from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.model import time """ Test multiplication of hierarchy and SS annotations in different combinations of MTRIX and BIOMT records presence. """ single_mtrix_txt = """ MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.479787 -0.038259 -0.876550 0.00000 MTRIX2 2 -0.530698 0.782918 -0.324654 0.00000 MTRIX3 2 0.698688 0.620947 0.355330 0.00000 """ mtrix_txt = """ MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.479787 -0.038259 -0.876550 0.00000 MTRIX2 2 -0.530698 0.782918 -0.324654 0.00000 MTRIX3 2 0.698688 0.620947 0.355330 0.00000 MTRIX1 3 -0.361936 -0.592602 -0.719600 0.00000 MTRIX2 3 -0.896947 0.431671 0.095646 0.00000 MTRIX3 3 0.253950 0.680060 -0.687769 0.00000 """ biomt_txt = """ REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 -0.809017 0.309017 0.00000 REMARK 350 BIOMT2 2 0.809017 0.309017 -0.500000 0.00000 REMARK 350 BIOMT3 2 0.309017 0.500000 0.809017 0.00000 REMARK 350 BIOMT1 3 -0.309017 -0.500000 0.809017 0.00000 REMARK 350 BIOMT2 3 0.500000 -0.809017 -0.309017 0.00000 REMARK 350 BIOMT3 3 0.809017 0.309017 0.500000 0.00000 """ ss_txt = """ HELIX 6 6 ARG A 316 LEU A 318 5 3 HELIX 7 7 SER A 335 ASN A 341 1 7 SHEET 1 E 2 TYR A 305 SER A 308 0 SHEET 2 E 2 GLN A 311 GLU A 314 -1 O ARG A 313 N PHE A 306 """ # 300 atoms atoms_txt = """ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 2065 N GLY A 304 3.950 -35.449 102.015 1.00 21.30 N ATOM 2066 CA GLY A 304 4.631 -35.764 103.257 1.00 19.87 C ATOM 2067 C GLY A 304 6.074 -36.196 103.097 1.00 19.37 C ATOM 2068 O GLY A 304 6.642 -36.823 103.994 1.00 18.69 O ATOM 2069 N TYR A 305 6.673 -35.863 101.957 1.00 19.21 N ATOM 2070 CA TYR A 305 8.065 -36.210 101.688 1.00 18.15 C ATOM 2071 C TYR A 305 8.975 -35.002 101.819 1.00 18.33 C ATOM 2072 O TYR A 305 8.673 -33.920 101.314 1.00 19.14 O ATOM 2073 CB TYR A 305 8.202 -36.803 100.289 1.00 17.45 C ATOM 2074 CG TYR A 305 7.826 -38.258 100.228 1.00 18.23 C ATOM 2075 CD1 TYR A 305 8.761 -39.250 100.515 1.00 18.89 C ATOM 2076 CD2 TYR A 305 6.526 -38.647 99.917 1.00 17.60 C ATOM 2077 CE1 TYR A 305 8.411 -40.595 100.493 1.00 18.65 C ATOM 2078 CE2 TYR A 305 6.166 -39.982 99.895 1.00 18.16 C ATOM 2079 CZ TYR A 305 7.112 -40.954 100.182 1.00 18.93 C ATOM 2080 OH TYR A 305 6.756 -42.284 100.149 1.00 20.67 O ATOM 2081 N PHE A 306 10.097 -35.200 102.498 1.00 18.08 N ATOM 2082 CA PHE A 306 11.061 -34.133 102.707 1.00 18.50 C ATOM 2083 C PHE A 306 12.458 -34.585 102.325 1.00 19.27 C ATOM 2084 O PHE A 306 12.737 -35.780 102.239 1.00 19.20 O ATOM 2085 CB PHE A 306 11.071 -33.720 104.181 1.00 18.35 C ATOM 2086 CG PHE A 306 9.784 -33.115 104.650 1.00 18.59 C ATOM 2087 CD1 PHE A 306 9.582 -31.744 104.580 1.00 18.76 