from __future__ import absolute_import, division, print_function from libtbx.test_utils import approx_equal, show_diff from scitbx import matrix from iotbx import pdb import mmtbx.model import iotbx.ncs import iotbx.ncs as ncs 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 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 1 N THR A 1 9.670 10.289 11.135 1.00 20.00 N ATOM 2 CA THR A 2 9.559 8.931 10.615 1.00 20.00 C ATOM 3 C THR A 3 9.634 7.903 11.739 1.00 20.00 C ATOM 4 O THR B 4 10.449 8.027 12.653 1.00 20.00 O ATOM 5 CB THR B 5 10.660 8.630 9.582 1.00 20.00 C ATOM 6 OG1 THR A 6 10.560 9.552 8.490 1.00 20.00 O ATOM 7 CG2 THR A 7 10.523 7.209 9.055 1.00 20.00 C TER """ pdb_str_3=""" REMARK 0 Test molecule with BIOMOLECULE: 1 REMARK 0 REMARK 0 The test will generate the biomolecule (the multimer assembly) REMARK 0 from the transformation matrices writen below REMARK 0 and then compare the results to the calculated expected one REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.000000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT2 2 0.000000 0.000000 -1.000000 0.000000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.000000 REMARK 350 BIOMT1 3 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.000000 REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 0.000000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT1 5 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.000000 REMARK 350 BIOMT3 5 -1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT1 6 0.000000 -1.000000 0.000000 0.000000 REMARK 350 BIOMT2 6 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT3 6 -1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT1 7 0.500000 -0.866025 0.000000 0.000000 REMARK 350 BIOMT2 7 0.866025 0.500000 0.000000 0.000000 REMARK 350 BIOMT3 7 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT1 8 -0.500000 -0.866025 0.000000 0.000000 REMARK 350 BIOMT2 8 0.866025 -0.500000 0.000000 0.000000 REMARK 350 BIOMT3 8 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT1 9 1.000000 0.000000 0.000000 0.000000 REMARK 350 BIOMT2 9 0.000000 1.000000 0.000000 0.500000 REMARK 350 BIOMT3 9 0.000000 0.000000 1.000000 0.000000 REMARK 350 BIOMT1 10 -0.500000 -0.866025 0.000000 0.000000 REMARK 350 BIOMT2 10 0.866025 -0.500000 0.000000 0.000000 REMARK 350 BIOMT3 10 0.000000 0.000000 1.000000 -1.000000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 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 1.000000 0.000000 0.000000 0.00000 MTRIX2 2 0.000000 0.000000 -1.000000 0.00000 MTRIX3 2 0.000000 1.000000 0.000000 0.00000 MTRIX1 3 0.500000 -0.866025 0.000000 0.00000 MTRIX2 3 0.866025 0.500000 0.000000 0.00000 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 MTRIX1 4 -0.500000 -0.866025 0.000000 0.00000 MTRIX2 4 0.866025 -0.500000 0.000000 0.00000 MTRIX3 4 0.000000 0.000000 1.000000 0.00000 MTRIX1 5 1.000000 0.000000 0.000000 0.00000 MTRIX2 5 0.000000 1.000000 0.000000 0.50000 MTRIX3 5 0.000000 0.000000 1.000000 0.00000 CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 