/*
FILE:     base_information.h
*/
/*
VERSION:  1.600
*/
/*
DATE:     2/3/2005
*/
/*
  Comments and Questions to: sw-help@rcsb.rutgers.edu
*/
/*
COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR
IMPLIED.  RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE
SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER
PROPRIETARY RIGHT.

The user of this software shall indemnify, hold harmless and defend
Rutgers, its governors, trustees, officers, employees, students,
agents and the authors against any and all claims, suits,
losses, liabilities, damages, costs, fees, and expenses including
reasonable attorneys' fees resulting from or arising out of the
use of this software.  This indemnification shall include, but is
not limited to, any and all claims alleging products liability.
*/
/*
               PDB SOFTWARE LICENSE AGREEMENT

BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING 
THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE  
SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS 
BECOMING A PARTY TO THIS AGREEMENT.  IF LICENSEE DOES NOT 
AGREE TO ALL OF THE TERMS OF THIS AGREEMENT
THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE.

1. LICENSE AGREEMENT

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at Rutgers, The State University of New Jersey (hereafter referred to 
as "RUTGERS").   The software is owned by RUTGERS and protected by 
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*/
#ifndef _BASE_INFORMATION_H_
#define _BASE_INFORMATION_H_

#define HBOND_TYPE_0    0
#define HBOND_TYPE_1    1
#define HBOND_TYPE_2    2
#define HBOND_TYPE_3    3
#define HBOND_TYPE_4    4
#define HBOND_TYPE_5    5
#define HBOND_TYPE_6    6
#define HBOND_TYPE_7    7
#define HBOND_TYPE_8    8
#define HBOND_TYPE_9    9
#define HBOND_TYPE_10  10
#define HBOND_TYPE_11  11
#define HBOND_TYPE_12  12
#define HBOND_TYPE_13  13
#define HBOND_TYPE_14  14
#define HBOND_TYPE_15  15
#define HBOND_TYPE_16  16
#define HBOND_TYPE_17  17
#define HBOND_TYPE_18  18
#define HBOND_TYPE_19  19
#define HBOND_TYPE_20  20
#define HBOND_TYPE_21  21
#define HBOND_TYPE_22  22
#define HBOND_TYPE_23  23
#define HBOND_TYPE_24  24
#define HBOND_TYPE_25  25
#define HBOND_TYPE_26  26
#define HBOND_TYPE_27  27
#define HBOND_TYPE_28  28
#define HBOND_TYPE_29  29

#define WATSON    1
#define HOOGSTEEN 2
#define SUGAR     3

#define R_RINGATOM     9
#define Y_RINGATOM     6

// #define PI        3.14159265358979323846
// #define XEPS      1.0e-7
#define HTWIST0   0.05
#define XBIG      1.0e+18
#define MAX_DORG  10.0
#define MAX_DPRJ  2.5
#define MAX_ANGLE 65.0
#define MIN_N91   6.0
#define HELIX_CHG 7.5
#define HLXANG    0.26
#define OLCRT     1.2 

#define CNUM      8
#define O3P_UPPER 2.5

#define MIN_CUTOFF 2.2
#define MAX_CUTOFF 3.5


typedef struct {
        int index;
        double d2dp;
        int type;
        int type_i;
        int type_j;
        int cis_or_trans;
} _PAIR_TO;

typedef struct {
        int num;
        int alloc_num;
        // int best_pair_to;
        // int pair_type;
        // double pair_score;
        _PAIR_TO **pair_to;
} _BASE_PAIR;

typedef struct {
        char chn_id[5];
        int sym;
        int transl[3];
        int count;
} SYM_OP;

typedef struct {
        char name[4];
} _ATOMNAME;

typedef struct {
        int num_atom;
        _ATOMNAME AtomName[12];
        double ref[12][3];
} REF_NA;

typedef struct {
        char atom[4];
        int  edge; /* WCE=1, CHE=2, SE=4 */
} _Atom_Edge;

