from __future__ import absolute_import, division, print_function import libtbx from libtbx import easy_run import iotbx.pdb from scitbx.array_family import flex from libtbx.test_utils import approx_equal, show_diff pdb_str_0 = """\ REMARK 350 BIOMT1 1 1.000000 -0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 -0.000000 1.000000 -0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 -0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.809017 -0.500000 0.309017 0.00000 REMARK 350 BIOMT2 2 -0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 2 0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 3 -0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.000000 -0.000000 -1.000000 0.00000 REMARK 350 BIOMT3 3 -1.000000 0.000000 -0.000000 0.00000 REMARK 350 BIOMT1 4 0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 4 -0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 4 0.309017 0.809017 -0.500000 -0.00000 REMARK 350 BIOMT1 5 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT2 5 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT3 5 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT1 6 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 6 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 6 0.500000 0.309017 -0.809017 -0.00000 REMARK 350 BIOMT1 7 -0.809017 0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 7 0.500000 0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 7 -0.309017 -0.809017 -0.500000 0.00000 REMARK 350 BIOMT1 8 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT2 8 0.500000 -0.309017 -0.809017 0.00000 REMARK 350 BIOMT3 8 0.309017 -0.809017 0.500000 0.00000 REMARK 350 BIOMT1 9 -0.309017 0.809017 -0.500000 0.00000 REMARK 350 BIOMT2 9 -0.809017 -0.500000 -0.309017 0.00000 REMARK 350 BIOMT3 9 -0.500000 0.309017 0.809017 0.00000 HELIX 1 1 PRO A 28 LEU A 33 1 6 HELIX 7 7 ASP B 74 ALA B 79 1 6 HELIX 12 12 LYS C 151 TYR C 159 1 9 SHEET 1 A 2 PRO A 28 LEU A 33 0 SHEET 2 A 2 ASP B 74 ALA B 79 -1 O ASP B 74 N PRO A 28 CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 ATOM 62 N PRO A 28 33.884 22.417 110.984 14.01 14.01 N ATOM 63 CA PRO A 28 34.083 23.080 112.268 12.01 12.01 C ATOM 64 C PRO A 28 32.908 24.004 112.604 12.01 12.01 C ATOM 65 O PRO A 28 32.254 24.556 111.723 16.00 16.00 O ATOM 66 CB PRO A 28 35.381 23.873 112.096 12.01 12.01 C ATOM 67 CG PRO A 28 35.369 24.249 110.611 12.01 12.01 C ATOM 68 CD PRO A 28 34.692 23.045 109.949 12.01 12.01 C ATOM 69 N ASN A 29 32.694 24.235 113.899 14.01 14.01 N ATOM 70 CA ASN A 29 31.700 25.147 114.485 12.01 12.01 C ATOM 71 C ASN A 29 30.215 24.812 114.276 12.01 12.01 C ATOM 72 O ASN A 29 29.406 25.211 115.111 16.00 16.00 O ATOM 73 CB ASN A 29 32.013 26.616 114.122 12.01 12.01 C ATOM 74 CG ASN A 29 33.381 27.082 114.575 12.01 12.01 C ATOM 75 OD1 ASN A 29 34.061 26.468 115.379 16.00 16.00 O ATOM 76 ND2 ASN A 29 33.841 28.204 114.073 14.01 14.01 N ATOM 77 N GLU A 30 30.550 21.845 114.346 14.01 14.01 N ATOM 78 CA GLU A 30 29.386 21.544 115.199 12.01 12.01 C ATOM 79 C GLU A 30 29.802 20.720 116.428 12.01 12.01 C ATOM 80 O GLU A 30 29.237 19.675 116.751 16.00 16.00 O ATOM 81 CB GLU A 30 28.306 20.825 114.365 12.01 12.01 C ATOM 82 CG GLU A 30 27.795 21.680 113.200 12.01 12.01 C ATOM 83 CD GLU A 30 26.582 21.020 112.532 12.01 12.01 C ATOM 84 OE1 GLU A 30 26.801 20.115 111.689 16.00 16.00 O ATOM 85 OE2 GLU A 30 25.450 21.412 112.878 16.00 16.00 O ATOM 86 N LEU A 31 29.828 23.005 116.792 14.01 14.01 N ATOM 87 CA LEU A 31 29.299 22.073 115.816 12.01 12.01 C ATOM 88 C LEU A 31 28.149 21.279 116.426 12.01 12.01 C ATOM 89 O LEU A 31 28.305 20.133 116.853 16.00 16.00 O ATOM 90 CB LEU A 31 30.413 21.167 115.268 12.01 12.01 C ATOM 91 CG LEU A 31 31.519 