biotite 1.4.0__cp312-cp312-macosx_11_0_arm64.whl → 1.5.0__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.
Files changed (46) hide show
  1. biotite/application/dssp/app.py +63 -6
  2. biotite/database/afdb/download.py +12 -6
  3. biotite/database/rcsb/download.py +1 -0
  4. biotite/database/rcsb/query.py +2 -2
  5. biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  7. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  8. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  9. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  10. biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
  11. biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
  12. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  13. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  14. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  15. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  16. biotite/sequence/codec.cpython-312-darwin.so +0 -0
  17. biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
  18. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  19. biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
  20. biotite/structure/atoms.py +1 -1
  21. biotite/structure/bonds.cpython-312-darwin.so +0 -0
  22. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  23. biotite/structure/chains.py +34 -0
  24. biotite/structure/charges.cpython-312-darwin.so +0 -0
  25. biotite/structure/filter.py +2 -1
  26. biotite/structure/geometry.py +164 -2
  27. biotite/structure/info/atoms.py +8 -0
  28. biotite/structure/info/components.bcif +0 -0
  29. biotite/structure/io/pdb/convert.py +1 -0
  30. biotite/structure/io/pdb/file.py +16 -2
  31. biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so +0 -0
  32. biotite/structure/io/pdbx/bcif.py +1 -1
  33. biotite/structure/io/pdbx/cif.py +1 -1
  34. biotite/structure/io/pdbx/compress.py +13 -9
  35. biotite/structure/io/pdbx/convert.py +17 -6
  36. biotite/structure/io/pdbx/encoding.cpython-312-darwin.so +0 -0
  37. biotite/structure/io/pdbx/encoding.pyx +39 -8
  38. biotite/structure/residues.py +173 -1
  39. biotite/structure/sasa.cpython-312-darwin.so +0 -0
  40. biotite/structure/segments.py +39 -3
  41. biotite/structure/util.py +14 -22
  42. biotite/version.py +16 -3
  43. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/METADATA +1 -1
  44. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/RECORD +46 -46
  45. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/WHEEL +0 -0
  46. {biotite-1.4.0.dist-info → biotite-1.5.0.dist-info}/licenses/LICENSE.rst +0 -0
@@ -1,8 +1,8 @@
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- biotite-1.4.0.dist-info/RECORD,,
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- biotite-1.4.0.dist-info/WHEEL,sha256=RemoLmiEETQWaDnkABcjmbI83SdF_gEdwFAlYn6e9o8,133
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- biotite-1.4.0.dist-info/METADATA,sha256=NZDvKedU4WJkuZIOpWAI3GXJIdbfP5jDh_CbaLSLfgU,5525
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- biotite-1.4.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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- biotite/version.py,sha256=rcWNYDlh913lujUvTfOu9iOIPdrTXg64R9wl7ENLjFU,511
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+ biotite-1.5.0.dist-info/RECORD,,
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+ biotite-1.5.0.dist-info/WHEEL,sha256=RemoLmiEETQWaDnkABcjmbI83SdF_gEdwFAlYn6e9o8,133
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+ biotite-1.5.0.dist-info/METADATA,sha256=UUKw6ATrAZtUc-I5_CvIIate_rM_OP8QyhHmLKF2tjY,5525
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+ biotite-1.5.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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+ biotite/version.py,sha256=sfeo6QRBwy3wEFaKhAEbFPpF98FLjoe4Car1c6NnghQ,704
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  biotite/copyable.py,sha256=C7ycTQxqanxT0SmXhzy5OLp7NpZdNWHyokozdoVDGNA,1897
