from __future__ import absolute_import, division, print_function from mmtbx.command_line import sort_hetatms from iotbx import file_reader from six.moves import cStringIO as StringIO import os.path as op import os def exercise(): pdb_raw = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 12.43 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 14.62 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 9.05 N TER ATOM 30 N GLN B 1 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN B 1 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN B 1 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN B 1 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN B 1 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN B 1 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN B 1 1.344 2.414 8.954 1.00 13.10 C ATOM 37 OE1 GLN B 1 0.774 1.325 9.002 1.00 10.65 O ATOM 38 NE2 GLN B 1 1.549 3.187 10.039 1.00 12.30 N ATOM 39 N ASN B 2 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN B 2 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN B 2 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN B 2 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN B 2 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN B 2 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN B 2 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN B 2 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR B 3 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR B 3 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR B 3 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR B 3 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR B 3 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR B 3 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR B 3 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR B 3 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR B 3 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR B 3 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR B 3 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR B 3 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR B 3 11.358 2.999 7.612 1.00 17.49 O TER HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 64 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 66 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 67 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O END """ pdb_file = "unsorted.pdb" with open(pdb_file, "w") as f: f.write(pdb_raw) if (op.exists("unsorted_sorted.pdb")): os.remove("unsorted_sorted.pdb") out = StringIO() sort_hetatms.run( args=[pdb_file, "--verbose"], out=out) assert ("""Residue group pdb=" O HOH 10 " added to chain A (distance = 2.814, symop = -x-1,y-1/2,-z)""" in out.getvalue()) pdb_in = file_reader.any_file("unsorted_sorted.pdb") hierarchy = pdb_in.file_object.hierarchy chains = hierarchy.models()[0].chains() assert (len(chains) == 4) rgsA = chains[-2].residue_groups() rgsB = chains[-1].residue_groups() assert (len(rgsA) == 3) and (len(rgsB) == 4) sort_hetatms.run( args=[pdb_file, "preserve_chain_id=True", "renumber=False"], out=StringIO()) pdb_in = file_reader.any_file("unsorted_sorted.pdb") hierarchy = pdb_in.file_object.hierarchy chains = hierarchy.models()[0].chains() assert (len(chains) == 3) assert (chains[-1].id == "A") pdb_raw2 = """\ CRYST1 21.937 10.000 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N TER 21 ASN A 3 HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 64 O HOH A 11 6.127 3.965 10.368 1.00 23.99 O HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 66 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 67 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O END """ pdb_file = "unsorted2.pdb" with open(pdb_file, "w") as f: f.write(pdb_raw2) if (op.exists("unsorted2_sorted.pdb")): os.remove("unsorted2_sorted.pdb") out = StringIO() sort_hetatms.run( args=[pdb_file, "--verbose", "--remove_waters_outside_radius"], out=out) assert ("Water 11 is not near any polymer chain, will delete" in out.getvalue()) out = StringIO() sort_hetatms.run( args=[pdb_file, "--verbose",], out=out) assert ("Residue group A 11 is not near any macromolecule chain" in out.getvalue()) pdb_raw = """\ HEADER LIGASE 31-AUG-98 1BS2 CRYST1 100.374 100.374 204.341 90.00 90.00 90.00 P 43 21 2 8 ATOM 1094 N LYS A 143 22.992 81.325 -18.373 1.00 63.31 N ATOM 1095 CA LYS A 143 24.003 82.214 -18.922 1.00 53.83 C ATOM 1096 C LYS A 143 24.725 81.433 -20.002 1.00 49.46 C ATOM 1097 O LYS A 143 25.026 80.249 -19.833 1.00 48.59 O ATOM 1098 CB LYS A 143 24.980 82.658 -17.835 1.00 58.17 C ATOM 1099 CG LYS A 143 24.831 84.114 -17.432 1.00 65.92 C ATOM 1100 CD LYS A 143 23.422 84.434 -16.967 1.00 69.21 C ATOM 1101 CE LYS A 143 23.253 85.929 -16.742 1.00 67.51 C ATOM 1102 NZ LYS A 143 21.905 86.254 -16.193 1.00 74.33 N ATOM 1103 N LYS A 144 24.985 82.095 -21.120 1.00 46.52 N ATOM 1104 CA LYS A 144 25.641 81.453 -22.246 1.00 48.43 C ATOM 1105 C LYS A 144 26.946 82.162 -22.583 1.00 49.19 C ATOM 1106 O LYS A 144 27.014 83.395 -22.623 1.00 47.13 O ATOM 1107 CB LYS A 144 24.704 81.475 -23.458 1.00 55.29 C ATOM 1108 CG LYS A 144 25.183 80.676 -24.659 1.00 63.36 C ATOM 1109 CD LYS A 144 24.334 80.964 -25.899 1.00 61.42 C ATOM 1110 CE LYS A 144 22.874 80.579 -25.705 1.00 58.72 C ATOM 1111 NZ LYS A 144 22.078 80.793 -26.946 1.00 61.59 N ATOM 1112 N VAL A 145 27.986 81.373 -22.819 1.00 42.70 N ATOM 1113 CA VAL A 145 29.280 81.932 -23.158 1.00 38.93 C ATOM 1114 C VAL A 145 29.869 81.233 -24.374 1.00 40.05 C ATOM 1115 O VAL A 145 29.715 80.021 -24.553 1.00 45.68 O ATOM 1116 CB VAL A 145 30.274 81.815 -21.972 1.00 30.33 C ATOM 1117 CG1 VAL A 145 30.431 80.356 -21.569 1.00 35.25 C ATOM 1118 CG2 VAL A 145 31.627 82.424 -22.351 1.00 15.32 C ATOM 1119 N ILE A 146 30.519 82.013 -25.225 1.00 36.19 N ATOM 1120 CA ILE A 146 31.157 81.457 -26.399 1.00 42.19 C ATOM 1121 C ILE A 146 32.640 81.522 -26.106 1.00 46.89 C ATOM 1122 O ILE A 146 33.161 82.577 -25.735 1.00 42.54 O ATOM 1123 CB ILE A 146 30.886 82.283 -27.666 1.00 43.82 C ATOM 1124 CG1 ILE A 146 29.406 82.226 -28.030 1.00 46.47 C ATOM 1125 CG2 ILE A 146 31.723 81.741 -28.816 1.00 39.50 C ATOM 1126 CD1 ILE A 146 29.048 83.115 -29.197 1.00 46.73 C ATOM 1127 N ILE A 147 33.311 80.387 -26.250 1.00 47.64 N ATOM 1128 CA ILE A 147 34.740 80.323 -26.019 1.00 47.32 C ATOM 1129 C ILE A 147 35.406 79.905 -27.326 1.00 49.89 C ATOM 1130 O ILE A 147 35.276 78.766 -27.777 1.00 46.22 O ATOM 1131 CB ILE A 147 35.078 79.325 -24.887 1.00 43.61 C ATOM 1132 CG1 ILE A 147 34.402 79.775 -23.586 1.00 40.57 C ATOM 1133 CG2 ILE A 147 36.585 79.257 -24.688 1.00 40.81 C ATOM 1134 CD1 ILE A 147 34.584 78.825 -22.424 1.00 34.81 C ATOM 1135 N GLU A 148 36.102 80.855 -27.940 1.00 49.93 N ATOM 1136 CA GLU A 148 36.788 80.613 -29.199 1.00 50.03 C ATOM 1137 C GLU A 148 38.263 80.328 -28.913 1.00 44.28 C ATOM 1138 O GLU A 148 38.943 81.145 -28.301 1.00 43.55 O ATOM 1139 CB GLU A 148 36.646 81.846 -30.106 1.00 47.09 C ATOM 1140 CG GLU A 148 37.243 81.679 -31.489 1.00 40.60 C ATOM 1141 CD GLU A 148 37.982 82.916 -31.943 1.00 48.19 C ATOM 1142 OE1 GLU A 148 37.324 83.935 -32.246 1.00 52.87 O ATOM 1143 OE2 GLU A 148 39.228 82.873 -31.982 1.00 45.83 O ATOM 1144 N PHE A 149 38.754 79.172 -29.347 1.00 37.67 N ATOM 1145 CA PHE A 149 40.147 78.828 -29.106 1.00 39.79 C ATOM 1146 C PHE A 149 40.775 77.925 -30.159 1.00 42.70 C ATOM 1147 O PHE A 149 40.079 77.314 -30.966 1.00 45.66 O ATOM 1148 CB PHE A 149 40.305 78.199 -27.718 1.00 37.53 C ATOM 1149 CG PHE A 149 39.387 77.039 -27.461 1.00 33.29 C ATOM 1150 CD1 PHE A 149 38.009 77.226 -27.387 1.00 29.22 C ATOM 1151 CD2 PHE A 149 39.903 75.760 -27.270 1.00 28.26 C ATOM 1152 CE1 PHE A 149 37.156 76.154 -27.124 1.00 26.87 C ATOM 1153 CE2 PHE A 149 39.062 74.681 -27.006 1.00 29.29 C ATOM 1154 CZ PHE A 149 37.683 74.879 -26.934 1.00 30.14 C ATOM 1155 N SER A 150 42.106 77.852 -30.120 1.00 44.78 N ATOM 1156 CA SER A 150 42.924 77.077 -31.057 1.00 38.94 C ATOM 1157 C SER A 150 42.996 77.839 -32.378 1.00 35.66 C ATOM 1158 O SER A 150 44.039 78.374 -32.718 1.00 38.02 O ATOM 1159 CB SER A 150 42.353 75.676 -31.283 1.00 32.93 C ATOM 1160 OG SER A 150 43.261 74.895 -32.047 1.00 31.61 O ATOM 1161 N SER A 151 41.879 77.879 -33.104 1.00 36.86 N ATOM 1162 CA SER A 151 41.745 78.598 -34.377 1.00 32.32 C ATOM 1163 C SER A 151 42.958 78.629 -35.304 1.00 36.45 C ATOM 1164 O SER A 151 43.531 79.692 -35.565 1.00 35.55 O ATOM 1165 CB SER A 151 41.305 80.038 -34.107 1.00 27.79 C ATOM 1166 OG SER A 151 40.065 80.069 -33.429 1.00 35.13 O ATOM 1167 N PRO A 152 43.356 77.468 -35.836 1.00 40.61 N ATOM 1168 CA PRO A 152 44.512 77.444 -36.736 1.00 42.49 C ATOM 1169 C PRO A 152 44.150 77.973 -38.125 1.00 42.14 C ATOM 1170 O PRO A 152 42.991 78.288 -38.397 1.00 40.80 O ATOM 1171 CB PRO A 152 44.883 75.968 -36.760 1.00 42.76 C ATOM 1172 CG PRO A 152 43.534 75.304 -36.693 1.00 42.42 C ATOM 1173 CD PRO A 152 42.812 76.112 -35.631 1.00 39.19 C ATOM 1174 N ASN A 153 45.148 78.086 -38.993 1.00 44.89 N ATOM 1175 CA ASN A 153 44.921 78.542 -40.362 1.00 45.11 C ATOM 1176 C ASN A 153 45.092 77.307 -41.232 1.00 46.15 C ATOM 1177 O ASN A 153 45.996 76.502 -41.003 1.00 50.16 O ATOM 1178 CB ASN A 153 45.951 79.592 -40.770 1.00 45.30 C ATOM 1179 CG ASN A 153 46.044 80.729 -39.781 1.00 43.47 C ATOM 1180 OD1 ASN A 153 45.093 81.487 -39.590 1.00 46.50 O ATOM 1181 ND2 ASN A 153 47.196 80.853 -39.143 1.00 33.35 N TER 4875 MET A 607 HETATM 4876 N ARG X 900 43.972 82.052 -36.884 1.00 37.31 N HETATM 4877 CA ARG X 900 44.639 83.205 -36.209 1.00 43.51 C HETATM 4878 C ARG X 900 46.150 83.005 -36.147 1.00 44.70 C HETATM 4879 O ARG X 900 46.842 83.928 -35.666 1.00 51.15 O HETATM 4880 CB ARG X 900 44.080 83.392 -34.788 1.00 31.47 C HETATM 4881 CG ARG X 900 42.619 83.803 -34.755 1.00 31.50 C HETATM 4882 CD ARG X 900 42.116 83.982 -33.337 1.00 38.70 C HETATM 4883 NE ARG X 900 40.700 84.343 -33.288 1.00 42.91 N HETATM 4884 CZ ARG X 900 40.206 85.521 -33.660 1.00 48.35 C HETATM 4885 NH1 ARG X 900 41.014 86.471 -34.114 1.00 45.64 N HETATM 4886 NH2 ARG X 900 38.899 85.751 -33.584 1.00 46.85 N HETATM 4887 OXT ARG X 900 46.623 81.932 -36.581 1.00 42.67 O HETATM 4963 O HOH X 976 48.036 82.421 -33.012 1.00 30.31 O HETATM 4964 O HOH X 977 44.190 81.253 -31.435 1.00 48.82 O HETATM 4965 O HOH X 978 41.198 81.209 -30.407 1.00 48.77 O """ pdb_file = "unsorted3.pdb" with open(pdb_file, "w") as f: f.write(pdb_raw) if (op.exists("unsorted3_sorted.pdb")): os.remove("unsorted3_sorted.pdb") out = StringIO() sort_hetatms.run( args=[pdb_file, "--verbose",], out=out) assert op.isfile("unsorted3_sorted.pdb") pdb_in = file_reader.any_file("unsorted3_sorted.pdb") for atom in pdb_in.file_object.hierarchy.atoms(): assert atom.fetch_labels().chain_id == "A" # now with ARG ligand minus waters, but still flagged as HETATM pdb_in = file_reader.any_file("unsorted3.pdb") sel_str = "not resname HOH" sel_cache = pdb_in.file_object.hierarchy.atom_selection_cache() sel = sel_cache.selection(sel_str) hierarchy_new = pdb_in.file_object.hierarchy.select(sel) with open("unsorted4.pdb", "w") as f: f.write(hierarchy_new.as_pdb_string( crystal_symmetry=pdb_in.file_object.crystal_symmetry())) if (op.exists("unsorted4_sorted.pdb")): os.remove("unsorted4_sorted.pdb") out = StringIO() sort_hetatms.run( args=["unsorted4.pdb", "--verbose",], out=out) assert op.isfile("unsorted4_sorted.pdb") pdb_in = file_reader.any_file("unsorted4_sorted.pdb") for atom in pdb_in.file_object.hierarchy.atoms(): assert atom.fetch_labels().chain_id == "A" print("OK") if (__name__ == "__main__"): exercise()