from __future__ import absolute_import, division, print_function from libtbx.test_utils import Exception_expected from libtbx.utils import null_out, Sorry from libtbx import easy_run from scitbx.array_family import flex from cctbx import uctbx, sgtbx import iotbx.pdb from iotbx import file_reader from mmtbx.refinement import select_best_starting_model import random from six.moves import range def exercise_main(): unit_cell = (24.937, 8.866, 25.477, 90.00, 107.08, 90.00) space_group = "P21" pdb_base = """\ CRYST1 24.937 8.866 25.477 90.00 107.08 90.00 P 1 21 1 SCALE1 0.040101 0.000000 0.012321 0.00000 SCALE2 0.000000 0.112790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.041062 0.00000 ATOM 1 N GLY A 1 8.992 0.474 -6.096 1.00 16.23 N ATOM 2 CA GLY A 1 9.033 0.047 -4.707 1.00 16.20 C ATOM 3 C GLY A 1 7.998 -1.029 -4.448 1.00 15.91 C ATOM 4 O GLY A 1 7.548 -1.689 -5.385 1.00 16.11 O ATOM 5 N ASN A 2 7.625 -1.218 -3.185 1.00 15.02 N ATOM 6 CA ASN A 2 6.523 -2.113 -2.848 1.00 13.92 C ATOM 7 C ASN A 2 5.220 -1.618 -3.428 1.00 12.24 C ATOM 8 O ASN A 2 4.955 -0.418 -3.432 1.00 11.42 O ATOM 9 CB ASN A 2 6.376 -2.261 -1.340 1.00 14.42 C ATOM 10 CG ASN A 2 7.620 -2.786 -0.697 1.00 13.92 C ATOM 11 OD1 ASN A 2 8.042 -3.915 -0.978 1.00 14.39 O ATOM 12 ND2 ASN A 2 8.232 -1.975 0.168 1.00 12.78 N ATOM 13 N ASN A 3 4.406 -2.553 -3.904 1.00 12.20 N ATOM 14 CA ASN A 3 3.164 -2.226 -4.594 1.00 11.81 C ATOM 15 C ASN A 3 1.925 -2.790 -3.910 1.00 10.59 C ATOM 16 O ASN A 3 1.838 -3.991 -3.653 1.00 10.32 O ATOM 17 CB ASN A 3 3.231 -2.727 -6.046 1.00 12.51 C ATOM 18 CG ASN A 3 1.973 -2.405 -6.848 1.00 12.59 C ATOM 19 OD1 ASN A 3 1.662 -1.239 -7.106 1.00 13.64 O ATOM 20 ND2 ASN A 3 1.260 -3.443 -7.268 1.00 12.39 N ATOM 21 N GLN A 4 0.973 -1.913 -3.608 1.00 10.34 N ATOM 22 CA GLN A 4 -0.366 -2.335 -3.208 1.00 10.00 C ATOM 23 C GLN A 4 -1.402 -1.637 -4.085 1.00 10.21 C ATOM 24 O GLN A 4 -1.514 -0.414 -4.070 1.00 8.99 O ATOM 25 CB GLN A 4 -0.656 -2.027 -1.736 1.00 10.00 C ATOM 26 CG GLN A 4 -1.927 -2.705 -1.229 1.00 10.50 C ATOM 27 CD GLN A 4 -2.482 -2.102 0.060 1.00 11.36 C ATOM 28 OE1 GLN A 4 -2.744 -0.900 0.151 1.00 12.29 O ATOM 29 NE2 GLN A 4 -2.684 -2.951 1.055 1.00 10.43 N ATOM 30 N GLN A 5 -2.154 -2.406 -4.857 1.00 10.48 N ATOM 31 CA GLN A 5 -3.247 -1.829 -5.630 1.00 11.24 C ATOM 32 C GLN A 5 -4.591 -2.382 -5.178 1.00 11.40 C ATOM 33 O GLN A 5 -4.789 -3.599 -5.092 1.00 11.94 O ATOM 34 CB GLN A 5 -3.024 -2.023 -7.129 1.00 11.14 C ATOM 35 CG GLN A 5 -1.852 -1.222 -7.653 1.00 10.65 C ATOM 36 CD GLN A 5 -1.338 -1.748 -8.965 1.00 10.73 C ATOM 37 OE1 GLN A 5 -0.794 -2.845 -9.028 1.00 10.14 O ATOM 38 NE2 GLN A 5 -1.511 -0.968 -10.027 1.00 11.31 N ATOM 39 N ASN A 6 -5.504 -1.471 -4.872 1.00 11.56 N ATOM 40 CA ASN A 6 -6.809 -1.838 -4.359 1.00 12.07 C ATOM 41 C ASN A 6 -7.856 -1.407 -5.353 1.00 13.18 C ATOM 42 O ASN A 6 -8.257 -0.251 -5.362 1.00 13.64 O ATOM 43 CB ASN A 6 -7.053 -1.149 -3.017 1.00 12.12 C ATOM 44 CG