from __future__ import absolute_import, division, print_function import os, time import mmtbx.model import iotbx.pdb from mmtbx.monomer_library.pdb_interpretation import grand_master_phil_str from libtbx.test_utils import approx_equal from mmtbx.hydrogens.validate_H import validate_H, validate_H_results from libtbx.utils import null_out from six.moves import zip #from validate_H_cl_app import master_params_str pdb_str = """ CRYST1 43.705 48.284 96.292 90.00 90.00 90.00 P 1 SCALE1 0.022881 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010385 0.00000 ATOM 1 N ASN A 1 25.174 -24.761 -21.940 1.00 16.59 N ATOM 2 CA ASN A 1 25.971 -25.578 -22.850 1.00 17.25 C ATOM 3 C ASN A 1 26.037 -24.941 -24.225 1.00 16.66 C ATOM 4 O ASN A 1 27.077 -24.979 -24.874 1.00 18.42 O ATOM 5 CB ASN A 1 25.498 -27.040 -22.913 1.00 18.30 C ATOM 6 CG ASN A 1 24.187 -27.208 -23.672 1.00 20.42 C ATOM 7 OD1 ASN A 1 23.167 -26.590 -23.335 1.00 20.87 O ATOM 8 ND2 ASN A 1 24.200 -28.069 -24.685 1.00 18.15 N ATOM 9 DA ASN A 1 26.975 -25.581 -22.461 1.00 15.99 D ATOM 10 DD21 ASN A 1 25.030 -28.545 -24.882 1.00 16.07 D ATOM 11 D AASN A 1 24.379 -25.105 -21.517 0.82 16.71 D ATOM 12 DB2AASN A 1 25.358 -27.400 -21.898 0.65 18.82 D ATOM 13 DB3AASN A 1 26.255 -27.641 -23.402 0.56 18.30 D ATOM 14 DD22AASN A 1 23.370 -28.163 -25.192 0.72 16.98 D ATOM 15 H BASN A 1 24.379 -25.105 -21.517 0.18 16.71 H ATOM 16 HB2BASN A 1 26.255 -27.641 -23.402 0.44 18.30 H ATOM 17 HB3BASN A 1 25.358 -27.400 -21.898 0.35 18.82 H ATOM 18 HD22BASN A 1 23.370 -28.163 -25.192 0.28 16.98 H ATOM 19 N ASN A 2 23.615 -22.281 -25.492 1.00 16.59 N ATOM 20 CA ASN A 2 24.412 -23.098 -26.402 1.00 17.25 C ATOM 21 C ASN A 2 24.478 -22.461 -27.777 1.00 16.66 C ATOM 22 O ASN A 2 25.518 -22.499 -28.426 1.00 18.42 O ATOM 23 CB ASN A 2 23.939 -24.560 -26.465 1.00 18.30 C ATOM 24 CG ASN A 2 22.628 -24.728 -27.224 1.00 20.42 C ATOM 25 OD1 ASN A 2 21.608 -24.110 -26.887 1.00 20.87 O ATOM 26 ND2 ASN A 2 22.641 -25.589 -28.237 1.00 18.15 N ATOM 27 DA ASN A 2 25.416 -23.101 -26.013 1.00 15.99 D ATOM 28 HD21 ASN A 2 23.471 -26.065 -28.434 1.00 16.07 H ATOM 29 D AASN A 2 22.820 -22.625 -25.069 0.82 16.71 D ATOM 30 DB2AASN A 2 23.799 -24.920 -25.450 0.65 18.82 D ATOM 31 DB3AASN A 2 24.696 -25.161 -26.954 0.56 18.30 D ATOM 32 DD22AASN A 2 21.811 -25.683 -28.744 0.72 16.98 D ATOM 33 H BASN A 2 22.820 -22.625 -25.069 0.18 16.71 H ATOM 34 HB2BASN A 2 24.696 -25.161 -26.954 0.44 18.30 H ATOM 35 HB3BASN A 2 23.799 -24.920 -25.450 0.35 18.82 H ATOM 36 HD22BASN A 2 21.811 -25.683 -28.744 0.28 16.98 H ATOM 37 N LEU A 3 23.374 -21.865 -28.222 1.00 15.90 N ATOM 38 CA LEU A 3 23.342 -21.224 -29.530 1.00 15.47 C ATOM 39 C LEU A 3 23.637 -19.727 -29.491 1.00 18.18 C ATOM 40 O LEU A 3 24.174 -19.175 -30.462 1.00 20.24 O ATOM 41 CB LEU A 3 22.021 -21.521 -30.238 1.00 15.76 C ATOM 42 CG LEU A 3 21.790 -23.005 -30.533 1.00 19.30 C ATOM 43 CD1 LEU A 3 20.460 -23.197 -31.290 1.00 20.74 C ATOM 44 CD2 LEU A 3 22.957 -23.627 -31.336 1.00 17.02 C ATOM 45 DA LEU A 3 24.132 -21.653 -30.101 1.00 12.76 D ATOM 46 DB3 LEU A 3 21.233 -21.196 -29.610 1.00 17.93 D ATOM 47 D ALEU A 3 22.567 -21.865 -27.663 0.91 16.63 D ATOM 48 DB2ALEU A 3 21.964 -20.976 -31.155 0.67 16.51 D ATOM 49 DG ALEU A 3 21.719 -23.530 -29.581 0.68 18.31 D ATOM 50 DD11ALEU A 3 19.620 -22.925 -30.652 0.74 20.52 D ATOM 51 DD12ALEU A 3 20.364 -24.239 -31.597 0.77 19.78 D ATOM 52 DD13ALEU A 3 20.458 -22.568 -32.171 0.49 20.26 D ATOM 53 DD21ALEU A 3 23.466 -22.855 -31.890 0.40 16.87 D ATOM 54 DD22ALEU A 3 22.563 -24.357 -32.028 0.00 16.68 D ATOM 55 DD23ALEU A 3 23.653 -24.109 -30.673 0.89 14.39 D ATOM 56 H BLEU A 3 22.567 -21.865 -27.663 0.09 16.63 H ATOM 57 HB2BLEU A 3 21.964 -20.976 -31.155 0.33 14.51 H ATOM 58 HG BLEU A 3 21.719 -23.530 -29.581 0.32 18.31 H ATOM 59 HD11BLEU A 3 19.620 -22.925 -30.652 0.26 20.52 H ATOM 60 HD12BLEU A 3 20.364 -24.239 -31.597 0.23 19.78 H ATOM 61 HD13BLEU A 3 20.458 -22.568 -32.171 0.51 20.26 H ATOM 62 HD21BLEU A 3 23.466 -22.855 -31.890 0.60 16.87 H ATOM 63 HD22BLEU A 3 22.563 -24.357 -32.028 0.58 16.68 H ATOM 64 HD23BLEU A 3 23.653 -24.109 -30.673 0.11 14.39 H ATOM 65 N SER A 4 9.243 -32.509 -36.471 1.00 38.02 N ATOM 66 CA SER A 4 10.063 -33.604 -36.981 1.00 39.55 C ATOM 67 C SER A 4 11.459 -33.153 -37.367 1.00 37.45 C ATOM 68 O SER A 4 11.633 -32.304 -38.239 1.00 38.82 O ATOM 69 CB SER A 4 9.384 -34.279 -38.180 1.00 41.66 C ATOM 70 OG SER A 4 8.375 -35.181 -37.753 1.00 44.91 O ATOM 71 DA SER A 4 10.165 -34.324 -36.187 1.00 38.72 D ATOM 72 D ASER A 4 8.730 -31.950 -37.103 0.62 38.48 D ATOM 73 DB2ASER A 4 10.116 -34.818 -38.774 0.63 41.36 D ATOM 74 DB3ASER A 4 8.918 -33.518 -38.793 0.36 41.73 D ATOM 75 DG ASER A 4 8.699 -36.084 -37.842 0.36 43.61 D ATOM 76 H BSER A 4 8.730 -31.950 -37.103 0.28 38.48 H ATOM 77 HB2BSER A 4 8.918 -33.518 -38.793 0.64 41.73 H ATOM 78 HB3BSER A 4 10.116 -34.818 -38.774 0.37 41.36 H ATOM 79 HG BSER A 4 8.699 -36.084 -37.842 0.64 43.61 H ATOM 80 N SER A 5 26.478 -19.398 45.776 1.00 19.78 N ATOM 81 C SER A 5 27.940 -19.562 43.818 1.00 21.99 C ATOM 82 O SER A 5 29.005 -19.770 43.306 1.00 21.20 O ATOM 83 CA ASER A 5 27.849 -19.441 45.318 0.64 18.99 C ATOM 84 CB ASER A 5 28.611 -20.590 45.987 0.64 21.66 C ATOM 85 OG ASER A 5 28.819 -20.337 47.363 0.64 23.21 O ATOM 86 DG ASER A 5 29.639 -20.155 47.499 0.64 22.10 D ATOM 87 H ASER A 5 26.064 -20.150 45.742 0.06 18.55 H ATOM 88 HA ASER A 5 28.296 -18.610 45.561 0.64 20.89 H ATOM 89 HB2ASER A 5 28.094 -21.408 45.903 0.00 22.17 H ATOM 90 HB3ASER A 5 29.468 -20.686 45.544 0.64 22.38 H ATOM 91 CA BSER A 5 27.851 -19.476 45.322 0.36 19.02 C ATOM 92 CB BSER A 5 28.561 -20.680 45.932 0.36 21.98 C ATOM 93 OG BSER A 5 28.005 -21.879 45.425 0.36 25.40 O ATOM 94 D BSER A 5 26.023 -20.128 45.688 0.94 18.55 D ATOM 95 HA BSER A 5 28.327 -18.675 45.599 0.36 21.03 H ATOM 96 HB2BSER A 5 29.498 -20.638 45.691 0.36 22.55 H ATOM 97 HB3BSER A 5 28.462 -20.665 46.898 0.36 23.83 H ATOM 98 HG BSER A 5 27.486 -22.196 46.000 0.36 22.10 H TER HETATM 100 O DOD B 1 25.202 -21.329 -23.306 1.00 30.00 O HETATM 101 D1 DOD B 1 25.963 -20.763 -23.255 1.00 30.00 D HETATM 102 D2 DOD B 1 24.439 -20.764 -23.305 1.00 30.00 D HETATM 103 O HOH B 2 26.442 -21.454 -25.349 1.00 30.00 O HETATM 104 D1 HOH B 2 27.249 -20.953 -25.339 1.00 30.00 D HETATM 105 O HOH B 3 24.970 -18.184 -24.460 1.00 30.00 O HETATM 106 O HOH B 4 21.573 -23.174 -24.023 1.00 30.00 O HETATM 107 D2 HOH B 4 20.731 -22.736 -24.071 1.00 30.00 D HETATM 108 D1 AHOH B 4 22.045 -22.784 -23.297 1.00 30.00 D HETATM 109 D1 BHOH B 4 22.145 -21.784 -22.297 1.00 30.00 D HETATM 110 D1 HOH B 5 21.772 -27.767 -28.880 1.00 30.00 D HETATM 111 O DOD B 6 17.493 -24.723 -25.229 1.00 20.00 O HETATM 112 D1 DOD B 6 17.492 -25.660 -25.470 1.00 20.00 D HETATM 113 D2 DOD B 6 18.304 -24.255 -25.470 1.00 20.00 D HETATM 114 D3 DOD B 6 16.682 -24.254 -25.470 1.00 20.00 D TER 115 HOH B 6 HETATM 1 PG ATP C 1 3.232 -0.948 -8.256 1.00 20.00 A P HETATM 2 O1G ATP C 1 4.490 -0.168 -7.985 1.00 20.00 A O HETATM 3 O2G ATP C 1 2.572 -0.420 -9.500 1.00 20.00 A O-1 HETATM 4 O3G ATP C 1 3.573 -2.392 -8.447 1.00 20.00 A O-1 HETATM 5 PB ATP C 1 2.368 0.364 -5.856 1.00 20.00 A P HETATM 6 O1B ATP C 1 3.702 0.219 -5.162 1.00 20.00 A O HETATM 7 O2B ATP C 1 2.287 1.719 -6.506 1.00 20.00 A O-1 HETATM 8 O3B ATP C 1 2.218 -0.793 -6.996 1.00 20.00 A O HETATM 9 PA ATP C 1 0.926 1.250 -3.494 1.00 20.00 A P HETATM 10 O1A ATP C 1 -0.200 2.200 -3.825 1.00 20.00 A O HETATM 11 O2A ATP C 1 2.197 2.037 -3.253 1.00 20.00 A O-1 HETATM 12 O3A ATP C 1 1.155 0.210 -4.753 1.00 20.00 A O HETATM 13 O5' ATP C 1 0.538 0.381 -2.115 1.00 20.00 A O HETATM 14 C5' ATP C 1 -0.378 0.948 -1.194 1.00 20.00 A C HETATM 15 C4' ATP C 1 -1.094 -0.162 -0.442 1.00 20.00 A C HETATM 16 O4' ATP C 1 -0.263 -0.783 0.344 1.00 20.00 A O HETATM 17 C3' ATP C 1 -2.258 0.478 0.549 1.00 20.00 A C HETATM 18 O3' ATP C 1 -3.508 0.701 -0.219 1.00 20.00 A O HETATM 19 C2' ATP C 1 -2.450 -0.373 1.436 1.00 20.00 A C HETATM 20 O2' ATP C 1 -3.564 -1.296 1.031 1.00 20.00 A O HETATM 21 C1' ATP C 1 -1.075 -1.183 1.553 1.00 20.00 A C HETATM 22 N9 ATP C 1 -0.436 -0.847 2.669 1.00 20.00 A N HETATM 23 C8 ATP C 1 0.891 -0.729 2.488 1.00 20.00 A C HETATM 24 N7 ATP C 1 1.445 -0.426 3.672 1.00 20.00 A N HETATM 25 C5 ATP C 1 0.455 -0.356 4.593 1.00 20.00 A C HETATM 26 C6 ATP C 1 0.464 -0.066 5.953 1.00 20.00 A C HETATM 27 N6 ATP C 1 1.576 0.468 6.779 1.00 20.00 A N HETATM 28 N1 ATP C 1 -0.678 -0.046 6.637 1.00 20.00 A N HETATM 29 C2 ATP C 1 -1.855 -0.311 6.004 1.00 20.00 A C HETATM 30 N3 ATP C 1 -1.865 -0.595 4.675 1.00 20.00 A N HETATM 31 C4 ATP C 1 -0.703 -0.615 3.975 1.00 20.00 A C HETATM 32 H5'1 ATP C 1 0.163 1.581 -0.485 1.00 20.00 A H HETATM 33 H5'2 ATP C 1 -1.105 1.545 -1.731 1.00 20.00 A H HETATM 34 H4' ATP C 1 -1.548 -0.870 -1.145 1.00 20.00 A H HETATM 35 H3' ATP C 1 -1.912 1.393 0.983 1.00 20.00 A H HETATM 36 HO3' ATP C 1 -3.892 1.548 0.031 1.00 20.00 A H HETATM 37 H2' ATP C 1 -2.680 0.114 2.384 1.00 20.00 A H HETATM 38 HO2' ATP C 1 -4.066 -1.553 1.810 1.00 20.00 A H HETATM 39 H1' ATP C 1 -1.273 -2.266 1.534 1.00 20.00 A H HETATM 40 H8 ATP C 1 1.431 -0.922 1.560 1.00 20.00 A H HETATM 41 HN61 ATP C 1 2.477 0.646 6.359 1.00 20.00 A H HETATM 42 HN62 ATP C 1 1.445 0.610 7.769 1.00 20.00 A H HETATM 43 H2 ATP C 1 -2.804 -0.294 6.573 1.00 20.00 A H TER END """ # exercise1 a) The C beta DB2 and DB3 atoms are swapped pdb_str1a = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.938 5.457 5.830 0.50 10.00 H ATOM 15 HB3ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.974 6.264 8.835 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH ATYR A 139 4.710 5.148 8.037 0.50 10.00 H ATOM 21 DA BTYR A 139 10.443 8.186 7.059 0.50 10.00 D ATOM 22 DB3BTYR A 139 10.938 5.457 5.830 0.50 10.00 D ATOM 23 DB2BTYR A 139 11.014 5.853 7.567 0.50 10.00 D ATOM 24 DD1BTYR A 139 8.799 5.277 4.695 0.50 10.00 D ATOM 25 DD2BTYR A 139 8.974 6.264 8.835 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.50 10.00 D ATOM 28 DH BTYR A 139 4.710 5.148 8.037 0.50 10.00 D """ # exercise1 b) The C beta HB2 and HB3 atoms are swapped pdb_str1b = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB3ATYR A 139 10.938 5.457 