from __future__ import absolute_import, division, print_function from iotbx import pdb from mmtbx import monomer_library import mmtbx.monomer_library.server import mmtbx.monomer_library.pdb_interpretation from libtbx.utils import Sorry, search_for, format_cpu_times, null_out from libtbx.test_utils import Exception_expected, block_show_diff, approx_equal import libtbx.load_env import iotbx.phil from libtbx import Auto from six.moves import cStringIO as StringIO import os import sys from cctbx.array_family import flex from six.moves import zip params = monomer_library.pdb_interpretation.master_params.extract() params.flip_symmetric_amino_acids = False def exercise_handle_case_insensitive(mon_lib_srv, ener_lib): def check(a, r, e): raw_records = ("""\ HETATM 1 %s %s F 1 -7.869 17.488 18.637 1.00 30.00 %s """ % (a,r,e)).splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, params=params, raw_records=raw_records, log=log) log_lines = log.getvalue().splitlines() lines=search_for( pattern="""\ Unusual residues: {' %s': 1}""" % r, mode="==", lines=log_lines) assert len(lines) == 1 assert len(log_lines) == 14 vars = ["ZN", "Zn"] for a in vars: for r in vars: for e in vars: check(a, r, e) def exercise_rna_v3(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 401.998 401.998 175.648 90.00 90.00 90.00 P 41 21 2 ATOM 25432 P G A1206 198.794 115.083 28.238 1.00 76.49 P ATOM 25433 OP1 G A1206 198.375 115.264 29.645 1.00 77.28 O ATOM 25434 OP2 G A1206 200.140 114.542 27.966 1.00 76.41 O ATOM 25435 O5' G A1206 197.705 114.233 27.449 1.00 76.56 O ATOM 25436 C5' G A1206 196.418 114.761 27.170 1.00 76.79 C ATOM 25437 C4' G A1206 195.633 113.833 26.279 1.00 77.12 C ATOM 25438 O4' G A1206 196.015 114.053 24.894 1.00 77.27 O ATOM 25439 C3' G A1206 195.867 112.344 26.510 1.00 77.37 C ATOM 25440 O3' G A1206 195.077 111.810 27.556 1.00 77.97 O ATOM 25441 C2' G A1206 195.569 111.736 25.150 1.00 77.22 C ATOM 25442 O2' G A1206 194.170 111.623 24.952 1.00 76.79 O ATOM 25443 C1' G A1206 196.112 112.819 24.214 1.00 77.65 C ATOM 25444 N9 G A1206 197.533 112.591 23.877 1.00 78.00 N ATOM 25445 C8 G A1206 198.581 113.321 24.380 1.00 78.03 C ATOM 25446 N7 G A1206 199.744 112.915 23.956 1.00 78.32 N ATOM 25447 C5 G A1206 199.447 111.851 23.119 1.00 77.90 C ATOM 25448 C6 G A1206 200.326 111.029 22.380 1.00 77.52 C ATOM 25449 O6 G A1206 201.557 111.100 22.331 1.00 77.98 O ATOM 25450 N1 G A1206 199.635 110.063 21.665 1.00 77.35 N ATOM 25451 C2 G A1206 198.270 109.923 21.660 1.00 76.93 C ATOM 25452 N2 G A1206 197.791 108.932 20.898 1.00 76.75 N ATOM 25453 N3 G A1206 197.437 110.686 22.346 1.00 77.12 N ATOM 25454 C4 G A1206 198.088 111.632 23.050 1.00 77.74 C HETATM25455 P 2MG A1207 195.612 110.560 28.417 1.00 79.39 P HETATM25456 OP1 2MG A1207 194.636 110.113 29.435 1.00 80.29 O HETATM25457 OP2 2MG A1207 196.934 111.063 28.860 1.00 79.14 O HETATM25458 O5' 2MG A1207 195.767 109.399 27.334 1.00 79.02 O HETATM25459 C5' 2MG A1207 194.639 108.661 26.891 1.00 79.38 C HETATM25460 C4' 2MG A1207 195.005 107.705 25.788 1.00 79.65 C HETATM25461 O4' 2MG A1207 195.607 108.447 24.695 1.00 80.37 O HETATM25462 C3' 2MG A1207 196.032 106.636 26.145 1.00 79.49 C HETATM25463 O3' 2MG A1207 195.452 105.486 26.729 1.00 79.21 O HETATM25464 C2' 2MG A1207 196.714 106.355 24.818 1.00 80.16 C HETATM25465 O2' 2MG A1207 195.930 105.477 24.030 1.00 80.10 O HETATM25466 C1' 2MG A1207 196.702 107.734 24.168 1.00 80.84 C HETATM25467 N9 2MG A1207 197.946 108.483 24.449 1.00 22.09 N HETATM25468 C8 2MG A1207 198.164 109.755 25.238 1.00 22.18 C HETATM25469 N7 2MG A1207 199.619 110.140 25.258 1.00 22.22 N HETATM25470 C5 2MG A1207 200.255 109.072 24.452 1.00 22.02 C HETATM25471 C6 2MG A1207 201.664 108.956 24.144 1.00 21.94 C HETATM25472 O6 2MG A1207 202.706 109.773 24.490 1.00 21.74 O HETATM25473 N1 2MG A1207 201.977 107.741 23.302 1.00 22.13 N HETATM25474 C2 2MG A1207 200.927 106.863 22.894 1.00 22.28 C HETATM25475 N2 2MG A1207 201.271 105.673 22.035 1.00 22.47 N HETATM25476 CM2 2MG A1207 200.196 105.202 20.911 1.00 22.37 C HETATM25477 N3 2MG A1207 199.581 107.007 23.199 1.00 22.01 N HETATM25478 C4 2MG A1207 199.263 108.076 23.968 1.00 22.00 C ATOM 25479 P C A1208 196.141 104.788 27.998 1.00 79.45 P ATOM 25480 OP1 C A1208 195.091 104.010 28.693 1.00 79.48 O ATOM 25481 OP2 C A1208 196.850 105.858 28.740 1.00 80.10 O ATOM 25482 O5' C A1208 197.196 103.794 27.347 1.00 80.15 O ATOM 25483 C5' C A1208 196.897 103.077 26.162 1.00 81.09 C ATOM 25484 C4' C A1208 198.159 102.657 25.458 1.00 82.10 C ATOM 25485 O4' C A1208 198.738 103.799 24.770 1.00 82.55 O ATOM 25486 C3' C A1208 199.268 102.155 26.367 1.00 82.68 C ATOM 25487 O3' C A1208 199.120 100.784 26.703 1.00 83.37 O ATOM 25488 C2' C A1208 200.542 102.467 25.585 1.00 82.81 C ATOM 25489 O2' C A1208 200.823 101.440 24.645 1.00 82.68 O ATOM 25490 C1' C A1208 200.147 103.738 24.821 1.00 83.10 C ATOM 25491 N1 C A1208 200.654 104.979 25.469 1.00 83.75 N ATOM 25492 C2 C A1208 202.030 105.208 25.539 1.00 84.04 C ATOM 25493 O2 C A1208 202.787 104.352 25.073 1.00 85.37 O ATOM 25494 N3 C A1208 202.504 106.336 26.117 1.00 83.20 N ATOM 25495 C4 C A1208 201.650 107.231 26.606 1.00 83.20 C ATOM 25496 N4 C A1208 202.152 108.331 27.170 1.00 82.99 N ATOM 25497 C5 C A1208 200.240 107.041 26.541 1.00 83.43 C ATOM 25498 C6 C A1208 199.794 105.918 25.966 1.00 83.75 C ATOM 25499 P C A1209 199.109 100.325 28.246 1.00 83.81 P ATOM 25500 OP1 C A1209 198.251 99.114 28.342 1.00 83.30 O ATOM 25501 OP2 C A1209 198.750 101.522 29.056 1.00 82.92 O ATOM 25502 O5' C A1209 200.633 99.930 28.499 1.00 84.20 O ATOM 25503 C5' C A1209 201.270 98.949 27.692 1.00 84.37 C ATOM 25504 C4' C A1209 202.741 99.244 27.501 1.00 84.82 C ATOM 25505 O4' C A1209 202.921 100.574 26.949 1.00 84.19 O ATOM 25506 C3' C A1209 203.597 99.255 28.757 1.00 85.06 C ATOM 25507 O3' C A1209 203.935 97.953 29.207 1.00 86.28 O ATOM 25508 C2' C A1209 204.805 100.090 28.332 1.00 84.19 C ATOM 25509 O2' C A1209 205.743 99.293 27.621 1.00 83.94 O ATOM 25510 C1' C A1209 204.174 101.087 27.350 1.00 83.23 C ATOM 25511 N1 C A1209 203.980 102.422 27.942 1.00 81.76 N ATOM 25512 C2 C A1209 205.090 103.092 28.456 1.00 81.49 C ATOM 25513 O2 C A1209 206.191 102.525 28.418 1.00 81.76 O ATOM 25514 N3 C A1209 204.936 104.327 28.991 1.00 81.01 N ATOM 25515 C4 C A1209 203.734 104.903 29.006 1.00 80.86 C ATOM 25516 N4 C A1209 203.625 106.122 29.534 1.00 79.98 N ATOM 25517 C5 C A1209 202.587 104.247 28.470 1.00 81.59 C ATOM 25518 C6 C A1209 202.754 103.021 27.948 1.00 81.60 C """.splitlines() cif_records = """\ # electronic Ligand Builder and Optimisation Workbench (eLBOW) # - a module of PHENIX version dev-550 (Mon Oct 6 00:28:00 2010) # - file written: Wed Nov 17 14:20:56 2010 # # Input file: sample.pdb # Random seed: 3628800 # Residue: 2MG # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level 2MG 2MG 'Unknown ' ligand 40 24 . # data_comp_2MG # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z 2MG P P P . 193.1922 110.7393 27.8108 2MG OP1 O OH1 . 193.2303 110.5959 29.4269 2MG OP2 O O . 193.8066 112.0430 27.1100 2MG O5' O O2 . 193.8090 109.3126 27.4983 2MG C5' C CH2 . 195.2238 109.1932 27.1837 2MG C4' C CR15 . 195.5915 108.2815 26.0928 2MG O4' O O . 196.8078 108.6487 25.5614 2MG C3' C CR15 . 195.7744 106.9078 26.6204 2MG O3' O OH1 . 195.9405 106.9603 27.9901 2MG C2' C CR15 . 196.9455 106.4187 26.0245 2MG O2' O OH1 . 196.6506 105.2541 25.2751 2MG C1' C CR15 . 197.4047 107.4689 25.1175 2MG N9 N NR5 . 198.8548 107.5902 25.1810 2MG C8 C CR15 . 199.6182 107.8273 26.3017 2MG N7 N N . 200.9440 107.9581 25.8975 2MG C5 C CR56 . 201.0035 107.8016 24.5249 2MG C6 C CR6 . 202.0016 107.9320 23.5649 2MG O6 O OH1 . 203.2939 108.1809 23.9568 2MG N1 N N . 201.6911 107.8327 22.1819 2MG C2 C CR6 . 200.3827 107.6027 21.7653 2MG N2 N NH1 . 200.1198 107.3807 20.4207 2MG CM2 C CH3 . 201.2316 107.4071 19.4380 2MG N3 N N . 199.4107 107.4740 22.6488 2MG C4 C CR56 . 199.6703 107.5658 24.0571 2MG HP1 H H . 191.9727 110.4452 27.6374 2MG HP11 H HOH1 . 192.6565 111.1706 29.7890 2MG H5'1 H HCH2 . 195.6955 108.8897 28.0106 2MG H5'2 H HCH2 . 195.5673 110.1131 26.9473 2MG H4'1 H HCR5 . 194.9037 108.3265 25.3852 2MG H3'1 H HCR5 . 195.0531 106.4463 26.3998 2MG H3'2 H HOH1 . 195.4753 106.3269 28.3657 2MG H2'1 H HCR5 . 197.5835 106.2824 26.7053 2MG H2'2 H HOH1 . 196.7242 104.5157 25.8120 2MG H1'1 H HCR5 . 197.2320 107.2825 24.2174 2MG H81 H HCR5 . 199.2996 107.8051 27.2342 2MG H61 H HOH1 . 203.7851 108.3067 23.2622 2MG H21 H HNH1 . 199.3048 107.1092 20.1655 2MG HM21 H HCH3 . 201.8876 108.1500 19.6848 2MG HM22 H HCH3 . 200.8866 107.5682 18.5764 2MG HM23 H HCH3 . 201.6753 106.5837 19.4482 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd 2MG P OP1 single 1.623 0.020 2MG P OP2 double 1.603 0.020 2MG P O5' single 1.586 0.020 2MG O5' C5' single 1.454 0.020 2MG C5' C4' single 1.468 0.020 2MG C4' O4' single 1.377 0.020 2MG C4' C3' single 1.483 0.020 2MG O4' C1' single 1.395 0.020 2MG C3' O3' single 1.381 0.020 2MG C3' C2' single 1.402 0.020 2MG C2' O2' single 1.416 0.020 2MG C2' C1' single 1.462 0.020 2MG C1' N9 single 1.457 0.020 2MG N9 C8 aromatic 1.377 0.020 2MG N9 C4 aromatic 1.389 0.020 2MG C8 N7 aromatic 1.392 0.020 2MG N7 C5 aromatic 1.383 0.020 2MG C5 C6 aromatic 1.391 0.020 2MG C5 C4 aromatic 1.432 0.020 2MG C6 O6 single 1.373 0.020 2MG C6 N1 aromatic 1.421 0.020 2MG N1 C2 aromatic 1.392 0.020 2MG C2 N2 single 1.388 0.020 2MG C2 N3 aromatic 1.320 0.020 2MG N3 C4 aromatic 1.435 0.020 2MG CM2 N2 single 1.484 0.020 2MG HP1 P single 1.266 0.020 2MG HP11 OP1 single 0.889 0.020 2MG H5'1 C5' single 0.999 0.020 2MG H5'2 C5' single 1.010 0.020 2MG H4'1 C4' single 0.988 0.020 2MG H3'1 C3' single 0.884 0.020 2MG H3'2 O3' single 0.871 0.020 2MG H2'1 C2' single 0.943 0.020 2MG H2'2 O2' single 0.916 0.020 2MG H1'1 C1' single 0.935 0.020 2MG H81 C8 single 0.986 0.020 2MG H61 O6 single 0.860 0.020 2MG H21 N2 single 0.896 0.020 2MG HM21 CM2 single 1.021 0.020 2MG HM22 CM2 single 0.942 0.020 2MG HM23 CM2 single 0.935 0.020 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd 2MG C5' O5' P 119.67 3.000 2MG OP2 P OP1 119.89 3.000 2MG O5' P OP1 96.17 3.000 2MG O5' P OP2 119.78 3.000 2MG C4' C5' O5' 117.08 3.000 2MG O4' C4' C5' 110.01 3.000 2MG C3' C4' C5' 109.98 3.000 2MG C1' O4' C4' 105.97 3.000 2MG O3' C3' C4' 109.42 3.000 2MG C2' C3' C4' 105.96 3.000 2MG C3' C4' O4' 105.98 3.000 2MG C2' C1' O4' 106.01 3.000 2MG N9 C1' O4' 109.98 3.000 2MG O2' C2' C3' 109.75 3.000 2MG C1' C2' C3' 105.99 3.000 2MG C2' C3' O3' 