from __future__ import absolute_import, division, print_function import iotbx.pdb from mmtbx.pair_interaction import pair_interaction pdb_str = """ REMARK PDB code: 1yjp, renumbered CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 0 N GLY A 0 -9.009 4.612 6.102 1.00 16.77 N ATOM 1 CA GLY A 0 -9.052 4.207 4.651 1.00 16.57 C ATOM 2 C GLY A 0 -8.015 3.140 4.419 1.00 16.16 C ATOM 3 O GLY A 0 -7.523 2.521 5.381 1.00 16.78 O ATOM 4 N ASN A 1 -7.656 2.923 3.155 1.00 15.02 N ATOM 5 CA ASN A 1 -6.522 2.038 2.831 1.00 14.10 C ATOM 6 C ASN A 1 -5.241 2.537 3.427 1.00 13.13 C ATOM 7 O ASN A 1 -4.978 3.742 3.426 1.00 11.91 O ATOM 8 CB ASN A 1 -6.346 1.881 1.341 1.00 15.38 C ATOM 9 CG ASN A 1 -7.584 1.342 0.692 1.00 14.08 C ATOM 10 OD1 ASN A 1 -8.025 0.227 1.016 1.00 17.46 O ATOM 11 ND2 ASN A 1 -8.204 2.155 -0.169 1.00 11.72 N ATOM 12 N ASN A 2 -4.438 1.590 3.905 1.00 12.26 N ATOM 13 CA ASN A 2 -3.193 1.904 4.589 1.00 11.74 C ATOM 14 C ASN A 2 -1.955 1.332 3.895 1.00 11.10 C ATOM 15 O ASN A 2 -1.872 0.119 3.648 1.00 10.42 O ATOM 16 CB ASN A 2 -3.259 1.378 6.042 1.00 12.15 C ATOM 17 CG ASN A 2 -2.006 1.739 6.861 1.00 12.82 C ATOM 18 OD1 ASN A 2 -1.702 2.925 7.072 1.00 15.05 O ATOM 19 ND2 ASN A 2 -1.271 0.715 7.306 1.00 13.48 N ATOM 20 N GLN A 3 -1.005 2.228 3.598 1.00 10.29 N ATOM 21 CA GLN A 3 0.384 1.888 3.199 1.00 10.53 C ATOM 22 C GLN A 3 1.435 2.606 4.088 1.00 10.24 C ATOM 23 O GLN A 3 1.547 3.843 4.115 1.00 8.86 O ATOM 24 CB GLN A 3 0.656 2.148 1.711 1.00 9.80 C ATOM 25 CG GLN A 3 1.944 1.458 1.213 1.00 10.25 C ATOM 26 CD GLN A 3 2.504 2.044 -0.089 1.00 12.43 C ATOM 27 OE1 GLN A 3 2.744 3.268 -0.190 1.00 14.62 O ATOM 28 NE2 GLN A 3 2.750 1.161 -1.091 1.00 9.05 N ATOM 29 N GLN A 4 2.154 1.821 4.871 1.00 10.38 N ATOM 30 CA GLN A 4 3.270 2.361 5.640 1.00 11.39 C ATOM 31 C GLN A 4 4.594 1.768 5.172 1.00 11.52 C ATOM 32 O GLN A 4 4.768 0.546 5.054 1.00 12.05 O ATOM 33 CB GLN A 4 3.056 2.183 7.147 1.00 11.96 C ATOM 34 CG GLN A 4 1.829 2.950 7.647 1.00 10.81 C ATOM 35 CD GLN A 4 1.344 2.414 8.954 1.00 13.10 C ATOM 36 OE1 GLN A 4 0.774 1.325 9.002 1.00 10.65 O ATOM 37 NE2 GLN A 4 1.549 3.187 10.039 1.00 12.30 N ATOM 38 N ASN A 5 5.514 2.664 4.856 1.00 11.99 N ATOM 39 CA ASN A 5 6.831 2.310 4.318 1.00 12.30 C ATOM 40 C ASN A 5 7.854 2.761 5.324 1.00 13.40 C ATOM 41 O ASN A 5 8.219 3.943 5.374 1.00 13.92 O ATOM 42 CB ASN A 5 7.065 3.016 2.993 1.00 12.13 C ATOM 43 CG ASN A 5 5.961 2.735 2.003 1.00 12.77 C ATOM 44 OD1 ASN A 5 5.798 1.604 1.551 1.00 14.27 O ATOM 45 ND2 ASN A 5 5.195 3.747 1.679 1.00 10.07 N ATOM 46 N TYR A 6 8.292 1.817 6.147 1.00 14.70 N ATOM 47 CA TYR A 6 9.159 2.144 7.299 1.00 15.18 C ATOM 48 C TYR A 6 10.603 2.331 6.885 1.00 15.91 C ATOM 49 O TYR A 6 11.041 1.811 5.855 1.00 15.76 O ATOM 50 CB TYR A 6 9.061 1.065 8.369 1.00 15.35 C ATOM 51 CG TYR A 6 7.665 0.929 8.902 1.00 14.45 C ATOM 52 CD1 TYR A 6 6.771 0.021 8.327 1.00 15.68 C ATOM 53 CD2 TYR A 6 7.210 1.756 9.920 1.00 14.80 C ATOM 54 CE1 TYR A 6 5.480 -0.094 8.796 1.00 13.46 C ATOM 55 CE2 TYR A 6 5.904 1.649 10.416 1.00 14.33 C ATOM 56 CZ TYR A 6 5.047 0.729 9.831 1.00 15.09 C ATOM 57 OH TYR A 6 3.766 0.589 10.291 1.00 14.39 O ATOM 58 OXT TYR A 6 11.358 2.999 7.612 1.00 17.49 O TER HETATM 59 O HOH A 7 -6.471 5.227 7.124 1.00 22.62 O HETATM 60 O HOH A 8 10.431 1.858 3.216 1.00 19.71 O HETATM 61 O HOH A 9 -11.286 1.756 -1.468 1.00 17.08 O HETATM 62 O HOH A 10 11.808 4.179 9.970 1.00 23.99 O HETATM 63 O HOH A 11 13.605 1.327 9.198 1.00 26.17 O HETATM 64 O HOH A 12 -2.749 3.429 10.024 1.00 39.15 O HETATM 65 O HOH A 13 -1.500 0.682 10.967 1.00 43.49 O END """ def run(): """ Exercise interaction graph construction. """ pdb_inp = iotbx.pdb.input(source_info=None, lines = pdb_str) ph = pdb_inp.construct_hierarchy() interaction_list = pair_interaction.run(ph) interaction_list.sort() # Changed as result of Python 2->3 conversion: #expected_list = [(1, 2), (1, 3), (1, 8), (2, 3), (2, 8), (2, 10), (3, 4), # (3, 5), (3, 13), (3, 14), (4, 5), (4, 6), (5, 6), (5, 7), # (5, 13), (5, 14), (6, 7), (6, 9), (7, 9), (7, 11), (7, 12), # (11, 12), (13, 14)] expected_list = [(1, 2), (1, 8), (2, 3), (2, 10), (3, 4), (3, 5), (3, 13), (3, 14), (4, 5), (4, 6), (5, 6), (5, 7), (5, 14), (6, 7), (6, 9), (7, 9), (7, 11), (7, 12), (11, 12), (13, 14)] assert interaction_list == expected_list #print(set(interaction_list).symmetric_difference(set(expected_list))) if(__name__ == "__main__"): run()