from __future__ import absolute_import, division, print_function # this is so useful that we might as well store it centrally model_1yjp = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 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 END """ model_1yjp_with_waters = model_1yjp.replace('END', '''TER HETATM 61 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 62 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 63 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 64 O HOH A 11 11.808 4.179 9.970 1.00 23.99 O HETATM 65 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 66 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 67 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O END ''') # smallest PDB with a "ligand" model_1aL1 = ''' CRYST1 62.350 62.350 62.350 90.00 90.00 90.00 I 41 3 2 48 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016038 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016038 0.00000 HETATM 1 C ACE A 0 31.227 38.585 11.521 1.00 25.00 C HETATM 2 O ACE A 0 30.433 37.878 10.859 1.00 25.00 O HETATM 3 CH3 ACE A 0 30.894 39.978 11.951 1.00 25.00 C ATOM 4 N GLU A 1 32.153 37.943 12.252 1.00 25.00 N ATOM 5 CA GLU A 1 32.594 36.639 11.811 1.00 25.00 C ATOM 6 C GLU A 1 32.002 35.428 12.514 1.00 25.00 C ATOM 7 O GLU A 1 32.521 34.279 12.454 1.00 25.00 O ATOM 8 CB GLU A 1 34.093 36.609 11.812 1.00 25.00 C ATOM 9 CG GLU A 1 34.609 36.464 13.285 1.00 25.00 C ATOM 10 CD GLU A 1 36.125 36.460 13.044 1.00 25.00 C ATOM 11 OE1 GLU A 1 36.442 35.745 12.084 1.00 25.00 O ATOM 12 OE2 GLU A 1 36.684 37.260 13.809 1.00 25.00 O ATOM 13 N LEU A 2 30.895 35.627 13.188 1.00 25.00 N ATOM 14 CA LEU A 2 30.067 34.612 13.814 1.00 25.00 C ATOM 15 C LEU A 2 29.025 34.315 12.695 1.00 25.00 C ATOM 16 O LEU A 2 28.665 33.168 12.395 1.00 25.00 O ATOM 17 CB LEU A 2 29.515 35.034 15.156 1.00 25.00 C ATOM 18 CG LEU A 2 28.434 34.122 15.752 1.00 25.00 C ATOM 19 CD1 LEU A 2 29.008 33.110 16.720 1.00 25.00 C ATOM 20 CD2 LEU A 2 27.350 34.963 16.399 1.00 25.00 C ATOM 21 N LEU A 3 28.628 35.417 12.027 1.00 25.00 N ATOM 22 CA LEU A 3 27.686 35.251 10.912 1.00 25.00 C ATOM 23 C LEU A 3 28.396 34.389 9.850 1.00 25.00 C ATOM 24 O LEU A 3 27.770 33.565 9.191 1.00 25.00 O ATOM 25 CB LEU A 3 27.084 36.547 10.374 1.00 25.00 C ATOM 26 CG LEU A 3 26.064 36.325 9.246 1.00 25.00 C ATOM 27 CD1 LEU A 3 24.784 35.715 9.770 1.00 25.00 C ATOM 28 CD2 LEU A 3 25.777 37.594 8.497 1.00 25.00 C ATOM 29 N LYS A 4 29.674 34.603 9.703 1.00 25.00 N ATOM 30 CA LYS A 4 30.512 33.899 8.748 1.00 25.00 C ATOM 31 C LYS A 4 30.578 32.417 9.098 1.00 25.00 C ATOM 32 O LYS A 4 30.261 31.531 8.280 1.00 25.00 O ATOM 33 CB LYS A 4 31.924 34.471 8.710 1.00 25.00 C ATOM 34 CG LYS A 4 32.539 34.431 7.317 1.00 25.00 C ATOM 35 CD LYS A 4 34.046 34.511 7.426 1.00 25.00 C ATOM 36 CE LYS A 4 34.729 33.782 6.289 1.00 25.00 C ATOM 37 NZ LYS A 4 34.710 34.603 5.059 1.00 25.00 N ATOM 38 N LYS A 5 30.993 32.153 10.327 1.00 25.00 N ATOM 39 CA LYS A 5 31.104 30.730 10.715 1.00 25.00 C ATOM 40 C LYS A 5 29.734 30.111 10.595 1.00 25.00 C ATOM 41 O LYS A 5 29.602 29.133 9.833 1.00 25.00 O ATOM 42 CB LYS