from __future__ import absolute_import, division, print_function import libtbx.load_env import sys from mmtbx.monomer_library import server from mmtbx.monomer_library import pdb_interpretation from six.moves import cStringIO as StringIO from libtbx.utils import format_cpu_times protein_pdb_str = """ ATOM 1 N SER C 2 34.351 13.914 38.850 1.00 25.20 N ATOM 2 CA SER C 2 35.564 14.555 38.349 1.00 23.89 C ATOM 3 C SER C 2 35.509 14.878 36.846 1.00 22.90 C ATOM 4 O SER C 2 35.800 16.010 36.460 1.00 23.08 O ATOM 5 CB SER C 2 36.790 13.687 38.657 1.00 23.11 C ATOM 6 OG SER C 2 36.939 13.492 40.053 1.00 21.13 O ATOM 7 N PRO C 3 35.146 13.899 35.989 1.00 22.39 N ATOM 8 CA PRO C 3 35.107 14.258 34.566 1.00 19.74 C ATOM 9 C PRO C 3 34.000 15.256 34.228 1.00 13.82 C ATOM 10 O PRO C 3 34.193 16.119 33.371 1.00 12.80 O ATOM 11 CB PRO C 3 34.857 12.915 33.872 1.00 23.07 C ATOM 12 CG PRO C 3 34.164 12.092 34.890 1.00 24.21 C ATOM 13 CD PRO C 3 34.778 12.485 36.199 1.00 23.79 C ATOM 14 N LEU C 4 32.857 15.135 34.897 1.00 11.29 N ATOM 15 CA LEU C 4 31.727 16.026 34.654 1.00 9.66 C ATOM 16 C LEU C 4 32.034 17.454 35.105 1.00 7.86 C ATOM 17 O LEU C 4 31.610 18.416 34.465 1.00 7.65 O ATOM 18 CB LEU C 4 30.456 15.496 35.345 1.00 10.57 C ATOM 19 CG LEU C 4 30.191 15.483 36.863 1.00 11.83 C ATOM 20 CD1 LEU C 4 29.728 16.845 37.386 1.00 12.67 C ATOM 21 CD2 LEU C 4 31.376 14.965 37.676 1.00 13.04 C ATOM 22 N ALA C 5 32.770 17.587 36.205 1.00 8.13 N ATOM 23 CA ALA C 5 33.144 18.900 36.719 1.00 8.04 C ATOM 24 C ALA C 5 34.126 19.589 35.777 1.00 7.24 C ATOM 25 O ALA C 5 34.030 20.794 35.529 1.00 6.98 O ATOM 26 CB ALA C 5 33.740 18.775 38.112 1.00 9.33 C ATOM 27 N GLN C 6 35.065 18.813 35.246 1.00 6.89 N ATOM 28 CA GLN C 6 36.032 19.335 34.292 1.00 7.52 C ATOM 29 C GLN C 6 35.326 19.718 33.000 1.00 5.67 C ATOM 30 O GLN C 6 35.664 20.719 32.364 1.00 5.64 O ATOM 31 CB GLN C 6 37.135 18.311 34.017 1.00 9.58 C ATOM 32 CG GLN C 6 38.024 18.016 35.215 1.00 12.45 C ATOM 33 CD GLN C 6 38.792 19.235 35.688 1.00 16.41 C ATOM 34 OE1 GLN C 6 39.169 20.095 34.891 1.00 17.91 O ATOM 35 NE2 GLN C 6 39.026 19.317 36.993 1.00 18.48 N ATOM 36 N GLN C 7 34.330 18.921 32.627 1.00 5.24 N ATOM 37 CA GLN C 7 33.571 19.174 31.411 1.00 4.92 C ATOM 38 C GLN C 7 32.744 20.449 31.523 1.00 4.44 C ATOM 39 O GLN C 7 32.739 21.270 30.609 1.00 4.63 O ATOM 40 CB GLN C 7 32.661 17.985 31.094 1.00 5.87 C ATOM 41 CG GLN C 7 31.868 18.136 29.805 1.00 8.74 C ATOM 42 CD GLN C 7 31.016 16.920 29.500 1.00 11.90 C ATOM 43 OE1 GLN C 7 31.059 15.921 30.219 1.00 17.10 O ATOM 44 NE2 GLN C 7 30.235 16.999 28.429 1.00 12.32 N ATOM 45 N ILE C 8 32.069 20.633 32.653 1.00 4.24 N ATOM 46 CA ILE C 8 31.246 21.823 32.833 1.00 4.30 C ATOM 47 C ILE C 8 32.114 23.072 33.008 1.00 4.16 C ATOM 48 O ILE C 8 31.758 24.146 32.517 1.00 5.21 O ATOM 49 CB ILE C 8 30.262 21.674 34.028 1.00 4.60 C ATOM 50 CG1 ILE C 8 29.291 22.857 34.076 1.00 5.10 C ATOM 51 CG2 ILE C 8 30.995 21.526 35.350 1.00 4.97 C ATOM 52 CD1 ILE C 8 28.415 22.977 32.848 1.00 5.70 C ATOM 53 N LYS C 9 33.252 22.941 33.687 1.00 4.57 N ATOM 54 CA LYS C 9 34.120 24.099 33.882 1.00 5.70 C ATOM 55 C LYS C 9 34.801 24.516 32.574 1.00 5.50 C ATOM 56 O LYS C 9 34.930 25.712 32.300 1.00 6.01 O ATOM 57 CB LYS C 9 35.164 23.834 34.978 1.00 8.15 C ATOM 58 CG LYS C 9 36.291 22.887 34.608 1.00 13.11 C ATOM 59 CD LYS C 9 37.294 22.751 35.743 1.00 17.07 C ATOM 60 CE LYS C 9 36.641 22.185 36.994 1.00 20.09 C ATOM 61 NZ LYS C 9 37.615 22.041 38.112 1.00 22.35 N ATOM 62 N ASN C 10 35.227 23.550 31.761 1.00 5.00 N ATOM 63 CA ASN C 10 35.842 23.898 30.484 1.00 5.09 C ATOM 64 C ASN C 10 34.792 24.427 29.512 1.00 4.73 C ATOM 65 O ASN C 10 35.075 25.320 28.711 1.00 4.79 O ATOM 66 CB ASN C 10 36.618 22.712 29.883 1.00 5.93 C ATOM 67 CG ASN C 10 35.730 21.547 29.469 1.00 6.66 C ATOM 68 OD1 ASN C 10 34.715 21.717 28.794 1.00 7.40 O ATOM 69 ND2 ASN C 10 36.134 20.344 29.858 1.00 8.16 N ATOM 70 N ILE C 11 33.579 23.881 29.591 1.00 4.14 N ATOM 71 CA ILE C 11 32.485 24.354 28.750 1.00 4.17 C ATOM 72 C ILE C 11 32.165 25.800 29.101 1.00 4.30 C ATOM 73 O ILE C 11 31.964 26.636 28.216 1.00 4.57 O ATOM 74 CB ILE C 11 31.217 23.481 28.900 1.00 4.26 C ATOM 75 CG1 ILE C 11 31.325 22.234 28.021 1.00 4.74 C ATOM 76 CG2 ILE C 11 29.969 24.260 28.518 1.00 5.09 C ATOM 77 CD1 ILE C 11 30.158 21.281 28.165 1.00 5.63 C ATOM 78 N GLU C 12 32.173 26.097 30.396 1.00 5.14 N ATOM 79 CA GLU C 12 31.933 27.453 30.866 1.00 6.72 C ATOM 80 C GLU C 12 33.067 28.362 30.404 1.00 5.62 C ATOM 81 O GLU C 12 32.845 29.523 30.048 1.00 6.01 O ATOM 82 CB GLU C 12 31.800 27.481 32.392 1.00 8.41 C ATOM 83 CG GLU C 12 31.326 28.810 32.968 1.00 10.55 C ATOM 84 CD GLU C 12 32.457 29.796 33.193 1.00 11.85 C ATOM 85 OE1 GLU C 12 33.623 29.358 33.274 1.00 13.15 O ATOM 86 OE2 GLU C 12 32.178 31.010 33.290 1.00 11.88 O ATOM 87 N SER C 13 34.281 27.822 30.391 1.00 5.36 N ATOM 88 CA SER C 13 35.443 28.605 29.996 0.48 5.54 C ATOM 89 C SER C 13 35.431 28.984 28.515 1.00 4.98 C ATOM 90 O SER C 13 35.623 30.158 28.175 1.00 5.24 O ATOM 91 CB SER C 13 36.728 27.839 30.320 0.48 7.24 C ATOM 92 OG SER C 13 37.874 28.579 29.935 0.48 8.58 O ATOM 93 N PHE C 14 