from __future__ import absolute_import, division, print_function from mmtbx import monomer_library import mmtbx.monomer_library.server import mmtbx.monomer_library.pdb_interpretation import sys try: from six.moves import cPickle as pickle except ImportError: import pickle from six.moves import cStringIO as StringIO from libtbx.test_utils import show_diff import iotbx.pdb from libtbx.utils import null_out # import dependency from time import time from libtbx.test_utils import approx_equal raw_records1 = """\ CRYST1 60.800 60.800 97.000 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016447 0.009496 0.000000 0.00000 SCALE2 0.000000 0.018992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010309 0.00000 ATOM 1050 N LYS A 135 31.992 14.930 -7.233 1.00 9.47 N ATOM 1051 CA LYS A 135 31.388 16.216 -7.637 1.00 12.89 C ATOM 1052 C LYS A 135 30.807 16.840 -6.406 1.00 6.47 C ATOM 1053 O LYS A 135 29.583 16.869 -6.191 1.00 15.74 O ATOM 1054 CB LYS A 135 30.263 16.059 -8.655 1.00 13.51 C ATOM 1055 CG LYS A 135 30.742 15.277 -9.843 1.00 16.23 C ATOM 1056 CD LYS A 135 29.612 15.131 -10.835 1.00 28.55 C ATOM 1057 CE LYS A 135 30.173 14.812 -12.216 1.00 34.52 C ATOM 1058 NZ LYS A 135 29.396 13.756 -12.899 1.00 46.18 N TER 1294 LYS A 162 END """ raw_records2 = """\ CRYST1 24.627 42.717 46.906 90.00 90.00 90.00 P 21 21 21 8 ATOM 184 P DG A 9 9.587 13.026 19.037 1.00 6.28 P ATOM 185 OP1 DG A 9 9.944 14.347 19.602 1.00 8.07 O ATOM 186 OP2 DG A 9 10.654 12.085 18.639 1.00 8.27 O ATOM 187 O5' DG A 9 8.717 12.191 20.048 1.00 5.88 O ATOM 188 C5' DG A 9 7.723 12.833 20.854 1.00 5.45 C ATOM 189 C4' DG A 9 7.145 11.818 21.807 1.00 5.40 C ATOM 190 O4' DG A 9 6.435 10.777 21.087 1.00 5.77 O ATOM 191 C3' DG A 9 8.142 11.036 22.648 1.00 5.10 C ATOM 192 O3' DG A 9 8.612 11.838 23.723 1.00 5.90 O ATOM 193 C2' DG A 9 7.300 9.857 23.068 1.00 5.97 C ATOM 194 C1' DG A 9 6.619 9.536 21.805 1.00 5.97 C ATOM 195 N9 DG A 9 7.390 8.643 20.931 1.00 5.97 N ATOM 196 C8 DG A 9 8.074 8.881 19.775 1.00 6.62 C ATOM 197 N7 DG A 9 8.647 7.820 19.249 1.00 6.57 N ATOM 198 C5 DG A 9 8.308 6.806 20.141 1.00 6.22 C ATOM 199 C6 DG A 9 8.620 5.431 20.136 1.00 6.03 C ATOM 200 O6 DG A 9 9.297 4.803 19.296 1.00 7.21 O ATOM 201 N1 DG A 9 8.101 4.773 21.247 1.00 6.10 N ATOM 202 C2 DG A 9 7.365 5.351 22.260 1.00 6.24 C ATOM 203 N2 DG A 9 6.948 4.569 23.241 1.00 7.88 N ATOM 204 N3 DG A 9 7.051 6.652 22.257 1.00 6.53 N ATOM 205 C4 DG A 9 7.539 7.295 21.184 1.00 5.69 C ATOM 206 P DC A 10 10.081 11.538 24.300 1.00 5.91 P ATOM 207 OP1 DC A 10 10.273 12.645 25.291 1.00 7.27 O ATOM 208 OP2 DC A 10 11.063 11.363 23.228 1.00 6.84 O ATOM 209 O5' DC A 10 9.953 10.128 25.026 1.00 5.75 O ATOM 210 C5' DC A 10 9.077 9.959 26.149 1.00 5.87 C ATOM 211 C4' DC A 10 9.188 8.549 26.672 1.00 5.56 C ATOM 212 O4' DC A 10 8.708 7.612 25.667 1.00 5.70 O ATOM 213 C3' DC A 10 10.580 8.059 27.007 1.00 5.27 C ATOM 214 O3' DC A 10 11.010 8.447 28.315 1.00 5.83 O ATOM 215 C2' DC A 10 10.422 6.549 26.893 1.00 5.34 C ATOM 216 C1' DC A 10 9.436 6.405 25.754 1.00 5.23 C ATOM 217 N1 DC A 10 10.113 6.168 24.448 1.00 5.30 N ATOM 218 C2 DC A 10 10.514 4.871 24.152 1.00 5.28 C ATOM 219 O2 DC A 10 10.283 3.972 25.000 1.00 5.75 O ATOM 220 N3 DC A 10 11.131 4.627 22.965 1.00 5.65 N ATOM 221 C4 DC A 10 11.395 5.628 22.138 1.00 5.80 C ATOM 222 N4 DC A 10 12.034 5.327 21.005 1.00 6.75 N ATOM 223 C5 DC A 10 11.029 6.970 