biotite 0.39.0__cp312-cp312-macosx_11_0_arm64.whl → 0.40.0__cp312-cp312-macosx_11_0_arm64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of biotite might be problematic. Click here for more details.

Files changed (104) hide show
  1. biotite/__init__.py +3 -3
  2. biotite/application/dssp/app.py +18 -18
  3. biotite/database/rcsb/download.py +19 -14
  4. biotite/sequence/align/banded.c +256 -235
  5. biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.c +241 -220
  7. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  8. biotite/sequence/align/kmersimilarity.c +213 -194
  9. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  10. biotite/sequence/align/kmertable.cpp +231 -203
  11. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  12. biotite/sequence/align/localgapped.c +256 -235
  13. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  14. biotite/sequence/align/localungapped.c +233 -212
  15. biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
  16. biotite/sequence/align/multiple.c +253 -232
  17. biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
  18. biotite/sequence/align/pairwise.c +272 -251
  19. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  20. biotite/sequence/align/permutation.c +213 -194
  21. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  22. biotite/sequence/align/selector.c +215 -195
  23. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  24. biotite/sequence/align/tracetable.c +213 -193
  25. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  26. biotite/sequence/codec.c +233 -212
  27. biotite/sequence/codec.cpython-312-darwin.so +0 -0
  28. biotite/sequence/phylo/nj.c +213 -194
  29. biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
  30. biotite/sequence/phylo/tree.c +225 -200
  31. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  32. biotite/sequence/phylo/upgma.c +213 -194
  33. biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
  34. biotite/structure/basepairs.py +7 -12
  35. biotite/structure/bonds.c +1173 -1224
  36. biotite/structure/bonds.cpython-312-darwin.so +0 -0
  37. biotite/structure/celllist.c +215 -195
  38. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  39. biotite/structure/charges.c +1050 -1099
  40. biotite/structure/charges.cpython-312-darwin.so +0 -0
  41. biotite/structure/filter.py +30 -37
  42. biotite/structure/info/__init__.py +5 -8
  43. biotite/structure/info/atoms.py +25 -67
  44. biotite/structure/info/bonds.py +46 -100
  45. biotite/structure/info/ccd/README.rst +8 -0
  46. biotite/structure/info/ccd/amino_acids.txt +1646 -0
  47. biotite/structure/info/ccd/carbohydrates.txt +1133 -0
  48. biotite/structure/info/ccd/components.bcif +0 -0
  49. biotite/structure/info/ccd/nucleotides.txt +797 -0
  50. biotite/structure/info/ccd.py +95 -0
  51. biotite/structure/info/groups.py +90 -0
  52. biotite/structure/info/masses.py +21 -20
  53. biotite/structure/info/misc.py +11 -22
  54. biotite/structure/info/standardize.py +17 -12
  55. biotite/structure/io/__init__.py +2 -4
  56. biotite/structure/io/ctab.py +1 -1
  57. biotite/structure/io/general.py +37 -43
  58. biotite/structure/io/mmtf/__init__.py +3 -0
  59. biotite/structure/io/mmtf/convertarray.c +217 -196
  60. biotite/structure/io/mmtf/convertarray.cpython-312-darwin.so +0 -0
  61. biotite/structure/io/mmtf/convertfile.c +215 -195
  62. biotite/structure/io/mmtf/convertfile.cpython-312-darwin.so +0 -0
  63. biotite/structure/io/mmtf/decode.c +223 -202
  64. biotite/structure/io/mmtf/decode.cpython-312-darwin.so +0 -0
  65. biotite/structure/io/mmtf/encode.c +213 -194
  66. biotite/structure/io/mmtf/encode.cpython-312-darwin.so +0 -0
  67. biotite/structure/io/mmtf/file.py +34 -26
  68. biotite/structure/io/npz/__init__.py +3 -0
  69. biotite/structure/io/npz/file.py +21 -18
  70. biotite/structure/io/pdb/__init__.py +3 -3
  71. biotite/structure/io/pdb/file.py +5 -3
  72. biotite/structure/io/pdb/hybrid36.c +63 -43
  73. biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so +0 -0
  74. biotite/structure/io/pdbqt/file.py +32 -32
  75. biotite/structure/io/pdbx/__init__.py +13 -6
  76. biotite/structure/io/pdbx/bcif.py +649 -0
  77. biotite/structure/io/pdbx/cif.py +1028 -0
  78. biotite/structure/io/pdbx/component.py +243 -0
  79. biotite/structure/io/pdbx/convert.py +707 -359
  80. biotite/structure/io/pdbx/encoding.c +112803 -0
  81. biotite/structure/io/pdbx/encoding.cpython-312-darwin.so +0 -0
  82. biotite/structure/io/pdbx/error.py +14 -0
  83. biotite/structure/io/pdbx/legacy.py +267 -0
  84. biotite/structure/molecules.py +151 -151
  85. biotite/structure/sasa.c +213 -194
  86. biotite/structure/sasa.cpython-312-darwin.so +0 -0
  87. biotite/structure/superimpose.py +158 -115
  88. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/METADATA +2 -2
  89. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/RECORD +92 -90
  90. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/WHEEL +1 -1
  91. biotite/structure/info/amino_acids.json +0 -1556
  92. biotite/structure/info/amino_acids.py +0 -42
  93. biotite/structure/info/carbohydrates.json +0 -1122
  94. biotite/structure/info/carbohydrates.py +0 -39
  95. biotite/structure/info/intra_bonds.msgpack +0 -0
  96. biotite/structure/info/link_types.msgpack +0 -1
  97. biotite/structure/info/nucleotides.json +0 -772
  98. biotite/structure/info/nucleotides.py +0 -39
  99. biotite/structure/info/residue_masses.msgpack +0 -0
  100. biotite/structure/info/residue_names.msgpack +0 -3
  101. biotite/structure/info/residues.msgpack +0 -0
  102. biotite/structure/io/pdbx/file.py +0 -652
  103. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/LICENSE.rst +0 -0
  104. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/top_level.txt +0 -0

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the package file manually.