from __future__ import absolute_import, division, print_function from libtbx.test_utils import approx_equal import iotbx.pdb from cctbx import maptbx from cctbx import maptbx from six.moves import zip raw_records = """\ CRYST1 26.880 33.600 31.920 90.00 90.00 90.00 P 1 ATOM 1 N META1 1 6.457 5.962 7.411 1.00945.14 N ATOM 2 CA META1 1 6.950 5.877 5.993 1.00928.61 C ATOM 3 C META1 1 8.223 6.699 5.793 1.00910.08 C ATOM 4 O META1 1 9.243 6.182 5.328 1.00910.73 O ATOM 5 CB META1 1 5.876 6.358 5.004 1.00932.69 C ATOM 6 CG META1 1 4.568 5.569 5.015 1.00937.71 C ATOM 7 SD META1 1 4.706 3.879 4.402 1.00945.00 S ATOM 8 CE META1 1 3.085 3.239 4.820 1.00941.13 C ATOM 9 N GLNA1 2 8.145 7.976 6.159 1.00985.67 N ATOM 10 CA GLNA1 2 9.224 8.943 5.958 1.00979.66 C ATOM 11 C GLNA1 2 10.241 9.025 7.112 1.00974.69 C ATOM 12 O GLNA1 2 11.358 9.495 6.896 1.00979.07 O ATOM 13 CB GLNA1 2 8.595 10.314 5.711 1.00980.23 C ATOM 14 CG GLNA1 2 9.537 11.423 5.259 1.00989.23 C ATOM 15 CD GLNA1 2 10.274 11.097 3.976 1.00902.03 C ATOM 16 OE1 GLNA1 2 9.763 10.385 3.110 1.00904.39 O ATOM 17 NE2 GLNA1 2 11.484 11.624 3.845 1.00937.18 N ATOM 18 N ARGA1 3 9.853 8.577 8.312 1.00964.30 N ATOM 19 CA ARGA1 3 10.716 8.560 9.520 1.00966.26 C ATOM 20 C ARGA1 3 10.999 9.975 10.053 1.00966.52 C ATOM 21 O ARGA1 3 11.841 10.691 9.509 1.00968.91 O ATOM 22 CB ARGA1 3 12.026 7.778 9.276 1.00972.03 C ATOM 23 CG ARGA1 3 13.003 7.724 10.446 1.00980.32 C ATOM 24 CD ARGA1 3 12.400 7.099 11.694 1.00993.10 C ATOM 25 NE ARGA1 3 13.347 7.098 12.809 1.00910.27 N ATOM 26 CZ ARGA1 3 13.072 6.692 14.050 1.00920.50 C ATOM 27 NH1 ARGA1 3 14.021 6.744 14.983 1.00930.56 N ATOM 28 NH2 ARGA1 3 11.860 6.234 14.373 1.00927.11 N ATOM 29 N SERA1 4 10.310 10.351 11.133 1.00970.10 N ATOM 30 CA SERA1 4 10.354 11.730 11.665 1.00969.72 C ATOM 31 C SERA1 4 11.636 12.037 12.458 1.00972.14 C ATOM 32 O SERA1 4 12.139 11.164 13.169 1.00972.46 O ATOM 33 CB SERA1 4 9.136 12.007 12.554 1.00967.95 C ATOM 34 OG SERA1 4 9.282 11.419 13.837 1.00966.18 O ATOM 35 N PROA1 5 12.143 13.288 12.370 1.00976.06 N ATOM 36 CA PROA1 5 13.432 13.642 12.995 1.00970.63 C ATOM 37 C PROA1 5 13.413 13.900 14.515 1.00962.60 C ATOM 38 O PROA1 5 14.460 13.795 15.158 1.00953.71 O ATOM 39 CB PROA1 5 13.835 14.912 12.244 1.00971.75 C ATOM 40 CG PROA1 5 12.538 15.556 11.904 1.00970.02 C ATOM 41 CD PROA1 5 11.546 14.450 11.681 1.00969.15 C ATOM 42 N VALA1 6 12.247 14.236 15.074 1.00957.91 N ATOM 43 CA VALA1 6 12.086 14.442 16.521 1.00956.66 C ATOM 44 C VALA1 6 12.466 13.191 17.316 1.00964.35 C ATOM 45 O VALA1 6 12.902 13.293 18.463 1.00963.11 O ATOM 46 CB VALA1 6 10.646 14.895 16.873 1.00953.86 C ATOM 47 CG1 VALA1 6 9.629 13.783 16.632 1.00955.04 C ATOM 48 CG2 VALA1 6 10.564 15.418 18.305 1.00951.21 C ATOM 49 N GLUA1 7 12.275 12.023 16.699 1.00981.64 N ATOM 