Add inchi type structs

[maneetgoyal]

/*
 * International Chemical Identifier (InChI)
 * Version 1
 * Software version 1.06
 * December 15, 2020
 *
 * 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.
 *
 * IUPAC/InChI-Trust Licence No.1.0 for the
 * International Chemical Identifier (InChI)
 * Copyright (C) IUPAC and InChI Trust
 *
 * This library is free software; you can redistribute it and/or modify it
 * under the terms of the IUPAC/InChI Trust InChI Licence No.1.0,
 * or any later version.
 *
 * Please note that this library is distributed WITHOUT ANY WARRANTIES
 * whatsoever, whether expressed or implied.
 * See the IUPAC/InChI-Trust InChI Licence No.1.0 for more details.
 *
 * You should have received a copy of the IUPAC/InChI Trust InChI
 * Licence No. 1.0 with this library; if not, please e-mail:
 *
 * info@inchi-trust.org
 *
 */

#ifndef _INHCH_API_H_
#define _INHCH_API_H_

#ifndef FIND_RING_SYSTEMS
#define FIND_RING_SYSTEMS 1
#endif
#ifndef FIND_RINS_SYSTEMS_DISTANCES
#define FIND_RINS_SYSTEMS_DISTANCES 0
#endif

#ifndef FIX_DOCANON_RETCODE_RESET_BUG
#define FIX_DOCANON_RETCODE_RESET_BUG 1
#endif

/* radical definitions */
typedef enum tagINCHIRadical {
    INCHI_RADICAL_NONE = 0,
    INCHI_RADICAL_SINGLET = 1,
    INCHI_RADICAL_DOUBLET = 2,
    INCHI_RADICAL_TRIPLET = 3
} inchi_Radical;

/* bond type definitions */
typedef enum tagINCHIBondType {
    INCHI_BOND_TYPE_NONE = 0,
    INCHI_BOND_TYPE_SINGLE = 1,
    INCHI_BOND_TYPE_DOUBLE = 2,
    INCHI_BOND_TYPE_TRIPLE = 3,
    INCHI_BOND_TYPE_ALTERN = 4  /* avoid by all means */
} inchi_BondType;
typedef enum tagINCHIBondStereo2D {
   /* stereocenter-related; positive: the sharp end points to this atom  */
    INCHI_BOND_STEREO_NONE = 0,
    INCHI_BOND_STEREO_SINGLE_1UP = 1,
    INCHI_BOND_STEREO_SINGLE_1EITHER = 4,
    INCHI_BOND_STEREO_SINGLE_1DOWN = 6,
    /* stereocenter-related; negative: the sharp end points to the opposite atom  */
    INCHI_BOND_STEREO_SINGLE_2UP = -1,
    INCHI_BOND_STEREO_SINGLE_2EITHER = -4,
    INCHI_BOND_STEREO_SINGLE_2DOWN = -6,
    /* stereobond-related */
    INCHI_BOND_STEREO_DOUBLE_EITHER = 3 /* unknown stereobond geometry */
} inchi_BondStereo2D;
/*************************************************************************
 * Notes on using INCHI_BOND_STEREO_SINGLE_*  from inchi_BondStereo2D    *
 *                                                                       *
 * These stereo markings are used by InChI to characterize a stereogenic *
 * atom if and only if all neighbors of this atom have same z-coordinate *
 * as this atom (that is, in case of 2D fragment).                       *
 * The only exception is INCHI_BOND_STEREO_SINGLE_?EITHER marking which  *
 * always assigns to the atom an "unknown" parity (u).                   *
 *                                                                       *
 * Note the behavior which is default for InChI software v.1.04/03/02std *
 * (at -NEWPSOFF option is not supplied) 2D stereo interpretation:       *
 * only bonds that have sharp end pointing to the stereogenic atom are   *
 * considered as being out of plane and only sharp ends of               *
 * INCHI_BOND_STEREO_SINGLE_?EITHER bonds are considered to determine    *
 * whether the stereochemistry is unknown.                               *
 *************************************************************************/

/* sizes definitions */
#define MAXVAL                   20 /* max number of bonds per atom                 */
#define ATOM_EL_LEN               6 /* length of ASCIIZ element symbol field        */
#define NUM_H_ISOTOPES            3 /* number of hydrogen isotopes: protium, D, T   */
#define ISOTOPIC_SHIFT_FLAG   10000 /* add to isotopic mass if isotopic_mass =      */
                                    /* (isotopic mass - average atomic mass)        */
#define ISOTOPIC_SHIFT_MAX      100 /* max abs(isotopic mass - average atomic mass) */

#ifndef INCHI_US_CHAR_DEF
typedef signed char   S_CHAR;
typedef unsigned char U_CHAR;
#define INCHI_US_CHAR_DEF
#endif

#ifndef INCHI_US_SHORT_DEF
typedef signed short   S_SHORT;
typedef unsigned short U_SHORT;
#define INCHI_US_SHORT_DEF
#endif

typedef  S_SHORT AT_NUM;        /* atom number; starts from 0 */

/*************************************************
 *
 *
 *  A T O M S   a n d   C O N N E C T I V I T Y
 *
 *
 *************************************************/

typedef struct tagInchiAtom {
    /* atom coordinates */
    double x;
    double y;
    double z;
    /* connectivity */
    AT_NUM  neighbor[MAXVAL];     /* adjacency list: ordering numbers of */
                                  /*            the adjacent atoms, >= 0 */
    S_CHAR  bond_type[MAXVAL];    /* inchi_BondType */
    /* 2D stereo */
    S_CHAR  bond_stereo[MAXVAL];  /* inchi_BondStereo2D; negative if the */
                                  /* sharp end points to opposite atom */
    /* other atom properties */
    char    elname[ATOM_EL_LEN];  /* zero-terminated chemical element name:*/
                                  /* "H", "Si", etc. */
    AT_NUM  num_bonds;            /* number of neighbors, bond types and bond*/
                                  /* stereo in the adjacency list */
    S_CHAR  num_iso_H[NUM_H_ISOTOPES + 1]; /* implicit hydrogen atoms */
                                  /* [0]: number of implicit non-isotopic H
                                       (exception: num_iso_H[0]=-1 means INCHI
                                       adds implicit H automatically),
                                     [1]: number of implicit isotopic 1H (protium),
                                     [2]: number of implicit 2H (deuterium),
                                     [3]: number of implicit 3H (tritium) */
    AT_NUM  isotopic_mass;        /* 0 => non-isotopic; isotopic mass or  */
                                  /* ISOTOPIC_SHIFT_FLAG + mass - (average atomic mass) */
    S_CHAR  radical;              /* inchi_Radical */
    S_CHAR  charge;               /* positive or negative; 0 => no charge */
}inchi_Atom;

