/*
 * International Chemical Identifier (InChI)
 * Version 1
 * Software version 1.02
 * October 31, 2008
 * Developed at NIST
 *
 * The InChI library and programs are free software developed under the
 * auspices of the International Union of Pure and Applied Chemistry (IUPAC);
 * you can redistribute this software and/or modify it under the terms of 
 * the GNU Lesser General Public License as published by the Free Software 
 * Foundation:
 * http://www.opensource.org/licenses/lgpl-license.php
 */


#ifndef __INCHI_H__
#define __INCHI_H__

#include "incomdef.h"

#define REQ_MODE_BASIC              0x000001    /* B include Fixed-H layer */
#define REQ_MODE_TAUT               0x000002    /* T include Mobile-H layer */
#define REQ_MODE_ISO                0x000004    /* I    */
#define REQ_MODE_NON_ISO            0x000008    /* NI   */
#define REQ_MODE_STEREO             0x000010    /* S    */
#define REQ_MODE_ISO_STEREO         0x000020    /* IS   */
#define REQ_MODE_NOEQ_STEREO        0x000040    /* SS   */
#define REQ_MODE_REDNDNT_STEREO     0x000080    /* RS   */
#define REQ_MODE_NO_ALT_SBONDS      0x000100    /* NASB */
/* new 10-10-2003 */
#define REQ_MODE_RELATIVE_STEREO    0x000200    /* REL All Relative Stereo */
#define REQ_MODE_RACEMIC_STEREO     0x000400    /* RAC All Racemic Stereo */
#define REQ_MODE_SC_IGN_ALL_UU      0x000800    /* IAUSC Ignore stereocenters if All Undef/Unknown */
#define REQ_MODE_SB_IGN_ALL_UU      0x001000    /* IAUSC Ignore stereobonds if All Undef/Unknown */
#define REQ_MODE_CHIR_FLG_STEREO    0x002000    /* SUCF  If Chiral flag then Abs otherwise Rel stereo */
/* end of 10-10-2003 */
#define REQ_MODE_MIN_SB_RING_MASK   0x0F0000    /* RSB  */
#define REQ_MODE_MIN_SB_RING_SHFT      16

#define REQ_MODE_DEFAULT  (REQ_MODE_BASIC | REQ_MODE_TAUT | REQ_MODE_ISO | REQ_MODE_NON_ISO | REQ_MODE_STEREO)

#define WARN_FAILED_STEREO          0x0001
#define WARN_FAILED_ISOTOPIC        0x0002
#define WARN_FAILED_ISOTOPIC_STEREO 0x0004
#define ERR_NO_CANON_RESULTS        0x0008