35.187 28.019 27.630 1.00 4.22 N ATOM 94 CA PHE C 14 35.185 28.362 26.211 1.00 4.26 C ATOM 95 C PHE C 14 33.912 29.116 25.824 1.00 3.83 C ATOM 96 O PHE C 14 33.946 29.930 24.905 1.00 4.21 O ATOM 97 CB PHE C 14 35.434 27.135 25.298 1.00 4.34 C ATOM 98 CG PHE C 14 34.346 26.085 25.291 1.00 4.32 C ATOM 99 CD1 PHE C 14 33.092 26.342 24.758 1.00 5.73 C ATOM 100 CD2 PHE C 14 34.625 24.799 25.721 1.00 4.92 C ATOM 101 CE1 PHE C 14 32.119 25.363 24.729 1.00 6.75 C ATOM 102 CE2 PHE C 14 33.661 23.811 25.681 1.00 5.77 C ATOM 103 CZ PHE C 14 32.404 24.096 25.189 1.00 6.41 C ATOM 104 N ILE C 15 32.795 28.855 26.500 1.00 3.71 N ATOM 105 CA ILE C 15 31.581 29.610 26.195 1.00 3.57 C ATOM 106 C ILE C 15 31.766 31.066 26.631 1.00 3.45 C ATOM 107 O ILE C 15 31.252 31.976 25.984 1.00 3.86 O ATOM 108 CB ILE C 15 30.304 29.004 26.847 1.00 4.42 C ATOM 109 CG1 ILE C 15 29.046 29.556 26.174 1.00 5.07 C ATOM 110 CG2 ILE C 15 30.234 29.286 28.335 1.00 5.27 C ATOM 111 CD1 ILE C 15 28.921 29.196 24.717 1.00 5.89 C ATOM 112 N HIS C 16 32.500 31.286 27.721 0.73 3.71 N ATOM 113 CA HIS C 16 32.766 32.646 28.182 0.73 3.79 C ATOM 114 C HIS C 16 33.758 33.374 27.274 0.73 3.39 C ATOM 115 O HIS C 16 33.541 34.536 26.904 0.73 3.85 O ATOM 116 CB HIS C 16 33.292 32.632 29.619 0.73 4.49 C ATOM 117 CG HIS C 16 33.579 33.994 30.170 0.73 5.87 C ATOM 118 ND1 HIS C 16 32.610 34.965 30.298 0.73 8.05 N ATOM 119 CD2 HIS C 16 34.728 34.546 30.627 0.73 5.56 C ATOM 120 CE1 HIS C 16 33.148 36.057 30.810 0.73 7.55 C ATOM 121 NE2 HIS C 16 34.432 35.830 31.019 0.73 6.08 N ATOM 122 N GLN C 17 34.833 32.685 26.896 0.73 3.40 N ATOM 123 CA GLN C 17 35.849 33.300 26.046 0.73 3.79 C ATOM 124 C GLN C 17 35.277 33.576 24.658 0.73 3.29 C ATOM 125 O GLN C 17 35.638 34.562 24.017 0.73 3.69 O ATOM 126 CB GLN C 17 37.107 32.426 25.957 0.73 4.26 C ATOM 127 CG GLN C 17 36.981 31.185 25.093 0.73 5.23 C ATOM 128 CD GLN C 17 38.258 30.368 25.057 0.73 7.38 C ATOM 129 OE1 GLN C 17 39.173 30.590 25.850 0.73 8.36 O ATOM 130 NE2 GLN C 17 38.326 29.416 24.133 0.73 9.04 N ATOM 131 N ALA C 18 34.390 32.700 24.196 1.00 3.36 N ATOM 132 CA ALA C 18 33.704 32.907 22.928 1.00 3.89 C ATOM 133 C ALA C 18 32.711 34.051 23.063 1.00 4.05 C ATOM 134 O ALA C 18 32.548 34.852 22.145 1.00 4.91 O ATOM 135 CB ALA C 18 33.001 31.643 22.480 1.00 4.53 C ATOM 136 N LYS C 19 32.068 34.137 24.225 1.00 4.37 N ATOM 137 CA LYS C 19 31.101 35.195 24.484 1.00 5.39 C ATOM 138 C LYS C 19 31.805 36.537 24.378 1.00 5.25 C ATOM 139 O LYS C 19 31.232 37.516 23.899 1.00 5.52 O ATOM 140 CB LYS C 19 30.456 35.032 25.862 1.00 6.50 C ATOM 141 CG LYS C 19 29.397 36.074 26.182 1.00 7.77 C ATOM 142 CD LYS C 19 28.842 35.886 27.585 1.00 10.16 C ATOM 143 CE LYS C 19 28.157 34.536 27.730 1.00 12.49 C ATOM 144 NZ LYS C 19 27.618 34.333 29.103 1.00 15.57 N ATOM 145 N ALA C 20 33.054 36.577 24.827 1.00 5.38 N ATOM 146 CA ALA C 20 33.869 37.769 24.640 1.00 5.88 C ATOM 147 C ALA C 20 34.255 37.929 23.167 1.00 5.38 C ATOM 148 O ALA C 20 34.229 39.034 22.626 1.00 6.73 O ATOM 149 CB ALA C 20 35.111 37.708 25.514 1.00 6.65 C ATOM 150 N ALA C 21 34.611 36.817 22.526 1.00 4.87 N ATOM 151 CA ALA C 21 35.030 36.822 21.124 1.00 5.54 C ATOM 152 C ALA C 21 33.874 36.868 20.120 1.00 4.89 C ATOM 153 O ALA C 21 33.628 37.898 19.493 1.00 5.59 O ATOM 154 CB ALA C 21 35.904 35.606 20.846 1.00 6.30 C ATOM 155 N GLY C 22 33.169 35.747 19.974 1.00 4.70 N ATOM 156 CA GLY C 22 32.123 35.622 18.971 1.00 4.84 C ATOM 157 C GLY C 22 31.060 34.606 19.349 1.00 4.56 C ATOM 158 O GLY C 22 31.318 33.683 20.120 1.00 5.92 O ATOM 159 N ARG C 23 29.869 34.747 18.777 1.00 4.30 N ATOM 160 CA ARG C 23 28.710 34.023 19.289 1.00 4.97 C ATOM 161 C ARG C 23 28.116 32.970 18.352 1.00 5.19 C ATOM 162 O ARG C 23 28.051 31.798 18.708 1.00 5.70 O ATOM 163 CB ARG C 23 27.613 35.021 19.669 1.00 5.52 C ATOM 164 CG ARG C 23 26.401 34.386 20.333 1.00 6.50 C ATOM 165 CD ARG C 23 25.368 35.434 20.715 1.00 7.51 C ATOM 166 NE ARG C 23 24.219 34.845 21.397 1.00 8.98 N ATOM 167 CZ ARG C 23 24.140 34.672 22.713 1.00 10.56 C ATOM 168 NH1 ARG C 23 23.055 34.128 23.248 1.00 10.81 N ATOM 169 NH2 ARG C 23 25.145 35.043 23.494 1.00 11.93 N ATOM 170 N MET C 24 27.705 33.380 17.156 0.69 5.87 seg N ATOM 171 CA MET C 24 26.942 32.498 16.270 0.69 7.12 seg C ATOM 172 C MET C 24 27.678 31.243 15.787 0.69 6.14 seg C ATOM 173 O MET C 24 27.095 30.156 15.762 0.69 5.80 seg O ATOM 174 CB MET C 24 26.452 33.294 15.055 0.69 9.83 seg C ATOM 175 CG MET C 24 27.541 34.062 14.321 0.69 13.17 seg C ATOM 176 SD MET C 24 26.891 35.077 12.980 0.69 13.65 seg S ATOM 177 CE MET C 24 25.967 36.304 13.900 0.69 13.09 seg C ATOM 178 N ASP C 25 28.948 31.378 15.421 1.00 6.26 seg N ATOM 179 CA ASP C 25 29.705 30.234 14.921 1.00 6.70 seg C ATOM 180 C ASP C 25 29.990 29.217 16.025 1.00 5.34 seg C ATOM 181 O ASP C 25 29.846 28.007 15.825 1.00 5.81 seg O ATOM 182 CB ASP C 25 31.016 30.700 14.281 1.00 9.38 seg C ATOM 183 CG ASP C 25 31.838 31.577 15.205 1.00 13.52 seg C ATOM 184 OD1 ASP C 25 31.266 32.128 16.169 1.00 14.07 seg O ATOM 185 OD2 ASP C 25 33.057 31.716 14.967 1.00 17.20 seg O ATOM 186 N GLU C 26 30.369 29.718 17.195 0.67 4.76 seg N ATOM 187 CA GLU C 26 30.676 