from __future__ import absolute_import, division, print_function from libtbx import easy_run import libtbx.load_env import os.path import time # taken from phenix_regression/refinement/ncs/tst_ncs_0.py pdb_str = """\ CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 ATOM 1395 N GLY A 95 55.545 77.050 62.972 1.00 67.65 N ATOM 1396 CA GLY A 95 54.815 76.493 64.067 1.00 66.50 C ATOM 1397 C GLY A 95 55.509 76.948 65.306 1.00 65.94 C ATOM 1398 O GLY A 95 56.728 77.057 65.338 1.00 66.27 O ATOM 1399 N LYS A 96 54.733 77.220 66.367 1.00 65.59 N ATOM 1400 CA LYS A 96 55.263 77.542 67.659 1.00 67.02 C ATOM 1401 C LYS A 96 55.940 76.308 68.162 1.00 65.59 C ATOM 1402 O LYS A 96 56.897 76.361 68.935 1.00 65.24 O ATOM 1403 CB LYS A 96 54.152 77.941 68.646 1.00 69.25 C ATOM 1404 CG LYS A 96 53.150 78.931 68.042 1.00 68.89 C ATOM 1405 CD LYS A 96 51.947 79.224 68.942 1.00 67.92 C ATOM 1406 CE LYS A 96 50.602 79.121 68.220 1.00 71.86 C ATOM 1407 NZ LYS A 96 50.769 78.385 66.946 1.00 70.05 N ATOM 1408 N GLU A 97 55.411 75.151 67.727 1.00 63.83 N ATOM 1409 CA GLU A 97 55.703 73.848 68.246 1.00 62.40 C ATOM 1410 C GLU A 97 57.109 73.451 67.909 1.00 56.41 C ATOM 1411 O GLU A 97 57.815 74.145 67.178 1.00 54.82 O ATOM 1412 CB GLU A 97 54.732 72.787 67.705 1.00 69.38 C ATOM 1413 CG GLU A 97 53.280 73.274 67.765 1.00 77.38 C ATOM 1414 CD GLU A 97 52.416 72.412 66.855 1.00 83.20 C ATOM 1415 OE1 GLU A 97 52.933 71.941 65.807 1.00 84.20 O ATOM 1416 OE2 GLU A 97 51.218 72.220 67.198 1.00 84.08 O ATOM 1417 N ASP A 98 57.560 72.337 68.527 1.00 54.83 N ATOM 1418 CA ASP A 98 58.945 71.963 68.620 1.00 52.52 C ATOM 1419 C ASP A 98 59.391 71.254 67.375 1.00 45.70 C ATOM 1420 O ASP A 98 58.695 70.397 66.837 1.00 45.06 O ATOM 1421 CB ASP A 98 59.220 71.021 69.805 1.00 61.00 C ATOM 1422 CG ASP A 98 58.309 71.431 70.957 1.00 64.25 C ATOM 1423 OD1 ASP A 98 57.123 71.006 70.957 1.00 65.51 O ATOM 1424 OD2 ASP A 98 58.789 72.174 71.855 1.00 63.23 O ATOM 1425 N ALA A 99 60.588 71.627 66.874 1.00 40.59 N ATOM 1426 CA ALA A 99 61.188 71.036 65.709 1.00 34.76 C ATOM 1427 C ALA A 99 61.566 69.603 65.956 1.00 31.73 C ATOM 1428 O ALA A 99 61.242 68.714 65.169 1.00 24.61 O ATOM 1429 CB ALA A 99 62.480 71.767 65.318 1.00 35.50 C ATOM 1430 N ALA A 100 62.263 69.356 67.081 1.00 29.14 N ATOM 1431 CA ALA A 100 62.905 68.103 67.363 1.00 26.25 C ATOM 1432 C ALA A 100 63.894 67.769 66.291 1.00 24.22 C ATOM 1433 O ALA A 100 63.646 67.922 65.096 1.00 25.43 O ATOM 1434 CB ALA A 100 61.940 66.914 67.494 1.00 30.57 C ATOM 1435 N ASN A 101 65.061 67.266 66.721 1.00 24.03 N ATOM 1436 CA ASN A 101 66.043 66.814 65.791 1.00 25.16 C ATOM 1437 C ASN A 101 65.760 65.366 65.582 1.00 22.14 C ATOM 1438 O ASN A 101 66.599 64.515 65.877 1.00 22.24 O ATOM 1439 CB ASN A 101 67.447 66.846 66.398 1.00 30.60 C ATOM 1440 CG ASN A 101 68.318 67.948 65.831 1.00 33.80 C ATOM 1441 OD1 ASN A 101 69.536 67.907 65.989 1.00 37.78 O ATOM 1442 ND2 ASN A 101 67.719 68.969 65.169 1.00 34.81 N ATOM 1443 N ASN A 102 64.577 65.034 65.045 1.00 18.33 N ATOM 1444 CA ASN A 102 64.423 63.668 64.678 1.00 15.90 C ATOM 1445 C ASN A 102 63.381 63.583 63.621 1.00 