/*
 * 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 __INCHITAUT_H__
#define __INCHITAUT_H__

#include "inpdef.h"
#include "ichi_bns.h"


/*******************************************************
  ---     Header of tautomers groups      ---
  ---  Each entry is AT_TAUTOMER_HDR type ---
          number of tautomer groups (nNumTautGroups)
          index of the first tautomer group (#1)
          ...
          index of the last tautomer group  (#nNumTautGroups)
  --- end of the Header of tautomers groups description ---
  
  ---  One endpoint group description  ---
  ---  Each entry has AT_TAUTOMER type members ---
    <fixed portion (6 entries)>
          number of endpoints  (0=end of list)
          number of mobile groups, including number of negative charges (=num(H)+num(-))
          number of negative charges
          number of 1H atoms
          number of 2H (deuterium) atoms
          number of 3H (tritium) atoms
     <variable portion, sorted in ascending order>
          atom rank #1 (ascending order)
          ...
          atom rank #endpoints
  --- end of the endpoint group description ----

  ----------------------------------------------
     Note:
     In the following Linear CT Tautomer descriptions
     we assume the tautomeric groups and the endpoints
     within them have been properly sorted
  
  --------- Linear CT Tautomer description -----
    <for each tautomeric group>
        -- fixed length part, non-isotopic --
        number of endpoints        = t_group->nNumEndpoints
        number of mobile atoms     = t_group->num[0]
        ...
        number of negative charges = t_group->num[T_NUM_NO_ISOTOPIC-1]
        -- fixed length part, isotopic --
        number of T (3H)           = t_group->num[T_NUM_NO_ISOTOPIC]
        ...
        number of 1H               = t_group->num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC-1]
        -- variable length part --
        rank of the first endpoint = nRank[t_group_info->nEndpointAtomNumber[t_group->nFirstEndpointAtNoPos]];
        ...
        rank of the last endpoint  = nRank[t_group_info->nEndpointAtomNumber[t_group->nFirstEndpointAtNoPos+t_group->nNumEndpoints-1]];
  
  --------- Linear CT Isotopic Tautomer description -----
    <for each isotopic tautomeric group>
        number of T (3H)           = t_group->num[T_NUM_NO_ISOTOPIC]
        ...
        number of 1H               = t_group->num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC-1]
        t-group ordering number in the Linear CT Tautomer, starts from 1
        
***************************************************************/


#define           T_NUM_NO_ISOTOPIC 2
#define           T_NUM_ISOTOPIC    NUM_H_ISOTOPES /* was 2, now 3 */

#define           T_GROUP_HDR_LEN   (1+T_NUM_NO_ISOTOPIC /*+T_NUM_ISOTOPIC*/) /* LinearCTTautomer */

typedef AT_NUMB   AT_TAUTOMER;  /* LinearCTTautomer */

typedef AT_ISO_SORT_KEY  T_GROUP_ISOWT; /* must hold value up to T_GROUP_ISOWT_MULT^3-1 */
                                     /* similar to AT_ISO_SORT_KEY */
/* = num_1H + T_GROUP_ISOWT_MULT*(num_D + T_GROUP_ISOWT_MULT*num_T) */


#define T_GROUP_ISOWT_MULT   1024 /* (max. number of identical isotopic hydrogens in a taut. group) + 1 */
                                   /* changed from 256U 9-12-2003 */
                                   /* (similar to AT_ISO_SORT_KEY_MULT ) */
/* note: (long)T_GROUP_ISOWT should always be positive (have zero sign bit) */

typedef struct tagIsotopicTautomerGroup {
    AT_NUMB  tgroup_num;  /* ordering number of a tautomer group with isotopes > 0 */
    /*
    union {
        struct {
            AT_NUMB num_T;
            AT_NUMB num_D;
            AT_NUMB num_1H;
        };
        AT_NUMB num[T_NUM_ISOTOPIC];
    };
    */
    AT_NUMB  num[T_NUM_ISOTOPIC]; /* inverted order: num_T, num_D, num_1H */
} AT_ISO_TGROUP;

