*n1 or cur2-*n2 is a stereo bond then reject if their stereo bond parities are different or */
/*    cannot be calculated without breaking ties. */
int GetAndCheckNextNeighbors( sp_ATOM *at, AT_RANK cur1, AT_RANK prev1, AT_RANK cur2, AT_RANK prev2,
                              AT_RANK *n1, AT_RANK *n2, AT_RANK *nVisited1, AT_RANK *nVisited2,
                              const AT_RANK *nRank, const AT_RANK *nCanonRank )
{
    AT_RANK cr1, cr2, s1, s2;
    int     i1, i2, k1, k2;
    cr1 = ( *n1 > MAX_ATOMS )? 0 : nCanonRank[(int)*n1];
    cr2 = ( *n2 > MAX_ATOMS )? 0 : nCanonRank[(int)*n2];
    if ( !GetNextNeighborAndRank( at, cur1, prev1, n1, &cr1, nCanonRank ) ||
         !GetNextNeighborAndRank( at, cur2, prev2, n2, &cr2, nCanonRank ) ||
         nRank[(int)*n1] != nRank[(int)*n2] || nVisited1[(int)*n1] != nVisited2[(int)*n2] ) {
        return 0;  /*  program error; no breakpoint here */ /*   <BRKPT> */
    }

    /*  Even though the bond or cumulene might have already been checked, check it: this is */
    /*  the only place we can check stereo bonds and cumulenes that are not edges of the DFS tree */
    /*  The code works both for a stereo bond and a stereogenic cumulene. */
    for ( i1 = 0, k1 = 0; i1 < MAX_NUM_STEREO_BONDS &&
                          (s1=at[cur1].stereo_bond_neighbor[i1]) &&
                         !(k1=(at[cur1].neighbor[(int)at[cur1].stereo_bond_ord[i1]] == *n1)); i1 ++ )
        ;
    for ( i2 = 0, k2 = 0; i2 < MAX_NUM_STEREO_BONDS &&
                          (s2=at[cur2].stereo_bond_neighbor[i2]) &&
                         !(k2=(at[cur2].neighbor[(int)at[cur2].stereo_bond_ord[i2]] == *n2)); i2 ++ )
        ;
    if ( k1 != k2 ) {    
        return 0; /*  possibly not an error: constit. equivalent atoms on a stereo bond and not on a stereo bond */
    }
    if ( k1 /* yes, it is a stero bond */ &&
         ( at[cur1].stereo_bond_parity[i1] != at[cur2].stereo_bond_parity[i2] ||
           /* PARITY_KNOWN (at[cur1].stereo_bond_parity[i1] ) */  /*  replaced 08-13-2002 with the next: */
           !PARITY_WELL_DEF (at[cur1].stereo_bond_parity[i1] ) /*  it suffices to check only one parity */
    ) ) {
        return 0; /*  different or (currently) unknown stereo bond parities */
    }
    return 1; /*  stereo bonds have known parities */
}

/**********************************************************************************/
/*  Simultaneously DFS-traverse 2 paths starting at the bonds prev1->cur1 and prev2->cur2 */
/*  The two paths MUST go through the pairs of constitutionally identical atoms, each atom being on one path. */
/*  Reject if encountered atoms having currently unknown (without breaking ties) */
/*      parities or having different known or unknown or undefined parities. */
/*  Save length of the path into nVisited[cur. atom number]. */
/*  Only one nVisited[] array is sufficient because the paths from the beginning are in different ring systems. */
AT_RANK PathsHaveIdenticalKnownParities( sp_ATOM *at, AT_RANK prev1, AT_RANK cur1, AT_RANK prev2, AT_RANK cur2,
                                         AT_RANK *nVisited1, AT_RANK *nVisited2,
                                         const AT_RANK *nRank, const AT_RANK *nCanonRank, AT_RANK nLength )
{
    int k;
    AT_RANK n1, n2;

    nLength ++;   /*  number of successfully traversed pairs of atoms */
    nVisited1[cur1] = nLength;
    nVisited2[cur2] = nLength;
    /*  the atoms must be either both stereogenic and have well-defined parities or non-stereogenic at all. */
    if ( at[cur1].stereo_atom_parity != at[cur2].stereo_atom_parity ||
         (at[cur1].stereo_atom_parity && !PARITY_WELL_DEF (at[cur1].stereo_atom_parity))
          ) {
        return 0;  /*  Reject: Different or unknown in advance parities */
    }

