from __future__ import absolute_import, division, print_function from libtbx.utils import null_out from six.moves import cStringIO as StringIO def exercise_dynamics_command(): pdb_in = """\ CRYST1 21.348 25.003 18.365 90.00 90.00 90.00 P 1 ATOM 1 N SER A 1 10.914 5.773 13.123 1.00 0.00 ATOM 2 CA SER A 1 12.373 5.809 13.123 1.00 0.00 ATOM 3 C SER A 1 12.880 7.231 13.123 1.00 0.00 ATOM 4 O SER A 1 12.115 8.196 13.123 1.00 0.00 ATOM 5 CB SER A 1 12.944 5.000 11.931 1.00 0.00 ATOM 6 N ASP A 2 14.192 7.378 13.123 1.00 0.00 ATOM 7 CA ASP A 2 14.822 8.695 13.123 1.00 0.00 ATOM 8 C ASP A 2 14.519 9.440 11.845 1.00 0.00 ATOM 9 O ASP A 2 14.263 10.684 11.836 1.00 0.00 ATOM 10 CB ASP A 2 16.348 8.559 13.365 1.00 0.00 ATOM 11 N PRO A 3 14.535 8.722 10.738 1.00 0.00 ATOM 12 CA PRO A 3 14.264 9.228 9.323 1.00 0.00 ATOM 13 C PRO A 3 12.793 9.507 9.027 1.00 0.00 ATOM 14 O PRO A 3 12.513 10.527 8.347 1.00 0.00 ATOM 15 CB PRO A 3 14.734 8.129 8.381 1.00 0.00 ATOM 16 N ALA A 4 11.844 8.703 9.470 1.00 0.00 ATOM 17 CA ALA A 4 10.431 8.949 9.199 1.00 0.00 ATOM 18 C ALA A 4 9.967 10.223 9.865 1.00 0.00 ATOM 19 O ALA A 4 9.185 11.004 9.310 1.00 0.00 ATOM 20 CB ALA A 4 9.645 7.712 9.664 1.00 0.00 ATOM 21 N ALA A 5 10.435 10.445 11.079 1.00 0.00 ATOM 22 CA ALA A 5 10.071 11.635 11.842 1.00 0.00 ATOM 23 C ALA A 5 10.591 12.886 11.175 1.00 0.00 ATOM 24 O ALA A 5 9.928 13.929 11.130 1.00 0.00 ATOM 25 CB ALA A 5 10.609 11.453 13.272 1.00 0.00 ATOM 26 N LEU A 6 11.801 12.803 10.654 1.00 0.00 ATOM 27 CA LEU A 6 12.432 13.934 9.979 1.00 0.00 ATOM 28 C LEU A 6 11.678 14.303 8.724 1.00 0.00 ATOM 29 O LEU A 6 11.492 15.483 8.391 1.00 0.00 ATOM 30 CB LEU A 6 13.921 13.618 9.660 1.00 0.00 ATOM 31 N LYS A 7 11.228 13.293 8.001 1.00 0.00 ATOM 32 CA LYS A 7 10.483 13.500 6.763 1.00 0.00 ATOM 33 C LYS A 7 9.162 14.181 7.033 1.00 0.00 ATOM 34 O LYS A 7 8.713 15.063 6.287 1.00 0.00 ATOM 35 CB LYS A 7 10.269 12.135 6.054 1.00 0.00 ATOM 36 N ARG A 8 8.515 13.780 8.112 1.00 0.00 ATOM 37 CA ARG A 8 7.227 14.350 8.498 1.00 0.00 ATOM 38 C ARG A 8 7.367 15.810 8.856 1.00 0.00 ATOM 39 O ARG A 8 6.516 16.641 8.545 1.00 0.00 ATOM 40 CB ARG A 8 6.648 13.528 9.682 1.00 0.00 ATOM 41 N ALA A 9 8.444 16.136 9.545 1.00 0.00 ATOM 42 CA ALA A 9 8.710 17.511 9.960 1.00 0.00 ATOM 43 C ALA A 9 8.937 18.403 8.764 1.00 0.00 ATOM 44 O ALA A 9 8.495 19.558 8.714 1.00 0.00 ATOM 45 CB ALA A 9 9.912 17.483 10.921 1.00 0.00 ATOM 46 N ARG A 10 9.646 17.883 7.780 1.00 0.00 ATOM 47 CA ARG A 10 9.944 18.630 6.562 1.00 0.00 ATOM 48 C ARG A 10 8.683 18.929 5.788 1.00 0.00 ATOM 49 O ARG A 10 8.510 20.003 5.215 1.00 0.00 ATOM 50 CB ARG A 10 10.955 17.817 5.707 1.00 0.00 ATOM 51 N ASN A 11 7.788 17.960 5.742 1.00 0.00 ATOM 52 CA ASN A 11 6.522 18.108 5.030 1.00 0.00 ATOM 53 C ASN A 11 5.662 19.170 5.672 1.00 0.00 ATOM 54 O ASN A 11 5.000 19.964 5.005 1.00 0.00 ATOM 55 CB ASN A 11 5.780 16.740 5.000 1.00 0.00 TER END """ open("tst_geo_min_ss_phil.pdb", "w").write(pdb_in) from mmtbx.command_line import secondary_structure_restraints out = StringIO() args = [ "tst_geo_min_ss_phil.pdb", ] secondary_structure_restraints.run(args, out=out, log=null_out()) # phenix.geometry_minimization from mmtbx.command_line import dynamics open("tst_geo_min_ss_phil.phil", "w").write(out.getvalue()) args = [ "tst_geo_min_ss_phil.pdb", "tst_geo_min_ss_phil.phil", "secondary_structure.enabled=True", ] dynamics.run(args=args, log=null_out()) pdb_new = "tst_geo_min_ss_phil_shaken.pdb" from iotbx import file_reader pdb_in = file_reader.any_file("tst_geo_min_ss_phil.pdb") pdb_in.assert_file_type("pdb") xrs_in = pdb_in.file_object.xray_structure_simple() pdb_out = file_reader.any_file(pdb_new) pdb_out.assert_file_type("pdb") xrs_out = pdb_out.file_object.xray_structure_simple() sites_in = xrs_in.sites_cart() sites_out = xrs_out.sites_cart() assert (sites_in.rms_difference(sites_out) > 0.3) if (__name__ == "__main__"): exercise_dynamics_command() print("OK")