109.54 3.000 2MG N9 C1' C2' 110.21 3.000 2MG C1' C2' O2' 109.14 3.000 2MG C8 N9 C1' 127.01 3.000 2MG C4 N9 C1' 123.21 3.000 2MG N7 C8 N9 107.94 3.000 2MG C5 C4 N9 106.21 3.000 2MG N3 C4 N9 133.57 3.000 2MG C4 N9 C8 109.65 3.000 2MG C5 N7 C8 108.57 3.000 2MG C6 C5 N7 134.85 3.000 2MG C4 C5 N7 107.63 3.000 2MG O6 C6 C5 119.70 3.000 2MG N1 C6 C5 120.55 3.000 2MG N3 C4 C5 119.96 3.000 2MG C4 C5 C6 117.25 3.000 2MG C2 N1 C6 120.54 3.000 2MG N1 C6 O6 119.74 3.000 2MG N2 C2 N1 119.62 3.000 2MG N3 C2 N1 120.53 3.000 2MG CM2 N2 C2 119.78 3.000 2MG C4 N3 C2 121.16 3.000 2MG N3 C2 N2 119.56 3.000 2MG HP11 OP1 P 109.46 3.000 2MG HP1 P OP1 97.96 3.000 2MG HP1 P OP2 119.89 3.000 2MG HP1 P O5' 97.97 3.000 2MG H5'1 C5' O5' 107.77 3.000 2MG H5'2 C5' O5' 107.86 3.000 2MG H4'1 C4' C5' 109.24 3.000 2MG H5'1 C5' C4' 107.94 3.000 2MG H5'2 C5' C4' 107.84 3.000 2MG H3'1 C3' C4' 107.10 3.000 2MG H4'1 C4' O4' 109.05 3.000 2MG H1'1 C1' O4' 113.32 3.000 2MG H4'1 C4' C3' 112.52 3.000 2MG H3'2 O3' C3' 109.63 3.000 2MG H2'1 C2' C3' 107.98 3.000 2MG H3'1 C3' O3' 111.44 3.000 2MG H3'1 C3' C2' 113.16 3.000 2MG H2'2 O2' C2' 109.64 3.000 2MG H1'1 C1' C2' 113.33 3.000 2MG H2'1 C2' O2' 113.84 3.000 2MG H2'1 C2' C1' 109.84 3.000 2MG H1'1 C1' N9 104.03 3.000 2MG H81 C8 N9 125.95 3.000 2MG H81 C8 N7 125.77 3.000 2MG H61 O6 C6 109.49 3.000 2MG H21 N2 C2 119.77 3.000 2MG HM21 CM2 N2 109.52 3.000 2MG HM22 CM2 N2 109.53 3.000 2MG HM23 CM2 N2 109.42 3.000 2MG H21 N2 CM2 119.88 3.000 2MG H5'2 C5' H5'1 108.04 3.000 2MG HM22 CM2 HM21 109.38 3.000 2MG HM23 CM2 HM21 109.45 3.000 2MG HM23 CM2 HM22 109.53 3.000 # loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period 2MG CONST_01 C5 N7 C8 N9 -0.02 0.0 0 2MG CONST_02 N7 C5 C4 N9 -0.02 0.0 0 2MG CONST_03 C6 C5 C4 N9 -174.95 0.0 0 2MG CONST_04 C2 N3 C4 N9 173.30 0.0 0 2MG CONST_05 C5 C4 N9 C8 0.00 0.0 0 2MG CONST_06 N3 C4 N9 C8 -173.94 0.0 0 2MG CONST_07 C6 C5 N7 C8 173.67 0.0 0 2MG CONST_08 C4 C5 N7 C8 0.03 0.0 0 2MG CONST_09 C4 N9 C8 N7 0.01 0.0 0 2MG CONST_10 N1 C6 C5 N7 -173.16 0.0 0 2MG CONST_11 N3 C4 C5 N7 174.92 0.0 0 2MG CONST_12 C2 N1 C6 C5 -0.02 0.0 0 2MG CONST_13 C2 N3 C4 C5 0.02 0.0 0 2MG CONST_14 N3 C4 C5 C6 -0.02 0.0 0 2MG CONST_15 N3 C2 N1 C6 0.02 0.0 0 2MG CONST_16 C4 C5 C6 N1 0.02 0.0 0 2MG CONST_17 C4 N3 C2 N1 -0.03 0.0 0 2MG CONST_18 N7 C8 N9 C1' -176.01 0.0 0 2MG CONST_19 C5 C4 N9 C1' 176.21 0.0 0 2MG CONST_20 N3 C4 N9 C1' 2.27 0.0 0 2MG CONST_21 O6 C6 C5 N7 5.76 0.0 0 2MG CONST_22 N2 C2 N1 C6 -173.82 0.0 0 2MG CONST_23 C4 C5 C6 O6 178.94 0.0 0 2MG CONST_24 C2 N1 C6 O6 -178.94 0.0 0 2MG CONST_25 C4 N3 C2 N2 173.82 0.0 0 2MG CONST_26 H81 C8 N9 C1' 10.40 0.0 0 2MG CONST_27 H81 C8 N7 C5 173.58 0.0 0 2MG CONST_28 H81 C8 N9 C4 -173.58 0.0 0 2MG Var_01 C4' C5' O5' P -138.25 30.0 3 2MG Var_02 C5' O5' P OP1 -98.80 30.0 3 2MG Var_03 C5' O5' P OP2 30.95 30.0 3 2MG Var_04 O4' C4' C5' O5' 156.12 30.0 3 2MG Var_05 C3' C4' C5' O5' -87.50 30.0 3 2MG Var_06 C1' O4' C4' C5' 149.03 30.0 1 2MG Var_07 O3' C3' C4' C5' -17.76 30.0 1 2MG Var_08 C2' C3' C4' C5' -135.78 30.0 1 2MG Var_09 N9 C1' O4' C4' -151.05 30.0 1 2MG Var_10 O2' C2' C3' C4' -120.19 30.0 1 2MG Var_11 O3' C3' C4' O4' 101.12 30.0 1 2MG Var_12 O2' C2' C1' O4' 138.94 30.0 1 2MG Var_13 C8 N9 C1' O4' 60.18 30.0 2 2MG Var_14 C4 N9 C1' O4' -115.34 30.0 2 2MG Var_15 N9 C1' C2' C3' 139.77 30.0 1 2MG Var_16 O2' C2' C3' O3' 121.88 30.0 1 2MG Var_17 C1' C2' C3' O3' -120.39 30.0 1 2MG Var_18 C8 N9 C1' C2' -56.35 30.0 2 2MG Var_19 C4 N9 C1' C2' 128.13 30.0 2 2MG Var_20 N9 C1' C2' O2' -102.09 30.0 1 2MG Var_21 CM2 N2 C2 N1 -0.75 30.0 2 2MG Var_22 N3 C2 N2 CM2 -174.66 30.0 2 2MG Var_23 H5'1 C5' O5' P 99.94 30.0 3 2MG Var_24 H5'2 C5' O5' P -16.48 30.0 3 2MG Var_25 HP11 OP1 P OP2 70.99 30.0 3 2MG Var_26 HP11 OP1 P O5' -159.34 30.0 3 2MG Var_27 H4'1 C4' C5' O5' 36.45 30.0 3 2MG Var_28 HP1 P O5' C5' 162.24 30.0 1 2MG Var_29 H3'1 C3' C4' C5' 103.17 30.0 1 2MG Var_30 H1'1 C1' O4' C4' 93.00 30.0 1 2MG Var_31 H3'2 O3' C3' C4' 136.99 30.0 3 2MG Var_32 H2'1 C2' C3' C4' 115.20 30.0 1 2MG Var_33 H5'1 C5' C4' O4' -82.15 30.0 2 2MG Var_34 H5'2 C5' C4' O4' 34.35 30.0 2 2MG Var_35 H3'1 C3' C4' O4' -137.95 30.0 1 2MG Var_36 H2'1 C2' C1' O4' -95.61 30.0 1 2MG Var_37 H5'1 C5' C4' C3' 34.22 30.0 2 2MG Var_38 H5'2 C5' C4' C3' 150.73 30.0 2 2MG Var_39 H2'2 O2' C2' C3' -89.07 30.0 3 2MG Var_40 H1'1 C1' C2' C3' -104.12 30.0 1 2MG Var_41 H4'1 C4' C3' O3' -139.78 30.0 1 2MG Var_42 H2'1 C2' C3' O3' -2.74 30.0 1 2MG Var_43 H4'1 C4' C3' C2' 102.20 30.0 1 2MG Var_44 H3'2 O3' C3' C2' -107.25 30.0 3 2MG Var_45 H3'1 C3' C2' O2' -3.13 30.0 1 2MG Var_46 H1'1 C1' C2' O2' 14.02 30.0 1 2MG Var_47 H4'1 C4' O4' C1' -91.18 30.0 1 2MG Var_48 H3'1 C3' C2' C1' 114.61 30.0 1 2MG Var_49 H2'2 O2' C2' C1' 155.18 30.0 3 2MG Var_50 H2'1 C2' C1' N9 23.37 30.0 1 2MG Var_51 H1'1 C1' N9 C8 -178.15 30.0 1 2MG Var_52 H61 O6 C6 C5 -174.96 30.0 2 2MG Var_53 H61 O6 C6 N1 3.97 30.0 2 2MG Var_54 H21 N2 C2 N1 170.63 30.0 2 2MG Var_55 HM21 CM2 N2 C2 -38.75 30.0 3 2MG Var_56 HM22 CM2 N2 C2 -158.70 30.0 3 2MG Var_57 HM23 CM2 N2 C2 81.23 30.0 3 2MG Var_58 H21 N2 C2 N3 -3.27 30.0 2 2MG Var_59 H1'1 C1' N9 C4 6.33 30.0 1 2MG Var_60 HP11 OP1 P HP1 -60.37 30.0 3 2MG Var_61 H4'1 C4' C5' H5'1 158.18 30.0 3 2MG Var_62 H4'1 C4' C5' H5'2 -85.32 30.0 3 2MG Var_63 H3'1 C3' C4' H4'1 -18.86 30.0 1 2MG Var_64 H3'2 O3' C3' H3'1 18.74 30.0 3 2MG Var_65 H2'1 C2' C3' H3'1 -127.74 30.0 1 2MG Var_66 H2'2 O2' C2' H2'1 32.08 30.0 3 2MG Var_67 H1'1 C1' C2' H2'1 139.48 30.0 1 2MG Var_68 HM21 CM2 N2 H21 149.88 30.0 3 2MG Var_69 HM22 CM2 N2 H21 29.93 30.0 3 2MG Var_70 HM23 CM2 N2 H21 -90.14 30.0 3 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign 2MG chir_01 P OP1 OP2 O5' both 2MG chir_02 C4' C5' O4' C3' both 2MG chir_03 C3' C4' O3' C2' both 2MG chir_04 C2' C3' O2' C1' both 2MG chir_05 C1' O4' C2' N9 both # # loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd 2MG plan-1 C1' 0.020 2MG plan-1 N9 0.020 2MG plan-1 C8 0.020 2MG plan-1 N7 0.020 2MG plan-1 C5 0.020 2MG plan-1 C6 0.020 2MG plan-1 O6 0.020 2MG plan-1 N1 0.020 2MG plan-1 C2 0.020 2MG plan-1 N2 0.020 2MG plan-1 N3 0.020 2MG plan-1 C4 0.020 2MG plan-1 H81 0.020 2MG plan-2 C2 0.020 2MG plan-2 N2 0.020 2MG plan-2 CM2 0.020 2MG plan-2 H21 0.020 """ import iotbx.cif log = StringIO() cif_object = iotbx.cif.reader(input_string=cif_records).model() mon_lib_srv.process_cif_object(cif_object=cif_object) processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params=params, force_symmetry=True, log=log) grm = processed_pdb_file.geometry_restraints_manager() mod_base_5p_link_op1 = False mod_base_5p_link_op2 = False for ap in grm.angle_proxies: if ap.i_seqs == (8,23,24): mod_base_5p_link_op1 = True if ap.i_seqs == (8,23,25): mod_base_5p_link_op2 = True assert mod_base_5p_link_op1 assert mod_base_5p_link_op2 def exercise_pdb_string(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 50.066 67.126 47.862 90.00 92.41 90.00 P 1 21 1 ATOM 0 N MET 0 18.670 12.527 40.988 1.00 52.89 N ATOM 1 CA MET 0 17.631 13.191 40.117 1.00 52.89 C ATOM 2 CB MET 0 18.110 13.132 38.643 1.00 52.89 C ATOM 3 CG MET 0 18.621 11.738 38.198 1.00 52.60 C ATOM 4 SD MET 0 19.279 11.706 36.483 1.00 52.89 S ATOM 5 CE MET 0 20.263 13.253 36.435 1.00 52.89 C ATOM 6 C MET 0 16.228 12.530 40.276 1.00 50.97 C ATOM 7 O MET 0 16.082 11.507 40.963 1.00 52.89 O ATOM 8 HA MET 0 17.568 14.136 40.375 1.00 52.89 D ATOM 9 HB1 MET 0 18.846 13.755 38.537 1.00 45.86 D ATOM 10 HB2 MET 0 17.375 13.382 38.060 1.00 52.35 D ATOM 11 HG1 MET 0 17.893 11.102 38.251 1.00 47.31 D ATOM 12 HG2 MET 0 19.339 11.465 38.791 1.00 52.89 D ATOM 13 HE1 MET 0 20.554 13.413 35.532 1.00 52.89 D ATOM 14 HE2 MET 0 21.028 13.143 37.008 1.00 52.89 D ATOM 15 HE3 MET 0 19.722 13.985 36.740 1.00 52.89 D ATOM 16 H1 MET 0 19.528 12.921 40.813 1.00 52.89 D ATOM 17 H2 MET 0 18.706 11.586 40.792 1.00 52.89 D ATOM 18 H3 MET 0 18.445 12.648 41.914 1.00 52.89 D END """.splitlines() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, params=params, raw_records=raw_records, force_symmetry=True) xray_structure = processed_pdb_file.xray_structure() assert xray_structure.scattering_type_registry().type_count_dict() \ == {"S": 1, "N": 1, "C": 5, "O": 1, "D": 11} raw_records = [line[:66] for line in raw_records] processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, params=params, file_name=None, raw_records=raw_records, force_symmetry=True) xray_structure = processed_pdb_file.xray_structure() assert xray_structure.scattering_type_registry().type_count_dict() \ == {"S": 1, "N": 1, "C": 5, "O": 1, "H": 11} # raw_records = """\ HETATM 1 N NH3 1 0.000 0.000 0.000 1.00 0.00 N HETATM 2 N NH3 2 0.000 0.000 0.000 1.00 0.00 HETATM 3 NH3 NH3 3 0.000 0.000 0.000 1.00 0.00 HETATM 4 X CH4 4 0.000 0.000 0.000 1.00 0.00 C HETATM 5 C CH4 5 0.000 0.000 0.000 1.00 0.00 HETATM 6 CH4 CH4 6 0.000 0.000 0.000 1.00 0.00 HETATM 7 U U 7 0.000 0.000 0.000 1.00 0.00 U END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, params=params, raw_records=raw_records, log=log) looking_for = "Ad-hoc single atom residues: " for line in log.getvalue().splitlines(): line = line.strip() if (not line.startswith(looking_for)): continue counts = eval(line[len(looking_for):]) assert counts == {"U ": 1} break else: raise RuntimeError('Expected string not found in output: "%s"' % looking_for) # raw_records = """\ CRYST1 106.820 62.340 114.190 90.00 90.00 90.00 P 21 21 21 ATOM 7 N SER A 4 64.059 32.579 18.554 1.00 14.95 ATOM 8 CA ASER A 4 64.561 31.418 17.802 1.00 9.04 ATOM 9 CA BSER A 4 64.804 31.635 18.406 1.00 12.07 ATOM 10 C SER A 4 65.282 31.515 17.187 1.00 10.69 ATOM 38 N ALA C 3 109.043 27.391 28.663 1.00 15.05 ATOM 39 CA ALA C 3 109.073 26.531 28.433 1.00 3.14 ATOM 40 C ALA C 3 108.930 26.867 26.637 1.00 15.22 ATOM 41 N SER C 4 109.311 25.012 25.749 1.00 6.18 ATOM 42 CA BSER C 4 109.271 25.165 25.154 1.00 11.32 ATOM 43 CA ASER C 4 109.508 25.337 25.273 1.00 4.97 ATOM 44 C SER C 4 109.045 24.408 24.187 1.00 15.28 END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) lines = search_for( pattern=" +bond proxies already assigned to first conformer: 3$", mode="re.match", lines=log.getvalue().splitlines()) assert len(lines) == 1 # test the atom_selection feature log = StringIO() pdb_inp = pdb.input(source_info = None, lines = raw_records) processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, atom_selection_string="resname ser", pdb_inp = pdb_inp, crystal_symmetry=pdb_inp.crystal_symmetry(), log=log) processed_pdb_file.geometry_restraints_manager() lines = search_for( pattern=" +Nonbonded interactions: 0$", mode="re.match", lines=log.getvalue().splitlines()) assert len(lines) == 1 processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, atom_selection_string="resname ser or resname ala", pdb_inp = pdb_inp, crystal_symmetry=pdb_inp.crystal_symmetry(), log=log) processed_pdb_file.geometry_restraints_manager() lines = search_for( pattern=" +Nonbonded interactions: 7$", mode="re.match", lines=log.getvalue().splitlines()) assert len(lines) == 1 # raw_records = """\ CRYST1 53.910 23.100 23.100 90.00 110.40 90.00 C 2 ATOM 561 N TYR X 39 11.814 -3.041 22.005 1.00 15.52 N ATOM 562 CA TYR X 39 13.044 -2.727 21.259 1.00 17.08 C ATOM 563 C TYR X 39 13.804 -1.593 21.948 1.00 19.46 C ATOM 564 O TYR X 39 14.993 -1.524 21.704 1.00 28.79 O ATOM 582 N VAL X 40 13.093 -0.787 22.711 1.00 23.32 N ATOM 583 CA VAL X 40 13.567 0.356 23.491 1.00 37.02 C ATOM 584 C VAL X 40 13.408 0.141 24.979 1.00 47.42 C ATOM 585 O VAL X 40 13.919 0.926 25.809 1.00 58.31 O ATOM 589 OXT VAL X 40 12.720 -0.842 25.372 1.00 48.85 O HETATM 600 C1 AEOH X 200 12.974 5.558 13.017 0.54 29.75 C HETATM 601 C1 BEOH X 200 14.446 4.322 12.408 0.46 32.58 C HETATM 602 C2 AEOH X 200 12.259 6.535 13.707 0.54 26.57 C HETATM 603 C2 BEOH X 200 13.905 4.879 13.576 0.46 32.29 C END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) lines = search_for( pattern="""\ +Inner-chain residues flagged as termini: \\['pdbres="VAL X 40 "'\\]$""", mode="re.match", lines=log.getvalue().splitlines()) assert len(lines) == 2 # raw_records = """\ CRYST1 53.910 23.100 23.100 90.00 110.40 90.00 C 2 ATOM 264 N GLU 21 3.822 -2.789 -0.368 1.00 11.74 N ATOM 265 CA GLU 21 5.032 -3.595 -0.485 1.00 11.86 C ATOM 266 C GLU 21 6.226 -2.698 -0.821 1.00 10.70 C ATOM 267 O GLU 21 6.118 -1.718 -1.512 1.00 11.93 O ATOM 268 CB AGLU 21 4.980 -4.649 -1.566 0.32 13.49 C ATOM 269 CB BGLU 21 4.769 -4.484 -1.766 0.68 14.37 C ATOM 270 CG AGLU 21 3.942 -5.699 -1.498 0.32 13.60 C ATOM 271 CG BGLU 21 5.737 -5.573 -1.952 0.68 19.43 C ATOM 272 CD AGLU 21 4.064 -6.621 -2.739 0.32 15.27 C ATOM 273 CD BGLU 21 5.251 -6.534 -3.036 0.68 19.91 C ATOM 274 OE1AGLU 21 5.043 -6.411 -3.478 0.32 16.46 O ATOM 276 OE2AGLU 21 3.193 -7.474 -2.870 0.32 19.03 O ATOM 277 OE2BGLU 21 6.037 -6.819 -3.934 0.68 23.06 O END """.splitlines() for i_pass in [0,1]: if (i_pass == 0): pattern = " +2.60 - 3.06: 2$" ci_counts = {0: 4, 1: 5, 2: 4} else: raw_records = raw_records[:1] + raw_records[5:] pattern = " +2.60 - 2.80: 1$" ci_counts = {1: 5, 2: 4} log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) grm = processed_pdb_file.geometry_restraints_manager() assert dict(grm.conformer_indices.counts()) == ci_counts lines = search_for( pattern=pattern, mode="re.match", lines=log.getvalue().splitlines()) assert len(lines) == 1 # raw_records = """\ REMARK HYDROLASE 05-SEP-07 2VB1 CRYST1 27.070 31.250 33.760 87.98 108.00 112.11 P 1 1 ATOM 1 N LYS A 1 1.984 5.113 14.226 1.00 6.14 N ATOM 2 CA LYS A 1 1.811 6.069 13.092 1.00 5.23 C ATOM 3 C LYS A 1 2.502 7.339 13.503 1.00 4.84 C ATOM 4 O LYS A 1 2.414 7.746 14.659 1.00 5.74 O ATOM 5 CB LYS A 1 0.325 6.305 12.891 1.00 5.48 C ATOM 6 CG LYS A 1 0.013 7.371 11.851 1.00 5.12 C ATOM 7 CD LYS A 1 -1.494 7.455 11.617 1.00 5.56 C ATOM 8 HA LYS A 1 2.215 5.709 12.275 1.00 6.28 H ATOM 9 HB2 LYS A 1 -0.091 5.472 12.620 1.00 6.57 H ATOM 10 HB3 LYS A 1 -0.068 6.569 13.738 1.00 6.57 H ATOM 11 HG2 LYS A 1 0.344 8.231 12.157 1.00 6.14 H ATOM 12 HG3 LYS A 1 0.461 7.155 11.018 1.00 6.14 H ATOM 13 CE ALYS A 1 -1.966 8.606 10.745 0.69 5.10 C ATOM 14 NZ ALYS A 1 -1.548 8.473 9.287 0.69 4.56 N ATOM 15 HD2ALYS A 1 -1.786 6.625 11.210 0.50 6.67 H ATOM 16 HD3ALYS A 1 -1.933 7.526 12.479 0.50 6.67 H ATOM 17 HE2ALYS A 1 -2.934 8.658 10.791 0.69 6.12 H ATOM 18 HE3ALYS A 1 -1.610 9.436 11.100 0.69 6.12 H ATOM 19 HZ1ALYS A 1 -1.884 7.721 8.949 0.69 6.84 H ATOM 20 HZ2ALYS A 1 -1.854 9.169 8.825 0.69 6.84 H ATOM 21 HZ3ALYS A 1 -0.659 8.450 9.234 0.69 6.84 H ATOM 22 CE BLYS A 1 -1.791 8.575 10.680 0.31 5.79 C ATOM 23 NZ BLYS A 1 -3.148 8.376 10.084 0.31 6.86 N ATOM 24 H1 BLYS A 1 2.852 4.975 14.368 0.50 9.20 H ATOM 25 H2 BLYS A 1 1.614 5.454 14.960 0.50 9.20 H ATOM 26 H3 BLYS A 1 1.589 4.341 14.026 0.50 9.20 H ATOM 27 HE2BLYS A 1 -1.763 9.419 11.157 0.31 6.95 H ATOM 28 HE3BLYS A 1 -1.124 8.601 9.977 0.31 6.95 H ATOM 29 HZ1BLYS A 1 -3.755 8.339 10.733 0.31 10.29 H ATOM 30 HZ2BLYS A 1 -3.335 9.055 9.540 0.31 10.29 H ATOM 31 HZ3BLYS A 1 -3.160 7.615 9.622 0.31 10.29 H END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) lines = search_for( pattern="""\ Number of resolved chirality restraint conflicts: 1""", mode="==", lines=log.getvalue().splitlines()) assert len(lines) == 1 # raw_records = """\ CRYST1 109.350 109.350 190.680 90.00 90.00 120.00 H 3 2 18 HETATM 2316 MG MG 401 85.173 71.732 16.992 1.00 77.96 MG HETATM 2317 MG MG 402 79.003 69.700 14.150 1.00 73.20 MG HETATM 2318 MG MG 403 9.596 62.411 13.402 1.00 62.56 MG HETATM 2319 MG MG 404 48.026 73.068 26.732 1.00 72.59 MG HETATM 2320 MG MG 405 63.623 79.773 28.694 1.00 86.62 MG HETATM 2321 MG MG 406 25.463 68.205 2.775 1.00 67.84 MG HETATM 2322 MG MG 407 64.693 59.956 7.476 1.00 81.20 MG HETATM 2323 MG MG 408 58.001 61.900 13.126 1.00 76.59 MG HETATM 2324 MG MG 409 79.965 84.253 23.275 1.00 73.36 MG HETATM 2325 MG MG 410 22.587 66.575 19.552 1.00 62.10 MG HETATM 2326 MG MG 411 53.007 73.668 38.880 1.00 89.72 MG HETATM 2327 MG MG 412 51.568 77.963 9.128 1.00 87.46 MG HETATM 2328 O HOH 301 32.853 56.507 0.571 1.00 41.94 O HETATM 2329 O HOH 302 27.055 59.115 12.335 1.00 46.41 O HETATM 2330 O HOH 303 21.956 61.533 10.963 1.00 42.68 O END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) lines = search_for( pattern="""\ Link IDs: {None: 14}""", mode="==", lines=log.getvalue().splitlines()) assert len(lines) == 1 # raw_records = """\ HETATM 1253 CD CD X 200 -0.849 19.743 0.211 1.00 14.82 END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, substitute_non_crystallographic_unit_cell_if_necessary=True, log=log) processed_pdb_file.xray_structure() lines = search_for( pattern="""\ Cd 1 47.96""", mode="==", lines=log.getvalue().splitlines()) assert len(lines) == 1 # raw_records = """\ HETATM 1253 ZN ZN X 200 -0.849 19.743 0.211 1.00 14.82 END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, substitute_non_crystallographic_unit_cell_if_necessary=True, log=log) processed_pdb_file.xray_structure() lines = search_for( pattern="""\ Zn 1 29.99""", mode="==", lines=log.getvalue().splitlines()) assert len(lines) == 1 # raw_records = """\ CRYST1 32.100 79.470 91.830 90.00 90.00 90.00 I 2 2 2 HETATM 709 NA NA A1398 -17.524 -7.858 -16.234 1.00 17.29 NA + HETATM 710 NA NA A1399 -11.813 -6.045 -17.742 1.00 25.01 NA1 HETATM 711 ZN ZN A1400 -1.928 -11.394 -27.827 1.00 17.21 ZN+2 HETATM 712 ZN ZN A1401 -2.733 -3.868 -16.577 1.00 20.27 ZN2+ """.splitlines() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, raw_records=raw_records) xray_structure = processed_pdb_file.xray_structure() assert xray_structure.scattering_type_registry().type_count_dict() \ == {"Na": 1, "Na1+": 1, "Zn2+": 2} # raw_records = """\ CRYST1 14.600 26.100 29.200 90.00 90.00 90.00 P 21 21 21 4 ATOM 107 N CYS A 16 -0.448 11.073 0.703 1.00 5.42 ATOM 108 CA CYS A 16 -1.464 10.253 1.359 1.00 6.46 ATOM 109 C CYS A 16 -2.718 11.036 1.746 1.00 6.39 ATOM 110 O CYS A 16 -3.805 10.424 1.754 1.00 7.99 ATOM 111 CB CYS A 16 -0.881 9.558 2.593 1.00 6.56 ATOM 112 SG CYS A 16 0.273 8.212 2.183 1.00 6.50 ATOM 113 H CYS A 16 0.296 11.370 1.301 1.00 5.42 ATOM 114 HA CYS A 16 -1.774 9.501 0.619 1.00 6.46 ATOM 115 HB2 CYS A 16 -0.360 10.303 3.212 1.00 6.56 ATOM 116 HB3 CYS A 16 -1.704 9.154 3.201 1.00 6.56 HETATM 117 N NH2 A 17 -2.607 12.317 2.071 1.00 6.64 HETATM 118 HN1 NH2 A 17 -1.710 12.757 2.069 1.00 6.64 HETATM 119 HN2 NH2 A 17 -3.421 12.843 2.318 1.00 6.64 """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, raw_records=raw_records, log=log) processed_pdb_file.xray_structure() lines=search_for( pattern="""\ Link IDs: {'NH2_CTERM': 1}""", mode="==", lines=log.getvalue().splitlines()) assert len(lines) == 1 def exercise_rna( mon_lib_srv, ener_lib, file_name, expected_block, expected_block_last_startswith=True, expected_modifications_used=None): file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/"+file_name, test=os.path.isfile) if (file_path is None): print('Skipping exercise_rna("%s"): input file not available' % file_name) return log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=file_path, log=log) lines = [] lines_modifications_used = [] for line in log.getvalue().splitlines(): if (line.startswith("""\ Modifications used: {""")): lines_modifications_used.append(line) else: lines.append(line) assert not block_show_diff( lines, expected_block, last_startswith=expected_block_last_startswith) if (expected_modifications_used is None): assert len(lines_modifications_used) == 0 else: assert len(lines_modifications_used) == len(expected_modifications_used) for line,expected in zip( lines_modifications_used, expected_modifications_used): modifications_used = eval(line.split(":", 1)[1]) assert modifications_used == expected def exercise_cns_rna(mon_lib_srv, ener_lib): exercise_rna( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name="cns_rna.pdb", expected_block= """\ Total number of atoms: 646 Number of models: 1 Model: "" Number of chains: 1 Chain: " " Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 646 Classifications: {'RNA': 20} Link IDs: {'rna3p': 19} Time building chain proxies: """, expected_modifications_used=\ [{'rna3p_pyr': 9, 'p5*END': 1, 'rna3p_pur': 11, '3*END': 1}]) def exercise_rna_3p_2p(mon_lib_srv, ener_lib): exercise_rna( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name="rna_3p_2p.pdb", expected_block= """\ Total number of atoms: 63 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Classifications: {'RNA': 3} Link IDs: {'rna2p': 1, 'rna3p': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P C A 857 " occ=0.30 ... (18 atoms not shown) pdb=" C6 C A 857 " occ=0.30 residue: pdb=" P U A 858 " occ=0.30 ... (18 atoms not shown) pdb=" C6 U A 858 " occ=0.30 Time building chain proxies: """, expected_modifications_used=[{'rna3p_pyr': 1, 'rna3p_pur': 1, 'rna2p_pyr': 1}]) # exercise_rna( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name="coords_rna_gap.pdb", expected_block= """\ Total number of atoms: 90 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 