biotite 0.39.0__cp312-cp312-macosx_11_0_arm64.whl → 0.40.0__cp312-cp312-macosx_11_0_arm64.whl

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Files changed (104) hide show
  1. biotite/__init__.py +3 -3
  2. biotite/application/dssp/app.py +18 -18
  3. biotite/database/rcsb/download.py +19 -14
  4. biotite/sequence/align/banded.c +256 -235
  5. biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.c +241 -220
  7. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  8. biotite/sequence/align/kmersimilarity.c +213 -194
  9. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  10. biotite/sequence/align/kmertable.cpp +231 -203
  11. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  12. biotite/sequence/align/localgapped.c +256 -235
  13. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  14. biotite/sequence/align/localungapped.c +233 -212
  15. biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
  16. biotite/sequence/align/multiple.c +253 -232
  17. biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
  18. biotite/sequence/align/pairwise.c +272 -251
  19. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  20. biotite/sequence/align/permutation.c +213 -194
  21. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  22. biotite/sequence/align/selector.c +215 -195
  23. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  24. biotite/sequence/align/tracetable.c +213 -193
  25. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  26. biotite/sequence/codec.c +233 -212
  27. biotite/sequence/codec.cpython-312-darwin.so +0 -0
  28. biotite/sequence/phylo/nj.c +213 -194
  29. biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
  30. biotite/sequence/phylo/tree.c +225 -200
  31. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  32. biotite/sequence/phylo/upgma.c +213 -194
  33. biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
  34. biotite/structure/basepairs.py +7 -12
  35. biotite/structure/bonds.c +1173 -1224
  36. biotite/structure/bonds.cpython-312-darwin.so +0 -0
  37. biotite/structure/celllist.c +215 -195
  38. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  39. biotite/structure/charges.c +1050 -1099
  40. biotite/structure/charges.cpython-312-darwin.so +0 -0
  41. biotite/structure/filter.py +30 -37
  42. biotite/structure/info/__init__.py +5 -8
  43. biotite/structure/info/atoms.py +25 -67
  44. biotite/structure/info/bonds.py +46 -100
  45. biotite/structure/info/ccd/README.rst +8 -0
  46. biotite/structure/info/ccd/amino_acids.txt +1646 -0
  47. biotite/structure/info/ccd/carbohydrates.txt +1133 -0
  48. biotite/structure/info/ccd/components.bcif +0 -0
  49. biotite/structure/info/ccd/nucleotides.txt +797 -0
  50. biotite/structure/info/ccd.py +95 -0
  51. biotite/structure/info/groups.py +90 -0
  52. biotite/structure/info/masses.py +21 -20
  53. biotite/structure/info/misc.py +11 -22
  54. biotite/structure/info/standardize.py +17 -12
  55. biotite/structure/io/__init__.py +2 -4
  56. biotite/structure/io/ctab.py +1 -1
  57. biotite/structure/io/general.py +37 -43
  58. biotite/structure/io/mmtf/__init__.py +3 -0
  59. biotite/structure/io/mmtf/convertarray.c +217 -196
  60. biotite/structure/io/mmtf/convertarray.cpython-312-darwin.so +0 -0
  61. biotite/structure/io/mmtf/convertfile.c +215 -195
  62. biotite/structure/io/mmtf/convertfile.cpython-312-darwin.so +0 -0
  63. biotite/structure/io/mmtf/decode.c +223 -202
  64. biotite/structure/io/mmtf/decode.cpython-312-darwin.so +0 -0
  65. biotite/structure/io/mmtf/encode.c +213 -194
  66. biotite/structure/io/mmtf/encode.cpython-312-darwin.so +0 -0
