biotite 1.4.0__cp311-cp311-macosx_11_0_arm64.whl → 1.5.0__cp311-cp311-macosx_11_0_arm64.whl

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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-311-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.cpython-311-darwin.so +0 -0
  7. biotite/sequence/align/kmersimilarity.cpython-311-darwin.so +0 -0
  8. biotite/sequence/align/kmertable.cpython-311-darwin.so +0 -0
  9. biotite/sequence/align/localgapped.cpython-311-darwin.so +0 -0
  10. biotite/sequence/align/localungapped.cpython-311-darwin.so +0 -0
  11. biotite/sequence/align/multiple.cpython-311-darwin.so +0 -0
  12. biotite/sequence/align/pairwise.cpython-311-darwin.so +0 -0
  13. biotite/sequence/align/permutation.cpython-311-darwin.so +0 -0
  14. biotite/sequence/align/selector.cpython-311-darwin.so +0 -0
  15. biotite/sequence/align/tracetable.cpython-311-darwin.so +0 -0
  16. biotite/sequence/codec.cpython-311-darwin.so +0 -0
  17. biotite/sequence/phylo/nj.cpython-311-darwin.so +0 -0
  18. biotite/sequence/phylo/tree.cpython-311-darwin.so +0 -0
  19. biotite/sequence/phylo/upgma.cpython-311-darwin.so +0 -0
  20. biotite/structure/atoms.py +1 -1
  21. biotite/structure/bonds.cpython-311-darwin.so +0 -0
  22. biotite/structure/celllist.cpython-311-darwin.so +0 -0
  23. biotite/structure/chains.py +34 -0
  24. biotite/structure/charges.cpython-311-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-311-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-311-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-311-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=fm1N917lvYihbGT4OyonPrhA6HCp511clhZcK6Fbvns,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=fm1N917lvYihbGT4OyonPrhA6HCp511clhZcK6Fbvns,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
@@ -74,7 +74,7 @@ biotite/application/clustalo/app.py,sha256=f5NEOkKCiTDlIVNJ1ozefzixwndVC4_vPQq8a
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  biotite/application/muscle/app3.py,sha256=Otgzi3VEYv0iQ_q5TesRJEfB6krbF7wXxfN87JzdKFg,7653
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  biotite/application/muscle/__init__.py,sha256=B1JrhQYjgwSKWxpcYgXS91f2GM5Tc1i9Ocs2wElslRs,338
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  biotite/application/muscle/app5.py,sha256=xYF-iLn-UVue-vu4yGJFaQVtnPi561rwoIVwVCIu_C8,4474
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- biotite/sequence/codec.cpython-311-darwin.so,sha256=P60kxyUVm_3HXONMv6wZpQZN3PODfhO9I7UP_7cVAw4,287736
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+ biotite/sequence/codec.cpython-311-darwin.so,sha256=SzVgeFWSkSowzyEk9eeT-0Iwxc3rxWPN4x_CS2Kx6c0,332504
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  biotite/sequence/annotation.py,sha256=L_TZL2Gmsuokbr6A6Y6gVa4hbEM3ox_NJ_P5PTsZ4V0,29705
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  biotite/sequence/codec.pyx,sha256=ed415FTMBJfiI9WbgKRFO3tF1f_SpRHxyEafLxW-g1k,4962
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  biotite/sequence/sequence.py,sha256=eIZ7Ugz9IwXlWXs_HC2NGyAtDDcP-Vf1z82jynT_PPE,11691
@@ -101,36 +101,36 @@ biotite/sequence/io/genbank/file.py,sha256=5XvuJCd_FuI2zh03_bLbLSAuORNw4tXr7p9sG
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  biotite/sequence/io/fastq/convert.py,sha256=x4rWn7WHdKxW1u7mwDgM8Z3qaML4lAO7r-JiMTQbvaI,3632
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  biotite/sequence/io/fastq/__init__.py,sha256=lhw9bxWS0eKPXzF1lg8fvrNmgAmJPLBzIB6jEP5GOVI,588
