from __future__ import absolute_import, division, print_function import os from libtbx import easy_run pdb_string = ''' CRYST1 589.160 589.160 589.160 90.00 90.00 90.00 P 1 SCALE1 0.001697 0.000000 0.000000 0.00000 SCALE2 0.000000 0.001697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001697 0.00000 ATOM 1 N CYS L 104 339.804 329.680 261.810 1.00 58.36 N ATOM 2 CA CYS L 104 338.530 329.122 261.395 1.00 60.90 C ATOM 3 C CYS L 104 337.438 329.433 262.396 1.00 63.21 C ATOM 4 O CYS L 104 336.436 330.048 262.048 1.00 65.22 O ATOM 5 CB CYS L 104 338.651 327.620 261.216 1.00 60.57 C ATOM 6 SG CYS L 104 339.341 326.788 262.654 1.00 60.22 S ATOM 7 N CYS L 108 338.113 325.778 267.745 1.00 68.92 N ATOM 8 CA CYS L 108 339.312 325.068 267.300 1.00 64.76 C ATOM 9 C CYS L 108 340.555 325.418 268.121 1.00 66.03 C ATOM 10 O CYS L 108 341.588 324.784 267.939 1.00 66.50 O ATOM 11 CB CYS L 108 339.571 325.286 265.807 1.00 60.82 C ATOM 12 SG CYS L 108 338.793 324.031 264.774 1.00 56.51 S ATOM 13 N CYS L 120 343.196 322.319 267.971 1.00 57.56 N ATOM 14 CA CYS L 120 342.863 321.598 266.735 1.00 57.89 C ATOM 15 C CYS L 120 344.051 321.463 265.784 1.00 59.16 C ATOM 16 O CYS L 120 344.945 322.303 265.759 1.00 57.82 O ATOM 17 CB CYS L 120 341.697 322.250 265.986 1.00 56.77 C ATOM 18 SG CYS L 120 341.374 321.502 264.369 1.00 53.53 S ATOM 19 N ILE L 121 344.035 320.383 265.006 1.00 61.55 N ATOM 20 CA ILE L 121 345.070 320.108 264.011 1.00 62.65 C ATOM 21 C ILE L 121 345.134 321.190 262.946 1.00 61.66 C ATOM 22 O ILE L 121 346.214 321.514 262.462 1.00 61.29 O ATOM 23 CB ILE L 121 344.869 318.724 263.337 1.00 64.79 C ATOM 24 CG1 ILE L 121 346.106 318.329 262.529 1.00 65.49 C ATOM 25 CG2 ILE L 121 343.629 318.694 262.442 1.00 64.60 C ATOM 26 CD1 ILE L 121 346.129 316.868 262.147 1.00 66.90 C ATOM 27 N CYS L 122 343.982 321.748 262.588 1.00 64.24 N ATOM 28 CA CYS L 122 343.921 322.801 261.579 1.00 68.72 C ATOM 29 C CYS L 122 344.962 323.861 261.847 1.00 69.64 C ATOM 30 O CYS L 122 345.597 324.371 260.927 1.00 73.06 O ATOM 31 CB CYS L 122 342.536 323.448 261.549 1.00 70.95 C ATOM 32 SG CYS L 122 342.155 324.561 262.930 1.00 73.02 S ATOM 33 N CYS L 145 338.912 319.344 260.063 1.00 94.97 N ATOM 34 CA CYS L 145 338.541 318.949 261.422 1.00 92.47 C ATOM 35 C CYS L 145 337.032 318.807 261.564 1.00 88.78 C ATOM 36 O CYS L 145 336.270 319.314 260.742 1.00 89.04 O ATOM 37 CB CYS L 145 339.074 319.959 262.435 1.00 93.38 C ATOM 38 SG CYS L 145 338.049 321.426 262.672 1.00 97.07 S ATOM 39 N CYS L 148 334.801 322.398 262.418 1.00 90.56 N ATOM 40 CA CYS L 148 334.536 323.276 261.291 1.00 88.35 C ATOM 41 C CYS L 148 335.420 322.848 260.130 1.00 93.31 C ATOM 42 O CYS L 148 336.536 322.377 260.342 1.00 95.93 O ATOM 43 CB CYS L 148 334.872 324.701 261.685 1.00 84.75 C ATOM 44 SG CYS L 148 336.541 324.858 262.342 1.00 79.52 S ATOM 45 N CYS L 150 338.090 323.242 257.957 1.00 99.57 N ATOM 46 CA CYS L 150 339.243 324.167 257.968 1.00 99.81 C ATOM 47 C CYS L 150 340.562 323.546 257.510 1.00 98.81 C ATOM 48 O CYS L 150 341.485 323.322 258.299 1.00 93.05 O ATOM 49 CB CYS L 150 339.390 324.814 259.342 1.00 97.02 C ATOM 50 SG CYS L 150 339.376 323.663 260.725 1.00 94.12 S TER HETATM 51 ZN ZN L1000 337.686 325.976 263.586 1.00 31.11 Zn HETATM 52 ZN ZN L1001 340.645 325.701 261.809 1.00 38.33 Zn HETATM 53 ZN ZN L1002 340.121 322.858 263.346 1.00 15.24 Zn END ''' def main(): with open('tst_mcl_02.pdb', 'w') as f: f.write(pdb_string) cmd = 'phenix.pdb_interpretation tst_mcl_02.pdb write_geo=1' print (cmd) rc = easy_run.go(cmd) assert os.path.exists('tst_mcl_02.pdb.geo') return rc.return_code if __name__ == '__main__': rc = main() assert not rc print('OK')