21.894 114.483 12.01 12.01 C ATOM 92 CD1 LEU A 31 32.517 20.866 113.958 12.01 12.01 C ATOM 93 CD2 LEU A 31 30.995 22.696 113.286 12.01 12.01 C ATOM 94 N GLY A 32 26.947 21.837 116.303 14.01 14.01 N ATOM 95 CA GLY A 32 25.679 21.115 116.378 12.01 12.01 C ATOM 96 C GLY A 32 25.506 20.004 115.323 12.01 12.01 C ATOM 97 O GLY A 32 24.382 19.638 114.991 16.00 16.00 O ATOM 98 N LEU A 33 26.624 19.470 114.815 14.01 14.01 N ATOM 99 CA LEU A 33 26.791 18.378 113.866 12.01 12.01 C ATOM 100 C LEU A 33 27.494 17.166 114.509 12.01 12.01 C ATOM 101 O LEU A 33 27.549 16.110 113.890 16.00 16.00 O ATOM 102 CB LEU A 33 27.595 18.877 112.644 12.01 12.01 C ATOM 103 CG LEU A 33 27.192 20.239 112.037 12.01 12.01 C ATOM 104 CD1 LEU A 33 28.098 20.578 110.853 12.01 12.01 C ATOM 105 CD2 LEU A 33 25.745 20.281 111.549 12.01 12.01 C ATOM 2090 N ASP B 74 21.209 34.482 113.075 14.01 14.01 N ATOM 2091 CA ASP B 74 20.506 33.939 114.233 12.01 12.01 C ATOM 2092 C ASP B 74 21.375 33.841 115.474 12.01 12.01 C ATOM 2093 O ASP B 74 22.182 32.923 115.611 16.00 16.00 O ATOM 2094 CB ASP B 74 19.906 32.571 113.907 12.01 12.01 C ATOM 2095 CG ASP B 74 18.979 32.068 114.997 12.01 12.01 C ATOM 2096 OD1 ASP B 74 19.110 32.533 116.149 16.00 16.00 O ATOM 2097 OD2 ASP B 74 18.121 31.208 114.708 16.00 16.00 O ATOM 2098 N MET B 75 21.194 34.811 116.364 14.01 14.01 N ATOM 2099 CA MET B 75 21.934 34.884 117.610 12.01 12.01 C ATOM 2100 C MET B 75 22.089 33.512 118.239 12.01 12.01 C ATOM 2101 O MET B 75 23.123 33.213 118.837 16.00 16.00 O ATOM 2102 CB MET B 75 21.234 35.824 118.583 12.01 12.01 C ATOM 2103 CG MET B 75 21.525 37.288 118.322 12.01 12.01 C ATOM 2104 SD MET B 75 23.242 37.703 118.659 32.07 32.07 S ATOM 2105 CE MET B 75 23.058 38.659 120.162 12.01 12.01 C ATOM 2106 N ILE B 76 21.067 32.672 118.091 14.01 14.01 N ATOM 2107 CA ILE B 76 21.116 31.324 118.645 12.01 12.01 C ATOM 2108 C ILE B 76 22.422 30.683 118.212 12.01 12.01 C ATOM 2109 O ILE B 76 22.994 29.858 118.922 16.00 16.00 O ATOM 2110 CB ILE B 76 19.929 30.457 118.191 12.01 12.01 C ATOM 2111 CG1 ILE B 76 20.068 30.070 116.720 12.01 12.01 C ATOM 2112 CG2 ILE B 76 18.618 31.182 118.436 12.01 12.01 C ATOM 2113 CD1 ILE B 76 18.979 29.144 116.230 12.01 12.01 C ATOM 2114 N LYS B 77 22.902 31.098 117.044 14.01 14.01 N ATOM 2115 CA LYS B 77 24.160 30.591 116.525 12.01 12.01 C ATOM 2116 C LYS B 77 25.209 30.734 117.613 12.01 12.01 C ATOM 2117 O LYS B 77 26.219 30.038 117.612 16.00 16.00 O ATOM 2118 CB LYS B 77 24.577 31.362 115.281 12.01 12.01 C ATOM 2119 CG LYS B 77 23.624 31.194 114.112 12.01 12.01 C ATOM 2120 CD LYS B 77 24.208 30.282 113.048 12.01 12.01 C ATOM 2121 CE LYS B 77 25.656 30.627 112.741 12.01 12.01 C ATOM 2122 NZ LYS B 77 25.986 32.047 113.045 14.01 14.01 N ATOM 2123 N ILE B 78 24.954 31.644 118.547 14.01 14.01 N ATOM 2124 CA ILE B 78 25.852 31.863 119.664 12.01 12.01 C ATOM 2125 C ILE B 78 25.432 30.891 120.752 12.01 12.01 C ATOM 2126 O ILE B 78 26.264 30.367 121.489 16.00 16.00 O ATOM 2127 CB ILE B 78 25.788 33.314 120.171 12.01 12.01 C ATOM 2128 CG1 ILE B 78 26.541 34.227 119.215 12.01 12.01 C ATOM 2129 CG2 ILE B 78 26.405 33.447 121.552 12.01 12.01 C ATOM 2130 CD1 ILE B 78 27.879 33.670 118.785 12.01 12.01 C ATOM 2131 N ALA B 79 24.131 30.644 120.844 14.01 14.01 N ATOM 2132 CA ALA B 79 23.615 29.721 121.839 12.01 12.01 C ATOM 2133 C ALA B 79 24.401 28.426 121.758 12.01 12.01 C ATOM 2134 O ALA B 79 25.260 28.159 122.591 16.00 16.00 O ATOM 2135 CB ALA B 79 22.140 29.461 121.605 12.01 12.01 C ATOM 4569 N LYS C 151 65.128 35.635 115.156 14.01 14.01 N ATOM 4570 CA LYS C 151 65.530 35.389 113.777 12.01 12.01 C ATOM 4571 C LYS C 151 64.991 36.467 112.836 12.01 12.01 C ATOM 4572 O LYS C 151 65.493 37.600 112.882 