  67. biotite/structure/io/mmtf/file.py +34 -26
  68. biotite/structure/io/npz/__init__.py +3 -0
  69. biotite/structure/io/npz/file.py +21 -18
  70. biotite/structure/io/pdb/__init__.py +3 -3
  71. biotite/structure/io/pdb/file.py +5 -3
  72. biotite/structure/io/pdb/hybrid36.c +63 -43
  73. biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so +0 -0
  74. biotite/structure/io/pdbqt/file.py +32 -32
  75. biotite/structure/io/pdbx/__init__.py +13 -6
  76. biotite/structure/io/pdbx/bcif.py +649 -0
  77. biotite/structure/io/pdbx/cif.py +1028 -0
  78. biotite/structure/io/pdbx/component.py +243 -0
  79. biotite/structure/io/pdbx/convert.py +707 -359
  80. biotite/structure/io/pdbx/encoding.c +112803 -0
  81. biotite/structure/io/pdbx/encoding.cpython-312-darwin.so +0 -0
  82. biotite/structure/io/pdbx/error.py +14 -0
  83. biotite/structure/io/pdbx/legacy.py +267 -0
  84. biotite/structure/molecules.py +151 -151
  85. biotite/structure/sasa.c +213 -194
  86. biotite/structure/sasa.cpython-312-darwin.so +0 -0
  87. biotite/structure/superimpose.py +158 -115
  88. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/METADATA +2 -2
  89. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/RECORD +92 -90
  90. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/WHEEL +1 -1
  91. biotite/structure/info/amino_acids.json +0 -1556
  92. biotite/structure/info/amino_acids.py +0 -42
  93. biotite/structure/info/carbohydrates.json +0 -1122
  94. biotite/structure/info/carbohydrates.py +0 -39
  95. biotite/structure/info/intra_bonds.msgpack +0 -0
  96. biotite/structure/info/link_types.msgpack +0 -1
  97. biotite/structure/info/nucleotides.json +0 -772
  98. biotite/structure/info/nucleotides.py +0 -39
  99. biotite/structure/info/residue_masses.msgpack +0 -0
  100. biotite/structure/info/residue_names.msgpack +0 -3
  101. biotite/structure/info/residues.msgpack +0 -0
  102. biotite/structure/io/pdbx/file.py +0 -652
  103. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/LICENSE.rst +0 -0
  104. {biotite-0.39.0.dist-info → biotite-0.40.0.dist-info}/top_level.txt +0 -0
@@ -1,10 +1,10 @@
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- biotite-0.39.0.dist-info/RECORD,,
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- biotite-0.39.0.dist-info/WHEEL,sha256=VdDmD53Z5Im3s3DzMnDRXVcjZVnzMxiqEPFSmUQBX3s,110
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- biotite-0.39.0.dist-info/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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- biotite-0.39.0.dist-info/top_level.txt,sha256=Tvj5T6Zfz3AhevTRlDRVhNC1WgPlFk-wDtSkzTgFM8w,8
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- biotite-0.39.0.dist-info/METADATA,sha256=-UBZ0t86SDwoIaX7_yt2-k1inbPtiKoesN0gFDVLfUg,7145
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+ biotite-0.40.0.dist-info/RECORD,,
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+ biotite-0.40.0.dist-info/WHEEL,sha256=Vo9YTsjXxZ5SWdH4n69oS5jU3YTIi3eHk0n-aUcTtlw,110
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+ biotite-0.40.0.dist-info/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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+ biotite-0.40.0.dist-info/top_level.txt,sha256=Tvj5T6Zfz3AhevTRlDRVhNC1WgPlFk-wDtSkzTgFM8w,8
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+ biotite-0.40.0.dist-info/METADATA,sha256=F_Wg3VF0txg1mUbDMmCGUR4_Omt6fNY_xpNmUqEeMoQ,7151
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  biotite/copyable.py,sha256=Rmsso_e9quxWc23SBQh2M45jTT36SerwSmt3ONng04M,1972
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- biotite/__init__.py,sha256=klQIUDyC3zcaYzVSTUd5vQaB-eMx5WDCoEu4fdrvLzg,524