/*********** compare components flags **********************************/
#define CMP_COMPONENTS              0x0001     /* perform compare components */
#define CMP_COMPONENTS_NONISO       0x0002     /* ignore isotopic */
#define CMP_COMPONENTS_NONTAUT      0x0004     /* compare non-tautomeric */
/****************** chemical identifier member definitions *************/
typedef struct tagINChI_IsotopicAtom {
    AT_NUMB   nAtomNumber;  /* Canonical atom number */
    NUM_H     nIsoDifference; /* 0=non-isotopic; 1=rounded avg. atomic mass */
    NUM_H     nNum_H;  /* number of 1H isotopic atoms attached */
    NUM_H     nNum_D;  /* number of 2H isotopic atoms attached */
    NUM_H     nNum_T;  /* number of 3H isotopic atoms attached */
} INChI_IsotopicAtom;
typedef struct tagINChI_IsotopicTGroup {
    AT_NUMB   nTGroupNumber;  /* Tautomeric group number */
    AT_NUMB   nNum_H;  /* number of 1H isotopic atoms */
    AT_NUMB   nNum_D;  /* number of 2H isotopic atoms */
    AT_NUMB   nNum_T;  /* number of 3H isotopic atoms */
} INChI_IsotopicTGroup;
typedef struct tagINChI_Stereo { /* [N] = allocated length */
    /* ---- possibly tetrahedral stereogenic atoms */
    int         nNumberOfStereoCenters;
    AT_NUMB    *nNumber;      /* Canonical number of a possibly tetrahedral
                               * stereogenic atom or allenes [nNumberOfAtoms] */
    S_CHAR     *t_parity;     /* tetrahedral (relative, see nCompInv2Abs) atom parities [nNumberOfAtoms] */
    /* ---- possibly tetrahedral stereogenic atoms of the iverted structure */
    AT_NUMB    *nNumberInv;   /* Canonical number of a possibly tetrahedral
                               * stereogenic atom or allene [nNumberOfAtoms] */
    S_CHAR     *t_parityInv;  /* tetrahedral inverted atom parities [nNumberOfAtoms] */
    /* bFlagAbsStereoIsInverted = nCompInv2Abs==-1: Abs stereo = Inverted  */
    int         nCompInv2Abs; /* 0=>Inv = Abs stereo; -1=> Inv < Abs stereo, +1=> Inv > Abs stereo; +2=> in reading InChI: no /m was found and in /sN N>0 */
    int         bTrivialInv;  /* 1=> nCompInv2Abs!= 0 && Inverted = Abs stereo with inverted parities 1<-->2 */
    /* ---- possibly stereogenic bonds and tetrahedral cumuleles */
    int         nNumberOfStereoBonds;
    AT_NUMB    *nBondAtom1; /* Canonical number of a first atom 
                             * [number of bonds] */
    AT_NUMB    *nBondAtom2; /* Canonical number of a second atom
                             * [number of bonds] */
    S_CHAR     *b_parity;   /* possibly stereogenic bond parities
                             * [number of bonds] */
} INChI_Stereo;
#define INCHI_FLAG_ACID_TAUT            0x0001   /* tautomerism of dissociated acid invoked */
#define INCHI_FLAG_REL_STEREO           0x0002   /* requested relative stereo */
#define INCHI_FLAG_RAC_STEREO           0x0004   /* requested racemic stereo */
#define INCHI_FLAG_SC_IGN_ALL_UU        0x0008   /* ignored all undefined/unknown stereocenters, non-isotopic */
#define INCHI_FLAG_SB_IGN_ALL_UU        0x0010   /* ignored all undefined/unknown stereocenters, non-isotopic */
#define INCHI_FLAG_SC_IGN_ALL_ISO_UU    0x0020   /* ignored all undefined/unknown stereocenters, isotopic */
#define INCHI_FLAG_SB_IGN_ALL_ISO_UU    0x0040   /* ignored all undefined/unknown stereocenters, isotopic */
#define INCHI_FLAG_HARD_ADD_REM_PROTON  0x0080   /* in normalization a proton has been added or removed along alt path */

#define INCHI_OUT_NO_AUX_INFO           0x0001   /* do not output Aux Info */
#define INCHI_OUT_SHORT_AUX_INFO        0x0002   /* output short version of Aux Info */
#define INCHI_OUT_ONLY_AUX_INFO         0x0004   /* output only Aux Info */
#define INCHI_OUT_EMBED_REC             0x0008   /* embed reconnected INChI into disconnected INChI */
#define INCHI_OUT_SDFILE_ONLY           0x0010   /* save input data in a Molfile instead of creating INChI */
#define INCHI_OUT_XML                   0x0020   /* output xml INChI */
#define INCHI_OUT_PLAIN_TEXT            0x0040   /* output plain text INChI */
#define INCHI_OUT_PLAIN_TEXT_COMMENTS   0x0080   /* output plain text annotation */
#define INCHI_OUT_XML_TEXT_COMMENTS     0x0100   /* output xml text annotation */
#define INCHI_OUT_WINCHI_WINDOW         0x0200   /* output into wINChI text window */
#define INCHI_OUT_TABBED_OUTPUT         0x0400   /* tab-delimited (only for plain text) */
#define INCHI_OUT_SDFILE_ATOMS_DT       0x0800   /* SDfile output H isotopes as D and T */
#define INCHI_OUT_SDFILE_SPLIT          0x1000   /* Split SDfile into components */
/*^^^ */
#define INCHI_OUT_FIX_TRANSPOSITION_CHARGE_BUG 0x2000   
                                    /* used to accomodate FIX_TRANSPOSITION_CHARGE_BUG */
/*^^^ */
#define INCHI_OUT_STANDARD_FLAG 0x4000   