16.00 16.00 O ATOM 4573 CB LYS C 151 65.144 33.970 113.358 12.01 12.01 C ATOM 4574 CG LYS C 151 65.912 32.877 114.088 12.01 12.01 C ATOM 4575 CD LYS C 151 67.128 32.399 113.304 12.01 12.01 C ATOM 4576 CE LYS C 151 67.638 31.055 113.817 12.01 12.01 C ATOM 4577 NZ LYS C 151 68.536 30.367 112.845 14.01 14.01 N ATOM 4578 N PRO C 152 63.957 36.119 111.972 14.01 14.01 N ATOM 4579 CA PRO C 152 63.508 37.232 111.112 12.01 12.01 C ATOM 4580 C PRO C 152 63.109 38.448 111.934 12.01 12.01 C ATOM 4581 O PRO C 152 63.440 39.574 111.564 16.00 16.00 O ATOM 4582 CB PRO C 152 62.297 36.661 110.371 12.01 12.01 C ATOM 4583 CG PRO C 152 62.611 35.226 110.237 12.01 12.01 C ATOM 4584 CD PRO C 152 63.111 34.901 111.606 12.01 12.01 C ATOM 4585 N ALA C 153 62.412 38.211 113.040 14.01 14.01 N ATOM 4586 CA ALA C 153 61.963 39.291 113.912 12.01 12.01 C ATOM 4587 C ALA C 153 63.098 40.266 114.150 12.01 12.01 C ATOM 4588 O ALA C 153 63.069 41.394 113.658 16.00 16.00 O ATOM 4589 CB ALA C 153 61.447 38.743 115.234 12.01 12.01 C ATOM 4590 N TYR C 154 64.115 39.823 114.883 14.01 14.01 N ATOM 4591 CA TYR C 154 65.267 40.665 115.165 12.01 12.01 C ATOM 4592 C TYR C 154 65.756 41.261 113.864 12.01 12.01 C ATOM 4593 O TYR C 154 66.400 42.302 113.847 16.00 16.00 O ATOM 4594 CB TYR C 154 66.376 39.866 115.831 12.01 12.01 C ATOM 4595 CG TYR C 154 67.016 40.606 116.973 12.01 12.01 C ATOM 4596 CD2 TYR C 154 67.159 40.015 118.220 12.01 12.01 C ATOM 4597 CD1 TYR C 154 67.468 41.902 116.804 12.01 12.01 C ATOM 4598 CE2 TYR C 154 67.743 40.697 119.266 12.01 12.01 C ATOM 4599 CE1 TYR C 154 68.055 42.593 117.842 12.01 12.01 C ATOM 4600 CZ TYR C 154 68.190 41.987 119.072 12.01 12.01 C ATOM 4601 OH TYR C 154 68.775 42.675 120.111 16.00 16.00 O ATOM 4602 N GLY C 155 65.432 40.583 112.771 14.01 14.01 N ATOM 4603 CA GLY C 155 65.788 41.039 111.449 12.01 12.01 C ATOM 4604 C GLY C 155 65.033 42.277 111.006 12.01 12.01 C ATOM 4605 O GLY C 155 64.881 43.241 111.751 16.00 16.00 O ATOM 4606 N GLN C 156 64.550 42.233 109.773 14.01 14.01 N ATOM 4607 CA GLN C 156 63.853 43.353 109.162 12.01 12.01 C ATOM 4608 C GLN C 156 62.850 43.968 110.123 12.01 12.01 C ATOM 4609 O GLN C 156 62.506 45.141 110.012 16.00 16.00 O ATOM 4610 CB GLN C 156 63.138 42.899 107.894 12.01 12.01 C ATOM 4611 CG GLN C 156 64.021 42.114 106.945 12.01 12.01 C ATOM 4612 CD GLN C 156 63.662 40.645 106.916 12.01 12.01 C ATOM 4613 OE1 GLN C 156 62.516 40.271 107.160 16.00 16.00 O ATOM 4614 NE2 GLN C 156 64.642 39.802 106.616 14.01 14.01 N ATOM 4615 N ALA C 157 62.387 43.173 111.075 14.01 14.01 N ATOM 4616 CA ALA C 157 61.412 43.650 112.046 12.01 12.01 C ATOM 4617 C ALA C 157 61.892 44.877 112.817 12.01 12.01 C ATOM 4618 O ALA C 157 61.110 45.516 113.514 16.00 16.00 O ATOM 4619 CB ALA C 157 61.039 42.537 113.014 12.01 12.01 C ATOM 4620 N LYS C 158 63.168 45.211 112.703 14.01 14.01 N ATOM 4621 CA LYS C 158 63.684 46.365 113.420 12.01 12.01 C ATOM 4622 C LYS C 158 63.183 47.677 112.829 12.01 12.01 C ATOM 4623 O LYS C 158 62.833 48.598 113.561 16.00 16.00 O ATOM 4624 CB LYS C 158 65.215 46.350 113.441 12.01 12.01 C ATOM 4625 CG LYS C 158 65.885 46.986 112.230 12.01 12.01 C ATOM 4626 CD LYS C 158 67.364 47.232 112.484 12.01 12.01 C ATOM 4627 CE LYS C 158 67.585 48.021 113.764 12.01 12.01 C ATOM 4628 NZ LYS C 158 67.696 47.123 114.945 14.01 14.01 N ATOM 4629 N TYR C 159 63.215 47.748 111.504 14.01 14.01 N ATOM 4630 CA TYR C 159 62.848 48.954 110.776 12.01 12.01 C ATOM 4631 C TYR C 159 61.362 49.227 110.625 12.01 12.01 C ATOM 4632 O TYR C 159 60.808 50.102 111.288 16.00 16.00 O ATOM 4633 CB TYR C 159 63.486 48.914 109.383 12.01 12.01 C ATOM 4634 CG TYR C 159 64.927 48.468 109.382 12.01 12.01 C ATOM 4635 CD2 TYR C 159 65.676 48.472 