biotite 1.0.0__cp311-cp311-macosx_11_0_arm64.whl → 1.1.0__cp311-cp311-macosx_11_0_arm64.whl

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Files changed (92) hide show
  1. biotite/application/dssp/app.py +13 -3
  2. biotite/application/localapp.py +34 -0
  3. biotite/application/muscle/app3.py +2 -15
  4. biotite/application/muscle/app5.py +2 -2
  5. biotite/application/util.py +1 -1
  6. biotite/application/viennarna/rnaplot.py +6 -2
  7. biotite/database/rcsb/query.py +6 -6
  8. biotite/database/uniprot/check.py +20 -15
  9. biotite/database/uniprot/download.py +1 -1
  10. biotite/database/uniprot/query.py +1 -1
  11. biotite/sequence/align/alignment.py +16 -3
  12. biotite/sequence/align/banded.cpython-311-darwin.so +0 -0
  13. biotite/sequence/align/banded.pyx +5 -5
  14. biotite/sequence/align/kmeralphabet.cpython-311-darwin.so +0 -0
  15. biotite/sequence/align/kmeralphabet.pyx +17 -0
  16. biotite/sequence/align/kmersimilarity.cpython-311-darwin.so +0 -0
  17. biotite/sequence/align/kmertable.cpython-311-darwin.so +0 -0
  18. biotite/sequence/align/kmertable.pyx +52 -42
  19. biotite/sequence/align/localgapped.cpython-311-darwin.so +0 -0
  20. biotite/sequence/align/localungapped.cpython-311-darwin.so +0 -0
  21. biotite/sequence/align/matrix.py +273 -55
  22. biotite/sequence/align/matrix_data/3Di.mat +24 -0
  23. biotite/sequence/align/matrix_data/PB.license +21 -0
  24. biotite/sequence/align/matrix_data/PB.mat +18 -0
  25. biotite/sequence/align/multiple.cpython-311-darwin.so +0 -0
  26. biotite/sequence/align/pairwise.cpython-311-darwin.so +0 -0
  27. biotite/sequence/align/permutation.cpython-311-darwin.so +0 -0
  28. biotite/sequence/align/selector.cpython-311-darwin.so +0 -0
  29. biotite/sequence/align/tracetable.cpython-311-darwin.so +0 -0
  30. biotite/sequence/alphabet.py +3 -0
  31. biotite/sequence/codec.cpython-311-darwin.so +0 -0
  32. biotite/sequence/graphics/color_schemes/3di_flower.json +48 -0
  33. biotite/sequence/graphics/color_schemes/pb_flower.json +2 -1
  34. biotite/sequence/graphics/colorschemes.py +44 -11
  35. biotite/sequence/phylo/nj.cpython-311-darwin.so +0 -0
  36. biotite/sequence/phylo/tree.cpython-311-darwin.so +0 -0
  37. biotite/sequence/phylo/upgma.cpython-311-darwin.so +0 -0
  38. biotite/sequence/profile.py +86 -4
  39. biotite/sequence/seqtypes.py +124 -3
  40. biotite/setup_ccd.py +197 -0
  41. biotite/structure/__init__.py +4 -3
  42. biotite/structure/alphabet/__init__.py +25 -0
  43. biotite/structure/alphabet/encoder.py +332 -0
  44. biotite/structure/alphabet/encoder_weights_3di.kerasify +0 -0
  45. biotite/structure/alphabet/i3d.py +110 -0
  46. biotite/structure/alphabet/layers.py +86 -0
  47. biotite/structure/alphabet/pb.license +21 -0
  48. biotite/structure/alphabet/pb.py +171 -0
  49. biotite/structure/alphabet/unkerasify.py +122 -0
  50. biotite/structure/atoms.py +156 -43
  51. biotite/structure/bonds.cpython-311-darwin.so +0 -0
  52. biotite/structure/bonds.pyx +72 -21
  53. biotite/structure/celllist.cpython-311-darwin.so +0 -0
  54. biotite/structure/charges.cpython-311-darwin.so +0 -0
  55. biotite/structure/filter.py +1 -1
  56. biotite/structure/geometry.py +60 -113
  57. biotite/structure/info/__init__.py +1 -0
  58. biotite/structure/info/atoms.py +13 -13
  59. biotite/structure/info/bonds.py +12 -6
  60. biotite/structure/info/ccd.py +125 -32
  61. biotite/structure/info/{ccd/components.bcif → components.bcif} +0 -0
  62. biotite/structure/info/groups.py +63 -17
  63. biotite/structure/info/masses.py +9 -6
  64. biotite/structure/info/misc.py +15 -21
  65. biotite/structure/info/standardize.py +3 -2
  66. biotite/structure/io/mol/sdf.py +41 -40
  67. biotite/structure/io/pdb/convert.py +2 -0
  68. biotite/structure/io/pdb/file.py +74 -3
  69. biotite/structure/io/pdb/hybrid36.cpython-311-darwin.so +0 -0
  70. biotite/structure/io/pdbqt/file.py +32 -32
  71. biotite/structure/io/pdbx/__init__.py +1 -0
  72. biotite/structure/io/pdbx/bcif.py +32 -8
  73. biotite/structure/io/pdbx/cif.py +148 -107
  74. biotite/structure/io/pdbx/component.py +9 -4
  75. biotite/structure/io/pdbx/compress.py +321 -0
  76. biotite/structure/io/pdbx/convert.py +227 -68
  77. biotite/structure/io/pdbx/encoding.cpython-311-darwin.so +0 -0
  78. biotite/structure/io/pdbx/encoding.pyx +98 -17
  79. biotite/structure/io/trajfile.py +16 -16
  80. biotite/structure/molecules.py +141 -141
  81. biotite/structure/sasa.cpython-311-darwin.so +0 -0
  82. biotite/structure/segments.py +1 -2
  83. biotite/structure/util.py +73 -1
  84. biotite/version.py +2 -2
  85. {biotite-1.0.0.dist-info → biotite-1.1.0.dist-info}/METADATA +4 -1
  86. {biotite-1.0.0.dist-info → biotite-1.1.0.dist-info}/RECORD +88 -78
  87. biotite/structure/info/ccd/README.rst +0 -8
  88. biotite/structure/info/ccd/amino_acids.txt +0 -1663
  89. biotite/structure/info/ccd/carbohydrates.txt +0 -1135
  90. biotite/structure/info/ccd/nucleotides.txt +0 -798
  91. {biotite-1.0.0.dist-info → biotite-1.1.0.dist-info}/WHEEL +0 -0
  92. {biotite-1.0.0.dist-info → biotite-1.1.0.dist-info}/licenses/LICENSE.rst +0 -0