1 N ILE A 40 1.000 1.000 1.000 1.00162.33 C ATOM 2 CA LEU A 40 94.618 -5.253 91.582 1.00 87.10 C ATOM 3 C ARG B 40 62.395 51.344 80.786 1.00107.25 C HETATM 4 C1 EDO A 40 39.954 51.526 72.372 0.33 60.93 C """ pdb_str_4 = """\ 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 0.309017 -0.951057 0.000000 0.00000 REMARK 350 BIOMT2 2 0.951057 0.309017 -0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 7.00000 REMARK 350 BIOMT1 3 -0.809017 -0.587785 0.000000 0.00000 REMARK 350 BIOMT2 3 0.587785 -0.809017 -0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 1 N ALA A 2 64.807-112.186 260.746 1.00160.99 N ATOM 2 CA ALA A 2 64.727-111.450 262.002 1.00159.36 C ATOM 3 C ALA A 2 63.960-110.148 261.805 1.00154.38 C ATOM 4 O ALA A 2 62.935-109.914 262.452 1.00149.47 O ATOM 5 CB ALA A 2 66.123-111.175 262.542 1.00156.98 C ATOM 6 N SER A 3 64.474-109.323 260.896 1.00135.75 N ATOM 7 CA SER A 3 63.887-108.040 260.510 1.00131.97 C ATOM 8 C SER A 3 64.863-107.340 259.575 1.00140.51 C ATOM 9 O SER A 3 65.864-107.925 259.165 1.00148.46 O ATOM 10 CB SER A 3 63.641-107.147 261.726 1.00126.01 C ATOM 11 OG SER A 3 64.002-105.804 261.453 1.00119.04 O END """ pdb_str_5 = """\ 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 0.309017 -0.951057 0.000000 0.00000 MTRIX2 2 0.951057 0.309017 -0.000000 0.00000 MTRIX3 2 0.000000 0.000000 1.000000 7.00000 MTRIX1 3 -0.809017 -0.587785 0.000000 0.00000 MTRIX2 3 0.587785 -0.809017 -0.000000 0.00000 MTRIX3 3 0.000000 0.000000 1.000000 0.00000 CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 757 N ASP A 247 16.068 -20.882 -28.984 1.00 35.93 N ATOM 758 CA ASP A 247 15.914 -22.265 -28.600 1.00 47.90 C ATOM 759 C ASP A 247 17.130 -23.042 -29.116 1.00 42.32 C ATOM 760 O ASP A 247 17.461 -22.986 -30.301 1.00 47.25 O ATOM 761 CB ASP A 247 14.621 -22.814 -29.198 1.00 47.22 C ATOM 762 CG ASP A 247 14.068 -23.974 -28.412 1.00 61.15 C ATOM 763 OD1 ASP A 247 14.359 -24.061 -27.196 1.00 63.66 O ATOM 764 OD2 ASP A 247 13.341 -24.798 -29.012 1.00 77.01 O ATOM 765 N VAL A 248 17.808 -23.746 -28.218 1.00 44.08 N ATOM 766 CA VAL A 248 19.008 -24.503 -28.584 1.00 46.18 C ATOM 767 C VAL A 248 18.668 -25.988 -28.583 1.00 53.97 C ATOM 768 O VAL A 248 18.049 -26.478 -27.638 1.00 51.48 O ATOM 769 CB VAL A 248 20.185 -24.226 -27.608 1.00 47.55 C ATOM 770 CG1 VAL A 248 21.414 -25.015 -28.012 1.00 41.43 C ATOM 771 CG2 VAL A 248 20.513 -22.743 -27.567 1.00 41.64 C ATOM 772 N VAL A 249 19.057 -26.697 -29.641 1.00 54.29 N ATOM 773 CA VAL A 249 18.662 -28.097 -29.810 1.00 60.17 C ATOM 774 C VAL A 249 19.859 -29.041 -29.982 1.00 57.98 C ATOM 775 O VAL A 249 20.731 -28.827 -30.828 1.00 58.31 O ATOM 776 CB VAL A 249 17.671 -28.280 -30.997 1.00 60.85 C ATOM 777 CG1 VAL A 249 16.500 -27.300 -30.884 1.00 48.00 C ATOM 778 CG2 VAL A 249 18.386 -28.110 -32.337 1.00 59.99 C TER ATOM 780 N LYS B 151 4.045 -6.858 -32.823 1.00 45.22 N ATOM 781 CA LYS B 151 4.686 -6.715 -34.123 1.00 50.40 C ATOM 782 C LYS B 151 5.707 -5.554 -34.172 1.00 47.13 C ATOM 783 O LYS B 151 6.820 -5.764 -34.625 1.00 52.91 O ATOM 784 