28.861 18.332 0.67 4.83 seg C ATOM 188 C GLU C 26 29.412 28.186 18.854 0.67 4.62 seg C ATOM 189 O GLU C 26 29.442 27.026 19.263 0.67 4.93 seg O ATOM 190 CB GLU C 26 31.358 29.666 19.440 0.67 5.41 seg C ATOM 191 CG GLU C 26 31.896 28.827 20.587 0.67 6.20 seg C ATOM 192 CD GLU C 26 30.908 28.695 21.727 0.67 7.05 seg C ATOM 193 OE1 GLU C 26 29.820 29.303 21.645 0.67 7.13 seg O ATOM 194 OE2 GLU C 26 31.224 27.991 22.709 0.67 8.43 seg O ATOM 195 N VAL C 27 28.304 28.920 18.836 1.00 4.54 seg N ATOM 196 CA VAL C 27 27.020 28.373 19.257 1.00 5.02 seg C ATOM 197 C VAL C 27 26.564 27.299 18.274 1.00 4.94 seg C ATOM 198 O VAL C 27 26.014 26.277 18.678 1.00 5.05 seg O ATOM 199 CB VAL C 27 25.941 29.477 19.381 1.00 5.29 seg C ATOM 200 CG1 VAL C 27 26.139 30.263 20.668 1.00 5.41 seg C ATOM 201 CG2 VAL C 27 24.541 28.882 19.346 1.00 6.00 seg C ATOM 202 N ARG C 28 26.816 27.519 16.987 1.00 5.20 seg N ATOM 203 CA ARG C 28 26.446 26.537 15.971 1.00 5.54 seg C ATOM 204 C ARG C 28 27.274 25.259 16.109 1.00 4.76 seg C ATOM 205 O ARG C 28 26.742 24.146 16.012 1.00 5.46 seg O ATOM 206 CB ARG C 28 26.617 27.126 14.569 1.00 6.82 seg C ATOM 207 CG ARG C 28 26.209 26.187 13.446 1.00 9.78 seg C ATOM 208 CD ARG C 28 26.389 26.843 12.087 1.00 13.05 seg C ATOM 209 NE ARG C 28 25.989 25.959 10.996 1.00 17.58 seg N ATOM 210 CZ ARG C 28 26.803 25.098 10.395 1.00 20.46 seg C ATOM 211 NH1 ARG C 28 26.353 24.333 9.410 1.00 20.45 seg N ATOM 212 NH2 ARG C 28 28.069 25.001 10.778 1.00 21.92 seg N ATOM 213 N THR C 29 28.570 25.421 16.364 1.00 4.62 seg N ATOM 214 CA THR C 29 29.451 24.272 16.550 1.00 5.38 seg C ATOM 215 C THR C 29 29.069 23.516 17.817 1.00 4.39 seg C ATOM 216 O THR C 29 29.128 22.286 17.862 1.00 5.02 seg O ATOM 217 CB THR C 29 30.932 24.687 16.629 1.00 7.77 seg C ATOM 218 OG1 THR C 29 31.098 25.687 17.643 1.00 9.68 seg O ATOM 219 CG2 THR C 29 31.405 25.239 15.293 1.00 8.93 seg C ATOM 220 N LEU C 30 28.673 24.262 18.843 1.00 4.10 seg N ATOM 221 CA LEU C 30 28.225 23.668 20.095 1.00 4.03 seg C ATOM 222 C LEU C 30 26.920 22.911 19.897 1.00 4.40 seg C ATOM 223 O LEU C 30 26.685 21.894 20.540 1.00 4.33 seg O ATOM 224 CB LEU C 30 28.056 24.737 21.175 1.00 4.41 seg C ATOM 225 CG LEU C 30 29.156 24.767 22.237 1.00 5.82 seg C ATOM 226 CD1 LEU C 30 30.514 25.010 21.597 1.00 7.43 seg C ATOM 227 CD2 LEU C 30 28.853 25.816 23.293 1.00 7.81 seg C ATOM 228 N GLN C 31 26.067 23.421 19.015 1.00 4.65 seg N ATOM 229 CA GLN C 31 24.813 22.752 18.697 1.00 5.33 seg C ATOM 230 C GLN C 31 25.085 21.453 17.952 1.00 5.02 seg C ATOM 231 O GLN C 31 24.417 20.445 18.186 1.00 5.56 seg O ATOM 232 CB GLN C 31 23.902 23.660 17.868 1.00 6.58 seg C ATOM 233 CG GLN C 31 23.231 24.766 18.667 1.00 9.50 seg C ATOM 234 CD GLN C 31 22.343 25.647 17.810 1.00 12.70 seg C ATOM 235 OE1 GLN C 31 22.452 25.652 16.584 1.00 14.44 seg O ATOM 236 NE2 GLN C 31 21.458 26.399 18.454 1.00 13.69 seg N ATOM 237 N GLU C 32 26.072 21.475 17.061 1.00 5.72 seg N ATOM 238 CA GLU C 32 26.439 20.268 16.326 1.00 6.90 seg C ATOM 239 C GLU C 32 27.043 19.221 17.261 1.00 5.82 seg C ATOM 240 O GLU C 32 26.741 18.028 17.155 1.00 6.63 seg O ATOM 241 CB GLU C 32 27.420 20.600 15.200 1.00 10.01 seg C ATOM 242 CG GLU C 32 26.842 21.491 14.114 1.00 16.02 seg C ATOM 243 CD GLU C 32 27.844 21.802 13.019 1.00 22.44 seg C ATOM 244 OE1 GLU C 32 29.028 21.435 13.174 1.00 25.00 seg O ATOM 245 OE2 GLU C 32 27.448 22.413 12.005 1.00 24.85 seg O ATOM 246 N ASN C 33 27.880 19.678 18.188 1.00 5.36 seg N ATOM 247 CA ASN C 33 28.513 18.787 19.154 1.00 5.56 seg C ATOM 248 C ASN C 33 27.501 18.199 20.132 1.00 5.07 seg C ATOM 249 O ASN C 33 27.587 17.029 20.503 1.00 6.19 seg O ATOM 250 CB ASN C 33 29.613 19.524 19.921 1.00 6.47 seg C ATOM 251 CG ASN C 33 30.768 19.936 19.030 1.00 8.34 seg C ATOM 252 OD1 ASN C 33 31.035 19.304 18.008 1.00 11.36 seg O ATOM 253 ND2 ASN C 33 31.461 21.002 19.415 1.00 8.04 seg N ATOM 254 N LEU C 34 26.543 19.020 20.547 1.00 4.51 seg N ATOM 255 CA LEU C 34 25.489 18.576 21.449 1.00 4.72 seg C ATOM 256 C LEU C 34 24.557 17.597 20.749 1.00 4.80 seg C ATOM 257 O LEU C 34 24.075 16.645 21.360 1.00 4.90 seg O ATOM 258 CB LEU C 34 24.696 19.769 21.988 1.00 4.81 seg C ATOM 259 CG LEU C 34 25.051 20.247 23.398 1.00 4.99 seg C ATOM 260 CD1 LEU C 34 26.525 20.610 23.505 1.00 5.66 seg C ATOM 261 CD2 LEU C 34 24.175 21.425 23.799 1.00 6.50 seg C ATOM 262 N HIS C 35 24.299 17.838 19.467 1.00 5.03 seg N ATOM 263 CA HIS C 35 23.442 16.949 18.691 1.00 5.85 seg C ATOM 264 C HIS C 35 24.105 15.596 18.443 1.00 5.91 seg C ATOM 265 O HIS C 35 23.460 14.554 18.568 1.00 6.51 seg O ATOM 266 CB HIS C 35 23.061 17.597 17.357 1.00 7.35 seg C ATOM 267 CG HIS C 35 21.980 18.626 17.472 1.00 10.07 seg C ATOM 268 ND1 HIS C 35 22.198 19.880 18.001 1.00 13.24 seg N ATOM 269 CD2 HIS C 35 20.672 18.587 17.125 1.00 10.94 seg C ATOM 270 CE1 HIS C 35 21.071 20.569 17.975 1.00 14.19 seg C ATOM 271 NE2 HIS C 35 20.130 19.807 17.449 1.00 13.06 seg N ATOM 272 N GLN C 36 25.393 15.607 18.107 1.00 5.86 seg N ATOM 273 CA GLN C 36 26.105 14.353 17.876 1.00 7.12 seg C ATOM 274 C GLN C 36 26.292 13.595 19.191 1.00 5.57 seg C ATOM 275 O GLN C 36 26.231 12.363 19.218 1.00 6.15 seg O