zClassLimits

 zClassLimits stores the cutoffs for the computer classification of pairs
 according to displacement, normal vector, and angle of rotation.  As such,
 it is the repository of expert knowledge of pair classifications.

0001 % zClassLimits stores the cutoffs for the computer classification of pairs
0002 % according to displacement, normal vector, and angle of rotation.  As such,
0003 % it is the repository of expert knowledge of pair classifications.
0004 
0005 % The main categories have integer values
0006 % The subcategories have decimal parts.
0007 % For decimal parts smaller than 0.5, the same hydrogen bonds will be checked
0008 % as for the main category.
0009 % For decimal parts 0.5 and larger, no hydrogen bonds will be checked
0010 
0011 function [ClassLimits, CurrentVersion] = zClassLimits;
0012 
0013 CurrentVersion = 6.2;                       % version number of class limits
0014 
0015 ClassLimits = zeros(50,12,16);
0016 
0017 % For each paircode there is a matrix B which tells the upper and lower
0018 % limits of various variables.
0019 % The first column of B is the category, as in zListCategoryNames
0020 % Some categories are further subdivided with decimal extensions.
0021 % Columns 2 and 3 of B are upper and lower limits on displ(1).
0022 % Columns 4 and 5 of B are upper and lower limits on displ(2).
0023 % Columns 6 and 7 of B are upper and lower limits on displ(3).
0024 % Columns 8 and 9 of B are upper and lower limits on normal(3).
0025 % Columns 10 and 11 of B are limits on Ang (FlipAng or RotAng, depending on
0026 % normal(3)).
0027 
0028 % AA pairs (paircode 1) ------------------------------------------------------
0029 
0030 B =    [  1    5.0  6.3  8.0 10.0 -3.0  3.0 -1.1 -0.7   70  105];  % cWw
0031 B = [B;[  2    5.1  8.0  7.7  9.8 -3.0  3.0  0.58  1.1  155  195]]; % tWW
0032 %B = [B;[  3    5.2  7.2 -1.9 -0.9 -3.5  3.5  0.6  1.1   45   75]]; % cis WC-H?
0033 B = [B;[  4    3.5  6.6  7.6  9.1 -3.0  3.0 -1.1 -0.7  145  190]]; % tr  H-WC
0034 B = [B;[  5    4.0  5.5  6.4  8.5 -3.0  3.0 -1.1 -0.7   15   45]]; % cis WC-S
0035 B = [B;[  6    2.3  3.3  8.1  9.1 -3.0  3.0  0.7  1.1  260  -70]]; % tr  S-WC
0036 B = [B;[  8   -3.1 -0.9  6.4  8.5 -3.0  3.0  0.7  1.1  165  205]]; % tHh
0037 B = [B;[  9   -4.7 -2.9  4.6  6.2 -3.0  3.0  0.7  1.1  -20   40]]; % cis H-S CLS 2008-07-01
0038 B = [B;[ 10   -1.5  0.6  7.1  8.9 -3.0  3.0 -1.1 -0.7   65  100]]; % tr  H-S
0039 B = [B;[ 11    2.5  5.5 -6.6 -5.0 -3.0  3.1 -1.1 -0.6  260  -65]]; % cSs
0040 B = [B;[ 12    6.1  8.2  1.1  4.1 -3.0  3.0  0.65 1.1  195  240]]; % tSs
0041 B = [B;[ 13    6.7  8.6  8.0  9.1 -3.0  3.0 -1.1 -0.7  120  155]]; % bifurcated
0042 B = [B;[ 21.1  2.0  4.8 -1.0  1.5  1.7  4.2  0.75 1.1   20   55]]; % s35 helix 1122
0043 %B = [B;[ 21.2 -2.5 -1.4  2.5  4.0  3.0  3.8  0.8  1.1  195  -35]]; % above, up
0044 %B = [B;[ 21.3  1.0  5.0 -1.5  3.0  3.0  4.2  0.4  1.1    0   50]]; % above, up
0045 B = [B;[-21.1 -4.5 -1.2 -0.6  3.6 -4.3 -1.1  0.7  1.1  -60  -15]]; % s53 helix 1122
0046 B = [B;[ 22.1  0.0  5.2   0.0  7.0  3.0  4.2 -1.1 -0.7   0  270]]; % above,down