typedef struct {
        int  num;
        _Atom_Edge _atoms[6];
} _Base_Edge;

typedef struct {
        int n_donor, n_acceptor;
        char donor[4][4];
        char acceptor[9][4];
        int  donor_type[4];
        int  acceptor_type[9];
} _Donor_Acceptor;

typedef struct {
        char type[2];
        _Donor_Acceptor *da;
        _Base_Edge *be;
} _DONOR_ACCEPTOR;

static _Base_Edge _EA = {
        6,
       {{ "C2", 5 },
        { "N1", 1 },
        { "N3", 4 },
        { "N6", 3 },
        { "N7", 2 },
        { "O2*",4 }}
};

static _Base_Edge _EC = {
       6,
       {{ "C5", 2 },
        { "C6", 2 },
        { "N3", 1 },
        { "N4", 3 },
        { "O2", 5 },
        { "O2*",4 }}
};

static _Base_Edge _EG = {
       6,
       {{ "N1", 1 },
        { "N2", 5 },
        { "N3", 4 },
        { "N7", 2 },
        { "O6", 3 },
        { "O2*",4 }}
};

static _Base_Edge _EI = {
       6,
       {{ "C2", 5 },
        { "N1", 1 },
        { "N3", 4 },
        { "N7", 2 },
        { "O6", 3 },
        { "O2*",4 }}
};

static _Base_Edge _ET = {
       5,
       {{ "C6", 2 },
        { "N3", 1 },
        { "O2", 5 },
        { "O2*",4 },
        { "O4", 3 }}
};

static _Base_Edge _EU = {
       6,
       {{ "C5", 2 },
        { "C6", 2 },
        { "N3", 1 },
        { "O2", 5 },
        { "O2*",4 },
        { "O4", 3 }}
};

static _Donor_Acceptor _baseA = {
        // 3, 9,
        3, 4,
        { "N6", "O2*", "C2" },
        { "N1", "N3",  "N7", "O2*", "O3*", "O4*", "O5*", "O1P", "O2P" },
        { 3, 1, 0 },
        { 3, 3, 3, 1, 1, 1, 1, 1, 1 }
};

static _Donor_Acceptor _baseC = {
        // 4, 8,
        4, 3,
        { "N4", "O2*", "C5", "C6" }, 
        { "O2", "N3", "O2*", "O3*", "O4*", "O5*", "O1P", "O2P" },
        { 3, 1, 0, 0 },
        { 3, 3, 1, 1, 1, 1, 1, 1 }
};

static _Donor_Acceptor _baseG = {
        // 3, 9,
        3, 4,
        { "N1", "N2", "O2*" },
        { "N3", "O6", "N7", "O2*", "O3*", "O4*", "O5*", "O1P", "O2P" },
        { 3, 3, 1 },
        { 3, 3, 3, 1, 1, 1, 1, 1, 1 }
};

static _Donor_Acceptor _baseI = {
        // 3,  9,
        3, 4,
        { "N1", "O2*", "C2" },
        { "N3", "O6", "N7", "O2*", "O3*", "O4*", "O5*", "O1P", "O2P" },
        { 3, 1, 0 },
        { 3, 3, 3, 1, 1, 1, 1, 1, 1 }
};

static _Donor_Acceptor _baseT = {
        // 3, 7,
        3, 3,
        { "N3", "O2*", "C6" },
        { "O2", "O4", "O3*", "O4*", "O5*", "O1P", "O2P" },
        { 3, 1, 0 },
        { 3, 3, 1, 1, 1, 1, 1 }
};

static _Donor_Acceptor _baseU = {
        // 4, 8, 
        4, 3,
        { "N3", "O2*", "C5", "C6" },
        { "O2", "O4", "O2*", "O3*", "O4*", "O5*", "O1P", "O2P" },
        { 3, 1, 0, 0 },
        { 3, 3, 1, 1, 1, 1, 1, 1 }
};

