from __future__ import absolute_import, division, print_function from libtbx import easy_run input_model = ''' CRYST1 130.690 260.300 281.800 90.00 90.00 90.00 P 21 21 21 SCALE1 0.007652 0.000000 0.000000 0.00000 SCALE2 0.000000 0.003842 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003549 0.00000 ATOM 91 N LEU A 54 20.742 150.819 94.874 1.00120.00 N ATOM 92 CA LEU A 54 20.638 151.937 95.856 1.00120.00 C ATOM 93 C LEU A 54 21.814 152.929 95.898 1.00120.00 C ATOM 94 O LEU A 54 22.823 152.732 95.186 1.00120.00 O ATOM 95 CB LEU A 54 20.461 151.285 97.237 1.00120.00 C ATOM 96 CG LEU A 54 19.658 149.983 97.288 1.00120.00 C ATOM 97 CD1 LEU A 54 18.167 150.245 97.141 1.00120.00 C ATOM 98 CD2 LEU A 54 19.941 149.218 98.572 1.00120.00 C ATOM 99 H LEU A 54 21.018 150.068 95.285 1.00120.00 H ATOM 100 HA LEU A 54 19.822 152.444 95.639 1.00120.00 H ATOM 101 HB2 LEU A 54 21.349 151.110 97.606 1.00120.00 H ATOM 102 HB3 LEU A 54 20.025 151.935 97.825 1.00120.00 H ATOM 103 HG LEU A 54 19.944 149.418 96.528 1.00120.00 H ATOM 104 HD11 LEU A 54 17.684 149.401 97.174 1.00120.00 H ATOM 105 HD12 LEU A 54 17.865 150.819 97.866 1.00120.00 H ATOM 106 HD13 LEU A 54 17.996 150.683 96.289 1.00120.00 H ATOM 107 HD21 LEU A 54 19.528 148.338 98.525 1.00120.00 H ATOM 108 HD22 LEU A 54 20.903 149.118 98.685 1.00120.00 H ATOM 109 HD23 LEU A 54 19.576 149.707 99.329 1.00120.00 H ATOM 110 N ASN A 55 21.617 153.948 96.766 1.00120.00 N ATOM 111 CA ASN A 55 22.531 155.021 97.266 1.00120.00 C ATOM 112 C ASN A 55 22.509 156.274 96.393 1.00120.00 C ATOM 113 O ASN A 55 23.555 156.637 95.831 1.00120.00 O ATOM 114 CB ASN A 55 23.913 154.482 97.623 1.00120.00 C ATOM 115 CG ASN A 55 23.739 153.392 98.653 1.00120.00 C ATOM 116 OD1 ASN A 55 22.618 153.017 98.980 1.00120.00 O ATOM 117 ND2 ASN A 55 24.791 152.757 99.098 1.00120.00 N ATOM 118 H ASN A 55 20.770 154.146 97.037 1.00120.00 H ATOM 119 HA ASN A 55 22.147 155.301 98.130 1.00120.00 H ATOM 120 HB2 ASN A 55 24.346 154.121 96.823 1.00120.00 H ATOM 121 HB3 ASN A 55 24.466 155.203 97.988 1.00120.00 H ATOM 122 N GLU A 56 21.318 156.876 96.301 1.00120.00 N ATOM 123 CA GLU A 56 20.966 158.175 95.651 1.00120.00 C ATOM 124 C GLU A 56 21.609 158.222 94.246 1.00120.00 C ATOM 125 O GLU A 56 21.438 157.225 93.524 1.00120.00 O ATOM 126 CB GLU A 56 21.082 159.334 96.668 1.00120.00 C ATOM 127 CG GLU A 56 22.375 159.494 97.470 1.00120.00 C ATOM 128 CD GLU A 56 23.607 159.913 96.688 1.00120.00 C ATOM 129 OE1 GLU A 56 23.490 160.899 95.937 1.00120.00 O ATOM 130 OE2 GLU A 56 24.665 159.272 96.825 1.00120.00 O ATOM 131 H GLU A 