from __future__ import absolute_import, division, print_function import os, sys from mmtbx.conformation_dependent_library.rdl_database import rdl_database from mmtbx.conformation_dependent_library import rotamers as rdl from iotbx import pdb import libtbx.load_env from mmtbx.conformation_dependent_library.testing_utils import get_geometry_restraints_manager pdbs = { "3sgs" : """ CRYST1 4.821 19.500 21.004 90.00 94.23 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 2.186 -1.809 10.234 1.00 10.29 N ATOM 2 CA GLY A 1 2.320 -0.815 9.141 1.00 9.80 C ATOM 3 C GLY A 1 1.418 -1.163 7.979 1.00 9.53 C ATOM 4 O GLY A 1 0.509 -1.993 8.106 1.00 10.48 O ATOM 5 N ASP A 2 1.661 -0.515 6.852 1.00 8.39 N ATOM 6 CA ASP A 2 0.811 -0.643 5.673 1.00 7.85 C ATOM 7 C ASP A 2 1.470 -1.495 4.602 1.00 6.99 C ATOM 8 O ASP A 2 2.696 -1.595 4.534 1.00 6.68 O ATOM 9 CB ASP A 2 0.516 0.739 5.087 1.00 7.92 C ATOM 10 CG ASP A 2 -0.103 1.696 6.094 1.00 8.88 C ATOM 11 OD1 ASP A 2 -0.972 1.260 6.879 1.00 9.26 O ATOM 12 OD2 ASP A 2 0.269 2.895 6.083 1.00 9.54 O ATOM 13 N VAL A 3 0.639 -2.089 3.747 1.00 5.97 N ATOM 14 CA VAL A 3 1.107 -2.730 2.539 1.00 5.50 C ATOM 15 C VAL A 3 0.524 -1.988 1.346 1.00 5.36 C ATOM 16 O VAL A 3 -0.705 -1.905 1.195 1.00 4.65 O ATOM 17 CB VAL A 3 0.686 -4.205 2.485 1.00 5.06 C ATOM 18 CG1 VAL A 3 1.198 -4.839 1.211 1.00 5.22 C ATOM 19 CG2 VAL A 3 1.197 -4.950 3.727 1.00 5.82 C ATOM 20 N ILE A 4 1.395 -1.423 0.522 1.00 5.14 N ATOM 21 CA ILE A 4 0.955 -0.615 -0.606 1.00 5.38 C ATOM 22 C ILE A 4 1.465 -1.216 -1.907 1.00 5.88 C ATOM 23 O ILE A 4 2.673 -1.309 -2.125 1.00 5.24 O ATOM 24 CB ILE A 4 1.414 0.853 -0.480 1.00 4.86 C ATOM 25 CG1 ILE A 4 0.807 1.508 0.765 1.00 6.05 C ATOM 26 CG2 ILE A 4 0.992 1.652 -1.697 1.00 3.89 C ATOM 27 CD1 ILE A 4 1.343 2.897 1.039 1.00 7.01 C ATOM 28 N GLU A 5 0.522 -1.599 -2.768 1.00 7.64 N ATOM 29 CA GLU A 5 0.797 -2.207 -4.071 1.00 9.57 C ATOM 30 C GLU A 5 0.245 -1.323 -5.182 1.00 11.31 C ATOM 31 O GLU A 5 -0.967 -1.167 -5.324 1.00 11.92 O ATOM 32 CB GLU A 5 0.155 -3.597 -4.151 1.00 9.45 C ATOM 33 CG GLU A 5 1.035 -4.713 -3.663 1.00 10.16 C ATOM 34 CD GLU A 5 2.009 -5.243 -4.706 1.00 10.01 C ATOM 35 OE1 GLU A 5 2.127 -4.680 -5.822 1.00 10.67 O ATOM 36 OE2 GLU A 5 2.653 -6.260 -4.403 1.00 10.98 O ATOM 37 N VAL A 6 1.129 -0.742 -5.983 1.00 13.27 N ATOM 38 CA VAL A 6 0.694 0.201 -7.016 1.00 15.08 C ATOM 39 C VAL A 6 1.239 -0.152 -8.414 1.00 16.11 C ATOM 40 O VAL A 6 2.388 0.136 -8.755 1.00 17.57 O ATOM 41 CB VAL A 6 1.089 1.654 -6.625 1.00 15.51 C ATOM 42 CG1 VAL A 6 0.230 2.140 -5.472 1.00 15.79 C ATOM 43 CG2 VAL A 6 2.539 1.722 -6.216 1.00 16.27 C ATOM 44 OXT VAL A 6 0.534 -0.718 -9.323 1.00 17.23 O END """, "mse.pdb" : """ HETATM 104 N MSE A 15 9.964 48.917 17.420 1.00 8.74 N HETATM 105 CA MSE A 15 10.216 47.479 17.369 1.00 8.79 C HETATM 106 C MSE A 15 11.068 47.049 18.526 1.00 8.17 C HETATM 107 