#!/usr/bin/python ############################################################################### # # This script tests various functions of reduce. I encourage you to add tests # as needs arise. When doing so, please update the info on what is ran here # below. The script uses python's unittest framework to compare reduce output # pdb strings to expected pdb strings which are stored as strings in this # script. # # The following is a list and description of the current tests ran herein: # - test_default_reduce tests default reduce # Compares output to default_answer # - test_flip_reduce test reduce's flip functionality using the # -flip flag, # Compares output to flip_answer # - test_nuc_reduce tests the addition of nuclear-centered Hs. # Compares output to nuc_answer # # TODO : Add N and H to the flip test # ############################################################################### import unittest import os import subprocess hs = 'you must go in the tst script and change the %s variable to point to %s' reduce_exe = '../reduce_src/reduce' assert os.path.exists(reduce_exe), hs % ('reduce_exe','a reduce executable') het_dict_path = '../reduce_het_dict.txt' assert os.path.exists(het_dict_path),hs%('het_dict_path','reduce_het_dict.txt') __author__ = 'bhintze' default_pdb_str = '''\ CRYST1 42.360 54.790 111.990 90.00 90.00 90.00 P 21 21 21 4 SCALE1 0.023607 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018252 0.000000 0.00000 ATOM 312 N THR A 68 33.568 21.278 46.864 1.00 44.97 N ATOM 313 CA THR A 68 32.890 20.190 47.567 1.00 46.61 C ATOM 314 C THR A 68 32.844 20.354 49.087 1.00 48.10 C ATOM 315 O THR A 68 32.371 19.466 49.797 1.00 50.47 O ATOM 316 CB THR A 68 33.558 18.847 47.259 1.00 46.45 C ATOM 317 OG1 THR A 68 34.862 18.831 47.845 1.00 54.25 O ATOM 318 CG2 THR A 68 33.679 18.648 45.760 1.00 45.17 C ATOM 319 N GLY A 69 33.330 21.483 49.591 1.00 46.02 N ATOM 320 CA GLY A 69 33.272 21.741 51.020 1.00 45.56 C ATOM 321 C GLY A 69 31.908 22.257 51.441 1.00 49.19 C ATOM 322 O GLY A 69 30.977 22.314 50.636 1.00 47.01 O ATOM 323 N GLY A 70 31.779 22.626 52.712 1.00 50.78 N ATOM 324 CA GLY A 70 30.561 23.259 53.190 1.00 47.53 C ATOM 325 C GLY A 70 29.348 22.361 53.314 1.00 51.12 C ATOM 326 O GLY A 70 28.258 22.831 53.644 1.00 49.03 O ATOM 327 N ASN A 71 29.534 21.069 53.061 1.00 58.93 N ATOM 328 CA ASN A 71 28.417 20.129 53.040 1.00 65.14 C ATOM 329 C ASN A 71 27.932 19.713 54.427 1.00 74.93 C ATOM 330 O ASN A 71 28.629 19.904 55.427 1.00 77.88 O ATOM 331 CB ASN A 71 28.791 18.894 52.225 1.00 61.19 C ATOM 332 CG ASN A 71 28.608 19.110 50.735 1.00 58.59 C ATOM 333 OD1 ASN A 71 27.771 18.468 50.099 1.00 62.04 O ATOM 334 ND2 ASN A 71 29.382 20.033 50.174 1.00 58.77 N ATOM 335 N ILE A 72 26.737 19.123 54.447 1.00 76.95 N ATOM 336 CA ILE A 72 25.929 18.894 55.651 1.00 80.49 C ATOM 337 C ILE A 72 26.679 18.458 56.914 1.00 91.67 C ATOM 338 O ILE A 72 27.103 19.298 57.714 1.00 90.79 O ATOM 339 N ARG A 73 26.813 17.144 57.090 1.00 96.55 N ATOM 340 CA ARG A 73 27.329 16.556 58.318 1.00 95.73 C ATOM 341 C ARG A 73 28.678 17.073 58.781 1.00 97.01 C ATOM 342 O ARG A 73 28.915 17.221 59.983 1.00 95.84 O ATOM 343 N ASN A 74 29.564 17.343 57.826 1.00 93.35 N ATOM 344 CA ASN A 74 30.868 17.899 58.135 1.00 93.98 C ATOM 345 C ASN A 74 30.791 19.397 58.361 1.00 90.89 C ATOM 346 O ASN A 74 31.261 20.183 57.536 1.00 80.51 O ATOM 347 N ASP A 75 30.194 19.790 59.484 1.00 91.06 N ATOM 348 CA ASP A 75 29.985 21.193 59.783 1.00 82.35 C ATOM 349 C ASP A 75 29.897 21.516 61.260 1.00 79.45 C ATOM 350 O ASP A 75 29.021 22.271 61.686 1.00 75.34 O ATOM 351 N ASP A 76 30.806 20.947 62.046 1.00 82.28 N ATOM 352 CA ASP A 76 30.916 21.299 63.449 1.00 79.21 C ATOM 353 C ASP A 76 31.526 22.681 63.584 1.00 76.33 C ATOM 354 O ASP A 76 31.412 23.327 64.622 1.00 79.14 O ATOM 355 N LYS A 77 32.175 23.136 62.515 1.00 77.70 N ATOM 356 CA LYS A 77 32.808 24.442 62.495 1.00 74.51 C ATOM 357 C LYS A 77 32.161 25.410 61.518 1.00 68.95 C ATOM 358 O LYS A 77 32.764 26.412 61.132 1.00 62.03 O ATOM 359 N TYR A 78 30.936 25.104 61.103 1.00 64.80 N ATOM 360 CA