from __future__ import absolute_import, division, print_function from libtbx import easy_run import libtbx.load_env import os.path import time cryst_str = """\n CRYST1 34.917 22.246 44.017 90.00 90.00 90.00 P 1 SCALE1 0.028639 0.000000 0.000000 0.00000 SCALE2 0.000000 0.044952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022718 0.00000 """ # taken from phenix_regression/refinement/ncs/tst_ncs_0.py pdb_str = """\ ATOM 1 N ALA A 1 27.344 16.348 30.784 1.00 10.00 N ATOM 2 CA ALA A 1 26.429 15.281 31.335 1.00 10.00 C ATOM 3 C ALA A 1 26.610 14.025 30.603 1.00 10.00 C ATOM 4 O ALA A 1 26.479 13.979 29.356 1.00 10.00 O ATOM 5 CB ALA A 1 24.874 15.800 31.300 1.00 10.00 C ATOM 1 N ALA A 2 26.812 12.925 31.345 1.00 10.00 N ATOM 2 CA ALA A 2 27.084 11.577 30.797 1.00 10.00 C ATOM 3 C ALA A 2 25.856 10.737 30.707 1.00 10.00 C ATOM 4 O ALA A 2 25.741 9.860 29.891 1.00 10.00 O ATOM 5 CB ALA A 2 28.151 10.950 31.721 1.00 10.00 C ATOM 1 N ALA A 3 25.009 10.973 31.714 1.00 10.00 N ATOM 2 CA ALA A 3 23.621 10.543 31.560 1.00 10.00 C ATOM 3 C ALA A 3 23.023 11.008 30.214 1.00 10.00 C ATOM 4 O ALA A 3 22.786 10.233 29.249 1.00 10.00 O ATOM 5 CB ALA A 3 22.760 11.040 32.654 1.00 10.00 C ATOM 1 N ALA A 4 22.798 12.304 30.175 1.00 10.00 N ATOM 2 CA ALA A 4 22.329 13.084 28.981 1.00 10.00 C ATOM 3 C ALA A 4 23.116 12.816 27.721 1.00 10.00 C ATOM 4 O ALA A 4 22.533 12.805 26.670 1.00 10.00 O ATOM 5 CB ALA A 4 22.372 14.607 29.318 1.00 10.00 C ATOM 1 N ALA A 5 24.448 12.622 27.823 1.00 10.00 N ATOM 2 CA ALA A 5 25.228 12.407 26.573 1.00 10.00 C ATOM 3 C ALA A 5 25.222 10.947 26.143 1.00 10.00 C ATOM 4 O ALA A 5 25.386 10.664 24.983 1.00 10.00 O ATOM 5 CB ALA A 5 26.634 12.906 26.746 1.00 10.00 C ATOM 1 N ALA A 6 24.976 10.048 27.071 1.00 10.00 N ATOM 2 CA ALA A 6 24.857 8.614 26.805 1.00 10.00 C ATOM 3 C ALA A 6 23.537 8.349 26.054 1.00 10.00 C ATOM 4 O ALA A 6 23.439 7.570 25.057 1.00 10.00 O ATOM 5 CB ALA A 6 24.874 7.845 28.114 1.00 10.00 C ATOM 1 N ALA A 7 22.542 9.039 26.580 1.00 10.00 N ATOM 2 CA ALA A 7 21.228 8.903 25.942 1.00 10.00 C ATOM 3 C ALA A 7 21.329 9.698 24.628 1.00 10.00 C ATOM 4 O ALA A 7 20.707 9.383 23.632 1.00 10.00 O ATOM 5 CB ALA A 7 20.146 9.465 26.862 1.00 10.00 C ATOM 1 N ALA A 8 22.181 10.696 24.613 1.00 10.00 N ATOM 2 CA ALA A 8 22.526 11.372 23.378 1.00 10.00 C ATOM 3 C ALA A 8 23.351 10.555 22.448 1.00 10.00 C ATOM 4 O ALA A 8 23.618 10.883 21.252 1.00 10.00 O