typedef enum tagTG_NumDA {  /* 2004-02-26 */
    TG_Num_dH, /* number of H donors that have only H (all single bonds) */
    TG_Num_dM, /* number of H donors that have (-)  (all single bonds) */
    TG_Num_aH, /* number of H acceptors that have H and no (-) (+a double bond) */
    TG_Num_aM, /* number of H acceptors that have (-) and possibly H (+ one double bond) */
    TG_Num_dO, /* number of H donors =C-OH or =C-O(-) */
    TG_Num_aO, /* number of H acceptors -C=O */
    TG_NUM_DA  /* number of elements in an array */
} TGNUMDA;

typedef struct tagTautomerGroup {
    /*
    union {
        struct {
               // T_NUM_NO_ISOTOPIC = 2 elements:
            AT_RANK num_Mobile; // Num_H+num_D+num_T+num_NegCharges
            AT_RANK num_NegCharges;
               // T_NUM_ISOTOPIC = 3 elements
            AT_RANK num_T;      // here the isotopic part (num+T_NUM_NO_ISOTOPIC) starts
            AT_RANK num_D;
            AT_RANK num_1H;
        };
        AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];  // same size and meaning as num[] in T_ENDPOINT
    };
    */
    AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];  /* same size and meaning as num[] in T_ENDPOINT */
                                                    /* isotopic inv. order: num_T, num_D, num_1H */
    AT_RANK num_DA[TG_NUM_DA];
    T_GROUP_ISOWT iWeight;   /* isotopic "weight" = T_GROUP_ISOWT_MULT*(T_GROUP_ISOWT_MULT*num_T + num_D)+num_1H; */
    AT_NUMB   nGroupNumber;  /* positive tautomer group ID = atom->endpoint */
    AT_NUMB   nNumEndpoints; /* number of the atom numbers in T_GROUP_INFO::nEndpointAtomNumber[] */
    AT_NUMB   nFirstEndpointAtNoPos; /* the first index of the atom number in T_GROUP_INFO::nEndpointAtomNumber[] */
} T_GROUP;

/* offsets/num_t_groups within T_GROUP_INFO::tGroupNumber  */
#define TGSO_CURR_ORDER  0  /* tGroupNumber:     current sorting order */
#define TGSO_SYMM_RANK   1  /* tSymmRank:     symmetry ranks (no isotopes) = min. ordering number > 0. */
#define TGSO_SYMM_IORDER 2  /* tiGroupNumber: isotopic symmetry rank sorting order */
#define TGSO_SYMM_IRANK  3  /* tiSymmRank:    isotopic symmetry ranks */
#define TGSO_TOTAL_LEN   4

/***************************************************/
/* flags for t_group_info->tni.bNormalizationFlags */
/***************************************************/
#define FLAG_PROTON_NPO_SIMPLE_REMOVED 0x0001
#define FLAG_PROTON_NP_HARD_REMOVED    0x0002
#define FLAG_PROTON_AC_SIMPLE_ADDED    0x0004
#define FLAG_PROTON_AC_SIMPLE_REMOVED  0x0008
#define FLAG_PROTON_AC_HARD_REMOVED    0x0010
#define FLAG_PROTON_AC_HARD_ADDED      0x0020
#define FLAG_PROTON_CHARGE_CANCEL      0x0040
#define FLAG_PROTON_SINGLE_REMOVED     0x0080

/* signifies tautomeric structure even though no t-group discovered */
#define FLAG_NORM_CONSIDER_TAUT      ( FLAG_PROTON_NPO_SIMPLE_REMOVED | \
                                       FLAG_PROTON_NP_HARD_REMOVED    | \
                                       FLAG_PROTON_AC_SIMPLE_ADDED    | \
                                       FLAG_PROTON_AC_SIMPLE_REMOVED  | \
                                       FLAG_PROTON_AC_HARD_REMOVED    | \
                                       FLAG_PROTON_AC_HARD_ADDED      | \
                                       FLAG_PROTON_SINGLE_REMOVED     | \
                                       FLAG_PROTON_CHARGE_CANCEL    )

