biotite 0.39.0__cp310-cp310-macosx_11_0_arm64.whl → 0.41.0__cp310-cp310-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 (121) hide show
  1. biotite/__init__.py +3 -3
  2. biotite/application/dssp/app.py +18 -18
  3. biotite/database/pubchem/download.py +23 -23
  4. biotite/database/pubchem/query.py +7 -7
  5. biotite/database/rcsb/download.py +19 -14
  6. biotite/file.py +17 -9
  7. biotite/sequence/align/banded.c +258 -237
  8. biotite/sequence/align/banded.cpython-310-darwin.so +0 -0
  9. biotite/sequence/align/cigar.py +60 -15
  10. biotite/sequence/align/kmeralphabet.c +243 -222
  11. biotite/sequence/align/kmeralphabet.cpython-310-darwin.so +0 -0
  12. biotite/sequence/align/kmersimilarity.c +215 -196
  13. biotite/sequence/align/kmersimilarity.cpython-310-darwin.so +0 -0
  14. biotite/sequence/align/kmertable.cpp +233 -205
  15. biotite/sequence/align/kmertable.cpython-310-darwin.so +0 -0
  16. biotite/sequence/align/localgapped.c +258 -237
  17. biotite/sequence/align/localgapped.cpython-310-darwin.so +0 -0
  18. biotite/sequence/align/localungapped.c +235 -214
  19. biotite/sequence/align/localungapped.cpython-310-darwin.so +0 -0
  20. biotite/sequence/align/multiple.c +255 -234
  21. biotite/sequence/align/multiple.cpython-310-darwin.so +0 -0
  22. biotite/sequence/align/pairwise.c +274 -253
  23. biotite/sequence/align/pairwise.cpython-310-darwin.so +0 -0
  24. biotite/sequence/align/permutation.c +215 -196
  25. biotite/sequence/align/permutation.cpython-310-darwin.so +0 -0
  26. biotite/sequence/align/selector.c +217 -197
  27. biotite/sequence/align/selector.cpython-310-darwin.so +0 -0
  28. biotite/sequence/align/tracetable.c +215 -195
  29. biotite/sequence/align/tracetable.cpython-310-darwin.so +0 -0
  30. biotite/sequence/annotation.py +2 -2
  31. biotite/sequence/codec.c +235 -214
  32. biotite/sequence/codec.cpython-310-darwin.so +0 -0
  33. biotite/sequence/io/fasta/convert.py +27 -24
  34. biotite/sequence/phylo/nj.c +215 -196
  35. biotite/sequence/phylo/nj.cpython-310-darwin.so +0 -0
  36. biotite/sequence/phylo/tree.c +227 -202
  37. biotite/sequence/phylo/tree.cpython-310-darwin.so +0 -0
  38. biotite/sequence/phylo/upgma.c +215 -196
  39. biotite/sequence/phylo/upgma.cpython-310-darwin.so +0 -0
  40. biotite/structure/__init__.py +2 -0
  41. biotite/structure/basepairs.py +7 -12
  42. biotite/structure/bonds.c +1437 -1279
  43. biotite/structure/bonds.cpython-310-darwin.so +0 -0
  44. biotite/structure/celllist.c +217 -197
  45. biotite/structure/celllist.cpython-310-darwin.so +0 -0
  46. biotite/structure/charges.c +1052 -1101
  47. biotite/structure/charges.cpython-310-darwin.so +0 -0
  48. biotite/structure/dotbracket.py +2 -0
  49. biotite/structure/filter.py +30 -37
  50. biotite/structure/info/__init__.py +5 -8
  51. biotite/structure/info/atoms.py +31 -68
  52. biotite/structure/info/bonds.py +47 -101
  53. biotite/structure/info/ccd/README.rst +8 -0
  54. biotite/structure/info/ccd/amino_acids.txt +1663 -0
  55. biotite/structure/info/ccd/carbohydrates.txt +1135 -0
  56. biotite/structure/info/ccd/components.bcif +0 -0
  57. biotite/structure/info/ccd/nucleotides.txt +798 -0
  58. biotite/structure/info/ccd.py +95 -0
  59. biotite/structure/info/groups.py +90 -0
  60. biotite/structure/info/masses.py +21 -20
  61. biotite/structure/info/misc.py +78 -25
  62. biotite/structure/info/standardize.py +17 -12
  63. biotite/structure/integrity.py +19 -70
  64. biotite/structure/io/__init__.py +2 -4
  65. biotite/structure/io/ctab.py +12 -106
  66. biotite/structure/io/general.py +167 -181
  67. biotite/structure/io/gro/file.py +16 -16