ATOM 5 CB ALA A 8 23.168 12.697 23.693 1.00 10.00 C ATOM 1 N ALA A 9 23.864 9.423 22.961 1.00 10.00 N ATOM 2 CA ALA A 9 24.785 8.541 22.264 1.00 10.00 C ATOM 3 C ALA A 9 24.057 7.451 21.484 1.00 10.00 C ATOM 4 O ALA A 9 24.127 7.381 20.257 1.00 10.00 O ATOM 5 CB ALA A 9 25.815 7.975 23.249 1.00 10.00 C ATOM 1 N ALA A 10 23.518 6.548 22.264 1.00 10.00 N ATOM 2 CA ALA A 10 22.629 5.525 21.690 1.00 10.00 C ATOM 3 C ALA A 10 21.549 6.308 21.009 1.00 10.00 C ATOM 4 O ALA A 10 21.114 5.933 19.930 1.00 10.00 O ATOM 5 CB ALA A 10 22.057 4.714 22.784 1.00 10.00 C ATOM 1 N ALA A 11 21.120 7.452 21.541 1.00 10.00 N ATOM 2 CA ALA A 11 20.186 8.260 20.874 1.00 10.00 C ATOM 3 C ALA A 11 20.978 9.215 19.937 1.00 10.00 C ATOM 4 O ALA A 11 20.386 10.177 19.507 1.00 10.00 O ATOM 5 CB ALA A 11 19.295 9.031 21.867 1.00 10.00 C ATOM 1 N ALA A 12 22.222 8.932 19.598 1.00 10.00 N ATOM 2 CA ALA A 12 22.896 9.709 18.563 1.00 10.00 C ATOM 3 C ALA A 12 22.924 8.925 17.308 1.00 10.00 C ATOM 4 O ALA A 12 22.982 9.445 16.193 1.00 10.00 O ATOM 5 CB ALA A 12 24.294 10.138 18.994 1.00 10.00 C ATOM 1 N ALA A 13 22.951 7.633 17.508 1.00 10.00 N ATOM 2 CA ALA A 13 22.709 6.629 16.554 1.00 10.00 C ATOM 3 C ALA A 13 21.275 6.673 16.206 1.00 10.00 C ATOM 4 O ALA A 13 20.870 6.521 15.092 1.00 10.00 O ATOM 5 CB ALA A 13 23.077 5.254 17.025 1.00 10.00 C ATOM 1 N ALA A 14 20.471 6.929 17.226 1.00 10.00 N ATOM 2 CA ALA A 14 19.039 6.992 17.025 1.00 10.00 C ATOM 3 C ALA A 14 18.676 8.380 16.528 1.00 10.00 C ATOM 4 O ALA A 14 17.748 8.556 15.761 1.00 10.00 O ATOM 5 CB ALA A 14 18.240 6.715 18.272 1.00 10.00 C ATOM 1 N ALA A 15 19.381 9.390 17.055 1.00 10.00 N ATOM 2 CA ALA A 15 19.204 10.743 16.669 1.00 10.00 C ATOM 3 C ALA A 15 19.407 10.807 15.174 1.00 10.00 C ATOM 4 O ALA A 15 18.402 10.987 14.424 1.00 10.00 O ATOM 5 CB ALA A 15 20.190 11.665 17.493 1.00 10.00 C ATOM 1 N ALA A 16 20.702 10.653 14.831 1.00 10.00 N ATOM 2 CA ALA A 16 21.206 10.546 13.480 1.00 10.00 C ATOM 3 C ALA A 16 20.484 9.612 12.585 1.00 10.00 C ATOM 4 O ALA A 16 20.380 9.918 11.386 1.00 10.00 O ATOM 5 CB ALA A 16 22.631 10.174 13.475 1.00 10.00 C ATOM 1 N ALA A 17 20.064 8.475 13.175 1.00 10.00 N ATOM 2 CA ALA A 17 19.355 7.473 12.426 1.00 10.00 C ATOM 3 C ALA A 17 17.924 7.807 12.064 1.00 10.00 C ATOM 4 O ALA A 17 17.535 7.721 10.871 1.00 10.00 O ATOM 5 CB ALA A 17 19.359 6.123 13.216 1.00 10.00 C ATOM 1 N ALA A 18 17.152 8.115 13.031 1.00 10.00 N