0047 B = [B;[ 23.1  4.0  7.5  0.5  4.1 -4.2 -2.9 -1.1 -0.8   20   60]]; % below,down
0048 B = [B;[ 23.2 -4.0  8.0 -4.0  8.0 -5.0 -2.0 -1.1 -0.7   90  155]]; % below,down
0049 
0050 s = size(B);
0051 ClassLimits(1:s(1),1:s(2),1) = B;                      % AA is paircode 1
0052 
0053 % AC pairs (paircode 5) ------------------------------------------------------
0054 
0055 B =    [  1    5.2  6.8  5.5  7.2 -3.0  3.0 -1.1 -0.7   54   95];  % cis WC-WC
0056 B = [B;[  1.1  8.0  9.9  1.5  4.0 -3.0  3.0 -1.1 -0.7   40   78]]; % cis WC-WC
0057 B = [B;[  1.2  6.4  7.6  4.3  6.6 -3.0  3.0 -1.1 -0.7   60   90]]; % cis WC-WC
0058 B = [B;[  2    3.3  4.3  8.2  9.2 -3.0  3.0  0.7  1.1  165  230]]; % tr  WC-WC
0059 B = [B;[ -4   -2.8 -0.6  7.2  8.9 -3.0  3.0 -1.1 -0.8  140  175]]; % tr   H-WC
0060 B = [B;[ -4.1 -4.0 -2.8  5.8  6.8 -3.0  3.0 -1.1 -0.8  150  180]]; % tr   H-WC
0061 B = [B;[  5    3.0  6.1  6.5  9.0 -3.0  3.0 -1.1 -0.5   10   54]]; % cis WC-S
0062 B = [B;[  5.1  1.6  2.6  7.3  9.3 -3.0  3.0 -1.1 -0.5   55   85]]; % cis WC-S
0063 B = [B;[ -5    3.5  6.0 -6.1 -4.6 -3.0  3.0 -1.1 -0.6  -60   50]]; % cis S-WC
0064 B = [B;[  6    1.7  3.3  7.8  9.0 -3.0  3.0  0.7  1.1  250  -50]]; % tr  WC-S
0065 B = [B;[ -6    5.9  7.1 -5.6 -4.4 -3.0  3.0  0.7  1.1   20   70]]; % tr  WC-S
0066 B = [B;[  8   -4.7 -2.6  6.4  7.9 -3.0  3.0  0.6  1.1  170  210]]; % tr   H-H
0067 B = [B;[  9   -4.3 -3.1  4.8  5.9 -3.0  3.0  0.65  1.1  -48    0]]; % cis H-S
0068 B = [B;[ -9    2.5  4.3 -6.0 -4.6 -3.0  3.0  0.8  1.1  -35    10]]; % cis S-H
0069 B = [B;[ 10   -2.5  1.6  7.4  9.5 -3.0  3.0 -1.1 -0.8   60  125]]; % tr   H-S 2008-05-20 CLZ
0070 B = [B;[-10    7.1  8.4 -4.0 -1.9 -3.0  3.0 -1.1 -0.8   50   92]]; % tr   S-H
0071 B = [B;[ 11.0  2.3  4.7 -7.4 -5.8 -3.0  3.0 -1.1 -0.5  250  -70]]; % cSs
0072 B = [B;[ 11.1  4.7  7.0 -7.4 -5.3 -3.0  3.0 -1.1 -0.7  235  -65]]; % cSs with water
0073 B = [B;[-11.0  5.7  7.7 -2.6 -0.0 -3.0  3.0 -1.1 -0.65 260  -40]]; % csS
0074 B = [B;[-11.1  3.9  5.8 -3.6 -2.1 -3.0  3.0 -1.1 -0.65 225  -80]]; % csS
0075 B = [B;[-11.2  5.8  7.3 -3.3 -2.6 -3.0  3.0 -1.1 -0.65 250  -50]]; % csS - Jesse 10_11_07, modified by CLZ 10-16-07
0076 B = [B;[ 12    6.5  8.6  1.0  5.0 -3.0  3.0  0.55 1.1  200  260]]; % tSs
0077 B = [B;[ 13    8.0 10.0  5.6  6.8 -3.0  3.0 -1.1 -0.7   85  130]]; % ac bif
0078 B = [B;[-13    1.0  2.2  8.3  9.4 -3.0  3.0 -1.1 -0.7   95  130]]; % ca bif
0079 B = [B;[-13.1  3.1  4.7  8.0  9.3 -3.0  3.0 -1.1 -0.7   65  100]]; % ca bif
0080 B = [B;[ 21.1  1.5  4.3 -0.6  2.0  2.7  4.3  0.8  1.1   20   55]]; % s35 helix 574
0081 B = [B;[-21.1 -3.9 -1.5  0.0  3.1 -4.5 -2.4  0.8  1.1  -55  -15]]; % s53 helix 610
0082 B = [B;[ 22.1  0.0  5.0 -4.0  8.0  3.0  4.2 -1.1 -0.4 -270  270]]; % above,down
0083 B = [B;[ 23.1  4.0  7.0  0.0  4.2 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0084 
0085 s = size(B);
0086 ClassLimits(1:s(1),1:s(2),5) = B;                      % AC is paircode 5
0087 
0088 % CC pairs (paircode 6) ------------------------------------------------------