    if ( at[cur1].valence != at[cur2].valence ) {
        return 0;  /*  program error */ /*   <BRKPT> */
    }
    if ( at[cur1].valence == 1 ) {
        return nLength; /*  so far success */
    }
    

    for ( k = 1, n1 = MAX_ATOMS+1, n2=MAX_ATOMS+1; k < at[cur1].valence; k ++ ) {
        /*  start from 1: since we do not go back, we have only (at[cur1].valence-1) bonds to try */
        if ( !GetAndCheckNextNeighbors( at, cur1, prev1, cur2, prev2,
                              &n1, &n2, nVisited1, nVisited2, nRank, nCanonRank ) ) {
            return 0; /*  different neighbors                       */
        }
        /*  In a DFS we do not traverse already visited atoms */
        if ( !nVisited1[n1] ) { /*  recursion */
            if ( ! (nLength = PathsHaveIdenticalKnownParities( at, cur1, n1, cur2, n2, nVisited1, nVisited2, nRank, nCanonRank, nLength ) ) ) {
                return 0;
            }
        }
    }
    /*  To be on a safe side, recheck after all nVisited[] have been set */
    for ( k = 1, n1 = MAX_ATOMS+1, n2=MAX_ATOMS+1; k < at[cur1].valence; k ++ ) {
        /*  start from 1: since we do not go back, we have only (at[cur1].valence-1) bonds to try */
        if ( !GetAndCheckNextNeighbors( at, cur1, prev1, cur2, prev2,
                              &n1, &n2, nVisited1, nVisited2, nRank, nCanonRank ) ) {
            return 0; /*  different neighbors */
        }
    }

    
    return nLength;

}

/**********************************************************************************/
/*  Remove stereo marks from the bonds that are known to be non-stereo */
/*  (compare neighbors if they are attached by cut-edges) */
int RemoveKnownNonStereoBondParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                      const AT_RANK *nRank, CANON_STAT *pCS)
{
    int j, n, m, ret;
    
    int i1, n1, s2;
    AT_RANK nAtomRank1, nAtomRank2, neigh[3], opposite_atom, *nVisited = NULL;
    ret = 0;
    for ( i1 = 0; i1 < num_atoms; i1 ++ ) {
        if ( at[i1].valence != 3 || !at[i1].stereo_bond_neighbor[0] ) {
            continue;
        }
        for ( n1 = 0; n1 < MAX_NUM_STEREO_BONDS && (s2=at[i1].stereo_bond_neighbor[n1]); n1++ ) {
            if ( !PARITY_CALCULATE(at[i1].stereo_bond_parity[n1]) && PARITY_WELL_DEF(at[i1].stereo_bond_parity[n1]) ) {
                continue;
            }
            opposite_atom = (AT_RANK)(s2-1);
            /* s2 = at[i1].neighbor[m=(int)at[i1].stereo_bond_ord[n1]]; */
            m=(int)at[i1].stereo_bond_ord[n1];
            for ( j = 0, n = 0; j < at[i1].valence; j ++ ) {      
                /* if ( at[i1].neighbor[j] != s2 ) */
                if ( j != m )
                {
                    neigh[n++] = at[i1].neighbor[j]; 
                }
            }
            if ( n > 2 ) {
                ret = CT_STEREOBOND_ERROR;  /*   <BRKPT> */
                goto exit_function;
            }
            if ( n != 2 || nRank[(int)neigh[0]] != nRank[(int)neigh[1]] ) {
                continue; /*  may happen if another half-bond has not a defined parity */
            }
            if ( at[i1].nRingSystem == at[(int)neigh[0]].nRingSystem ) {
                continue;  /*  no more ring system membership check is necessary because     */
            }              /*  the two neighbors are to be constitutionally equivalent atoms */
            if ( !nVisited && !(nVisited = (AT_RANK*) inchi_malloc( sizeof(nVisited[0])*num_atoms ) ) ) {
                ret = CT_OUT_OF_RAM;  /*   <BRKPT> */
                goto exit_function;
            }
            memset( nVisited, 0, sizeof(nVisited[0])*num_atoms );
            nVisited[i1] = 1;
            if ( PathsHaveIdenticalKnownParities( at, (AT_RANK)i1, neigh[0], (AT_RANK)i1, neigh[1], nVisited, nVisited, nRank, nCanonRank, 1 ) ) {
                if ( !RemoveOneStereoBond( at, i1, /* atom number*/ n1 /* stereo bond number*/ ) ) {
                    ret = CT_STEREOBOND_ERROR;  /*   <BRKPT> */
                    goto exit_function;
                }
                n1 --; /*  cycle counter may temporarily become negative */
                /*  Remove from pCS */
                nAtomRank1 = inchi_max( nCanonRank[i1], nCanonRank[opposite_atom]);
                nAtomRank2 = inchi_min( nCanonRank[i1], nCanonRank[opposite_atom]);
                for ( n = 0, m = pCS->nLenLinearCTStereoDble-1; n <= m; n ++ ) {
                    if ( pCS->LinearCTStereoDble[n].at_num1 == nAtomRank1 &&
                         pCS->LinearCTStereoDble[n].at_num2 == nAtomRank2 ) {
                        if ( n < m ) { /*  remove pCS->LinearCTStereoDble[n] */
                            memmove( pCS->LinearCTStereoDble + n,
                                     pCS->LinearCTStereoDble + n + 1,
                                     (m-n)*sizeof(pCS->LinearCTStereoDble[0]) );
                        }
                        pCS->nLenLinearCTStereoDble --;
#if ( bRELEASE_VERSION == 0 )
                        pCS->bExtract |= EXTR_KNOWN_USED_TO_REMOVE_PARITY;
#endif
                        m = -1;   /*  set flag "found" */
                        break;
                    }
                }
                if ( m >= 0) {
                    ret = CT_STEREOCOUNT_ERR;  /*  bond not found  <BRKPT> */
                    goto exit_function;
                }
                ret ++;  /*  number of removed known in advance non-stereo bonds */
            }
        }
    }