C ATOM 2088 CD2 PHE A 306 8.765 -33.919 105.141 1.00 18.71 C ATOM 2089 CE1 PHE A 306 8.379 -31.180 104.994 1.00 19.56 C ATOM 2090 CE2 PHE A 306 7.558 -33.366 105.557 1.00 20.09 C ATOM 2091 CZ PHE A 306 7.365 -31.993 105.483 1.00 20.22 C ATOM 2092 N MET A 307 13.330 -33.615 102.088 1.00 20.68 N ATOM 2093 CA MET A 307 14.717 -33.899 101.773 1.00 21.16 C ATOM 2094 C MET A 307 15.423 -33.667 103.103 1.00 22.68 C ATOM 2095 O MET A 307 15.811 -32.544 103.417 1.00 23.48 O ATOM 2096 CB MET A 307 15.243 -32.920 100.729 1.00 20.61 C ATOM 2097 CG MET A 307 16.666 -33.197 100.265 1.00 21.45 C ATOM 2098 SD MET A 307 16.835 -34.726 99.306 1.00 21.53 S ATOM 2099 CE MET A 307 18.018 -35.567 100.270 1.00 21.98 C ATOM 2100 N SER A 308 15.551 -34.726 103.900 1.00 23.90 N ATOM 2101 CA SER A 308 16.196 -34.629 105.204 1.00 25.50 C ATOM 2102 C SER A 308 17.711 -34.736 105.044 1.00 26.51 C ATOM 2103 O SER A 308 18.287 -35.817 105.177 1.00 26.25 O ATOM 2104 CB SER A 308 15.681 -35.736 106.127 1.00 25.33 C ATOM 2105 OG SER A 308 16.066 -35.503 107.471 1.00 28.15 O ATOM 2106 N ASN A 309 18.344 -33.602 104.754 1.00 27.44 N ATOM 2107 CA ASN A 309 19.787 -33.533 104.556 1.00 28.19 C ATOM 2108 C ASN A 309 20.235 -34.192 103.260 1.00 28.98 C ATOM 2109 O ASN A 309 20.106 -33.612 102.183 1.00 30.58 O ATOM 2110 CB ASN A 309 20.522 -34.170 105.737 1.00 28.18 C ATOM 2111 CG ASN A 309 20.631 -33.238 106.923 1.00 28.56 C ATOM 2112 OD1 ASN A 309 21.308 -32.212 106.855 1.00 28.58 O ATOM 2113 ND2 ASN A 309 19.963 -33.585 108.017 1.00 27.94 N ATOM 2114 N ASP A 310 20.753 -35.410 103.369 1.00 28.99 N ATOM 2115 CA ASP A 310 21.249 -36.144 102.212 1.00 28.59 C ATOM 2116 C ASP A 310 20.246 -37.125 101.612 1.00 27.76 C ATOM 2117 O ASP A 310 20.386 -37.526 100.457 1.00 28.39 O ATOM 2118 CB ASP A 310 22.514 -36.904 102.598 1.00 30.83 C ATOM 2119 CG ASP A 310 22.271 -37.900 103.717 1.00 33.72 C ATOM 2120 OD1 ASP A 310 21.917 -37.469 104.838 1.00 32.95 O ATOM 2121 OD2 ASP A 310 22.426 -39.118 103.473 1.00 34.80 O ATOM 2122 N GLN A 311 19.238 -37.512 102.388 1.00 26.40 N ATOM 2123 CA GLN A 311 18.239 -38.461 101.910 1.00 24.95 C ATOM 2124 C GLN A 311 16.812 -37.956 101.941 1.00 23.86 C ATOM 2125 O GLN A 311 16.499 -36.941 102.561 1.00 23.90 O ATOM 2126 CB GLN A 311 18.268 -39.739 102.741 1.00 27.17 C ATOM 2127 CG GLN A 311 19.513 -40.558 102.642 1.00 31.00 C ATOM 2128 CD GLN A 311 19.343 -41.880 103.340 1.00 32.73 C ATOM 2129 OE1 GLN A 311 18.986 -41.928 104.519 1.00 32.73 O ATOM 2130 NE2 GLN A 311 19.591 -42.969 102.618 1.00 35.40 N ATOM 2131 N ILE A 312 15.948 -38.706 101.272 1.00 22.64 N ATOM 2132 CA ILE A 312 14.529 -38.409 101.221 1.00 20.51 C ATOM 2133 C ILE A 312 13.903 -39.134 102.404 1.00 21.02 C ATOM 2134 