#if( FIX_N_MINUS_NORN_BUG == 1 )
#define FLAG_FORCE_SALT_TAUT         ( FLAG_PROTON_NP_HARD_REMOVED  | \
                                       FLAG_PROTON_AC_HARD_REMOVED  | \
                                       FLAG_PROTON_AC_HARD_ADDED    | \
                                       FLAG_PROTON_CHARGE_CANCEL    )
#else
/* force salt tautomerism exploration */
#define FLAG_FORCE_SALT_TAUT         ( FLAG_PROTON_NP_HARD_REMOVED  | \
                                       FLAG_PROTON_AC_HARD_REMOVED  | \
                                       FLAG_PROTON_AC_HARD_ADDED    )
#endif

typedef struct tagTautomerNormInfo {
    NUM_H       nNumRemovedExplicitH; /* keeps track of explicit H */
    NUM_H       nNumRemovedProtons;
    NUM_H       nNumRemovedProtonsIsotopic[NUM_H_ISOTOPES];
    INCHI_MODE   bNormalizationFlags;
} TNI;

/***************************************************/
/*      t_group_info definition                    */
/***************************************************/
typedef struct tagTautomerGroupsInfo {
    T_GROUP   *t_group;  /* max_num_t_groups elements */
    AT_NUMB   *nEndpointAtomNumber; /* nNumEndpoints elements; also see comments to T_GROUP */
    AT_NUMB   *tGroupNumber;
    int       nNumEndpoints;
    int       num_t_groups;
    int       max_num_t_groups;
    int       bIgnoreIsotopic;

    AT_NUMB   *nIsotopicEndpointAtomNumber; /* [0]: number of the following atoms; [1...]: non-tautomeric atoms that may have isotopic H */
    int       nNumIsotopicEndpoints;     /* allocated length of nIsotopicEndpointAtomNumber */
    NUM_H     num_iso_H[NUM_H_ISOTOPES]; /* isotopic H on tautomeric atoms and those in nIsotopicEndpointAtomNumber */
    
    TNI       tni;
    
    INCHI_MODE bTautFlags;      
    INCHI_MODE bTautFlagsDone;      
} T_GROUP_INFO;

#define CANON_FLAG_NO_H_RECANON           0x0001  /* iOther: second canonicalization of the no H structure */
#define CANON_FLAG_NO_TAUT_H_DIFF         0x0002  /* iOther: NoTautH eq. partition differs from NoH */
#define CANON_FLAG_ISO_ONLY_NON_TAUT_DIFF 0x0004  /* iOther: eq. partition in isotopic only non-taut differs from non-isotopic */
#define CANON_FLAG_ISO_TAUT_DIFF          0x0008  /* iBase:  isotopic eq. partition in isotopic taut differs from non-isotopic taut */
#define CANON_FLAG_ISO_FIXED_H_DIFF       0x0010  /* iOther: isotopic eq. partition in fixed H non-taut differs from non-isotopic fixed H */

/* Note: rank of tautomer atom #i = Rank[nEndpointAtomNumber[i]] */
/*       for each tautomer atom group (t_group) t_group.nFirstEndpointAtNoPos */
/*       is the first index of the atom number in nEndpointAtomNumber[] */

typedef struct tagTautomerEndpoint {
    /*
    union {
        struct {
            AT_RANK num_Mobile; // Num_H+num_D+num_T+num_NegCharges
            AT_RANK num_NegCharges;
            AT_RANK num_T;
            AT_RANK num_D;
        };
        AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];    // same size and meaning as num[] in T_GROUP
    };
    */
    AT_RANK num[T_NUM_NO_ISOTOPIC+T_NUM_ISOTOPIC];    /* same size and meaning as num[] in T_GROUP */
    AT_RANK num_DA[TG_NUM_DA];
    AT_NUMB nGroupNumber;
    AT_NUMB nEquNumber;  /* same for endpoints connected by alt paths */
    AT_NUMB nAtomNumber;
    /*AT_NUMB neighbor_index; */
} T_ENDPOINT;