/*******************************************************************
 * Notes: 1. Atom ordering numbers (i, k, and atom[i].neighbor[j] below)
 *           start from zero; max. ordering number is (num_atoms-1).
 *        2. inchi_Atom atom[i] is connected to the atom[atom[i].neighbor[j]]
 *           by a bond that has type atom[i].bond_type[j] and 2D stereo type
 *           atom[i].bond_stereo[j] (in case of no stereo
 *           atom[i].bond_stereo[j] = INCHI_BOND_STEREO_NONE)
 *           Index j is in the range 0 <= j <= (atom[i].num_bonds-1)
 *        3. Any connection (represented by atom[i].neighbor[j],
 *           atom[i].bond_type[j], and atom[i].bond_stereo[j])
 *           should be present in one or both adjacency list:
 *             if k = atom[i].neighbor[j] then i may or may not be present in
 *           atom[k].neighbor[] list. For example, the adjacency lists may be
 *           populated with only such neighbors that atom[i].neighbor[j] < i
 *           All elements of an adjacency list must be different, that is,
 *           a bond must be specified in an adjacency list only once.
 *        4. in Molfiles usually
 *           (number of implicit H) = Valence - SUM(bond_type[])
 *        5. Seemingly illogical order of the inchi_Atom members was
 *           chosen in an attempt to avoid alignment problems when
 *           accessing inchi_Atom from unrelated to C programming
 *           languages such as Visual Basic.
 *******************************************************************/

/*******************************************************************
    0D Stereo Parity and Type definitions
 *******************************************************************
            Note:
            =====
            o Below #A is the ordering number of atom A, starting from 0
            o See parity values corresponding to 'o', 'e', and 'u' in
              inchi_StereoParity0D definition below)

           =============================================
            stereogenic bond >A=B< or cumulene >A=C=C=B<
           =============================================

                                 neighbor[4]  : {#X,#A,#B,#Y} in this order
     X                           central_atom : NO_ATOM
      \            X      Y      type         : INCHI_StereoType_DoubleBond
       A==B         \    /
           \         A==B
            Y

    parity= 'e'    parity= 'o'   unknown parity = 'u'

    Limitations:
    ============
    o Atoms A and B in cumulenes MUST be connected by a chain of double bonds;
      atoms A and B in a stereogenic 'double bond' may be connected by a double,
      single, or alternating bond.
    o One atom may belong to up to 3 stereogenic bonds (i.g. in a fused
      aromatic structure).
    o Multiple stereogenic bonds incident to any given atom should
      either all except possibly one have (possibly different) defined
      parities ('o' or 'e') or should all have an unknown parity 'u'.

      Note on parities of alternating stereobonds
      ===========================================
                                                     D--E
      In large rings  (see Fig. 1, all              //   \\
      atoms are C) all alternating bonds         B--C      F--G
      are treated as stereogenic.              //              \\
      To avoid "undefined" bond parities      A                  H
      for bonds BC, DE, FG, HI, JK, LM, AN     \               /
      it is recommended to mark them with       N==M       J==I
      parities.                                     \     /
                                                      L==K    Fig. 1
      Such a marking will make
      the stereochemical layer unambiguous
      and it will be different from the          B--C      F--G
      stereochemical layer of the second       //   \\   //    \\
      structure (Fig. 2).                     A      D--E        H
                                               \               /
                                                N==M       J==I
      By default, double and alternating            \     /
      bonds in 8-member and greater rings             L==K    Fig. 2
      are treated by InChI as stereogenic.

           =============================================
            tetrahedral atom
           =============================================

   4 neighbors

            X                    neighbor[4] : {#W, #X, #Y, #Z}
            |                    central_atom: #A
         W--A--Y                 type        : INCHI_StereoType_Tetrahedral
            |
            Z
   parity: if (X,Y,Z) are clockwize when seen from W then parity is 'e' otherwise 'o'
   Example (see AXYZW above): if W is above the plane XYZ then parity = 'e'

   3 neighbors

              Y          Y       neighbor[4] : {#A, #X, #Y, #Z}
             /          /        central_atom: #A
         X--A  (e.g. O=S   )     type        : INCHI_StereoType_Tetrahedral
             \          \
              Z          Z

   parity: if (X,Y,Z) are clockwize when seen from A then parity is 'e',
                                                          otherwise 'o'
   unknown parity = 'u'
   Example (see AXYZ above): if A is above the plane XYZ then parity = 'e'
   This approach may be used also in case of an implicit H attached to A.

           =============================================
            allene
           =============================================

       X       Y                 neighbor[4]  : {#X,#A,#B,#Y}
        \     /                  central_atom : #C
         A=C=B                   type         : INCHI_StereoType_Allene

                                      Y      X
                                      |      |
     when seen from A along A=C=B:  X-A    Y-A

                          parity:   'e'    'o'

   parity: if A, B, Y are clockwise when seen from X then parity is 'e',
                                                          otherwise 'o'
   unknown parity = 'u'
   Example (see XACBY above): if X on the diagram is above the plane ABY
                                                      then parity is 'o'

   Limitations
   ===========
   o Atoms A and B in allenes MUST be connected by a chain of double bonds;

   How InChI uses 0D parities
   ==========================

   1. 0D parities are used if all atom coordinates are zeroes.

   In addition to that:

   2. 0D parities are used for Stereobonds, Allenes, or Cumulenes if:

   2a. A bond to the end-atom is shorter than MIN_BOND_LEN=0.000001
   2b. A ratio of two bond lengths to the end-atom is smaller than MIN_SINE=0.03
   2c. In case of a linear fragment X-A=B end-atom A is treated as satisfying 2a-b

       0D parities are used if 2a or 2b or 2c applies to one or both end-atoms.

   3. 0D parities are used for Tetrahedral Atoms if at least one of 3a-c is true:

   3a. One of bonds to the central atom is shorter than MIN_BOND_LEN=0.000001
   3b. A ratio of two bond lengths to the central atom is smaller than MIN_SINE=0.03
   3c. The four neighbors are almost in one plane or the central atom and
       its only 3 explicit neighbors are almost in one plane

   Notes on 0D parities and 'undefined' stereogenic elements
   =========================================================

   If 0D parity is to be used according to 1-3 but    CH3     CH3
   has not been provided then the corresponding         \    /
   stereogenic element is considered 'undefined'.        C=CH
                                                        /
   For example, if in the structure (Fig. 3)           H
   the explicit H has been moved so that it                Fig. 3
   has same coordinates as atom >C= (that is,
   the length of the bond H-C became zero)
   then the double bond is assigned 'undefined'       CH3      CH3
   parity which by default is omitted from the          \     /
   Identifier.                                           CH=CH

   However, the structure on Fig. 4 will have double        Fig. 4
   bond parity 'o' and its parity in the Identifier is (-).