#define NUM_BASE_TYPE        6

static _DONOR_ACCEPTOR _base_type[NUM_BASE_TYPE] = {
       { "A", &_baseA, &_EA },
       { "C", &_baseC, &_EC },
       { "G", &_baseG, &_EG },
       { "I", &_baseI, &_EI },
       { "T", &_baseT, &_ET },
       { "U", &_baseU, &_EU }
};

static const char *_base_pair_type[] = {
       "",
       "TYPE_1_PAIR",
       "TYPE_2_PAIR",
       "TYPE_3_PAIR",
       "TYPE_4_PAIR",
       "TYPE_5_PAIR",
       "TYPE_6_PAIR",
       "TYPE_7_PAIR",
       "TYPE_8_PAIR",
       "TYPE_9_PAIR",
       "TYPE_10_PAIR",
       "TYPE_11_PAIR",
       "TYPE_12_PAIR",
       "TYPE_13_PAIR",
       "TYPE_14_PAIR",
       "TYPE_15_PAIR",
       "TYPE_16_PAIR",
       "TYPE_17_PAIR",
       "TYPE_18_PAIR",
       "WATSON-CRICK",
       "WATSON-CRICK",
       "REVERSED WATSON-CRICK",
       "REVERSED WATSON-CRICK",
       "HOOGSTEEN",
       "REVERSED HOOGSTEEN",
       "TYPE_25_PAIR",
       "TYPE_26_PAIR",
       "TYPE_27_PAIR",
       "TYPE_28_PAIR",
       "TYPE_29_PAIR"
};
/*
static char *_saenger_classification[] = {
       "",
       "I",
       "II",
       "III",
       "IV",
       "V",
       "VI",
       "VII",
       "VIII",
       "IX",
       "X",
       "XI",
       "XII",
       "XIII",
       "XIV",
       "XV",
       "XVI",
       "XVII",
       "XVIII",
       "Watson-Crick",
       "Watson-Crick",
       "reversed Watson-Crick",
       "reversed Watson-Crick",
       "Hoogsteen",
       "reversed Hoogsteen",
       "XXV",
       "XXVI",
       "XXVII",
       "XXVIII",
       "XXIX"
};

static char *_edges[] = {
       "",
       "Watson-Crick",
       "Hoogsteen",
       "Sugar Edge"
};

static char *_gb_dir[] = {
       "",
       "Cis",
       "Trans"
};
*/
static int _leontis_westhof_index[2][3][3] = {
        { { 1,  3,  5 },  { 3,  7,  9 },  { 5,  9, 11 } },
        { { 2,  4,  6 },  { 4,  8, 10 },  { 6, 10, 12 } }
};

typedef struct {
        char a_atomtyp[4];
        char b_atomtyp[4];
} ATOM_PAIR;

typedef struct {
        int type;
        int num;
        ATOM_PAIR atom_pair[3];
} BASE_TYPE;

typedef struct {
        int  num_base_type;
        BASE_TYPE base_type[6];
} BASEPAIR_TYPE;

typedef struct {
        char type[7];
        BASEPAIR_TYPE *btype;
} BASE_HBOND_TYPE;

static BASEPAIR_TYPE _base_AA = {
       4, {
       { HBOND_TYPE_1, 2, 
         {{"N6", "N1"},
          {"N1", "N6"}}
       },
       { HBOND_TYPE_2, 2,
         {{"N6", "N7"},
          {"N7", "N6"}}
       },
       { HBOND_TYPE_5, 2,
         {{"N6", "N1"},
          {"N7", "N6"}}
       },
       { HBOND_TYPE_5, 2,
         {{"N1", "N6"},
          {"N6", "N7"}}
       } }
};

static BASEPAIR_TYPE _base_AC = {
       2, {
       { HBOND_TYPE_25, 2,
         {{"N6", "N3"},
          {"N7", "N4"}}
       },
       { HBOND_TYPE_26, 2,
         {{"N6", "N3"},
          {"N1", "N4"}}
       } }
};

