from __future__ import absolute_import, division, print_function import os from libtbx import easy_run pdb_string = ''' CRYST1 111.035 111.035 103.765 90.00 90.00 90.00 P 42 21 2 SCALE1 0.009006 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009637 0.00000 ATOM 1 CG HIS A 94 4.447 42.151 13.943 0.77 17.81 C ATOM 2 ND1 HIS A 94 5.032 40.915 13.774 0.73 17.16 N ATOM 3 CD2 HIS A 94 4.981 42.659 15.076 0.74 17.98 C ATOM 4 CE1 HIS A 94 5.861 40.696 14.786 0.74 16.72 C ATOM 5 NE2 HIS A 94 5.842 41.736 15.605 0.77 17.63 N ATOM 6 HD1 HIS A 94 4.884 40.375 13.121 0.80 20.60 H ATOM 7 HD2 HIS A 94 4.794 43.496 15.436 1.00 21.59 H ATOM 8 HE1 HIS A 94 6.375 39.930 14.902 1.00 20.08 H ATOM 9 C GLU A 95 2.025 43.133 17.485 0.67 19.15 C ATOM 10 O GLU A 95 2.858 42.410 18.055 0.71 20.41 O ATOM 11 N PHE A 96 2.183 44.438 17.387 0.71 19.57 N ATOM 12 CA PHE A 96 3.407 45.155 17.764 0.71 20.32 C ATOM 13 C PHE A 96 3.295 45.550 19.225 0.74 20.62 C ATOM 14 CD1 PHE A 96 6.139 46.430 16.838 0.81 22.37 C ATOM 15 CE1 PHE A 96 7.333 47.130 16.925 0.71 22.35 C ATOM 16 HA PHE A 96 4.182 44.577 17.687 1.00 24.39 H ATOM 17 HD1 PHE A 96 6.161 45.512 16.690 1.00 26.85 H ATOM 18 HE1 PHE A 96 8.139 46.677 16.825 1.00 26.83 H ATOM 19 N LYS A 97 3.603 44.608 20.107 0.77 20.43 N ATOM 20 CA LYS A 97 3.415 44.727 21.542 0.72 20.44 C ATOM 21 C LYS A 97 4.641 44.097 22.190 0.78 20.27 C ATOM 22 O LYS A 97 4.610 42.973 22.721 0.74 20.47 O ATOM 23 H LYS A 97 3.940 43.850 19.882 1.00 24.53 H ATOM 24 HA LYS A 97 3.377 45.661 21.803 1.00 24.54 H ATOM 25 HB2 LYS A 97 2.092 43.190 21.621 1.00 25.53 H ATOM 26 N CYS A 98 5.742 44.842 22.169 0.68 19.66 N ATOM 27 CA CYS A 98 7.031 44.270 22.542 0.67 19.58 C ATOM 28 O CYS A 98 7.973 43.190 24.445 0.77 21.13 O ATOM 29 CB CYS A 98 8.182 45.122 22.026 0.60 19.62 C ATOM 30 SG CYS A 98 8.101 45.543 20.265 0.76 20.50 S ATOM 31 H CYS A 98 5.771 45.672 21.946 1.00 23.60 H ATOM 32 HA CYS A 98 7.094 43.403 22.111 1.00 23.51 H ATOM 33 HB2 CYS A 98 8.193 45.954 22.523 1.00 23.55 H ATOM 34 HB3 CYS A 98 9.009 44.637 22.171 0.93 23.55 H ATOM 35 CA CYS A 101 7.161 39.577 23.994 0.62 17.59 C ATOM 36 CB CYS A 101 7.310 40.364 22.701 0.65 17.76 C ATOM 37 SG CYS A 101 7.640 39.283 21.296 0.72 18.31 S ATOM 38 HA CYS A 101 6.486 38.892 23.868 1.00 21.12 H ATOM 39 HB2 CYS A 101 6.488 40.849 22.525 1.00 21.32 H ATOM 40 HB3 CYS A 101 8.049 40.985 22.788 1.00 21.32 H ATOM 41 N ARG A 103 10.777 37.930 22.421 0.66 17.18 N ATOM 42 CA ARG A 103 11.924 38.373 21.621 0.72 17.68 C ATOM 43 C ARG A 103 12.256 39.854 21.815 0.73 17.82 