CB LYS B 151 3.657 -6.646 -35.268 1.00 40.73 C ATOM 785 CG LYS B 151 4.264 -6.627 -36.661 1.00 55.98 C ATOM 786 CD LYS B 151 3.272 -7.051 -37.745 1.00 72.14 C ATOM 787 CE LYS B 151 2.529 -8.338 -37.375 1.00 75.11 C ATOM 788 NZ LYS B 151 3.451 -9.400 -36.884 1.00 75.46 N ATOM 789 N ARG B 152 5.369 -4.349 -33.709 1.00 42.01 N ATOM 790 CA ARG B 152 6.399 -3.290 -33.702 1.00 40.51 C ATOM 791 C ARG B 152 6.155 -2.002 -32.909 1.00 34.21 C ATOM 792 O ARG B 152 5.015 -1.605 -32.636 1.00 33.77 O ATOM 793 CB ARG B 152 6.845 -2.937 -35.130 1.00 40.62 C ATOM 794 CG ARG B 152 5.842 -2.126 -35.925 1.00 45.94 C ATOM 795 CD ARG B 152 6.341 -1.926 -37.341 1.00 42.75 C ATOM 796 NE ARG B 152 7.478 -1.006 -37.404 1.00 45.27 N ATOM 797 CZ ARG B 152 8.177 -0.763 -38.509 1.00 49.68 C ATOM 798 NH1 ARG B 152 7.860 -1.382 -39.644 1.00 47.81 N ATOM 799 NH2 ARG B 152 9.192 0.096 -38.482 1.00 48.06 N END """ pdb_str_8 = """\ 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 1 MTRIX2 2 0.867925 0.376088 -0.324443 0.00000 1 MTRIX3 2 -0.010221 0.666588 0.745356 0.00000 1 MTRIX1 3 -0.317946 -0.173437 0.932111 0.00000 1 MTRIX2 3 0.760735 -0.633422 0.141629 0.00000 1 MTRIX3 3 0.565855 0.754120 0.333333 0.00000 1 CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 ATOM 1 N THR A 1 9.670 10.289 11.135 1.00 20.00 N ATOM 2 CA THR A 2 9.559 8.931 10.615 1.00 20.00 C ATOM 3 C THR A 3 9.634 7.903 11.739 1.00 20.00 C ATOM 4 O THR B 4 10.449 8.027 12.653 1.00 20.00 O ATOM 5 CB THR B 5 10.660 8.630 9.582 1.00 20.00 C ATOM 6 OG1 THR A 6 10.560 9.552 8.490 1.00 20.00 O ATOM 7 CG2 THR A 7 10.523 7.209 9.055 1.00 20.00 C END """ # A dimer pdb_str_9=\ """ CRYST1 18.411 24.923 19.598 90.00 90.00 90.00 P 1 ATOM 1 N LEU A 219 12.476 8.570 6.342 1.00 30.00 N ATOM 2 CA LEU A 219 11.029 8.720 6.198 1.00 30.00 C ATOM 3 C LEU A 219 10.371 9.171 7.496 1.00 30.00 C ATOM 4 O LEU A 219 9.422 9.957 7.469 1.00 30.00 O ATOM 5 CB LEU A 219 10.404 7.413 5.700 1.00 30.00 C ATOM 6 CG LEU A 219 8.894 7.444 5.410 1.00 30.00 C ATOM 7 CD1 LEU A 219 8.567 6.777 4.078 1.00 30.00 C ATOM 8 CD2 LEU A 219 8.092 6.808 6.540 1.00 30.00 C ATOM 9 N ARG A 220 10.878 8.672 8.622 1.00 30.00 N ATOM 10 CA ARG A 220 10.381 9.053 9.938 1.00 30.00 C ATOM 11 C ARG A 220 10.603 10.531 10.185 1.00 30.00 C ATOM 12 O ARG A 220 9.715 11.202 10.728 1.00 30.00 O ATOM 13 CB ARG A 220 11.065 8.236 11.041 1.00 30.00 C ATOM 14 CG ARG A 220 10.661 6.771 11.083 1.00 30.00 C ATOM 15 CD ARG A 220 9.321 6.571 11.776 1.00 30.00 C ATOM 16 NE ARG A 220 8.945 5.157 11.847 1.00 30.00 N ATOM 17 CZ ARG A 220 9.446 4.259 12.701 1.00 30.00 C ATOM 18 NH1 ARG A 220 10.377 4.593 13.598 1.00 30.00 N ATOM 19 NH2 ARG A 220 9.012 3.000 12.656 1.00 30.00 N ATOM 20 N LEU A 221 11.792 11.006 9.803 1.00 30.00 N ATOM 21 CA LEU A 221 12.179 12.402 9.990 1.00 30.00 C ATOM 22 C LEU A 221 11.192 13.323 9.293 1.00 30.00 C ATOM 23 O LEU A 221 10.739 14.325 9.874 1.00 30.00 O ATOM 24 CB LEU A 221 13.578 12.678 9.432 1.00 30.00 C ATOM 25 CG LEU A 221 14.169 14.072 9.673 1.00 30.00 C ATOM 26 CD1 LEU A 221 14.503 14.277 11.143 