TYR A 78 30.137 26.048 60.333 1.00 56.64 C ATOM 361 C TYR A 78 29.133 26.715 61.259 1.00 48.87 C ATOM 362 O TYR A 78 28.369 27.587 60.844 1.00 44.48 O ATOM 363 CB TYR A 78 29.417 25.352 59.173 1.00 57.64 C ATOM 364 CG TYR A 78 30.352 24.788 58.130 1.00 61.82 C ATOM 365 CD1 TYR A 78 31.582 25.388 57.872 1.00 63.84 C ATOM 366 CD2 TYR A 78 30.012 23.654 57.406 1.00 64.20 C ATOM 367 CE1 TYR A 78 32.446 24.873 56.916 1.00 58.36 C ATOM 368 CE2 TYR A 78 30.869 23.128 56.458 1.00 65.24 C ATOM 369 CZ TYR A 78 32.083 23.743 56.212 1.00 61.98 C ATOM 370 OH TYR A 78 32.941 23.224 55.265 1.00 63.38 O ATOM 371 N THR A 79 29.156 26.301 62.523 1.00 49.22 N ATOM 372 CA THR A 79 28.229 26.804 63.524 1.00 42.21 C ATOM 373 C THR A 79 28.321 28.320 63.691 1.00 38.81 C ATOM 374 O THR A 79 27.364 28.958 64.127 1.00 40.18 O ATOM 375 CB THR A 79 28.468 26.130 64.895 1.00 48.93 C ATOM 376 OG1 THR A 79 29.771 26.471 65.381 1.00 55.67 O ATOM 377 CG2 THR A 79 28.367 24.620 64.768 1.00 56.67 C ATOM 378 N HIS A 80 29.463 28.905 63.347 1.00 33.78 N ATOM 379 CA HIS A 80 29.612 30.349 63.476 1.00 31.59 C ATOM 380 C HIS A 80 28.915 31.110 62.336 1.00 28.85 C ATOM 381 O HIS A 80 28.790 32.333 62.393 1.00 28.35 O ATOM 382 CB HIS A 80 31.095 30.737 63.556 1.00 36.80 C ATOM 383 CG HIS A 80 31.885 30.403 62.328 1.00 44.69 C ATOM 384 ND1 HIS A 80 31.515 29.411 61.446 1.00 46.50 N ATOM 385 CD2 HIS A 80 33.036 30.929 61.843 1.00 44.38 C ATOM 386 CE1 HIS A 80 32.398 29.346 60.463 1.00 43.56 C ATOM 387 NE2 HIS A 80 33.329 30.257 60.679 1.00 44.44 N ATOM 388 N PHE A 81 28.455 30.392 61.314 1.00 26.91 N ATOM 389 CA PHE A 81 27.611 31.013 60.293 1.00 26.80 C ATOM 390 C PHE A 81 26.207 31.294 60.819 1.00 27.58 C ATOM 391 O PHE A 81 25.485 32.115 60.260 1.00 23.87 O ATOM 392 CB PHE A 81 27.512 30.132 59.040 1.00 26.61 C ATOM 393 CG PHE A 81 28.820 29.946 58.313 1.00 25.55 C ATOM 394 CD1 PHE A 81 29.045 28.809 57.565 1.00 27.17 C ATOM 395 CD2 PHE A 81 29.815 30.911 58.372 1.00 26.18 C ATOM 396 CE1 PHE A 81 30.242 28.624 56.897 1.00 27.35 C ATOM 397 CE2 PHE A 81 31.018 30.732 57.703 1.00 24.11 C ATOM 398 CZ PHE A 81 31.229 29.587 56.967 1.00 26.35 C ATOM 399 N PHE A 82 25.818 30.632 61.909 1.00 26.96 N ATOM 400 CA PHE A 82 24.448 30.780 62.397 1.00 28.96 C ATOM 401 C PHE A 82 24.398 31.122 63.878 1.00 29.75 C ATOM 402 O PHE A 82 25.280 30.748 64.630 1.00 34.14 O ATOM 403 CB PHE A 82 23.654 29.503 62.128 1.00 32.61 C ATOM 404 CG PHE A 82 23.702 29.060 60.693 1.00 32.62 C ATOM 405 CD1 PHE A 82 24.535 28.027 60.297 1.00 31.95 C ATOM 406 CD2 PHE A 82 22.930 29.691 59.738 1.00 28.66 C ATOM 407 CE1 PHE A 82 24.584 27.632 58.973 1.00 30.64 C ATOM 408 CE2 PHE A 82 22.978 29.296 58.407 1.00 30.13 C ATOM 409 CZ PHE A 82 23.805 28.268 58.032 1.00 30.16 C ATOM 410 N SER A 83 23.367 31.856 64.279 1.00 28.83 N ATOM 411 CA SER A 83 23.146 32.159 65.686 1.00 33.49 C ATOM 412 C SER A 83 22.802 30.880 66.450 1.00 39.39 C ATOM 413 O SER A 83 22.535 29.841 65.854 1.00 37.63 O ATOM 414 CB SER A 83 22.026 33.183 65.849 1.00 32.43 C ATOM 415 OG SER A 83 20.768 32.557 65.653 1.00 44.84 O ATOM 416 N GLY A 84 22.812 30.954 67.775 1.00 46.57 N ATOM 417 CA GLY A 84 22.555 29.775 68.586 1.00 49.01 C ATOM 418 C GLY A 84 21.110 29.319 68.510 1.00 46.09 C ATOM 419 O GLY A 84 20.830 28.124 68.567 1.00 53.68 O HETATM 1739 C1 EOH A 717 34.026 19.250 53.995 0.90 63.57 C HETATM 1740 C2 EOH A 717 33.701 20.048 55.258 0.90 61.11 C HETATM 1741 O EOH A 717 32.822 18.995 53.269 0.90 65.41 O HETATM 1755 C MOH A 724 24.486 26.604 64.638 1.00 43.73 C HETATM 1756 O MOH A 724 25.220 27.577 65.381 1.00 45.19 O END ''' default_answer = '''\ USER MOD reduce.3.3.160422 H: found=0, std=0, add=78, rem=0, adj=5 CRYST1 42.360 54.790 111.990 90.00 90.00 90.00 P 21 21 21 4 SCALE1 0.023607 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018252 0.000000 0.00000 USER MOD ----------------------------------------------------------------- USER MOD scores for adjustable sidechains, with "set" totals for H,N and Q USER MOD "o" means original, "f" means flipped, "180deg" is methyl default USER MOD "!" flags a clash with