from __future__ import division from libtbx import easy_run pdb = ''' ATOM 1 P C A 1 0.226 -10.894 0.425 1.00 76.88 P ATOM 2 OP1 C A 1 0.482 -11.761 1.602 1.00 78.59 O ATOM 3 OP2 C A 1 -0.746 -9.788 0.472 1.00 75.20 O ATOM 4 O5' C A 1 1.619 -10.251 -0.015 1.00 78.76 O ATOM 5 C5' C A 1 2.889 -10.871 0.240 1.00 77.93 C ATOM 6 C4' C A 1 4.016 -9.909 -0.104 1.00 78.66 C ATOM 7 O4' C A 1 3.904 -9.426 -1.486 1.00 79.49 O ATOM 8 C3' C A 1 4.077 -8.641 0.739 1.00 78.23 C ATOM 9 O3' C A 1 4.714 -8.922 1.993 1.00 77.17 O ATOM 10 C2' C A 1 4.872 -7.722 -0.207 1.00 79.34 C ATOM 11 O2' C A 1 6.269 -7.992 -0.276 1.00 79.34 O ATOM 12 C1' C A 1 4.252 -8.053 -1.569 1.00 78.22 C ATOM 13 N1 C A 1 3.007 -7.180 -1.992 1.00 20.00 N ATOM 14 C2 C A 1 3.150 -5.813 -2.248 1.00 20.00 C ATOM 15 N3 C A 1 2.064 -5.098 -2.618 1.00 20.00 N ATOM 16 C4 C A 1 0.877 -5.697 -2.729 1.00 20.00 C ATOM 17 C5 C A 1 0.707 -7.085 -2.458 1.00 20.00 C ATOM 18 C6 C A 1 1.784 -7.778 -2.098 1.00 20.00 C ATOM 19 O2 C A 1 4.275 -5.294 -2.125 1.00 20.00 O ATOM 20 N4 C A 1 -0.163 -4.952 -3.107 1.00 20.00 N ATOM 21 P G A 2 4.132 -8.090 3.235 1.00 76.88 P ATOM 22 OP1 G A 2 4.816 -8.681 4.412 1.00 78.59 O ATOM 23 OP2 G A 2 2.717 -7.684 3.282 1.00 75.20 O ATOM 24 O5' G A 2 4.957 -6.796 2.795 1.00 78.76 O ATOM 25 C5' G A 2 6.360 -6.632 3.050 1.00 77.93 C ATOM 26 C4' G A 2 6.789 -5.214 2.706 1.00 78.66 C ATOM 27 O4' G A 2 6.434 -4.868 1.324 1.00 79.49 O ATOM 28 C3' G A 2 6.156 -4.114 3.549 1.00 78.23 C ATOM 29 O3' G A 2 6.843 -4.006 4.803 1.00 77.17 O ATOM 30 C2' G A 2 6.328 -2.911 2.603 1.00 79.34 C ATOM 31 O2' G A 2 7.650 -2.383 2.534 1.00 79.34 O ATOM 32 C1' G A 2 5.985 -3.524 1.241 1.00 78.22 C ATOM 33 N9 G A 2 4.566 -3.455 0.848 1.00 20.00 N ATOM 34 C8 G A 2 3.693 -4.506 0.681 1.00 20.00 C ATOM 35 N7 G A 2 2.484 -4.139 0.318 1.00 20.00 N ATOM 36 C5 G A 2 2.545 -2.754 0.231 1.00 20.00 C ATOM 37 C4 G A 2 3.812 -2.311 0.556 1.00 20.00 C ATOM 38 N1 G A 2 2.016 -0.497 -0.062 1.00 20.00 N ATOM 39 C2 G A 2 3.298 -0.143 0.266 1.00 20.00 C ATOM 40 N3 G A 2 4.242 -1.013 0.586 1.00 20.00 N ATOM 41 C6 G A 2 1.539 -1.808 -0.102 1.00 20.00 C ATOM 42 O6 G A 2 0.354 -2.021 -0.408 1.00 20.00 O ATOM 43 N2 G A 2 3.585 1.155 0.252 1.00 20.00 N ATOM 44 P A A 3 5.904 -3.620 6.045 1.00 76.88 P ATOM 45 OP1 A A 3 6.799 -3.748 7.222 1.00 78.59 O ATOM 46 OP2 A A 3 4.494 -4.043 6.092 1.00 75.20 O ATOM 47 O5' A A 3 5.899 -2.086 5.605 1.00 78.76 O ATOM 48 C5' A A 3 6.991 -1.189 