strutil.h

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/*
 * 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
 *
 */
 
#ifndef _STRUTIL_H_
#define _STRUTIL_H_
 
/* Mol structure utlities */
 
#include "inpdef.h"
#include "ichi.h"
#include "util.h"            /* (@nnuk : Nauman Ullah Khan) :: utilizing defined macros */
#include "incomdef.h"
 
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C"
{
#endif
#endif
 
    /*(@nnuk : Nauman Ullah Khan)
    * Metal definitions for molecular inorganics (MolInOrg)
    */
#define MolInOrg1           1          /* takes the lowest valence of an element */
#define MolInOrg2           3          /* takes the two lowest valences of an element */
#define MolInOrg3           7          /* takes the three lowest valences of an element */
#define MolInOrg4           15         /* takes the four lowest valences of an element */
 
    /* forward declaration */
    struct tagTautomerGroupsInfo;
    struct tagCANON_GLOBALS;
 
      /*(@nnuk : Nauman Ullah Khan)
    * CHEMICAL ELEMENTS & ATOMIC VALENCE MODEL FOR VARIOUS OXIDATION STATES
    */
    typedef struct tagMolecularInorganicsArray
    {
        /*    Element chemical symbol */
        const char* szElName;
        /*    Average atomic mass from the Periodic Chart of the Elements
        (Fisher cat. no. 05-702-10) */
        int     nAtMass;
        /*    (not used currently) Atomic mass of the most abundant isotope */
        int     nNormAtMass;
        /*    (not used currently) Exact mw of the most abundant isotope (not used)    */
        double  dAtMass;
        /*    MolInOrg1, MolInOrg2, MolInOrg3 or MolInOrg4 */
        int     nType;
        /*    (not used currently) Pauling electronegativity x 10; 0 means unknown    */
        int     nElNegPauling10;
        /*    InChI does not add implicit H to atoms that have non-zero bSkipAddingH */
        /*    NB: was called bDoNotAddH, renamed to avoid confusion with other procedures */
        int     bSkipAddingH;
        S_CHAR  cValence[NUM_ATOM_CHARGES][MAX_NUM_VALENCES];
    } MolecularInorganicsElData;
 
    /*(@nnuk : Nauman Ullah Khan) :: Structure to hold variables for the array of all chemical elements, further used by MolecularInorganics function*/
    typedef struct tagElementsMolecularInorganics
    {
        int atomic_number;
        char symbol[3];  /* Fixed length for symbol, up to 2 characters + null terminator */
 
    } ElementsMolecularInorganics;
 
    /* (@nnuk : Nauman Ullah Khan) :: Main function for molecular inorganics */
    int MolecularInorganicsPreprocessing(ORIG_ATOM_DATA* orig_at_data, INPUT_PARMS* ip);
    /* (@nnuk : Nauman Ullah Khan) :: Function related to molecular inorganics, for getting the binary value of the electronegativity difference between any two elements */
    int shouldBondBeCut(int atom1, int atom2);
    /* (@nnuk : Nauman Ullah Khan) :: Function related to molecular inorganics, for updating the neighbour's list in the main molecular inorganics function processing */
    void updateNeighborListMolecularInorganics(inp_ATOM* at, int atom_idx, int neighbor_idx);
    /* (@nnuk : Nauman Ullah Khan) :: Function related to molecular inorganics, decides for the specific metal bonds to be kept or disconnected. */
    int MolecularInorganicsIsMetalToDisconnect(inp_ATOM* at, int atom_idx);
    /* Function retrieves valence values for molecular inorganics functionality*/
    int getElValenceforMolecularInorganics(int nPeriodicNum, int charge, int val_num);
    /* Function retrieves element type value for molecular inorganics functionality*/
    int getElTypeforMolecularInorganics(int nPeriodicNum);
  
    int set_EnhancedStereo_t_m_layers(const ORIG_ATOM_DATA *orig_inp_data,
                                      const INChI *inchi,
                                      const INChI_Aux *aux);
 
    int get_canonical_atom_number( const INChI_Aux *aux,
                                   int orig_atom_num);
 
    int get_parity_idx_from_canonical_atom_number( int canon_atom_num,
                                                   const AT_NUMB *nNumber,
                                                   int nof_atoms);
 
    int invert_parities(const INChI *inchi,
                        const INChI_Aux *aux,
                        int **list_atoms,
                        int nof_lists,
                        int is_absolute);
 
    int ExtractConnectedComponent(inp_ATOM *at, int num_at,
                                  int component_number,
                                  inp_ATOM *component_at);
    int SetConnectedComponentNumber(inp_ATOM *at, int num_at, int component_number);
 
