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): # pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) # initial model model_initial = mmtbx.model.manager(model_input = pdb_inp, log = null_out()) hd_sel_initial = model_initial.get_hd_selection() number_h_expected = hd_sel_initial.count(True) ph_initial = model_initial.get_hierarchy() h_atoms_initial = ph_initial.select(hd_sel_initial).atoms() h_names_initial = list(h_atoms_initial.extract_name()) # remove H atoms model_without_h = model_initial.select(~hd_sel_initial) 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) # place H atoms again 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() h_atoms_added = ph_h_added.select(hd_sel_h_added).atoms() h_names_added = list(h_atoms_added.extract_name()) number_h_added = hd_sel_h_added.count(True) #f = open("bla_intermediate.pdb","w") #f.write(model_h_added.model_as_pdb()) #f.close() assert ph_initial.is_similar_hierarchy(other=ph_h_added) assert(number_h_expected == number_h_added) 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))} for name, sc in d2.items(): assert(name in d1) assert approx_equal(sc, d1[name], 0.01), name # ------------------------------------------------------------------------------ def test_000(): ''' CDL is true by default. Will crash for this example if is False. ''' compare_models(pdb_str = pdb_str_000) # ------------------------------------------------------------------------------ def test_001(): ''' clash between LYS 246 NZ & Tam 2 C5 --> fails in REDUCE Removing either Lys 246 NZ, or TAM 2 C5, or both of Lys 246 HZ1 and HZ3 will allow Reduce to run to completion and produce a usable result. However, Lys 246 HZ1 and HZ3 will not be added back by Reduce. ''' compare_models(pdb_str = pdb_str_001) # ------------------------------------------------------------------------------ def test_002(): ''' Test if multi-model file is supported ''' compare_models(pdb_str = pdb_str_002) # ------------------------------------------------------------------------------ def test_003(): ''' Check if normal and modified nucleic acid work. ''' compare_models(pdb_str = pdb_str_003) # ------------------------------------------------------------------------------ def test_004(): ''' Check if dc is processed correctly: TYR dc with every atom in either A or B ''' compare_models(pdb_str = pdb_str_004) # ------------------------------------------------------------------------------ def test_005(): ''' Check if dc is processed correctly: Glu dc with atoms in A or B or '' (blank) ''' compare_models(pdb_str = pdb_str_005) # ------------------------------------------------------------------------------ def test_006(): ''' Check if model without H to be placed is correctly processed ''' compare_models(pdb_str = pdb_str_006) # ------------------------------------------------------------------------------ def test_007(): ''' Check if mmCIF file format works ''' compare_models(pdb_str = pdb_str_007) # ------------------------------------------------------------------------------ def test_008(): ''' Test CYS-CYS disulfide with double conformation ''' compare_models(pdb_str = pdb_str_008) # ------------------------------------------------------------------------------ def test_009(): ''' 1KYC: SIN linked to GLU1, but later in file. Goal: no