from __future__ import absolute_import, division, print_function pdb_string = ''' CRYST1 74.120 110.220 88.210 90.00 111.08 90.00 P 1 21 1 SCALE1 0.013492 0.000000 0.005201 0.00000 SCALE2 0.000000 0.009073 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012150 0.00000 ATOM 1 N MET A 18 15.215 -9.367 61.781 1.00 4.60 N ATOM 2 CA MET A 18 15.994 -9.639 60.573 1.00 4.33 C ATOM 3 C MET A 18 16.745 -8.406 60.090 1.00 4.51 C ATOM 4 O MET A 18 16.143 -7.509 59.515 1.00 4.82 O ATOM 5 CB MET A 18 15.126 -10.183 59.422 1.00 4.76 C ATOM 6 CG MET A 18 14.343 -11.416 59.813 1.00 5.58 C ATOM 7 SD MET A 18 13.572 -12.228 58.401 1.00 6.39 S ATOM 8 CE MET A 18 14.906 -13.295 57.886 1.00 6.54 C ATOM 9 N PRO A 19 18.064 -8.360 60.319 1.00 5.05 N ATOM 10 CA PRO A 19 18.906 -7.408 59.619 1.00 5.21 C ATOM 11 C PRO A 19 19.235 -7.982 58.236 1.00 5.15 C ATOM 12 O PRO A 19 19.074 -9.179 58.005 1.00 5.57 O ATOM 13 CB PRO A 19 20.167 -7.364 60.481 1.00 5.61 C ATOM 14 CG PRO A 19 20.273 -8.777 60.996 1.00 5.96 C ATOM 15 CD PRO A 19 18.864 -9.259 61.175 1.00 5.46 C ATOM 16 N GLY A 20 19.718 -7.162 57.313 1.00 5.38 N ATOM 17 CA GLY A 20 20.123 -7.718 56.021 1.00 5.56 C ATOM 18 C GLY A 20 21.352 -8.618 56.134 1.00 5.51 C ATOM 19 O GLY A 20 21.447 -9.635 55.447 1.00 6.08 O ATOM 20 N MET A 45 23.492 -17.747 55.646 1.00 5.92 N ATOM 21 CA MET A 45 22.469 -16.820 56.107 1.00 5.49 C ATOM 22 C MET A 45 22.107 -17.166 57.544 1.00 5.48 C ATOM 23 O MET A 45 21.090 -17.797 57.833 1.00 6.28 O ATOM 24 CB MET A 45 21.247 -16.804 55.194 1.00 5.38 C ATOM 25 CG MET A 45 20.401 -15.567 55.446 1.00 6.08 C ATOM 26 SD MET A 45 21.221 -13.984 55.142 1.00 6.66 S ATOM 27 CE MET A 45 21.440 -13.998 53.389 1.00 10.50 C ATOM 28 N AMET A 60 17.784 -13.489 62.293 0.50 4.96 N ATOM 29 CA AMET A 60 18.366 -14.113 61.111 0.50 4.63 C ATOM 30 C AMET A 60 18.517 -13.083 60.009 0.50 4.62 C ATOM 31 O AMET A 60 17.645 -12.235 59.816 0.50 5.04 O ATOM 32 CB AMET A 60 17.486 -15.268 60.628 0.50 5.40 C ATOM 33 CG AMET A 60 18.030 -15.953 59.379 0.50 5.79 C ATOM 34 SD AMET A 60 17.293 -17.563 59.033 0.50 8.88 S ATOM 35 CE AMET A 60 15.691 -17.103 58.425 0.50 9.84 C ATOM 36 N BMET A 60 17.808 -13.468 62.300 0.50 4.99 N ATOM 37 CA BMET A 60 18.372 -14.103 61.122 0.50 4.66 C ATOM 38 C BMET A 60 18.520 -13.079 60.013 0.50 4.61 C ATOM 39 O BMET A 60 17.651 -12.228 59.822 0.50 5.05 O ATOM 40 CB BMET A 60 17.463 -15.242 60.671 0.50 5.34 C ATOM 41 CG BMET A 60 17.993 -16.000 59.469 0.50 5.73 C ATOM 42 SD BMET A 60 16.961 -17.415 59.051 0.50 7.74 S ATOM 43 CE BMET A 60 17.480 -17.628 57.356 0.50 6.86 C ATOM 44 N GLY A 61 19.623 -13.141 59.279 1.00 4.61 N ATOM 45 CA GLY A 61 19.790 -12.275 58.124 1.00 4.53 C ATOM 46 C GLY A 61 18.763 -12.558 57.033 1.00 4.33 C ATOM 47 O GLY A 61 18.268 -13.677 56.885 1.00 4.88 O ATOM 48 N HIS A 62 18.445 -11.511 56.263 1.00 4.67 N ATOM 49 CA HIS A 62 17.535 -11.671 55.130 1.00 4.67 C ATOM 50 C HIS A 62 18.172 -11.460 53.753 1.00 4.62 C ATOM 51 O HIS A 62 17.509 -11.713 52.751 1.00 5.66 O ATOM 52 CB HIS A 62 16.245 -10.808 55.263 1.00 5.00 C ATOM 53 CG HIS A 62 16.453 -9.324 55.365 1.00 5.03 C ATOM 54 ND1 HIS A 62 17.096 -8.584 54.399 1.00 5.27 N ATOM 55 CD2 HIS A 62 15.999 -8.429 56.281 1.00 5.73 C ATOM 56 CE1 HIS A 62 17.081 -7.304 54.759 1.00 5.40 C ATOM 57 NE2 HIS A 62 16.409 -7.182 55.884 1.00 5.91 N ATOM 58 N GLY A 63 19.414 -10.999 53.682 1.00 4.54 N ATOM 59 CA GLY A 63 20.077 -10.720 52.424 1.00 5.11 C ATOM 60 C GLY A 63 19.597 -9.432 51.792 1.00 5.28 C ATOM 61 O GLY A 63 18.676 -8.784 52.268 1.00 10.32 O ATOM 62 N MET A 64 20.188 -9.032 50.690 1.00 4.88 N ATOM 63 CA MET A 64 19.875 -7.722 50.110 1.00 4.61 C ATOM 64 C MET A 64 18.802 -7.851 49.034 1.00 4.01 C ATOM 65 O MET A 64 18.950 -8.608 48.072 1.00 5.02 O ATOM 66 CB MET A 64 21.123 -7.109 49.485 1.00 5.88 C ATOM 67 CG MET A 64 22.189 -6.837 50.547 1.00 7.27 C ATOM 68 SD MET A 64 23.536 -5.778 50.026 1.00 10.02 S ATOM 69 CE MET A 64 24.268 -6.809 48.769 1.00 9.52 C ATOM 70 N SER A 68 15.441 -11.601 47.812 1.00 3.72 N ATOM 71 CA SER A 68 16.098 -12.378 48.866 1.00 4.05 C ATOM 72 C SER A 68 15.232 -12.433 50.117 1.00 4.18 C ATOM 73 O SER A 68 14.960 -13.517 50.652 1.00 4.38 O ATOM 74 CB SER A 68 17.456 -11.763 49.191 1.00 4.18 C ATOM 75 OG SER A 68 18.137 -12.530 50.159 1.00 5.33 O ATOM 76 N CYS A 69 14.801 -11.268 50.599 1.00 4.15 N ATOM 77 CA CYS A 69 14.051 -11.277 51.835 1.00 4.21 C ATOM 78 C CYS A 69 12.676 -11.926 51.689 1.00 3.95 C ATOM 79 O CYS A 69 12.147 -12.460 52.674 1.00 5.01 O ATOM 80 CB CYS A 69 13.942 -9.887 52.432 1.00 4.97 C ATOM 81 SG CYS A 69 12.884 -8.739 51.550 1.00 5.68 S ATOM 82 N TYR A 72 13.108 -15.718 52.476 1.00 4.39 N ATOM 83 CA TYR A 72 13.265 -16.077 53.880 1.00 4.87 C ATOM 84 C TYR A 72 12.019 -15.828 54.678 1.00 4.47 C ATOM 85 O TYR A 72 11.644 -16.649 55.510 1.00 5.33 O ATOM 86 CB TYR A 72 14.470 -15.353 54.494 1.00 5.22 C ATOM 87 CG TYR A 72 15.777 -15.839 53.953 1.00 5.47 C ATOM 88 CD1 TYR A 72 16.251 -17.119 54.274 1.00 6.76 C ATOM 89 CD2 TYR A 72 16.537 -15.067 53.084 1.00 6.32 C ATOM 90 CE1 TYR A 72 17.428 -17.590 53.743 1.00 7.24 C ATOM 91 CE2 TYR A 72 17.727 -15.532 52.569 1.00 7.02 C ATOM 92 CZ TYR A 72 18.173 -16.793 52.898 1.00 6.65 C ATOM 93 OH TYR A 72 19.366 -17.214 52.363 1.00 8.74 O ATOM 94 N ARG A 87 12.058 -6.379 60.531 1.00 4.03 N ATOM 95 CA ARG A 87 13.280 -6.007 59.840 1.00 4.44 C ATOM 96 C ARG A 87 13.927 -4.837 60.581 1.00 4.37 C ATOM 97 O ARG A 87 13.242 -3.890 60.978 1.00 4.52 O ATOM 98 CB ARG A 87 13.005 -5.622 58.385 1.00 4.97 C ATOM 99 CG ARG A 87 14.195 -4.965 57.708 1.00 5.40 C ATOM 100 CD ARG A 87 13.976 -4.770 56.203 1.00 5.93 C ATOM 101 NE ARG A 87 14.676 -3.589 55.713 1.00 6.34 N ATOM 102 CZ ARG A 87 15.987 -3.377 55.798 1.00 5.76 C ATOM 103 NH1 ARG A 87 16.787 -4.315 56.242 1.00 6.21 N ATOM 104 NH2 ARG A 87 16.487 -2.207 55.442 1.00 6.66 N ATOM 105 N GLU A 181 13.993 -3.488 51.085 1.00 4.28 N ATOM 106 CA GLU A 181 13.274 -4.704 51.468 1.00 4.20 C ATOM 107 C GLU A 181 11.842 -4.541 51.980 1.00 3.76 C ATOM 108 O GLU A 181 11.044 -5.466 51.776 1.00 4.13 O ATOM 109 CB GLU A 181 14.066 -5.476 52.519 1.00 4.85 C ATOM 110 CG GLU A 181 15.375 -6.034 51.998 1.00 5.84 C ATOM 111 CD GLU A 181 16.565 -5.108 52.105 1.00 5.87 C ATOM 112 OE1 GLU A 181 17.620 -5.461 51.537 1.00 6.33 O ATOM 113 OE2 GLU A 181 16.481 -4.053 52.751 1.00 7.97 O ATOM 114 N ILE A 185 8.764 -7.518 52.166 1.00 4.11 N ATOM 115 CA ILE A 185 8.380 -8.207 53.399 1.00 4.15 C ATOM 116 C ILE A 185 6.887 -7.955 53.683 1.00 3.80 C ATOM 117 O ILE A 185 6.158 -8.888 54.046 1.00 4.10 O ATOM 118 CB ILE A 185 9.244 -7.743 54.571 1.00 4.79 C ATOM 119 CG1 ILE A 185 10.711 -8.123 54.320 1.00 5.83 C ATOM 120 CG2 ILE A 185 8.742 -8.362 55.870 1.00 5.63 C ATOM 121 CD1 ILE A 185 11.673 -7.661 55.373 1.00 6.69 C TER HETATM 122 C1 AGOL A 301 19.343 -2.253 53.379 0.25 11.18 C HETATM 123 C2 AGOL A 301 19.099 -3.727 53.183 0.25 10.86 C HETATM 124 C3 AGOL A 301 19.755 -4.689 54.142 0.25 11.90 C HETATM 125 O1 AGOL A 301 18.265 -1.622 52.704 0.25 8.81 O HETATM 126 O2 AGOL A 301 19.693 -4.136 51.959 0.25 8.60 O HETATM 127 O3 AGOL A 301 20.239 -5.795 53.373 0.25 7.42 O HETATM 128 C1 BGOL A 301 21.418 -2.460 54.579 0.25 14.24 C HETATM 129 C2 BGOL A 301 21.388 -3.327 55.820 0.25 13.76 C HETATM 130 C3 BGOL A 301 19.940 -3.430 56.209 0.25 9.95 C HETATM 131 O1 BGOL A 301 21.378 -3.406 53.502 0.25 10.70 O HETATM 132 O2 BGOL A 301 21.860 -4.628 55.469 0.25 11.34 O HETATM 133 O3 BGOL A 301 19.286 -2.256 55.666 0.25 5.65 O HETATM 134 C1 CGOL A 301 22.179 -2.132 55.772 0.50 11.93 C HETATM 135 C2 CGOL A 301 21.418 -3.361 55.236 0.50 11.64 C HETATM 136 C3 CGOL A 301 20.007 -3.217 55.753 0.50 12.10 C HETATM 137 O1 CGOL A 301 23.559 -2.106 55.373 0.50 16.86 O HETATM 138 O2 CGOL A 301 21.976 -4.600 55.688 0.50 12.26 O HETATM 139 O3 CGOL A 301 19.681 -4.230 56.700 0.50 8.36 O HETATM 140 O HOH A 422 20.632 -13.536 49.381 1.00 16.15 O END ''' import time from libtbx import easy_run def main(run_mopac=None): try: run_mopac=int(run_mopac) except Exception: run_mopac=True preamble = 'tst_flipping_his' selection = 'chain A and resid 62 and resname HIS' f=open('%s.pdb' % preamble, 'w') f.write(pdb_string) del f cmd = 'phenix.ready_set %(preamble)s.pdb' % locals() print('\n ~> %s' % cmd) rc = easy_run.go(cmd) assert rc.return_code==0 cmd = 'mmtbx.quantum_interface %(preamble)s.pdb' % locals() print('\n ~> %s' % cmd) rc = easy_run.go(cmd) assert rc.return_code cmd = 'mmtbx.quantum_interface %(preamble)s.updated.pdb write_qmr_phil=1 qi.selection="%(selection)s"' % locals() cmd += ' format=quantum_interface' print('\n ~> %s' % cmd) rc = easy_run.go(cmd) assert rc.return_code==0 t0=time.time() cmd = 'mmtbx.quantum_interface %(preamble)s.updated.pdb run_qmr=True %(preamble)s.updated_A_62_HIS.phil' % locals() cmd += ' iterate_histidine=True only_i=1' if type(run_mopac)==type(1): cmd += ' qi.nproc=%d' % run_mopac print('\n ~> %s' % cmd) if run_mopac: rc = easy_run.go(cmd) print('Time : %0.fs' % (time.time()-t0)) assert rc.return_code==0 print('DONE') if __name__ == '__main__': import sys main(*tuple(sys.argv[1:]))