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add broken PDB tests
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@stefdoerr
stefdoerr committed Dec 7, 2023
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105 changes: 105 additions & 0 deletions moleculekit/test-data/molecule-readers/broken_cases/broken_bond_indexes.pdb
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HETATM 1630 CA CA A 480 -10.300 4.358 36.895 1.00 10.61 1 CA
HETATM 1631 C1 BEN A 1 -1.853 14.311 16.658 1.00 19.86 1 C
HETATM 1632 C2 BEN A 1 -2.107 15.653 16.758 1.00 19.86 1 C
HETATM 1633 C3 BEN A 1 -1.774 16.341 17.932 1.00 19.86 1 C
HETATM 1634 C4 BEN A 1 -1.175 15.662 19.005 1.00 19.86 1 C
HETATM 1635 C5 BEN A 1 -0.914 14.295 18.885 1.00 19.86 1 C
HETATM 1636 C6 BEN A 1 -1.257 13.634 17.708 1.00 19.86 1 C
HETATM 1637 C BEN A 1 -2.193 13.627 15.496 1.00 19.86 1 C
HETATM 1638 N1 BEN A 1 -2.797 14.235 14.491 1.00 19.86 1 N
HETATM 1639 N2 BEN A 1 -1.762 12.391 15.309 1.00 19.86 1 N
HETATM 1640 O HOH A 401 -2.927 13.819 40.756 1.00 24.70 1 O
HETATM 1641 O HOH A 406 4.889 5.909 25.265 1.00 10.10 1 O
HETATM 1642 O HOH A 408 8.850 13.873 17.142 1.00 12.46 1 O
HETATM 1643 O HOH A 410 -3.870 9.452 26.413 1.00 4.19 1 O
HETATM 1644 O HOH A 412 -11.374 0.654 26.976 1.00 4.60 1 O
HETATM 1645 O HOH A 415 -4.496 15.265 10.737 1.00 12.69 1 O
HETATM 1646 O HOH A 416 0.950 11.375 16.494 1.00 7.25 1 O
HETATM 1647 O HOH A 429 -12.070 6.651 18.466 1.00 12.69 1 O
HETATM 1648 O HOH A 430 -9.270 8.506 22.731 1.00 5.98 1 O
HETATM 1649 O HOH A 439 11.040 20.653 27.812 1.00 33.08 1 O
HETATM 1650 O HOH A 457 -5.843 10.561 34.958 1.00 7.31 1 O
HETATM 1651 O HOH A 470 -8.705 0.135 14.338 1.00 10.73 1 O
HETATM 1652 O HOH A 473 7.336 7.289 8.139 1.00 8.89 1 O
HETATM 1653 O HOH A 482 7.664 21.532 24.985 1.00 24.39 1 O
HETATM 1654 O HOH A 499 17.457 20.536 24.689 1.00 24.73 1 O
HETATM 1655 O HOH A 516 -4.428 -1.630 32.617 1.00 14.74 1 O
HETATM 1656 O HOH A 530 2.122 11.727 1.634 1.00 28.70 1 O
HETATM 1657 O HOH A 561 -10.284 -2.115 35.691 1.00 25.93 1 O
HETATM 1658 O HOH A 562 -4.808 11.535 9.447 1.00 16.14 1 O
HETATM 1659 O HOH A 583 -3.359 -2.958 40.024 1.00 26.45 1 O
HETATM 1660 O HOH A 604 -8.098 0.011 30.017 1.00 11.83 1 O
HETATM 1661 O HOH A 700 -8.200 13.812 37.881 1.00 9.95 1 O
HETATM 1662 O HOH A 701 -1.973 7.926 24.818 1.00 1.53 1 O
HETATM 1663 O HOH A 702 -1.245 17.671 22.998 1.00 7.65 1 O
HETATM 1664 O HOH A 703 11.391 12.930 17.496 1.00 8.18 1 O
HETATM 1665 O HOH A 704 -1.935 8.071 13.249 1.00 5.41 1 O
HETATM 1666 O HOH A 705 -3.835 8.922 10.084 1.00 10.34 1 O
HETATM 1667 O HOH A 706 -9.067 0.122 36.996 1.00 8.60 1 O
HETATM 1668 O HOH A 707 -7.612 9.020 36.477 1.00 7.89 1 O
HETATM 1669 O HOH A 708 -3.411 3.419 33.133 1.00 6.19 1 O
HETATM 1670 O HOH A 709 -4.364 0.823 31.016 1.00 14.93 1 O
