from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.model from mmtbx.building.cablam_idealization import cablam_idealization, master_phil import sys import libtbx.load_env ss_1aon = """\ SHEET 1 D 3 MET A 193 PHE A 195 0 SHEET 2 D 3 THR A 330 ILE A 332 -1 N ILE A 332 O MET A 193 SHEET 3 D 3 VAL A 323 ILE A 325 -1 N VAL A 324 O THR A 331 """ ss_phenix = """\ SHEET 1 C 2 VAL A 323 ASN A 326 0 SHEET 2 C 2 THR A 329 ILE A 332 -1 O THR A 331 N VAL A 324 """ pdb_str = """\ CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 ATOM 1361 N VAL A 190 180.789 103.980 72.202 1.00121.81 N ATOM 1362 CA VAL A 190 179.994 104.660 71.186 1.00133.83 C ATOM 1363 C VAL A 190 180.110 106.158 71.432 1.00156.81 C ATOM 1364 O VAL A 190 180.495 106.598 72.517 1.00196.34 O ATOM 1365 CB VAL A 190 178.524 104.204 71.198 1.00 96.01 C ATOM 1366 CG1 VAL A 190 177.849 104.682 72.446 1.00118.41 C ATOM 1367 CG2 VAL A 190 177.794 104.682 69.960 1.00 96.01 C ATOM 1368 N GLU A 191 179.779 106.947 70.414 1.00168.27 N ATOM 1369 CA GLU A 191 180.167 108.351 70.413 1.00180.29 C ATOM 1370 C GLU A 191 179.043 109.249 70.910 1.00152.32 C ATOM 1371 O GLU A 191 178.000 109.369 70.267 1.00152.32 O ATOM 1372 CB GLU A 191 180.583 108.775 69.010 1.00214.56 C ATOM 1373 CG GLU A 191 181.784 108.024 68.439 1.00248.72 C ATOM 1374 CD GLU A 191 183.031 108.128 69.299 1.00239.34 C ATOM 1375 OE1 GLU A 191 183.268 109.204 69.893 1.00224.38 O ATOM 1376 OE2 GLU A 191 183.785 107.132 69.366 1.00218.48 O ATOM 1377 N GLY A 192 179.283 109.909 72.039 1.00190.08 N ATOM 1378 CA GLY A 192 178.378 110.877 72.631 1.00151.92 C ATOM 1379 C GLY A 192 179.177 111.867 73.451 1.00151.92 C ATOM 1380 O GLY A 192 180.405 111.763 73.491 1.00173.70 O ATOM 1381 N MET A 193 178.533 112.823 74.114 1.00141.34 N ATOM 1382 CA MET A 193 179.325 113.903 74.691 1.00144.10 C ATOM 1383 C MET A 193 179.366 113.927 76.210 1.00173.20 C ATOM 1384 O MET A 193 180.456 113.878 76.786 1.00176.78 O ATOM 1385 CB MET A 193 178.856 115.262 74.186 1.00193.39 C ATOM 1386 CG MET A 193 179.696 116.389 74.760 1.00195.75 C ATOM 1387 SD MET A 193 179.453 117.985 73.974 1.00281.89 S ATOM 1388 CE MET A 193 180.418 117.738 72.488 1.00157.97 C ATOM 1389 N GLN A 194 178.210 114.050 76.862 1.00187.33 N ATOM 1390 CA GLN A 194 178.165 114.307 78.300 1.00191.17 C ATOM 1391 C GLN A 194 178.790 115.645 78.661 1.00149.29 C ATOM 1392 O GLN A 194 179.935 115.711 79.113 1.00149.29 O ATOM 1393 CB GLN A 194 178.859 113.193 79.090 1.00211.88 C ATOM 1394 CG GLN A 194 178.874 113.421 80.594 1.00205.55 C ATOM 1395 CD GLN A 194 177.506 113.379 81.191 1.00174.59 C ATOM 1396 OE1 GLN A 194 176.865 112.339 81.197 1.00132.86 O ATOM 1397 NE2 GLN A 194 177.023 114.523 81.652 1.00189.30 N ATOM 1398 N PHE A 195 178.085 116.719 78.386 1.00125.89 N ATOM 1399 