   Notes on 0D parities in structures containing metals
   ====================================================
   Since InChI disconnects bonds to metals the 0D parities upon the
   disconnection may change in several different ways:

   1) previously non-stereogenic bond may become stereogenic:

         \     /                            \     /
          CH==CH          disconnection      CH==CH
           \ /               ======>
            M                                  M

     before the disconnection:    after the disconnection:
     atoms C have valence=5 and   the double bond may become
     the double bond is not       stereogenic
     recognized as stereogenic

   2) previously stereogenic bond may become non-stereogenic:

       M                           M(+)
        \    /                             /
         N==C      disconnection    (-)N==C
             \        ======>              \

   3) Oddball structures, usually resulting from projecting 3D
      structures on the plane, may contain fragment like that
      depicted on Fig. 5:

              M   A                      M   A
              |\ /   B                      /   B
              | X   /     disconnection    /   /
              |/ \ /         ======>      /   /
              C===C                      C===C
             Fig. 5
     (X stands for bond intersection)

     A-C=C-B parity is              A-C=C-B parity is
     trans (e)                      cis (o) or undefined
     because the bond               because C valence = 3,
     orientation is same            not 4.
     as on Fig, 6 below:

          A       M
           \     /     Removal of M from the structure
            C===C      on Fig. 5 changes the geometry from trans
           /     \     to cis.
          M'      B    Removal of M and M' from the structure
          Fig. 6       on Fig. 6 does not change the A-C=C-B
                       geometry: it is trans.

   To resolve the problem InChI API accepts the second parity
   corresponding to the metal-disconnected structure.
   To store both bond parities use left shift by 3 bits:

   inchi_Stereo0D::parity = ParityOfConnected | (ParityOfDisconnected<<3)

   In case when only disconnected structure parity exists set
   ParityOfConnected = INCHI_PARITY_UNDEFINED.
   This is the only case when INCHI_PARITY_UNDEFINED parity
   may be fed to the InChI.

   In cases when the bond parity in a disconnected structure exists and
   differs from the parity in the connected structure the atoms A and B
   should be non-metals.

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

#define NO_ATOM          (-1) /* non-existent (central) atom */

/* 0D parity types */
typedef enum tagINCHIStereoType0D {
    INCHI_StereoType_None = 0,
    INCHI_StereoType_DoubleBond = 1,
    INCHI_StereoType_Tetrahedral = 2,
    INCHI_StereoType_Allene = 3
} inchi_StereoType0D;

/* 0D parities */
typedef enum tagINCHIStereoParity0D {
    INCHI_PARITY_NONE = 0,
    INCHI_PARITY_ODD = 1,  /* 'o' */
    INCHI_PARITY_EVEN = 2,  /* 'e' */
    INCHI_PARITY_UNKNOWN = 3,  /* 'u' */ /* (see also readinch.c)
                                           used in: Extract0DParities, InchiToAtom  */
    INCHI_PARITY_UNDEFINED = 4   /* '?' -- should not be used; however, see Note above */
} inchi_StereoParity0D;

/*************************************************
 *
 *
 *  0D - S T E R E O  (if no coordinates given)
 *
 *
 *************************************************/

typedef struct tagINCHIStereo0D {
    AT_NUM  neighbor[4];    /* 4 atoms always */
    AT_NUM  central_atom;   /* central tetrahedral atom or a central */
                            /* atom of allene; otherwise NO_ATOM */
    S_CHAR  type;           /* inchi_StereoType0D */
    S_CHAR  parity;         /* inchi_StereoParity0D: may be a combination of two parities: */
                            /* ParityOfConnected | (ParityOfDisconnected << 3), see Note above */
}inchi_Stereo0D;

/*************************************************
 *
 *
 *  I N C h I    D L L     I n p u t
 *
 *
 *************************************************/

/*
    Structure -> InChI

    GetINCHI()
    GetStdINCHI()
    GetINCHIEx()

*/

typedef struct tagINCHI_Input
{
    /* the caller is responsible for the data allocation and deallocation               */
    inchi_Atom     *atom;         /* array of num_atoms elements                        */
    inchi_Stereo0D *stereo0D;     /* array of num_stereo0D 0D stereo elements or NULL   */
    char           *szOptions;    /* InChI options: space-delimited; each is preceded by*/
                                  /* '/' or '-' depending on OS and compiler            */
    AT_NUM          num_atoms;    /* number of atoms in the structure < MAX_ATOMS       */
    AT_NUM          num_stereo0D; /* number of 0D stereo elements                       */
}inchi_Input;

/*
    Extended input supporting v. 1.05+ extensions: V3000; polymers

    Mainly follows Accelrys CTFile cpecification.

    See:
    CTFile Formats. Accelrys, December 2011.
    http://accelrys.com/products/collaborative-science/biovia-draw/ctfile-no-fee.html

    Note that V3000 extensions are supported onlyprovisionally: the data are read but not used

*/

/* Polymers */

typedef struct inchi_Input_PolymerUnit
{
    int id;             /* Unit id; it is what is called 'Sgroup number'        */
                        /* in CTFile (not used, kept for compatibility)         */
    int type;           /* Unit type as per CTFile format (STY)                 */
    int subtype;        /* Unit subtype as per CTFile format (SST)              */
    int conn;           /* Unit connection scheme  as per CTFile format (SCN)   */
    int label;          /* One more unit id; what is called 'unique Sgroup      */
                        /* identifier' in CTFile (not used, for compatibility)  */
    int na;             /* Number of atoms in the unit                          */
    int nb;             /* Number of bonds in the unit                          */
    double xbr1[4];     /* Bracket ends coordinates (SDI)                       */
    double xbr2[4];     /* Bracket ends coordinates (SDI)                       */
    char smt[80];       /* Sgroup Subscript (SMT) ('n' or so )                  */
    int *alist;         /* List of atoms in the unit (SAL), atomic numbers      */
    int *blist;         /* List of crossing bonds of unit:                      */
                        /* [bond1end1, bond1end2, bond2end1, bond2end2]         */
}  inchi_Input_PolymerUnit;

typedef struct inchi_Input_Polymer
{
    /* List of pointers to polymer units        */
    inchi_Input_PolymerUnit **units;
    int        n;   /* Number of polymer units  */
} inchi_Input_Polymer;