90 Classifications: {'RNA': 5} Link IDs: {'rna3p': 4} Chain breaks: 1 """, expected_block_last_startswith=False, expected_modifications_used=[{'rna3p_pyr': 2, 'rna3p_pur': 2}]) def exercise_rna_dna_hybrid(mon_lib_srv, ener_lib): exercise_rna( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name="da_a.pdb", expected_block= """\ Total number of atoms: 63 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Classifications: {'DNA': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Classifications: {'RNA': 1} Time building chain proxies: """, expected_modifications_used=[{'5*END': 1}, {'rna3p_pur': 1}]) def exercise_hydrogen_deuterium_aliases(): file_paths = [] for file_name in ["NAD_594_HD.pdb", "NAD_594_HD.cif"]: file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/"+file_name, test=os.path.isfile) if (file_path is None): print("Skipping exercise_hydrogen_deuterium_aliases():", \ "input file not available:", file_name) return file_paths.append(file_path) log = StringIO() monomer_library.pdb_interpretation.run(args=file_paths, params=params, log=log) assert not block_show_diff( log.getvalue(), """\ Histogram of bond lengths: 0.94 - 1.13: 56 1.13 - 1.32: 4 1.32 - 1.51: 56 1.51 - 1.69: 18 1.69 - 1.88: 1 Bond restraints: 135 """) def exercise_corrupt_cif_link(): file_paths = [] for file_name in ["hem_no.pdb", "hem_no.cif"]: file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/misc/"+file_name, test=os.path.isfile) if (file_path is None): print("Skipping exercise_corrupt_cif_link():", \ "input file not available:", file_name) return file_paths.append(file_path) log = StringIO() try: monomer_library.pdb_interpretation.run(args=file_paths, params=params, log=log) except Sorry as e: assert str(e).startswith("Corrupt CIF link definition:") else: raise Exception_expected def exercise_dna_cns_cy5_th6(): file_paths = [] for file_name in ["dna_cns_cy5_th6.pdb", "dna_cns_cy5.cif", "dna_cns_th6.cif"]: file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/misc/"+file_name, test=os.path.isfile) if (file_path is None): print("Skipping exercise_dna_cns_cy5_th6():", \ "input file not available:", file_name) return file_paths.append(file_path) log = StringIO() monomer_library.pdb_interpretation.run(args=file_paths, params=params, log=log) assert not block_show_diff(log.getvalue(), """\ Number of residues, atoms: 12, 244 Classifications: %s Modifications used: {'5*END': 1} Link IDs: %s """ % ( str({'DNA': 12}), str({'rna3p': 11}))) def exercise_sym_excl_indices(mon_lib_srv, ener_lib): file_name = "so4_on_two_fold.pdb" file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/"+file_name, test=os.path.isfile) if (file_path is None): print("Skipping exercise_sym_excl_indices():", \ "input file not available:", file_name) return log = StringIO() pdb_interpretation_params = monomer_library.pdb_interpretation.master_params.extract() pdb_interpretation_params.sort_atoms=False pdb_interpretation_params.flip_symmetric_amino_acids=False processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=file_path, params=pdb_interpretation_params, log=log) processed_pdb_file.geometry_restraints_manager() lines = log.getvalue().splitlines() assert not block_show_diff( lines, """\ Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" S SO4 A 13 " occ=0.50 ... (3 atoms not shown) pdb=" O4 SO4 A 13 " occ=0.50 Time building chain proxies: """, last_startswith=True) assert not block_show_diff( lines, """\ Sorted by model distance: nonbonded pdb=" OE1 GLU A 9 " pdb=" O4 SO4 A 13 " model vdw sym.op. 2.134 3.040 z+1/4,y-1/4,-x+3/4 """) def exercise_auto_alias_h_h1(): file_paths = [] for file_name in ["dpn.pdb", "dpn.cif"]: file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/"+file_name, test=os.path.isfile) if (file_path is None): print("Skipping exercise_auto_alias_h_h1():", \ "input file not available:", file_name) return file_paths.append(file_path) log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.run( params=params, args=file_paths, log=log) assert log.getvalue().find("Modifications used: {'NH3': 1}") >= 0 assert processed_pdb_file.all_chain_proxies.fatal_problems_message() is None def exercise_d_aa_resnames(): file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/dpn.pdb", test=os.path.isfile) if (file_path is None): print("Skipping exercise_d_aa_resnames():", \ "input file not available: dpn.pdb") return log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.run( params=params, args=[file_path], log=log) assert log.getvalue().find("'PEPT-D': 1") >= 0 assert log.getvalue().find("'NH1NOTPRO': 1") >= 0 assert processed_pdb_file.all_chain_proxies.fatal_problems_message() is None def exercise_d_amino_acid_chain_perfect_in_box_peptide_plane(): file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/d_amino_acid_chain_perfect_in_box.pdb", test=os.path.isfile) if (file_path is None): print("Skipping exercise_d_aa_resnames():", \ "input file not available: d_amino_acid_chain_perfect_in_box.pdb") return log = StringIO() pdb_interpretation_params = monomer_library.pdb_interpretation.master_params.extract() pdb_interpretation_params.sort_atoms=False pdb_interpretation_params.flip_symmetric_amino_acids=False pdb_interpretation_params.peptide_link.apply_peptide_plane=True processed_pdb_file = monomer_library.pdb_interpretation.run( args=[file_path], params=pdb_interpretation_params, log=log) grm = processed_pdb_file.geometry_restraints_manager() lv = log.getvalue() assert lv.find("Classifications: {'peptide': 16}") >= 0 assert lv.find("Link IDs: {'PCIS': 1, 'TRANS': 14, 'peptide plane': 15}")>=0 def exercise_d_amino_acid_chain_perfect_in_box(): file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/d_amino_acid_chain_perfect_in_box.pdb", test=os.path.isfile) if (file_path is None): print("Skipping exercise_d_aa_resnames():", \ "input file not available: d_amino_acid_chain_perfect_in_box.pdb") return log = StringIO() pdb_interpretation_params = monomer_library.pdb_interpretation.master_params.extract() pdb_interpretation_params.sort_atoms=False pdb_interpretation_params.flip_symmetric_amino_acids=False processed_pdb_file = monomer_library.pdb_interpretation.run( args=[file_path], params=pdb_interpretation_params, log=log) grm = processed_pdb_file.geometry_restraints_manager() lv = log.getvalue() print(lv) assert lv.find("Classifications: {'peptide': 16}") >= 0 assert lv.find("'PEPT-D': 1") >= 0 assert lv.find("'TRANS': 14") >= 0 assert lv.find("'PCIS': 1") >= 0 assert lv.find("Link IDs: {'PCIS': 1, 'TRANS': 14}")>=0 assert lv.find("""\ Simple disulfide: pdb=" SG DCY A 4 " - pdb=" SG DCY A 19 " distance=2.03 """) >= 0 assert not block_show_diff(lv, """\ Bond restraints: 121 Sorted by residual: bond pdb=" CZ DAR A 14 " pdb=" NH2 DAR A 14 " ideal model delta sigma weight residual 1.330 1.326 0.004 1.30e-02 5.92e+03 1.15e-01 """) assert not block_show_diff(lv, """\ Bond angle restraints: 161 Sorted by residual: angle pdb=" NE DAR A 14 " pdb=" CZ DAR A 14 " pdb=" NH1 DAR A 14 " ideal model delta sigma weight residual 121.50 120.07 1.43 1.00e+00 1.00e+00 2.04e+00 """) assert not block_show_diff(lv, """\ Dihedral angle restraints: 50 sinusoidal: 34 harmonic: 16 Sorted by residual: dihedral pdb=" CA DCY A 4 " pdb=" CB DCY A 4 " pdb=" SG DCY A 4 " pdb=" SG DCY A 19 " ideal model delta sinusoidal sigma weight residual 79.00 18.71 60.29 1 2.00e+01 2.50e-03 1.21e+01 """) assert processed_pdb_file.all_chain_proxies.fatal_problems_message() is None log = StringIO() acp = processed_pdb_file.all_chain_proxies grm.show_sorted( sites_cart=acp.sites_cart_exact(), site_labels=[atom.id_str() for atom in acp.pdb_atoms], f=log) lv = log.getvalue() assert not block_show_diff(lv, """\ chirality pdb=" CB DIL A 10 " pdb=" CA DIL A 10 " pdb=" CG1 DIL A 10 " pdb=" CG2 DIL A 10 " both_signs ideal model delta sigma weight residual True 2.64 2.65 -0.00 2.00e-01 2.50e+01 5.99e-06 """) assert not block_show_diff(lv, """\ chirality pdb=" CB DTH A 18 " pdb=" CA DTH A 18 " pdb=" CG2 DTH A 18 " pdb=" OG1 DTH A 18 " both_signs ideal model delta sigma weight residual True 2.55 -2.55 -0.00 2.00e-01 2.50e+01 4.37e-06 """) def exercise_asp_glu_acid(): for resname in ["ASP", "GLU"]: file_name = resname.lower() + "_acid.pdb" file_path = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/"+file_name, test=os.path.isfile) if (file_path is None): print("Skipping exercise_asp_glu_acid():", \ "input file not available:", file_name) else: log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.run( params=params, args=[file_path], log=log) if (resname == "ASP"): pat = "Modifications used: {'ACID-ASP': 1}" else: pat = "Modifications used: {'ACID-GLU': 1, 'COOH': 1, 'NH1NOTPRO': 1}" assert log.getvalue().find(pat) >= 0 assert processed_pdb_file.all_chain_proxies \ .fatal_problems_message() is None # tests automatic aliasing of OP1/O1P etc. when the residue is not detected as # RNA/DNA but the monomer entry is def exercise_rna_dna_synonyms(): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/PGP.pdb", test=os.path.isfile) cif_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/cif_files/PGP.cif", test=os.path.isfile) if (None in [pdb_file, cif_file]): print("Skipping exercise_rna_dna_synonyms() - input file(s) unavailable.") else : log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.run( params=params, args=[pdb_file, cif_file], log=log) msg = processed_pdb_file.all_chain_proxies.fatal_problems_message( ignore_unknown_scattering_types=False, ignore_unknown_nonbonded_energy_types=False) assert (msg is None) def exercise_geostd_cif_links(mon_lib_srv, ener_lib): raw_records = """\ ATOM 6707 C1 MAN D9032 -82.149 64.388 127.264 1.00 20.00 C ATOM 6708 C2 MAN D9032 -82.661 63.644 128.508 1.00 20.00 C ATOM 6709 O2 MAN D9032 -81.755 62.603 128.885 1.00 20.00 O ATOM 6710 C3 MAN D9032 -83.112 64.561 129.660 1.00 20.00 C ATOM 6711 O3 MAN D9032 -83.036 63.857 130.877 1.00 20.00 O ATOM 6712 C4 MAN D9032 -82.378 65.900 129.641 1.00 20.00 C ATOM 6713 O4 MAN D9032 -82.870 66.786 130.611 1.00 20.00 O ATOM 6714 C5 MAN D9032 -82.589 66.508 128.255 1.00 20.00 C ATOM 6715 O5 MAN D9032 -81.778 65.758 127.405 1.00 20.00 O ATOM 6716 C6 MAN D9032 -82.234 68.002 128.113 1.00 20.00 C ATOM 6717 O6 MAN D9032 -83.296 68.629 127.421 1.00 20.00 O ATOM 6718 O1 MAN D8032 -82.173 69.386 124.623 1.00 20.00 O ATOM 6719 C1 MAN D8032 -82.135 70.338 125.650 1.00 20.00 C ATOM 6720 C2 MAN D8032 -83.046 69.904 126.785 1.00 20.00 C ATOM 6721 