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  biotite/sequence/io/fastq/file.py,sha256=Q5jrBN21Fi0hp6rU5cc68kQPYc1jWdZfMwhx0Ze6oGw,17817
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- biotite/sequence/align/selector.cpython-311-darwin.so,sha256=V0hKUkFJ6Ia8XOjH8ycHK-UV6AMyJvK8VkP7KnFVj0I,316176
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+ biotite/sequence/align/selector.cpython-311-darwin.so,sha256=mUuOCVns1n9XgLh_QFvWJxBrFitPq-zVxUvhM1HWxPQ,351648
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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/kmeralphabet.cpython-311-darwin.so,sha256=bEeioCJN5P5IlicMFtOMOpTty9A-a3npGX4Kw5MhqXc,406384
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+ biotite/sequence/align/kmeralphabet.cpython-311-darwin.so,sha256=5R8VYBfSiAusBNCpEDMlL5BaPUTe_lVfaOwjZ2xkkOA,455408
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  biotite/sequence/align/primes.txt,sha256=7pKfLGN1vjYl_KJ3y5uuo8np_5DDUH52UAkhb3fJfWE,10140
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- biotite/sequence/align/kmertable.cpython-311-darwin.so,sha256=eV1PwoHqJkV-Ugc2k1vl_qOY4U6B73rkhWOANhnnk3g,715984
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+ biotite/sequence/align/kmertable.cpython-311-darwin.so,sha256=U-HjbXd1jULZITeJGXlzr-VHiUCEcxTBxWjMjYiKVI4,795424
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- biotite/sequence/align/kmersimilarity.cpython-311-darwin.so,sha256=0V7iJYYGGANBnAunndf2dxnBiDbhTv509kNkZNgpZ70,217704
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+ biotite/sequence/align/kmersimilarity.cpython-311-darwin.so,sha256=OjJO6pEaMdfsTW5Ci9IJJVx4ssaHzdLrKN8OhLrlCWM,243432
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- biotite/sequence/align/tracetable.cpython-311-darwin.so,sha256=1j5E9GU-d2BuEFBy2IiQzgZSXWkwy0RGoznlKXQvBbI,187520
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+ biotite/sequence/align/tracetable.cpython-311-darwin.so,sha256=kTbp5b378e5cdtFPcCS8aryuYw3_nLl0GyMX2ooamDU,208720
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- biotite/sequence/align/multiple.cpython-311-darwin.so,sha256=JOe_Qmag9X7RbuoNKhvliLwXaYQWIDChEmyk648Y9T0,488992
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+ biotite/sequence/align/multiple.cpython-311-darwin.so,sha256=Lfg1IkTI_x2jCb0xJ57LYjW4M3BE7TZ709253FMCQgE,557488
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- biotite/sequence/align/permutation.cpython-311-darwin.so,sha256=ZowW7kOiOTifDoBT6RIoAqM65ZBo3eNhfKMou1Mbtys,237552
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+ biotite/sequence/align/permutation.cpython-311-darwin.so,sha256=qktWIZTelPEtom4XNVDRozLV3MwYhUZyBa1LX3nTJR8,262672
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- biotite/sequence/align/pairwise.cpython-311-darwin.so,sha256=jlEfjohsRllSSPValVM5Od34deA7axJ6rOhWVvOZ16o,583120
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- biotite/sequence/align/banded.cpython-311-darwin.so,sha256=wBLBVsERjSc48ZEBykPpMlBQmQdeBbAjNnVQYJEMjSU,528336
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+ biotite/sequence/align/pairwise.cpython-311-darwin.so,sha256=i-C_POCjGtn0E4TSV5Cr47dqUSw474ikCPrvwSUY6wg,691648
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+ biotite/sequence/align/banded.cpython-311-darwin.so,sha256=jv5RDBBVIt3uw0SQuKgAteGddwrRyPdmNfjCOxMY5Z8,632000
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- biotite/sequence/align/localgapped.cpython-311-darwin.so,sha256=blwPwnXW5sDpMhGDrLjon2Rsac8YpzOqcfbcj_jRFew,1138800