    INChI *Alloc_INChI(inp_ATOM *at, int num_at, int *found_num_bonds,
                       int *found_num_isotopic, int nAllocMode);
 
    int Free_INChI(INChI **ppINChI);
 
    int Free_INChI_Members(INChI *pINChI);
 
    int Free_INChI_Stereo(INChI_Stereo *pINChI_Stereo);
 
    INChI_Aux *Alloc_INChI_Aux(int num_at, int num_isotopic_atoms,
                               int nAllocMode, int bOrigData);
 
    int Free_INChI_Aux(INChI_Aux **ppINChI_Aux);
 
    int Create_INChI(struct tagCANON_GLOBALS *pCG,
                     struct tagINCHI_CLOCK *ic,
                     INPUT_PARMS *ip,
                     INChI **ppINChI,
                     INChI_Aux **ppINChI_Aux,
                     ORIG_ATOM_DATA *orig_inp_data,
                     inp_ATOM *inp_at,
                     INP_ATOM_DATA *inp_norm_data[2],
                     int num_inp_at,
                     INCHI_MODE nUserMode,
                     INCHI_MODE *pbTautFlags,
                     INCHI_MODE *pbTautFlagsDone,
                     struct tagInchiTime *ulMaxTime,
                     struct tagTautomerGroupsInfo *ti_out,
                     char *pStrErrStruct);
 
    int FillOutInfAtom(struct tagCANON_GLOBALS *pCG,
                       inp_ATOM *norm_at,
                       INF_ATOM_DATA *inf_norm_at_data,
                       int init_num_at,
                       int num_removed_H,
                       int bAdd_DT_to_num_H,
                       int nNumRemovedProtons,
                       NUM_H *nNumRemovedProtonsIsotopic,
                       int bIsotopic,
                       INChI *pINChI,
                       INChI_Aux *pINChI_Aux,
                       int bAbcNumbers,
                       INCHI_MODE nMode);
 
    int FillOutCompositeCanonInfAtom(struct tagCANON_GLOBALS *pCG,
                                     COMP_ATOM_DATA *composite_norm_data,
                                     INF_ATOM_DATA *inf_norm_at_data,
                                     int bIsotopic,
                                     int bTautomeric,
                                     PINChI2 *pINChI2,
                                     PINChI_Aux2 *pINChI_Aux2,
                                     int bAbcNumbers,
                                     INCHI_MODE nMode);
 
#if (FIX_DALKE_BUGS == 1)
    char *AllocateAndFillHillFormula(INChI *pINChI);
#endif
 