HETATM 1671 O HOH A 710 1.643 17.857 19.582 1.00 13.54 1 O
HETATM 1672 O HOH A 711 -9.490 6.317 38.193 1.00 10.77 1 O
HETATM 1673 O HOH A 712 12.881 15.826 38.107 1.00 16.78 1 O
HETATM 1674 O HOH A 713 16.319 2.991 38.344 1.00 17.46 1 O
HETATM 1675 O HOH A 714 -10.352 2.286 35.742 1.00 9.07 1 O
HETATM 1676 O HOH A 715 -8.947 13.763 33.942 1.00 18.33 1 O
HETATM 1677 O HOH A 716 -1.261 0.368 33.097 1.00 11.30 1 O
HETATM 1678 O HOH A 717 -5.709 -1.127 29.306 1.00 14.70 1 O
HETATM 1679 O HOH A 718 -13.888 0.087 28.304 1.00 17.89 1 O
HETATM 1680 O HOH A 719 12.450 22.857 26.008 1.00 16.95 1 O
HETATM 1681 O HOH A 720 13.546 22.707 23.451 1.00 17.22 1 O
HETATM 1682 O HOH A 721 -0.813 0.453 22.355 1.00 8.79 1 O
HETATM 1683 O HOH A 722 11.081 2.688 16.695 1.00 6.65 1 O
HETATM 1684 O HOH A 723 9.877 19.379 12.494 1.00 16.57 1 O
HETATM 1685 O HOH A 724 14.027 18.220 9.118 1.00 25.72 1 O
HETATM 1686 O HOH A 725 9.930 16.190 5.865 1.00 18.43 1 O
HETATM 1687 O HOH A 726 2.515 1.626 4.656 1.00 15.63 1 O
HETATM 1688 O HOH A 727 3.320 4.101 2.884 1.00 20.91 1 O
HETATM 1689 O HOH A 728 -14.059 9.003 16.556 1.00 19.27 1 O
HETATM 1690 O HOH A 729 8.286 -4.150 16.486 1.00 16.24 1 O
HETATM 1691 O HOH A 730 -11.173 1.601 14.409 1.00 21.46 1 O
HETATM 1692 O HOH A 731 4.054 21.913 4.296 1.00 17.68 1 O
HETATM 1693 O HOH A 800 16.519 19.931 15.883 1.00 25.07 1 O
HETATM 1694 O HOH A 801 -12.130 23.265 15.927 1.00 25.98 1 O
HETATM 1695 O HOH A 802 -10.358 18.093 16.449 1.00 28.23 1 O
HETATM 1696 O HOH A 803 16.477 -0.727 18.616 1.00 31.58 1 O
HETATM 1697 O HOH A 804 12.812 -3.910 27.238 1.00 30.53 1 O
HETATM 1698 O HOH A 805 8.315 20.399 27.434 1.00 24.88 1 O
HETATM 1699 O HOH A 807 5.803 20.922 28.430 1.00 30.29 1 O
HETATM 1700 O HOH A 808 17.331 18.227 28.215 1.00 30.47 1 O
HETATM 1701 O HOH A 809 17.388 20.916 27.945 1.00 29.88 1 O
CONECT 48 1007
CONECT 185 298
CONECT 298 185
CONECT 384 1630
CONECT 397 1630
CONECT 421 1630
CONECT 461 1630
CONECT 811 1521
CONECT 853 1327
CONECT 1007 48
CONECT 1084 1190
CONECT 1190 1084
CONECT 1265 1422
CONECT 1327 853
CONECT 1422 1265
CONECT 1521 811
CONECT 1630 384 397 421
CONECT 1630 461 1672 1675
CONECT 1631 1632 1636 1637
CONECT 1632 1631 1633
CONECT 1633 1632 1634
CONECT 1634 1633 1635
CONECT 1635 1634 1636
CONECT 1636 1631 1635
CONECT 1637 1631 1638 1639
CONECT 1638 1637
CONECT 1639 1637
CONECT 1672 1630
CONECT 9999 1630
CONECT 1675 1630
CONECT 1675 9999 9998
ENDMDL
END
55 changes: 55 additions & 0 deletions moleculekit/test-data/molecule-readers/broken_cases/broken_crystal_info.pdb
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HEADER LIGASE 01-JAN-01 1HTO
TITLE CRYSTALLOGRAPHIC STRUCTURE OF A RELAXED GLUTAMINE SYNTHETASE FROM
TITLE 2 MYCOBACTERIUM TUBERCULOSIS