1.00 30.00 C ATOM 27 CD2 LEU A 221 15.411 14.272 8.823 1.00 30.00 C ATOM 28 N GLN A 222 10.879 12.956 8.053 1.00 30.00 N ATOM 29 CA GLN A 222 9.943 13.723 7.218 1.00 30.00 C ATOM 30 C GLN A 222 8.591 13.825 7.903 1.00 30.00 C ATOM 31 O GLN A 222 7.994 14.910 7.968 1.00 30.00 O ATOM 32 CB GLN A 222 9.767 13.081 5.840 1.00 30.00 C ATOM 33 CG GLN A 222 8.924 13.893 4.867 1.00 30.00 C ATOM 34 CD GLN A 222 8.715 13.178 3.545 1.00 30.00 C ATOM 35 OE1 GLN A 222 9.626 12.537 3.018 1.00 30.00 O ATOM 36 NE2 GLN A 222 7.507 13.285 3.000 1.00 30.00 N ATOM 37 N GLN A 223 8.143 12.676 8.406 1.00 30.00 N ATOM 38 CA GLN A 223 6.857 12.566 9.106 1.00 30.00 C ATOM 39 C GLN A 223 6.827 13.513 10.297 1.00 30.00 C ATOM 40 O GLN A 223 5.844 14.249 10.510 1.00 30.00 O ATOM 41 CB GLN A 223 6.617 11.147 9.642 1.00 30.00 C ATOM 42 CG GLN A 223 6.137 10.118 8.636 1.00 30.00 C ATOM 43 CD GLN A 223 5.812 8.791 9.300 1.00 30.00 C ATOM 44 OE1 GLN A 223 6.419 7.765 8.994 1.00 30.00 O ATOM 45 NE2 GLN A 223 4.859 8.809 10.228 1.00 30.00 N ATOM 46 N ALA A 224 7.918 13.468 11.053 1.00 30.00 N ATOM 47 CA ALA A 224 8.090 14.293 12.253 1.00 30.00 C ATOM 48 C ALA A 224 7.967 15.770 11.893 1.00 30.00 C ATOM 49 O ALA A 224 7.262 16.539 12.568 1.00 30.00 O ATOM 50 CB ALA A 224 9.437 14.024 12.914 1.00 30.00 C ATOM 51 N TYR A 225 8.666 16.128 10.822 1.00 30.00 N ATOM 52 CA TYR A 225 8.683 17.504 10.316 1.00 30.00 C ATOM 53 C TYR A 225 7.279 17.961 9.973 1.00 30.00 C ATOM 54 O TYR A 225 6.865 19.071 10.346 1.00 30.00 O ATOM 55 CB TYR A 225 9.677 17.738 9.178 1.00 30.00 C ATOM 56 CG TYR A 225 10.896 18.350 9.759 1.00 30.00 C ATOM 57 CD1 TYR A 225 10.898 19.695 10.102 1.00 30.00 C ATOM 58 CD2 TYR A 225 12.010 17.578 10.072 1.00 30.00 C ATOM 59 CE1 TYR A 225 11.998 20.273 10.696 1.00 30.00 C ATOM 60 CE2 TYR A 225 13.126 18.149 10.660 1.00 30.00 C ATOM 61 CZ TYR A 225 13.112 19.496 10.970 1.00 30.00 C ATOM 62 OH TYR A 225 14.197 20.075 11.563 1.00 30.00 O ATOM 63 N LEU A 226 6.569 17.081 9.279 1.00 30.00 N ATOM 64 CA LEU A 226 5.188 17.332 8.848 1.00 30.00 C ATOM 65 C LEU A 226 4.312 17.613 10.059 1.00 30.00 C ATOM 66 O LEU A 226 3.523 18.584 10.065 1.00 30.00 O ATOM 67 CB LEU A 226 4.587 16.155 8.061 1.00 30.00 C ATOM 68 CG LEU A 226 4.521 16.312 6.542 1.00 30.00 C ATOM 69 CD1 LEU A 226 5.914 16.258 5.943 1.00 30.00 C ATOM 70 CD2 LEU A 226 3.643 15.232 5.923 1.00 30.00 C ATOM 71 N ILE A 227 4.476 16.749 11.064 1.00 30.00 N ATOM 72 CA ILE A 227 3.690 16.855 12.301 1.00 30.00 C ATOM 73 C ILE A 227 3.952 18.198 12.969 1.00 30.00 C ATOM 74 O ILE A 227 3.000 18.870 13.405 1.00 30.00 O ATOM 75 CB ILE A 227 3.668 15.644 13.279 1.00 30.00 C ATOM 76 CG1 ILE A 227 5.016 15.359 13.918 1.00 30.00 C ATOM 77 CG2 ILE A 227 3.107 14.410 12.588 1.00 30.00 C ATOM 78 CD1 ILE A 227 4.926 14.502 15.160 1.00 30.00 C ATOM 79 N MET A 228 5.227 18.566 13.017 1.00 30.00 N ATOM 80 CA MET A 228 5.663 19.830 13.617 1.00 30.00 C ATOM 81 C MET A 228 4.991 21.002 12.916 1.00 30.00 C ATOM 82 O MET A 228 4.472 21.923 13.572 1.00 30.00 O ATOM 83 CB MET A 228 7.192 19.985 13.595 