from __future__ import absolute_import, division, print_function from six.moves import cStringIO as StringIO from libtbx.test_utils import approx_equal, Exception_expected, \ show_diff, assert_lines_in_text from libtbx.utils import null_out import iotbx.cif from iotbx.pdb.mmcif import pdb_hierarchy_builder import mmtbx.model import libtbx.load_env from six.moves import range input_1ab1 = """\ data_1AB1 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.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _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 17 C CA A THR A 1 2 13.800 11.354 5.944 0.70 2.98 2 THR A CA 1 ATOM 18 C CA B THR A 1 2 13.872 10.918 5.772 0.30 5.01 2 THR A CA 1 ATOM 19 C C . THR A 1 2 14.118 10.664 7.274 1.00 2.92 2 THR A C 1 ATOM 20 O O . THR A 1 2 15.013 9.787 7.376 1.00 3.70 2 THR A O 1 ATOM 21 C CB A THR A 1 2 12.784 10.610 5.099 0.70 4.35 2 THR A CB 1 ATOM 22 C CB B THR A 1 2 12.938 9.905 5.108 0.30 1.07 2 THR A CB 1 ATOM 23 O OG1 A THR A 1 2 13.364 9.360 4.756 0.70 5.60 2 THR A OG1 1 ATOM 24 O OG1 B THR A 1 2 12.559 10.450 3.917 0.30 5.43 2 THR A OG1 1 ATOM 25 C CG2 A THR A 1 2 12.451 11.323 3.797 0.70 7.65 2 THR A CG2 1 ATOM 26 C CG2 B THR A 1 2 11.642 9.729 5.862 0.30 2.71 2 THR A CG2 1 ATOM 27 H H . THR A 1 2 15.500 10.728 5.006 1.00 1.74 2 THR A H 1 ATOM 28 H HA . THR A 1 2 13.437 12.241 6.128 1.00 4.09 2 THR A HA 1 ATOM 29 H HB A THR A 1 2 11.947 10.457 5.635 0.70 1.11 2 THR A HB 1 ATOM 30 H HB B THR A 1 2 13.426 9.030 5.019 0.30 4.20 2 THR A HB 1 ATOM 31 H HG21 A THR A 1 2 13.241 11.856 3.510 0.70 1.00 2 THR A HG21 1 ATOM 32 H HG21 B THR A 1 2 11.196 10.615 5.970 0.30 2.01 2 THR A HG21 1 ATOM 33 H HG22 A THR A 1 2 12.211 10.692 3.092 0.70 5.54 2 THR A HG22 1 ATOM 34 H HG22 B THR A 1 2 11.027 9.120 5.405 0.30 10.62 2 THR A HG22 1 ATOM 35 H HG23 A THR A 1 2 11.693 11.979 3.928 0.70 9.26 2 THR A HG23 1 ATOM 36 H HG23 B THR A 1 2 11.801 9.381 6.801 0.30 8.15 2 THR A HG23 1 # ...trunacted... HETATM 679 C C1 A EOH B 2 . 16.083 0.909 12.713 0.60 15.95 66 EOH A C1 1 HETATM 680 C C1 B EOH B 2 . 15.565 1.042 13.226 0.40 14.21 66 EOH A C1 1 HETATM 681 C C2 A EOH B 2 . 15.130 -0.269 13.016 0.60 14.85 66 EOH A C2 1 HETATM 682 C C2 B EOH B 2 . 14.830 -0.303 13.058 0.40 15.17 66 EOH A C2 1 HETATM 683 O O A EOH B 2 . 15.378 1.984 12.104 0.60 12.07 66 EOH A O 1 HETATM 684 O O B EOH B 2 . 14.811 2.078 12.602 0.40 5.53 66 EOH A O 1 """ def exercise_cif_show(): cif_model = iotbx.cif.reader(input_string=input_1ab1).model() builder = pdb_hierarchy_builder(cif_model["1AB1"]) hierarchy = builder.hierarchy h_cif = hierarchy.as_cif_block() builder = pdb_hierarchy_builder(h_cif) # this runs OK, why? # output h_cif: s = StringIO() h_cif.show(out=s, align_columns=False) builder = pdb_hierarchy_builder(h_cif) # Now it fails. def exercise_pdb_hierachy_builder(): cif_model = iotbx.cif.reader(input_string=input_1ab1).model() builder = pdb_hierarchy_builder(cif_model["1AB1"]) #assert builder.crystal_symmetry is None hierarchy = builder.hierarchy atoms = hierarchy.atoms() assert atoms[0].segid == " " # some code relies on this s = StringIO() hierarchy.show(out=s) assert not show_diff(s.getvalue(), """\ model id="" #chains=1 chain id="A" #residue_groups=2 resid=" 2 " #atom_groups=3 altloc="" resname="THR" #atoms=4 " C " " O " " H " " HA " altloc="A" resname="THR" #atoms=8 " CA " " CB " " OG1" " CG2" " HB " "HG21" "HG22" "HG23" altloc="B" resname="THR" #atoms=8 " CA " " CB " " OG1" " CG2" " HB " "HG21" "HG22" "HG23" resid=" 66 " #atom_groups=2 altloc="A" resname="EOH" #atoms=3 " C1 " " C2 " " O " altloc="B" resname="EOH" #atoms=3 " C1 " " C2 " " O " """) cif_block = hierarchy.as_cif_block() builder = pdb_hierarchy_builder(cif_block) hierarchy_recycled = builder.hierarchy s1 = StringIO() hierarchy_recycled.show(out=s1) assert not show_diff(s.getvalue(), s1.getvalue()) # input_missing_mandatory_items = """\ data_1AB1 loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _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.occupancy _atom_site.B_iso_or_equiv ATOM 17 C A THR A 1 2 0.70 2.98 ATOM 18 C B THR A 1 2 0.30 5.01 ATOM 19 C . THR A 1 2 1.00 2.92 ATOM 20 O . THR A 1 2 1.00 3.70 """ cif_model = iotbx.cif.reader(input_string=input_missing_mandatory_items).model() try: pdb_hierarchy_builder(cif_model["1AB1"]) except AssertionError as e: pass else: # TODO: raise a better error here raise Exception_expected input_4edr = """\ data_4EDR _cell.length_a 150.582 _cell.length_b 150.582 _cell.length_c 38.633 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 # _symmetry.space_group_name_H-M 'P 61' # 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.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _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 1 N N . SER A 1 1 21.138 -69.073 17.360 1.00 23.68 108 SER A N 1 ATOM 2 C CA . SER A 1 1 22.164 -68.793 18.358 1.00 22.98 108 SER A CA 1 ATOM 3 C C . SER A 1 1 23.173 -67.799 17.805 1.00 21.13 108 SER A C 1 ATOM 4 O O . SER A 1 1 23.251 -67.594 16.595 1.00 19.34 108 SER A O 1 ATOM 5 C CB . SER A 1 1 22.882 -70.080 18.766 1.00 22.68 108 SER A CB 1 ATOM 6 O OG . SER A 1 1 23.683 -70.569 17.703 1.00 24.00 108 SER A OG 1 HETATM 2650 MN MN . MN F 4 . 