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 pdb_str = """\ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 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 """ def exercise_no_sidechains(prefix="tst_one_resid_rotation_no_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()) s = model.selection("name N or name CA or name C or name O") model = model.select(s) ci = cablam_idealization(model = model, params=master_phil.extract().cablam_idealization, log=sys.stdout) pdb_txt = model.model_as_pdb() def exercise_yes_sidechains(prefix="tst_one_resid_rotation_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()