/*
    V3000 Extensions

    Note that V3000 extensions are supported only
    provisionally, the data are read but not used
*/
typedef struct inchi_Input_V3000
{
    int n_non_star_atoms;
    int n_star_atoms;
    int *atom_index_orig;       /* Index as supplied for atoms                      */
    int *atom_index_fin;        /* = index or -1 for star atom                      */
    int n_sgroups;              /* Not used yet.                                    */
    int n_3d_constraints;       /* Not used yet.                                    */
    int n_collections;
    int n_non_haptic_bonds;
    int n_haptic_bonds;
    int **lists_haptic_bonds;   /* Haptic_bonds[i] is pointer to int                */
                                /*    array which contains:                         */
                                /* bond_type, non-star atom number,                 */
                                /* nendpts, then endpts themselves                  */
    /* Enhanced stereo collections */
    int n_steabs;
    int **lists_steabs;         /* steabs[k][0] - not used                          */
                                /* steabs[k][1] -  number of members in collection  */
                                /* steabs[k][2..] - member atom numbers             */
    int n_sterel;
    int **lists_sterel;         /* sterel[k][0] - n from "STERELn" tag              */
                                /* sterel[k][1] -  number of members in collection  */
                                /* sterel[k][2..] - member atom numbers             */
    int n_sterac;
    int **lists_sterac;         /* sterac[k][0] - n from "STERACn" tag              */
                                /* sterac[k][1] -  number of members in collection  */
                                /* sterac[k][0] - number from "STERACn" tag         */
} inchi_Input_V3000;

/* Input data structure for GetINCHIEx() */

typedef struct inchi_InputEx
{
    /* the caller is responsible for the data allocation and deallocation                           */

    /* same as in older inchi_Input                                                                 */
    inchi_Atom *atom;                       /* array of num_atoms elements                          */
    /* same as in older inchi_Input                                                                 */
    inchi_Stereo0D *stereo0D;               /* array of num_stereo0D 0D stereo elements or NULL     */
    /* same as in older inchi_Input                                                                 */
    char *szOptions;                        /* InChI options: space-delimited; each is preceded by  */
                                            /* '/' or '-' depending on OS and compiler              */
    /* same as in older inchi_Input                                                                 */
    AT_NUM num_atoms;                       /* number of atoms in the structure                     */
    /* same as in older inchi_Input                                                                 */
    AT_NUM num_stereo0D;                    /* number of 0D stereo elements                         */
    inchi_Input_Polymer *polymer;           /* v. 1.05+ extended data, polymers                      */
                                            /* NULL if not a polymer                                */
    inchi_Input_V3000 *v3000;               /* v. 1.05+ extended data, V3000 Molfile features        */
                                            /* NULL if no V3000 extensions present                  */
} inchi_InputEx;

/*
    InChI -> Structure

    GetStructFromINCHI()
    GetStructFromStdINCHI()
    GetStructFromINCHIEx()
*/
typedef struct tagINCHI_InputINCHI
{
    /* the caller is responsible for the data allocation and deallocation       */
    char *szInChI;      /* InChI ASCIIZ string to be converted to a strucure    */
    char *szOptions;    /* InChI options: space-delimited; each is preceded by  */
                        /* '/' or '-' depending on OS and compiler */
} inchi_InputINCHI;

typedef inchi_Input_PolymerUnit inchi_Output_PolymerUnit;
typedef inchi_Input_Polymer inchi_Output_Polymer;
typedef inchi_Input_V3000 inchi_Output_V3000;

/*************************************************
 *
 *
 *  I N C h I     D L L     O u t p u t
 *
 *
 *************************************************/

/*
    Structure -> InChI
*/

typedef struct tagINCHI_Output
{
    /* zero-terminated C-strings allocated by GetStdINCHI() */
    /* to deallocate all of them call FreeStdINCHI() (see below) */
    char *szInChI;     /* InChI ASCIIZ string */
    char *szAuxInfo;   /* Aux info ASCIIZ string */
    char *szMessage;   /* Error/warning ASCIIZ message */
    char *szLog;       /* log-file ASCIIZ string, contains a human-readable list */
                       /* of recognized options and possibly an Error/warning message */
} inchi_Output;

/* InChI -> Structure */

typedef struct tagINCHI_OutputStruct
{
    /* Pointers are allocated by GetStructFromINCHI()/GetStructFromStdINCHI()                       */
    /* to deallocate all of them call FreeStructFromStdINCHI()/FreeStructFromStdINCHI()             */
    inchi_Atom     *atom;               /* array of num_atoms elements                              */
    inchi_Stereo0D *stereo0D;           /* array of num_stereo0D 0D stereo elements or NULL         */
    AT_NUM          num_atoms;          /* number of atoms in the structure                         */
    AT_NUM          num_stereo0D;       /* number of 0D stereo elements                             */
    char           *szMessage;          /* Error/warning ASCIIZ message                             */
    char           *szLog;              /* log-file ASCIIZ string, contains a human-readable list   */
                                        /* of recognized options and possibly an Error/warn message */
    unsigned long  WarningFlags[2][2];  /* warnings, see INCHIDIFF in inchicmp.h                    */
                                        /* [x][y]:                                                  */
                                        /*  x=0 => Reconnected if present in InChI                  */
                                        /*         otherwise Disconnected/Normal                    */
                                        /*  x=1 => Disconnected layer if Reconn. layer is present   */
                                        /*  y=1 => Main layer or Mobile-H                           */
                                        /*  y=0 => Fixed-H layer                                    */
}inchi_OutputStruct;

typedef struct tagINCHI_OutputStructEx
{
    /* Pointers are allocated by GetStructFromINCHIEx()                                                 */
    /* to deallocate all of them call FreeStructFromNCHIEx()                                            */
    inchi_Atom           *atom;             /* array of num_atoms elements                              */
    inchi_Stereo0D       *stereo0D;         /* array of num_stereo0D 0D stereo elements or NULL         */
    AT_NUM               num_atoms;         /* number of atoms in the structure                         */
    AT_NUM               num_stereo0D;      /* number of 0D stereo elements                             */
    char                 *szMessage;        /* Error/warning ASCIIZ message                             */
    char                 *szLog;            /* log-file ASCIIZ string, contains a human-readable list   */
                                            /* of recognized options and possibly an Error/Warn message */
    unsigned long        WarningFlags[2][2];/* warnings, see INCHIDIFF in inchicmp.h                    */
                                            /* [x][y]: x=0 => Reconnected if present in InChI           */
                                            /*                otherwise Disconnected/Normal             */
                                            /*  x=1 => Disconnected layer if Reconne layer is present   */
                                            /*  y=1 => Main layer or Mobile-H                           */
                                            /*  y=0 => Fixed-H layer                                    */
    inchi_Output_Polymer *polymer;          /* v. 1.05+ extended data, polymers                          */
    inchi_Output_V3000   *v3000;            /* v. 1.05+ extended data, V3000 Molfile features            */
} inchi_OutputStructEx;

void FreeInChIExtInput( inchi_Input_Polymer    *polymer, inchi_Input_V3000 *v3000 );