50 CA GLUA1 7 12.746 10.740 17.244 1.00986.88 C ATOM 51 C GLUA1 7 14.251 10.751 17.542 1.00984.08 C ATOM 52 O GLUA1 7 14.682 10.288 18.602 1.00981.69 O ATOM 53 CB GLUA1 7 12.428 9.594 16.274 1.00992.25 C ATOM 54 CG GLUA1 7 10.942 9.304 16.075 1.00998.55 C ATOM 55 CD GLUA1 7 10.255 8.692 17.292 1.00908.01 C ATOM 56 OE1 GLUA1 7 10.945 8.223 18.225 1.00917.52 O ATOM 57 OE2 GLUA1 7 9.006 8.674 17.310 1.00911.20 O ATOM 58 N ASPA1 8 15.029 11.281 16.597 1.00981.90 N ATOM 59 CA ASPA1 8 16.486 11.412 16.728 1.00973.55 C ATOM 60 C ASPA1 8 16.859 12.874 16.984 1.00968.82 C ATOM 61 O ASPA1 8 17.526 13.518 16.167 1.00967.38 O ATOM 62 CB ASPA1 8 17.181 10.885 15.466 1.00972.03 C ATOM 63 CG ASPA1 8 16.797 9.452 15.138 1.00970.76 C ATOM 64 OD1 ASPA1 8 16.670 8.634 16.072 1.00971.90 O ATOM 65 OD2 ASPA1 8 16.624 9.145 13.939 1.00969.04 O ATOM 66 N ALAA1 9 16.415 13.379 18.132 1.00961.64 N ATOM 67 CA ALAA1 9 16.603 14.784 18.516 1.00966.44 C ATOM 68 C ALAA1 9 17.351 14.937 19.844 1.00967.19 C ATOM 69 O ALAA1 9 17.283 14.063 20.712 1.00961.82 O ATOM 70 CB ALAA1 9 15.256 15.486 18.591 1.00968.54 C ATOM 71 N ASNA1 10 18.056 16.065 19.975 1.00973.18 N ATOM 72 CA ASNA1 10 18.795 16.429 21.183 1.00964.26 C ATOM 73 C ASNA1 10 18.003 17.403 22.070 1.00968.71 C ATOM 74 O ASNA1 10 17.219 18.228 21.577 1.00959.02 O ATOM 75 CB ASNA1 10 20.144 17.045 20.791 1.00956.30 C ATOM 76 CG ASNA1 10 21.141 17.087 21.939 1.00955.13 C ATOM 77 OD1 ASNA1 10 20.945 16.476 22.991 1.00949.89 O ATOM 78 ND2 ASNA1 10 22.228 17.814 21.732 1.00958.95 N ATOM 79 N CYSA1 11 18.240 17.302 23.378 1.00 20.00 N ATOM 80 CA CYSA1 11 17.509 18.064 24.406 1.00 20.00 C ATOM 81 C CYSA1 11 17.457 19.576 24.165 1.00 20.00 C ATOM 82 O CYSA1 11 16.456 20.218 24.484 1.00 20.00 O ATOM 83 CB CYSA1 11 18.093 17.773 25.796 1.00 20.00 C ATOM 84 SG CYSA1 11 19.900 17.783 25.877 1.00 20.00 S ATOM 85 N LEUA1 12 18.530 20.132 23.607 1.00 20.00 N ATOM 86 CA LEUA1 12 18.578 21.549 23.243 1.00 20.00 C ATOM 87 C LEUA1 12 17.781 21.794 21.968 1.00 20.00 C ATOM 88 O LEUA1 12 16.997 22.747 21.888 1.00 20.00 O ATOM 89 CB LEUA1 12 20.023 22.024 23.056 1.00 20.00 C ATOM 90 CG LEUA1 12 20.775 22.412 24.332 1.00 20.00 C ATOM 91 CD1 LEUA1 12 21.100 21.195 25.188 1.00 20.00 C ATOM 92 CD2 LEUA1 12 22.051 23.166 23.986 1.00 20.00 C ATOM 93 N SERA1 13 17.979 20.922 20.982 1.00 20.00 N ATOM 94 CA SERA1 13 17.342 21.072 19.672 1.00 20.00 C ATOM 95 C SERA1 13 15.823 20.970 19.753 1.00 20.00 C ATOM 96 O SERA1 13 15.111 21.701 19.049 1.00 20.00 O ATOM 97 CB SERA1 13 17.897 20.057 18.667 1.00 20.00 C ATOM 98 OG SERA1 13 17.826 18.736 19.165 1.00 20.00 O ATOM 99 N ARGA1 14 15.340 20.073 20.614 1.00 20.00 N ATOM 100 CA ARGA1 14 13.895 19.927 20.840 1.00 20.00 C ATOM 101 C ARGA1 14 13.283 21.099 21.632 1.00 20.00 C ATOM 102 O ARGA1 14 12.119 