22.449 1.00 5.99 C ATOM 224 C6 DC A 10 10.394 7.203 23.612 1.00 5.56 C ATOM 226 O5' DG B 11 12.424 -4.393 18.427 1.00 22.70 O ATOM 227 C5' DG B 11 12.380 -5.516 19.282 1.00 14.75 C ATOM 228 C4' DG B 11 11.969 -5.112 20.676 1.00 10.42 C ATOM 229 O4' DG B 11 12.972 -4.192 21.210 1.00 10.51 O ATOM 230 C3' DG B 11 10.649 -4.394 20.782 1.00 8.57 C ATOM 231 O3' DG B 11 9.618 -5.363 20.846 1.00 8.69 O ATOM 232 C2' DG B 11 10.822 -3.597 22.051 1.00 8.63 C ATOM 233 C1' DG B 11 12.236 -3.233 21.980 1.00 9.81 C ATOM 234 N9 DG B 11 12.509 -1.902 21.305 1.00 8.66 N ATOM 235 C8 DG B 11 13.175 -1.667 20.135 1.00 9.57 C ATOM 236 N7 DG B 11 13.255 -0.407 19.824 1.00 9.04 N ATOM 237 C5 DG B 11 12.613 0.235 20.869 1.00 7.63 C ATOM 238 C6 DG B 11 12.388 1.612 21.119 1.00 7.05 C ATOM 239 O6 DG B 11 12.723 2.590 20.419 1.00 7.81 O ATOM 240 N1 DG B 11 11.715 1.819 22.317 1.00 6.27 N ATOM 241 C2 DG B 11 11.264 0.828 23.159 1.00 6.05 C ATOM 242 N2 DG B 11 10.611 1.219 24.248 1.00 5.85 N ATOM 243 N3 DG B 11 11.483 -0.457 22.942 1.00 6.55 N ATOM 244 C4 DG B 11 12.150 -0.687 21.797 1.00 6.84 C ATOM 245 P DC B 12 8.134 -5.009 20.350 1.00 8.13 P ATOM 246 OP1 DC B 12 7.367 -6.252 20.459 1.00 10.02 O ATOM 247 OP2 DC B 12 8.172 -4.307 19.052 1.00 9.79 O ATOM 248 O5' DC B 12 7.564 -3.912 21.389 1.00 8.18 O ATOM 249 C5' DC B 12 7.275 -4.296 22.719 1.00 8.00 C ATOM 250 C4' DC B 12 6.856 -3.057 23.487 1.00 8.01 C ATOM 251 O4' DC B 12 8.006 -2.146 23.615 1.00 7.35 O ATOM 252 C3' DC B 12 5.763 -2.208 22.890 1.00 7.04 C ATOM 253 O3' DC B 12 4.456 -2.800 23.100 1.00 9.82 O ATOM 254 C2' DC B 12 6.019 -0.916 23.630 1.00 6.50 C ATOM 255 C1' DC B 12 7.467 -0.808 23.608 1.00 7.35 C ATOM 256 N1 DC B 12 8.040 -0.143 22.396 1.00 6.64 N ATOM 257 C2 DC B 12 8.017 1.257 22.382 1.00 5.68 C ATOM 258 O2 DC B 12 7.524 1.832 23.357 1.00 6.32 O ATOM 259 N3 DC B 12 8.543 1.930 21.312 1.00 6.18 N ATOM 260 C4 DC B 12 9.009 1.236 20.266 1.00 6.48 C ATOM 261 N4 DC B 12 9.518 1.926 19.243 1.00 7.43 N ATOM 262 C5 DC B 12 9.012 -0.198 20.248 1.00 6.83 C ATOM 263 C6 DC B 12 8.502 -0.825 21.311 1.00 6.80 C """ raw_records3 = """\ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 1 ATOM 1 N ALA A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 2 CA ALA A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 3 C ALA A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 4 O ALA A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 5 CB ALA A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 7 N ALA A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 8 CA ALA A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 9 C ALA A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 10 O ALA A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 11 CB ALA A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 13 N ALA A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 14 CA ALA A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 15 C ALA A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 16 O ALA A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 17 CB ALA A 4 0.656 2.148 1.711 1.00 9.80 C END """ def make_initial_grm(mon_lib_srv, ener_lib, records): processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, raw_records = records, force_symmetry = True) geometry = processed_pdb_file.geometry_restraints_manager( show_energies = True, plain_pairs_radius = 5.0) xrs = processed_pdb_file.xray_structure() return geometry, xrs def make_geo_pickle_unpickle(geometry, xrs, prefix): init_out = StringIO() from_file_out = StringIO() geometry.show_sorted( sites_cart=xrs.sites_cart(), site_labels=xrs.scatterers().extract_labels(), f=init_out) energy_original = geometry.energies_sites(sites_cart=xrs.sites_cart()) t0 = time() #import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) ) pklstr = pickle.dumps(geometry) t1 = time() grm_from_file = pickle.loads(pklstr) t2 = time() # Fails here: energy_from_pickle = grm_from_file.energies_sites(sites_cart=xrs.sites_cart()) assert approx_equal(energy_original.target, energy_from_pickle.target) print("Time pickling/unpickling: %.4f, %.4f" % (t1-t0, t2-t1)) grm_from_file.show_sorted( sites_cart=xrs.sites_cart(), site_labels=xrs.scatterers().extract_labels(), f=from_file_out) # print "INITIAL" init_v = init_out.getvalue() # print init_v # print "="*50 # print "From disc" from_file_v = from_file_out.getvalue() # print from_file_v # STOP() assert not show_diff(init_v, from_file_v) return grm_from_file def test_simple_protein( mon_lib_srv, ener_lib, prefix="tst_grm_pickling_simple_protein"): geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, raw_records1) make_geo_pickle_unpickle(geometry, xrs, prefix) def test_nucleic_acid(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_na"): with open("%s.pdb" % prefix, "w") as f: f.write(raw_records2) from mmtbx import monomer_library params = monomer_library.pdb_interpretation.master_params.extract() params.secondary_structure.enabled=True processed_pdb_file = monomer_library.pdb_interpretation.run( args=["%s.pdb" % prefix], params=params, strict_conflict_handling=False, log=sys.stdout) geo = processed_pdb_file.geometry_restraints_manager() assert geo.get_n_hbond_proxies() == 6 assert geo.get_n_hangle_proxies() == 12 assert geo.get_n_stacking_proxies() == 2 assert geo.get_n_parallelity_bp_proxies() == 2 make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix) def test_ramachandran(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_rama"): with open("%s.pdb" % prefix, "w") as f: f.write(raw_records3) from mmtbx import monomer_library params = monomer_library.pdb_interpretation.master_params.extract() params.peptide_link.ramachandran_restraints=True processed_pdb_file = monomer_library.pdb_interpretation.run( args=["%s.pdb" % prefix], params=params, strict_conflict_handling=False, log=sys.stdout) geo = processed_pdb_file.geometry_restraints_manager() assert geo.get_n_ramachandran_proxies() == 1 make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix) def test_cbeta(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_cbeta"): with open("%s.pdb" % prefix, "w") as f: f.write(raw_records3) from mmtbx import monomer_library params = monomer_library.pdb_interpretation.master_params.extract() params.c_beta_restraints=True processed_pdb_file = monomer_library.pdb_interpretation.run( args=["%s.pdb" % prefix], params=params, strict_conflict_handling=False, log=sys.stdout) geo = processed_pdb_file.geometry_restraints_manager() assert geo.get_n_c_beta_torsion_proxies() == 6 make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix) def test_reference_coordinate(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_ref_coor"): from mmtbx.geometry_restraints import reference # for some strange reason