from __future__ import absolute_import, division, print_function import mmtbx.monomer_library.pdb_interpretation import iotbx.mtz from cctbx.array_family import flex import time from mmtbx import monomer_library import iotbx.pdb from libtbx import group_args import mmtbx.restraints import mmtbx.refinement.real_space pdb_str_answer="""\ CRYST1 16.960 19.455 19.841 90.00 90.00 90.00 P 1 ATOM 1 N ASP A 18 14.727 11.381 11.191 1.00 21.41 N ATOM 2 CA ASP A 18 14.022 12.655 11.131 1.00 34.70 C ATOM 3 C ASP A 18 13.805 13.085 9.684 1.00 35.50 C ATOM 4 O ASP A 18 14.760 13.408 8.976 1.00 38.48 O ATOM 5 CB ASP A 18 14.798 13.731 11.893 1.00 38.15 C ATOM 6 CG ASP A 18 14.068 15.059 11.937 1.00 27.39 C ATOM 7 OD1 ASP A 18 13.282 15.275 12.883 1.00 35.78 O ATOM 8 OD2 ASP A 18 14.282 15.889 11.028 1.00 30.67 O ATOM 9 N ASN A 19 12.544 13.082 9.257 1.00 22.94 N ATOM 10 CA ASN A 19 12.169 13.463 7.896 1.00 22.82 C ATOM 11 C ASN A 19 12.886 12.623 6.841 1.00 20.25 C ATOM 12 O ASN A 19 13.859 13.069 6.233 1.00 33.24 O ATOM 13 CB ASN A 19 12.419 14.959 7.663 1.00 28.83 C ATOM 14 CG ASN A 19 11.659 15.505 6.465 1.00 26.44 C ATOM 15 OD1 ASN A 19 11.356 14.780 5.518 1.00 22.64 O ATOM 16 ND2 ASN A 19 11.350 16.797 6.504 1.00 28.91 N ATOM 17 N TYR A 20 12.397 11.404 6.631 1.00 23.81 N ATOM 18 CA TYR A 20 12.992 10.492 5.662 1.00 35.69 C ATOM 19 C TYR A 20 11.909 9.888 4.773 1.00 28.94 C ATOM 20 O TYR A 20 11.281 10.589 3.980 1.00 25.26 O ATOM 21 CB TYR A 20 13.765 9.382 6.379 1.00 33.37 C ATOM 22 CG TYR A 20 13.470 9.266 7.861 1.00 31.48 C ATOM 23 CD1 TYR A 20 12.437 8.463 8.327 1.00 36.91 C ATOM 24 CD2 TYR A 20 14.228 9.963 8.794 1.00 21.36 C ATOM 25 CE1 TYR A 20 12.169 8.355 9.678 1.00 36.56 C ATOM 26 CE2 TYR A 20 13.967 9.862 10.147 1.00 29.56 C ATOM 27 CZ TYR A 20 12.936 9.057 10.583 1.00 35.08 C ATOM 28 OH TYR A 20 12.671 8.953 11.930 1.00 38.73 O ATOM 29 N ARG A 21 11.695 8.584 4.914 1.00 38.95 N ATOM 30 CA ARG A 21 10.695 7.881 4.120 1.00 38.77 C ATOM 31 C ARG A 21 9.825 6.998 5.010 1.00 27.69 C ATOM 32 O ARG A 21 8.635 6.819 4.750 1.00 22.82 O ATOM 33 CB ARG A 21 11.373 7.048 3.027 1.00 20.00 C ATOM 34 CG ARG A 21 10.419 6.410 2.025 1.00 20.00 C ATOM 35 CD ARG A 21 10.098 4.968 2.391 1.00 20.00 C ATOM 36 NE ARG A 21 9.189 4.346 1.434 1.00 20.00 N ATOM 37 CZ ARG A 21 8.730 3.103 1.542 1.00 20.00 C ATOM 38 NH1 ARG A 21 9.094 2.347 2.569 1.00 20.00 N ATOM 39 NH2 ARG A 21 7.906 2.617 0.625 1.00 20.00 N TER ATOM 41 N ASP B 3 10.807 10.584 13.275 1.00 21.41 N ATOM 42 CA ASP B 3 10.009 11.773 13.002 1.00 