from __future__ import absolute_import, division, print_function from libtbx import easy_run import sys pdb1exr_fragment = """\ CRYST1 25.015 29.415 52.761 89.54 86.10 82.39 P 1 1 ATOM 43 N GLU A 7 53.533 13.702 12.116 1.00 20.13 N ATOM 44 CA GLU A 7 53.762 12.263 12.038 1.00 18.74 C ATOM 45 C GLU A 7 52.498 11.484 11.693 1.00 16.59 C ATOM 46 O GLU A 7 52.569 10.583 10.885 1.00 17.01 O ATOM 47 CB GLU A 7 54.372 11.761 13.341 1.00 20.40 C ATOM 48 CG GLU A 7 54.593 10.273 13.376 1.00 25.03 C ATOM 49 CD GLU A 7 55.520 9.719 12.310 1.00 28.18 C ATOM 50 OE1 GLU A 7 56.482 10.353 11.807 1.00 41.67 O ATOM 51 OE2 GLU A 7 55.305 8.552 11.930 1.00 33.78 O ATOM 52 N GLN A 8 51.345 11.827 12.274 1.00 16.10 N ATOM 53 CA GLN A 8 50.125 11.194 11.846 1.00 15.79 C ATOM 54 C GLN A 8 49.860 11.431 10.346 1.00 14.53 C ATOM 55 O GLN A 8 49.477 10.500 9.631 1.00 14.74 O ATOM 56 CB GLN A 8 48.901 11.729 12.636 1.00 17.49 C ATOM 57 CG GLN A 8 48.898 11.267 14.104 1.00 19.61 C ATOM 58 CD GLN A 8 47.721 11.984 14.800 1.00 22.58 C ATOM 59 OE1 GLN A 8 47.751 13.197 14.980 1.00 23.84 O ATOM 60 NE2 GLN A 8 46.715 11.193 15.121 1.00 25.44 N ATOM 61 N AILE A 9 50.042 12.619 9.863 0.60 15.47 N ATOM 62 N BILE A 9 50.064 12.669 9.955 0.40 15.79 N ATOM 63 CA AILE A 9 49.760 12.880 8.443 0.60 16.16 C ATOM 64 CA BILE A 9 49.894 13.068 8.557 0.40 14.97 C ATOM 65 C AILE A 9 50.740 12.096 7.568 0.60 16.68 C ATOM 66 C BILE A 9 50.739 12.182 7.629 0.40 15.01 C ATOM 67 O AILE A 9 50.344 11.527 6.549 0.60 13.30 O ATOM 68 O BILE A 9 50.215 11.661 6.634 0.40 13.83 O ATOM 69 CB AILE A 9 49.712 14.388 8.233 0.60 17.94 C ATOM 70 CB BILE A 9 50.201 14.546 8.306 0.40 15.90 C ATOM 71 CG1AILE A 9 48.529 15.065 8.881 0.60 19.71 C ATOM 72 CG1BILE A 9 49.111 15.466 8.868 0.40 14.83 C ATOM 73 CG2AILE A 9 49.644 14.632 6.712 0.60 18.98 C ATOM 74 CG2BILE A 9 50.339 14.857 6.814 0.40 13.92 C ATOM 75 CD1AILE A 9 48.524 16.563 9.024 0.60 23.19 C ATOM 76 CD1BILE A 9 49.568 16.907 8.941 0.40 21.29 C ATOM 77 N ALA A 10 52.006 12.040 7.976 1.00 16.22 N ATOM 78 CA ALA A 10 52.970 11.271 7.207 1.00 15.86 C ATOM 79 C ALA A 10 52.525 9.824 7.134 1.00 14.08 C ATOM 80 O ALA A 10 52.586 9.200 6.066 1.00 14.53 O ATOM 81 CB ALA A 10 54.346 11.404 7.820 1.00 18.40 C HETATM 1515 O AHOH 2041 44.207 4.663 -11.870 0.33 8.04 O HETATM 1516 O BHOH 2042 44.917 5.551 -12.815 0.33 11.39 O HETATM 1517 O CHOH 2043 43.481 3.315 -12.617 0.33 10.33 O END """ def exercise(args): assert len(args) == 0 open("tmp_altloc_chain_break.pdb", "w").write(pdb1exr_fragment) command = " ".join([ "phenix.geometry_minimization", "cdl=False", "tmp_altloc_chain_break.pdb", "pdb_interpretation.nonbonded_weight=16", ">tmp_altloc_chain_break.zlog"]) easy_run.call(command=command) target_values = [] for line in open("tmp_altloc_chain_break.zlog","r").readlines(): line = line.strip() if (line.startswith("target: ")): target_values.append(float(line.split()[-1])) print(target_values) assert len(target_values) == 6 assert target_values[0] > 100 assert target_values[5] < 7 print("OK") if (__name__ == "__main__"): exercise(sys.argv[1:])