NH3 to GLU. ''' compare_models(pdb_str = pdb_str_009) assert 0 # ------------------------------------------------------------------------------ pdb_str_000 = """ REMARK This will crash if CDL is set to FALSE CRYST1 72.240 72.010 86.990 90.00 90.00 90.00 P 21 21 21 ATOM 1 N PRO H 1 52.628 -74.147 33.427 1.00 20.43 N ATOM 2 CA PRO H 1 53.440 -73.630 34.533 1.00 20.01 C ATOM 3 C PRO H 1 54.482 -72.584 34.124 1.00 20.76 C ATOM 4 O PRO H 1 55.025 -72.627 33.021 1.00 16.34 O ATOM 5 CB PRO H 1 54.055 -74.895 35.134 1.00 22.06 C ATOM 6 CG PRO H 1 54.084 -75.862 33.972 1.00 25.16 C ATOM 7 CD PRO H 1 52.770 -75.608 33.294 1.00 17.36 C ATOM 8 H2 PRO H 1 51.760 -73.969 33.583 1.00 20.43 H ATOM 9 H3 PRO H 1 52.881 -73.753 32.659 1.00 20.43 H ATOM 10 HA PRO H 1 52.877 -73.212 35.203 1.00 20.01 H ATOM 11 HB2 PRO H 1 54.949 -74.711 35.461 1.00 22.06 H ATOM 12 HB3 PRO H 1 53.499 -75.228 35.856 1.00 22.06 H ATOM 13 HG2 PRO H 1 54.830 -75.664 33.385 1.00 25.16 H ATOM 14 HG3 PRO H 1 54.147 -76.775 34.292 1.00 25.16 H ATOM 15 HD3 PRO H 1 52.801 -75.872 32.361 1.00 17.36 H ATOM 16 HD2 PRO H 1 52.048 -76.072 33.746 1.00 17.36 H ATOM 17 N SER H 2 54.727 -71.646 35.038 1.00 21.70 N ATOM 18 CA SER H 2 55.670 -70.537 34.874 1.00 25.33 C ATOM 19 C SER H 2 55.049 -69.401 34.057 1.00 24.78 C ATOM 20 O SER H 2 55.581 -68.291 34.023 1.00 27.51 O ATOM 21 CB SER H 2 56.982 -71.005 34.219 1.00 25.20 C ATOM 22 OG SER H 2 56.914 -70.938 32.802 1.00 28.91 O ATOM 23 H SER H 2 54.335 -71.634 35.803 1.00 21.70 H ATOM 24 HA SER H 2 55.899 -70.163 35.739 1.00 25.33 H ATOM 25 HB2 SER H 2 57.705 -70.434 34.524 1.00 25.20 H ATOM 26 HB3 SER H 2 57.151 -71.924 34.481 1.00 25.20 H ATOM 27 HG SER H 2 56.769 -70.147 32.558 1.00 28.91 H ATOM 28 N GLN H 3 53.918 -69.678 33.412 1.00 24.55 N ATOM 29 CA GLN H 3 53.224 -68.673 32.611 1.00 29.39 C ATOM 30 C GLN H 3 52.340 -67.778 33.475 1.00 28.13 C ATOM 31 O GLN H 3 52.234 -67.987 34.681 1.00 26.35 O ATOM 32 CB GLN H 3 52.371 -69.346 31.533 1.00 31.67 C ATOM 33 CG GLN H 3 53.196 -70.112 30.524 1.00 44.80 C ATOM 34 CD GLN H 3 54.379 -69.303 30.030 1.00 48.55 C ATOM 35 OE1 GLN H 3 54.213 -68.269 29.386 1.00 52.45 O ATOM 36 NE2 GLN H 3 55.584 -69.766 30.342 1.00 55.07 N ATOM 37 H GLN H 3 53.530 -70.445 33.423 1.00 24.55 H ATOM 38 HA GLN H 3 53.888 -68.112 32.179 1.00 29.39 H ATOM 39 HB2 GLN H 3 51.871 -68.665 31.056 1.00 31.67 H ATOM 40 HB3 GLN H 3 51.761 -69.970 31.957 1.00 31.67 H ATOM 41 HG2 GLN H 3 53.533 -70.922 30.937 1.00 44.80 H ATOM 42 HG3 GLN H 3 52.641 -70.335 29.761 1.00 44.80 H ATOM 43 HE21 GLN H 3 56.287 -69.343 30.085 1.00 55.07 H ATOM 44 HE22 GLN H 3 55.661 -70.489 30.801 1.00 55.07 H """ pdb_str_001 = """ REMARK this fails in REDUCE because of clash between LYS 246 NZ & Tam 2 C5 CRYST1 24.984 25.729 23.590 90.00 90.00 90.00 P 1 ATOM 1 N PRO A 245 13.194 10.192 16.658 1.00 41.32 N ATOM 2 CA PRO A 245 12.939 11.276 15.705 1.00 43.09 C ATOM 3 C PRO A 245 13.983 11.305 14.601 1.00 46.16 C ATOM 4 O PRO A 245 15.086 10.768 14.728 1.00 44.69 O ATOM 5 CB PRO A 245 13.007 12.541 16.569 1.00 42.50 C ATOM 6 CG PRO A 245 13.795 12.147 17.772 1.00 47.69 C ATOM 7 CD PRO A 245 13.504 10.698 18.006 1.00 45.37 C REMARK ATOM 8 H2 PRO A 245 12.414 9.635 16.709 1.00 41.32 H REMARK ATOM 9 H3 PRO A 245 13.938 9.673 16.344 1.00 41.32 H ATOM 10 HA PRO A 245 12.051 