0089 
0090 B =    [  1    6.3  7.2 -0.7  1.3 -2.9  2.9 -1.1 -0.7   30   65];  % cWw
0091 B = [B;[  2    4.3  5.8  4.3  6.5 -3.0  3.0  0.7  1.1  160  190]]; % tWW - JS_7_4_08
0092 B = [B;[  3    6.8  8.2  1.0  3.6 -3.0  3.0  0.7  1.1   60  100]]; % cis WC-H
0093 B = [B;[  4    5.6  7.6  2.0  5.0 -3.0  3.0 -1.1 -0.7  115  165]]; % tr   H-WC
0094 B = [B;[  5    3.6  5.8  5.2  6.8 -3.0  3.0 -1.1 -0.7  -40   35]]; % cis WC-S
0095 B = [B;[  5.1  2.2  4.8  7.0  8.6 -3.0  3.0 -1.1 -0.7   70   80]]; % cis WC-S?
0096 B = [B;[  6    2.4  3.5  7.1  8.4 -3.0  3.0  0.5  1.1  240  -80]]; % tr   WC-S
0097 % B = [B;[  8   -4.7 -2.6  6.4  7.5 -3.0  3.0  0.6  1.1  170  210]]; % tHh Removed 12-14-2007 JS
0098 B = [B;[  9   -6.0 -4.0  3.0  5.4 -3.0  3.0  0.6  1.1  -30   55]]; % cis H-S
0099 B = [B;[ 10   -3.1 -1.1  6.5  8.5 -3.0  3.0 -1.1 -0.7   60  105]]; % tr   H-S
0100 B = [B;[ 11    1.6  3.0 -7.8 -6.4 -3.0  3.0 -1.1 -0.7  240  -80]]; % cSs  CLZ 2008-04-22
0101 B = [B;[ 13    7.5  8.8  1.2  3.2 -3.0  3.0 -1.1 -0.7   70   95]]; % cis WC-WC
0102 B = [B;[ 13.1  6.9  7.9  4.3  5.4 -3.0  3.0 -1.1 -0.7   60   80]]; % ???
0103 B = [B;[ 21.1  1.0  4.5 -1.0  2.0  3.0  4.6  0.7  1.1   20   50]]; % above, up
0104 B = [B;[-21.1 -4.5 -1.0 -0.3  3.5 -4.5 -2.3  0.7  1.1  -55  -15]]; % s53 helix 1775
0105 B = [B;[ 22.1  0.0  5.0 -4.0  8.0  3.0  4.2 -1.1 -0.4 -270  270]]; % above,down
0106 B = [B;[ 23.1  4.0  7.0  0.0  4.0 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0107 
0108 s = size(B);
0109 ClassLimits(1:s(1),1:s(2),6) = B;                      % CC is paircode 6
0110 
0111 % GC pairs (paircode 7) ------------------------------------------------------
0112 
0113 B =    [  1    5.6  9.0  2.8  6.9 -3.0  3.0 -1.1 -0.7   45   90];  % cis WC-WC
0114 B = [B;[  1.1  5.4  6.3  6.6  7.6 -3.0  3.0 -1.1 -0.7   70  110]]; % cis WC-WC
0115 B = [B;[  2    6.4  7.7  4.2  6.1 -3.0  3.0  0.7  1.1  185  220]]; % tr  WC-WC
0116 B = [B;[  3   -4.8 -2.1  4.5  8.0 -3.0  3.0  0.7  1.1  245  -50]]; % cis WC-H
0117 B = [B;[  4   -1.9 -0.7  7.6  8.8 -3.0  3.0 -1.1 -0.7  135  175]]; % tr  H-WC
0118 B = [B;[  4.1 -0.4  2.6  9.1 11.9 -3.0  3.0 -1.1 -0.7  135  170]]; % tr  H-WC
0119 B = [B;[  5    4.2  5.2 -6.3 -5.3 -3.0  3.0 -1.1 -0.6   30   60]]; % cis WC-S
0120 B = [B;[ -5    6.5  7.6  4.0  5.4 -3.0  3.0 -1.1 -0.7   15   40]]; % cis S-WC
0121 B = [B;[  6    6.8  7.7 -3.7 -2.6 -3.0  3.0  0.7  1.1   70  110]]; % tr  S-WC
0122 B = [B;[ -6    4.7  6.2  5.9  7.3 -3.0  3.0  0.7  1.1  235  -80]]; % tr  S-WC
0123 B = [B;[  7   -3.8 -2.6  4.7  5.9 -3.0  3.0 -1.1 -0.7  -40    0]]; % cis H-H
0124 B = [B;[  8   -4.1 -3.1  6.7  7.8 -3.0  3.0  0.7  1.1  160  220]]; % tr  H-H
0125 B = [B;[  8.1 -2.6 -1.6  8.1  9.1 -3.0  3.0  0.7  1.1  180  220]]; % tr  H-H