ATOM 276 CB GLN C 36 27.454 14.599 17.187 1.00 10.81 seg C ATOM 277 CG GLN C 36 28.480 15.354 18.009 1.00 15.82 seg C ATOM 278 CD GLN C 36 29.782 15.569 17.262 1.00 20.43 seg C ATOM 279 OE1 GLN C 36 29.786 16.007 16.112 1.00 21.72 seg O ATOM 280 NE2 GLN C 36 30.896 15.259 17.915 1.00 22.23 seg N ATOM 281 N LEU C 37 26.508 14.332 20.278 1.00 4.79 seg N ATOM 282 CA LEU C 37 26.654 13.725 21.597 1.00 5.02 seg C ATOM 283 C LEU C 37 25.338 13.101 22.046 1.00 4.81 seg C ATOM 284 O LEU C 37 25.320 12.023 22.640 1.00 5.11 seg O ATOM 285 CB LEU C 37 27.123 14.760 22.622 1.00 5.48 seg C ATOM 286 CG LEU C 37 27.185 14.318 24.086 1.00 7.48 seg C ATOM 287 CD1 LEU C 37 28.176 13.180 24.270 1.00 8.34 seg C ATOM 288 CD2 LEU C 37 27.539 15.492 24.986 1.00 9.38 seg C ATOM 289 N MET C 38 24.237 13.784 21.751 1.00 5.10 seg N ATOM 290 CA MET C 38 22.913 13.286 22.098 0.60 5.87 seg C ATOM 291 C MET C 38 22.569 12.054 21.271 1.00 5.55 seg C ATOM 292 O MET C 38 21.963 11.108 21.775 1.00 5.83 seg O ATOM 293 CB MET C 38 21.856 14.374 21.892 0.60 7.11 seg C ATOM 294 CG MET C 38 20.443 13.946 22.255 0.60 8.46 seg C ATOM 295 SD MET C 38 19.234 15.263 22.019 0.60 10.21 seg S ATOM 296 CE MET C 38 19.348 15.514 20.249 0.60 11.26 seg C ATOM 297 N HIS C 39 22.962 12.067 20.001 1.00 5.90 seg N ATOM 298 CA HIS C 39 22.700 10.937 19.117 1.00 6.60 seg C ATOM 299 C HIS C 39 23.515 9.706 19.503 1.00 6.76 seg C ATOM 300 O HIS C 39 22.995 8.589 19.502 1.00 7.35 seg O ATOM 301 CB HIS C 39 22.987 11.318 17.663 1.00 7.90 seg C ATOM 302 CG HIS C 39 21.937 12.189 17.047 1.00 9.99 seg C ATOM 303 ND1 HIS C 39 21.807 13.527 17.349 1.00 11.79 seg N ATOM 304 CD2 HIS C 39 20.966 11.912 16.144 1.00 10.09 seg C ATOM 305 CE1 HIS C 39 20.802 14.037 16.660 1.00 11.60 seg C ATOM 306 NE2 HIS C 39 20.275 13.078 15.921 1.00 10.84 seg N ATOM 307 N GLU C 40 24.787 9.905 19.838 1.00 6.24 seg N ATOM 308 CA GLU C 40 25.634 8.786 20.240 1.00 7.45 seg C ATOM 309 C GLU C 40 25.229 8.261 21.617 1.00 6.69 seg C ATOM 310 O GLU C 40 25.306 7.060 21.874 1.00 7.99 seg O ATOM 311 CB GLU C 40 27.117 9.177 20.221 1.00 8.91 seg C ATOM 312 CG GLU C 40 27.533 10.220 21.241 1.00 12.58 seg C ATOM 313 CD GLU C 40 29.006 10.566 21.145 1.00 17.22 seg C ATOM 314 OE1 GLU C 40 29.755 9.803 20.500 1.00 19.50 seg O ATOM 315 OE2 GLU C 40 29.414 11.601 21.712 1.00 19.12 seg O ATOM 316 N TYR C 41 24.800 9.160 22.499 1.00 6.31 seg N ATOM 317 CA TYR C 41 24.342 8.761 23.827 1.00 6.52 seg C ATOM 318 C TYR C 41 23.036 7.980 23.732 1.00 6.93 seg C ATOM 319 O TYR C 41 22.826 7.011 24.461 1.00 7.89 seg O ATOM 320 CB TYR C 41 24.164 9.982 24.731 1.00 6.84 seg C ATOM 321 CG TYR C 41 23.671 9.653 26.123 1.00 7.08 seg C ATOM 322 CD1 TYR C 41 24.546 9.195 27.100 1.00 8.09 seg C ATOM 323 CD2 TYR C 41 22.333 9.805 26.462 1.00 8.31 seg C ATOM 324 CE1 TYR C 41 24.102 8.894 28.373 1.00 8.88 seg C ATOM 325 CE2 TYR C 41 21.879 9.506 27.733 1.00 8.84 seg C ATOM 326 CZ TYR C 41 22.768 9.051 28.684 1.00 9.01 seg C ATOM 327 OH TYR C 41 22.321 8.753 29.951 1.00 9.91 seg O ATOM 328 N PHE C 42 22.160 8.412 22.829 1.00 7.44 seg N ATOM 329 CA PHE C 42 20.888 7.733 22.609 1.00 9.29 seg C ATOM 330 C PHE C 42 21.110 6.371 21.963 1.00 11.50 seg C ATOM 331 O PHE C 42 20.420 5.402 22.282 1.00 13.50 seg O ATOM 332 CB PHE C 42 19.964 8.589 21.740 1.00 9.49 seg C ATOM 333 CG PHE C 42 18.635 7.948 21.453 1.00 9.99 seg C ATOM 334 CD1 PHE C 42 17.617 7.983 22.392 1.00 11.43 seg C ATOM 335 CD2 PHE C 42 18.400 7.318 20.241 1.00 10.35 seg C ATOM 336 CE1 PHE C 42 16.393 7.397 22.131 1.00 11.84 seg C ATOM 337 CE2 PHE C 42 17.178 6.730 19.974 1.00 11.43 seg C ATOM 338 CZ PHE C 42 16.174 6.770 20.921 1.00 12.29 seg C ATOM 339 N GLN C 43 22.076 6.305 21.052 1.00 11.97 seg N ATOM 340 CA GLN C 43 22.408 5.056 20.376 1.00 13.21 seg C ATOM 341 C GLN C 43 23.035 4.058 21.345 1.00 16.37 seg C ATOM 342 O GLN C 43 22.759 2.860 21.283 1.00 17.39 seg O ATOM 343 CB GLN C 43 23.353 5.318 19.202 1.00 11.79 seg C ATOM 344 CG GLN C 43 23.738 4.071 18.421 1.00 11.86 seg C ATOM 345 CD GLN C 43 24.676 4.372 17.268 1.00 12.53 seg C ATOM 346 OE1 GLN C 43 24.443 5.296 16.489 1.00 14.19 seg O ATOM 347 NE2 GLN C 43 25.744 3.592 17.155 1.00 13.65 seg N ATOM 348 N GLN C 44 23.879 4.562 22.241 1.00 19.32 seg N ATOM 349 CA GLN C 44 24.531 3.721 23.238 1.00 22.77 seg C ATOM 350 C GLN C 44 23.530 3.198 24.263 1.00 25.16 seg C ATOM 351 O GLN C 44 23.747 2.157 24.882 1.00 27.03 seg O ATOM 352 CB GLN C 44 25.648 4.493 23.942 1.00 23.69 seg C TER """ rna_pdb_str = """ ATOM 1 C5' DG A 1 -3.978 -5.685 17.586 1.00 10.33 C ATOM 2 C4' DG A 1 -3.637 -6.940 16.870 1.00 7.67 C ATOM 3 O4' DG A 1 -4.730 -7.294 15.970 1.00 7.90 O ATOM 4 C3' DG A 1 -2.415 -6.913 15.950 1.00 7.02 C ATOM 5 O3' DG A 1 -1.253 -7.199 16.735 1.00 7.48 O ATOM 6 C2' DG A 1 -2.743 -7.953 14.919 1.00 6.34 C ATOM 7 C1' DG A 1 -4.181 -7.833 14.764 1.00 7.13 C ATOM 8 N9 DG A 1 -4.669 -6.929 13.664 1.00 7.10 N ATOM 9 C8 DG A 1 -5.410 -5.780 13.735 1.00 8.55 C ATOM 10 N7 DG A 1 -5.682 -5.281 12.554 1.00 8.50 N ATOM 11 C5 DG A 1 -5.105 -6.154 11.649 1.00 6.84 C ATOM 12 C6 DG A 1 -5.074 -6.171 10.236 1.00 7.07 C ATOM 13 O6 DG A 1 -5.560 -5.361 9.442 1.00 8.18 O