ASN A 6 -5.966 -1.446 -1.998 1.00 12.31 C ATOM 45 OD1 ASN A 6 -5.833 -2.579 -1.517 1.00 13.43 O ATOM 46 ND2 ASN A 6 -5.198 -0.423 -1.645 1.00 11.88 N ATOM 47 N TYR A 7 -8.298 -2.332 -6.193 1.00 14.34 N ATOM 48 CA TYR A 7 -9.162 -1.980 -7.317 1.00 15.00 C ATOM 49 C TYR A 7 -10.603 -1.792 -6.893 1.00 15.64 C ATOM 50 O TYR A 7 -11.013 -2.278 -5.838 1.00 15.68 O ATOM 51 CB TYR A 7 -9.064 -3.041 -8.412 1.00 15.31 C ATOM 52 CG TYR A 7 -7.657 -3.197 -8.931 1.00 15.06 C ATOM 53 CD1 TYR A 7 -6.785 -4.118 -8.368 1.00 15.24 C ATOM 54 CD2 TYR A 7 -7.193 -2.400 -9.960 1.00 14.96 C ATOM 55 CE1 TYR A 7 -5.489 -4.253 -8.830 1.00 14.94 C ATOM 56 CE2 TYR A 7 -5.905 -2.526 -10.429 1.00 15.13 C ATOM 57 CZ TYR A 7 -5.055 -3.451 -9.861 1.00 14.97 C ATOM 58 OH TYR A 7 -3.768 -3.572 -10.335 1.00 14.93 O ATOM 59 OXT TYR A 7 -11.378 -1.149 -7.601 1.00 15.89 O TER """ pdb_base_water = """\ HETATM 64 O HOH S 1 -10.466 -2.347 -3.168 1.00 17.57 O HETATM 65 O HOH S 2 6.469 1.081 -7.070 1.00 21.27 O HETATM 66 O HOH S 3 -11.809 0.108 -9.956 1.00 27.52 O HETATM 67 O HOH S 4 1.580 -3.455 -11.035 1.00 44.76 O END """ with open("tst_start_model_base.pdb", "w") as f: f.write(pdb_base+pdb_base_water) params = """ high_resolution = 1.75 add_sigmas = True pdb_file = tst_start_model_base.pdb output { label = F type = *real complex file_name = tst_start_model_base.mtz } """ with open("tst_start_model_fmodel.eff", "w") as f: f.write(params) assert (easy_run.fully_buffered( "phenix.fmodel tst_start_model_fmodel.eff" ).raise_if_errors().return_code == 0) mtz_in = file_reader.any_file("tst_start_model_base.mtz") f_obs = mtz_in.file_server.miller_arrays[0] symm = f_obs.crystal_symmetry().customized_copy( space_group_info=sgtbx.space_group_info("P2")) f_obs = f_obs.customized_copy(crystal_symmetry=symm) random.seed(12345) # XXX makes results more predictable flags = f_obs.generate_r_free_flags(fraction=0.1) mtz_data = f_obs.as_mtz_dataset( column_root_label="F") mtz_data.add_miller_array(flags, column_root_label="FreeR_flag") mtz_data.mtz_object().write("tst_start_model.mtz") pdb_in = file_reader.any_file("tst_start_model_base.pdb") hierarchy_in = pdb_in.file_object.hierarchy xrs_in = pdb_in.file_object.xray_structure_simple() selection = hierarchy_in.atom_selection_cache().selection # Model 1: very few changes, but shifted by (1,0,0.5) symm2 = xrs_in.crystal_symmetry().customized_copy( unit_cell=uctbx.unit_cell((24.932, 8.841, 25.501, 90.00, 107.5, 90.00))) #u_iso = xrs_in.extract_u_iso_or_u_equiv() #xrs_out = xrs_in.deep_copy_scatterers().set_u_iso( # selection=flex.bool(u_iso.size(), True), values=u_iso*1.1) xrs_out = xrs_in.deep_copy_scatterers() sites_cart = xrs_out.sites_cart() sites_cart += flex.vec3_double(sites_cart.size(), (1.0, 0.0, 0.5)) xrs_out.set_sites_cart(sites_cart) hierarchy_out = hierarchy_in.deep_copy() hierarchy_out.adopt_xray_structure(xrs_out) with open("tst_start_model_1.pdb", "w") as f: f.write(hierarchy_out.as_pdb_string(crystal_symmetry=symm2)) # Model 2: no sidechains mc_sele = selection("(name N or name C or name O or name CA or name CB)") hierarchy_out = hierarchy_in.select(mc_sele) xrs_out = xrs_in.select(mc_sele) with open("tst_start_model_2.pdb", "w") as f: f.write(hierarchy_out.as_pdb_string(crystal_symmetry=xrs_out)) # Model 3: P1 symmetry symm3 = xrs_in.crystal_symmetry().customized_copy( space_group_info=sgtbx.space_group_info("P1")) with open("tst_start_model_3.pdb", "w") as f: f.write(hierarchy_out.as_pdb_string(crystal_symmetry=symm3)) # Model 4: shaken coordinates and ADPs def random_double(size, factor=1): d = flex.double() for x in range(size): d.append(random.random() * factor) return d xrs_out = xrs_in.customized_copy() xrs_out.shake_sites_in_place(0.3, random_double=random_double) xrs_out.shake_adp() hierarchy_out = hierarchy_in.deep_copy() hierarchy_out.adopt_xray_structure(xrs_out) with open("tst_start_model_4.pdb", "w") as f: f.write(hierarchy_out.as_pdb_string(crystal_symmetry=xrs_out)) # Model 5: perfect, but missing CRYST1 with open("tst_start_model_5.pdb", "w") as f: f.write(hierarchy_in.as_pdb_string()) # run method params = select_best_starting_model.master_phil.extract() params.rigid_body_refine = False model_names = [ "tst_start_model_1.pdb", "tst_start_model_2.pdb", "tst_start_model_3.pdb", "tst_start_model_4.pdb", "tst_start_model_5.pdb", ] result = select_best_starting_model.select_model( model_names=model_names, model_data=None, f_obs=f_obs, r_free_flags=flags, params=params, skip_twin_detection=True, log=null_out()) # result.show(verbose=True) assert (result.best_model_name == "tst_start_model_4.pdb"), result.best_model_name params.rigid_body_refine = True result = select_best_starting_model.select_model( model_names=model_names, model_data=None, f_obs=f_obs, r_free_flags=flags, params=params, skip_twin_detection=True, log=null_out()) # result.show(verbose=True) assert (result.best_model_name == "tst_start_model_1.pdb"), result.best_model_name def exercise_misc(): pdb_str = """\ REMARK this is a remark record! CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.009 4.612 6.102 0.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 0.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 0.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 0.00 16.78 O ATOM 5 H1 GLY A 1 -9.802 4.938 6.343 0.00 16.77 H ATOM 6 H2 GLY A 1 -8.816 3.902 6.603 0.00 16.77 H ATOM 7 H3 GLY A 1 -8.385 5.236 6.218 0.00 16.77 H ATOM 8 HA2 GLY A 1 -9.928 3.856 4.426 0.00 16.57 H ATOM 9 HA3 GLY A 1 -8.858 4.970 4.084 0.00 16.57 H ATOM 10 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 11 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 12 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 13 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 14 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 15 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 16 