1.00 30.00 C ATOM 84 CG MET A 228 7.960 19.118 14.591 1.00 30.00 C ATOM 85 SD MET A 228 7.511 19.311 16.335 1.00 30.00 S ATOM 86 CE MET A 228 7.660 21.082 16.598 1.00 30.00 C TER ATOM 1 N LEU B 219 -12.476 -8.570 6.342 1.00 30.00 N ATOM 2 CA LEU B 219 -11.029 -8.720 6.198 1.00 30.00 C ATOM 3 C LEU B 219 -10.371 -9.171 7.496 1.00 30.00 C ATOM 4 O LEU B 219 -9.422 -9.957 7.469 1.00 30.00 O ATOM 5 CB LEU B 219 -10.404 -7.413 5.700 1.00 30.00 C ATOM 6 CG LEU B 219 -8.894 -7.444 5.410 1.00 30.00 C ATOM 7 CD1 LEU B 219 -8.567 -6.777 4.078 1.00 30.00 C ATOM 8 CD2 LEU B 219 -8.092 -6.808 6.540 1.00 30.00 C ATOM 9 N ARG B 220 -10.878 -8.672 8.622 1.00 30.00 N ATOM 10 CA ARG B 220 -10.381 -9.053 9.938 1.00 30.00 C ATOM 11 C ARG B 220 -10.603 -10.531 10.185 1.00 30.00 C ATOM 12 O ARG B 220 -9.715 -11.202 10.728 1.00 30.00 O ATOM 13 CB ARG B 220 -11.065 -8.236 11.041 1.00 30.00 C ATOM 14 CG ARG B 220 -10.661 -6.771 11.083 1.00 30.00 C ATOM 15 CD ARG B 220 -9.321 -6.571 11.776 1.00 30.00 C ATOM 16 NE ARG B 220 -8.945 -5.157 11.847 1.00 30.00 N ATOM 17 CZ ARG B 220 -9.446 -4.259 12.701 1.00 30.00 C ATOM 18 NH1 ARG B 220 -10.377 -4.593 13.598 1.00 30.00 N ATOM 19 NH2 ARG B 220 -9.012 -3.000 12.656 1.00 30.00 N ATOM 20 N LEU B 221 -11.792 -11.006 9.803 1.00 30.00 N ATOM 21 CA LEU B 221 -12.179 -12.402 9.990 1.00 30.00 C ATOM 22 C LEU B 221 -11.192 -13.323 9.293 1.00 30.00 C ATOM 23 O LEU B 221 -10.739 -14.325 9.874 1.00 30.00 O ATOM 24 CB LEU B 221 -13.578 -12.678 9.432 1.00 30.00 C ATOM 25 CG LEU B 221 -14.169 -14.072 9.673 1.00 30.00 C ATOM 26 CD1 LEU B 221 -14.503 -14.277 11.143 1.00 30.00 C ATOM 27 CD2 LEU B 221 -15.411 -14.272 8.823 1.00 30.00 C ATOM 28 N GLN B 222 -10.879 -12.956 8.053 1.00 30.00 N ATOM 29 CA GLN B 222 -9.943 -13.723 7.218 1.00 30.00 C ATOM 30 C GLN B 222 -8.591 -13.825 7.903 1.00 30.00 C ATOM 31 O GLN B 222 -7.994 -14.910 7.968 1.00 30.00 O ATOM 32 CB GLN B 222 -9.767 -13.081 5.840 1.00 30.00 C ATOM 33 CG GLN B 222 -8.924 -13.893 4.867 1.00 30.00 C ATOM 34 CD GLN B 222 -8.715 -13.178 3.545 1.00 30.00 C ATOM 35 OE1 GLN B 222 -9.626 -12.537 3.018 1.00 30.00 O ATOM 36 NE2 GLN B 222 -7.507 -13.285 3.000 1.00 30.00 N ATOM 37 N GLN B 223 -8.143 -12.676 8.406 1.00 30.00 N ATOM 38 CA GLN B 223 -6.857 -12.566 9.106 1.00 30.00 C ATOM 39 C GLN B 223 -6.827 -13.513 10.297 1.00 30.00 C ATOM 40 O GLN B 223 -5.844 -14.249 10.510 1.00 30.00 O ATOM 41 CB GLN B 223 -6.617 -11.147 9.642 1.00 30.00 C ATOM 42 CG GLN B 223 -6.137 -10.118 8.636 1.00 30.00 C ATOM 43 CD GLN B 223 -5.812 -8.791 9.300 1.00 30.00 C ATOM 44 OE1 GLN B 223 -6.419 -7.765 8.994 1.00 30.00 O ATOM 45 NE2 GLN B 223 -4.859 -8.809 10.228 1.00 30.00 N ATOM 46 N ALA B 224 -7.918 -13.468 11.053 1.00 30.00 N ATOM 47 CA ALA B 224 -8.090 -14.293 12.253 1.00 30.00 C ATOM 48 C ALA B 224 -7.967 -15.770 11.893 1.00 30.00 C ATOM 49 O ALA B 224 -7.262 -16.539 12.568 1.00 30.00 O ATOM 50 CB ALA B 224 -9.437 -14.024 12.914 1.00 30.00 C ATOM 51 N TYR B 225 -8.666 -16.128 10.822 1.00 30.00 N ATOM 52 CA TYR B 225 -8.683 -17.504 10.316 1.00 30.00 C ATOM 53 