34.70 C ATOM 43 C ASP B 3 9.681 11.887 11.519 1.00 35.50 C ATOM 44 O ASP B 3 10.577 11.850 10.675 1.00 38.48 O ATOM 45 CB ASP B 3 10.741 13.031 13.473 1.00 38.15 C ATOM 46 CG ASP B 3 9.956 14.298 13.202 1.00 27.39 C ATOM 47 OD1 ASP B 3 9.139 14.688 14.063 1.00 35.78 O ATOM 48 OD2 ASP B 3 10.155 14.906 12.130 1.00 30.67 O ATOM 49 N ASN B 4 8.392 12.025 11.215 1.00 22.94 N ATOM 50 CA ASN B 4 7.914 12.139 9.839 1.00 22.82 C ATOM 51 C ASN B 4 8.362 10.974 8.963 1.00 20.25 C ATOM 52 O ASN B 4 8.974 11.171 7.914 1.00 33.24 O ATOM 53 CB ASN B 4 8.347 13.472 9.221 1.00 28.83 C ATOM 54 CG ASN B 4 7.800 14.668 9.976 1.00 26.44 C ATOM 55 OD1 ASN B 4 6.697 14.622 10.520 1.00 22.64 O ATOM 56 ND2 ASN B 4 8.572 15.747 10.013 1.00 28.91 N ATOM 57 N ARG B 5 8.056 9.759 9.405 1.00 23.81 N ATOM 58 CA ARG B 5 8.452 8.557 8.682 1.00 35.69 C ATOM 59 C ARG B 5 7.240 7.898 8.028 1.00 28.94 C ATOM 60 O ARG B 5 7.119 6.673 8.018 1.00 25.26 O ATOM 61 CB ARG B 5 9.150 7.569 9.619 1.00 20.00 C ATOM 62 CG ARG B 5 10.498 8.049 10.133 1.00 20.00 C ATOM 63 CD ARG B 5 11.214 7.048 11.026 1.00 20.00 C ATOM 64 NE ARG B 5 12.468 7.581 11.550 1.00 20.00 N ATOM 65 CZ ARG B 5 13.227 6.959 12.441 1.00 20.00 C ATOM 66 NH1 ARG B 5 12.864 5.773 12.913 1.00 20.00 N ATOM 67 NH2 ARG B 5 14.354 7.519 12.862 1.00 20.00 N ATOM 68 N ARG B 6 6.348 8.727 7.490 1.00 38.95 N ATOM 69 CA ARG B 6 5.152 8.255 6.792 1.00 38.77 C ATOM 70 C ARG B 6 4.304 7.308 7.640 1.00 27.69 C ATOM 71 O ARG B 6 3.395 7.741 8.349 1.00 22.82 O ATOM 72 CB ARG B 6 5.531 7.599 5.460 1.00 20.00 C ATOM 73 CG ARG B 6 4.458 6.697 4.873 1.00 20.00 C ATOM 74 CD ARG B 6 4.877 5.236 4.948 1.00 20.00 C ATOM 75 NE ARG B 6 3.881 4.343 4.364 1.00 20.00 N ATOM 76 CZ ARG B 6 4.001 3.020 4.317 1.00 20.00 C ATOM 77 NH1 ARG B 6 5.077 2.431 4.821 1.00 20.00 N ATOM 78 NH2 ARG B 6 3.045 2.284 3.766 1.00 20.00 N TER END """ pdb_str_poor="""\n CRYST1 16.960 19.455 19.841 90.00 90.00 90.00 P 1 ATOM 1 N ASP A 18 14.727 11.381 11.191 1.00 21.41 N ATOM 2 CA ASP A 18 14.022 12.655 11.131 1.00 34.70 C ATOM 3 C ASP A 18 13.805 13.085 9.684 1.00 35.50 C ATOM 4 O ASP A 18 14.760 13.408 8.976 1.00 38.48 O ATOM 5 CB ASP A 18 14.798 13.731 11.893 1.00 38.15 C ATOM 6 CG ASP A 18 14.068 15.059 11.937 1.00 27.39 C ATOM 7 OD1 ASP A 18 13.282 15.275 12.883 1.00 35.78 O ATOM 8 OD2 ASP A 18 14.282 15.889 11.028 1.00 30.67 O ATOM 9 N ASN A 19 12.544 13.082 9.257 1.00 22.94 N ATOM 10 CA ASN A 19 12.169 13.463 7.896 1.00 22.82 C ATOM 11 C ASN A 19 12.886 12.623 6.841 1.00 20.25 C ATOM 12 O ASN A 19 13.859 13.069 