/*************************************************
 *
 *
 *  I N C h I      D L L     I n t e r f a c e
 *
 *
 *************************************************/

#if (defined( _WIN32 ) && defined( _MSC_VER ) && defined(BUILD_LINK_AS_DLL) )
    /* Win32 & MS VC ++, compile and link as a DLL */
#ifdef _USRDLL
    /* InChI library dll */
#define INCHI_API __declspec(dllexport)
#define EXPIMP_TEMPLATE
#define INCHI_DECL
#else
   /* calling the InChI dll program */
#define INCHI_API __declspec(dllimport)
#define EXPIMP_TEMPLATE extern
#define INCHI_DECL
#endif
#else
    /* create a statically linked InChI library or link to an executable */
#define INCHI_API
#define EXPIMP_TEMPLATE
#define INCHI_DECL
#endif

/* Return codes for
        GetINCHI
        GetStdINCHI
        GetINCHIEx
        Get_inchi_Input_FromAuxInfo
        Get_std_inchi_Input_FromAuxInfo
        GetStructFromINCHI
        GetStructFromStdINCHI
        GetStructFromINCHIEx
*/

typedef enum tagRetValGetINCHI
{
    inchi_Ret_BREAK = -100,
    inchi_Ret_SKIP = -2, /* not used in InChI library */
    inchi_Ret_EOF = -1, /* no structural data has been provided */
    inchi_Ret_OKAY = 0, /* Success; no errors or warnings */
    inchi_Ret_WARNING = 1, /* Success; warning(s) issued */
    inchi_Ret_ERROR = 2, /* Error: no InChI has been created */
    inchi_Ret_FATAL = 3, /* Severe error: no InChI has been created (typically, memory allocation failure) */
    inchi_Ret_UNKNOWN = 4, /* Unknown program error */
    inchi_Ret_BUSY = 5  /* Previuos call to InChI has not returned yet */
} RetValGetINCHI;

/* Return codes for
        MakeINCHIFromMolfileText
*/
typedef enum tagRetValMOL2INCHI
{
    mol2inchi_Ret_OKAY = 0, /* Success; no errors or warnings */
    mol2inchi_Ret_WARNING = 1, /* Success; warning(s) issued */
    mol2inchi_Ret_EOF = -1, /* generic Error: no InChI has been created */
    mol2inchi_Ret_ERROR = 2, /* generic Error: no InChI has been created */
    mol2inchi_Ret_ERROR_get = 4, /* get structure Error: no InChI has been created */
    mol2inchi_Ret_ERROR_comp = 5  /* compute InChI Error: no InChI has been created */
} RetValMol2INCHI;

/* Return codes for CheckINCHI */
typedef enum tagRetValCheckINCHI
{
    INCHI_VALID_STANDARD = 0,
    INCHI_VALID_NON_STANDARD = 1,
    INCHI_VALID_BETA = 2,
    INCHI_INVALID_PREFIX = 3,
    INCHI_INVALID_VERSION = 4,
    INCHI_INVALID_LAYOUT = 5,
    INCHI_FAIL_I2I = 6
} RetValCheckINCHI;

/* to compile all InChI code as a C++ code #define COMPILE_ALL_CPP */
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif

/* InChI PREFIX */
#define INCHI_STRING_PREFIX "InChI="
#define LEN_INCHI_STRING_PREFIX 6

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Format:

    Standard InChI starts with: InChI=1S/
    Non-standard one with:      InChI=1/
    Empty std InChI:            InChI=1S//
    Empty InChI:                InChI=1//
                                AuxInfo=1//
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/

/* EXPORTED FUNCTIONS */

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetINCHI / GetStdINCHI

    inchi_Input is created by the user; strings in inchi_Output are allocated and deallocated by InChI
    inchi_Output does not need to be initilized out to zeroes; see FreeNCHI()/FreeSTDINCHI() on how to deallocate it

    Valid options for GetINCHI:
    (use - instead of / for O.S. other than MS Windows)

    Structure perception (compatible with stdInChI)
        /NEWPSOFF   /DoNotAddH   /SNon
    Stereo interpretation (lead to generation of non-standard InChI)
        /SRel /SRac /SUCF /ChiralFlagON /ChiralFlagOFF
    InChI creation options (lead to generation of non-standard InChI)
        /SUU /SLUUD   /FixedH  /RecMet  /KET /15T

    GetINCHI produces standard InChI if no InChI creation/stereo modification options
    are specified. Inveresely, if any of SUU/SLUUD/RecMet/FixedH/Ket/15T/SRel/SRac/SUCF
    options are specified, generated InChI will be non-standard one.

    GetStdINCHI produces standard InChI only.
    The valid structure perception options are:
        /NEWPSOFF   /DoNotAddH   /SNon

    Other options are:
        /AuxNone    Omit auxiliary information (default: Include)
        /Wnumber    Set time-out per structure in seconds; W0 means unlimited
                    In InChI library the default value is unlimited
        /WMnumber   Set time-out per structure in milliseconds; WM0 means unlimited
                    In InChI library the default value is unlimited
        /OutputSDF  Output SDfile instead of InChI
        /WarnOnEmptyStructure
                    Warn and produce empty InChI for empty structure
        /SaveOpt    Save custom InChI creation options (non-standard InChI)

 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHI( inchi_Input *inp, inchi_Output *out );
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStdINCHI( inchi_Input *inp, inchi_Output *out );

    /* Extended version of GetINCHI supporting v. 1.05+ extensions: V3000; polymers */
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHIEx( inchi_InputEx *inp, inchi_Output *out );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    FreeINCHI / FreeStdINCHI

        should be called to deallocate char* pointers
        obtained from each GetINCHI /GetStdINCHI call

