from __future__ import division pdbs = {'one' : [''' CRYST1 71.765 48.519 56.920 90.00 90.00 90.00 P 1 SCALE1 0.013934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017569 0.00000 ATOM 1 N ASNDE 1 -7.656 -1.943 3.155 1.00 15.02 N ATOM 2 CA ASNDE 1 -6.522 -2.828 2.831 1.00 14.10 C ATOM 3 C ASNDE 1 -5.241 -2.329 3.427 1.00 13.13 C ATOM 4 O ASNDE 1 -4.978 -1.124 3.426 1.00 11.91 O ATOM 5 CB ASNDE 1 -6.346 -2.985 1.341 1.00 15.38 C ATOM 6 CG ASNDE 1 -7.584 -3.524 0.692 1.00 14.08 C ATOM 7 OD1 ASNDE 1 -8.025 -4.639 1.016 1.00 17.46 O ATOM 8 ND2 ASNDE 1 -8.204 -2.711 -0.169 1.00 11.72 N ATOM 9 D ASNDE 1 -8.117 -1.532 2.343 1.00 15.02 D ATOM 10 DA ASNDE 1 -6.744 -3.809 3.252 1.00 14.10 D ATOM 11 DB2 ASNDE 1 -6.124 -2.013 0.900 1.00 15.38 D ATOM 12 DB3 ASNDE 1 -5.528 -3.678 1.146 1.00 15.38 D ATOM 13 DD21 ASNDE 1 -9.052 -3.021 -0.643 1.00 11.72 D ATOM 14 DD22 ASNDE 1 -7.829 -1.780 -0.352 1.00 11.72 D ATOM 15 N ASNDE 2 -4.438 -3.276 3.905 1.00 12.26 N ATOM 16 CA ASNDE 2 -3.193 -2.962 4.589 1.00 11.74 C ATOM 17 C ASNDE 2 -1.955 -3.534 3.895 1.00 11.10 C ATOM 18 O ASNDE 2 -1.872 -4.747 3.648 1.00 10.42 O ATOM 19 CB ASNDE 2 -3.259 -3.488 6.042 1.00 12.15 C ATOM 20 CG ASNDE 2 -2.006 -3.127 6.861 1.00 12.82 C ATOM 21 OD1 ASNDE 2 -1.702 -1.941 7.072 1.00 15.05 O ATOM 22 ND2 ASNDE 2 -1.271 -4.151 7.306 1.00 13.48 N ATOM 23 D ASNDE 2 -4.626 -4.276 3.832 1.00 12.26 D ATOM 24 DA ASNDE 2 -3.074 -1.879 4.586 1.00 11.74 D ATOM 25 DB2 ASNDE 2 -4.125 -3.051 6.539 1.00 12.15 D ATOM 26 DB3 ASNDE 2 -3.349 -4.574 6.023 1.00 12.15 D ATOM 27 DD21 ASNDE 2 -0.429 -3.974 7.854 1.00 13.48 D ATOM 28 DD22 ASNDE 2 -1.552 -5.109 7.097 1.00 13.48 D ATOM 29 N GLNDE 3 -1.005 -2.638 3.598 1.00 10.29 N ATOM 30 CA GLNDE 3 0.384 -2.978 3.199 1.00 10.53 C ATOM 31 C GLNDE 3 1.435 -2.260 4.088 1.00 10.24 C ATOM 32 O GLNDE 3 1.547 -1.023 4.115 1.00 8.86 O ATOM 33 CB GLNDE 3 0.656 -2.718 1.711 1.00 9.80 C ATOM 34 CG GLNDE 3 1.944 -3.408 1.213 1.00 10.25 C ATOM 35 CD GLNDE 3 2.504 -2.822 -0.089 1.00 12.43 C ATOM 36 OE1 GLNDE 3 2.744 -1.598 -0.190 1.00 14.62 O ATOM 37 NE2 GLNDE 3 2.750 -3.705 -1.091 1.00 9.05 N ATOM 38 D GLNDE 3 -1.162 -1.630 3.622 1.00 10.29 D ATOM 39 DA GLNDE 3 0.505 -4.051 3.346 1.00 10.53 D ATOM 40 DB2 GLNDE 3 -0.180 -3.100 1.125 1.00 9.80 D ATOM 41 DB3 GLNDE 3 0.764 -1.645 1.552 1.00 9.80 D ATOM 42 DG2 GLNDE 3 2.713 -3.307 1.979 1.00 10.25 D ATOM 43 DG3 GLNDE 3 1.730 -4.462 1.036 1.00 10.25 D ATOM 44 DE21 GLNDE 3 2.562 -4.698 -0.953 1.00 9.05 D ATOM 45 DE22 GLNDE 3 