from __future__ import division from libtbx.utils import null_out from libtbx.test_utils import show_diff from cStringIO import StringIO def exercise_metal_coordination () : pdb_in = """\ HETATM 6 PA ANP A 1 -2.347 2.100 -17.803 1.00 10.27 P HETATM 7 PB ANP A 1 0.438 2.937 -18.222 1.00 10.85 P HETATM 8 PG ANP A 1 1.125 2.500 -21.112 1.00 10.56 P HETATM 9 C5' ANP A 1 -1.973 -0.334 -17.074 1.00 10.24 C HETATM 10 O5' ANP A 1 -2.737 0.857 -16.887 1.00 9.76 O HETATM 11 C4' ANP A 1 -2.889 -1.539 -17.210 1.00 10.40 C HETATM 12 O4' ANP A 1 -3.627 -1.699 -15.990 1.00 10.47 O HETATM 13 C3' ANP A 1 -3.936 -1.477 -18.319 1.00 9.24 C HETATM 14 O3' ANP A 1 -3.371 -1.834 -19.590 1.00 10.01 O HETATM 15 C2' ANP A 1 -4.953 -2.483 -17.795 1.00 9.88 C HETATM 16 O2' ANP A 1 -4.490 -3.826 -17.960 1.00 11.25 O HETATM 17 C1' ANP A 1 -4.915 -2.225 -16.303 1.00 11.21 C HETATM 18 N1 ANP A 1 -9.509 -1.559 -14.126 1.00 11.19 N HETATM 19 O1A ANP A 1 -3.108 3.253 -17.261 1.00 10.62 O HETATM 20 O1B ANP A 1 0.034 4.332 -18.573 1.00 10.23 O HETATM 21 O1G ANP A 1 2.434 1.809 -21.423 1.00 12.01 O HETATM 22 C2 ANP A 1 -8.855 -2.697 -14.422 1.00 11.32 C HETATM 23 O2A ANP A 1 -2.510 1.726 -19.235 1.00 9.76 O HETATM 24 O2B ANP A 1 1.600 2.764 -17.285 1.00 12.69 O HETATM 25 O2G ANP A 1 -0.014 2.061 -22.037 1.00 10.31 O HETATM 26 N3 ANP A 1 -7.636 -2.728 -14.988 1.00 10.83 N HETATM 27 N3B ANP A 1 0.614 2.050 -19.591 1.00 13.13 N HETATM 28 O3A ANP A 1 -0.783 2.257 -17.423 1.00 11.18 O HETATM 29 O3G ANP A 1 1.269 4.014 -21.065 1.00 10.83 O HETATM 30 C4 ANP A 1 -7.053 -1.540 -15.290 1.00 10.41 C HETATM 31 C5 ANP A 1 -7.703 -0.266 -15.019 1.00 10.36 C HETATM 32 C6 ANP A 1 -9.013 -0.333 -14.380 1.00 10.39 C HETATM 33 N6 ANP A 1 -9.709 0.784 -14.079 1.00 10.34 N HETATM 34 N7 ANP A 1 -6.889 0.732 -15.437 1.00 10.05 N HETATM 35 C8 ANP A 1 -5.791 0.126 -15.942 1.00 10.13 C HETATM 36 N9 ANP A 1 -5.898 -1.223 -15.869 1.00 10.39 N HETATM 37 MG MG A 2 -1.727 1.886 -21.040 1.00 8.15 MG HETATM 38 MG MG A 3 -0.077 5.289 -20.356 1.00 9.42 MG HETATM 1 O HOH A 4 -3.435 1.768 -22.164 1.00 8.59 O HETATM 3 O HOH A 5 -2.158 5.884 -19.807 1.00 9.00 O HETATM 4 O HOH A 6 -1.791 4.005 -20.881 1.00 7.86 O HETATM 39 O HOH A 7 -1.518 -0.155 -21.151 1.00 13.31 O HETATM 40 O HOH A 8 -0.256 6.271 -22.179 1.00 12.97 O HETATM 41 O HOH A 9 0.913 6.863 -19.633 1.00 13.62 O """ open("tst_geo_min_metal_coord.pdb", "w").write(pdb_in) params1 = """\ geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 2 atom_selection_2 = name O2A and chain A and resname ANP and resseq 1 distance_ideal = 2.090000 sigma = 0.250 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 2 atom_selection_2 = name O2G and chain A and resname ANP and resseq 1 distance_ideal = 2.090000 sigma = 0.250 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 2 atom_selection_2 = name O and chain A and resname HOH and resseq 4 distance_ideal = 2.070000 sigma = 0.050 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 2 atom_selection_2 = name O and chain A and resname HOH and resseq 7 distance_ideal = 2.070000 sigma = 0.050 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 2 atom_selection_2 = name O and chain A and resname HOH and resseq 6 distance_ideal = 2.070000 sigma = 0.050 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 3 atom_selection_2 = name O3G and chain A and resname ANP and resseq 1 distance_ideal = 2.090000 sigma = 0.250 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 3 atom_selection_2 = name O and chain A and resname HOH and resseq 9 distance_ideal = 2.070000 sigma = 0.050 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 3 atom_selection_2 = name O1B and chain A and resname ANP and resseq 1 distance_ideal = 2.090000 sigma = 0.250 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 3 atom_selection_2 = name O and chain A and resname HOH and resseq 8 distance_ideal = 2.070000 sigma = 0.050 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 3 atom_selection_2 = name O and chain A and resname HOH and resseq 6 distance_ideal = 2.070000 sigma = 0.050 } bond { action = *add atom_selection_1 = name MG and chain A and resname MG and resseq 3 atom_selection_2 = name O and chain A and resname HOH and resseq 5 distance_ideal = 2.070000 sigma = 0.050 } }""" params2 = "refinement {\n%s\n}" % params1 open("tst_geo_min_metal_coord_1.phil", "w").write(params1) open("tst_geo_min_metal_coord_2.phil", "w").write(params2) # phenix.geometry_minimization from mmtbx.command_line import geometry_minimization args = [ "file_name=tst_geo_min_metal_coord.pdb", "output_file_name_prefix=tst_geo_min_metal_coord_1", "write_geo_file=True", "tst_geo_min_metal_coord_1.phil", ] geometry_minimization.run(args=args, log=null_out()) geo_file_1 = open("tst_geo_min_metal_coord_1.geo").read() args = [ "file_name=tst_geo_min_metal_coord.pdb", "output_file_name_prefix=tst_geo_min_metal_coord_2", "write_geo_file=True", "tst_geo_min_metal_coord_2.phil", ] geometry_minimization.run(args=args, log=null_out()) geo_file_2 = open("tst_geo_min_metal_coord_2.geo").read() show_diff(geo_file_1, geo_file_2) # phenix.pdbtools from mmtbx import pdbtools args = [ "tst_geo_min_metal_coord.pdb", "tst_geo_min_metal_coord_1.phil", "model_statistics=True", ] out1 = StringIO() pdbtools.run(args=args, out=out1, replace_stderr=False) args = [ "tst_geo_min_metal_coord.pdb", "tst_geo_min_metal_coord_2.phil", "model_statistics=True", ] out2 = StringIO() pdbtools.run(args=args, out=out2, replace_stderr=False) assert (""" atom 1: \"HETATM 37 MG MG A 2 .*. Mg \"""" in out1.getvalue()) assert (""" atom 1: \"HETATM 37 MG MG A 2 .*. Mg \"""" in out2.getvalue()) for line1, line2 in zip(out1.getvalue().splitlines(), out2.getvalue().splitlines()) : line1 = line1.strip() line2 = line2.strip() if (line1.startswith("Date") or line1.startswith("PID") or line1.startswith("Command line") or line1.startswith("Time")): continue else : assert not show_diff(line1, line2) def exercise_secondary_structure () : 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 geometry_minimization 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", ] geometry_minimization.run(args=args, log=null_out()) # TODO phenix.pdbtools? if (__name__ == "__main__") : exercise_metal_coordination() exercise_secondary_structure() print "OK"