from __future__ import absolute_import, division, print_function from mmtbx.secondary_structure import sec_str_master_phil_str, manager import iotbx.pdb import iotbx.pdb.secondary_structure as ioss from libtbx.utils import null_out def exercise_helix_bonding_pattern_with_insertions(): alpha_h1_ends = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N ALA 1 1.643 -2.366 -1.408 1.00 0.00 N ATOM 2 CA ALA 1 1.280 -3.608 -2.069 1.00 0.00 C ATOM 3 C ALA 1 -0.114 -3.466 -2.684 1.00 0.00 C ATOM 4 O ALA 1 -0.327 -3.827 -3.840 1.00 0.00 O ATOM 5 CB ALA 1 1.361 -4.762 -1.068 1.00 0.00 C ATOM 6 N ALA 1A -1.028 -2.938 -1.882 1.00 0.00 N ATOM 7 CA ALA 1A -2.395 -2.743 -2.332 1.00 0.00 C ATOM 8 C ALA 1A -2.396 -1.855 -3.579 1.00 0.00 C ATOM 9 O ALA 1A -3.059 -2.167 -4.567 1.00 0.00 O ATOM 10 CB ALA 1A -3.228 -2.150 -1.194 1.00 0.00 C ATOM 11 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N ATOM 12 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C ATOM 13 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C ATOM 14 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O ATOM 15 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C ATOM 16 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N ATOM 17 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C ATOM 18 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C ATOM 19 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O ATOM 20 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C ATOM 21 N ALA 5 -1.184 -3.711 -6.463 1.00 0.00 N ATOM 22 CA ALA 5 -2.231 -4.619 -6.901 1.00 0.00 C ATOM 23 C ALA 5 -3.253 -3.847 -7.737 1.00 0.00 C ATOM 24 O ALA 5 -3.647 -4.296 -8.813 1.00 0.00 O ATOM 25 CB ALA 5 -2.864 -5.294 -5.683 1.00 0.00 C ATOM 26 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N ATOM 27 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C ATOM 28 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C ATOM 29 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O ATOM 30 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C ATOM 31 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 32 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 33 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 34 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 35 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 36 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 37 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 38 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 39 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 40 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 41 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 42 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 43 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 44 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 45 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 46 N ALA 9A -5.617 -2.338 -12.812 1.00 