O MSE A 15 10.735 46.094 19.248 1.00 8.75 O HETATM 108 CB MSE A 15 10.919 47.112 16.062 1.00 9.55 C HETATM 109 CG MSE A 15 10.029 47.299 14.827 1.00 10.59 C HETATM 110 SE MSE A 15 8.751 45.831 14.563 1.00 15.23 SE HETATM 111 CE MSE A 15 10.035 44.485 13.975 1.00 10.87 C """, "met.pdb" : """ ATOM 104 N MET A 15 9.964 48.917 17.420 1.00 8.74 N ATOM 105 CA MET A 15 10.216 47.479 17.369 1.00 8.79 C ATOM 106 C MET A 15 11.068 47.049 18.526 1.00 8.17 C ATOM 107 O MET A 15 10.735 46.094 19.248 1.00 8.75 O ATOM 108 CB MET A 15 10.919 47.112 16.062 1.00 9.55 C ATOM 109 CG MET A 15 10.029 47.299 14.827 1.00 10.59 C ATOM 110 SD MET A 15 8.751 45.831 14.563 1.00 15.23 S ATOM 111 CE MET A 15 10.035 44.485 13.975 1.00 10.87 C """, "tyr.pdb" : """ ATOM 1235 N TYR A 150 9.126 58.830 20.254 1.00 12.80 N ATOM 1236 CA TYR A 150 8.222 58.422 19.190 1.00 12.53 C ATOM 1237 C TYR A 150 8.121 56.907 19.022 1.00 13.12 C ATOM 1238 O TYR A 150 9.136 56.226 18.861 1.00 14.16 O ATOM 1239 CB TYR A 150 8.667 59.045 17.856 1.00 14.51 C ATOM 1240 CG TYR A 150 7.875 58.505 16.688 1.00 14.22 C ATOM 1241 CD1 TYR A 150 6.561 58.914 16.461 1.00 17.43 C ATOM 1242 CD2 TYR A 150 8.415 57.534 15.849 1.00 14.20 C ATOM 1243 CE1 TYR A 150 5.825 58.388 15.409 1.00 19.08 C ATOM 1244 CE2 TYR A 150 7.692 57.012 14.796 1.00 17.26 C ATOM 1245 CZ TYR A 150 6.401 57.437 14.581 1.00 18.47 C ATOM 1246 OH TYR A 150 5.685 56.901 13.541 1.00 20.26 O """, } def run(filename): print(filename) if 0: print("RDL") for aa in sorted(rdl_database): print(" %s" % aa) for key, value in rdl_database[aa].items(): print(" %s" % key) for names, values in rdl_database[aa][key].items(): print(" %s : %s" % (names, values)) assert 0 # if filename=="3sgs.pdb": from libtbx import easy_run f=open("mse.pdb", "w") f.write(pdbs["mse.pdb"]) f.close() f=open("met.pdb", "w") f.write(pdbs["met.pdb"]) f.close() cmd="phenix.pdb_interpretation rdl=True write_geo=1 mse.pdb" print(cmd) easy_run.call(cmd) cmd="phenix.pdb_interpretation rdl=True write_geo=1 met.pdb" print(cmd) easy_run.call(cmd) # pdb_inp = pdb.input(filename) pdb_hierarchy = pdb_inp.construct_hierarchy() geometry_restraints_manager = get_geometry_restraints_manager(filename) pdb_hierarchy.reset_i_seq_if_necessary() rdl.update_restraints(pdb_hierarchy, geometry_restraints_manager, assert_rotamer_found=True, verbose=True, ) print("OK") mmtbx_dir = libtbx.env.dist_path("mmtbx") props = os.path.join(mmtbx_dir,"rotamer","rotamer_names.props") f=open(props, "r") props = f.readlines() f.close() for prop in props: print(prop) key = prop.split("=")[0] residue, rotamer_name = key.split() residue = residue.upper() if residue in ["MSE"]: continue assert residue in rdl_database assert rotamer_name in rdl_database[residue] if __name__=="__main__": if len(sys.argv)==1: f=open("3sgs.pdb", "w") f.write(pdbs["3sgs"]) f.close() run("3sgs.pdb") else: run(sys.argv[1])