static BASEPAIR_TYPE _base_AG = {
       4, {
       { HBOND_TYPE_8, 2,
         {{"N6", "O6"},
          {"N1", "N1"}}
       },
       { HBOND_TYPE_9, 2,
         {{"N6", "O6"},
          {"N7", "N1"}}
       },
       { HBOND_TYPE_10, 2,
         {{"N1", "N2"},
          {"N6", "N3"}}
       },
       { HBOND_TYPE_11, 2,
         {{"N6", "N3"},
          {"N7", "N2"}}
       } }
};

static BASEPAIR_TYPE _base_AI = {
       2, {
       { HBOND_TYPE_8, 2,
         {{"N6", "O6"},
          {"N1", "N1"}}
       },
       { HBOND_TYPE_9, 2,
         {{"N6", "O6"},
          {"N7", "N1"}}
       } }
};

static BASEPAIR_TYPE _base_AT = {
       4, {
       { HBOND_TYPE_20, 2,
         {{"N1", "N3"},
          {"N6", "O4"}}
       },
       { HBOND_TYPE_21, 2,
         {{"N1", "N3"},
          {"N6", "O2"}}
       },
       { HBOND_TYPE_23, 2,
         {{"N7", "N3"},
          {"N6", "O4"}}
       },
       { HBOND_TYPE_24, 2,
         {{"N7", "N3"},
          {"N6", "O2"}}
       } }
};

static BASEPAIR_TYPE _base_CC = {
       2, {
       { HBOND_TYPE_14, 2,
         {{"N3", "N4"},
          {"N4", "N3"}}
       },
       { HBOND_TYPE_15, 2,
         {{"O2", "N4"},
          {"N4", "O2"}}
       } }
};

static BASEPAIR_TYPE _base_CG = {
       2, {
       { HBOND_TYPE_19, 3,
         {{"O2", "N2"},
          {"N3", "N1"},
          {"N4", "O6"}}
       },
       { HBOND_TYPE_22, 2,
         {{"O2", "N1"},
          {"N3", "N2"}}
       } }
};

static BASEPAIR_TYPE _base_CI = {
       1, {
       { HBOND_TYPE_29, 2,
         {{"N3", "N1"},
          {"N4", "O6"}}
       } }
};

static BASEPAIR_TYPE _base_CT = {
       2, {
       { HBOND_TYPE_17, 2,
         {{"N3", "N3"},
          {"N4", "O2"}}
       },
       { HBOND_TYPE_18, 2,
         {{"N3", "N3"},
          {"N4", "O4"}}
       } }
};

static BASEPAIR_TYPE _base_GG = {
       6, {
       { HBOND_TYPE_3, 2,
         {{"O6", "N1"},
          {"N1", "O6"}}
       },
       { HBOND_TYPE_4, 2,
         {{"N3", "N2"},
          {"N2", "N3"}}
       },
       { HBOND_TYPE_6, 2,
         {{"O6", "N1"},
          {"N7", "N2"}}
       },
       { HBOND_TYPE_6, 2,
         {{"N1", "O6"},
          {"N2", "N7"}}
       },
       { HBOND_TYPE_7, 2,
         {{"O6", "N2"},
          {"N7", "N1"}}
       },
       { HBOND_TYPE_7, 2,
         {{"N2", "O6"},
          {"N1", "N7"}}
       } }
};

static BASEPAIR_TYPE _base_GI = {
       3, {
       { HBOND_TYPE_3, 2,
         {{"O6", "N1"},
          {"N1", "O6"}}
       },
       { HBOND_TYPE_6, 2,
         {{"N1", "O6"},
          {"N2", "N7"}}
       },
       { HBOND_TYPE_7, 2,
         {{"N2", "O6"},
          {"N1", "N7"}}
       } }
};