0.00 N ATOM 47 CA ALA 9A -5.879 -1.301 -13.795 1.00 0.00 C ATOM 48 C ALA 9A -5.242 -1.695 -15.130 1.00 0.00 C ATOM 49 O ALA 9A -5.880 -1.605 -16.177 1.00 0.00 O ATOM 50 CB ALA 9A -5.358 0.040 -13.274 1.00 0.00 C TER """).construct_hierarchy() alpha_h1_ac = iotbx.pdb.input(source_info=None, lines="""\ ATOM 1 N AALA 1 1.643 -2.366 -1.408 0.50 0.00 N ATOM 2 CA AALA 1 1.280 -3.608 -2.069 0.50 0.00 C ATOM 3 C AALA 1 -0.114 -3.466 -2.684 0.50 0.00 C ATOM 4 O AALA 1 -0.327 -3.827 -3.840 0.50 0.00 O ATOM 5 CB AALA 1 1.361 -4.762 -1.068 0.50 0.00 C ATOM 6 N BALA 1 1.743 -2.366 -1.408 0.50 0.00 N ATOM 7 CA BALA 1 1.380 -3.608 -2.069 0.50 0.00 C ATOM 8 C BALA 1 -0.014 -3.466 -2.684 0.50 0.00 C ATOM 9 O BALA 1 -0.227 -3.827 -3.840 0.50 0.00 O ATOM 10 CB BALA 1 1.461 -4.762 -1.068 0.50 0.00 C ATOM 11 N ALA 1A -1.028 -2.938 -1.882 1.00 0.00 N ATOM 12 CA ALA 1A -2.395 -2.743 -2.332 1.00 0.00 C ATOM 13 C ALA 1A -2.396 -1.855 -3.579 1.00 0.00 C ATOM 14 O ALA 1A -3.059 -2.167 -4.567 1.00 0.00 O ATOM 15 CB ALA 1A -3.228 -2.150 -1.194 1.00 0.00 C ATOM 16 N ALA 3 -1.646 -0.767 -3.491 1.00 0.00 N ATOM 17 CA ALA 3 -1.551 0.168 -4.599 1.00 0.00 C ATOM 18 C ALA 3 -1.044 -0.568 -5.841 1.00 0.00 C ATOM 19 O ALA 3 -1.601 -0.419 -6.927 1.00 0.00 O ATOM 20 CB ALA 3 -0.646 1.337 -4.205 1.00 0.00 C ATOM 21 N ALA 4 0.008 -1.348 -5.639 1.00 0.00 N ATOM 22 CA ALA 4 0.597 -2.109 -6.728 1.00 0.00 C ATOM 23 C ALA 4 -0.466 -3.023 -7.340 1.00 0.00 C ATOM 24 O ALA 4 -0.611 -3.085 -8.559 1.00 0.00 O ATOM 25 CB ALA 4 1.808 -2.887 -6.211 1.00 0.00 C ATOM 26 N AALA 5 -1.184 -3.711 -6.463 0.50 0.00 N ATOM 27 CA AALA 5 -2.231 -4.619 -6.901 0.50 0.00 C ATOM 28 C AALA 5 -3.253 -3.847 -7.737 0.50 0.00 C ATOM 29 O AALA 5 -3.647 -4.296 -8.813 0.50 0.00 O ATOM 30 CB AALA 5 -2.864 -5.294 -5.683 0.50 0.00 C ATOM 31 N BALA 5 -1.084 -3.711 -6.463 0.50 0.00 N ATOM 32 CA BALA 5 -2.131 -4.619 -6.901 0.50 0.00 C ATOM 33 C BALA 5 -3.153 -3.847 -7.737 0.50 0.00 C ATOM 34 O BALA 5 -3.547 -4.296 -8.813 0.50 0.00 O ATOM 35 CB BALA 5 -2.764 -5.294 -5.683 0.50 0.00 C ATOM 36 N ALA 6 -3.654 -2.699 -7.211 1.00 0.00 N ATOM 37 CA ALA 6 -4.623 -1.860 -7.896 1.00 0.00 C ATOM 38 C ALA 6 -4.090 -1.499 -9.284 1.00 0.00 C ATOM 39 O ALA 6 -4.809 -1.602 -10.276 1.00 0.00 O ATOM 40 CB ALA 6 -4.919 -0.623 -7.045 1.00 0.00 C ATOM 41 N ALA 7 -2.831 -1.084 -9.309 1.00 0.00 N ATOM 42 CA ALA 7 -2.192 -0.708 -10.559 1.00 0.00 C ATOM 43 C ALA 7 -2.243 -1.890 -11.529 1.00 0.00 C ATOM 44 O ALA 7 -2.600 -1.727 -12.695 1.00 0.00 O ATOM 45 CB ALA 7 -0.761 -0.243 -10.281 1.00 0.00 C ATOM 46 N ALA 8 -1.881 -3.055 -11.012 1.00 0.00 N ATOM 47 CA ALA 8 -1.882 -4.264 -11.817 1.00 0.00 C ATOM 48 C ALA 8 -3.285 -4.496 -12.382 1.00 0.00 C ATOM 49 O ALA 8 -3.442 -4.772 -13.570 1.00 0.00 O ATOM 50 CB ALA 8 -1.391 -5.441 -10.972 1.00 0.00 C ATOM 51 N ALA 9 -4.269 -4.376 -11.503 1.00 0.00 N ATOM 52 CA ALA 9 -5.653 -4.568 -11.898 1.00 0.00 C ATOM 53 C ALA 9 -6.000 -3.590 -13.022 