5.830 0.50 10.00 H ATOM 15 HB2ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.974 6.264 8.835 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH ATYR A 139 4.710 5.148 8.037 0.50 10.00 H ATOM 21 DA BTYR A 139 10.443 8.186 7.059 0.50 10.00 D ATOM 22 DB2BTYR A 139 10.938 5.457 5.830 0.50 10.00 D ATOM 23 DB3BTYR A 139 11.014 5.853 7.567 0.50 10.00 D ATOM 24 DD1BTYR A 139 8.799 5.277 4.695 0.50 10.00 D ATOM 25 DD2BTYR A 139 8.974 6.264 8.835 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.50 10.00 D ATOM 28 DH BTYR A 139 4.710 5.148 8.037 0.50 10.00 D """ pdb_str2 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.938 5.457 5.830 0.50 10.00 H ATOM 15 HB3ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 8.00 H ATOM 17 HD2ATYR A 139 8.974 6.264 8.835 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH ATYR A 139 4.564 5.706 7.633 0.60 10.00 H ATOM 21 DA BTYR A 139 10.543 8.286 7.059 0.50 10.00 D ATOM 22 DB2BTYR A 139 10.938 5.457 5.830 0.50 10.00 D ATOM 23 DB3BTYR A 139 11.014 5.853 7.567 0.50 10.00 D ATOM 24 DD1BTYR A 139 8.799 5.277 4.695 0.50 10.00 D ATOM 25 DD2BTYR A 139 8.974 6.264 8.835 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.50 10.00 D ATOM 28 DH BTYR A 139 4.710 5.148 8.037 0.40 10.00 D """ pdb_str3 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.938 5.457 5.830 0.00 10.00 H ATOM 15 HB3ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1 TYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.974 6.264 8.835 0.40 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH ATYR A 139 4.710 5.148 8.037 0.50 10.00 H ATOM 21 DA BTYR A 139 10.443 8.186 7.059 0.50 10.00 D ATOM 22 DB2BTYR A 139 10.938 5.457 5.830 1.00 10.00 D ATOM 23 DB3BTYR A 139 11.014 5.853 7.567 0.50 10.00 D ATOM 25 DD2BTYR A 139 8.974 6.264 8.835 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.60 10.00 D ATOM 28 DH BTYR A 139 4.710 5.148 8.037 0.50 10.00 D """ pdb_str4 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA TYR A 139 10.443 8.186 7.059 1.00 10.00 H ATOM 15 HB3 TYR A 139 11.014 5.853 7.567 1.00 10.00 H ATOM 16 HD1 TYR A 139 8.799 5.277 4.695 1.00 10.00 H ATOM 17 HD2 TYR A 139 8.974 6.264 8.835 1.00 10.00 H ATOM 19 HE2 TYR A 139 6.575 5.788 9.051 1.00 10.00 H ATOM 20 HH TYR A 139 4.710 5.148 8.037 1.00 10.00 H """ pdb_str5 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 DA TYR A 139 10.443 8.186 7.059 1.00 10.00 D ATOM 15 DB3 TYR A 139 11.014 5.853 7.567 1.00 10.00 D ATOM 16 DD1 TYR A 139 8.799 5.277 4.695 1.00 10.00 D ATOM 17 DD2 TYR A 139 8.974 6.264 8.835 1.00 10.00 D ATOM 19 DE2 TYR A 139 6.575 5.788 9.051 1.00 10.00 D ATOM 20 DH TYR A 139 4.710 5.148 8.037 1.00 10.00 D """ pdb_str6 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.938 5.457 5.830 0.50 10.00 H ATOM 15 HB3ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH TYR A 139 4.710 5.148 8.037 1.00 10.00 H ATOM 21 DA BTYR A 139 10.443 8.186 7.059 0.50 10.00 D ATOM 22 DB2BTYR A 139 10.938 5.457 5.830 0.50 10.00 D ATOM 24 DD1BTYR A 139 8.799 5.277 4.695 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.50 10.00 D """ pdb_str7 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 8 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 7 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 10 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 9 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB2ATYR A 139 11.057 5.645 5.981 0.50 10.00 H ATOM 15 HB3ATYR A 139 10.870 5.954 7.475 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.792 6.377 9.033 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH ATYR A 139 4.837 5.050 7.863 0.50 10.00 H """ pdb_str8 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 21 DA TYR A 139 10.443 8.186 7.059 1.00 10.00 D ATOM 14 DB2 TYR A 139 10.783 5.595 5.785 1.00 10.00 D ATOM 15 DB3 TYR A 139 11.112 5.843 7.715 1.00 10.00 D ATOM 16 DD1 TYR A 139 8.781 5.167 4.530 1.00 10.00 D ATOM 25 DD2 TYR A 139 8.974 6.264 8.835 1.00 10.00 D ATOM 26 DE1 TYR A 139 6.400 4.801 4.908 1.00 10.00 D ATOM 19 DE2 TYR A 139 6.754 5.829 8.900 1.00 10.00 D ATOM 28 DH TYR A 139 4.710 5.148 8.037 1.00 10.00 D """ pdb_str9 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.443 8.186 7.059 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.968 5.639 5.981 0.50 10.00 H ATOM 15 HB3ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.974 6.264 8.835 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.648 5.677 8.989 0.50 10.00 H ATOM 20 HH ATYR A 139 4.710 5.148 8.037 0.50 10.00 H ATOM 21 DA BTYR A 139 10.443 8.186 7.059 0.50 10.00 D ATOM 22 DB2BTYR A 139 10.938 5.457 5.830 0.50 10.00 D ATOM 23 DB3BTYR A 139 11.014 5.853 7.567 0.50 10.00 D ATOM 24 DD1BTYR A 139 8.832 5.349 4.523 0.50 10.00 D ATOM 25 DD2BTYR A 139 8.974 6.264 8.835 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.50 10.00 D ATOM 28 DH BTYR A 139 4.823 5.165 8.210 0.50 10.00 D """ pdb_str10 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 10.241 7.920 5.000 1.00 10.00 N ATOM 2 CA TYR A 139 10.853 7.555 6.271 1.00 10.00 C ATOM 3 C TYR A 139 12.362 7.771 6.227 1.00 10.00 C ATOM 4 O