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeINCHI( inchi_Output *out );
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStdINCHI( inchi_Output *out );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    GetStringLength

        helper: get string length

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStringLength( char *p );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    GetStructFromINCHI / GetStructFromStdINCHI / GetStructFromINCHIEx

        inchi_Inputinchi_InputINCHI is created by the user; pointers in inchi_OutputStruct are allocated and deallocated by InChI
        inchi_OutputStruct does not need to be initialized out to zeroes; see FreeStructFromStdINCHI() on how to deallocate it
        Option /Inchi2Struct is not needed for GetStructFromINCHI()/GetStructFromStdINCHI()

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStructFromINCHI( inchi_InputINCHI *inpInChI, inchi_OutputStruct *outStruct );
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStructFromStdINCHI( inchi_InputINCHI *inpInChI, inchi_OutputStruct *outStruct );
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStructFromINCHIEx( inchi_InputINCHI *inpInChI, inchi_OutputStructEx *outStruct );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    FreeStructFromINCHI / FreeStructFromStdINCHI / FreeStructFromINCHIEx

        should be called to deallocate pointers obtained from each
        GetStructFromStdINCHI / GetStructFromINCHI / GetStructFromINCHIEx

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStructFromINCHI( inchi_OutputStruct *out );
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStructFromStdINCHI( inchi_OutputStruct *out );
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL FreeStructFromINCHIEx( inchi_OutputStructEx *out );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    GetINCHIfromINCHI

        GetINCHIfromINCHI does same as -InChI2InChI option: converts InChI into InChI for validation purposes
        It may also be used to filter out specific layers. For instance, /Snon would remove stereochemical layer
        Omitting /FixedH and/or /RecMet would remove Fixed-H or Reconnected layers
        To keep all InChI layers use options string "/FixedH /RecMet"; option /InChI2InChI is not needed
        inchi_InputINCHI is created by the user; strings in inchi_Output are allocated and deallocated by InChI
        inchi_Output does not need to be initilized out to zeroes; see FreeINCHI() on how to deallocate it

        Note: there is no explicit tool to conversion from/to standard InChI

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHIfromINCHI( inchi_InputINCHI *inpInChI, inchi_Output *out );

#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif

/*****************************************************************
 *
 *
 *   C o n v e r s i o n:   InChI  AuxInfo string => inchi_Input
 *
 *
 *****************************************************************/

#ifndef STR_ERR_LEN
#define STR_ERR_LEN     256
#endif

typedef struct tagInchiInpData {
    inchi_Input *pInp;    /* a pointer to pInp that has all items 0 or NULL */
    int          bChiral; /* 1 => the structure was marked as chiral, 2=> not chiral, 0=> not marked */
    char         szErrMsg[STR_ERR_LEN];
} InchiInpData;

/* to compile all InChI code as a C++ code #define COMPILE_ALL_CPP */
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Get_inchi_Input_FromAuxInfo / Get_std_inchi_Input_FromAuxInfo

Input:
    szInchiAuxInfo: contains ASCIIZ string of InChI output for a single
                   structure or only the AuxInfo line
    bDoNotAddH:    if 0 then InChI will be allowed to add implicit H
    bDiffUnkUndfStereo
                   if not 0, use different labels for unknown and undefined stereo
    pInchiInp:     should have a valid pointer pInchiInp->pInp to an empty
                   (all members = 0) inchi_Input structure

Output:
    pInchiInp:     The following members of pInp may be filled during the call:
                   atom, num_atoms, stereo0D, num_stereo0D
    Return value:  see RetValGetINCHI

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL Get_inchi_Input_FromAuxInfo(
                                                            char *szInchiAuxInfo,
                                                            int bDoNotAddH,
                                                            int bDiffUnkUndfStereo,
                                                            InchiInpData *pInchiInp );
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL Get_std_inchi_Input_FromAuxInfo( char *szInchiAuxInfo,
                                                            int bDoNotAddH,
                                                            InchiInpData *pInchiInp );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    Free_inchi_Input / Free_std_inchi_Input

        To deallocate and write zeroes into the changed members of pInchiInp->pInp call
        Free_inchi_Input( inchi_Input *pInp )

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL Free_inchi_Input( inchi_Input *pInp );
    EXPIMP_TEMPLATE INCHI_API void INCHI_DECL Free_std_inchi_Input( inchi_Input *pInp );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    CheckINCHI

    Check if the string represents valid InChI/standard InChI.
    Input:
        szINCHI     source InChI
        strict      if 0, just briefly check for proper layout (prefix, version, etc.)
                    The result may not be strict.
                    If not 0, try to perform InChI2InChI conversion and
                    returns success if a resulting InChI string exactly match source.
                    The result may be 'false alarm' due to imperfectness of conversion.
    Returns:
        success/errors codes

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL CheckINCHI( const char *szINCHI, const int strict );

#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

                                InChIKey API

    InChIKey description

    The InChIKey is a character signature based on a hash code of the InChI string.
    Standard InChIKey is produced out of standard InChI.
    Non-standard InChIKey is produced out of non-standard InChI.

                    AAAAAAAAAAAAAA-BBBBBBBBCD-P

    InChIKey layout is as follows:

    AAAAAAAAAAAAAA
        First block (14 letters)
        Encodes molecular skeleton (connectivity)

    BBBBBBBB
        Second block (8 letters)
        Encodes tautomers, stereochemistry, isotopomers, reconnected layer
    C
        'S' for standard
        'N' for non-standard
    D
        InChI version ('A' for 1)
    P - (de)protonation flag
        Protonization encoding:
        N 0
        O +1 P +2 Q +3 R +4 S +5 T +6 U +7 V +8 W +9 X +10 Y +11 Z +12
        M -1 L-2 K -3 J -4 I -5 H -6 G -7 F -8 E -9 D -10 C -11 B -12
        A < -12 or > +12

    All symbols except delimiter (dash, that is, minus) are uppercase English
    letters representing a "base 26" encoding.