110.547 12.01 12.01 C ATOM 4636 CD1 TYR C 159 65.540 48.048 108.213 12.01 12.01 C ATOM 4637 CE2 TYR C 159 66.996 48.072 110.545 12.01 12.01 C ATOM 4638 CE1 TYR C 159 66.858 47.646 108.202 12.01 12.01 C ATOM 4639 CZ TYR C 159 67.578 47.660 109.370 12.01 12.01 C ATOM 4640 OH TYR C 159 68.888 47.260 109.362 16.00 16.00 O END """ pdb_str_1=""" MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.496590 -0.643597 0.582393 0.00000 MTRIX2 2 0.867925 0.376088 -0.324443 0.00000 MTRIX3 2 -0.010221 0.666588 0.745356 0.00000 MTRIX1 3 -0.317946 -0.173437 0.932111 0.00000 MTRIX2 3 0.760735 -0.633422 0.141629 0.00000 MTRIX3 3 0.565855 0.754120 0.333333 0.00000 CRYST1 11.101 13.080 14.163 90.00 90.00 90.00 P 1 SCALE1 0.090082 0.000000 0.000000 0.00000 SCALE2 0.000000 0.076453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.070607 0.00000 ATOM 1 N THR A 1 5.111 8.080 7.645 1.00 20.00 N ATOM 2 CA THR A 2 5.000 6.722 7.125 1.00 20.00 C ATOM 3 C THR A 3 5.075 5.694 8.249 1.00 20.00 C TER ATOM 4 O THR B 4 5.890 5.818 9.163 1.00 20.00 O ATOM 5 CB THR B 5 6.101 6.421 6.092 1.00 20.00 C TER ATOM 6 OG1 THR A 6 6.001 7.343 5.000 1.00 20.00 O ATOM 7 CG2 THR A 7 5.964 5.000 5.565 1.00 20.00 C TER END """ pdb_str_1a=""" CRYST1 11.101 13.080 14.163 90.00 90.00 90.00 P 1 SCALE1 0.090082 0.000000 0.000000 0.00000 SCALE2 0.000000 0.076453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.070607 0.00000 ATOM 1 N THRA1 1 5.111 8.080 7.645 1.00 20.00 N ATOM 2 CA THRA1 2 5.000 6.722 7.125 1.00 20.00 C ATOM 3 C THRA1 3 5.075 5.694 8.249 1.00 20.00 C TER ATOM 4 O THRB1 4 5.890 5.818 9.163 1.00 20.00 O ATOM 5 CB THRB1 5 6.101 6.421 6.092 1.00 20.00 C TER ATOM 6 OG1 THRA1 6 6.001 7.343 5.000 1.00 20.00 O ATOM 7 CG2 THRA1 7 5.964 5.000 5.565 1.00 20.00 C TER ATOM 1 N THRA2 1 1.790 4.994 11.032 1.00 20.00 N ATOM 2 CA THRA2 2 2.306 4.556 9.740 1.00 20.00 C ATOM 3 C THRA2 3 3.660 3.870 9.892 1.00 20.00 C TER ATOM 4 O THRB2 4 4.517 4.327 10.648 1.00 20.00 O ATOM 5 CB THRB2 5 2.445 5.734 8.759 1.00 20.00 C TER ATOM 6 OG1 THRA2 6 1.166 6.348 8.560 1.00 20.00 O ATOM 7 CG2 THRA2 7 2.985 5.251 7.420 1.00 20.00 C TER ATOM 1 N THRA3 1 4.100 -0.147 11.534 1.00 20.00 N ATOM 2 CA THRA3 2 3.886 0.555 10.273 1.00 20.00 C ATOM 3 C THRA3 3 5.088 1.422 9.915 1.00 20.00 C TER ATOM 4 O THRB3 4 5.659 2.093 10.775 1.00 20.00 O ATOM 5 CB THRB3 5 2.625 1.437 10.325 1.00 20.00 C TER ATOM 6 OG1 THRA3 6 1.479 0.622 10.600 1.00 20.00 O ATOM 7 CG2 THRA3 7 2.424 2.158 9.000 1.00 20.00 C TER END """ pdb_str_2=""" MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.496590 -0.643597 0.582393 0.00000 MTRIX2 2 0.867925 0.376088 -0.324443 0.00000 MTRIX3 2 -0.010221 0.666588 0.745356 0.00000 MTRIX1 3 -0.317946 -0.173437 0.932111 0.00000 MTRIX2 3 0.760735 -0.633422 0.141629 0.00000 MTRIX3 3 0.565855 0.754120 0.333333 0.00000 ATOM 1 N THR A 1 5.111 8.080 7.645 1.00 20.00 N ATOM 2 CA THR A 2 5.000 6.722 7.125 1.00 20.00 C ATOM 3 C THR A 3 5.075 5.694 8.249 1.00 20.00 C TER ATOM 4 O THR B 4 5.890 5.818 9.163 1.00 20.00 O ATOM 5 CB THR B 5 6.101 6.421 6.092 1.00 20.00 C TER ATOM 6 OG1 THR A 6 6.001 7.343 5.000 1.00 20.00 O ATOM 7 CG2 THR A 7 5.964 5.000 5.565 1.00 20.00 C TER END """ pdb_str_2a=""" ATOM 1 N THRA1 1 5.111 8.080 7.645 1.00 20.00 N ATOM 2 CA THRA1 2 5.000 6.722 7.125 1.00 20.00 C ATOM 3 C THRA1 3 5.075 5.694 8.249 1.00 20.00 C TER ATOM 4 O THRB1 4 5.890 5.818 9.163 1.00 20.00 O ATOM 5 CB THRB1 5 6.101 6.421 6.092 1.00 20.00 C TER ATOM 6 OG1 THRA1 6 6.001 7.343 5.000 1.00 20.00 O ATOM 7 CG2 THRA1 7 5.964 5.000 5.565 1.00 20.00 C TER ATOM 1 N THRA2 1 1.790 4.994 11.032 1.00 20.00 N ATOM 2 CA THRA2 2 2.306 4.556 9.740 1.00 20.00 C ATOM 3 C THRA2 3 3.660 3.870 9.892 1.00 20.00 C TER ATOM 4 