1.00 0.00 C ATOM 54 O ALA 9 -6.590 -3.978 -14.029 1.00 0.00 O ATOM 55 CB ALA 9 -6.561 -4.400 -10.678 1.00 0.00 C ATOM 56 N AALA 9A -5.617 -2.338 -12.812 0.50 0.00 N ATOM 57 CA AALA 9A -5.879 -1.301 -13.795 0.50 0.00 C ATOM 58 C AALA 9A -5.242 -1.695 -15.130 0.50 0.00 C ATOM 59 O AALA 9A -5.880 -1.605 -16.177 0.50 0.00 O ATOM 60 CB AALA 9A -5.358 0.040 -13.274 0.50 0.00 C ATOM 62 N BALA 9A -5.517 -2.338 -12.812 0.50 0.00 N ATOM 63 CA BALA 9A -5.779 -1.301 -13.795 0.50 0.00 C ATOM 64 C BALA 9A -5.142 -1.695 -15.130 0.50 0.00 C ATOM 65 O BALA 9A -5.780 -1.605 -16.177 0.50 0.00 O ATOM 66 CB BALA 9A -5.258 0.040 -13.274 0.50 0.00 C END """).construct_hierarchy() alpha_annot_1_1 = """\ HELIX 1 1 ALA 1 ALA 9A 1 10 """ alpha_annot_1_2 = """\ HELIX 1 1 ALA 1A ALA 9 1 10 """ alpha_annot_1_3 = """\ HELIX 1 1 ALA 1A ALA 9A 1 10 """ alpha_annot_1_4 = """\ HELIX 1 1 ALA 1 ALA 9 1 10 """ alpha_annot_2 = """\ HELIX 1 1 ALA 2 ALA 5 1 10 """ log = null_out() n_hbonds = [] n_hangles = [] for pdb_h, recs in [ (alpha_h1_ends, alpha_annot_1_1), #6 (alpha_h1_ends, alpha_annot_1_2), #4 (alpha_h1_ends, alpha_annot_1_3), #5 (alpha_h1_ends, alpha_annot_1_4), #5 (alpha_h1_ac, alpha_annot_1_1), #9 (alpha_h1_ac, alpha_annot_1_2), #5 (alpha_h1_ac, alpha_annot_1_3), #7 (alpha_h1_ac, alpha_annot_1_4), #7 ]: ioss_annotation = ioss.annotation.from_records(records = recs.split('\n')) ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure") defpars = iotbx.phil.parse(sec_str_master_phil_str) custom_pars = defpars.fetch(iotbx.phil.parse(ann)) custom_pars_ex = custom_pars.extract() ss_manager = manager( pdb_h, sec_str_from_pdb_file=None, params=custom_pars_ex.secondary_structure, verbose=-1) proxies_for_grm, hangles = ss_manager.create_protein_hbond_proxies( annotation= None, log = log) n_hbonds.append(proxies_for_grm.size()) n_hangles.append(hangles.size()) print(n_hbonds, n_hangles) assert n_hbonds == [6, 4, 5, 5, 9, 5, 7, 7] assert n_hangles == [18, 12, 15, 15, 28, 16, 22, 22] def exercise_sheets_bonding_pattern_with_insertions(): pdb_apar_h = iotbx.pdb.input(source_info=None, lines = """\ SCRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1 SCALE1 0.021524 0.012427 0.000000 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005176 0.00000 ATOM 5 N TYR A 2 27.208 -20.701 0.590 1.00 7.29 N ATOM 6 CA TYR A 2 27.617 -19.424 0.052 1.00 7.96 C ATOM 7 C TYR A 2 26.483 -18.436 0.263 1.00 6.87 C ATOM 8 O TYR A 2 25.303 -18.771 0.249 1.00 6.97 O ATOM 9 CB TYR A 2 27.861 -19.541 -1.451 1.00 7.90 C ATOM 10 CG TYR A 2 28.902 -20.556 -1.857 1.00 9.09 C ATOM 11 CD1 TYR A 2 30.255 -20.336 -1.592 1.00 11.43 C ATOM 12 CD2 TYR A 2 28.566 -21.697 -2.545 1.00 10.59 C ATOM 13 CE1 TYR A 2 31.227 -21.244 -1.987 1.00 13.93 C ATOM 14 CE2 TYR A 2 29.518 -22.630 -2.915 1.00 11.76 C ATOM 15 CZ TYR A 2 30.847 -22.395 -2.659 1.00 13.67 C ATOM 16 OH TYR A 2 31.792 -23.309 -3.059 1.00 18.26 O ATOM 17 N SER A 2A 26.854 -17.177 