from __future__ import division from libtbx.utils import null_out from cStringIO import StringIO def exercise_dynamics_command () : pdb_in = """\ ATOM 1 N SER A 1 0.043 -0.056 0.000 1.00 0.00 ATOM 2 CA SER A 1 1.502 -0.020 0.000 1.00 0.00 ATOM 3 C SER A 1 2.009 1.402 0.000 1.00 0.00 ATOM 4 O SER A 1 1.244 2.367 0.000 1.00 0.00 ATOM 5 CB SER A 1 2.073 -0.829 -1.192 1.00 0.00 ATOM 6 N ASP A 2 3.321 1.549 0.000 1.00 0.00 ATOM 7 CA ASP A 2 3.951 2.866 0.000 1.00 0.00 ATOM 8 C ASP A 2 3.648 3.611 -1.278 1.00 0.00 ATOM 9 O ASP A 2 3.392 4.855 -1.287 1.00 0.00 ATOM 10 CB ASP A 2 5.477 2.730 0.242 1.00 0.00 ATOM 11 N PRO A 3 3.664 2.893 -2.385 1.00 0.00 ATOM 12 CA PRO A 3 3.393 3.399 -3.800 1.00 0.00 ATOM 13 C PRO A 3 1.922 3.678 -4.096 1.00 0.00 ATOM 14 O PRO A 3 1.642 4.698 -4.776 1.00 0.00 ATOM 15 CB PRO A 3 3.863 2.300 -4.742 1.00 0.00 ATOM 16 N ALA A 4 0.973 2.874 -3.653 1.00 0.00 ATOM 17 CA ALA A 4 -0.440 3.120 -3.924 1.00 0.00 ATOM 18 C ALA A 4 -0.904 4.394 -3.258 1.00 0.00 ATOM 19 O ALA A 4 -1.686 5.175 -3.813 1.00 0.00 ATOM 20 CB ALA A 4 -1.226 1.883 -3.459 1.00 0.00 ATOM 21 N ALA A 5 -0.436 4.616 -2.044 1.00 0.00 ATOM 22 CA ALA A 5 -0.800 5.806 -1.281 1.00 0.00 ATOM 23 C ALA A 5 -0.280 7.057 -1.948 1.00 0.00 ATOM 24 O ALA A 5 -0.943 8.100 -1.993 1.00 0.00 ATOM 25 CB ALA A 5 -0.262 5.624 0.149 1.00 0.00 ATOM 26 N LEU A 6 0.930 6.974 -2.469 1.00 0.00 ATOM 27 CA LEU A 6 1.561 8.105 -3.144 1.00 0.00 ATOM 28 C LEU A 6 0.807 8.474 -4.399 1.00 0.00 ATOM 29 O LEU A 6 0.621 9.654 -4.732 1.00 0.00 ATOM 30 CB LEU A 6 3.050 7.789 -3.463 1.00 0.00 ATOM 31 N LYS A 7 0.357 7.464 -5.122 1.00 0.00 ATOM 32 CA LYS A 7 -0.388 7.671 -6.360 1.00 0.00 ATOM 33 C LYS A 7 -1.709 8.352 -6.090 1.00 0.00 ATOM 34 O LYS A 7 -2.158 9.234 -6.836 1.00 0.00 ATOM 35 CB LYS A 7 -0.602 6.306 -7.069 1.00 0.00 ATOM 36 N ARG A 8 -2.356 7.951 -5.011 1.00 0.00 ATOM 37 CA ARG A 8 -3.644 8.521 -4.625 1.00 0.00 ATOM 38 C ARG A 8 -3.504 9.981 -4.267 1.00 0.00 ATOM 39 O ARG A 8 -4.355 10.812 -4.578 1.00 0.00 ATOM 40 CB ARG A 8 -4.223 7.699 -3.441 1.00 0.00 ATOM 41 N ALA A 9 -2.427 10.307 -3.578 1.00 0.00 ATOM 42 CA ALA A 9 -2.161 11.682 -3.163 1.00 0.00 ATOM 43 C ALA A 9 -1.934 12.574 -4.359 1.00 0.00 ATOM 44 O ALA A 9 -2.376 13.729 -4.409 1.00 0.00 ATOM 45 CB ALA A 9 -0.959 11.654 -2.202 1.00 0.00 ATOM 46 N ARG A 10 -1.225 12.054 -5.343 1.00 0.00 ATOM 47 CA ARG A 10 -0.927 12.801 -6.561 1.00 0.00 ATOM 48 C ARG A 10 -2.188 13.100 -7.335 1.00 0.00 ATOM 49 O ARG A 10 -2.361 14.174 -7.908 1.00 0.00 ATOM 50 CB ARG A 10 0.084 11.988 -7.416 1.00 0.00 ATOM 51 N ASN A 11 -3.083 12.131 -7.381 1.00 0.00 ATOM 52 CA ASN A 11 -4.349 12.279 -8.093 1.00 0.00 ATOM 53 C ASN A 11 -5.209 13.341 -7.451 1.00 0.00 ATOM 54 O ASN A 11 -5.871 14.135 -8.118 1.00 0.00 ATOM 55 CB ASN A 11 -5.091 10.911 -8.123 1.00 0.00 """ 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", "use_ksdssp=False", ] 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_restraints=True", "secondary_structure.input.find_automatically=False", ] 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"