O THRB2 4 4.517 4.327 10.648 1.00 20.00 O ATOM 5 CB THRB2 5 2.445 5.734 8.759 1.00 20.00 C TER ATOM 6 OG1 THRA2 6 1.166 6.348 8.560 1.00 20.00 O ATOM 7 CG2 THRA2 7 2.985 5.251 7.420 1.00 20.00 C TER ATOM 1 N THRA3 1 4.100 -0.147 11.534 1.00 20.00 N ATOM 2 CA THRA3 2 3.886 0.555 10.273 1.00 20.00 C ATOM 3 C THRA3 3 5.088 1.422 9.915 1.00 20.00 C TER ATOM 4 O THRB3 4 5.659 2.093 10.775 1.00 20.00 O ATOM 5 CB THRB3 5 2.625 1.437 10.325 1.00 20.00 C TER ATOM 6 OG1 THRA3 6 1.479 0.622 10.600 1.00 20.00 O ATOM 7 CG2 THRA3 7 2.424 2.158 9.000 1.00 20.00 C TER END """ pdb_str_2b=""" HELIX 1 1 THR A 1 THR A 2 1 6 SHEET 1 A 2 THR A 1 THR A 3 0 SHEET 2 A 2 THR B 4 THR B 5 -1 O THR B 4 N THR A 2 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.496590 -0.643597 0.582393 0.00000 MTRIX2 2 0.867925 0.376088 -0.324443 0.00000 MTRIX3 2 -0.010221 0.666588 0.745356 0.00000 MTRIX1 3 -0.317946 -0.173437 0.932111 0.00000 MTRIX2 3 0.760735 -0.633422 0.141629 0.00000 MTRIX3 3 0.565855 0.754120 0.333333 0.00000 ATOM 1 N THR A 1 5.111 8.080 7.645 1.00 20.00 N ATOM 2 CA THR A 2 5.000 6.722 7.125 1.00 20.00 C ATOM 3 C THR A 3 5.075 5.694 8.249 1.00 20.00 C TER ATOM 4 O THR B 4 5.890 5.818 9.163 1.00 20.00 O ATOM 5 CB THR B 5 6.101 6.421 6.092 1.00 20.00 C TER ATOM 6 OG1 THR A 6 6.001 7.343 5.000 1.00 20.00 O ATOM 7 CG2 THR A 7 5.964 5.000 5.565 1.00 20.00 C TER END """ pdb_str_3=""" data_1A37 # loop_ _database_PDB_rev_record.rev_num _database_PDB_rev_record.type _database_PDB_rev_record.details 2 SOURCE ? 2 COMPND ? 2 REMARK ? 2 SEQRES ? 2 KEYWDS ? 2 HEADER ? 3 VERSN ? 4 MTRIX1 ? 4 MTRIX2 ? 4 MTRIX3 ? # _cell.entry_id 1A37 _cell.length_a 94.730 _cell.length_b 94.730 _cell.length_c 250.870 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 # _symmetry.entry_id 1A37 _symmetry.space_group_name_H-M 'P 65' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number ? _symmetry.space_group_name_Hall ? # loop_ _struct_ncs_oper.id _struct_ncs_oper.code _struct_ncs_oper.details _struct_ncs_oper.matrix[1][1] _struct_ncs_oper.matrix[1][2] _struct_ncs_oper.matrix[1][3] _struct_ncs_oper.matrix[2][1] _struct_ncs_oper.matrix[2][2] _struct_ncs_oper.matrix[2][3] _struct_ncs_oper.matrix[3][1] _struct_ncs_oper.matrix[3][2] _struct_ncs_oper.matrix[3][3] _struct_ncs_oper.vector[1] _struct_ncs_oper.vector[2] _struct_ncs_oper.vector[3] 1 given ? 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 2 generate ? -0.997443 0.000760 -0.071468 -0.000162 -0.999965 -0.008376 -0.071472 -0.008343 0.997408 59.52120 80.32820 2.38680 # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.Cartn_x_esd _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd _atom_site.occupancy_esd _atom_site.B_iso_or_equiv_esd _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . MET A 1 1 ? 10.710 38.460 14.825 1.00 89.21 ? ? ? ? ? ? 1 MET A N 1 ATOM 2 C CA . MET A 1 1 ? 11.257 39.553 13.961 1.00 89.21 ? ? ? ? ? ? 1 MET A CA 1 ATOM 3 C C . MET A 1 1 ? 11.385 40.985 14.516 1.00 89.21 ? ? ? ? ? ? 1 MET A C 1 ATOM 4 O O . MET A 1 1 ? 12.376 41.648 14.218 1.00 89.21 ? ? ? ? ? ? 1 MET A O 1 ATOM 5 C CB . MET A 1 1 ? 10.514 39.584 12.633 1.00 72.05 ? ? ? ? ? ? 1 MET A CB 1 ATOM 6 C CG . MET A 1 1 ? 11.115 38.664 11.596 1.00 72.05 ? ? ? ? ? ? 1 MET A CG 1 ATOM 7 S SD . MET A 1 1 ? 12.048 39.609 10.386 1.00 72.05 ? ? ? ? ? ? 1 MET A SD 1 ATOM 8 C CE . MET A 1 1 ? 13.456 40.084 11.391 1.00 72.05 ? ? ? ? ? ? 1 MET A CE 1 ATOM 9 N N . ASP A 1 2 ? 10.381 41.467 15.263 1.00 81.99 ? ? ? ? ? ? 2 ASP A N 1 ATOM 10 C CA . ASP A 1 2 ? 10.350 42.822 15.886 1.00 81.99 ? ? ? ? ? ? 2 ASP A CA 1 ATOM 11 C C . ASP A 1 2 ? 10.651 44.060 15.038 1.00 81.99 ? ? ? ? ? ? 2 ASP A C 1 ATOM 12 O O . ASP A 1 2 ? 