14.00 C ATOM 1446 O ASN A 102 62.490 64.426 63.515 1.00 12.14 O ATOM 1447 CB ASN A 102 64.070 62.725 65.846 1.00 18.46 C ATOM 1448 CG ASN A 102 62.726 63.100 66.443 1.00 21.95 C ATOM 1449 OD1 ASN A 102 62.629 63.981 67.295 1.00 27.01 O ATOM 1450 ND2 ASN A 102 61.656 62.391 65.994 1.00 27.14 N ATOM 1451 N TYR A 103 63.516 62.534 62.799 1.00 10.81 N ATOM 1452 CA TYR A 103 62.708 62.269 61.655 1.00 6.91 C ATOM 1453 C TYR A 103 61.309 62.060 62.142 1.00 2.00 C ATOM 1454 O TYR A 103 60.349 62.519 61.526 1.00 2.00 O ATOM 1455 CB TYR A 103 63.217 60.995 60.944 1.00 3.80 C ATOM 1456 CG TYR A 103 62.318 60.589 59.826 1.00 9.36 C ATOM 1457 CD1 TYR A 103 62.305 61.252 58.626 1.00 9.82 C ATOM 1458 CD2 TYR A 103 61.478 59.505 59.974 1.00 8.69 C ATOM 1459 CE1 TYR A 103 61.465 60.854 57.606 1.00 8.11 C ATOM 1460 CE2 TYR A 103 60.651 59.094 58.966 1.00 13.62 C ATOM 1461 CZ TYR A 103 60.638 59.771 57.765 1.00 13.62 C ATOM 1462 OH TYR A 103 59.782 59.351 56.728 1.00 17.18 O ATOM 1463 N ALA A 104 61.153 61.334 63.263 1.00 4.07 N ATOM 1464 CA ALA A 104 59.857 60.824 63.598 1.00 6.65 C ATOM 1465 C ALA A 104 58.853 61.920 63.825 1.00 7.19 C ATOM 1466 O ALA A 104 57.788 61.896 63.211 1.00 6.00 O ATOM 1467 CB ALA A 104 59.885 59.966 64.870 1.00 11.87 C ATOM 1468 N ARG A 105 59.131 62.918 64.696 1.00 7.49 N ATOM 1469 CA ARG A 105 58.072 63.870 64.909 1.00 10.39 C ATOM 1470 C ARG A 105 57.876 64.604 63.636 1.00 11.29 C ATOM 1471 O ARG A 105 56.754 64.797 63.170 1.00 11.85 O ATOM 1472 CB ARG A 105 58.328 64.974 65.957 1.00 11.69 C ATOM 1473 CG ARG A 105 59.547 64.795 66.856 1.00 12.68 C ATOM 1474 CD ARG A 105 59.356 65.416 68.245 1.00 13.62 C ATOM 1475 NE ARG A 105 58.864 66.817 68.080 1.00 14.65 N ATOM 1476 CZ ARG A 105 57.573 67.139 68.396 1.00 16.77 C ATOM 1477 NH1 ARG A 105 56.696 66.163 68.773 1.00 18.53 N ATOM 1478 NH2 ARG A 105 57.160 68.439 68.341 1.00 18.02 N END """ def exercise_04(prefix="tst_mi_map_test_05"): """ Actually will try to CCD. Should include actual check for success. """ # without cryst pdb_file = open("%s_start.pdb" % prefix, "w") pdb_file.write(pdb_str) pdb_file.close() cmd = " ".join([ "phenix.model_idealization", "%s_start.pdb" % prefix, "use_map_for_reference=True", "run_minimization_first=False", "run_minimization_last=False", "loop_idealization.minimize_whole=False", "loop_idealization.number_of_ccd_trials=1", "number_of_refinement_cycles=1", "n_macro=1", "debug=True", # ">%s.log" % prefix, ]) print(cmd) assert not easy_run.call(cmd) # assert os.path.isfile("%s_start.pdb_all_idealized.pdb" % prefix) # res_log = open("%s.log" % prefix, "r") # log_lines = res_log.readlines() # # NCS constraints with map are not implemented yet # for l in [ # # "Using ncs\n", # "Using map as reference\n", # " Minimizing... (NCS)\n", # # "Ramachandran outliers: 0.00 0.00 0.00 0.00 0.00\n", # "All done.\n"]: # assert l in log_lines, "'%s' not in log file." % l # res_log.close() if (__name__ == "__main__"): t0 = time.time() if (not libtbx.env.has_module(name="probe")): print("Skipping: probe not configured") else: exercise_04() print("Time: %.2f" % (time.time() - t0)) print("OK")