5.860 1.00 77.93 C ATOM 49 C4' A A 3 6.586 0.236 5.516 1.00 78.66 C ATOM 50 O4' A A 3 6.100 0.335 4.134 1.00 79.49 O ATOM 51 C3' A A 3 5.459 0.819 6.359 1.00 78.23 C ATOM 52 O3' A A 3 5.979 1.282 7.613 1.00 77.17 O ATOM 53 C2' A A 3 4.954 1.925 5.413 1.00 79.34 C ATOM 54 O2' A A 3 5.781 3.083 5.344 1.00 79.34 O ATOM 55 C1' A A 3 4.997 1.223 4.051 1.00 78.22 C ATOM 56 N9 A A 3 3.745 0.511 3.653 1.00 20.00 N ATOM 57 C8 A A 3 3.592 -0.836 3.491 1.00 20.00 C ATOM 58 N7 A A 3 2.386 -1.187 3.127 1.00 20.00 N ATOM 59 C5 A A 3 1.698 0.009 3.047 1.00 20.00 C ATOM 60 C4 A A 3 2.524 1.076 3.368 1.00 20.00 C ATOM 61 N1 A A 3 -0.009 1.601 2.733 1.00 20.00 N ATOM 62 C2 A A 3 0.899 2.529 3.062 1.00 20.00 C ATOM 63 N3 A A 3 2.181 2.373 3.392 1.00 20.00 N ATOM 64 C6 A A 3 0.372 0.307 2.716 1.00 20.00 C ATOM 65 N6 A A 3 -0.525 -0.629 2.388 1.00 20.00 N ATOM 66 P A B 1 -10.978 -1.171 1.417 1.00 76.88 P ATOM 67 OP1 A B 1 -11.872 -1.039 0.240 1.00 78.59 O ATOM 68 OP2 A B 1 -9.746 -1.977 1.370 1.00 75.20 O ATOM 69 O5' A B 1 -10.538 0.299 1.857 1.00 78.76 O ATOM 70 C5' A B 1 -11.330 1.469 1.602 1.00 77.93 C ATOM 71 C4' A B 1 -10.536 2.720 1.946 1.00 78.66 C ATOM 72 O4' A B 1 -10.043 2.677 3.328 1.00 79.49 O ATOM 73 C3' A B 1 -9.290 2.959 1.103 1.00 78.23 C ATOM 74 O3' A B 1 -9.658 3.550 -0.151 1.00 77.17 O ATOM 75 C2' A B 1 -8.492 3.875 2.049 1.00 79.34 C ATOM 76 O2' A B 1 -8.956 5.220 2.118 1.00 79.34 O ATOM 77 C1' A B 1 -8.732 3.215 3.411 1.00 78.22 C ATOM 78 N9 A B 1 -7.735 2.176 3.810 1.00 20.00 N ATOM 79 C8 A B 1 -7.971 0.841 3.972 1.00 20.00 C ATOM 80 N7 A B 1 -6.914 0.162 4.336 1.00 20.00 N ATOM 81 C5 A B 1 -5.915 1.113 4.416 1.00 20.00 C ATOM 82 C4 A B 1 -6.403 2.371 4.095 1.00 20.00 C ATOM 83 N1 A B 1 -3.825 2.154 4.730 1.00 20.00 N ATOM 84 C2 A B 1 -4.432 3.302 4.401 1.00 20.00 C ATOM 85 N3 A B 1 -5.706 3.517 4.071 1.00 20.00 N ATOM 86 C6 A B 1 -4.559 1.022 4.747 1.00 20.00 C ATOM 87 N6 A B 1 -3.964 -0.130 5.075 1.00 20.00 N ATOM 88 P U B 2 -8.752 3.091 -1.393 1.00 76.88 P ATOM 89 OP1 U B 2 -9.433 3.685 -2.570 1.00 78.59 O ATOM 90 OP2 U B 2 -8.151 1.747 -1.440 1.00 75.20 O ATOM 91 O5' U B 2 -7.587 4.090 -0.953 1.00 78.76 O ATOM 92 C5' U B 2 -7.622 5.503 -1.208 1.00 77.93 C ATOM 93 C4' U B 2 -6.279 6.127 -0.864 1.00 78.66 C ATOM 94 O4' U B 2 -5.886 5.824 0.518 1.00 79.49 O ATOM 95 C3' U B 2 -5.100 5.654 -1.707 1.00 78.23 C ATOM 96 O3' U B 2 -5.091 6.351 -2.961 1.00 77.17 O ATOM 97 C2' U B 2 -3.934 5.995 -0.761 