0.412 1.00 6.66 N ATOM 18 CA SER A 2A 25.899 -16.083 0.383 0.53 6.83 C ATOM 20 C SER A 2A 26.500 -14.946 -0.440 1.00 5.61 C ATOM 21 O SER A 2A 27.729 -14.822 -0.565 1.00 8.14 O ATOM 22 CB SER A 2A 25.569 -15.634 1.795 0.53 7.38 C ATOM 24 OG SER A 2A 26.740 -15.136 2.390 0.53 9.79 O ATOM 26 N CYS A 2B 25.627 -14.135 -0.995 1.00 5.11 N ATOM 27 CA CYS A 2B 26.070 -13.062 -1.865 1.00 5.65 C ATOM 28 C CYS A 2B 25.043 -11.934 -1.798 1.00 4.54 C ATOM 29 O CYS A 2B 23.856 -12.180 -1.528 1.00 5.60 O ATOM 30 CB CYS A 2B 26.253 -13.557 -3.295 1.00 7.00 C ATOM 31 SG CYS A 2B 24.806 -14.269 -4.119 1.00 8.88 S ATOM 32 N ARG A 5 25.486 -10.691 -2.002 1.00 4.69 N ATOM 33 CA ARG A 5 24.558 -9.545 -2.064 1.00 4.87 C ATOM 34 C ARG A 5 25.196 -8.395 -2.796 1.00 4.57 C ATOM 35 O ARG A 5 26.416 -8.238 -2.793 1.00 5.50 O ATOM 36 CB ARG A 5 24.061 -9.108 -0.700 1.00 6.43 C ATOM 37 CG ARG A 5 25.121 -8.566 0.219 1.00 6.96 C ATOM 38 CD ARG A 5 24.461 -8.032 1.494 1.00 7.25 C ATOM 39 NE ARG A 5 25.452 -7.547 2.440 1.00 7.63 N ATOM 40 CZ ARG A 5 26.107 -8.341 3.280 1.00 9.10 C ATOM 41 NH1 ARG A 5 25.867 -9.642 3.297 1.00 9.68 N ATOM 42 NH2 ARG A 5 26.974 -7.836 4.146 1.00 10.30 N ATOM 43 N ALA A 6 24.325 -7.563 -3.358 1.00 4.39 N ATOM 44 CA ALA A 6 24.723 -6.362 -4.067 1.00 4.73 C ATOM 45 C ALA A 6 23.693 -5.275 -3.769 1.00 4.15 C ATOM 46 O ALA A 6 22.482 -5.458 -3.987 1.00 4.96 O ATOM 47 CB ALA A 6 24.831 -6.626 -5.558 1.00 5.96 C ATOM 48 N VAL A 7 24.165 -4.139 -3.284 1.00 4.97 N ATOM 49 CA VAL A 7 23.374 -2.917 -3.085 1.00 4.42 C ATOM 50 C VAL A 7 23.482 -2.046 -4.325 1.00 4.45 C ATOM 51 O VAL A 7 24.589 -1.663 -4.717 1.00 5.55 O ATOM 52 CB VAL A 7 23.830 -2.159 -1.806 1.00 5.09 C ATOM 53 CG1 VAL A 7 23.111 -0.842 -1.686 1.00 5.65 C ATOM 54 CG2 VAL A 7 23.612 -2.998 -0.570 1.00 6.88 C ATOM 204 N MET A 31 18.177 -3.966 -4.656 1.00 4.72 N ATOM 205 CA MET A 31 18.833 -4.887 -3.744 1.00 5.29 C ATOM 206 C MET A 31 18.765 -6.294 -4.322 1.00 4.60 C ATOM 207 O MET A 31 17.661 -6.738 -4.657 1.00 4.98 O ATOM 208 CB MET A 31 18.097 -4.868 -2.387 1.00 6.39 C ATOM 209 CG MET A 31 18.723 -5.755 -1.334 1.00 8.61 C ATOM 210 SD MET A 31 20.248 -5.074 -0.655 1.00 11.04 S ATOM 211 CE MET A 31 21.358 -6.427 -0.777 1.00 8.94 C ATOM 212 N ALA A 32 19.899 -6.986 -4.412 1.00 3.90 N ATOM 213 CA ALA A 32 19.934 -8.380 -4.864 1.00 3.55 C ATOM 214 C ALA A 32 20.720 -9.194 -3.858 1.00 3.90 C ATOM 215 O ALA A 32 21.762 -8.763 -3.393 1.00 5.01 O ATOM 216 CB ALA A 32 20.552 -8.500 -6.255 1.00 4.55 C ATOM 217 N SER A 33 20.230 -10.407 -3.567 1.00 4.02 N ATOM 218 CA SER A 33 20.980 -11.288 -2.645 1.00 3.79 C ATOM 219 C SER A 33 20.591 -12.727 -2.850 1.00 4.33 C ATOM 220 O SER A 33 19.532 -13.045 -3.412 1.00 4.84 O ATOM 221 CB SER A 33 20.830 -10.880 -1.167 1.00 4.55 C ATOM 222 OG SER A 33 19.498 -11.105 -0.710 1.00 5.25 O ATOM 223 N GLY A 34 21.415 -13.600 -2.283 1.00 4.96 N ATOM 224 CA GLY A 34 21.104 -14.997 -2.335 1.00 4.50 C