    typedef enum tagInchiDiffBits
    {
        IDIF_PROBLEM = 0x00000001,           /* severe: at least one InChI does not exist */
        IDIF_NUM_AT = 0x00000001,            /* severe: different number of atoms in the skeleton */
        IDIF_ATOMS = 0x00000001,             /* severe: diiferent types of skeleton atoms */
        IDIF_NUM_EL = 0x00000001,            /* severe: formulas differ in another element */
        IDIF_CON_LEN = 0x00000001,           /* severe: different connection table lengths */
        IDIF_CON_TBL = 0x00000001,           /* severe: different connection tables */
        IDIF_POSITION_H = 0x00000002,        /* difference in non-taut (Mobile-H) or all H (Fixed-H) location/number */
        IDIF_MORE_FH = 0x00000004,           /* extra fixed H */
        IDIF_LESS_FH = 0x00000008,           /* missing fixed H */
        IDIF_MORE_H = 0x00000010,            /* formulas differ in number of H */
        IDIF_LESS_H = 0x00000020,            /* formulas differ in number of H */
        /*IDIF_TAUT_LEN      = 0x00000008,*/ /* different lengths of tautomer lists */
        IDIF_NO_TAUT = 0x00000040,           /* restored structure has no taut groups while the original InChI has some */
        IDIF_WRONG_TAUT = 0x00000080,        /* restored has tautomerism while the original does not have it */
        IDIF_SINGLE_TG = 0x00000100,         /* restored has 1 taut. group while the original InChI has multiple tg */
        IDIF_MULTIPLE_TG = 0x00000200,       /* restored has multiple tg while the original InChI has only one tg */
        IDIF_NUM_TG = 0x00000400,            /* different number of tautomeric groups */
        /*IDIF_LESS_TG_ENDP  = 0x00000200,*/ /* restores structure has less taut. endpoints */
        /*IDIF_MORE_TG_ENDP  = 0x00000400,*/ /* restores structure has more taut. endpoints */
        IDIF_EXTRA_TG_ENDP = 0x00000800,     /* extra tautomeric endpoint(s) in restored structure */
        IDIF_MISS_TG_ENDP = 0x00001000,      /* one or more tg endpoint is not in the restored structure */
        IDIF_DIFF_TG_ENDP = 0x00002000,      /* lists of tg endpoints are different */
        IDIF_TG = 0x00004000,                /* different tautomeric groups */
        IDIF_NUM_ISO_AT = 0x00008000,        /* ?severe: restored struct. has different number of isotopic atoms */
        IDIF_ISO_AT = 0x00010000,            /* ?severe: restored struct. has different locations/isotopes of isotopic atoms */
        IDIF_CHARGE = 0x00020000,            /* restored structure has different charge */
        IDIF_REM_PROT = 0x00040000,          /* proton(s) removed/added from the restored structure */
        IDIF_REM_ISO_H = 0x00080000,         /* isotopic H removed */
        IDIF_SC_INV = 0x00100000,            /* restores structure has different inversion stereocenter mark */
        IDIF_SC_PARITY = 0x00200000,         /* restored structure has stereoatoms or allenes with different parity */
        IDIF_SC_EXTRA_UNDF = 0x00400000,     /* restored structure has extra undefined stereocenter(s) */
        IDIF_SC_EXTRA = 0x00800000,          /* restored structure has extra stereocenter(s) */
        IDIF_SC_MISS_UNDF = 0x01000000,      /* restored structure has not some undefined stereocenter(s) */
        IDIF_SC_MISS = 0x02000000,           /* restored structure has not some stereocenters that are not undefined */
        IDIF_SB_PARITY = 0x04000000,         /* restored structure has stereobonds or cumulenes with different parity */
        IDIF_SB_EXTRA_UNDF = 0x08000000,     /* restored structure has extra undefined stereobond(s) */
        IDIF_SB_EXTRA = 0x10000000,          /* restored structure has extra stereobond(s) */
        IDIF_SB_MISS_UNDF = 0x20000000,      /* restored structure has not some undefined stereocenters */
        IDIF_SB_MISS = 0x40000000            /* restored structure has not some stereobonds that are not undefined */
    } IDIF;
 
#define IDIFF_SB (IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS)
#define IDIFF_SC (IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA | IDIF_SC_MISS_UNDF | IDIF_SC_MISS)
 
#define IDIFF_CONSTIT (IDIF_POSITION_H | IDIF_MORE_FH | IDIF_LESS_FH | IDIF_MORE_H | IDIF_LESS_H |    \
                       IDIF_NO_TAUT | IDIF_WRONG_TAUT | IDIF_SINGLE_TG | IDIF_MULTIPLE_TG |           \
                       IDIF_NUM_TG | IDIF_EXTRA_TG_ENDP | IDIF_MISS_TG_ENDP | IDIF_TG |               \
                       IDIF_NUM_ISO_AT | IDIF_ISO_AT | IDIF_CHARGE | IDIF_REM_PROT | IDIF_REM_ISO_H | \
                       IDIF_DIFF_TG_ENDP)
#define IDIFF_STEREO (IDIF_SC_INV | IDIF_SC_PARITY | IDIF_SC_EXTRA_UNDF | IDIF_SC_EXTRA |      \
                      IDIF_SC_MISS_UNDF | IDIF_SC_MISS | IDIF_SB_PARITY | IDIF_SB_EXTRA_UNDF | \
                      IDIF_SB_EXTRA | IDIF_SB_MISS_UNDF | IDIF_SB_MISS)
 
