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 TER ATOM 1 N ALA B 1 16.348 17.420 35.897 1.00 50.00 N ATOM 2 CA ALA B 1 16.783 16.083 36.351 1.00 50.00 C ATOM 3 C ALA B 1 16.794 15.172 35.139 1.00 50.00 C ATOM 4 O ALA B 1 16.167 15.477 34.133 1.00 50.00 O ATOM 5 CB ALA B 1 15.785 15.534 37.468 1.00 50.00 C ATOM 1 N ALA B 2 17.491 14.058 35.255 1.00 50.00 N ATOM 2 CA ALA B 2 17.790 13.267 34.127 1.00 50.00 C ATOM 3 C ALA B 2 16.716 12.232 33.688 1.00 50.00 C ATOM 4 O ALA B 2 16.676 11.869 32.543 1.00 50.00 O ATOM 5 CB ALA B 2 19.125 12.656 34.415 1.00 50.00 C ATOM 1 N ALA B 3 15.904 11.687 34.605 1.00 50.00 N ATOM 2 CA ALA B 3 14.798 10.901 34.173 1.00 50.00 C ATOM 3 C ALA B 3 13.740 11.723 33.536 1.00 50.00 C ATOM 4 O ALA B 3 13.398 11.501 32.356 1.00 50.00 O ATOM 5 CB ALA B 3 14.148 10.176 35.403 1.00 50.00 C ATOM 1 N ALA B 4 13.239 12.708 34.247 1.00 50.00 N ATOM 2 CA ALA B 4 12.158 13.487 33.709 1.00 50.00 C ATOM 3 C ALA B 4 12.674 14.248 32.495 1.00 50.00 C ATOM 4 O ALA B 4 11.935 14.376 31.526 1.00 50.00 O ATOM 5 CB ALA B 4 11.553 14.432 34.712 1.00 50.00 C ATOM 1 N ALA B 5 13.947 14.627 32.479 1.00 50.00 N ATOM 2 CA ALA B 5 14.416 15.490 31.405 1.00 50.00 C ATOM 3 C ALA B 5 14.960 14.730 30.186 1.00 50.00 C ATOM 4 O ALA B 5 14.575 14.940 29.054 1.00 50.00 O ATOM 5 CB ALA B 5 15.464 16.431 31.928 1.00 50.00 C ATOM 1 N ALA B 6 15.867 13.827 30.546 1.00 50.00 N ATOM 2 CA ALA B 6 16.575 12.918 29.615 1.00 50.00 C ATOM 3 C ALA B 6 15.465 12.002 28.975 1.00 50.00 C ATOM 4 O ALA B 6 15.450 11.709 27.742 1.00 50.00 O ATOM 5 CB ALA B 6 17.632 12.157 30.362 1.00 50.00 C ATOM 1 N ALA B 7 14.542 11.597 29.783 1.00 50.00 N ATOM 2 CA ALA B 7 13.529 10.701 29.277 1.00 50.00 C ATOM 3 C ALA B 7 12.175 11.364 28.835 1.00 50.00 C ATOM 4 O ALA B 7 11.466 10.770 27.969 1.00 50.00 O ATOM 5 CB ALA B 7 13.161 9.644 30.376 1.00 50.00 C ATOM 1 N ALA B 8 11.753 12.455 29.452 1.00 50.00 N ATOM 2 CA ALA B 8 10.536 13.193 28.972 1.00 50.00 C ATOM 3 C ALA B 8 10.919 13.923 27.670 1.00 50.00 C ATOM 4 O ALA B 8 10.171 14.036 26.729 1.00 50.00 O ATOM 5 CB ALA B 8 10.032 14.139 30.014 1.00 50.00 C ATOM 1 N ALA B 9 12.185 14.247 27.579 1.00 50.00 N ATOM 2 CA ALA B 9 12.754 14.849 26.385 1.00 50.00 C ATOM 3 C ALA B 9 12.892 13.859 25.320 1.00 50.00 C ATOM 4 O ALA B 9 12.234 13.980 24.290 1.00 50.00 O ATOM 5 CB ALA B 9 14.108 15.448 26.695 1.00 50.00 C ATOM 1 N ALA B 10 13.655 12.794 25.566 1.00 50.00 N ATOM 2 CA ALA B 10 13.831 11.803 24.529 1.00 50.00 C ATOM 3 C ALA B 10 12.551 10.987 24.319 1.00 50.00 C ATOM 4 O ALA B 10 12.514 10.237 23.390 1.00 50.00 O ATOM 5 CB ALA B 10 15.024 10.750 24.992 1.00 50.00 C ATOM 1 N ALA B 11 11.558 11.184 25.126 1.00 50.00 N ATOM 2 CA ALA B 11 10.334 10.457 24.931 1.00 50.00 C ATOM 3 C ALA B 11 9.326 11.284 24.168 1.00 50.00 C ATOM 4 O ALA B 11 8.566 10.707 23.476 1.00 50.00 O ATOM 5 CB ALA B 11 9.644 10.042 26.251 1.00 50.00 C ATOM 1 N ALA B 12 9.277 12.611 24.334 1.00 50.00 N ATOM 2 CA ALA B 12 8.354 13.375 23.644 1.00 50.00 C ATOM 3 C ALA B 12 9.019 13.546 