from __future__ import absolute_import, division, print_function import time, os, sys import mmtbx.model import iotbx.pdb import libtbx.load_env from libtbx import easy_run from libtbx.utils import null_out from libtbx.test_utils import approx_equal from cctbx.array_family import flex from cctbx import xray from libtbx.utils import Sorry from six.moves import cStringIO as StringIO import mmtbx.validation.clashscore as mvc import cctbx.geometry_restraints.process_nonbonded_proxies as pnp chem_data = libtbx.env.find_in_repositories( relative_path="chem_data/geostd", test=os.path.isdir) def obtain_model(raw_records, stop_for_unknowns = True): ''' Helper function to obtain model class from raw records ''' params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.allow_polymer_cross_special_position=True pdb_inp = iotbx.pdb.input(lines=raw_records.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, stop_for_unknowns = stop_for_unknowns, log = null_out()) model.process(pdb_interpretation_params=params, make_restraints=True) return model def get_clashes_result(raw_records, sel=None): ''' Helper function to get clashes results from raw records ''' params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.allow_polymer_cross_special_position=True params.pdb_interpretation.clash_guard.nonbonded_distance_threshold = None pdb_inp = iotbx.pdb.input(lines=raw_records.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) model.process(pdb_interpretation_params=params, make_restraints=True) if sel is not None: model = model.select(sel) pnps = pnp.manager(model = model) clashes = pnps.get_clashes() return clashes def test_overlap_atoms(): ''' Test that overlapping atoms are being counted ''' print(raw_records_5) clashes = get_clashes_result(raw_records=raw_records_5) results = clashes.get_results() assert(results.n_clashes == 6), 'Overlapping atoms are not counted properly.' assert(results.clashscore == 1500), 'Clashscore is wrong' clashes = get_clashes_result(raw_records=raw_records_4) results = clashes.get_results() assert(results.n_clashes == 15) assert approx_equal(results.clashscore, 2500, eps=1) def test_inline_overlaps(): ''' Test non-bonded overlaps of C with H-C. Check when valid overlaps and when it's considered to be inline - test when all are in the same residue - test when C and H-C are in different residues ''' clashes = get_clashes_result(raw_records=raw_records_2) results = clashes.get_results() assert(results.n_clashes == 4), 'Total nonbonded overlaps are incorrect.' assert approx_equal(results.clashscore, 85.11, eps=0.1), 'Wrong clashscore.' def test_manager_and_clashes_functions(): ''' Test some functions of the manager and the clashes class ''' model = obtain_model(raw_records=raw_records_7) pnps = pnp.manager(model = model) assert(pnps.has_clashes()) clashes = pnps.get_clashes() # sorted by overlap (default) clashes.sort_clashes(by_value='overlap') assert(list(clashes._clashes_dict.items())[11][0] == ((38, 39))) # sorted by symmetry clashes.sort_clashes(by_value='symmetry') assert(list(clashes._clashes_dict.items())[11][0] == (27, 27)) assert(clashes.iseq_is_clashing(iseq=27)) assert(clashes.iseq_is_clashing(iseq=44)) assert(clashes.iseq_is_clashing(iseq=13)) assert(clashes.iseq_is_clashing(iseq=38)) assert(clashes.iseq_is_clashing(iseq=3)) def test_vdw_dist(): ''' Test that overlaps are identified properly Test overlaps that are set to be on the limit of the overlap distance 0.40 Test evaluation of vdw distances. if the parameters 1) assume_hydrogens_all_missing=False 2) hard_minimum_nonbonded_distance=0.0 are not set properly, the number of overlaps will change ''' clashes = get_clashes_result(raw_records=raw_records_0) results = clashes.get_results() assert(results.n_clashes == 2) assert approx_equal(results.clashscore, 38.46, eps=0.1) assert(results.n_clashes_sym == 2) assert approx_equal(results.clashscore_sym, 38.46, eps=0.1) assert(results.n_clashes_macro_mol == 0) assert(results.clashscore_macro_mol == 0) clashes = get_clashes_result(raw_records=raw_records_1) results = clashes.get_results() assert(results.n_clashes == 4) assert approx_equal(results.clashscore, 28.77, eps=0.1) assert(results.n_clashes_sym == 0) assert approx_equal(results.clashscore_sym, 0, eps=0.1) assert(results.n_clashes_macro_mol == 4) assert approx_equal(results.clashscore_macro_mol, 28.77, eps=0.1) def test_atom_selection(): ''' Test clashes when atom is removed ''' clashes = get_clashes_result(raw_records=raw_records_3) results = clashes.get_results() assert(results.n_clashes == 3) assert approx_equal(results.clashscore, 1000, eps=0.1) sel = flex.bool([True, True, False]) clashes = get_clashes_result(raw_records=raw_records_3, sel = sel) results = clashes.get_results() assert(results.n_clashes == 1) assert approx_equal(results.clashscore, 500, eps=0.1) def test_addition_scatterers(): ''' Test overlaps when adding and moving scatterers Test water scatterers with and without labels ''' clashes = get_clashes_result(raw_records=raw_records_3) results = clashes.get_results() assert(results.n_clashes == 3) assert approx_equal(results.clashscore, 1000, eps=0.1) # Add water scatterers model = clashes.model xrs = model.get_xray_structure() new_scatterers = flex.xray_scatterer( xrs.scatterers().size(), xray.scatterer(occupancy = 1, b = 10, scattering_type = "O")) new_sites_frac = xrs.unit_cell().fractionalize(xrs.sites_cart()+[0.5,0,0]) new_scatterers.set_sites(new_sites_frac) new_xrs = xray.structure( special_position_settings = xrs, scatterers = new_scatterers) model.add_solvent( solvent_xray_structure = new_xrs, refine_occupancies = False, refine_adp = "isotropic") pnps = pnp.manager(model = model) clashes = pnps.get_clashes() results = clashes.get_results() assert(results.n_clashes == 15) assert approx_equal(results.clashscore, 2500, eps=5) def test_show(): ''' Test show ''' clashes = get_clashes_result(raw_records=raw_records_7) results = clashes.get_results() assert(results.n_clashes == 12) assert(results.n_clashes_sym == 2) assert(results.n_clashes_macro_mol == 3) assert approx_equal(results.clashscore, 260.87, eps=1) assert approx_equal(results.clashscore_sym, 43.48, eps=1) assert approx_equal(results.clashscore_macro_mol, 78.95, eps=1) string_io = StringIO() clashes.show(log=string_io) lines = string_io.getvalue().split('\n') assert(lines[8].startswith('--------')) assert(lines[21].startswith('--------')) def test_unknown_pair_type(): ''' Make sure unknown pair types are not processed ''' sorry = None try: clashes = get_clashes_result(raw_records=raw_records_6) except Sorry as e: sorry = e assert(sorry is not None) def test_running_from_command_line(): ''' Make sure mmtbx.nonbonded_overlaps can run without errors ''' file_name = 'test_pdb_file.pdb' if not os.path.isfile(file_name): open(file_name,'w').write(raw_records_1) #self.file_to_delete.append(self.file_name) cmd = 'mmtbx.nonbonded_overlaps {}' cmd = cmd.format(file_name) r = easy_run.go(cmd, join_stdout_stderr=False) assert(not bool(r.stderr_lines)) #def test_file_with_unknown_pair_type(): # ''' # Verify that file with unknown_pair_type fails # --> retire this test as functionality is already tested above # also, this test becomes a failure whenever the unknown entity is # added to geostd. # ''' # model = obtain_model(raw_records = unknown_pairs_pdb_str, # stop_for_unknowns = False) # ph = model.get_hierarchy() # pdb_with_h, h_were_added = mvc.check_and_add_hydrogen( # pdb_hierarchy = ph, # allow_multiple_models = False, # crystal_symmetry = model.crystal_symmetry(), # log = null_out()) # sorry = None # try: # model = obtain_model(raw_records=pdb_with_h) # except Sorry as e: # sorry = e # assert(sorry is not None) # # test = nbo.unknown_pairs_present(grm=grm,sites_cart=sites,site_labels=labels) # # make sure we have unknown pairs # self.assertTrue(test) # pdb_ready_set_file_names = nbo.create_cif_file_using_ready_set( # file_name=fn_with_h, # log=null_out()) # [fn_cif,fn_pdb] = pdb_ready_set_file_names # # check that we can run overlaps # if fn_cif: # self.file_to_delete.extend(pdb_ready_set_file_names) # overlaps_count_info = process_overlaps_count( # file_name=fn_pdb, # cif_file_name=fn_cif) def test_small_cell(): ''' Test what happens with small cell. ''' clashes = get_clashes_result(raw_records=raw_records_8) results = clashes.get_results() assert(results.n_clashes == 0) assert