0126 B = [B;[  9    3.7  5.2 -8.2 -6.6 -3.0  3.0  0.7  1.1    5   50]]; % cis H-S  CLZ 2007-12-14
0127 B = [B;[  9.1  2.0  3.3 -6.5 -5.3 -3.0  3.0  0.7  1.1  -40   10]]; % cis H-S  No instances found
0128 B = [B;[ 11    6.1  7.6 -3.8 -2.2 -3.0  3.0 -1.1 -0.7  250  -60]]; % cSs
0129 B = [B;[ 11.1  5.7  6.1 -4.0 -3.2 -3.0  3.0 -1.1 -0.7  -50  -20]]; % cSs
0130 %B = [B;[-11    2.6  3.9 -7.1 -5.6 -3.0  3.0 -1.1 -0.7  250  -70]]; % cis S-S
0131 B = [B;[-11    1.8  3.9 -8.7 -6.3 -3.0  3.0 -1.1 -0.7  230  -70]]; % csS CLZ 2007-12-13
0132 B = [B;[-12    7.8  9.0 -1.9 -0.5 -3.0  3.0  0.7  1.1  140  200]]; % tsS
0133 
0134 B = [B;[ 21.1  1.0  5.0 -1.0  2.5  3.0  4.4  0.5  1.1   20   60]]; % above, up
0135 B = [B;[-21.1 -4.5 -1.4 -0.3  3.2 -4.2 -2.2  0.8  1.1  -55  -15]]; % s53 helix 1258
0136 B = [B;[ 22.1 -2.0  2.0  1.0  5.0  2.7  4.1 -1.1 -0.5  200  -50]]; % above,down
0137 B = [B;[ 22.1  1.0  5.0  1.0  6.0  2.5  4.2 -1.1 -0.5   50  160]]; % above,down
0138 B = [B;[ 23.1  4.0  7.0  0.0  4.0 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0139 
0140 
0141 s = size(B);
0142 ClassLimits(1:s(1),1:s(2),7) = B;
0143 
0144 % AG pairs (paircode 9) ------------------------------------------------------
0145 
0146 B =    [  1    7.0  9.0  5.6  8.4 -3.5  3.5 -1.1 -0.65  65  100];  % cis WC-WC
0147 B = [B;[  1.1  8.6  9.6  3.2  4.6 -3.0  3.0 -1.1 -0.7   50   75]]; % cis WC-WC
0148 B = [B;[  1.2  5.8  7.0  7.6  8.6 -3.0  3.0 -1.1 -0.5   90  125]]; % cis WC-WC
0149 B = [B;[  3    6.7  7.8  4.4  5.4 -3.0  3.0  0.7  1.1   70  100]]; % cis WC-H
0150 B = [B;[  3.1  4.4  5.4  7.0  8.3 -3.0  3.04  0.7  1.1   75  110]]; % cis WC-H
0151 B = [B;[ -3   -6.0 -4.9  6.5  7.8 -3.0  3.0  0.7  1.1  250  -80]]; % cis H-WC
0152 B = [B;[  4    4.3  5.4  7.2  8.5 -3.0  3.02 -1.1 -0.7  155  185]]; % tr  H-WC
0153 B = [B;[  5    3.7  4.7  6.9  8.7 -3.0  3.0 -1.1 -0.5   15   65]]; % cis WC-S
0154 B = [B;[ -5    6.6  8.6 -4.8 -2.8 -3.0  3.0 -1.1 -0.5  -90   -5]]; % cis S-WC - Jesse 10_11_07
0155 B = [B;[  6    1.5  3.3  8.0  9.4 -3.0  3.0  0.6  1.1  260  -50]]; % tr  WC-S
0156 B = [B;[  6.1  6.3  7.8  6.4  8.5 -3.0  3.0  0.7  1.1  220  265]]; % tr  WC-S
0157 B = [B;[  7   -4.6 -3.6  7.8  8.8 -3.0  3.0 -1.1 -0.7  180  225]]; % cis H-H
0158 B = [B;[  8   -3.3 -1.5  8.5 10.2 -3.0  3.02  0.7  1.1  195  245]]; % tr  H-H
0159 B = [B;[  9   -6.6 -5.6  2.5  3.6 -3.0  3.0  0.7  1.1   20   60]]; % cis H-S
0160 B = [B;[  9.1 -2.6 -0.5  7.2 8.75 -3.0  3.0  0.7  1.1  -50   35]]; % cis H-S - Jesse 4_21_08
0161 B = [B;[ -9    3.5  7.0 -5.1 -3.1 -3.0  3.0  0.7  1.1    0   60]]; % cis S-H - Jesse 4_18_08
0162 B = [B;[ 10   -2.0  0.7  7.1  9.0 -3.0  3.0 -1.1 -0.6   55  100]]; % tr  H-S
0163 B = [B;[ 10.1 -3.3 -2.0  7.1  9.0 -3.0  3.0 -1.1 -0.6   55  100]]; % tr  H-S