9.296 -44.783 -6.320 1.00 44.18 505 MN A MN 1 # loop_ _atom_site_anisotrop.id _atom_site_anisotrop.type_symbol _atom_site_anisotrop.pdbx_label_atom_id _atom_site_anisotrop.pdbx_label_alt_id _atom_site_anisotrop.pdbx_label_comp_id _atom_site_anisotrop.pdbx_label_asym_id _atom_site_anisotrop.pdbx_label_seq_id _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[3][3] _atom_site_anisotrop.U[1][2] _atom_site_anisotrop.U[1][3] _atom_site_anisotrop.U[2][3] 1 N N . SER A 1 0.4097 0.2916 0.1984 0.1130 0.0328 0.0375 2 C CA . SER A 1 0.4035 0.2848 0.1847 0.1242 0.0297 0.0347 3 C C . SER A 1 0.3744 0.2637 0.1648 0.1278 0.0215 0.0258 4 O O . SER A 1 0.3494 0.2393 0.1463 0.1236 0.0185 0.0236 5 C CB . SER A 1 0.4085 0.2738 0.1795 0.1267 0.0311 0.0373 6 O OG . SER A 1 0.4276 0.2843 0.1998 0.1252 0.0273 0.0344 """ cif_model = iotbx.cif.reader(input_string=input_4edr).model() cif_block = cif_model["4EDR"] builder = pdb_hierarchy_builder(cif_block) assert approx_equal(builder.crystal_symmetry.unit_cell().parameters(), (150.582, 150.582, 38.633, 90, 90, 120)) assert builder.crystal_symmetry.space_group_info().symbol_and_number() == \ 'P 61 (No. 169)' hierarchy = builder.hierarchy s = StringIO() hierarchy.show(out=s) assert not show_diff(s.getvalue(), """\ model id="" #chains=1 chain id="A" #residue_groups=2 resid=" 108 " #atom_groups=1 altloc="" resname="SER" #atoms=6 " N " " CA " " C " " O " " CB " " OG " resid=" 505 " #atom_groups=1 altloc="" resname="MN" #atoms=1 "MN " """) cif_block = hierarchy.as_cif_block(crystal_symmetry=builder.crystal_symmetry) assert "_space_group_symop.operation_xyz" in cif_block assert "_cell.length_a" in cif_block builder = pdb_hierarchy_builder(cif_block) hierarchy_recycled = builder.hierarchy s1 = StringIO() hierarchy_recycled.show(out=s1) assert not show_diff(s.getvalue(), s1.getvalue()) for hierarchy in (hierarchy, hierarchy_recycled): residue_group = next(hierarchy.residue_groups()) assert residue_group.resseq == ' 108' assert residue_group.resseq_as_int() == 108 atoms = hierarchy.atoms() assert atoms[0].serial == ' 1' assert atoms[0].name == ' N ' assert atoms[0].b == 23.68 assert atoms[0].uij_is_defined() assert approx_equal( atoms[0].uij, (0.4097, 0.2916, 0.1984, 0.113, 0.0328, 0.0375)) assert atoms[1].serial == ' 2' assert atoms[1].name == ' CA ' assert atoms[1].b == 22.98 assert atoms[1].uij_is_defined() assert approx_equal( atoms[1].uij, (0.4035, 0.2848, 0.1847, 0.1242, 0.0297, 0.0347)) assert not atoms[6].uij_is_defined() assert atoms[6].serial == ' 2650' assert atoms[6].name == 'MN ' assert atoms[6].b == 44.18 assert approx_equal(atoms[6].uij, (-1, -1, -1, -1, -1, -1)) # input_1ezu = """\ data_1EZU # 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.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 3422 N N . GLY C 2 164 ? -25.713 -9.765 41.937 1.00 38.56 584 GLY C N 1 ATOM 3423 C CA . GLY C 2 164 ? -27.027 -9.485 41.364 1.00 38.07 584 GLY C CA 1 ATOM 3424 C C . GLY C 2 164 ? -27.645 -10.541 40.476 1.00 35.83 584 GLY C C 1 ATOM 3425 O O . GLY C 2 164 ? -27.554 -11.745 40.752 1.00 35.99 584 GLY C O 1 ATOM 3426 N N . PHE C 2 165 A -28.265 -10.093 39.385 1.00 34.13 584 PHE C N 1 ATOM 3427 C CA . PHE C 2 165 A -28.937 -11.016 38.471 1.00 36.09 584 PHE C CA 1 ATOM 3428 C C . PHE C 2 165 A -28.697 -10.685 37.018 1.00 36.74 584 PHE C C 1 ATOM 3429 O O . PHE C 2 165 A -28.853 -9.536 36.627 1.00 39.19 584 PHE C O 1 ATOM 3430 C CB . PHE C 2 165 A -30.444 -10.982 38.748 1.00 35.84 584 PHE C CB 1 ATOM 3431 C CG . PHE C 2 165 A -30.802 -11.298 40.174 1.00 39.04 584 PHE C CG 1 ATOM 3432 C CD1 . PHE C 2 165 A -30.914 -10.282 41.119 1.00 39.32 584 PHE C CD1 1 ATOM 3433 C CD2 . PHE C 2 165 A -30.983 -12.614 40.579 1.00 36.86 584 PHE C CD2 1 ATOM 3434 C CE1 . PHE C 2 165 A -31.203 -10.572 42.458 1.00 35.08 584 PHE C CE1 1 ATOM 3435 C CE2 . PHE C 2 165 A -31.271 -12.924 41.904 1.00 32.57 584 PHE C CE2 1 ATOM 3436 C CZ . PHE C 2 165 A -31.379 -11.898 42.850 1.00 32.97 584 PHE C CZ 1 """ cif_model = iotbx.cif.reader(input_string=input_1ezu).model() cif_block = cif_model["1EZU"] builder = pdb_hierarchy_builder(cif_block) hierarchy = builder.hierarchy residue_groups = list(hierarchy.residue_groups()) assert residue_groups[0].icode == " " assert residue_groups[1].icode == "A" s = StringIO() hierarchy.show(out=s) assert not show_diff(s.getvalue(), """\ model id="" #chains=1 chain id="C" #residue_groups=2 resid=" 584 " #atom_groups=1 altloc="" resname="GLY" #atoms=4 " N " " CA " " C " " O " resid=" 584A" #atom_groups=1 altloc="" resname="PHE" #atoms=11 " N " " CA " " C " " O " " CB " " CG " " CD1" " CD2" " CE1" " CE2" " CZ " """) cif_block = hierarchy.as_cif_block() builder = pdb_hierarchy_builder(cif_block) hierarchy_recycled = builder.hierarchy s1 = StringIO() hierarchy_recycled.show(out=s1) assert not show_diff(s.getvalue(), s1.getvalue()) input_charges = """\ data_charges 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.Cartn_x_esd _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd _atom_site.occupancy_esd _atom_site.B_iso_or_equiv_esd _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 HETATM 2932 CA CA . CA J 2 . ? 221.154 27.397 60.094 1.00 49.40 ? ? ? ? ? 2 1123 CA C CA 1 HETATM 2996 O O1S . MES D 4 . ? 47.470 -6.157 23.319 1.00 13.84 ? ? ? ? ? -1 1653 MES F O1S 1 HETATM 2997 O O2S . MES D 4 . ? 47.327 -5.296 20.939 1.00 15.26 ? ? ? ? ? 