static BASEPAIR_TYPE _base_GT = {
       2, {
       { HBOND_TYPE_27, 2,
         {{"O6", "N3"},
          {"N1", "O4"}}
       },
       { HBOND_TYPE_28, 2,
         {{"O6", "N3"},
          {"N1", "O2"}}
       } }
};

static BASEPAIR_TYPE _base_II = {
       1, {
       { HBOND_TYPE_3, 2,
         {{"N1", "O6"},
          {"O6", "N1"}}
       } }
};

static BASEPAIR_TYPE _base_TT = {
       4, {
       { HBOND_TYPE_12, 2,
         {{"N3", "O4"},
          {"O4", "N3"}}
       },
       { HBOND_TYPE_13, 2,
         {{"O2", "N3"},
          {"N3", "O2"}}
       },
       { HBOND_TYPE_16, 2,
         {{"N3", "O4"},
          {"O2", "N3"}}
       },
       { HBOND_TYPE_16, 2,
         {{"O4", "N3"},
          {"N3", "O2"}}
       } }
};

#define NUM_BASE_HBOND_TYPE  21

static BASE_HBOND_TYPE base_hbond_type[NUM_BASE_HBOND_TYPE] = {
     { "AA", &_base_AA },
     { "AC", &_base_AC },
     { "AG", &_base_AG },
     { "AI", &_base_AI },
     { "AT", &_base_AT },
     { "AU", &_base_AT },
     { "CC", &_base_CC },
     { "CG", &_base_CG },
     { "CI", &_base_CI },
     { "CT", &_base_CT },
     { "CU", &_base_CT },
     { "GG", &_base_GG },
     { "GI", &_base_GI },
     { "GT", &_base_GT },
     { "GU", &_base_GT },
     { "II", &_base_II },
     { "IT", &_base_GT },
     { "IU", &_base_GT },
     { "TT", &_base_TT },
     { "TU", &_base_TT },
     { "UU", &_base_TT }
};

static const char *R_RingAtom[R_RINGATOM] = { "N9", "C8", "N7", "C5", "C6", "N1", "C2", "N3", "C4" };
static const char *Y_RingAtom[Y_RINGATOM] = { "N1", "C2", "N3", "C4", "C5", "C6" };

static double R_BLOCK[8][3] = {
       { -2.2500,  5.0000,  0.2500 },
       { -2.2500,  0.5000,  0.2500 },
       { -2.2500,  0.5000, -0.2500 },
       { -2.2500,  5.0000, -0.2500 },
       {  2.2500,  5.0000,  0.2500 },
       {  2.2500,  0.5000,  0.2500 },
       {  2.2500,  0.5000, -0.2500 },
       {  2.2500,  5.0000, -0.2500 }
};

static double Y_BLOCK[8][3] = {
       { -2.2500,  5.0000,  0.2500 },
       { -2.2500,  2.0000,  0.2500 },
       { -2.2500,  2.0000, -0.2500 },
       { -2.2500,  5.0000, -0.2500 },
       {  2.2500,  5.0000,  0.2500 },
       {  2.2500,  2.0000,  0.2500 },
       {  2.2500,  2.0000, -0.2500 },
       {  2.2500,  5.0000, -0.2500 }
};

static REF_NA STAND_A = { 11, 
        { { "C1*" }, { "C2" }, { "C4" }, { "C5" }, { "C6" }, { "C8" },
          { "N1" }, { "N3" }, { "N6" }, { "N7" }, { "N9" }, { "" }
        },
        { { -2.479,  5.346,  0.000 },
          { -1.912,  1.023,  0.000 },
          { -1.267,  3.124,  0.000 },
          {  0.071,  2.771,  0.000 },
          {  0.369,  1.398,  0.000 },
          {  0.024,  4.897,  0.000 },
          { -0.668,  0.532,  0.000 },
          { -2.320,  2.290,  0.000 },
          {  1.611,  0.909,  0.000 },
          {  0.877,  3.902,  0.000 },
          { -1.291,  4.498,  0.000 },
          {  0.000,  0.000,  0.000 }
        }
};