C3 MAN D8032 -83.124 71.033 127.800 1.00 20.00 C ATOM 6722 O3 MAN D8032 -83.760 70.573 128.974 1.00 20.00 O ATOM 6723 C4 MAN D8032 -81.746 71.580 128.181 1.00 20.00 C ATOM 6724 O4 MAN D8032 -81.878 72.934 128.571 1.00 20.00 O ATOM 6725 C5 MAN D8032 -80.638 71.462 127.125 1.00 20.00 C ATOM 6726 O5 MAN D8032 -80.827 70.430 126.159 1.00 20.00 O ATOM 6727 C6 MAN D8032 -79.314 71.191 127.833 1.00 20.00 C ATOM 6728 O6 MAN D8032 -79.563 70.916 129.196 1.00 20.00 O """.splitlines() link_def = """\ apply_cif_link { data_link = ALPHA2-6 residue_selection_1 = chain D and resname MAN and resseq 9032 residue_selection_2 = chain D and resname MAN and resseq 8032 } """ links_phil = iotbx.phil.parse( mmtbx.monomer_library.pdb_interpretation.master_params_str, process_includes=True, ) links = libtbx.phil.parse(link_def) params_links = links_phil.fetch(source=links) #params_links.show() params_links = params_links.extract() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, #force_symmetry=True, params=params_links, log=log, ) #print log.getvalue() pat = "data_link: ALPHA2-6" assert log.getvalue().find(pat) >= 0 def exercise_flattened_cif_loop(): # Previously our code would not interpret properly files where CIF loops with # only one row were "flattened" - i.e. listed as tag-value pairs rather than # in a loop construct pdb_string = """\ CRYST1 15.000 15.000 15.000 80.00 70.00 100.00 P 1 HETATM 13 O HOH 1 13.866 16.009 12.098 1.00 3.00 O HETATM 14 H1 HOH 1 13.327 16.140 12.905 1.00 3.00 H HETATM 15 H2 HOH 1 14.117 16.901 11.777 1.00 3.00 H """ restraints_cif_string = """\ # data_comp_list _chem_comp.id HOH _chem_comp.three_letter_code . _chem_comp.name 'water ' _chem_comp.group solvent _chem_comp.number_atoms_all 3 _chem_comp.number_atoms_nh 1 _chem_comp.desc_level . # data_comp_HOH # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge HOH O O OH2 -0.408 HOH H1 H HOH2 0.204 HOH H2 H HOH2 0.204 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type HOH O n/a . END HOH H1 O . . HOH H2 O . . loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd _chem_comp_bond.value_dist_neutron HOH O H1 coval 0.840 0.020 0.950 HOH O H2 coval 0.840 0.020 0.950 _chem_comp_angle.comp_id HOH _chem_comp_angle.atom_id_1 H1 _chem_comp_angle.atom_id_2 O _chem_comp_angle.atom_id_3 H2 _chem_comp_angle.value_angle 106.800 _chem_comp_angle.value_angle_esd 3.000 """ from libtbx.test_utils import open_tmp_file from libtbx import easy_run pdb_file = open_tmp_file(suffix="HOH.pdb") pdb_file.write(pdb_string) pdb_file.close() restraints_file = open_tmp_file(suffix="HOH.cif") restraints_file.write(restraints_cif_string) restraints_file.close() cmd = "phenix.pdb_interpretation \"%s\" \"%s\" write_geo_files=True" %( pdb_file.name, restraints_file.name) result = easy_run.fully_buffered(cmd).raise_if_errors() geo_file = open(pdb_file.name+".geo", "r") geo_file_str = geo_file.read() geo_file.close() assert "Bond angle restraints: 1" in geo_file_str def exercise_do_not_link(mon_lib_srv, ener_lib): """ Do not attempt to link two residues below. """ raw_records = """\ CRYST1 48.273 28.843 18.740 90.00 90.00 90.00 P 1 ATOM 17464 C1 BOG R 16 30.175 -15.554 9.755 1.00 35.95 R C ATOM 17465 O1 BOG R 16 31.099 -15.296 8.697 1.00 42.53 R O ATOM 17466 C2 BOG R 16 29.782 -17.026 9.758 1.00 39.47 R C ATOM 17467 O2 BOG R 16 29.087 -17.331 8.552 1.00 40.97 R O ATOM 17468 C3 BOG R 16 28.901 -17.357 10.950 1.00 40.73 R C ATOM 17469 O3 BOG R 16 28.635 -18.764 10.974 1.00 46.27 R O ATOM 17470 C4 BOG R 16 29.617 -16.951 12.225 1.00 40.76 R C ATOM 17471 O4 BOG R 16 28.755 -17.165 13.351 1.00 42.98 R O ATOM 17472 C5 BOG R 16 29.971 -15.472 12.137 1.00 39.41 R C ATOM 17473 O5 BOG R 16 30.787 -15.208 10.993 1.00 37.94 R O ATOM 17474 C6 BOG R 16 30.688 -14.989 13.394 1.00 40.91 R C ATOM 17475 O6 BOG R 16 31.999 -15.553 13.445 1.00 37.31 R O ATOM 17476 C1' BOG R 16 31.264 -13.898 8.462 1.00 38.79 R C ATOM 17477 C2' BOG R 16 32.250 -13.694 7.317 1.00 39.57 R C ATOM 17478 C3' BOG R 16 32.609 -12.219 7.133 1.00 44.82 R C ATOM 17479 C4' BOG R 16 31.515 -11.448 6.400 1.00 50.44 R C ATOM 17480 C5' BOG R 16 31.977 -10.037 6.047 1.00 48.33 R C ATOM 1 C1 BOG R 18 66.170 -7.947 8.034 1.00 55.33 R C ATOM 2 O1 BOG R 18 65.900 -6.739 8.753 1.00 55.00 R O ATOM 3 C2 BOG R 18 65.682 -9.113 8.883 1.00 55.62 R C ATOM 4 O2 BOG R 18 66.397 -9.125 10.123 1.00 61.39 R O ATOM 5 C3 BOG R 18 65.843 -10.438 8.147 1.00 60.20 R C ATOM 6 O3 BOG R 18 65.302 -11.514 8.924 1.00 64.46 R O ATOM 7 C4 BOG R 18 65.106 -10.358 6.821 1.00 55.23 R C ATOM 8 O4 BOG R 18 65.294 -11.575 6.088 1.00 58.17 R O ATOM 9 C5 BOG R 18 65.635 -9.174 6.022 1.00 55.29 R C ATOM 10 O5 BOG R 18 65.506 -7.953 6.761 1.00 55.00 R O ATOM 11 C6 BOG R 18 64.879 -9.032 4.705 1.00 50.53 R C ATOM 12 O6 BOG R 18 63.593 -8.452 4.947 1.00 41.70 R O ATOM 13 C1' BOG R 18 66.554 -5.574 8.243 1.00 52.47 R C ATOM 14 C2' BOG R 18 66.138 -4.389 9.113 1.00 55.51 R C ATOM 15 C3' BOG R 18 66.908 -3.115 8.772 1.00 56.45 R C ATOM 16 C4' BOG R 18 66.061 -2.210 7.826 1.00 56.42 R C ATOM 17 C5' BOG R 18 66.250 -0.997 7.016 1.00 58.47 R C ATOM 18 C6' BOG R 18 66.002 0.079 5.931 1.00 59.92 R C """.splitlines() cif_records = """ # ------------------------------------------------ # # --- LIST OF MONOMERS --- # data_comp_list loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level BOG BOG 'B-OCTYLGLUCOSIDE ' pyranose 48 20 . # ------------------------------------------------------ # ------------------------------------------------------ # # --- DESCRIPTION OF MONOMERS --- # data_comp_BOG # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z BOG C1 C CH1 0.000 0.000 0.000 0.000 BOG H1 H H 0.000 0.135 -1.086 0.103 BOG O1 O O2 0.000 -1.360 0.279 -0.341 BOG "C1'" C CH2 0.000 -2.165 -0.233 0.721 BOG "H1'1" H H 0.000 -1.890 0.259 1.656 BOG "H1'2" H H 0.000 -2.001 -1.309 0.815 BOG "C2'" C CH2 0.000 -3.640 0.035 0.417 BOG "H2'1" H H 0.000 -3.913 -0.458 -0.519 BOG "H2'2" H H 0.000 -3.801 1.110 0.321 BOG "C3'" C CH2 0.000 -4.504 -0.514 1.554 BOG "H3'1" H H 0.000 -4.228 -0.021 2.489 BOG "H3'2" H H 0.000 -4.340 -1.589 1.649 BOG "C4'" C CH2 0.000 -5.979 -0.246 1.250 BOG "H4'1" H H 0.000 -6.252 -0.737 0.314 BOG "H4'2" H H 0.000 -6.141 0.830 1.155 BOG "C5'" C CH2 0.000 -6.843 -0.795 2.386 BOG "H5'1" H H 0.000 -6.567 -0.303 3.322 BOG "H5'2" H H 0.000 -6.679 -1.870 2.480 BOG "C6'" C CH2 0.000 -8.318 -0.527 2.083 BOG "H6'1" H H 0.000 -8.591 -1.019 1.147 BOG "H6'2" H H 0.000 -8.479 0.549 1.988 BOG "C7'" C CH2 0.000 -9.181 -1.075 3.219 BOG "H7'1" H H 0.000 -8.906 -0.583 4.154 BOG "H7'2" H H 0.000 -9.017 -2.151 3.314 BOG "C8'" C CH3 0.000 -10.656 -0.807 2.915 BOG "H8'3" H H 0.000 -10.818 0.237 2.823 BOG "H8'2" H H 0.000 -10.926 -1.285 2.008 BOG "H8'1" H H 0.000 -11.257 -1.186 3.702 BOG O5 O O2 0.000 0.320 0.635 1.235 BOG C5 C CH1 0.000 1.615 0.188 1.628 BOG H5 H H 0.000 1.639 -0.911 1.621 BOG C4 C CH1 0.000 2.668 0.725 0.656 BOG H4 H H 0.000 2.630 1.824 0.644 BOG O4 O OH1 0.000 3.965 0.296 1.072 BOG HO4 H H 0.000 4.629 0.637 0.457 BOG C3 C CH1 0.000 2.372 0.187 -0.747 BOG H3 H H 0.000 2.512 -0.903 -0.761 BOG O3 O OH1 0.000 3.255 0.796 -1.691 BOG HO3 H H 0.000 3.066 0.455 -2.575 BOG C2 C CH1 0.000 0.919 0.523 -1.105 BOG H2 H H 0.000 0.805 1.612 -1.194 BOG O2 O OH1 0.000 0.577 -0.095 -2.346 BOG HO2 H H 0.000 -0.339 0.119 -2.570 BOG C6 C CH2 0.000 1.922 0.693 3.039 BOG H61 H H 0.000 1.898 1.785 3.047 BOG H62 H H 0.000 2.914 0.349 3.340 BOG O6 O OH1 0.000 0.944 0.187 3.950 BOG HO6 H H 0.000 1.174 0.528 4.825 loop_ _chem_comp_tree.comp_id _chem_comp_tree.atom_id _chem_comp_tree.atom_back _chem_comp_tree.atom_forward _chem_comp_tree.connect_type BOG C1 n/a O5 START BOG H1 C1 . . BOG O1 C1 "C1'" . BOG "C1'" O1 "C2'" . BOG "H1'1" "C1'" . . BOG "H1'2" "C1'" . . BOG "C2'" "C1'" "C3'" . BOG "H2'1" "C2'" . . BOG "H2'2" "C2'" . . BOG "C3'" "C2'" "C4'" . BOG "H3'1" "C3'" . . BOG "H3'2" "C3'" . . BOG "C4'" "C3'" "C5'" . BOG "H4'1" "C4'" . . BOG "H4'2" "C4'" . . BOG "C5'" "C4'" "C6'" . BOG "H5'1" "C5'" . . BOG "H5'2" "C5'" . . BOG "C6'" "C5'" "C7'" . BOG "H6'1" "C6'" . . BOG "H6'2" "C6'" . . BOG "C7'" "C6'" "C8'" . BOG "H7'1" "C7'" . . BOG "H7'2" "C7'" . . BOG "C8'" "C7'" "H8'1" . BOG "H8'3" "C8'" . . BOG "H8'2" "C8'" . . BOG "H8'1" "C8'" . . BOG O5 C1 . END BOG C5 O5 C6 . BOG H5 C5 . . BOG C4 C5 C3 . BOG H4 C4 . . BOG O4 C4 HO4 . BOG HO4 O4 . . BOG C3 C4 C2 . BOG H3 C3 . . BOG O3 C3 HO3 . BOG HO3 O3 . . BOG C2 C3 O2 . BOG H2 C2 . . BOG O2 C2 HO2 . BOG HO2 O2 . . BOG C6 C5 O6 . BOG H61 C6 . . BOG H62 C6 . . BOG O6 C6 . . BOG HO6 O6 . . BOG C1 C2 . ADD loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd BOG O1 C1 single 1.426 0.020 BOG C1 C2 single 1.524 0.020 BOG O5 C1 single 1.426 0.020 BOG H1 C1 single 1.099 0.020 BOG "C1'" O1 single 1.426 0.020 BOG O2 C2 single 1.432 0.020 BOG C2 C3 single 1.524 0.020 BOG H2 C2 single 1.099 0.020 BOG HO2 O2 single 0.967 0.020 BOG O3 C3 single 1.432 0.020 BOG C3 C4 single 1.524 0.020 BOG H3 C3 single 1.099 0.020 BOG HO3 O3 single 0.967 0.020 BOG O4 C4 single 1.432 0.020 BOG C4 C5 single 1.524 0.020 BOG H4 C4 single 1.099 0.020 BOG HO4 O4 single 0.967 0.020 BOG C5 O5 single 1.426 0.020 BOG C6 C5 single 1.524 0.020 BOG H5 C5 single 1.099 0.020 BOG O6 C6 single 1.432 0.020 BOG H61 C6 single 1.092 0.020 BOG H62 C6 single 1.092 0.020 BOG HO6 O6 single 0.967 0.020 BOG "C2'" "C1'" single 1.524 0.020 BOG "H1'1" "C1'" single 1.092 0.020 BOG "H1'2" "C1'" single 1.092 0.020 BOG "C3'" "C2'" single 1.524 0.020 BOG "H2'1" "C2'" single 1.092 0.020 BOG "H2'2" "C2'" single 1.092 0.020 BOG "C4'" "C3'" single 1.524 0.020 BOG "H3'1" "C3'" single 1.092 0.020 BOG "H3'2" "C3'" single 1.092 0.020 BOG "C5'" "C4'" single 1.524 0.020 BOG "H4'1" "C4'" single 1.092 0.020 BOG "H4'2" "C4'" single 1.092 0.020 BOG "C6'" "C5'" single 1.524 0.020 BOG "H5'1" "C5'" single 1.092 0.020 BOG "H5'2" "C5'" single 1.092 0.020 BOG "C7'" "C6'" single 1.524 0.020 BOG "H6'1" "C6'" single 1.092 0.020 BOG "H6'2" "C6'" single 1.092 0.020 BOG "C8'" "C7'" single 1.513 0.020 BOG "H7'1" "C7'" single 1.092 0.020 BOG "H7'2" "C7'" single 1.092 0.020 BOG "H8'1" "C8'" single 1.059 0.020 BOG "H8'2" "C8'" single 1.059 0.020 BOG "H8'3" "C8'" single 1.059 0.020 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd BOG H1 C1 O1 109.470 3.000 BOG H1 C1 O5 109.470 3.000 BOG O1 C1 O5 109.470 3.000 BOG H1 C1 C2 108.340 3.000 BOG O1 C1 C2 109.470 3.000 BOG O5 C1 C2 109.470 3.000 BOG C1 O1 "C1'" 111.800 3.000 BOG O1 "C1'" "H1'1" 109.470 3.000 BOG O1 "C1'" "H1'2" 