0164 B = [B;[ 10.2  0.2  1.7  9.0  9.7 -3.0  3.0 -1.1 -0.6   55  100]]; % tr  H-S
0165 B = [B;[ 11    2.6  4.9 -6.6 -5.4 -3.0  3.0 -1.1 -0.5  260  -75]]; % cSs
0166 B = [B;[-11    5.2  7.5 -2.5  0.5 -3.0  3.0 -1.1 -0.6  230  -50]]; % csS
0167 B = [B;[ 12    5.4  8.3 -0.6  3.5 -4.2  3.5  0.5  1.1  195  230]]; % tSs
0168 B = [B;[ 14    5.8  7.7 -5.2 -2.3 -2.5  2.0  0.3  0.9  170  200]]; % tr S-S CLZ
0169 B = [B;[-12    7.4  8.7 -1.3 -0.1 -3.0  3.0  0.7  1.1  170  195]]; % tr  S-S
0170 B = [B;[ 21.1  1.6  4.5 -0.8  2.1  2.6  4.5  0.8  1.1   20   55]]; % s35 helix 509
0171 B = [B;[-21.1 -4.6 -1.2 -0.2  3.0 -4.3 -2.2  0.8  1.1  -50  -15]]; % s53 helix 551
0172 B = [B;[ 22.1  0.0  5.0 -2.0  4.0  3.0  4.2 -1.1 -0.4  -90  270]]; % above,down
0173 B = [B;[ 23.1  4.0  7.0  0.0  4.0 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0174 
0175 s = size(B);
0176 ClassLimits(1:s(1),1:s(2),9) = B;                      % AG is paircode 9
0177 
0178 % GG pairs (paircode 11) -----------------------------------------------------
0179 
0180 %B =    [  1    5.4  6.5  7.7  9.6 -3.6  3.6 -1.1 -0.5   70  105];  % cis WC-WC These only exist when modeled wrong!
0181 B =    [  2    5.2  7.2  7.8  9.8 -3.0  3.0  0.7  1.1  160  210];  % tWW - Jesse 10_11_07
0182 B = [B;[  3    7.9  9.6  2.6  4.8 -3.0  3.0  0.7  1.1   70  110]]; % cis WC-H
0183 B = [B;[  4    4.6  6.6  6.0  7.1 -3.0  3.0 -1.1 -0.7  155  200]]; % tr  H-WC
0184 B = [B;[  5    5.4  8.1  5.9  7.5 -3.0  3.0 -1.1 -0.7    0   45]]; % cis WC-S CLZ 2008-07-03
0185 B = [B;[  7   -2.1 -0.9  5.5  6.7 -3.0  3.0 -1.1 -0.7  -45    0]]; % cHh
0186 B = [B;[  8   -0.8  0.4  7.5  8.7 -3.0  3.0  0.7  1.1  100  140]]; % tHh
0187 B = [B;[  9   -6.1 -4.5  4.9  6.9 -3.0  3.0  0.7  1.1  -45    0]]; % cis H-S
0188 B = [B;[ 10   -1.6  1.3  8.8 10.4 -3.0  3.0 -1.1 -0.7   70  105]]; % tr  H-S
0189 B = [B;[ 10.1  1.3  2.0  9.1  9.9 -3.0  3.0 -1.1 -0.7   55   75]]; % tr  H-S
0190 B = [B;[ 11    1.0  3.4 -6.9 -4.9 -3.0  3.0 -1.1 -0.7  230  265]]; % cSs
0191 B = [B;[ 12    7.0  8.5 -3.0 -0.6 -3.0  3.0  0.7  1.1  160  195]]; % tSs
0192 B = [B;[ 14    5.8  8.0 -6.0 -3.8 -3.5  0.5  0.2  0.8  160  195]]; % tr  S-S CLZ
0193 B = [B;[ 13    6.6  8.0  7.3  8.6 -3.0  3.0 -1.1 -0.7  125  150]]; % bifurcated
0194 B = [B;[ 21.1  0.0  4.6 -2.0  3.0  3.0  4.8  0.4  1.1    0   70]]; % above, up
0195 B = [B;[-21.1 -4.6 -1.2 -0.8  3.2 -4.3 -2.0  0.8  1.1  -55  -10]]; % s53 helix 1775
0196 B = [B;[ 22.1  0.0  7.0  0.0  6.0  2.0  4.2 -1.1 -0.4  -90  270]]; % above,down
0197 B = [B;[ 23.1  4.0  7.5 -5.0  6.0 -5.0 -2.0 -1.1 -0.7    0   60]]; % below,down
0198 
0199 s = size(B);
0200 ClassLimits(1:s(1),1:s(2),11) = B;                      % GG is paircode 11
0201 
0202 % AU pairs (paircode 13) ------------------------------------------------------