O ILE A 312 14.209 -40.300 102.653 1.00 21.21 O ATOM 2135 CB ILE A 312 13.886 -38.956 99.933 1.00 19.13 C ATOM 2136 CG1 ILE A 312 14.452 -38.229 98.715 1.00 18.32 C ATOM 2137 CG2 ILE A 312 12.375 -38.824 100.008 1.00 17.77 C ATOM 2138 CD1 ILE A 312 13.918 -38.745 97.395 1.00 17.16 C ATOM 2139 N ARG A 313 13.042 -38.442 103.140 1.00 21.29 N ATOM 2140 CA ARG A 313 12.363 -39.049 104.275 1.00 21.69 C ATOM 2141 C ARG A 313 10.872 -38.764 104.223 1.00 22.24 C ATOM 2142 O ARG A 313 10.445 -37.705 103.766 1.00 22.50 O ATOM 2143 CB ARG A 313 12.932 -38.539 105.601 1.00 21.74 C ATOM 2144 CG ARG A 313 14.216 -39.223 106.028 1.00 23.27 C ATOM 2145 CD ARG A 313 14.488 -39.007 107.511 1.00 24.27 C ATOM 2146 NE ARG A 313 15.647 -39.768 107.970 1.00 26.04 N ATOM 2147 CZ ARG A 313 16.906 -39.483 107.652 1.00 26.93 C ATOM 2148 NH1 ARG A 313 17.177 -38.443 106.873 1.00 26.76 N ATOM 2149 NH2 ARG A 313 17.895 -40.244 108.103 1.00 27.18 N ATOM 2150 N GLU A 314 10.085 -39.729 104.686 1.00 23.21 N ATOM 2151 CA GLU A 314 8.637 -39.591 104.709 1.00 23.33 C ATOM 2152 C GLU A 314 8.256 -39.096 106.107 1.00 23.56 C ATOM 2153 O GLU A 314 8.950 -39.370 107.084 1.00 23.95 O ATOM 2154 CB GLU A 314 7.990 -40.946 104.405 1.00 23.60 C ATOM 2155 CG GLU A 314 6.517 -40.906 104.006 1.00 25.54 C ATOM 2156 CD GLU A 314 5.571 -40.837 105.196 1.00 27.64 C ATOM 2157 OE1 GLU A 314 5.803 -41.568 106.184 1.00 27.37 O ATOM 2158 OE2 GLU A 314 4.586 -40.068 105.137 1.00 27.35 O ATOM 2159 N ARG A 315 7.162 -38.349 106.187 1.00 23.65 N ATOM 2160 CA ARG A 315 6.672 -37.790 107.443 1.00 22.98 C ATOM 2161 C ARG A 315 6.921 -38.651 108.687 1.00 22.60 C ATOM 2162 O ARG A 315 7.532 -38.196 109.653 1.00 22.85 O ATOM 2163 CB ARG A 315 5.173 -37.516 107.323 1.00 23.23 C ATOM 2164 CG ARG A 315 4.735 -36.167 107.842 1.00 24.91 C ATOM 2165 CD ARG A 315 3.231 -36.143 108.070 1.00 28.73 C ATOM 2166 NE ARG A 315 2.444 -36.339 106.853 1.00 31.17 N ATOM 2167 CZ ARG A 315 2.358 -35.454 105.863 1.00 34.22 C ATOM 2168 NH1 ARG A 315 3.018 -34.301 105.937 1.00 36.07 N ATOM 2169 NH2 ARG A 315 1.596 -35.715 104.805 1.00 32.99 N ATOM 2170 N ARG A 316 6.447 -39.893 108.657 1.00 22.00 N ATOM 2171 CA ARG A 316 6.578 -40.806 109.792 1.00 21.99 C ATOM 2172 C ARG A 316 7.984 -41.091 110.302 1.00 23.09 C ATOM 2173 O ARG A 316 8.149 -41.529 111.439 1.00 23.65 O ATOM 2174 CB ARG A 316 5.886 -42.136 109.475 1.00 21.22 C ATOM 2175 CG ARG A 316 4.373 -42.042 109.402 1.00 23.38 C ATOM 2176 CD ARG A 316 3.836 -42.668 108.123 1.00 26.73 C ATOM 2177 NE ARG A 316 3.995 -44.121 108.085 1.00 28.42 N ATOM 2178 CZ ARG A 316 4.479 -44.789 107.040 1.00 28.61 C ATOM 2179 NH1 ARG A 316 4.857 -44.132 105.954 1.00 29.34 N ATOM 2180 NH2 ARG A 316 4.571 -46.113 