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  biotite/__init__.py,sha256=rL8ZyaCUjOrECEvRxyHj8MOMp4FHMJ8n6KKgrYf5OAQ,545
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  biotite/visualize.py,sha256=GSxIL8PLXMDlaULG-ckSghRifQnBnkseZ-OWsnuno4M,13955
@@ -25,10 +25,10 @@ biotite/database/pubchem/query.py,sha256=Z_DVRY62HhelCtMr3xwUOZBBUpNCwTKVC8ey9dG
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  biotite/database/pubchem/download.py,sha256=p1UtPJ1YuccDWLsXE4Zd410RwqgbwCHj5ZDcISQ6-5U,9870
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  biotite/database/pubchem/__init__.py,sha256=xjwfutIL4-JeTs7v4wCkRyy5q4KE7fGWDvo46ubkXt4,669
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  biotite/database/pubchem/throttle.py,sha256=HXf2l7EW5RLdW0bg72uSdXCDZXFXOE49akhfgKhEdc8,3286
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- biotite/database/rcsb/query.py,sha256=Ar2uZRuOCMm0RQeMATHfAeTeW5G8eNfg2Iy5qMMZ8JU,32895
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- biotite/database/rcsb/download.py,sha256=AtRljEV60NReeuWno-YFNrzrpFY_hetghO31-8VojtE,5676
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+ biotite/database/rcsb/query.py,sha256=svweSjUNDOuZRLDfYTN17goFPOeHKhHs_qPvi9VkKs8,32897
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+ biotite/database/rcsb/download.py,sha256=a2Epoari3qItLTbBpjKWgBL-H4tbOAP9UQlUnhkXSS4,5757
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  biotite/database/rcsb/__init__.py,sha256=sTJnL4vYwhO7gSszMuT_Lr91uwX0wM1h-fZWiZkITYA,332
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- biotite/database/afdb/download.py,sha256=sIaGz0hTj1MBA_XIw9HCP6NGnPfNAyPgryOhLuRa9i8,6367
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+ biotite/database/afdb/download.py,sha256=cSi6x4KXSDHBm4qv7-dK4Q4k09uefNSoVGZjHWHfjQs,6679
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  biotite/database/afdb/__init__.py,sha256=VqRn4WE6wJWS4Sd916xchmMz7tyPpEflnwOVnInhEOs,333
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  biotite/interface/version.py,sha256=1duxoIDwBB6onugS5QqrM1iyM_O644Dw0FGai0V9ssc,2952
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  biotite/interface/__init__.py,sha256=CEbr_8h6pt3za2ybSeePcNKMsA2vkNUbzYhzP62g2Lg,717
@@ -52,7 +52,7 @@ biotite/application/__init__.py,sha256=gOy5iGp5uuKTd0qpR9LgsmanB3ZfdQaTnZcKMRDwS
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  biotite/application/application.py,sha256=MLMft5z1ocBMsTOXkUg-ZeZj0jC8l6WHrYSjgkE7iW8,8096
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  biotite/application/msaapp.py,sha256=6e88Q7vgGSK_5uKdOVPcZF6wMKDRGYEKrvc9tb0yjbs,11974
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  biotite/application/dssp/__init__.py,sha256=lUf-A2rJzPLJYZQZGpZUt7HtA0M59KaX6zQSCrkhfF4,323
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- biotite/application/dssp/app.py,sha256=tHoG8uFmX8WaBHm0Fhjc7D0NXEaMa-zkLvwFzyP4FQk,5323
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+ biotite/application/dssp/app.py,sha256=Xs0A764NKchkGFVEfB4bqBinFC5r2wNyAmKEk4G06dQ,7612
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  biotite/application/viennarna/rnaalifold.py,sha256=QawXG9hYKQzdRt8-J_WiXUcoJx7Whps-iSCzq7DFJEA,10683
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  biotite/application/viennarna/util.py,sha256=racSlWGMtRRNtc_wh-ggIJWPDNoxIqwejc_Ztgusk8Q,2635
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  biotite/application/viennarna/__init__.py,sha256=m2obwXBnkDzRDzjrffsGdnp7YxAFz6CctsSmmg03xVI,473
@@ -83,7 +83,7 @@ biotite/sequence/__init__.py,sha256=fSWhobaPGRMJI6-8UYFpjguxVtP4O4cAHmiRxNAGzYI,
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  biotite/sequence/seqtypes.py,sha256=I5OaC9IOJoA9G610Tod67cgCWDQqTAgYpK1FHF8Ofok,23246
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  biotite/sequence/codon.py,sha256=Scua9XHD-TnWfCaKHRegKQGSP3XK3wW3zLgxen45ux0,16346
