from __future__ import division pdbs = {'FES' : [''' CRYST1 69.637 83.783 289.575 90.00 90.00 90.00 P 21 21 21 SCALE1 0.014360 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003453 0.00000 ATOM 2 N CYS B 65 27.906 13.996 110.876 1.00 38.84 N ATOM 3 CB CYS B 65 25.655 13.129 111.327 1.00 45.32 C ATOM 4 SG CYS B 65 24.970 12.918 109.662 1.00 48.54 S ATOM 6 CB CYS B 70 24.347 16.552 110.907 1.00 35.56 C ATOM 7 SG CYS B 70 25.742 16.540 109.744 1.00 38.98 S ATOM 9 CB CYS B 73 28.351 16.094 103.957 1.00 38.81 C ATOM 10 SG CYS B 73 27.104 14.870 103.769 1.00 54.50 S ATOM 11 CB CYS B 85 27.375 11.085 104.799 1.00 53.46 C ATOM 12 SG CYS B 85 25.854 11.959 105.192 1.00 43.66 S TER HETATM 13 S1 FES B1001 27.661 14.411 107.356 1.00 45.15 S HETATM 14 S2 FES B1001 24.426 14.718 106.631 1.00 50.67 S HETATM 15 FE1 FES B1001 26.274 13.994 105.655 1.00 45.74 Fe HETATM 16 FE2 FES B1001 25.714 14.660 108.456 1.00 54.80 Fe END ''', '''Iron sulfur cluster coordination pdb=" FES B1001 " pdb="FE1 FES B1001 " - pdb=" SG CYS B 85 " pdb="FE1 FES B1001 " - pdb=" SG CYS B 73 " pdb="FE2 FES B1001 " - pdb=" SG CYS B 65 " pdb="FE2 FES B1001 " - pdb=" SG CYS B 70 " Number of angles added : 6''' ], 'SF4' : [''' CRYST1 69.637 83.783 289.575 90.00 90.00 90.00 P 21 21 21 SCALE1 0.014360 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003453 0.00000 ATOM 1 CB CYS B 158 13.213 19.933 106.619 1.00 39.32 C ATOM 2 SG CYS B 158 14.305 21.083 105.791 1.00 40.40 S ATOM 4 SG CYS B 161 19.842 19.147 102.318 1.00 39.67 S ATOM 6 CB CYS B 164 15.403 21.627 98.258 1.00 32.61 C ATOM 7 SG CYS B 164 15.348 22.627 99.764 1.00 45.66 S ATOM 8 CB CYS B 225 14.524 16.612 99.097 1.00 42.52 C ATOM 9 SG CYS B 225 14.453 16.183 100.856 1.00 47.12 S TER HETATM 10 S1 SF4 B1002 16.060 18.164 103.702 1.00 42.49 S HETATM 11 S2 SF4 B1002 16.763 21.423 103.093 1.00 39.97 S HETATM 12 S3 SF4 B1002 16.716 19.174 100.702 1.00 47.37 S HETATM 13 S4 SF4 B1002 13.852 20.036 102.235 1.00 41.04 S HETATM 14 FE1 SF4 B1002 15.572 20.996 101.237 1.00 44.15 Fe HETATM 15 FE2 SF4 B1002 15.000 18.186 101.701 1.00 44.87 Fe HETATM 16 FE3 SF4 B1002 15.185 20.158 104.048 1.00 43.71 Fe HETATM 17 FE4 SF4 B1002 17.638 19.418 102.765 1.00 45.13 Fe END ''', '''Iron sulfur cluster coordination pdb=" SF4 B1002 " pdb="FE3 SF4 B1002 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B1002 " - pdb=" SG CYS B 164 " pdb="FE2 SF4 B1002 " - pdb=" SG CYS B 225 " pdb="FE4 SF4 B1002 " - pdb=" SG CYS B 161 " Number of angles added : 12''' ], 'F3S' : [''' CRYST1 69.637 83.783 289.575 90.00 90.00 90.00 P 21 21 21 SCALE1 0.014360 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011936 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003453 0.00000 ATOM 1 CB CYS B 168 15.203 26.368 93.567 1.00 47.04 C ATOM 2 SG CYS B 168 13.943 27.456 92.871 1.00 47.62 S ATOM 4 CB CYS B 215 7.764 28.960 93.921 1.00 37.98 C ATOM 5 SG CYS B 215 7.441 27.195 93.528 1.00 39.80 S ATOM 10 CB CYS B 221 12.828 21.872 95.639 1.00 37.15 C ATOM 11 SG CYS B 221 11.108 21.981 95.007 1.00 44.00 S TER HETATM 12 S1 F3S B1003 12.639 23.857 92.203 1.00 32.42 S HETATM 13 S2 F3S B1003 10.627 27.040 91.359 1.00 41.10 S HETATM 14 S3 F3S B1003 11.078 25.992 94.637 1.00 40.00 S HETATM 15 S4 F3S B1003 8.840 23.963 92.856 1.00 38.57 S HETATM 16 FE1 F3S B1003 12.222 26.021 92.644 1.00 44.92 Fe HETATM 17 FE3 F3S B1003 10.970 23.908 93.675 1.00 48.58 Fe HETATM 18 FE4 F3S B1003 9.433 26.146 93.042 1.00 47.61 Fe END ''', '''Iron sulfur cluster coordination pdb=" F3S B1003 " pdb="FE4 F3S B1003 " - pdb=" SG CYS B 215 " pdb="FE1 F3S B1003 " - pdb=" SG CYS B 168 " pdb="FE3 F3S B1003 " - pdb=" SG CYS B 221 " Number of angles added : 9''' ], } 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_fe_s_%s.pdb' % code with open(pf, 'w') as f: f.write(item[0]) cmd = 'phenix.pdb_interpretation %(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.log' % pf, lines=line) if __name__ == '__main__': main()