0203 
0204 B =    [  1    5.6  8.5  3.2  6.8 -3.0  3.0 -1.1 -0.8   50   90];  % cis WC-WC
0205 B = [B;[  2    4.8  6.4  6.0  7.8 -3.0  3.0  0.7  1.1  180  220]]; % tr   WC-WC
0206 B = [B;[  3    6.0  8.0  6.0  8.0 -3.0  3.0  0.7  1.1   80  120]]; % cis WC-H
0207 B = [B;[  3.1  8.0 10.0 -0.2  1.8 -3.0  3.0  0.7  1.1   60   90]]; % cis WC-H
0208 B = [B;[ -3   -6.0 -4.0  3.0  5.5 -3.0  3.0  0.7  1.1  -85  -45]]; % cis H-WC
0209 B = [B;[ -3.1 -6.5 -5.2  6.5  7.5 -3.0  3.0  0.7  1.1  -55  -40]]; % cis H-WC?
0210 B = [B;[ -4   -5.0 -1.9  5.0  7.8 -3.0  3.0 -1.1 -0.7  140  190]]; % tr   H-WC
0211 B = [B;[ -4.1 -2.1  0.0  7.7  9.5 -3.0  3.0 -1.1 -0.8   98  155]]; % tr   H-WC
0212 B = [B;[  5    3.8  6.3  6.0  8.6 -3.0  3.0 -1.1 -0.6   10   60]]; % cis WC-S
0213 B = [B;[ -5    3.8  5.2 -4.8 -3.3 -3.0  3.0 -1.1 -0.7  -55  -15]]; % cis S-WC
0214 B = [B;[  6   -0.7  2.7  7.8  9.6 -3.0  3.0  0.6  1.1  -90  -45]]; % tr  WC-S  Exchanged with 6.1 CLZ 12-14-2007 - Jesse_4_18_08
0215 B = [B;[  6.1  2.0  3.2  7.8  9.0 -3.0  3.0  0.7  1.1  250  -50]]; % tr  WC-S Exchanged with 6.0 CLZ 12-14-2007
0216 B = [B;[ -6    5.8  7.0 -3.2 -1.8 -3.0  3.0  0.7  1.1   90  120]]; % tr   S-WC
0217 B = [B;[  8   -3.2 -1.0  8.3 10.5 -3.0  3.0  0.8  1.1  180  210]]; % tHh
0218 B = [B;[  8.1 -4.0 -3.0  5.5  6.5 -3.0  3.0  0.7  1.1  163  183]]; % tr   H-H
0219 B = [B;[  8.2 -0.8  1.8  9.5 11.0 -3.0  3.0  0.8  1.1  180  220]]; % tr   H-H
0220 B = [B;[  9   -3.2 -1.8  6.2  7.6 -3.0  3.0  0.6  1.1  -60  -35]]; % cis H-S
0221 B = [B;[  9.1 -4.2 -3.5  4.5  5.8 -3.0  3.0  0.6  1.1   10   35]]; % cis H-S
0222 B = [B;[ -9    6.6  8.0 -4.5 -3.5 -3.0  3.0  0.7  1.1   40   80]]; % cis H-S
0223 B = [B;[ 10   -3.0  1.0  7.0  9.0 -3.0  3.0 -1.1 -0.8   60   98]]; % tr   H-S
0224 B = [B;[ 10.1 -6.5 -3.8  1.0  4.0 -3.0  3.0 -1.1 -0.7  105  165]]; % tr   H-S
0225 B = [B;[-10    9.3 11.0 -0.7  1.6 -3.0  3.0 -1.1 -0.7   60  115]]; % tr   H-S
0226 B = [B;[ 11    3.8  5.3 -6.2 -3.4 -3.0  3.0 -1.1 -0.7  260  -55]]; % cSs
0227 B = [B;[-11    5.7  7.3 -2.5  0.5 -3.5  3.9 -1.1 -0.6  260  -50]]; % csS
0228 B = [B;[ 12    7.0  8.7  0.9  3.7 -3.0  3.0  0.7  1.1  205  255]]; % tSs
0229 B = [B;[ 21.1  1.5  4.5 -0.8  2.0  3.1  4.3  0.8  1.1   20   55]]; % s35 helix 224
0230 B = [B;[-21.1 -3.8 -1.5  0.0  2.9 -4.2 -2.6  0.8  1.1  -50  -20]]; % s53 helix 220
0231 B = [B;[ 22.1  0.0  5.0 -2.0  4.0  3.0  4.2 -1.1 -0.4  -90  270]]; % above,down
0232 B = [B;[ 23.1  4.0  7.0  0.0  4.0 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0233 
0234 s = size(B);
0235 ClassLimits(1:s(1),1:s(2),13) = B;
0236 
0237 % CU pairs (paircode 14) -----------------------------------------------------
0238 