21.445 21.419 1.00 20.00 O ATOM 103 CB ARGA1 14 13.570 18.579 21.500 1.00 20.00 C ATOM 104 CG ARGA1 14 14.072 18.405 22.922 1.00 20.00 C ATOM 105 CD ARGA1 14 13.841 16.988 23.418 1.00 20.00 C ATOM 106 NE ARGA1 14 12.423 16.714 23.658 1.00 20.00 N ATOM 107 CZ ARGA1 14 11.935 15.592 24.195 1.00 20.00 C ATOM 108 NH1 ARGA1 14 10.619 15.463 24.369 1.00 20.00 N ATOM 109 NH2 ARGA1 14 12.742 14.594 24.564 1.00 20.00 N ATOM 110 N TYRA1 15 14.065 21.700 22.532 1.00 20.00 N ATOM 111 CA TYRA1 15 13.624 22.854 23.325 1.00 20.00 C ATOM 112 C TYRA1 15 13.416 24.094 22.457 1.00 20.00 C ATOM 113 O TYRA1 15 12.343 24.698 22.482 1.00 20.00 O ATOM 114 CB TYRA1 15 14.648 23.155 24.422 1.00 20.00 C ATOM 115 CG TYRA1 15 14.241 24.242 25.389 1.00 20.00 C ATOM 116 CD1 TYRA1 15 13.524 23.941 26.547 1.00 20.00 C ATOM 117 CD2 TYRA1 15 14.590 25.574 25.161 1.00 20.00 C ATOM 118 CE1 TYRA1 15 13.156 24.935 27.445 1.00 20.00 C ATOM 119 CE2 TYRA1 15 14.226 26.577 26.050 1.00 20.00 C ATOM 120 CZ TYRA1 15 13.510 26.254 27.191 1.00 20.00 C ATOM 121 OH TYRA1 15 13.147 27.244 28.077 1.00 20.00 O ATOM 122 N PHEA1 16 14.448 24.460 21.697 1.00 20.00 N ATOM 123 CA PHEA1 16 14.402 25.621 20.779 1.00 20.00 C ATOM 124 C PHEA1 16 13.776 25.358 19.393 1.00 20.00 C ATOM 125 O PHEA1 16 13.545 26.313 18.643 1.00 20.00 O ATOM 126 CB PHEA1 16 15.814 26.192 20.575 1.00 20.00 C ATOM 127 CG PHEA1 16 16.319 26.997 21.734 1.00 20.00 C ATOM 128 CD1 PHEA1 16 16.018 28.349 21.840 1.00 20.00 C ATOM 129 CD2 PHEA1 16 17.110 26.410 22.712 1.00 20.00 C ATOM 130 CE1 PHEA1 16 16.490 29.099 22.909 1.00 20.00 C ATOM 131 CE2 PHEA1 16 17.581 27.153 23.785 1.00 20.00 C ATOM 132 CZ PHEA1 16 17.272 28.501 23.883 1.00 20.00 C ATOM 133 N PHEA1 17 13.499 24.089 19.068 1.00 20.00 N ATOM 134 CA PHEA1 17 13.061 23.671 17.724 1.00 20.00 C ATOM 135 C PHEA1 17 14.112 23.971 16.634 1.00 20.00 C ATOM 136 O PHEA1 17 13.961 24.927 15.864 1.00 20.00 O ATOM 137 CB PHEA1 17 11.696 24.288 17.357 1.00 20.00 C ATOM 138 CG PHEA1 17 10.643 24.113 18.413 1.00 20.00 C ATOM 139 CD1 PHEA1 17 9.834 22.986 18.423 1.00 20.00 C ATOM 140 CD2 PHEA1 17 10.451 25.082 19.394 1.00 20.00 C ATOM 141 CE1 PHEA1 17 8.855 22.825 19.394 1.00 20.00 C ATOM 142 CE2 PHEA1 17 9.476 24.925 20.369 1.00 20.00 C ATOM 143 CZ PHEA1 17 8.675 23.795 20.370 1.00 20.00 C ATOM 144 N TRPA1 18 15.177 23.164 16.593 1.00 20.00 N ATOM 145 CA TRPA1 18 16.173 23.217 15.500 1.00 20.00 C ATOM 146 C TRPA1 18 15.755 22.365 14.287 1.00 20.00 C ATOM 147 O TRPA1 18 16.241 22.588 13.175 1.00 20.00 O ATOM 148 CB TRPA1 18 17.555 22.750 15.985 1.00 20.00 C ATOM 149 CG TRPA1 18 18.326 23.748 16.815 1.00 20.00 C ATOM 150 CD1 TRPA1 18 17.963 24.262 18.026 1.00 20.00 C ATOM 151 CD2 TRPA1 18 19.609 24.321 16.505 1.00 20.00 C ATOM 152 NE1 TRPA1 18 18.931 25.126 18.488 1.00 20.00 N ATOM 153 CE2 