22.264 1.00 50.00 C ATOM 4 O ALA B 12 8.400 13.891 21.317 1.00 50.00 O ATOM 5 CB ALA B 12 8.056 14.678 24.287 1.00 50.00 C ATOM 1 N ALA B 13 10.333 13.339 22.264 1.00 50.00 N ATOM 2 CA ALA B 13 11.239 13.471 21.127 1.00 50.00 C ATOM 3 C ALA B 13 11.096 12.161 20.325 1.00 50.00 C ATOM 4 O ALA B 13 11.145 12.175 19.123 1.00 50.00 O ATOM 5 CB ALA B 13 12.584 13.665 21.596 1.00 50.00 C ATOM 1 N ALA B 14 11.051 11.078 21.086 1.00 50.00 N ATOM 2 CA ALA B 14 10.953 9.771 20.454 1.00 50.00 C ATOM 3 C ALA B 14 9.550 9.463 20.117 1.00 50.00 C ATOM 4 O ALA B 14 9.233 8.571 19.367 1.00 50.00 O ATOM 5 CB ALA B 14 11.461 8.697 21.413 1.00 50.00 C ATOM 1 N ALA B 15 8.669 10.215 20.743 1.00 50.00 N ATOM 2 CA ALA B 15 7.282 10.010 20.486 1.00 50.00 C ATOM 3 C ALA B 15 6.825 10.982 19.376 1.00 50.00 C ATOM 4 O ALA B 15 5.855 10.783 18.619 1.00 50.00 O ATOM 5 CB ALA B 15 6.367 10.306 21.797 1.00 50.00 C ATOM 1 N ALA B 16 7.511 12.143 19.430 1.00 50.00 N ATOM 2 CA ALA B 16 7.233 13.302 18.551 1.00 50.00 C ATOM 3 C ALA B 16 7.912 13.082 17.205 1.00 50.00 C ATOM 4 O ALA B 16 7.492 13.573 16.111 1.00 50.00 O ATOM 5 CB ALA B 16 7.762 14.594 19.165 1.00 50.00 C ATOM 1 N ALA B 17 9.071 12.427 17.269 1.00 50.00 N ATOM 2 CA ALA B 17 9.595 11.771 16.091 1.00 50.00 C ATOM 3 C ALA B 17 8.883 10.519 15.763 1.00 50.00 C ATOM 4 O ALA B 17 8.890 10.193 14.597 1.00 50.00 O ATOM 5 CB ALA B 17 11.046 11.518 16.265 1.00 50.00 C ATOM 1 N ALA B 18 8.315 9.809 16.722 1.00 50.00 N ATOM 2 CA ALA B 18 7.515 8.647 16.448 1.00 50.00 C ATOM 3 C ALA B 18 6.253 9.063 15.707 1.00 50.00 C ATOM 4 O ALA B 18 5.559 8.173 15.198 1.00 50.00 O ATOM 5 CB ALA B 18 7.129 7.915 17.695 1.00 50.00 C ATOM 1 N ALA B 19 5.866 10.332 15.772 1.00 50.00 N ATOM 2 CA ALA B 19 4.686 10.808 15.089 1.00 50.00 C ATOM 3 C ALA B 19 5.011 11.578 13.803 1.00 50.00 C ATOM 4 O ALA B 19 4.291 11.514 12.837 1.00 50.00 O ATOM 5 CB ALA B 19 3.854 11.710 15.960 1.00 50.00 C ATOM 1 N ALA B 20 6.176 12.195 13.822 1.00 50.00 N ATOM 2 CA ALA B 20 6.614 13.121 12.789 1.00 50.00 C ATOM 3 C ALA B 20 7.933 12.759 12.098 1.00 50.00 C ATOM 4 O ALA B 20 8.620 13.613 11.585 1.00 50.00 O ATOM 5 CB ALA B 20 6.823 14.498 13.449 1.00 50.00 C ATOM 1 N ALA B 21 8.284 11.511 12.050 1.00 50.00 N ATOM 2 CA ALA B 21 9.513 11.117 11.323 1.00 50.00 C ATOM 3 C ALA B 21 9.313 9.628 11.029 1.00 50.00 C ATOM 4 O ALA B 21 9.731 8.751 11.795 1.00 50.00 O ATOM 5 CB ALA B 21 10.799 11.332 12.178 1.00 50.00 C TER """ def exercise_03(prefix="tst_mi_map_test_03"): """ Run with reference map. Check if working with NCS in the model with symmetry. """ # with cryst pdb_file = open("%s_start.pdb" % prefix, "w") pdb_file.write(cryst_str) pdb_file.write(pdb_str) pdb_file.close() cmd = " ".join([ "phenix.model_idealization", "%s_start.pdb" % prefix, "use_map_for_reference=True", "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", " Minimizing... (NCS)\n", "Using map as reference\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_03() print("Time: %.2f" % (time.time() - t0)) print("OK")