A 5 31.793 30.525 12.023 1.00 25.00 C ATOM 43 CG LYS A 5 33.284 30.906 12.043 1.00 25.00 C ATOM 44 N LEU A 6 28.753 30.676 11.269 1.00 25.00 N ATOM 45 CA LEU A 6 27.375 30.124 11.257 1.00 25.00 C ATOM 46 C LEU A 6 26.938 29.849 9.827 1.00 25.00 C ATOM 47 O LEU A 6 26.490 28.746 9.489 1.00 25.00 O ATOM 48 CB LEU A 6 26.459 31.026 12.062 1.00 25.00 C ATOM 49 CG LEU A 6 24.966 30.925 11.913 1.00 25.00 C ATOM 50 CD1 LEU A 6 24.329 29.894 12.837 1.00 25.00 C ATOM 51 CD2 LEU A 6 24.339 32.286 12.234 1.00 25.00 C ATOM 52 N LEU A 7 27.110 30.857 9.002 1.00 25.00 N ATOM 53 CA LEU A 7 26.760 30.849 7.586 1.00 25.00 C ATOM 54 C LEU A 7 27.408 29.683 6.868 1.00 25.00 C ATOM 55 O LEU A 7 26.743 29.154 5.950 1.00 25.00 O ATOM 56 CB LEU A 7 27.003 32.249 6.971 1.00 25.00 C ATOM 57 CG LEU A 7 25.878 33.239 6.752 1.00 25.00 C ATOM 58 CD1 LEU A 7 26.241 34.705 6.949 1.00 25.00 C ATOM 59 CD2 LEU A 7 25.397 33.158 5.297 1.00 25.00 C ATOM 60 N GLU A 8 28.603 29.243 7.208 1.00 25.00 N ATOM 61 CA GLU A 8 29.260 28.146 6.496 1.00 25.00 C ATOM 62 C GLU A 8 28.759 26.751 6.831 1.00 25.00 C ATOM 63 O GLU A 8 28.974 25.822 6.023 1.00 25.00 O ATOM 64 CB GLU A 8 30.742 28.009 6.785 1.00 25.00 C ATOM 65 CG GLU A 8 31.432 29.271 7.271 1.00 25.00 C ATOM 66 CD GLU A 8 32.846 28.933 7.703 1.00 25.00 C ATOM 67 OE1 GLU A 8 33.727 28.886 6.851 1.00 25.00 O ATOM 68 OE2 GLU A 8 32.945 28.685 8.934 1.00 25.00 O ATOM 69 N GLU A 9 28.216 26.687 8.024 1.00 25.00 N ATOM 70 CA GLU A 9 27.676 25.450 8.602 1.00 25.00 C ATOM 71 C GLU A 9 26.228 25.197 8.197 1.00 25.00 C ATOM 72 O GLU A 9 25.741 24.063 8.299 1.00 25.00 O ATOM 73 CB GLU A 9 27.655 25.571 10.131 1.00 25.00 C ATOM 74 CG GLU A 9 28.212 24.450 10.999 1.00 25.00 C ATOM 75 CD GLU A 9 29.424 24.893 11.771 1.00 25.00 C ATOM 76 OE1 GLU A 9 29.571 24.773 12.967 1.00 25.00 O ATOM 77 OE2 GLU A 9 30.236 25.448 10.993 1.00 25.00 O ATOM 78 N LEU A 10 25.547 26.243 7.776 1.00 25.00 N ATOM 79 CA LEU A 10 24.138 26.200 7.405 1.00 25.00 C ATOM 80 C LEU A 10 23.858 25.477 6.104 1.00 25.00 C ATOM 81 O LEU A 10 24.653 25.474 5.162 1.00 25.00 O ATOM 82 CB LEU A 10 23.611 27.641 7.410 1.00 25.00 C ATOM 83 CG LEU A 10 22.355 27.821 8.248 1.00 25.00 C ATOM 84 CD1 LEU A 10 22.565 27.116 9.582 1.00 25.00 C ATOM 85 CD2 LEU A 10 22.151 29.317 8.369 1.00 25.00 C ATOM 86 N LYS A 11 22.674 24.898 6.074 1.00 25.00 N ATOM 87 CA LYS A 11 22.163 24.138 4.939 1.00 25.00 C ATOM 88 C LYS A 11 21.851 25.032 3.731 1.00 25.00 C ATOM 89 O LYS A 11 21.403 26.185 3.840 1.00 25.00 O ATOM 90 CB LYS A 11 20.933 23.323 5.327 1.00 25.00 C ATOM 91 N GLY A 12 22.109 24.411 2.573 1.00 25.00 N ATOM 92 CA GLY A 12 21.938 24.917 1.234 1.00 25.00 C ATOM 93 C GLY A 12 21.882 26.448 1.133 1.00 25.00 C ATOM 94 O GLY A 12 22.838 26.994 0.516 1.00 25.00 O ATOM 95 OXT GLY A 12 20.888 27.022 1.650 1.00 25.00 O TER 96 GLY A 12 HETATM 97 S SO4 A 13 31.477 38.950 15.821 0.50 25.00 S HETATM 98 O1 SO4 A 13 31.243 38.502 17.238 0.50 25.00 O HETATM 99 O2 SO4 A 13 30.616 40.133 15.527 0.50 25.00 O HETATM 100 O3 SO4 A 13 31.158 37.816 14.905 0.50 25.00 O HETATM 101 O4 SO4 A 13 32.916 39.343 15.640 0.50 25.00 O END '''