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  biotite/sequence/search.py,sha256=G__T-GHMJODWmgh87z5wxs_g9-t1DtvEOd-USp-Qizg,3088
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- biotite/sequence/codec.cpython-312-darwin.so,sha256=O7FGM9Oic43byqnxAvO7mlMdrfU5RScwtXeoe-VejU4,286600
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+ biotite/sequence/codec.cpython-312-darwin.so,sha256=A4ifsFqHEKHdkVi7PzXM-anjBhUumzr_rQKCgYCGWyE,332120
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  biotite/sequence/alphabet.py,sha256=3iTSuuAsaPtTyqyTjeU0OF5y_17wuhC3lMVbcJGwqe8,17227
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  biotite/sequence/io/__init__.py,sha256=4K13uxFWe8IpNC8yuVxjDiI7-8lmXu7qT6iMmVSqPs4,314
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  biotite/sequence/io/general.py,sha256=sD03pLnkxsT6vFh8806ZhErC8GEG3LF_70NMcVJyGe0,6694
@@ -104,33 +104,33 @@ biotite/sequence/io/fastq/file.py,sha256=Q5jrBN21Fi0hp6rU5cc68kQPYc1jWdZfMwhx0Ze
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  biotite/sequence/align/matrix.py,sha256=A1PUA43ltUnvYqB_RO6WPbvAtCzZI3zSfeKHP3aVSNQ,22360
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  biotite/sequence/align/permutation.pyx,sha256=xbbw5DJ7c5SXnuSUl2hJUMxzvinKP1Khc7CSdH5cEE0,10028
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  biotite/sequence/align/selector.pyx,sha256=BstkOkz-nB2dPtkZIZbU5QlCT-h3QHxdsGg1pGUh-Qo,33471
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- biotite/sequence/align/pairwise.cpython-312-darwin.so,sha256=PaNJInnCvVClZC_ZejiQ08VQLRpkaPKkozH7Q5WeahI,553232
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+ biotite/sequence/align/pairwise.cpython-312-darwin.so,sha256=7rc5RwDbibEeuyjgXEMCALZhQ3JsoTqb1GWKiXrOpC0,679744
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  biotite/sequence/align/primes.txt,sha256=7pKfLGN1vjYl_KJ3y5uuo8np_5DDUH52UAkhb3fJfWE,10140
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- biotite/sequence/align/localgapped.cpython-312-darwin.so,sha256=hYVBCGWVDlAYCseSDeKsTaqCTvzUxyI_2oyJWlku8j0,1016368
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- biotite/sequence/align/banded.cpython-312-darwin.so,sha256=W98ybWXiwZ39NFzBRLgNpJE9N8wbK6EkpocCyhsID34,514912
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+ biotite/sequence/align/localgapped.cpython-312-darwin.so,sha256=KUtOf9Lvy_0stKdL9dmmu7DQfHMAbNY7RNIHqm19Fuw,1184816
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+ biotite/sequence/align/banded.cpython-312-darwin.so,sha256=_ZQ1zDqmI5TkilS9ejvQcUDNm47XyOzLfVnRTPj7Uh4,620064
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  biotite/sequence/align/kmeralphabet.pyx,sha256=t4MKs3uIXGn_2AB8NRKQxY73RoBLDa-IlKVnSdANkCU,18636
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- biotite/sequence/align/localungapped.cpython-312-darwin.so,sha256=_sU15Qez5wCr4Wr6aqP2z9B6OhnYYk2VD-uMBqcarn4,305712
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+ biotite/sequence/align/localungapped.cpython-312-darwin.so,sha256=EyMb4gOPhmULxlyiFaI-AtFc_cn7TYFPJBrcyRwJ320,354416
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- biotite/sequence/align/permutation.cpython-312-darwin.so,sha256=ImB7h3udWe-BThqS3PQ_o8IQ3R0ecS5lL1D9guJIPEU,232384
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- biotite/sequence/align/multiple.cpython-312-darwin.so,sha256=2Rqb_f1Dpshw0yzP5pyE73bnBAOmInBUyjFKiZbmJCw,463488
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+ biotite/sequence/align/permutation.cpython-312-darwin.so,sha256=Rar8-PXrd4CpA168Q2pFgAGDE4q1gETnNCYKmpldOtg,257088
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+ biotite/sequence/align/multiple.cpython-312-darwin.so,sha256=cy1mBkrzY6C35SbB_JbmEfx8eex7XhCYKeGXza-LXAs,548304
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- biotite/sequence/align/kmersimilarity.cpython-312-darwin.so,sha256=QFfDES-KIsAc6iCtYTr34HjZqVnvzghprxoJSKoxfTM,213848