typedef struct tagTautomerBondLocation {
    AT_NUMB nAtomNumber;
    AT_NUMB neighbor_index;
} T_BONDPOS;

typedef struct tagEndpointInfo {
    S_CHAR cMoveableCharge;
    S_CHAR cNeutralBondsValence;
    S_CHAR cMobile;
    S_CHAR cDonor;
    S_CHAR cAcceptor;
    S_CHAR cKetoEnolCode; /* 1 => carbon, 2 => oxygen */ /* post v.1 feature */
} ENDPOINT_INFO;


/* positive charge group (extended onium) */

#define CHARGED_CPOINT(X,i) ((X)[i].charge==1)

typedef struct tagChargeCandidate {
    AT_NUMB   atnumber;
    S_CHAR    type;
    S_CHAR    subtype;
} C_CANDIDATE;

typedef struct tagChargeGroup {
    AT_RANK   num[2]; /* [0]: number of (+), [1]: number atoms that have H, including H accessible through tautomerism */
    AT_RANK   num_CPoints;
    AT_NUMB   nGroupNumber;
    U_CHAR    cGroupType;
} C_GROUP;
    
typedef struct tagChargeGroupsInfo {
    C_GROUP *c_group;
    int     num_c_groups;
    int     max_num_c_groups;
    
    C_CANDIDATE *c_candidate;
    int          max_num_candidates;
    int          num_candidates; /* 0=>unimitialized, -1=>no candidates found */
} C_GROUP_INFO;

/* salts */
typedef struct tagSaltChargeCandidate {
    AT_NUMB   atnumber;
    S_CHAR    type;
    S_CHAR    subtype;
    AT_NUMB   endpoint; /* MAX_ATOMS+1 => found alt path to the candidate */
} S_CANDIDATE;

typedef struct tagSaltGroupInfo {
    S_CANDIDATE *s_candidate;
    int          max_num_candidates;
    int          num_candidates; /* 0=>unimitialized, -1=>no candidates found */
    int          num_other_candidates; /* num. non-"acidic O" candidates */
    int          num_p_only_candidates; /* num. non-tautomeric p-donor/acceptor candidates like -CH2-SH */
} S_GROUP_INFO;

/********************* ATOM_SIZES *******************************/
/* sizes of a component */
typedef struct tagAtomSizes {
    /* for tautomeric and non-tautomeric structures */
    int nMaxNumStereoAtoms; /* max. number of stereo atoms in isotopic case */
    int nMaxNumStereoBonds; /* max. number of stereo bonds in isotopic case */
    int num_isotopic_atoms;  /* includes atoms that have isotopic tautomeric H */
    int nLenCT;
    int nLenBonds;
    int nLenIsotopic;
    int nLenCTAtOnly;
    int nLenLinearCTStereoDble; /* max. number of stereo bonds in non-isotopic case */
    int nLenLinearCTStereoCarb; /* max. number of stereo atoms in non-isotopic case */
    /* int bHasIsotopicAtoms; */
    int bMayHaveStereo;

    int bIgnoreIsotopic;

    /* tautomeric structure only; zeroes in non-tautomeric */
    int nLenLinearCTTautomer;
    int nLenLinearCTIsotopicTautomer;
    int bHasIsotopicTautGroups;
    int nLenIsotopicEndpoints;

} ATOM_SIZES;


typedef struct tagDfsPath {
    AT_RANK       at_no;
    /*AT_RANK       nDfsLevel;*/
    U_CHAR        bond_type;
    S_CHAR        bond_pos;
} DFS_PATH;


