biotite 0.40.0__cp312-cp312-win_amd64.whl → 0.41.0__cp312-cp312-win_amd64.whl

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Files changed (90) hide show
  1. biotite/__init__.py +1 -1
  2. biotite/database/pubchem/download.py +23 -23
  3. biotite/database/pubchem/query.py +7 -7
  4. biotite/file.py +17 -9
  5. biotite/sequence/align/banded.c +117 -117
  6. biotite/sequence/align/banded.cp312-win_amd64.pyd +0 -0
  7. biotite/sequence/align/cigar.py +60 -15
  8. biotite/sequence/align/kmeralphabet.c +117 -117
  9. biotite/sequence/align/kmeralphabet.cp312-win_amd64.pyd +0 -0
  10. biotite/sequence/align/kmersimilarity.c +117 -117
  11. biotite/sequence/align/kmersimilarity.cp312-win_amd64.pyd +0 -0
  12. biotite/sequence/align/kmertable.cp312-win_amd64.pyd +0 -0
  13. biotite/sequence/align/kmertable.cpp +117 -117
  14. biotite/sequence/align/localgapped.c +117 -117
  15. biotite/sequence/align/localgapped.cp312-win_amd64.pyd +0 -0
  16. biotite/sequence/align/localungapped.c +117 -117
  17. biotite/sequence/align/localungapped.cp312-win_amd64.pyd +0 -0
  18. biotite/sequence/align/multiple.c +117 -117
  19. biotite/sequence/align/multiple.cp312-win_amd64.pyd +0 -0
  20. biotite/sequence/align/pairwise.c +117 -117
  21. biotite/sequence/align/pairwise.cp312-win_amd64.pyd +0 -0
  22. biotite/sequence/align/permutation.c +117 -117
  23. biotite/sequence/align/permutation.cp312-win_amd64.pyd +0 -0
  24. biotite/sequence/align/selector.c +117 -117
  25. biotite/sequence/align/selector.cp312-win_amd64.pyd +0 -0
  26. biotite/sequence/align/tracetable.c +117 -117
  27. biotite/sequence/align/tracetable.cp312-win_amd64.pyd +0 -0
  28. biotite/sequence/annotation.py +2 -2
  29. biotite/sequence/codec.c +117 -117
  30. biotite/sequence/codec.cp312-win_amd64.pyd +0 -0
  31. biotite/sequence/io/fasta/convert.py +27 -24
  32. biotite/sequence/phylo/nj.c +117 -117
  33. biotite/sequence/phylo/nj.cp312-win_amd64.pyd +0 -0
  34. biotite/sequence/phylo/tree.c +117 -117
  35. biotite/sequence/phylo/tree.cp312-win_amd64.pyd +0 -0
  36. biotite/sequence/phylo/upgma.c +117 -117
  37. biotite/sequence/phylo/upgma.cp312-win_amd64.pyd +0 -0
  38. biotite/structure/__init__.py +2 -0
  39. biotite/structure/bonds.c +1122 -913
  40. biotite/structure/bonds.cp312-win_amd64.pyd +0 -0
  41. biotite/structure/celllist.c +117 -117
  42. biotite/structure/celllist.cp312-win_amd64.pyd +0 -0
  43. biotite/structure/charges.c +117 -117
  44. biotite/structure/charges.cp312-win_amd64.pyd +0 -0
  45. biotite/structure/dotbracket.py +2 -0
  46. biotite/structure/info/atoms.py +6 -1
  47. biotite/structure/info/bonds.py +1 -1
  48. biotite/structure/info/ccd/amino_acids.txt +17 -0
  49. biotite/structure/info/ccd/carbohydrates.txt +2 -0
  50. biotite/structure/info/ccd/components.bcif +0 -0
  51. biotite/structure/info/ccd/nucleotides.txt +1 -0
  52. biotite/structure/info/misc.py +69 -5
  53. biotite/structure/integrity.py +19 -70
  54. biotite/structure/io/ctab.py +12 -106
  55. biotite/structure/io/general.py +157 -165
  56. biotite/structure/io/gro/file.py +16 -16
  57. biotite/structure/io/mmtf/convertarray.c +117 -117
  58. biotite/structure/io/mmtf/convertarray.cp312-win_amd64.pyd +0 -0
  59. biotite/structure/io/mmtf/convertfile.c +117 -117
  60. biotite/structure/io/mmtf/convertfile.cp312-win_amd64.pyd +0 -0
  61. biotite/structure/io/mmtf/decode.c +117 -117
  62. biotite/structure/io/mmtf/decode.cp312-win_amd64.pyd +0 -0
  63. biotite/structure/io/mmtf/encode.c +117 -117
  64. biotite/structure/io/mmtf/encode.cp312-win_amd64.pyd +0 -0
  65. biotite/structure/io/mol/__init__.py +4 -2
  66. biotite/structure/io/mol/convert.py +71 -7
  67. biotite/structure/io/mol/ctab.py +414 -0
  68. biotite/structure/io/mol/header.py +116 -0
  69. biotite/structure/io/mol/{file.py → mol.py} +69 -82
  70. biotite/structure/io/mol/sdf.py +909 -0
  71. biotite/structure/io/pdb/file.py +84 -31
  72. biotite/structure/io/pdb/hybrid36.cp312-win_amd64.pyd +0 -0
  73. biotite/structure/io/pdbx/__init__.py +0 -1
  74. biotite/structure/io/pdbx/bcif.py +2 -3
  75. biotite/structure/io/pdbx/cif.py +9 -5
  76. biotite/structure/io/pdbx/component.py +4 -1
  77. biotite/structure/io/pdbx/convert.py +203 -79
  78. biotite/structure/io/pdbx/encoding.c +117 -117
  79. biotite/structure/io/pdbx/encoding.cp312-win_amd64.pyd +0 -0
  80. biotite/structure/repair.py +253 -0
  81. biotite/structure/sasa.c +117 -117
  82. biotite/structure/sasa.cp312-win_amd64.pyd +0 -0
  83. biotite/structure/sequence.py +112 -0
  84. biotite/structure/superimpose.py +472 -13
  85. {biotite-0.40.0.dist-info → biotite-0.41.0.dist-info}/METADATA +2 -2
  86. {biotite-0.40.0.dist-info → biotite-0.41.0.dist-info}/RECORD +89 -85
  87. biotite/structure/io/pdbx/error.py +0 -14
  88. {biotite-0.40.0.dist-info → biotite-0.41.0.dist-info}/LICENSE.rst +0 -0
  89. {biotite-0.40.0.dist-info → biotite-0.41.0.dist-info}/WHEEL +0 -0
  90. {biotite-0.40.0.dist-info → biotite-0.41.0.dist-info}/top_level.txt +0 -0
biotite/sequence/annotation.py CHANGED
@@ -455,7 +455,7 @@ class Annotation(Copyable):
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  i_last = sys.maxsize
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  else:
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  i_last = index.stop - 1
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-
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+
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  sub_annot = Annotation()
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  for feature in self:
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  locs_in_scope = []
@@ -744,7 +744,7 @@ class AnnotatedSequence(Copyable):
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  locs, key=lambda loc: loc.last, reverse=True
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  )
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  # Merge the sequences corresponding to the ordered locations
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- for loc in sorted(locs, key=lambda loc: loc.first):
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+ for loc in sorted_locs:
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  slice_start = loc.first - self._seqstart
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  # +1 due to exclusive stop
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  slice_stop = loc.last - self._seqstart +1