static REF_NA STAND_C = { 9,
        { { "C1*" }, { "C2" }, { "C4" }, { "C5" }, { "C6" }, { "N1" },
          { "N3" }, { "N4" }, { "O2" }, { "" }, { "" }, { "" }
        },
        { {  -2.477,  5.402,  0.000 },
          {  -1.472,  3.158,  0.000 },
          {   0.837,  2.868,  0.000 },
          {   1.056,  4.275,  0.000 },
          {  -0.023,  5.068,  0.000 },
          {  -1.285,  4.542,  0.000 },
          {  -0.391,  2.344,  0.000 },
          {   1.875,  2.027,  0.001 },
          {  -2.628,  2.709,  0.001 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 }
        }
};

static REF_NA STAND_G = { 12,
        { { "C1*" }, { "C2" }, { "C4" }, { "C5" }, { "C6" }, { "C8" },
          { "N1" }, { "N2" }, { "N3" }, { "N7" }, { "N9" }, { "O6" }
        },
        { {  -2.477,  5.399,  0.000 },
          {  -1.999,  1.087,  0.000 },
          {  -1.265,  3.177,  0.000 },
          {   0.071,  2.833,  0.000 },
          {   0.424,  1.460,  0.000 },
          {   0.023,  4.962,  0.000 },
          {  -0.700,  0.641,  0.000 },
          {  -2.949,  0.139, -0.001 },
          {  -2.342,  2.364,  0.001 },
          {   0.870,  3.969,  0.000 },
          {  -1.289,  4.551,  0.000 },
          {   1.554,  0.955,  0.000 }
        }
};

static REF_NA STAND_P = { 9,
        { { "C1*" }, { "C2" }, { "C4" }, { "C5" }, { "C6" }, { "N1" },
          { "N3" }, { "O2" }, { "O4" }, { "" }, { "" }, { "" }
        },
        {
          {  -2.506,  5.371,  0.000 },
          {   1.037,  2.915,  0.000 },
          {  -1.422,  3.076,  0.000 },
          {  -1.284,  4.500,  0.000 },
          {  -0.064,  5.048,  0.000 },
          {   1.087,  4.295,  0.000 },
          {  -0.229,  2.383,  0.000 },
          {   2.036,  2.217,  0.000 },
          {  -2.485,  2.453,  0.000 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 }
        }
};

static REF_NA STAND_T = { 10,
        { { "C1*" }, { "C2" }, { "C4" }, { "C5" }, { "C5M" }, { "C6" },
          { "N1" },  { "N3" }, { "O2" }, { "O4" }, { "" },    { "" }
        },
        {
          {  -2.481,  5.354,  0.000 },
          {  -1.462,  3.135,  0.000 },
          {   0.994,  2.897,  0.000 },
          {   1.106,  4.338,  0.000 },
          {   2.466,  4.961,  0.001 },
          {  -0.024,  5.057,  0.000 },
          {  -1.284,  4.500,  0.000 },
          {  -0.298,  2.407,  0.000 },
          {  -2.562,  2.608,  0.000 },
          {   1.944,  2.119,  0.000 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 }
        }
};

static REF_NA STAND_U = { 9,
        { { "C1*" },  { "C2" }, { "C4" }, { "C5" }, { "C6" }, { "N1" },
          { "N3"  },  { "O2" }, { "O4" }, { ""   }, { ""   }, { "" }
        },
        {
          {  -2.481,  5.354,  0.000 },
          {  -1.462,  3.131,  0.000 },
          {   0.989,  2.884,  0.000 },
          {   1.089,  4.311,  0.000 },
          {  -0.024,  5.053,  0.000 },
          {  -1.284,  4.500,  0.000 },
          {  -0.302,  2.397,  0.000 },
          {  -2.563,  2.608,  0.000 },
          {   1.935,  2.094, -0.001 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 },
          {   0.000,  0.000,  0.000 }
        }
};

#endif