exit_function:

    if ( nVisited ) {
        inchi_free( nVisited );
    }
    return ret;
}
#endif /* } REMOVE_KNOWN_NONSTEREO */
/**********************************************************************************/
/*  Find stereo center parities known in advance */
int SetKnownStereoCenterParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                  const AT_RANK *nRank, const AT_RANK *nAtomNumber )
{
    int i, j, n, m, j1, k, num_neigh, iMax, trans_i, trans_k, prev_trans, num_set;
    AT_RANK nAtomRank;
    AT_RANK nNeighRank[MAX_NUM_STEREO_ATOM_NEIGH];
    AT_RANK nNeighCanonRank[MAX_NUM_STEREO_ATOM_NEIGH];
    for ( i = 0, num_set = 0; i < num_atoms; i ++ ) {
        if ( !at[i].parity || at[i].stereo_bond_neighbor[0] ) {
            continue;
        }
        if ( at[i].stereo_atom_parity != AB_PARITY_CALC || !PARITY_WELL_DEF(at[i].parity) ) {
            continue;
        }
        num_neigh = at[i].valence;
        for ( j = 0; j < num_neigh; j ++ ) {
            nNeighRank[j] = nRank[(int)at[i].neighbor[j]];
        }
        nAtomRank = nRank[i];
        if ( num_neigh == 1 ) {  /* other neighbors must be implicit H */
            at[i].stereo_atom_parity = at[i].parity;
            trans_i = 0;
        } else {
            /* sort constitutional equivalence ranks of the neighbors */
            trans_i = insertions_sort(nNeighRank, num_neigh, sizeof(nNeighRank[0]), comp_AT_RANK);
            for ( j = 1; j < num_neigh; j ++ ) {
                if ( nNeighRank[j-1] == nNeighRank[j] )
                    break; /* at[i] has consitutionally identical neighbors */
            }
            if ( j < num_neigh ) {
                /*  at least 2 neighbors are const. identical; parity cannot be calculated at this time */
                continue; /*  try next stereo atom */
            }
        }
        prev_trans = -1;
        trans_k    =  0;
        /*  find neighbors of constitutionally equivalent stereo centers */
        /*  and at[i] parities in case those centers are mapped on at[i] */
        for ( iMax = (int)nAtomRank-1, j1 = 0; j1 <= iMax && nAtomRank==nRank[k=(int)nAtomNumber[iMax-j1]]; j1 ++ ) {
            /*  at[k] is constitutionally equivalent to at[i] */
            if ( (int)at[k].valence != num_neigh ) {
                return CT_STEREOCOUNT_ERR;  /*   <BRKPT> */
            }
            /* -- commented out to accept  non-stereogenic atoms since     --
               -- they may participate in mapping stereocenters 12-16-2003 --
            if ( !PARITY_VAL(at[k].parity) ) {
                continue; // not a stereogenic atom
            }
            */
            for ( j = 0, m = 0; m < num_neigh; m ++ ) {
                for ( n = 0; n < num_neigh; n ++ ) {
                    if ( nRank[(int)at[k].neighbor[n]] == nNeighRank[m] ) {
                        /* save canonical numbers (ranks) of the neighbors in
                         * order of increasing constit. equivalence ranks */
                        nNeighCanonRank[m] = nCanonRank[(int)at[k].neighbor[n]];
                        j ++;
                        break;
                    }
                }
            }
            if ( j != num_neigh ) {
                return CT_STEREOCOUNT_ERR;  /*   <BRKPT> */
            }
            trans_k = insertions_sort(nNeighCanonRank, num_neigh, sizeof(nNeighCanonRank[0]), comp_AT_RANK);
            trans_k %= 2;
            if ( prev_trans < 0 ) {
                prev_trans = trans_k;
            } else
            if ( trans_k != prev_trans ) {
                /*  different mappings may produce different parities. Cannot find the parity at this time */
                /*  this may happen when a set of constit. equivalent atoms has non-contiguous canonical numbers */
               break;
            }
        }
        if ( trans_k == prev_trans ) {
            at[i].stereo_atom_parity = 2 - (at[i].parity + trans_i + prev_trans ) % 2;
            num_set ++;
        }
    }
    return num_set;
}