an overlap of 0.40A or greater USER MOD flip categories: "K"=keep, "C"=clashes, "X"=uncertain, "F"=flip USER MOD Single : A 68 THR OG1 : rot -40:sc= 0.00645 USER MOD Single : A 78 TYR OH : rot 63:sc= -0.281 USER MOD Single : A 79 THR OG1 : rot 180:sc= 0 USER MOD Single : A 83 SER OG : rot 180:sc= 0 USER MOD Single : A 717 EOH O : rot 180:sc= 0 USER MOD ----------------------------------------------------------------- ATOM 312 N THR A 68 33.568 21.278 46.864 1.00 44.97 N ATOM 313 CA THR A 68 32.890 20.190 47.567 1.00 46.61 C ATOM 314 C THR A 68 32.844 20.354 49.087 1.00 48.10 C ATOM 315 O THR A 68 32.371 19.466 49.797 1.00 50.47 O ATOM 316 CB THR A 68 33.558 18.847 47.259 1.00 46.45 C ATOM 317 OG1 THR A 68 34.862 18.831 47.845 1.00 54.25 O ATOM 318 CG2 THR A 68 33.679 18.648 45.760 1.00 45.17 C ATOM 0 HA THR A 68 31.977 20.217 47.240 1.00 46.61 H new ATOM 0 HB THR A 68 33.017 18.131 47.627 1.00 46.45 H new ATOM 0 HG1 THR A 68 35.224 19.582 47.745 1.00 54.25 H new ATOM 0 HG21 THR A 68 34.103 17.795 45.580 1.00 45.17 H new ATOM 0 HG22 THR A 68 32.796 18.660 45.359 1.00 45.17 H new ATOM 0 HG23 THR A 68 34.216 19.362 45.381 1.00 45.17 H new ATOM 319 N GLY A 69 33.330 21.483 49.591 1.00 46.02 N ATOM 320 CA GLY A 69 33.272 21.741 51.020 1.00 45.56 C ATOM 321 C GLY A 69 31.908 22.257 51.441 1.00 49.19 C ATOM 322 O GLY A 69 30.977 22.314 50.636 1.00 47.01 O ATOM 0 H GLY A 69 33.694 22.107 49.125 1.00 46.02 H new ATOM 0 HA2 GLY A 69 33.474 20.926 51.505 1.00 45.56 H new ATOM 0 HA3 GLY A 69 33.952 22.390 51.260 1.00 45.56 H new ATOM 323 N GLY A 70 31.779 22.626 52.712 1.00 50.78 N ATOM 324 CA GLY A 70 30.561 23.259 53.190 1.00 47.53 C ATOM 325 C GLY A 70 29.348 22.361 53.314 1.00 51.12 C ATOM 326 O GLY A 70 28.258 22.831 53.644 1.00 49.03 O ATOM 0 H GLY A 70 32.386 22.518 53.311 1.00 50.78 H new ATOM 0 HA2 GLY A 70 30.741 23.650 54.059 1.00 47.53 H new ATOM 0 HA3 GLY A 70 30.341 23.989 52.590 1.00 47.53 H new ATOM 327 N ASN A 71 29.534 21.069 53.061 1.00 58.93 N ATOM 328 CA ASN A 71 28.417 20.129 53.040 1.00 65.14 C ATOM 329 C ASN A 71 27.932 19.713 54.427 1.00 74.93 C ATOM 330 O ASN A 71 28.629 19.904 55.427 1.00 77.88 O ATOM 331 CB ASN A 71 28.791 18.894 52.225 1.00 61.19 C ATOM 332 CG ASN A 71 28.608 19.110 50.735 1.00 58.59 C ATOM 333 OD1 ASN A 71 27.771 18.468 50.099 1.00 62.04 O ATOM 334 ND2 ASN A 71 29.382 20.033 50.174 1.00 58.77 N ATOM 0 H ASN A 71 30.301 20.716 52.899 1.00 58.93 H new ATOM 0 HA ASN A 71 27.676 20.597 52.624 1.00 65.14 H new ATOM 0 HB2 ASN A 71 29.715 18.658 52.404 1.00 61.19 H new ATOM 0 HB3 ASN A 71 28.246 18.144 52.510 1.00 61.19 H new ATOM 0 HD21 ASN A 71 29.309 20.202 49.334 1.00 58.77 H new ATOM 0 HD22 ASN A 71 29.955 20.461 50.651 1.00 58.77 H new ATOM 335 N ILE A 72 26.737 19.123 54.447 1.00 76.95 N ATOM 336 CA ILE A 72 25.929 18.894 55.651 1.00 80.49 C ATOM 337 C ILE A 72 26.679 18.458 56.914 1.00 91.67 C ATOM 338 O ILE A 72 27.103 19.298 57.714 1.00 90.79 O ATOM 0 H ILE A 72 26.358 18.833 53.732 1.00 76.95 H new ATOM 339 N ARG A 73 26.813 17.144 57.090 1.00 96.55 N ATOM 340 CA ARG A 73 27.329 16.556 58.318 1.00 95.73 C ATOM 341 C ARG A 73 28.678 17.073 58.781 1.00 97.01 C ATOM 342 O ARG A 73 28.915 17.221 59.983 1.00 95.84 O ATOM 0 H ARG A 73 26.603 16.564 56.490 1.00 96.55 H new ATOM 343 N ASN A 74 29.564 17.343 57.826 1.00 93.35 N ATOM 344 CA ASN A 74 30.868 17.899 58.135 1.00 93.98 C ATOM 345 C ASN A 74 30.791 19.397 58.361 1.00 90.89 C ATOM 346 O ASN A 74 31.261 20.183 57.536 1.00 80.51 O ATOM 0 H ASN A 74 29.424 17.209 56.988 1.00 93.35 H new ATOM 347 N ASP A 75 30.194 19.790 59.484 1.00 91.06 N ATOM 348 CA ASP A 75 29.985 21.193 59.783 1.00 82.35 C ATOM 349 C ASP A 75 29.897 21.516 61.260 1.00 79.45 C ATOM 350 O ASP A 75 29.021 22.271 61.686 1.00 75.34 O ATOM 0 H ASP A 75 29.902 19.251 60.087 1.00 91.06 H new ATOM 351 N ASP A 76 30.806 20.947 62.046 1.00 82.28 N ATOM 352 CA ASP A 76 30.916 21.299 63.449 1.00 79.21 C ATOM 353 C ASP A 76 31.526 22.681 63.584 1.00 76.33 C ATOM 354 O ASP A 76 31.412 23.327 64.622 1.00 79.14 O ATOM 0 H ASP A 76 31.369 20.353 61.781 1.00 82.28 H new