0239 B =    [  1    5.6  7.1  5.5  7.2 -3.0  3.0 -1.1 -0.7   85  105];  % cis WC-WC
0240 B = [B;[  1.1  5.0  6.5  6.8  8.5 -3.0  3.0 -1.1 -0.7   100 115]]; % cis WC-WC
0241 B = [B;[  1.2  5.7  6.8  2.3  4.0 -3.0  3.0 -1.1 -0.7   40   85]]; % cis WC-WC
0242 B = [B;[  2    4.6  5.8  4.4  5.6 -3.0  3.0  0.7  1.1  160  200]]; % tr  WC-WC
0243 B = [B;[  3    5.4  8.1  2.0  4.0 -3.0  3.0  0.7  1.1   45   95]]; % cis WC-H CLZ 2007-12-13
0244 B = [B;[  5    3.5  5.0  5.6  7.3 -3.0  3.0 -1.1 -0.7   30   70]]; % cis WC-S
0245 B = [B;[ -5    4.8  6.8 -3.9 -1.9 -3.0  3.0 -1.1 -0.7  -45    0]]; % cis  S-WC
0246 B = [B;[  6    2.5  4.5  7.3  9.3 -3.0  3.0  0.7  1.1  240  270]]; % tr   WC-S CLZ 2007-12-12
0247 B = [B;[ -6    6.5  7.7 -1.9 -0.7 -3.0  3.0  0.7  1.1  105  145]]; % tr   S-WC
0248 B = [B;[  8   -3.9 -1.9  7.7  9.5 -3.0  3.0  0.7  1.1  175  210]]; % tHh
0249 B = [B;[  9   -5.6 -3.9  3.4  6.2 -3.0  3.0  0.7  1.1  -40   40]]; % cis H-S
0250 B = [B;[  9.1 -2.5 -0.7  7.5  8.7 -3.0  3.0  0.7  1.1  -80  -35]]; % cis H-S
0251 B = [B;[ -9    3.2  5.3 -5.9 -4.5 -3.0  3.0  0.7  1.1  -40    5]]; % cis H-S
0252 B = [B;[ 10   -3.4 -0.8  6.9  8.6 -3.0  3.0 -1.1 -0.7   65  120]]; % tr   H-S
0253 B = [B;[ 11    2.4  4.2 -8.0 -6.0 -3.0  3.0 -1.1 -0.7  240  270]]; % cSs
0254 B = [B;[-11    5.1  6.9 -3.7 -0.9 -3.3  3.3 -1.1 -0.7  -90  -30]]; % csS
0255 %B = [B;[ 21.1  0.0  5.0 -1.0  3.0  3.0  4.2  0.4  1.1   20   80]]; % above, up
0256 B = [B;[-21.1 -4.5 -1.0 -0.9  3.3 -4.5 -2.0  0.7  1.1  -55  -15]]; % s53 helix 551
0257 %B = [B;[ 22.1  0.0  5.0 -4.0  8.0  3.0  4.2 -1.1 -0.4 -270  270]]; % above,down
0258 %B = [B;[-21.1 -5.0 -1.0  0.0  4.0 -4.2 -2.9  0.7  1.1  -60  -20]]; % below, up
0259 %B = [B;[ 23.1  4.0  7.0  0.0  4.0 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0260 
0261 s = size(B);
0262 ClassLimits(1:s(1),1:s(2),14) = B;                      % CU is paircode 14
0263 
0264 % GU pairs (paircode 15) ------------------------------------------------------
0265 
0266 B =    [  1    5.0  6.9  6.0  7.5 -3.0  3.0 -1.1 -0.7   50   90];  % cis WC-WC
0267 B = [B;[  1.1  3.9  5.0  6.7  7.8 -3.0  3.0 -1.1 -0.7   50  100]]; % cis WC-WC
0268 B = [B;[  1.2  5.5  7.5  4.7  6.0 -3.0  3.0 -1.1 -0.7   50   90]]; % cis WC-WC
0269 B = [B;[  2    2.8  3.9  7.1  9.1 -3.4  3.0  0.7  1.1  180  215]]; % tr  WC-WC
0270 B = [B;[ -3   -6.1 -5.1  2.7  3.4 -3.0  3.0  0.7  1.1  -65  -35]]; % cis H-WC
0271 B = [B;[  4    5.1  7.9  6.5  8.2 -3.0  3.0 -1.1 -0.7  145  180]]; % tr  WC-H
0272 B = [B;[ -4   -5.8 -4.8  5.1  6.1 -3.0  3.0 -1.1 -0.7  180  210]]; % tr  H-WC
0273 B = [B;[  5    6.1  7.8  4.0  5.9 -3.0  3.0 -1.1 -0.7   15   40]]; % cis WC-S