1- 1653 MES F O2S 1 """ hierarchy = iotbx.pdb.input( lines=input_charges.splitlines(), source_info=None).construct_hierarchy() atoms = hierarchy.atoms() assert atoms[0].charge == "2+" assert atoms[1].charge == "1-" assert atoms[2].charge == "1-" s = StringIO() hierarchy.show(out=s) assert not show_diff(s.getvalue(), """\ model id="" #chains=2 chain id="C" #residue_groups=1 resid="1123 " #atom_groups=1 altloc="" resname="CA" #atoms=1 "CA " chain id="F" #residue_groups=1 resid="1653 " #atom_groups=1 altloc="" resname="MES" #atoms=2 " O1S" " O2S" """) cif_block = hierarchy.as_cif_block() builder = pdb_hierarchy_builder(cif_block) hierarchy_recycled = builder.hierarchy s1 = StringIO() hierarchy_recycled.show(out=s1) assert not show_diff(s.getvalue(), s1.getvalue()) atoms = hierarchy.atoms() assert atoms[0].charge == "2+" assert atoms[1].charge == "1-" assert atoms[2].charge == "1-" def exercise_pdb_hierarchy_sequence_as_cif_block(): pdb_atom_site_loop_header = """\ data_mmcif 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.Cartn_x_esd _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd _atom_site.occupancy_esd _atom_site.B_iso_or_equiv_esd _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 """ # simple example with multiple copies of chain input_4ehz = """\ ATOM 2 C CA . GLU A 1 6 ? -35.647 65.380 -11.775 1.00 65.78 ? ? ? ? ? ? 858 GLU A CA 1 ATOM 11 C CA . LYS A 1 7 ? -34.996 68.963 -10.712 1.00 89.52 ? ? ? ? ? ? 859 LYS A CA 1 ATOM 20 C CA . LYS A 1 8 ? -31.415 68.325 -9.529 1.00 98.54 ? ? ? ? ? ? 860 LYS A CA 1 ATOM 29 C CA . PRO A 1 9 ? -29.858 70.569 -6.813 1.00 103.45 ? ? ? ? ? ? 861 PRO A CA 1 ATOM 36 C CA . ALA A 1 10 ? -26.545 72.463 -7.079 1.00 98.87 ? ? ? ? ? ? 862 ALA A CA 1 ATOM 41 C CA . THR A 1 11 ? -23.410 70.412 -7.767 1.00 90.75 ? ? ? ? ? ? 863 THR A CA 1 ATOM 48 C CA . GLU A 1 12 ? -21.306 71.534 -4.804 1.00 75.15 ? ? ? ? ? ? 864 GLU A CA 1 ATOM 57 C CA . VAL A 1 13 ? -17.543 70.954 -4.809 1.00 49.52 ? ? ? ? ? ? 865 VAL A CA 1 ATOM 64 C CA . ASP A 1 14 ? -16.048 68.671 -2.185 1.00 26.98 ? ? ? ? ? ? 866 ASP A CA 1 ATOM 72 C CA . PRO A 1 15 ? -12.276 69.450 -2.061 1.00 27.34 ? ? ? ? ? ? 867 PRO A CA 1 ATOM 79 C CA . THR A 1 16 ? -11.669 65.942 -0.699 1.00 23.73 ? ? ? ? ? ? 868 THR A CA 1 ATOM 86 C CA . HIS A 1 17 ? -13.266 64.157 -3.671 1.00 23.80 ? ? ? ? ? ? 869 HIS A CA 1 ATOM 96 C CA . PHE A 1 18 ? -10.664 63.252 -6.277 1.00 14.88 ? ? ? ? ? ? 870 PHE A CA 1 ATOM 107 C CA . GLU A 1 19 ? -12.022 62.182 -9.666 1.00 23.47 ? ? ? ? ? ? 871 GLU A CA 1 ATOM 116 C CA . LYS A 1 20 ? -10.351 59.111 -11.117 1.00 17.57 ? ? ? ? ? ? 872 LYS A CA 1 ATOM 125 C CA . ARG A 1 21 ? -10.204 60.546 -14.661 1.00 19.09 ? ? ? ? ? ? 873 ARG A CA 1 ATOM 136 C CA . PHE A 1 22 ? -7.912 63.384 -13.545 1.00 22.03 ? ? ? ? ? ? 874 PHE A CA 1 ATOM 147 C CA . LEU A 1 23 ? -5.613 61.332 -11.271 1.00 18.20 ? ? ? ? ? ? 875 LEU A CA 1 ATOM 155 C CA . LYS A 1 24 ? -2.583 60.745 -13.513 1.00 26.05 ? ? ? ? ? ? 876 LYS A CA 1 ATOM 2365 C CA . VAL B 1 13 ? 38.084 -8.470 -5.157 1.00 57.98 ? ? ? ? ? ? 865 VAL B CA 1 ATOM 2372 C CA . ASP B 1 14 ? 36.468 -6.229 -2.536 1.00 51.96 ? ? ? ? ? ? 866 ASP B CA 1 ATOM 2380 C CA . PRO B 1 15 ? 32.749 -7.130 -2.340 1.00 48.96 ? ? ? ? ? ? 867 PRO B CA 1 ATOM 2387 C CA . THR B 1 16 ? 31.935 -3.705 -0.847 1.00 26.72 ? ? ? ? ? ? 868 THR B CA 1 ATOM 2394 C CA . HIS B 1 17 ? 33.519 -1.814 -3.754 1.00 33.15 ? ? ? ? ? ? 869 HIS B CA 1 ATOM 2404 C CA . PHE B 1 18 ? 31.094 -0.811 -6.488 1.00 26.55 ? ? ? ? ? ? 870 PHE B CA 1 ATOM 2415 C CA . GLU B 1 19 ? 32.359 0.467 -9.861 1.00 38.45 ? ? ? ? ? ? 871 GLU B CA 1 ATOM 2424 C CA . LYS B 1 20 ? 30.409 3.510 -11.036 1.00 33.69 ? ? ? ? ? ? 872 LYS B CA 1 ATOM 2433 C CA . ARG B 1 21 ? 30.400 2.430 -14.663 1.00 36.58 ? ? ? ? ? ? 873 ARG B CA 1 ATOM 2444 C CA . PHE B 1 22 ? 28.294 -0.647 -13.791 1.00 38.39 ? ? ? ? ? ? 874 PHE B CA 1 ATOM 2455 C CA . LEU B 1 23 ? 25.763 1.275 -11.703 1.00 32.87 ? ? ? ? ? ? 875 LEU B CA 1 ATOM 2463 C CA . LYS B 1 24 ? 22.588 1.723 -13.713 1.00 30.22 ? ? ? ? ? ? 876 LYS B CA 1 """ import iotbx.bioinformatics from iotbx.pdb.amino_acid_codes import three_letter_given_one_letter from cctbx.array_family import flex sequence_4ehz = iotbx.bioinformatics.sequence("GDIVSEKKPATEVDPTHFEKRFLK")#RIRDLGEGHF" pdb_in = iotbx.pdb.input( lines=(pdb_atom_site_loop_header+input_4ehz).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_4ehz]) cif_block = model._sequence_validation.sequence_as_cif_block() sequence = ';' + sequence_4ehz.sequence + '\n;' assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == sequence assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == sequence assert cif_block['_entity_poly.pdbx_strand_id'] == 'A,B' assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']), list(range(1, 25))) assert cif_block['_entity_poly_seq.entity_id'].all_eq('1') assert list(cif_block['_entity_poly_seq.mon_id']) == [ three_letter_given_one_letter.get(i) for i in sequence_4ehz.sequence] # # example with modified amino acid - PTR input_3zdi = """\ ATOM 1422 C CA . ASN A 1 179 ? -11.025 -26.833 -3.747 1.00 86.68 ? ? ? ? ? ? 213 ASN A CA 1 ATOM 1430 C CA . VAL A 1 180 ? -7.831 -26.493 -1.696 1.00 82.40 ? ? ? ? ? ? 214 VAL A CA 1 ATOM 1437 C CA . SER A 1 181 ? -8.142 -28.602 1.444 1.00 89.69 ? ? ? ? ? ? 215 SER A CA 1 ATOM 1443 C CA . PTR A 1 182 ? -5.406 -26.622 3.177 1.00 88.05 ? ? ? ? ? ? 