TYR A 139 12.955 8.272 7.181 1.00 10.00 O ATOM 5 CB TYR A 139 10.540 6.098 6.617 1.00 10.00 C ATOM 6 CG TYR A 139 9.063 5.805 6.749 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.316 5.391 5.654 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.414 5.943 7.969 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.966 5.122 5.770 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.064 5.676 8.095 1.00 10.00 C ATOM 11 CZ TYR A 139 6.345 5.266 6.993 1.00 10.00 C ATOM 12 OH TYR A 139 5.000 5.000 7.113 1.00 10.00 O ATOM 13 HA ATYR A 139 10.583 7.992 7.177 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.938 5.457 5.830 0.50 10.00 H ATOM 15 HB3ATYR A 139 11.014 5.853 7.567 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.799 5.277 4.695 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.974 6.264 8.835 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.400 4.801 4.908 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.575 5.788 9.051 0.50 10.00 H ATOM 20 HH ATYR A 139 4.710 5.148 8.037 0.50 10.00 H ATOM 21 DA BTYR A 139 10.557 8.334 6.899 0.50 10.00 D ATOM 22 DB2BTYR A 139 10.938 5.457 5.830 0.50 10.00 D ATOM 23 DB3BTYR A 139 11.014 5.853 7.567 0.50 10.00 D ATOM 24 DD1BTYR A 139 8.799 5.277 4.695 0.50 10.00 D ATOM 25 DD2BTYR A 139 8.974 6.264 8.835 0.50 10.00 D ATOM 26 DE1BTYR A 139 6.400 4.801 4.908 0.50 10.00 D ATOM 27 DE2BTYR A 139 6.575 5.788 9.051 0.50 10.00 D ATOM 28 DH BTYR A 139 4.710 5.148 8.037 0.50 10.00 D """ pdb_str11 = """ CRYST1 17.955 13.272 13.095 90.00 90.00 90.00 P 1 SCALE1 0.055695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.075347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.076365 0.00000 ATOM 1 N TYR A 139 11.036 5.830 4.803 1.00 10.00 N ATOM 2 CA TYR A 139 11.024 6.967 5.716 1.00 10.00 C ATOM 3 C TYR A 139 12.431 7.528 5.890 1.00 10.00 C ATOM 4 O TYR A 139 12.649 8.448 6.679 1.00 10.00 O ATOM 5 CB TYR A 139 10.449 6.559 7.076 1.00 10.00 C ATOM 6 CG TYR A 139 8.999 6.118 7.041 1.00 10.00 C ATOM 7 CD1 TYR A 139 8.187 6.397 5.948 1.00 10.00 C ATOM 8 CD2 TYR A 139 8.444 5.421 8.106 1.00 10.00 C ATOM 9 CE1 TYR A 139 6.865 5.994 5.918 1.00 10.00 C ATOM 10 CE2 TYR A 139 7.123 5.014 8.084 1.00 10.00 C ATOM 11 CZ TYR A 139 6.339 5.303 6.988 1.00 10.00 C ATOM 12 OH TYR A 139 5.023 4.900 6.962 1.00 10.00 O ATOM 13 HA ATYR A 139 10.470 7.671 5.345 0.50 10.00 H ATOM 14 HB2ATYR A 139 10.973 5.821 7.425 0.50 10.00 H ATOM 15 HB3ATYR A 139 10.511 7.317 7.679 0.50 10.00 H ATOM 16 HD1ATYR A 139 8.536 6.863 5.223 0.50 10.00 H ATOM 17 HD2ATYR A 139 8.970 5.224 8.847 0.50 10.00 H ATOM 18 HE1ATYR A 139 6.334 6.188 5.179 0.50 10.00 H ATOM 19 HE2ATYR A 139 6.765 4.548 8.805 0.50 10.00 H ATOM 20 HH ATYR A 139 4.834 4.492 7.672 0.50 10.00 H """ pdb_str12a = """ CRYST1 19.968 16.881 14.617 90.00 90.00 90.00 P 1 SCALE1 0.050080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.059238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.068413 0.00000 ATOM 62 P A A 3 24.641 -3.951 -5.491 1.00 29.43 P ANISOU 62 P A A 3 4128 3373 3681 -371 815 -398 P ATOM 63 OP1 A A 3 25.708 -4.265 -6.475 1.00 31.32 O ANISOU 63 OP1 A A 3 4348 3730 3823 -437 1123 -264 O ATOM 64 OP2 A A 3 23.848 -2.702 -5.549 1.00 33.50 O ANISOU 64 OP2 A A 3 5180 3675 3874 -38 594 -122 O ATOM 65 O5' A A 3 23.568 -5.100 -5.644 1.00 27.30 O ANISOU 65 O5' A A 3 3750 3254 3367 -244 624 -238 O ATOM 66 C5' A A 3 24.008 -6.432 -5.684 1.00 26.59 C ANISOU 66 C5' A A 3 3613 3318 3174 -268 449 -24 C ATOM 67 C4' A A 3 22.856 -7.369 -5.558 1.00 24.31 C ANISOU 67 C4' A A 3 2940 3360 2938 -132 191 158 C ATOM 68 O4' A A 3 22.216 -7.202 -4.268 1.00 23.51 O ANISOU 68 O4' A A 3 2669 3549 2716 229 -49 181 O ATOM 69 C3' A A 3 21.713 -7.204 -6.543 1.00 22.64 C ANISOU 69 C3' A A 3 2570 3095 2939 23 108 75 C ATOM 70 O3' A A 3 22.036 -7.703 -7.822 1.00 21.70 O ANISOU 70 O3' A A 3 2381 2989 2875 340 -63 -119 O ATOM 71 C2' A A 3 20.618 -7.974 -5.834 1.00 22.54 C ANISOU 71 C2' A A 3 2683 2965 2917 254 -84 254 C ATOM 72 O2' A A 3 20.877 -9.368 -5.907 1.00 24.68 O ANISOU 72 O2' A A 3 3062 3194 3120 501 -66 167 O ATOM 73 C1' A A 3 20.844 -7.504 -4.393 1.00 22.32 C ANISOU 73 C1' A A 3 2600 3126 2756 137 -50 130 C ATOM 74 N9 A A 3 20.071 -6.281 -4.150 1.00 22.38 N ANISOU 74 N9 A A 3 2766 3075 2660 40 47 -196 N ATOM 75 C8 A A 3 20.479 -4.970 -4.244 1.00 21.65 C ANISOU 75 C8 A A 3 2769 2846 2611 60 91 -156 C ATOM 76 N7 A A 3 19.514 -4.113 -4.001 1.00 22.55 N ANISOU 76 N7 A A 3 2915 3122 2532 126 220 -226 N ATOM 77 C5 A A 3 18.408 -4.919 -3.782 1.00 22.50 C ANISOU 77 C5 A A 3 2913 3131 2505 96 130 -148 C ATOM 78 C6 A A 3 17.070 -4.648 -3.477 1.00 22.18 C ANISOU 78 C6 A A 3 3024 3082 2321 -26 -12 -123 C ATOM 79 N6 A A 3 16.576 -3.426 -3.369 1.00 22.36 N ANISOU 79 N6 A A 3 3152 3016 2329 -60 -158 -237 N ATOM 80 N1 A A 3 16.209 -5.667 -3.317 1.00 23.05 N ANISOU 80 N1 A A 3 3000 3481 2278 36 174 -84 N ATOM 81 C2 A A 3 16.692 -6.903 -3.440 1.00 23.27 C ANISOU 81 C2 A A 3 2794 3522 2524 122 366 11 C ATOM 82 N3 A A 3 17.931 -7.310 -3.719 1.00 23.07 N ANISOU 82 N3 A A 3 2685 3428 2651 -328 327 261 N ATOM 83 C4 A A 3 