1.00 79.34 C ATOM 98 O2' U B 2 -3.598 7.377 -0.692 1.00 79.34 O ATOM 99 C1' U B 2 -4.493 5.569 0.601 1.00 78.22 C ATOM 100 N1 U B 2 -4.200 4.068 1.024 1.00 20.00 N ATOM 101 C2 U B 2 -2.904 3.668 1.275 1.00 20.00 C ATOM 102 N3 U B 2 -2.757 2.346 1.647 1.00 20.00 N ATOM 103 C4 U B 2 -3.761 1.415 1.783 1.00 20.00 C ATOM 104 C5 U B 2 -5.081 1.922 1.496 1.00 20.00 C ATOM 105 C6 U B 2 -5.264 3.207 1.136 1.00 20.00 C ATOM 106 O2 U B 2 -1.952 4.421 1.179 1.00 20.00 O ATOM 107 O4 U B 2 -3.505 0.253 2.122 1.00 20.00 O ATOM 108 P C B 3 -4.576 5.475 -4.203 1.00 76.88 P ATOM 109 OP1 C B 3 -4.829 6.343 -5.380 1.00 78.59 O ATOM 110 OP2 C B 3 -4.796 4.019 -4.250 1.00 75.20 O ATOM 111 O5' C B 3 -3.056 5.687 -3.763 1.00 78.76 O ATOM 112 C5' C B 3 -2.323 6.894 -4.018 1.00 77.93 C ATOM 113 C4' C B 3 -0.855 6.694 -3.674 1.00 78.66 C ATOM 114 O4' C B 3 -0.688 6.227 -2.292 1.00 79.49 O ATOM 115 C3' C B 3 -0.118 5.660 -4.517 1.00 78.23 C ATOM 116 O3' C B 3 0.266 6.240 -5.771 1.00 77.17 O ATOM 117 C2' C B 3 1.047 5.316 -3.571 1.00 79.34 C ATOM 118 O2' C B 3 2.077 6.298 -3.502 1.00 79.34 O ATOM 119 C1' C B 3 0.347 5.259 -2.209 1.00 78.22 C ATOM 120 N1 C B 3 -0.229 3.852 -1.785 1.00 20.00 N ATOM 121 C2 C B 3 0.630 2.778 -1.530 1.00 20.00 C ATOM 122 N3 C B 3 0.102 1.591 -1.159 1.00 20.00 N ATOM 123 C4 C B 3 -1.221 1.453 -1.048 1.00 20.00 C ATOM 124 C5 C B 3 -2.113 2.530 -1.319 1.00 20.00 C ATOM 125 C6 C B 3 -1.581 3.694 -1.679 1.00 20.00 C ATOM 126 O2 C B 3 1.856 2.950 -1.652 1.00 20.00 O ATOM 127 N4 C B 3 -1.693 0.265 -0.670 1.00 20.00 N ATOM 128 P G B 4 0.226 5.226 -7.013 1.00 76.88 P ATOM 129 OP1 G B 4 0.482 6.093 -8.190 1.00 78.59 O ATOM 130 OP2 G B 4 -0.746 4.120 -7.060 1.00 75.20 O ATOM 131 O5' G B 4 1.619 4.583 -6.573 1.00 78.76 O ATOM 132 C5' G B 4 2.889 5.203 -6.828 1.00 77.93 C ATOM 133 C4' G B 4 4.016 4.241 -6.484 1.00 78.66 C ATOM 134 O4' G B 4 3.904 3.758 -5.102 1.00 79.49 O ATOM 135 C3' G B 4 4.077 2.973 -7.327 1.00 78.23 C ATOM 136 O3' G B 4 4.714 3.254 -8.581 1.00 77.17 O ATOM 137 C2' G B 4 4.872 2.054 -6.381 1.00 79.34 C ATOM 138 O2' G B 4 6.269 2.324 -6.312 1.00 79.34 O ATOM 139 C1' G B 4 4.252 2.385 -5.019 1.00 78.22 C ATOM 140 N9 G B 4 3.095 1.560 -4.626 1.00 20.00 N ATOM 141 C8 G B 4 1.793 1.973 -4.459 1.00 20.00 C ATOM 142 N7 G B 4 0.973 1.011 -4.096 1.00 20.00 N ATOM 143 C5 G B 4 1.773 -0.122 -4.009 1.00 20.00 C ATOM 144 C4 G B 4 3.079 0.190 -4.334 1.00 20.00 C ATOM 145 N1 G B 4 2.547 -2.307 -3.716 1.00 20.00 N ATOM 146 C2 G B 4 3.817 -1.912 -4.044 1.00 20.00 C ATOM 147 N3 G B 4 4.142 -0.670 -4.364 1.00 20.00 N ATOM 148 C6 G B 4 1.437 -1.461 -3.676 1.00 20.00 C ATOM 149 O6 G B 4 0.325 -1.922 -3.370 1.00 20.00 O ATOM 150 N2 G B 4 4.760 -2.849 -4.030 1.00 20.00 N ''' std_asserts = [ [ 'enable = 0', 'esd = *phenix csd', ], [ 'enable = 0', 'esd = phenix *csd', ], [ 'enable = 1', 'esd = *phenix csd', ], [ 'enable = 1', 'esd = phenix *csd', ], ] geo_asserts = [] geo_asserts.append( ['''bond pdb=" P G A 2 " pdb=" OP1 G A 2 " ideal model delta sigma weight residual 1.485 1.484 0.001 2.00e-02 2.50e+03 2.16e-03''', '''angle pdb=" O3' C B 3 " pdb=" P G B 4 " pdb=" O5' G B 4 " ideal model delta sigma weight residual 104.00 91.11 12.89 1.50e+00 4.44e-01 7.38e+01''', ]) geo_asserts.append(geo_asserts[0]) geo_asserts.append( ['''bond pdb=" P G A 2 " pdb=" OP1 G A 2 " ideal model delta sigma weight residual 1.484 1.484 -0.000 2.00e-02 2.50e+03 1.25e-05''', '''angle pdb=" O3' C B 3 " pdb=" P G B 4 " pdb=" O5' G B 4 " ideal model delta sigma weight residual 104.20 91.11 13.09 1.50e+00 4.44e-01 7.61e+01''', ]) geo_asserts.append( ['''bond pdb=" P G A 2 " pdb=" OP1 G A 2 " ideal model delta sigma weight residual 1.484 1.484 -0.000 1.20e-02 6.94e+03 3.48e-05''', '''angle pdb=" O3' C B 3 " pdb=" P G B 4 " pdb=" O5' G B 4 " ideal model delta sigma weight residual 104.20 91.11 13.09 1.50e+00 4.44e-01 7.61e+01''', ]) restraintlib_installed=True try: from restraintlib import launcher # special import from restraintlib.printer import TuplePrinter # special import from restraintlib.restraints import analyze_pdb_hierarhy # special import except ImportError as e: restraintlib_installed = False def main(): i=0 filename = 'cdl_nucleotide.pdb' with open(filename, 'w') as f: f.write(pdb) for param1 in range(2): if param1 and not restraintlib_installed: break for param2 in ['phenix', 'csd']: cmd = 'phenix.pdb_interpretation %s write_geo=True cdl_nucleotides.enable=%s cdl_nucleotides.esd=%s' % ( filename, param1, param2, ) cmd += ' cdl_nucleotides.factor=1.' print(i, param1, param2, cmd) rc = easy_run.go(cmd) lines=[] for line in rc.stdout_lines: lines.append(line.strip()) for line in std_asserts[i]: assert line in lines, 'missing %s' % line with open('%s.geo' % filename, 'r') as f: lines=f.read() for line in geo_asserts[i]: assert lines.find(line)>-1, 'missing %s' % line i+=1 print('OK') print('OK') if __name__ == '__main__': main()