0274 B = [B;[  5.1  7.0  8.5  3.2  4.7 -3.0  3.0 -1.1 -0.7   40   55]]; % cis WC-S
0275 B = [B;[  5.2  7.7  8.7  3.7  4.8 -3.0  3.0 -1.1 -0.7   65   95]]; % cis WC-S
0276 B = [B;[ -5    2.8  3.8 -4.8 -3.8 -3.1  3.0 -1.1 -0.7  -65  -35]]; % cis S-WC
0277 B = [B;[  6    4.9  7.5  5.1  7.6 -3.0  3.0  0.7  1.1  235  -80]]; % tr  WC-S
0278 B = [B;[ -6    6.6  8.1 -3.7 -1.7 -3.0  3.0  0.7  1.1  115  155]]; % tr  S-WC
0279 B = [B;[ -9    2.8  5.8 -6.2 -4.3 -3.0  3.0  0.7  1.1  -50    0]]; % cis H-S
0280 B = [B;[ -9.1  8.0  9.2 -4.7 -3.7 -3.0  3.0  0.7  1.1  10    50]]; % cis H-S
0281 B = [B;[ -9.2  5.6  6.4 -5.3 -4.3 -3.0  3.0  0.7  1.1  10    50]]; % cis H-S
0282 B = [B;[-10    8.4 10.1 -3.7 -1.0 -3.0  3.0 -1.1 -0.7   60  100]]; % tr  S-H
0283 B = [B;[ 11    1.6  4.1 -8.7 -5.9 -3.0  3.0 -1.1 -0.7  230  -70]]; % cSs
0284 B = [B;[-11    5.7  7.5 -3.6 -1.9 -3.0  3.0 -1.1 -0.7  255  -50]]; % csS
0285 B = [B;[-11.1  4.3  5.2 -4.0 -3.0 -3.0  3.0 -1.1 -0.7  230  260]]; % csS
0286 B = [B;[ 12    8.1  8.9 -1.7  0.2 -3.0  3.0  0.7  1.1  180  220]]; % tSs
0287 B = [B;[ 13    7.5  9.2  5.6  7.5 -3.0  3.0 -1.1 -0.7  110  145]]; % bifurcated
0288 B = [B;[-21.1 -4.0 -1.2 -0.3  3.1 -4.3 -2.3  0.8  1.1  -55  -10]]; % s53 helix 610
0289 
0290 B = [B;[ 25   -5.4 -3.7  1.6  3.3 -3.0  3.0 -1.1 -0.7  125  165]]; % motif
0291 
0292 s = size(B);
0293 ClassLimits(1:s(1),1:s(2),15) = B;
0294 
0295 % UU pairs (paircode 16) -----------------------------------------------------
0296 
0297 B =    [  1    3.4  5.7  4.1  6.8 -3.0  3.0 -1.1 -0.7   35   80];  % cWw
0298 B = [B;[  2    5.2  6.5  2.0  4.0 -3.0  3.0  0.7  1.1  160  200]]; % tWW 2008-10-23
0299 B = [B;[  2.1  3.0  4.2  6.9  8.1 -3.4  3.0  0.7  1.1  170  200]]; % tWW
0300 B = [B;[  3    6.6  7.6  0.8  3.2 -3.0  3.0  0.7  1.1   55  100]]; % cis WC-H - Jesse_7_4_08
0301 B = [B;[  4    3.8  5.3  6.2  7.1 -3.0  3.0 -1.1 -0.7  145  180]]; % tr  WC-H
0302 B = [B;[  5    5.0  6.5  1.2  5.0 -3.0  3.0 -1.1 -0.7  -80   45]]; % cis WC-S - Jesse_4_18_08
0303 B = [B;[  6    5.6  7.0  2.8  4.2 -3.0  3.0  0.7  1.1  200  230]]; % tr  WC-S
0304 B = [B;[  9   -5.7 -4.5  4.1  5.3 -3.0  3.0  0.7  1.1    0   30]]; % cis H-S
0305 B = [B;[ 11    3.0  5.5 -6.5 -4.6 -3.0  3.0 -1.1 -0.7  260  -50]]; % cSs
0306 %B = [B;[ 21.1 -3.0  5.0 -1.0  3.0  3.0  4.2  0.4  1.1   20   80]]; % above, up
0307 B = [B;[-21.1 -4.2 -1.3 -0.4  3.9 -4.2 -1.5  0.7  1.1  -60  -20]]; % s53 helix 1122
0308 %B = [B;[ 22.1  0.0  5.0 -4.0  8.0  3.0  4.2 -1.1 -0.4 -270  270]]; % above,down
0309 %B = [B;[ 23.1  4.0  7.0  0.0  4.0 -4.2 -2.9 -1.1 -0.8   20   50]]; % below,down
0310 
0311 s = size(B);
0312 ClassLimits(1:s(1),1:s(2),16) = B;                      % UU is paircode 16
0313