    /*************************************************************************************/
#define ICR_MAX_ENDP_IN1_ONLY 32
#define ICR_MAX_ENDP_IN2_ONLY 32
#define ICR_MAX_DIFF_FIXED_H 32
#define ICR_MAX_SB_IN1_ONLY 32
#define ICR_MAX_SB_IN2_ONLY 32
#define ICR_MAX_SC_IN1_ONLY 32
#define ICR_MAX_SC_IN2_ONLY 32
#define ICR_MAX_SB_UNDF 32
#define ICR_MAX_SC_UNDF 32
 
    typedef struct tagInChICompareResults
    {
        INCHI_MODE flags;
 
        int tot_num_H1;
        int tot_num_H2;
        int num_taut_H1;
        int num_taut_H2;
        int num_taut_M1;
        int num_taut_M2;
 
        /* 1 => InChI from reversed struct. 2 => input InChI */
 
        AT_NUMB endp_in1_only[ICR_MAX_ENDP_IN1_ONLY]; /* endpoint canonical number = index+1 */
        int num_endp_in1_only;
 
        AT_NUMB endp_in2_only[ICR_MAX_ENDP_IN2_ONLY]; /* endpoint canonical number = index+1 */
        int num_endp_in2_only;
 
        AT_NUMB diff_pos_H_at[ICR_MAX_DIFF_FIXED_H]; /* non-tautomeric H */
        S_CHAR diff_pos_H_nH[ICR_MAX_DIFF_FIXED_H];
        int num_diff_pos_H;
 
        AT_NUMB fixed_H_at1_more[ICR_MAX_DIFF_FIXED_H]; /* extra fixed_H */
        S_CHAR fixed_H_nH1_more[ICR_MAX_DIFF_FIXED_H];
        int num_fixed_H1_more;
 
        AT_NUMB fixed_H_at2_more[ICR_MAX_DIFF_FIXED_H]; /* missed fixed_H */
        S_CHAR fixed_H_nH2_more[ICR_MAX_DIFF_FIXED_H];
        int num_fixed_H2_more;
 
        AT_NUMB sc_in1_only[ICR_MAX_SC_IN1_ONLY];
        int num_sc_in1_only;
        AT_NUMB sc_in2_only[ICR_MAX_SC_IN2_ONLY];
        int num_sc_in2_only;
 
        AT_NUMB sb_in1_only[ICR_MAX_SB_IN1_ONLY];
        int num_sb_in1_only;
        AT_NUMB sb_in2_only[ICR_MAX_SB_IN2_ONLY];
        int num_sb_in2_only;
 
        AT_NUMB sb_undef_in1_only[ICR_MAX_SC_UNDF];
        int num_sb_undef_in1_only;
        AT_NUMB sb_undef_in2_only[ICR_MAX_SC_UNDF];
        int num_sb_undef_in2_only;
 
        AT_NUMB sc_undef_in1_only[ICR_MAX_SB_UNDF];
        int num_sc_undef_in1_only;
        AT_NUMB sc_undef_in2_only[ICR_MAX_SB_UNDF];
        int num_sc_undef_in2_only;
    } ICR; /* tagInChICompareResults */
 
    INCHI_MODE CompareReversedINChI2(INChI *i1 /* InChI from reversed struct */,
                                     INChI *i2 /* input InChI */,
                                     INChI_Aux *a1, INChI_Aux *a2,
                                     ICR *picr, int *err);
 
    int CompareIcr(ICR *picr1, ICR *picr2, INCHI_MODE *pin1, INCHI_MODE *pin2, INCHI_MODE mask);
 
    int CompareReversedINChI(INChI *i1, INChI *i2, INChI_Aux *a1, INChI_Aux *a2);
 
    // Where is this function?
    const char *CompareReversedInchiMsg(int code);
 
#define EQL_EXISTS 1
#define EQL_SP3 2
#define EQL_SP3_INV 4
#define EQL_SP2 8
 
    int Eql_INChI_Stereo(INChI_Stereo *s1, int eql1, INChI_Stereo *s2, int eql2, int bRelRac);
 
    int Eql_INChI_Isotopic(INChI *i1, INChI *i2);
 