ATOM 355 N LYS A 77 32.175 23.136 62.515 1.00 77.70 N ATOM 356 CA LYS A 77 32.808 24.442 62.495 1.00 74.51 C ATOM 357 C LYS A 77 32.161 25.410 61.518 1.00 68.95 C ATOM 358 O LYS A 77 32.764 26.412 61.132 1.00 62.03 O ATOM 0 H LYS A 77 32.258 22.693 61.783 1.00 77.70 H new ATOM 359 N TYR A 78 30.936 25.104 61.103 1.00 64.80 N ATOM 360 CA TYR A 78 30.137 26.048 60.333 1.00 56.64 C ATOM 361 C TYR A 78 29.133 26.715 61.259 1.00 48.87 C ATOM 362 O TYR A 78 28.369 27.587 60.844 1.00 44.48 O ATOM 363 CB TYR A 78 29.417 25.352 59.173 1.00 57.64 C ATOM 364 CG TYR A 78 30.352 24.788 58.130 1.00 61.82 C ATOM 365 CD1 TYR A 78 31.582 25.388 57.872 1.00 63.84 C ATOM 366 CD2 TYR A 78 30.012 23.654 57.406 1.00 64.20 C ATOM 367 CE1 TYR A 78 32.446 24.873 56.916 1.00 58.36 C ATOM 368 CE2 TYR A 78 30.869 23.128 56.458 1.00 65.24 C ATOM 369 CZ TYR A 78 32.083 23.743 56.212 1.00 61.98 C ATOM 370 OH TYR A 78 32.941 23.224 55.265 1.00 63.38 O ATOM 0 H TYR A 78 30.549 24.352 61.258 1.00 64.80 H new ATOM 0 HA TYR A 78 30.724 26.717 59.949 1.00 56.64 H new ATOM 0 HB2 TYR A 78 28.869 24.634 59.527 1.00 57.64 H new ATOM 0 HB3 TYR A 78 28.816 25.985 58.749 1.00 57.64 H new ATOM 0 HD1 TYR A 78 31.829 26.147 58.349 1.00 63.84 H new ATOM 0 HD2 TYR A 78 29.193 23.241 57.561 1.00 64.20 H new ATOM 0 HE1 TYR A 78 33.263 25.286 56.751 1.00 58.36 H new ATOM 0 HE2 TYR A 78 30.630 22.363 55.987 1.00 65.24 H new ATOM 0 HH TYR A 78 33.653 22.977 55.637 1.00 63.38 H new ATOM 371 N THR A 79 29.156 26.301 62.523 1.00 49.22 N ATOM 372 CA THR A 79 28.229 26.804 63.524 1.00 42.21 C ATOM 373 C THR A 79 28.321 28.320 63.691 1.00 38.81 C ATOM 374 O THR A 79 27.364 28.958 64.127 1.00 40.18 O ATOM 375 CB THR A 79 28.468 26.130 64.895 1.00 48.93 C ATOM 376 OG1 THR A 79 29.771 26.471 65.381 1.00 55.67 O ATOM 377 CG2 THR A 79 28.367 24.620 64.768 1.00 56.67 C ATOM 0 H THR A 79 29.713 25.718 62.822 1.00 49.22 H new ATOM 0 HA THR A 79 27.340 26.585 63.203 1.00 42.21 H new ATOM 0 HB THR A 79 27.791 26.445 65.515 1.00 48.93 H new ATOM 0 HG1 THR A 79 29.897 26.105 66.126 1.00 55.67 H new ATOM 0 HG21 THR A 79 28.519 24.211 65.634 1.00 56.67 H new ATOM 0 HG22 THR A 79 27.483 24.380 64.448 1.00 56.67 H new ATOM 0 HG23 THR A 79 29.034 24.303 64.140 1.00 56.67 H new ATOM 378 N HIS A 80 29.463 28.905 63.347 1.00 33.78 N ATOM 379 CA HIS A 80 29.612 30.349 63.476 1.00 31.59 C ATOM 380 C HIS A 80 28.915 31.110 62.336 1.00 28.85 C ATOM 381 O HIS A 80 28.790 32.333 62.393 1.00 28.35 O ATOM 382 CB HIS A 80 31.095 30.737 63.556 1.00 36.80 C ATOM 383 CG HIS A 80 31.885 30.403 62.328 1.00 44.69 C ATOM 384 ND1 HIS A 80 31.515 29.411 61.446 1.00 46.50 N ATOM 385 CD2 HIS A 80 33.036 30.929 61.843 1.00 44.38 C ATOM 386 CE1 HIS A 80 32.398 29.346 60.463 1.00 43.56 C ATOM 387 NE2 HIS A 80 33.329 30.257 60.679 1.00 44.44 N ATOM 0 H HIS A 80 30.153 28.492 63.042 1.00 33.78 H new ATOM 0 HA HIS A 80 29.176 30.607 64.303 1.00 31.59 H new ATOM 0 HB2 HIS A 80 31.161 31.691 63.721 1.00 36.80 H new ATOM 0 HB3 HIS A 80 31.495 30.289 64.318 1.00 36.80 H new ATOM 0 HD2 HIS A 80 33.534 31.615 62.225 1.00 44.38 H new ATOM 0 HE1 HIS A 80 32.368 28.759 59.743 1.00 43.56 H new ATOM 388 N PHE A 81 28.455 30.392 61.314 1.00 26.91 N ATOM 389 CA PHE A 81 27.611 31.013 60.293 1.00 26.80 C ATOM 390 C PHE A 81 26.207 31.294 60.819 1.00 27.58 C ATOM 391 O PHE A 81 25.485 32.115 60.260 1.00 23.87 O ATOM 392 CB PHE A 81 27.512 30.132 59.040 1.00 26.61 C ATOM 393 CG PHE A 81 28.820 29.946 58.313 1.00 25.55 C ATOM 394 CD1 PHE A 81 29.045 28.809 57.565 1.00 27.17 C ATOM 395 CD2 PHE A 81 29.815 30.911 58.372 1.00 26.18 C ATOM 396 CE1 PHE A 81 30.242 28.624 56.897 1.00 27.35 C ATOM 397 CE2 PHE A 81 31.018 30.732 57.703 1.00 24.11 C ATOM 398 CZ PHE A 81 31.229 29.587 56.967 1.00 26.35 C ATOM 0 H PHE A 81 28.616 29.556 61.193 1.00 26.91 H new ATOM 0 HA PHE A 81 28.033 31.855 60.059 1.00 26.80 H new ATOM 0 HB2 PHE A 81 27.168 29.262 59.295 1.00 26.61 H new ATOM 0 HB3 PHE A 81 26.867 30.524 58.431 1.00 26.61 H new ATOM 0 HD1 PHE A 81 28.383 28.158 57.509 1.00 27.17 H new ATOM 0 HD2 PHE A 81 29.674 31.687 58.865 1.00 26.18 