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+ biotite/__init__.py,sha256=xHwZNZlRcAlkSZFw6EMrVf5GqBoft7VfnmLDkqxF2Fo,522
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  biotite/visualize.py,sha256=mLME6fOGwdcUZLUzDTbwUpZokC4D1cVE6ICdtJDc0yw,9842
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  biotite/file.py,sha256=flQknYLaLSlbX38D8_I3fG9DAo4D3ExeoRzweMoZMno,7335
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  biotite/temp.py,sha256=AenIC7m3rrezikJDKgTEnLZigACubfsw_UcmYMGyGa8,2045
@@ -26,7 +26,7 @@ biotite/database/pubchem/download.py,sha256=rio_-ykW1xAZhhWcd-U88NYrwcI1lsJNrG75
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  biotite/database/pubchem/__init__.py,sha256=Lnk0h85FzSFBu6KAG3P5ssbGfXE2lX-EMYXWCafPF0o,668
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  biotite/database/pubchem/throttle.py,sha256=RzMFaBKJVWygH2QlLQEFO_EBcN7nGxj6Sq-sAB7njvY,3534
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  biotite/database/rcsb/query.py,sha256=I5eAsdsW8FT-O0cKz_71dpS-HrEe0VtauliAPQMPBSo,33065
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- biotite/database/rcsb/download.py,sha256=LcuB7UnjGyra6ERPrljnrNoWxfp15ZyD7SIiQ6FBQTg,5787
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+ biotite/database/rcsb/download.py,sha256=A34iNIVufjUu1b21hj3jhcxIlXmUWDLt5I5jCMBOW1I,5996
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  biotite/application/util.py,sha256=KmvdyozUayuvlmGZ2QYkXeJCkqayvEmpQJDSXPL8I7w,2104
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  biotite/application/localapp.py,sha256=RA6MVIn5lSOhfv62H1QP6ymkiiMvzjK3swb9JSY6xAs,9450
@@ -35,7 +35,7 @@ biotite/application/__init__.py,sha256=ZsDk_A34W4W1jrA2zlHWhXXqe2uBKQVWDMa58d0IZ
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  biotite/application/application.py,sha256=6-UfFW1ssAeU6Xfd17ovjOREoa6owFIYWWDDIHVNUgE,8129
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  biotite/application/msaapp.py,sha256=tAXy8OKqHProreN4zDgNGcFFC7vFGoK6YFgNLeD9QxA,12346
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  biotite/application/dssp/__init__.py,sha256=CdRcAe_Uc_kGl_I0_Cn1Qk_4RsFn_n-u8SbLrklvYEM,322
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- biotite/application/dssp/app.py,sha256=PLSsCMi2EuxygpDJu-_QPUj_xxg0Vr6W7mvu3K5glqw,4929
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+ biotite/application/dssp/app.py,sha256=5l3ZKHHacp18w1L3tC1MImpfIWWyltQkV-cATlDmCvc,4828
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  biotite/application/viennarna/rnaalifold.py,sha256=4petrddQWumjtUzWxjVKqategejEczthqkwMIjkPvDE,10556
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@@ -57,7 +57,7 @@ biotite/application/clustalo/app.py,sha256=tPZFZ5SP1jCE1OQlTz7WzFOmdZ5B6JHTTjaCU
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  biotite/application/muscle/app3.py,sha256=tm51pw2zuDcuua-an5eaD_oBGh_PBL8vdlGdfUkXLF4,8450
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  biotite/application/muscle/app5.py,sha256=9tbw6XISmu9CEvFPDxoXW72HnrpAPf0MZY4jH7F8jK0,4799
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- biotite/sequence/codec.c,sha256=Yq4Z77uBYK3BViCHpkJEvbGvCSexYSCh2paPRNVXdfg,1533203
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+ biotite/sequence/codec.c,sha256=CHnLyRwGKFYW8lAuFWGenZz3Wj_avp12rdXnUHXXODc,1533571
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@@ -66,7 +66,7 @@ biotite/sequence/__init__.py,sha256=jwkyw2DlOVCyeZAfT5V1P-q6lZN7c7kINhNbtF2tODs,
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- biotite/sequence/codec.cpython-312-darwin.so,sha256=NocEmpwbumD5zkPn4BwNaIvX3CSynIQqI8htLyvAWis,318776