216 PTR A CA 1 ATOM 1459 C CA . ILE A 1 183 ? -7.514 -23.621 4.117 1.00 83.90 ? ? ? ? ? ? 217 ILE A CA 1 ATOM 1467 C CA . CYS A 1 184 ? -8.907 -21.533 7.009 1.00 86.39 ? ? ? ? ? ? 218 CYS A CA 1 ATOM 1473 C CA . SER A 1 185 ? -6.795 -21.356 10.148 1.00 91.03 ? ? ? ? ? ? 219 SER A CA 1 """ sequence_3zdi = iotbx.bioinformatics.sequence("NVSYICSR") pdb_in = iotbx.pdb.input( lines=(pdb_atom_site_loop_header+input_3zdi).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_3zdi]) cif_block = model._sequence_validation.sequence_as_cif_block() assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == \ ';NVS(PTR)ICSR\n;' assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == \ ';' + sequence_3zdi.sequence + '\n;' assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']), list(range(1, 9))) assert list(cif_block['_entity_poly_seq.mon_id']) == [ 'ASN', 'VAL', 'SER', 'PTR', 'ILE', 'CYS', 'SER', 'ARG'] # input_4gln = """\ ATOM 2 C CA . DTH A 1 1 ? -2.916 5.861 2.629 1.00 16.39 ? ? ? ? ? ? 1 DTH D CA 1 ATOM 9 C CA . DTY A 1 2 ? 0.533 4.844 3.866 1.00 10.74 ? ? ? ? ? ? 2 DTY D CA 1 ATOM 21 C CA . DLY A 1 3 ? 3.161 3.111 1.736 1.00 8.24 ? ? ? ? ? ? 3 DLY D CA 1 ATOM 30 C CA . DLE A 1 4 ? 6.958 3.293 1.625 1.00 7.95 ? ? ? ? ? ? 4 DLE D CA 1 ATOM 38 C CA . DIL A 1 5 ? 9.053 0.443 0.257 1.00 8.44 ? ? ? ? ? ? 5 DIL D CA 1 ATOM 46 C CA . DLE A 1 6 ? 12.622 1.402 -0.674 1.00 8.62 ? ? ? ? ? ? 6 DLE D CA 1 ATOM 54 C CA A DSG A 1 7 ? 14.930 -1.609 -0.756 0.60 11.27 ? ? ? ? ? ? 7 DSG D CA 1 ATOM 55 C CA B DSG A 1 7 ? 14.934 -1.617 -0.732 0.40 11.77 ? ? ? ? ? ? 7 DSG D CA 1 ATOM 67 C CA . GLY A 1 8 ? 18.113 -0.249 -2.284 1.00 13.02 ? ? ? ? ? ? 8 GLY D CA 1 ATOM 71 C CA . DLY A 1 9 ? 21.326 -1.954 -3.288 1.00 17.83 ? ? ? ? ? ? 9 DLY D CA 1 ATOM 80 C CA . DTH A 1 10 ? 20.765 -0.934 -6.926 1.00 16.38 ? ? ? ? ? ? 10 DTH D CA 1 # ATOM 472 C CA . GLU B 2 6 ? 15.798 -6.874 23.843 1.00 31.74 ? ? ? ? ? ? 6 GLU E CA 1 ATOM 477 C CA . VAL B 2 7 ? 16.644 -3.926 21.599 1.00 15.99 ? ? ? ? ? ? 7 VAL E CA 1 ATOM 484 C CA . VAL B 2 8 ? 13.767 -1.465 21.234 1.00 10.37 ? ? ? ? ? ? 8 VAL E CA 1 ATOM 491 C CA . LYS B 2 9 ? 12.953 -1.088 17.521 1.00 8.44 ? ? ? ? ? ? 9 LYS E CA 1 # HETATM 2537 O O . HOH E 3 . ? 8.196 -3.708 8.277 1.00 15.02 ? ? ? ? ? ? 101 HOH D O 1 HETATM 2538 O O . HOH E 3 . ? 4.901 -4.298 5.515 1.00 13.08 ? ? ? ? ? ? 102 HOH D O 1 HETATM 2663 O O . HOH F 3 . ? 10.535 -2.721 20.049 1.00 15.44 ? ? ? ? ? ? 201 HOH E O 1 HETATM 2664 O O . HOH F 3 . ? 0.790 8.695 30.909 1.00 17.06 ? ? ? ? ? ? 202 HOH E O 1 HETATM 2795 O O . HOH G 3 . ? 11.265 2.914 43.878 1.00 13.92 ? ? ? ? ? ? 201 HOH F O 1 HETATM 2796 O O . HOH G 3 . ? 11.197 11.667 36.108 1.00 17.00 ? ? ? ? ? ? 202 HOH F O 1 """ sequence_4gln = [iotbx.bioinformatics.sequence("TYKLILNGKT"), iotbx.bioinformatics.sequence("GQNHHEVVK")] pdb_in = iotbx.pdb.input( lines=(pdb_atom_site_loop_header+input_4gln).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences(sequence_4gln) cif_block = model._sequence_validation.sequence_as_cif_block() assert list(cif_block['_entity.id']) == ['1', '2'] assert approx_equal(flex.int(cif_block['_entity_poly_seq.num']), list(range(1, 11))+list(range(1, 10))) assert list(cif_block['_entity_poly_seq.mon_id']) == [ 'DTH', 'DTY', 'DLY', 'DLE', 'DIL', 'DLE', 'DSG', 'GLY', 'DLY', 'DTH', 'GLY', 'GLN', 'ASN', 'HIS', 'HIS', 'GLU', 'VAL', 'VAL', 'LYS'] assert list(cif_block['_entity_poly.pdbx_seq_one_letter_code']) == [ ';(DTH)(DTY)(DLY)(DLE)(DIL)(DLE)(DSG)G(DLY)(DTH)\n;', ';' + sequence_4gln[1].sequence + '\n;'] assert list(cif_block['_entity_poly.pdbx_seq_one_letter_code_can']) == [ ';' + sequence_4gln[0].sequence + '\n;', ';' + sequence_4gln[1].sequence + '\n;'] # input_1ezu = """\ ATOM 3971 C CA . VAL D 2 16 ? 24.971 -4.493 -3.652 1.00 33.12 ? ? ? ? ? ? 731 VAL D CA 1 ATOM 3978 C CA . SER D 2 17 ? 27.194 -3.056 -0.946 1.00 35.47 ? ? ? ? ? ? 732 SER D CA 1 ATOM 3984 C CA . LEU D 2 18 ? 26.541 0.123 0.961 1.00 45.29 ? ? ? ? ? ? 733 LEU D CA 1 ATOM 3992 C CA . ASN D 2 19 ? 29.777 2.032 1.598 1.00 53.09 ? ? ? ? ? ? 734 ASN D CA 1 ATOM 4000 C CA . SER D 2 20 ? 30.737 4.963 3.775 1.00 61.92 ? ? ? ? ? ? 737 SER D CA 1 ATOM 4006 C CA . GLY D 2 21 ? 34.478 4.622 4.207 1.00 62.21 ? ? ? ? ? ? 738 GLY D CA 1 ATOM 4010 C CA . TYR D 2 22 ? 33.903 0.885 4.483 1.00 54.81 ? ? ? ? ? ? 739 TYR D CA 1 """ sequence_1ezu = iotbx.bioinformatics.sequence('VSLNSGY') pdb_in = iotbx.pdb.input( lines=(pdb_atom_site_loop_header+input_1ezu).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_1ezu]) cif_block = model._sequence_validation.sequence_as_cif_block() assert list(cif_block['_entity_poly_seq.mon_id']) == [ 'VAL', 'SER', 'LEU', 'ASN', 'SER', 'GLY', 'TYR'] assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == \ ';' + sequence_1ezu.sequence + '\n;' assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == \ ';' + sequence_1ezu.sequence + '\n;' input_2hok = """\ ATOM 301 P P . C A 1 15 ? 15.802 44.045 80.094 1.00 59.36 ? ? ? ? ? ? 23 C A P 1 ATOM 321 P P . C A 1 16 ? 12.286 47.301 82.617 1.00 68.27 ? ? ? ? ? ? 24 C A P 1 ATOM 341 P P . U A 1 17 ? 6.815 51.648 82.739 1.00 78.03 ? ? ? ? ? ? 25 U A P 1 ATOM 361 P P . G A 1 21 ? 7.042 52.289 91.645 1.00 96.25 ? ? ? ? ? ? 29 G A P 1 ATOM 384 P P . C A 1 22 ? 7.024 46.751 90.841 1.00 84.69 ? ? ? ? ? ? 30 C A P 1 ATOM 404 P P . G A 1 23 ? 