H new ATOM 0 HE1 PHE A 81 30.382 27.850 56.400 1.00 27.35 H new ATOM 0 HE2 PHE A 81 31.680 31.384 57.752 1.00 24.11 H new ATOM 0 HZ PHE A 81 32.034 29.463 56.518 1.00 26.35 H new ATOM 399 N PHE A 82 25.818 30.632 61.909 1.00 26.96 N ATOM 400 CA PHE A 82 24.448 30.780 62.397 1.00 28.96 C ATOM 401 C PHE A 82 24.398 31.122 63.878 1.00 29.75 C ATOM 402 O PHE A 82 25.280 30.748 64.630 1.00 34.14 O ATOM 403 CB PHE A 82 23.654 29.503 62.128 1.00 32.61 C ATOM 404 CG PHE A 82 23.702 29.060 60.693 1.00 32.62 C ATOM 405 CD1 PHE A 82 24.535 28.027 60.297 1.00 31.95 C ATOM 406 CD2 PHE A 82 22.930 29.691 59.738 1.00 28.66 C ATOM 407 CE1 PHE A 82 24.584 27.632 58.973 1.00 30.64 C ATOM 408 CE2 PHE A 82 22.978 29.296 58.407 1.00 30.13 C ATOM 409 CZ PHE A 82 23.805 28.268 58.032 1.00 30.16 C ATOM 0 H PHE A 82 26.318 30.105 62.370 1.00 26.96 H new ATOM 0 HA PHE A 82 24.048 31.521 61.915 1.00 28.96 H new ATOM 0 HB2 PHE A 82 23.998 28.792 62.691 1.00 32.61 H new ATOM 0 HB3 PHE A 82 22.729 29.645 62.385 1.00 32.61 H new ATOM 0 HD1 PHE A 82 25.066 27.595 60.927 1.00 31.95 H new ATOM 0 HD2 PHE A 82 22.370 30.390 59.989 1.00 28.66 H new ATOM 0 HE1 PHE A 82 25.144 26.935 58.717 1.00 30.64 H new ATOM 0 HE2 PHE A 82 22.452 29.727 57.773 1.00 30.13 H new ATOM 0 HZ PHE A 82 23.840 28.000 57.142 1.00 30.16 H new ATOM 410 N SER A 83 23.367 31.856 64.279 1.00 28.83 N ATOM 411 CA SER A 83 23.146 32.159 65.686 1.00 33.49 C ATOM 412 C SER A 83 22.802 30.880 66.450 1.00 39.39 C ATOM 413 O SER A 83 22.535 29.841 65.854 1.00 37.63 O ATOM 414 CB SER A 83 22.026 33.183 65.849 1.00 32.43 C ATOM 415 OG SER A 83 20.768 32.557 65.653 1.00 44.84 O ATOM 0 H SER A 83 22.780 32.190 63.747 1.00 28.83 H new ATOM 0 HA SER A 83 23.962 32.537 66.050 1.00 33.49 H new ATOM 0 HB2 SER A 83 22.065 33.579 66.734 1.00 32.43 H new ATOM 0 HB3 SER A 83 22.141 33.904 65.210 1.00 32.43 H new ATOM 0 HG SER A 83 20.155 33.124 65.745 1.00 44.84 H new ATOM 416 N GLY A 84 22.812 30.954 67.775 1.00 46.57 N ATOM 417 CA GLY A 84 22.555 29.775 68.586 1.00 49.01 C ATOM 418 C GLY A 84 21.110 29.319 68.510 1.00 46.09 C ATOM 419 O GLY A 84 20.830 28.124 68.567 1.00 53.68 O ATOM 0 H GLY A 84 22.965 31.673 68.221 1.00 46.57 H new ATOM 0 HA2 GLY A 84 23.134 29.054 68.295 1.00 49.01 H new ATOM 0 HA3 GLY A 84 22.782 29.966 69.509 1.00 49.01 H new HETATM 1739 C1 EOH A 717 34.026 19.250 53.995 0.90 63.57 C HETATM 1740 C2 EOH A 717 33.701 20.048 55.258 0.90 61.11 C HETATM 1741 O EOH A 717 32.822 18.995 53.269 0.90 65.41 O HETATM 0 3H2 EOH A 717 33.288 20.890 55.011 0.90 61.11 H new HETATM 0 2H2 EOH A 717 33.090 19.539 55.814 0.90 61.11 H new HETATM 0 2H1 EOH A 717 34.651 19.743 53.441 0.90 63.57 H new HETATM 0 1H2 EOH A 717 34.518 20.221 55.751 0.90 61.11 H new HETATM 0 1H1 EOH A 717 34.456 18.413 54.231 0.90 63.57 H new HETATM 0 HO EOH A 717 33.001 18.558 52.574 0.90 65.41 H new HETATM 1755 C MOH A 724 24.486 26.604 64.638 1.00 43.73 C HETATM 1756 O MOH A 724 25.220 27.577 65.381 1.00 45.19 O END ''' flip_test_str = '''\ ATOM 800 N ASN B 3 6.076 89.982 59.411 1.00 4.63 N ATOM 801 CA ASN B 3 5.450 88.943 60.224 1.00 4.43 C ATOM 802 C ASN B 3 5.198 89.487 61.636 1.00 4.66 C ATOM 803 O ASN B 3 4.110 89.265 62.214 1.00 4.93 O ATOM 804 CB ASN B 3 6.301 87.657 60.231 1.00 4.34 C ATOM 805 CG ASN B 3 5.552 86.456 60.791 1.00 3.94 C ATOM 806 OD1 ASN B 3 4.451 86.590 61.345 1.00 2.54 O ATOM 807 ND2 ASN B 3 6.148 85.267 60.647 1.00 4.44 N ATOM 1837 N HIS B 4 6.171 90.222 62.163 1.00 2.00 N ATOM 1838 CA HIS B 4 6.033 90.827 63.489 1.00 2.00 C ATOM 1839 C HIS B 4 4.816 91.761 63.577 1.00 2.00 C ATOM 1840 O HIS B 4 4.170 91.880 64.649 1.00 2.00 O ATOM 1841 CB HIS B 4 7.302 91.606 63.860 1.00 2.00 C ATOM 1842 CG HIS B 4 8.501 90.745 64.094 1.00 2.00 C ATOM 1843 ND1 HIS B 4 9.700 90.948 63.443 1.00 2.00 N ATOM 1844 CD2 HIS B 4 8.696 89.694 64.924 1.00 2.00 C ATOM 1845 CE1 HIS B 4 10.576 90.049 63.853 1.00 2.00 C ATOM 1846 NE2 HIS B 4 9.995 89.282 64.757 1.00 2.00 N ATOM 151 N ARG B 5 4.459 92.414 62.487 1.00 18.73 N ATOM 152 CA ARG B 5 3.320 93.335 62.497 1.00 19.66 C ATOM 153 C ARG B 5 2.032 92.680 62.014 