from __future__ import absolute_import, division, print_function import time import mmtbx.model import iotbx.pdb from mmtbx.hydrogens import reduce_hydrogen from libtbx.utils import null_out from libtbx.test_utils import approx_equal # ------------------------------------------------------------------------------ def run(): test_000() test_001() test_002() test_003() test_004() test_005() test_006() test_007() test_008() test_009() # ------------------------------------------------------------------------------ def compare_models(pdb_str, contains = None, not_contains = None): ''' Function to compare model with new H to the known answer (pdb_str) ''' # pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) model_initial = mmtbx.model.manager(model_input = pdb_inp, log = null_out()) ph_initial = model_initial.get_hierarchy() hd_sel_initial = model_initial.get_hd_selection() h_atoms_initial = ph_initial.select(hd_sel_initial).atoms() h_names_initial = list(h_atoms_initial.extract_name()) # number of H in pdb string (right answer) number_h_expected = hd_sel_initial.count(True) # get model obj without H atoms model_without_h = model_initial.select(~hd_sel_initial) # make sure model without H indeed has no H atoms hd_sel_without_h = model_without_h.get_hd_selection() assert (hd_sel_without_h is not None) assert (hd_sel_without_h.count(True) == 0) #model_h_added = reduce.add(model = model_without_h) # place H atoms reduce_add_h_obj = reduce_hydrogen.place_hydrogens(model = model_without_h) reduce_add_h_obj.run() model_h_added = reduce_add_h_obj.get_model() hd_sel_h_added = model_h_added.get_hd_selection() ph_h_added = model_h_added.get_hierarchy() assert ph_initial.is_similar_hierarchy(other=ph_h_added) number_h_added = hd_sel_h_added.count(True) assert(number_h_expected == number_h_added) h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms() h_names_added = list(h_atoms_added.extract_name()) if not_contains: assert (not_contains not in h_names_added) if contains: assert (contains in h_names_added) sc_h_initial = model_initial.select(hd_sel_initial).get_sites_cart() sc_h_added = model_h_added.select(hd_sel_h_added).get_sites_cart() d1 = {h_names_initial[i]: sc_h_initial[i] for i in range(len(h_names_initial))} d2 = {h_names_added[i]: sc_h_added[i] for i in range(len(h_names_added))} # check that coordinates are correct for name, sc in d2.items(): assert(name in d1) assert approx_equal(sc, d1[name], 0.01) # ------------------------------------------------------------------------------ def test_000(): ''' Incomplete peptide unit at the N-terminal --> H should not be placed. ''' compare_models(pdb_str = pdb_str_000) # ------------------------------------------------------------------------------ def test_001(): ''' CD1 is missing --> H, HD1, HE1 can't be parameterized --> should not be added. ''' compare_models(pdb_str = pdb_str_001, not_contains = ' HE1') # ------------------------------------------------------------------------------ def test_002(): ''' If there is a disulfide bond --> don't add H on CYS ''' compare_models(pdb_str = pdb_str_002, not_contains = ' HG ') # ------------------------------------------------------------------------------ def test_003(): ''' If CYS is not in disulfide or does not coordinate --> place HG ''' compare_models(pdb_str = pdb_str_003, contains = ' HG ') # ------------------------------------------------------------------------------ def test_004(): ''' N atom is missing --> make sure peptide H is not placed ''' compare_models(pdb_str = pdb_str_004, not_contains = ' H ') # ------------------------------------------------------------------------------ def test_005(): ''' CYS coordinates a metal --> HG should not be placed ''' compare_models(pdb_str = pdb_str_005, not_contains = ' HG ') # ------------------------------------------------------------------------------ def test_006(): ''' CYS forms a disulfid with symmetry mate --> don't place HG ''' compare_models(pdb_str = pdb_str_006, not_contains = ' HG ') # ------------------------------------------------------------------------------ def test_007(): ''' CYS forms a disulfid with symmetry mate --> don't place HG ''' compare_models(pdb_str = pdb_str_007, not_contains = ' HG ') # ------------------------------------------------------------------------------ def test_008(): ''' disulfide bridge between neighboring residues --> don't place HG atoms ''' compare_models(pdb_str = pdb_str_008, not_contains = ' HG ') # ------------------------------------------------------------------------------ def test_009(): ''' Incomplete peptide unit at the N-terminal --> H should not be placed. ''' compare_models(pdb_str = pdb_str_009) # ------------------------------------------------------------------------------ pdb_str_000 = """ REMARK two AA fragments, GLY peptide H atom is not expected to be placed CRYST1 14.074 14.385 15.410 90.00 90.00 90.00 P 1 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 H1 GLY A 1 -8.818 5.479 6.162 1.00 16.77 H ATOM 6 H2 GLY A 1 -9.801 4.456 6.477 1.00 16.77 H ATOM 7 H3 GLY A 1 -8.383 4.140 6.523 1.00 16.77 H ATOM 8 HA3 GLY A 1 -9.929 3.858 4.426 1.00 16.57 H ATOM 9 HA2 GLY A 1 -8.861 4.970 4.084 1.00 16.57 H ATOM 10 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 11 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 12 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 13 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 