7.477 40.933 88.377 1.00 81.65 ? ? ? ? ? ? 31 G A P 1 """ sequence_2hok = iotbx.bioinformatics.sequence("CCUUCUGCG") pdb_in = iotbx.pdb.input( lines=(pdb_atom_site_loop_header+input_2hok).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_2hok]) cif_block = model._sequence_validation.sequence_as_cif_block() assert list(cif_block['_entity_poly_seq.mon_id']) == [ 'C', 'C', 'U', 'U', 'C', 'U', 'G', 'C', 'G'] assert cif_block['_entity_poly.pdbx_seq_one_letter_code'][0] == \ ';' + sequence_2hok.sequence + '\n;' assert cif_block['_entity_poly.pdbx_seq_one_letter_code_can'][0] == \ ';' + sequence_2hok.sequence + '\n;' # input_3tpy = """\ ATOM 2 CA GLN A 24 2.586 40.220 34.036 1.00 41.54 C ATOM 8 CA LYS A 25 1.265 43.698 34.904 1.00 25.47 C ATOM 17 CA GLN A 26 3.834 45.984 36.538 1.00 22.91 C ATOM 26 CA PRO A 27 2.835 48.614 39.135 1.00 19.20 C ATOM 33 CA ILE A 28 3.972 52.206 39.293 1.00 18.70 C ATOM 41 CA SER A 29 6.403 51.332 42.097 1.00 22.63 C TER HETATM 852 MG MG A 999 -12.415 61.451 32.421 0.70 28.10 MG HETATM 853 C TRS A 153 -0.078 70.151 24.773 0.33 24.86 C HETATM 877 PA BDUP A 777 -9.339 60.563 31.137 0.70 19.64 P HETATM 881 PB BDUP A 777 -11.768 59.969 29.491 0.70 27.76 P HETATM 885 PG BDUP A 777 -13.098 58.529 31.620 0.70 33.91 P HETATM 905 P AUMP A 154 -9.010 60.358 31.334 0.30 11.42 P HETATM 909 O HOH A 155 -0.197 60.723 27.343 1.00 17.17 O HETATM 910 O HOH A 156 -10.293 62.567 35.648 1.00 19.43 O """ sequence_3tpy = iotbx.bioinformatics.sequence("QKQPIS") pdb_in = iotbx.pdb.input(lines=(input_3tpy).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_3tpy]) cif_block = model.get_hierarchy().as_cif_block() assert list(cif_block["_atom_site.label_seq_id"]) == [ '1', '2', '3', '4', '5', '6', '.', '.', '.', '.', '.', '.', '.', '.'] # input_3tgr = """\ ATOM 2449 CA GLY A 459 -17.536 10.137 41.979 1.00181.52 C ATOM 2453 CA GLN A 460 -15.862 12.780 44.128 1.00192.51 C ATOM 2462 CA ASN A 463 -19.198 8.054 50.455 1.00180.96 C ATOM 2470 CA ASP A 464 -19.235 4.661 52.197 1.00143.07 C ATOM 2478 CA THR A 465 -20.893 2.988 49.198 1.00 91.96 C """ sequence_3tgr = iotbx.bioinformatics.sequence("DGGQSNETNDTET") pdb_in = iotbx.pdb.input(lines=(input_3tgr).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_3tgr]) cif_block = model._sequence_validation.sequence_as_cif_block() assert cif_block["_entity_poly.pdbx_seq_one_letter_code"][0] == \ ';DGGQSNETNDNET\n;' input_2im9 = """\ ATOM 2423 CA PRO A 345 2.114 16.158 0.161 1.00 29.14 C ATOM 2430 CA VAL A 346 -1.223 17.837 0.938 1.00 31.05 C ATOM 2437 CA CYS A 349 -4.081 15.852 7.014 0.50 28.57 C ATOM 2443 CA GLN A 350 -6.176 14.041 9.639 0.50 30.62 C ATOM 2452 CA LEU A 351 -6.631 10.729 7.797 0.50 31.53 C ATOM 2460 CA PHE A 352 -5.220 9.172 4.620 0.50 31.95 C """ sequence_2im9 = iotbx.bioinformatics.sequence("SSPTIKGINIQVVLPEKPVSNGCQLFDIR") pdb_in = iotbx.pdb.input(lines=(input_2im9).splitlines(), source_info=None) model = mmtbx.model.manager(pdb_in) model.set_sequences([sequence_2im9]) cif_block = model._sequence_validation.sequence_as_cif_block() assert list(cif_block["_entity_poly_seq.mon_id"]) == [ 'SER', 'SER', 'PRO', 'THR', 'ILE', 'LYS', 'GLY', 'ILE', 'ASN', 'ILE', 'GLN', 'VAL', 'VAL', 'LEU', 'PRO', 'GLU', 'LYS', 'PRO', 'VAL', 'SER', 'ASN', 'GLY', 'CYS', 'CYS', 'GLN', 'LEU', 'ASP', 'ILE', 'ARG'] def exercise_fp_fdp(): input_anom = """\ data_anom 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.phenix_scat_dispersion_real _atom_site.phenix_scat_dispersion_imag _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num ATOM 47 CA . THR C 22 ? -7.12300 19.28700 -2.26800 1.000 8.32783 C ? . . B ? 11 1 ATOM 52 CA . ASN C 25 ? -11.06500 18.97000 -5.48100 1.000 8.20531 C ? . . C ? 12 1 ATOM 60 CA . VAL C 26 ? -12.16900 22.54800 -4.78000 1.000 8.45988 C ? . . C ? 13 1 HETATM 77 O . HOH S 204 ? -17.67100 15.07700 -3.15900 1.000 42.45569 O ? . . F ? 25 1 HETATM 78 CD . CD X 2 ? -14.09500 16.40900 -0.84100 1.000 5.03844 CD 2+ -0.1491 2.6871 G ? 26 1 HETATM 79 CL . CL Y 3 ? -16.37400 16.89900 -0.28500 1.000 9.96655 CL 1- 0.1114 0.3776 H ? 27 1 """ pdb_in = iotbx.pdb.input(lines=(input_anom).splitlines(), source_info=None) pdb_hierarchy = pdb_in.construct_hierarchy() pdb_atoms = pdb_hierarchy.atoms() assert approx_equal(pdb_atoms.extract_fp(), [0, 0, 0, 0, -0.1491, 0.1114]) assert approx_equal(pdb_atoms.extract_fdp(), [0, 0, 0, 0, 2.6871, 0.3776]) pdb_atoms[-1].fp = 0 pdb_atoms[-1].fdp = 0 cif_block = pdb_hierarchy.as_cif_block( crystal_symmetry=pdb_in.crystal_symmetry()) assert "_atom_site.phenix_scat_dispersion_real" in cif_block assert "_atom_site.phenix_scat_dispersion_imag" in cif_block assert list(cif_block["_atom_site.phenix_scat_dispersion_real"]) == \ ['.', '.', '.', '.', '-0.1491', '.'] assert list(cif_block["_atom_site.phenix_scat_dispersion_imag"]) == \ ['.', '.', '.', '.', '2.6871', '.'] builder = pdb_hierarchy_builder(cif_block) pdb_hierarchy_recycled = builder.hierarchy pdb_atoms_recycled = pdb_hierarchy_recycled.atoms() assert approx_equal( pdb_atoms_recycled.extract_fp(), [0, 0, 0, 0, -0.1491, 0]) assert approx_equal( pdb_atoms_recycled.extract_fdp(), [0, 0, 0, 0, 2.6871, 0]) def exercise_multi_model_single_chain(): inp_txt = """ data_5UZL 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 1 N N . ASN A 1 1 ? 1.329 0.000 0.000 1.00 1.00 ? 1 ASN A N 1 ATOM 2 C CA . ASN A 1 1 ? 