1.00 19.66 C ATOM 154 O ARG B 5 0.950 93.273 62.111 1.00 21.95 O ATOM 155 CB ARG B 5 3.638 94.541 61.601 1.00 23.29 C ATOM 156 CG ARG B 5 4.881 95.354 62.034 1.00 23.24 C ATOM 157 CD ARG B 5 5.365 96.251 60.910 1.00 29.00 C ATOM 158 NE ARG B 5 6.449 97.202 61.226 1.00 32.94 N ATOM 159 CZ ARG B 5 7.728 96.894 61.473 1.00 34.16 C ATOM 160 NH1 ARG B 5 8.157 95.628 61.480 1.00 30.53 N ATOM 161 NH2 ARG B 5 8.606 97.884 61.648 1.00 35.22 N ATOM 112 N GLN B 9 10.186 91.359 59.521 1.00 15.79 N ATOM 113 CA GLN B 9 9.578 92.637 59.819 1.00 18.37 C ATOM 114 C GLN B 9 8.076 92.653 59.539 1.00 17.17 C ATOM 115 O GLN B 9 7.278 93.226 60.303 1.00 16.99 O ATOM 116 CB GLN B 9 10.255 93.750 59.036 1.00 19.44 C ATOM 117 CG GLN B 9 11.594 94.138 59.641 1.00 24.67 C ATOM 118 CD GLN B 9 11.403 94.696 61.052 0.00 27.67 C ATOM 119 NE2 GLN B 9 10.724 95.708 61.264 1.00 31.74 O ATOM 120 OE1 GLN B 9 11.983 94.024 62.020 1.00 31.80 N HETATM 7573 O HOH B 407 6.633 88.635 66.643 1.00 11.41 O HETATM 7693 O HOH B 527 3.491 85.743 61.660 1.00 4.12 O ''' flip_answer = '''\ USER MOD reduce.3.3.160422 H: found=0, std=0, add=33, rem=0, adj=3 USER MOD ----------------------------------------------------------------- USER MOD scores for adjustable sidechains, with "set" totals for H,N and Q USER MOD "o" means original, "f" means flipped, "180deg" is methyl default USER MOD "!" flags a clash with an overlap of 0.40A or greater USER MOD flip categories: "K"=keep, "C"=clashes, "X"=uncertain, "F"=flip USER MOD Single : B 3 ASN :FLIP amide:sc= -4.98! C(o=-12!,f=-5!) USER MOD Single : B 4 HIS :FLIP no HD1:sc= 0.634 F(o=-2.1!,f=0.63) USER MOD Single : B 9 GLN :FLIP amide:sc= 0.716 F(o=-4.8!,f=0.72) USER MOD ----------------------------------------------------------------- ATOM 800 N ASN B 3 6.076 89.982 59.411 1.00 4.63 N ATOM 801 CA ASN B 3 5.450 88.943 60.224 1.00 4.43 C ATOM 802 C ASN B 3 5.198 89.487 61.636 1.00 4.66 C ATOM 803 O ASN B 3 4.110 89.265 62.214 1.00 4.93 O ATOM 804 CB ASN B 3 6.341 87.684 60.206 1.00 4.34 C ATOM 805 CG ASN B 3 5.632 86.451 60.747 1.00 3.94 C ATOM 806 OD1 ASN B 3 6.138 85.324 60.640 1.00 2.54 O flip ATOM 807 ND2 ASN B 3 4.447 86.658 61.332 1.00 4.44 N flip ATOM 0 HA ASN B 3 4.594 88.700 59.838 1.00 4.43 H new ATOM 0 HB2 ASN B 3 6.632 87.512 59.297 1.00 4.34 H new ATOM 0 HB3 ASN B 3 7.138 87.850 60.733 1.00 4.34 H new ATOM 0 HD21 ASN B 3 4.004 85.995 61.653 1.00 4.44 H new ATOM 0 HD22 ASN B 3 4.128 87.455 61.387 1.00 4.44 H new ATOM 1837 N HIS B 4 6.171 90.222 62.163 1.00 2.00 N ATOM 1838 CA HIS B 4 6.033 90.827 63.489 1.00 2.00 C ATOM 1839 C HIS B 4 4.816 91.761 63.577 1.00 2.00 C ATOM 1840 O HIS B 4 4.170 91.880 64.649 1.00 2.00 O ATOM 1841 CB HIS B 4 7.265 91.675 63.832 1.00 2.00 C ATOM 1842 CG HIS B 4 8.531 90.890 63.957 1.00 2.00 C ATOM 1843 ND1 HIS B 4 8.652 89.803 64.797 1.00 2.00 N flip ATOM 1844 CD2 HIS B 4 9.736 91.040 63.360 1.00 2.00 C flip ATOM 1845 CE1 HIS B 4 9.881 89.327 64.720 1.00 2.00 C flip ATOM 1846 NE2 HIS B 4 10.556 90.054 63.850 1.00 2.00 N flip ATOM 0 H HIS B 4 6.920 90.384 61.772 1.00 2.00 H new ATOM 0 HA HIS B 4 5.899 90.100 64.117 1.00 2.00 H new ATOM 0 HB2 HIS B 4 7.382 92.351 63.147 1.00 2.00 H new ATOM 0 HB3 HIS B 4 7.102 92.142 64.667 1.00 2.00 H new ATOM 0 HD2 HIS B 4 9.966 91.690 62.735 1.00 2.00 H new ATOM 0 HE1 HIS B 4 10.215 88.602 65.198 1.00 2.00 H new ATOM 0 HE2 HIS B 4 11.377 89.930 63.625 1.00 2.00 H new ATOM 151 N ARG B 5 4.459 92.414 62.487 1.00 18.73 N ATOM 152 CA ARG B 5 3.320 93.335 62.497 1.00 19.66 C ATOM 153 C ARG B 5 2.032 92.680 62.014 1.00 19.66 C ATOM 154 O ARG B 5 0.950 93.273 62.111 1.00 21.95 O ATOM 155 CB ARG B 5 3.638 94.541 61.601 1.00 23.29 C ATOM 156 CG ARG B 5 4.881 95.354 62.034 1.00 23.24 C ATOM 157 CD ARG B 5 5.365 96.251 60.910 1.00 29.00 C ATOM 158 NE ARG B 5 6.449 97.202 61.226 1.00 32.94 N ATOM 159 CZ ARG B 5 7.728 96.894 61.473 1.00 34.16 C ATOM 160 NH1 ARG B 5 8.157 95.628 61.480 1.00 30.53 N ATOM 161 NH2 ARG B 5 8.606 97.884 61.648 1.00 35.22 N ATOM 0 H ARG B 5 4.857 92.344 61.728 1.00 18.73 H new ATOM 0 HA ARG B 5 3.179 93.612 63.416 1.00 19.66 H new