14 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 15 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 16 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 17 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 18 H ASN A 2 -8.045 3.269 2.470 1.00 15.02 H ATOM 19 HA ASN A 2 -6.719 1.165 3.206 1.00 14.10 H ATOM 20 HB2 ASN A 2 -6.148 2.746 0.949 1.00 15.38 H ATOM 21 HB3 ASN A 2 -5.618 1.264 1.168 1.00 15.38 H ATOM 22 HD21 ASN A 2 -8.919 1.893 -0.569 1.00 11.72 H ATOM 23 HD22 ASN A 2 -7.888 2.940 -0.323 1.00 11.72 H TER """ pdb_str_001 = """ REMARK CD1 is missing --> HD1, HE1 cannot not be placed; H is not placed CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 8 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 9 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 10 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 11 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 12 HA TYR A 139 10.487 8.115 6.973 1.00 10.00 H ATOM 13 HB2 TYR A 139 10.961 5.881 7.464 1.00 10.00 H ATOM 14 HB3 TYR A 139 10.893 5.529 5.916 1.00 10.00 H ATOM 15 HD2 TYR A 139 8.896 6.220 8.714 1.00 10.00 H ATOM 16 HE2 TYR A 139 6.643 5.772 8.919 1.00 10.00 H ATOM 17 HH TYR A 139 4.752 5.127 7.905 1.00 10.00 H TER """ pdb_str_002 = """ REMARK fragment of disulfide bridge --> don't place H on Cys SG atom CRYST1 14.197 15.507 16.075 90.00 90.00 90.00 P 1 ATOM 1 N CYS A 128 14.558 -30.378 -19.478 1.00 11.73 N ATOM 2 CA CYS A 128 13.499 -29.511 -19.901 1.00 11.51 C ATOM 3 C CYS A 128 12.454 -30.316 -20.640 1.00 11.99 C ATOM 4 O CYS A 128 12.765 -31.329 -21.265 1.00 16.86 O ATOM 5 CB CYS A 128 14.059 -28.357 -20.691 1.00 12.94 C ATOM 6 SG CYS A 128 15.213 -27.350 -19.760 1.00 12.36 S ATOM 7 HA CYS A 128 13.044 -29.102 -19.148 1.00 11.51 H ATOM 8 HB2 CYS A 128 14.526 -28.706 -21.466 1.00 12.94 H ATOM 9 HB3 CYS A 128 13.327 -27.787 -20.974 1.00 12.94 H ATOM 10 N CYS A 232 13.105 -25.822 -15.371 1.00 4.75 N ATOM 11 CA CYS A 232 14.298 -26.646 -15.573 1.00 5.50 C ATOM 12 C CYS A 232 15.596 -25.838 -15.551 1.00 5.70 C ATOM 14 O CYS A 232 16.651 -26.346 -15.190 1.00 8.25 O ATOM 15 CB CYS A 232 14.178 -27.497 -16.824 1.00 6.69 C ATOM 16 SG CYS A 232 14.060 -26.477 -18.360 1.00 7.70 S ATOM 17 HA CYS A 232 14.363 -27.258 -14.823 1.00 5.50 H ATOM 18 HB2 CYS A 232 14.961 -28.065 -16.898 1.00 6.69 H ATOM 19 HB3 CYS A 232 13.378 -28.042 -16.761 1.00 6.69 H TER """ pdb_str_003 = """ REMARK fragment of lone CYS --> place the HG atom CRYST1 14.197 15.507 16.075 90.00 90.00 90.00 P 1 ATOM 1 N CYS A 128 14.558 -30.378 -19.478 1.00 11.73 N ATOM 2 CA CYS A 128 13.499 -29.511 -19.901 1.00 11.51 C ATOM 3 C CYS A 128 12.454 -30.316 -20.640 1.00 11.99 C ATOM 4 O CYS A 128 12.765 -31.329 -21.265 1.00 