Biskit.surfaceRacerTools

Source Code for Module Biskit.surfaceRacerTools

1 ## 2 ## Biskit, a toolkit for the manipulation of macromolecular structures 3 ## Copyright (C) 2004-2005 Raik Gruenberg & Johan Leckner 4 ## 5 ## This program is free software; you can redistribute it and/or 6 ## modify it under the terms of the GNU General Public License as 7 ## published by the Free Software Foundation; either version 2 of the 8 ## License, or any later version. 9 ## 10 ## This program is distributed in the hope that it will be useful, 11 ## but WITHOUT ANY WARRANTY; without even the implied warranty of 12 ## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 13 ## General Public License for more details. 14 ## 15 ## You find a copy of the GNU General Public License in the file 16 ## license.txt along with this program; if not, write to the Free 17 ## Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. 18 ## 19 ## 20 ## last $Author: leckner $ 21 ## last $Date: 2006/09/12 06:34:36 $ 22 ## $Revision: 1.6 $ 23 """ 24 Reference data for SurfaceRacer. 25 """ 26 27 import Numeric 28 29 30 ## dictionary with average accessabilities in 500 random 31 ## GLY-XX-GLY peptides calculated with SurfaceRacer using 32 ## a probe radius of 1.4 A and the Richards vdw radii set 33 34 ## random coil molecular surface in a GLY-XXX-GLY peptide 35 ranMS = {'CYS': {'C' : 1.969, 'CB' : 21.339, 'CA' : 8.077, 36 'O' : 14.038, 'N' : 5.713, 'SG' : 34.959}, 37 'GLN': {'C' : 1.736, 'CB' : 18.742, 'CA' : 6.384, 38 'CG' : 20.672, 'O' : 14.136, 'CD' : 2.825, 39 'N' : 7.409, 'NE2': 23.326, 'OE1': 14.894}, 40 'ILE': {'C' : 1.151, 'CB' : 7.933, 'CA' : 4.369, 41 'O' : 14.185, 'N' : 5.428, 'CD1': 31.332, 42 'CG1': 17.690, 'CG2': 28.741}, 43 'SER': {'C' : 2.336, 'OG' : 17.413, 'CB' : 26.667, 44 'CA' : 8.803, 'O' : 13.894, 'N' : 6.849}, 45 'VAL': {'C' : 1.332, 'CB' : 7.877, 'CA' : 6.509, 46 'O' : 13.741, 'N' : 4.786, 'CG1': 31.049, 47 'CG2': 30.663}, 48 'LYS': {'C' : 1.722, 'CB' : 18.077, 'CA' : 6.360, 49 'CG' : 16.832, 'CE' : 18.940, 'CD' : 16.329, 50 'NZ' : 32.635, 'O' : 14.175, 'N' : 7.007}, 51 'ASN': {'C' : 2.050, 'CB' : 13.362, 'CA' : 15.158, 52 'CG' : 20.928, 'O' : 6.352, 'N' : 1.645, 53 'OD1': 14.146, 'ND2': 6.379 }, 54 'PRO': {'C' : 15.067, 'CB' : 14.374, 'CA' : 5.090, 55 'CG' : 4.201, 'O' : 15.123, 'CD' : 15.837, 56 'N' : 1.779}, 57 'GLY': {'CA' : 20.259, 'C' : 5.731, 'O' : 21.192, 58 'N' : 15.386}, 59 'THR': {'C' : 19.678, 'CB' : 0.712, 'CA' : 1.439, 60 'OG1': 11.571, 'O' : 8.170, 'N' : 15.934, 61 'CG2': 14.310}, 62 'PHE': {'C' : 6.163, 'CE1': 32.630, 'CB' : 1.976, 63 'CA' : 12.422, 'CG' : 21.216, 'O' : 7.309, 64 'N' : 1.825, 'CZ' : 14.120, 'CD1': 6.826, 65 'CD2': 15.219, 'CE2': 12.588}, 66 'ALA': {'CB' : 15.389, 'CA' : 15.277, 'C' : 34.475, 67 'O' : 9.672, 'N' : 1.697}, 68 'HIS': {'C' : 14.138, 'CE1': 7.174, 'CB' : 26.080, 69 'CA' : 3.136, 'CG' : 13.978, 'O' : 8.065, 70 'N' : 1.666, 'CD2': 14.372, 'ND1': 21.724, 71 'NE2': 8.415}, 72 'MET': {'C' : 1.564, 'CB' : 14.093, 'CA' : 7.444, 73 'CG' : 15.702, 'CE' : 10.286, 'N' : 15.480, 74 'O' : 2.250, 'SD' : 19.502}, 75 'ASP': {'C' : 7.110, 'CB' : 22.634, 'CA' : 14.257, 76 'CG' : 3.331, 'O' : 14.934, 'N' : 5.535, 