#if ( REMOVE_KNOWN_NONSTEREO == 1 ) /* { */
/**********************************************************************************/
/*  DFS along paths starting from the stereocenter through pairs of cut-edges  */
int RemoveKnownNonStereoCenterParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank,
                                        const AT_RANK *nRank, CANON_STAT *pCS)
{
    int i, j, n, m, k, num_neigh, ret = 0;
    /*AT_RANK nAtomRank;*/
    AT_RANK nNeighRank[MAX_NUM_STEREO_ATOM_NEIGH], nNeighOrd[MAX_NUM_STEREO_ATOM_NEIGH];
    
    AT_RANK *nVisited = NULL;
    
    for ( i = 0; i < num_atoms; i ++ ) {
        if ( !at[i].parity || at[i].stereo_bond_neighbor[0] ) {
            continue;
        }
        if ( !PARITY_CALCULATE(at[i].stereo_atom_parity) && PARITY_WELL_DEF(at[i].stereo_atom_parity) ) {
            continue;
        }
        num_neigh = at[i].valence;
        for ( j = 0; j < num_neigh; j ++ ) {
            nNeighRank[j] = nRank[(int)at[i].neighbor[j]];
            nNeighOrd[j]  = j;
        }
        /*nAtomRank = nRank[i];*/
        if ( num_neigh == 1 ) {
            continue;
        }
        pn_RankForSort = nNeighRank;
        insertions_sort(nNeighOrd, num_neigh, sizeof(nNeighRank[0]), CompRanksOrd);
        for ( j = k = 1; k && j < num_neigh; j ++ ) {
            if ( at[i].nRingSystem != at[(int)at[i].neighbor[(int)nNeighOrd[j]]].nRingSystem &&
                 /*  no more ring system membership check is necessary because */
                 /*  the two neighbors are to be constitutionally equivalent atoms: */
                nNeighRank[nNeighOrd[j-1]] == nNeighRank[nNeighOrd[j]] ) {
                k = j;
                do {
                    if ( !nVisited && !(nVisited = (AT_RANK*) inchi_malloc( sizeof(nVisited[0])*num_atoms ) ) ) {
                        ret = CT_OUT_OF_RAM;  /*   <BRKPT> */
                        goto exit_function;
                    }
                    memset( nVisited, 0, sizeof(nVisited[0])*num_atoms );
                    nVisited[i] = 1;
                    if ( PathsHaveIdenticalKnownParities( at, (AT_RANK)i, at[i].neighbor[(int)nNeighOrd[j-1]],
                                                              (AT_RANK)i, at[i].neighbor[(int)nNeighOrd[k]],
                                                              nVisited, nVisited, nRank, nCanonRank, 1 ) ) {
                        at[i].parity             = 0; /*  remove parity */
                        at[i].stereo_atom_parity = 0;
                        at[i].final_parity       = 0;
                        /* at[i].bHasStereoOrEquToStereo = 0; */
                        for ( n = 0, m = pCS->nLenLinearCTStereoCarb-1; n <= m; n ++ ) {
                            if ( pCS->LinearCTStereoCarb[n].at_num == nCanonRank[i] ) {
                                if ( n < m ) { /*  remove pCS->LinearCTStereoCarb[n] */
                                    memmove( pCS->LinearCTStereoCarb + n,
                                             pCS->LinearCTStereoCarb + n + 1,
                                             (m-n)*sizeof(pCS->LinearCTStereoCarb[0]) );
                                }
                                pCS->nLenLinearCTStereoCarb --;
                                k = 0;
#if ( bRELEASE_VERSION == 0 )
                                pCS->bExtract |= EXTR_KNOWN_USED_TO_REMOVE_PARITY;
#endif
                                break;
                            }
                        }
                        if ( k ) {
                            ret = CT_STEREOCOUNT_ERR;  /*   <BRKPT> */
                            goto exit_function;
                        }
                        ret ++;
                        break;
                    }
                } while ( ++k < num_neigh && nNeighRank[nNeighOrd[j-1]] == nNeighRank[nNeighOrd[k]] );
            }
        }
    }

exit_function:

    if ( nVisited ) {
        inchi_free( nVisited );
    }

    return ret;
}
#endif /* } REMOVE_KNOWN_NONSTEREO */
/**********************************************************************************/
/*  Find stereo center parities known in advance */
int MarkKnownEqualStereoCenterParities( sp_ATOM *at, int num_atoms,
                                        const AT_RANK *nRank, const AT_RANK *nAtomNumber )
{
    int i, j1, k, num_centers, iMax, bDifferentParities;
    AT_RANK nAtomRank;
    int  parity, parity_k;
    num_centers = 0;
    for ( i = 0; i < num_atoms; i ++ ) {
        if ( !at[i].parity || at[i].stereo_bond_neighbor[0] ) {
            continue;
        }
        if ( at[i].bHasStereoOrEquToStereo ) {
            continue; /* already marked */
        }
        if ( /*!PARITY_KNOWN(at[i].stereo_atom_parity) ||*/ (at[i].stereo_atom_parity & KNOWN_PARITIES_EQL) ) {
            continue;
        }
        parity    = PARITY_VAL(at[i].stereo_atom_parity);
        if ( parity == AB_PARITY_NONE ) {
            continue;
        }
        nAtomRank = nRank[i];
        bDifferentParities = -1;
        /*  find constitutionally equivalent stereo centers and compare their known at this time parities */
        for ( iMax = (int)nAtomRank-1, j1 = 0; j1 <= iMax && nAtomRank==nRank[k=(int)nAtomNumber[iMax-j1]]; j1 ++ ) {
            /*  at[k] is constitutionally equivalent to at[i] */
            parity_k = PARITY_VAL(at[k].stereo_atom_parity);
            if ( parity_k != parity ) {
                bDifferentParities = 1;
            } else
            if ( parity_k == parity && bDifferentParities < 0 ) {
                bDifferentParities = 0;
            }
            if ( !parity_k ) {
                at[k].bHasStereoOrEquToStereo = 2;
            } else
            if ( !at[k].bHasStereoOrEquToStereo ) {
                at[k].bHasStereoOrEquToStereo = 1;
            }
        }
        if ( 0 == bDifferentParities && PARITY_KNOWN( parity ) ) {
            for ( iMax = (int)nAtomRank-1, j1 = 0; j1 <= iMax && nAtomRank==nRank[k=(int)nAtomNumber[iMax-j1]]; j1 ++ ) {
                /*  at[k] is constitutionally equivalent to at[i] */
                at[k].stereo_atom_parity |= KNOWN_PARITIES_EQL;
                num_centers ++;
            }
        }
    }
    return num_centers;
}
/*****************************************************************************/
/* invert known parities in at[] and in pCS->LinearCTStereoDble              */
/*                                      pCS->LinearCTStereoCarb              */
/* nCanonRank[] contains canonical ranks used to fill pCS->LinearCTStereo... */
/* nAtomNumberCanon[] will be filled with atom numbers in canonical order    */
/*****************************************************************************/
int InvertStereo( sp_ATOM *at, int num_at_tg,
                  AT_RANK *nCanonRank, AT_RANK *nAtomNumberCanon,
                  CANON_STAT *pCS, int bInvertLinearCTStereo )
{
    int i, j, j1, j2, num_changes, parity, cumulene_len;
    num_changes = 0;