16.86 O ATOM 5 CB CYS A 128 14.059 -28.357 -20.691 1.00 12.94 C ATOM 6 SG CYS A 128 15.213 -27.350 -19.760 1.00 12.36 S ATOM 7 HA CYS A 128 13.044 -29.102 -19.148 1.00 11.51 H ATOM 8 HB2 CYS A 128 14.526 -28.706 -21.466 1.00 12.94 H ATOM 9 HB3 CYS A 128 13.327 -27.787 -20.974 1.00 12.94 H ATOM 10 HG CYS A 128 16.134 -28.034 -19.410 1.00 12.36 H TER """ pdb_str_004 = """ REMARK peptide N is missing --> peptide H atom should not be placed CRYST1 15.000 15.000 15.000 90.00 90.00 90.00 P 1 ATOM 1 CA PHE H 1 7.000 7.000 7.000 1.00 15.00 C ATOM 2 C PHE H 1 7.956 7.811 6.133 1.00 15.00 C ATOM 3 O PHE H 1 8.506 7.237 5.169 1.00 15.00 O ATOM 4 CB PHE H 1 7.767 5.853 7.671 1.00 15.00 C ATOM 5 CG PHE H 1 6.935 5.032 8.622 1.00 15.00 C ATOM 6 CD1 PHE H 1 5.918 4.176 8.140 1.00 15.00 C ATOM 7 CD2 PHE H 1 7.161 5.107 10.012 1.00 15.00 C ATOM 8 CE1 PHE H 1 5.126 3.395 9.038 1.00 15.00 C ATOM 9 CE2 PHE H 1 6.382 4.336 10.930 1.00 15.00 C ATOM 10 CZ PHE H 1 5.360 3.476 10.439 1.00 15.00 C ATOM 11 HZ PHE H 1 4.849 2.971 11.029 1.00 15.00 H ATOM 12 HE2 PHE H 1 6.542 4.396 11.844 1.00 15.00 H ATOM 13 HD2 PHE H 1 7.828 5.668 10.337 1.00 15.00 H ATOM 14 HD1 PHE H 1 5.762 4.120 7.225 1.00 15.00 H ATOM 16 HE1 PHE H 1 4.460 2.836 8.708 1.00 15.00 H ATOM 17 HA PHE H 1 6.622 7.575 7.683 1.00 15.00 H ATOM 18 HB3 PHE H 1 8.101 5.258 6.982 1.00 15.00 H ATOM 19 HB2 PHE H 1 8.507 6.227 8.174 1.00 15.00 H TER """ pdb_str_005 = """ REMARK CYS coordinates a metal --> HG should not be placed CRYST1 108.910 108.910 108.910 90.00 90.00 90.00 I 4 3 2 ATOM 1 N CYS A 48 -40.561 -16.057 6.830 1.00 99.72 N ATOM 2 CA CYS A 48 -41.351 -14.915 6.380 1.00106.82 C ATOM 3 C CYS A 48 -41.146 -13.719 7.305 1.00104.36 C ATOM 4 O CYS A 48 -40.407 -13.794 8.283 1.00104.56 O ATOM 5 CB CYS A 48 -42.835 -15.275 6.303 1.00105.79 C ATOM 6 SG CYS A 48 -43.707 -15.186 7.879 1.00101.00 S ATOM 7 HA CYS A 48 -41.063 -14.664 5.488 1.00106.82 H ATOM 8 HB2 CYS A 48 -43.271 -14.661 5.692 1.00105.79 H ATOM 9 HB3 CYS A 48 -42.916 -16.184 5.974 1.00105.79 H TER HETATM 12 ZN ZN A 102 -44.322 -17.446 8.351 1.00 98.67 Zn END """ pdb_str_006 = """ REMARK CYS forms a disulfide bridge with symmetry mate --> don't place HG CRYST1 108.910 108.910 108.910 90.00 90.00 90.00 I 4 3 2 ATOM 1 N CYS A 12 -50.777 -13.205 -12.246 1.00 95.50 N ATOM 2 CA CYS A 12 -51.774 -13.797 -13.124 1.00103.68 C ATOM 3 C CYS A 12 -51.135 -14.327 -14.399 1.00101.77 C ATOM 4 O CYS A 12 -50.987 -13.597 -15.382 1.00106.09 O ATOM 5 CB CYS A 12 -52.861 -12.775 -13.466 1.00103.91 C ATOM 6 SG CYS A 12 -54.064 -13.357 -14.680 1.00106.39 S ATOM 7 HA CYS A 12 -52.194 -14.542 -12.667 1.00103.68 H ATOM 8 HB2 CYS A 12 -52.438 -11.981 -13.828 1.00103.91 H ATOM 9 HB3 CYS A 12 -53.344 -12.553 -12.655 1.00103.91 H TER """ pdb_str_007 = """ REMARK CYS forms a disulfide with symmetry mate --> don't place HG REMARK from PDB 5c11 CRYST1 108.910 108.910 108.910 90.00 90.00 90.00 I 4 3 2 ATOM 1 N PRO A 1 -50.110 -12.340 -8.990 1.00 87.52 N ATOM 2 CA PRO A 1 -49.518 -12.918 -10.200 1.00 88.41 C ATOM 3 C PRO A 1 -50.549 -13.676 -11.025 1.00 97.43 C ATOM 4 O PRO A 1 -51.129 -14.656 -10.556 1.00 93.89 O ATOM 5 CB PRO A 1 -48.446 -13.865 -9.649 1.00 78.46 C ATOM 6 CG PRO A 1 -48.110 -13.314 -8.317 1.00 80.77 C ATOM 7 CD PRO A 1 -49.402 -12.783 -7.777 1.00 92.02 C ATOM 8 H2 PRO A 1 -50.010 -11.446 -9.004 1.00 87.52 H ATOM 9 H3 PRO A 1 -50.986 -12.543 -8.958 1.00 87.52 H ATOM 10 HA PRO A 1 -49.092 -12.241 -10.748 1.00 88.41 H ATOM 11 HB2 PRO A 1 -48.804 -14.764 -9.574 1.00 78.46 H ATOM 12 HB3 PRO A 1 -47.671 -13.864 -10.232 1.00 78.46 H ATOM 13 HG2 PRO A 1 -47.455 -12.604 -8.409 1.00 80.77 H ATOM 14 HG3 PRO A 1 -47.760 -14.017 -7.748 1.00 80.77 H ATOM 15 HD2 PRO A 1 -49.899 -13.480 -7.321 1.00 92.02 H ATOM 16 HD3 PRO A 1 -49.246 -12.038 -7.175 1.00 92.02 H ATOM 17 N CYS A 2 -50.777 -13.205 -12.246 1.00 95.50 N ATOM 18 CA CYS A 2 -51.774 -13.797 -13.124 1.00103.68 C ATOM 19 C CYS A 2 -51.135 -14.327 -14.399 1.00101.77 C ATOM 20 O CYS A 2 -50.987 -13.597 -15.382 1.00106.09 O ATOM 21 CB CYS A 2 -52.861 -12.775 -13.466 1.00103.91 C ATOM 22 SG CYS A 2 -54.064 -13.357 -14.680 1.00106.39 S ATOM 23 H CYS A 2 -50.361 -12.536 -12.590 1.00 95.50 H ATOM 24 HA CYS A 2 -52.147 -14.558 -12.653 1.00103.68 H ATOM 25 HB2 CYS A 2 -52.438 -11.981 -13.828 1.00103.91 H ATOM 26 HB3 CYS A 2 -53.344 -12.553 -12.655 1.00103.91 H ATOM 28 N LYS A 3 -50.756 -15.600 -14.375 1.00105.98 N ATOM 29 CA LYS A 3 -50.135 -16.230 -15.528 1.00115.21 C ATOM 30 C LYS A 3 -50.110 -17.740 -15.357 1.00105.26 C ATOM 31 O LYS A 3 -50.331 -18.255 -14.264 1.00118.65 O ATOM 32 CB LYS A 3 -48.714 -15.704 -15.737 1.00110.03 C ATOM 33 CG LYS A 3 -47.784 -15.954 -14.563 1.00100.14 C ATOM 34 CD LYS A 3 -46.379 -15.452 -14.853 1.00101.77 C ATOM 35 CE LYS A 3 -45.456 -15.678 -13.663 1.00112.21 C ATOM 36 NZ LYS A 3 -44.063 -15.229 -13.941 1.00110.68 N ATOM 37 H LYS A 3 -50.849 -16.122 -13.698 1.00105.98 H ATOM 38 HA LYS A 3 -50.648 -16.015 -16.323 1.00115.21 H ATOM 39 HB2 LYS A 3 -48.755 -14.746 -15.882 1.00110.03 H ATOM 40 HB3 LYS A 3 -48.332 -16.141 -16.514 1.00110.03 H ATOM 41 HG2 LYS A 3 -48.120 -15.488 -13.782 1.00100.14 H ATOM 42 HG3 LYS A 3 -47.738 -16.907 -14.386 1.00100.14 H ATOM 43 HD2 LYS A 3 -46.409 -14.501 -15.041 1.00101.77 H ATOM 44 HD3 LYS A 3 -46.017 -15.929 -15.616 1.00101.77 H ATOM 45 HE2 LYS A 3 -45.789 -15.178 -12.902 1.00112.21 H ATOM 46 HE3 LYS A 3 -45.432 -16.625 -13.453 1.00112.21 H ATOM 47 HZ1 LYS A 3 -43.731 -15.679 -14.633 1.00110.68 H ATOM 48 HZ2 LYS A 3 -43.549 -15.374 -13.229 1.00110.68 H ATOM 49 HZ3 LYS A 3 -44.056 -14.360 -14.131 1.00110.68 H TER """ pdb_str_008 = """ REMARK disulfide bridge between neighboring residues --> don't place HG atoms REMARK from PDB 3cu9 CRYST1 86.141 89.579 76.041 90.00 90.00 90.00 C 2 2 21 ATOM 1 N CYS A 221 -25.409 6.530 5.604 1.00 8.50 N ATOM 2 CA CYS A 221 -25.611 7.909 5.995 1.00 8.62 C ATOM 3 C CYS A 221 -25.469 8.835 4.795 1.00 8.84 C ATOM 4 O CYS A 221 -25.131 8.426 3.672 1.00 9.51 O ATOM 5 CB CYS A 221 -24.546 8.272 7.047 1.00 9.34 C ATOM 6 SG CYS A 221 -22.908 8.520 6.302 1.00 10.59 S ATOM 7 HA CYS A 221 -26.500 8.030 6.365 1.00 8.62 H ATOM 8 HB2 CYS A 221 -24.805 9.094 7.491 1.00 9.34 H ATOM 9 HB3 CYS A 221 -24.479 7.552 7.694 1.00 9.34 H ATOM 10 N CYS A 222 -25.649 10.119 5.071 1.00 8.82 N ATOM 11 CA CYS A 222 -25.005 11.177 4.321 1.00 8.99 C ATOM 12 C CYS A 222 -25.532 11.323 2.911 1.00 9.12 C ATOM 14 O CYS A 222 -24.803 11.847 2.036 1.00 11.09 O ATOM 15 CB CYS A 222 -23.463 10.894 4.313 1.00 11.23 C ATOM 16 SG CYS A 222 -22.792 10.598 5.958 1.00 11.91 S ATOM 17 H CYS A 222 -26.153 10.408 5.705 1.00 8.82 H ATOM 18 HA CYS A 222 -25.188 12.029 4.746 1.00 8.99 H ATOM 19 HB2 CYS A 222 -23.004 11.661 3.936 1.00 11.23 H ATOM 20 HB3 CYS A 222 -23.291 10.107 3.773 1.00 11.23 H TER """ pdb_str_009 = """ CRYST1 22.251 49.068 23.478 90.00 90.00 90.00 P 1 ATOM 1 N HIS A 44 5.727 38.590 5.000 1.00 7.72 N ATOM 2 CA HIS A 44 6.991 38.641 5.686 1.00 8.00 C ATOM 3 C HIS A 44 7.274 37.329 6.472 1.00 8.78 C ATOM 4 O HIS A 44 6.403 36.603 6.844 1.00 9.64 O ATOM 5 CB HIS A 44 6.917 39.719 6.794 1.00 11.03 C ATOM 6 CG HIS A 44 6.477 41.058 6.353 1.00 9.11 C ATOM 7 ND1 HIS A 44 5.698 41.854 7.162 1.00 9.47 N ATOM 8 CD2 HIS A 44 6.675 41.756 5.230 1.00 10.66 C ATOM 9 CE1 HIS A 44 5.476 43.005 6.544 1.00 11.24 C ATOM 10 NE2 HIS A 44 6.065 42.976 5.358 1.00 9.90 N ATOM 11 HA HIS A 44 7.678 38.811 5.022 1.00 8.00 H ATOM 12 HB2 HIS A 44 7.801 39.819 7.181 1.00 11.03 H ATOM 13 HB3 HIS A 44 6.290 39.418 7.471 1.00 11.03 H ATOM 14 HD1 HIS A 44 5.404 41.639 7.941 1.00 9.47 H ATOM 15 HD2 HIS A 44 7.148 41.462 4.485 1.00 10.66 H ATOM 16 HE1 HIS A 44 4.986 43.717 6.887 1.00 11.24 H ATOM 17 HE2 HIS A 44 6.065 43.608 4.775 1.00 9.90 H ATOM 18 N SER A 60 8.719 39.746 15.915 1.00 9.28 N ATOM 19 CA SER A 60 8.995 40.756 14.888 1.00 8.34 C ATOM 20 C SER A 60 9.663 40.135 13.685 1.00 9.31 C ATOM 21 O SER A 60 9.754 38.932 13.513 1.00 9.78 O ATOM 22 CB ASER A 60 9.760 41.944 15.459 0.50 11.89 C ATOM 23 OG ASER A 60 9.077 42.510 16.590 0.33 10.99 O ATOM 24 HA ASER A 60 8.159 41.130 14.569 1.00 8.34 H ATOM 25 HB2ASER A 60 10.639 41.645 15.740 0.50 11.89 H ATOM 26 HB3ASER