CA PHE A 195 178.445 118.003 78.948 1.00125.89 C ATOM 1400 C PHE A 195 177.667 118.197 80.242 1.00150.60 C ATOM 1401 O PHE A 195 177.061 117.259 80.764 1.00125.89 O ATOM 1402 CB PHE A 195 178.191 119.117 77.943 1.00158.30 C ATOM 1403 CG PHE A 195 176.761 119.286 77.577 1.00181.66 C ATOM 1404 CD1 PHE A 195 175.980 120.214 78.231 1.00179.67 C ATOM 1405 CD2 PHE A 195 176.191 118.520 76.582 1.00194.09 C ATOM 1406 CE1 PHE A 195 174.663 120.388 77.890 1.00157.65 C ATOM 1407 CE2 PHE A 195 174.866 118.685 76.241 1.00181.78 C ATOM 1408 CZ PHE A 195 174.101 119.618 76.897 1.00151.70 C ATOM 1409 N ASP A 196 177.704 119.420 80.776 1.00190.62 N ATOM 1410 CA ASP A 196 177.127 119.719 82.087 1.00171.67 C ATOM 1411 C ASP A 196 176.050 120.788 82.002 1.00158.10 C ATOM 1412 O ASP A 196 176.309 121.922 81.594 1.00155.93 O ATOM 1413 CB ASP A 196 178.182 120.170 83.080 1.00219.72 C ATOM 1414 CG ASP A 196 177.591 120.440 84.449 1.00192.59 C ATOM 1415 OD1 ASP A 196 176.393 120.147 84.661 1.00175.54 O ATOM 1416 OD2 ASP A 196 178.320 120.964 85.312 1.00205.97 O ATOM 1417 N ARG A 197 174.860 120.418 82.445 1.00165.07 N ATOM 1418 CA ARG A 197 173.754 121.323 82.706 1.00155.71 C ATOM 1419 C ARG A 197 172.696 120.470 83.385 1.00155.71 C ATOM 1420 O ARG A 197 172.934 119.301 83.688 1.00186.86 O ATOM 1421 CB ARG A 197 173.262 121.990 81.422 1.00126.62 C ATOM 1422 CG ARG A 197 172.280 123.113 81.630 1.00162.31 C ATOM 1423 CD ARG A 197 172.919 124.202 82.445 1.00126.62 C ATOM 1424 NE ARG A 197 174.099 124.734 81.779 1.00130.61 N ATOM 1425 CZ ARG A 197 174.882 125.674 82.293 1.00150.12 C ATOM 1426 NH1 ARG A 197 174.599 126.197 83.475 1.00193.70 N ATOM 1427 NH2 ARG A 197 175.941 126.099 81.621 1.00132.73 N ATOM 2327 N GLY A 318 169.195 115.930 63.690 1.00216.32 N ATOM 2328 CA GLY A 318 169.975 114.907 64.348 1.00193.16 C ATOM 2329 C GLY A 318 169.246 113.598 64.539 1.00197.19 C ATOM 2330 O GLY A 318 168.148 113.399 64.016 1.00193.16 O ATOM 2331 N GLN A 319 169.849 112.700 65.308 1.00184.03 N ATOM 2332 CA GLN A 319 169.232 111.415 65.589 1.00195.95 C ATOM 2333 C GLN A 319 169.246 111.137 67.080 1.00193.64 C ATOM 2334 O GLN A 319 168.185 111.047 67.708 1.00229.34 O ATOM 2335 CB GLN A 319 169.941 110.308 64.822 1.00201.09 C ATOM 2336 CG GLN A 319 169.719 110.407 63.336 1.00236.37 C ATOM 2337 CD GLN A 319 168.255 110.312 62.966 1.00254.36 C ATOM 2338 OE1 GLN A 319 167.506 109.520 63.536 1.00280.71 O ATOM 2339 NE2 GLN A 319 167.836 111.126 62.007 1.00220.80 N ATOM 2340 N ALA A 320 170.446 111.006 67.646 1.00140.99 N ATOM 2341 CA ALA A 320 170.595 110.942 69.090 1.00197.51 C ATOM 2342 C ALA A 320 169.906 109.734 69.704 1.00203.65 C ATOM 2343 O ALA A 320 168.789 109.863 70.203 1.00242.54 O ATOM 2344 CB ALA A 320 170.069 112.226 69.727 1.00240.45 C ATOM 2345 N LYS