ATOM 14 N1 DG A 1 -4.385 -7.274 9.738 1.00 6.07 N ATOM 15 C2 DG A 1 -3.792 -8.250 10.486 1.00 5.88 C ATOM 16 N2 DG A 1 -3.158 -9.232 9.863 1.00 6.30 N ATOM 17 N3 DG A 1 -3.814 -8.251 11.818 1.00 6.14 N ATOM 18 C4 DG A 1 -4.475 -7.184 12.328 1.00 6.40 C ATOM 19 O5' DG A 1 -4.129 -4.616 16.670 1.00 13.23 O ATOM 20 P DC A 2 0.159 -6.607 16.354 1.00 7.17 P ATOM 21 OP1 DC A 2 1.032 -7.098 17.438 1.00 9.49 O ATOM 22 OP2 DC A 2 0.079 -5.157 16.084 1.00 8.19 O ATOM 23 O5' DC A 2 0.540 -7.259 14.978 1.00 6.67 O ATOM 24 C5' DC A 2 0.845 -8.687 14.933 1.00 6.21 C ATOM 25 C4' DC A 2 1.061 -9.042 13.480 1.00 5.85 C ATOM 26 O4' DC A 2 -0.171 -8.807 12.756 1.00 5.64 O ATOM 27 C3' DC A 2 2.080 -8.258 12.694 1.00 5.87 C ATOM 28 O3' DC A 2 3.384 -8.830 12.944 1.00 6.20 O ATOM 29 C2' DC A 2 1.621 -8.416 11.264 1.00 5.92 C ATOM 30 C1' DC A 2 0.149 -8.416 11.402 1.00 5.36 C ATOM 31 N1 DC A 2 -0.536 -7.095 11.175 1.00 5.25 N ATOM 32 C2 DC A 2 -0.789 -6.771 9.851 1.00 5.43 C ATOM 33 O2 DC A 2 -0.402 -7.525 8.959 1.00 5.62 O ATOM 34 N3 DC A 2 -1.483 -5.633 9.585 1.00 5.07 N ATOM 35 C4 DC A 2 -1.832 -4.811 10.582 1.00 5.35 C ATOM 36 N4 DC A 2 -2.459 -3.681 10.271 1.00 6.32 N ATOM 37 C5 DC A 2 -1.489 -5.072 11.930 1.00 6.06 C ATOM 38 C6 DC A 2 -0.863 -6.228 12.175 1.00 5.82 C ATOM 39 P DG A 3 4.694 -7.979 12.612 1.00 6.44 P ATOM 40 OP1 DG A 3 5.824 -8.863 12.983 1.00 8.30 O ATOM 41 OP2 DG A 3 4.632 -6.627 13.229 1.00 7.47 O ATOM 42 O5' DG A 3 4.565 -7.883 11.033 1.00 6.85 O ATOM 43 C5' DG A 3 5.087 -6.782 10.277 1.00 6.15 C ATOM 44 C4' DG A 3 4.628 -6.912 8.863 1.00 5.98 C ATOM 45 O4' DG A 3 3.198 -6.768 8.835 1.00 6.93 O ATOM 46 C3' DG A 3 5.140 -5.841 7.909 1.00 6.17 C ATOM 47 O3' DG A 3 6.438 -6.239 7.429 1.00 6.98 O ATOM 48 C2' DG A 3 4.093 -5.795 6.848 1.00 6.25 C ATOM 49 C1' DG A 3 2.922 -6.068 7.584 1.00 7.07 C ATOM 50 N9 DG A 3 2.090 -4.883 8.068 1.00 5.57 N ATOM 51 C8 DG A 3 1.731 -4.500 9.337 1.00 6.21 C ATOM 52 N7 DG A 3 0.978 -3.447 9.375 1.00 5.89 N ATOM 53 C5 DG A 3 0.800 -3.101 8.043 1.00 5.50 C ATOM 54 C6 DG A 3 0.052 -2.059 7.446 1.00 5.33 C ATOM 55 O6 DG A 3 -0.613 -1.177 8.002 1.00 6.41 O ATOM 56 N1 DG A 3 0.162 -2.064 6.056 1.00 5.28 N ATOM 57 C2 DG A 3 0.904 -2.968 5.338 1.00 5.04 C ATOM 58 N2 DG A 3 0.882 -2.763 4.024 1.00 5.53 N ATOM 59 N3 DG A 3 1.579 -3.967 5.878 1.00 5.25 N ATOM 60 C4 DG A 3 1.481 -3.975 7.228 1.00 5.17 C ATOM 61 P DT A 4 7.494 -5.119 7.002 1.00 6.95 P ATOM 62 OP1 DT A 4 8.729 -5.879 6.636 1.00 8.83 O ATOM 63 OP2 DT A 4 7.560 -4.065 8.008 1.00 8.54 O ATOM 64 O5' DT A 4 6.867 -4.454 5.706 1.00 6.35 O ATOM 65 C5' DT A 4 6.991 -5.019 4.402 1.00 6.40 C ATOM 66 C4' DT A 4 6.569 -3.963 3.385 1.00 6.14 C ATOM 67 O4' DT A 4 5.172 -3.691 3.509 1.00 5.85 O ATOM 68 C3' DT A 4 7.260 -2.609 3.531 1.00 5.96 C ATOM 69 O3' DT A 4 8.570 -2.657 2.955 1.00 7.00 O ATOM 70 C2' DT A 4 6.281 -1.694 2.834 1.00 5.83 C ATOM 71 C1' DT A 4 4.995 -2.269 3.199 1.00 5.50 C ATOM 72 N1 DT A 4 4.319 -1.695 4.408 1.00 4.88 N ATOM 73 C2 DT A 4 3.479 -0.614 4.203 1.00 4.89 C ATOM 74 O2 DT A 4 3.238 -0.157 3.100 1.00 5.46 O ATOM 75 N3 DT A 4 2.870 -0.136 5.336 1.00 4.98 N ATOM 76 C4 DT A 4 3.060 -0.549 6.631 1.00 5.07 C ATOM 77 O4 DT A 4 2.451 -0.030 7.571 1.00 5.20 O ATOM 78 C5 DT A 4 4.052 -1.592 6.790 1.00 5.28 C ATOM 79 C7 DT A 4 4.391 -2.043 8.172 1.00 5.73 C ATOM 80 C6 DT A 4 4.601 -2.115 5.688 1.00 4.94 C ATOM 81 P DA A 5 9.713 -1.721 3.558 1.00 7.31 P ATOM 82 OP1 DA A 5 10.936 -2.057 2.755 1.00 10.22 O ATOM 83 OP2 DA A 5 9.792 -1.797 5.019 1.00 8.84 O ATOM 84 O5' DA A 5 9.202 -0.284 3.122 1.00 6.72 O ATOM 85 C5' DA A 5 9.353 0.848 3.965 1.00 7.16 C ATOM 86 C4' DA A 5 8.507 1.956 3.432 1.00 6.26 C ATOM 87 O4' DA A 5 7.101 1.592 3.512 1.00 6.16 O ATOM 88 C3' DA A 5 8.616 3.260 4.198 1.00 6.67 C ATOM 89 O3' DA A 5 9.773 3.987 3.773 1.00 8.06 O ATOM 90 C2' DA A 5 7.309 3.930 3.859 1.00 6.69 C ATOM 91 C1' DA A 5 6.348 2.752 3.827 1.00 5.98 C ATOM 92 N9 DA A 5 5.704 2.499 5.127 1.00 5.34 N ATOM 93 C8 DA A 5 5.954 1.516 6.040 1.00 5.75 C ATOM 94 N7 DA A 5 5.193 1.582 7.116 1.00 5.44 N ATOM 95 C5 DA A 5 4.395 2.695 6.888 1.00 5.38 C ATOM 96 C6 DA A 5 3.346 3.282 7.618 1.00 5.28 C ATOM 97 N6 DA A 5 2.951 2.826 8.808 1.00 5.35 N ATOM 98 N1 DA A 5 2.743 4.365 7.111 1.00 5.45 N ATOM 99 C2 DA A 5 3.146 4.832 5.915 1.00 5.47 C ATOM 100 N3 DA A 5 4.105 4.372 5.121 1.00 5.80 N ATOM 101 C4 DA A 5 4.691 3.277 5.672 1.00 5.05 C ATOM 102 P DA A 7 10.361 9.907 7.735 1.00 7.99 seg P ATOM 103 OP1 DA A 7 11.390 11.000 7.496 1.00 10.78 seg O ATOM 104 OP2 DA A 7 10.815 8.642 8.293 1.00 9.63 seg O ATOM 105 N9 DA A 7 6.334 9.455 11.116 1.00 5.65 seg N ATOM 106 C8 DA A 7 7.224 8.572 10.573 1.00 6.17 seg C ATOM 107 N7 DA A 7 7.120 7.360 11.049 1.00 6.56 seg N ATOM 108 C5 DA A 7 6.093 7.459 11.988 1.00 5.71 seg C ATOM 109 C6 DA A 7 5.502 6.522 12.853 1.00 6.10 seg C ATOM 110 N6 DA A 7 5.857 5.242 12.917 1.00 7.10 seg N ATOM 111 N1 DA A 7 4.527 6.967 13.680 1.00 6.05 seg N ATOM 112 C2 DA A 7 4.148 8.245 13.617 1.00 6.15 seg C ATOM 113 N3 DA A 7 4.623 9.210 12.837 1.00 6.29 seg N ATOM 114 C4 DA A 7 5.590 8.748 12.022 1.00 5.70 seg C ATOM 115 O5' DA A 7 9.260 10.485 8.777 1.00 6.82 seg O