77 'OD1': 14.057, 'OD2': 1.949}, 78 'LEU': {'C' : 16.627, 'CB' : 5.280, 'CA' : 8.389, 79 'CG' : 14.299, 'O' : 5.688, 'N' : 30.423, 80 'CD1': 29.766, 'CD2': 1.777}, 81 'ARG': {'C' : 18.112, 'CB' : 5.241, 'CA' : 16.730, 82 'CG' : 16.616, 'NE' : 13.828, 'O' : 15.959, 83 'CD' : 1.912, 'CZ' : 21.727, 'NH1': 21.265, 84 'NH2': 7.178, 'N' : 1.769}, 85 'TRP': {'C' : 22.097, 'CZ2': 9.303, 'CB' : 4.131, 86 'CA' : 14.342, 'CG' : 5.499, 'O' : 16.075, 87 'N' : 15.575, 'CH2': 1.621, 'CE3': 22.125, 88 'CE2': 8.268, 'CD2': 2.468, 'CZ3': 13.935, 89 'NE1': 7.413, 'CD1': 15.173}, 90 'GLU': {'C' : 22.925, 'CB' : 2.084, 'CA' : 15.389, 91 'CG' : 20.656, 'O' : 21.058, 'CD' : 7.101, 92 'OE2': 2.090, 'N' : 14.298, 'OE1': 6.603}, 93 'TYR': {'C' : 5.766, 'CD2': 12.756, 'OH' : 13.124, 94 'CB' : 15.263, 'CA' : 1.525, 'CG' : 18.792, 95 'O' : 6.204, 'N' : 18.807, 'CZ' : 35.593, 96 'CD1': 7.103, 'CE1': 14.230, 'CE2': 14.968}} 97 98 ## random coil solvent accessible surface in a GLY-XXX-GLY peptide 99 ranAS = {'CYS': {'C' : 0.833, 'CB' : 34.358, 'CA' : 7.768, 100 'O' : 29.027, 'N' : 5.159, 'SG' : 76.311}, 101 'GLN': {'C' : 0.694, 'CB' : 28.846, 'CA' : 3.896, 102 'CG' : 32.484, 'O' : 28.716, 'CD' : 2.467, 103 'N' : 7.736, 'NE2': 54.470, 'OE1': 32.637}, 104 'ILE': {'C' : 0.336, 'CB' : 10.203, 'CA' : 2.117, 105 'O' : 26.670, 'N' : 4.723, 'CD1': 63.709, 106 'CG1': 32.543, 'CG2': 50.456}, 107 'SER': {'C' : 1.003, 'OG' : 47.009, 'CB' : 44.666, 108 'CA' : 8.688, 'O' : 29.511, 'N' : 6.051}, 109 'VAL': {'C' : 0.491, 'CB' : 9.140, 'CA' : 5.240, 110 'O' : 23.612, 'N' : 2.422, 'CG1': 65.475, 111 'CG2': 59.022}, 112 'LYS': {'C' : 0.713, 'CB' : 27.111, 'CA' : 4.234, 113 'CG' : 24.319, 'CE' : 35.072, 'CD' : 23.182, 114 'NZ' : 76.704, 'O' : 27.814, 'N' : 7.147}, 115 'ASN': {'C' : 0.671, 'CB' : 33.549, 'CA' : 6.662, 116 'CG' : 2.403, 'O' : 27.881, 'N' : 7.635, 117 'OD1': 36.200, 'ND2': 50.093}, 118 'PRO': {'C' : 0.696, 'CB' : 34.966, 'CA' : 4.790, 119 'CG' : 46.846, 'O' : 34.264, 'CD' : 32.028, 120 'N' : 0.314}, 121 'GLY': {'CA' : 43.741, 'C' : 2.298, 'O' : 31.107, 122 'N' : 12.702}, 123 'THR': {'C' : 0.709, 'CB' : 15.180, 'CA' : 7.358, 124 'OG1': 38.230, 'O' : 27.475, 'N' : 4.937, 125 'CG2': 62.021}, 126 'PHE': {'C' : 0.876, 'CE1': 33.974, 'CB' : 30.431, 127 'CA' : 4.790, 'CG' : 1.388, 'O' : 28.205, 128 'N' : 6.352, 'CZ' : 34.444, 'CD1': 19.752, 129 'CD2': 18.580, 'CE2': 32.812}, 130 'ALA': {'CB' : 70.070, 'CA' : 11.256, 'C' : 0.717, 131 'O' : 27.891, 'N' : 7.782}, 132 'HIS': {'C' : 0.923, 'CE1': 32.391, 'CB' : 31.658, 133 'CA' : 6.665, 'CG' : 1.280, 'O' : 27.750, 134 'N' : 7.365, 'CD2': 27.492, 'ND1': 15.030, 135 'NE2': 36.247}, 136 'MET': {'C' : 0.590, 'CB' : 28.322, 'CA' : 3.961, 137 'CG' : 29.567, 'CE' : 74.891, 'N' : 7.345, 138 'O' : 27.658, 'SD' : 29.550}, 139 'ASP': {'C' : 0.972, 'CB' : 37.245, 'CA' : 10.246, 140 'CG' : 3.665, 'O' : 25.235, 'N' : 3.251, 141 'OD1': 37.525, 'OD2': 33.852}, 142 'LEU': {'C' : 0.793, 'CB' : 21.950, 'CA' : 2.852, 143 'CG' : 14.129, 'O' : 27.978, 'N' : 5.231, 144 'CD1': 61.814, 'CD2': 59.042}, 145 'ARG': {'C' : 0.829, 'CB' : 28.313, 'CA' : 2.930, 146 'CG' : 27.099, 'NE' : 23.452, 'O' : 28.419, 147 'CD' : 23.936, 'CZ' : 1.719, 'NH1': 50.063, 