from __future__ import absolute_import, division, print_function from cctbx.array_family import flex from mmtbx.geometry_restraints import c_beta import mmtbx.model import iotbx pdb_str_1 = """\ CRYST1 26.960 29.455 29.841 90.00 90.00 90.00 P 21 21 21 ATOM 1 N TYR A 20 10.702 10.331 8.954 1.00 23.81 N ATOM 2 CA TYR A 20 11.170 9.547 7.817 1.00 35.69 C ATOM 3 C TYR A 20 10.082 8.601 7.319 1.00 28.94 C ATOM 4 O TYR A 20 9.756 7.616 7.982 1.00 25.26 O ATOM 5 CB TYR A 20 12.426 8.758 8.192 1.00 33.37 C ATOM 6 CG TYR A 20 13.016 7.958 7.052 1.00 31.48 C ATOM 7 CD1 TYR A 20 13.847 8.558 6.115 1.00 36.91 C ATOM 8 CD2 TYR A 20 12.747 6.602 6.916 1.00 21.36 C ATOM 9 CE1 TYR A 20 14.389 7.832 5.071 1.00 36.56 C ATOM 10 CE2 TYR A 20 13.285 5.868 5.875 1.00 29.56 C ATOM 11 CZ TYR A 20 14.105 6.487 4.957 1.00 35.08 C ATOM 12 OH TYR A 20 14.644 5.760 3.920 1.00 38.73 O ATOM 13 N ARG A 21 9.530 8.915 6.149 1.00 38.95 N ATOM 14 CA ARG A 21 8.473 8.118 5.525 1.00 38.77 C ATOM 15 C ARG A 21 7.250 7.963 6.428 1.00 27.69 C ATOM 16 O ARG A 21 7.134 6.992 7.176 1.00 22.82 O ATOM 17 CB ARG A 21 9.004 6.747 5.093 1.00 20.00 C ATOM 18 CG ARG A 21 8.015 5.920 4.285 1.00 20.00 C ATOM 19 CD ARG A 21 8.608 4.577 3.893 1.00 20.00 C ATOM 20 NE ARG A 21 7.671 3.771 3.116 1.00 20.00 N ATOM 21 CZ ARG A 21 7.939 2.556 2.649 1.00 20.00 C ATOM 22 NH1 ARG A 21 9.121 2.001 2.879 1.00 20.00 N ATOM 23 NH2 ARG A 21 7.025 1.895 1.951 1.00 20.00 N ATOM 24 N GLY A 22 6.340 8.929 6.351 1.00 24.85 N ATOM 25 CA GLY A 22 5.132 8.903 7.154 1.00 29.53 C ATOM 26 C GLY A 22 5.373 9.358 8.580 1.00 33.22 C ATOM 27 O GLY A 22 5.196 10.531 8.906 1.00 30.06 O """ pdb_str_2 = """\ CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1 ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C ATOM 538 HA GLU B 3 8.761 12.248 22.034 1.00 20.00 H ATOM 539 H AGLU B 3 7.474 10.360 20.122 0.50 20.00 H ATOM 540 D BGLU B 3 7.474 10.360 20.122 0.50 20.00 D """ pdb_str_3 = """\ CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1 ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N ATOM 534 CA AGLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 534 CA BGLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C """ pdb_str_4 = """\ CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1 ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N ATOM 534 CA AGLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C """ pdb_str_5 = """\ ATOM 1 N DAL A 1 -1.425 -0.261 -0.246 1.00 20.00 A N ATOM 2 CA DAL A 1 0.026 -0.261 -0.246 1.00 20.00 A C ATOM 3 CB DAL A 1 0.535 -0.261 1.194 1.00 20.00 A C ATOM 4 C DAL A 1 0.535 0.986 -0.965 1.00 20.00 A C ATOM 5 O DAL A 1 1.425 0.883 -1.851 1.00 20.00 A O ATOM 6 OXT DAL A 1 0.066 2.117 -0.674 1.00 20.00 A O-1 """ pdb_str_6 = """ ATOM 1 N ALA A 1 -1.425 -0.261 -0.246 1.00 20.00 A N ATOM 2 CA ALA A 1 0.026 -0.261 -0.246 1.00 20.00 A C ATOM 3 CB ALA A 1 0.535 -0.261 1.194 1.00 20.00 A C ATOM 4 C ALA A 1 0.535 0.986 -0.965 1.00 20.00 A C ATOM 5 O ALA A 1 1.425 0.883 -1.851 1.00 20.00 A O ATOM 6 OXT ALA A 1 0.066 2.117 -0.674 1.00 20.00 A O-1 """ pdb_str_7 = """ CRYST1 405.833 405.833 236.667 90.00 90.00 90.00 P 1 ATOM 10021 N ALA E1273 302.855 197.287 175.926 1.00 96.14 N ATOM 10022 CA ALA E1273 303.086 195.852 176.039 1.00 96.14 C ATOM 10023 C ALA E1273 303.598 195.351 174.696 1.00 96.14 C ATOM 10024 O ALA E1273 303.769 196.123 173.749 1.00 96.14 O ATOM 10025 CB ALA E1273 301.819 195.120 176.456 1.00174.39 C ATOM 10026 N HIS E1274 303.840 194.045 174.612 1.00 96.33 N ATOM 10027 CA HIS E1274 304.277 193.409 173.371 1.00 96.33 C ATOM 10028 C HIS E1274 303.842 191.944 173.370 1.00 96.33 C ATOM 10029 O HIS E1274 303.670 191.358 174.436 1.00 96.33 O ATOM 10030 CB HIS E1274 305.794 193.523 173.216 1.00174.39 C ATOM 10031 CG HIS E1274 306.463 192.245 172.818 