11.211 15.320 1.00 43.09 H ATOM 11 HB2 PRO A 245 13.452 13.251 16.080 1.00 42.50 H ATOM 12 HB3 PRO A 245 12.112 12.820 16.817 1.00 42.50 H ATOM 13 HG2 PRO A 245 14.740 12.283 17.601 1.00 47.69 H ATOM 14 HG3 PRO A 245 13.515 12.679 18.533 1.00 47.69 H ATOM 15 HD2 PRO A 245 14.279 10.246 18.375 1.00 45.37 H ATOM 16 HD3 PRO A 245 12.744 10.590 18.598 1.00 45.37 H ATOM 17 N LYS A 246 13.611 11.942 13.495 1.00 42.99 N ATOM 18 CA LYS A 246 14.551 12.132 12.404 1.00 43.44 C ATOM 19 C LYS A 246 15.633 13.122 12.832 1.00 46.25 C ATOM 20 O LYS A 246 15.332 14.110 13.510 1.00 45.93 O ATOM 21 CB LYS A 246 13.837 12.652 11.156 1.00 49.81 C ATOM 22 CG LYS A 246 12.652 11.809 10.713 1.00 54.70 C ATOM 23 CD LYS A 246 13.071 10.649 9.829 1.00 62.40 C ATOM 24 CE LYS A 246 11.928 9.661 9.640 1.00 71.25 C ATOM 25 NZ LYS A 246 10.594 10.329 9.556 1.00 76.52 N ATOM 26 H LYS A 246 12.828 12.269 13.355 1.00 42.99 H ATOM 27 HA LYS A 246 14.966 11.285 12.179 1.00 43.44 H ATOM 28 HB2 LYS A 246 14.472 12.674 10.423 1.00 49.81 H ATOM 29 HB3 LYS A 246 13.509 13.547 11.338 1.00 49.81 H ATOM 30 HG2 LYS A 246 12.208 11.447 11.496 1.00 54.70 H ATOM 31 HG3 LYS A 246 12.036 12.365 10.210 1.00 54.70 H ATOM 32 HD2 LYS A 246 13.815 10.182 10.241 1.00 62.40 H ATOM 33 HD3 LYS A 246 13.332 10.985 8.958 1.00 62.40 H ATOM 34 HE2 LYS A 246 11.910 9.050 10.393 1.00 71.25 H ATOM 35 HE3 LYS A 246 12.069 9.168 8.816 1.00 71.25 H REMARK ATOM 36 HZ1 LYS A 246 9.955 9.720 9.446 1.00 76.52 H REMARK ATOM 37 HZ2 LYS A 246 10.578 10.892 8.867 1.00 76.52 H REMARK ATOM 38 HZ3 LYS A 246 10.434 10.784 10.304 1.00 76.52 H ATOM 39 N PRO A 247 16.897 12.890 12.459 1.00 44.07 N ATOM 40 CA PRO A 247 17.961 13.810 12.905 1.00 39.69 C ATOM 41 C PRO A 247 17.659 15.272 12.622 1.00 41.96 C ATOM 42 O PRO A 247 17.848 16.127 13.497 1.00 43.51 O ATOM 43 CB PRO A 247 19.188 13.316 12.126 1.00 43.94 C ATOM 44 CG PRO A 247 18.912 11.884 11.852 1.00 47.67 C ATOM 45 CD PRO A 247 17.430 11.781 11.650 1.00 44.76 C ATOM 46 HA PRO A 247 18.124 13.716 13.857 1.00 39.69 H ATOM 47 HB3 PRO A 247 19.279 13.817 11.300 1.00 43.94 H ATOM 48 HB2 PRO A 247 19.987 13.419 12.667 1.00 43.94 H ATOM 49 HG2 PRO A 247 19.193 11.346 12.609 1.00 47.67 H ATOM 50 HG3 PRO A 247 19.387 11.607 11.053 1.00 47.67 H ATOM 51 HD2 PRO A 247 17.201 11.896 10.714 1.00 44.76 H ATOM 52 HD3 PRO A 247 17.097 10.929 11.971 1.00 44.76 H TER HETATM 48 N TAM H 2 9.323 12.496 7.335 1.00 20.00 N HETATM 49 C TAM H 2 8.060 12.492 8.002 1.00 20.00 C HETATM 50 C1 TAM H 2 7.540 13.901 8.071 1.00 20.00 C HETATM 51 C2 TAM H 2 8.386 11.881 9.335 1.00 20.00 C HETATM 52 C3 TAM H 2 7.035 11.686 7.294 1.00 20.00 C HETATM 53 C4 TAM H 2 7.128 14.539 6.744 1.00 20.00 C HETATM 54 C5 TAM H 2 8.930 10.458 9.271 1.00 20.00 C HETATM 55 C6 TAM H 2 5.660 11.992 7.821 1.00 20.00 C HETATM 56 O4 TAM H 2 5.710 14.391 6.585 1.00 20.00 O HETATM 57 O5 TAM H 2 7.872 9.487 9.299 1.00 20.00 O HETATM 58 O6 TAM H 2 5.714 12.262 9.200 1.00 20.00 O HETATM 59 H11 TAM H 2 6.779 13.910 8.672 1.00 20.00 H HETATM 60 H12 TAM H 2 8.223 14.452 8.485 1.00 20.00 H HETATM 61 H21 TAM H 2 7.589 11.879 9.888 1.00 20.00 H HETATM 62 H22 TAM H 2 9.038 12.437 9.790 1.00 20.00 H HETATM 63 H31 TAM H 2 7.225 10.740 7.392 1.00 20.00 H HETATM 64 H32 TAM H 2 7.071 11.859 6.340 1.00 20.00 H HETATM 65 H41 TAM H 2 7.600 14.117 6.009 