C TYR B 225 -7.279 -17.961 9.973 1.00 30.00 C ATOM 54 O TYR B 225 -6.865 -19.071 10.346 1.00 30.00 O ATOM 55 CB TYR B 225 -9.677 -17.738 9.178 1.00 30.00 C ATOM 56 CG TYR B 225 -10.896 -18.350 9.759 1.00 30.00 C ATOM 57 CD1 TYR B 225 -10.898 -19.695 10.102 1.00 30.00 C ATOM 58 CD2 TYR B 225 -12.010 -17.578 10.072 1.00 30.00 C ATOM 59 CE1 TYR B 225 -11.998 -20.273 10.696 1.00 30.00 C ATOM 60 CE2 TYR B 225 -13.126 -18.149 10.660 1.00 30.00 C ATOM 61 CZ TYR B 225 -13.112 -19.496 10.970 1.00 30.00 C ATOM 62 OH TYR B 225 -14.197 -20.075 11.563 1.00 30.00 O ATOM 63 N LEU B 226 -6.569 -17.081 9.279 1.00 30.00 N ATOM 64 CA LEU B 226 -5.188 -17.332 8.848 1.00 30.00 C ATOM 65 C LEU B 226 -4.312 -17.613 10.059 1.00 30.00 C ATOM 66 O LEU B 226 -3.523 -18.584 10.065 1.00 30.00 O ATOM 67 CB LEU B 226 -4.587 -16.155 8.061 1.00 30.00 C ATOM 68 CG LEU B 226 -4.521 -16.312 6.542 1.00 30.00 C ATOM 69 CD1 LEU B 226 -5.914 -16.258 5.943 1.00 30.00 C ATOM 70 CD2 LEU B 226 -3.643 -15.232 5.923 1.00 30.00 C ATOM 71 N ILE B 227 -4.476 -16.749 11.064 1.00 30.00 N ATOM 72 CA ILE B 227 -3.690 -16.855 12.301 1.00 30.00 C ATOM 73 C ILE B 227 -3.952 -18.198 12.969 1.00 30.00 C ATOM 74 O ILE B 227 -3.000 -18.870 13.405 1.00 30.00 O ATOM 75 CB ILE B 227 -3.668 -15.644 13.279 1.00 30.00 C ATOM 76 CG1 ILE B 227 -5.016 -15.359 13.918 1.00 30.00 C ATOM 77 CG2 ILE B 227 -3.107 -14.410 12.588 1.00 30.00 C ATOM 78 CD1 ILE B 227 -4.926 -14.502 15.160 1.00 30.00 C ATOM 79 N MET B 228 -5.227 -18.566 13.017 1.00 30.00 N ATOM 80 CA MET B 228 -5.663 -19.830 13.617 1.00 30.00 C ATOM 81 C MET B 228 -4.991 -21.002 12.916 1.00 30.00 C ATOM 82 O MET B 228 -4.472 -21.923 13.572 1.00 30.00 O ATOM 83 CB MET B 228 -7.192 -19.985 13.595 1.00 30.00 C ATOM 84 CG MET B 228 -7.960 -19.118 14.591 1.00 30.00 C ATOM 85 SD MET B 228 -7.511 -19.311 16.335 1.00 30.00 S ATOM 86 CE MET B 228 -7.660 -21.082 16.598 1.00 30.00 C TER """ def exercise_02(): """ Generate ncs operators """ from mmtbx.ncs.ncs import generate_ncs_ops assert generate_ncs_ops(symmetry='d7')[0].max_operators()==14 assert generate_ncs_ops(symmetry='c7')[0].max_operators()==7 assert generate_ncs_ops(symmetry='o')[0].max_operators()==24 assert generate_ncs_ops(symmetry='t')[0].max_operators()==12 assert generate_ncs_ops(symmetry='i')[0].max_operators()==60 def exercise_03(): """ Verify that there are no errors processing the write command No inception of the output is done. Just making sure it does not break """ pdb_inp = pdb.input(source_info=None, lines=pdb_str_1) transform_info = pdb_inp.process_MTRIX_records() transforms_obj = iotbx.ncs.input( hierarchy=pdb_inp.construct_hierarchy()) pdb_inp = pdb.input(source_info=None, lines=pdb_str_1) transforms_obj.get_ncs_info_as_spec() def exercise_04(): """Test MTRIX record processing""" expected = """\ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 SCALE1 0.100000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.100000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.100000 0.00000 ATOM 1 N ILE A 40 1.000 1.000 1.000 1.00162.33 C ATOM 