from __future__ import absolute_import, division, print_function from libtbx import easy_run import libtbx.load_env import os.path import time pdb_lines = """\ CRYST1 194.138 101.751 80.651 90.00 105.74 90.00 C 1 2 1 4 ATOM 1 N MET A 1 -63.482 31.658 20.489 1.00 88.61 N ATOM 2 CA MET A 1 -64.594 31.042 19.724 1.00 87.28 C ATOM 3 C MET A 1 -65.689 30.614 20.691 1.00 85.59 C ATOM 4 O MET A 1 -65.419 30.412 21.876 1.00 85.68 O ATOM 5 CB MET A 1 -64.075 29.831 18.973 1.00 89.26 C ATOM 6 CG MET A 1 -62.902 30.150 18.065 1.00 92.21 C ATOM 7 SD MET A 1 -62.278 28.659 17.271 1.00 96.77 S ATOM 8 CE MET A 1 -63.798 27.825 16.920 1.00 94.61 C ATOM 9 N THR A 2 -66.924 30.488 20.211 1.00 83.63 N ATOM 10 CA THR A 2 -68.002 30.078 21.106 1.00 83.02 C ATOM 11 C THR A 2 -69.152 29.283 20.508 1.00 81.29 C ATOM 12 O THR A 2 -69.485 29.420 19.332 1.00 79.88 O ATOM 13 CB THR A 2 -68.642 31.264 21.829 1.00 84.34 C ATOM 14 OG1 THR A 2 -69.678 31.807 21.006 1.00 86.38 O ATOM 15 CG2 THR A 2 -67.602 32.328 22.151 1.00 86.86 C ATOM 16 N MET A 3 -69.768 28.490 21.387 1.00 79.99 N ATOM 17 CA MET A 3 -70.888 27.620 21.082 1.00 77.22 C ATOM 18 C MET A 3 -70.424 26.519 20.160 1.00 76.93 C ATOM 19 O MET A 3 -69.748 25.598 20.606 1.00 78.22 O ATOM 20 CB MET A 3 -72.019 28.431 20.476 1.00 76.32 C ATOM 21 CG MET A 3 -72.439 29.543 21.406 1.00 75.48 C ATOM 22 SD MET A 3 -72.756 28.964 23.098 1.00 75.99 S ATOM 23 CE MET A 3 -71.183 29.165 23.909 1.00 73.62 C ATOM 24 N ASP A 4 -70.753 26.588 18.880 1.00 76.31 N ATOM 25 CA ASP A 4 -70.290 25.529 18.001 1.00 75.92 C ATOM 26 C ASP A 4 -69.444 26.061 16.882 1.00 75.06 C ATOM 27 O ASP A 4 -69.938 26.667 15.939 1.00 75.09 O ATOM 28 CB ASP A 4 -71.451 24.727 17.426 1.00 76.22 C ATOM 29 CG ASP A 4 -70.984 23.449 16.763 1.00 76.96 C ATOM 30 OD1 ASP A 4 -70.169 23.538 15.816 1.00 76.92 O ATOM 31 OD2 ASP A 4 -71.428 22.362 17.205 1.00 77.39 O ATOM 32 N PHE A 5 -68.156 25.798 17.003 1.00 74.26 N ATOM 33 CA PHE A 5 -67.167 26.224 16.037 1.00 74.26 C ATOM 34 C PHE A 5 -67.515 25.771 14.623 1.00 72.79 C ATOM 35 O PHE A 5 -67.028 26.337 13.644 1.00 72.51 O ATOM 36 CB PHE A 5 -65.831 25.636 16.442 1.00 77.83 C ATOM 37 CG PHE A 5 -65.602 25.613 17.931 1.00 82.00 C ATOM 38 CD1 PHE A 5 -64.713 24.690 18.492 1.00 84.76 C ATOM 39 CD2 PHE A 5 -66.249 26.521 18.775 1.00 84.12 C ATOM 40 CE1 PHE A 5 -64.473 24.672 19.871 1.00 85.57 C ATOM 41 CE2 PHE A 5 -66.017 26.516 20.156 1.00 85.19 C ATOM 42 CZ PHE A 5 -65.127 25.589 20.708 1.00 86.02 C HETATM 8902 C1 MLI A1001 -35.107 -8.183 19.606 