C ATOM 44 O ARG A 103 13.074 40.388 21.068 0.76 19.13 O ATOM 45 CB ARG A 103 11.725 38.036 20.147 0.73 18.00 C ATOM 46 H ARG A 103 10.036 38.305 22.200 1.00 20.63 H ATOM 47 HB2 ARG A 103 10.867 38.386 19.860 1.00 21.62 H ATOM 48 HB3 ARG A 103 12.439 38.448 19.634 1.00 21.62 H ATOM 49 N ARG A 104 11.684 40.513 22.818 0.73 18.25 N ATOM 50 CA ARG A 104 11.837 41.939 23.001 0.71 19.44 C ATOM 51 C ARG A 104 13.290 42.386 22.948 0.79 20.04 C ATOM 52 O ARG A 104 13.564 43.489 22.450 0.74 21.77 O ATOM 53 CB ARG A 104 11.180 42.351 24.315 0.65 20.65 C ATOM 54 H ARG A 104 11.191 40.146 23.419 1.00 21.92 H ATOM 55 HA ARG A 104 11.387 42.396 22.274 1.00 23.33 H ATOM 56 HB2 ARG A 104 10.224 42.216 24.216 1.00 24.79 H ATOM 57 HG3 ARG A 104 10.929 44.363 24.199 1.00 26.63 H ATOM 58 CA CYS A 107 14.141 40.912 17.640 0.74 16.49 C ATOM 59 CB CYS A 107 12.803 41.522 18.025 0.67 16.85 C ATOM 60 SG CYS A 107 11.577 41.287 16.684 0.72 16.87 S ATOM 61 HA CYS A 107 14.061 39.968 17.432 1.00 19.80 H ATOM 62 HB2 CYS A 107 12.470 41.091 18.828 1.00 20.23 H ATOM 63 HB3 CYS A 107 12.913 42.473 18.181 1.00 20.23 H ATOM 64 CA PHE A 109 11.822 43.112 13.160 0.70 16.48 C ATOM 65 C PHE A 109 11.778 44.447 13.912 0.71 16.79 C ATOM 66 CB PHE A 109 10.477 42.411 13.152 0.76 17.33 C ATOM 67 CG PHE A 109 9.396 43.177 12.443 0.75 17.14 C ATOM 68 CD2 PHE A 109 8.246 43.568 13.102 0.74 18.13 C ATOM 69 CE2 PHE A 109 7.222 44.234 12.410 0.74 18.70 C ATOM 70 H PHE A 109 12.563 41.592 14.165 1.00 19.86 H ATOM 71 HB3 PHE A 109 10.190 42.276 14.069 1.00 20.81 H ATOM 72 HD2 PHE A 109 8.150 43.389 14.009 1.00 21.76 H ATOM 73 HE2 PHE A 109 6.431 44.453 12.848 1.00 22.46 H ATOM 74 N LEU A 110 11.819 44.413 15.247 0.72 17.76 N ATOM 75 CA LEU A 110 11.851 45.667 16.003 0.78 18.06 C ATOM 76 CB LEU A 110 11.929 45.370 17.496 0.74 18.64 C ATOM 77 CG LEU A 110 12.054 46.598 18.401 0.76 19.61 C ATOM 78 CD1 LEU A 110 10.914 47.577 18.191 0.61 19.05 C ATOM 79 CD2 LEU A 110 12.114 46.135 19.824 0.68 20.47 C ATOM 80 H LEU A 110 11.830 43.699 15.727 1.00 21.32 H ATOM 81 HA LEU A 110 11.032 46.164 15.853 1.00 21.69 H ATOM 82 HB2 LEU A 110 11.122 44.899 17.756 1.00 22.38 H ATOM 83 HB3 LEU A 110 12.706 44.812 17.656 1.00 22.38 H ATOM 84 HD13 LEU A 110 10.071 47.104 18.279 1.00 22.87 H ATOM 85 HD22 LEU A 110 11.317 45.621 20.024 1.00 24.58 H ATOM 86 HD23 LEU A 110 12.903 45.582 19.943 1.00 24.58 H ATOM 87 HG21 VAL A 113 8.468 47.188 13.530 1.00 22.60 H ATOM 88 CB LYS A 146 4.922 37.238 16.068 0.63 16.22 C ATOM 89 CG LYS A 146 4.385 37.431 17.504 0.55 15.69 C ATOM 