from __future__ import absolute_import, division, print_function import sys from six.moves import cStringIO as StringIO from libtbx import easy_run import iotbx.pdb pdbs = { "ASP" : """ ATOM 1 N ASP L 1 55.410 -0.618 -1.595 1.00 33.13 N ATOM 2 CA ASP L 1 55.727 -2.042 -1.664 1.00 50.61 C ATOM 3 C ASP L 1 56.021 -2.621 -0.277 1.00 42.48 C ATOM 4 O ASP L 1 56.306 -1.887 0.661 1.00 36.07 O ATOM 5 CB ASP L 1 56.856 -2.319 -2.677 1.00 50.51 C ATOM 6 CG ASP L 1 58.182 -1.647 -2.310 1.00 51.45 C ATOM 7 OD1 ASP L 1 59.243 -2.181 -2.696 1.00 52.89 O ATOM 8 OD2 ASP L 1 58.188 -0.585 -1.659 1.00 51.81 O ATOM 9 H1 ASP L 1 55.244 -0.311 -2.414 1.00 33.13 H ATOM 10 H2 ASP L 1 54.692 -0.498 -1.082 1.00 33.13 H ATOM 11 H3 ASP L 1 56.100 -0.177 -1.247 1.00 33.13 H ATOM 12 HA ASP L 1 54.941 -2.506 -1.993 1.00 50.61 H ATOM 13 HB2 ASP L 1 56.994 -3.277 -2.743 1.00 50.51 H ATOM 14 HB3 ASP L 1 56.577 -2.012 -3.554 1.00 50.51 H """, "GLU" : """ ATOM 1691 N GLU B 1 -45.832-106.231 -7.917 1.00 56.97 N ATOM 1692 CA GLU B 1 -45.794-105.198 -8.995 1.00 52.47 C ATOM 1693 C GLU B 1 -45.700-103.803 -8.381 1.00 46.38 C ATOM 1694 O GLU B 1 -46.454-103.456 -7.470 1.00 44.22 O ATOM 1695 CB GLU B 1 -47.033-105.306 -9.893 1.00 63.38 C ATOM 1696 CG GLU B 1 -46.783-104.967 -11.365 1.00 61.17 C ATOM 1697 CD GLU B 1 -46.547-103.486 -11.609 1.00 56.72 C ATOM 1698 OE1 GLU B 1 -46.005-103.137 -12.680 1.00 64.27 O ATOM 1699 OE2 GLU B 1 -46.904-102.668 -10.735 1.00 57.61 O ATOM 1700 H1 GLU B 1 -46.103-107.006 -8.258 1.00 68.38 H ATOM 1701 H2 GLU B 1 -45.018-106.327 -7.570 1.00 68.38 H ATOM 1702 H3 GLU B 1 -46.397-105.973 -7.279 1.00 68.38 H ATOM 1703 HA GLU B 1 -45.009-105.340 -9.546 1.00 62.98 H ATOM 1704 HB2 GLU B 1 -47.366-106.216 -9.853 1.00 76.07 H ATOM 1705 HB3 GLU B 1 -47.710-104.695 -9.561 1.00 76.07 H ATOM 1706 HG2 GLU B 1 -45.998-105.449 -11.670 1.00 73.41 H ATOM 1707 HG3 GLU B 1 -47.557-105.235 -11.885 1.00 73.41 H """, "PHE" : """ ATOM 1206 N PHE L 83 77.038 -23.401 3.393 1.00 55.55 N ATOM 1207 CA PHE L 83 77.649 -22.073 3.419 1.00 53.48 C ATOM 1208 C PHE L 83 77.083 -21.233 2.280 1.00 48.61 C ATOM 1209 O PHE L 83 77.325 -21.514 1.106 1.00 54.11 O ATOM 1210 CB PHE L 83 79.177 -22.165 3.306 1.00 55.82 C ATOM 1211 CG PHE L 83 79.833 -20.881 2.882 1.00 60.50 C ATOM 1212 CD1 PHE L 83 80.317 -20.728 1.593 1.00 64.71 C ATOM 1213 CD2 PHE L 83 79.954 -19.821 3.767 1.00 65.07 C ATOM 1214 CE1 PHE L 83 80.912 -19.543 1.196 1.00 68.67 C ATOM 1215 CE2 PHE L 83 80.549 -18.634 3.373 1.00 68.71 C ATOM 1216 CZ PHE L 83 81.028 -18.497 2.086 1.00 69.85 C ATOM 1217 H PHE L 83 77.591 -24.047 3.262 1.00 55.55 H ATOM 1218 HA PHE L 83 77.440 -21.651 4.267 1.00 53.48 H ATOM 1219 HB2 PHE L 83 79.540 -22.436 4.163 1.00 55.82 H ATOM 1220 HB3 PHE L 83 79.404 -22.860 2.669 1.00 55.82 H ATOM 1221 HD1 PHE L 83 80.241 -21.430 0.987 1.00 64.71 H ATOM 1222 HD2 PHE L 83 79.632 -19.908 4.635 1.00 65.07 H ATOM 1223 HE1 PHE L 83 81.234 -19.453 0.328 1.00 68.67 H ATOM 1224 HE2 PHE L 83 80.626 -17.930 3.975 1.00 68.71 H ATOM 1225 HZ PHE L 83 81.428 -17.701 1.820 1.00 69.85 H """, "TYR" : """ ATOM 1271 N TYR L 87 67.948 -15.639 0.990 1.00 39.05 N ATOM 1272 CA TYR L 87 66.992 -14.569 0.769 1.00 35.23 C ATOM 1273 C TYR L 87 65.567 -15.103 0.846 1.00 35.65 C ATOM 1274 O TYR L 87 65.270 -16.177 0.327 1.00 40.62 O ATOM 1275 CB TYR L 87 67.220 -13.932 -0.604 1.00 33.62 C ATOM 1276 CG TYR L 87 68.586 -13.316 -0.803 1.00 33.61 C ATOM 1277 CD1 TYR L 87 68.792 -11.955 -0.608 1.00 30.41 C ATOM 1278 CD2 TYR L 87 69.669 -14.092 -1.206 1.00 36.13 C ATOM 1279 CE1 TYR L 87 70.042 -11.388 -0.799 1.00 36.04 C ATOM 1280 CE2 TYR L 87 70.920 -13.529 -1.399 1.00 38.98 C ATOM 1281 CZ TYR L 87 71.099 -12.181 -1.194 1.00 40.09 C ATOM 1282 OH TYR L 87 72.345 -11.628 -1.387 1.00 41.66 O ATOM 1283 H TYR L 87 67.946 -16.244 0.379 1.00 39.05 H ATOM 1284 HA TYR L 87 67.119 -13.901 1.460 1.00 35.23 H ATOM 1285 HB2 TYR L 87 67.082 -14.608 -1.286 1.00 33.62 H ATOM 1286 HB3 TYR L 87 66.548 -13.247 -0.744 1.00 33.62 H ATOM 1287 HD1 TYR L 87 68.080 -11.417 -0.345 1.00 30.41 H ATOM 1288 HD2 TYR L 87 69.551 -15.003 -1.348 1.00 36.13 H ATOM 1289 HE1 TYR L 87 70.168 -10.477 -0.661 1.00 36.04 H ATOM 1290 HE2 TYR L 87 71.635 -14.060 -1.666 1.00 38.98 H ATOM 1291 HH TYR L 87 72.884 -12.227 -1.623 1.00 41.66 H """, "ARG" : """ ATOM 6724 N ARG A 465 -8.114 20.359 -8.988 1.00 49.56 N ATOM 6725 CA ARG A 465 -8.113 21.468 -8.039 1.00 52.45 C ATOM 6726 C ARG A 465 -9.335 21.427 -7.136 1.00 54.28 C ATOM 6727 O ARG A 465 -9.283 21.899 -5.996 1.00 54.38 O ATOM 6728 CB ARG A 465 -8.072 22.802 -8.784 1.00 53.89 C ATOM 6729 CG ARG A 465 -6.707 23.162 -9.350 1.00 55.53 C ATOM 6730 CD ARG A 465 -6.579 24.655 -9.586 1.00 57.77 C ATOM 6731 NE ARG A 465 -6.803 25.405 -8.354 1.00 59.92 N ATOM 6732 CZ ARG A 465 -6.632 26.716 -8.223 1.00 61.69 C ATOM 6733 NH1 ARG A 465 -6.849 27.289 -7.047 1.00 62.84 N ATOM 6734 NH2 ARG A 465 -6.242 27.453 -9.254 1.00 62.15 N ATOM 6735 H ARG A 465 -8.015 20.588 -9.811 1.00 49.56 H ATOM 6736 HA ARG A 465 -7.321 21.380 -7.486 1.00 52.45 H ATOM 6737 HB2 ARG A 465 -8.714 22.775 -9.510 1.00 53.89 H ATOM 6738 HB3 ARG A 465 -8.356 23.506 -8.180 1.00 53.89 H ATOM 6739 HG2 ARG A 465 -6.014 22.870 -8.737 1.00 55.53 H ATOM 6740 HG3 ARG A 465 -6.566 22.688 -10.185 1.00 55.53 H ATOM 6741 HD2 ARG A 465 -5.696 24.856 -9.934 1.00 57.77 H ATOM 6742 HD3 ARG A 465 -7.219 24.935 -10.259 1.00 57.77 H ATOM 6743 HE ARG A 465 -7.065 24.966 -7.662 1.00 59.92 H ATOM 6744 HH11 ARG A 465 -7.099 26.812 -6.376 1.00 62.84 H ATOM 6745 HH12 ARG A 465 -6.740 28.137 -6.955 1.00 62.84 H ATOM 6746 HH21 ARG A 465 -6.097 27.083 -10.017 1.00 62.15 H ATOM 6747 HH22 ARG A 465 -6.134 28.301 -9.160 1.00 62.15 H """, "PHE_missing_CE2" : """ ATOM 810 N PHE A 105 27.518 -30.761 62.509 1.00 24.66 N ANISOU 810 N PHE A 105 3396 2930 3044 46 490 24 N ATOM 811 CA PHE A 105 27.910 -31.927 61.750 1.00 22.63 C ANISOU 811 CA PHE A 105 3141 2671 2786 43 489 25 C ATOM 812 C PHE A 105 26.878 -32.113 60.659 1.00 22.52 C ANISOU 812 C PHE A 105 3123 2661 2773 39 491 25 C ATOM 813 O PHE A 105 25.759 -31.615 60.765 1.00 23.79 O ANISOU 813 O PHE A 105 3280 2824 2934 38 493 26 O ATOM 814 CB PHE A 105 27.958 -33.165 62.645 1.00 23.99 C ANISOU 814 CB PHE A 105 3321 2841 2955 42 491 24 C ATOM 815 CG PHE A 105 26.609 -33.618 63.120 1.00 28.62 C ANISOU 815 CG PHE A 105 3906 3429 3538 38 495 25 C ATOM 816 CD1 PHE A 105 26.093 -33.177 64.320 1.00 30.02 C ANISOU 816 CD1 PHE A 105 4085 3607 3715 40 497 24 C ATOM 817 CD2 PHE A 105 25.841 -34.478 62.353 1.00 30.68 C ANISOU 817 CD2 PHE A 105 4166 3691 3798 34 497 25 C ATOM 818 CE1 PHE A 105 24.849 -33.596 64.733 1.00 32.03 C ANISOU 818 CE1 PHE A 105 4339 3863 3968 36 500 24 C """, "PHE_2" : """ ATOM 3264 N PHE A 217 30.776 -28.100 -17.162 1.00 15.42 N ATOM 3265 CA PHE A 217 31.363 -27.624 -18.384 1.00 14.70 C ATOM 3266 C PHE A 217 32.212 -28.677 -19.046 1.00 15.01 C ATOM 3267 O PHE A 217 33.021 -29.350 -18.413 1.00 16.31 O ATOM 3268 CB PHE A 217 32.177 -26.335 -18.136 1.00 16.76 C ATOM 3269 CG PHE A 217 31.302 -25.242 -17.626 1.00 16.55 C ATOM 3270 CD1 PHE A 217 31.215 -24.983 -16.284 1.00 16.83 C ATOM 3271 CD2 PHE A 217 30.503 -24.516 -18.502 1.00 18.31 C ATOM 3272 CE1 PHE A 217 30.337 -24.029 -15.786 1.00 16.65 C ATOM 3273 CE2 PHE A 217 29.624 -23.532 -18.011 1.00 15.24 C ATOM 3274 CZ PHE A 217 29.561 -23.283 -16.645 1.00 17.98 C ATOM 3275 H PHE A 217 31.327 -28.470 -16.616 1.00 18.51 H ATOM 3276 HA PHE A 217 30.648 -27.401 -18.999 1.00 17.64 H ATOM 3277 HB2 PHE A 217 32.864 -26.510 -17.475 1.00 20.11 H ATOM 3278 HB3 PHE A 217 32.577 -26.042 -18.970 1.00 20.11 H ATOM 3279 HD1 PHE A 217 31.726 -25.485 -15.690 1.00 20.20 H ATOM 3280 HD2 PHE A 217 30.540 -24.690 -19.415 1.00 21.98 H ATOM 3281 HE1 PHE A 217 30.310 -23.859 -14.872 1.00 19.99 H ATOM 3282 HE2 PHE A 217 29.101 -23.038 -18.600 1.00 18.29 H ATOM 3283 HZ PHE A 217 28.992 -22.626 -16.313 1.00 21.58 H ATOM 4166 CD1 TYR A 277 41.891 -14.126 -14.217 1.00 26.09 C """, 'LEU' : ''' ATOM 1142 N LEU B 158 12.672 -5.202 21.045 1.00 12.10 B N ATOM 1143 CA LEU B 158 12.719 -4.364 19.855 1.00 9.96 B C ATOM 1144 C LEU B 158 14.074 -3.681 19.767 1.00 13.93 B C ATOM 1145 O LEU B 158 14.542 -3.091 20.750 1.00 10.55 B O ATOM 1146 CB LEU B 158 11.594 -3.321 19.891 1.00 9.63 B C ATOM 1147 CG LEU B 158 11.380 -2.482 18.634 1.00 11.09 B C ATOM 1148 CD1 LEU B 158 9.897 -2.151 18.478 1.00 11.88 B C ATOM 1149 CD2 LEU B 158 11.900 -3.216 17.391 1.00 15.14 B C ''', 'VAL' : ''' HETATM 1 N VAL A 1 -0.458 -1.800 -0.548 1.00 20.00 A N HETATM 2 CA VAL A 1 -0.329 -0.702 0.393 1.00 20.00 A C HETATM 3 C VAL A 1 -1.671 -0.463 1.082 1.00 20.00 A C HETATM 4 O VAL A 1 -2.646 -0.015 0.423 1.00 20.00 A O HETATM 5 CB VAL A 1 0.092 0.561 -0.354 1.00 20.00 A C HETATM 6 CG2 VAL A 1 0.584 1.604 0.647 1.00 20.00 A C HETATM 7 CG1 VAL A 1 1.215 0.224 -1.332 1.00 20.00 A C HETATM 8 OXT VAL A 1 -1.802 -0.713 2.309 1.00 20.00 A O-1 HETATM 9 H VAL A 1 -1.391 -2.165 -0.511 1.00 20.00 A H HETATM 10 H2 VAL A 1 0.193 -2.524 -0.308 1.00 20.00 A H HETATM 11 HA VAL A 1 0.419 -0.949 1.136 1.00 20.00 A H HETATM 12 HB VAL A 1 -0.755 0.957 -0.900 1.00 20.00 A H HETATM 13 HG21 VAL A 1 -0.219 1.854 1.334 1.00 20.00 A H HETATM 14 HG22 VAL A 1 0.897 2.498 0.115 1.00 20.00 A H HETATM 15 HG23 VAL A 1 1.426 1.202 1.204 1.00 20.00 A H HETATM 16 HG11 VAL A 1 0.813 -0.349 -2.162 1.00 20.00 A H HETATM 17 HG12 VAL A 1 1.975 -0.362 -0.822 1.00 20.00 A H HETATM 18 HG13 VAL A 1 1.657 1.143 -1.707 1.00 20.00 A H ''', } geo_strs = { "ASP" : """dihedral pdb=" CA ASP L 1 " pdb=" CB ASP L 1 " pdb=" CG ASP L 1 " pdb=" OD1 ASP L 1 " """, "GLU" : """ dihedral pdb=" CB GLU B 1 " pdb=" CG GLU B 1 " pdb=" CD GLU B 1 " pdb=" OE1 GLU B 1 " """, "PHE" : """dihedral pdb=" CA PHE L 83 " pdb=" CB PHE L 83 " pdb=" CG PHE L 83 " pdb=" CD1 PHE L 83 " """, "TYR" : """dihedral pdb=" CA TYR L 87 " pdb=" CB TYR L 87 " pdb=" CG TYR L 87 " pdb=" CD1 TYR L 87 " """, "ARG" : """dihedral pdb=" CD ARG A 465 " pdb=" NE ARG A 465 " pdb=" CZ ARG A 465 " pdb=" NH1 ARG A 465 " """, "PHE_missing_CE2" : 'Residue "A PHE 105": not complete - not flipped', "PHE_2" : """dihedral pdb=" CA PHE A 217 " pdb=" CB PHE A 217 " pdb=" CG PHE A 217 " pdb=" CD1 PHE A 217 " """, 'LEU' : '''chirality pdb=" CG LEU B 158 " segid="B " pdb=" CB LEU B 158 " segid="B " pdb=" CD1 LEU B 158 " segid="B " pdb=" CD2 LEU B 158 " segid="B " ''', 'VAL' : '''chirality pdb=" CB VAL A 1 " segid="A " pdb=" CA VAL A 1 " segid="A " pdb=" CG1 VAL A 1 " segid="A " pdb=" CG2 VAL A 1 " segid="A " ''', } values = { "ASP" : [ 152, -82, -999, -999], "GLU" : [ 162, -162, -18, 18], "PHE" : [-105, 15, 74, 16], "TYR" : [ -96, 6, 85, 5], "ARG" : [-179, 179, -999, -999], "PHE_missing_CE2" : [-999,-999,-999,-999], "PHE_2" : [97, -7, -79, -11], # chiral 'LEU' : [2.65, -5.24, -2.65, 0.06], 'VAL' : [2.65, -5.37, -2.75, 0.11], } def largest_torsion(s, f, i): t = s.split(f) if len(t)==1: return -999 s=t[1].splitlines() f="ideal model delta sinusoidal sigma weight residual" reading = False for line in s: print(line) if reading: break if line.find(f)>-1: reading=True d=line.split() print(d) return float(d[i]) def largest_chiral(s, f, i): t = s.split(f) if len(t)==1: return -999 s=t[1].splitlines() f="both_signs ideal model delta sigma weight residual" reading = False for line in s: print(line) if reading: break if line.find(f)>-1: reading=True d=line.split() print(d) return float(d[i]) def run(): for code, lines in pdbs.items(): #if code!='VAL': continue print(('-%s- ' % code)*10) with open("tst_symmetric_flips_%s.pdb" % code, "w") as f: f.write(lines) cmd = "phenix.pdb_interpretation tst_symmetric_flips_%s.pdb" % code cmd += ' flip_symmetric_amino_acids=None' print(cmd) ero = easy_run.fully_buffered(command=cmd) out = StringIO() ero.show_stdout(out=out) i=0 if code in ['LEU', 'VAL']: d = largest_chiral(out.getvalue(), geo_strs[code], i+2) print('chiral',d) assert abs(d-values[code][i])<.1, '%s %s' % (d, values[code][i]) else: d = largest_torsion(out.getvalue(), geo_strs[code], i+1) print('torsion',d) assert abs(d-values[code][i])<1, '%s %s' % (d, values[code][i]) i+=1 if code in ['LEU', 'VAL']: d = largest_chiral(out.getvalue(), geo_strs[code], i+2) print('delta',d) assert abs(d-values[code][i])<.1, '%s %s' % (d, values[code][i]) else: d = largest_torsion(out.getvalue(), geo_strs[code], i+1) print('delta',d) assert abs(d-values[code][i])<1, '%s %s' % (d, values[code][i]) pdb_inp = iotbx.pdb.input('tst_symmetric_flips_%s.pdb' % code) hierarchy = pdb_inp.construct_hierarchy() rc = hierarchy.flip_symmetric_amino_acids() print(rc) hierarchy.write_pdb_file("tst_symmetric_flips_%s.pdb" % code) cmd = "phenix.pdb_interpretation tst_symmetric_flips_%s.pdb" % code cmd += ' flip_symmetric_amino_acids=None' print(cmd) ero = easy_run.fully_buffered(command=cmd) out = StringIO() ero.show_stdout(out=out) i+=1 if code in ['LEU', 'VAL']: d = largest_chiral(out.getvalue(), geo_strs[code], i) print('chiral',d) assert abs(d-values[code][i])<.1, '%s %s' % (d, values[code][i]) else: d = largest_torsion(out.getvalue(), geo_strs[code], i-1) print('torsion',d) assert abs(d-values[code][i])<1, '%s %s' % (d, values[code][i]) i+=1 if code in ['LEU', 'VAL']: d = largest_chiral(out.getvalue(), geo_strs[code], i) print('delta',d) assert abs(d-values[code][i])<.1, '%s %s' % (d, values[code][i]) else: d = largest_torsion(out.getvalue(), geo_strs[code], i-1) print('delta',d) assert abs(d-values[code][i])<1, '%s %s' % (d, values[code][i]) if __name__=="__main__": import libtbx.load_env if libtbx.env.find_in_repositories('chem_data') is not None: args = sys.argv[1:] del sys.argv[1:] run(*tuple(args)) else: print('chem_data is missing, skipping test')