#define EQL_EQU 0
#define EQL_EQU_TG 1
#define EQL_EQU_ISO 2
 
    int Eql_INChI_Aux_Equ(INChI_Aux *a1, int eql1, INChI_Aux *a2, int eql2);
 
#define EQL_NUM 0
#define EQL_NUM_INV 1
#define EQL_NUM_ISO 2
 
    int Eql_INChI_Aux_Num(INChI_Aux *a1, int eql1, INChI_Aux *a2, int eql2);
 
    int bHasEquString(AT_NUMB *LinearCT, int nLenCT);
 
    int CompINChINonTaut2(const void *p1, const void *p2);
 
    int CompINChITaut2(const void *p1, const void *p2);
 
    int CompINChI2(const INCHI_SORT *p1, const INCHI_SORT *p2, int bTaut, int bCompareIsotopic);
 
    int CompINChITautVsNonTaut(const INCHI_SORT *p1, const INCHI_SORT *p2, int bCompareIsotopic);
 
    typedef enum tagDiffINChISegments
    {                  /* r = repetitive, n = non-repetitive */
      DIFS_f_FORMULA,  /*  0 r; fixed-H <-> mobile-H */
      DIFS_c_CONNECT,  /*  1 n; connection table; mobile-H only */
      DIFS_h_H_ATOMS,  /*  2 n; hydrogen atoms: mobile-H and Fixed-H; have different meanings */
      DIFS_q_CHARGE,   /*  3 r; charge; fixed-H <-> mobile-H */
      DIFS_p_PROTONS,  /*  4 n; protons; mobile-H only */
      DIFS_b_SBONDS,   /*  5 r: stereobonds: fixed-H <-> mobile-H * isotopic <-> non-isotopic */
      DIFS_t_SATOMS,   /*  6 r: stereoatoms: fixed-H <-> mobile-H * isotopic <-> non-isotopic */
      DIFS_m_SP3INV,   /*  7 r: stereo-abs-inv: fixed-H <-> mobile-H * isotopic <-> non-isotopic */
      DIFS_s_STYPE,    /*  8 r: stereo-type: fixed-H <-> mobile-H * isotopic <-> non-isotopic */
      DIFS_i_IATOMS,   /*  9 r: isotopic atoms: fixed-H <-> mobile-H * isotopic <-> non-isotopic */
      DIFS_o_TRANSP,   /* 10 n: Fixed-H transposition */
      DIFS_idf_LENGTH, /* 11    length of the array relevant to the INChI Identifier */
      /* later elements referring to AuxInfo may be added */
      DIFS_LENGTH = DIFS_idf_LENGTH /* length of the array */
    } DIF_SEGMENTS;
 
    typedef enum tagDiffINChILayers
    {
        DIFL_M,     /* 0 main layer */
        DIFL_MI,    /* 1 main isotopic */
        DIFL_F,     /* 2 fixed-H */
        DIFL_FI,    /* 3 fixed-H isotopic */
        DIFL_LENGTH /* number of layers */
    } DIF_LAYERS;
 
    /* Value meaning */
    typedef enum tagMarkDiff
    {
        DIFV_BOTH_EMPTY = 0, /* both this and the component in the preceding namesake segment are empty  */
        DIFV_EQL2PRECED = 1, /* equal to the component in the preceding namesake segment                 */
        DIFV_NEQ2PRECED = 2, /* different from the component in the preceding namesake segment           */
        DIFV_IS_EMPTY = 4,   /* is empty while the preceding namesake segment is not empty               */
        DIFV_FI_EQ_MI = 8,   /* FI stereo component is equal to the component in the MI namesake segment */
                             /* while M and F components are empty                                       */
        /* decision_F = bitmask: bits that should not be present */
        /* decision_T = bitmask: at least one of the bits should be present */
        /* decision = true if( !( BITS & decision_F ) && ( BITS & decision_F ) ) */
        DIFV_OUTPUT_EMPTY_T = (DIFV_IS_EMPTY),                                     /* bits present for empty segment output */
        DIFV_OUTPUT_EMPTY_F = (DIFV_EQL2PRECED | DIFV_NEQ2PRECED | DIFV_FI_EQ_MI), /* bits NOT present */
 