TRPA1 18 19.949 25.185 17.575 1.00 20.00 C ATOM 154 CE3 TRPA1 18 20.499 24.197 15.427 1.00 20.00 C ATOM 155 CZ2 TRPA1 18 21.145 25.922 17.598 1.00 20.00 C ATOM 156 CZ3 TRPA1 18 21.692 24.933 15.451 1.00 20.00 C ATOM 157 CH2 TRPA1 18 22.000 25.783 16.532 1.00 20.00 C ATOM 158 N TRPA1 19 14.858 21.401 14.508 1.00 20.00 N ATOM 159 CA TRPA1 19 14.551 20.352 13.512 1.00 20.00 C ATOM 160 C TRPA1 19 13.654 20.762 12.341 1.00 20.00 C ATOM 161 O TRPA1 19 13.665 20.095 11.303 1.00 20.00 O ATOM 162 CB TRPA1 19 13.982 19.092 14.183 1.00 20.00 C ATOM 163 CG TRPA1 19 12.647 19.247 14.852 1.00 20.00 C ATOM 164 CD1 TRPA1 19 12.423 19.644 16.133 1.00 20.00 C ATOM 165 CD2 TRPA1 19 11.359 18.966 14.289 1.00 20.00 C ATOM 166 NE1 TRPA1 19 11.079 19.648 16.401 1.00 20.00 N ATOM 167 CE2 TRPA1 19 10.400 19.233 15.289 1.00 20.00 C ATOM 168 CE3 TRPA1 19 10.921 18.522 13.036 1.00 20.00 C ATOM 169 CZ2 TRPA1 19 9.025 19.072 15.080 1.00 20.00 C ATOM 170 CZ3 TRPA1 19 9.548 18.359 12.825 1.00 20.00 C ATOM 171 CH2 TRPA1 19 8.619 18.635 13.845 1.00 20.00 C ATOM 172 N THRA1 20 12.893 21.842 12.494 1.00 20.00 N ATOM 173 CA THRA1 20 12.024 22.334 11.408 1.00 20.00 C ATOM 174 C THRA1 20 12.757 22.960 10.196 1.00 20.00 C ATOM 175 O THRA1 20 12.143 23.126 9.131 1.00 20.00 O ATOM 176 CB THRA1 20 10.981 23.340 11.942 1.00 20.00 C ATOM 177 OG1 THRA1 20 11.638 24.387 12.665 1.00 20.00 O ATOM 178 CG2 THRA1 20 9.986 22.643 12.860 1.00 20.00 C """.splitlines() raw_records_2 = """\ CRYST1 26.880 33.600 31.920 90.00 90.00 90.00 P 1 ATOM 1 N META1 1 6.457 5.962 7.411 1.00200.00 N ATOM 2 CA META1 1 6.950 5.877 5.993 1.00200.00 C ATOM 3 C META1 1 8.223 6.699 5.793 1.00200.00 C ATOM 4 O META1 1 9.243 6.182 5.328 1.00200.00 O ATOM 5 CB META1 1 5.876 6.358 5.004 1.00200.00 C ATOM 6 CG META1 1 4.568 5.569 5.015 1.00200.00 C ATOM 7 SD META1 1 4.706 3.879 4.402 1.00200.00 S ATOM 8 CE META1 1 3.085 3.239 4.820 1.00200.00 C ATOM 9 N GLNA1 2 8.145 7.976 6.159 1.00200.00 N ATOM 10 CA GLNA1 2 9.224 8.943 5.958 1.00200.00 C ATOM 11 C GLNA1 2 10.241 9.025 7.112 1.00200.00 C ATOM 12 O GLNA1 2 11.358 9.495 6.896 1.00200.00 O ATOM 13 CB GLNA1 2 8.595 10.314 5.711 1.00200.00 C ATOM 14 CG GLNA1 2 9.537 11.423 5.259 1.00200.00 C ATOM 15 CD GLNA1 2 10.274 11.097 3.976 1.00200.00 C ATOM 16 OE1 GLNA1 2 9.763 10.385 3.110 1.00200.00 O ATOM 17 NE2 GLNA1 2 11.484 11.624 3.845 1.00200.00 N ATOM 18 N ARGA1 3 9.853 8.577 8.312 1.00200.00 N ATOM 19 CA ARGA1 3 10.716 8.560 9.520 1.00200.00 C ATOM 20 C ARGA1 3 10.999 9.975 10.053 1.00200.00 C ATOM 21 O ARGA1 3 11.841 10.691 9.509 1.00200.00 O ATOM 22 CB ARGA1 3 12.026 7.778 9.276 1.00200.00 C ATOM 23 CG ARGA1 3 13.003 7.724 10.446 1.00200.00 C ATOM 24 CD ARGA1 3 12.400 7.099 11.694 1.00200.00 C ATOM 25 NE ARGA1 3 13.347 7.098 12.809 1.00200.00 N ATOM 26 CZ ARGA1 3 13.072 