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 17 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 18 H ASN A 2 -8.044 3.269 2.470 1.00 15.02 H ATOM 19 HA ASN A 2 -6.698 1.159 3.202 1.00 14.10 H ATOM 20 HB2 ASN A 2 -6.150 2.746 0.949 1.00 15.38 H ATOM 21 HB3 ASN A 2 -5.619 1.262 1.169 1.00 15.38 H ATOM 22 HD21 ASN A 2 -8.919 1.893 -0.569 1.00 11.72 H ATOM 23 HD22 ASN A 2 -7.888 2.940 -0.323 1.00 11.72 H ATOM 24 N AASN A 3 -4.438 1.590 3.905 0.50 12.26 N ATOM 25 CA AASN A 3 -3.193 1.904 4.589 0.50 11.74 C ATOM 26 C AASN A 3 -1.955 1.332 3.895 0.50 11.10 C ATOM 27 O AASN A 3 -1.872 0.119 3.648 0.50 10.42 O ATOM 28 CB AASN A 3 -3.259 1.378 6.042 0.50 12.15 C ATOM 29 CG AASN A 3 -2.006 1.739 6.861 0.50 12.82 C ATOM 30 OD1AASN A 3 -1.702 2.925 7.072 0.50 15.05 O ATOM 31 ND2AASN A 3 -1.271 0.715 7.306 0.50 13.48 N ATOM 32 H AASN A 3 -4.597 0.747 3.843 0.50 12.26 H ATOM 33 HA AASN A 3 -3.083 2.866 4.633 0.50 11.74 H ATOM 34 HB2AASN A 3 -4.029 1.767 6.485 0.50 12.15 H ATOM 35 HB3AASN A 3 -3.339 0.411 6.025 0.50 12.15 H ATOM 36 HD21AASN A 3 -0.560 0.864 7.766 0.50 13.48 H ATOM 37 HD22AASN A 3 -1.509 -0.093 7.132 0.50 13.48 H ATOM 38 N BASN A 3 -4.338 1.590 3.905 0.50 12.26 N ATOM 39 CA BASN A 3 -3.093 1.904 4.589 0.50 11.74 C ATOM 40 C BASN A 3 -1.855 1.332 3.895 0.50 11.10 C ATOM 41 O BASN A 3 -1.772 0.119 3.648 0.50 10.42 O ATOM 42 CB BASN A 3 -3.159 1.378 6.042 0.50 12.15 C ATOM 43 CG BASN A 3 -4.127 2.189 6.923 0.50 12.82 C ATOM 44 OD1BASN A 3 -4.598 1.573 8.012 0.50 15.05 O ATOM 45 ND2BASN A 3 -4.430 3.358 6.630 0.50 13.48 N ATOM 46 H BASN A 3 -4.464 0.743 3.823 0.50 12.26 H ATOM 47 HA BASN A 3 -2.983 2.866 4.621 0.50 11.74 H ATOM 48 HB2BASN A 3 -3.463 0.457 6.031 0.50 12.15 H ATOM 49 HB3BASN A 3 -2.275 1.432 6.438 0.50 12.15 H ATOM 50 HD21BASN A 3 -3.922 3.821 6.115 0.50 13.48 H ATOM 51 HD22BASN A 3 -5.147 3.708 6.952 0.50 13.48 H ATOM 52 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 53 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 54 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 55 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 56 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 57 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 58 CD GLN A 4 2.504 2.044 -0.089 1.00 12.43 C ATOM 59 OE1 GLN A 4 2.744 3.268 -0.190 1.00 14.62 O ATOM 60 NE2 GLN A 4 2.750 1.161 -1.091 1.00 9.05 N ATOM 61 HA GLN A 4 0.509 0.941 3.335 1.00 10.53 H ATOM 62 HB2 GLN A 4 -0.088 1.808 1.189 1.00 9.80 H ATOM 63 HB3 GLN A 4 0.752 3.103 1.569 1.00 9.80 H ATOM 64 HG2 GLN A 4 2.630 1.544 1.893 1.00 10.25 H ATOM 65 HG3 GLN A 4 1.753 0.520 1.057 1.00 10.25 H ATOM 66 HE21 GLN A 4 2.592 0.324 -0.975 1.00 9.05 H ATOM 67 HE22 GLN A 4 3.064 1.439 -1.842 1.00 9.05 H ATOM 68 H AGLN A 4 -1.142 3.077 3.620 0.50 10.29 H ATOM 69 H BGLN A 4 -1.168 3.072 3.606 0.50 10.29 H ATOM 70 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 71 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 72 