1.00 20.00 H HETATM 66 H42 TAM H 2 7.377 15.476 6.732 1.00 20.00 H HETATM 67 H61 TAM H 2 5.264 12.763 7.385 1.00 20.00 H HETATM 68 H62 TAM H 2 5.044 11.254 7.689 1.00 20.00 H HETATM 69 HN1 TAM H 2 9.235 12.859 6.527 1.00 20.00 H HETATM 70 HN2 TAM H 2 9.942 12.134 7.862 1.00 20.00 H """ pdb_str_002 = """ REMARK This is a multi model file --> check if this works CRYST1 16.760 20.171 17.648 90.00 90.00 90.00 P 1 MODEL 1 ATOM 1 N GLY A -3 14.573 7.304 5.082 1.00 23.20 N ATOM 2 CA GLY A -3 15.503 6.752 6.050 1.00 43.12 C ATOM 3 C GLY A -3 16.822 7.516 6.092 1.00 10.33 C ATOM 4 O GLY A -3 17.833 7.000 5.608 1.00 34.23 O ATOM 5 HA2 GLY A -3 15.692 5.828 5.822 1.00 43.12 H ATOM 6 HA3 GLY A -3 15.103 6.784 6.933 1.00 43.12 H ATOM 7 N PRO A -2 16.855 8.759 6.667 1.00 43.42 N ATOM 8 CA PRO A -2 18.084 9.573 6.756 1.00 72.12 C ATOM 9 C PRO A -2 19.050 9.085 7.843 1.00 24.33 C ATOM 10 O PRO A -2 20.269 9.138 7.662 1.00 1.42 O ATOM 11 CB PRO A -2 17.569 10.986 7.098 1.00 65.32 C ATOM 12 CG PRO A -2 16.078 10.915 7.005 1.00 23.11 C ATOM 13 CD PRO A -2 15.713 9.483 7.257 1.00 3.14 C ATOM 14 HA PRO A -2 18.527 9.578 5.893 1.00 72.12 H ATOM 15 HB2 PRO A -2 17.846 11.226 7.996 1.00 65.32 H ATOM 16 HB3 PRO A -2 17.923 11.625 6.460 1.00 65.32 H ATOM 17 HG2 PRO A -2 15.793 11.190 6.120 1.00 23.11 H ATOM 18 HG3 PRO A -2 15.682 11.493 7.676 1.00 23.11 H ATOM 19 HD2 PRO A -2 15.639 9.304 8.207 1.00 3.14 H ATOM 20 HD3 PRO A -2 14.884 9.250 6.810 1.00 3.14 H ATOM 21 N SER A -1 18.485 8.603 8.974 1.00 54.30 N ATOM 22 CA SER A -1 19.258 8.090 10.133 1.00 74.21 C ATOM 23 C SER A -1 20.126 9.182 10.770 1.00 44.31 C ATOM 24 O SER A -1 20.919 9.834 10.087 1.00 24.24 O ATOM 25 CB SER A -1 20.129 6.881 9.741 1.00 35.31 C ATOM 26 OG SER A -1 20.678 6.247 10.885 1.00 34.24 O ATOM 27 H SER A -1 17.635 8.561 9.098 1.00 54.30 H ATOM 28 HA SER A -1 18.623 7.790 10.802 1.00 74.21 H ATOM 29 HB2 SER A -1 20.854 7.187 9.174 1.00 35.31 H ATOM 30 HB3 SER A -1 19.580 6.241 9.261 1.00 35.31 H ATOM 31 HG SER A -1 21.157 6.789 11.312 1.00 34.24 H TER ENDMDL MODEL 2 ATOM 35 N GLY A -3 15.598 12.155 12.730 1.00 23.20 N ATOM 36 CA GLY A -3 15.801 13.217 11.761 1.00 43.12 C ATOM 37 C GLY A -3 15.603 12.746 10.322 1.00 10.33 C ATOM 38 O GLY A -3 14.940 11.727 10.105 1.00 34.23 O ATOM 39 HA3 GLY A -3 15.172 13.934 11.936 1.00 43.12 H ATOM 40 HA2 GLY A -3 16.704 13.561 11.848 1.00 43.12 H ATOM 41 N PRO A -2 16.164 13.467 9.301 1.00 43.42 N ATOM 42 CA PRO A -2 16.028 13.090 7.880 1.00 72.12 C ATOM 43 C PRO A -2 16.904 11.891 7.491 1.00 24.33 C ATOM 44 O PRO A -2 16.479 11.039 6.705 1.00 1.42 O ATOM 45 CB PRO A -2 16.479 14.351 7.114 1.00 65.32 C ATOM 46 CG PRO A -2 16.651 15.418 8.147 1.00 23.11 C ATOM 47 CD PRO A -2 16.953 14.708 9.432 1.00 3.14 C ATOM 48 HA PRO A -2 15.094 12.906 7.692 1.00 72.12 H ATOM 49 HB2 PRO A -2 17.317 14.174 6.659 1.00 65.32 H ATOM 50 HB3 PRO A -2 15.799 14.602 6.470 1.00 65.32 H ATOM 51 HG3 PRO A -2 15.832 15.932 8.224 1.00 23.11 H ATOM 52 HG2 PRO A -2 17.386 15.999 7.896 1.00 23.11 H ATOM 53 HD2 PRO A -2 17.900 14.513 9.508 1.00 3.14 H ATOM 54 HD3 PRO A -2 16.659 15.229 10.196 1.00 3.14 H ATOM 55 N SER A -1 18.123 11.839 8.047 1.00 54.30 N ATOM 56 CA SER A -1 19.064 10.752 7.768 1.00 74.21 C ATOM 57 C SER A -1 19.650 10.188 9.066 1.00 44.31 C ATOM 58 O SER A -1 19.683 8.969 