approx_equal(results.clashscore, 0, eps=0.1) def test_inline_angle(): ''' Test cos_vec(u,v) ''' u = (40.196,3.261,-48.474) v = (39.466,4.279,-52.202) w = (37.407,5.077,-51.025) result = pnp.cos_vec(u, v, w) expected = 0.5072 msg = 'The difference is: {}'.format(result - expected) assert approx_equal(result, expected, eps=0.001), msg def test_1_5_overlaps(): ''' Test if 1_5 overlaps are correctly identified ''' model = obtain_model(raw_records_0) hd_sel = model.get_hd_selection() grm = model.get_restraints_manager().geometry full_connectivity_table = grm.shell_sym_tables[0].full_simple_connectivity() outstring = '1-5 Interaction test error. {}' # check that direction of function calling does not matter tst = pnp.check_if_1_5_interaction(21, 33,hd_sel,full_connectivity_table) msg = 'Test results depend on atoms order' assert(tst), msg tst = pnp.check_if_1_5_interaction(33, 21,hd_sel,full_connectivity_table) assert(tst), msg # check 1-4 interaction tst = pnp.check_if_1_5_interaction(33, 20,hd_sel,full_connectivity_table) msg = 'Test fails on 1-4 interaction' assert(not tst), msg # check 1-6 interaction tst = pnp.check_if_1_5_interaction(33, 38,hd_sel,full_connectivity_table) msg = 'Test fails on 1-6 interaction' assert(not tst), msg # 1-5 interaction of atoms other than hydrogen tst = pnp.check_if_1_5_interaction(38, 25,hd_sel,full_connectivity_table) msg = 'Test fails on 1-5 non hydrogen interaction' assert(not tst), msg # 1-5 interaction of two hydrogens tst = pnp.check_if_1_5_interaction(33, 31,hd_sel,full_connectivity_table) msg = 'Test fails on 1-5 two hydrogen interaction' assert(not tst), msg def test_no_unit_cell(): ''' Make sure NBO code does not crash if no unit cell provided ''' clashes = get_clashes_result(raw_records=raw_records_9) results = clashes.get_results() assert(results.n_clashes == 15) assert approx_equal(results.clashscore, 468, eps=2.0) raw_records_0 = """ CRYST1 80.020 97.150 49.850 90.00 90.00 90.00 C 2 2 21 ATOM 1271 N ILE A 83 31.347 4.310 -43.960 1.00 9.97 N ATOM 1272 CA ILE A 83 32.076 3.503 -44.918 1.00 19.49 C ATOM 1273 C ILE A 83 32.062 4.261 -46.243 1.00 15.26 C ATOM 1274 O ILE A 83 31.006 4.660 -46.740 1.00 16.12 O ATOM 1275 CB ILE A 83 31.486 2.080 -45.048 1.00 18.05 C ATOM 1276 CG1 ILE A 83 32.328 1.263 -46.027 1.00 17.98 C ATOM 1277 CG2 ILE A 83 30.020 2.134 -45.469 1.00 28.62 C ATOM 1278 CD1 ILE A 83 32.130 -0.226 -45.888 1.00 38.88 C ATOM 1279 H ILE A 83 30.735 4.798 -44.316 1.00 9.97 H ATOM 1280 HA ILE A 83 32.999 3.421 -44.630 1.00 19.49 H ATOM 1281 HB ILE A 83 31.534 1.655 -44.178 1.00 18.05 H ATOM 1282 HG12 ILE A 83 32.087 1.512 -46.933 1.00 17.98 H ATOM 1283 HG13 ILE A 83 33.266 1.454 -45.871 1.00 17.98 H ATOM 1284 HG21 ILE A 83 29.627 1.256 -45.347 1.00 28.62 H ATOM 1285 HG22 ILE A 83 29.554 2.783 -44.919 1.00 28.62 H ATOM 1286 HG23 ILE A 83 29.967 2.392 -46.402 1.00 28.62 H ATOM 1287 HD11 ILE A 83 33.003 -0.644 -45.858 1.00 38.88 H ATOM 1288 HD12 ILE A 83 31.654 -0.404 -45.062 1.00 38.88 H ATOM 1289 HD13 ILE A 83 31.608 -0.541 -46.640 1.00 38.88 H ATOM 1290 N ILE A 84 33.252 4.542 -46.758 1.00 11.36 N ATOM 1291 CA ILE A 84 33.381 5.290 -47.993 1.00 9.27 C ATOM 1292 C ILE A 84 33.906 4.417 -49.101 1.00 11.06 C ATOM 1293 O ILE A 84 34.881 3.694 -48.921 1.00 14.52 O ATOM 1294 CB ILE A 84 34.308 6.508 -47.813 1.00 11.89 C ATOM 1295 CG1 ILE A 84 33.730 7.436 -46.746 1.00 9.03 C ATOM 1296 CG2 ILE A 84 34.471 7.257 -49.132 1.00 10.52 C ATOM 1297 CD1 ILE A 84 34.436 8.761 -46.632 1.00 12.96 C ATOM 1298 H ILE A 84 34.002 4.308 -46.408 1.00 11.36 H ATOM 1299 HA ILE A 84 32.515 5.625 -48.269 1.00 9.27 H ATOM 1300 HB ILE A 84 35.179 6.198 -47.520 1.00 11.89 H ATOM 1301 HG12 ILE A 84 32.800 7.587 -46.942 1.00 9.03 H ATOM 1302 HG13 ILE A 84 33.808 6.995 -45.886 1.00 9.03 H ATOM 1303 HG21 ILE A 84 35.193 7.898 -49.045 1.00 10.52 H ATOM 1304 HG22 ILE A 84 34.688 6.643 -49.848 1.00 10.52 H ATOM 1305 HG23 ILE A 84 33.642 7.718 -49.335 1.00 10.52 H ATOM 1306 HD11 ILE A 84 33.911 9.335 -46.052 1.00 12.96 H ATOM 1307 HD12 ILE A 84 35.300 8.606 -46.229 1.00 12.96 H ATOM 1308 HD13 ILE A 84 34.530 9.185 -47.497 1.00 12.96 H ATOM 1309 N THR A 85 33.228 4.470 -50.242 1.00 17.41 N ATOM 1310 CA THR A 85 33.615 3.692 -51.411 