biotite 0.38.0__cp311-cp311-macosx_11_0_arm64.whl → 0.40.0__cp311-cp311-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 (124) hide show
  1. biotite/__init__.py +3 -3
  2. biotite/application/application.py +33 -28
  3. biotite/application/dssp/app.py +18 -18
  4. biotite/application/sra/__init__.py +5 -0
  5. biotite/application/sra/app.py +337 -55
  6. biotite/database/entrez/__init__.py +2 -1
  7. biotite/database/entrez/check.py +14 -3
  8. biotite/database/entrez/download.py +20 -13
  9. biotite/database/entrez/key.py +44 -0
  10. biotite/database/entrez/query.py +38 -34
  11. biotite/database/pubchem/query.py +44 -44
  12. biotite/database/rcsb/download.py +19 -14
  13. biotite/database/rcsb/query.py +46 -46
  14. biotite/sequence/align/__init__.py +5 -1
  15. biotite/sequence/align/banded.c +1408 -1025
  16. biotite/sequence/align/banded.cpython-311-darwin.so +0 -0
  17. biotite/sequence/align/buckets.py +69 -0
  18. biotite/sequence/align/cigar.py +389 -0
  19. biotite/sequence/align/kmeralphabet.c +3220 -2850
  20. biotite/sequence/align/kmeralphabet.cpython-311-darwin.so +0 -0
  21. biotite/sequence/align/kmersimilarity.c +713 -663
  22. biotite/sequence/align/kmersimilarity.cpython-311-darwin.so +0 -0
  23. biotite/sequence/align/kmertable.cpp +68398 -0
  24. biotite/sequence/align/kmertable.cpython-311-darwin.so +0 -0
  25. biotite/sequence/align/localgapped.c +1507 -1074
  26. biotite/sequence/align/localgapped.cpython-311-darwin.so +0 -0
  27. biotite/sequence/align/localungapped.c +1143 -833
  28. biotite/sequence/align/localungapped.cpython-311-darwin.so +0 -0
  29. biotite/sequence/align/multiple.c +1569 -1092
  30. biotite/sequence/align/multiple.cpython-311-darwin.so +0 -0
  31. biotite/sequence/align/pairwise.c +1612 -1212
  32. biotite/sequence/align/pairwise.cpython-311-darwin.so +0 -0
  33. biotite/sequence/align/permutation.c +33259 -0
  34. biotite/sequence/align/permutation.cpython-311-darwin.so +0 -0
  35. biotite/sequence/align/primes.txt +821 -0
  36. biotite/sequence/align/{kmertable.c → selector.c} +9129 -16497
  37. biotite/sequence/align/selector.cpython-311-darwin.so +0 -0
  38. biotite/sequence/align/tracetable.c +685 -646
  39. biotite/sequence/align/tracetable.cpython-311-darwin.so +0 -0
  40. biotite/sequence/codec.c +1159 -841
  41. biotite/sequence/codec.cpython-311-darwin.so +0 -0
  42. biotite/sequence/graphics/alignment.py +212 -2
  43. biotite/sequence/io/genbank/annotation.py +11 -11
  44. biotite/sequence/phylo/nj.c +684 -636
  45. biotite/sequence/phylo/nj.cpython-311-darwin.so +0 -0
  46. biotite/sequence/phylo/tree.c +970 -673
  47. biotite/sequence/phylo/tree.cpython-311-darwin.so +0 -0
  48. biotite/sequence/phylo/upgma.c +672 -626
  49. biotite/sequence/phylo/upgma.cpython-311-darwin.so +0 -0
  50. biotite/structure/__init__.py +1 -1
  51. biotite/structure/atoms.py +1 -1
  52. biotite/structure/basepairs.py +7 -12
  53. biotite/structure/bonds.c +3861 -3749
  54. biotite/structure/bonds.cpython-311-darwin.so +0 -0
  55. biotite/structure/celllist.c +727 -707
  56. biotite/structure/celllist.cpython-311-darwin.so +0 -0
  57. biotite/structure/charges.c +1561 -1560
  58. biotite/structure/charges.cpython-311-darwin.so +0 -0
  59. biotite/structure/filter.py +30 -37
  60. biotite/structure/info/__init__.py +5 -8
  61. biotite/structure/info/atoms.py +25 -67
  62. biotite/structure/info/bonds.py +46 -100