    for ( i = 0; i < num_at_tg; i ++ ) {
        nAtomNumberCanon[(int)nCanonRank[i]-1] = i;
    }
    for ( i = 0; i < pCS->nLenLinearCTStereoCarb; i ++ ) {
        parity = pCS->LinearCTStereoCarb[i].parity;
        if ( ATOM_PARITY_WELL_DEF( parity ) ) {
            j = nAtomNumberCanon[(int)pCS->LinearCTStereoCarb[i].at_num-1];
            if ( PARITY_WELL_DEF(at[j].parity) ) {
                at[j].parity ^= AB_INV_PARITY_BITS;
            } else {
                goto exit_error; /* inconsistency */
            }
            if ( bInvertLinearCTStereo ) {
                pCS->LinearCTStereoCarb[i].parity ^= AB_INV_PARITY_BITS;
            }
            num_changes ++;
            if ( PARITY_WELL_DEF(at[j].stereo_atom_parity) ) {
                at[j].stereo_atom_parity ^= AB_INV_PARITY_BITS;
            }
            if ( PARITY_WELL_DEF(at[j].final_parity) ) {
                at[j].final_parity ^= AB_INV_PARITY_BITS;
            }
        }
    }
    for ( i = 0; i < pCS->nLenLinearCTStereoDble; i ++ ) {
        parity = pCS->LinearCTStereoDble[i].parity;
        if ( ATOM_PARITY_WELL_DEF( parity ) ) {
            j1 = nAtomNumberCanon[(int)pCS->LinearCTStereoDble[i].at_num1-1];
            cumulene_len = BOND_CHAIN_LEN(at[j1].stereo_bond_parity[0]);
            if ( cumulene_len % 2 ) {
                /* invert only in case of allene */
                j2 = nAtomNumberCanon[(int)pCS->LinearCTStereoDble[i].at_num2-1];
                /* checks for debug only */
                if ( 1 < MAX_NUM_STEREO_BONDS ) {
                    if ( at[j1].stereo_bond_neighbor[1] ||
                         at[j2].stereo_bond_neighbor[1] ) {
                        goto exit_error; /* inconsitency: atom has more than one cumulene bond */
                    }
                }
                if ( cumulene_len != BOND_CHAIN_LEN(at[j2].stereo_bond_parity[0]) ||
                     j1+1 != at[j2].stereo_bond_neighbor[0] ||
                     j2+1 != at[j1].stereo_bond_neighbor[0] ) {
                    goto exit_error; /* inconsitency: atoms should refer to each other */
                }
                /* invert parities */
                if ( PARITY_WELL_DEF(at[j1].parity) && PARITY_WELL_DEF(at[j2].parity) ) {
                    j  = inchi_min( j1, j2 ); 
                    at[j].parity ^= AB_INV_PARITY_BITS; /* for reversability always invert only atom with the smaller number */
                } else {
                    goto exit_error; /* inconsistency */
                }
                if ( bInvertLinearCTStereo ) {
                    pCS->LinearCTStereoDble[i].parity ^= AB_INV_PARITY_BITS;
                }
                num_changes ++;
                if ( PARITY_WELL_DEF(at[j1].stereo_bond_parity[0]) ) {
                    at[j1].stereo_bond_parity[0] ^= AB_INV_PARITY_BITS;
                }
                if ( PARITY_WELL_DEF(at[j2].stereo_bond_parity[0]) ) {
                    at[j2].stereo_bond_parity[0] ^= AB_INV_PARITY_BITS;
                }
            }
        }
    }