148 'NH2': 46.094, 'N' : 7.109}, 149 'TRP': {'C' : 0.856, 'CZ2': 31.924, 'CB' : 28.556, 150 'CA' : 3.339, 'CG' : 1.337, 'O' : 28.269, 151 'N' : 5.626, 'CH2': 34.844, 'CE3': 20.285, 152 'CE2': 4.521, 'CD2': 3.335, 'CZ3': 34.289, 153 'NE1': 32.834, 'CD1': 23.722}, 154 'GLU': {'C' : 0.987, 'CB' : 27.019, 'CA' : 5.321, 155 'CG' : 41.443, 'O' : 29.082, 'CD' : 3.502, 156 'OE2': 35.857, 'N' : 4.529, 'OE1': 32.074}, 157 'TYR': {'C' : 0.777, 'CD2': 20.732, 'OH' : 56.712, 158 'CB' : 29.172, 'CA' : 4.380, 'CG' : 1.517, 159 'O' : 28.824, 'N' : 5.930, 'CZ' : 6.352, 160 'CD1': 19.637, 'CE1': 30.502, 'CE2': 30.358}} 161 162 ## C-terminal random coil molecular surface in a GLY-GLY-XXX peptide 163 ranMS_C = {'CYS': {'C' : 4.901, 'OXT': 16.009, 'CB' : 21.505, 'CA' : 8.895, 164 'O' : 15.937, 'N' : 5.493, 'SG' : 32.718}, 165 'GLN': {'C' : 4.268, 'OXT': 16.327, 'CB' : 18.696, 'CA' : 6.661, 166 'CG' : 21.508, 'O' : 15.993, 'N' : 6.289, 'CD' : 2.908, 167 'NE2': 23.350, 'OE1': 15.560}, 168 'ILE': {'C' : 3.954, 'OXT': 15.895, 'CB' : 7.210, 'CA' : 6.836, 169 'O' : 15.297, 'N' : 5.218, 'CD1': 32.674, 'CG1': 17.185, 170 'CG2': 29.494 }, 171 'SER': {'C' : 4.935, 'OG' : 17.498, 'CB' : 26.752, 'CA' : 9.621, 172 'O' : 15.997, 'N' : 6.296, 'OXT': 16.009 }, 173 'VAL': {'C' : 3.886, 'OXT': 16.344, 'CB' : 8.237, 'CA' : 6.639, 174 'O' : 16.111, 'N' : 5.403, 'CG1': 31.003, 'CG2': 30.984}, 175 'LYS': {'C' : 4.543, 'OXT': 15.863, 'CB' : 17.773, 'CA' : 9.434, 176 'CG' : 16.113, 'O' : 15.696, 'N' : 5.357, 'NZ' : 32.439, 177 'CE' : 18.742, 'CD' : 17.682}, 178 'TRP': {'C' : 4.480, 'CD1': 13.511, 'CZ2': 15.023, 'CB' : 21.117, 179 'CA' : 7.578, 'CG' : 1.631, 'O' : 16.137, 'N' : 6.173, 180 'OXT': 16.517, 'CH2': 15.027, 'CE3': 13.489, 'CE2': 4.452, 181 'CD2': 3.832, 'CZ3': 14.883, 'NE1': 15.688}, 182 'PRO': {'C' : 4.198, 'OXT': 16.105, 'CB' : 20.472, 'CA' : 10.419, 183 'CG' : 21.513, 'O' : 16.161, 'CD' : 19.308, 'N' : 0.553}, 184 'THR': {'C' : 4.033, 'OXT': 16.336, 'CB' : 11.889, 'CA' : 7.479, 185 'OG1': 15.555, 'O' : 16.001, 'N' : 5.930, 'CG2': 33.396}, 186 'PHE': {'C' : 4.941, 'CD2': 10.800, 'OXT': 16.072, 'CB' : 21.817, 187 'CA' : 7.746, 'CG' : 1.710, 'O' : 15.997, 'N' : 5.831, 188 'CZ' : 15.263, 'CD1': 12.185, 'CE1': 15.259, 'CE2': 14.726}, 189 'ALA': {'C' : 4.785, 'OXT': 15.918, 'CB' : 34.751, 'CA' : 10.288, 190 'O' : 15.844, 'N' : 6.609}, 191 'GLY': {'OXT': 15.901, 'CA' : 26.945, 'C' : 5.589, 'O' : 15.783, 192 'N' : 8.017}, 193 'HIS': {'C' : 4.537, 'CD2': 13.867, 'OXT': 15.778, 'CB' : 22.103, 194 'CA' : 9.755, 'CG' : 1.686, 'O' : 15.257, 'N' : 5.629, 195 'CE1': 15.805, 'ND1': 12.331, 'NE2': 15.544 }, 196 'GLU': {'C' : 4.787, 'OXT': 16.161, 'CB' : 20.204, 'CA' : 7.939, 197 'CG' : 20.793, 'O' : 16.023, 'N' : 5.478, 'OE2': 15.843, 198 'CD' : 4.832, 'OE1': 15.462}, 199 'LEU': {'C' : 4.225, 'OXT': 16.433, 'CB' : 15.593, 'CA' : 6.733, 200 'CG' : 8.037, 'O' : 16.122, 'N' : 5.857, 'CD1': 31.131, 201 'CD2': 31.326}, 202 'ARG': {'C' : 4.178, 'OXT': 16.028, 'CB' : 18.280, 'CA' : 9.543, 203 'CG' : 16.758, 'NE' : 20.127, 'O' : 14.080, 'N' : 4.504, 204 'CZ' : 2.192, 'NH1': 20.770, 'NH2': 22.158, 'CD' : 13.552}, 205 'ASP': {'C' : 4.437, 'OXT': 16.092, 'CB' : 22.783, 'CA' : 