ATOM 0 HB2 ARG B 5 3.771 94.228 60.693 1.00 23.29 H new ATOM 0 HB3 ARG B 5 2.868 95.131 61.588 1.00 23.29 H new ATOM 0 HG2 ARG B 5 4.664 95.893 62.811 1.00 23.24 H new ATOM 0 HG3 ARG B 5 5.592 94.749 62.298 1.00 23.24 H new ATOM 0 HD2 ARG B 5 5.664 95.685 60.181 1.00 29.00 H new ATOM 0 HD3 ARG B 5 4.606 96.758 60.582 1.00 29.00 H new ATOM 0 HE ARG B 5 6.238 98.035 61.254 1.00 32.94 H new ATOM 0 HH11 ARG B 5 7.606 94.986 61.323 1.00 30.53 H new ATOM 0 HH12 ARG B 5 8.984 95.455 61.641 1.00 30.53 H new ATOM 0 HH21 ARG B 5 8.346 98.702 61.601 1.00 35.22 H new ATOM 0 HH22 ARG B 5 9.432 97.703 61.808 1.00 35.22 H new ATOM 112 N GLN B 9 10.186 91.359 59.521 1.00 15.79 N ATOM 113 CA GLN B 9 9.578 92.637 59.819 1.00 18.37 C ATOM 114 C GLN B 9 8.076 92.653 59.539 1.00 17.17 C ATOM 115 O GLN B 9 7.278 93.226 60.303 1.00 16.99 O ATOM 116 CB GLN B 9 10.229 93.787 59.068 1.00 19.44 C ATOM 117 CG GLN B 9 11.591 94.142 59.641 1.00 24.67 C ATOM 118 CD GLN B 9 11.455 94.628 61.084 0.00 27.67 C ATOM 119 NE2 GLN B 9 11.988 94.028 62.025 1.00 31.74 O flip ATOM 120 OE1 GLN B 9 10.723 95.704 61.263 1.00 31.80 N flip ATOM 0 HA GLN B 9 9.701 92.785 60.770 1.00 18.37 H new ATOM 0 HB2 GLN B 9 10.324 93.549 58.133 1.00 19.44 H new ATOM 0 HB3 GLN B 9 9.651 94.565 59.105 1.00 19.44 H new ATOM 0 HG2 GLN B 9 12.173 93.367 59.608 1.00 24.67 H new ATOM 0 HG3 GLN B 9 12.006 94.831 59.099 1.00 24.67 H new ATOM 0 HE21 GLN B 9 12.462 93.326 61.874 1.00 31.74 H new ATOM 0 HE22 GLN B 9 11.885 94.312 62.830 1.00 31.74 H new HETATM 7573 O HOH B 407 6.633 88.635 66.643 1.00 11.41 O HETATM 7693 O HOH B 527 3.491 85.743 61.660 1.00 4.12 O ''' nuc_answer = '''\ USER MOD reduce.3.3.160422 H: found=0, std=0, add=33, rem=0, adj=3 USER MOD ----------------------------------------------------------------- USER MOD scores for adjustable sidechains, with "set" totals for H,N and Q USER MOD "o" means original, "f" means flipped, "180deg" is methyl default USER MOD "!" flags a clash with an overlap of 0.40A or greater USER MOD flip categories: "K"=keep, "C"=clashes, "X"=uncertain, "F"=flip USER MOD Single : B 3 ASN :FLIP amide:sc= -4.08! C(o=-13!,f=-4.1!) USER MOD Single : B 4 HIS :FLIP no HE2:sc= 0.911 F(o=-2.8!,f=0.91) USER MOD Single : B 9 GLN :FLIP amide:sc= 0.688 F(o=-5.3!,f=0.69) USER MOD ----------------------------------------------------------------- ATOM 800 N ASN B 3 6.076 89.982 59.411 1.00 4.63 N ATOM 801 CA ASN B 3 5.450 88.943 60.224 1.00 4.43 C ATOM 802 C ASN B 3 5.198 89.487 61.636 1.00 4.66 C ATOM 803 O ASN B 3 4.110 89.265 62.214 1.00 4.93 O ATOM 804 CB ASN B 3 6.341 87.684 60.206 1.00 4.34 C ATOM 805 CG ASN B 3 5.632 86.451 60.747 1.00 3.94 C ATOM 806 OD1 ASN B 3 6.138 85.324 60.640 1.00 2.54 O flip ATOM 807 ND2 ASN B 3 4.447 86.658 61.332 1.00 4.44 N flip ATOM 0 HA ASN B 3 4.488 88.669 59.790 1.00 4.43 H new ATOM 0 HB2 ASN B 3 6.668 87.491 59.184 1.00 4.34 H new ATOM 0 HB3 ASN B 3 7.237 87.871 60.798 1.00 4.34 H new ATOM 0 HD21 ASN B 3 3.921 85.871 61.713 1.00 4.44 H new ATOM 0 HD22 ASN B 3 4.069 87.603 61.397 1.00 4.44 H new ATOM 1837 N HIS B 4 6.171 90.222 62.163 1.00 2.00 N ATOM 1838 CA HIS B 4 6.033 90.827 63.489 1.00 2.00 C ATOM 1839 C HIS B 4 4.816 91.761 63.577 1.00 2.00 C ATOM 1840 O HIS B 4 4.170 91.880 64.649 1.00 2.00 O ATOM 1841 CB HIS B 4 7.265 91.675 63.832 1.00 2.00 C ATOM 1842 CG HIS B 4 8.531 90.890 63.957 1.00 2.00 C ATOM 1843 ND1 HIS B 4 8.652 89.803 64.797 1.00 2.00 N flip ATOM 1844 CD2 HIS B 4 9.736 91.040 63.360 1.00 2.00 C flip ATOM 1845 CE1 HIS B 4 9.881 89.327 64.720 1.00 2.00 C flip ATOM 1846 NE2 HIS B 4 10.556 90.054 63.850 1.00 2.00 N flip ATOM 0 H HIS B 4 7.059 90.414 61.699 1.00 2.00 H new ATOM 0 HA HIS B 4 5.883 90.010 64.195 1.00 2.00 H new ATOM 0 HB2 HIS B 4 7.396 92.434 63.062 1.00 2.00 H new ATOM 0 HB3 HIS B 4 7.082 92.200 64.770 1.00 2.00 H new ATOM 0 HD1 HIS B 4 7.909 89.426 65.386 1.00 2.00 H new ATOM 0 HD2 HIS B 4 10.003 91.795 62.635 1.00 2.00 H new ATOM 0 HE1 HIS B 4 10.268 88.485 65.275 1.00 2.00 H new ATOM 151 N ARG B 5 4.459 92.414 62.487 1.00 18.73 N ATOM 152 CA ARG B 5 3.320 93.335 62.497 1.00 19.66 