from __future__ import division from cctbx.geometry_restraints.manager import nonbonded_clashscore as nb from cStringIO import StringIO from mmtbx import monomer_library import mmtbx.monomer_library.server import mmtbx.monomer_library.pdb_interpretation from cctbx.array_family import flex from cctbx import xray from libtbx.utils import Sorry import libtbx.load_env import mmtbx.model import unittest import os.path #from cctbx.array_family import flex #from cctbx import geometry_restraints #from scitbx import matrix #from libtbx.test_utils import approx_equal, not_approx_equal, eps_eq, show_diff #from libtbx.utils import null_out # #import math #import sys ''' Test non-bonded clashscore @author Youval Dar (LBL 2013) ''' # Raw data for the test cases chem_data = libtbx.env.find_in_repositories( relative_path="chem_data/geostd", test=os.path.isdir) if chem_data is not None: mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() raw_records0 = """\ 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 """.splitlines() raw_records1 = """\ 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 """.splitlines() raw_records2 = '''\ 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 '''.splitlines() raw_records3="""\n 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 TER END """ raw_records4='''\n 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_records5="""\n 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 """.splitlines() raw_records6="""\n 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 """.splitlines() class test_nb_clashscore(unittest.TestCase): #def setUp(self): #''' #Called to perform set-up steps prior to running any of the testing methods #''' def test_inline_angle(self): ''' Test cos_vec(u,v) ''' u = (37.407,5.077,-51.025,40.196,3.261,-48.474) v = (39.466,4.279,-52.202,37.407,5.077,-51.025) result = nb.cos_vec(u, v) expected = 0.5072 msg = 'The difference is: {}'.format(result - expected) self.assertAlmostEqual(result,expected, delta=0.001, msg =msg) def test_vdw_dist(self): ''' Test that clashes are identified properly Test clashes that are set to be on the limit of the clash distance 0.41 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 clashes will change ''' outstring = '{0} , expected {1:.2f}, actual {2:.2f}' for i in [0,1]: grm = self.process_raw_records(raw_record_number=i) nb_clash_sym = grm.nb_clashscore_due_to_sym_op expected = [38.46,0][i] msg = outstring.format('symmetry related clashscore', expected, nb_clash_sym) self.assertAlmostEqual(nb_clash_sym, expected, delta=0.01,msg=msg) # nb_clash_no_sym = grm.nb_clashscore_simple expected = [0,28.77][i] msg = outstring.format('non-symmetry related clashscore', expected, nb_clash_no_sym) self.assertAlmostEqual(nb_clash_no_sym, expected, delta=0.01,msg=msg) # nb_clash_total = grm.nb_clashscore_all_clashes expected = [38.46,28.77][i] msg = outstring.format('total clashscore', expected, nb_clash_total) self.assertAlmostEqual(nb_clash_total, expected, delta=0.01,msg=msg) # nb_list_sym = len(grm.nb_clash_proxies_due_to_sym_op) expected = [2,0][i] msg = outstring.format('Number of clashes, symmetry related', expected, nb_list_sym) self.assertEqual(nb_list_sym, expected,msg=msg) # nb_list_no_sym = len(grm.nb_clash_proxies_simple) expected = [0,4][i] msg = outstring.format('Number of clashes, not symmetry related', expected, nb_list_no_sym) self.assertEqual(nb_list_no_sym, expected, msg=msg) # nb_list_all = len(grm.nb_clash_proxies_all_clashes) expected = [2,4][i] msg = outstring.format('Total number of clashes', expected, nb_list_all) self.assertEqual(nb_list_all, expected, msg=msg) def test_inline_clash(self): ''' Test clashes of C with H-C. Check when valid clash 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 ''' outstring = '{0} , expected {1:.2f}, actual {2:.2f}' for use_site_labels in [True,False]: grm = self.process_raw_records(raw_record_number=2, use_site_labels=use_site_labels) nb_clashscore_total = grm.nb_clashscore_all_clashes expected = 127.66 msg = outstring.format('Total clashscore', expected, nb_clashscore_total) self.assertAlmostEqual(nb_clashscore_total, expected, delta=0.1,msg=msg) def test_1_5_clash(self): ''' Test that 1-5 clashes are not being counted ''' outstring = '1-5 Interaction test error. {}' grm = self.process_raw_records(raw_record_number=0) # check that direction of function calling does not matter tst = nb.is_1_5_interaction(21, 33,grm.hd_sel,grm.full_connectivty_table) msg = outstring.format('Test results depand on atoms order') self.assertTrue(tst,msg=msg) tst = nb.is_1_5_interaction(33, 21,grm.hd_sel,grm.full_connectivty_table) self.assertTrue(tst,msg=msg) # check 1-4 interaction tst = nb.is_1_5_interaction(33, 20,grm.hd_sel,grm.full_connectivty_table) msg = outstring.format('Test fails on 1-4 interaction') self.assertFalse(tst,msg=msg) # check 1-6 interaction tst = nb.is_1_5_interaction(33, 38,grm.hd_sel,grm.full_connectivty_table) msg = outstring.format('Test fails on 1-6 interaction') self.assertFalse(tst,msg=msg) # test 1-5 interaction of atoms other then hydrogen tst = nb.is_1_5_interaction(38, 25,grm.hd_sel,grm.full_connectivty_table) msg = outstring.format('Test fails on 1-5 non hydrogen interaction') self.assertFalse(tst,msg=msg) # test 1-5 interaction of two hydrogens tst = nb.is_1_5_interaction(33, 31,grm.hd_sel,grm.full_connectivty_table) msg = outstring.format('Test fails on 1-5 two hydrogen interaction') self.assertFalse(tst,msg=msg) def test_overlap_atoms(self): ''' Test that overlapping atoms are being counted ''' msg = 'Overlapping atoms are not counted properly.' grm = self.process_raw_records(raw_record_number=5, nonbonded_distance_threshold=None) self.assertEqual(grm.nb_clashscore_all_clashes, 1500,msg) def test_atom_selection(self): ''' Test that working correctly when atom is removed ''' outstring = '{0} , expected {1:.2f}, actual {2:.2f}' processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, raw_records = raw_records3, force_symmetry = True) grm = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5.0) xrs = processed_pdb_file.xray_structure() sites_cart,site_labels,hd_sel,full_connectivty_table = self.get_clashscore_param(xrs,grm) nb_clashscore = grm.get_nonbonded_clashscore( sites_cart=sites_cart, site_labels=site_labels, hd_sel=hd_sel) expected = 1000 result = nb_clashscore.nb_clashscore_all_clashes msg = outstring.format('Selection related clashscore', expected, result) self.assertEqual(result, expected, msg=msg) # Select sel = flex.bool([True, True, False]) grm = grm.select(selection=sel) xrs = xrs.select(selection=sel) sites_cart,site_labels,hd_sel,full_connectivty_table = self.get_clashscore_param(xrs,grm) nb_clashscore = grm.get_nonbonded_clashscore( sites_cart=sites_cart, site_labels=site_labels, hd_sel=hd_sel) expected = 500 result = nb_clashscore.nb_clashscore_all_clashes msg = outstring.format('Selection related clashscore', expected, result) self.assertEqual(result, expected, msg=msg) def test_solvent(self): ''' Test if solvent is counted properly Consider solvent as (O, O-H, H-O-H, O-D, D-O-D) or any other single, double and triple atoms molecules ''' processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, raw_records = raw_records4, force_symmetry = True) geometry = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5.0) xrs = processed_pdb_file.xray_structure() grm = geometry.get_nonbonded_clashscore( sites_cart = xrs.sites_cart(), site_labels = xrs.scatterers().extract_labels(), hd_sel = xrs.hd_selection()) clashscore_total = grm.nb_clashscore_all_clashes clashscore_due_to_sym_op = grm.nb_clashscore_due_to_sym_op clashscore_solvent_solvent = grm.nb_clashscore_solvent_solvent clashscore_simple = grm.nb_clashscore_simple outstring = '{0} , expected {1:.2f}, actual {2:.2f}' expected = 2500 msg = outstring.format('Total clashscore', expected, clashscore_solvent_solvent) self.assertEqual(clashscore_solvent_solvent, expected,msg=msg) def test_labels_and_addition_scatterers(self): ''' Test clashes when adding and movning scatterers Test water scatterers with and without labels ''' outstring = '{0} , expected {1:.2f}, actual {2:.2f}' processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, raw_records = raw_records3, force_symmetry = True) geometry = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5.0) xrs = processed_pdb_file.xray_structure() nb_clashscore = geometry.get_nonbonded_clashscore( sites_cart = xrs.sites_cart(), site_labels = xrs.scatterers().extract_labels(), hd_sel = xrs.hd_selection()) expected = 1000 result = nb_clashscore.nb_clashscore_all_clashes msg = outstring.format('Selection related clashscore', expected, result) self.assertEqual(result, expected, msg=msg) # Add water scatterers restraints_manager = mmtbx.restraints.manager(geometry = geometry, normalization = False) mol = mmtbx.model.manager( restraints_manager = restraints_manager, xray_structure = xrs, pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy) # 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) mol.add_solvent( solvent_xray_structure = new_xrs, refine_occupancies = False, refine_adp = "isotropic") nb_clashscore = mol.restraints_manager.geometry.get_nonbonded_clashscore( sites_cart = mol.xray_structure.sites_cart(), site_labels = mol.xray_structure.scatterers().extract_labels(), hd_sel = mol.xray_structure.hd_selection()) expected = 2500 result = nb_clashscore.nb_clashscore_all_clashes msg = outstring.format('Selection related clashscore', expected, result) self.assertEqual(result, expected, msg=msg) # Test the modified pdb data with scatterers lables processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, raw_records = raw_records4, force_symmetry = True) geometry = processed_pdb_file.geometry_restraints_manager( show_energies = False, plain_pairs_radius = 5.0) xrs = processed_pdb_file.xray_structure() nb_clashscore = geometry.get_nonbonded_clashscore( sites_cart = xrs.sites_cart(), site_labels = xrs.scatterers().extract_labels(), hd_sel = xrs.hd_selection()) expected = 2500 result = nb_clashscore.nb_clashscore_all_clashes msg = outstring.format('Selection related clashscore', expected, result) self.assertEqual(result, expected, msg=msg) def test_unknown_pair_type(self): '''Make sure unknown pair types are not processed''' self.assertRaises(Sorry,self.process_raw_records,raw_record_number=6) def process_raw_records( self, raw_record_number, use_site_labels=True, hard_minimum_nonbonded_distance=0, nonbonded_distance_threshold=0.5): '''(int,bool,int,int) -> geomerty_restraints object hard_minimum_nonbonded_distance: by defult this value is 0.01 which will prevent testing closer nonbonded interaction nonbonded_distance_threshold: 0.5 is the default, it does not allow overlapping atoms to test overlapping atoms use "None" Argument: raw_record_number: select whcih raw records to use use_site_labels: use site_labels (atom description) or leave as None ''' records = [] if raw_record_number == 0: records = raw_records0 elif raw_record_number == 1: records = raw_records1 elif raw_record_number == 2: records = raw_records2 elif raw_record_number == 4: records = raw_records4 elif raw_record_number == 5: records = raw_records5 elif raw_record_number == 6: records = raw_records6 else: print ('Wrong raw_records number') # create a geometry_restraints_manager (grm) log = StringIO() # process pdb data pdb_processed_file = monomer_library.pdb_interpretation.process( file_name=None, raw_records=records, substitute_non_crystallographic_unit_cell_if_necessary=True, mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, log=log, ) # get geometry restraints object #grm = pdb.geometry_restraints_manager() grm = pdb_processed_file.geometry_restraints_manager( assume_hydrogens_all_missing=False, hard_minimum_nonbonded_distance=hard_minimum_nonbonded_distance, nonbonded_distance_threshold=nonbonded_distance_threshold) xrs = pdb_processed_file.xray_structure() sites_cart,site_labels,hd_sel,full_connectivty_table = self.get_clashscore_param( xrs, grm, use_site_labels=use_site_labels) return grm.get_nonbonded_clashscore(sites_cart=sites_cart, site_labels=site_labels, hd_sel=hd_sel) def get_clashscore_param(self,xrs,grm,use_site_labels=True): ''' Process input parameters for non_bonded_clashscore Arguments: xrs: xray_structure object grm: geometry restraints manager object Returns: sites_cart,site_labels,hd_sel,full_connectivty_table ''' hd_sel = xrs.hd_selection() sites_cart = xrs.sites_cart() if use_site_labels: site_labels = xrs.scatterers().extract_labels() else: site_labels = None table_bonds = grm.shell_sym_tables[0] full_connectivty_table = table_bonds.full_simple_connectivity() return sites_cart,site_labels,hd_sel,full_connectivty_table if (__name__ == "__main__"): if (chem_data is None) : print "chem_data not present, skipping" else : unittest.main()