    return num_changes;

exit_error:

    return CT_STEREOCOUNT_ERR;
}
/**********************************************************************************/
/*  Make sure atoms stereo descriptors fit molecular symmetry and remove */
/*  parity from obviously non-stereo atoms and bonds */
int FillOutStereoParities( sp_ATOM *at, int num_atoms, const AT_RANK *nCanonRank, const AT_RANK *nAtomNumberCanon,
                           const AT_RANK *nRank, const AT_RANK *nAtomNumber, CANON_STAT *pCS, int bIsotopic )
{
    int ret;
    /*  unmark atoms with 2 or more constitutionally equivalent neighbors */
    /*  such that there is no path through them to an atom with parity */
    ret = UnmarkNonStereo( at, num_atoms, nRank, nAtomNumber, bIsotopic );
    if ( ret < 0 )
        return ret;  /*  program error? */ /*   <BRKPT> */
    ret = FillAllStereoDescriptors( at, num_atoms, nCanonRank, nAtomNumberCanon, pCS ); /*  ret<0: error */
    if ( !ret ) {
        ret = pCS->nLenLinearCTStereoCarb + pCS->nLenLinearCTStereoDble;
    }
    if ( ret < 0 ) {
        return ret; /*  program error? */ /*   <BRKPT> */
    }

    if ( ret >= 0 ) {
        int ret2;
        ret2 = SetKnownStereoCenterParities( at, num_atoms, nCanonRank, nRank, nAtomNumber );
        if ( ret2 >= 0 ) {
            ret2 = MarkKnownEqualStereoCenterParities( at, num_atoms, nRank, nAtomNumber );
        }
        if ( ret2 >= 0 ) {
            ret2 = SetKnownStereoBondParities( at, num_atoms, nCanonRank, nRank, nAtomNumber );
            if ( ret2 >= 0 ) {
                ret2 = MarkKnownEqualStereoBondParities( at, num_atoms, nRank, nAtomNumber);
            }
        }
#if ( REMOVE_KNOWN_NONSTEREO == 1 ) /* { */
        if ( ret2 >= 0 ) {
            int ret3;
            do {
                ret2 = RemoveKnownNonStereoCenterParities( at, num_atoms, nCanonRank, nRank, pCS);
                if ( ret2 >= 0 ) {
                    ret3 = RemoveKnownNonStereoBondParities( at, num_atoms, nCanonRank, nRank, pCS);
                    ret2 = ret3 >= 0? ret2+ret3 : ret3;
                }
            }
            while( ret2 > 0 );  
        }
        if ( RETURNED_ERROR( ret2 ) ) {
            ret = ret2;
        }
#endif /* } REMOVE_KNOWN_NONSTEREO */
    }

    return ret; /*  non-zero means error */
}
/**********************************************************************************/
int GetStereoNeighborPos( sp_ATOM *at, int iAt1, int iAt2 )
{
    int k1;
    AT_RANK sNeigh = (AT_RANK)(iAt2+1);
    AT_RANK s;
    for ( k1 = 0; k1 < MAX_NUM_STEREO_BONDS && (s = at[iAt1].stereo_bond_neighbor[k1]); k1 ++ ) {
        if ( s == sNeigh ) {
            return k1;
        }
    }
    return -1; /*  neighbor not found */
}

/**********************************************************************************/
/*  Extracted from FillSingleStereoDescriptors(...) */
/**********************************************************************************/
int GetStereoBondParity(sp_ATOM *at, int i, int n, AT_RANK *nRank )
{
int k1, k2, s, parity;
        
    if ( at[i].stereo_bond_neighbor[0] ) {
        for ( k1 = 0; k1 < MAX_NUM_STEREO_BONDS && (s = (int)at[i].stereo_bond_neighbor[k1]); k1 ++ ) {
            if ( --s == n ) {
                goto neigh1_found;
            }
        }
        return -1; /*  error: not a stereo neighbor */
neigh1_found:
        if ( PARITY_KNOWN( at[i].stereo_bond_parity[k1] ) ) {
            return PARITY_VAL( at[i].stereo_bond_parity[k1] );
        }
        for ( k2 = 0; k2 < MAX_NUM_STEREO_BONDS && (s = (int)at[n].stereo_bond_neighbor[k2]); k2 ++ ) {
            if ( --s == i ) {
                goto neigh2_found;
            }
        }
        return -1; /*  error: not a stereo neighbor */
neigh2_found:;
    } else {
        return -1; /*  error: not a stereo bond */
    }