11.725 44.645 15.140 1.00 81.99 ? ? ? ? ? ? 2 ASP A O 1 ATOM 13 C CB . ASP A 1 2 ? 11.208 42.882 17.167 1.00 70.41 ? ? ? ? ? ? 2 ASP A CB 1 ATOM 14 C CG . ASP A 1 2 ? 11.000 44.178 17.963 1.00 70.41 ? ? ? ? ? ? 2 ASP A CG 1 ATOM 15 O OD1 . ASP A 1 2 ? 10.015 44.907 17.702 1.00 70.41 ? ? ? ? ? ? 2 ASP A OD1 1 ATOM 16 O OD2 . ASP A 1 2 ? 11.821 44.453 18.866 1.00 70.41 ? ? ? ? ? ? 2 ASP A OD2 1 # """ pdb_str_3a=""" data_default _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.length_b 94.730 _cell.length_c 250.870 _cell.angle_alpha 90.000 _cell.volume 1949640.043 _cell.length_a 94.730 _space_group.crystal_system hexagonal _space_group.name_H-M_alt 'P 65' _space_group.IT_number 170 _space_group.name_Hall ' P 65' _symmetry.space_group_name_H-M 'P 65' _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ' P 65' loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x-y,x,z+5/6 3 y,-x+y,z+1/6 4 -y,x-y,z+2/3 5 -x+y,-x,z+1/3 6 -x,-y,z+1/2 loop_ _atom_site.group_PDB _atom_site.id _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.type_symbol _atom_site.pdbx_formal_charge _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num ATOM 1 N . MET A1 1 ? 10.71000 38.46000 14.82500 1.000 89.21000 N ? A ? 1 1 ATOM 2 CA . MET A1 1 ? 11.25700 39.55300 13.96100 1.000 89.21000 C ? A ? 1 1 ATOM 3 C . MET A1 1 ? 11.38500 40.98500 14.51600 1.000 89.21000 C ? A ? 1 1 ATOM 4 O . MET A1 1 ? 12.37600 41.64800 14.21800 1.000 89.21000 O ? A ? 1 1 ATOM 5 CB . MET A1 1 ? 10.51400 39.58400 12.63300 1.000 72.05000 C ? A ? 1 1 ATOM 6 CG . MET A1 1 ? 11.11500 38.66400 11.59600 1.000 72.05000 C ? A ? 1 1 ATOM 7 SD . MET A1 1 ? 12.04800 39.60900 10.38600 1.000 72.05000 S ? A ? 1 1 ATOM 8 CE . MET A1 1 ? 13.45600 40.08400 11.39100 1.000 72.05000 C ? A ? 1 1 ATOM 9 N . ASP A1 2 ? 10.38100 41.46700 15.26300 1.000 81.99000 N ? A ? 2 1 ATOM 10 CA . ASP A1 2 ? 10.35000 42.82200 15.88600 1.000 81.99000 C ? A ? 2 1 ATOM 11 C . ASP A1 2 ? 10.65100 44.06000 15.03800 1.000 81.99000 C ? A ? 2 1 ATOM 12 O . ASP A1 2 ? 11.72500 44.64500 15.14000 1.000 81.99000 O ? A ? 2 1 ATOM 13 CB . ASP A1 2 ? 11.20800 42.88200 17.16700 1.000 70.41000 C ? A ? 2 1 ATOM 14 CG . ASP A1 2 ? 11.00000 44.17800 17.96300 1.000 70.41000 C ? A ? 2 1 ATOM 15 OD1 . ASP A1 2 ? 10.01500 44.90700 17.70200 1.000 70.41000 O ? A ? 2 1 ATOM 16 OD2 . ASP A1 2 ? 11.82100 44.45300 18.86600 1.000 70.41000 O ? A ? 2 1 ATOM 1 N . MET A2 1 ? 47.80830 41.74364 16.08704 1.000 89.21000 N ? B ? 3 1 ATOM 2 CA . MET A2 1 ? 47.32528 40.65782 15.17706 1.000 89.21000 C ? B ? 3 1 ATOM 3 C . MET A2 1 ? 47.15903 39.22120 15.70953 1.000 89.21000 C ? B ? 3 1 ATOM 4 O . MET A2 1 ? 46.19237 38.56056 15.33594 1.000 89.21000 O ? B ? 3 1 ATOM 5 CB . MET A2 1 ? 48.16131 40.63807 13.90535 1.000 72.05000 C ? B ? 3 1 ATOM 6 CG . MET A2 1 ? 47.63526 41.56662 12.83576 1.000 72.05000 C ? B ? 3 1 ATOM 7 SD . MET A2 1 ? 46.79184 40.63164 11.55433 1.000 72.05000 S ? B ? 3 1 ATOM 8 CE . MET A2 1 ? 45.31598 40.14801 12.45213 1.000 72.05000 C ? B ? 3 1 ATOM 9 N . ASP A2 2 ? 48.10744 38.73313 16.52233 1.000 81.99000 N ? B ? 4 1 ATOM 10 CA . ASP A2 2 ? 48.09487 37.37296 17.13462 1.000 81.99000 C ? B ? 4 1 ATOM 11 C . ASP A2 2 ? 47.85618 36.14206 16.25698 1.000 81.99000 C ? B ? 4 1 ATOM 12 O . ASP A2 2 ? 46.77809 35.55605 16.27707 1.000 81.99000 O ? B ? 4 1 ATOM 13 CB . ASP A2 2 ? 47.14756 37.30209 18.35048 1.000 70.41000 C ? B ? 4 1 ATOM 14 CG . ASP A2 2 ? 47.29912 35.99951 19.14847 1.000 70.41000 C ? B ? 4 1 ATOM 15 OD1 . ASP A2 2 ? 48.30081 35.27288 18.95247 1.000 70.41000 O ? B ? 4 1 ATOM 16 OD2 . ASP A2 2 ? 46.41590 35.71682 19.98816 1.000 70.41000 O ? B ? 