C ATOM 153 C ARG B 5 2.032 92.680 62.014 1.00 19.66 C ATOM 154 O ARG B 5 0.950 93.273 62.111 1.00 21.95 O ATOM 155 CB ARG B 5 3.638 94.541 61.601 1.00 23.29 C ATOM 156 CG ARG B 5 4.881 95.354 62.034 1.00 23.24 C ATOM 157 CD ARG B 5 5.365 96.251 60.910 1.00 29.00 C ATOM 158 NE ARG B 5 6.449 97.202 61.226 1.00 32.94 N ATOM 159 CZ ARG B 5 7.728 96.894 61.473 1.00 34.16 C ATOM 160 NH1 ARG B 5 8.157 95.628 61.480 1.00 30.53 N ATOM 161 NH2 ARG B 5 8.606 97.884 61.648 1.00 35.22 N ATOM 0 H ARG B 5 4.932 92.330 61.587 1.00 18.73 H new ATOM 0 HA ARG B 5 3.162 93.646 63.530 1.00 19.66 H new ATOM 0 HB2 ARG B 5 3.787 94.189 60.580 1.00 23.29 H new ATOM 0 HB3 ARG B 5 2.773 95.204 61.586 1.00 23.29 H new ATOM 0 HG2 ARG B 5 4.638 95.959 62.907 1.00 23.24 H new ATOM 0 HG3 ARG B 5 5.679 94.674 62.330 1.00 23.24 H new ATOM 0 HD2 ARG B 5 5.701 95.615 60.091 1.00 29.00 H new ATOM 0 HD3 ARG B 5 4.512 96.821 60.541 1.00 29.00 H new ATOM 0 HE ARG B 5 6.199 98.190 61.259 1.00 32.94 H new ATOM 0 HH11 ARG B 5 7.504 94.867 61.294 1.00 30.53 H new ATOM 0 HH12 ARG B 5 9.138 95.423 61.671 1.00 30.53 H new ATOM 0 HH21 ARG B 5 8.298 98.855 61.593 1.00 35.22 H new ATOM 0 HH22 ARG B 5 9.585 97.670 61.837 1.00 35.22 H new ATOM 112 N GLN B 9 10.186 91.359 59.521 1.00 15.79 N ATOM 113 CA GLN B 9 9.578 92.637 59.819 1.00 18.37 C ATOM 114 C GLN B 9 8.076 92.653 59.539 1.00 17.17 C ATOM 115 O GLN B 9 7.278 93.226 60.303 1.00 16.99 O ATOM 116 CB GLN B 9 10.229 93.787 59.068 1.00 19.44 C ATOM 117 CG GLN B 9 11.591 94.142 59.641 1.00 24.67 C ATOM 118 CD GLN B 9 11.455 94.628 61.084 0.00 27.67 C ATOM 119 NE2 GLN B 9 11.988 94.028 62.025 1.00 31.74 O flip ATOM 120 OE1 GLN B 9 10.723 95.704 61.263 1.00 31.80 N flip ATOM 0 HA GLN B 9 9.716 92.803 60.887 1.00 18.37 H new ATOM 0 HB2 GLN B 9 10.336 93.519 58.017 1.00 19.44 H new ATOM 0 HB3 GLN B 9 9.579 94.661 59.109 1.00 19.44 H new ATOM 0 HG2 GLN B 9 12.245 93.271 59.604 1.00 24.67 H new ATOM 0 HG3 GLN B 9 12.057 94.917 59.032 1.00 24.67 H new ATOM 0 HE21 GLN B 9 12.550 93.196 61.846 1.00 31.74 H new ATOM 0 HE22 GLN B 9 11.866 94.365 62.980 1.00 31.74 H new HETATM 7573 O HOH B 407 6.633 88.635 66.643 1.00 11.41 O HETATM 7693 O HOH B 527 3.491 85.743 61.660 1.00 4.12 O ''' #theoretically this should flip when symmetry is detected sym_flip = ''' CRYST1 14.000 11.000 14.000 90.00 90.00 90.00 P 21 21 21 8 ATOM 1837 N HIS B 4 0.0 -1.090 1.356 1.00 2.00 N ATOM 1838 CA HIS B 4 0.0 -0.537 0.00 1.00 2.00 C ATOM 1839 C HIS B 4 0.0 1.000 0.0 1.00 2.00 C ATOM 1840 O HIS B 4 0.588 1.645 -0.904 1.00 2.00 O ATOM 1841 CB HIS B 4 -1.212 -1.046 -0.789 1.00 2.00 C ATOM 1842 CG HIS B 4 -1.164 -2.506 -1.107 1.00 2.00 C ATOM 1843 ND1 HIS B 4 -2.193 -3.37 -0.7915 1.00 2.00 N ATOM 1844 CD2 HIS B 4 -0.225 -3.252 -1.734 1.00 2.00 C ATOM 1845 CE1 HIS B 4 -1.880 -4.586 -1.198 1.00 2.00 C ATOM 1846 NE2 HIS B 4 -0.696 -4.541 -1.781 1.00 2.00 N HETATM 7693 O HOH B 527 -2.263 -7.663 -4.291 1.00 4.12 O ''' class TestReduce(unittest.TestCase) : def test_default_reduce(self) : args = [reduce_exe,'-q','-DB',het_dict_path,'-'] pop = subprocess.Popen(args,stdout=subprocess.PIPE,stdin=subprocess.PIPE) out = pop.communicate(input=default_pdb_str)[0] #fle = open('default_reduce.pdb','w') #fle.write(out) #fle.close() self.assertEqual(out,default_answer) def test_flip_reduce(self) : args = [reduce_exe,'-q','-flip','-DB',het_dict_path,'-'] pop = subprocess.Popen(args,stdout=subprocess.PIPE,stdin=subprocess.PIPE) out = pop.communicate(input=flip_test_str)[0] #fle = open('flip_reduce.pdb','w') #fle.write(out) #fle.close() self.assertEqual(out,flip_answer) def test_nuc_reduce(self) : args = [reduce_exe,'-q','-nuc','-flip','-DB',het_dict_path,'-'] pop = subprocess.Popen(args,stdout=subprocess.PIPE,stdin=subprocess.PIPE) out = pop.communicate(input=flip_test_str)[0] #fle = open('nuc_reduce.pdb','w') #fle.write(out) #fle.close() self.assertEqual(out,nuc_answer) self.assertNotEqual(out,flip_answer) if __name__ == '__main__' : unittest.main() #suite = unittest.TestLoader().loadTestsFromTestCase(TestReduce) #unittest.TextTestRunner(verbosity=2).run(suite)