ATOM 116 C5' DA A 7 8.750 11.813 8.635 1.00 7.00 seg C ATOM 117 C4' DA A 7 7.804 12.093 9.780 1.00 6.45 seg C ATOM 118 O4' DA A 7 6.598 11.282 9.642 1.00 4.73 seg O ATOM 119 C3' DA A 7 8.274 11.755 11.194 1.00 5.90 seg C ATOM 120 O3' DA A 7 9.154 12.775 11.689 1.00 6.00 seg O ATOM 121 C2' DA A 7 6.975 11.670 11.899 1.00 4.64 seg C ATOM 122 C1' DA A 7 6.132 10.895 10.898 1.00 5.64 seg C ATOM 123 N1 DC A 8 6.735 9.699 15.920 1.00 5.92 seg N ATOM 124 C2 DC A 8 6.159 8.694 16.692 1.00 6.04 seg C ATOM 125 O2 DC A 8 5.281 9.024 17.522 1.00 6.66 seg O ATOM 126 N3 DC A 8 6.569 7.420 16.535 1.00 6.40 seg N ATOM 127 C4 DC A 8 7.504 7.119 15.618 1.00 6.85 seg C ATOM 128 N4 DC A 8 7.874 5.856 15.500 1.00 8.97 seg N ATOM 129 C5 DC A 8 8.129 8.134 14.832 1.00 7.62 seg C ATOM 130 C6 DC A 8 7.715 9.401 15.007 1.00 6.89 seg C ATOM 131 P DC A 8 10.149 12.560 12.869 1.00 7.33 seg P ATOM 132 OP1 DC A 8 10.964 13.795 12.977 1.00 11.24 seg O ATOM 133 OP2 DC A 8 10.865 11.262 12.719 1.00 11.23 seg O ATOM 134 O5' DC A 8 9.256 12.419 14.149 1.00 5.64 seg O ATOM 135 C5' DC A 8 8.458 13.523 14.600 1.00 7.95 seg C ATOM 136 C4' DC A 8 7.513 13.014 15.672 1.00 5.78 seg C ATOM 137 O4' DC A 8 6.736 11.895 15.132 1.00 5.71 seg O ATOM 138 C3' DC A 8 8.072 12.394 16.940 1.00 5.19 seg C ATOM 139 O3' DC A 8 8.587 13.377 17.832 1.00 5.00 seg O ATOM 140 C2' DC A 8 6.847 11.654 17.449 1.00 5.70 seg C ATOM 141 C1' DC A 8 6.269 11.067 16.181 1.00 6.41 seg C ATOM 142 P DG A 9 9.587 13.026 19.037 1.00 6.28 seg P ATOM 143 OP1 DG A 9 9.944 14.347 19.602 1.00 8.07 seg O ATOM 144 OP2 DG A 9 10.654 12.085 18.639 1.00 8.27 seg O ATOM 145 O5' DG A 9 8.717 12.191 20.048 1.00 5.88 seg O ATOM 146 C5' DG A 9 7.723 12.833 20.854 1.00 5.45 seg C ATOM 147 C4' DG A 9 7.145 11.818 21.807 1.00 5.40 seg C ATOM 148 O4' DG A 9 6.435 10.777 21.087 1.00 5.77 seg O ATOM 149 C3' DG A 9 8.142 11.036 22.648 1.00 5.10 seg C ATOM 150 O3' DG A 9 8.612 11.838 23.723 1.00 5.90 seg O ATOM 151 C2' DG A 9 7.300 9.857 23.068 1.00 5.97 seg C ATOM 152 C1' DG A 9 6.619 9.536 21.805 1.00 5.97 seg C ATOM 153 N9 DG A 9 7.390 8.643 20.931 1.00 5.97 seg N ATOM 154 C8 DG A 9 8.074 8.881 19.775 1.00 6.62 seg C ATOM 155 N7 DG A 9 8.647 7.820 19.249 1.00 6.57 seg N ATOM 156 C5 DG A 9 8.308 6.806 20.141 1.00 6.22 seg C ATOM 157 C6 DG A 9 8.620 5.431 20.136 1.00 6.03 seg C ATOM 158 O6 DG A 9 9.297 4.803 19.296 1.00 7.21 seg O ATOM 159 N1 DG A 9 8.101 4.773 21.247 1.00 6.10 seg N ATOM 160 C2 DG A 9 7.365 5.351 22.260 1.00 6.24 seg C ATOM 161 N2 DG A 9 6.948 4.569 23.241 1.00 7.88 seg N ATOM 162 N3 DG A 9 7.051 6.652 22.257 1.00 6.53 seg N ATOM 163 C4 DG A 9 7.539 7.295 21.184 1.00 5.69 seg C ATOM 164 P DC A 10 10.081 11.538 24.300 1.00 5.91 seg P ATOM 165 OP1 DC A 10 10.273 12.645 25.291 1.00 7.27 seg O ATOM 166 OP2 DC A 10 11.063 11.363 23.228 1.00 6.84 seg O ATOM 167 O5' DC A 10 9.953 10.128 25.026 1.00 5.75 seg O ATOM 168 C5' DC A 10 9.077 9.959 26.149 1.00 5.87 seg C ATOM 169 C4' DC A 10 9.188 8.549 26.672 1.00 5.56 seg C ATOM 170 O4' DC A 10 8.708 7.612 25.667 1.00 5.70 seg O ATOM 171 C3' DC A 10 10.580 8.059 27.007 1.00 5.27 seg C ATOM 172 O3' DC A 10 11.010 8.447 28.315 1.00 5.83 seg O ATOM 173 C2' DC A 10 10.422 6.549 26.893 1.00 5.34 seg C ATOM 174 C1' DC A 10 9.436 6.405 25.754 1.00 5.23 seg C ATOM 175 N1 DC A 10 10.113 6.168 24.448 1.00 5.30 seg N ATOM 176 C2 DC A 10 10.514 4.871 24.152 1.00 5.28 seg C ATOM 177 O2 DC A 10 10.283 3.972 25.000 1.00 5.75 seg O ATOM 178 N3 DC A 10 11.131 4.627 22.965 1.00 5.65 seg N ATOM 179 C4 DC A 10 11.395 5.628 22.138 1.00 5.80 seg C ATOM 180 N4 DC A 10 12.034 5.327 21.005 1.00 6.75 seg N ATOM 181 C5 DC A 10 11.029 6.970 22.449 1.00 5.99 seg C ATOM 182 C6 DC A 10 10.394 7.203 23.612 1.00 5.56 seg C TER ATOM 183 O5' DG B 11 12.424 -4.393 18.427 1.00 22.70 seg O ATOM 184 C5' DG B 11 12.380 -5.516 19.282 1.00 14.75 seg C ATOM 185 C4' DG B 11 11.969 -5.112 20.676 1.00 10.42 seg C ATOM 186 O4' DG B 11 12.972 -4.192 21.210 1.00 10.51 seg O ATOM 187 C3' DG B 11 10.649 -4.394 20.782 1.00 8.57 seg C ATOM 188 O3' DG B 11 9.618 -5.363 20.846 1.00 8.69 seg O ATOM 189 C2' DG B 11 10.822 -3.597 22.051 1.00 8.63 seg C ATOM 190 C1' DG B 11 12.236 -3.233 21.980 1.00 9.81 seg C ATOM 191 N9 DG B 11 12.509 -1.902 21.305 1.00 8.66 seg N ATOM 192 C8 DG B 11 13.175 -1.667 20.135 1.00 9.57 seg C ATOM 193 N7 DG B 11 13.255 -0.407 19.824 1.00 9.04 seg N ATOM 194 C5 DG B 11 12.613 0.235 20.869 1.00 7.63 seg C ATOM 195 C6 DG B 11 12.388 1.612 21.119 1.00 7.05 seg C ATOM 196 O6 DG B 11 12.723 2.590 20.419 1.00 7.81 seg O ATOM 197 N1 DG B 11 11.715 1.819 22.317 1.00 6.27 seg N ATOM 198 C2 DG B 11 11.264 0.828 23.159 1.00 6.05 seg C ATOM 199 N2 DG B 11 10.611 1.219 24.248 1.00 5.85 seg N ATOM 200 N3 DG B 11 11.483 -0.457 22.942 1.00 6.55 seg N ATOM 201 C4 DG B 11 12.150 -0.687 21.797 1.00 6.84 seg C ATOM 202 P DC B 12 8.134 -5.009 20.350 1.00 8.13 seg P ATOM 203 OP1 DC B 12 7.367 -6.252 20.459 1.00 10.02 seg O ATOM 204 OP2 DC B 12 8.172 -4.307 19.052 1.00 9.79 seg O ATOM 205 O5' DC B 12 7.564 -3.912 21.389 1.00 8.18 seg O ATOM 206 C5' DC B 12 7.275 -4.296 22.719 1.00 8.00 seg C ATOM 207 C4' DC B 12 6.856 -3.057 23.487 1.00 