9.256 1.00 24.24 O ATOM 59 CB SER A -1 20.187 11.243 6.843 1.00 35.31 C ATOM 60 OG SER A -1 20.983 10.164 6.382 1.00 34.24 O ATOM 61 H SER A -1 18.429 12.428 8.594 1.00 54.30 H ATOM 62 HA SER A -1 18.597 10.032 7.316 1.00 74.21 H ATOM 63 HB2 SER A -1 20.750 11.861 7.334 1.00 35.31 H ATOM 64 HB3 SER A -1 19.791 11.690 6.079 1.00 35.31 H ATOM 65 HG SER A -1 21.333 9.767 7.034 1.00 34.24 H TER ENDMDL """ pdb_str_003 = """ REMARK PDB snippet with a normal and a modified nucleic acid CRYST1 17.826 22.060 19.146 90.00 90.00 90.00 P 1 ATOM 1 P U A 2 7.236 16.525 9.726 1.00 37.21 P ATOM 2 OP1 U A 2 6.663 17.060 10.993 1.00 38.75 O ATOM 3 OP2 U A 2 8.650 16.805 9.385 1.00 34.84 O ATOM 4 O5' U A 2 7.029 14.947 9.685 1.00 34.31 O ATOM 5 C5' U A 2 5.756 14.354 9.974 1.00 37.02 C ATOM 6 C4' U A 2 5.821 12.860 9.763 1.00 36.81 C ATOM 7 O4' U A 2 5.957 12.552 8.350 1.00 36.96 O ATOM 8 C3' U A 2 7.025 12.178 10.388 1.00 36.55 C ATOM 9 O3' U A 2 6.846 11.969 11.775 1.00 36.22 O ATOM 10 C2' U A 2 7.106 10.884 9.592 1.00 36.94 C ATOM 11 O2' U A 2 6.138 9.930 9.980 1.00 38.55 O ATOM 12 C1' U A 2 6.755 11.383 8.191 1.00 36.22 C ATOM 13 N1 U A 2 7.938 11.735 7.391 1.00 34.47 N ATOM 14 C2 U A 2 8.652 10.705 6.795 1.00 33.67 C ATOM 15 O2 U A 2 8.375 9.526 6.954 1.00 33.54 O ATOM 16 N3 U A 2 9.706 11.110 6.014 1.00 33.13 N ATOM 17 C4 U A 2 10.119 12.408 5.784 1.00 32.43 C ATOM 18 O4 U A 2 11.043 12.620 5.000 1.00 31.05 O ATOM 19 C5 U A 2 9.352 13.409 6.464 1.00 33.80 C ATOM 20 C6 U A 2 8.316 13.048 7.223 1.00 33.46 C ATOM 21 H4* U A 2 5.000 12.459 10.088 1.00 36.81 H ATOM 22 H3* U A 2 7.826 12.702 10.232 1.00 36.55 H ATOM 23 H2* U A 2 7.997 10.505 9.648 1.00 36.94 H ATOM 24 HO2* U A 2 5.578 9.841 9.360 1.00 38.55 H ATOM 25 H1* U A 2 6.256 10.694 7.724 1.00 36.22 H ATOM 26 H5 U A 2 9.576 14.307 6.377 1.00 33.80 H ATOM 27 H5*2 U A 2 5.515 14.540 10.895 1.00 37.02 H ATOM 28 H5*1 U A 2 5.082 14.734 9.388 1.00 37.02 H ATOM 29 H3 U A 2 10.157 10.489 5.626 1.00 33.13 H ATOM 30 H6 U A 2 7.829 13.711 7.657 1.00 33.46 H HETATM 31 P UMS A 3 8.115 12.049 12.757 1.00 35.65 P HETATM 32 OP1 UMS A 3 7.608 12.006 14.146 1.00 37.56 O HETATM 33 OP2 UMS A 3 8.986 13.173 12.329 1.00 35.79 O HETATM 34 O5' UMS A 3 8.946 10.722 12.449 1.00 37.12 O HETATM 35 C5' UMS A 3 8.323 9.447 12.591 1.00 36.88 C HETATM 36 C4' UMS A 3 9.203 8.363 12.041 1.00 39.11 C HETATM 37 O4' UMS A 3 9.187 8.277 10.585 1.00 38.36 O HETATM 38 C3' UMS A 3 10.640 8.278 12.458 1.00 40.33 C HETATM 39 O3' UMS A 3 10.895 8.001 13.828 1.00 40.80 O HETATM 40 C2' UMS A 3 11.291 7.467 11.374 1.00 40.93 C HETATM 41 C1' UMS A 3 10.496 7.904 10.133 1.00 38.75 C HETATM 42 N1 UMS A 3 11.106 9.042 9.429 1.00 36.80 N HETATM 43 C2 UMS A 3 12.013 8.736 8.436 1.00 35.25 C HETATM 44 O2 UMS A 3 12.328 7.589 8.163 1.00 36.36 O HETATM 45 N3 UMS A 3 12.557 9.822 7.786 1.00 33.98 N HETATM 46 C4 UMS A 3 12.275 11.159 7.996 1.00 32.51 C HETATM 47 O4 UMS A 3 12.826 12.001 7.302 1.00 33.01 O HETATM 48 C5 UMS A 3 11.323 11.402 9.046 1.00 33.90 C HETATM 49 C6 UMS A 3 10.817 10.354 9.743 1.00 34.62 C HETATM 50 CA' UMS A 3 11.776 5.000 13.480 1.00 46.26 C HETATM 51 SE2' UMS A 3 10.815 5.400 11.905 1.00 48.17 Se HETATM 53 H3* UMS A 3 11.022 9.152 12.279 1.00 40.33 H HETATM 54 H3 UMS A 3 13.140 9.648 7.179 1.00 33.98 H HETATM 55 H1* UMS A 3 10.387 7.156 9.525 