from __future__ import absolute_import, division, print_function import sys from libtbx import easy_run pdbs = {'4udx_sf4.pdb' : ''' HETATM 9499 FE1 SF4 X1001 39.663 2.346 22.723 1.00 6.06 FE HETATM 9500 FE2 SF4 X1001 42.157 2.138 23.788 1.00 5.97 FE HETATM 9501 FE3 SF4 X1001 41.050 0.016 22.600 1.00 6.18 FE HETATM 9502 FE4 SF4 X1001 41.899 2.128 21.073 1.00 6.14 FE HETATM 9503 S1 SF4 X1001 41.420 3.878 22.535 1.00 6.14 S HETATM 9504 S2 SF4 X1001 40.249 1.068 24.522 1.00 6.06 S HETATM 9505 S3 SF4 X1001 43.249 0.748 22.278 1.00 6.36 S HETATM 9506 S4 SF4 X1001 39.895 0.913 20.872 1.00 6.51 S ''', '4udx_sf4_cys.pdb' : ''' ATOM 683 N CYS X 48 44.683 -0.694 27.648 1.00 5.76 N ATOM 684 CA CYS X 48 44.043 0.578 27.358 1.00 5.66 C ATOM 685 C CYS X 48 42.533 0.474 27.608 1.00 5.45 C ATOM 686 O CYS X 48 41.867 -0.426 27.113 1.00 6.44 O ATOM 687 CB CYS X 48 44.312 1.012 25.919 1.00 5.93 C ATOM 688 SG CYS X 48 43.598 2.633 25.504 1.00 5.98 S ATOM 734 N CYS X 51 38.525 4.088 25.616 1.00 5.96 N ATOM 735 CA CYS X 51 37.209 4.232 25.021 1.00 6.18 C ATOM 736 C CYS X 51 36.381 2.999 25.357 1.00 5.94 C ATOM 737 O CYS X 51 36.866 2.008 25.906 1.00 6.63 O ATOM 738 CB CYS X 51 37.245 4.495 23.514 1.00 6.07 C ATOM 739 SG CYS X 51 37.502 3.012 22.476 1.00 6.27 S ATOM 801 N CYS X 56 41.197 -2.946 25.932 1.00 6.08 N ATOM 802 CA CYS X 56 42.138 -3.527 25.009 1.00 6.07 C ATOM 803 C CYS X 56 43.396 -3.916 25.747 1.00 5.94 C ATOM 804 O CYS X 56 43.802 -3.243 26.704 1.00 7.17 O ATOM 805 CB CYS X 56 42.512 -2.569 23.889 1.00 6.66 C ATOM 806 SG CYS X 56 41.086 -2.294 22.740 1.00 6.50 S ATOM 1022 N CYS X 70 41.337 0.053 17.877 1.00 6.60 N ATOM 1023 CA CYS X 70 41.399 1.221 16.973 1.00 6.52 C ATOM 1024 C CYS X 70 42.679 1.255 16.144 1.00 6.45 C ATOM 1025 O CYS X 70 42.824 2.158 15.296 1.00 7.57 O ATOM 1026 CB CYS X 70 41.302 2.516 17.784 1.00 6.74 C ATOM 1027 SG CYS X 70 42.684 2.663 18.965 1.00 6.45 S HETATM 9499 FE1 SF4 X1001 39.663 2.346 22.723 1.00 6.06 FE HETATM 9500 FE2 SF4 X1001 42.157 2.138 23.788 1.00 5.97 FE HETATM 9501 FE3 SF4 X1001 41.050 0.016 22.600 1.00 6.18 FE HETATM 9502 FE4 SF4 X1001 41.899 2.128 21.073 1.00 6.14 FE HETATM 9503 S1 SF4 X1001 41.420 3.878 22.535 1.00 6.14 S HETATM 9504 S2 SF4 X1001 40.249 1.068 24.522 1.00 6.06 S HETATM 9505 S3 SF4 X1001 43.249 0.748 22.278 1.00 6.36 S HETATM 9506 S4 SF4 X1001 39.895 0.913 20.872 1.00 6.51 S ''', '4u9h_f3s_cys.pdb' : ''' CRYST1 66.530 97.950 125.850 90.00 90.00 90.00 P 21 21 21 SCALE1 0.015031 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007946 0.00000 ATOM 1 N CYS S 231 -40.840 -6.337 14.851 1.00 5.51 N ATOM 2 CA CYS S 231 -40.013 -5.494 14.018 1.00 5.50 C ATOM 3 C CYS S 231 -40.789 -4.444 13.235 1.00 5.59 C ATOM 4 O CYS S 231 -40.377 -3.294 13.181 1.00 6.08 O ATOM 5 CB CYS S 231 -39.137 -6.330 13.077 1.00 5.85 C ATOM 6 SG CYS S 231 -38.302 -7.647 14.022 1.00 5.36 S ATOM 7 H CYS S 231 -40.715 -7.176 14.722 1.00 8.43 H ATOM 8 HA CYS S 231 -39.406 -5.011 14.590 1.00 4.25 H ATOM 9 HB2 CYS S 231 -39.693 -6.723 12.387 1.00 8.29 H ATOM 10 HB3 CYS S 231 -38.460 -5.757 12.678 1.00 6.29 H ATOM 11 N CYS S 249 -36.838 -10.889 5.704 1.00 5.29 N ATOM 12 CA CYS S 249 -36.582 -11.388 7.062 1.00 5.34 C ATOM 13 C CYS S 249 -35.867 -12.738 6.948 1.00 5.19 C ATOM 14 O CYS S 249 -36.217 -13.566 6.098 1.00 5.72 O ATOM 15 CB CYS S 249 -37.959 -11.517 7.758 1.00 5.35 C ATOM 16 SG CYS S 249 -37.935 -12.287 9.420 1.00 5.03 S ATOM 17 H CYS S 249 -37.663 -10.835 5.492 1.00 6.38 H ATOM 18 HA CYS S 249 -36.025 -10.764 7.557 1.00 6.71 H ATOM 19 HB2 CYS S 249 -38.359 -10.636 7.819 1.00 7.35 H ATOM 20 HB3 CYS S 