2 CA LEU A 40 94.618 -5.253 91.582 1.00 87.10 C TER ATOM 3 C ARG B 40 62.395 51.344 80.786 1.00107.25 C TER HETATM 4 C1 EDO A 40 39.954 51.526 72.372 0.33 60.93 C ATOM 5 N ILE C 40 1.000 -1.000 1.000 1.00162.33 C ATOM 6 CA LEU C 40 94.618 -91.582 -5.253 1.00 87.10 C TER ATOM 7 C ARG D 40 62.395 -80.786 51.344 1.00107.25 C TER HETATM 8 C1 EDO C 40 39.954 -72.372 51.526 0.33 60.93 C ATOM 9 N ILE E 40 1.000 1.000 -1.000 1.00162.33 C ATOM 10 CA LEU E 40 91.582 -5.253 -94.618 1.00 87.10 C TER ATOM 11 C ARG F 40 80.786 51.344 -62.395 1.00107.25 C TER HETATM 12 C1 EDO E 40 72.372 51.526 -39.954 0.33 60.93 C ATOM 13 N ILE G 40 -1.000 1.000 1.000 1.00162.33 C ATOM 14 CA LEU G 40 5.253 94.618 91.582 1.00 87.10 C TER ATOM 15 C ARG H 40 -51.344 62.395 80.786 1.00107.25 C TER HETATM 16 C1 EDO G 40 -51.526 39.954 72.372 0.33 60.93 C ATOM 17 N ILE I 40 1.000 1.000 -1.000 1.00162.33 C ATOM 18 CA LEU I 40 91.582 -5.253 -94.618 1.00 87.10 C TER ATOM 19 C ARG J 40 80.786 51.344 -62.395 1.00107.25 C TER HETATM 20 C1 EDO I 40 72.372 51.526 -39.954 0.33 60.93 C ATOM 21 N ILE K 40 -1.000 1.000 -1.000 1.00162.33 C ATOM 22 CA LEU K 40 5.253 91.582 -94.618 1.00 87.10 C TER ATOM 23 C ARG L 40 -51.344 80.786 -62.395 1.00107.25 C TER HETATM 24 C1 EDO K 40 -51.526 72.372 -39.954 0.33 60.93 C ATOM 25 N ILE M 40 -0.366 1.366 1.000 1.00162.33 C ATOM 26 CA LEU M 40 51.858 79.315 91.582 1.00 87.10 C TER ATOM 27 C ARG N 40 -13.268 79.708 80.786 1.00107.25 C TER HETATM 28 C1 EDO M 40 -24.646 60.364 72.372 0.33 60.93 C ATOM 29 N ILE O 40 -1.366 0.366 1.000 1.00162.33 C ATOM 30 CA LEU O 40 -42.760 84.568 91.582 1.00 87.10 C TER ATOM 31 C ARG P 40 -75.663 28.364 80.786 1.00107.25 C TER HETATM 32 C1 EDO O 40 -64.600 8.838 72.372 0.33 60.93 C ATOM 33 N ILE Q 40 1.000 1.500 1.000 1.00162.33 C ATOM 34 CA LEU Q 40 94.618 -4.753 91.582 1.00 87.10 C TER ATOM 35 C ARG R 40 62.395 51.844 80.786 1.00107.25 C TER HETATM 36 C1 EDO Q 40 39.954 52.026 72.372 0.33 60.93 C ATOM 37 N ILE S 40 -1.366 0.366 0.000 1.00162.33 C ATOM 38 CA LEU S 40 -42.760 84.568 90.582 1.00 87.10 C TER ATOM 39 C ARG T 40 -75.663 28.364 79.786 1.00107.25 C TER HETATM 40 C1 EDO S 40 -64.600 8.838 71.372 0.33 60.93 C END """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_3) model = mmtbx.model.manager(pdb_inp, expand_with_mtrix=False) model.expand_with_BIOMT_records() assert not show_diff(expected, model.model_as_pdb()) def exercise_05(): """Test MTRIX record processing""" cau_expected_results = """\ CRYST1 10.000 10.000 10.000 90.00 90.00 90.00 P 1 SCALE1 0.100000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.100000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.100000 0.00000 ATOM 1 N ILE A 40 1.000 1.000 1.000 1.00162.33 C ATOM 2 CA LEU A 40 94.618 -5.253 91.582 1.00 87.10 C TER ATOM 3 C ARG B 40 62.395 51.344 80.786 1.00107.25 C TER HETATM 4 C1 EDO A 40 39.954 51.526 72.372 0.33 60.93 C ATOM 5 N ILE C 40 1.000 -1.000 1.000 1.00162.33 C ATOM 6 CA LEU C 40 94.618 -91.582 -5.253 1.00 87.10 C TER ATOM 7 C ARG D 40 62.395 -80.786 51.344 1.00107.25 C TER HETATM 