109.470 3.000 BOG O1 "C1'" "C2'" 109.470 3.000 BOG "H1'1" "C1'" "H1'2" 107.900 3.000 BOG "H1'1" "C1'" "C2'" 109.470 3.000 BOG "H1'2" "C1'" "C2'" 109.470 3.000 BOG "C1'" "C2'" "H2'1" 109.470 3.000 BOG "C1'" "C2'" "H2'2" 109.470 3.000 BOG "C1'" "C2'" "C3'" 111.000 3.000 BOG "H2'1" "C2'" "H2'2" 107.900 3.000 BOG "H2'1" "C2'" "C3'" 109.470 3.000 BOG "H2'2" "C2'" "C3'" 109.470 3.000 BOG "C2'" "C3'" "H3'1" 109.470 3.000 BOG "C2'" "C3'" "H3'2" 109.470 3.000 BOG "C2'" "C3'" "C4'" 111.000 3.000 BOG "H3'1" "C3'" "H3'2" 107.900 3.000 BOG "H3'1" "C3'" "C4'" 109.470 3.000 BOG "H3'2" "C3'" "C4'" 109.470 3.000 BOG "C3'" "C4'" "H4'1" 109.470 3.000 BOG "C3'" "C4'" "H4'2" 109.470 3.000 BOG "C3'" "C4'" "C5'" 111.000 3.000 BOG "H4'1" "C4'" "H4'2" 107.900 3.000 BOG "H4'1" "C4'" "C5'" 109.470 3.000 BOG "H4'2" "C4'" "C5'" 109.470 3.000 BOG "C4'" "C5'" "H5'1" 109.470 3.000 BOG "C4'" "C5'" "H5'2" 109.470 3.000 BOG "C4'" "C5'" "C6'" 111.000 3.000 BOG "H5'1" "C5'" "H5'2" 107.900 3.000 BOG "H5'1" "C5'" "C6'" 109.470 3.000 BOG "H5'2" "C5'" "C6'" 109.470 3.000 BOG "C5'" "C6'" "H6'1" 109.470 3.000 BOG "C5'" "C6'" "H6'2" 109.470 3.000 BOG "C5'" "C6'" "C7'" 111.000 3.000 BOG "H6'1" "C6'" "H6'2" 107.900 3.000 BOG "H6'1" "C6'" "C7'" 109.470 3.000 BOG "H6'2" "C6'" "C7'" 109.470 3.000 BOG "C6'" "C7'" "H7'1" 109.470 3.000 BOG "C6'" "C7'" "H7'2" 109.470 3.000 BOG "C6'" "C7'" "C8'" 111.000 3.000 BOG "H7'1" "C7'" "H7'2" 107.900 3.000 BOG "H7'1" "C7'" "C8'" 109.470 3.000 BOG "H7'2" "C7'" "C8'" 109.470 3.000 BOG "C7'" "C8'" "H8'3" 109.470 3.000 BOG "C7'" "C8'" "H8'2" 109.470 3.000 BOG "C7'" "C8'" "H8'1" 109.470 3.000 BOG "H8'3" "C8'" "H8'2" 109.470 3.000 BOG "H8'3" "C8'" "H8'1" 109.470 3.000 BOG "H8'2" "C8'" "H8'1" 109.470 3.000 BOG C1 O5 C5 111.800 3.000 BOG O5 C5 H5 109.470 3.000 BOG O5 C5 C4 109.470 3.000 BOG O5 C5 C6 109.470 3.000 BOG H5 C5 C4 108.340 3.000 BOG H5 C5 C6 108.340 3.000 BOG C4 C5 C6 111.000 3.000 BOG C5 C4 H4 108.340 3.000 BOG C5 C4 O4 109.470 3.000 BOG C5 C4 C3 111.000 3.000 BOG H4 C4 O4 109.470 3.000 BOG H4 C4 C3 108.340 3.000 BOG O4 C4 C3 109.470 3.000 BOG C4 O4 HO4 109.470 3.000 BOG C4 C3 H3 108.340 3.000 BOG C4 C3 O3 109.470 3.000 BOG C4 C3 C2 111.000 3.000 BOG H3 C3 O3 109.470 3.000 BOG H3 C3 C2 108.340 3.000 BOG O3 C3 C2 109.470 3.000 BOG C3 O3 HO3 109.470 3.000 BOG C3 C2 H2 108.340 3.000 BOG C3 C2 O2 109.470 3.000 BOG C3 C2 C1 111.000 3.000 BOG H2 C2 O2 109.470 3.000 BOG H2 C2 C1 108.340 3.000 BOG O2 C2 C1 109.470 3.000 BOG C2 O2 HO2 109.470 3.000 BOG C5 C6 H61 109.470 3.000 BOG C5 C6 H62 109.470 3.000 BOG C5 C6 O6 109.470 3.000 BOG H61 C6 H62 107.900 3.000 BOG H61 C6 O6 109.470 3.000 BOG H62 C6 O6 109.470 3.000 BOG C6 O6 HO6 109.470 3.000 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period BOG var_1 O5 C1 O1 "C1'" -59.799 20.000 1 BOG var_2 C1 O1 "C1'" "C2'" 179.999 20.000 1 BOG var_3 O1 "C1'" "C2'" "C3'" -179.965 20.000 3 BOG var_4 "C1'" "C2'" "C3'" "C4'" 180.000 20.000 3 BOG var_5 "C2'" "C3'" "C4'" "C5'" 179.946 20.000 3 BOG var_6 "C3'" "C4'" "C5'" "C6'" 179.980 20.000 3 BOG var_7 "C4'" "C5'" "C6'" "C7'" -179.963 20.000 3 BOG var_8 "C5'" "C6'" "C7'" "C8'" -179.980 20.000 3 BOG var_9 "C6'" "C7'" "C8'" "H8'1" -179.975 20.000 3 BOG var_10 C1 O5 C5 C6 180.000 20.000 1 BOG var_11 O5 C5 C4 C3 -60.000 20.000 3 BOG var_12 C5 C4 O4 HO4 -179.949 20.000 1 BOG var_13 C5 C4 C3 C2 60.000 20.000 3 BOG var_14 C4 C3 O3 HO3 -179.973 20.000 1 BOG var_15 C4 C3 C2 O2 180.000 20.000 3 BOG var_16 C3 C2 C1 O5 60.000 20.000 3 BOG var_17 C3 C2 O2 HO2 -179.932 20.000 1 BOG var_18 O5 C5 C6 O6 59.890 20.000 3 BOG var_1 C5 O5 C1 C2 -55.000 20.000 1 # loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign BOG chir_01 C1 O1 C2 O5 negativ BOG chir_02 C2 C1 O2 C3 positiv BOG chir_03 C3 C2 O3 C4 negativ BOG chir_04 C4 C3 O4 C5 positiv BOG chir_05 C5 C4 O5 C6 positiv # ------------------------------------------------------ """ import iotbx.cif log = StringIO() cif_object = iotbx.cif.reader(input_string=cif_records).model() mon_lib_srv.process_cif_object(cif_object=cif_object) processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, force_symmetry=False, log = log) # this is to check there is no covalent bonds between two residues xrs = processed_pdb_file.xray_structure() grm = processed_pdb_file.geometry_restraints_manager() rgs=list(processed_pdb_file.all_chain_proxies.pdb_hierarchy.residue_groups()) rg1_i_seqs_1 = rgs[0].atoms().extract_i_seq() rg1_i_seqs_2 = rgs[1].atoms().extract_i_seq() bps, asu = grm.get_covalent_bond_proxies(sites_cart = xrs.sites_cart()) for bps in bps: for i_seq in bps.i_seqs: r = [] r.append(i_seq in rg1_i_seqs_1) r.append(i_seq in rg1_i_seqs_2) assert r.count(True)==1 def exercise_bogus_crystal_symmetry(mon_lib_srv, ener_lib): raw_records = """\ REMARK taken from 4arg CRYST1 1.000 1.000 1.000 1.00 1.00 1.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ATOM 1 CA PRO A 1 58.034 68.065 61.446 1.00 0.00 C ATOM 2 CA ARG A 2 59.821 66.269 58.634 1.00 0.00 C ATOM 3 CA THR A 3 56.972 63.793 58.378 1.00 0.00 C ATOM 4 CA LEU A 4 54.332 66.493 58.625 1.00 0.00 C ATOM 5 CA ASN A 5 55.845 68.102 55.551 1.00 0.00 C ATOM 6 CA ALA A 6 55.922 64.739 53.816 1.00 0.00 C ATOM 7 CA TRP A 7 52.227 64.264 54.482 1.00 0.00 C ATOM 8 CA VAL A 8 51.590 67.865 53.504 1.00 0.00 C ATOM 9 CA LYS A 9 52.954 66.907 50.106 1.00 0.00 C ATOM 10 CA VAL A 10 50.711 63.858 50.117 1.00 0.00 C """.splitlines() try: processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, force_symmetry=True) except Sorry as e: assert str(e).startswith( "Unit cell volume is incompatible with number of atoms") else: raise Exception_expected # Test automatic detection of CDL def exercise_cdl_automatic(): pdbstring = """\ ATOM 0 CA GLY A 3 5.804 -2.100 7.324 1.00 1.36 C ATOM 1 C GLY A 3 4.651 -1.149 7.578 1.00 1.01 C ATOM 2 O GLY A 3 3.598 -1.553 8.071 1.00 1.38 O ATOM 3 N GLY A 3 6.706 -1.622 6.294 1.00 1.11 N ATOM 4 CA PHE A 4 3.819 1.134 7.419 1.00 0.89 C ATOM 5 CB PHE A 4 4.397 2.380 8.094 1.00 1.13 C ATOM 6 C PHE A 4 3.185 1.509 6.084 1.00 0.94 C ATOM 7 N PHE A 4 4.852 0.121 7.242 1.00 0.88 N ATOM 8 O PHE A 4 2.361 2.421 6.010 1.00 1.47 O ATOM 9 CA LEU A 5 3.055 1.059 3.693 1.00 0.87 C ATOM 10 CB LEU A 5 3.965 0.435 2.634 1.00 1.13 C ATOM 11 C LEU A 5 1.634 0.527 3.541 1.00 0.87 C ATOM 12 N LEU A 5 3.576 0.800 5.030 1.00 0.92 N ATOM 13 O LEU A 5 1.246 -0.440 4.196 1.00 1.23 O """ pdb_1 = "REMARK 3 GEOSTD + MON.LIB. + CDL v1.2\n" + pdbstring pdb_2 = pdbstring with open("tst_cdl_auto_1.pdb", "w") as f: f.write(pdb_1) with open("tst_cdl_auto_2.pdb", "w") as f: f.write(pdb_2) cifstring = """\ data_cdl_refine %s loop_ _atom_site.group_PDB _atom_site.id _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.auth_asym_id _atom_site.auth_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.type_symbol _atom_site.pdbx_formal_charge _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num ATOM 1 N . GLY A 1 ? -9.12200 4.64529 5.82028 1.000 21.01594 N ? A ? 1 1 ATOM 2 CA . GLY A 1 ? -9.14139 4.15860 4.44999 1.000 17.74125 C ? A ? 1 1 ATOM 3 C . GLY A 1 ? -8.06917 3.11022 4.29606 1.000 17.40881 C ? A ? 1 1 ATOM 4 O . GLY A 1 ? -7.63359 2.52149 5.28628 1.000 17.89287 O ? A ? 1 1 ATOM 5 N . ASN A 2 ? -7.62610 2.88495 3.06334 1.000 16.11630 N ? A ? 2 1 ATOM 6 CA . ASN A 2 ? -6.52361 1.96527 2.82704 1.000 15.02052 C ? A ? 2 1 ATOM 7 C . ASN A 2 ? -5.24111 2.51732 3.42319 1.000 13.75642 C ? A ? 2 1 ATOM 8 O . ASN A 2 ? -5.04518 3.73206 3.51450 1.000 13.09303 O ? A ? 2 1 ATOM 9 CB . ASN A 2 ? -6.34271 1.71701 1.33679 1.000 14.87486 C ? A ? 2 1 ATOM 10 CG . ASN A 2 ? -7.61171 1.23635 0.68846 1.000 16.71339 C ? A ? 2 1 ATOM 11 OD1 . ASN A 2 ? -8.11028 0.15702 1.01777 1.000 19.77837 O ? A ? 2 1 ATOM 12 ND2 . ASN A 2 ? -8.16730 2.04317 -0.21593 1.000 14.75765 N ? A ? 2 1 """ cif_1 = cifstring % """\ _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' """ cif_2 = cifstring % "" with open("tst_cdl_auto_1.cif", "w") as f: f.write(cif_1) with open("tst_cdl_auto_2.cif", "w") as f: f.write(cif_2) model_files = [ ("tst_cdl_auto_1.pdb", "tst_cdl_auto_2.pdb"), ("tst_cdl_auto_1.cif", "tst_cdl_auto_2.cif"), ] for file1, file2 in model_files : # mmtbx.monomer_library.pdb_interpretation.run will not work with mmCIF, # so I'm testing via the command-line tool instead from mmtbx.command_line.pdb_interpretation import run stdout_save = sys.stdout sys.stdout = null_out() ppf_1 = run(args=[file1, "cdl=False"])[0] ppf_2 = run(args=[file2, "cdl=False"])[0] grm_1 = ppf_1.geometry_restraints_manager() grm_2 = ppf_2.geometry_restraints_manager() assert not None in [grm_1, grm_2] assert ppf_1.all_chain_proxies.use_cdl is None, ppf_1.all_chain_proxies.use_cdl assert ppf_2.all_chain_proxies.use_cdl is None, ppf_2.all_chain_proxies.use_cdl ppf_1 = run(args=[file1, "cdl=Auto"])[0] ppf_2 = run(args=[file2, "cdl=Auto"])[0] grm_1 = ppf_1.geometry_restraints_manager() grm_2 = ppf_2.geometry_restraints_manager() assert ppf_1.all_chain_proxies.use_cdl == True assert ppf_2.all_chain_proxies.use_cdl is None sys.stdout = stdout_save def exercise_unk_and_cys(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 182.247 207.944 177.997 90.00 90.00 90.00 P 21 21 21 8 ATOM 27637 N CYS X 25 162.023 328.719 193.119 1.00 48.83 N ATOM 27638 CA CYS X 25 160.744 328.717 192.370 1.00 48.38 C ATOM 27639 C CYS X 25 160.840 329.477 191.030 1.00 48.55 C ATOM 27640 O CYS X 25 160.447 328.960 189.978 1.00 47.05 O ATOM 27641 CB CYS X 25 159.647 329.420 193.185 1.00 49.20 C ATOM 27642 SG CYS X 25 158.050 329.117 192.457 1.00 48.43 S TER HETATM28972 UNK UNX C 262 92.003 325.919 218.014 1.00 80.36 X END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) def exercise_ss_bond_angles(mon_lib_srv, ener_lib): raw_records = """\ HEADER HYDROLASE/IMMUNE SYSTEM 11-MAR-07 2P45 CRYST1 73.447 73.070 42.539 90.00 90.00 90.00 P 21 21 21 4 ATOM 1119 N CYS B 22 48.085 17.330 19.679 1.00 11.80 N ATOM 1120 CA CYS B 22 47.337 16.587 18.675 1.00 11.61 C ATOM 1121 C CYS B 22 46.034 17.288 18.406 1.00 11.47 C ATOM 1122 O CYS B 22 45.392 17.844 19.314 1.00 12.66 O ATOM 1123 CB CYS B 22 47.077 15.179 19.161 1.00 13.15 C ATOM 1124 SG CYS B 22 45.959 14.196 18.149 1.00 14.55 S ATOM 1687 N CYS B 96 48.918 9.850 18.634 1.00 12.25 N ATOM 1688 CA CYS B 96 47.641 10.223 19.169 1.00 11.51 C ATOM 1689 C CYS B 96 46.539 9.414 18.528 1.00 10.27 C ATOM 1690 O CYS B 96 46.654 8.958 17.371 1.00 12.04 O ATOM 1691 CB CYS B 96 47.460 11.706 19.105 1.00 16.73 C ATOM 1692 SG ACYS B 96 45.815 12.414 19.205 0.50 