249 -38.524 -12.071 7.205 1.00 6.05 H ATOM 40 N CYS S 252 -34.737 -14.293 12.518 1.00 5.11 N ATOM 41 CA CYS S 252 -33.673 -14.292 13.509 1.00 4.88 C ATOM 42 C CYS S 252 -34.097 -14.398 14.968 1.00 5.08 C ATOM 43 O CYS S 252 -33.221 -14.580 15.827 1.00 5.63 O ATOM 44 CB CYS S 252 -32.706 -13.130 13.306 1.00 5.00 C ATOM 45 SG CYS S 252 -33.261 -11.513 13.953 1.00 5.02 S ATOM 46 H CYS S 252 -34.873 -13.554 12.121 1.00 4.62 H ATOM 47 HA CYS S 252 -33.162 -15.093 13.343 0.99 4.06 H ATOM 48 HB2 CYS S 252 -31.880 -13.344 13.777 1.00 5.77 H ATOM 49 HB3 CYS S 252 -32.490 -13.045 12.358 1.00 4.19 H TER HETATM 50 S1 F3S S1003 -37.373 -8.610 10.393 1.00 5.80 S HETATM 51 S2 F3S S1003 -34.483 -11.028 10.412 1.00 5.12 S HETATM 52 S3 F3S S1003 -37.067 -11.059 12.944 1.00 5.03 S HETATM 53 S4 F3S S1003 -34.752 -8.309 13.065 1.00 5.36 S HETATM 54 FE1 F3S S1003 -36.744 -10.733 10.683 1.00 4.93 Fe2+ HETATM 55 FE3 F3S S1003 -36.932 -8.794 12.568 1.00 5.27 Fe2+ HETATM 56 FE4 F3S S1003 -34.843 -10.514 12.587 1.00 4.74 Fe2+ END ''' } results = {'4udx_sf4.pdb' : [[722, 9714, 12002, 8287], [0,0,13,4], ], } def run(): fn = '4udx_sf4.pdb' f=open(fn, 'w') f.write(pdbs[fn]) f.close() for i, superpose in enumerate(['None', 'all']): cmd = 'phenix.geometry_minimization %s superpose_ideal=%s' % (fn, superpose, ) print(cmd) rc = easy_run.go(cmd) for line in rc.stdout_lines: #print line if line.find('bond_residual_sum')>-1: bond_value = round(float(line.split()[-1])) if line.find('angle_residual_sum')>-1: angle_value = round(float(line.split()[-1])) # in the second iteration bond_value and angle_value are expected to be 0! # assert bond_value, "%f %f" % (bond_value, results[fn][i][0]) # assert angle_value, angle_value assert bond_value==results[fn][i][0], 'not matching %s to %s' % ( bond_value, results[fn][i][0], ) assert angle_value==results[fn][i][1], 'not matching %s to %s' % ( angle_value, results[fn][i][1], ) for i, superpose in enumerate(['None', 'all']): cmd = 'phenix.pdb_interpretation %s superpose_ideal=%s' % (fn, superpose, ) print(cmd) rc = easy_run.go(cmd) for line in rc.stdout_lines: #print line if line.find('bond_residual_sum')>-1: value = round(float(line.split()[-1])) print('value',value) assert value==results[fn][i][2], 'not matching %s to %s' % ( value, results[fn][i][2], ) if line.find('angle_residual_sum')>-1: value = round(float(line.split()[-1])) print('value',value) assert value==results[fn][i][3], 'not matching %s to %s' % ( value, results[fn][i][3], ) from libtbx.test_utils import assert_lines_in_file fn = '4udx_sf4_cys.pdb' f=open(fn, 'w') f.write(pdbs[fn]) f.close() lines = [ 'Iron sulfur cluster coordination', 'SF4 X1001', 'pdb="FE1 SF4 X1001 " - pdb=" SG CYS X 51 "', 'pdb="FE4 SF4 X1001 " - pdb=" SG CYS X 70 "', 'pdb="FE3 SF4 X1001 " - pdb=" SG CYS X 56 "', 'pdb="FE2 SF4 X1001 " - pdb=" SG CYS X 48 "', ] cmd = 'phenix.pdb_interpretation %s link_all=True > %s.log' % (fn, fn) print(cmd) assert not easy_run.call(cmd) for line in lines: print(line) assert_lines_in_file(file_name='%s.log' % fn, lines=line) fn = '4u9h_f3s_cys.pdb' with open(fn, 'w') as f: f.write(pdbs[fn]) lines = [ 'Iron sulfur cluster coordination', 'F3S S1003', 'pdb="FE1 F3S S1003 " - pdb=" SG CYS S 249 "', 'pdb="FE3 F3S S1003 " - pdb=" SG CYS S 231 "', 'pdb="FE4 F3S S1003 " - pdb=" SG CYS S 252 "', ] cmd = 'phenix.pdb_interpretation %s link_all=True > %s.log' % (fn, fn) print(cmd) assert not easy_run.call(cmd) for line in lines: print(line) assert_lines_in_file(file_name='%s.log' % fn, lines=line) return 0 if __name__=="__main__": rc = run()#sys.argv[1]) assert rc==0