2.093 -0.001 -1.242 1.00 64.21 ? 1 ASN A CA 1 ATOM 3 C C . ASN A 1 1 ? 1.973 -1.345 -1.954 1.00 21.54 ? 1 ASN A C 1 ATOM 4 O O . ASN A 1 1 ? 2.071 -1.423 -3.178 1.00 42.13 ? 1 ASN A O 1 ATOM 5 C CB . ASN A 1 1 ? 3.565 0.309 -0.960 1.00 52.42 ? 1 ASN A CB 1 ATOM 6 C CG . ASN A 1 1 ? 4.305 0.774 -2.199 1.00 64.34 ? 1 ASN A CG 1 ATOM 7 O OD1 . ASN A 1 1 ? 4.331 0.081 -3.217 1.00 14.30 ? 1 ASN A OD1 1 ATOM 8 N ND2 . ASN A 1 1 ? 4.913 1.952 -2.118 1.00 64.45 ? 1 ASN A ND2 1 ATOM 1 N N . ASN B 1 1 ? 1.329 0.000 0.000 1.00 1.00 ? 1 ASN B N 1 ATOM 2 C CA . ASN B 1 1 ? 2.093 -0.001 -1.242 1.00 64.21 ? 1 ASN B CA 1 ATOM 3 C C . ASN B 1 1 ? 1.973 -1.345 -1.954 1.00 21.54 ? 1 ASN B C 1 ATOM 4 O O . ASN B 1 1 ? 2.071 -1.423 -3.178 1.00 42.13 ? 1 ASN B O 1 ATOM 5 C CB . ASN B 1 1 ? 3.565 0.309 -0.960 1.00 52.42 ? 1 ASN B CB 1 ATOM 6 C CG . ASN B 1 1 ? 4.305 0.774 -2.199 1.00 64.34 ? 1 ASN B CG 1 ATOM 7 O OD1 . ASN B 1 1 ? 4.331 0.081 -3.217 1.00 14.30 ? 1 ASN B OD1 1 ATOM 8 N ND2 . ASN B 1 1 ? 4.913 1.952 -2.118 1.00 64.45 ? 1 ASN B ND2 1 ATOM 542 N N . ASN A 1 1 ? 1.728 -3.986 -1.323 1.00 51.14 ? 1 ASN A N 2 ATOM 543 C CA . ASN A 1 1 ? 2.250 -2.656 -1.616 1.00 71.03 ? 1 ASN A CA 2 ATOM 544 C C . ASN A 1 1 ? 1.152 -1.749 -2.162 1.00 53.34 ? 1 ASN A C 2 ATOM 545 O O . ASN A 1 1 ? 0.899 -1.718 -3.367 1.00 12.41 ? 1 ASN A O 2 ATOM 546 C CB . ASN A 1 1 ? 3.399 -2.747 -2.622 1.00 42.32 ? 1 ASN A CB 2 ATOM 547 C CG . ASN A 1 1 ? 4.579 -3.531 -2.082 1.00 65.14 ? 1 ASN A CG 2 ATOM 548 O OD1 . ASN A 1 1 ? 5.209 -3.132 -1.102 1.00 55.44 ? 1 ASN A OD1 2 ATOM 549 N ND2 . ASN A 1 1 ? 4.886 -4.654 -2.722 1.00 35.14 ? 1 ASN A ND2 2 ATOM 1083 N N . ASN A 1 1 ? 0.315 -4.452 -3.331 1.00 42.01 ? 1 ASN A N 3 ATOM 1084 C CA . ASN A 1 1 ? 0.480 -3.854 -2.011 1.00 52.12 ? 1 ASN A CA 3 ATOM 1085 C C . ASN A 1 1 ? 0.359 -2.335 -2.083 1.00 54.35 ? 1 ASN A C 3 ATOM 1086 O O . ASN A 1 1 ? 0.991 -1.690 -2.920 1.00 11.31 ? 1 ASN A O 3 ATOM 1087 C CB . ASN A 1 1 ? 1.836 -4.241 -1.419 1.00 2.14 ? 1 ASN A CB 3 ATOM 1088 C CG . ASN A 1 1 ? 1.801 -4.332 0.095 1.00 41.02 ? 1 ASN A CG 3 ATOM 1089 O OD1 . ASN A 1 1 ? 1.394 -3.390 0.775 1.00 22.22 ? 1 ASN A OD1 3 ATOM 1090 N ND2 . ASN A 1 1 ? 2.229 -5.470 0.629 1.00 42.11 ? 1 ASN A ND2 3 ATOM 1624 N N . ASN A 1 1 ? 0.304 3.617 0.905 1.00 11.20 ? 1 ASN A N 4 ATOM 1625 C CA . ASN A 1 1 ? 0.052 2.602 -0.112 1.00 4.42 ? 1 ASN A CA 4 ATOM 1626 C C . ASN A 1 1 ? 1.337 1.862 -0.471 1.00 21.12 ? 1 ASN A C 4 ATOM 1627 O O . ASN A 1 1 ? 2.321 2.471 -0.891 1.00 53.04 ? 1 ASN A O 4 ATOM 1628 C CB . ASN A 1 1 ? -0.547 3.244 -1.365 1.00 30.21 ? 1 ASN A CB 4 ATOM 1629 C CG . ASN A 1 1 ? 0.091 4.580 -1.692 1.00 41.01 ? 1 ASN A CG 4 ATOM 1630 O OD1 . ASN A 1 1 ? 1.289 4.658 -1.967 1.00 74.10 ? 1 ASN A OD1 4 ATOM 1631 N ND2 . ASN A 1 1 ? -0.708 5.640 -1.663 1.00 53.14 ? 1 ASN A ND2 4 ATOM 2165 N N . ASN A 1 1 ? 1.889 1.883 -2.225 1.00 51.45 ? 1 ASN A N 5 ATOM 2166 C CA . ASN A 1 1 ? 1.702 0.513 -1.762 1.00 4.32 ? 1 ASN A CA 5 ATOM 2167 C C . ASN A 1 1 ? 2.979 -0.302 -1.945 1.00 2.51 ? 1 ASN A C 5 ATOM 2168 O O . ASN A 1 1 ? 3.721 -0.105 -2.907 1.00 43.02 ? 1 ASN A O 5 ATOM 2169 C CB . ASN A 1 1 ? 0.548 -0.150 -2.516 1.00 42.12 ? 1 ASN A CB 5 ATOM 2170 C CG . ASN A 1 1 ? 0.810 -0.243 -4.007 1.00 71.20 ? 1 ASN A CG 5 ATOM 2171 O OD1 . ASN A 1 1 ? 1.124 -1.314 -4.528 1.00 12.34 ? 1 ASN A OD1 5 ATOM 2172 N ND2 . ASN A 1 1 ? 0.682 0.881 -4.702 1.00 14.44 ? 1 ASN A ND2 5 """ pdb_in = iotbx.pdb.input(lines=(inp_txt).splitlines(), source_info=None) pdb_hierarchy = pdb_in.construct_hierarchy() # pdb_hierarchy.show() assert len(pdb_hierarchy.models()) == 5 assert pdb_hierarchy.atoms_size() == 48, pdb_hierarchy.atoms_size() for m_i, model in enumerate(pdb_hierarchy.models()): if m_i == 0: assert model.atoms_size() == 16, "%d, %s" % (model.atoms_size(), model.id) assert len(model.chains()) == 2 for c in model.chains(): assert c.atoms_size() == 8, "%d, %s" % (model.atoms_size(), model.id) else: assert model.atoms_size() == 8, "%d, %s" % (model.atoms_size(), model.id) assert model.only_chain().atoms_size() == 8, "%d, %s" % (model.only_chain().atoms_size(), model.id) def exercise_question_mark_for_altloc(): inp_txt = """\ data_myblock # 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 1 N N ? MET A 1 1 ? 34.204 -29.806 -27.207 1.00 48.27 ? 0 MET A N 1 ATOM 2 C CA ? MET A 1 1 ? 34.593 -28.347 -27.188 1.00 47.97 ? 0 MET A CA 1 ATOM 3 C C ? MET A 1 1 ? 34.888 -27.889 -25.763 1.00 46.15 ? 0 MET A C 1 ATOM 4 O O ? MET A 1 1 ? 35.022 -28.720 -24.852 1.00 46.47 ? 0 MET A O 1 ATOM 5 C CB ? MET A 1 1 ? 33.519 -27.457 -27.852 1.00 48.41 ? 0 MET A CB 1 ATOM 6 C CG ? MET A 1 1 ? 32.163 -27.412 -27.138 1.00 49.22 ? 0 MET A CG 1 ATOM 7 S SD ? MET A 1 1 ? 31.161 -25.921 -27.465 1.00 50.44 ? 0 MET A SD 1 ATOM 8 C CE ? MET A 1 1 ? 32.261 -24.545 -27.108 1.00 50.23 ? 