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 73 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 74 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 75 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 76 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C ATOM 77 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O ATOM 78 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N ATOM 79 H GLN A 5 2.021 0.978 4.977 1.00 10.38 H ATOM 80 HA GLN A 5 3.333 3.315 5.487 1.00 11.39 H ATOM 81 HB2 GLN A 5 2.924 1.242 7.341 1.00 11.96 H ATOM 82 HB3 GLN A 5 3.834 2.516 7.621 1.00 11.96 H ATOM 83 HG2 GLN A 5 2.063 3.883 7.769 1.00 10.81 H ATOM 84 HG3 GLN A 5 1.111 2.866 7.000 1.00 10.81 H ATOM 85 HE21 GLN A 5 1.943 3.947 9.957 1.00 12.30 H ATOM 86 HE22 GLN A 5 1.286 2.920 10.813 1.00 12.30 H ATOM 87 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 88 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 89 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 90 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 91 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 92 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 93 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 94 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 95 H ASN A 6 5.401 3.512 4.945 1.00 11.99 H ATOM 96 HA ASN A 6 6.909 1.352 4.189 1.00 12.30 H ATOM 97 HB2 ASN A 6 7.098 3.974 3.140 1.00 12.13 H ATOM 98 HB3 ASN A 6 7.901 2.707 2.610 1.00 12.13 H ATOM 99 HD21 ASN A 6 4.553 3.638 1.117 1.00 10.07 H ATOM 100 HD22 ASN A 6 5.334 4.521 2.028 1.00 10.07 H ATOM 101 N MSE A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 102 CA MSE A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 103 C MSE A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 104 O MSE A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 105 CB MSE A 7 9.071 1.027 8.337 1.00 20.00 C ATOM 106 CG MSE A 7 7.703 0.904 8.987 1.00 20.00 C ATOM 107 SE MSE A 7 7.114 2.484 9.902 1.00 20.00 Se ATOM 108 CE MSE A 7 8.400 2.453 11.367 1.00 20.00 C ATOM 109 H MSE A 7 8.109 0.980 6.070 1.00 14.70 H ATOM 110 HA MSE A 7 8.841 2.961 7.708 1.00 15.18 H ATOM 111 HB2 MSE A 7 9.270 0.186 7.900 1.00 20.00 H ATOM 112 HB3 MSE A 7 9.724 1.195 9.033 1.00 20.00 H ATOM 113 HG2 MSE A 7 7.042 0.539 8.377 1.00 20.00 H ATOM 114 HG3 MSE A 7 8.123 0.264 9.563 1.00 20.00 H ATOM 115 HE1 MSE A 7 8.976 3.219 11.304 1.00 20.00 H ATOM 116 HE2 MSE A 7 8.333 2.133 12.198 1.00 20.00 H ATOM 117 HE3 MSE A 7 9.010 1.805 10.983 1.00 20.00 H TER HETATM 118 CL CL 1 -6.471 5.227 7.124 1.00 30.00 Cl TER HETATM 119 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 120 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 121 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 122 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 123 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 124 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O TER END """ pdb_file = "tst_start_model_misc.pdb" with open(pdb_file, "w") as f: f.write(pdb_str) pdb_in = iotbx.pdb.input(file_name=pdb_file) pdb_hierarchy = pdb_in.construct_hierarchy() xray_structure = pdb_in.xray_structure_simple() hd_sel = xray_structure.hd_selection() assert hd_sel.count(True) == 55 xray_structure.convert_to_anisotropic(selection=~hd_sel) pdb_hierarchy.adopt_xray_structure(xray_structure) hierarchy_new, xrs_new = select_best_starting_model.strip_model( pdb_hierarchy=pdb_hierarchy, xray_structure=xray_structure, output_file="tst_start_model_misc_new.pdb", log=null_out()) # basic changes hd_sel = xray_structure.hd_selection() assert hd_sel.count(True) == 55 # should be left alone assert xrs_new.hd_selection().count(True) == 0 sel = hierarchy_new.atom_selection_cache().selection mse_sel = sel("resname MSE") assert mse_sel.count(True) == 0 hoh_sel = sel("resname HOH") assert hoh_sel.count(True) == 0 alt_sel = sel("altloc 'B'") assert alt_sel.count(True) == 0 cl_sel = sel("element CL") assert cl_sel.count(True) == 1 occ_xrs = xrs_new.scatterers().extract_occupancies() occ_pdb = hierarchy_new.atoms().extract_occ() assert occ_xrs.all_eq(occ_pdb) and occ_xrs.all_eq(1.0) assert xrs_new.use_u_aniso().all_eq(False) # remove all ligands assert xray_structure.hd_selection().count(True) == 55 hierarchy_new, xrs_new = select_best_starting_model.strip_model( pdb_hierarchy=pdb_hierarchy, xray_structure=xray_structure, remove_ligands=True, remove_hydrogens=False, output_file="tst_start_model_misc_new2.pdb", log=null_out()) sel = hierarchy_new.atom_selection_cache().selection assert sel("resname CL").count(True) == 0 assert xrs_new.hd_selection().count(True) == 48 # multi-model hierarchy model2 = pdb_hierarchy.models()[0].detached_copy() pdb_hierarchy.append_model(model2) try : hierarchy_new, xrs_new = select_best_starting_model.strip_model( pdb_hierarchy=pdb_hierarchy, xray_structure=xray_structure, log=null_out()) except Sorry : pass else : raise Exception_expected # both structure and file name passed try : hierarchy_new, xrs_new = select_best_starting_model.strip_model( pdb_hierarchy=pdb_hierarchy, xray_structure=xray_structure, file_name=pdb_file, log=null_out()) except AssertionError : pass else : raise Exception_expected # preserve REMARK hierarchy_new, xrs_new = select_best_starting_model.strip_model( file_name=pdb_file, preserve_remarks=True, output_file="tst_start_model_misc_new.pdb", log=null_out()) pdb_new = iotbx.pdb.input(file_name="tst_start_model_misc_new.pdb") assert len(pdb_new.remark_section()) == 1 # reset HETATM hierarchy_new, xrs_new = select_best_starting_model.strip_model( file_name=pdb_file, preserve_remarks=True, reset_hetatm_flag=True, output_file="tst_start_model_misc_new.pdb", log=null_out()) with open("tst_start_model_misc_new.pdb") as f: lines = f.readlines() for line in lines : assert (not line.startswith("HETATM")) if (__name__ == "__main__"): exercise_misc() exercise_main() print("OK")