4 1 """ def exercise_000(file_name="tst_mtrix_biomt_cmdl_000.pdb"): """ Make sure SS gets populated by BIOMT """ of = open(file_name,"w") print(pdb_str_0, file=of) of.close() # template when pdb_as_cif will handle BIOMT records as well... # easy_run.call("phenix.pdb_as_cif %s"%file_name) # for file_type in ['pdb', 'cif']: for file_type in ['pdb']: print("file_type:", file_type) easy_run.call("phenix.pdb.biomt_reconstruction %s.%s" % (file_name[:-4], file_type)) pdb_inp = iotbx.pdb.input( file_name="%s_BIOMT_expanded.%s" % (file_name[:-4], file_type)) a = pdb_inp.extract_secondary_structure() assert a.get_n_helices() == 27 assert a.get_n_sheets() == 9, "%d" % a.get_n_sheets() # checking chain ids. If this part is failing, then something is changed in # chain expanding which made chain ids in hierarchy.py:join_roots() # not compatible with those used in secondary_structure.py:multiply_to_asu chain_ids = [h.start_chain_id for h in a.helices] assert chain_ids == ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '0'], chain_ids # checking sheets for i, sh in enumerate(a.sheets): assert sh.n_strands == 2 assert sh.registrations[0] == None assert sh.registrations[1].cur_chain_id == chain_ids[i*3+1] assert sh.registrations[1].prev_chain_id == chain_ids[i*3] assert sh.strands[0].start_chain_id == chain_ids[i*3], sh.strands[0].start_chain_id assert sh.strands[0].end_chain_id == chain_ids[i*3] assert sh.strands[1].start_chain_id == chain_ids[i*3+1], sh.strands[1].start_chain_id assert sh.strands[1].end_chain_id == chain_ids[i*3+1] def exercise_001(file_name="tst_mtrix_biomt_cmdl_001.pdb"): """ Make sure SS gets populated by MTRIX """ of = open(file_name,"w") print(pdb_str_2b, file=of) of.close() easy_run.call("phenix.pdb.mtrix_reconstruction %s"%file_name) pdb_inp = iotbx.pdb.input( file_name="tst_mtrix_biomt_cmdl_001_MTRIX_expanded.pdb") a = pdb_inp.extract_secondary_structure() assert a.get_n_helices() == 3, a.get_n_helices() assert a.get_n_sheets() == 3, "%d" % a.get_n_sheets() # checking chain ids. If this part is failing, then something is changed in # chain expanding which made chain ids in hierarchy.py:join_roots() # not compatible with those used in secondary_structure.py:multiply_to_asu chain_ids = [h.start_chain_id for h in a.helices] assert chain_ids == ['A', 'C', 'E'], chain_ids # checking sheets assert not show_diff (a.as_pdb_str(),"""\ HELIX 1 1 THR A 1 THR A 2 1 6 HELIX 2 2 THR C 1 THR C 2 1 6 HELIX 3 3 THR E 1 THR E 2 1 6 SHEET 1 1 2 THR A 1 THR A 3 0 SHEET 2 1 2 THR B 4 THR B 5 -1 O THR B 4 N THR A 2 SHEET 1 2 2 THR C 1 THR C 3 0 SHEET 2 2 2 THR D 4 THR D 5 -1 O THR D 4 N THR C 2 SHEET 1 3 2 THR E 1 THR E 3 0 SHEET 2 3 2 THR F 4 THR F 5 -1 O THR F 4 N THR E 2""") def exercise_002(file_name="tst_mtrix_biomt_cmdl_002.pdb"): """ Make sure SS is fine when expanding without MTRIX """ of = open(file_name,"w") print(pdb_str_0, file=of) of.close() easy_run.call("phenix.pdb.mtrix_reconstruction %s"%file_name) pdb_inp = iotbx.pdb.input( file_name="tst_mtrix_biomt_cmdl_002_MTRIX_expanded.pdb") a = pdb_inp.extract_secondary_structure() assert a.get_n_helices() == 3, a.get_n_helices() assert a.get_n_sheets() == 1, "%d" % a.get_n_sheets() # checking chain ids. If this part is failing, then something is changed in # chain expanding which made chain ids in hierarchy.py:join_roots() # not compatible with those used in secondary_structure.py:multiply_to_asu chain_ids = [h.start_chain_id for h in a.helices] assert chain_ids == ['A', 'B', 'C'], chain_ids # checking sheets for i, sh in enumerate(a.sheets): assert sh.n_strands == 2 assert sh.registrations[0] == None assert sh.registrations[1].cur_chain_id == 'B' assert sh.registrations[1].prev_chain_id == 'A' assert sh.strands[0].start_chain_id == 'A' assert sh.strands[0].end_chain_id == 