56 20.593 156.517 96.721 1.00120.00 H ATOM 132 HA GLU A 56 20.000 158.107 95.471 1.00120.00 H ATOM 133 HB2 GLU A 56 20.925 160.170 96.181 1.00120.00 H ATOM 134 HB3 GLU A 56 20.345 159.236 97.307 1.00120.00 H ATOM 135 HG2 GLU A 56 22.217 160.188 98.145 1.00120.00 H ATOM 136 HG3 GLU A 56 22.570 158.680 97.960 1.00120.00 H ATOM 226 C1 NAG A2001 26.288 152.579 99.625 1.00120.00 C ATOM 227 C2 NAG A2001 26.292 152.561 101.153 1.00120.00 C ATOM 228 C3 NAG A2001 27.587 152.013 101.713 1.00120.00 C ATOM 229 C4 NAG A2001 27.713 150.595 101.193 1.00120.00 C ATOM 230 C5 NAG A2001 27.692 150.594 99.662 1.00120.00 C ATOM 231 C6 NAG A2001 27.611 149.183 99.103 1.00120.00 C ATOM 232 C7 NAG A2001 25.896 154.087 102.985 1.00120.00 C ATOM 233 C8 NAG A2001 25.579 155.489 103.409 1.00120.00 C ATOM 234 N2 NAG A2001 25.996 153.879 101.677 1.00120.00 N ATOM 235 O3 NAG A2001 27.573 151.975 103.140 1.00120.00 O ATOM 236 O4 NAG A2001 28.804 149.907 101.844 1.00120.00 O ATOM 237 O5 NAG A2001 26.501 151.233 99.203 1.00120.00 O ATOM 238 O6 NAG A2001 28.880 148.767 98.602 1.00120.00 O ATOM 239 O7 NAG A2001 26.050 153.186 103.791 1.00120.00 O ATOM 240 H1 NAG A2001 27.390 152.977 99.425 1.00120.00 H ATOM 241 H2 NAG A2001 25.486 151.888 101.475 1.00120.00 H ATOM 242 H3 NAG A2001 28.406 152.641 101.354 1.00120.00 H ATOM 243 H4 NAG A2001 26.791 150.081 101.500 1.00120.00 H ATOM 244 H5 NAG A2001 28.561 151.116 99.240 1.00120.00 H ATOM 245 H61 NAG A2001 27.285 148.496 99.886 1.00120.00 H ATOM 246 H62 NAG A2001 26.873 149.154 98.299 1.00120.00 H ATOM 247 H81 NAG A2001 24.530 155.631 103.405 1.00120.00 H ATOM 248 H82 NAG A2001 25.958 155.658 104.383 1.00120.00 H ATOM 249 H83 NAG A2001 26.026 156.170 102.733 1.00120.00 H ATOM 250 HN2 NAG A2001 25.863 154.643 101.030 1.00120.00 H ATOM 251 HO3 NAG A2001 28.407 151.606 103.462 1.00120.00 H ATOM 252 HO6 NAG A2001 28.770 147.934 98.122 1.00120.00 H ATOM 253 C1 NAG A2002 30.262 150.211 101.739 1.00120.00 C ATOM 254 C2 NAG A2002 31.006 150.060 103.073 1.00120.00 C ATOM 255 C3 NAG A2002 32.407 149.482 102.952 1.00120.00 C ATOM 256 C4 NAG A2002 32.454 148.412 101.885 1.00120.00 C ATOM 257 C5 NAG A2002 32.105 149.120 100.586 1.00120.00 C ATOM 258 C6 NAG A2002 32.380 148.310 99.327 1.00120.00 C ATOM 259 C7 NAG A2002 31.892 151.549 104.798 1.00120.00 C ATOM 260 C8 NAG A2002 31.972 152.967 105.272 1.00120.00 C ATOM 261 N2 NAG A2002 31.169 151.363 103.693 1.00120.00 N ATOM 262 O3 NAG A2002 32.826 148.946 104.211 1.00120.00 O ATOM 263 O4 NAG A2002 33.752 147.807 101.946 1.00120.00 O ATOM 264 O5 NAG A2002 30.712 149.394 100.650 