9.494, 206 'CG' : 4.258, 'O' : 16.423, 'N' : 5.150, 'OD1': 16.141, 207 'OD2': 16.226}, 208 'ASN': {'C' : 4.200, 'OXT': 16.330, 'CB' : 22.238, 'CA' : 8.738, 209 'CG' : 2.759, 'O' : 16.268, 'N' : 6.718, 'OD1': 15.585, 210 'ND2': 23.497}, 211 'TYR': {'C' : 4.257, 'CE1': 15.574, 'OH' : 20.805, 'OXT': 16.007, 212 'CB' : 21.243, 'CA' : 9.453, 'CG' : 1.708, 'O' : 16.290, 213 'N' : 4.981, 'CZ' : 5.799, 'CD1': 10.416, 'CD2': 12.459, 214 'CE2': 15.491}, 215 'MET': {'C' : 4.692, 'OXT': 16.239, 'CB' : 18.674, 'CA' : 7.639, 216 'CG' : 19.206, 'O' : 15.957, 'N' : 6.066, 'CE' : 36.053, 217 'SD' : 15.153 }} 218 219 220 221 ## N-terminal random coil molecular surface in a XXX-GLY-GLY peptide 222 ranMS_N = {'CYS': {'C' : 1.881, 'CB' : 20.689, 'CA' : 12.751, 'O' : 12.456, 223 'N' : 17.890, 'SG' : 33.579}, 224 'GLN': {'C' : 1.838, 'CB' : 18.800, 'CA' : 12.632, 'CG' : 18.923, 225 'O' : 12.560, 'CD' : 3.315, 'N' : 17.352, 'NE2': 23.831, 226 'OE1': 13.464}, 227 'ILE': {'C' : 1.681, 'CB' : 7.893, 'CA' : 8.675, 'O' : 13.221, 228 'N' : 18.819, 'CD1': 31.268, 'CG1': 17.636, 'CG2': 27.787}, 229 'SER': {'C' : 2.303, 'OG' : 16.770, 'CB' : 26.889, 'CA' : 13.107, 230 'O' : 13.152, 'N' : 19.013}, 231 'VAL': {'C' : 1.649, 'CB' : 8.327, 'CA' : 10.304, 'O' : 13.305, 232 'N' : 18.515, 'CG1': 29.069, 'CG2': 30.586}, 233 'LYS': {'C' : 2.076, 'CB' : 16.542, 'CA' : 11.608, 'CG' : 17.298, 234 'CE' : 18.221, 'CD' : 17.673, 'NZ' : 32.602, 'O' : 13.474, 235 'N' : 19.247}, 236 'TRP': {'C' : 1.788, 'CD1': 9.793, 'CZ2': 14.896, 'CB' : 19.663, 237 'CA' : 12.625, 'CG' : 1.542, 'O' : 12.968, 'N' : 18.599, 238 'CH2': 14.820, 'CE3': 13.676, 'CE2': 4.877, 'CD2': 4.279, 239 'CZ3': 14.890, 'NE1': 15.654}, 240 'PRO': {'C' : 2.460, 'CB' : 21.196, 'CA' : 12.083, 'CG' : 21.410, 241 'O' : 13.475, 'CD' : 24.855, 'N' : 8.681 }, 242 'THR': {'C' : 2.049, 'CB' : 11.750, 'CA' : 11.666, 'OG1': 15.173, 243 'O' : 13.350, 'N' : 18.585, 'CG2': 32.218}, 244 'PHE': {'C' : 1.806, 'CD2': 12.542, 'CB' : 20.567, 'CA' : 12.435, 245 'CG' : 1.700, 'O' : 12.991, 'N' : 18.878, 'CZ' : 15.122, 246 'CD1': 9.868, 'CE1': 15.353, 'CE2': 15.245}, 247 'ALA': {'CB' : 34.147, 'CA' : 13.086, 'C' : 2.120, 'O' : 13.312, 248 'N' : 19.125}, 249 'GLY': {'CA' : 29.487, 'C' : 3.092, 'O' : 13.362, 'N' : 19.552}, 250 'HIS': {'C' : 1.800, 'CD2': 13.812, 'CB' : 21.222, 'CA' : 12.204, 251 'CG' : 1.448, 'O' : 12.229, 'N' : 19.066, 'CE1': 15.538, 252 'ND1': 10.390, 'NE2': 15.168}, 253 'GLU': {'C' : 2.148, 'CB' : 19.736, 'CA' : 11.607, 'CG' : 21.964, 254 'O' : 13.334, 'CD' : 4.935, 'OE2': 15.359, 'N' : 18.703, 255 'OE1': 15.546}, 256 'LEU': {'C' : 1.846, 'CB' : 15.176, 'CA' : 12.338, 'CG' : 7.083, 257 'O' : 12.648, 'N' : 18.191, 'CD1': 29.800, 'CD2': 30.607}, 258 'ARG': {'C' : 1.822, 'CB' : 16.419, 'CA' : 12.537, 'CG' : 16.382, 259 'NE' : 18.534, 'O' : 12.524, 'CD' : 17.014, 'CZ' : 2.161, 260 'NH1': 22.420, 'NH2': 21.693, 'N' : 18.034}, 261 'ASP': {'C' : 1.943, 'CB' : 22.100, 'CA' : 13.127, 'CG' : 3.754, 262 'O' : 13.528, 'N' : 18.370, 'OD1': 14.891, 'OD2': 15.499}, 263 'ASN': {'C' : 1.781, 'CB' : 21.494, 'CA' : 12.711, 'CG' : 2.215, 264 'O' : 12.685, 'N' : 18.523, 'OD1': 13.989, 'ND2': 21.674}, 265 'TYR': {'C' : 1.891, 'CE1': 15.296, 