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 103.86000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 137.25000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 128.84500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 137.25000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 103.86000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 128.84500
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
CRYST1 207.720 257.690 274.500 90.00 90.00 90.00 P 21 21 21 96
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 0.004810 0.000000 0.000000 0.00000
SCALE2 0.000000 0.003880 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003640 0.00000
ATOM 1 N THR A 601 103.936 52.601 136.940 1.00 87.38 N
ATOM 2 CA THR A 601 104.798 52.889 138.123 1.00100.00 C
ATOM 3 C THR A 601 106.262 52.526 137.849 1.00100.00 C
ATOM 4 O THR A 601 107.144 53.386 137.932 1.00100.00 O
ATOM 5 CB THR A 601 104.306 52.129 139.397 1.00100.00 C
ATOM 6 OG1 THR A 601 102.935 52.458 139.660 1.00100.00 O
ATOM 7 CG2 THR A 601 105.143 52.515 140.620 1.00 90.85 C
ATOM 8 N GLU A 602 106.509 51.266 137.494 1.00100.00 N
ATOM 9 CA GLU A 602 107.871 50.806 137.230 1.00 99.67 C
ATOM 10 C GLU A 602 108.155 50.148 135.878 1.00 94.54 C
ATOM 11 O GLU A 602 109.321 50.000 135.505 1.00 99.67 O
ENDMDL
END
55 changes: 55 additions & 0 deletions moleculekit/test-data/molecule-readers/broken_cases/broken_crystal_info2.pdb
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HEADER LIGASE 01-JAN-01 1HTO
TITLE CRYSTALLOGRAPHIC STRUCTURE OF A RELAXED GLUTAMINE SYNTHETASE FROM
TITLE 2 MYCOBACTERIUM TUBERCULOSIS
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 103.86000
REMARK 290 SMTRY2 2 0.000000 -1.0aa000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 137.25000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 128.84500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 137.25000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 103.86000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 128.84500
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
CRYST1 207.720 257.690 274.500 90.00 90.00 90.00 P 21 21 21 96
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 0.004810 0.000000 0.000000 0.00000
SCALE2 0.000000 0.003880 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003640 0.00000
ATOM 1 N THR A 601 103.936 52.601 136.940 1.00 87.38 N
ATOM 2 CA THR A 601 104.798 52.889 138.123 1.00100.00 C
ATOM 3 C THR A 601 106.262 52.526 137.849 1.00100.00 C
ATOM 4 O THR A 601 107.144 53.386 137.932 1.00100.00 O
ATOM 5 CB THR A 601 104.306 52.129 139.397 1.00100.00 C
ATOM 6 OG1 THR A 601 102.935 52.458 139.660 1.00100.00 O
ATOM 7 CG2 THR A 601 105.143 52.515 140.620 1.00 90.85 C
ATOM 8 N GLU A 602 106.509 51.266 137.494 1.00100.00 N
ATOM 9 CA GLU A 602 107.871 50.806 137.230 1.00 99.67 C
ATOM 10 C GLU A 602 108.155 50.148 135.878 1.00 94.54 C