1.00 14.87 C ATOM 1311 C THR A 85 33.743 4.584 -52.633 1.00 15.68 C ATOM 1312 O THR A 85 33.232 5.702 -52.660 1.00 10.37 O ATOM 1313 CB THR A 85 32.581 2.585 -51.737 1.00 13.04 C ATOM 1314 OG1 THR A 85 31.285 3.169 -51.914 1.00 19.63 O ATOM 1315 CG2 THR A 85 32.524 1.546 -50.626 1.00 14.50 C ATOM 1316 H THR A 85 32.530 4.957 -50.365 1.00 17.41 H ATOM 1317 HA THR A 85 34.473 3.268 -51.259 1.00 14.87 H ATOM 1318 HB THR A 85 32.872 2.178 -52.553 1.00 13.04 H ATOM 1319 HG1 THR A 85 31.049 3.564 -51.211 1.00 19.63 H ATOM 1320 HG21 THR A 85 32.000 0.780 -50.908 1.00 14.50 H ATOM 1321 HG22 THR A 85 33.420 1.251 -50.402 1.00 14.50 H ATOM 1322 HG23 THR A 85 32.116 1.932 -49.835 1.00 14.50 H """ raw_records_1 = """ CRYST1 80.020 97.150 49.850 90.00 90.00 90.00 C 2 2 21 HETATM 1819 N NPH A 117 23.870 15.268 -50.490 1.00 25.06 N HETATM 1820 CA NPH A 117 23.515 14.664 -49.210 1.00 22.94 C HETATM 1821 CB NPH A 117 23.658 15.702 -48.113 1.00 21.44 C HETATM 1822 SG NPH A 117 25.281 16.410 -47.839 1.00 31.29 S HETATM 1823 CD NPH A 117 25.498 16.310 -46.059 0.50 33.70 C HETATM 1824 CE NPH A 117 26.971 16.492 -45.820 0.50 39.92 C HETATM 1825 OZ NPH A 117 27.815 15.348 -45.806 0.50 43.26 O HETATM 1826 NZ NPH A 117 27.411 17.709 -45.649 0.50 43.87 N HETATM 1827 C6 NPH A 117 28.830 18.015 -45.436 0.50 51.14 C HETATM 1828 C5 NPH A 117 29.800 17.009 -45.411 0.50 51.26 C HETATM 1829 C6A NPH A 117 29.195 19.344 -45.262 0.50 52.54 C HETATM 1830 C4A NPH A 117 31.137 17.332 -45.219 0.50 52.42 C HETATM 1831 C10 NPH A 117 30.543 19.684 -45.064 0.50 54.23 C HETATM 1832 C7 NPH A 117 28.201 20.331 -45.288 0.50 53.28 C HETATM 1833 C4 NPH A 117 32.087 16.314 -45.202 0.50 53.40 C HETATM 1834 C1A NPH A 117 31.522 18.669 -45.046 0.50 55.19 C HETATM 1835 N10 NPH A 117 30.892 21.027 -44.889 0.50 53.87 N HETATM 1836 C8 NPH A 117 28.549 21.670 -45.111 0.50 54.83 C HETATM 1837 C3 NPH A 117 33.439 16.599 -45.020 0.50 53.96 C HETATM 1838 N1 NPH A 117 32.879 18.963 -44.861 0.50 57.78 N HETATM 1839 C9 NPH A 117 29.889 22.011 -44.911 0.50 55.29 C HETATM 1840 C2 NPH A 117 33.832 17.924 -44.852 0.50 55.79 C HETATM 1841 C NPH A 117 22.061 14.206 -49.245 1.00 23.82 C HETATM 1842 O NPH A 117 21.158 15.023 -49.423 1.00 24.62 O HETATM 1843 HZ NPH A 117 26.743 18.445 -45.689 0.50 43.87 H HETATM 1844 HD3 NPH A 117 24.961 17.137 -45.534 0.50 33.70 H HETATM 1845 HD2 NPH A 117 25.185 15.321 -45.644 0.50 33.70 H HETATM 1846 HC2 NPH A 117 34.904 18.122 -44.711 0.50 55.79 H HETATM 1847 HB3 NPH A 117 22.975 16.550 -48.341 1.00 21.44 H HETATM 1848 HB2 NPH A 117 23.315 15.232 -47.181 1.00 21.44 H HETATM 1849 H9 NPH A 117 30.113 23.063 -44.748 0.50 55.29 H HETATM 1850 H8 NPH A 117 27.786 22.458 -45.117 0.50 54.83 H HETATM 1851 H7 NPH A 117 27.137 20.098 -45.429 0.50 53.28 H HETATM 1852 H5 NPH A 117 29.623 15.938 -45.543 0.50 51.26 H HETATM 1853 H4 NPH A 117 31.708 15.307 -45.324 0.50 53.40 H HETATM 1854 H3 NPH A 117 34.196 15.804 -45.008 0.50 53.96 H ATOM 1855 N VAL A 118 21.831 12.913 -49.037 1.00 28.67 N ATOM 1856 CA VAL A 118 20.474 12.371 -49.062 1.00 33.96 C ATOM 1857 C VAL A 118 20.069 11.729 -47.737 1.00 36.17 C ATOM 1858 O VAL A 118 20.854 11.018 -47.109 1.00 40.12 O ATOM 1859 CB VAL A 118 20.297 11.336 -50.209 1.00 39.91 C ATOM 1860 CG1 VAL A 118 18.831 10.915 -50.336 1.00 38.68 C ATOM 1861 CG2 VAL A 118 20.791 11.918 -51.524 1.00 43.67 C ATOM 1862 H VAL A 118 22.442 12.328 -48.879 1.00 28.67 H ATOM 1863 HA VAL A 118 19.848 13.087 -49.232 1.00 33.96 H ATOM 1864 HB VAL A 118 20.823 10.546 -50.010 1.00 39.91 H ATOM 1865 HG11 VAL A 118 18.723 10.392 -51.146 1.00 38.68 H ATOM 1866 HG12 VAL A 118 18.585 10.381 -49.564 1.00 38.68 H ATOM 1867 HG13 VAL A 118 18.277 11.710 -50.381 1.00 38.68 H ATOM 1868 HG21 VAL A 118 20.576 11.302 -52.242 1.00 43.67 H ATOM 1869 HG22 VAL A 118 20.352 12.770 -51.676 1.00 43.67 H ATOM 1870 HG23 VAL A 118 21.751 12.045 -51.474 1.00 43.67 H ATOM 1871 N MET A 119 18.829 11.986 -47.328 1.00 39.11 N ATOM 1872 CA MET A 119 18.273 11.449 -46.092 1.00 39.84 C ATOM 1873 C MET A 119 16.761 11.361 -46.256 1.00 45.51 C ATOM 1874 O MET A 119 16.066 12.375 -46.173 1.00 45.08 O ATOM 1875 CB MET A 119 18.616 12.370 -44.916 1.00 46.77 C ATOM 1876 CG MET A 119 19.314 11.688 -43.740 