6.692 14.050 1.00200.00 C ATOM 27 NH1 ARGA1 3 14.021 6.744 14.983 1.00200.00 N ATOM 28 NH2 ARGA1 3 11.860 6.234 14.373 1.00200.00 N ATOM 29 N SERA1 4 10.310 10.351 11.133 1.00200.00 N ATOM 30 CA SERA1 4 10.354 11.730 11.665 1.00200.00 C ATOM 31 C SERA1 4 11.636 12.037 12.458 1.00200.00 C ATOM 32 O SERA1 4 12.139 11.164 13.169 1.00200.00 O ATOM 33 CB SERA1 4 9.136 12.007 12.554 1.00200.00 C ATOM 34 OG SERA1 4 9.282 11.419 13.837 1.00200.00 O ATOM 35 N PROA1 5 12.143 13.288 12.370 1.00200.00 N ATOM 36 CA PROA1 5 13.432 13.642 12.995 1.00200.00 C ATOM 37 C PROA1 5 13.413 13.900 14.515 1.00200.00 C ATOM 38 O PROA1 5 14.460 13.795 15.158 1.00200.00 O ATOM 39 CB PROA1 5 13.835 14.912 12.244 1.00200.00 C ATOM 40 CG PROA1 5 12.538 15.556 11.904 1.00200.00 C ATOM 41 CD PROA1 5 11.546 14.450 11.681 1.00200.00 C ATOM 42 N VALA1 6 12.247 14.236 15.074 1.00200.00 N ATOM 43 CA VALA1 6 12.086 14.442 16.521 1.00200.00 C ATOM 44 C VALA1 6 12.466 13.191 17.316 1.00200.00 C ATOM 45 O VALA1 6 12.902 13.293 18.463 1.00200.00 O ATOM 46 CB VALA1 6 10.646 14.895 16.873 1.00200.00 C ATOM 47 CG1 VALA1 6 9.629 13.783 16.632 1.00200.00 C ATOM 48 CG2 VALA1 6 10.564 15.418 18.305 1.00200.00 C ATOM 49 N GLUA1 7 12.275 12.023 16.699 1.00200.00 N ATOM 50 CA GLUA1 7 12.746 10.740 17.244 1.00200.00 C ATOM 51 C GLUA1 7 14.251 10.751 17.542 1.00200.00 C ATOM 52 O GLUA1 7 14.682 10.288 18.602 1.00200.00 O ATOM 53 CB GLUA1 7 12.428 9.594 16.274 1.00200.00 C ATOM 54 CG GLUA1 7 10.942 9.304 16.075 1.00200.00 C ATOM 55 CD GLUA1 7 10.255 8.692 17.292 1.00200.00 C ATOM 56 OE1 GLUA1 7 10.945 8.223 18.225 1.00200.00 O ATOM 57 OE2 GLUA1 7 9.006 8.674 17.310 1.00200.00 O ATOM 58 N ASPA1 8 15.029 11.281 16.597 1.00200.00 N ATOM 59 CA ASPA1 8 16.486 11.412 16.728 1.00200.00 C ATOM 60 C ASPA1 8 16.859 12.874 16.984 1.00200.00 C ATOM 61 O ASPA1 8 17.526 13.518 16.167 1.00200.00 O ATOM 62 CB ASPA1 8 17.181 10.885 15.466 1.00200.00 C ATOM 63 CG ASPA1 8 16.797 9.452 15.138 1.00200.00 C ATOM 64 OD1 ASPA1 8 16.670 8.634 16.072 1.00200.00 O ATOM 65 OD2 ASPA1 8 16.624 9.145 13.939 1.00200.00 O ATOM 66 N ALAA1 9 16.415 13.379 18.132 1.00200.00 N ATOM 67 CA ALAA1 9 16.603 14.784 18.516 1.00200.00 C ATOM 68 C ALAA1 9 17.351 14.937 19.844 1.00200.00 C ATOM 69 O ALAA1 9 17.283 14.063 20.712 1.00200.00 O ATOM 70 CB ALAA1 9 15.256 15.486 18.591 1.00200.00 C ATOM 71 N ASNA1 10 18.056 16.065 19.975 1.00200.00 N ATOM 72 CA ASNA1 10 18.795 16.429 21.183 1.00200.00 C ATOM 73 C ASNA1 10 18.003 17.403 22.070 1.00200.00 C ATOM 74 O ASNA1 10 17.219 18.228 21.577 1.00200.00 O ATOM 75 CB ASNA1 10 20.144 17.045 20.791 1.00200.00 C ATOM 76 CG ASNA1 10 21.141 17.087 21.939 1.00200.00 C ATOM 77 OD1 ASNA1 10 20.945 16.476 22.991 1.00200.00 O ATOM 78 ND2 ASNA1 10 22.228 17.814 21.732 1.00200.00 N ATOM 79 N CYSA1 11 18.240 