'OH' : 20.825, 'CB' : 20.631, 266 'CA' : 12.481, 'CG' : 1.666, 'O' : 12.892, 'N' : 18.798, 267 'CZ' : 5.542, 'CD1': 12.374, 'CD2': 10.473, 'CE2': 14.935}, 268 'MET': {'C' : 1.970, 'CB' : 17.536, 'CA' : 11.852, 'CG' : 18.881, 269 'CE' : 36.194, 'N' : 19.261, 'O' : 13.279, 'SD' : 15.618}} 270 271 ## C-terminal random coil solvent accessible surface in a GLY-GLY-XXX peptide 272 ranAS_C = {'CYS': {'C' : 3.576, 'OXT': 44.000, 'CB' : 35.823, 'CA' : 7.883, 273 'O' : 40.390, 'N' : 3.953, 'SG' : 63.386}, 274 'GLN': {'C' : 2.560, 'OXT': 39.663, 'CB' : 23.902, 'CA' : 3.636, 275 'CG' : 35.848, 'O' : 39.558, 'N' : 5.031, 'CD' : 2.604, 276 'NE2': 52.310, 'OE1': 37.289}, 277 'ILE': {'C' : 2.192, 'OXT': 38.990, 'CB' : 6.897, 'CA' : 4.449, 278 'O' : 35.608, 'N' : 3.047, 'CD1': 73.231, 'CG1': 27.316, 279 'CG2': 53.373}, 280 'SER': {'C' : 3.562, 'OG' : 44.874, 'CB' : 45.772, 'CA' : 9.377, 281 'O' : 40.102, 'N' : 5.281, 'OXT': 44.024}, 282 'VAL': {'C' : 1.947, 'OXT': 40.714, 'CB' : 10.749, 'CA' : 4.843, 283 'O' : 38.524, 'N' : 4.350, 'CG1': 64.304, 'CG2': 61.298}, 284 'LYS': {'C' : 3.209, 'OXT': 43.059, 'CB' : 25.382, 'CA' : 9.294, 285 'CG' : 17.124, 'O' : 37.874, 'N' : 3.358, 'NZ' : 78.334, 286 'CE' : 34.282, 'CD' : 28.882}, 287 'TRP': {'C' : 2.864, 'CD1': 23.471, 'CZ2': 30.132, 'CB' : 27.372, 288 'CA' : 4.926, 'CG' : 1.362, 'O' : 39.445, 'N' : 4.670, 289 'OXT': 42.192, 'CH2': 33.477, 'CE3': 21.297, 'CE2': 3.987, 290 'CD2': 3.165, 'CZ3': 32.837, 'NE1': 31.635}, 291 'PRO': {'C' : 2.522, 'OXT': 42.757, 'CB' : 39.165, 'CA' : 12.754, 292 'CG' : 45.959, 'O' : 36.644, 'CD' : 30.229, 'N' : 0.162}, 293 'THR': {'C' : 2.135, 'OXT': 41.079, 'CB' : 16.180, 'CA' : 5.510, 294 'OG1': 31.767, 'O' : 39.334, 'N' : 4.732, 'CG2': 69.879}, 295 'PHE': {'C' : 3.491, 'CD2': 16.338, 'OXT': 43.822, 'CB' : 31.885, 296 'CA' : 5.300, 'CG' : 1.482, 'O' : 40.849, 'N' : 4.425, 297 'CZ' : 32.891, 'CD1': 20.269, 'CE1': 32.231, 'CE2': 27.941}, 298 'ALA': {'C' : 3.470, 'OXT': 44.166, 'CB' : 69.869, 'CA' : 10.822, 299 'O' : 40.456, 'N' : 5.644 }, 300 'GLY': {'OXT': 44.099, 'CA' : 44.499, 'C' : 5.688, 'O' : 44.236, 301 'N' : 10.787}, 302 'HIS': {'C' : 3.235, 'CD2': 26.008, 'OXT': 42.132, 'CB' : 35.445, 303 'CA' : 9.836, 'CG' : 1.313, 'O' : 34.817, 'N' : 3.437, 304 'CE1': 36.648, 'ND1': 16.111, 'NE2': 36.711}, 305 'GLU': {'C' : 3.233, 'OXT': 43.638, 'CB' : 25.879, 'CA' : 6.755, 306 'CG' : 28.174, 'O' : 40.299, 'N' : 4.009, 'OE2': 38.602, 307 'CD' : 4.560, 'OE1': 43.505}, 308 'LEU': {'C' : 2.492, 'OXT': 41.188, 'CB' : 13.565, 'CA' : 3.909, 309 'CG' : 9.503, 'O' : 38.884, 'N' : 4.293, 310 'CD1': 62.247, 'CD2': 70.859}, 311 'ARG': {'C' : 2.842, 'OXT': 43.324, 'CB' : 30.232, 'CA' : 9.378, 312 'CG' : 26.275, 'NE' : 31.446, 'O' : 28.475, 'N' : 2.424, 313 'CZ' : 2.091, 'NH1': 39.892, 'NH2': 58.200, 'CD' : 16.212}, 314 'ASP': {'C' : 2.712, 'OXT': 42.871, 'CB' : 37.628, 'CA' : 9.681, 315 'CG' : 3.708, 'O' : 35.649, 'N' : 2.738, 'OD1': 35.467, 316 'OD2': 41.483}, 317 'ASN': {'C' : 2.654, 'OXT': 40.748, 'CB' : 30.645, 'CA' : 6.482, 318 'CG' : 2.489, 'O' : 38.499, 'N' : 5.569, 'OD1': 38.650, 319 'ND2': 54.095}, 320 'TYR': {'C' : 3.012, 'CE1': 25.434, 'OH' : 56.665, 'OXT': 43.093, 321 'CB' : 