1.00 45.80 C ATOM 1877 SD MET A 119 18.225 10.980 -42.492 1.00 41.41 S ATOM 1878 CE MET A 119 17.987 9.359 -43.118 1.00 44.09 C ATOM 1879 H MET A 119 18.277 12.482 -47.762 1.00 39.11 H ATOM 1880 HA MET A 119 18.637 10.566 -45.922 1.00 39.84 H ATOM 1881 HB2 MET A 119 19.202 13.071 -45.238 1.00 46.77 H ATOM 1882 HB3 MET A 119 17.801 12.765 -44.571 1.00 46.77 H ATOM 1883 HG2 MET A 119 19.854 10.965 -44.091 1.00 45.80 H ATOM 1884 HG3 MET A 119 19.885 12.336 -43.300 1.00 45.80 H ATOM 1885 HE1 MET A 119 17.086 9.072 -42.908 1.00 44.09 H ATOM 1886 HE2 MET A 119 18.121 9.364 -44.078 1.00 44.09 H ATOM 1887 HE3 MET A 119 18.627 8.768 -42.693 1.00 44.09 H ATOM 1888 N LYS A 120 16.265 10.152 -46.521 1.00 52.01 N ATOM 1889 CA LYS A 120 14.834 9.908 -46.706 1.00 55.50 C ATOM 1890 C LYS A 120 14.220 10.827 -47.764 1.00 61.07 C ATOM 1891 O LYS A 120 13.324 11.621 -47.467 1.00 63.20 O ATOM 1892 CB LYS A 120 14.079 10.073 -45.381 1.00 57.57 C ATOM 1893 CG LYS A 120 14.393 9.026 -44.324 1.00 62.80 C ATOM 1894 CD LYS A 120 13.804 9.426 -42.977 1.00 66.61 C ATOM 1895 CE LYS A 120 14.483 10.683 -42.438 1.00 72.33 C ATOM 1896 NZ LYS A 120 13.902 11.173 -41.155 1.00 69.78 N ATOM 1897 H LYS A 120 16.747 9.444 -46.600 1.00 52.01 H ATOM 1898 HA LYS A 120 14.711 8.993 -47.004 1.00 55.50 H ATOM 1899 HB2 LYS A 120 14.293 10.951 -45.043 1.00 57.57 H ATOM 1900 HB3 LYS A 120 13.127 10.019 -45.560 1.00 57.57 H ATOM 1901 HG2 LYS A 120 14.005 8.177 -44.587 1.00 62.80 H ATOM 1902 HG3 LYS A 120 15.354 8.943 -44.230 1.00 62.80 H ATOM 1903 HD2 LYS A 120 12.857 9.611 -43.082 1.00 66.61 H ATOM 1904 HD3 LYS A 120 13.940 8.707 -42.340 1.00 66.61 H ATOM 1905 HE2 LYS A 120 15.421 10.490 -42.285 1.00 72.33 H ATOM 1906 HE3 LYS A 120 14.396 11.408 -43.068 1.00 72.33 H ATOM 1907 HZ1 LYS A 120 14.332 11.905 -40.886 1.00 69.78 H ATOM 1908 HZ2 LYS A 120 13.041 11.368 -41.266 1.00 69.78 H ATOM 1909 HZ3 LYS A 120 13.977 10.546 -40.528 1.00 69.78 H ATOM 1910 N GLY A 121 14.729 10.739 -48.990 1.00 62.98 N ATOM 1911 CA GLY A 121 14.207 11.559 -50.072 1.00 61.51 C ATOM 1912 C GLY A 121 14.804 12.947 -50.225 1.00 57.12 C ATOM 1913 O GLY A 121 15.145 13.351 -51.339 1.00 61.31 O ATOM 1914 H GLY A 121 15.372 10.216 -49.218 1.00 62.98 H ATOM 1915 HA2 GLY A 121 14.350 11.088 -50.908 1.00 61.51 H ATOM 1916 HA3 GLY A 121 13.250 11.662 -49.955 1.00 61.51 H ATOM 1917 N VAL A 122 14.909 13.687 -49.123 1.00 48.05 N ATOM 1918 CA VAL A 122 15.464 15.042 -49.144 1.00 40.46 C ATOM 1919 C VAL A 122 16.907 15.047 -49.643 1.00 37.52 C ATOM 1920 O VAL A 122 17.717 14.230 -49.217 1.00 47.57 O ATOM 1921 CB VAL A 122 15.397 15.699 -47.740 1.00 38.05 C ATOM 1922 CG1 VAL A 122 16.099 17.054 -47.747 1.00 31.26 C ATOM 1923 CG2 VAL A 122 13.940 15.863 -47.312 1.00 35.36 C ATOM 1924 H VAL A 122 14.663 13.425 -48.342 1.00 48.05 H ATOM 1925 HA VAL A 122 14.938 15.586 -49.751 1.00 40.46 H ATOM 1926 HB VAL A 122 15.842 15.127 -47.095 1.00 38.05 H ATOM 1927 HG11 VAL A 122 15.813 17.560 -46.970 1.00 31.26 H ATOM 1928 HG12 VAL A 122 17.059 16.917 -47.715 1.00 31.26 H ATOM 1929 HG13 VAL A 122 15.857 17.530 -48.557 1.00 31.26 H ATOM 1930 HG21 VAL A 122 13.910 16.341 -46.469 1.00 35.36 H ATOM 1931 HG22 VAL A 122 13.466 16.365 -47.994 1.00 35.36 H ATOM 1932 HG23 VAL A 122 13.540 14.985 -47.210 1.00 35.36 H ATOM 1933 N THR A 123 17.222 15.963 -50.553 1.00 32.61 N ATOM 1934 CA THR A 123 18.571 16.046 -51.098 1.00 28.67 C ATOM 1935 C THR A 123 19.130 17.463 -51.045 1.00 29.81 C ATOM 1936 O THR A 123 18.492 18.416 -51.489 1.00 32.53 O ATOM 1937 CB THR A 123 18.627 15.533 -52.561 1.00 29.86 C ATOM 1938 OG1 THR A 123 18.176 14.175 -52.612 1.00 31.25 O ATOM 1939 CG2 THR A 123 20.054 15.598 -53.103 1.00 32.10 C ATOM 1940 H THR A 123 16.675 16.546 -50.870 1.00 32.61 H ATOM 1941 HA THR A 123 19.160 15.485 -50.579 1.00 28.67 H ATOM 1942 HB THR A 123 18.059 16.085 -53.121 1.00 29.86 H ATOM 1943 HG1 THR A 123 18.204 13.892 -53.403 1.00 31.25 H ATOM 1944 HG21 THR A 123 20.120 15.079 -53.920 1.00 32.10 H ATOM 1945 HG22 THR A 123 20.298 16.517 -53.295 1.00 32.10 H ATOM 1946 HG23 THR A 123 20.673 15.236 -52.450 1.00 32.10 H ATOM 1947 N SER A 124 20.324 17.583 -50.480 1.00 25.77 N ATOM 1948 CA SER A 124 21.012 18.858 -50.362 1.00 25.34 C