from __future__ import absolute_import, division, print_function from mmtbx.disorder import backbone import iotbx.pdb from six.moves import cStringIO as StringIO pdb_raw = """ CRYST1 21.937 6.000 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 AASN A 3 -4.438 1.590 3.905 0.50 12.26 N ATOM 14 CA AASN A 3 -3.193 1.904 4.589 0.50 11.74 C ATOM 15 C AASN A 3 -1.955 1.332 3.895 0.50 11.10 C ATOM 16 O AASN A 3 -1.872 0.119 3.648 0.50 10.42 O ATOM 17 CB AASN A 3 -3.259 1.378 6.042 0.50 12.15 C ATOM 18 CG AASN A 3 -2.006 1.739 6.861 0.50 12.82 C ATOM 19 OD1AASN A 3 -1.702 2.925 7.072 0.50 15.05 O ATOM 20 ND2AASN A 3 -1.271 0.715 7.306 0.50 13.48 N ATOM 13 N BASN A 3 -4.438 1.590 3.905 0.50 12.26 N ATOM 14 CA BASN A 3 -3.193 1.904 4.589 0.50 11.74 C ATOM 15 C BASN A 3 -1.993 1.011 4.266 0.50 11.10 C ATOM 16 O BASN A 3 -2.000 -0.192 4.568 0.50 10.42 O ATOM 17 CB BASN A 3 -3.259 1.378 6.042 0.50 12.15 C ATOM 18 CG BASN A 3 -2.006 1.739 6.861 0.50 12.82 C ATOM 19 OD1BASN A 3 -1.702 2.925 7.072 0.50 15.05 O ATOM 20 ND2BASN A 3 -1.271 0.715 7.306 0.50 13.48 N ATOM 21 N AGLN A 4 -1.005 2.228 3.598 0.50 10.29 N ATOM 22 CA AGLN A 4 0.384 1.888 3.199 0.50 10.53 C ATOM 23 C AGLN A 4 1.435 2.606 4.088 0.50 10.24 C ATOM 24 O AGLN A 4 1.547 3.843 4.115 0.50 8.86 O ATOM 25 CB AGLN A 4 0.656 2.148 1.711 0.50 9.80 C ATOM 26 CG AGLN A 4 1.944 1.458 1.213 0.50 10.25 C ATOM 27 CD AGLN A 4 2.504 2.044 -0.089 0.50 12.43 C ATOM 28 OE1AGLN A 4 2.744 3.268 -0.190 0.50 14.62 O ATOM 29 NE2AGLN A 4 2.750 1.161 -1.091 0.50 9.05 N ATOM 21 N BGLN A 4 -0.972 1.629 3.658 0.50 10.29 N ATOM 22 CA BGLN A 4 0.392 1.063 3.508 0.50 10.53 C ATOM 23 C BGLN A 4 1.482 2.027 4.050 0.50 10.24 C ATOM 24 O BGLN A 4 1.689 3.145 3.548 0.50 8.86 O ATOM 25 CB BGLN A 4 0.705 0.638 2.067 0.50 9.80 C ATOM 26 CG BGLN A 4 1.943 -0.280 1.974 0.50 10.25 C ATOM 27 CD BGLN A 4 2.565 -0.350 0.574 0.50 12.43 C ATOM 28 OE1BGLN A 4 2.900 0.692 -0.032 0.50 14.62 O ATOM 29 NE2BGLN A 4 2.757 -1.593 0.061 0.50 9.05 N ATOM 30 N AGLN A 5 2.154 1.821 4.871 0.50 10.38 N ATOM 31 CA AGLN A 5 3.270 2.361 5.640 0.50 11.39 C ATOM 32 C AGLN A 5 4.594 1.768 5.172 0.50 11.52 C ATOM 33 O AGLN A 5 4.768 0.546 5.054 0.50 12.05 O ATOM 34 CB AGLN A 5 3.056 2.183 7.147 0.50 11.96 C ATOM 35 CG AGLN A 5 1.829 2.950 7.647 0.50 10.81 C ATOM 36 CD AGLN A 5 1.344 2.414 8.954 0.50 13.10 C ATOM 37 OE1AGLN A 5 0.774 1.325 9.002 0.50 10.65 O ATOM 38 NE2AGLN A 5 1.549 3.187 10.039 0.50 12.30 N ATOM 30 N BGLN A 5 2.127 1.614 5.127 0.50 10.38 N ATOM 31 CA BGLN A 5 3.270 2.361 5.640 0.50 11.39 C ATOM 32 C BGLN A 5 4.594 1.768 5.172 0.50 11.52 C ATOM 33 O BGLN A 5 4.768 0.546 5.054 0.50 12.05 O ATOM 34 CB BGLN A 5 3.056 2.183 7.147 0.50 11.96 C ATOM 35 CG BGLN A 5 1.829 2.950 7.647 0.50 10.81 C ATOM 36 CD BGLN A 5 1.344 2.414 8.954 0.50 13.10 C ATOM 37 OE1BGLN A 5 0.774 1.325 9.002 0.50 10.65 O ATOM 38 NE2BGLN A 5 1.549 3.187 10.039 0.50 12.30 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O TER 60 TYR A 7 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 """ def exercise(): hierarchy = iotbx.pdb.input(source_info=None, lines=pdb_raw).construct_hierarchy() with open("tmp.pdb", "w") as f: f.write(hierarchy.as_pdb_string()) backrubs = backbone.find_backrubs( pdb_hierarchy=hierarchy) assert (len(backrubs) == 1) out = StringIO() backrubs[0].show(out=out) assert (out.getvalue() == """backrub A 4 (A,B): angle=-26.0\n"""), \ out.getvalue() if (__name__ == "__main__"): exercise() print("OK")