1.00 38.75 H HETATM 56 H6 UMS A 3 10.252 10.527 10.462 1.00 34.62 H HETATM 57 H4* UMS A 3 8.782 7.553 12.369 1.00 39.11 H HETATM 58 H5*2 UMS A 3 7.481 9.448 12.109 1.00 36.88 H HETATM 59 H5 UMS A 3 11.056 12.270 9.246 1.00 33.90 H HETATM 60 H5* UMS A 3 8.158 9.276 13.531 1.00 36.88 H HETATM 64 H2* UMS A 3 12.022 6.833 11.440 1.00 40.93 H """ pdb_str_004 = ''' REMARK TYR double conformation where *every* atom is in either A or B CRYST1 15.639 15.148 16.657 90.00 90.00 90.00 P 1 ATOM 1 N ATYR A 59 5.624 5.492 5.997 0.63 5.05 N ATOM 2 CA ATYR A 59 6.283 5.821 7.250 0.63 5.48 C ATOM 3 C ATYR A 59 5.451 6.841 8.030 0.63 6.01 C ATOM 4 O ATYR A 59 5.000 7.863 7.506 0.63 6.38 O ATOM 5 CB ATYR A 59 7.724 6.421 6.963 0.63 5.57 C ATOM 6 CG ATYR A 59 8.212 7.215 8.170 0.63 6.71 C ATOM 7 CD1ATYR A 59 8.690 6.541 9.297 0.63 7.05 C ATOM 8 CD2ATYR A 59 8.071 8.583 8.242 0.63 8.31 C ATOM 9 CE1ATYR A 59 9.100 7.172 10.481 0.63 7.99 C ATOM 10 CE2ATYR A 59 8.408 9.230 9.447 0.63 9.07 C ATOM 11 CZ ATYR A 59 8.919 8.547 10.507 0.63 9.01 C ATOM 12 OH ATYR A 59 9.211 9.255 11.657 0.63 12.31 O ATOM 13 HA ATYR A 59 6.384 5.020 7.788 0.63 5.48 H ATOM 14 HB2ATYR A 59 7.683 7.014 6.196 0.63 5.57 H ATOM 15 HB3ATYR A 59 8.349 5.699 6.792 0.63 5.57 H ATOM 16 HD1ATYR A 59 8.740 5.613 9.260 0.63 7.05 H ATOM 17 HD2ATYR A 59 7.760 9.068 7.512 0.63 8.31 H ATOM 18 HE1ATYR A 59 9.466 6.703 11.196 0.63 7.99 H ATOM 19 HE2ATYR A 59 8.278 10.148 9.520 0.63 9.07 H ATOM 20 HH ATYR A 59 9.058 10.072 11.538 0.63 12.31 H ATOM 21 N BTYR A 59 5.613 5.513 5.963 0.37 5.75 N ATOM 22 CA BTYR A 59 6.322 5.809 7.211 0.37 5.49 C ATOM 23 C BTYR A 59 5.795 6.953 8.094 0.37 5.14 C ATOM 24 O BTYR A 59 5.668 8.090 7.641 0.37 6.42 O ATOM 25 CB BTYR A 59 7.798 6.076 6.900 0.37 7.77 C ATOM 26 CG BTYR A 59 8.556 6.722 8.038 0.37 5.20 C ATOM 27 CD1BTYR A 59 9.162 5.951 9.021 0.37 8.94 C ATOM 28 CD2BTYR A 59 8.665 8.103 8.129 0.37 6.25 C ATOM 29 CE1BTYR A 59 9.856 6.537 10.063 0.37 11.97 C ATOM 30 CE2BTYR A 59 9.357 8.699 9.167 0.37 9.52 C ATOM 31 CZ BTYR A 59 9.950 7.911 10.131 0.37 12.68 C ATOM 32 OH BTYR A 59 10.639 8.500 11.166 0.37 26.50 O ATOM 33 HA BTYR A 59 6.185 5.019 7.758 0.37 5.49 H ATOM 34 HB2BTYR A 59 7.853 6.669 6.134 0.37 7.77 H ATOM 35 HB3BTYR A 59 8.231 5.232 6.698 0.37 7.77 H ATOM 36 HD1BTYR A 59 9.100 5.024 8.978 0.37 8.94 H ATOM 37 HD2BTYR A 59 8.266 8.637 7.480 0.37 6.25 H ATOM 38 HE1BTYR A 59 10.257 6.008 10.714 0.37 11.97 H ATOM 39 HE2BTYR A 59 9.422 9.625 9.215 0.37 9.52 H ATOM 40 HH BTYR A 59 10.618 9.336 11.086 0.37 26.50 H ''' pdb_str_005 = ''' REMARK Glu double conformation where atoms are either A, B or '' (blank) CRYST1 13.702 13.985 14.985 90.00 90.00 90.00 P 1 ATOM 1 N GLU A 78 8.702 8.360 5.570 1.00 35.65 N ATOM 2 C GLU A 78 6.379 7.842 5.202 1.00 35.59 C ATOM 3 O GLU A 78 5.975 8.985 5.000 1.00 35.38 O ATOM 4 CA AGLU A 78 7.598 7.571 6.076 0.70 35.57 C ATOM 5 CB AGLU A 78 7.301 7.887 7.536 0.70 35.75 C ATOM 6 CG AGLU A 78 6.481 6.798 8.188 0.70 36.10 C ATOM 7 CD AGLU A 78 5.833 7.232 9.476 0.70 37.70 C ATOM 8 OE1AGLU A 78 6.155 8.333 9.982 0.70 38.74 O ATOM 9 OE2AGLU A 78 5.000 6.456 9.985 0.70 37.65 O ATOM 10 HA AGLU A 78 7.819 6.627 6.051 0.70 35.57 H ATOM 11 HB2AGLU A 78 6.802 8.717 7.588 0.70 35.75 H ATOM 12 HB3AGLU A 78 8.137 7.971 8.021 0.70 35.75 H ATOM 13 HG2AGLU A 78 5.778 