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/

/* Return codes for key generation procedure */
#define INCHIKEY_OK 0
#define INCHIKEY_UNKNOWN_ERROR 1
#define INCHIKEY_EMPTY_INPUT 2
#define INCHIKEY_INVALID_INCHI_PREFIX 3
#define INCHIKEY_NOT_ENOUGH_MEMORY 4
#define INCHIKEY_INVALID_INCHI 20
#define INCHIKEY_INVALID_STD_INCHI 21

/* Return codes for CheckINCHIKey */
typedef enum tagRetValGetINCHIKey
{
    INCHIKEY_VALID_STANDARD = 0,
    INCHIKEY_VALID_NON_STANDARD = -1,
    INCHIKEY_INVALID_LENGTH = 1,
    INCHIKEY_INVALID_LAYOUT = 2,
    INCHIKEY_INVALID_VERSION = 3
} RetValCheckINCHIKeyv;

/* EXPORTED FUNCTIONS */

/* To compile all InChI code as a C++ code #define COMPILE_ALL_CPP */

#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
GetINCHIKeyFromINCHI

Calculate InChIKey by InChI string.

Input:
        szINCHISource
            source InChI string
        xtra1
            =1 calculate hash extension (up to 256 bits; 1st block)
        xtra2
            =1 calculate hash extension (up to 256 bits; 2nd block)

Output:
        szINCHIKey
            InChIKey string
            The user-supplied buffer szINCHIKey should be at least 28 bytes long.
        szXtra1
            hash extension (up to 256 bits; 1st block) string
            Caller should allocate space for 64 characters + trailing NULL
        szXtra2
            hash extension (up to 256 bits; 2nd block) string
            Caller should allocate space for 64 characters + trailing NULL

Returns:
        success/errors codes

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetINCHIKeyFromINCHI( const char* szINCHISource,
                                                                  const int xtra1,
                                                                  const int xtra2,
                                                                  char* szINCHIKey,
                                                                  char* szXtra1,
                                                                  char* szXtra2 );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    GetStdINCHIKeyFromStdINCHI

        "Standard" counterpart

        For compatibility with v. 1.02std, no extra hash calculation is allowed.
        To calculate extra hash(es), use GetINCHIKeyFromINCHI with stdInChI as input.

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL GetStdINCHIKeyFromStdINCHI( const char* szINCHISource,
                                                                        char* szINCHIKey );

    /*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    CheckINCHIKey

    Check if the string represents valid InChIKey.
    Input:
            szINCHIKey
                source InChIKey string
    Returns:
            success/errors codes

    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
    EXPIMP_TEMPLATE INCHI_API int INCHI_DECL CheckINCHIKey( const char *szINCHIKey );

#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

                          Modularized InChI generation API

    Note. Functions with STDINCHIGEN prefix are
    retained for compatibility with v. 1.02std

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/

/* Data structures holding intermediate (normalization) results */

#ifndef MAX_NUM_STEREO_ATOM_NEIGH
#define MAX_NUM_STEREO_ATOM_NEIGH 4
#endif
#ifndef MAX_NUM_STEREO_BONDS
#define MAX_NUM_STEREO_BONDS      3
#endif
#ifndef INCHI_NUM
#define INCHI_NUM            2    /* = array size; member indexes: */
#endif

typedef unsigned short AT_NUMBR;
typedef signed short NUM_HS;
typedef unsigned long INCHI_MODES;

typedef struct tagNormAtom
{
    char          elname[ATOM_EL_LEN];      /* chem. element name */
    U_CHAR        el_number;                /* number of the element in the Periodic Table */
    AT_NUMBR      neighbor[MAXVAL];         /* positions (from 0) of the neighbors in the NORM_ATOM array */
    AT_NUMBR      orig_at_number;           /* original atom number, starts from 1 */
    AT_NUMBR      orig_compt_at_numb;       /* atom number within a component before terminal H removal */
    S_CHAR        bond_stereo[MAXVAL];      /* 1=Up,4=Either,6=Down (this atom is at the pointing wedge)
                                               negative => on the opposite side of the wedge; 3=Either double bond  */
    U_CHAR        bond_type[MAXVAL];        /* 1=single, 2=double, 3=triple, 4=1/2 (bond order is 1 or 2) */
                                            /* 5=1/2/3, 6=1/3, 7=2/3, 8=tautomeric, 9=1/2 non-stereogenic */

    S_CHAR        valence;                  /* number of bonds = number of neighbors not greater than MAXVAL */
    S_CHAR        chem_bonds_valence;       /* sum of bond types (1,2,3); type 4 needs special treatment */
    S_CHAR        num_H;                    /* number of adjacent implicit hydrogen atoms including D and T    */
    S_CHAR        num_iso_H[NUM_H_ISOTOPES];/* number of adjacent implicit 1H(protium), 2H(D), 3H(T) < 16 */
    S_CHAR        iso_atw_diff;             /* =0 => natural isotopic abundances  */
                                            /* >0 => (isotopic mass) - (rounded average atomic mass) + 1 */
                                            /* <0 => (isotopic mass) - (rounded average atomic mass) */
    S_CHAR        charge;                   /* charge */
    S_CHAR        radical;                  /* RADICAL_SINGLET, RADICAL_DOUBLET, or RADICAL_TRIPLET */
    S_CHAR        bAmbiguousStereo;         /* flag of detected stereo ambiguity */
    S_CHAR        cFlags;                   /* AT_FLAG_ISO_H_POINT: atom may have exchangeable isotopic H */
    AT_NUMBR      at_type;                  /* ATT_NONE, ATT_ACIDIC, etc. See InChI normalization code */
    AT_NUMBR      component;                /* number of the structure component > 0 */
    AT_NUMBR      endpoint;                 /* id of a tautomeric group */
    AT_NUMBR      c_point;                  /* id of a positive charge group */
    double        x;                        /* x coordinate */
    double        y;                        /* y coordinate */
    double        z;                        /* x coordinate */
    /*---------  0D parities ----------*/
    S_CHAR        bUsed0DParity;            /* bit=1 => stereobond; bit=2 => stereocenter */
    /*-----  tetrahedral stereo parity */
    S_CHAR        p_parity;                 /* tetrahedral (sp3) cml parity */
    AT_NUMBR      p_orig_at_num[MAX_NUM_STEREO_ATOM_NEIGH]; /* orig_at_number of each neighbor > 0; 0=> no neighbor */
    /*----- stereo bond (SB) parities */
    S_CHAR        sb_ord[MAX_NUM_STEREO_BONDS];  /* neighbor[] index of another end of this SB, starts from 0 */
    S_CHAR        sn_ord[MAX_NUM_STEREO_BONDS];  /* neighbor[] index of a bond that is not this SB; starts from 0;
                                                  -1 means the neighbor is a removed explicit H */
    /* atoms on both ends of a stereobond have same parity => trans/T/E/2, diff. parities => cis/C/Z/1 */
    S_CHAR        sb_parity[MAX_NUM_STEREO_BONDS];       /* parities of stereobonds (sp2) incident to this atom */
    AT_NUMBR      sn_orig_at_num[MAX_NUM_STEREO_BONDS];  /* orig_at_number of sn_ord[] neighbor > 0 */