ATOM 1949 C SER A 124 22.166 18.863 -51.358 1.00 23.45 C ATOM 1950 O SER A 124 22.899 17.881 -51.477 1.00 26.73 O ATOM 1951 CB SER A 124 21.543 19.037 -48.938 1.00 24.00 C ATOM 1952 OG SER A 124 22.400 20.159 -48.851 1.00 27.42 O ATOM 1953 H SER A 124 20.766 16.923 -50.150 1.00 25.77 H ATOM 1954 HA SER A 124 20.410 19.588 -50.567 1.00 25.34 H ATOM 1955 HB2 SER A 124 20.793 19.168 -48.338 1.00 24.00 H ATOM 1956 HB3 SER A 124 22.034 18.250 -48.682 1.00 24.00 H ATOM 1957 HG SER A 124 21.984 20.856 -49.068 1.00 27.42 H """ raw_records_2 = """ CRYST1 80.020 97.150 49.850 90.00 90.00 90.00 C 2 2 21 HETATM 1819 N NPH A 117 24.064 15.944 -50.623 1.00 25.06 N HETATM 1820 CA NPH A 117 23.709 15.340 -49.343 1.00 22.94 C HETATM 1821 CB NPH A 117 23.852 16.378 -48.246 1.00 21.44 C HETATM 1822 SG NPH A 117 25.475 17.086 -47.972 1.00 31.29 S HETATM 1823 CD NPH A 117 25.692 16.986 -46.192 0.50 33.70 C HETATM 1824 CE NPH A 117 27.165 17.168 -45.953 0.50 39.92 C HETATM 1825 OZ NPH A 117 28.009 16.024 -45.939 0.50 43.26 O HETATM 1826 NZ NPH A 117 27.605 18.385 -45.782 0.50 43.87 N HETATM 1827 C6 NPH A 117 29.024 18.691 -45.569 0.50 51.14 C HETATM 1828 C5 NPH A 117 29.994 17.685 -45.544 0.50 51.26 C HETATM 1829 C6A NPH A 117 29.389 20.020 -45.395 0.50 52.54 C HETATM 1830 C4A NPH A 117 31.331 18.008 -45.352 0.50 52.42 C HETATM 1831 C10 NPH A 117 30.737 20.360 -45.197 0.50 54.23 C HETATM 1832 C7 NPH A 117 28.395 21.007 -45.421 0.50 53.28 C HETATM 1833 C4 NPH A 117 32.281 16.990 -45.335 0.50 53.40 C HETATM 1834 C1A NPH A 117 31.716 19.345 -45.179 0.50 55.19 C HETATM 1835 N10 NPH A 117 31.086 21.703 -45.022 0.50 53.87 N HETATM 1836 C8 NPH A 117 28.743 22.346 -45.244 0.50 54.83 C HETATM 1837 C3 NPH A 117 33.633 17.275 -45.153 0.50 53.96 C HETATM 1838 N1 NPH A 117 33.073 19.639 -44.994 0.50 57.78 N HETATM 1839 C9 NPH A 117 30.083 22.687 -45.044 0.50 55.29 C HETATM 1840 C2 NPH A 117 34.026 18.600 -44.985 0.50 55.79 C HETATM 1841 C NPH A 117 22.255 14.882 -49.378 1.00 23.82 C HETATM 1842 O NPH A 117 21.352 15.699 -49.556 1.00 24.62 O HETATM 1843 HZ NPH A 117 26.937 19.121 -45.822 0.50 43.87 H HETATM 1844 HD3 NPH A 117 25.155 17.813 -45.667 0.50 33.70 H HETATM 1845 HD2 NPH A 117 25.379 15.997 -45.777 0.50 33.70 H HETATM 1846 HC2 NPH A 117 35.098 18.798 -44.844 0.50 55.79 H HETATM 1847 HB3 NPH A 117 23.169 17.226 -48.474 1.00 21.44 H HETATM 1848 HB2 NPH A 117 23.509 15.908 -47.314 1.00 21.44 H HETATM 1849 H9 NPH A 117 30.307 23.739 -44.881 0.50 55.29 H HETATM 1850 H8 NPH A 117 27.980 23.134 -45.250 0.50 54.83 H HETATM 1851 H7 NPH A 117 27.331 20.774 -45.562 0.50 53.28 H HETATM 1852 H5 NPH A 117 29.817 16.614 -45.676 0.50 51.26 H HETATM 1853 H4 NPH A 117 31.902 15.983 -45.457 0.50 53.40 H HETATM 1854 H3 NPH A 117 34.390 16.480 -45.141 0.50 53.96 H ATOM 1947 N SER B 124 20.843 16.929 -50.266 1.00 25.77 N ATOM 1948 CA SER B 124 21.084 18.355 -50.408 1.00 25.34 C ATOM 1949 C SER B 124 22.267 18.540 -51.353 1.00 23.45 C ATOM 1950 O SER B 124 23.277 17.846 -51.239 1.00 26.73 O ATOM 1951 CB SER B 124 21.398 18.973 -49.044 1.00 24.00 C ATOM 1952 OG SER B 124 21.849 20.306 -49.179 1.00 27.42 O ATOM 1953 H SER B 124 21.437 16.527 -49.790 1.00 25.77 H ATOM 1954 HA SER B 124 20.306 18.795 -50.781 1.00 25.34 H ATOM 1955 HB2 SER B 124 20.592 18.968 -48.505 1.00 24.00 H ATOM 1956 HB3 SER B 124 22.084 18.454 -48.612 1.00 24.00 H ATOM 1957 HG SER B 124 21.258 20.773 -49.552 1.00 27.42 H """ raw_records_3=""" CRYST1 20.000 20.000 20.000 90.00 90.00 90.00 P 1 ATOM 1 N LYS 1 5.000 5.000 5.000 1.00 20.00 N ATOM 1 N LYS 2 6.000 5.000 5.000 1.00 20.00 N ATOM 1 N LYS 4 5.000 5.500 5.500 1.00 20.00 N """ raw_records_4=""" CRYST1 20.000 20.000 20.000 90.00 90.00 90.00 P 1 SCALE1 0.050000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.050000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.050000 0.00000 ATOM 1 N LYS 1 5.000 5.000 5.000 1.00 20.00 N ATOM 2 N LYS 2 6.000 5.000 5.000 1.00 20.00 N ATOM 3 N LYS 4 5.000 5.500 5.500 1.00 20.00 N TER HETATM 4 O HOH 1 5.500 5.000 5.000 1.00 10.00 O HETATM 5 O HOH 2 6.500 5.000 5.000 1.00 10.00 O HETATM 6 O HOH 3 5.500 5.500 5.500 1.00 10.00 O TER END """ raw_records_5 = """ CRYST1 20.000 20.000 20.000 90.00 90.00 90.00 P 1 ATOM 1 N LYS 1 5.000 5.000 5.000 1.00 20.00 N ATOM 1 N LYS 2 6.000 5.000 5.000 1.00 20.00 N ATOM 1 N LYS 3 5.000 5.500 5.500 1.00 20.00 N ATOM 1 N LYS 4 5.000 5.500 5.500 1.00 20.00 N """ raw_records_6=""" CRYST1 44.060 35.400 48.340 90.00 95.00 90.00 C 1 2 1 8 HETATM 410 O3' A44 B 17 21.829 8.287 7.189 1.00 36.66 O HETATM 411 C2' A44 B 17 23.214 6.318 6.661 1.00 33.97 C HETATM 412 O2' A44 B 17 23.644 7.009 5.493 1.00 33.08 O HETATM 413 z!