17.302 23.378 1.00 20.00 N ATOM 80 CA CYSA1 11 17.509 18.064 24.406 1.00 20.00 C ATOM 81 C CYSA1 11 17.457 19.576 24.165 1.00 20.00 C ATOM 82 O CYSA1 11 16.456 20.218 24.484 1.00 20.00 O ATOM 83 CB CYSA1 11 18.093 17.773 25.796 1.00 20.00 C ATOM 84 SG CYSA1 11 19.900 17.783 25.877 1.00 20.00 S ATOM 85 N LEUA1 12 18.530 20.132 23.607 1.00 20.00 N ATOM 86 CA LEUA1 12 18.578 21.549 23.243 1.00 20.00 C ATOM 87 C LEUA1 12 17.781 21.794 21.968 1.00 20.00 C ATOM 88 O LEUA1 12 16.997 22.747 21.888 1.00 20.00 O ATOM 89 CB LEUA1 12 20.023 22.024 23.056 1.00 20.00 C ATOM 90 CG LEUA1 12 20.775 22.412 24.332 1.00 20.00 C ATOM 91 CD1 LEUA1 12 21.100 21.195 25.188 1.00 20.00 C ATOM 92 CD2 LEUA1 12 22.051 23.166 23.986 1.00 20.00 C ATOM 93 N SERA1 13 17.979 20.922 20.982 1.00 20.00 N ATOM 94 CA SERA1 13 17.342 21.072 19.672 1.00 20.00 C ATOM 95 C SERA1 13 15.823 20.970 19.753 1.00 20.00 C ATOM 96 O SERA1 13 15.111 21.701 19.049 1.00 20.00 O ATOM 97 CB SERA1 13 17.897 20.057 18.667 1.00 20.00 C ATOM 98 OG SERA1 13 17.826 18.736 19.165 1.00 20.00 O ATOM 99 N ARGA1 14 15.340 20.073 20.614 1.00 20.00 N ATOM 100 CA ARGA1 14 13.895 19.927 20.840 1.00 20.00 C ATOM 101 C ARGA1 14 13.283 21.099 21.632 1.00 20.00 C ATOM 102 O ARGA1 14 12.119 21.445 21.419 1.00 20.00 O ATOM 103 CB ARGA1 14 13.570 18.579 21.500 1.00 20.00 C ATOM 104 CG ARGA1 14 14.072 18.405 22.922 1.00 20.00 C ATOM 105 CD ARGA1 14 13.841 16.988 23.418 1.00 20.00 C ATOM 106 NE ARGA1 14 12.423 16.714 23.658 1.00 20.00 N ATOM 107 CZ ARGA1 14 11.935 15.592 24.195 1.00 20.00 C ATOM 108 NH1 ARGA1 14 10.619 15.463 24.369 1.00 20.00 N ATOM 109 NH2 ARGA1 14 12.742 14.594 24.564 1.00 20.00 N ATOM 110 N TYRA1 15 14.065 21.700 22.532 1.00 20.00 N ATOM 111 CA TYRA1 15 13.624 22.854 23.325 1.00 20.00 C ATOM 112 C TYRA1 15 13.416 24.094 22.457 1.00 20.00 C ATOM 113 O TYRA1 15 12.343 24.698 22.482 1.00 20.00 O ATOM 114 CB TYRA1 15 14.648 23.155 24.422 1.00 20.00 C ATOM 115 CG TYRA1 15 14.241 24.242 25.389 1.00 20.00 C ATOM 116 CD1 TYRA1 15 13.524 23.941 26.547 1.00 20.00 C ATOM 117 CD2 TYRA1 15 14.590 25.574 25.161 1.00 20.00 C ATOM 118 CE1 TYRA1 15 13.156 24.935 27.445 1.00 20.00 C ATOM 119 CE2 TYRA1 15 14.226 26.577 26.050 1.00 20.00 C ATOM 120 CZ TYRA1 15 13.510 26.254 27.191 1.00 20.00 C ATOM 121 OH TYRA1 15 13.147 27.244 28.077 1.00 20.00 O ATOM 122 N PHEA1 16 14.448 24.460 21.697 1.00 20.00 N ATOM 123 CA PHEA1 16 14.402 25.621 20.779 1.00 20.00 C ATOM 124 C PHEA1 16 13.776 25.358 19.393 1.00 20.00 C ATOM 125 O PHEA1 16 13.545 26.313 18.643 1.00 20.00 O ATOM 126 CB PHEA1 16 15.814 26.192 20.575 1.00 20.00 C ATOM 127 CG PHEA1 16 16.319 26.997 21.734 1.00 20.00 C ATOM 128 CD1 PHEA1 16 16.018 28.349 21.840 1.00 20.00 C ATOM 129 CD2 PHEA1 16 17.110 26.410 22.712 1.00 20.00 C ATOM 130 CE1 PHEA1 16 16.490 29.099 22.909 