6.233 1.00 33.24 O ATOM 13 CB ASN A 19 12.419 14.959 7.663 1.00 28.83 C ATOM 14 CG ASN A 19 11.659 15.505 6.465 1.00 26.44 C ATOM 15 OD1 ASN A 19 11.356 14.780 5.518 1.00 22.64 O ATOM 16 ND2 ASN A 19 11.350 16.797 6.504 1.00 28.91 N ATOM 17 N TYR A 20 12.397 11.404 6.631 1.00 23.81 N ATOM 18 CA TYR A 20 12.992 10.492 5.662 1.00 35.69 C ATOM 19 C TYR A 20 11.909 9.888 4.773 1.00 28.94 C ATOM 20 O TYR A 20 11.281 10.589 3.980 1.00 25.26 O ATOM 21 CB TYR A 20 13.765 9.382 6.379 1.00 33.37 C ATOM 22 CG TYR A 20 13.470 9.266 7.861 0.10 5.48 C ATOM 23 CD1 TYR A 20 12.437 8.463 8.327 1.50 5.91 C ATOM 24 CD2 TYR A 20 14.228 9.963 8.794 0.50 95.36 C ATOM 25 CE1 TYR A 20 12.169 8.355 9.678 0.50 5.56 C ATOM 26 CE2 TYR A 20 13.967 9.862 10.147 0.50 5.56 C ATOM 27 CZ TYR A 20 12.936 9.057 10.583 0.30 5.08 C ATOM 28 OH TYR A 20 12.671 8.953 11.930 1.00 38.73 O ATOM 29 N ARG A 21 11.695 8.584 4.914 1.00 38.95 N ATOM 30 CA ARG A 21 10.695 7.881 4.120 1.00 38.77 C ATOM 31 C ARG A 21 9.825 6.998 5.010 1.00 27.69 C ATOM 32 O ARG A 21 8.635 6.819 4.750 1.00 22.82 O ATOM 33 CB ARG A 21 11.373 7.048 3.027 1.00 20.00 C ATOM 34 CG ARG A 21 10.419 6.410 2.025 1.00 20.00 C ATOM 35 CD ARG A 21 10.098 4.968 2.391 1.00 20.00 C ATOM 36 NE ARG A 21 9.189 4.346 1.434 1.00 20.00 N ATOM 37 CZ ARG A 21 8.730 3.103 1.542 1.00 20.00 C ATOM 38 NH1 ARG A 21 9.094 2.347 2.569 1.00 20.00 N ATOM 39 NH2 ARG A 21 7.906 2.617 0.625 1.00 20.00 N TER ATOM 41 N ASP B 3 10.807 10.584 13.275 1.00 21.41 N ATOM 42 CA ASP B 3 10.009 11.773 13.002 1.00 34.70 C ATOM 43 C ASP B 3 9.681 11.887 11.519 1.00 35.50 C ATOM 44 O ASP B 3 10.577 11.850 10.675 1.00 38.48 O ATOM 45 CB ASP B 3 10.741 13.031 13.473 1.00 38.15 C ATOM 46 CG ASP B 3 9.956 14.298 13.202 1.00 27.39 C ATOM 47 OD1 ASP B 3 9.139 14.688 14.063 1.00 35.78 O ATOM 48 OD2 ASP B 3 10.155 14.906 12.130 1.00 30.67 O ATOM 49 N ASN B 4 8.392 12.025 11.215 1.00 22.94 N ATOM 50 CA ASN B 4 7.914 12.139 9.839 1.00 22.82 C ATOM 51 C ASN B 4 8.362 10.974 8.963 1.00 20.25 C ATOM 52 O ASN B 4 8.974 11.171 7.914 1.00 33.24 O ATOM 53 CB ASN B 4 8.347 13.472 9.221 1.00 28.83 C ATOM 54 CG ASN B 4 7.800 14.668 9.976 1.00 26.44 C ATOM 55 OD1 ASN B 4 6.697 14.622 10.520 1.00 22.64 O ATOM 56 ND2 ASN B 4 8.572 15.747 10.013 1.00 28.91 N ATOM 57 N ARG B 5 8.056 9.759 9.405 1.00 23.81 N ATOM 58 CA ARG B 5 8.452 8.557 8.682 1.00 35.69 C ATOM 59 C ARG B 5 7.240 7.898 8.028 1.00 28.94 C ATOM 60 O ARG B 5 7.119 6.673 8.018 1.00 25.26 O ATOM 61 CB ARG B 5 9.150 7.569 9.619 1.00 20.00 C ATOM 62 CG ARG B 5 10.498 