ATOM 225 C GLY A 34 21.914 -15.837 -1.397 1.00 4.64 C ATOM 226 O GLY A 34 22.836 -15.343 -0.732 1.00 4.96 O ATOM 227 N THR A 35 21.521 -17.105 -1.329 1.00 4.35 N ATOM 228 CA THR A 35 22.277 -18.138 -0.654 1.00 4.02 C ATOM 229 C THR A 35 22.226 -19.392 -1.495 1.00 4.55 C ATOM 230 O THR A 35 21.221 -19.652 -2.170 1.00 4.35 O ATOM 231 CB THR A 35 21.715 -18.436 0.762 1.00 5.12 C ATOM 232 OG1 THR A 35 20.356 -18.929 0.668 1.00 5.51 O ATOM 233 CG2 THR A 35 21.733 -17.222 1.670 1.00 5.97 C ATOM 234 N SER A 35A 23.294 -20.178 -1.426 1.00 4.63 N ATOM 235 CA SER A 35A 23.402 -21.406 -2.221 1.00 4.58 C ATOM 236 C SER A 35A 24.387 -22.368 -1.553 1.00 5.05 C ATOM 237 O SER A 35A 24.929 -22.095 -0.497 1.00 6.22 O ATOM 238 CB SER A 35A 23.881 -21.071 -3.639 1.00 5.69 C ATOM 239 OG SER A 35A 25.213 -20.561 -3.633 1.00 7.12 O """).construct_hierarchy() pdb_par_h = iotbx.pdb.input(source_info=None, lines = """\ CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1 SCALE1 0.021524 0.012427 0.000000 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005176 0.00000 ATOM 67 N ALA A 15 5.011 -5.031 -8.967 1.00 5.73 N ATOM 68 CA ALA A 15 4.943 -6.455 -9.287 1.00 6.16 C ATOM 69 C ALA A 15 5.610 -7.252 -8.166 1.00 6.39 C ATOM 70 O ALA A 15 6.751 -7.007 -7.857 1.00 9.87 O ATOM 71 CB ALA A 15 5.684 -6.739 -10.604 1.00 7.46 C ATOM 72 N THR A 15A 4.929 -8.263 -7.636 1.00 5.49 N ATOM 73 C THR A 15A 5.316 -10.600 -7.084 1.00 5.07 C ATOM 74 O THR A 15A 4.214 -11.002 -7.422 1.00 6.51 O ATOM 75 CA THR A 15A 5.513 -9.172 -6.657 1.00 5.70 C ATOM 76 CB THR A 15A 4.864 -9.001 -5.276 1.00 8.31 C ATOM 77 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N ATOM 78 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C ATOM 79 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C ATOM 80 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O ATOM 81 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N ATOM 82 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C ATOM 83 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C ATOM 84 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O ATOM 85 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C ATOM 86 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N ATOM 87 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C ATOM 88 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C ATOM 89 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O ATOM 90 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C ATOM 91 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N ATOM 92 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C ATOM 93 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C ATOM 94 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O ATOM 95 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C ATOM 96 N THR A 20A 10.560 -24.542 -5.569 1.00 4.00 N ATOM 97 CA THR A 20A 10.597 -25.962 -5.876 1.00 4.05 C ATOM 98 C THR A 20A 10.984 -26.770 -4.636 1.00 4.53 C ATOM 99 O THR A 20A 11.770 -26.361 -3.802 1.00 5.04 O ATOM 100 CB THR A 20A 11.488 -26.293 -7.083 1.00 4.38 C ATOM 189 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N ATOM 190 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C ATOM 191 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C ATOM 192 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O ATOM 193 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C ATOM 194 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N ATOM 195 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C ATOM 196 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C ATOM 197 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O ATOM 198 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C ATOM 199 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N ATOM 200 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C ATOM 201 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C ATOM 202 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O ATOM 203 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C ATOM 204 N LYS A 42A 2.479 -16.398 -7.978 1.00 6.26 N ATOM 205 CA LYS A 42A 3.247 -17.395 -7.256 1.00 6.48 C ATOM 206 C LYS A 42A 3.186 -18.741 -7.955 1.00 5.78 C ATOM 207 O LYS A 42A 2.206 -19.041 -8.623 1.00 9.40 O ATOM 208 CB LYS A 42A 2.727 -17.535 -5.836 1.00 8.81 C ATOM 209 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N ATOM 210 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C ATOM 211 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C ATOM 212 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O ATOM 213 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C ATOM 214 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N ATOM 215 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C ATOM 216 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C ATOM 217 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O ATOM 218 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C ATOM 219 N ALA A 45A 6.347 -26.119 -7.403 1.00 3.62 N ATOM 220 CA ALA A 45A 6.443 -27.338 -8.202 1.00 3.99 C ATOM 221 C ALA A 45A 7.579 -28.205 -7.717 1.00 4.57 C ATOM 222 O ALA A 45A 8.479 -27.750 -7.000 1.00 4.79 O ATOM 223 CB ALA A 45A 6.607 -27.026 -9.678 1.00 4.52 C TER END """).construct_hierarchy() pdb_par_ac_h = iotbx.pdb.input(source_info=None, lines = """\ CRYST1 46.460 46.460 193.210 90.00 90.00 120.00 P 31 2 1 SCALE1 0.021524 0.012427 0.000000 0.00000 SCALE2 0.000000 0.024854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005176 0.00000 ATOM 1 N AALA A 15 5.011 -5.031 -8.967 0.50 5.73 N ATOM 2 CA AALA A 15 4.943 -6.455 -9.287 0.50 6.16 C ATOM 3 C AALA A 15 5.610 -7.252 -8.166 0.50 6.39 C ATOM 4 O AALA A 15 6.751 -7.007 -7.857 0.50 9.87 O ATOM 5 CB AALA A 15 5.684 -6.739 -10.604 0.50 7.46 C ATOM 6 N BALA A 15 5.111 -5.031 -8.967 0.50 5.73 N ATOM 7 CA BALA A 15 5.043 -6.455 -9.287 0.50 6.16 