6.526 7.578 0.70 36.10 H ATOM 14 HG3AGLU A 78 7.059 6.044 8.385 0.70 36.10 H ATOM 15 CA BGLU A 78 7.581 7.608 6.115 0.30 35.61 C ATOM 16 CB BGLU A 78 7.269 8.093 7.534 0.30 35.70 C ATOM 17 CG BGLU A 78 6.166 7.322 8.245 0.30 36.05 C ATOM 18 CD BGLU A 78 6.683 6.115 9.003 0.30 36.79 C ATOM 19 OE1BGLU A 78 7.585 6.285 9.856 0.30 37.19 O ATOM 20 OE2BGLU A 78 6.173 5.000 8.760 0.30 37.31 O ATOM 21 HA BGLU A 78 7.779 6.660 6.170 0.30 35.61 H ATOM 22 HB2BGLU A 78 8.073 8.013 8.070 0.30 35.70 H ATOM 23 HB3BGLU A 78 6.992 9.022 7.488 0.30 35.70 H ATOM 24 HG3BGLU A 78 5.525 7.010 7.587 0.30 36.05 H ATOM 25 HG2BGLU A 78 5.730 7.910 8.881 0.30 36.05 H ''' pdb_str_006 = ''' REMARK Hg, Sr and HOH: no H atoms are expected to be placed CRYST1 10.286 24.260 13.089 90.00 90.00 90.00 P 1 HETATM 1 HG HG A 101 5.000 7.056 5.951 0.60 17.71 HG HETATM 2 SR SR A 102 5.182 10.793 8.089 0.85 18.78 SR HETATM 3 O HOH A 201 5.093 5.000 5.000 1.00 25.34 O HETATM 4 O HOH A 202 5.286 19.260 7.818 1.00 28.43 O ''' # check if mmCIF file works pdb_str_007 = ''' data_1UBQ # _entry.id 1UBQ # _cell.entry_id 1UBQ _cell.length_a 50.840 _cell.length_b 42.770 _cell.length_c 28.950 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 # _symmetry.entry_id 1UBQ _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.Int_Tables_number 19 # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 594 N N . GLY A 1 75 ? 41.165 35.531 31.898 0.25 36.31 ? 75 GLY A N 1 ATOM 595 C CA . GLY A 1 75 ? 41.845 36.550 32.686 0.25 36.07 ? 75 GLY A CA 1 ATOM 596 C C . GLY A 1 75 ? 41.251 37.941 32.588 0.25 36.16 ? 75 GLY A C 1 ATOM 597 O O . GLY A 1 75 ? 41.102 38.523 31.500 0.25 36.26 ? 75 GLY A O 1 ATOM 598 H HA2 . GLY A 1 75 ? 42.768 36.603 32.393 0.25 36.07 ? 75 GLY A HA3 1 ATOM 599 H HA3 . GLY A 1 75 ? 41.823 36.286 33.619 0.25 36.07 ? 75 GLY A HA2 1 ATOM 600 N N . GLY A 1 76 ? 40.946 38.472 33.757 0.25 36.05 ? 76 GLY A N 1 ATOM 601 C CA . GLY A 1 76 ? 40.373 39.813 33.944 0.25 36.19 ? 76 GLY A CA 1 ATOM 602 C C . GLY A 1 76 ? 40.031 39.992 35.432 0.25 36.20 ? 76 GLY A C 1 ATOM 603 O O . GLY A 1 76 ? 38.933 40.525 35.687 0.25 36.13 ? 76 GLY A O 1 ATOM 604 O OXT . GLY A 1 76 ? 40.862 39.575 36.251 0.25 36.27 ? 76 GLY A OXT 1 ATOM 605 H H . GLY A 1 76 ? 41.063 38.062 34.504 0.25 36.05 ? 76 GLY A H 1 ATOM 606 H HA3 . GLY A 1 76 ? 39.566 39.910 33.413 0.25 36.19 ? 76 GLY A HA3 1 ATOM 607 H HA2 . GLY A 1 76 ? 41.011 40.491 33.675 0.25 36.19 ? 76 GLY A HA2 1 HETATM 611 O O . HOH B 2 . ? 45.747 30.081 19.708 1.00 12.43 ? 77 HOH A O 1 ''' pdb_str_008 = ''' REMARK disulfide bond with altloc CRYST1 13.626 15.799 17.617 90.00 90.00 90.00 P 1 ATOM 1 N CYS A 27 17.541 4.439 12.897 1.00 13.99 N ATOM 2 CA CYS A 27 16.566 5.527 12.862 1.00 14.57 C ATOM 3 C CYS A 27 16.236 6.026 11.467 1.00 14.53 C ATOM 4 O CYS A 27 15.254 6.760 11.351 1.00 16.95 O ATOM 5 CB CYS A 27 17.114 6.698 13.662 1.00 15.77 C ATOM 6 SG CYS A 27 17.230 6.332 15.443 1.00 17.57 S ATOM 7 HA CYS A 27 15.739 5.186 13.237 1.00 14.57 H ATOM 8 HB2 CYS A 27 16.526 7.461 13.549 1.00 15.77 H ATOM 9 HB3 CYS A 27 18.003 6.913 13.340 1.00 15.77 H ATOM 10 CB CYS A 123 14.607 7.591 16.260 1.00 24.16 C ATOM 11 SG CYS A 123 15.316 5.939 15.946 1.00 20.05 S ATOM 12 N ACYS A 123 15.023 7.279 18.624 0.58 26.40 N ATOM 14 CA ACYS A 123 15.266 8.190 17.491 0.58 25.69 C ATOM 