A 321 170.554 108.566 69.662 1.00164.18 N ATOM 2346 CA LYS A 321 169.963 107.306 70.104 1.00134.95 C ATOM 2347 C LYS A 321 169.103 107.477 71.344 1.00134.95 C ATOM 2348 O LYS A 321 167.904 107.194 71.302 1.00134.95 O ATOM 2349 CB LYS A 321 171.040 106.265 70.421 1.00145.47 C ATOM 2350 CG LYS A 321 171.950 105.868 69.279 1.00164.10 C ATOM 2351 CD LYS A 321 171.197 105.229 68.138 1.00145.47 C ATOM 2352 CE LYS A 321 172.173 104.777 67.070 1.00145.80 C ATOM 2353 NZ LYS A 321 171.487 104.149 65.918 1.00145.93 N ATOM 2354 N ARG A 322 169.682 107.900 72.454 1.00185.62 N ATOM 2355 CA ARG A 322 168.888 108.089 73.652 1.00142.57 C ATOM 2356 C ARG A 322 169.546 109.124 74.551 1.00128.56 C ATOM 2357 O ARG A 322 170.758 109.341 74.474 1.00128.56 O ATOM 2358 CB ARG A 322 168.719 106.769 74.369 1.00115.16 C ATOM 2359 CG ARG A 322 167.669 106.817 75.430 1.00133.21 C ATOM 2360 CD ARG A 322 167.578 105.605 76.270 1.00149.50 C ATOM 2361 NE ARG A 322 168.665 105.482 77.219 1.00115.16 N ATOM 2362 CZ ARG A 322 168.912 104.370 77.883 1.00115.16 C ATOM 2363 NH1 ARG A 322 168.133 103.302 77.715 1.00116.90 N ATOM 2364 NH2 ARG A 322 169.915 104.340 78.745 1.00115.16 N ATOM 2365 N VAL A 323 168.740 109.783 75.382 1.00121.29 N ATOM 2366 CA VAL A 323 169.198 110.884 76.220 1.00121.29 C ATOM 2367 C VAL A 323 168.668 110.712 77.632 1.00139.86 C ATOM 2368 O VAL A 323 167.480 110.430 77.835 1.00121.29 O ATOM 2369 CB VAL A 323 168.795 112.246 75.654 1.00117.56 C ATOM 2370 CG1 VAL A 323 168.912 113.310 76.710 1.00151.93 C ATOM 2371 CG2 VAL A 323 169.721 112.603 74.534 1.00121.07 C ATOM 2372 N VAL A 324 169.553 110.915 78.601 1.00186.06 N ATOM 2373 CA VAL A 324 169.257 110.860 80.023 1.00145.81 C ATOM 2374 C VAL A 324 169.680 112.181 80.632 1.00137.41 C ATOM 2375 O VAL A 324 170.842 112.582 80.510 1.00178.72 O ATOM 2376 CB VAL A 324 169.998 109.700 80.699 1.00111.15 C ATOM 2377 CG1 VAL A 324 169.991 109.869 82.194 1.00111.15 C ATOM 2378 CG2 VAL A 324 169.361 108.392 80.320 1.00174.59 C ATOM 2379 N ILE A 325 168.750 112.858 81.291 1.00135.50 N ATOM 2380 CA ILE A 325 169.053 114.082 82.010 1.00135.50 C ATOM 2381 C ILE A 325 168.433 113.999 83.385 1.00169.00 C ATOM 2382 O ILE A 325 167.250 113.672 83.524 1.00221.23 O ATOM 2383 CB ILE A 325 168.540 115.326 81.277 1.00128.37 C ATOM 2384 CG1 ILE A 325 169.308 115.511 79.987 1.00157.49 C ATOM 2385 CG2 ILE A 325 168.652 116.540 82.152 1.00128.37 C ATOM 2386 CD1 ILE A 325 168.664 116.495 79.084 1.00250.18 C ATOM 2387 N ASN A 326 169.238 114.283 84.395 1.00199.74 N ATOM 2388 CA ASN A 326 168.756 114.523 85.740 1.00188.01 C ATOM 2389 C ASN A 326 168.984 115.989 86.024 1.00186.66 C ATOM 2390 O ASN A 326 169.421 116.729 85.142 1.00228.60 O ATOM 2391 CB ASN A 326 169.515 113.691 86.752 1.00191.53 C ATOM 2392 CG ASN A 326 