8 C1 EDO C 40 39.954 -72.372 51.526 0.33 60.93 C ATOM 9 N ILE E 40 -0.366 1.366 1.000 1.00162.33 C ATOM 10 CA LEU E 40 51.858 79.315 91.582 1.00 87.10 C TER ATOM 11 C ARG F 40 -13.268 79.708 80.786 1.00107.25 C TER HETATM 12 C1 EDO E 40 -24.646 60.364 72.372 0.33 60.93 C ATOM 13 N ILE G 40 -1.366 0.366 1.000 1.00162.33 C ATOM 14 CA LEU G 40 -42.760 84.568 91.582 1.00 87.10 C TER ATOM 15 C ARG H 40 -75.663 28.364 80.786 1.00107.25 C TER HETATM 16 C1 EDO G 40 -64.600 8.838 72.372 0.33 60.93 C ATOM 17 N ILE I 40 1.000 1.500 1.000 1.00162.33 C ATOM 18 CA LEU I 40 94.618 -4.753 91.582 1.00 87.10 C TER ATOM 19 C ARG J 40 62.395 51.844 80.786 1.00107.25 C TER HETATM 20 C1 EDO I 40 39.954 52.026 72.372 0.33 60.93 C END """ # use MTRIX data pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_3) model = mmtbx.model.manager(pdb_inp) assert not show_diff(cau_expected_results, model.model_as_pdb()) def exercise_06(): """ Test that when building bio-molecule and then finding NCS relations from it, we get the same rotation and translation""" pdb_strings = [pdb_str_4, pdb_str_5] for method,pdb_string in enumerate(pdb_strings): pdb_inp = pdb.input(source_info=None, lines=pdb_string) model = mmtbx.model.manager(pdb_inp, expand_with_mtrix=False) crystal_symmetry = model.crystal_symmetry() # The exact transforms from pdb_string r1_expected = matrix.sqr( [0.309017, -0.951057, 0.0,0.951057, 0.309017,-0.0,0.0,0.0,1.0]) r2_expected = matrix.sqr( [-0.809017,-0.587785,0.0,0.587785,-0.809017,-0.0,0.0,0.0,1.0]) t1_expected = matrix.col([0,0,7]) t2_expected = matrix.col([0,0,0]) # Look at biomt records retrieved from PDB file if method == 0: rec = model._model_input.process_BIOMT_records() model.expand_with_BIOMT_records() h = model.get_hierarchy() else: rec = model._model_input.process_MTRIX_records() model.expand_with_MTRIX_records() h = model.get_hierarchy() r1 = rec.r[1] r2 = rec.r[2] t1 = rec.t[1] t2 = rec.t[2] assert approx_equal(r1, r1_expected, eps=0.001) assert approx_equal(t1, t1_expected, eps=0.1) assert approx_equal(r2, r2_expected, eps=0.001) assert approx_equal(t2, t2_expected, eps=0.1) # Look at the rotation and translation found by the NCS search s = h.as_pdb_string(crystal_symmetry=crystal_symmetry) ncs_obj = ncs.input(hierarchy=pdb.input( source_info=None, lines=s).construct_hierarchy()) nrgl = ncs_obj.get_ncs_restraints_group_list() assert approx_equal(r1_expected, nrgl[0].copies[0].r, eps=0.001) assert approx_equal(t1_expected, nrgl[0].copies[0].t, eps=0.1) assert approx_equal(r2_expected, nrgl[0].copies[1].r, eps=0.001) assert approx_equal(t2_expected, nrgl[0].copies[1].t, eps=0.1) if method == 0: assert nrgl.get_n_groups() == 1 elif method == 1: assert nrgl.get_n_groups() == 2 def exercise_08(): """ Test for MTRIX record when copies already present in file """ pdb_inp = pdb.input(source_info=None, lines=pdb_str_8) model = mmtbx.model.manager(pdb_inp) assert model.get_number_of_atoms() == 7 if(__name__=='__main__'): exercise_02() exercise_03() exercise_04() exercise_05() exercise_06() exercise_08()