3.123 -3.375 -1.981 1.00 9.05 D ATOM 46 N GLNDE 4 2.154 -3.045 4.871 1.00 10.38 N ATOM 47 CA GLNDE 4 3.270 -2.505 5.640 1.00 11.39 C ATOM 48 C GLNDE 4 4.594 -3.098 5.172 1.00 11.52 C ATOM 49 O GLNDE 4 4.768 -4.320 5.054 1.00 12.05 O ATOM 50 CB GLNDE 4 3.056 -2.683 7.147 1.00 11.96 C ATOM 51 CG GLNDE 4 1.829 -1.916 7.647 1.00 10.81 C ATOM 52 CD GLNDE 4 1.344 -2.452 8.954 1.00 13.10 C ATOM 53 OE1 GLNDE 4 0.774 -3.541 9.002 1.00 10.65 O ATOM 54 NE2 GLNDE 4 1.549 -1.679 10.039 1.00 12.30 N ATOM 55 D GLNDE 4 1.995 -4.045 4.996 1.00 10.38 D ATOM 56 DA GLNDE 4 3.328 -1.429 5.475 1.00 11.39 D ATOM 57 DB2 GLNDE 4 2.909 -3.741 7.365 1.00 11.96 D ATOM 58 DB3 GLNDE 4 3.931 -2.311 7.679 1.00 11.96 D ATOM 59 DG2 GLNDE 4 2.090 -0.866 7.782 1.00 10.81 D ATOM 60 DG3 GLNDE 4 1.024 -2.009 6.918 1.00 10.81 D ATOM 61 DE21 GLNDE 4 2.015 -0.777 9.942 1.00 12.30 D ATOM 62 DE22 GLNDE 4 1.238 -1.996 10.957 1.00 12.30 D ATOM 63 N ASNDE 5 5.514 -2.202 4.856 1.00 11.99 N ATOM 64 CA ASNDE 5 6.831 -2.556 4.318 1.00 12.30 C ATOM 65 C ASNDE 5 7.854 -2.105 5.324 1.00 13.40 C ATOM 66 O ASNDE 5 8.219 -0.923 5.374 1.00 13.92 O ATOM 67 CB ASNDE 5 7.065 -1.850 2.993 1.00 12.13 C ATOM 68 CG ASNDE 5 5.961 -2.131 2.003 1.00 12.77 C ATOM 69 OD1 ASNDE 5 5.798 -3.262 1.551 1.00 14.27 O ATOM 70 ND2 ASNDE 5 5.195 -1.119 1.679 1.00 10.07 N ATOM 71 D ASNDE 5 5.383 -1.196 4.960 1.00 11.99 D ATOM 72 DA ASNDE 5 6.915 -3.627 4.132 1.00 12.30 D ATOM 73 DB2 ASNDE 5 7.106 -0.774 3.162 1.00 12.13 D ATOM 74 DB3 ASNDE 5 8.005 -2.196 2.563 1.00 12.13 D ATOM 75 DD21 ASNDE 5 4.432 -1.249 1.014 1.00 10.07 D ATOM 76 DD22 ASNDE 5 5.361 -0.201 2.091 1.00 10.07 D TER ATOM 77 D2 ASNDE 1 -8.282 -2.409 3.603 1.00 15.02 D ATOM 78 DC ASNDE 5 8.249 -2.763 5.965 1.00 13.40 D TER END ''', '''bond pdb=" N ASNDE 1 " pdb=" D2 ASNDE 1 " ideal model delta sigma weight residual 0.960 0.900 0.060 2.00e-02 2.50e+03 9.04e+00 bond pdb=" C ASNDE 5 " pdb=" DC ASNDE 5 " ideal model delta sigma weight residual 1.000 1.000 0.000 2.00e-02 2.50e+03 1.06e-05''' ], } from libtbx import easy_run from libtbx.test_utils import assert_lines_in_file def main(): for code, item in pdbs.items(): print(code) pf = 'tst_deuterium_end_%s.pdb' % code with open(pf, 'w') as f: f.write(item[0]) cmd = 'phenix.pdb_interpretation write_geo=True %(pf)s > %(pf)s.log' % locals() print(cmd) easy_run.go(cmd) print(item[1]) for line in item[1].split('\n'): print(line) assert_lines_in_file(file_name='%s.geo' % pf, lines=line) if __name__ == '__main__': main()