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

int is_centerpoint_elem( U_CHAR el_number );
int is_centerpoint_elem_strict( U_CHAR el_number );
#if ( KETO_ENOL_TAUT == 1 )
int is_centerpoint_elem_KET( U_CHAR el_number );
#endif
int bIsCenterPointStrict( inp_ATOM *atom, int iat );

int nGetEndpointInfo( inp_ATOM *atom, int iat, ENDPOINT_INFO *eif );
#if ( KETO_ENOL_TAUT == 1 )
int nGetEndpointInfo_KET( inp_ATOM *atom, int iat, ENDPOINT_INFO *eif );
#endif
void AddAtom2DA( AT_RANK num_DA[], inp_ATOM *atom, int at_no, int bSubtract );
int AddAtom2num(  AT_RANK num[], inp_ATOM *atom, int at_no, int bSubtract );
int AddEndPoint( T_ENDPOINT *pEndPoint, inp_ATOM *at, int iat );
int bHasAcidicHydrogen( inp_ATOM *at, int i );
int bHasOtherExchangableH ( inp_ATOM *at, int i );
int bHasAcidicMinus( inp_ATOM *at, int i );


int nGet15TautIn6MembAltRing( inp_ATOM *atom, int nStartAtom, AT_RANK  *nBfsTreePos,
                              DFS_PATH *DfsPath, int nMaxLenBfsTree,
                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
                              int *pnNumEndPoint, int *pnNumBondPos,
                              struct BalancedNetworkStructure *pBNS,
                              struct BalancedNetworkData *pBD, int num_atoms );

int nGet12TautIn5MembAltRing( inp_ATOM *atom, int nStartAtom, int nStartAtomNeighbor,
                              AT_RANK  *nBfsTreePos, DFS_PATH *DfsPath, int nMaxLenBfsTree,
                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
                              int *pnNumEndPoint, int *pnNumBondPos,
                              struct BalancedNetworkStructure *pBNS,
                              struct BalancedNetworkData *pBD, int num_atoms );
int nGet14TautIn7MembAltRing( inp_ATOM *atom, int nStartAtom, int nStartAtomNeighbor,
                              int nStartAtomNeighborEndpoint, int nStartAtomNeighborNeighborEndpoint,
                              AT_RANK  *nDfsPathPos, DFS_PATH *DfsPath, int nMaxLenDfsPath,
                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
                              int *pnNumEndPoint, int *pnNumBondPos,
                              struct BalancedNetworkStructure *pBNS,
                              struct BalancedNetworkData *pBD, int num_atoms );
int nGet14TautIn5MembAltRing( inp_ATOM *atom, int nStartAtom, int nStartAtomNeighbor,
                              int nStartAtomNeighborEndpoint, int nStartAtomNeighborNeighborEndpoint,
                              AT_RANK  *nDfsPathPos, DFS_PATH *DfsPath, int nMaxLenDfsPath,
                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
                              int *pnNumEndPoint, int *pnNumBondPos,
                              struct BalancedNetworkStructure *pBNS,
                              struct BalancedNetworkData *pBD, int num_atoms );

int nGet15TautInAltPath( inp_ATOM *atom, int nStartAtom, AT_RANK  *nDfsPathPos,
                              DFS_PATH *DfsPath, int nMaxLenDfsPath,
                              T_ENDPOINT *EndPoint, int nMaxNumEndPoint,
                              T_BONDPOS  *BondPos, int nMaxNumBondPos,
                              int *pnNumEndPoint, int *pnNumBondPos,
                              struct BalancedNetworkStructure *pBNS,
                              struct BalancedNetworkData *pBD, int num_atoms );


#if( RING2CHAIN == 1 )
int Ring2Chain( ORIG_ATOM_DATA *orig_inp_data );
#endif

#if( UNDERIVATIZE == 1 )
int underivatize( ORIG_ATOM_DATA *orig_inp_data );
#endif

#ifndef INCHI_ALL_CPP
#ifdef __cplusplus
}
#endif
#endif

#endif /* __INCHITAUT_H__ */