90 CD LYS A 146 4.168 38.856 17.880 0.56 17.24 C ATOM 91 CE LYS A 146 3.869 38.984 19.365 0.63 18.84 C ATOM 92 NZ LYS A 146 3.526 40.252 19.782 0.48 19.13 N ATOM 93 HA LYS A 146 3.917 38.713 15.052 1.00 19.83 H ATOM 94 HB3 LYS A 146 5.761 37.720 15.999 1.00 19.48 H ATOM 95 HG3 LYS A 146 5.024 37.055 18.129 1.00 18.84 H ATOM 96 HD2 LYS A 146 4.968 39.368 17.682 1.00 20.70 H ATOM 97 HD3 LYS A 146 3.415 39.211 17.383 1.00 20.70 H ATOM 98 HE2 LYS A 146 3.128 38.397 19.581 0.49 22.62 H ATOM 99 HE3 LYS A 146 4.659 38.719 19.862 1.00 22.62 H ATOM 100 HZ1 LYS A 146 2.809 40.535 19.337 1.00 22.96 H ATOM 101 HZ2 LYS A 146 3.343 40.246 20.653 1.00 22.96 H ATOM 102 HZ3 LYS A 146 4.200 40.814 19.632 1.00 22.96 H ATOM 103 CA VAL A 202 10.548 37.321 15.536 0.69 15.15 C ATOM 104 C VAL A 202 10.068 36.258 16.517 0.71 15.90 C ATOM 105 CB VAL A 202 9.385 37.927 14.733 0.65 14.91 C ATOM 106 CG1 VAL A 202 9.864 39.187 13.988 0.68 16.53 C ATOM 107 CG2 VAL A 202 8.776 36.926 13.790 0.63 15.08 C ATOM 108 HA VAL A 202 10.956 38.035 16.051 1.00 18.20 H ATOM 109 HB VAL A 202 8.681 38.185 15.349 1.00 17.90 H ATOM 110 HG11 VAL A 202 9.123 39.557 13.484 1.00 19.84 H ATOM 111 HG12 VAL A 202 10.180 39.836 14.636 1.00 19.84 H ATOM 112 HG13 VAL A 202 10.584 38.943 13.386 1.00 19.84 H ATOM 113 HG21 VAL A 202 8.044 37.346 13.312 1.00 18.10 H ATOM 114 HG23 VAL A 202 8.447 36.170 14.301 1.00 18.10 H ATOM 115 N ALA A 203 9.030 36.578 17.292 0.72 15.95 N ATOM 116 CA ALA A 203 8.509 35.669 18.316 0.64 15.23 C ATOM 117 CB ALA A 203 8.039 36.486 19.524 0.52 14.58 C ATOM 118 H ALA A 203 8.606 37.324 17.242 1.00 19.15 H ATOM 119 HB1 ALA A 203 7.701 35.881 20.202 1.00 17.51 H ATOM 120 HB2 ALA A 203 8.790 36.990 19.876 1.00 17.51 H ATOM 121 HB3 ALA A 203 7.337 37.093 19.242 1.00 17.51 H TER HETATM 122 S1 SF4 A 605 6.161 42.357 19.418 0.72 18.36 S HETATM 123 S2 SF4 A 605 8.515 43.542 16.879 0.72 17.81 S HETATM 124 S3 SF4 A 605 9.700 42.134 20.034 0.73 18.33 S HETATM 125 S4 SF4 A 605 8.153 39.962 17.476 0.75 17.07 S HETATM 126 FE1 SF4 A 605 9.599 41.722 17.775 0.72 17.00 Fe HETATM 127 FE2 SF4 A 605 7.863 40.820 19.591 0.72 17.44 Fe HETATM 128 FE3 SF4 A 605 6.948 41.912 17.304 0.74 17.32 Fe HETATM 129 FE4 SF4 A 605 8.114 43.542 19.144 0.73 18.33 Fe END ''' def main(): with open('tst_mcl_03.pdb', 'w') as f: f.write(pdb_string) cmd = 'phenix.pdb_interpretation tst_mcl_03.pdb write_geo=1' print (cmd) rc = easy_run.go(cmd) assert os.path.exists('tst_mcl_03.pdb.geo') return rc.return_code if __name__ == '__main__': rc = main() assert not rc print('OK')