  68. biotite/structure/io/mmtf/__init__.py +3 -0
  69. biotite/structure/io/mmtf/convertarray.c +219 -198
  70. biotite/structure/io/mmtf/convertarray.cpython-310-darwin.so +0 -0
  71. biotite/structure/io/mmtf/convertfile.c +217 -197
  72. biotite/structure/io/mmtf/convertfile.cpython-310-darwin.so +0 -0
  73. biotite/structure/io/mmtf/decode.c +225 -204
  74. biotite/structure/io/mmtf/decode.cpython-310-darwin.so +0 -0
  75. biotite/structure/io/mmtf/encode.c +215 -196
  76. biotite/structure/io/mmtf/encode.cpython-310-darwin.so +0 -0
  77. biotite/structure/io/mmtf/file.py +34 -26
  78. biotite/structure/io/mol/__init__.py +4 -2
  79. biotite/structure/io/mol/convert.py +71 -7
  80. biotite/structure/io/mol/ctab.py +414 -0
  81. biotite/structure/io/mol/header.py +116 -0
  82. biotite/structure/io/mol/{file.py → mol.py} +69 -82
  83. biotite/structure/io/mol/sdf.py +909 -0
  84. biotite/structure/io/npz/__init__.py +3 -0
  85. biotite/structure/io/npz/file.py +21 -18
  86. biotite/structure/io/pdb/__init__.py +3 -3
  87. biotite/structure/io/pdb/file.py +89 -34
  88. biotite/structure/io/pdb/hybrid36.c +63 -43
  89. biotite/structure/io/pdb/hybrid36.cpython-310-darwin.so +0 -0
  90. biotite/structure/io/pdbqt/file.py +32 -32
  91. biotite/structure/io/pdbx/__init__.py +12 -6
  92. biotite/structure/io/pdbx/bcif.py +648 -0
  93. biotite/structure/io/pdbx/cif.py +1032 -0
  94. biotite/structure/io/pdbx/component.py +246 -0
  95. biotite/structure/io/pdbx/convert.py +858 -386
  96. biotite/structure/io/pdbx/encoding.c +112813 -0
  97. biotite/structure/io/pdbx/encoding.cpython-310-darwin.so +0 -0
  98. biotite/structure/io/pdbx/legacy.py +267 -0
  99. biotite/structure/molecules.py +151 -151
  100. biotite/structure/repair.py +253 -0
  101. biotite/structure/sasa.c +215 -196
  102. biotite/structure/sasa.cpython-310-darwin.so +0 -0
  103. biotite/structure/sequence.py +112 -0
  104. biotite/structure/superimpose.py +618 -116
  105. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/METADATA +3 -3
  106. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/RECORD +109 -103
  107. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/WHEEL +1 -1
  108. biotite/structure/info/amino_acids.json +0 -1556
  109. biotite/structure/info/amino_acids.py +0 -42
  110. biotite/structure/info/carbohydrates.json +0 -1122
  111. biotite/structure/info/carbohydrates.py +0 -39
  112. biotite/structure/info/intra_bonds.msgpack +0 -0
  113. biotite/structure/info/link_types.msgpack +0 -1
  114. biotite/structure/info/nucleotides.json +0 -772
  115. biotite/structure/info/nucleotides.py +0 -39
  116. biotite/structure/info/residue_masses.msgpack +0 -0
  117. biotite/structure/info/residue_names.msgpack +0 -3
  118. biotite/structure/info/residues.msgpack +0 -0
  119. biotite/structure/io/pdbx/file.py +0 -652
  120. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/LICENSE.rst +0 -0
  121. {biotite-0.39.0.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):
455
455
  i_last = sys.maxsize
456
456
  else:
457
457
  i_last = index.stop - 1
458
-
458
+
459
459
  sub_annot = Annotation()
460
460
  for feature in self:
461
461
  locs_in_scope = []
@@ -744,7 +744,7 @@ class AnnotatedSequence(Copyable):
744
744
  locs, key=lambda loc: loc.last, reverse=True
745
745
  )
746
746
  # Merge the sequences corresponding to the ordered locations
747
- for loc in sorted(locs, key=lambda loc: loc.first):
747
+ for loc in sorted_locs:
748
748
  slice_start = loc.first - self._seqstart
749
749
  # +1 due to exclusive stop
750
750
  slice_stop = loc.last - self._seqstart +1