Skip to content

Instantly share code, notes, and snippets.

@ajasja

ajasja/pyrosetta-pdb-coords.ipynb

Last active August 29, 2015 14:08
Show Gist options
  • Save ajasja/b9ee7816415d742c1909 to your computer and use it in GitHub Desktop.
Save ajasja/b9ee7816415d742c1909 to your computer and use it in GitHub Desktop.
Download ZIP
Display the source blob
Display the rendered blob
Raw
pyrosetta-pdb-coords.ipynb
{
"worksheets": [
{
"cells": [
{
"metadata": {},
"cell_type": "code",
"input": "import numpy as np\nimport rosetta as r\nimport random\nr.init()\nr.__version__",
"prompt_number": 1,
"outputs": [
{
"output_type": "stream",
"text": "low_memory_mode?\n",
"stream": "stdout"
},
{
"text": "'56891:56891:6efc58f8abb54611ace5a6cdd7e69e6c970a01ef'",
"output_type": "pyout",
"metadata": {},
"prompt_number": 1
}
],
"language": "python",
"trusted": true,
"collapsed": false
},
{
"metadata": {},
"cell_type": "code",
"input": "pdbstring = \"\"\"CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1\nATOM 1 N ALA P 1 0.212 1.255 -26.668 1.00 1.00 P N\nATOM 2 HT1 ALA P 1 0.510 1.910 -27.419 0.00 0.00 P H\nATOM 3 HT2 ALA P 1 0.076 0.305 -27.068 0.00 0.00 P H\nATOM 4 HT3 ALA P 1 0.942 1.219 -25.928 0.00 0.00 P H\nATOM 5 CA ALA P 1 -1.065 1.727 -26.078 1.00 1.00 P C\nATOM 6 HA ALA P 1 -0.878 2.708 -25.666 1.00 0.00 P H\nATOM 7 CB ALA P 1 -2.157 1.806 -27.166 1.00 0.00 P C\nATOM 8 HB1 ALA P 1 -3.116 2.160 -26.731 1.00 0.00 P H\nATOM 9 HB2 ALA P 1 -1.856 2.526 -27.957 1.00 0.00 P H\nATOM 10 HB3 ALA P 1 -2.329 0.819 -27.645 1.00 0.00 P H\nATOM 11 C ALA P 1 -1.503 0.812 -24.976 1.00 1.00 P C\nATOM 12 O ALA P 1 -1.571 1.219 -23.817 1.00 1.00 P O\nATOM 13 N ALA P 2 -1.811 -0.462 -25.325 1.00 1.00 P N\nATOM 14 HN ALA P 2 -1.737 -0.755 -26.275 0.00 0.00 P H\nATOM 15 CA ALA P 2 -2.279 -1.485 -24.419 1.00 1.00 P C\nATOM 16 HA ALA P 2 -3.156 -1.100 -23.919 1.00 0.00 P H\nATOM 17 CB ALA P 2 -2.656 -2.778 -25.168 1.00 0.00 P C\nATOM 18 HB1 ALA P 2 -3.050 -3.543 -24.466 1.00 0.00 P H\nATOM 19 HB2 ALA P 2 -3.443 -2.560 -25.921 1.00 0.00 P H\nATOM 20 HB3 ALA P 2 -1.776 -3.199 -25.699 1.00 0.00 P H\nATOM 21 C ALA P 2 -1.250 -1.836 -23.377 1.00 1.00 P C\nATOM 22 O ALA P 2 -1.588 -2.025 -22.211 1.00 1.00 P O\nATOM 23 N ALA P 3 0.040 -1.917 -23.788 1.00 1.00 P N\nATOM 24 HN ALA P 3 0.279 -1.755 -24.743 0.00 0.00 P H\nATOM 25 CA ALA P 3 1.160 -2.228 -22.929 1.00 1.00 P C\nATOM 26 HA ALA P 3 0.943 -3.166 -22.436 1.00 0.00 P H\nATOM 27 CB ALA P 3 2.467 -2.370 -23.731 1.00 0.00 P C\nATOM 28 HB1 ALA P 3 3.314 -2.642 -23.065 1.00 0.00 P H\nATOM 29 HB2 ALA P 3 2.355 -3.170 -24.493 1.00 0.00 P H\nATOM 30 HB3 ALA P 3 2.715 -1.423 -24.257 1.00 0.00 P H\nATOM 31 C ALA P 3 1.373 -1.170 -21.876 1.00 1.00 P C\nATOM 32 O ALA P 3 1.630 -1.489 -20.717 1.00 1.00 P O\nATOM 33 N ALA P 4 1.250 0.121 -22.271 1.00 1.00 P N\nATOM 34 HN ALA P 4 1.034 0.343 -23.219 0.00 0.00 P H\nATOM 35 CA ALA P 4 1.402 1.266 -21.402 1.00 1.00 P C\nATOM 36 HA ALA P 4 2.363 1.180 -20.915 1.00 0.00 P H\nATOM 37 CB ALA P 4 1.357 2.589 -22.189 1.00 0.00 P C\nATOM 38 HB1 ALA P 4 1.518 3.457 -21.514 1.00 0.00 P H\nATOM 