1.00 48.70 C HETATM 8903 C2 MLI A1001 -34.404 -7.934 20.966 1.00 47.76 C HETATM 8904 C3 MLI A1001 -35.406 -7.002 18.730 1.00 51.13 C HETATM 8905 O6 MLI A1001 -33.181 -7.738 21.141 1.00 48.11 O HETATM 8906 O7 MLI A1001 -35.151 -7.962 21.978 1.00 44.44 O HETATM 8907 O8 MLI A1001 -34.422 -6.274 18.392 1.00 48.51 O HETATM 8908 O9 MLI A1001 -36.601 -6.959 18.453 1.00 53.02 O """ cif_lines = """\ # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level MLI MLI "Unknown " ligand 9 7 . # data_comp_MLI # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z MLI C1 C CH2 0 . -0.3524 -0.0000 -0.4983 MLI C2 C C 0 . 1.1747 -0.0000 -0.4983 MLI C3 C C 0 . -0.8614 -0.0000 0.9415 MLI O6 O O 0 . 1.8042 1.0799 -0.3478 MLI O7 O OC -1 . 1.8042 -1.0799 -0.6489 MLI O8 O O 0 . -1.2112 1.0802 1.4855 MLI O9 O OC -1 . -0.9313 -1.0802 1.5844 MLI H11 H HCH2 0 . -0.7135 0.8845 -1.0090 MLI H12 H HCH2 0 . -0.7135 -0.8845 -1.0090 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd _chem_comp_bond.value_dist_neutron MLI C1 C2 single 1.527 0.020 1.527 MLI C1 C3 single 1.527 0.020 1.527 MLI C1 H11 single 0.970 0.020 1.090 MLI C1 H12 single 0.970 0.020 1.090 MLI C2 O6 deloc 1.259 0.020 1.259 MLI C2 O7 deloc 1.259 0.020 1.259 MLI C3 O8 deloc 1.259 0.020 1.259 MLI C3 O9 deloc 1.259 0.020 1.259 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd MLI H12 C1 H11 109.47 3.000 MLI H12 C1 C3 109.47 3.000 MLI H11 C1 C3 109.47 3.000 MLI H12 C1 C2 109.47 3.000 MLI H11 C1 C2 109.47 3.000 MLI C3 C1 C2 109.47 3.000 MLI O7 C2 O6 120.00 3.000 MLI O7 C2 C1 120.00 3.000 MLI O6 C2 C1 120.00 3.000 MLI O9 C3 O8 120.00 3.000 MLI O9 C3 C1 120.00 3.000 MLI O8 C3 C1 120.00 3.000 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period MLI Var_01 O8 C3 C1 C2 97.82 30.0 3 MLI Var_02 O6 C2 C1 C3 -82.06 30.0 3 # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd MLI plan-1 C1 0.020 MLI plan-1 C2 0.020 MLI plan-1 O6 0.020 MLI plan-1 O7 0.020 MLI plan-2 C1 0.020 MLI plan-2 C3 0.020 MLI plan-2 O8 0.020 MLI plan-2 O9 0.020 """ def exercise_01(prefix="tst_mi_ligands_test_01"): """ Simple run to a completion with reference map. no SS annotations. """ pdb_file = open("%s_start.pdb" % prefix, "w") pdb_file.write(pdb_lines) pdb_file.close() cif_file = open("%s_start.cif" % prefix, "w") cif_file.write(cif_lines) cif_file.close() cmd = " ".join([ "phenix.model_idealization", "%s_start.pdb" % prefix, "%s_start.cif" % 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", # "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")