8.01 seg C ATOM 208 O4' DC B 12 8.006 -2.146 23.615 1.00 7.35 seg O ATOM 209 C3' DC B 12 5.763 -2.208 22.890 1.00 7.04 seg C ATOM 210 O3' DC B 12 4.456 -2.800 23.100 1.00 9.82 seg O ATOM 211 C2' DC B 12 6.019 -0.916 23.630 1.00 6.50 seg C ATOM 212 C1' DC B 12 7.467 -0.808 23.608 1.00 7.35 seg C ATOM 213 N1 DC B 12 8.040 -0.143 22.396 1.00 6.64 seg N ATOM 214 C2 DC B 12 8.017 1.257 22.382 1.00 5.68 seg C ATOM 215 O2 DC B 12 7.524 1.832 23.357 1.00 6.32 seg O ATOM 216 N3 DC B 12 8.543 1.930 21.312 1.00 6.18 seg N ATOM 217 C4 DC B 12 9.009 1.236 20.266 1.00 6.48 seg C ATOM 218 N4 DC B 12 9.518 1.926 19.243 1.00 7.43 seg N ATOM 219 C5 DC B 12 9.012 -0.198 20.248 1.00 6.83 seg C ATOM 220 C6 DC B 12 8.502 -0.825 21.311 1.00 6.80 seg C ATOM 221 P DG B 13 3.317 -2.567 21.984 1.00 10.53 seg P ATOM 222 OP1 DG B 13 2.138 -3.315 22.464 1.00 12.90 seg O ATOM 223 OP2 DG B 13 3.797 -2.910 20.692 1.00 15.34 seg O ATOM 224 O5' DG B 13 3.058 -1.005 22.003 1.00 8.16 seg O ATOM 225 C5' DG B 13 2.486 -0.453 23.175 1.00 7.96 seg C ATOM 226 C4' DG B 13 2.422 1.049 23.015 1.00 7.52 seg C ATOM 227 O4' DG B 13 3.776 1.585 22.972 1.00 8.03 seg O ATOM 228 C3' DG B 13 1.786 1.610 21.766 1.00 6.71 seg C ATOM 229 O3' DG B 13 0.374 1.467 21.862 1.00 6.44 seg O ATOM 230 C2' DG B 13 2.313 3.016 21.879 1.00 7.13 seg C ATOM 231 C1' DG B 13 3.801 2.784 22.295 1.00 7.50 seg C ATOM 232 N9 DG B 13 4.601 2.712 21.088 1.00 7.08 seg N ATOM 233 C8 DG B 13 5.173 1.609 20.512 1.00 6.87 seg C ATOM 234 N7 DG B 13 5.814 1.892 19.415 1.00 7.15 seg N ATOM 235 C5 DG B 13 5.655 3.258 19.245 1.00 6.53 seg C ATOM 236 C6 DG B 13 6.091 4.135 18.221 1.00 6.23 seg C ATOM 237 O6 DG B 13 6.762 3.865 17.217 1.00 7.02 seg O ATOM 238 N1 DG B 13 5.657 5.437 18.454 1.00 6.37 seg N ATOM 239 C2 DG B 13 4.896 5.858 19.514 1.00 6.35 seg C ATOM 240 N2 DG B 13 4.599 7.146 19.531 1.00 6.42 seg N ATOM 241 N3 DG B 13 4.501 5.043 20.466 1.00 6.38 seg N ATOM 242 C4 DG B 13 4.904 3.776 20.267 1.00 6.57 seg C ATOM 243 P DT B 14 -0.502 1.442 20.533 1.00 6.12 seg P ATOM 244 OP1 DT B 14 -1.889 1.279 21.023 1.00 7.43 seg O ATOM 245 OP2 DT B 14 0.064 0.495 19.535 1.00 7.35 seg O ATOM 246 O5' DT B 14 -0.296 2.900 19.897 1.00 5.91 seg O ATOM 247 C5' DT B 14 -0.864 4.029 20.559 1.00 6.72 seg C ATOM 248 C4' DT B 14 -0.613 5.258 19.743 1.00 5.90 seg C ATOM 249 O4' DT B 14 0.836 5.541 19.679 1.00 5.83 seg O ATOM 250 C3' DT B 14 -1.009 5.225 18.272 1.00 5.92 seg C ATOM 251 O3' DT B 14 -2.417 5.269 18.155 1.00 6.57 seg O ATOM 252 C2' DT B 14 -0.248 6.446 17.791 1.00 5.66 seg C ATOM 253 C1' DT B 14 1.089 6.266 18.502 1.00 5.37 seg C ATOM 254 N1 DT B 14 2.007 5.496 17.631 1.00 5.56 seg N ATOM 255 C2 DT B 14 2.567 6.214 16.592 1.00 5.65 seg C ATOM 256 O2 DT B 14 2.348 7.401 16.401 1.00 6.01 seg O ATOM 257 N3 DT B 14 3.389 5.484 15.771 1.00 5.43 seg N ATOM 258 C4 DT B 14 3.637 4.136 15.836 1.00 5.80 seg C ATOM 259 O4 DT B 14 4.363 3.617 14.997 1.00 6.83 seg O ATOM 260 C5 DT B 14 3.027 3.447 16.945 1.00 5.92 seg C ATOM 261 C7 DT B 14 3.264 1.982 17.116 1.00 7.13 seg C ATOM 262 C6 DT B 14 2.257 4.156 17.789 1.00 5.79 seg C ATOM 263 P DA B 15 -3.107 4.614 16.844 1.00 6.33 seg P ATOM 264 OP1 DA B 15 -4.536 4.501 17.215 1.00 7.81 seg O ATOM 265 OP2 DA B 15 -2.355 3.433 16.355 1.00 7.39 seg O ATOM 266 O5' DA B 15 -2.903 5.712 15.734 1.00 6.64 seg O ATOM 267 C5' DA B 15 -3.456 7.019 15.917 1.00 7.02 seg C ATOM 268 C4' DA B 15 -2.863 7.975 14.857 1.00 6.49 seg C ATOM 269 O4' DA B 15 -1.417 8.002 15.006 1.00 6.33 seg O ATOM 270 C3' DA B 15 -3.120 7.639 13.418 1.00 6.56 seg C ATOM 271 O3' DA B 15 -4.406 8.139 13.055 1.00 7.27 seg O ATOM 272 C2' DA B 15 -1.969 8.325 12.734 1.00 6.18 seg C ATOM 273 C1' DA B 15 -0.855 8.099 13.667 1.00 5.84 seg C ATOM 274 N9 DA B 15 -0.080 6.863 13.448 1.00 5.58 seg N ATOM 275 C8 DA B 15 -0.139 5.693 14.139 1.00 5.46 seg C ATOM 276 N7 DA B 15 0.721 4.783 13.706 1.00 5.24 seg N ATOM 277 C5 DA B 15 1.390 5.435 12.679 1.00 5.11 seg C ATOM 278 C6 DA B 15 2.451 5.017 11.838 1.00 5.10 seg C ATOM 279 N6 DA B 15 3.032 3.818 11.887 1.00 5.80 seg N ATOM 280 N1 DA B 15 2.867 5.905 10.917 1.00 5.50 seg N ATOM 281 C2 DA B 15 2.312 7.119 10.854 1.00 5.61 seg C ATOM 282 N3 DA B 15 1.319 7.610 11.607 1.00 5.67 seg N ATOM 283 C4 DA B 15 0.916 6.720 12.504 1.00 5.30 seg C ATOM 284 P DA B 17 -5.863 7.587 6.066 1.00 7.46 P ATOM 285 OP1 DA B 17 -7.082 8.055 5.372 1.00 9.84 O ATOM 286 OP2 DA B 17 -6.010 6.428 6.951 1.00 9.05 O ATOM 287 O5' DA B 17 -4.763 7.131 4.982 1.00 6.87 O ATOM 288 C5' DA B 17 -4.584 7.937 3.825 1.00 7.49 C ATOM 289 C4' DA B 17 -3.539 7.243 2.937 1.00 6.83 C ATOM 290 O4' DA B 17 -2.295 7.168 3.631 1.00 7.04 O ATOM 291 C3' DA B 17 -3.829 5.816 2.525 1.00 7.02 C ATOM 292 O3' DA B 17 -4.804 5.781 1.477 1.00 8.14 O ATOM 293 C2' DA B 17 -2.450 5.387 2.108 1.00 7.22 C ATOM 294 C1' DA B 17 -1.587 6.010 3.166 1.00 6.66 C ATOM 295 N9 DA B 17 -1.369 5.144 4.326 1.00 5.85 N ATOM 296 C8 DA B 17 -2.072 5.079 5.492 1.00 6.17 C ATOM 297 N7 DA B 17 -1.643 4.156 6.319 1.00 6.03 N ATOM 298 C5 DA B 17 -0.591 3.552 5.643 1.00 5.68 C ATOM 299 C6 DA B 17 0.268 2.480 5.946 1.00 5.42 C ATOM 300 N6 DA B 17 0.257 1.834 7.114 1.00 5.69 N ATOM 