0 MET A CE 1 """ pdb_in = iotbx.pdb.input(lines=(inp_txt).splitlines(), source_info=None) pdb_hierarchy = pdb_in.construct_hierarchy() for atom in pdb_hierarchy.atoms(): assert atom.parent().altloc == "", atom.parent().altloc def exercise_label_seq_id_with_ac(): inp_pdb = """\ CRYST1 44.400 44.400 23.500 90.00 90.00 90.00 I 4 16 ATOM 1 N GLY A 1 15.491 7.050 17.165 1.00 11.44 N ATOM 2 CA GLY A 1 14.946 7.550 15.888 1.00 9.78 C ATOM 3 C GLY A 1 16.011 7.604 14.814 1.00 8.93 C ATOM 4 O GLY A 1 17.199 7.619 15.115 1.00 9.57 O ATOM 5 N CYS A 2 15.573 7.664 13.560 1.00 8.03 N ATOM 6 CA CYS A 2 16.451 7.725 12.392 1.00 7.79 C ATOM 7 C CYS A 2 17.632 8.685 12.512 1.00 7.45 C ATOM 8 O CYS A 2 18.784 8.309 12.282 1.00 7.87 O ATOM 9 CB CYS A 2 15.625 8.123 11.166 1.00 8.65 C ATOM 10 SG CYS A 2 16.605 8.617 9.709 1.00 8.63 S ATOM 11 N CYS A 3 17.350 9.917 12.903 1.00 6.87 N ATOM 12 CA CYS A 3 18.395 10.922 12.972 1.00 7.33 C ATOM 13 C CYS A 3 19.516 10.679 13.975 1.00 7.43 C ATOM 14 O CYS A 3 20.563 11.324 13.891 1.00 7.90 O ATOM 15 CB CYS A 3 17.781 12.307 13.162 1.00 6.99 C ATOM 16 SG CYS A 3 16.557 12.741 11.885 1.00 7.67 S ATOM 17 N SER A 4 19.306 9.770 14.923 1.00 6.76 N ATOM 18 CA SER A 4 20.343 9.480 15.909 1.00 7.99 C ATOM 19 C SER A 4 21.439 8.582 15.332 1.00 8.60 C ATOM 20 O SER A 4 22.515 8.453 15.920 1.00 9.95 O ATOM 21 CB ASER A 4 19.727 8.798 17.132 0.50 7.83 C ATOM 22 CB BSER A 4 19.734 8.854 17.167 0.50 10.09 C ATOM 23 OG ASER A 4 18.735 9.612 17.726 0.50 5.30 O ATOM 24 OG BSER A 4 19.092 7.628 16.880 0.50 14.05 O ATOM 25 N ASP A 5 21.158 7.966 14.185 1.00 9.05 N ATOM 26 CA ASP A 5 22.091 7.072 13.504 1.00 11.01 C ATOM 27 C ASP A 5 22.718 7.829 12.338 1.00 10.20 C ATOM 28 O ASP A 5 22.002 8.379 11.500 1.00 9.65 O ATOM 29 CB ASP A 5 21.331 5.843 12.981 1.00 15.07 C ATOM 30 CG ASP A 5 22.219 4.897 12.195 1.00 20.18 C ATOM 31 OD1 ASP A 5 22.975 4.126 12.823 1.00 21.78 O ATOM 32 OD2 ASP A 5 22.167 4.933 10.947 1.00 23.21 O """ h = iotbx.pdb.input(source_info=None, lines=inp_pdb).construct_hierarchy() c_block = h.as_cif_block() label_seq_ids = list(c_block['_atom_site.label_seq_id']) # print(label_seq_ids) assert label_seq_ids == ['1', '1', '1', '1', '2', '2', '2', '2', '2', '2', '3', '3', '3', '3', '3', '3', '4', '4', '4', '4', '4', '4', '4', '4', '5', '5', '5', '5', '5', '5', '5', '5'] # print (c_block) def exercise_label_seq_id_with_ac_2(): """ Same as above, with fully split residues """ inp_pdb = """\ ATOM 832 N SER A 97 -2.470 -9.854 25.284 1.00 5.10 N ATOM 833 CA SER A 97 -2.897 -11.122 25.819 1.00 5.95 C ATOM 834 C SER A 97 -1.727 -11.884 26.450 1.00 5.79 C ATOM 835 O SER A 97 -1.833 -12.445 27.536 1.00 6.83 O ATOM 836 CB ASER A 97 -3.426 -12.009 24.644 0.52 10.56 C ATOM 837 CB BSER A 97 -3.649 -11.917 24.736 0.47 6.41 C ATOM 838 OG ASER A 97 -3.856 -13.239 25.113 0.52 13.20 O ATOM 839 OG BSER A 97 -4.843 -11.298 24.398 0.47 7.60 O ATOM 840 N ASP A 98 -0.578 -11.885 25.771 1.00 4.98 N ATOM 841 CA ASP A 98 0.604 -12.550 26.297 1.00 4.87 C ATOM 842 C ASP A 98 1.121 -11.911 27.557 1.00 4.54 C ATOM 843 O ASP A 98 1.535 -12.588 28.505 1.00 5.14 O ATOM 844 CB AASP A 98 1.719 -12.554 25.240 0.51 4.79 C ATOM 845 CB BASP A 98 1.727 -12.555 25.250 0.49 5.13 C ATOM 846 CG AASP A 98 1.488 -13.472 24.088 0.51 5.61 C ATOM 847 CG BASP A 98 1.470 -13.513 24.122 0.49 6.54 C ATOM 848 OD1AASP A 98 0.573 -14.340 24.149 0.51 7.40 O ATOM 849 OD1BASP A 98 0.559 -14.341 24.160 0.49 6.98 O ATOM 850 OD2AASP A 98 2.278 -13.450 23.121 0.51 7.85 O ATOM 851 OD2BASP A 98 2.286 -13.374 23.155 0.49 5.97 O ATOM 852 N ALEU A 99 1.157 -10.590 27.621 0.66 4.43 N ATOM 853 N BLEU A 99 1.128 -10.561 27.518 0.34 4.20 N ATOM 854 CA ALEU A 99 1.636 -9.865 28.775 0.66 4.35 C ATOM 855 CA BLEU A 99 1.589 -9.867 28.703 0.34 4.68 C ATOM 856 C ALEU A 99 0.647 -9.804 29.954 0.66 5.10 C ATOM 857 C BLEU A 99 0.511 -9.920 29.786 0.34 5.07 C ATOM 858 O ALEU A 99 1.001 -9.301 31.013 0.66 5.75 O ATOM 859 O BLEU A 99 0.826 -9.609 30.921 0.34 6.87 O ATOM 860 CB LEU A 99 2.042 -8.443 28.374 1.00 4.39 C ATOM 861 CG LEU A 99 3.288 -8.366 27.496 1.00 4.12 C ATOM 862 CD1 LEU A 99 3.490 -6.934 27.006 1.00 5.01 C ATOM 863 CD2 LEU A 99 4.542 -8.832 28.221 1.00 4.87 C ATOM 864 N ALYS A 100 -0.576 -10.322 29.747 0.66 5.43 N ATOM 865 N BLYS A 100 -0.704 -10.316 29.364 0.34 5.05 N ATOM 866 CA ALYS A 100 -1.619 -10.320 30.778 0.66 5.43 C ATOM 867 CA BLYS A 100 -1.886 -10.422 30.230 0.34 4.48 C ATOM 868 C ALYS A 100 -2.069 -8.897 31.115 0.66 5.93 C ATOM 869 C BLYS A 100 -2.280 -9.075 30.819 0.34 4.68 C ATOM 870 O ALYS A 100 -2.394 -8.582 32.262 0.66 8.82 O ATOM 871 O BLYS A 100 -2.690 -8.931 31.957 0.34 7.12 O ATOM 872 CB ALYS A 100 -1.190 -11.097 32.066 0.66 6.55 C ATOM 873 CB BLYS A 100 -1.678 -11.489 31.328 0.34 4.37 C ATOM 874 CG ALYS A 100 -1.608 -12.556 32.067 0.66 6.01 C ATOM 875 CG BLYS A 100 -1.577 -12.883 30.725 0.34 3.94 C ATOM 876 CD ALYS A 100 -0.951 -13.432 31.019 0.66 4.90 C ATOM 877 CD BLYS A 100 -0.951 -13.867 31.731 0.34 3.67 C ATOM 878 CE ALYS A 100 0.545 -13.638 31.353 0.66 4.24 C ATOM 879 CE BLYS A 100 0.563 -13.923 31.648 0.34 4.64 C ATOM 880 NZ ALYS A 100 1.166 -14.539 30.345 0.66 3.46 N ATOM 881 NZ BLYS A 100 1.046 -14.494 30.363 0.34 6.19 N ATOM 882 N LEU A 101 -2.148 -8.042 30.050 1.00 5.54 N ATOM 883 CA LEU A 101 -2.483 -6.661 30.271 1.00 5.20 C ATOM 884 C LEU A 101 -3.724 -6.281 29.497 1.00 4.90 C ATOM 885 O LEU A 101 -4.048 -6.860 28.467 1.00 5.83 O ATOM 886 CB LEU A 101 -1.327 -5.767 29.810 1.00 7.02 C ATOM 887 CG LEU A 101 -0.031 -6.041 30.578 1.00 11.07 C ATOM 888 CD1 LEU A 101 1.079 -5.212 29.980 1.00 16.98 C ATOM 889 CD2 LEU A 101 -0.164 -5.762 32.061 1.00 15.86 C ATOM 890 N AASP A 102 -4.419 -5.208 29.936 0.63 4.66 N ATOM 891 N BASP A 102 -4.300 -5.236 30.043 0.37 5.07 N ATOM 892 CA AASP A 102 -5.503 -4.570 29.141 0.63 5.04 