from __future__ import absolute_import, division, print_function import sys from iotbx import pdb from six.moves import range pdb_lines = ''' ATOM 18755 N LYS N 56 48.225 62.706 -53.862 1.00 69.77 N ATOM 18756 CA LYS N 56 47.122 61.816 -53.629 1.00 70.02 C ATOM 18757 C LYS N 56 46.793 61.775 -52.151 1.00 70.49 C ATOM 18758 O LYS N 56 45.732 62.272 -51.762 1.00 70.82 O ATOM 18759 CB LYS N 56 47.445 60.405 -54.119 1.00 69.96 C ATOM 18760 CG LYS N 56 47.862 60.366 -55.558 1.00 69.09 C ATOM 18761 CD LYS N 56 46.738 60.829 -56.449 1.00 69.14 C ATOM 18762 CE LYS N 56 47.154 60.761 -57.900 1.00 68.65 C ATOM 18763 NZ LYS N 56 46.070 61.230 -58.799 1.00 67.64 N ATOM 18764 N LYS N 57 47.630 61.207 -51.295 1.00 70.59 N ATOM 18765 CA LYS N 57 47.259 61.174 -49.888 1.00 70.64 C ATOM 18766 C LYS N 57 48.216 61.977 -49.013 1.00 71.13 C ATOM 18767 O LYS N 57 47.781 62.990 -48.461 1.00 71.98 O ATOM 18768 CB LYS N 57 47.055 59.726 -49.452 1.00 70.28 C ATOM 18769 CG LYS N 57 45.619 59.278 -49.768 1.00 70.08 C ATOM 18770 CD LYS N 57 45.350 58.763 -51.161 1.00 68.27 C ATOM 18771 CE LYS N 57 43.872 58.439 -51.282 1.00 67.38 C ATOM 18772 NZ LYS N 57 43.719 57.886 -52.654 1.00 66.40 N ATOM 18773 N VAL N 58 49.522 61.811 -49.121 1.00 71.03 N ATOM 18774 CA VAL N 58 50.479 60.749 -49.246 1.00 70.78 C ATOM 18775 C VAL N 58 50.801 60.494 -47.743 1.00 70.09 C ATOM 18776 O VAL N 58 50.009 60.889 -46.880 1.00 70.44 O ATOM 18777 CB VAL N 58 51.665 61.148 -50.115 1.00 71.15 C ATOM 18778 CG1 VAL N 58 51.233 61.264 -51.566 1.00 71.41 C ATOM 18779 CG2 VAL N 58 52.289 62.461 -49.638 1.00 71.37 C ATOM 18780 N PRO N 59 51.836 59.722 -47.347 1.00 69.26 N ATOM 18781 CA PRO N 59 53.160 59.201 -46.949 1.00 68.80 C ATOM 18782 C PRO N 59 54.389 59.494 -47.837 1.00 68.33 C ATOM 18783 O PRO N 59 54.177 59.842 -48.977 1.00 68.60 O ATOM 18784 CB PRO N 59 52.909 57.680 -46.892 1.00 68.81 C ATOM 18785 CG PRO N 59 51.511 57.540 -46.598 1.00 69.03 C ATOM 18786 CD PRO N 59 50.868 58.605 -47.385 1.00 69.11 C ATOM 18787 N PHE N 60 55.619 59.124 -47.487 1.00 67.22 N ATOM 18788 CA PHE N 60 56.155 58.824 -46.158 1.00 65.75 C ATOM 18789 C PHE N 60 57.465 59.615 -46.163 1.00 65.03 C ATOM 18790 O PHE N 60 58.327 59.487 -45.292 1.00 64.85 O ATOM 18791 CB PHE N 60 56.325 57.317 -45.873 1.00 65.65 C ATOM 18792 CG PHE N 60 57.281 56.587 -46.787 1.00 65.73 C ATOM 18793 CD1 PHE N 60 56.849 56.085 -48.007 1.00 66.68 C ATOM 18794 CD2 PHE N 60 58.580 56.314 -46.380 1.00 66.05 C ATOM 18795 CE1 PHE N 60 57.713 55.378 -48.834 1.00 67.64 C ATOM 18796 CE2 PHE N 60 59.451 55.605 -47.199 1.00 67.13 C ATOM 18797 CZ PHE N 60 59.015 55.134 -48.427 1.00 67.63 C ATOM 18798 N LEU N 61 57.540 60.450 -47.206 1.00 64.08 N ATOM 18799 CA LEU N 61 58.603 61.375 -47.593 1.00 63.10 C ATOM 18800 C LEU N 61 57.880 62.245 -48.648 1.00 62.48 C ATOM 18801 O LEU N 61 56.647 62.255 -48.570 1.00 62.00 O ATOM 18802 CB LEU N 61 59.905 60.590 -47.871 1.00 62.99 C ATOM 18803 CG LEU N 61 60.257 59.711 -49.072 1.00 62.57 C ATOM 18804 CD1 LEU N 61 61.732 59.308 -49.013 1.00 62.70 C ATOM 18805 CD2 LEU N 61 59.353 58.526 -49.229 1.00 61.75 C ATOM 18806 N SER N 62 58.466 63.043 -49.565 1.00 61.91 N ATOM 18807 CA SER N 62 59.847 63.261 -50.010 1.00 61.11 C ATOM 18808 C SER N 62 60.085 64.721 -50.329 1.00 60.49 C ATOM 18809 O SER N 62 59.168 65.539 -50.236 1.00 60.11 O ATOM 18810 CB SER N 62 60.128 62.434 -51.262 1.00 60.97 C ATOM 18811 OG SER N 62 61.494 62.508 -51.606 1.00 61.00 O ''' def run(): filename = 'tst_multi.pdb' f=open(filename, 'w') f.write(pdb_lines) f.close() pdb_inp = pdb.input(filename) pdb_hierarchy = pdb_inp.construct_hierarchy() from mmtbx.conformation_dependent_library.testing_utils import \ get_geometry_restraints_manager geometry_restraints_manager = get_geometry_restraints_manager(filename) pdb_hierarchy.reset_i_seq_if_necessary() refine = [False, # -179 True, # -44 False, # 86 True, # -22 False, # -179 ] refine += [True]*5 refine += [False]*14 omegalyze = [False, False, False, True, False, ] omegalyze += [True]*3 omegalyze += [False]*16 from mmtbx.conformation_dependent_library import generate_protein_threes for i, threes in enumerate(generate_protein_threes(pdb_hierarchy, geometry_restraints_manager, cdl_class=True, #verbose=verbose, )): print(i, threes) print(' omega %5.1f' % threes.get_omega_value()) print(" cis? %-5s %s" % (threes.cis_group(), threes.cis_group(limit=30))) print(" trans? %-5s %s" % (threes.trans_group(), threes.trans_group(limit=30))) print(" rama %s" % threes.get_ramalyze_key()) print(' conf %s' % threes.is_pure_main_conf()) assert threes.cis_group()==refine[i], '%s!=%s' % (threes.cis_group(), refine[i]) assert threes.cis_group(limit=30)==omegalyze[i] for j in range(0,181,10): i+=1 print(" %3d %-5s %-8s %-5s" % ( j, threes._define_omega_a_la_duke_using_limit(j)=='cis', threes._define_omega_a_la_duke_using_limit(j, limit=30), refine[i], )) assert (threes._define_omega_a_la_duke_using_limit(j)=='cis')==refine[i] if __name__=="__main__": args = sys.argv[1:] del sys.argv[1:] run()