107.074 1.00 27.85 N ATOM 2181 N ASP A 317 9.000 -40.846 109.485 1.00 25.17 N ATOM 2182 CA ASP A 317 10.363 -41.127 109.913 1.00 26.92 C ATOM 2183 C ASP A 317 11.076 -39.946 110.566 1.00 26.95 C ATOM 2184 O ASP A 317 12.094 -40.123 111.234 1.00 27.91 O ATOM 2185 CB ASP A 317 11.184 -41.652 108.733 1.00 31.20 C ATOM 2186 CG ASP A 317 12.583 -42.075 109.139 1.00 35.93 C ATOM 2187 OD1 ASP A 317 13.435 -41.187 109.360 1.00 40.17 O ATOM 2188 OD2 ASP A 317 12.831 -43.295 109.250 1.00 37.90 O ATOM 2189 N LEU A 318 10.550 -38.741 110.378 1.00 26.49 N ATOM 2190 CA LEU A 318 11.155 -37.560 110.985 1.00 26.24 C ATOM 2191 C LEU A 318 10.717 -37.537 112.448 1.00 26.95 C ATOM 2192 O LEU A 318 9.800 -36.810 112.828 1.00 27.99 O ATOM 2193 CB LEU A 318 10.693 -36.301 110.252 1.00 24.34 C ATOM 2194 CG LEU A 318 11.071 -36.288 108.768 1.00 23.72 C ATOM 2195 CD1 LEU A 318 10.394 -35.132 108.065 1.00 24.49 C ATOM 2196 CD2 LEU A 318 12.580 -36.193 108.629 1.00 24.02 C ATOM 2197 N THR A 319 11.392 -38.343 113.259 1.00 27.73 N ATOM 2198 CA THR A 319 11.076 -38.486 114.676 1.00 27.93 C ATOM 2199 C THR A 319 11.764 -37.518 115.637 1.00 28.67 C ATOM 2200 O THR A 319 11.364 -37.407 116.795 1.00 29.01 O ATOM 2201 CB THR A 319 11.379 -39.919 115.137 1.00 27.93 C ATOM 2202 OG1 THR A 319 12.746 -40.235 114.841 1.00 27.70 O ATOM 2203 CG2 THR A 319 10.472 -40.911 114.417 1.00 26.51 C ATOM 2204 N THR A 320 12.797 -36.826 115.169 1.00 29.46 N ATOM 2205 CA THR A 320 13.513 -35.872 116.011 1.00 29.47 C ATOM 2206 C THR A 320 12.739 -34.564 116.150 1.00 30.76 C ATOM 2207 O THR A 320 12.574 -34.041 117.251 1.00 31.05 O ATOM 2208 CB THR A 320 14.900 -35.571 115.435 1.00 29.84 C ATOM 2209 OG1 THR A 320 15.722 -36.738 115.556 1.00 28.30 O ATOM 2210 CG2 THR A 320 15.548 -34.398 116.168 1.00 30.39 C ATOM 2211 N SER A 321 12.274 -34.035 115.023 1.00 31.46 N ATOM 2212 CA SER A 321 11.505 -32.799 115.014 1.00 31.46 C ATOM 2213 C SER A 321 10.184 -33.067 114.316 1.00 30.56 C ATOM 2214 O SER A 321 10.104 -33.934 113.448 1.00 32.00 O ATOM 2215 CB SER A 321 12.270 -31.700 114.277 1.00 33.39 C ATOM 2216 OG SER A 321 13.478 -31.389 114.950 1.00 37.51 O ATOM 2217 N VAL A 322 9.149 -32.325 114.694 1.00 28.32 N ATOM 2218 CA VAL A 322 7.829 -32.503 114.103 1.00 25.27 C ATOM 2219 C VAL A 322 7.760 -31.974 112.671 1.00 24.50 C ATOM 2220 O VAL A 322 8.001 -30.794 112.424 1.00 24.31 O ATOM 2221 CB VAL A 322 6.756 -31.795 114.945 1.00 24.16 C ATOM 2222 CG1 VAL A 322 5.380 -32.058 114.362 1.00 24.15 C ATOM 2223 CG2 VAL A 322 6.830 -32.275 116.380 1.00 23.55 C ATOM 2224 N PRO A 323 7.429 -32.850 111.708 1.00 23.60 N ATOM 2225 CA PRO A 323 7.325 -32.477 110.294 1.00 22.62 C ATOM 2226 C PRO A 323 6.166 -31.512 110.044 1.00 22.04 C