39 HB2 ALA P 4 2.157 2.596 -22.959 1.00 0.00 P H\nATOM 40 HB3 ALA P 4 0.380 2.714 -22.704 1.00 0.00 P H\nATOM 41 C ALA P 4 0.331 1.314 -20.343 1.00 1.00 P C\nATOM 42 O ALA P 4 0.613 1.614 -19.185 1.00 1.00 P O\nATOM 43 N ALA P 5 -0.929 1.000 -20.732 1.00 1.00 P N\nATOM 44 HN ALA P 5 -1.119 0.755 -21.680 0.00 0.00 P H\nATOM 45 CA ALA P 5 -2.084 0.980 -19.863 1.00 1.00 P C\nATOM 46 HA ALA P 5 -2.144 1.944 -19.379 1.00 0.00 P H\nATOM 47 CB ALA P 5 -3.383 0.732 -20.653 1.00 0.00 P C\nATOM 48 HB1 ALA P 5 -4.267 0.759 -19.980 1.00 0.00 P H\nATOM 49 HB2 ALA P 5 -3.510 1.521 -21.425 1.00 0.00 P H\nATOM 50 HB3 ALA P 5 -3.355 -0.252 -21.167 1.00 0.00 P H\nATOM 51 C ALA P 5 -1.969 -0.084 -18.802 1.00 1.00 P C\nATOM 52 O ALA P 5 -2.308 0.152 -17.644 1.00 1.00 P O\nATOM 53 N ALA P 6 -1.469 -1.283 -19.189 1.00 1.00 P N\nATOM 54 HN ALA P 6 -1.200 -1.435 -20.137 0.00 0.00 P H\nATOM 55 CA ALA P 6 -1.271 -2.418 -18.318 1.00 1.00 P C\nATOM 56 HA ALA P 6 -2.213 -2.623 -17.829 1.00 0.00 P H\nATOM 57 CB ALA P 6 -0.831 -3.667 -19.106 1.00 0.00 P C\nATOM 58 HB1 ALA P 6 -0.719 -4.542 -18.431 1.00 0.00 P H\nATOM 59 HB2 ALA P 6 -1.595 -3.916 -19.873 1.00 0.00 P H\nATOM 60 HB3 ALA P 6 0.134 -3.490 -19.626 1.00 0.00 P H\nATOM 61 C ALA P 6 -0.232 -2.140 -17.263 1.00 1.00 P C\nATOM 62 O ALA P 6 -0.410 -2.506 -16.103 1.00 1.00 P O\nATOM 63 N ALA P 7 0.874 -1.464 -17.658 1.00 1.00 P N\nATOM 64 HN ALA P 7 0.981 -1.180 -18.607 0.00 0.00 P H\nATOM 65 CA ALA P 7 1.969 -1.093 -16.791 1.00 1.00 P C\nATOM 66 HA ALA P 7 2.317 -1.991 -16.300 1.00 0.00 P H\nATOM 67 CB ALA P 7 3.135 -0.471 -17.584 1.00 0.00 P C\nATOM 68 HB1 ALA P 7 3.985 -0.226 -16.913 1.00 0.00 P H\nATOM 69 HB2 ALA P 7 3.494 -1.191 -18.351 1.00 0.00 P H\nATOM 70 HB3 ALA P 7 2.812 0.455 -18.106 1.00 0.00 P H\nATOM 71 C ALA P 7 1.539 -0.105 -15.737 1.00 1.00 P C\nATOM 72 O ALA P 7 1.932 -0.221 -14.578 1.00 1.00 P O\nATOM 73 N ALA P 8 0.701 0.884 -16.132 1.00 1.00 P N\nATOM 74 HN ALA P 8 0.400 0.943 -17.081 0.00 0.00 P H\nATOM 75 CA ALA P 8 0.170 1.913 -15.268 1.00 1.00 P C\nATOM 76 HA ALA P 8 1.006 2.394 -14.781 1.00 0.00 P H\nATOM 77 CB ALA P 8 -0.625 2.967 -16.062 1.00 0.00 P C\nATOM 78 HB1 ALA P 8 -0.994 3.772 -15.392 1.00 0.00 P H\nATOM 79 HB2 ALA P 8 0.030 3.429 -16.832 1.00 0.00 P H\nATOM 80 HB3 ALA P 8 -1.492 2.505 -16.579 1.00 0.00 P H\nATOM 81 C ALA P 8 -0.738 1.341 -14.209 1.00 1.00 P C\nATOM 82 O ALA P 8 -0.680 1.751 -13.052 1.00 1.00 P O\nATOM 83 N ALA P 9 -1.589 0.361 -14.598 1.00 1.00 P N\nATOM 84 HN ALA P 9 -1.604 0.051 -15.546 0.00 0.00 P H\nATOM 85 CA ALA P 9 -2.523 -0.318 -13.728 1.00 1.00 P C\nATOM 86 HA ALA P 9 -3.125 0.437 -13.242 1.00 0.00 P H\nATOM 87 CB ALA P 9 -3.446 -1.266 -14.517 1.00 0.00 P C\nATOM 88 HB1 ALA P 9 -4.184 -1.752 -13.843 1.00 0.00 P H\nATOM 89 HB2 ALA P 9 -4.004 -0.692 -15.287 1.00 0.00 P H\nATOM 90 HB3 ALA P 9 -2.859 -2.055 -15.033 1.00 0.00 P H\nATOM 91 C ALA P 9 -1.817 -1.124 -12.669 1.00 1.00 P C\nATOM 92 O ALA P 9 -2.227 -1.125 -11.510 1.00 1.00 P O\nATOM 93 N ALA P 10 -0.719 -1.818 -13.059 1.00 1.00 P N\nATOM 94 HN ALA P 10 -0.414 -1.789 -14.008 0.00 0.00 P H\nATOM 