without importing this the code doesn't work... from cctbx import adp_restraints # import dependency pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records3) params = monomer_library.pdb_interpretation.master_params.extract() params.reference_coordinate_restraints.enabled=False processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=params, strict_conflict_handling=False, pdb_inp=pdb_inp, log=sys.stdout) geo = processed_pdb_file.geometry_restraints_manager() pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy sites_cart = pdb_hierarchy.atoms().extract_xyz() rcp = reference.add_coordinate_restraints(sites_cart=sites_cart) geo.adopt_reference_coordinate_restraints_in_place(rcp) # print "number of rcr proxies:", geo.get_n_reference_coordinate_proxies() make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix) def test_secondary_structure(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_ss"): pdb_str = """ HELIX 2 2 ASP A 37 GLY A 48 1 12 CRYST1 113.068 113.068 53.292 90.00 90.00 90.00 I 41 8 ATOM 266 N ASP A 37 6.265 61.752 14.145 1.00 35.17 N ATOM 267 CA ASP A 37 5.251 62.335 15.056 1.00 37.08 C ATOM 268 C ASP A 37 5.433 61.900 16.511 1.00 37.79 C ATOM 269 O ASP A 37 6.443 61.316 16.858 1.00 37.54 O ATOM 270 CB ASP A 37 3.827 62.120 14.521 1.00 37.53 C ATOM 271 CG ASP A 37 3.427 60.683 14.400 1.00 38.76 C ATOM 272 OD1 ASP A 37 4.001 59.819 15.070 1.00 38.84 O ATOM 273 OD2 ASP A 37 2.506 60.327 13.624 1.00 41.78 O ATOM 274 N ASP A 38 4.467 62.205 17.382 1.00 38.31 N ATOM 275 CA ASP A 38 4.609 61.829 18.786 1.00 38.69 C ATOM 276 C ASP A 38 4.781 60.335 18.955 1.00 37.78 C ATOM 277 O ASP A 38 5.598 59.886 19.760 1.00 38.31 O ATOM 278 CB ASP A 38 3.376 62.258 19.608 1.00 39.51 C ATOM 279 CG ASP A 38 3.378 63.724 19.972 1.00 42.76 C ATOM 280 OD1 ASP A 38 4.462 64.343 20.161 1.00 48.07 O ATOM 281 OD2 ASP A 38 2.295 64.337 20.144 1.00 47.65 O ATOM 282 N ALA A 39 4.003 59.561 18.209 1.00 36.68 N ATOM 283 CA ALA A 39 4.065 58.107 18.287 1.00 36.58 C ATOM 284 C ALA A 39 5.433 57.607 17.773 1.00 35.91 C ATOM 285 O ALA A 39 6.014 56.661 18.319 1.00 35.28 O ATOM 286 CB ALA A 39 2.947 57.491 17.483 1.00 36.33 C ATOM 287 N GLY A 40 5.948 58.257 16.745 1.00 35.33 N ATOM 288 CA GLY A 40 7.296 57.938 16.267 1.00 35.20 C ATOM 289 C GLY A 40 8.386 58.218 17.295 1.00 34.81 C ATOM 290 O GLY A 40 9.320 57.432 17.456 1.00 34.92 O ATOM 291 N ARG A 41 8.297 59.351 17.981 1.00 35.65 N ATOM 292 CA ARG A 41 9.300 59.698 18.970 1.00 35.75 C ATOM 293 C ARG A 41 9.257 58.681 20.093 1.00 37.10 C ATOM 294 O ARG A 41 10.295 58.291 20.642 1.00 37.65 O ATOM 295 CB ARG A 41 9.090 61.118 19.494 1.00 36.15 C ATOM 296 CG ARG A 41 9.575 62.196 18.563 1.00 35.51 C ATOM 297 CD ARG A 41 9.383 63.592 19.134 1.00 38.98 C ATOM 298 NE ARG A 41 7.999 64.012 18.913 1.00 40.46 N ATOM 299 CZ ARG A 41 7.537 64.446 17.753 1.00 41.44 C ATOM 300 NH1 ARG A 41 8.326 64.534 16.682 1.00 42.62 N ATOM 301 NH2 ARG A 41 6.261 64.776 17.649 1.00 43.05 N ATOM 302 N ALA A 42 8.053 58.238 20.441 1.00 38.18 N ATOM 303 CA ALA A 42 7.878 57.270 21.524 1.00 38.42 C ATOM 304 C ALA A 42 8.398 55.909 21.116 1.00 38.32 C ATOM 305 O ALA A 42 8.952 55.181 21.927 1.00 37.15 O ATOM 306 CB ALA A 42 6.387 57.158 21.948 1.00 38.91 C ATOM 307 N THR A 43 8.209 55.567 19.842 1.00 37.57 N ATOM 308 CA THR A 43 8.756 54.324 19.328 1.00 37.21 C ATOM 309 C THR A 43 10.284 54.321 19.472 