#define INCHI_OUT_PRINT_OPTIONS       (INCHI_OUT_EMBED_REC |           \
                                       INCHI_OUT_XML |                 \
                                       INCHI_OUT_PLAIN_TEXT |          \
                                       INCHI_OUT_PLAIN_TEXT_COMMENTS | \
                                       INCHI_OUT_XML_TEXT_COMMENTS)


/*******REQ_MODE_SB_IGN_ALL_UU*************** chemical identifier definition *****************/
typedef struct tagINChI {  /* [N] = allocated length */
    
    int        nErrorCode;  /* 0 = success */
    INCHI_MODE  nFlags;      /* INCHI_FLAG_ACID_TAUT            tautomerism of dissociated acid invoked
                                INCHI_FLAG_REL_STEREO           requested relative stereo
                                INCHI_FLAG_RAC_STEREO           requested racemic stereo
                                INCHI_FLAG_SC_IGN_ALL_UU        ignored all undefined/unknown stereocenters, non-isotopic
                                INCHI_FLAG_SB_IGN_ALL_UU        ignored all undefined/unknown stereocenters, non-isotopic
                                INCHI_FLAG_SC_IGN_ALL_ISO_UU    ignored all undefined/unknown stereocenters, isotopic
                                INCHI_FLAG_SB_IGN_ALL_ISO_UU    ignored all undefined/unknown stereocenters, isotopic
                                INCHI_FLAG_HARD_ADD_REM_PROTON  in normalization a proton has been added or removed along alt path
                              */
    /* ---- basic & tautomer layer */
    int        nTotalCharge;
    int        nNumberOfAtoms;
    char      *szHillFormula;
    U_CHAR    *nAtom;       /* atomic numbers [nNumberOfAtoms] from the Periodic Table */
    int        lenConnTable;
    AT_NUMB   *nConnTable;  /* Connection table [nNumberOfAtoms+NumberOfBonds] */
    int        lenTautomer;
    AT_NUMB   *nTautomer;   /* NumGroups; ((NumAt+1, NumH,         At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 1} - old
                             * NumGroups; ((NumAt+2, NumH, Num(-), At1..AtNumAt),...); {INCHI_T_NUM_MOVABLE = 2} - new
                             * Allocated length: [5*nNumberOfAtoms/2+1], see Alloc_INChI(...) */
    S_CHAR    *nNum_H;      /* number of terminal hydrogen atoms on each atom; in tautomeric
                             * representation these H on tautomeric atoms are not included [nNumberOfAtoms] */
    S_CHAR    *nNum_H_fixed;/* number of terminal hydrogen atoms on tautomeric atoms,
                             * in non-atautomeric representation only [nNumberOfAtoms] */
    /* ---- isotopic & isotopic tautomeric layer */
    int                  nNumberOfIsotopicAtoms;
    INChI_IsotopicAtom   *IsotopicAtom;              /* [nNumberOfIsotopicAtoms] */
    int                  nNumberOfIsotopicTGroups;
    /* in reversing InChI keeps a pointer to stolen from AuxInfo coordinates */
    INChI_IsotopicTGroup *IsotopicTGroup;             /* [nNumberOfIsotopicAtoms] */
    /* ---- stereo layer */
    INChI_Stereo *Stereo;
    INChI_Stereo *StereoIsotopic;
                                                /* not including mobile H groups */
    AT_NUMB *nPossibleLocationsOfIsotopicH;     /* [0]=> length including 0th element, location1,...*/
    int      bDeleted;
#if( bREUSE_INCHI == 1 )
    int nRefCount;
#endif
#if( bRELEASE_VERSION == 0 )
    int bExtract;
#endif
#if( READ_INCHI_STRING == 1 )
    int nLink;  /* negative: ignore InChI; positive: index of (Reconnected component) + 1 linked to it */
#endif
} INChI;