95 CA ALA P 10 0.096 -2.634 -12.189 1.00 1.00 P C\nATOM 96 HA ALA P 10 -0.557 -3.342 -11.699 1.00 0.00 P H\nATOM 97 CB ALA P 10 1.172 -3.405 -12.978 1.00 0.00 P C\nATOM 98 HB1 ALA P 10 1.766 -4.058 -12.304 1.00 0.00 P H\nATOM 99 HB2 ALA P 10 0.687 -4.047 -13.744 1.00 0.00 P H\nATOM 100 HB3 ALA P 10 1.861 -2.706 -13.499 1.00 0.00 P H\nATOM 101 C ALA P 10 0.788 -1.809 -11.135 1.00 1.00 P C\nATOM 102 O ALA P 10 0.855 -2.211 -9.975 1.00 1.00 P O\nATOM 103 N ALA P 11 1.306 -0.621 -11.530 1.00 1.00 P N\nATOM 104 HN ALA P 11 1.228 -0.327 -12.480 0.00 0.00 P H\nATOM 105 CA ALA P 11 1.991 0.313 -10.666 1.00 1.00 P C\nATOM 106 HA ALA P 11 2.792 -0.224 -10.176 1.00 0.00 P H\nATOM 107 CB ALA P 11 2.587 1.490 -11.461 1.00 0.00 P C\nATOM 108 HB1 ALA P 11 3.144 2.179 -10.791 1.00 0.00 P H\nATOM 109 HB2 ALA P 11 3.293 1.106 -12.228 1.00 0.00 P H\nATOM 110 HB3 ALA P 11 1.790 2.063 -11.981 1.00 0.00 P H\nATOM 111 C ALA P 11 1.074 0.875 -9.611 1.00 1.00 P C\nATOM 112 O ALA P 11 1.465 1.007 -8.452 1.00 1.00 P O\nATOM 113 N ALA P 12 -0.180 1.205 -10.003 1.00 1.00 P N\nATOM 114 HN ALA P 12 -0.462 1.079 -10.951 0.00 0.00 P H\nATOM 115 CA ALA P 12 -1.204 1.743 -9.137 1.00 1.00 P C\nATOM 116 HA ALA P 12 -0.795 2.618 -8.652 1.00 0.00 P H\nATOM 117 CB ALA P 12 -2.461 2.149 -9.930 1.00 0.00 P C\nATOM 118 HB1 ALA P 12 -3.225 2.597 -9.259 1.00 0.00 P H\nATOM 119 HB2 ALA P 12 -2.192 2.902 -10.700 1.00 0.00 P H\nATOM 120 HB3 ALA P 12 -2.908 1.273 -10.445 1.00 0.00 P H\nATOM 121 C ALA P 12 -1.617 0.755 -8.077 1.00 1.00 P C\nATOM 122 O ALA P 12 -1.802 1.125 -6.919 1.00 1.00 P O\nATOM 123 N ALA P 13 -1.753 -0.537 -8.465 1.00 1.00 P N\nATOM 124 HN ALA P 13 -1.590 -0.799 -9.413 0.00 0.00 P H\nATOM 125 CA ALA P 13 -2.126 -1.628 -7.594 1.00 1.00 P C\nATOM 126 HA ALA P 13 -3.051 -1.355 -7.106 1.00 0.00 P H\nATOM 127 CB ALA P 13 -2.338 -2.935 -8.381 1.00 0.00 P C\nATOM 128 HB1 ALA P 13 -2.662 -3.756 -7.706 1.00 0.00 P H\nATOM 129 HB2 ALA P 13 -3.126 -2.786 -9.149 1.00 0.00 P H\nATOM 130 HB3 ALA P 13 -1.406 -3.244 -8.898 1.00 0.00 P H\nATOM 131 C ALA P 13 -1.083 -1.881 -6.536 1.00 1.00 P C\nATOM 132 O ALA P 13 -1.416 -2.116 -5.377 1.00 1.00 P O\nATOM 133 N ALA P 14 0.213 -1.820 -6.928 1.00 1.00 P N\nATOM 134 HN ALA P 14 0.445 -1.621 -7.878 0.00 0.00 P H\nATOM 135 CA ALA P 14 1.351 -2.020 -6.061 1.00 1.00 P C\nATOM 136 HA ALA P 14 1.223 -2.975 -5.570 1.00 0.00 P H\nATOM 137 CB ALA P 14 2.673 -2.035 -6.852 1.00 0.00 P C\nATOM 138 HB1 ALA P 14 3.535 -2.228 -6.180 1.00 0.00 P H\nATOM 139 HB2 ALA P 14 2.643 -2.838 -7.618 1.00 0.00 P H\nATOM 140 HB3 ALA P 14 2.835 -1.067 -7.373 1.00 0.00 P H\nATOM 141 C ALA P 14 1.448 -0.947 -5.007 1.00 1.00 P C\nATOM 142 O ALA P 14 1.735 -1.238 -3.847 1.00 1.00 P O\nATOM 143 N ALA P 15 1.190 0.324 -5.401 1.00 1.00 P N\nATOM 144 HN ALA P 15 0.956 0.520 -6.351 0.00 0.00 P H\nATOM 145 CA ALA P 15 1.221 1.481 -4.536 1.00 1.00 P C\nATOM 146 HA ALA P 15 2.186 1.499 -4.049 1.00 0.00 P H\nATOM 147 CB ALA P 15 1.034 2.787 -5.331 1.00 0.00 P C\nATOM 148 HB1 ALA P 15 1.098 3.671 -4.660 1.00 0.00 P H\nATOM 149 HB2 ALA P 15 1.831 2.877 -6.099 1.00 0.00 P