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- biotite/sequence/align/localungapped.cpython-311-darwin.so,sha256=nHz9TnXR3qOZCRAY8SdP9On0vR7ESXL6mtJirnFRZFg,307968
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+ biotite/sequence/align/localgapped.cpython-311-darwin.so,sha256=5fZfj3LQK81eSn3FZKW5_u4v2Fh1Gyn6MxHPxjIBLkw,1304096
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+ biotite/sequence/align/localungapped.cpython-311-darwin.so,sha256=8Qgy5zsQA2gaMe9I64KYS9_V9Wo4vQT5ugxhaCLGO8k,354160
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+ biotite/sequence/phylo/nj.cpython-311-darwin.so,sha256=B8iNVD-MMuUMfGdAmSZJ40YeD-1IGkvj7-JSAYQ3uEQ,239928
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- biotite/sequence/phylo/upgma.cpython-311-darwin.so,sha256=45uyuOAs2_8FpBbih99gRMT3JFo4cpvmsTs_bVzkAb8,214120
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+ biotite/sequence/phylo/tree.cpython-311-darwin.so,sha256=bZUGS4e8FRh1mFG79o8p9dko8X5xBrShM6dxGd9Tg94,300808
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+ biotite/sequence/phylo/upgma.cpython-311-darwin.so,sha256=4uocVtmCMAGOf6jHbRjEXHjiSRnrf_Yt6Ycn4jy8rtU,237000
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- biotite/structure/sasa.cpython-311-darwin.so,sha256=UPBrc7XiVgvrHFK1KsztSVvYc1YEWSp_RKnr-gUjxQI,256840
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- biotite/structure/chains.py,sha256=_E4oEhXRg2AxsyZVy623fRkylzAFonDTDSLGSbh3-M8,8324
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+ biotite/structure/sasa.cpython-311-darwin.so,sha256=gXz-sSlRZ00yiXS9YM7jAo93P6MwwTIZ94qfGiqUQ14,282568
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+ biotite/structure/atoms.py,sha256=7-QBLs4E04PwHBV7DSB9gDpSqyfGruiIONUmKMeGSa4,50837
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+ biotite/structure/charges.cpython-311-darwin.so,sha256=dIg521TFu_sxpdpY9As0IL47bxWsYGNoisPyDz9drTA,309392
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+ biotite/structure/residues.py,sha256=DsI_ia4B2ZbWeBpxOvKxAJ3dlu7iYyiqgXIP8AkKjOs,28403
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@@ -302,14 +302,14 @@ biotite/structure/io/dcd/__init__.py,sha256=tYiiTSmqDrsSgg_sZaoQgx2D8N9OeqlooxH4
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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/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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- biotite/structure/io/pdbx/encoding.cpython-311-darwin.so,sha256=5MJ6s0-rjET9LtIIFo0Py2ucWP_h_FXb5LUuK-BJ7ak,1166320
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+ biotite/structure/io/pdbx/encoding.cpython-311-darwin.so,sha256=G4td_-Wqlc7GOTYEqoivDkm2kgUfDeWFKz9rhY8BUi0,1405712
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@@ -325,11 +325,11 @@ biotite/structure/io/mol/__init__.py,sha256=WvcNPDdf9W1zPyJ0tjTvGNxA83ht18uRQA8B
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- biotite/structure/io/pdb/convert.py,sha256=ECG8KFmduPN2xd7HWqJweYabn-IFdnhxVNtO3AkzLaQ,13800
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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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- biotite/structure/io/pdb/hybrid36.cpython-311-darwin.so,sha256=Js8Mig8a1Xad8ScUlbrqWthUd0eLgN_aQZRfWt5nMAE,194480
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+ biotite/structure/io/pdb/hybrid36.cpython-311-darwin.so,sha256=G7WKVXNaz52YCC8d9uegLipE8TYhdm_5cOaDWzSoPBw,236080
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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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