1.00120.00 O ATOM 265 O6 NAG A2002 33.791 148.107 99.189 1.00120.00 O ATOM 266 O7 NAG A2002 32.453 150.645 105.392 1.00120.00 O ATOM 267 H1 NAG A2002 30.373 151.261 101.436 1.00120.00 H ATOM 268 H2 NAG A2002 30.414 149.417 103.739 1.00120.00 H ATOM 269 H3 NAG A2002 33.090 150.291 102.656 1.00120.00 H ATOM 270 H4 NAG A2002 31.679 147.664 102.100 1.00120.00 H ATOM 271 H5 NAG A2002 32.671 150.061 100.533 1.00120.00 H ATOM 272 H61 NAG A2002 31.996 148.844 98.454 1.00120.00 H ATOM 273 H62 NAG A2002 31.871 147.346 99.388 1.00120.00 H ATOM 274 H81 NAG A2002 30.999 153.323 105.488 1.00120.00 H ATOM 275 H82 NAG A2002 32.408 153.567 104.516 1.00120.00 H ATOM 276 H83 NAG A2002 32.567 153.014 106.147 1.00120.00 H ATOM 277 HN2 NAG A2002 30.731 152.159 103.253 1.00120.00 H ATOM 278 HO3 NAG A2002 33.766 148.727 104.169 1.00120.00 H ATOM 279 HO6 NAG A2002 33.969 147.611 98.378 1.00120.00 H ATOM 280 C1 BMA A2003 33.732 146.369 102.120 1.00120.00 C ATOM 281 C2 BMA A2003 33.505 145.870 103.554 1.00120.00 C ATOM 282 C3 BMA A2003 33.759 144.371 103.613 1.00120.00 C ATOM 283 C4 BMA A2003 32.968 143.668 102.521 1.00120.00 C ATOM 284 C5 BMA A2003 33.280 144.312 101.185 1.00120.00 C ATOM 285 C6 BMA A2003 32.604 143.536 100.068 1.00120.00 C ATOM 286 O2 BMA A2003 32.172 146.059 104.040 1.00120.00 O ATOM 287 O3 BMA A2003 33.360 143.861 104.889 1.00120.00 O ATOM 288 O4 BMA A2003 33.303 142.277 102.454 1.00120.00 O ATOM 289 O5 BMA A2003 32.868 145.676 101.229 1.00120.00 O ATOM 290 O6 BMA A2003 32.891 142.146 100.256 1.00120.00 O ATOM 291 H1 BMA A2003 34.747 146.032 101.870 1.00120.00 H ATOM 292 H2 BMA A2003 34.221 146.372 104.221 1.00120.00 H ATOM 293 H3 BMA A2003 34.831 144.185 103.453 1.00120.00 H ATOM 294 H4 BMA A2003 31.896 143.786 102.728 1.00120.00 H ATOM 295 H5 BMA A2003 34.366 144.267 101.026 1.00120.00 H ATOM 296 H61 BMA A2003 32.984 143.868 99.099 1.00120.00 H ATOM 297 H62 BMA A2003 31.526 143.704 100.092 1.00120.00 H ATOM 298 HO2 BMA A2003 32.067 146.963 104.365 1.00120.00 H ATOM 299 HO3 BMA A2003 33.846 144.320 105.588 1.00120.00 H ATOM 300 HO4 BMA A2003 33.053 141.845 103.282 1.00120.00 H ''' result = '''Links applied BETA1-4 " NAG A2001 " - " NAG A2002 " " NAG A2002 " - " BMA A2003 " NAG-ASN " NAG A2001 " - " ASN A 55 "''' def main(): input_model_filename = 'carbo_linking_output.pdb' with open(input_model_filename, 'w') as f: f.write(input_model) cmd = 'phenix.pdb_interpretation %s' % input_model_filename rc = easy_run.go(cmd) lines = '\n'.join(rc.stdout_lines) assert lines.find(result)>-1 print('OK') if __name__ == '__main__': main()