H\nATOM 150 HB3 ALA P 15 0.052 2.801 -5.849 1.00 0.00 P H\nATOM 151 C ALA P 15 0.150 1.417 -3.479 1.00 1.00 P C\nATOM 152 O ALA P 15 0.399 1.743 -2.320 1.00 1.00 P O\nATOM 153 N ALA P 16 -1.070 0.974 -3.871 1.00 1.00 P N\nATOM 154 HN ALA P 16 -1.231 0.714 -4.820 0.00 0.00 P H\nATOM 155 CA ALA P 16 -2.217 0.830 -3.004 1.00 1.00 P C\nATOM 156 HA ALA P 16 -2.380 1.781 -2.517 1.00 0.00 P H\nATOM 157 CB ALA P 16 -3.482 0.447 -3.797 1.00 0.00 P C\nATOM 158 HB1 ALA P 16 -4.364 0.376 -3.125 1.00 0.00 P H\nATOM 159 HB2 ALA P 16 -3.692 1.221 -4.565 1.00 0.00 P H\nATOM 160 HB3 ALA P 16 -3.347 -0.526 -4.315 1.00 0.00 P H\nATOM 161 C ALA P 16 -1.990 -0.219 -1.947 1.00 1.00 P C\nATOM 162 O ALA P 16 -2.354 -0.026 -0.789 1.00 1.00 P O\nATOM 163 N ALA P 17 -1.361 -1.353 -2.339 1.00 1.00 P N\nATOM 164 HN ALA P 17 -1.078 -1.472 -3.288 0.00 0.00 P H\nATOM 165 CA ALA P 17 -1.040 -2.463 -1.473 1.00 1.00 P C\nATOM 166 HA ALA P 17 -1.954 -2.773 -0.987 1.00 0.00 P H\nATOM 167 CB ALA P 17 -0.462 -3.652 -2.263 1.00 0.00 P C\nATOM 168 HB1 ALA P 17 -0.257 -4.513 -1.592 1.00 0.00 P H\nATOM 169 HB2 ALA P 17 -1.191 -3.980 -3.035 1.00 0.00 P H\nATOM 170 HB3 ALA P 17 0.480 -3.368 -2.778 1.00 0.00 P H\nATOM 171 C ALA P 17 -0.041 -2.076 -0.414 1.00 1.00 P C\nATOM 172 O ALA P 17 -0.175 -2.473 0.742 1.00 1.00 P O\nATOM 173 O1 R1A P 18 8.042 -1.478 5.639 0.00 0.00 P O\nATOM 174 N1 R1A P 18 7.016 -1.451 4.891 0.00 0.00 P O\nATOM 175 C2 R1A P 18 7.013 -2.109 3.556 0.00 0.00 P C\nATOM 176 C5 R1A P 18 5.752 -0.836 5.355 0.00 0.00 P C\nATOM 177 C8 R1A P 18 8.095 -1.399 2.710 0.00 0.00 P C\nATOM 178 H81 R1A P 18 7.859 -0.322 2.572 0.00 0.00 P H\nATOM 179 H82 R1A P 18 8.167 -1.873 1.708 0.00 0.00 P H\nATOM 180 H83 R1A P 18 9.093 -1.482 3.189 0.00 0.00 P H\nATOM 181 C6 R1A P 18 6.009 0.671 5.577 0.00 0.00 P C\nATOM 182 H61 R1A P 18 5.075 1.171 5.908 0.00 0.00 P H\nATOM 183 H62 R1A P 18 6.359 1.166 4.646 0.00 0.00 P H\nATOM 184 H63 R1A P 18 6.774 0.827 6.367 0.00 0.00 P H\nATOM 185 C9 R1A P 18 7.304 -3.612 3.778 0.00 0.00 P C\nATOM 186 H91 R1A P 18 7.296 -4.148 2.805 0.00 0.00 P H\nATOM 187 H93 R1A P 18 6.544 -4.079 4.441 0.00 0.00 P H\nATOM 188 H92 R1A P 18 8.306 -3.756 4.235 0.00 0.00 P H\nATOM 189 C7 R1A P 18 5.297 -1.591 6.626 0.00 0.00 P C\nATOM 190 H71 R1A P 18 5.198 -2.682 6.438 0.00 0.00 P H\nATOM 191 H72 R1A P 18 4.313 -1.210 6.969 0.00 0.00 P H\nATOM 192 H73 R1A P 18 6.024 -1.441 7.452 0.00 0.00 P H\nATOM 193 C3 R1A P 18 5.579 -1.810 3.173 0.00 0.00 P C\nATOM 194 C4 R1A P 18 4.938 -1.154 4.139 0.00 0.00 P C\nATOM 195 H41 R1A P 18 3.888 -0.829 4.143 0.00 0.00 P H\nATOM 196 CE R1A P 18 5.001 -2.366 1.892 0.00 0.00 P C\nATOM 197 HE1 R1A P 18 5.238 -3.449 1.820 0.00 0.00 P H\nATOM 198 HE2 R1A P 18 3.894 -2.304 1.915 0.00 0.00 P H\nATOM 199 SD R1A P 18 5.609 -1.550 0.379 0.00 0.00 P S\nATOM 200 N R1A P 18 0.985 -1.275 -0.798 1.00 1.00 P N\nATOM 201 HN R1A P 18 1.060 -0.963 -1.742 0.00 0.00 P H\nATOM 202 CA R1A P 18 2.039 -0.819 0.079 1.00 1.00 P C\nATOM 203 HA R1A P 18 2.445 -1.697 0.557 1.00 0.00 P H\nATOM 204 CB R1A P 18 3.162 -0.087 -0.699 1.00 0.00 P C\nATOM 205 HB1 R1A P 18 