33.823, 'CA' : 9.198, 'CG' : 1.325, 'O' : 35.242, 322 'N' : 2.741, 'CZ' : 5.893, 'CD1': 11.890, 'CD2': 18.390, 323 'CE2': 30.470}, 324 'MET': {'C' : 3.048, 'OXT': 43.014, 'CB' : 23.902, 'CA' : 5.848, 325 'CG' : 28.573, 'O' : 39.775, 'N' : 4.874, 'CE' : 76.639, 326 'SD' : 32.812}} 327 328 329 330 ## N-terminal random coil solvent accessible surface in a XXX-GLY-GLY peptide 331 ranAS_N = {'CYS': {'C' : 1.431, 'CB' : 38.159, 'CA' : 19.289, 'O' : 23.438, 332 'N' : 43.276, 'SG' : 67.559}, 333 'GLN': {'C' : 1.649, 'CB' : 31.979, 'CA' : 19.263, 'CG' : 23.964, 334 'O' : 21.682, 'CD' : 2.755, 'N' : 38.957, 'NE2': 56.478, 335 'OE1': 31.267}, 336 'ILE': {'C' : 1.024, 'CB' : 9.940, 'CA' : 8.458, 'O' : 24.997, 337 'N' : 42.475, 'CD1': 68.526, 'CG1': 33.941, 'CG2': 46.229}, 338 'SER': {'C' : 1.629, 'OG' : 48.780, 'CB' : 42.463, 'CA' : 18.962, 339 'O' : 26.451, 'N' : 43.920}, 340 'VAL': {'C' : 0.936, 'CB' : 10.647, 'CA' : 12.837, 'O' : 25.260, 341 'N' : 42.960, 'CG1': 52.342, 'CG2': 66.747}, 342 'LYS': {'C' : 1.326, 'CB' : 17.475, 'CA' : 15.471, 'CG' : 28.459, 343 'CE' : 32.971, 'CD' : 32.126, 'NZ' : 75.829, 'O' : 27.414, 344 'N' : 45.390}, 345 'TRP': {'C' : 1.715, 'CD1': 10.467, 'CZ2': 31.117, 'CB' : 32.211, 346 'CA' : 19.563, 'CG' : 1.157, 'O' : 23.389, 'N' : 38.572, 347 'CH2': 34.299, 'CE3': 21.185, 'CE2': 4.574, 'CD2': 3.138, 348 'CZ3': 34.416, 'NE1': 27.704}, 349 'PRO': {'C' : 1.586, 'CB' : 36.124, 'CA' : 17.336, 'CG' : 47.576, 350 'O' : 27.825, 'CD' : 51.994, 'N' : 19.511}, 351 'THR': {'C' : 1.375, 'CB' : 15.023, 'CA' : 15.341, 'OG1': 40.161, 352 'O' : 26.875, 'N' : 42.884, 'CG2': 61.218}, 353 'PHE': {'C' : 1.579, 'CD2': 19.828, 'CB' : 34.960, 'CA' : 18.791, 354 'CG' : 1.281, 'O' : 22.256, 'N' : 42.396, 'CZ' : 34.159, 355 'CD1': 10.942, 'CE1': 28.856, 'CE2': 34.476}, 356 'ALA': {'CB' : 70.762, 'CA' : 19.700, 'C' : 1.248, 'O' : 27.698, 357 'N' : 48.593}, 358 'GLY': {'CA' : 54.054, 'C' : 2.369, 'O' : 30.073, 'N' : 53.879}, 359 'HIS': {'C' : 1.443, 'CD2': 26.112, 'CB' : 35.612, 'CA' : 17.834, 360 'CG' : 1.116, 'O' : 21.813, 'N' : 45.116, 'CE1': 32.814, 361 'ND1': 12.827, 'NE2': 35.149}, 362 'GLU': {'C' : 1.532, 'CB' : 21.289, 'CA' : 15.421, 'CG' : 34.752, 363 'O' : 27.491, 'CD' : 4.877, 'OE2': 43.069, 'N' : 43.177, 364 'OE1': 44.404}, 365 'LEU': {'C' : 1.453, 'CB' : 22.380, 'CA' : 18.248, 'CG' : 7.839, 366 'O' : 24.519, 'N' : 42.514, 'CD1': 57.000, 'CD2': 66.283}, 367 'ARG': {'C' : 1.558, 'CB' : 25.193, 'CA' : 18.837, 'CG' : 21.292, 368 'NE' : 23.924, 'O' : 20.214, 'CD' : 24.711, 'CZ' : 2.057, 369 'NH1': 57.939, 'NH2': 50.567, 'N' : 39.687}, 370 'ASP': {'C' : 1.748, 'CB' : 38.818, 'CA' : 20.482, 'CG' : 3.560, 371 'O' : 25.296, 'N' : 42.730, 'OD1': 31.978, 'OD2': 36.750}, 372 'ASN': {'C' : 1.576, 'CB' : 36.560, 'CA' : 19.196, 'CG' : 2.215, 373 'O' : 22.760, 'N' : 44.258, 'OD1': 29.512, 'ND2': 44.276}, 374 'TYR': {'C' : 1.626, 'CE1': 30.412, 'OH' : 55.461, 'CB' : 34.783, 375 'CA' : 18.887, 'CG' : 1.309, 'O' : 22.818, 'N' : 42.020, 376 'CZ' : 5.631, 'CD1': 19.492, 'CD2': 12.154, 'CE2': 24.738}, 377 'MET': {'C' : 1.458, 'CB' : 18.265, 'CA' : 16.140, 'CG' : 28.567, 378 'CE' : 79.176, 'N' : 45.454, 'O' : 25.118, 'SD' : 36.038}} 379 380 381