#if ( FIND_RING_SYSTEMS == 1 )
    S_CHAR  bCutVertex;                    /* is the atom a cut-vertex or not */
    AT_NUMBR nRingSystem;                  /* starts from 1; number of a ring system */
    AT_NUMBR nNumAtInRingSystem;           /* number of atoms in a ring system to which this at belongs */
    AT_NUMBR nBlockSystem;                 /* ambiguous if the atom is a cut-vertex: better apply this to bonds */

#if ( FIND_RINS_SYSTEMS_DISTANCES == 1 )
    AT_NUMBR nDistanceFromTerminal;        /* not used */
#endif

#endif
} NORM_ATOM;

typedef struct tagNormAtomData
{
    NORM_ATOM *at;                  /* atom list */
    NORM_ATOM *at_fixed_bonds;      /* atom list with added or removed protons only */
    int       num_at;               /* number of atoms except removed terminal H */
    int       num_removed_H;        /* number of removed H; at[] has (num_at+num_removed_H) elements */
    int       num_bonds;
    int       num_isotopic;         /* number of isotopic atoms */
    int       bExists;              /* for internal use */
    int       bDeleted;             /* for internal use */
    int       bHasIsotopicLayer;
    int       bTautomeric;
    int       bTautPreprocessed;    /* for internal use */
    int       nNumRemovedProtons;
    NUM_HS    nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES];
                                    /* isotopic composition of removed protons, not included in num_iso_H[] */
    NUM_HS    num_iso_H[NUM_H_ISOTOPES];
                                    /* isotopic H on tautomeric atoms and those
                                       in nIsotopicEndpointAtomNumber */
    INCHI_MODES bTautFlags;         /* for internal use */
    INCHI_MODES bTautFlagsDone;     /* for internal use */
    INCHI_MODES bNormalizationFlags;/* for internal use */
} NORM_ATOMS;

typedef struct tagINCHIGEN_DATA
{

    char          pStrErrStruct[STR_ERR_LEN]; /* intermediate log (warning/error report) */
    int           num_components[INCHI_NUM];  /* number of allocated INChI, INChI_Aux data structures */
                                              /* index=0 => disconnected, 1 => reconnected structure */

    /* The results of normalization stage */
    /* for each member of pair disconnected/reconnected structures: */
    NORM_ATOMS   *NormAtomsNontaut[INCHI_NUM];
    NORM_ATOMS   *NormAtomsTaut[INCHI_NUM];
} INCHIGEN_DATA;

/* InChI Generator Handle */

typedef void* INCHIGEN_HANDLE;

/* EXPORTED FUNCTIONS */

/* to compile all InChI code as a C++ code #define COMPILE_ALL_CPP */
#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
extern "C" {
#endif
#endif

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_Create / STDINCHIGEN_Create

InChI Generator: create generator
Returns handle of generator object or NULL on failure

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API INCHIGEN_HANDLE INCHI_DECL INCHIGEN_Create( void );
EXPIMP_TEMPLATE INCHI_API INCHIGEN_HANDLE INCHI_DECL STDINCHIGEN_Create( void );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_Setup / STDINCHIGEN_Setup

InChI Generator: setup

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL INCHIGEN_Setup( INCHIGEN_HANDLE HGen,
                                                         INCHIGEN_DATA * pGenData,
                                                         inchi_Input * pInp );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL STDINCHIGEN_Setup( INCHIGEN_HANDLE HGen,
                                                            INCHIGEN_DATA * pGenData,
                                                            inchi_Input * pInp );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_DoNormalization / STDINCHIGEN_DoNormalization

InChI Generator: structure normalization stage

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL INCHIGEN_DoNormalization( INCHIGEN_HANDLE HGen,
                                                                   INCHIGEN_DATA * pGenData );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL STDINCHIGEN_DoNormalization( INCHIGEN_HANDLE HGen,
                                                                      INCHIGEN_DATA * pGenData );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_DoCanonicalization / STDINCHIGEN_DoCanonicalization

InChI Generator: structure canonicalization stage

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL INCHIGEN_DoCanonicalization( INCHIGEN_HANDLE HGen,
                                                                      INCHIGEN_DATA * pGenData );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL STDINCHIGEN_DoCanonicalization( INCHIGEN_HANDLE HGen,
                                                                         INCHIGEN_DATA * pGenData );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_DoSerialization / STDINCHIGEN_DoSerialization

InChI Generator: InChI serialization stage

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL INCHIGEN_DoSerialization( INCHIGEN_HANDLE HGen,
                                                                   INCHIGEN_DATA * pGenData,
                                                                   inchi_Output * pResults );
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL STDINCHIGEN_DoSerialization( INCHIGEN_HANDLE HGen,
                                                                      INCHIGEN_DATA * pGenData,
                                                                      inchi_Output * pResults );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_Reset / STDINCHIGEN_Reset

    InChI Generator: reset stage (use before get next structure)

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL INCHIGEN_Reset( INCHIGEN_HANDLE HGen,
                                                          INCHIGEN_DATA * pGenData,
                                                          inchi_Output * pResults );
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL STDINCHIGEN_Reset( INCHIGEN_HANDLE HGen,
                                                             INCHIGEN_DATA * pGenData,
                                                             inchi_Output * pResults );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
INCHIGEN_Destroy / STDINCHIGEN_Destroy

    InChI Generator: destroy generator

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL INCHIGEN_Destroy( INCHIGEN_HANDLE HGen );
EXPIMP_TEMPLATE INCHI_API void INCHI_DECL STDINCHIGEN_Destroy( INCHIGEN_HANDLE HGen );

/*^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
MakeINCHIFromMolfileText

    Direct generation of InChI from Molfile supplied as text

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^*/
EXPIMP_TEMPLATE INCHI_API int INCHI_DECL MakeINCHIFromMolfileText( const char *moltext,
                                                                   char *options,
                                                                   inchi_Output *result );

#ifndef COMPILE_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif

#include "ixa.h"

#endif    /* _INHCH_API_H_ */

[maneetgoyal]

InCHI API Reference: InChI_API_Reference.pdf

[maneetgoyal]

How to map C types to NodeJS friendly FFI types?

Via: https://github.com/node-ffi/node-ffi/wiki/Node-FFI-Tutorial

[maneetgoyal]

Fixed by #7