2.764 0.864 -1.115 1.00 0.00 P H\nATOM 206 HB2 R1A P 18 3.446 -0.721 -1.567 1.00 0.00 P H\nATOM 207 SG R1A P 18 4.666 0.250 0.284 0.00 0.00 P S\nATOM 208 C R1A P 18 1.495 0.109 1.139 1.00 1.00 P C\nATOM 209 O R1A P 18 1.885 0.027 2.301 1.00 1.00 P O\nATOM 210 N ALA P 19 0.564 1.011 0.740 1.00 1.00 P N\nATOM 211 HN ALA P 19 0.270 1.044 -0.213 0.00 0.00 P H\nATOM 212 CA ALA P 19 -0.079 1.977 1.600 1.00 1.00 P C\nATOM 213 HA ALA P 19 0.699 2.544 2.092 1.00 0.00 P H\nATOM 214 CB ALA P 19 -0.975 2.942 0.801 1.00 0.00 P C\nATOM 215 HB1 ALA P 19 -1.431 3.704 1.469 1.00 0.00 P H\nATOM 216 HB2 ALA P 19 -0.368 3.471 0.035 1.00 0.00 P H\nATOM 217 HB3 ALA P 19 -1.787 2.392 0.279 1.00 0.00 P H\nATOM 218 C ALA P 19 -0.927 1.312 2.653 1.00 1.00 P C\nATOM 219 O ALA P 19 -0.929 1.733 3.807 1.00 1.00 P O\nATOM 220 N ALA P 20 -1.658 0.240 2.263 1.00 1.00 P N\nATOM 221 HN ALA P 20 -1.631 -0.074 1.317 0.00 0.00 P H\nATOM 222 CA ALA P 20 -2.507 -0.542 3.133 1.00 1.00 P C\nATOM 223 HA ALA P 20 -3.193 0.139 3.617 1.00 0.00 P H\nATOM 224 CB ALA P 20 -3.313 -1.592 2.346 1.00 0.00 P C\nATOM 225 HB1 ALA P 20 -3.991 -2.159 3.020 1.00 0.00 P H\nATOM 226 HB2 ALA P 20 -3.934 -1.089 1.574 1.00 0.00 P H\nATOM 227 HB3 ALA P 20 -2.639 -2.309 1.832 1.00 0.00 P H\nATOM 228 C ALA P 20 -1.712 -1.258 4.194 1.00 1.00 P C\nATOM 229 O ALA P 20 -2.120 -1.304 5.353 1.00 1.00 P O\nATOM 230 N ALA P 21 -0.540 -1.820 3.807 1.00 1.00 P N\nATOM 231 HN ALA P 21 -0.241 -1.759 2.858 0.00 0.00 P H\nATOM 232 CA ALA P 21 0.370 -2.525 4.681 1.00 1.00 P C\nATOM 233 HA ALA P 21 -0.193 -3.302 5.179 1.00 0.00 P H\nATOM 234 CB ALA P 21 1.529 -3.168 3.896 1.00 0.00 P C\nATOM 235 HB1 ALA P 21 2.204 -3.733 4.575 1.00 0.00 P H\nATOM 236 HB2 ALA P 21 1.126 -3.874 3.140 1.00 0.00 P H\nATOM 237 HB3 ALA P 21 2.123 -2.396 3.365 1.00 0.00 P H\nATOM 238 C ALA P 21 0.960 -1.614 5.725 1.00 1.00 P C\nATOM 239 O ALA P 21 1.091 -1.999 6.885 1.00 1.00 P O\nATOM 240 N ALA P 22 1.315 -0.370 5.320 1.00 1.00 P N\nATOM 241 HN ALA P 22 1.190 -0.095 4.370 0.00 0.00 P H\nATOM 242 CA ALA P 22 1.878 0.653 6.171 1.00 1.00 P C\nATOM 243 HA ALA P 22 2.750 0.237 6.652 1.00 0.00 P H\nATOM 244 CB ALA P 22 2.296 1.894 5.360 1.00 0.00 P C\nATOM 245 HB1 ALA P 22 2.774 2.652 6.016 1.00 0.00 P H\nATOM 246 HB2 ALA P 22 3.028 1.601 4.578 1.00 0.00 P H\nATOM 247 HB3 ALA P 22 1.421 2.356 4.857 1.00 0.00 P H\nATOM 248 C ALA P 22 0.910 1.092 7.236 1.00 1.00 P C\nATOM 249 O ALA P 22 1.290 1.266 8.392 1.00 1.00 P O\nATOM 250 N ALA P 23 -0.379 1.263 6.853 1.00 1.00 P N\nATOM 251 HN ALA P 23 -0.649 1.104 5.907 0.00 0.00 P H\nATOM 252 CA ALA P 23 -1.455 1.671 7.726 1.00 1.00 P C\nATOM 253 HA ALA P 23 -1.153 2.589 8.210 1.00 0.00 P H\nATOM 254 CB ALA P 23 -2.757 1.921 6.940 1.00 0.00 P C\nATOM 255 HB1 ALA P 23 -3.566 2.272 7.615 1.00 0.00 P H\nATOM 256 HB2 ALA P 23 -2.586 2.701 6.168 1.00 0.00 P H\nATOM 257 HB3 ALA P 23 -3.095 0.996 6.425 1.00 0.00 P H\nATOM 258 C ALA P 23 -1.738 0.639 8.785 1.00 1.00 P C\nATOM 259 O ALA P 23 -1.960 0.981 9.945 1.00 1.00 P O\nATOM 260 N ALA P 24 -1.719 -0.659 8.395 1.00 1.00 P N\nATOM 261 HN ALA P 24 -1.530 -0.898 