# A44 B 17 24.403 5.690 7.395 1.00 32.76 C """ raw_records_7=""" CRYST1 44.060 35.400 48.340 90.00 95.00 90.00 C 1 2 1 4 ATOM 1 N GLY A 1 -6.724 4.519 10.133 1.00 16.77 N ATOM 2 CA GLY A 1 -7.194 4.166 8.745 1.00 16.57 C ATOM 3 C GLY A 1 -6.271 3.120 8.177 1.00 16.16 C ATOM 4 O GLY A 1 -5.516 2.473 8.927 1.00 16.78 O ATOM 5 N ASN A 2 -6.301 2.953 6.856 1.00 15.02 N ATOM 6 CA ASN A 2 -5.313 2.093 6.179 1.00 14.10 C ATOM 7 C ASN A 2 -3.913 2.586 6.388 1.00 13.13 C ATOM 8 O ASN A 2 -3.663 3.793 6.355 1.00 11.91 O ATOM 9 CB ASN A 2 -5.585 1.992 4.699 1.00 15.38 C ATOM 10 CG ASN A 2 -6.959 1.462 4.424 1.00 14.08 C ATOM 11 OD1 ASN A 2 -7.284 0.331 4.822 1.00 17.46 O ATOM 12 ND2 ASN A 2 -7.807 2.298 3.816 1.00 11.72 N ATOM 13 N ASN A 3 -3.004 1.632 6.572 1.00 12.26 N ATOM 14 CA ASN A 3 -1.613 1.936 6.869 1.00 11.74 C ATOM 15 C ASN A 3 -0.635 1.404 5.819 1.00 11.10 C ATOM 16 O ASN A 3 -0.628 0.202 5.513 1.00 10.42 O ATOM 17 CB ASN A 3 -1.246 1.358 8.256 1.00 12.15 C ATOM 18 CG ASN A 3 0.193 1.704 8.681 1.00 12.82 C ATOM 19 OD1 ASN A 3 0.544 2.886 8.837 1.00 15.05 O ATOM 20 ND2 ASN A 3 1.027 0.674 8.850 1.00 13.48 N ATOM 21 N GLN A 4 0.718 2.275 5.803 1.00 10.29 N ATOM 22 CA GLN A 4 1.399 2.012 4.510 1.00 10.53 C ATOM 23 C GLN A 4 2.797 2.684 4.444 1.00 10.24 C ATOM 24 O GLN A 4 2.943 3.917 4.484 1.00 8.86 O ATOM 25 CB GLN A 4 0.545 2.406 3.297 1.00 9.80 C ATOM 26 CG GLN A 4 1.072 1.800 1.978 1.00 10.25 C ATOM 27 CD GLN A 4 0.565 2.510 0.717 1.00 12.43 C ATOM 28 OE1 GLN A 4 0.710 3.745 0.575 1.00 14.62 O ATOM 29 NE2 GLN A 4 -0.007 1.723 -0.230 1.00 9.05 N ATOM 30 N GLN A 5 3.828 1.858 4.418 1.00 10.38 N ATOM 31 CA GLN A 5 4.819 1.038 5.107 1.00 11.39 C ATOM 32 C GLN A 5 5.215 -0.166 4.260 1.00 11.52 C ATOM 33 O GLN A 5 4.376 -0.926 3.752 1.00 12.05 O ATOM 34 CB GLN A 5 4.342 0.629 6.505 1.00 11.96 C ATOM 35 CG GLN A 5 4.135 1.841 7.417 1.00 10.81 C ATOM 36 CD GLN A 5 3.241 1.514 8.568 1.00 13.10 C ATOM 37 OE1 GLN A 5 2.035 1.354 8.386 1.00 10.65 O ATOM 38 NE2 GLN A 5 3.822 1.429 9.781 1.00 12.30 N TER HETATM 61 O HOH A 8 -0.511 4.797 12.393 1.00 22.62 O HETATM 62 O HOH A 9 -0.513 4.516 12.150 1.00 19.71 O TER HETATM 2800 S SO4 A 701 -3.889 1.786 10.440 1.00 55.67 S HETATM 2801 O1 SO4 A 701 -3.645 1.548 9.055 1.00 57.05 O HETATM 2802 O2 SO4 A 701 -4.464 3.089 10.608 1.00 55.53 O HETATM 2803 O3 SO4 A 701 -4.744 0.755 10.958 1.00 56.44 O HETATM 2804 O4 SO4 A 701 -2.664 1.753 11.146 1.00 56.08 O ATOM 60 O HOH C 37 -0.639 -0.486 5.076 1.00 0.00 O END """ raw_records_8 = """ CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 1 -6.724 4.519 10.133 1.00 16.77 N ATOM 2 CA GLY A 1 -7.194 4.166 8.745 1.00 16.57 C ATOM 3 C GLY A 1 -6.271 3.120 8.177 1.00 16.16 C ATOM 4 O GLY A 1 -5.516 2.473 8.927 1.00 16.78 O ATOM 5 H1 GLY A 1 -7.327 4.247 10.729 1.00 16.77 H ATOM 6 H2 GLY A 1 -5.946 4.118 10.294 1.00 16.77 H ATOM 7 H3 GLY A 1 -6.621 5.401 10.197 1.00 16.77 H ATOM 8 HA2 GLY A 1 -8.104 3.833 8.772 1.00 16.57 H ATOM 9 HA3 GLY A 1 -7.198 4.954 8.180 1.00 16.57 H """ raw_records_9 = """ HETATM 7 O HOH S 14 -18.253 -4.465 -12.178 1.00 27.19 O HETATM 13 O HOH S 25 -19.834 -4.638 -10.686 1.00 27.54 O HETATM 14 O HOH S 27 -15.855 -5.767 -12.479 1.00 27.85 O HETATM 22 O HOH S 63 -18.424 -6.217 -12.820 1.00 34.44 O HETATM 23 O HOH S 70 -20.622 -6.101 -13.748 1.00 36.15 O HETATM 27 O HOH S 85 -18.252 -5.783 -14.957 1.00 35.55 O ATOM 124 N ALA U1093 -20.236 -1.950 -10.882 1.00 40.90 N ATOM 125 CA ALA U1093 -18.894 -2.526 -11.105 1.00 40.85 C ATOM 126 C ALA U1093 -18.981 -4.042 -11.306 1.00 42.09 C ATOM 127 O ALA U1093 -19.762 -4.688 -10.593 1.00 44.16 O ATOM 128 CB ALA U1093 -18.001 -2.171 -9.946 1.00 41.35 C ATOM 129 H ALA U1093 -20.351 -1.498 -10.080 1.00 40.90 H ATOM 130 HA ALA U1093 -18.495 -2.165 -11.940 1.00 40.85 H