'A' assert sh.strands[1].start_chain_id == 'B' assert sh.strands[1].end_chain_id == 'B' def exercise_003(file_name="tst_mtrix_biomt_cmdl_003.pdb"): """ Make sure SS is fine when expanding without BIOMT """ of = open(file_name,"w") print(pdb_str_2b, file=of) of.close() easy_run.call("phenix.pdb.biomt_reconstruction %s"%file_name) pdb_inp = iotbx.pdb.input( file_name="tst_mtrix_biomt_cmdl_003_BIOMT_expanded.pdb") a = pdb_inp.extract_secondary_structure() assert a.get_n_helices() == 1, a.get_n_helices() assert a.get_n_sheets() == 1, "%d" % a.get_n_sheets() # checking chain ids. If this part is failing, then something is changed in # chain expanding which made chain ids in hierarchy.py:join_roots() # not compatible with those used in secondary_structure.py:multiply_to_asu chain_ids = [h.start_chain_id for h in a.helices] assert chain_ids == ['A'], chain_ids # checking sheets for i, sh in enumerate(a.sheets): assert sh.n_strands == 2 assert sh.registrations[0] == None assert sh.registrations[1].cur_chain_id == 'B' assert sh.registrations[1].prev_chain_id == 'A' assert sh.strands[0].start_chain_id == 'A' assert sh.strands[0].end_chain_id == 'A' assert sh.strands[1].start_chain_id == 'B' assert sh.strands[1].end_chain_id == 'B' def exercise_01(file_name="tst_mtrix_biomt_cmdl_01.pdb"): """ Use MTRIX. """ of = open(file_name,"w") print(pdb_str_1, file=of) of.close() easy_run.call("phenix.pdb.mtrix_reconstruction %s"%file_name) pdb_inp1 = iotbx.pdb.input( file_name="tst_mtrix_biomt_cmdl_01_MTRIX_expanded.pdb") pdb_inp2 = iotbx.pdb.input(source_info=None, lines=pdb_str_1a) dist = flex.sqrt(( pdb_inp1.atoms().extract_xyz() - pdb_inp2.atoms().extract_xyz()).dot()) assert approx_equal(dist.min_max_mean().as_tuple(), [0,0,0]) assert pdb_inp1.crystal_symmetry().is_similar_symmetry( pdb_inp2.crystal_symmetry()) assert pdb_inp1.crystal_symmetry() is not None assert pdb_inp2.crystal_symmetry() is not None assert pdb_inp1.crystal_symmetry().unit_cell() is not None assert pdb_inp2.crystal_symmetry().unit_cell() is not None def exercise_02(file_name="tst_mtrix_biomt_cmdl_02.pdb"): """ Make sure it's not going to make up CRYST1. """ of = open(file_name,"w") print(pdb_str_2, file=of) of.close() easy_run.call("phenix.pdb.mtrix_reconstruction %s"%file_name) pdb_inp1 = iotbx.pdb.input( file_name="tst_mtrix_biomt_cmdl_02_MTRIX_expanded.pdb") pdb_inp2 = iotbx.pdb.input(source_info=None, lines=pdb_str_2a) dist = flex.sqrt(( pdb_inp1.atoms().extract_xyz() - pdb_inp2.atoms().extract_xyz()).dot()) assert approx_equal(dist.min_max_mean().as_tuple(), [0,0,0]) assert [pdb_inp1.crystal_symmetry(), pdb_inp2.crystal_symmetry()].count(None)==2 def exercise_03(file_name="tst_mtrix_biomt_cmdl_03.cif"): """ Handle mmCIF. """ of = open(file_name,"w") print(pdb_str_3, file=of) of.close() easy_run.call("phenix.pdb.mtrix_reconstruction %s"%file_name) pdb_inp1 = iotbx.pdb.input( file_name="tst_mtrix_biomt_cmdl_03_MTRIX_expanded.cif") pdb_inp2 = iotbx.pdb.input(source_info=None, lines=pdb_str_3a) dist = flex.sqrt(( pdb_inp1.atoms().extract_xyz() - pdb_inp2.atoms().extract_xyz()).dot()) assert approx_equal(dist.min_max_mean().as_tuple(), [0,0,0]) assert pdb_inp1.crystal_symmetry().is_similar_symmetry( pdb_inp2.crystal_symmetry()) assert pdb_inp1.crystal_symmetry() is not None assert pdb_inp2.crystal_symmetry() is not None assert pdb_inp1.crystal_symmetry().unit_cell() is not None assert pdb_inp2.crystal_symmetry().unit_cell() is not None if(__name__=='__main__'): if libtbx.env.has_module("phenix"): # SS records handling exercise_000() exercise_001() exercise_002() exercise_003() # # other exercise_01() exercise_02() exercise_03() else: print("Skipping tests: phenix not found")