1.00 20.00 C ATOM 131 CE2 PHEA1 16 17.581 27.153 23.785 1.00 20.00 C ATOM 132 CZ PHEA1 16 17.272 28.501 23.883 1.00 20.00 C ATOM 133 N PHEA1 17 13.499 24.089 19.068 1.00 20.00 N ATOM 134 CA PHEA1 17 13.061 23.671 17.724 1.00 20.00 C ATOM 135 C PHEA1 17 14.112 23.971 16.634 1.00 20.00 C ATOM 136 O PHEA1 17 13.961 24.927 15.864 1.00 20.00 O ATOM 137 CB PHEA1 17 11.696 24.288 17.357 1.00 20.00 C ATOM 138 CG PHEA1 17 10.643 24.113 18.413 1.00 20.00 C ATOM 139 CD1 PHEA1 17 9.834 22.986 18.423 1.00 20.00 C ATOM 140 CD2 PHEA1 17 10.451 25.082 19.394 1.00 20.00 C ATOM 141 CE1 PHEA1 17 8.855 22.825 19.394 1.00 20.00 C ATOM 142 CE2 PHEA1 17 9.476 24.925 20.369 1.00 20.00 C ATOM 143 CZ PHEA1 17 8.675 23.795 20.370 1.00 20.00 C ATOM 144 N TRPA1 18 15.177 23.164 16.593 1.00 20.00 N ATOM 145 CA TRPA1 18 16.173 23.217 15.500 1.00 20.00 C ATOM 146 C TRPA1 18 15.755 22.365 14.287 1.00 20.00 C ATOM 147 O TRPA1 18 16.241 22.588 13.175 1.00 20.00 O ATOM 148 CB TRPA1 18 17.555 22.750 15.985 1.00 20.00 C ATOM 149 CG TRPA1 18 18.326 23.748 16.815 1.00 20.00 C ATOM 150 CD1 TRPA1 18 17.963 24.262 18.026 1.00 20.00 C ATOM 151 CD2 TRPA1 18 19.609 24.321 16.505 1.00 20.00 C ATOM 152 NE1 TRPA1 18 18.931 25.126 18.488 1.00 20.00 N ATOM 153 CE2 TRPA1 18 19.949 25.185 17.575 1.00 20.00 C ATOM 154 CE3 TRPA1 18 20.499 24.197 15.427 1.00 20.00 C ATOM 155 CZ2 TRPA1 18 21.145 25.922 17.598 1.00 20.00 C ATOM 156 CZ3 TRPA1 18 21.692 24.933 15.451 1.00 20.00 C ATOM 157 CH2 TRPA1 18 22.000 25.783 16.532 1.00 20.00 C ATOM 158 N TRPA1 19 14.858 21.401 14.508 1.00 20.00 N ATOM 159 CA TRPA1 19 14.551 20.352 13.512 1.00 20.00 C ATOM 160 C TRPA1 19 13.654 20.762 12.341 1.00 20.00 C ATOM 161 O TRPA1 19 13.665 20.095 11.303 1.00 20.00 O ATOM 162 CB TRPA1 19 13.982 19.092 14.183 1.00 20.00 C ATOM 163 CG TRPA1 19 12.647 19.247 14.852 1.00 20.00 C ATOM 164 CD1 TRPA1 19 12.423 19.644 16.133 1.00 20.00 C ATOM 165 CD2 TRPA1 19 11.359 18.966 14.289 1.00 20.00 C ATOM 166 NE1 TRPA1 19 11.079 19.648 16.401 1.00 20.00 N ATOM 167 CE2 TRPA1 19 10.400 19.233 15.289 1.00 20.00 C ATOM 168 CE3 TRPA1 19 10.921 18.522 13.036 1.00 20.00 C ATOM 169 CZ2 TRPA1 19 9.025 19.072 15.080 1.00 20.00 C ATOM 170 CZ3 TRPA1 19 9.548 18.359 12.825 1.00 20.00 C ATOM 171 CH2 TRPA1 19 8.619 18.635 13.845 1.00 20.00 C ATOM 172 N THRA1 20 12.893 21.842 12.494 1.00 20.00 N ATOM 173 CA THRA1 20 12.024 22.334 11.408 1.00 20.00 C ATOM 174 C THRA1 20 12.757 22.960 10.196 1.00 20.00 C ATOM 175 O THRA1 20 12.143 23.126 9.131 1.00 20.00 O ATOM 176 CB THRA1 20 10.981 23.340 11.942 1.00 20.00 C ATOM 177 OG1 THRA1 20 11.638 24.387 12.665 1.00 20.00 O ATOM 178 CG2 THRA1 20 9.986 22.643 12.860 1.00 20.00 C """.splitlines() def get_b_and_occ(hierarchy=None,atom_selection=None): atom_selection="name CA and (resid 5 or resid 