15 C ACYS A 123 14.764 9.599 17.776 0.58 26.33 C ATOM 16 O ACYS A 123 14.197 10.238 16.886 0.58 28.70 O ATOM 17 OXTACYS A 123 14.975 10.081 18.878 0.58 28.31 O ATOM 18 HA ACYS A 123 16.217 8.287 17.324 0.58 25.69 H ATOM 19 HB2ACYS A 123 13.652 7.502 16.408 1.00 24.16 H ATOM 20 HB3ACYS A 123 14.772 8.157 15.490 1.00 24.16 H ATOM 22 N BCYS A 123 15.023 7.288 18.685 0.42 25.68 N ATOM 23 CA BCYS A 123 15.108 8.205 17.548 0.42 25.86 C ATOM 24 C BCYS A 123 14.270 9.460 17.813 0.42 26.42 C ATOM 26 O BCYS A 123 13.915 10.125 16.837 0.42 27.75 O ATOM 27 OXTBCYS A 123 13.981 9.728 18.968 0.42 28.04 O ATOM 28 HA BCYS A 123 16.045 8.426 17.432 0.42 25.86 H ATOM 29 HB2BCYS A 123 13.642 7.500 16.307 1.00 24.16 H ATOM 30 HB3BCYS A 123 14.850 8.168 15.519 1.00 24.16 H ''' pdb_str_009 = ''' REMARK 1KYC: SIN is linked to GLU 1, but at end of model file CRYST1 19.769 30.000 32.270 90.00 90.00 90.00 P 1 ATOM 1 N GLU A 1 9.100 10.903 6.846 1.00 18.32 N ATOM 2 CA GLU A 1 8.321 10.315 7.917 1.00 16.97 C ATOM 3 C GLU A 1 9.162 9.612 8.973 1.00 15.25 C ATOM 4 O GLU A 1 8.910 9.774 10.170 1.00 14.23 O ATOM 5 CB GLU A 1 7.291 9.304 7.380 1.00 17.54 C ATOM 6 CG GLU A 1 6.485 8.581 8.454 1.00 19.79 C ATOM 7 CD GLU A 1 5.488 9.479 9.156 1.00 20.81 C ATOM 8 OE1 GLU A 1 5.000 10.445 8.534 1.00 23.39 O ATOM 9 OE2 GLU A 1 5.180 9.223 10.333 1.00 21.60 O ATOM 10 HA GLU A 1 7.863 11.056 8.343 1.00 16.97 H ATOM 11 HB2 GLU A 1 6.662 9.777 6.812 1.00 17.54 H ATOM 12 HB3 GLU A 1 7.761 8.630 6.865 1.00 17.54 H ATOM 13 HG2 GLU A 1 7.094 8.232 9.123 1.00 19.79 H ATOM 14 HG3 GLU A 1 5.993 7.854 8.042 1.00 19.79 H ATOM 15 N GLU A 2 10.111 8.769 8.574 1.00 15.28 N ATOM 16 CA GLU A 2 10.916 8.018 9.519 1.00 14.99 C ATOM 17 C GLU A 2 11.541 8.882 10.615 1.00 13.85 C ATOM 18 O GLU A 2 11.362 8.667 11.822 1.00 13.88 O ATOM 19 CB GLU A 2 12.024 7.270 8.757 1.00 16.20 C ATOM 20 CG GLU A 2 12.869 6.426 9.713 1.00 17.22 C ATOM 21 CD GLU A 2 14.152 5.903 9.124 1.00 17.43 C ATOM 22 OE1 GLU A 2 14.556 6.396 8.052 1.00 18.62 O ATOM 23 OE2 GLU A 2 14.769 5.000 9.734 1.00 17.26 O ATOM 24 H GLU A 2 10.307 8.616 7.751 1.00 15.28 H ATOM 25 HA GLU A 2 10.334 7.388 9.972 1.00 14.99 H ATOM 26 HB2 GLU A 2 12.604 7.912 8.318 1.00 16.20 H ATOM 27 HB3 GLU A 2 11.622 6.681 8.099 1.00 16.20 H ATOM 28 HG2 GLU A 2 13.101 6.970 10.482 1.00 17.22 H ATOM 29 HG3 GLU A 2 12.344 5.661 9.995 1.00 17.22 H HETATM 30 O1 SO4 A 101 11.629 25.000 26.048 0.50 20.11 O HETATM 31 O2 SO4 A 101 10.541 22.822 26.297 0.50 21.85 O HETATM 32 O3 SO4 A 101 9.524 24.537 24.875 0.50 20.45 O HETATM 33 O4 SO4 A 101 9.520 24.852 27.270 0.50 19.22 O HETATM 34 S SO4 A 101 10.313 24.291 26.126 0.50 19.91 S HETATM 35 C1 SIN A 0 10.126 11.723 7.051 1.00 19.39 C HETATM 36 C2 SIN A 0 10.828 12.260 5.817 1.00 21.62 C HETATM 37 C3 SIN A 0 11.448 13.629 6.056 1.00 22.69 C HETATM 38 C4 SIN A 0 10.468 14.784 6.095 1.00 23.92 C HETATM 39 O1 SIN A 0 10.519 11.999 8.189 1.00 19.91 O HETATM 40 O3 SIN A 0 10.949 15.933 6.216 1.00 24.14 O HETATM 41 O4 SIN A 0 9.264 14.547 6.337 1.00 25.37 O HETATM 42 H21 SIN A 0 10.110 12.330 5.000 1.00 21.62 H HETATM 43 H22 SIN A 0 11.609 11.561 5.518 1.00 21.62 H HETATM 44 H31 SIN A 0 11.985 13.602 7.004 1.00 22.69 H HETATM 45 H32 SIN A 0 12.173 13.820 5.265 1.00 22.69 H ''' if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))