18.742 -6.255 -3.880 1.00 22.38 C ANISOU 83 C4 A A 3 2707 3187 2607 -200 133 38 C ATOM 84 H5' A A 3 24.629 -6.587 -4.955 1.00 31.92 H ATOM 85 H5'' A A 3 24.462 -6.594 -6.526 1.00 31.92 H ATOM 86 H4' A A 3 23.200 -8.273 -5.635 1.00 29.18 H ATOM 87 H3' A A 3 21.456 -6.273 -6.629 1.00 27.18 H ATOM 88 H2' A A 3 19.729 -7.755 -6.155 1.00 27.05 H ATOM 89 HO2' A A 3 21.392 -9.583 -5.278 1.00 29.62 H ATOM 90 H1' A A 3 20.611 -8.194 -3.752 1.00 26.79 H ATOM 91 H8 A A 3 21.348 -4.717 -4.457 1.00 25.99 H ATOM 92 H61 A A 3 15.740 -3.313 -3.205 1.00 26.84 H ATOM 93 H62 A A 3 17.091 -2.744 -3.464 1.00 26.84 H ATOM 94 H2 A A 3 16.073 -7.585 -3.310 1.00 27.93 H """ pdb_str12b = """ CRYST1 19.968 16.881 14.617 90.00 90.00 90.00 P 1 SCALE1 0.050080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.059238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.068413 0.00000 ATOM 62 P A A 3 24.641 -3.951 -5.491 1.00 29.43 P ANISOU 62 P A A 3 4128 3373 3681 -371 815 -398 P ATOM 63 OP1 A A 3 25.708 -4.265 -6.475 1.00 31.32 O ANISOU 63 OP1 A A 3 4348 3730 3823 -437 1123 -264 O ATOM 64 OP2 A A 3 23.848 -2.702 -5.549 1.00 33.50 O ANISOU 64 OP2 A A 3 5180 3675 3874 -38 594 -122 O ATOM 65 O5' A A 3 23.568 -5.100 -5.644 1.00 27.30 O ANISOU 65 O5' A A 3 3750 3254 3367 -244 624 -238 O ATOM 66 C5' A A 3 24.008 -6.432 -5.684 1.00 26.59 C ANISOU 66 C5' A A 3 3613 3318 3174 -268 449 -24 C ATOM 67 C4' A A 3 22.856 -7.369 -5.558 1.00 24.31 C ANISOU 67 C4' A A 3 2940 3360 2938 -132 191 158 C ATOM 68 O4' A A 3 22.216 -7.202 -4.268 1.00 23.51 O ANISOU 68 O4' A A 3 2669 3549 2716 229 -49 181 O ATOM 69 C3' A A 3 21.713 -7.204 -6.543 1.00 22.64 C ANISOU 69 C3' A A 3 2570 3095 2939 23 108 75 C ATOM 70 O3' A A 3 22.036 -7.703 -7.822 1.00 21.70 O ANISOU 70 O3' A A 3 2381 2989 2875 340 -63 -119 O ATOM 71 C2' A A 3 20.618 -7.974 -5.834 1.00 22.54 C ANISOU 71 C2' A A 3 2683 2965 2917 254 -84 254 C ATOM 72 O2' A A 3 20.877 -9.368 -5.907 1.00 24.68 O ANISOU 72 O2' A A 3 3062 3194 3120 501 -66 167 O ATOM 73 C1' A A 3 20.844 -7.504 -4.393 1.00 22.32 C ANISOU 73 C1' A A 3 2600 3126 2756 137 -50 130 C ATOM 74 N9 A A 3 20.071 -6.281 -4.150 1.00 22.38 N ANISOU 74 N9 A A 3 2766 3075 2660 40 47 -196 N ATOM 75 C8 A A 3 20.479 -4.970 -4.244 1.00 21.65 C ANISOU 75 C8 A A 3 2769 2846 2611 60 91 -156 C ATOM 76 N7 A A 3 19.514 -4.113 -4.001 1.00 22.55 N ANISOU 76 N7 A A 3 2915 3122 2532 126 220 -226 N ATOM 77 C5 A A 3 18.408 -4.919 -3.782 1.00 22.50 C ANISOU 77 C5 A A 3 2913 3131 2505 96 130 -148 C ATOM 78 C6 A A 3 17.070 -4.648 -3.477 1.00 22.18 C ANISOU 78 C6 A A 3 3024 3082 2321 -26 -12 -123 C ATOM 79 N6 A A 3 16.576 -3.426 -3.369 1.00 22.36 N ANISOU 79 N6 A A 3 3152 3016 2329 -60 -158 -237 N ATOM 80 N1 A A 3 16.209 -5.667 -3.317 1.00 23.05 N ANISOU 80 N1 A A 3 3000 3481 2278 36 174 -84 N ATOM 81 C2 A A 3 16.692 -6.903 -3.440 1.00 23.27 C ANISOU 81 C2 A A 3 2794 3522 2524 122 366 11 C ATOM 82 N3 A A 3 17.931 -7.310 -3.719 1.00 23.07 N ANISOU 82 N3 A A 3 2685 3428 2651 -328 327 261 N ATOM 83 C4 A A 3 18.742 -6.255 -3.880 1.00 22.38 C ANISOU 83 C4 A A 3 2707 3187 2607 -200 133 38 C ATOM 86 H4' A A 3 23.200 -8.273 -5.635 1.00 29.18 H ATOM 87 H3' A A 3 21.456 -6.273 -6.629 1.00 27.18 H ATOM 88 H2' A A 3 19.729 -7.755 -6.155 1.00 27.05 H ATOM 89 HO2' A A 3 21.392 -9.583 -5.278 1.00 29.62 H ATOM 90 H1' A A 3 20.611 -8.194 -3.752 1.00 26.79 H ATOM 91 H8 A A 3 21.348 -4.717 -4.457 1.00 25.99 H ATOM 92 H61 A A 3 15.740 -3.313 -3.205 1.00 26.84 H ATOM 93 H62 A A 3 17.091 -2.744 -3.464 1.00 26.84 H ATOM 94 H2 A A 3 16.073 -7.585 -3.310 1.00 27.93 H """ def get_results_from_validate_H(neutron_distances, pdb_str): pdb_interpretation_phil = iotbx.phil.parse( input_string = grand_master_phil_str, process_includes = True) pi_params = pdb_interpretation_phil.extract() pi_params.pdb_interpretation.use_neutron_distances = neutron_distances pi_params.pdb_interpretation.flip_symmetric_amino_acids=False pdb_inp = iotbx.pdb.input(lines=pdb_str.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, stop_for_unknowns = False, log = null_out()) model.process(pdb_interpretation_params=pi_params, make_restraints=True) c = validate_H(model = model, use_neutron_distances = neutron_distances) r = c.validate_inputs() c.run() results = c.get_results() return results def test_output(results): out = validate_H_results(results) log = open(os.devnull, 'w') out.print_results(prefix=' ', log=log) log.close() # export data for wxGUI out.export_renamed_for_wxGUI() out.export_occupancies_0_for_wxGUI() out.export_occupancies_lt_1_for_wxGUI() out.export_missing_HD_atoms_for_wxGUI() out.export_outliers_bonds_for_wxGUI() out.export_outliers_angles_for_wxGUI() out.export_sites_different_xyz_for_wxGUI() out.export_sites_different_b_for_wxGUI() out.export_sites_sum_occ_for_wxGUI() out.export_sites_occ_scattering_for_wxGUI() def exercise(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str) oc = results.overall_counts_hd hd_atoms_with_occ_0 = oc.hd_atoms_with_occ_0 assert (oc.count_h == 42) assert (oc.count_d == 39) assert (oc.count_h_protein == 30) assert (oc.count_d_protein == 