ATOM 11 O GLU A 602 109.321 50.000 135.505 1.00 99.67 O
ENDMDL
END
48 changes: 48 additions & 0 deletions moleculekit/test-data/molecule-readers/broken_cases/non_numeric_resid.pdb
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ATOM 1586 N GLN A 240 20.882 3.280 29.367 1.00 16.18 0 N
ATOM 1587 CA GLN A 240 21.945 4.015 30.108 1.00 16.18 0 C
ATOM 1588 C GLN A 240 21.352 4.831 31.274 1.00 16.18 0 C
ATOM 1589 O GLN A 240 21.954 4.892 32.384 1.00 16.18 0 O
ATOM 1590 CB GLN A 240 22.672 4.993 29.126 1.00 16.18 0 C
ATOM 1591 CG GLN A 240 23.639 6.000 29.790 0.00 0.00 0 C
ATOM 1592 CD GLN A 240 24.773 5.283 30.518 0.00 0.00 0 C
ATOM 1593 OE1 GLN A 240 25.406 4.366 29.937 0.00 0.00 0 O
ATOM 1594 NE2 GLN A 240 24.774 5.468 31.824 0.00 0.00 0 N
ATOM 1595 N THR A 241 20.271 5.555 30.892 1.00 12.30 0 N
ATOM 1596 CA THR A 241 19.640 6.449 31.852 1.00 12.30 0 C
ATOM 1597 C THR A 241 19.127 5.679 33.047 1.00 12.30 0 C
ATOM 1598 O THR A 241 19.397 6.107 34.209 1.00 12.30 0 O
ATOM 1599 CB THR A 241 18.558 7.414 31.263 1.00 12.30 0 C
ATOM 1600 OG1 THR A 241 19.197 8.159 30.210 1.00 10.37 0 O
ATOM 1601 CG2 THR A 241 18.088 8.464 32.289 1.00 10.37 0 C
ATOM 1602 N ILE A 242 18.389 4.648 32.726 1.00 12.54 0 N
ATOM 1603 CA ILE A 242 17.711 3.915 33.784 1.00 12.54 0 C
ATOM 1604 C ILE A 242 18.746 3.196 34.642 1.00 12.54 0 C
ATOM 1605 O ILE A 242 18.540 3.065 35.889 1.00 12.54 0 O
ATOM 1606 CB ILE A 242 16.761 2.814 33.189 1.00 12.54 0 C
ATOM 1607 CG1 ILE A 242 15.393 3.371 32.933 1.00 26.84 0 C
ATOM 1608 CG2 ILE A 242 16.586 1.642 34.193 1.00 26.84 0 C
ATOM 1609 CD1 ILE A 242 15.381 4.340 31.766 1.00 26.84 0 C
ATOM 1610 N ALA A 243 19.847 2.815 34.041 1.00 16.55 0 N
ATOM 1611 CA ALA A 243 20.925 2.121 34.801 1.00 16.55 0 C
ATOM 1612 C ALA A 243 21.633 3.042 35.812 1.00 16.55 0 C
ATOM 1613 O ALA A 243 22.249 2.521 36.788 1.00 16.55 0 O
ATOM 1614 CB ALA A 243 22.001 1.631 33.824 1.00 16.55 0 C
ATOM 1615 N SER A 2B4 21.520 4.357 35.602 1.00 18.50 0 N
ATOM 1616 CA SER A 244 22.288 5.308 36.418 1.00 18.50 0 C
ATOM 1617 C SER A 244 21.419 6.233 37.249 1.00 18.50 0 C
ATOM 1618 O SER A 244 21.912 7.209 37.870 1.00 18.50 0 O
ATOM 1619 CB SER A 244 23.258 6.144 35.552 1.00 18.50 0 C
ATOM 1620 OG SER A 244 23.969 5.281 34.652 0.00 0.00 0 O
ATOM 1621 N ASN A 245 20.140 6.014 37.228 1.00 16.03 0 N
ATOM 1622 CA ASN A 24X 19.247 6.871 37.964 1.00 16.03 0 C
ATOM 1623 C ASN A 245 18.167 6.050 38.662 1.00 16.03 0 C
ATOM 1624 O ASN A 245 17.332 6.695 39.341 1.00 16.03 0 O
ATOM 1625 CB ASN A 245 18.546 7.785 36.941 1.00 16.03 0 C
ATOM 1626 CG ASN A 245 19.506 8.823 36.333 1.00 18.49 0 C
ATOM 1627 OD1 ASN A 245 19.679 9.885 36.980 1.00 18.49 0 O
ATOM 1628 ND2 ASN A 245 20.188 8.572 35.247 1.00 18.49 0 N
ATOM 1629 OXT ASN A 245V 18.437 4.875 39.012 1.00 18.49 0 O
TER
ENDMDL
END
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