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+ biotite/sequence/align/kmersimilarity.cpython-312-darwin.so,sha256=eZsCq6NeS3csjubcCtEdjYhGvmxBx-3DaDpzb3HMvdo,255400
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- biotite/sequence/align/tracetable.cpython-312-darwin.so,sha256=-XmsPBOGaLDK4tWihbZTEF5nM93D8r8xZcbnKap25Lk,186544
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+ biotite/sequence/align/tracetable.cpython-312-darwin.so,sha256=ST1De-jShEKUnB66PXmaqfX3m0XDdlx7uprv37C3jtg,224176
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- biotite/sequence/align/selector.cpython-312-darwin.so,sha256=hW3GAT0Zx1148izLN0pycozouD1vsWzL6e0bfDyL5dE,308256
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+ biotite/sequence/align/selector.cpython-312-darwin.so,sha256=w52GLC2XIJoGiRETfgW9FLicZOINt_n3ibk_ywOCphA,360320
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- biotite/sequence/align/kmeralphabet.cpython-312-darwin.so,sha256=MMihAmc42n0d8ZZqPy-XQUS4QJ4bjp5Qj-viTTvZqTQ,388400
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+ biotite/sequence/align/kmeralphabet.cpython-312-darwin.so,sha256=Wb1UBkqJGwwyFT_HB7OS7oVeh39KFec4xpxMziuPn2g,458016
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- biotite/sequence/align/kmertable.cpython-312-darwin.so,sha256=UVG4V3xyN9nbWH1xnL_C85FNZFN3OoDhMDZvfnT5abM,672032
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+ biotite/sequence/align/kmertable.cpython-312-darwin.so,sha256=Nd60gxzhzS9ZvF2V5N22_KG6FF-0Q8hbY5pg0tUXFWw,756224
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@@ -250,25 +250,25 @@ biotite/sequence/graphics/color_schemes/autumn.json,sha256=usp-Y70tk39LCJV64vi7t
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- biotite/sequence/phylo/upgma.cpython-312-darwin.so,sha256=997TfGbmQ20RufCo_MnPGRlMxYuAzSOeI2AcughlgTs,210904
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+ biotite/sequence/phylo/tree.cpython-312-darwin.so,sha256=jEScQRR075MkHb1zbwBMGd7yxoFYamepbqBmgN-OA-U,313752
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+ biotite/sequence/phylo/upgma.cpython-312-darwin.so,sha256=PAVZv737sLIaE2yITzMBybpJgkeq0Iyzi1I4aWpEaVc,233032
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+ biotite/sequence/phylo/nj.cpython-312-darwin.so,sha256=JdqxIk7qD6xEFQZVSS7zvU4FHjnKOXXsp_vZkNAu0As,233912
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- biotite/structure/chains.py,sha256=_E4oEhXRg2AxsyZVy623fRkylzAFonDTDSLGSbh3-M8,8324
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+ biotite/structure/charges.cpython-312-darwin.so,sha256=kHct2RVnNHxyf-yHr4lDyvIp3OFvCm3WnEx22uy5x-M,296784
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- biotite/structure/segments.py,sha256=1Z094xZWFsLTx_d5w67I-oHlEPCj2sbtLvZWaZfbgF4,9741
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+ biotite/structure/util.py,sha256=naGADXePMb635MdtYKxO_5BFPEMz-YYF2Q2cH7ImAjA,4398
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+ biotite/structure/segments.py,sha256=7ORMe1q_2LFSP9efwAvIM3UhL0KhRlURXMnUGPfoJaw,10785
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- biotite/structure/bonds.cpython-312-darwin.so,sha256=X5koFxYXLe8hNNLqlTYvbVpR2Yw6SNarerd0u0gSww0,549336
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+ biotite/structure/bonds.cpython-312-darwin.so,sha256=sBReKANRGk4EmxQu9UXjDD7nBsx38loABZiz52VoVr4,631944
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@@ -276,22 +276,22 @@ biotite/structure/sse.py,sha256=OHXohnYi4ipBcSas9XTi9Pm8oNasM49Oxr7DBvYbe1U,1140
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+ biotite/structure/celllist.cpython-312-darwin.so,sha256=t5uk1nsBCvx_j5f8_0W_Q9_MeVfv76XTrahXx3TNLas,338624
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- biotite/structure/geometry.py,sha256=7FtPNJtTUn691xw6kbVk90s8a9rAd98zC-rKD23ikdU,23676