29) assert (oc.count_h_water == 0) assert (oc.count_d_water == 10) assert (oc.count_water == 5 + 1) assert (oc.count_water_0h == 1) assert (oc.count_water_1h == 1) assert (oc.count_water_2h == 1) assert (oc.count_water_altconf == 1) assert (oc.count_water_no_oxygen == 1) assert (oc.count_h_other == 12) assert (oc.count_d_other == 0) answer = ['DD22ALEU A 3 ', ' HB2ASER A 5 '] for item, answer in zip(hd_atoms_with_occ_0, answer): assert(item[0][5:-1] == answer) renamed_answer = [('DB2', 'DB3'), ('DB3', 'DB2'),('DB2', 'DB3'), ('DB3', 'DB2'),('DB2', 'DB3'), ('DB3', 'DB2')] renamed = results.renamed for entry, answer in zip(renamed, renamed_answer): oldname = entry[2].strip() newname = entry[1].strip() assert(oldname == answer[0]) assert(newname == answer[1]) assert (entry[3] is not None) assert (results.count_exchanged_sites == 22) hd_sites_analysis = results.hd_sites_analysis sites_different_xyz = hd_sites_analysis.sites_different_xyz xyz_answer = [0.0712] for item, answer in zip(sites_different_xyz, xyz_answer): assert approx_equal(item[2],answer, 1.e-2) sites_different_b = hd_sites_analysis.sites_different_b b_answer = [-2] for item, answer in zip(sites_different_b, b_answer): assert approx_equal(item[2],answer, 1.e-1) sites_sum_occ_not_1 = hd_sites_analysis.sites_sum_occ_not_1 sum_occ_answer=[0.58, 0.9] for item, answer in zip(sites_sum_occ_not_1, sum_occ_answer): assert approx_equal(item[2], answer, 1.e-2) sites_occ_sum_no_scattering = hd_sites_analysis.sites_occ_sum_no_scattering sum_scatt_answer=[0.4, 0.36] for item, answer in zip(sites_occ_sum_no_scattering, sum_scatt_answer): assert approx_equal(item[3], answer, 1.e-2) missing_HD_atoms = results.missing_HD_atoms test_output(results) # XXX TODO # ------------------------------------------------------------------------------ # Input has H and D everywhere (all exchanged) # a) The C beta DB2 and DB3 atoms are swapped # b) The C beta HB2 and HB3 atoms are swapped # ------------------------------------------------------------------------------ def exercise1(): renamed_answer = [('DB2', 'DB3')] # DB2 and DB3 swapped results1 = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str1a) for entry, answer in zip(results1.renamed, renamed_answer): oldname = entry[2].strip() newname = entry[1].strip() assert(oldname == answer[0]) assert(newname == answer[1]) assert (entry[3] is not None) # HB2 and HB3 swapped --> D atoms are renamed results2 = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str1b) for entry, answer in zip(results1.renamed, renamed_answer): oldname = entry[2].strip() newname = entry[1].strip() assert(oldname == answer[0]) assert(newname == answer[1]) assert (entry[3] is not None) test_output(results1) test_output(results2) # ------------------------------------------------------------------------------ # PROPERTIES H/D SITES # a) HA and DA have different coordinates # b) HD1 and DD1 have different B factors # c) HH and DH have different coordinates and are within cutoff distance to # create a warning for zero scattering sum # ------------------------------------------------------------------------------ def exercise2(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str2) hd_sites_analysis = results.hd_sites_analysis assert (results.count_exchanged_sites == 8) sites_different_xyz = hd_sites_analysis.sites_different_xyz xyz_answer = [ ('pdb=" HA ATYR A 139 "', 'pdb=" DA BTYR A 139 "', 0.141), ('pdb=" HH ATYR A 139 "', 'pdb=" DH BTYR A 139 "', 0.704)] for item, answer in zip(sites_different_xyz, xyz_answer): assert approx_equal(item[2],answer[2], 1.e-2) assert (item[3] is not None and item[4] is not None) # make sure xyz exist assert (item[0].strip() == answer[0].strip()) assert (item[1].strip() == answer[1].strip()) sites_different_b = hd_sites_analysis.sites_different_b b_answer = [('pdb=" HD1ATYR A 139 "', 'pdb=" DD1BTYR A 139 "', -2)] for item, answer in zip(sites_different_b, b_answer): assert approx_equal(item[2],answer[2], 1.e-1) assert (item[3] is not None and item[4] is not None) # make sure xyz exist assert (item[0].strip() == answer[0].strip()) assert (item[1].strip() == answer[1].strip()) sites_occ_sum_no_scattering = hd_sites_analysis.sites_occ_sum_no_scattering sum_scatt_answer=[('pdb=" HH ATYR A 139 "', 'pdb=" DH BTYR A 139 "', 0.6, 0.4)] for item, answer in zip(sites_occ_sum_no_scattering, sum_scatt_answer): assert approx_equal(item[3], answer[3], 1.e-2) assert (item[3] is not None and item[4] is not None) # make sure xyz exist assert (item[0].strip() == answer[0].strip()) assert (item[1].strip() == answer[1].strip()) test_output(results) # ------------------------------------------------------------------------------ # OCCUPANCIES # a) HD2 and DD2 have sum occupancy < 1 # b) HE2 and DD2 have sum occupancy > 1 # c) HB2 has 0 occupancy (while having exchanged partner DB2) # d) HD1 has occupancy < 1 (no exchanged partner) # ------------------------------------------------------------------------------ def exercise3(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str3) hd_sites_analysis = results.hd_sites_analysis sites_sum_occ_not_1 = hd_sites_analysis.sites_sum_occ_not_1 sum_occ_answer=[ ('pdb=" HD2ATYR A 139 "', 'pdb=" DD2BTYR A 139 "', 0.9), ('pdb=" HE2ATYR A 139 "', 'pdb=" DE2BTYR A 139 "', 1.1)] for item, answer in zip(sites_sum_occ_not_1, sum_occ_answer): assert approx_equal(item[2], answer[2], 1.e-2) assert (item[3] is not None and item[4] is not None) # make sure xyz exist assert (item[0].strip() == answer[0].strip()) assert (item[1].strip() == answer[1].strip()) oc = results.overall_counts_hd hd_atoms_with_occ_0 = oc.hd_atoms_with_occ_0 single_hd_atoms_occ_lt_1 = oc.single_hd_atoms_occ_lt_1 occ_0_answer = ['pdb=" HB2ATYR A 139 "'] for item, answer in zip(hd_atoms_with_occ_0, occ_0_answer): assert (item[0].strip() == answer.strip()) assert (item[1] is not None) # make sure xyz exist occ_lt_1_answer = [('pdb=" HD1 TYR A 139 "', 0.5)] for item, answer in zip(single_hd_atoms_occ_lt_1, occ_lt_1_answer): assert (item[0].strip() == answer[0].strip()) assert (item[1] == answer[1]) assert (item[2] is not None) # make sure xyz exist test_output(results) # ------------------------------------------------------------------------------ # MISSING ATOMS # Model has only H atoms # H, HE1 and HB2 are missing # (takes into account naming ambiguity HB1+HB2 and HB2+HB3) # ------------------------------------------------------------------------------ def exercise4(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str4) missing = results.missing_HD_atoms missing_answer = [('pdbres="TYR A 139 "', ['HE1', 'H', 'HB2'])] for item, answer in zip(missing, missing_answer): assert (item[0].strip() == answer[0].strip()) assert (item[2] is not None) # make sure xyz exist for atom, aatom in zip(sorted(item[1]), sorted(answer[1])): assert (atom.strip() == aatom.strip()) test_output(results) # ------------------------------------------------------------------------------ # MISSING ATOMS # Model has only D atoms # H, HE1 and HB2 are missing --> result uses H naming convention! # (takes into account naming ambiguity HB1+HB2 and HB2+HB3) # ------------------------------------------------------------------------------ def exercise5(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str5) missing = results.missing_HD_atoms missing_answer = [('pdbres="TYR A 139 "', ['HE1', 'H', 'HB2'])] for item, answer in zip(missing, missing_answer): assert (item[0].strip() == answer[0].strip()) assert (item[2] is not None) # make sure xyz exist for atom, aatom in zip(sorted(item[1]), sorted(answer[1])): assert (atom.strip() == aatom.strip()) test_output(results) # ------------------------------------------------------------------------------ # MISSING ATOMS # Model has exchanged sites # H --> missing # HD2 --> missing # CG --> missing, should not be in results because it is non-H atom # HE1 --> is present as DE1 in conf B but missing HE1 in conf A # HB3 --> is present as HB3 in conf A but missing DB3 in conf B # ------------------------------------------------------------------------------ def exercise6(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str6) missing = results.missing_HD_atoms #missing_answer = [('pdbres="TYR A 139 "', ['HE1', 'H', 'HD2', 'HB3'])] # XXX HB3 was never compared because missing only had 3 items. Removed it # for compatibility with python 3.8 missing_answer = [('pdbres="TYR A 139 "', ['HE1', 'H', 'HD2'])] for item, answer in zip(missing, missing_answer): assert (item[0].strip() == answer[0].strip()) assert (item[2] is not None) # make sure xyz exist for atom, aatom in zip(sorted(item[1]), sorted(answer[1])): assert (atom.strip() == aatom.strip()) assert (atom.strip() != 'CG') test_output(results) # ------------------------------------------------------------------------------ # BOND OUTLIERS # Model has only H atoms and only following outliers # Bond OH--HH, observed: 0.769, delta from target: 0.210 # Bond CB--HB3, observed: 0.930, delta from target: 0.159 # Bond CB--HB2, observed: 0.936, delta from target: 0.153 # Bond CD2--HD2, observed: 1.209, delta from target: -0.129 # ------------------------------------------------------------------------------ def exercise7(): print('exercise7') results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str7) outliers_bonds = results.outliers_bonds outliers_bond_answer = [ [' A 139 ATYR HD2', 1.209, 1.08 ], [' A 139 ATYR HB2', 0.936, 1.09 ], [' A 139 ATYR HB3', 0.930, 1.09 ], [' A 139 ATYR HH ', 0.769, 0.98 ] ] for item, answer in zip(outliers_bonds, outliers_bond_answer): #print(item) #print(answer) assert (item[0].strip() == answer[0].strip()) # pdb_str assert (item[5] is not None) # make sure xyz exist assert approx_equal(item[2],answer[1], 1.e-2) # bond length model assert approx_equal(item[4],answer[2], 1.e-1) # target test_output(results) # ------------------------------------------------------------------------------ # BOND OUTLIERS # Model has only D atoms and only following outliers # Bond CE2--DE2, observed: 0.876, delta from target: 0.203 # Bond CB--DB3, observed: 1.264, delta from target: -0.174 # Bond CD1--DD1, observed: 