8.049 10.133 1.00 20.00 C ATOM 63 CD ARG B 5 11.214 7.048 11.026 1.00 20.00 C ATOM 64 NE ARG B 5 12.468 7.581 11.550 1.00 20.00 N ATOM 65 CZ ARG B 5 13.227 6.959 12.441 1.00 20.00 C ATOM 66 NH1 ARG B 5 12.864 5.773 12.913 1.00 20.00 N ATOM 67 NH2 ARG B 5 14.354 7.519 12.862 1.00 20.00 N ATOM 68 N ARG B 6 6.348 8.727 7.490 1.00 38.95 N ATOM 69 CA ARG B 6 5.152 8.255 6.792 1.00 38.77 C ATOM 70 C ARG B 6 4.304 7.308 7.640 1.00 27.69 C ATOM 71 O ARG B 6 3.395 7.741 8.349 1.00 22.82 O ATOM 72 CB ARG B 6 5.531 7.599 5.460 1.00 20.00 C ATOM 73 CG ARG B 6 4.458 6.697 4.873 1.00 20.00 C ATOM 74 CD ARG B 6 4.877 5.236 4.948 1.00 20.00 C ATOM 75 NE ARG B 6 3.881 4.343 4.364 1.00 20.00 N ATOM 76 CZ ARG B 6 4.001 3.020 4.317 1.00 20.00 C ATOM 77 NH1 ARG B 6 5.077 2.431 4.821 1.00 20.00 N ATOM 78 NH2 ARG B 6 3.045 2.284 3.766 1.00 20.00 N TER END """ def exercise(d_min=1.5, resolution_factor = 0.25): # answer pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_answer) pdb_inp.write_pdb_file(file_name = "answer.pdb") xrs_answer = pdb_inp.xray_structure_simple() f_calc = xrs_answer.structure_factors(d_min = d_min).f_calc() fft_map = f_calc.fft_map(resolution_factor=resolution_factor) fft_map.apply_sigma_scaling() target_map = fft_map.real_map_unpadded() mtz_dataset = f_calc.as_mtz_dataset(column_root_label = "FCmap") mtz_object = mtz_dataset.mtz_object() mtz_object.write(file_name = "answer.mtz") # poor mon_lib_srv = monomer_library.server.server() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = monomer_library.server.ener_lib(), raw_records = flex.std_string(pdb_str_poor.splitlines()), strict_conflict_handling = True, force_symmetry = True, log = None) pdb_hierarchy_poor = processed_pdb_file.all_chain_proxies.pdb_hierarchy xrs_poor = processed_pdb_file.xray_structure() sites_cart_poor = xrs_poor.sites_cart() pdb_hierarchy_poor.write_pdb_file(file_name = "poor.pdb") #### target_map_object = group_args( map_data = target_map, miller_array = f_calc, crystal_gridding = fft_map, d_min = d_min) grm = mmtbx.restraints.manager( geometry=processed_pdb_file.geometry_restraints_manager(show_energies=False), normalization = True) sm = mmtbx.refinement.real_space.structure_monitor( pdb_hierarchy = pdb_hierarchy_poor, xray_structure = xrs_poor, target_map_object = target_map_object, geometry_restraints_manager = grm.geometry) sm.show(prefix="start") sm.show_residues(map_cc_all=2) # XXX assert printed output table: if(__name__ == "__main__"): t0 = time.time() exercise() print("Time: %6.4f"%(time.time()-t0))