170.974 114.019 86.751 1.00177.51 C ATOM 2393 OD1 ASN A 326 171.477 114.588 85.789 1.00181.89 O ATOM 2394 ND2 ASN A 326 171.662 113.699 87.832 1.00177.51 N ATOM 2395 N LYS A 327 168.723 116.428 87.237 1.00150.02 N ATOM 2396 CA LYS A 327 169.141 117.765 87.589 1.00152.41 C ATOM 2397 C LYS A 327 170.660 117.829 87.576 1.00183.89 C ATOM 2398 O LYS A 327 171.338 116.972 88.151 1.00182.77 O ATOM 2399 CB LYS A 327 168.573 118.168 88.941 1.00149.83 C ATOM 2400 CG LYS A 327 168.941 117.264 90.077 1.00149.83 C ATOM 2401 CD LYS A 327 168.258 117.747 91.336 1.00157.59 C ATOM 2402 CE LYS A 327 168.760 119.125 91.726 1.00149.83 C ATOM 2403 NZ LYS A 327 168.070 119.626 92.943 1.00160.60 N ATOM 2404 N ASP A 328 171.184 118.819 86.857 1.00218.03 N ATOM 2405 CA ASP A 328 172.591 119.218 86.870 1.00213.19 C ATOM 2406 C ASP A 328 173.533 118.188 86.255 1.00226.70 C ATOM 2407 O ASP A 328 174.694 118.091 86.655 1.00223.51 O ATOM 2408 CB ASP A 328 173.025 119.554 88.294 1.00211.95 C ATOM 2409 CG ASP A 328 172.325 120.779 88.820 1.00217.32 C ATOM 2410 OD1 ASP A 328 171.820 121.567 87.993 1.00181.79 O ATOM 2411 OD2 ASP A 328 172.246 120.937 90.055 1.00264.08 O ATOM 2412 N THR A 329 173.062 117.425 85.275 1.00238.65 N ATOM 2413 CA THR A 329 173.929 116.603 84.444 1.00191.16 C ATOM 2414 C THR A 329 173.151 116.297 83.171 1.00195.25 C ATOM 2415 O THR A 329 171.922 116.379 83.170 1.00197.03 O ATOM 2416 CB THR A 329 174.350 115.322 85.178 1.00198.74 C ATOM 2417 OG1 THR A 329 174.966 115.668 86.424 1.00151.38 O ATOM 2418 CG2 THR A 329 175.348 114.535 84.371 1.00227.62 C ATOM 2419 N THR A 330 173.852 115.960 82.094 1.00192.15 N ATOM 2420 CA THR A 330 173.180 115.643 80.843 1.00174.21 C ATOM 2421 C THR A 330 174.004 114.667 80.018 1.00177.58 C ATOM 2422 O THR A 330 175.235 114.683 80.064 1.00155.50 O ATOM 2423 CB THR A 330 172.912 116.904 80.037 1.00149.29 C ATOM 2424 OG1 THR A 330 172.189 116.561 78.853 1.00196.16 O ATOM 2425 CG2 THR A 330 174.209 117.553 79.663 1.00171.73 C ATOM 2426 N THR A 331 173.312 113.823 79.255 1.00154.85 N ATOM 2427 CA THR A 331 173.933 112.727 78.527 1.00139.34 C ATOM 2428 C THR A 331 173.347 112.631 77.131 1.00126.25 C ATOM 2429 O THR A 331 172.136 112.788 76.950 1.00126.25 O ATOM 2430 CB THR A 331 173.689 111.400 79.219 1.00198.41 C ATOM 2431 OG1 THR A 331 172.286 111.139 79.199 1.00216.30 O ATOM 2432 CG2 THR A 331 174.132 111.456 80.641 1.00185.45 C ATOM 2433 N ILE A 332 174.192 112.324 76.158 1.00 96.15 N ATOM 2434 CA ILE A 332 173.754 112.026 74.805 1.00 96.15 C ATOM 2435 C ILE A 332 174.531 110.821 74.318 1.00 96.15 C ATOM 2436 O ILE A 332 175.766 110.853 74.273 1.00 96.15 O ATOM 2437 CB ILE A 332 173.963 113.208 73.857 1.00 81.50 C ATOM 2438 CG1 ILE A 332 173.003 114.333 74.196 1.00 81.50 C ATOM 2439 CG2 ILE A 332 173.758 