301 N1 DA B 17 1.178 2.113 5.031 1.00 5.65 N ATOM 302 C2 DA B 17 1.212 2.780 3.868 1.00 5.86 C ATOM 303 N3 DA B 17 0.472 3.809 3.457 1.00 5.97 N ATOM 304 C4 DA B 17 -0.423 4.147 4.410 1.00 5.68 C ATOM 305 P DC B 18 -5.850 4.605 1.415 1.00 8.75 P ATOM 306 OP1 DC B 18 -6.730 4.928 0.276 1.00 12.93 O ATOM 307 OP2 DC B 18 -6.479 4.382 2.720 1.00 11.49 O ATOM 308 N1 DC B 18 -2.088 0.995 2.743 1.00 5.94 N ATOM 309 C2 DC B 18 -1.320 0.079 3.454 1.00 5.53 C ATOM 310 O2 DC B 18 -0.464 -0.570 2.845 1.00 6.20 O ATOM 311 N3 DC B 18 -1.531 -0.063 4.785 1.00 5.53 N ATOM 312 C4 DC B 18 -2.510 0.618 5.387 1.00 5.87 C ATOM 313 N4 DC B 18 -2.692 0.431 6.686 1.00 6.96 N ATOM 314 C5 DC B 18 -3.324 1.552 4.679 1.00 6.40 C ATOM 315 C6 DC B 18 -3.077 1.692 3.371 1.00 6.07 C ATOM 316 O5' DC B 18 -4.980 3.312 1.052 1.00 9.67 O ATOM 317 C5' DC B 18 -4.326 3.201 -0.208 1.00 18.33 C ATOM 318 C4' DC B 18 -3.395 1.992 -0.189 1.00 7.63 C ATOM 319 O4' DC B 18 -2.311 2.271 0.750 1.00 6.13 O ATOM 320 C3' DC B 18 -3.906 0.638 0.289 1.00 6.36 C ATOM 321 O3' DC B 18 -4.745 0.062 -0.685 1.00 6.90 O ATOM 322 C2' DC B 18 -2.552 -0.024 0.545 1.00 4.15 C ATOM 323 C1' DC B 18 -1.815 1.074 1.293 1.00 6.79 C ATOM 324 N9 DG B 19 -2.358 -3.762 3.056 1.00 5.17 N ATOM 325 C8 DG B 19 -3.242 -2.728 3.235 1.00 5.72 C ATOM 326 N7 DG B 19 -3.594 -2.570 4.492 1.00 5.81 N ATOM 327 C5 DG B 19 -2.879 -3.533 5.177 1.00 5.12 C ATOM 328 C6 DG B 19 -2.800 -3.847 6.569 1.00 4.99 C ATOM 329 O6 DG B 19 -3.414 -3.301 7.509 1.00 6.20 O ATOM 330 N1 DG B 19 -1.958 -4.914 6.801 1.00 5.03 N ATOM 331 C2 DG B 19 -1.245 -5.621 5.857 1.00 4.92 C ATOM 332 N2 DG B 19 -0.506 -6.630 6.310 1.00 5.16 N ATOM 333 N3 DG B 19 -1.281 -5.323 4.563 1.00 4.95 N ATOM 334 C4 DG B 19 -2.111 -4.279 4.311 1.00 4.86 C ATOM 335 P DG B 19 -5.394 -1.368 -0.434 1.00 6.03 P ATOM 336 OP1 DG B 19 -6.386 -1.588 -1.504 1.00 10.24 O ATOM 337 OP2 DG B 19 -5.801 -1.496 0.951 1.00 7.31 O ATOM 338 O5' DG B 19 -4.162 -2.301 -0.650 1.00 16.06 O ATOM 339 C5' DG B 19 -4.125 -3.645 -0.798 1.00 22.50 C ATOM 340 C4' DG B 19 -2.783 -4.124 -0.249 1.00 4.64 C ATOM 341 O4' DG B 19 -2.316 -3.216 0.749 1.00 6.27 O ATOM 342 C3' DG B 19 -2.908 -5.468 0.394 1.00 4.51 C ATOM 343 O3' DG B 19 -2.826 -6.486 -0.621 1.00 8.79 O ATOM 344 C2' DG B 19 -1.790 -5.568 1.388 1.00 3.09 C ATOM 345 C1' DG B 19 -1.724 -4.162 1.780 1.00 3.64 C ATOM 346 P DC B 20 -3.827 -7.730 -0.547 1.00 7.39 P ATOM 347 OP1 DC B 20 -3.528 -8.515 -1.781 1.00 10.52 O ATOM 348 OP2 DC B 20 -5.200 -7.318 -0.309 1.00 9.09 O ATOM 349 O5' DC B 20 -3.338 -8.510 0.743 1.00 7.10 O ATOM 350 C5' DC B 20 -2.082 -9.184 0.769 1.00 6.85 C ATOM 351 C4' DC B 20 -1.886 -9.845 2.096 1.00 5.89 C ATOM 352 O4' DC B 20 -1.809 -8.845 3.109 1.00 5.69 O ATOM 353 C3' DC B 20 -3.027 -10.776 2.575 1.00 6.11 C ATOM 354 O3' DC B 20 -2.893 -12.101 2.117 1.00 6.77 O ATOM 355 C2' DC B 20 -2.924 -10.707 4.083 1.00 6.12 C ATOM 356 C1' DC B 20 -2.345 -9.366 4.353 1.00 5.64 C ATOM 357 N1 DC B 20 -3.277 -8.343 4.869 1.00 5.40 N ATOM 358 C2 DC B 20 -3.487 -8.319 6.251 1.00 5.46 C ATOM 359 O2 DC B 20 -2.925 -9.189 6.930 1.00 5.71 O ATOM 360 N3 DC B 20 -4.256 -7.344 6.779 1.00 5.66 N ATOM 361 C4 DC B 20 -4.870 -6.469 5.972 1.00 5.89 C ATOM 362 N4 DC B 20 -5.635 -5.536 6.565 1.00 6.38 N ATOM 363 C5 DC B 20 -4.742 -6.533 4.557 1.00 5.85 C ATOM 364 C6 DC B 20 -3.917 -7.457 4.043 1.00 5.82 C TER END""" def get_grm(pdb_str, mon_lib_srv, ener_lib, log): pdb_int_pars = pdb_interpretation.master_params.extract() pdb_int_pars.secondary_structure.enabled=True processed_pdb_file = pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=pdb_int_pars, raw_records=pdb_str, substitute_non_crystallographic_unit_cell_if_necessary=True, log=log) return processed_pdb_file.geometry_restraints_manager() def exercise_protein(mon_lib_srv, ener_lib, log): grm = get_grm(protein_pdb_str.split('\n'), mon_lib_srv, ener_lib, log) print(grm.get_n_hbond_proxies(), "want 30") # 31 hbonds, with segids 30 print(grm.get_n_hangle_proxies(), "want 90") assert grm.get_n_hbond_proxies() == 30 # 31 hbonds, with segids 30 assert grm.get_n_hangle_proxies() == 90 def exercise_rna(mon_lib_srv, ener_lib, log): grm = get_grm(rna_pdb_str.split('\n'), mon_lib_srv, ener_lib, log) print(grm.get_n_hbond_proxies(), "want 22") # 22 hbonds, with segids print(grm.get_n_hangle_proxies(), "want 44") assert grm.get_n_hbond_proxies() == 22 assert grm.get_n_hangle_proxies() == 44 def exercise_both(mon_lib_srv, ener_lib, log): grm = get_grm(protein_pdb_str.split('\n') + rna_pdb_str.split('\n'), mon_lib_srv, ener_lib, log) print(grm.get_n_hbond_proxies(), "want 52") print(grm.get_n_hangle_proxies(), "want 44+90=134") # 90 from protein assert grm.get_n_hbond_proxies() == 52 assert grm.get_n_hangle_proxies() == 134 if __name__ == "__main__": if (not libtbx.env.has_module(name="ksdssp")): print("Skipping KSDSSP tests: ksdssp module not available.") else: mon_lib_srv = server.server() ener_lib = server.ener_lib() # log = sys.stdout log = StringIO() exercise_protein(mon_lib_srv, ener_lib, log) exercise_rna(mon_lib_srv, ener_lib, log) exercise_both(mon_lib_srv, ener_lib, log) print(format_cpu_times()) print("OK")