7.445 0.00 0.00 P H\nATOM 262 CA ALA P 24 -1.958 -1.789 9.264 1.00 1.00 P C\nATOM 263 HA ALA P 24 -2.908 -1.629 9.753 1.00 0.00 P H\nATOM 264 CB ALA P 24 -2.014 -3.110 8.473 1.00 0.00 P C\nATOM 265 HB1 ALA P 24 -2.235 -3.965 9.147 1.00 0.00 P H\nATOM 266 HB2 ALA P 24 -2.816 -3.055 7.707 1.00 0.00 P H\nATOM 267 HB3 ALA P 24 -1.052 -3.304 7.953 1.00 0.00 P H\nATOM 268 C ALA P 24 -0.890 -1.920 10.318 1.00 1.00 P C\nATOM 269 O ALA P 24 -1.190 -2.195 11.478 1.00 1.00 P O\nATOM 270 N ALA P 25 0.389 -1.705 9.923 1.00 1.00 P N\nATOM 271 HN ALA P 25 0.593 -1.479 8.974 0.00 0.00 P H\nATOM 272 CA ALA P 25 1.545 -1.771 10.787 1.00 1.00 P C\nATOM 273 HA ALA P 25 1.534 -2.736 11.276 1.00 0.00 P H\nATOM 274 CB ALA P 25 2.857 -1.626 9.991 1.00 0.00 P C\nATOM 275 HB1 ALA P 25 3.739 -1.715 10.660 1.00 0.00 P H\nATOM 276 HB2 ALA P 25 2.921 -2.426 9.223 1.00 0.00 P H\nATOM 277 HB3 ALA P 25 2.900 -0.646 9.470 1.00 0.00 P H\nATOM 278 C ALA P 25 1.516 -0.697 11.843 1.00 1.00 P C\nATOM 279 O ALA P 25 1.834 -0.955 13.003 1.00 1.00 P O\nATOM 280 N ALA P 26 1.110 0.535 11.450 1.00 1.00 P N\nATOM 281 HN ALA P 26 0.855 0.704 10.501 0.00 0.00 P H\nATOM 282 CA ALA P 26 1.003 1.686 12.317 1.00 1.00 P C\nATOM 283 HA ALA P 26 1.959 1.818 12.804 1.00 0.00 P H\nATOM 284 CB ALA P 26 0.664 2.963 11.524 1.00 0.00 P C\nATOM 285 HB1 ALA P 26 0.622 3.847 12.194 1.00 0.00 P H\nATOM 286 HB2 ALA P 26 1.444 3.146 10.755 1.00 0.00 P H\nATOM 287 HB3 ALA P 26 -0.313 2.861 11.005 1.00 0.00 P H\nATOM 288 C ALA P 26 -0.053 1.496 13.374 1.00 1.00 P C\nATOM 289 O ALA P 26 0.154 1.852 14.532 1.00 1.00 P O\nATOM 290 N ALA P 27 -1.211 0.910 12.984 1.00 1.00 P N\nATOM 291 HN ALA P 27 -1.340 0.629 12.035 0.00 0.00 P H\nATOM 292 CA ALA P 27 -2.333 0.633 13.851 1.00 1.00 P C\nATOM 293 HA ALA P 27 -2.607 1.560 14.336 1.00 0.00 P H\nATOM 294 CB ALA P 27 -3.543 0.101 13.060 1.00 0.00 P C\nATOM 295 HB1 ALA P 27 -4.411 -0.071 13.732 1.00 0.00 P H\nATOM 296 HB2 ALA P 27 -3.843 0.843 12.289 1.00 0.00 P H\nATOM 297 HB3 ALA P 27 -3.295 -0.851 12.545 1.00 0.00 P H\nATOM 298 C ALA P 27 -1.985 -0.379 14.912 1.00 1.00 P C\nATOM 299 O ALA P 27 -2.367 -0.224 16.070 1.00 1.00 P O\nATOM 300 N ALA P 28 -1.230 -1.436 14.524 1.00 1.00 P N\nATOM 301 HN ALA P 28 -0.934 -1.524 13.575 0.00 0.00 P H\nATOM 302 CA ALA P 28 -0.785 -2.499 15.395 1.00 1.00 P C\nATOM 303 HA ALA P 28 -1.658 -2.908 15.884 1.00 0.00 P H\nATOM 304 CB ALA P 28 -0.078 -3.619 14.607 1.00 0.00 P C\nATOM 305 HB1 ALA P 28 0.225 -4.448 15.281 1.00 0.00 P H\nATOM 306 HB2 ALA P 28 -0.768 -4.030 13.839 1.00 0.00 P H\nATOM 307 HB3 ALA P 28 0.824 -3.232 14.087 1.00 0.00 P H\nATOM 308 C ALA P 28 0.166 -1.997 16.450 1.00 1.00 P C\nATOM 309 O ALA P 28 0.075 -2.394 17.610 1.00 1.00 P O\nATOM 310 N ALA P 29 1.096 -1.093 16.056 1.00 1.00 P N\nATOM 311 HN ALA P 29 1.136 -0.792 15.106 0.00 0.00 P H\nATOM 312 CA ALA P 29 2.082 -0.489 16.922 1.00 1.00 P C\nATOM 313 HA ALA P 29 2.619 -1.289 17.413 1.00 0.00 P H\nATOM 314 CB ALA P 29 3.081 0.375 16.128 1.00 0.00 P C\nATOM 315 HB1 ALA P 29 3.856 0.802 16.799 1.00 0.00 P H\nATOM 316 HB2 ALA P 29 3.590 -0.248 15.362 1.00 0.00 