112.766 72.446 1.00106.08 C ATOM 2440 CD1 ILE A 332 173.300 115.594 73.446 1.00 81.50 C ATOM 2441 N ILE A 333 173.817 109.784 73.902 1.00140.99 N ATOM 2442 CA ILE A 333 174.460 108.513 73.612 1.00146.25 C ATOM 2443 C ILE A 333 175.126 108.570 72.252 1.00156.54 C ATOM 2444 O ILE A 333 176.350 108.684 72.164 1.00137.40 O ATOM 2445 CB ILE A 333 173.443 107.365 73.678 1.00124.68 C ATOM 2446 CG1 ILE A 333 172.994 107.169 75.120 1.00124.68 C ATOM 2447 CG2 ILE A 333 174.026 106.090 73.113 1.00124.68 C ATOM 2448 CD1 ILE A 333 171.909 106.157 75.279 1.00124.68 C ATOM 2449 N ASP A 334 174.337 108.493 71.187 1.00184.11 N ATOM 2450 CA ASP A 334 174.900 108.642 69.855 1.00191.95 C ATOM 2451 C ASP A 334 173.822 109.118 68.901 1.00201.36 C ATOM 2452 O ASP A 334 172.661 108.726 69.012 1.00169.42 O ATOM 2453 CB ASP A 334 175.500 107.328 69.352 1.00229.86 C ATOM 2454 CG ASP A 334 176.076 107.454 67.967 1.00209.90 C ATOM 2455 OD1 ASP A 334 177.073 108.185 67.807 1.00194.49 O ATOM 2456 OD2 ASP A 334 175.530 106.825 67.040 1.00201.57 O ATOM 2457 N GLY A 335 174.222 109.961 67.961 1.00230.09 N ATOM 2458 CA GLY A 335 173.372 110.262 66.835 1.00158.73 C ATOM 2459 C GLY A 335 173.912 109.583 65.604 1.00155.16 C ATOM 2460 O GLY A 335 175.061 109.134 65.593 1.00158.08 O ATOM 2461 N VAL A 336 173.117 109.523 64.548 1.00175.68 N ATOM 2462 CA VAL A 336 173.631 108.975 63.306 1.00190.55 C ATOM 2463 C VAL A 336 174.373 110.102 62.610 1.00175.68 C ATOM 2464 O VAL A 336 173.792 111.149 62.310 1.00178.92 O ATOM 2465 CB VAL A 336 172.509 108.405 62.425 1.00188.43 C ATOM 2466 CG1 VAL A 336 173.083 107.857 61.137 1.00208.89 C ATOM 2467 CG2 VAL A 336 171.737 107.334 63.172 1.00161.96 C """ def exercise_no_sidechains(prefix="tst_single_outliers_sur_no_sidechains"): pdb_inp = iotbx.pdb.input(lines=pdb_str.split('\n'), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp) s = model.selection("name N or name CA or name C or name O") model = model.select(s) with open("%s_start.pdb" % prefix, 'w') as f: f.write(model.model_as_pdb()) ci = cablam_idealization(model = model, params=master_phil.extract().cablam_idealization, log=sys.stdout) with open("%s_end.pdb" % prefix, 'w') as f: f.write(model.model_as_pdb()) def exercise_yes_sidechains(prefix="tst_single_outliers_sur_yes_sidechains"): pdb_inp = iotbx.pdb.input(lines=pdb_str.split('\n'), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp) with open("%s_start.pdb" % prefix, 'w') as f: f.write(model.model_as_pdb()) ci = cablam_idealization(model = model, params=master_phil.extract().cablam_idealization, log=sys.stdout) pdb_txt = model.model_as_pdb() if __name__ == '__main__': if (not libtbx.env.has_module(name="probe")): print("Skipping: probe not configured") else: exercise_no_sidechains() exercise_yes_sidechains()