ATOM 2 CA ALA A 18 15.835 8.594 12.861 1.00 10.00 C ATOM 3 C ALA A 18 15.811 9.835 11.861 1.00 10.00 C ATOM 4 O ALA A 18 15.020 9.889 10.868 1.00 10.00 O ATOM 5 CB ALA A 18 15.272 8.918 14.234 1.00 10.00 C ATOM 1 N ALA A 19 16.661 10.845 12.100 1.00 10.00 N ATOM 2 CA ALA A 19 16.435 12.061 11.275 1.00 10.00 C ATOM 3 C ALA A 19 17.004 11.815 9.833 1.00 10.00 C ATOM 4 O ALA A 19 16.334 12.117 8.857 1.00 10.00 O ATOM 5 CB ALA A 19 17.059 13.242 11.866 1.00 10.00 C ATOM 1 N ALA A 20 18.191 11.200 9.841 1.00 10.00 N ATOM 2 CA ALA A 20 19.091 11.247 8.697 1.00 10.00 C ATOM 3 C ALA A 20 19.549 9.835 8.231 1.00 10.00 C ATOM 4 O ALA A 20 20.670 9.692 7.663 1.00 10.00 O ATOM 5 CB ALA A 20 20.326 12.105 9.035 1.00 10.00 C ATOM 1 N ALA A 21 18.654 8.850 8.523 1.00 10.00 N ATOM 2 CA ALA A 21 18.827 7.437 8.168 1.00 10.00 C ATOM 3 C ALA A 21 17.565 6.607 8.282 1.00 10.00 C ATOM 4 O ALA A 21 16.485 6.992 7.820 1.00 10.00 O ATOM 5 CB ALA A 21 19.888 6.838 8.983 1.00 10.00 C """ def exercise_01(prefix="tst_mi_ext_map_test_01"): """ Simple run to a completion with reference map. no SS annotations. """ pdb_file = open("%s_start.pdb" % prefix, "w") pdb_file.write(cryst_str) pdb_file.write(pdb_str) pdb_file.close() # making map fmodel_cmd = " ".join([ "phenix.fmodel", "%s_start.pdb" % prefix, "high_resolution=5", # "generate_fake_p1_symmetry=True", ]) print(fmodel_cmd) easy_run.call(fmodel_cmd) mtz2map_cmd = " ".join([ "phenix.mtz2map", "%s_start.pdb.mtz" % prefix, "include_fmodel=True"]) print(mtz2map_cmd) easy_run.call(mtz2map_cmd) # STOP() cmd = " ".join([ "phenix.model_idealization", "%s_start.pdb" % prefix, "%s_start.pdb_fmodel.ccp4" % prefix, "use_map_for_reference=True", "number_of_refinement_cycles=1", "run_minimization_first=False", "loop_idealization.number_of_ccd_trials=1", "n_macro=1", "debug=True", ">%s.log" % prefix]) print(cmd) assert not easy_run.call(cmd) res_log = open("%s.log" % prefix, "r") log_lines = res_log.readlines() for l in [ # "Secondary structure substitution step will be skipped\n", " Minimizing...\n", "Using map as reference\n", "Preparing user map...\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() # assert os.path.isfile("%s_start.pdb_idealized.pdb" % prefix) if (__name__ == "__main__"): t0 = time.time() if (not libtbx.env.has_module(name="probe")): print("Skipping: probe not configured") else: exercise_01() print("Time: %.2f" % (time.time() - t0)) print("OK")