ATOM 131 HB1 ALA U1093 -16.981 -2.694 -10.196 1.00 41.35 H ATOM 132 HB2 ALA U1093 -17.763 -0.991 -9.899 1.00 41.35 H ATOM 133 HB3 ALA U1093 -18.382 -2.648 -8.901 1.00 41.35 H ATOM 134 N VAL U1094 -18.217 -4.564 -12.261 1.00 42.56 N ATOM 135 CA VAL U1094 -18.145 -6.038 -12.472 1.00 49.14 C ATOM 136 C VAL U1094 -16.659 -6.420 -12.427 1.00 61.05 C ATOM 137 O VAL U1094 -16.393 -7.631 -12.342 1.00 68.50 O ATOM 138 CB VAL U1094 -18.803 -6.451 -13.798 1.00 53.70 C ATOM 139 CG1 VAL U1094 -20.319 -6.313 -13.759 1.00 52.46 C ATOM 140 CG2 VAL U1094 -18.227 -5.687 -14.979 1.00 42.89 C ATOM 141 H VAL U1094 -17.692 -4.093 -12.848 1.00 42.56 H ATOM 142 HA VAL U1094 -18.467 -6.478 -11.486 1.00 49.14 H ATOM 143 HB VAL U1094 -18.688 -7.451 -14.019 1.00 53.70 H ATOM 144 HG11 VAL U1094 -20.335 -6.928 -14.723 1.00 52.46 H ATOM 145 HG12 VAL U1094 -20.360 -6.983 -12.826 1.00 52.46 H ATOM 146 HG13 VAL U1094 -19.966 -5.155 -13.742 1.00 52.46 H ATOM 147 HG21 VAL U1094 -18.868 -5.778 -15.987 1.00 42.89 H ATOM 148 HG22 VAL U1094 -18.229 -4.543 -14.732 1.00 42.89 H ATOM 149 HG23 VAL U1094 -17.077 -5.935 -15.188 1.00 42.89 H """ unknown_pairs_pdb_str = """ CRYST1 117.569 80.626 62.614 90.00 121.09 90.00 C 1 2 1 4 SCALE1 0.008506 0.000000 0.005128 0.00000 SCALE2 0.000000 0.012403 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018649 0.00000 HETATM 1816 N CAS A 380 12.871 17.119 3.514 1.00 50.96 N HETATM 1817 CA CAS A 380 11.787 16.447 4.266 1.00 53.12 C HETATM 1818 CB CAS A 380 11.217 15.255 3.530 1.00 54.75 C HETATM 1819 C CAS A 380 12.248 15.763 5.514 1.00 51.35 C HETATM 1820 O CAS A 380 11.648 15.861 6.584 1.00 50.96 O HETATM 1821 SG CAS A 380 10.161 15.814 2.259 1.00 63.65 S HETATM 1822 AS CAS A 380 9.628 14.063 0.831 1.00 79.64 AS HETATM 1823 CE1 CAS A 380 7.742 13.464 1.110 1.00 74.47 C HETATM 1824 CE2 CAS A 380 9.928 14.352 -1.138 1.00 75.18 C ATOM 2021 N VAL A 404 24.522 15.315 13.625 1.00 53.07 N ATOM 2022 CA VAL A 404 24.335 15.650 12.189 1.00 55.02 C ATOM 2023 C VAL A 404 23.047 16.466 11.861 1.00 56.25 C ATOM 2024 O VAL A 404 23.079 17.480 11.116 1.00 55.31 O ATOM 2025 CB VAL A 404 24.462 14.424 11.288 1.00 54.08 C ATOM 2026 CG1AVAL A 404 24.258 14.838 9.847 1.00 56.77 C ATOM 2027 CG2AVAL A 404 25.822 13.869 11.450 1.00 54.99 C TER HETATM 2049 C1 T3 A 1 21.311 4.072 5.543 1.00 52.81 C HETATM 2050 C2 T3 A 1 17.344 6.064 8.054 1.00 43.91 C HETATM 2051 C3 T3 A 1 20.783 3.905 6.673 1.00 53.50 C HETATM 2052 C4 T3 A 1 16.533 6.250 8.959 1.00 40.96 C HETATM 2053 C5 T3 A 1 19.781 4.009 7.424 1.00 52.40 C HETATM 2054 C6 T3 A 1 16.098 7.066 9.816 1.00 46.33 C HETATM 2055 C7 T3 A 1 18.736 4.583 6.685 1.00 51.52 C HETATM 2056 C8 T3 A 1 16.706 8.313 9.621 1.00 49.35 C HETATM 2057 C9 T3 A 1 18.988 4.926 5.307 1.00 53.87 C HETATM 2058 C10 T3 A 1 17.561 8.051 8.696 1.00 46.75 C HETATM 2059 C11 T3 A 1 20.306 4.642 4.770 1.00 52.69 C HETATM 2060 C12 T3 A 1 18.054 7.225 7.882 1.00 44.35 C HETATM 2061 C13 T3 A 1 22.687 3.698 5.078 1.00 48.08 C HETATM 2062 C15 T3 A 1 22.757 3.421 3.584 1.00 44.34 C HETATM 2063 C17 T3 A 1 24.163 3.014 3.224 1.00 43.53 C HETATM 2064 I1 T3 A 1 19.604 3.521 9.441 1.00 48.60 I HETATM 2065 I2 T3 A 1 14.653 6.812 11.273 1.00 48.77 I HETATM 2066 I3 T3 A 1 17.518 5.847 3.966 1.00 58.43 I HETATM 2067 N1 T3 A 1 21.771 2.499 3.028 1.00 41.57 N HETATM 2068 O1 T3 A 1 16.352 9.490 10.263 1.00 43.23 O HETATM 2069 O2 T3 A 1 17.531 4.821 7.328 1.00 50.96 O HETATM 2070 O3 T3 A 1 24.437 2.050 2.495 1.00 43.66 O HETATM 2071 O4 T3 A 1 25.057 3.683 3.704 1.00 44.34 O HETATM 2072 O HOH A 411 5.940 15.281 10.898 1.00 20.25 O HETATM 2073 O HOH A 412 20.790 1.172 -9.857 1.00 30.79 O END """ if (__name__ == "__main__"): if not os.getenv("MMTBX_CCP4_MONOMER_LIB") and not os.getenv("CLIBD_MONCLIBD") and chem_data is None: print("Test skipped, need monomer library") sys.exit() t0 = time.time() test_1_5_overlaps() test_inline_angle() test_inline_overlaps() test_overlap_atoms() test_vdw_dist() test_atom_selection() test_addition_scatterers() test_show() test_unknown_pair_type() test_running_from_command_line() #test_file_with_unknown_pair_type() test_small_cell() test_manager_and_clashes_functions() test_no_unit_cell() print("OK. Time: %8.3f"%(time.time()-t0))