1.236, delta from target: -0.156 # Bond CB--DB2, observed: 1.002, delta from target: 0.087 # ------------------------------------------------------------------------------ def exercise8(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str8) outliers_bonds = results.outliers_bonds outliers_bond_answer = [ [' A 139 TYR DB2', 1.002, 1.09], [' A 139 TYR DD1', 1.236, 1.08], [' A 139 TYR DB3', 1.264, 1.09], [' A 139 TYR DE2', 0.876, 1.08] ] for item, answer in zip(outliers_bonds, outliers_bond_answer): assert (item[0].strip() == answer[0].strip()) # pdb_str assert (item[5] is not None) # make sure xyz exist assert approx_equal(item[2],answer[1], 1.e-2) # bond length model assert approx_equal(item[4],answer[2], 1.e-1) # target test_output(results) # ------------------------------------------------------------------------------ # BOND OUTLIERS # Model has H and D atoms, and only the following outliers # Bond CE2--DE2, observed: 0.876, delta from target: 0.203 # Bond CB--DB3, observed: 1.264, delta from target: -0.174 # Bond CD1--DD1, observed: 1.236, delta from target: -0.156 # Bond CB--DB2, observed: 1.002, delta from target: 0.087 # ------------------------------------------------------------------------------ def exercise9(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str9) outliers_bonds = results.outliers_bonds outliers_bond_answer = [ [' A 139 ATYR HE2', 0.986, 1.08], [' A 139 BTYR DH ', 1.123, 0.98], [' A 139 BTYR DD1', 1.243, 1.08], [' A 139 ATYR HB2', 0.893, 1.09], ] for item, answer in zip(outliers_bonds, outliers_bond_answer): assert (item[0].strip() == answer[0].strip()) # pdb_str assert (item[5] is not None) # make sure xyz exist assert approx_equal(item[2],answer[1], 1.e-2) # bond length model assert approx_equal(item[4],answer[2], 1.e-1) # target test_output(results) # ------------------------------------------------------------------------------ # ANGLE OUTLIERS # Model has H and D atoms, and only the two following outliers # Angle 'N-CA-HA', observed: 123.01, delta from target: -13.01 # Angle 'CB-CA-DA',observed: 121.11, delta from target: -12.11 # ------------------------------------------------------------------------------ def exercise10(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str10) outliers_angles = results.outliers_angles outliers_angles_answer = [ [' A 139 BTYR DA ', 121.11, 109.0, (10.557, 8.334, 6.899)], [' A 139 ATYR HA ', 123.01, 110.0, (10.583, 7.992, 7.177)] ] for item, answer in zip(outliers_angles, outliers_angles_answer): assert (item[0].strip() == answer[0].strip()) # pdb_str assert (item[5] is not None) # make sure xyz exist assert approx_equal(item[2],answer[1], 1.e-2) # angle in model assert approx_equal(item[4],answer[2], 1.e-1) # target test_output(results) # ------------------------------------------------------------------------------ # Mismatch between expected restraints and X-H(D) bond lengths # Input model has H at X-ray distances but use_neutron_distances flag is True # --> xray_distances_used flag should be True # ------------------------------------------------------------------------------ def exercise11(): results = get_results_from_validate_H( neutron_distances = True, pdb_str = pdb_str11) bond_results = results.bond_results assert(bond_results.xray_distances_used == True) test_output(results) def exercise12(): ''' Make sure that RNA H atoms are correctly identified as missing or present These atoms have names with '*' in libraries, but most recent used is "'" for example: H5*2 is in the database and in the file is H5'' (issue raised by Jermaine Jenkins July 2019) ''' results = get_results_from_validate_H( neutron_distances = False, pdb_str = pdb_str12a) missing = results.missing_HD_atoms assert (len(missing)==0) test_output(results) results = get_results_from_validate_H( neutron_distances = False, pdb_str = pdb_str12b) missing = results.missing_HD_atoms mt = missing[0] atom_names = mt[1] assert ("H5''" in atom_names and "H5'" in atom_names) assert (len(atom_names) == 2) def exercise_hd_state(): ''' CHECK HD STATE (hd_state) This is not a result but used internally to decide if H/D site analysis is necessary or not ''' pdb_inp = iotbx.pdb.input(lines=pdb_str4.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, log = null_out()) c = validate_H(model = model, use_neutron_distances = True) assert (c.get_hd_state() == 'all_h') pdb_inp = iotbx.pdb.input(lines=pdb_str5.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp) c = validate_H(model = model, use_neutron_distances = True) assert (c.get_hd_state() == 'all_d') pdb_inp = iotbx.pdb.input(lines=pdb_str3.split("\n"), source_info=None) model = mmtbx.model.manager( model_input = pdb_inp) c = validate_H(model = model, use_neutron_distances = True) assert (c.get_hd_state() == 'h_and_d') def run(): exercise() exercise1() exercise2() exercise3() exercise4() exercise5() exercise6() exercise7() exercise8() exercise9() exercise10() exercise11() exercise12() exercise_hd_state() if (__name__ == "__main__"): t0 = time.time() run() print("OK. Time: %8.3f"%(time.time()-t0))