  63. biotite/structure/info/ccd/README.rst +8 -0
  64. biotite/structure/info/ccd/amino_acids.txt +1646 -0
  65. biotite/structure/info/ccd/carbohydrates.txt +1133 -0
  66. biotite/structure/info/ccd/components.bcif +0 -0
  67. biotite/structure/info/ccd/nucleotides.txt +797 -0
  68. biotite/structure/info/ccd.py +95 -0
  69. biotite/structure/info/groups.py +90 -0
  70. biotite/structure/info/masses.py +21 -20
  71. biotite/structure/info/misc.py +11 -22
  72. biotite/structure/info/standardize.py +17 -12
  73. biotite/structure/io/__init__.py +2 -4
  74. biotite/structure/io/ctab.py +1 -1
  75. biotite/structure/io/general.py +37 -43
  76. biotite/structure/io/mmtf/__init__.py +3 -0
  77. biotite/structure/io/mmtf/convertarray.c +528 -365
  78. biotite/structure/io/mmtf/convertarray.cpython-311-darwin.so +0 -0
  79. biotite/structure/io/mmtf/convertfile.c +725 -676
  80. biotite/structure/io/mmtf/convertfile.cpython-311-darwin.so +0 -0
  81. biotite/structure/io/mmtf/decode.c +1070 -754
  82. biotite/structure/io/mmtf/decode.cpython-311-darwin.so +0 -0
  83. biotite/structure/io/mmtf/encode.c +727 -677
  84. biotite/structure/io/mmtf/encode.cpython-311-darwin.so +0 -0
  85. biotite/structure/io/mmtf/file.py +34 -26
  86. biotite/structure/io/npz/__init__.py +3 -0
  87. biotite/structure/io/npz/file.py +21 -18
  88. biotite/structure/io/pdb/__init__.py +3 -3
  89. biotite/structure/io/pdb/file.py +72 -70
  90. biotite/structure/io/pdb/hybrid36.c +540 -478
  91. biotite/structure/io/pdb/hybrid36.cpython-311-darwin.so +0 -0
  92. biotite/structure/io/pdbqt/file.py +82 -68
  93. biotite/structure/io/pdbx/__init__.py +13 -6
  94. biotite/structure/io/pdbx/bcif.py +649 -0
  95. biotite/structure/io/pdbx/cif.py +1028 -0
  96. biotite/structure/io/pdbx/component.py +243 -0
  97. biotite/structure/io/pdbx/convert.py +707 -359
  98. biotite/structure/io/pdbx/encoding.c +112813 -0
  99. biotite/structure/io/pdbx/encoding.cpython-311-darwin.so +0 -0
  100. biotite/structure/io/pdbx/error.py +14 -0
  101. biotite/structure/io/pdbx/legacy.py +267 -0
  102. biotite/structure/molecules.py +151 -151
  103. biotite/structure/residues.py +40 -40
  104. biotite/structure/sasa.c +713 -644
  105. biotite/structure/sasa.cpython-311-darwin.so +0 -0
  106. biotite/structure/superimpose.py +158 -115
  107. biotite/visualize.py +9 -11
  108. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/METADATA +2 -2
  109. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/RECORD +112 -102
  110. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/WHEEL +1 -1
  111. biotite/structure/info/amino_acids.json +0 -1556
  112. biotite/structure/info/amino_acids.py +0 -42
  113. biotite/structure/info/carbohydrates.json +0 -1122
  114. biotite/structure/info/carbohydrates.py +0 -39
  115. biotite/structure/info/intra_bonds.msgpack +0 -0
  116. biotite/structure/info/link_types.msgpack +0 -1
  117. biotite/structure/info/nucleotides.json +0 -772
  118. biotite/structure/info/nucleotides.py +0 -39
  119. biotite/structure/info/residue_masses.msgpack +0 -0
  120. biotite/structure/info/residue_names.msgpack +0 -3
  121. biotite/structure/info/residues.msgpack +0 -0
  122. biotite/structure/io/pdbx/file.py +0 -652
  123. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/LICENSE.rst +0 -0
  124. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/top_level.txt +0 -0