C ATOM 8 C BALA A 15 5.710 -7.252 -8.166 0.50 6.39 C ATOM 9 O BALA A 15 6.851 -7.007 -7.857 0.50 9.87 O ATOM 10 CB BALA A 15 5.784 -6.739 -10.604 0.50 7.46 C ATOM 11 N ATHR A 15A 4.929 -8.263 -7.636 0.50 5.49 N ATOM 12 C ATHR A 15A 5.316 -10.600 -7.084 0.50 5.07 C ATOM 13 O ATHR A 15A 4.214 -11.002 -7.422 0.50 6.51 O ATOM 14 CA ATHR A 15A 5.513 -9.172 -6.657 0.50 5.70 C ATOM 15 CB ATHR A 15A 4.864 -9.001 -5.276 0.50 8.31 C ATOM 16 N BTHR A 15A 5.029 -8.263 -7.636 0.50 5.49 N ATOM 17 C BTHR A 15A 5.416 -10.600 -7.084 0.50 5.07 C ATOM 18 O BTHR A 15A 4.314 -11.002 -7.422 0.50 6.51 O ATOM 19 CA BTHR A 15A 5.613 -9.172 -6.657 0.50 5.70 C ATOM 20 CB BTHR A 15A 4.964 -9.001 -5.276 0.50 8.31 C ATOM 21 N GLY A 17 6.393 -11.375 -7.067 1.00 4.56 N ATOM 22 CA GLY A 17 6.325 -12.770 -7.439 1.00 4.26 C ATOM 23 C GLY A 17 7.219 -13.654 -6.621 1.00 4.41 C ATOM 24 O GLY A 17 8.263 -13.233 -6.114 1.00 5.01 O ATOM 25 N SER A 18 6.827 -14.921 -6.561 1.00 4.24 N ATOM 26 CA SER A 18 7.657 -15.945 -5.959 1.00 4.02 C ATOM 27 C SER A 18 7.539 -17.244 -6.724 1.00 3.64 C ATOM 28 O SER A 18 6.482 -17.526 -7.331 1.00 4.07 O ATOM 29 CB SER A 18 7.335 -16.157 -4.481 1.00 5.86 C ATOM 30 N ALA A 19 8.573 -18.049 -6.627 1.00 3.19 N ATOM 31 CA ALA A 19 8.578 -19.414 -7.195 1.00 3.31 C ATOM 32 C ALA A 19 9.370 -20.307 -6.238 1.00 3.20 C ATOM 33 O ALA A 19 10.484 -19.956 -5.817 1.00 4.21 O ATOM 34 CB ALA A 19 9.235 -19.415 -8.574 1.00 3.85 C ATOM 35 N THR A 20 8.825 -21.476 -5.940 1.00 3.77 N ATOM 36 CA THR A 20 9.478 -22.432 -5.047 1.00 3.70 C ATOM 37 C THR A 20 9.444 -23.827 -5.640 1.00 3.56 C ATOM 38 O THR A 20 8.383 -24.281 -6.108 1.00 4.14 O ATOM 39 CB THR A 20 8.787 -22.430 -3.673 1.00 4.76 C ATOM 40 N THR A 21 10.560 -24.542 -5.569 1.00 4.00 N ATOM 41 CA THR A 21 10.597 -25.962 -5.876 1.00 4.05 C ATOM 42 C THR A 21 10.984 -26.770 -4.636 1.00 4.53 C ATOM 43 O THR A 21 11.770 -26.361 -3.802 1.00 5.04 O ATOM 44 CB THR A 21 11.488 -26.293 -7.083 1.00 4.38 C ATOM 45 N GLN A 40 0.280 -6.099 -9.049 1.00 6.35 N ATOM 46 CA GLN A 40 0.087 -7.454 -9.580 1.00 6.35 C ATOM 47 C GLN A 40 0.964 -8.417 -8.788 1.00 6.09 C ATOM 48 O GLN A 40 2.080 -8.093 -8.393 1.00 6.87 O ATOM 49 CB GLN A 40 0.461 -7.523 -11.060 1.00 7.52 C ATOM 50 N THR A 41 0.419 -9.596 -8.544 1.00 6.66 N ATOM 51 CA THR A 41 1.108 -10.640 -7.800 1.00 6.93 C ATOM 52 C THR A 41 0.932 -12.005 -8.414 1.00 6.82 C ATOM 53 O THR A 41 -0.069 -12.258 -9.104 1.00 8.79 O ATOM 54 CB THR A 41 0.633 -10.636 -6.352 1.00 10.84 C ATOM 55 N ALA A 42 1.951 -12.847 -8.263 1.00 6.44 N ATOM 56 CA ALA A 42 1.923 -14.209 -8.797 1.00 6.59 C ATOM 57 C ALA A 42 2.829 -15.117 -7.992 1.00 5.51 C ATOM 58 O ALA A 42 3.835 -14.684 -7.420 1.00 5.94 O ATOM 59 CB ALA A 42 2.327 -14.218 -10.264 1.00 9.02 C ATOM 60 N LYS A 42A 2.479 -16.398 -7.978 1.00 6.26 N ATOM 61 CA LYS A 42A 3.247 -17.395 -7.256 1.00 6.48 C ATOM 62 C LYS A 42A 3.186 -18.741 -7.955 1.00 5.78 C ATOM 63 O LYS A 42A 