P H\nATOM 317 HB3 ALA P 29 2.561 1.206 15.606 1.00 0.00 P H\nATOM 318 C ALA P 29 1.445 0.379 17.975 1.00 1.00 P C\nATOM 319 O ALA P 29 1.852 0.352 19.135 1.00 1.00 P O\nATOM 320 N ALA P 30 0.410 1.160 17.579 1.00 1.00 P N\nATOM 321 HN ALA P 30 0.105 1.151 16.630 0.00 0.00 P H\nATOM 322 CA ALA P 30 -0.336 2.046 18.443 1.00 1.00 P C\nATOM 323 HA ALA P 30 0.373 2.700 18.930 1.00 0.00 P H\nATOM 324 CB ALA P 30 -1.343 2.898 17.647 1.00 0.00 P C\nATOM 325 HB1 ALA P 30 -1.883 3.602 18.316 1.00 0.00 P H\nATOM 326 HB2 ALA P 30 -0.805 3.494 16.878 1.00 0.00 P H\nATOM 327 HB3 ALA P 30 -2.086 2.256 17.128 1.00 0.00 P H\nATOM 328 C ALA P 30 -1.096 1.288 19.500 1.00 1.00 P C\nATOM 329 O ALA P 30 -1.134 1.701 20.657 1.00 1.00 P O\nATOM 330 N ALA P 31 -1.708 0.143 19.110 1.00 1.00 P N\nATOM 331 HN ALA P 31 -1.651 -0.163 18.163 0.00 0.00 P H\nATOM 332 CA ALA P 31 -2.472 -0.725 19.977 1.00 1.00 P C\nATOM 333 HA ALA P 31 -3.228 -0.121 20.458 1.00 0.00 P H\nATOM 334 CB ALA P 31 -3.159 -1.855 19.187 1.00 0.00 P C\nATOM 335 HB1 ALA P 31 -3.774 -2.490 19.858 1.00 0.00 P H\nATOM 336 HB2 ALA P 31 -3.826 -1.419 18.413 1.00 0.00 P H\nATOM 337 HB3 ALA P 31 -2.409 -2.495 18.675 1.00 0.00 P H\nATOM 338 C ALA P 31 -1.610 -1.353 21.041 1.00 1.00 P C\nATOM 339 O ALA P 31 -2.018 -1.444 22.197 1.00 1.00 P O\nATOM 340 N ALA P 32 -0.384 -1.788 20.660 1.00 1.00 P N\nATOM 341 HN ALA P 32 -0.085 -1.693 19.714 0.00 0.00 P H\nATOM 342 CA ALA P 32 0.583 -2.404 21.540 1.00 1.00 P C\nATOM 343 HA ALA P 32 0.097 -3.237 22.028 1.00 0.00 P H\nATOM 344 CB ALA P 32 1.808 -2.921 20.761 1.00 0.00 P C\nATOM 345 HB1 ALA P 32 2.526 -3.425 21.442 1.00 0.00 P H\nATOM 346 HB2 ALA P 32 1.482 -3.656 19.994 1.00 0.00 P H\nATOM 347 HB3 ALA P 32 2.330 -2.089 20.242 1.00 0.00 P H\nATOM 348 C ALA P 32 1.069 -1.445 22.596 1.00 1.00 P C\nATOM 349 O ALA P 32 1.201 -1.815 23.762 1.00 1.00 P O\nATOM 350 N ALA P 33 1.327 -0.176 22.195 1.00 1.00 P N\nATOM 351 HN ALA P 33 1.199 0.088 21.241 0.00 0.00 P H\nATOM 352 CA ALA P 33 1.790 0.888 23.057 1.00 1.00 P C\nATOM 353 HA ALA P 33 2.684 0.539 23.554 1.00 0.00 P H\nATOM 354 CB ALA P 33 2.123 2.161 22.255 1.00 0.00 P C\nATOM 355 HB1 ALA P 33 2.513 2.959 22.922 1.00 0.00 P H\nATOM 356 HB2 ALA P 33 2.901 1.933 21.495 1.00 0.00 P H\nATOM 357 HB3 ALA P 33 1.225 2.544 21.725 1.00 0.00 P H\nATOM 358 C ALA P 33 0.765 1.246 24.102 1.00 1.00 P C\nATOM 359 O ALA P 33 1.107 1.451 25.266 1.00 1.00 P O\nATOM 360 N ALA P 34 -0.526 1.306 23.693 1.00 1.00 P N\nATOM 361 HN ALA P 34 -0.762 1.125 22.742 0.00 0.00 P H\nATOM 362 CA ALA P 34 -1.655 1.614 24.542 1.00 1.00 P C\nATOM 363 HA ALA P 34 -1.450 2.558 25.027 1.00 0.00 P H\nATOM 364 CB ALA P 34 -2.958 1.736 23.730 1.00 0.00 P C\nATOM 365 HB1 ALA P 34 -3.811 2.009 24.387 1.00 0.00 P H\nATOM 366 HB2 ALA P 34 -2.847 2.528 22.958 1.00 0.00 P H\nATOM 367 HB3 ALA P 34 -3.196 0.782 23.213 1.00 0.00 P H\nATOM 368 C ALA P 34 -1.858 0.563 25.602 1.00 1.00 P C\nATOM 369 O ALA P 34 -2.132 0.883 26.757 1.00 1.00 P O\nATOM 370 C ALA P 35 -0.684 -1.962 27.096 1.00 1.00 P C\nATOM 371 OT1 ALA P 35 0.296 -1.180 26.981 0.00 1.00 P O\nATOM 372 