        DIFV_OUTPUT_OMIT_F = (DIFV_NEQ2PRECED | DIFV_IS_EMPTY), /* bits NOT present for omitting */
 
        DIFV_OUTPUT_FILL_T = (DIFV_EQL2PRECED | DIFV_NEQ2PRECED | DIFV_FI_EQ_MI)
    } DIF_VALUES;
 
    typedef enum tagINChISegmAction
    {
        INCHI_SEGM_OMIT = 0,
        INCHI_SEGM_FILL = 1, /* the value is used in str_LineEnd() */
        INCHI_SEGM_EMPTY = 2 /* the value is used in str_LineEnd() */
    } INCHI_SEGM_ACTION;
 
    int CompINChILayers(const INCHI_SORT *p1, const INCHI_SORT *p2,
                        char sDifSegs[][DIFS_LENGTH], int bFixTranspChargeBug);
 
    int MarkUnusedAndEmptyLayers(char sDifSegs[][DIFS_LENGTH]);
 
    int INChI_SegmentAction(char cDifSegs);
 
#define FLAG_SORT_PRINT_TRANSPOS_BAS 1   /* transposition in the main InChI layer */
#define FLAG_SORT_PRINT_TRANSPOS_REC 2   /* transposition in the reconnected InChI layer */
#define FLAG_SORT_PRINT_NO_NFIX_H_BAS 4  /* no fixed H non-isotopic in the main InChI layer */
#define FLAG_SORT_PRINT_NO_NFIX_H_REC 8  /* no fixed H non-isotopic in the reconnected InChI layer */
#define FLAG_SORT_PRINT_NO_IFIX_H_BAS 16 /* no fixed H isotopic in the main InChI layer */
#define FLAG_SORT_PRINT_NO_IFIX_H_REC 32 /* no fixed H isotopic in the the reconnected InChI layer */
#define FLAG_SORT_PRINT_ReChI_PREFIX 64  /* Output ReChI instead of InChI */
 
    struct tagCANON_GLOBALS;
 
    int OutputINChI1(struct tagCANON_GLOBALS *pCG,
                     INCHI_IOS_STRING *strbuf,
                     INCHI_SORT *pINChISortTautAndNonTaut2[][TAUT_NUM],
                     int iINChI,
                     ORIG_ATOM_DATA *orig_inp_data,
                     ORIG_STRUCT *pOrigStruct,
                     INPUT_PARMS *ip,
                     int bDisconnectedCoord,
                     int bOutputType,
                     int bINChIOutputOptions,
                     int num_components2[],
                     int num_non_taut2[],
                     int num_taut2[],
                     INCHI_IOSTREAM *out_file,
                     INCHI_IOSTREAM *log_file,
                     int num_input_struct,
                     int *pSortPrintINChIFlags,
                     unsigned char save_opt_bits);
 
    int OutputINChI2(struct tagCANON_GLOBALS *pCG,
                     INCHI_IOS_STRING *strbuf,
                     INCHI_SORT *pINChISortTautAndNonTaut2[][TAUT_NUM],
                     int INCHI_basic_or_INCHI_reconnected,
                     ORIG_ATOM_DATA *orig_inp_data,
                     ORIG_STRUCT *pOrigStruct,
                     INPUT_PARMS *ip,
                     int bDisconnectedCoord,
                     int bOutputType,
                     int bINChIOutputOptions,
                     int num_components2[],
                     int num_non_taut2[],
                     int num_taut2[],
                     INCHI_IOSTREAM *out_file,
                     INCHI_IOSTREAM *log_file,
                     int num_input_struct,
                     int *pSortPrintINChIFlags,
                     unsigned char save_opt_bits);
 
    int SaveEquComponentsInfoAndSortOrder(int iINChI,
                                          INCHI_SORT *pINChISort[TAUT_NUM],
                                          int *num_components,
                                          ORIG_ATOM_DATA *orig_inp_data,
                                          ORIG_ATOM_DATA *prep_inp_data,
                                          COMP_ATOM_DATA composite_norm_data[TAUT_NUM + 1],
                                          int bCompareComponents); /* djb-rwth: matching composite_norm_data bounds */
 
    int OutputINChIPlainError(INCHI_IOSTREAM *out_file,
                              char *pErrorText,
                              int bError);
 
    int GetInpStructErrorType(INPUT_PARMS *ip, int err, char *pStrErrStruct, int num_inp_atoms);
 
    int ProcessStructError(INCHI_IOSTREAM *out_file,
                           INCHI_IOSTREAM *log_file,
                           char *pStrErrStruct,
                           int nErrorType,
                           long num_inp,
                           INPUT_PARMS *ip);
 
    int bNumHeterAtomHasIsotopicH(inp_ATOM *atom, int num_atoms);
 
