from __future__ import absolute_import, division, print_function import mmtbx.model import iotbx.pdb import time from libtbx.utils import null_out pdb_str = """ CRYST1 20.645 25.843 29.055 90.00 90.00 90.00 P 1 SCALE1 0.048438 0.000000 0.000000 0.00000 SCALE2 0.000000 0.038695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.034417 0.00000 ATOM 1 N CYS C 284 13.554 13.652 6.082 1.00 43.53 EA N ATOM 2 CA CYS C 284 14.504 14.116 7.088 1.00 43.46 EA C ATOM 3 C CYS C 284 13.857 14.177 8.466 1.00 46.41 EA C ATOM 4 O CYS C 284 14.509 13.899 9.480 1.00 34.73 EA O ATOM 5 CB CYS C 284 15.043 15.493 6.699 1.00 37.37 EA C ATOM 6 SG CYS C 284 15.645 15.628 5.000 1.00 30.55 EA S ATOM 7 N HIS C 285 12.571 14.535 8.520 1.00 81.03 EA N ATOM 8 CA HIS C 285 11.880 14.644 9.799 1.00 78.99 EA C ATOM 9 C HIS C 285 11.736 13.290 10.481 1.00 78.91 EA C ATOM 10 O HIS C 285 11.798 13.206 11.713 1.00 83.81 EA O ATOM 11 CB HIS C 285 10.507 15.286 9.600 1.00 87.56 EA C ATOM 12 CG HIS C 285 9.755 15.507 10.875 1.00100.53 EA C ATOM 13 ND1 HIS C 285 10.129 16.454 11.804 1.00102.57 EA N ATOM 14 CD2 HIS C 285 8.650 14.905 11.376 1.00110.92 EA C ATOM 15 CE1 HIS C 285 9.288 16.426 12.823 1.00110.54 EA C ATOM 16 NE2 HIS C 285 8.381 15.495 12.588 1.00115.69 EA N ATOM 17 N GLU C 286 11.547 12.223 9.702 1.00 41.43 EA N ATOM 18 CA GLU C 286 11.389 10.896 10.285 1.00 45.81 EA C ATOM 19 C GLU C 286 12.742 10.245 10.550 1.00 45.31 EA C ATOM 20 O GLU C 286 12.996 9.747 11.652 1.00 47.64 EA O ATOM 21 CB GLU C 286 10.559 10.014 9.350 1.00 31.98 EA C ATOM 22 CG GLU C 286 9.189 10.568 9.001 1.00 31.19 EA C ATOM 23 CD GLU C 286 8.308 10.778 10.211 1.00 46.04 EA C ATOM 24 OE1 GLU C 286 7.157 11.227 10.033 1.00 37.93 EA O ATOM 25 OE2 GLU C 286 8.766 10.496 11.337 1.00 53.32 EA O1- ATOM 26 N GLY C 289 14.202 12.615 13.228 1.00120.10 EA N ATOM 27 CA GLY C 289 13.414 12.984 14.388 1.00114.20 EA C ATOM 28 C GLY C 289 12.937 11.824 15.240 1.00106.50 EA C ATOM 29 O GLY C 289 12.978 11.900 16.472 1.00135.13 EA O ATOM 30 N HIS C 290 12.487 10.744 14.604 1.00 38.52 EA N ATOM 31 CA HIS C 290 11.863 9.625 15.301 1.00 48.73 EA C ATOM 32 C HIS C 290 12.756 8.398 15.399 1.00 53.95 EA C ATOM 33 O HIS C 290 12.984 7.888 16.500 1.00 51.44 EA O ATOM 34 CB HIS C 290 10.542 9.248 14.614 1.00 62.93 EA C ATOM 35 CG HIS C 290 9.496 10.316 14.686 1.00 56.22 EA C ATOM 36 ND1 HIS C 290 9.507 11.425 13.869 1.00 61.73 EA N ATOM 37 CD2 HIS C 290 8.406 10.444 15.480 1.00 51.42 EA C ATOM 38 CE1 HIS C 290 8.469 12.190 14.155 1.00 65.43 EA C ATOM 39 NE2 HIS C 290 7.785 11.618 15.129 1.00 66.69 EA N ATOM 40 N VAL C 291 13.265 7.902 14.267 1.00 73.68 EA N ATOM 41 CA VAL C 291 13.909 6.587 14.249 1.00 64.37 EA C ATOM 42 C VAL C 291 14.982 6.458 15.326 1.00 63.70 EA C ATOM 43 O VAL C 291 14.977 5.453 16.052 1.00 75.32 EA O ATOM 44 CB VAL C 291 14.446 6.282 12.842 1.00 66.63 EA C ATOM 45 CG1 VAL C 291 15.263 5.000 12.850 1.00 61.40 EA C ATOM 46 CG2 VAL C 291 13.298 6.187 11.848 1.00 83.70 EA C ATOM 47 N VAL C 329 6.501 13.140 22.870 1.00 30.06 EA N ATOM 48 CA VAL C 329 7.335 12.486 21.868 1.00 29.12 EA C ATOM 49 C VAL C 329 7.839 13.498 20.849 1.00 29.42 EA C ATOM 50 O VAL C 329 8.982 13.414 20.387 1.00 30.09 EA O ATOM 51 CB VAL C 329 6.561 11.337 21.192 1.00 26.47 EA C ATOM 52 CG1 VAL C 329 7.384 10.727 20.069 1.00 25.53 EA C ATOM 53 CG2 VAL C 329 6.187 10.272 22.214 1.00 26.38 EA C ATOM 54 N GLU C 330 7.004 14.476 20.493 1.00 54.98 EA N ATOM 55 CA GLU C 330 7.375 15.437 19.461 1.00 50.88 EA C ATOM 56 C GLU C 330 8.233 16.564 20.026 1.00 53.96 EA C ATOM 57 O GLU C 330 9.287 16.890 19.469 1.00 56.09 EA O ATOM 58 CB GLU C 330 6.115 16.006 18.806 1.00 54.40 EA C ATOM 59 CG GLU C 330 6.312 16.485 17.380 1.00 54.09 EA C ATOM 60 CD GLU C 330 6.616 15.348 16.429 1.00 51.73 EA C ATOM 61 OE1 GLU C 330 6.385 14.180 16.807 1.00 45.43 EA O ATOM 62 OE2 GLU C 330 7.084 15.620 15.304 1.00 72.06 EA O1- ATOM 63 N PHE C 331 7.801 17.165 21.133 1.00 52.30 EA N ATOM 64 CA PHE C 331 8.480 18.302 21.750 1.00 45.16 EA C ATOM 65 C PHE C 331 8.595 18.100 23.255 1.00 38.54 EA C ATOM 66 O PHE C 331 8.298 18.989 24.055 1.00 40.25 EA O ATOM 67 CB PHE C 331 7.748 19.603 21.437 1.00 51.35 EA C ATOM 68 CG PHE C 331 7.634 19.893 19.970 1.00 50.90 EA C ATOM 69 CD1 PHE C 331 8.639 20.575 19.305 1.00 48.59 EA C ATOM 70 CD2 PHE C 331 6.523 19.482 19.254 1.00 41.82 EA C ATOM 71 CE1 PHE C 331 8.537 20.843 17.953 1.00 56.15 EA C ATOM 72 CE2 PHE C 331 6.416 19.747 17.902 1.00 48.23 EA C ATOM 73 CZ PHE C 331 7.423 20.429 17.251 1.00 52.08 EA C TER HETATM 74 FE FE E 9 6.958 14.164 13.719 1.00129.77 Fe TER HETATM 75 O HOH G 21 5.000 12.310 14.576 1.00 60.96 O HETATM 76 O HOH G 22 5.115 15.599 12.863 1.00 38.47 O HETATM 77 O HOH G 23 6.308 12.238 11.815 1.00 68.93 O TER END""" def run(): """ Check metal linking (make sure CE1 is not included). """ pdb_inp = iotbx.pdb.input(lines=pdb_str, source_info=None) params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.automatic_linking.link_metals=True m = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) m.process(pdb_interpretation_params=params, make_restraints=True) grm = m.get_restraints_manager() ph = m.get_hierarchy() atoms = list(ph.atoms()) assert atoms[73].element.strip().upper() == "FE" bond_proxies_simple, asu = grm.geometry.get_all_bond_proxies( sites_cart = ph.atoms().extract_xyz()) expected_link_atoms = ['NE2', "NE2", "OE1", "OE2", "O", "O", "O"] expected_link_atoms.sort() linked_atoms_found = [] for p in bond_proxies_simple: if(73 in p.i_seqs): i,j = p.i_seqs a1 = atoms[i].name.strip().upper() a2 = atoms[j].name.strip().upper() if(i!=73): linked_atoms_found.append(a1) else: linked_atoms_found.append(a2) linked_atoms_found.sort() assert expected_link_atoms == linked_atoms_found, '%s != %s' % (expected_link_atoms, linked_atoms_found) if (__name__ == "__main__"): t0 = time.time() run() print("Time: %6.3f"%(time.time()-t0))