typedef INChI *PINChI2[TAUT_NUM];

typedef struct tagOrigInfo {
    S_CHAR cCharge;
    S_CHAR cRadical;       /* 0=none, 1=doublet, 2=triplet, 3=unknown */
    S_CHAR cUnusualValence; /* see get_unusual_el_valence() */
} ORIG_INFO;
/******************** auxiliary chemical identifier info **************/
typedef struct tagINChI_Aux { /* [N] = allocated length */

    int        nErrorCode;  /* 0 = success */
    int        nNumberOfAtoms;
    int        nNumberOfTGroups;   /* non-zero only in tautomeric representation */
    int        bIsIsotopic;        /* filled out even though isotopic has not been requested */
    int        bIsTautomeric;      /* filled out even though tautomeric has not been requested; non-zero if taut exists */
    /* canonical numbers of the atoms: nOrigAtNosInCanonOrd[i-1]+1 =       */
    /*                       input atom number for the canonical number i  */
    AT_NUMB   *nOrigAtNosInCanonOrd;             /* [nNumberOfInputAtoms*1.5]; */
    AT_NUMB   *nIsotopicOrigAtNosInCanonOrd;     /* [nNumberOfInputAtoms*1.5]; */
    /* same for the inverted structure */
    AT_NUMB   *nOrigAtNosInCanonOrdInv;          /* inveterted stereo [nNumberOfInputAtoms*1.5]; */
    AT_NUMB   *nIsotopicOrigAtNosInCanonOrdInv;  /* [nNumberOfInputAtoms*1.5]; */
    AT_NUMB   *nConstitEquNumbers;               /* [nNumberOfAtoms*1.5] */
    AT_NUMB   *nConstitEquTGroupNumbers;         /* [nNumberOfAtoms/2] */
    AT_NUMB   *nConstitEquIsotopicNumbers;       /* [nNumberOfAtoms*1.5] */
    AT_NUMB   *nConstitEquIsotopicTGroupNumbers; /* [nNumberOfAtoms/2] */
#if( bREUSE_INCHI == 1 )
    int nRefCount;
#endif
#if( TEST_RENUMB_ATOMS == 1 )
    unsigned long ulNormTime;
    unsigned long ulCanonTime;
#endif

    ORIG_INFO *OrigInfo;
    MOL_COORD *szOrigCoord;
    NUM_H   nNumRemovedProtons;
    NUM_H   nNumRemovedIsotopicH[NUM_H_ISOTOPES]; /* isotopic H that may be exchanged and considered
                                                     randomly distributed, including removed protons;
                                                     order: 0=>1H, 1=>D, 2=>T */
    int     bDeleted;
    INCHI_MODE  bTautFlags;             /* t_group_info->bTautFlags */
    INCHI_MODE  bTautFlagsDone;         /* t_group_info->bTautFlagsDone */
    INCHI_MODE  bNormalizationFlags;    /* t_group_info->tni.bNormalizationFlags */
    int        nCanonFlags;
} INChI_Aux;

typedef INChI_Aux *PINChI_Aux2[TAUT_NUM];

/********************* array of pointers for sorting components and INChI output *********/
typedef struct tagINChIforSort {
    INChI     *pINChI[TAUT_NUM];
    INChI_Aux *pINChI_Aux[TAUT_NUM];
    short      ord_number;    /* for stable sort */
    short      n1; /* points to the original; used in structure reconstruction only */
    short      n2; /* points to the original; used in structure reconstruction only */
    short      n3; /* points to the original; used in structure reconstruction only */
}INCHI_SORT;

#endif /* __INCHI_H__ */