1.00 36.33 C ATOM 310 O THR A 43 10.842 53.315 19.824 1.00 36.44 O ATOM 311 CB THR A 43 8.316 54.130 17.873 1.00 37.54 C ATOM 312 OG1 THR A 43 6.890 53.948 17.829 1.00 38.41 O ATOM 313 CG2 THR A 43 8.897 52.837 17.280 1.00 36.05 C ATOM 314 N LEU A 44 10.948 55.436 19.192 1.00 36.74 N ATOM 315 CA LEU A 44 12.410 55.504 19.283 1.00 36.66 C ATOM 316 C LEU A 44 12.877 55.316 20.729 1.00 37.24 C ATOM 317 O LEU A 44 13.840 54.613 20.978 1.00 36.26 O ATOM 318 CB LEU A 44 12.957 56.819 18.725 1.00 36.22 C ATOM 319 CG LEU A 44 12.786 57.061 17.209 1.00 34.97 C ATOM 320 CD1 LEU A 44 13.386 58.400 16.795 1.00 33.89 C ATOM 321 CD2 LEU A 44 13.399 55.928 16.404 1.00 33.15 C ATOM 322 N ARG A 45 12.147 55.914 21.675 1.00 38.31 N ATOM 323 CA ARG A 45 12.485 55.801 23.095 1.00 39.49 C ATOM 324 C ARG A 45 12.296 54.381 23.589 1.00 39.97 C ATOM 325 O ARG A 45 13.113 53.864 24.338 1.00 40.63 O ATOM 326 CB ARG A 45 11.614 56.757 23.935 1.00 39.94 C ATOM 327 N ARG A 46 11.186 53.775 23.179 1.00 41.00 N ATOM 328 CA ARG A 46 10.849 52.397 23.503 1.00 41.33 C ATOM 329 C ARG A 46 11.912 51.412 23.025 1.00 40.34 C ATOM 330 O ARG A 46 12.278 50.485 23.731 1.00 39.81 O ATOM 331 CB ARG A 46 9.524 52.063 22.835 1.00 41.72 C ATOM 332 CG ARG A 46 8.773 50.911 23.395 1.00 46.36 C ATOM 333 CD ARG A 46 7.352 50.836 22.851 1.00 51.59 C ATOM 334 NE ARG A 46 7.345 50.162 21.548 1.00 57.79 N ATOM 335 CZ ARG A 46 6.851 50.659 20.399 1.00 61.01 C ATOM 336 NH1 ARG A 46 6.282 51.872 20.344 1.00 62.67 N ATOM 337 NH2 ARG A 46 6.918 49.916 19.290 1.00 61.73 N ATOM 338 N LEU A 47 12.402 51.620 21.809 1.00 39.47 N ATOM 339 CA LEU A 47 13.439 50.765 21.223 1.00 38.25 C ATOM 340 C LEU A 47 14.826 51.006 21.800 1.00 37.39 C ATOM 341 O LEU A 47 15.742 50.247 21.530 1.00 38.19 O ATOM 342 CB LEU A 47 13.502 51.010 19.712 1.00 38.57 C ATOM 343 CG LEU A 47 12.264 50.556 18.951 1.00 38.58 C ATOM 344 CD1 LEU A 47 12.346 51.046 17.517 1.00 38.92 C ATOM 345 CD2 LEU A 47 12.101 49.038 19.050 1.00 38.51 C ATOM 346 N GLY A 48 14.997 52.083 22.557 1.00 36.96 N ATOM 347 CA GLY A 48 16.262 52.383 23.191 1.00 35.72 C ATOM 348 C GLY A 48 17.323 52.969 22.286 1.00 34.43 C ATOM 349 O GLY A 48 18.512 52.912 22.607 1.00 34.93 O """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) params = monomer_library.pdb_interpretation.master_params.extract() params.secondary_structure.enabled=True processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=params, strict_conflict_handling=False, pdb_inp=pdb_inp, log=sys.stdout) geo = processed_pdb_file.geometry_restraints_manager() assert geo.get_n_hbond_proxies() == 8 make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix) def test_secondary_structure_2(mon_lib_srv, ener_lib, prefix="tst_grm_pickling_ss2"): from iotbx.pdb.tst_secondary_structure import pdb_1ywf_sample_strings pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_1ywf_sample_strings) params = monomer_library.pdb_interpretation.master_params.extract() params.secondary_structure.enabled=True processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=params, strict_conflict_handling=False, pdb_inp=pdb_inp, log=sys.stdout) geo = processed_pdb_file.geometry_restraints_manager() assert geo.get_n_hbond_proxies() == 103, geo.get_n_hbond_proxies() make_geo_pickle_unpickle(geo, processed_pdb_file.xray_structure(), prefix) def test_across_symmetry(mon_lib_srv, ener_lib, prefix="tst_across_symmetry"): raw_records1 = """\ CRYST1 60.800 60.800 97.000 90.00 90.00 120.00 P 32 2 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016447 0.009496 0.000000 0.00000 SCALE2 0.000000 0.018992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010309 0.00000 ATOM 1050 N LYS A 135 31.992 14.930 -7.233 1.00 9.47 N ATOM 1051 CA LYS A 135 31.388 16.216 -7.637 1.00 12.89 C ATOM 1052 C LYS A 135 30.807 16.840 -6.406 1.00 6.47 C ATOM 1053 O LYS A 135 29.583 16.869 -6.191 1.00 15.74 O ATOM 1054 CB LYS A 135 30.263 16.059 -8.655 1.00 13.51 C ATOM 1055 CG LYS A 135 30.742 15.277 -9.843 1.00 16.23 C ATOM 1056 CD LYS A 135 29.612 15.131 -10.835 1.00 28.55 C ATOM 1057 CE LYS A 135 30.173 14.812 -12.216 1.00 34.52 C ATOM 1058 NZ LYS A 135 29.396 13.756 -12.899 1.00 46.18 N HETATM 1406 O HOH A 282 32.366 19.942 24.727 1.00 38.09 O END """ geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, raw_records1) make_geo_pickle_unpickle(geometry, xrs, prefix) def test_reference_model(mon_lib_srv, ener_lib, prefix="tst_reference_model"): from mmtbx.geometry_restraints.torsion_restraints.tst_reference_model import \ model_raw_records, reference_raw_records from mmtbx.geometry_restraints.torsion_restraints.reference_model import \ reference_model import mmtbx.model # mstream = StringIO() from libtbx.utils import multi_out mstream = multi_out() mstream.register("stdout", sys.stdout) mstream_file_name = "polder.log" mstreamfile = open(mstream_file_name, "w") mstream.register("logfile", mstreamfile) work_params = mmtbx.model.manager.get_default_pdb_interpretation_params() work_params.reference_model.enabled = True work_params.reference_model.use_starting_model_as_reference = True work_params.reference_model.fix_outliers = False pdb_inp = iotbx.pdb.input(lines=model_raw_records.split('\n'), source_info=None) model = mmtbx.model.manager(model_input = pdb_inp) model.process(pdb_interpretation_params=work_params, make_restraints=True) reference_hierarchy_list = [] tmp_hierarchy = iotbx.pdb.input( source_info=None, lines=reference_raw_records.split('\n')).construct_hierarchy() reference_hierarchy_list.append(tmp_hierarchy) rm = reference_model( model = model, reference_hierarchy_list=reference_hierarchy_list, params=work_params.reference_model, log=mstream) assert rm.get_n_proxies() == 5, "Got %d, expected 5" % rm.get_n_proxies() geometry, xrs = make_initial_grm(mon_lib_srv, ener_lib, model_raw_records) geometry.adopt_reference_dihedral_manager(rm) make_geo_pickle_unpickle(geometry, xrs, prefix) mstream.close() def exercise_all(args): mon_lib_srv = None ener_lib = None try: mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() except Exception: print("Can not initialize monomer_library, skipping test.") return 0 import libtbx.load_env if libtbx.env.find_in_repositories(relative_path="chem_data") is None: print("Skipping exercise(): chem_data directory not available") return test_simple_protein(mon_lib_srv, ener_lib) test_nucleic_acid(mon_lib_srv, ener_lib) # test_ramachandran(mon_lib_srv, ener_lib) # test_cbeta(mon_lib_srv, ener_lib) # test_reference_coordinate(mon_lib_srv, ener_lib) # test_secondary_structure(mon_lib_srv, ener_lib) # test_secondary_structure_2(mon_lib_srv, ener_lib) # test_across_symmetry(mon_lib_srv, ener_lib) test_reference_model(mon_lib_srv, ener_lib) if (__name__ == "__main__"): exercise_all(sys.argv[1:])