2.206 -19.041 -8.623 1.00 9.40 O ATOM 64 CB LYS A 42A 2.727 -17.535 -5.836 1.00 8.81 C ATOM 65 N SER A 44 4.243 -19.534 -7.818 1.00 4.43 N ATOM 66 CA SER A 44 4.241 -20.890 -8.325 1.00 4.28 C ATOM 67 C SER A 44 4.998 -21.811 -7.358 1.00 4.09 C ATOM 68 O SER A 44 5.865 -21.377 -6.584 1.00 4.53 O ATOM 69 CB SER A 44 4.831 -20.949 -9.731 1.00 5.33 C ATOM 70 N PHE A 45 4.660 -23.091 -7.444 1.00 4.39 N ATOM 71 CA PHE A 45 5.198 -24.135 -6.576 1.00 4.44 C ATOM 72 C PHE A 45 5.222 -25.415 -7.389 1.00 4.16 C ATOM 73 O PHE A 45 4.183 -25.754 -7.979 1.00 5.11 O ATOM 74 CB PHE A 45 4.254 -24.281 -5.370 1.00 5.22 C ATOM 75 N ALA A 46 6.347 -26.119 -7.403 1.00 3.62 N ATOM 76 CA ALA A 46 6.443 -27.338 -8.202 1.00 3.99 C ATOM 77 C ALA A 46 7.579 -28.205 -7.717 1.00 4.57 C ATOM 78 O ALA A 46 8.479 -27.750 -7.000 1.00 4.79 O ATOM 79 CB ALA A 46 6.607 -27.026 -9.678 1.00 4.52 C TER 80 ALA A 46 END """).construct_hierarchy() s_apar_records1 = """\ SHEET 1 A 2 TYR A 2 VAL A 7 0 SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 35A N ALA A 2 """ s_apar_records2 = """\ SHEET 1 A 2 TYR A 2 VAL A 7 0 SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 32 N ALA A 6 """ s_apar_records3 = """\ SHEET 1 A 2 SER A 2A VAL A 7 0 SHEET 2 A 2 MET A 31 SER A 35A-1 O ALA A 32 N ALA A 6 """ s_par_records1 = """\ SHEET 1 B 2 ALA A 15 THR A 20A 0 SHEET 2 B 2 GLN A 40 ALA A 45A 1 O GLN A 40 N THR A 15A """ s_par_records2 = """\ SHEET 1 B 2 ALA A 15 THR A 20A 0 SHEET 2 B 2 GLN A 40 ALA A 45A 1 O GLN A 44 N THR A 20 """ s_par_records3 = """\ SHEET 1 B 2 ALA A 15A THR A 20A 0 SHEET 2 B 2 GLN A 40 ALA A 45 1 O GLN A 44 N THR A 20 """ log = null_out() # defpars = sec_str_master_phil n_hbonds = [] n_hangles = [] for pdb_h, recs in [ (pdb_apar_h, s_apar_records1), # 6 (pdb_apar_h, s_apar_records2), # 6 (pdb_apar_h, s_apar_records3), # 4 (pdb_par_h, s_par_records1), # 6 (pdb_par_h, s_par_records2), # 6 (pdb_par_h, s_par_records3), # 5 (pdb_par_ac_h, s_par_records1), # 8 hbonds ]: ioss_annotation = ioss.annotation.from_records(records = recs.split('\n')) ann = ioss_annotation.as_restraint_groups(prefix_scope="secondary_structure") defpars = iotbx.phil.parse(sec_str_master_phil_str) custom_pars = defpars.fetch(iotbx.phil.parse(ann)) custom_pars_ex = custom_pars.extract() ss_manager = manager( pdb_h, sec_str_from_pdb_file=None, params=custom_pars_ex.secondary_structure, verbose=-1) proxies_for_grm, hangles = ss_manager.create_protein_hbond_proxies( annotation= None, log = log) # print proxies_for_grm.size() n_hbonds.append(proxies_for_grm.size()) n_hangles.append(hangles.size()) print(n_hbonds, n_hangles) assert n_hbonds == [6, 6, 4, 6, 6, 5, 8] assert n_hangles == [15, 15, 12, 18, 18, 12, 24] def exercise_phil_generation(): log = null_out() defpars = sec_str_master_phil.fetch() if __name__ == "__main__" : exercise_helix_bonding_pattern_with_insertions() exercise_sheets_bonding_pattern_with_insertions() print("OK")