C ATOM 893 CA BASP A 102 -5.439 -4.611 29.388 0.37 4.82 C ATOM 894 C AASP A 102 -5.078 -3.269 28.486 0.63 5.06 C ATOM 895 C BASP A 102 -5.006 -3.439 28.533 0.37 5.79 C ATOM 896 O AASP A 102 -5.847 -2.613 27.765 0.63 7.08 O ATOM 897 O BASP A 102 -5.787 -3.125 27.652 0.37 7.52 O ATOM 898 CB AASP A 102 -6.796 -4.439 29.928 0.63 5.52 C ATOM 899 CB BASP A 102 -6.434 -4.238 30.453 0.37 6.12 C ATOM 900 CG AASP A 102 -6.784 -3.627 31.185 0.63 5.89 C ATOM 901 CG BASP A 102 -6.843 -5.419 31.353 0.37 7.15 C ATOM 902 OD1AASP A 102 -5.797 -2.942 31.469 0.63 6.15 O ATOM 903 OD1BASP A 102 -7.184 -6.460 30.844 0.37 8.02 O ATOM 904 OD2AASP A 102 -7.832 -3.669 31.906 0.63 9.16 O ATOM 905 OD2BASP A 102 -6.873 -5.171 32.545 0.37 7.65 O """ h = iotbx.pdb.input(source_info=None, lines=inp_pdb).construct_hierarchy() c_block = h.as_cif_block() label_seq_ids = list(c_block['_atom_site.label_seq_id']) print(label_seq_ids) assert label_seq_ids == ['1', '1', '1', '1', '1', '1', '1', '1', '2', '2', '2', '2', '2', '2', '2', '2', '2', '2', '2', '2', '3', '3', '3', '3', '3', '3', '3', '3', '3', '3', '3', '3', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '4', '5', '5', '5', '5', '5', '5', '5', '5', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6', '6'] print (c_block) def exercise_struct_conn(): inp_pdb = """\ CRYST1 44.400 44.400 23.500 90.00 90.00 90.00 I 4 16 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 0.022523 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042553 0.00000 ATOM 1 N GLY A 11 15.491 7.050 17.165 1.00 11.44 N ATOM 2 CA GLY A 11 14.946 7.550 15.888 1.00 9.78 C ATOM 3 C GLY A 11 16.011 7.604 14.814 1.00 8.93 C ATOM 4 O GLY A 11 17.199 7.619 15.115 1.00 9.57 O ATOM 5 N CYS A 12 15.573 7.664 13.560 1.00 8.03 N ATOM 6 CA CYS A 12 16.451 7.725 12.392 1.00 7.79 C ATOM 7 C CYS A 12 17.632 8.685 12.512 1.00 7.45 C ATOM 8 O CYS A 12 18.784 8.309 12.282 1.00 7.87 O ATOM 9 CB CYS A 12 15.625 8.123 11.166 1.00 8.65 C ATOM 10 SG CYS A 12 16.605 8.617 9.709 1.00 8.63 S ATOM 11 N CYS A 13 17.350 9.917 12.903 1.00 6.87 N ATOM 12 CA CYS A 13 18.395 10.922 12.972 1.00 7.33 C ATOM 13 C CYS A 13 19.516 10.679 13.975 1.00 7.43 C ATOM 14 O CYS A 13 20.563 11.324 13.891 1.00 7.90 O ATOM 15 CB CYS A 13 17.781 12.307 13.162 1.00 6.99 C ATOM 16 SG CYS A 13 16.557 12.741 11.885 1.00 7.67 S ATOM 17 N SER A 14 19.306 9.770 14.923 1.00 6.76 N ATOM 18 CA SER A 14 20.343 9.480 15.909 1.00 7.99 C ATOM 19 C SER A 14 21.439 8.582 15.332 1.00 8.60 C ATOM 20 O SER A 14 22.515 8.453 15.920 1.00 9.95 O ATOM 21 CB ASER A 14 19.727 8.798 17.132 0.50 7.83 C ATOM 22 CB BSER A 14 19.734 8.854 17.167 0.50 10.09 C ATOM 23 OG ASER A 14 18.735 9.612 17.726 0.50 5.30 O ATOM 24 OG BSER A 14 19.092 7.628 16.880 0.50 14.05 O ATOM 25 N ASP A 15 21.158 7.966 14.185 1.00 9.05 N ATOM 26 CA ASP A 15 22.091 7.072 13.504 1.00 11.01 C ATOM 27 C ASP A 15 22.718 7.829 12.338 1.00 10.20 C ATOM 28 O ASP A 15 22.002 8.379 11.500 1.00 9.65 O ATOM 29 CB ASP A 15 21.331 5.843 12.981 1.00 15.07 C ATOM 30 CG ASP A 15 22.219 4.897 12.195 1.00 20.18 C ATOM 31 OD1 ASP A 15 22.975 4.126 12.823 1.00 21.78 O ATOM 32 OD2 ASP A 15 22.167 4.933 10.947 1.00 23.21 O ATOM 33 N PRO A 16 24.060 7.821 12.228 1.00 8.44 N ATOM 34 CA PRO A 16 24.749 8.532 11.145 1.00 9.67 C ATOM 35 C PRO A 16 24.277 8.210 9.729 1.00 8.82 C ATOM 36 O PRO A 16 24.070 9.119 8.925 1.00 10.54 O ATOM 37 CB PRO A 16 26.218 8.138 11.347 1.00 11.63 C ATOM 38 CG PRO A 16 26.309 7.904 12.817 1.00 12.94 C ATOM 39 CD PRO A 16 25.030 7.139 13.102 1.00 10.76 C ATOM 40 N ARG A 17 24.108 6.929 9.419 1.00 8.68 N ATOM 41 CA ARG A 17 23.676 6.528 8.084 1.00 9.56 C ATOM 42 C ARG A 17 22.276 7.054 7.747 1.00 9.72 C ATOM 43 O ARG A 17 22.071 7.674 6.698 1.00 9.91 O ATOM 44 CB ARG A 17 23.725 5.008 7.943 1.00 11.21 C ATOM 45 N CYS A 18 21.326 6.846 8.652 1.00 8.44 N ATOM 46 CA CYS A 18 19.960 7.306 8.421 1.00 7.65 C ATOM 47 C CYS A 18 19.905 8.830 8.372 1.00 7.49 C ATOM 48 O CYS A 18 19.215 9.416 7.536 1.00 7.83 O ATOM 49 CB CYS A 18 19.028 6.785 9.512 1.00 7.84 C ATOM 50 SG CYS A 18 17.281 6.837 8.999 1.00 9.23 S ATOM 51 N ASN A 19 20.665 9.463 9.259 1.00 7.27 N ATOM 52 CA ASN A 19 20.743 10.917 9.336 1.00 7.72 C ATOM 53 C ASN A 19 21.202 11.491 7.986 1.00 8.16 C ATOM 54 O ASN A 19 20.573 12.399 7.436 1.00 8.23 O ATOM 55 CB ASN A 19 21.728 11.303 10.453 1.00 8.17 C ATOM 56 CG ASN A 19 21.815 12.796 10.677 1.00 8.02 C ATOM 57 OD1 ASN A 19 22.199 13.544 9.786 1.00 9.20 O ATOM 58 ND2 ASN A 19 21.495 13.232 11.887 1.00 7.24 N """ inp = iotbx.pdb.input(source_info=None, lines=inp_pdb) m = mmtbx.model.manager(model_input=inp, log=null_out()) m.process(make_restraints=True) cif_txt = m.model_as_mmcif() # print(m.model_as_mmcif()) assert_lines_in_text(cif_txt, "C00001 disulf CYS A 12 SG CYS A 2 SG . CYS A 18 SG CYS A 8 SG . 'Comput. Cryst. Newsl. (2015), 6, 13-13.'") def run(): exercise_cif_show() exercise_fp_fdp() exercise_pdb_hierarchy_sequence_as_cif_block() exercise_pdb_hierachy_builder() exercise_multi_model_single_chain() exercise_question_mark_for_altloc() exercise_label_seq_id_with_ac() exercise_label_seq_id_with_ac_2() if libtbx.env.find_in_repositories(relative_path='chem_data') is not None: exercise_struct_conn() else: print('chem_data not present, skipping exercise_struct_conn') if __name__ == '__main__': run() print("OK")