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+ biotite/structure/geometry.py,sha256=LojdE15YFkFAUhVH65GQS-UJDMTG8yurrB7H5pfalTA,29281
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+ biotite/structure/atoms.py,sha256=7-QBLs4E04PwHBV7DSB9gDpSqyfGruiIONUmKMeGSa4,50837
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+ biotite/structure/sasa.cpython-312-darwin.so,sha256=rmORwvEWh6eiThVMTrYE5Ky5euvFUbtTw-8GcL1KF3w,273336
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+ biotite/structure/residues.py,sha256=DsI_ia4B2ZbWeBpxOvKxAJ3dlu7iYyiqgXIP8AkKjOs,28403
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@@ -302,13 +302,13 @@ biotite/structure/io/dcd/__init__.py,sha256=tYiiTSmqDrsSgg_sZaoQgx2D8N9OeqlooxH4
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- biotite/structure/io/pdbx/bcif.py,sha256=y5ueesX3G-5JSVj0chX6LiJ71IYdjgaF5x0nR6stiD0,21247
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- biotite/structure/io/pdbx/convert.py,sha256=hEBw0QeRNGRX70z3W0i7cDjVgIOD7RFrOnZGrUMa_gM,79916
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+ biotite/structure/io/pdbx/encoding.cpython-312-darwin.so,sha256=q1wt-YL60L7fh6vZX-uDCH5bUKwyCX_dLpLgZRZGFa0,1332320
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+ biotite/structure/io/pdbx/bcif.py,sha256=8dQyPCtQho4tV2dRK52hOsifOOGnXPMLI7SDJt_UgaU,21248
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+ biotite/structure/io/pdbx/convert.py,sha256=gNdslGuHHQwixoacevhxLgUpCtY3AZEvSNUYvP0W3UQ,80733
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+ biotite/structure/io/pdbx/encoding.pyx,sha256=gqTnq2qONPRdv5lz2JkJIhjK4k3J9k-Fp8YOVbeE9N0,33609
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- biotite/structure/io/pdbx/cif.py,sha256=1gyMDANR51yNXsV0aFIAK4VSUYl32nBIC94RwQf57PE,34978
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+ biotite/structure/io/pdbx/compress.py,sha256=YAUaMsaXwmxpFOnbYgkrTl4k-k3PiBXyC6tKWAajxfI,13407
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+ biotite/structure/io/pdbx/cif.py,sha256=1hY4-brq_kX_Hg5-OJm600zcdXV6KDidZhTdHKQunYY,34979
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@@ -325,10 +325,10 @@ biotite/structure/io/mol/__init__.py,sha256=WvcNPDdf9W1zPyJ0tjTvGNxA83ht18uRQA8B
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- biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so,sha256=DT_ZAr9LDjaCNCCJ_fY53tkj74Qa7FfiMgZ8PbN-2IY,210672
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- biotite/structure/io/pdb/convert.py,sha256=ECG8KFmduPN2xd7HWqJweYabn-IFdnhxVNtO3AkzLaQ,13800
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+ biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so,sha256=zz87-sPRME-1j83Iz9rC8vv-b0FqXNYS001pHYcUYyk,236272
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+ biotite/structure/io/pdb/convert.py,sha256=nnRZl5cG5N6UQURG_oSfLZ1z32uXeiF9pOMcpOTFNcI,13826
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- biotite/structure/io/pdb/file.py,sha256=Ppb0bFqmp8xi-L-_dA3JzEuMBjLdUUJKZEDB4DUeblw,54085
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+ biotite/structure/io/pdb/file.py,sha256=GCS8qD-efyXswe5acr2Erz3qurGfY52J60n06BqA7jc,54557
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@@ -338,7 +338,7 @@ biotite/structure/alphabet/encoder.py,sha256=2BWLMdGBr2bHw09vMhbzPztMKSnVt8UhUf8
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- biotite/structure/info/components.bcif,sha256=y9ysqudHo8BQmtqI5JEMnEFXQtG1yt1X9WBtyw8yD2Y,60736935
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+ biotite/structure/info/components.bcif,sha256=mQrO6PEOkPNw2i1DHp5qugNyDx0g-2d_uV-T4KD1bwI,62070945
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@@ -347,7 +347,7 @@ biotite/structure/info/radii.py,sha256=PGpl5WoaFBzAktxNodzb_mCz8jp0AwW3GNXk9jKN3
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+ biotite/structure/info/atoms.py,sha256=8GoHM5owz0-Tnx9OzV8Q41sz-WU7TAJfy4sTgAW939Q,3271
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