ATOM 2227 O PRO A 323 5.076 -31.683 110.594 1.00 21.04 O ATOM 2228 CB PRO A 323 7.097 -33.816 109.596 1.00 22.18 C ATOM 2229 CG PRO A 323 7.725 -34.803 110.523 1.00 23.36 C ATOM 2230 CD PRO A 323 7.282 -34.306 111.868 1.00 23.35 C ATOM 2231 N PRO A 324 6.389 -30.483 109.214 1.00 21.26 N ATOM 2232 CA PRO A 324 5.345 -29.504 108.905 1.00 20.28 C ATOM 2233 C PRO A 324 4.265 -30.149 108.052 1.00 20.15 C ATOM 2234 O PRO A 324 4.394 -31.297 107.620 1.00 21.43 O ATOM 2235 CB PRO A 324 6.093 -28.424 108.128 1.00 20.19 C ATOM 2236 CG PRO A 324 7.499 -28.565 108.593 1.00 22.05 C ATOM 2237 CD PRO A 324 7.676 -30.054 108.644 1.00 21.65 C ATOM 2238 N VAL A 325 3.207 -29.394 107.797 1.00 18.93 N ATOM 2239 CA VAL A 325 2.106 -29.878 106.986 1.00 17.74 C ATOM 2240 C VAL A 325 1.533 -28.648 106.265 1.00 18.27 C ATOM 2241 O VAL A 325 1.462 -27.564 106.845 1.00 19.21 O ATOM 2242 CB VAL A 325 1.065 -30.589 107.891 1.00 15.23 C ATOM 2243 CG1 VAL A 325 0.310 -29.581 108.721 1.00 16.64 C ATOM 2244 CG2 VAL A 325 0.144 -31.438 107.066 1.00 16.39 C ATOM 2245 N ALA A 326 1.160 -28.802 104.998 1.00 18.66 N ATOM 2246 CA ALA A 326 0.636 -27.680 104.211 1.00 19.12 C ATOM 2247 C ALA A 326 -0.783 -27.267 104.588 1.00 19.46 C ATOM 2248 O ALA A 326 -1.755 -27.780 104.035 1.00 22.10 O ATOM 2249 CB ALA A 326 0.699 -28.016 102.723 1.00 17.55 C ATOM 2250 N LEU A 327 -0.898 -26.324 105.516 1.00 17.63 N ATOM 2251 CA LEU A 327 -2.205 -25.855 105.961 1.00 16.12 C ATOM 2252 C LEU A 327 -2.471 -24.440 105.467 1.00 16.88 C ATOM 2253 O LEU A 327 -1.590 -23.795 104.901 1.00 18.47 O ATOM 2254 CB LEU A 327 -2.279 -25.897 107.487 1.00 13.74 C ATOM 2255 CG LEU A 327 -1.897 -27.240 108.115 1.00 11.17 C ATOM 2256 CD1 LEU A 327 -1.930 -27.126 109.624 1.00 9.68 C ATOM 2257 CD2 LEU A 327 -2.840 -28.330 107.633 1.00 9.69 C ATOM 2258 N THR A 328 -3.692 -23.962 105.683 1.00 16.51 N ATOM 2259 CA THR A 328 -4.076 -22.623 105.254 1.00 15.88 C ATOM 2260 C THR A 328 -3.155 -21.559 105.881 1.00 15.66 C ATOM 2261 O THR A 328 -3.011 -21.475 107.101 1.00 14.78 O ATOM 2262 CB THR A 328 -5.577 -22.379 105.580 1.00 14.98 C ATOM 2263 OG1 THR A 328 -5.835 -20.975 105.690 1.00 15.31 O ATOM 2264 CG2 THR A 328 -5.968 -23.098 106.862 1.00 16.50 C ATOM 2265 N ALA A 329 -2.535 -20.758 105.015 1.00 15.68 N ATOM 2266 CA ALA A 329 -1.570 -19.718 105.391 1.00 15.70 C ATOM 2267 C ALA A 329 -2.002 -18.573 106.305 1.00 16.13 C ATOM 2268 O ALA A 329 -3.165 -18.169 106.317 1.00 15.82 O ATOM 2269 CB ALA A 329 -0.949 -19.136 104.123 1.00 15.02 C ATOM 2270 N THR A 330 -1.028 -18.050 107.054 1.00 17.52 N ATOM 2271 CA THR A 330 -1.220 -16.930 107.984 1.00 18.76 C ATOM 2272 C THR A 330 0.039 -16.068 108.050 1.00 18.94 C ATOM 2273 O THR A 330 1.134 -16.520 