382 -def relExposure( model, absSurf, key='AS', clip=1 ):

383 """ 384 Calculate how exposed an atom is relative to the same 385 atom in a GLY-XXX-GLY tripeptide, an approximation of 386 the unfolded state. 387 388 @param absSurf: Absolute MS OR AS values 389 @type absSurf: [float] 390 @param key: MS or AS 391 @type key: MS|AS 392 @param clip: clip values above 100% (default: 1) 393 @type clip: 1|0 394 395 @return: rel - list of relative accessible surfaces 396 @rtype: [float] 397 """ 398 if not key=='MS' and not key=='AS': 399 raise Exception,\ 400 'Incorrect key for relative exposiure: %s '%key 401 402 rel = [] 403 i=0 404 405 ## loop over chains 406 for j in range( model.lenChains()): 407 c = model.takeChains([j]) 408 409 k=0 410 cIdx = c.resIndex() 411 ## and loop over atoms in chain 412 for a in c.atoms: 413 ## N-terminal residue 414 if k < cIdx[1]: 415 rel = __Nter( a, rel, absSurf, key, i ) 416 ## C-terminal residue 417 if k >= cIdx[-1]: 418 rel = __Cter( a, rel, absSurf, key, i ) 419 ## everything but N- and C termini 420 if not k < cIdx[1] and not k >= cIdx[-1]: 421 rel = __bulk( a, rel, absSurf, key, i ) 422 i+=1 423 k+=1 424 425 if clip: 426 return Numeric.clip( Numeric.array(rel), 0.0, 100.0 ) 427 else: 428 return Numeric.array(rel)