OT2 ALA P 35 -0.767 -2.844 27.992 0.00 1.00 P O\nATOM 373 N ALA P 35 -1.697 -0.725 25.219 1.00 1.00 P N\nATOM 374 HN ALA P 35 -1.457 -0.956 24.279 0.00 0.00 P H\nATOM 375 CA ALA P 35 -1.857 -1.852 26.105 1.00 1.00 P C\nATOM 376 HA ALA P 35 -2.773 -1.708 26.663 1.00 0.00 P H\nATOM 377 CB ALA P 35 -1.950 -3.175 25.321 1.00 0.00 P C\nATOM 378 HB1 ALA P 35 -2.121 -4.032 26.006 1.00 0.00 P H\nATOM 379 HB2 ALA P 35 -2.797 -3.129 24.603 1.00 0.00 P H\nATOM 380 HB3 ALA P 35 -1.017 -3.355 24.746 1.00 0.00 P H\nEND\"\"\";\nwith open(\"test.pdb\", \"w\") as text_file:\n text_file.write(pdbstring)",
"prompt_number": 5,
"outputs": [],
"language": "python",
"trusted": true,
"collapsed": false
},
{
"metadata": {},
"cell_type": "code",
"input": "!ls *.pdb",
"prompt_number": 6,
"outputs": [
{
"output_type": "stream",
"text": "1YY8.clean.pdb\t1YY8.pdb A35_R1A18.clean.pdb A35_R1A18.pdb test.pdb\r\n",
"stream": "stdout"
}
],
"language": "python",
"trusted": true,
"collapsed": false
},
{
"metadata": {},
"cell_type": "code",
"input": "pose = r.pose_from_pdb(\"A35_R1A18.pdb\")\ntarget_resid = 18\nprint pose.pdb_info()",
"prompt_number": 7,
"outputs": [
{
"output_type": "stream",
"text": "PDB file name: A35_R1A18.pdb\n Pose Range Chain PDB Range | #Residues #Atoms\n\n0001 -- 0035 P 0001 -- 0035 | 0035 residues; 00380 atoms\n TOTAL | 0035 residues; 00380 atoms\n\n",
"stream": "stdout"
}
],
"language": "python",
"trusted": true,
"collapsed": false
},
{
"metadata": {},
"cell_type": "code",
"input": "pr=np.array(list(pose.residue(target_resid).atom('CA').xyz()))\npdb=np.array([2.039, -0.819, 0.079])\nprint pdb-pr\npr=np.array(list(pose.residue(target_resid).atom('CB').xyz()))\npdb=np.array([3.162, -0.087, -0.699])\nprint pdb-pr\npr=np.array(list(pose.residue(target_resid).atom('SG').xyz()))\npdb=np.array([4.666, 0.250, 0.284 ])\nprint pdb-pr\npr=np.array(list(pose.residue(target_resid).atom('N1').xyz()))\npdb=np.array([7.016, -1.451, 4.891 ])\nprint pdb-pr",
"prompt_number": 9,
"outputs": [
{
"output_type": "stream",
"text": "[ 0. 0. 0.]\n[ 0.19247554 -0.02155985 0.1735812 ]\n[ 0.35272151 -0.57848878 0.34102605]\n[-0.12854559 1.76254473 0.43158213]\n",
"stream": "stdout"
}
],
"language": "python",
"trusted": true,
"collapsed": false
},
{
"metadata": {},
"cell_type": "code",
"input": "#Other residues are OK\npr=np.array(list(pose.residue(16).atom('CA').xyz()))\npdb=np.array([-2.217, 0.830, -3.004])\nprint pdb-pr\npr=np.array(list(pose.residue(16).atom('CB').xyz()))\npdb=np.array([-3.482, 0.447, -3.797])\nprint pdb-pr",
"prompt_number": 12,
"outputs": [
{
"output_type": "stream",
"text": "[ 0. 0. 0.]\n[ 0. 0. 0.]\n",
"stream": "stdout"
}
],
"language": "python",
"trusted": true,
"collapsed": false
},
{
"metadata": {},
"cell_type": "code",
"input": "",
"outputs": [],
"language": "python",
"trusted": true,
"collapsed": false
}
],
"metadata": {}
}
],
"metadata": {
"name": "",
"signature": "sha256:d336dc43cd1a87ac4b7fb27acabd93aef08ee30e82c0fdcf2865b2f2c9696f65",
"gist_id": "b9ee7816415d742c1909"
},
"nbformat": 3
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment