from __future__ import absolute_import, division, print_function from scitbx.array_family import flex import iotbx.pdb from mmtbx.conformation_dependent_library import generate_protein_threes from six.moves import range rec_1_residue = """\ CRYST1 41.566 72.307 92.870 108.51 93.02 90.06 P 1 4 ATOM 5466 N ASN C 236 17.899 72.943 29.028 1.00 60.13 N ATOM 5467 CA ASN C 236 16.519 72.435 29.114 1.00 60.52 C ATOM 5468 C ASN C 236 16.377 70.925 29.327 1.00 60.49 C ATOM 5469 O ASN C 236 15.429 70.294 28.863 1.00 60.60 O ATOM 5470 CB ASN C 236 15.689 72.896 27.916 1.00 60.55 C ATOM 5471 CG ASN C 236 14.357 73.447 28.338 1.00 61.75 C ATOM 5472 OD1 ASN C 236 14.256 74.609 28.768 1.00 62.86 O ATOM 5473 ND2 ASN C 236 13.319 72.616 28.247 1.00 61.22 N """ rec_2_residues = """\ CRYST1 41.566 72.307 92.870 108.51 93.02 90.06 P 1 4 ATOM 5466 N ASN C 236 17.899 72.943 29.028 1.00 60.13 N ATOM 5467 CA ASN C 236 16.519 72.435 29.114 1.00 60.52 C ATOM 5468 C ASN C 236 16.377 70.925 29.327 1.00 60.49 C ATOM 5469 O ASN C 236 15.429 70.294 28.863 1.00 60.60 O ATOM 5470 CB ASN C 236 15.689 72.896 27.916 1.00 60.55 C ATOM 5471 CG ASN C 236 14.357 73.447 28.338 1.00 61.75 C ATOM 5472 OD1 ASN C 236 14.256 74.609 28.768 1.00 62.86 O ATOM 5473 ND2 ASN C 236 13.319 72.616 28.247 1.00 61.22 N ATOM 5474 N LEU C 237 17.316 70.364 30.068 1.00 60.55 N ATOM 5475 CA LEU C 237 17.444 68.931 30.166 1.00 60.48 C ATOM 5476 C LEU C 237 17.815 68.555 31.581 1.00 60.06 C ATOM 5477 O LEU C 237 17.335 67.547 32.097 1.00 60.41 O ATOM 5478 CB LEU C 237 18.518 68.464 29.178 1.00 60.91 C ATOM 5479 CG LEU C 237 18.542 67.095 28.491 1.00 62.25 C ATOM 5480 CD1 LEU C 237 17.407 66.153 28.923 1.00 63.18 C ATOM 5481 CD2 LEU C 237 18.563 67.309 26.965 1.00 62.89 C """ rec_3_residues = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 4 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 6 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 8 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 12 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 13 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 17 N GLY A 4 49.963 44.013 20.917 1.00 79.31 N ATOM 18 CA GLY A 4 49.030 44.458 19.892 1.00 79.31 C ATOM 21 C GLY A 4 48.761 43.480 18.761 1.00 79.31 C ATOM 22 O GLY A 4 47.790 42.725 18.808 1.00 79.31 O ATOM 24 N ALA A 5 49.581 43.499 17.715 1.00 78.81 N ATOM 25 CA ALA A 5 49.395 42.604 16.581 1.00 78.81 C ATOM 27 CB ALA A 5 49.774 43.314 15.283 1.00 77.40 C ATOM 31 C ALA A 5 50.195 41.315 16.714 1.00 78.81 C ATOM 32 O ALA A 5 50.258 40.537 15.757 1.00 78.81 O """ rec_4_residues = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 4 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 6 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 8 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 12 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 13 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 17 N GLY A 4 49.963 44.013 20.917 1.00 79.31 N ATOM 18 CA GLY A 4 49.030 44.458 19.892 1.00 79.31 C ATOM 21 C GLY A 4 48.761 43.480 18.761 1.00 79.31 C ATOM 22 O GLY A 4 47.790 42.725 18.808 1.00 79.31 O ATOM 24 N ALA A 5 49.581 43.499 17.715 1.00 78.81 N ATOM 25 CA ALA A 5 49.395 42.604 16.581 1.00 78.81 C ATOM 27 CB ALA A 5 49.774 43.314 15.283 1.00 77.40 C ATOM 31 C ALA A 5 50.195 41.315 16.714 1.00 78.81 C ATOM 32 O ALA A 5 50.258 40.537 15.757 1.00 78.81 O ATOM 34 N GLN A 6 50.816 41.073 17.872 1.00 80.55 N ATOM 35 CA GLN A 6 51.642 39.880 18.018 1.00 80.55 C ATOM 37 CB GLN A 6 52.383 39.879 19.354 1.00 79.84 C ATOM 40 CG GLN A 6 53.264 41.072 19.596 1.00 79.84 C ATOM 43 CD GLN A 6 52.490 42.211 20.225 1.00 79.84 C ATOM 44 OE1 GLN A 6 51.290 42.091 20.489 1.00 79.84 O ATOM 45 NE2 GLN A 6 53.167 43.325 20.468 1.00 79.84 N ATOM 48 C GLN A 6 50.788 38.631 17.945 1.00 80.55 C ATOM 49 O GLN A 6 51.148 37.659 17.273 1.00 80.55 O """ rec_2_chains = """ CRYST1 49.945 53.842 33.425 90.00 90.00 90.00 P 1 ATOM 5466 N ASN C 236 10.328 45.698 25.449 1.00 60.13 N ATOM 5467 CA ASN C 236 8.971 45.973 25.787 1.00 60.52 C ATOM 5468 C ASN C 236 8.271 44.664 25.724 1.00 60.49 C ATOM 5469 O ASN C 236 7.276 44.532 25.017 1.00 60.60 O ATOM 5470 CB ASN C 236 8.337 46.962 24.776 1.00 60.55 C ATOM 5471 CG ASN C 236 7.235 47.762 25.415 1.00 61.75 C ATOM 5472 OD1 ASN C 236 6.331 47.222 26.063 1.00 62.86 O ATOM 5473 ND2 ASN C 236 7.315 49.079 25.302 1.00 61.22 N ATOM 5474 N LEU C 237 8.820 43.663 26.441 1.00 60.55 N ATOM 5475 CA LEU C 237 8.420 42.305 26.286 1.00 60.48 C ATOM 5476 C LEU C 237 8.713 41.508 27.558 1.00 60.06 C ATOM 5477 O LEU C 237 7.907 41.421 28.503 1.00 60.41 O ATOM 5478 CB LEU C 237 9.159 41.598 25.114 1.00 60.91 C ATOM 5479 CG LEU C 237 9.365 42.136 23.662 1.00 62.25 C ATOM 5480 CD1 LEU C 237 10.605 42.996 23.496 1.00 63.18 C ATOM 5481 CD2 LEU C 237 9.419 40.966 22.765 1.00 62.89 C TER ATOM 1 N THR A 3 40.527 19.363 20.612 1.00 80.52 N ATOM 2 CA THR A 3 41.278 18.625 19.636 1.00 80.52 C ATOM 4 CB THR A 3 40.971 17.090 19.710 1.00 79.62 C ATOM 6 OG1 THR A 3 40.039 16.849 20.760 1.00 79.62 O ATOM 8 CG2 THR A 3 42.308 16.246 19.999 1.00 79.62 C ATOM 12 C THR A 3 40.899 19.134 18.229 1.00 80.52 C ATOM 13 O THR A 3 39.780 19.542 17.983 1.00 80.52 O ATOM 17 N GLY A 4 41.890 19.246 17.384 1.00 79.31 N ATOM 18 CA GLY A 4 41.732 19.850 16.092 1.00 79.31 C ATOM 21 C GLY A 4 41.306 18.930 14.985 1.00 79.31 C ATOM 22 O GLY A 4 40.121 18.885 14.657 1.00 79.31 O """ rec_2_segids = """ CRYST1 49.945 53.842 33.425 90.00 90.00 90.00 P 1 ATOM 5466 N ASN A 236 10.328 45.698 25.449 1.00 60.13 N ATOM 5467 CA ASN A 236 8.971 45.973 25.787 1.00 60.52 C ATOM 5468 C ASN A 236 8.271 44.664 25.724 1.00 60.49 C ATOM 5469 O ASN A 236 7.276 44.532 25.017 1.00 60.60 O ATOM 5470 CB ASN A 236 8.337 46.962 24.776 1.00 60.55 C ATOM 5471 CG ASN A 236 7.235 47.762 25.415 1.00 61.75 C ATOM 5472 OD1 ASN A 236 6.331 47.222 26.063 1.00 62.86 O ATOM 5473 ND2 ASN A 236 7.315 49.079 25.302 1.00 61.22 N ATOM 5474 N LEU A 237 8.820 43.663 26.441 1.00 60.55 N ATOM 5475 CA LEU A 237 8.420 42.305 26.286 1.00 60.48 C ATOM 5476 C LEU A 237 8.713 41.508 27.558 1.00 60.06 C ATOM 5477 O LEU A 237 7.907 41.421 28.503 1.00 60.41 O ATOM 5478 CB LEU A 237 9.159 41.598 25.114 1.00 60.91 C ATOM 5479 CG LEU A 237 9.365 42.136 23.662 1.00 62.25 C ATOM 5480 CD1 LEU A 237 10.605 42.996 23.496 1.00 63.18 C ATOM 5481 CD2 LEU A 237 9.419 40.966 22.765 1.00 62.89 C TER ATOM 1 N THR A 3 40.527 19.363 20.612 1.00 80.52 seg N ATOM 2 CA THR A 3 41.278 18.625 19.636 1.00 80.52 seg C ATOM 4 CB THR A 3 40.971 17.090 19.710 1.00 79.62 seg C ATOM 6 OG1 THR A 3 40.039 16.849 20.760 1.00 79.62 seg O ATOM 8 CG2 THR A 3 42.308 16.246 19.999 1.00 79.62 seg C ATOM 12 C THR A 3 40.899 19.134 18.229 1.00 80.52 seg C ATOM 13 O THR A 3 39.780 19.542 17.983 1.00 80.52 seg O ATOM 17 N GLY A 4 41.890 19.246 17.384 1.00 79.31 seg N ATOM 18 CA GLY A 4 41.732 19.850 16.092 1.00 79.31 seg C ATOM 21 C GLY A 4 41.306 18.930 14.985 1.00 79.31 seg C ATOM 22 O GLY A 4 40.121 18.885 14.657 1.00 79.31 seg O """ rec_2_acs_edge = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 3 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 4 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 5 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 6 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 7 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 8 N GLY A 4 49.963 44.013 20.917 1.00 79.31 N ATOM 9 CA GLY A 4 49.030 44.458 19.892 1.00 79.31 C ATOM 10 C GLY A 4 48.761 43.480 18.761 1.00 79.31 C ATOM 11 O GLY A 4 47.790 42.725 18.808 1.00 79.31 O ATOM 12 N AALA A 5 49.581 43.499 17.715 0.50 78.81 N ATOM 13 CA AALA A 5 49.395 42.604 16.581 0.50 78.81 C ATOM 14 CB AALA A 5 49.774 43.314 15.283 0.50 77.40 C ATOM 15 C AALA A 5 50.195 41.315 16.714 0.50 78.81 C ATOM 16 O AALA A 5 50.258 40.537 15.757 0.50 78.81 O ATOM 17 N BALA A 5 49.681 43.499 17.715 0.50 78.81 N ATOM 18 CA BALA A 5 49.495 42.604 16.581 0.50 78.81 C ATOM 19 CB BALA A 5 49.874 43.314 15.283 0.50 77.40 C ATOM 20 C BALA A 5 50.295 41.315 16.714 0.50 78.81 C ATOM 21 O BALA A 5 50.358 40.537 15.757 0.50 78.81 O END """ rec_2_acs_middle = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 3 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 4 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 5 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 6 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 7 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 8 N AGLY A 4 49.963 44.013 20.917 0.50 79.31 N ATOM 9 CA AGLY A 4 49.030 44.458 19.892 0.50 79.31 C ATOM 10 C AGLY A 4 48.761 43.480 18.761 0.50 79.31 C ATOM 11 O AGLY A 4 47.790 42.725 18.808 0.50 79.31 O ATOM 12 N BGLY A 4 50.063 44.013 20.917 0.50 79.31 N ATOM 13 CA BGLY A 4 49.130 44.458 19.892 0.50 79.31 C ATOM 14 C BGLY A 4 48.861 43.480 18.761 0.50 79.31 C ATOM 15 O BGLY A 4 47.890 42.725 18.808 0.50 79.31 O ATOM 16 N ALA A 5 49.581 43.499 17.715 1.00 78.81 N ATOM 17 CA ALA A 5 49.395 42.604 16.581 1.00 78.81 C ATOM 18 CB ALA A 5 49.774 43.314 15.283 1.00 77.40 C ATOM 19 C ALA A 5 50.195 41.315 16.714 1.00 78.81 C ATOM 20 O ALA A 5 50.258 40.537 15.757 1.00 78.81 O END """ rec_2_acs_middle_one_atom_1 = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 3 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 4 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 5 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 6 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 7 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 8 N AGLY A 4 49.963 44.013 20.917 0.50 79.31 N ATOM 9 N BGLY A 4 50.063 44.013 20.917 0.50 79.31 N ATOM 10 CA GLY A 4 49.030 44.458 19.892 0.50 79.31 C ATOM 11 C GLY A 4 48.761 43.480 18.761 0.50 79.31 C ATOM 12 O GLY A 4 47.790 42.725 18.808 0.50 79.31 O ATOM 16 N ALA A 5 49.581 43.499 17.715 1.00 78.81 N ATOM 17 CA ALA A 5 49.395 42.604 16.581 1.00 78.81 C ATOM 18 CB ALA A 5 49.774 43.314 15.283 1.00 77.40 C ATOM 19 C ALA A 5 50.195 41.315 16.714 1.00 78.81 C ATOM 20 O ALA A 5 50.258 40.537 15.757 1.00 78.81 O END """ rec_2_acs_middle_one_atom_2 = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 3 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 4 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 5 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 6 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 7 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 8 N GLY A 4 49.963 44.013 20.917 0.50 79.31 N ATOM 9 CA AGLY A 4 49.030 44.458 19.892 0.50 79.31 C ATOM 13 CA BGLY A 4 49.130 44.458 19.892 0.50 79.31 C ATOM 10 C GLY A 4 48.761 43.480 18.761 0.50 79.31 C ATOM 11 O GLY A 4 47.790 42.725 18.808 0.50 79.31 O ATOM 16 N ALA A 5 49.581 43.499 17.715 1.00 78.81 N ATOM 17 CA ALA A 5 49.395 42.604 16.581 1.00 78.81 C ATOM 18 CB ALA A 5 49.774 43.314 15.283 1.00 77.40 C ATOM 19 C ALA A 5 50.195 41.315 16.714 1.00 78.81 C ATOM 20 O ALA A 5 50.258 40.537 15.757 1.00 78.81 O END """ rec_2_acs_middle_one_atom_3 = """\ CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1 SCALE1 0.013875 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029383 0.00000 ATOM 519 N HIS B 1 5.000 8.515 18.112 1.00 20.00 N ATOM 520 CA HIS B 1 5.999 8.713 17.074 1.00 20.00 C ATOM 521 C HIS B 1 7.157 9.627 17.517 1.00 20.00 C ATOM 522 O HIS B 1 8.302 9.165 17.614 1.00 20.00 O ATOM 523 CB HIS B 1 5.315 9.226 15.797 1.00 20.00 C ATOM 524 HA HIS B 1 6.434 7.742 16.835 1.00 20.00 H ATOM 525 N TRP B 2 6.845 10.900 17.805 1.00 20.00 N ATOM 526 CA ATRP B 2 7.853 11.954 18.083 0.50 20.00 C ATOM 556 CA BTRP B 2 7.453 11.454 18.083 0.50 20.00 C ATOM 527 C TRP B 2 8.071 12.262 19.565 1.00 20.00 C ATOM 528 O TRP B 2 8.355 13.406 19.941 1.00 20.00 O ATOM 529 CB TRP B 2 7.516 13.257 17.336 1.00 20.00 C ATOM 530 HA TRP B 2 8.809 11.606 17.692 1.00 20.00 H ATOM 531 H ATRP B 2 5.886 11.243 17.855 0.50 20.00 H ATOM 532 D BTRP B 2 5.886 11.243 17.855 0.50 20.00 D ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C ATOM 538 HA GLU B 3 8.761 12.248 22.034 1.00 20.00 H ATOM 539 H AGLU B 3 7.474 10.360 20.122 0.50 20.00 H ATOM 540 D BGLU B 3 7.474 10.360 20.122 0.50 20.00 D """ rec_4_residues_isertions = """ CRYST1 69.211 49.956 52.557 90.00 90.00 90.00 P 1 ATOM 1 N THR A 3 51.193 44.956 23.993 1.00 80.52 N ATOM 2 CA THR A 3 50.812 43.732 23.211 1.00 80.52 C ATOM 4 CB THR A 3 50.446 42.559 24.181 1.00 79.62 C ATOM 6 OG1 THR A 3 50.206 41.358 23.433 1.00 79.62 O ATOM 8 CG2 THR A 3 49.239 42.888 25.066 1.00 79.62 C ATOM 12 C THR A 3 49.657 44.014 22.221 1.00 80.52 C ATOM 13 O THR A 3 48.520 44.223 22.631 1.00 80.52 O ATOM 17 N GLY A 3A 49.963 44.013 20.917 1.00 79.31 N ATOM 18 CA GLY A 3A 49.030 44.458 19.892 1.00 79.31 C ATOM 21 C GLY A 3A 48.761 43.480 18.761 1.00 79.31 C ATOM 22 O GLY A 3A 47.790 42.725 18.808 1.00 79.31 O ATOM 24 N ALA A 3B 49.581 43.499 17.715 1.00 78.81 N ATOM 25 CA ALA A 3B 49.395 42.604 16.581 1.00 78.81 C ATOM 27 CB ALA A 3B 49.774 43.314 15.283 1.00 77.40 C ATOM 31 C ALA A 3B 50.195 41.315 16.714 1.00 78.81 C ATOM 32 O ALA A 3B 50.258 40.537 15.757 1.00 78.81 O ATOM 34 N GLN A 4 50.816 41.073 17.872 1.00 80.55 N ATOM 35 CA GLN A 4 51.642 39.880 18.018 1.00 80.55 C ATOM 37 CB GLN A 4 52.383 39.879 19.354 1.00 79.84 C ATOM 40 CG GLN A 4 53.264 41.072 19.596 1.00 79.84 C ATOM 43 CD GLN A 4 52.490 42.211 20.225 1.00 79.84 C ATOM 44 OE1 GLN A 4 51.290 42.091 20.489 1.00 79.84 O ATOM 45 NE2 GLN A 4 53.167 43.325 20.468 1.00 79.84 N ATOM 48 C GLN A 4 50.788 38.631 17.945 1.00 80.55 C ATOM 49 O GLN A 4 51.148 37.659 17.273 1.00 80.55 O """ pdb_1yjp = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 21 N GLN A 4 -1.005 2.228 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.384 1.888 3.199 1.00 10.53 C ATOM 23 C GLN A 4 1.435 2.606 4.088 1.00 10.24 C ATOM 24 O GLN A 4 1.547 3.843 4.115 1.00 8.86 O ATOM 25 CB GLN A 4 0.656 2.148 1.711 1.00 9.80 C ATOM 26 CG GLN A 4 1.944 1.458 1.213 1.00 10.25 C ATOM 27 CD GLN A 4 2.504 2.044 -0.089 1.00 12.43 C ATOM 28 OE1 GLN A 4 2.744 3.268 -0.190 1.00 14.62 O ATOM 29 NE2 GLN A 4 2.750 1.161 -1.091 1.00 9.05 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O """ pdb_1yjp_minus_4 = """ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O ATOM 5 N ASN A 2 -7.656 2.923 3.155 1.00 15.02 N ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 7 C ASN A 2 -5.241 2.537 3.427 1.00 13.13 C ATOM 8 O ASN A 2 -4.978 3.742 3.426 1.00 11.91 O ATOM 9 CB ASN A 2 -6.346 1.881 1.341 1.00 15.38 C ATOM 10 CG ASN A 2 -7.584 1.342 0.692 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.025 0.227 1.016 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.204 2.155 -0.169 1.00 11.72 N ATOM 13 N ASN A 3 -4.438 1.590 3.905 1.00 12.26 N ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 15 C ASN A 3 -1.955 1.332 3.895 1.00 11.10 C ATOM 16 O ASN A 3 -1.872 0.119 3.648 1.00 10.42 O ATOM 17 CB ASN A 3 -3.259 1.378 6.042 1.00 12.15 C ATOM 18 CG ASN A 3 -2.006 1.739 6.861 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.702 2.925 7.072 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.271 0.715 7.306 1.00 13.48 N ATOM 30 N GLN A 5 2.154 1.821 4.871 1.00 10.38 N ATOM 31 CA GLN A 5 3.270 2.361 5.640 1.00 11.39 C ATOM 32 C GLN A 5 4.594 1.768 5.172 1.00 11.52 C ATOM 33 O GLN A 5 4.768 0.546 5.054 1.00 12.05 O ATOM 34 CB GLN A 5 3.056 2.183 7.147 1.00 11.96 C ATOM 35 CG GLN A 5 1.829 2.950 7.647 1.00 10.81 C ATOM 36 CD GLN A 5 1.344 2.414 8.954 1.00 13.10 C ATOM 37 OE1 GLN A 5 0.774 1.325 9.002 1.00 10.65 O ATOM 38 NE2 GLN A 5 1.549 3.187 10.039 1.00 12.30 N ATOM 39 N ASN A 6 5.514 2.664 4.856 1.00 11.99 N ATOM 40 CA ASN A 6 6.831 2.310 4.318 1.00 12.30 C ATOM 41 C ASN A 6 7.854 2.761 5.324 1.00 13.40 C ATOM 42 O ASN A 6 8.219 3.943 5.374 1.00 13.92 O ATOM 43 CB ASN A 6 7.065 3.016 2.993 1.00 12.13 C ATOM 44 CG ASN A 6 5.961 2.735 2.003 1.00 12.77 C ATOM 45 OD1 ASN A 6 5.798 1.604 1.551 1.00 14.27 O ATOM 46 ND2 ASN A 6 5.195 3.747 1.679 1.00 10.07 N ATOM 47 N TYR A 7 8.292 1.817 6.147 1.00 14.70 N ATOM 48 CA TYR A 7 9.159 2.144 7.299 1.00 15.18 C ATOM 49 C TYR A 7 10.603 2.331 6.885 1.00 15.91 C ATOM 50 O TYR A 7 11.041 1.811 5.855 1.00 15.76 O ATOM 51 CB TYR A 7 9.061 1.065 8.369 1.00 15.35 C ATOM 52 CG TYR A 7 7.665 0.929 8.902 1.00 14.45 C ATOM 53 CD1 TYR A 7 6.771 0.021 8.327 1.00 15.68 C ATOM 54 CD2 TYR A 7 7.210 1.756 9.920 1.00 14.80 C ATOM 55 CE1 TYR A 7 5.480 -0.094 8.796 1.00 13.46 C ATOM 56 CE2 TYR A 7 5.904 1.649 10.416 1.00 14.33 C ATOM 57 CZ TYR A 7 5.047 0.729 9.831 1.00 15.09 C ATOM 58 OH TYR A 7 3.766 0.589 10.291 1.00 14.39 O ATOM 59 OXT TYR A 7 11.358 2.999 7.612 1.00 17.49 O """ rec_3_res_ac_h = """\ CRYST1 72.072 33.173 34.033 90.00 90.00 90.00 P 1 ATOM 519 N HIS B 1 5.000 8.515 18.112 1.00 20.00 N ATOM 520 CA HIS B 1 5.999 8.713 17.074 1.00 20.00 C ATOM 521 C HIS B 1 7.157 9.627 17.517 1.00 20.00 C ATOM 522 O HIS B 1 8.302 9.165 17.614 1.00 20.00 O ATOM 523 CB HIS B 1 5.315 9.226 15.797 1.00 20.00 C ATOM 524 HA HIS B 1 6.434 7.742 16.835 1.00 20.00 H ATOM 525 N TRP B 2 6.845 10.900 17.805 1.00 20.00 N ATOM 526 CA TRP B 2 7.853 11.954 18.083 1.00 20.00 C ATOM 527 C TRP B 2 8.071 12.262 19.565 1.00 20.00 C ATOM 528 O TRP B 2 8.355 13.406 19.941 1.00 20.00 O ATOM 529 CB TRP B 2 7.516 13.257 17.336 1.00 20.00 C ATOM 530 HA TRP B 2 8.809 11.606 17.692 1.00 20.00 H ATOM 531 H ATRP B 2 5.886 11.243 17.855 0.50 20.00 H ATOM 532 D BTRP B 2 5.886 11.243 17.855 0.50 20.00 D ATOM 533 N GLU B 3 7.910 11.239 20.396 1.00 20.00 N ATOM 534 CA GLU B 3 8.310 11.284 21.798 1.00 20.00 C ATOM 535 C GLU B 3 9.344 10.190 21.979 1.00 20.00 C ATOM 536 O GLU B 3 10.197 10.267 22.867 1.00 20.00 O ATOM 537 CB GLU B 3 7.115 11.041 22.731 1.00 20.00 C ATOM 538 HA GLU B 3 8.761 12.248 22.034 1.00 20.00 H ATOM 539 H AGLU B 3 7.474 10.360 20.122 0.50 20.00 H ATOM 540 D BGLU B 3 7.474 10.360 20.122 0.50 20.00 D """ def exercise_phi_psi_extraction(): for n_prox, raw_records in [ ([0, 0], rec_1_residue), ([0, 0], rec_2_residues), ([4, 2], rec_3_residues), ([6, 4], rec_4_residues), ([0, 0], rec_2_chains), ([0, 0], rec_2_segids), ([8, 4], rec_2_acs_edge), ([8, 4], rec_2_acs_middle), ([6, 4], rec_4_residues_isertions), ([12, 10], pdb_1yjp), ([8, 4], pdb_1yjp_minus_4), ([4, 2], rec_3_res_ac_h), ([8, 4], rec_2_acs_middle_one_atom_1), ([8, 4], rec_2_acs_middle_one_atom_2), ([8, 4], rec_2_acs_middle_one_atom_3), ]: tmp_hierarchy = iotbx.pdb.input( source_info=None, lines=flex.split_lines(raw_records)).construct_hierarchy() for opp in range(2): proxies = [] for three in generate_protein_threes( hierarchy=tmp_hierarchy, geometry=None): ppp = three.get_dummy_dihedral_proxies(only_psi_phi_pairs=opp) print(three,'ppp',len(ppp)) proxies.extend(ppp) print(len(proxies), n_prox) assert len(proxies) == n_prox[opp], \ "Expected %d, got %d" % ( n_prox[opp], len(proxies), ) if (__name__ == "__main__"): exercise_phi_psi_extraction()