429 430

431 -def __Nter( a, rel, absSurf, key, i ):

432 """ 433 Get N-terminal relative exposures. 434 435 @param rel: list in which relative exposures are collected 436 @type rel: [float] 437 @param absSurf: Absolute MS OR AS values 438 @type absSurf: [float] 439 @param key: MS or AS 440 @type key: MS|AS 441 442 @return: rel - list of relative accessible surfaces with data from 443 N-terminal residues appended. 444 @rtype: [float] 445 """ 446 atom = a['name'] 447 resi = a['residue_name'] 448 ## don't want to divide with zero 449 if absSurf[i] != 0: 450 ## if solvent accessible surface 451 if key == 'AS': 452 rel += [ (absSurf[i] / ranAS_N[resi][atom]) *100 ] 453 ## if molecular surface 454 if key == 'MS': 455 rel += [ (absSurf[i] / ranMS_N[resi][atom]) *100 ] 456 else: 457 rel += [0.0] 458 return rel

459 460

461 -def __Cter( a, rel, absSurf, key, i ):

462 """ 463 Get C-terminal relative exposures 464 465 @param rel: list in which relative exposures are collected 466 @type rel: [float] 467 @param absSurf: Absolute MS OR AS values 468 @type absSurf: [float] 469 @param key: MS or AS 470 @type key: MS|AS 471 472 @return: rel - list of relative accessible surfaces with data from 473 C-terminal residues appended. 474 @rtype: [float] 475 """ 476 atom = a['name'] 477 resi = a['residue_name'] 478 if absSurf[i] != 0: 479 if key == 'AS': 480 rel += [ (absSurf[i] / ranAS_C[resi][atom]) *100 ] 481 if key == 'MS': 482 rel += [ (absSurf[i] / ranMS_C[resi][atom]) *100 ] 483 else: 484 rel += [0.0] 485 return rel

486 487

488 -def __bulk( a, rel, absSurf, key, i ):

489 """ 490 Get relative exposures for everything else. 491 492 @param rel: list in which relative exposures are collected 493 @type rel: [float] 494 @param absSurf: Absolute MS OR AS values 495 @type absSurf: [float] 496 @param key: MS or AS 497 @type key: MS|AS 498 499 @return: rel - list of relative accessible surfaces with data from 500 ' none-terminal residues appended. 501 @rtype: [float] 502 """ 503 atom = a['name'] 504 resi = a['residue_name'] 505 if absSurf[i] != 0: 506 if key == 'AS': 507 rel += [ (absSurf[i] / ranAS[resi][atom]) *100 ] 508 if key == 'MS': 509 rel += [ (absSurf[i] / ranMS[resi][atom]) *100 ] 510 else: 511 rel += [0.0] 512 return rel

513 514 515 516 ############# 517 ## TESTING 518 ############# 519

520 -class Test:

521 """ 522 Test class 523 """ 524

525 - def run( self, local=0 ):

526 """ 527 run function test 528 529 @param local: transfer local variables to global and perform 530 other tasks only when run locally 531 @type local: 1|0 532 533 @return: something 534 @rtype: float 535 """ 536 from Biskit import PDBModel 537 import Biskit.tools as T 538 539 ## load a structure 540 m = PDBModel( T.testRoot()+'/lig/1A19.pdb' ) 541 m = m.compress( m.maskProtein() ) 542 m = m.compress( m.maskHeavy() ) 543 544 ## some fake surface data 545 surf = Numeric.ones( m.lenAtoms()) * 10.0 546 547 relExp = relExposure( m, surf ) 548 549 if local: 550 globals().update( locals() ) 551 552 return Numeric.sum(relExp)

553 554

555 - def expected_result( self ):

556 """ 557 Precalculated result to check for consistent performance. 558 559 @return: something 560 @rtype: float 561 """ 562 return 44276.860852223857

563 564 565 if __name__ == '__main__': 566 567 test = Test() 568 569 assert test.run( local=1 ) == test.expected_result() 570