A 60 9.844 42.623 14.771 0.50 11.89 H ATOM 27 HG ASER A 60 9.512 43.162 16.891 0.33 10.99 H ATOM 28 CB BSER A 60 9.680 41.954 15.550 0.50 12.25 C ATOM 29 OG BSER A 60 10.939 41.568 16.145 0.66 17.46 O ATOM 30 HA BSER A 60 8.196 41.138 14.493 1.00 8.34 H ATOM 31 HB2BSER A 60 9.099 42.306 16.243 0.50 12.25 H ATOM 32 HB3BSER A 60 9.845 42.634 14.878 0.50 12.25 H ATOM 33 HG BSER A 60 11.303 42.234 16.504 0.66 17.46 H ATOM 34 N HIS A 61 10.095 40.969 12.694 1.00 7.19 N ATOM 35 CA HIS A 61 10.687 40.443 11.504 1.00 7.24 C ATOM 36 C HIS A 61 12.059 39.821 11.742 1.00 7.38 C ATOM 37 O HIS A 61 12.874 40.275 12.498 1.00 9.97 O ATOM 38 CB HIS A 61 10.837 41.605 10.486 1.00 9.38 C ATOM 39 CG HIS A 61 9.512 42.014 9.909 1.00 8.78 C ATOM 40 ND1 HIS A 61 9.298 43.039 9.081 1.00 9.06 N ATOM 41 CD2 HIS A 61 8.304 41.455 10.105 1.00 11.08 C ATOM 42 CE1 HIS A 61 7.997 43.118 8.789 1.00 12.84 C ATOM 43 NE2 HIS A 61 7.381 42.061 9.398 1.00 11.66 N ATOM 44 H HIS A 61 10.043 41.827 12.717 1.00 7.19 H ATOM 45 HA HIS A 61 10.119 39.738 11.156 1.00 7.24 H ATOM 46 HB2 HIS A 61 11.225 42.374 10.933 1.00 9.38 H ATOM 47 HB3 HIS A 61 11.411 41.320 9.758 1.00 9.38 H ATOM 48 HD1 HIS A 61 9.906 43.568 8.781 1.00 9.06 H ATOM 49 HD2 HIS A 61 8.144 40.733 10.669 1.00 11.08 H ATOM 50 HE1 HIS A 61 7.587 43.770 8.268 1.00 12.84 H ATOM 51 HE2 HIS A 61 6.553 41.838 9.331 1.00 11.66 H ATOM 52 N PHE A 62 12.300 38.781 10.945 1.00 7.37 N ATOM 53 CA PHE A 62 13.573 38.090 10.989 1.00 7.69 C ATOM 54 C PHE A 62 14.659 39.009 10.437 1.00 8.66 C ATOM 55 O PHE A 62 14.567 39.469 9.302 1.00 8.67 O ATOM 56 CB PHE A 62 13.468 36.801 10.201 1.00 9.12 C ATOM 57 CG PHE A 62 14.736 35.956 10.204 1.00 8.46 C ATOM 58 CD1 PHE A 62 15.452 35.723 11.369 1.00 10.92 C ATOM 59 CD2 PHE A 62 15.186 35.393 9.017 1.00 12.32 C ATOM 60 CE1 PHE A 62 16.602 34.930 11.343 1.00 13.49 C ATOM 61 CE2 PHE A 62 16.297 34.631 8.988 1.00 14.14 C ATOM 62 CZ PHE A 62 16.979 34.320 10.172 1.00 13.67 C ATOM 63 H PHE A 62 11.741 38.462 10.375 1.00 7.37 H ATOM 64 HA PHE A 62 13.822 37.850 11.895 1.00 7.69 H ATOM 65 HB2 PHE A 62 13.263 37.018 9.278 1.00 9.12 H ATOM 66 HB3 PHE A 62 12.756 36.263 10.581 1.00 9.12 H ATOM 67 HD1 PHE A 62 15.165 36.096 12.171 1.00 10.92 H ATOM 68 HD2 PHE A 62 14.714 35.544 8.230 1.00 12.32 H ATOM 69 HE1 PHE A 62 17.109 34.816 12.114 1.00 13.49 H ATOM 70 HE2 PHE A 62 16.614 34.309 8.175 1.00 14.14 H ATOM 71 HZ PHE A 62 17.679 33.708 10.165 1.00 13.67 H TER HETATM 72 CU CU A 1 5.421 41.446 9.097 1.00 13.22 Cu HETATM 73 ZN ZN A 152 10.669 44.068 7.982 1.00 9.34 Zn HETATM 74 O HOH A 167 5.000 43.153 10.522 1.00 24.06 O HETATM 75 O HOH A 204 13.077 42.283 14.236 1.00 35.24 O """ if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))