107.713 1.00 18.98 O ATOM 2274 CB THR A 330 -1.486 -17.400 109.427 1.00 18.55 C ATOM 2275 OG1 THR A 330 -2.582 -18.314 109.441 1.00 25.08 O ATOM 2276 CG2 THR A 330 -1.826 -16.215 110.316 1.00 17.33 C ATOM 2277 N LYS A 331 -0.130 -14.826 108.494 1.00 18.76 N ATOM 2278 CA LYS A 331 0.981 -13.893 108.648 1.00 18.12 C ATOM 2279 C LYS A 331 1.276 -13.801 110.140 1.00 18.19 C ATOM 2280 O LYS A 331 2.396 -13.505 110.551 1.00 19.51 O ATOM 2281 CB LYS A 331 0.595 -12.500 108.149 1.00 17.57 C ATOM 2282 CG LYS A 331 0.218 -12.405 106.686 1.00 18.42 C ATOM 2283 CD LYS A 331 -0.306 -11.007 106.356 1.00 18.16 C ATOM 2284 CE LYS A 331 0.701 -9.919 106.725 1.00 16.46 C ATOM 2285 NZ LYS A 331 0.187 -8.552 106.431 1.00 15.24 N ATOM 2286 N LEU A 332 0.247 -14.064 110.937 1.00 18.16 N ATOM 2287 CA LEU A 332 0.315 -14.001 112.393 1.00 18.94 C ATOM 2288 C LEU A 332 1.112 -15.152 113.006 1.00 20.72 C ATOM 2289 O LEU A 332 1.034 -15.408 114.207 1.00 21.12 O ATOM 2290 CB LEU A 332 -1.111 -13.996 112.944 1.00 17.77 C ATOM 2291 CG LEU A 332 -2.055 -13.055 112.181 1.00 15.45 C ATOM 2292 CD1 LEU A 332 -3.501 -13.375 112.509 1.00 14.04 C ATOM 2293 CD2 LEU A 332 -1.723 -11.617 112.522 1.00 12.75 C ATOM 2294 N ASN A 333 1.880 -15.838 112.166 1.00 23.44 N ATOM 2295 CA ASN A 333 2.703 -16.971 112.578 1.00 23.93 C ATOM 2296 C ASN A 333 4.150 -16.545 112.728 1.00 24.70 C ATOM 2297 O ASN A 333 4.853 -16.992 113.632 1.00 24.54 O ATOM 2298 CB ASN A 333 2.646 -18.062 111.515 1.00 26.61 C ATOM 2299 CG ASN A 333 1.858 -19.250 111.956 1.00 29.55 C ATOM 2300 OD1 ASN A 333 2.146 -19.843 112.991 1.00 33.22 O ATOM 2301 ND2 ASN A 333 0.853 -19.617 111.173 1.00 34.06 N ATOM 2302 N GLN A 334 4.586 -15.696 111.803 1.00 24.83 N ATOM 2303 CA GLN A 334 5.948 -15.190 111.768 1.00 24.33 C ATOM 2304 C GLN A 334 6.154 -14.072 112.782 1.00 23.29 C ATOM 2305 O GLN A 334 5.292 -13.209 112.949 1.00 23.17 O ATOM 2306 CB GLN A 334 6.257 -14.671 110.362 1.00 26.56 C ATOM 2307 CG GLN A 334 7.356 -15.429 109.623 1.00 29.28 C ATOM 2308 CD GLN A 334 7.077 -16.915 109.515 1.00 28.54 C ATOM 2309 OE1 GLN A 334 6.021 -17.330 109.038 1.00 28.36 O ATOM 2310 NE2 GLN A 334 8.031 -17.725 109.954 1.00 29.34 N ATOM 2311 N SER A 335 7.298 -14.094 113.459 1.00 21.22 N ATOM 2312 CA SER A 335 7.616 -13.065 114.439 1.00 19.84 C ATOM 2313 C SER A 335 8.243 -11.891 113.700 1.00 19.90 C ATOM 2314 O SER A 335 8.584 -12.005 112.522 1.00 19.68 O ATOM 2315 CB SER A 335 8.600 -13.597 115.479 1.00 19.73 C ATOM 2316 OG SER A 335 9.870 -13.836 114.897 1.00 20.23 O ATOM 2317 N ALA A 336 8.401 -10.767 114.393 1.00 19.82 N ATOM 2318 CA ALA A 336 8.988 -9.579 113.787 1.00 18.90 C ATOM 2319 C ALA A 336 10.408 -9.856 113.309 1.00 19.44 C ATOM 2320 O ALA A 336 10.807 -9.413 112.232 1.00 18.92 O ATOM 2321 CB ALA A 336 8.987 -8.436 114.780 1.00 18.18 C ATOM 2322 N SER A 337 11.169 -10.592 114.112 1.00 20.65 N ATOM 2323 CA SER A 337 12.543 -10.918 113.756 1.00 21.77 C ATOM 2324 C SER A 337 12.601 -11.896 112.588 1.00 21.99 C ATOM 2325 O SER A 337 13.536 -11.852 111.790 1.00 22.49 O ATOM 2326 CB SER A 337 13.280 -11.495 114.963 1.00 21.52 C ATOM 2327 OG SER A 337 12.584 -12.609 115.487 1.00 27.59 O ATOM 2328 N ASN A 338 11.610 -12.779 112.484 1.00 22.03 N ATOM 2329 CA ASN A 338 11.584 -13.729 111.378 1.00 22.50 C ATOM 2330 C ASN A 338 11.427 -12.965 110.068 1.00 22.06 C ATOM 2331 O ASN A 338 12.155 -13.213 109.108 1.00 21.25 O ATOM 2332 CB ASN A 338 10.430 -14.727 111.517 1.00 25.28 C ATOM 2333 CG ASN A 338 10.682 -15.778 112.586 1.00 27.64 C ATOM 2334 OD1 ASN A 338 11.812 -16.237 112.773 1.00 28.04 O ATOM 2335 ND2 ASN A 338 9.620 -16.181 113.280 1.00 28.11 N ATOM 2336 N ASN A 339 10.477 -12.032 110.038 1.00 21.49 N ATOM 2337 CA ASN A 339 10.232 -11.229 108.844 1.00 20.40 C ATOM 2338 C ASN A 339 11.511 -10.562 108.357 1.00 19.57 C ATOM 2339 O ASN A 339 11.764 -10.496 107.156 1.00 20.36 O ATOM 2340 CB ASN A 339 9.186 -10.147 109.115 1.00 20.32 C ATOM 2341 CG ASN A 339 7.869 -10.714 109.585 1.00 20.71 C ATOM 2342 OD1 ASN A 339 7.471 -11.806 109.178 1.00 22.61 O ATOM 2343 ND2 ASN A 339 7.174 -9.969 110.435 1.00 19.61 N ATOM 2344 N LEU A 340 12.312 -10.065 109.294 1.00 17.69 N ATOM 2345 CA LEU A 340 13.561 -9.405 108.942 1.00 16.22 C ATOM 2346 C LEU A 340 14.507 -10.326 108.185 1.00 16.58 C ATOM 2347 O LEU A 340 15.286 -9.866 107.349 1.00 18.23 O ATOM 2348 CB LEU A 340 14.251 -8.872 110.198 1.00 13.20 C ATOM 2349 CG LEU A 340 13.589 -7.648 110.832 1.00 10.55 C ATOM 2350 CD1 LEU A 340 14.276 -7.322 112.136 1.00 9.92 C ATOM 2351 CD2 LEU A 340 13.663 -6.465 109.877 1.00 9.35 C ATOM 2352 N ASN A 341 14.435 -11.624 108.468 1.00 16.36 N ATOM 2353 CA ASN A 341 15.295 -12.597 107.798 1.00 15.90 C ATOM 2354 C ASN A 341 14.594 -13.269 106.626 1.00 15.59 C ATOM 2355 O ASN A 341 14.917 -14.403 106.269 1.00 15.34 O ATOM 2356 CB ASN A 341 15.754 -13.670 108.782 1.00 15.76 C ATOM 2357 CG ASN A 341 16.460 -13.089 109.977 1.00 16.78 C ATOM 2358 OD1 ASN A 341 17.302 -12.200 109.841 1.00 19.51 O ATOM 2359 ND2 ASN A 341 16.132 -13.593 111.161 1.00 16.09 N ATOM 2360 N ALA A 342 13.640 -12.566 106.027 1.00 14.50 N ATOM 2361 CA ALA A 342 12.894 -13.105 104.900 1.00 13.77 C ATOM 2362 C ALA A 342 13.788 -13.386 103.695 1.00 14.02 C ATOM 2363 O ALA A 342 14.703 -12.618 103.392 1.00 14.49 O ATOM 2364 CB ALA A 342 11.782 -12.143 104.511 1.00 12.29 C """ def exercise_single_mtrix(): inp = iotbx.pdb.input(lines=single_mtrix_txt+ss_txt+atoms_txt, source_info=None) model = mmtbx.model.manager( model_input = inp) # print (model.model_as_pdb()) assert model.get_number_of_atoms() == 600, model.get_number_of_atoms() assert model.get_hierarchy().atoms_size() == 600 assert model.get_xray_structure().scatterers().size() == 600 ss_ann = model.get_ss_annotation() # print ss_ann.as_pdb_str() assert ss_ann.get_n_helices() == 4 assert ss_ann.get_n_sheets() == 2 def exercise_mtrix(): inp = iotbx.pdb.input(lines=mtrix_txt+ss_txt+atoms_txt, source_info=None) model = mmtbx.model.manager( model_input = inp) assert model.get_number_of_atoms() == 900, model.get_number_of_atoms() assert model.get_hierarchy().atoms_size() == 900 assert model.get_xray_structure().scatterers().size() == 900 ss_ann = model.get_ss_annotation() # print ss_ann.as_pdb_str() assert ss_ann.get_n_helices() == 6 assert ss_ann.get_n_sheets() == 3 def exercise_biomt(): inp = iotbx.pdb.input(lines=biomt_txt+ss_txt+atoms_txt, source_info=None) model = mmtbx.model.manager( model_input = inp) assert model.get_number_of_atoms() == 300, model.get_number_of_atoms() assert model.get_hierarchy().atoms_size() == 300 assert model.get_xray_structure().scatterers().size() == 300 ss_ann = model.get_ss_annotation() assert ss_ann.get_n_helices() == 2 assert ss_ann.get_n_sheets() == 1 model.expand_with_BIOMT_records() assert model.get_number_of_atoms() == 900, model.get_number_of_atoms() assert model.get_hierarchy().atoms_size() == 900 assert model.get_xray_structure().scatterers().size() == 900, model.get_xray_structure().scatterers().size() ss_ann = model.get_ss_annotation() assert ss_ann.get_n_helices() == 6 assert ss_ann.get_n_sheets() == 3 def exercise_both(): inp = iotbx.pdb.input(lines=mtrix_txt+biomt_txt+ss_txt+atoms_txt, source_info=None) model = mmtbx.model.manager( model_input = inp) assert model.get_number_of_atoms() == 900, model.get_number_of_atoms() assert model.get_hierarchy().atoms_size() == 900 assert model.get_xray_structure().scatterers().size() == 900 ss_ann = model.get_ss_annotation() # print ss_ann.as_pdb_str() # print "="*30 assert ss_ann.get_n_helices() == 6 assert ss_ann.get_n_sheets() == 3 model.expand_with_BIOMT_records() assert model.get_number_of_atoms() == 2700, model.get_number_of_atoms() assert model.get_hierarchy().atoms_size() == 2700 assert model.get_xray_structure().scatterers().size() == 2700, model.get_xray_structure().scatterers().size() ss_ann = model.get_ss_annotation() # print ss_ann.as_pdb_str() assert ss_ann.get_n_helices() == 18 assert ss_ann.get_n_sheets() == 9 return if (__name__ == "__main__"): t0 = time.time() exercise_single_mtrix() exercise_mtrix() exercise_biomt() exercise_both() print("Total time: %8.3f"%(time.time() - t0)) print("OK.")