    // does this function exist?
    int WriteToSDfile(const INP_ATOM_DATA *inp_at_data, INCHI_IOSTREAM *fcb, const char *name, const char *comment,
                      const char *szLabel, const char *szValue);
 
    int bIsMetalSalt(inp_ATOM *at, int i);
 
    int bIsSameBond(int a1, int a2, int b1, int b2);
 
    extern const char gsMissing[];
    extern const char gsEmpty[];
    extern const char gsSpace[];
    extern const char gsEqual[];
 
#define SDF_LBL_VAL(L, V) ((L) && (L)[0]) ? gsSpace : gsEmpty, ((L) && (L)[0]) ? L : gsEmpty, ((L) && (L)[0]) ? (((V) && (V)[0]) ? gsEqual : gsSpace) : gsEmpty, ((V) && (V)[0]) ? V : ((L) && (L)[0]) ? gsMissing \
                                                                                                                                                                                                       : gsEmpty
 
    /* Handle integer matrix [mxn] */
    int imat_new(int m, int n, int ***a);
 
    void imat_free(int m, int **a);
 
    /* Light-weight {nodes, connections} subgraph of molecule, subgraf
       refers to parent structure via orig atom numbers stored internally
            nodes and edges: are living in 0-based node numbers domain
            atoms and bonds: are living in 1-based orig atom numbers domain
    */
 
    /* subgraf_edge is node connections element */
    typedef struct subgraf_edge
    {
        int nbr;   /* node neighbor                                 */
        int etype; /* edge type echoing corresponding bond type     */
    } subgraf_edge;
    /* subgraf is set of nodes and their connections */
    typedef struct subgraf
    {
        int nnodes;         /* number of nodes (atoms)                          */
        int *nodes;         /* nodes[i]  is 1-based orig atom number of node #i */
                            /* (i = 0 to nnodes)                                */
        int *degrees;       /* degrees of nodes                                 */
        int *orig2node;     /* orig2node[k] is 0-based node number for orig #k  */
        subgraf_edge **adj; /* node connections representing adjacency relation */
                            /* adj[i] is vector[0-degree] of edges at node #i   */
    } subgraf;
    /* helper structure for finding paths in subgraf*/
    typedef struct subgraf_pathfinder
    {
        subgraf *sg;  /* base subgraf                                       */
        int start;    /* start node of path, 0-based                        */
        int end;      /* end node of path                                   */
        int maxbonds; /* max number of bonds in path                        */
        int nbonds;   /* actual number of bonds in path                 */
        int nseen;    /* number of nodes of found path(s)                   */
        int *seen;    /* nodes of found path(s)                         */
    } subgraf_pathfinder;
 
    subgraf *subgraf_new(ORIG_ATOM_DATA *orig_inp_data,
                         int nnodes,
                         int *nodes);
 
    void subgraf_free(subgraf *sg);
    void subgraf_debug_trace(subgraf *sg);
 
    subgraf_pathfinder *subgraf_pathfinder_new(subgraf *sg,
                                               ORIG_ATOM_DATA *orig_inp_data,
                                               int start,
                                               int end);
 
    void subgraf_pathfinder_free(subgraf_pathfinder *spf);
 
    void subgraf_pathfinder_run(subgraf_pathfinder *spf,
                                int nforbidden,
                                int *forbidden_orig,
                                int *nbonds, int **bonds,
                                int *natoms, int *atoms);
 
    int subgraf_pathfinder_collect_all(subgraf_pathfinder *spf,
                                       int nforbidden,
                                       int *forbidden,
                                       int *atnums);
 
    void CompAtomData_GetNumMapping(COMP_ATOM_DATA *adata, int *orig_num, int *curr_num);
 
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif
 
#endif /* _STRUTIL_H_ */