1.00174.39 C ATOM 10032 ND1 HIS E1274 306.808 191.271 173.730 1.00174.39 N ATOM 10033 CD2 HIS E1274 306.848 191.779 171.606 1.00174.39 C ATOM 10034 CE1 HIS E1274 307.379 190.261 173.098 1.00174.39 C ATOM 10035 NE2 HIS E1274 307.416 190.544 171.809 1.00174.39 N ATOM 10036 N ARG E1275 303.671 191.339 172.195 1.00 96.53 N ATOM 10037 CA ARG E1275 303.301 189.931 172.174 1.00 96.53 C ATOM 10038 C ARG E1275 304.315 189.194 173.039 1.00 96.53 C ATOM 10039 O ARG E1275 305.308 188.665 172.530 1.00 96.53 O ATOM 10040 CB ARG E1275 303.279 189.375 170.749 1.00174.39 C ATOM 10041 N UNK E1276 304.062 189.142 174.347 1.00 95.20 N ATOM 10042 CA UNK E1276 305.103 188.914 175.332 1.00 95.20 C ATOM 10043 C UNK E1276 305.569 187.487 175.535 1.00 95.20 C ATOM 10044 O UNK E1276 305.814 187.071 176.671 1.00 95.20 O ATOM 10045 CB UNK E1276 304.640 189.472 176.669 1.00161.31 C ATOM 10046 N UNK E1277 305.690 186.727 174.455 1.00 94.99 N ATOM 10047 CA UNK E1277 306.151 185.349 174.528 1.00 94.99 C ATOM 10048 C UNK E1277 306.888 185.034 173.233 1.00 94.99 C ATOM 10049 O UNK E1277 307.382 185.940 172.554 1.00 94.99 O ATOM 10050 CB UNK E1277 304.991 184.389 174.752 1.00161.31 C TER END """ def exercise_1(): pdb_inp = iotbx.pdb.input(lines=flex.std_string(pdb_str_1.splitlines()), source_info=None) model = mmtbx.model.manager(model_input = pdb_inp) model.process(make_restraints=True) grm = model.get_restraints_manager().geometry pdb_hierarchy = model.get_hierarchy() sites_cart = model.get_sites_cart() # c-beta restraints are added by default!!! assert len(grm.get_c_beta_torsion_proxies()) == 4 #test global selection and removing c-beta restraints tst_boolsel = pdb_hierarchy.atom_selection_cache().selection("resname TYR") tst_iselection = tst_boolsel.iselection() #test global selection grm2 = grm.select(iselection=tst_iselection) assert len(grm2.get_c_beta_torsion_proxies()) == 2 grm2 = grm.select(selection=tst_boolsel) assert len(grm2.get_c_beta_torsion_proxies()) == 2 #remove a selection grm.remove_c_beta_torsion_restraints_in_place(selection=tst_iselection) assert len(grm.get_c_beta_torsion_proxies()) == 2 #add a selection grm.remove_c_beta_torsion_restraints_in_place() assert len(grm.get_c_beta_torsion_proxies()) == 0 c_beta_torsion_proxies = c_beta.get_c_beta_torsion_proxies( pdb_hierarchy, selection=tst_iselection, sigma=2.5) assert len(c_beta_torsion_proxies) == 2 def exercise_2(): """ Testing with ACs """ pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_2).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 2 pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_3).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 4 pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_4).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 2 def exercise_3(): """ Testing d-peptide """ pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_5).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 0 assert len(c_beta_skip.get("d-peptide", []))==1 assert len(c_beta_skip.get("-ve", []))==0 pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_6).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert len(c_beta_restrs) == 0 assert len(c_beta_skip.get("d-peptide", []))==0 assert len(c_beta_skip.get("-ve", []))==1 def exercise_4(): """ Testing UNK to be equivalent to ALA """ pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_7).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert c_beta_restrs.size()==10 assert c_beta_skip == {} # pdb_h = iotbx.pdb.input( source_info=None, lines=pdb_str_7.replace("UNK","ALA")).construct_hierarchy() c_beta_restrs, c_beta_skip = c_beta.get_c_beta_torsion_proxies(pdb_h) assert c_beta_restrs.size()==10 assert c_beta_skip == {} if (__name__ == "__main__"): exercise_1() exercise_2() exercise_3() exercise_4() print("OK")