    if ( ATOM_PARITY_WELL_DEF(at[i].parity) &&
         ATOM_PARITY_WELL_DEF(at[n].parity) &&
         MIN_DOT_PROD <= abs(at[i].stereo_bond_z_prod[k1]) ) {
        /*  bond parity can be calculated */
        int half_parity1, half_parity2;
        /*  check whether all neighbors are defined */


        half_parity1 = HalfStereoBondParity( at, i, k1, nRank );
        half_parity2 = HalfStereoBondParity( at, n, k2, nRank );
        if ( !half_parity1 || !half_parity2 )
            return 0; /*  ranks undefined or not a stereo bond */
        if ( ATOM_PARITY_WELL_DEF(half_parity1) &&
             ATOM_PARITY_WELL_DEF(half_parity2)  ) {
            parity = 2 - ( half_parity1 + half_parity2
                     + (at[i].stereo_bond_z_prod[k1] < 0))%2; 
        } else {
            return CT_STEREOBOND_ERROR;  /*   <BRKPT> */
        }
    } else {
        /*  parity cannot be calculated: not enough info or 'unknown' */
        if ( AB_PARITY_NONE != (parity = inchi_max(at[i].parity, at[n].parity)) ) {
            parity = AB_PARITY_UNDF; /*  should not happen */
        }
    }
    return parity;
}




/**********************************************************************************/
/*  Extracted from FillSingleStereoDescriptors(...) */
/**********************************************************************************/
int GetPermutationParity( sp_ATOM *at, AT_RANK nAvoidNeighbor, AT_RANK *nCanonRank )
{
    AT_RANK nNeighRank[MAX_NUM_STEREO_ATOM_NEIGH];
    int     j, k, parity;
    if ( at->valence > MAX_NUM_STEREO_ATOM_NEIGH ) {
        parity = -1; /*  error */
    } else {
        for ( j = k = 0; j < at->valence; j ++ ) {
            if ( at->neighbor[j] != nAvoidNeighbor ) {
                nNeighRank[k++] = nCanonRank[(int)at->neighbor[j]];
            }
        }
        if ( k ) {
            parity = insertions_sort( nNeighRank, k, sizeof(nNeighRank[0]), comp_AT_RANK);
            if ( nNeighRank[0] ) {
                parity = 2 - parity % 2;
            } else {
                parity = 0; /*  not all ranks are known */
            }
        } else {
            /* special case: HX= with implicit H */
            parity = 2;
        }
    }
    return parity;
}
/**********************************************************************************/
int GetStereoCenterParity(sp_ATOM *at, int i, AT_RANK *nRank )
{
    AT_NUMB  nNeighborNumber2[MAXVAL];
    int      parity;
    int      k, num_trans;

    if ( !at[i].parity ) {
        return 0; /*  not a stereo center */
    }
    if ( at[i].stereo_bond_neighbor[0] ) {
        return -1;  /*  a stereo bond atom, not a stereo center */
    }

    if ( ATOM_PARITY_WELL_DEF(at[i].parity) ) {
        /*  number of neighbors transpositions to the sorted order is unknown. Find it. */
        /*  If parity is not well-defined then doing this is a waste of time */
        int num_neigh = at[i].valence;
        for ( k = 0; k < num_neigh; k ++) {
            if ( !nRank[(int)at[i].neighbor[k]] )
                return 0; /*  stereo at[i] does not belong to the traversed part of the structure */
            nNeighborNumber2[k] = k;
        }
        pNeighborsForSort = at[i].neighbor;
        pn_RankForSort    = nRank;
        num_trans=insertions_sort( nNeighborNumber2, num_neigh, sizeof(nNeighborNumber2[0]), CompNeighborsAT_NUMBER );
#ifndef CT_NEIGH_INCREASE
        num_trans += ((num_neigh*(num_neigh-1))/2)%2;  /*  get correct parity for ascending order */
#endif
        parity = 2 - (at[i].parity + num_trans)%2;
    } else {
        parity = at[i].parity;
    }

    return parity;
}