15)" asc1=hierarchy.atom_selection_cache() sel1 = asc1.selection(string = atom_selection) b_values=list(hierarchy.select(sel1).atoms().extract_b()) resolutions=list(hierarchy.select(sel1).atoms().extract_occ()) return b_values,resolutions def make_map_from_pdb(raw_records=None,set_b_iso=None): pdb_inp = iotbx.pdb.input(source_info=None, lines=raw_records) ph = pdb_inp.construct_hierarchy() xrs = pdb_inp.xray_structure_simple() if set_b_iso: xrs.set_b_iso(value=set_b_iso) crystal_symmetry=xrs.crystal_symmetry() fc = xrs.structure_factors(d_min = 3, algorithm = "direct").f_calc() fft_map = fc.fft_map(resolution_factor = 0.25) fft_map.apply_sigma_scaling() map_data = fft_map.real_map_unpadded() # Create model instead of pdb_hierarchy ph.adopt_xray_structure(xrs) import mmtbx.model model=mmtbx.model.manager( model_input = ph.as_pdb_input(), crystal_symmetry = crystal_symmetry) return model,map_data,crystal_symmetry def tst_0(): model,map_data,crystal_symmetry=make_map_from_pdb(raw_records=raw_records) method="rscc" pdb_hierarchy_new = maptbx.loc_res( map = map_data, model = model, crystal_symmetry = crystal_symmetry, chunk_size = 10, soft_mask_radius = 3., method = method) b_values,occs=get_b_and_occ(hierarchy=pdb_hierarchy_new, atom_selection="name CA and (resid 5 or resid 15)") print("\nBvalues (resolutions): for %s: %s" %(method,str(b_values))) assert approx_equal(b_values,[7.5, 3.0]) method = "fsc" pdb_hierarchy_new = maptbx.loc_res( map = map_data, model= model, crystal_symmetry = crystal_symmetry, chunk_size = 10, soft_mask_radius = 3., method = method, fsc_cutoff = 0.143) b_values,occs=get_b_and_occ(hierarchy=pdb_hierarchy_new, atom_selection="name CA and (resid 5 or resid 15)") print("\nBvalues (resolutions): for %s: %s" %(method,str(b_values))) assert approx_equal(b_values,[2.72, 2.27],eps=.05) def tst_1(): for set_b_iso,expected_b_values,expected_occs in zip( [-200,0,200], [[200.0, 200.0],[-20.0, -20.0],[-160.0, -180.0]], [[3.0, 3.0],[3.4, 3.0],[3.2, 3.1]] ): model,map_data,crystal_symmetry=make_map_from_pdb(raw_records=raw_records_2, set_b_iso=set_b_iso) method = "rscc_d_min_b" print("Running test of rscc_d_min_b") pdb_hierarchy_new = maptbx.loc_res( map = map_data, model = model, crystal_symmetry = crystal_symmetry, chunk_size = 10, method = method, soft_mask_radius = 3., hard_d_min=3., b_range_low=-1000, b_range_high=1000,) b_values,occs=get_b_and_occ(hierarchy=pdb_hierarchy_new, atom_selection="name CA and (resid 5 or resid 15)") print("Bvalues (b_sharpen) expected: %s found: %s " %( str(expected_b_values),str(b_values))) print("Occ values(d_min) expected: %s found: %s " %( str(expected_occs),str(occs))) assert approx_equal(expected_b_values,b_values) assert approx_equal(expected_occs,occs) if (__name__ == "__main__"): tst_0() tst_1() print("OK")