12.31 S ATOM 1693 SG BCYS B 96 47.259 12.563 17.544 0.50 18.06 S END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) grm = processed_pdb_file.geometry_restraints_manager() assert grm.angle_proxies.size() == 15 assert grm.get_dihedral_proxies().size() == 3 selected_dihedrals = grm.dihedral_proxies.proxy_select( n_seq=13, iselection=flex.size_t([4,5,10,11,12])) # select SS dihedrals, 2 in this case because of alternative SG atom assert selected_dihedrals.size() == 2 # assert exact values from cif library... assert approx_equal(selected_dihedrals[0].angle_ideal, 93.0) assert approx_equal(selected_dihedrals[0].alt_angle_ideals[0], -86.0) deltas = grm.dihedral_proxies.deltas( processed_pdb_file.xray_structure().sites_cart()) assert approx_equal(deltas[3], -19.6324864704) # --> -86 degrees assert approx_equal(deltas[6], 23.2807269272) # --> 93 degrees def exercise_ss_bond_angles_alt_loc(mon_lib_srv, ener_lib): raw_records = """\ HEADER HYDROLASE 19-OCT-05 2BCH CRYST1 45.908 45.908 101.372 90.00 90.00 120.00 P 31 2 1 6 ATOM 274 N CYS A 27 17.541 4.439 12.897 1.00 13.99 N ATOM 275 CA CYS A 27 16.566 5.527 12.862 1.00 14.57 C ATOM 276 C CYS A 27 16.236 6.026 11.467 1.00 14.53 C ATOM 277 O CYS A 27 15.254 6.760 11.351 1.00 16.95 O ATOM 278 CB CYS A 27 17.114 6.698 13.662 1.00 15.77 C ATOM 279 SG CYS A 27 17.230 6.332 15.443 1.00 17.57 S ATOM 1225 CB CYS A 123 14.607 7.591 16.260 1.00 24.16 C ATOM 1226 SG CYS A 123 15.316 5.939 15.946 1.00 20.05 S ATOM 1217 N ACYS A 123 15.023 7.279 18.624 0.58 26.40 N ATOM 1219 CA ACYS A 123 15.266 8.190 17.491 0.58 25.69 C ATOM 1221 C ACYS A 123 14.764 9.599 17.776 0.58 26.33 C ATOM 1223 O ACYS A 123 14.197 10.238 16.886 0.58 28.70 O ATOM 1227 OXTACYS A 123 14.975 10.081 18.878 0.58 28.31 O ATOM 1218 N BCYS A 123 15.023 7.288 18.685 0.42 25.68 N ATOM 1220 CA BCYS A 123 15.108 8.205 17.548 0.42 25.86 C ATOM 1222 C BCYS A 123 14.270 9.460 17.813 0.42 26.42 C ATOM 1224 O BCYS A 123 13.915 10.125 16.837 0.42 27.75 O ATOM 1228 OXTBCYS A 123 13.981 9.728 18.968 0.42 28.04 O END """.splitlines() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) grm = processed_pdb_file.geometry_restraints_manager() assert grm.angle_proxies.size() == 21 assert grm.get_dihedral_proxies().size() == 5, \ "dihedrals %d" % grm.get_dihedral_proxies().size() def exercise_bad_water(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 34.035 17.923 13.510 90.00 90.00 90.00 P 1 SCALE1 0.029382 0.000000 0.000000 0.00000 SCALE2 0.000000 0.055794 0.000000 0.00000 SCALE3 0.000000 0.000000 0.074019 0.00000 ATOM 5961 W HOH 21100 44.341 86.390 -10.071 1.000 50.00 ATOM 5962 W HOH 21101 56.357 78.467 -11.839 1.000 50.00 ATOM 5963 W HOH 21102 32.322 79.906 -13.581 1.000 50.00 END """.splitlines() e = None log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, log=log) msg = processed_pdb_file.all_chain_proxies.fatal_problems_message() assert msg == """Fatal problems interpreting model file: Number of atoms with unknown scattering type symbols: 3 Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. It is best practice to define the element names in columns 77-78 of the PDB file.""", msg def exercise_edits_parallelity(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 47.935 37.102 30.520 90.00 90.00 90.00 P 1 ATOM 55 N PHE A 431 31.800 18.971 9.354 1.00187.57 N ATOM 56 CA PHE A 431 30.664 18.262 9.908 1.00187.57 C ATOM 57 C PHE A 431 29.679 19.392 10.042 1.00187.57 C ATOM 58 O PHE A 431 29.961 20.372 10.729 1.00187.57 O ATOM 59 CB PHE A 431 30.976 17.709 11.288 1.00192.11 C ATOM 60 CG PHE A 431 32.191 16.840 11.330 1.00192.11 C ATOM 61 CD1 PHE A 431 32.307 15.750 10.487 1.00192.11 C ATOM 62 CD2 PHE A 431 33.209 17.101 12.221 1.00192.11 C ATOM 63 CE1 PHE A 431 33.426 14.943 10.527 1.00192.11 C ATOM 64 CE2 PHE A 431 34.331 16.298 12.265 1.00192.11 C ATOM 65 CZ PHE A 431 34.439 15.217 11.418 1.00192.11 C ATOM 225 P A P 36 27.448 9.314 19.851 1.00 76.88 P ATOM 226 OP1 A P 36 26.648 9.676 21.048 1.00 78.59 O ATOM 227 OP2 A P 36 28.571 8.351 19.976 1.00 75.20 O ATOM 228 O5' A P 36 27.998 10.652 19.190 1.00 78.76 O ATOM 229 C5' A P 36 29.217 11.250 19.656 1.00 77.93 C ATOM 230 C4' A P 36 30.389 10.753 18.844 1.00 78.66 C ATOM 231 O4' A P 36 29.987 10.611 17.462 1.00 79.49 O ATOM 232 C3' A P 36 31.616 11.662 18.873 1.00 78.23 C ATOM 233 O3' A P 36 32.665 11.095 19.647 1.00 77.17 O ATOM 234 C2' A P 36 32.056 11.820 17.411 1.00 79.34 C ATOM 235 O2' A P 36 33.369 11.376 17.124 1.00 79.34 O ATOM 236 C1' A P 36 31.046 10.987 16.617 1.00 78.22 C ATOM 237 N9 A P 36 30.484 11.736 15.494 1.00 20.00 N ATOM 238 C8 A P 36 29.463 12.653 15.522 1.00 20.00 C ATOM 239 N7 A P 36 29.182 13.166 14.348 1.00 20.00 N ATOM 240 C5 A P 36 30.081 12.548 13.491 1.00 20.00 C ATOM 241 C6 A P 36 30.298 12.660 12.106 1.00 20.00 C ATOM 242 N6 A P 36 29.597 13.468 11.310 1.00 20.00 N ATOM 243 N1 A P 36 31.274 11.902 11.561 1.00 20.00 N ATOM 244 C2 A P 36 31.978 11.092 12.360 1.00 20.00 C ATOM 245 N3 A P 36 31.869 10.898 13.673 1.00 20.00 N ATOM 246 C4 A P 36 30.890 11.665 14.184 1.00 20.00 C END """.splitlines() edits = """\ pdb_interpretation.geometry_restraints { edits { plane1 = chain A and resseq 431 and (name cg or name ce1 or name ce2) plane2 = chain P and resseq 36 and (name c2 or name c4 or name c6) parallelity { action = *add delete change atom_selection_1 = $plane1 atom_selection_2 = $plane2 sigma = 0.027 target_angle_deg = 0 } } }""" gm_phil = iotbx.phil.parse( monomer_library.pdb_interpretation.grand_master_phil_str, process_includes=True) edits_phil = iotbx.phil.parse(edits) working_phil = gm_phil.fetch(edits_phil) params = working_phil.extract() # print params.geometry_restraints.edits.parallelity[0].atom_selection_1 assert params.geometry_restraints.edits.parallelity[0].atom_selection_1 == \ "chain A and resseq 431 and (name cg or name ce1 or name ce2)" processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params = params.pdb_interpretation, log=None) grm = processed_pdb_file.geometry_restraints_manager( params_edits=params.geometry_restraints.edits, params_remove=params.geometry_restraints.remove) assert grm.parallelity_proxies.size() == 1 pp = grm.parallelity_proxies[0] # print dir(pp) assert list(pp.i_seqs) == [5,8,9] assert list(pp.j_seqs) == [27,30,32] assert approx_equal(pp.weight, 1371.74211248) assert approx_equal(pp.target_angle_deg, 0) def exercise_edits_planarity(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 47.935 37.102 30.520 90.00 90.00 90.00 P 1 ATOM 55 N PHE A 431 31.800 18.971 9.354 1.00187.57 N ATOM 56 CA PHE A 431 30.664 18.262 9.908 1.00187.57 C ATOM 57 C PHE A 431 29.679 19.392 10.042 1.00187.57 C ATOM 58 O PHE A 431 29.961 20.372 10.729 1.00187.57 O ATOM 59 CB PHE A 431 30.976 17.709 11.288 1.00192.11 C ATOM 60 CG PHE A 431 32.191 16.840 11.330 1.00192.11 C ATOM 61 CD1 PHE A 431 32.307 15.750 10.487 1.00192.11 C ATOM 62 CD2 PHE A 431 33.209 17.101 12.221 1.00192.11 C ATOM 63 CE1 PHE A 431 33.426 14.943 10.527 1.00192.11 C ATOM 64 CE2 PHE A 431 34.331 16.298 12.265 1.00192.11 C ATOM 65 CZ PHE A 431 34.439 15.217 11.418 1.00192.11 C ATOM 225 P A P 36 27.448 9.314 19.851 1.00 76.88 P ATOM 226 OP1 A P 36 26.648 9.676 21.048 1.00 78.59 O ATOM 227 OP2 A P 36 28.571 8.351 19.976 1.00 75.20 O ATOM 228 O5' A P 36 27.998 10.652 19.190 1.00 78.76 O ATOM 229 C5' A P 36 29.217 11.250 19.656 1.00 77.93 C ATOM 230 C4' A P 36 30.389 10.753 18.844 1.00 78.66 C ATOM 231 O4' A P 36 29.987 10.611 17.462 1.00 79.49 O ATOM 232 C3' A P 36 31.616 11.662 18.873 1.00 78.23 C ATOM 233 O3' A P 36 32.665 11.095 19.647 1.00 77.17 O ATOM 234 C2' A P 36 32.056 11.820 17.411 1.00 79.34 C ATOM 235 O2' A P 36 33.369 11.376 17.124 1.00 79.34 O ATOM 236 C1' A P 36 31.046 10.987 16.617 1.00 78.22 C ATOM 237 N9 A P 36 30.484 11.736 15.494 1.00 20.00 N ATOM 238 C8 A P 36 29.463 12.653 15.522 1.00 20.00 C ATOM 239 N7 A P 36 29.182 13.166 14.348 1.00 20.00 N ATOM 240 C5 A P 36 30.081 12.548 13.491 1.00 20.00 C ATOM 241 C6 A P 36 30.298 12.660 12.106 1.00 20.00 C ATOM 242 N6 A P 36 29.597 13.468 11.310 1.00 20.00 N ATOM 243 N1 A P 36 31.274 11.902 11.561 1.00 20.00 N ATOM 244 C2 A P 36 31.978 11.092 12.360 1.00 20.00 C ATOM 245 N3 A P 36 31.869 10.898 13.673 1.00 20.00 N ATOM 246 C4 A P 36 30.890 11.665 14.184 1.00 20.00 C END """.splitlines() edits = """\ pdb_interpretation.geometry_restraints { edits { planarity { action = *add delete change atom_selection = resid 431 and (name N or name CA or name C) sigma = 0.027 } } }""" gm_phil = iotbx.phil.parse( monomer_library.pdb_interpretation.grand_master_phil_str, process_includes=True) edits_phil = iotbx.phil.parse(edits) working_phil = gm_phil.fetch(edits_phil) params = working_phil.extract() # print params.geometry_restraints.edits.planarity[0].atom_selection assert params.geometry_restraints.edits.planarity[0].atom_selection == \ "resid 431 and (name N or name CA or name C)" processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params = params.pdb_interpretation, log=None) grm = processed_pdb_file.geometry_restraints_manager( params_edits=params.geometry_restraints.edits, params_remove=params.geometry_restraints.remove) assert grm.planarity_proxies.size() == 3 pp = grm.planarity_proxies[2] # print dir(pp) assert list(pp.i_seqs) == [0,1,2] assert approx_equal(list(pp.weights)[0], 1371.7421124828534) def exercise_edits_bond(mon_lib_srv, ener_lib): from cctbx.geometry_restraints.linking_class import linking_class origin_ids = linking_class() raw_records = """\ CRYST1 47.935 37.102 30.520 90.00 90.00 90.00 P 1 ATOM 55 N PHE A 431 31.800 18.971 9.354 1.00187.57 N ATOM 56 CA PHE A 431 30.664 18.262 9.908 1.00187.57 C ATOM 57 C PHE A 431 29.679 19.392 10.042 1.00187.57 C ATOM 58 O PHE A 431 29.961 20.372 10.729 1.00187.57 O ATOM 59 CB PHE A 431 30.976 17.709 11.288 1.00192.11 C ATOM 60 CG PHE A 431 32.191 16.840 11.330 1.00192.11 C ATOM 61 CD1 PHE A 431 32.307 15.750 10.487 1.00192.11 C ATOM 62 CD2 PHE A 431 33.209 17.101 12.221 1.00192.11 C ATOM 63 CE1 PHE A 431 33.426 14.943 10.527 1.00192.11 C ATOM 64 CE2 PHE A 431 34.331 16.298 12.265 1.00192.11 C ATOM 65 CZ PHE A 431 34.439 15.217 11.418 1.00192.11 C END """.splitlines() edits = """\ pdb_interpretation.geometry_restraints { edits { bond { action = *add delete change atom_selection_1 = name N atom_selection_2 = name CB symmetry_operation = None distance_ideal = 3 sigma = 0.1 slack = None limit = 1.0 top_out = True } } }""" gm_phil = iotbx.phil.parse( monomer_library.pdb_interpretation.grand_master_phil_str, process_includes=True) edits_phil = iotbx.phil.parse(edits) working_phil = gm_phil.fetch(edits_phil) params = working_phil.extract() # print params.geometry_restraints.edits.parallelity[0].atom_selection_1 assert params.geometry_restraints.edits.bond[0].atom_selection_1 == \ "name N" processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params = params.pdb_interpretation, log=None) grm = processed_pdb_file.geometry_restraints_manager( params_edits=params.geometry_restraints.edits, params_remove=params.geometry_restraints.remove) simple = grm.pair_proxies().bond_proxies.simple assert simple.size() == 12 user_defined = simple.proxy_select(origin_id=origin_ids.get_origin_id('edits')) assert user_defined.size() == 1 udp = user_defined[0] assert list(udp.i_seqs) == [0,4] assert udp.limit == 1 assert udp.top_out assert approx_equal(udp.distance_ideal, 3, eps=1e-4) assert approx_equal(udp.weight, 100, eps=1e-4) def exercise_bad_custom_bonds(mon_lib_srv, ener_lib): raw_records = """ CRYST1 21.213 24.878 21.468 90.00 90.00 90.00 P 1 SCALE1 0.047141 0.000000 0.000000 0.00000 SCALE2 0.000000 0.040196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046581 0.00000 ATOM 1 N SER A 92 10.967 6.937 5.256 1.00 19.08 N ATOM 2 CA SER A 92 11.206 7.027 6.703 1.00 14.61 C ATOM 3 C SER A 92 10.010 7.586 7.440 1.00 17.30 C ATOM 4 O SER A 92 9.590 7.129 8.497 1.00 21.21 O ATOM 5 CB SER A 92 12.423 7.902 6.959 1.00 16.36 C ATOM 6 OG SER A 92 12.172 9.246 6.637 1.00 23.58 O ATOM 7 N HIS A 93 9.395 8.633 6.883 1.00 19.20 N ATOM 8 CA HIS A 93 8.283 9.235 7.604 1.00 16.97 C ATOM 9 C HIS A 93 7.034 8.370 7.604 1.00 17.87 C ATOM 10 O HIS A 93 6.276 8.484 8.570 1.00 24.29 O ATOM 11 CB HIS A 93 7.948 10.619 7.018 1.00 17.10 C ATOM 12 CG HIS A 93 8.966 11.616 7.493 1.00 18.72 C ATOM 13 ND1 HIS A 93 10.278 11.564 7.100 1.00 19.80 N ATOM 14 CD2 HIS A 93 8.875 12.654 8.337 1.00 20.88 C ATOM 15 CE1 HIS A 93 10.963 12.535 7.666 1.00 20.04 C ATOM 16 NE2 HIS A 93 10.126 13.212 8.419 1.00 23.24 N ATOM 17 N ALA A 94 6.823 7.568 6.564 1.00 15.69 N ATOM 18 CA ALA A 94 5.666 6.670 6.556 1.00 18.31 C ATOM 19 C ALA A 94 5.873 5.431 7.418 1.00 18.40 C ATOM 20 O ALA A 94 5.000 5.000 8.170 1.00 19.22 O ATOM 21 CB ALA A 94 5.323 6.241 5.146 1.00 18.06 C HETATM 22 C1A HEM A 154 13.653 13.778 9.638 1.00 18.41 C HETATM 23 C1B HEM A 154 11.623 16.547 7.120 1.00 20.12 C HETATM 24 C1C HEM A 154 8.120 16.126 9.474 1.00 13.75 C HETATM 25 C1D HEM A 154 10.162 13.422 12.047 1.00 14.87 C HETATM 26 C2A HEM A 154 14.872 13.734 8.859 1.00 21.34 C HETATM 27 C2B HEM A 154 11.083 17.515 6.191 1.00 18.28 C HETATM 28 C2C HEM A 154 6.847 16.067 10.168 1.00 20.20 C HETATM 29 C2D HEM A 154 10.746 12.535 13.032 1.00 18.53 C HETATM 30 C3A HEM A 154 14.709 14.571 7.805 1.00 19.89 C HETATM 31 C3B HEM A 154 9.804 17.783 6.579 1.00 14.10 C HETATM 32 C3C HEM A 154 7.053 15.362 11.318 1.00 20.16 C HETATM 33 C3D HEM A 154 12.057 12.389 12.708 1.00 17.55 C HETATM 34 C4A HEM A 154 13.376 15.131 7.909 1.00 14.01 C HETATM 35 C4B HEM A 154 9.545 16.955 7.748 1.00 15.74 C HETATM 36 C4C HEM A 154 8.385 14.781 11.212 1.00 11.44 C HETATM 37 C4D HEM A 154 12.258 13.048 11.435 1.00 12.93 C HETATM 38 CAA HEM A 154 16.084 12.838 9.160 1.00 17.09 C HETATM 39 CAB HEM A 154 8.764 18.621 6.096 1.00 18.06 C HETATM 40 CAC HEM A 154 6.304 15.113 12.506 1.00 17.18 C HETATM 41 CAD HEM A 154 13.170 11.725 13.527 1.00 19.52 C HETATM 42 CBA HEM A 154 16.213 11.573 8.272 1.00 15.28 C HETATM 43 CBB HEM A 154 8.972 19.878 5.454 1.00 10.31 C HETATM 44 CBC HEM A 154 5.104 15.868 12.800 1.00 23.40 C HETATM 45 CBD HEM A 154 13.800 12.570 14.648 1.00 26.70 C HETATM 46 CGA HEM A 154 14.900 10.799 8.148 1.00 14.87 C HETATM 47 CGD HEM A 154 14.961 11.923 15.376 1.00 23.81 C HETATM 48 CHA HEM A 154 13.453 12.992 10.753 1.00 13.26 C HETATM 49 CHB HEM A 154 12.882 16.011 6.977 1.00 14.01 C HETATM 50 CHC HEM A 154 8.314 16.918 8.363 1.00 13.33 C HETATM 51 CHD HEM A 154 8.874 13.897 12.145 1.00 11.65 C HETATM 52 CMA HEM A 154 15.692 14.910 6.685 1.00 14.40 C HETATM 53 CMB HEM A 154 11.855 18.090 5.000 1.00 11.05 C HETATM 54 CMC HEM A 154 5.571 16.713 9.646 1.00 21.38 C HETATM 55 CMD HEM A 154 10.000 11.931 14.225 1.00 17.96 C HETATM 56 N A HEM A 154 12.773 14.670 9.058 1.00 10.68 N HETATM 57 N B HEM A 154 10.689 16.271 8.094 1.00 18.79 N HETATM 58 N C HEM A 154 9.011 15.278 10.091 1.00 15.30 N HETATM 59 N D HEM A 154 11.098 13.702 11.072 1.00 15.13 N HETATM 60 O1A HEM A 154 14.486 10.248 9.192 1.00 22.79 O HETATM 61 O1D HEM A 154 14.703 11.366 16.468 1.00 47.56 O HETATM 62 O2A HEM A 154 14.357 10.789 7.028 1.00 31.78 O HETATM 63 O2D HEM A 154 16.078 11.998 14.825 1.00 40.84 O HETATM 64 FE HEM A 154 10.863 14.901 9.518 1.00 17.04 Fe HETATM 65 O MTO A 155 11.461 16.396 10.964 1.00 20.08 O TER END """.splitlines() edits = """\ pdb_interpretation.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname HIS and resid 93 and name NE2 distance_ideal = 2.1 sigma = 0.01 } bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = x,y,z distance_ideal = 2.2 sigma = 0.01 } bond { atom_selection_2 = chain N and resname O and name NE } bond { distance_ideal = -1 } bond { distance_ideal = 2 } bond { distance_ideal = 2 sigma = -1 } }""" gm_phil = iotbx.phil.parse( monomer_library.pdb_interpretation.grand_master_phil_str, process_includes=True) edits_phil = iotbx.phil.parse(edits) working_phil = gm_phil.fetch(edits_phil) params = working_phil.extract() log = StringIO() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params = params.pdb_interpretation, log = log) grm = processed_pdb_file.geometry_restraints_manager( params_edits=params.geometry_restraints.edits) expected = """ Custom bonds: bond: atom 1: "HETATM 64 FE HEM A 154 .*. Fe " atom 2: "ATOM 16 NE2 HIS A 93 .*. N " symmetry operation: x,y,z distance_model: 2.146 distance_ideal: 2.100 ideal - model: -0.046 slack: 0.000 delta_slack: -0.046 sigma: 0.0100 bond: atom 1: "HETATM 64 FE HEM A 154 .*. Fe " atom 2: "HETATM 65 O MTO A 155 .*. O " symmetry operation: x,y,z distance_model: 2.164 distance_ideal: 2.200 ideal - model: 0.036 slack: 0.000 delta_slack: 0.036 sigma: 0.0100 Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = "chain N and resname O and name NE" Warning: Ignoring bond with distance_ideal < 0: atom_selection_1 = None atom_selection_2 = None distance_ideal = -1 Warning: Ignoring bond with sigma = None: atom_selection_1 = None atom_selection_2 = None distance_ideal = 2 Warning: Ignoring bond with sigma <= 0: atom_selection_1 = None atom_selection_2 = None distance_ideal = 2 sigma = -1 slack = 0 Total number of added/changed bonds: 2""" log = log.getvalue().splitlines() found = 0 for e in expected.splitlines(): if(e in log): found += 1 assert found > 39, found def exercise_allow_polymer_cross_special_position(mon_lib_srv, ener_lib): raw_records = """\ CRYST1 257.160 257.160 125.289 90.00 90.00 90.00 P 42 21 2 ATOM 6125 N GLU B 219 2.256 -0.004 52.800 1.00556.70 B N ATOM 6126 CA GLU B 219 2.976 -0.009 54.101 1.00553.07 B C ATOM 6127 C GLU B 219 2.020 -0.291 55.269 1.00548.53 B C ATOM 6128 O GLU B 219 2.412 -1.087 56.152 1.00563.96 B O ATOM 6129 CB GLU B 219 3.635 1.353 54.312 1.00549.67 B C ATOM 6130 N VAL B 220 0.817 0.295 55.291 1.00579.40 B N ATOM 6131 CA VAL B 220 -0.101 -0.076 56.415 1.00536.12 B C ATOM 6132 C VAL B 220 -0.931 -1.312 56.040 1.00595.15 B C ATOM 6133 O VAL B 220 -1.615 -1.845 56.941 1.00560.98 B O ATOM 6134 CB VAL B 220 -0.969 1.109 56.872 1.00506.94 B C ATOM 6135 CG1 VAL B 220 -1.904 0.713 58.004 1.00516.72 B C ATOM 6136 CG2 VAL B 220 -0.110 2.296 57.278 1.00493.38 B C ATOM 6137 N GLN B 221 -0.855 -1.759 54.781 1.00618.59 B N ATOM 6138 CA GLN B 221 -1.583 -2.967 54.295 1.00643.31 B C ATOM 6139 C GLN B 221 -0.837 -4.237 54.735 1.00659.80 B C ATOM 6140 O GLN B 221 -1.504 -5.170 55.254 1.00664.86 B O ATOM 6141 CB GLN B 221 -1.633 -2.914 52.766 1.00632.59 B C ATOM 6142 CG GLN B 221 -2.226 -4.158 52.118 1.00628.14 B C ATOM 6143 CD GLN B 221 -3.524 -3.878 51.400 1.00607.81 B C ATOM 6144 OE1 GLN B 221 -3.819 -2.746 51.025 1.00587.02 B O ATOM 6145 NE2 GLN B 221 -4.309 -4.921 51.188 1.00611.94 B N END """.splitlines() params = iotbx.phil.parse( monomer_library.pdb_interpretation.grand_master_phil_str, process_includes=True).extract() exp_lines = [ "Polymer crosses special position element:", "ATOM 7 CA VAL B 220 0.000 -0.000 56.415 1.00536.12 B C", "Use 'allow_polymer_cross_special_position=True' to keep going."] cntr=0 try: processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params = params.pdb_interpretation, log=None).xray_structure() except KeyboardInterrupt: raise except Exception as e: for line in str(e).splitlines(): if(line.strip() in exp_lines): cntr+=1 assert cntr>=2 # params.pdb_interpretation.allow_polymer_cross_special_position=True processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv=mon_lib_srv, ener_lib=ener_lib, file_name=None, raw_records=raw_records, params = params.pdb_interpretation, log=None).xray_structure() def run(args): assert len(args) == 0 mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() exercise_allow_polymer_cross_special_position(mon_lib_srv, ener_lib) exercise_bad_custom_bonds(mon_lib_srv, ener_lib) exercise_bad_water(mon_lib_srv, ener_lib) exercise_unk_and_cys(mon_lib_srv, ener_lib) exercise_cdl_automatic() exercise_flattened_cif_loop() exercise_bogus_crystal_symmetry(mon_lib_srv, ener_lib) exercise_do_not_link(mon_lib_srv, ener_lib) exercise_geostd_cif_links(mon_lib_srv, ener_lib) exercise_handle_case_insensitive(mon_lib_srv, ener_lib) exercise_pdb_string(mon_lib_srv, ener_lib) exercise_cns_rna(mon_lib_srv, ener_lib) exercise_rna_3p_2p(mon_lib_srv, ener_lib) exercise_rna_dna_hybrid(mon_lib_srv, ener_lib) exercise_hydrogen_deuterium_aliases() exercise_corrupt_cif_link() exercise_dna_cns_cy5_th6() exercise_sym_excl_indices(mon_lib_srv, ener_lib) exercise_auto_alias_h_h1() exercise_d_aa_resnames() exercise_d_amino_acid_chain_perfect_in_box() exercise_d_amino_acid_chain_perfect_in_box_peptide_plane() exercise_rna_v3(mon_lib_srv, ener_lib) exercise_asp_glu_acid() exercise_rna_dna_synonyms() exercise_ss_bond_angles(mon_lib_srv, ener_lib) exercise_ss_bond_angles_alt_loc(mon_lib_srv, ener_lib) exercise_edits_parallelity(mon_lib_srv, ener_lib) exercise_edits_planarity(mon_lib_srv, ener_lib) exercise_edits_bond(mon_lib_srv, ener_lib) print(format_cpu_times()) if (__name__ == "__main__"): import sys run(args=sys.argv[1:])