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+ biotite/sequence/codec.cpython-312-darwin.so,sha256=KDyGGE5fcpr1Jc1IVGDzbKL84ygKGW08rEvaKXpjL24,318776
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- biotite/sequence/align/localungapped.c,sha256=XTv0MAcWbrlEwzGJ8F_TE8iUQ63wWOkQxps9OEAWxeA,1610051
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+ biotite/sequence/align/banded.c,sha256=Lx01w-j7NyXtUQPxeY-vYv5h_k8nt26dOQve1XmTVug,2583113
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+ biotite/sequence/align/localungapped.c,sha256=mYe5D-O-MThCLc34vVJDZDPs6bOUhylX_3IQIy3vitI,1610419
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+ biotite/sequence/align/pairwise.cpython-312-darwin.so,sha256=ok8sDcpp5chw3djXRGM168Db2aqkNRRTHb0RJT8v3-k,631067
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- biotite/sequence/align/localgapped.c,sha256=gQ5R0H3sFB0yiRfUip9c16jbdHvc1IDWAyxT4MuNulQ,4603624
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+ biotite/sequence/align/localgapped.c,sha256=HlAXw6zn2b_s3vLnlNADbwmAacX6DKjmCZ2-zdJJ4eU,4604175
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+ biotite/sequence/align/banded.cpython-312-darwin.so,sha256=sP4QjF7cxaWBvaiVd9rUrk-VYU5bsevpQo749YBUKzc,578025
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+ biotite/sequence/align/localungapped.cpython-312-darwin.so,sha256=7hd8Ra-QZdNDteDAa7OZlcJZTcHiVyVtZ57kbgxcPUg,321328
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+ biotite/sequence/align/multiple.cpython-312-darwin.so,sha256=zZCN6v7gbadp3QjPTG9xwxxvaxV2roNoirtYVDyxVnc,546715
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+ biotite/sequence/align/kmersimilarity.c,sha256=Mrh07wdD3OGKS7G8EoSZnTOBeJ63uvt52cDBK56G20Q,1259825
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+ biotite/sequence/align/kmertable.cpp,sha256=cG7VxjolvxZjU-p2wmL09JNzy7p8S0JyOolDh21A570,3037407
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+ biotite/sequence/align/kmersimilarity.cpython-312-darwin.so,sha256=-vgDxvQVG6-Cnsfo_aHi38yaDcu2XFN78UGcY2ATTPM,247681
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- biotite/sequence/align/tracetable.cpython-312-darwin.so,sha256=wK_MYwq-1K9oj8LGiJCtbhXUDV8INYDPnJ25sp8btVE,204941
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+ biotite/sequence/align/selector.c,sha256=Vvkls1Mp044wjISJTuuaRlc5vX0xQAfeMZhtfC2pq1M,1637193
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+ biotite/sequence/align/tracetable.cpython-312-darwin.so,sha256=Mv7wZ6sZ3zT4dS2v9mbBhNlFQdhLaZHb32jAD1tL7lo,204941
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+ biotite/sequence/align/multiple.c,sha256=fhKUw5ngZaEuy74Qa503yemBqqueM0iAPMaBRzRKqJQ,2282358
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- biotite/sequence/phylo/upgma.cpython-312-darwin.so,sha256=kYfGBFFtXR_1NLbvywzCQn88wj9mYPcznC8WOB45gec,227704
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+ biotite/sequence/phylo/nj.c,sha256=Rx6pNLsYCsGvmuU3k5pzWknUgE6Dkl4RNPiYoF1Zu4w,1228289
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+ biotite/structure/io/pdbx/legacy.py,sha256=01mS2bA5_GptHDpe_F7_6IyueQ8_tlgB_X_m9dRa694,8842
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+ biotite/structure/io/pdbx/error.py,sha256=uY2i4nscyB2_QwbUv_-T8i9-3xrxogFUQf2B4U6C1wo,380
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+ biotite/structure/io/pdbx/__init__.py,sha256=dVWVJMjgOljsjYcoXtpyIcWnCX4qd4cxoZArK8h64DU,735
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+ biotite/structure/io/pdbx/cif.py,sha256=29QXV5gMJSiI1-pJOY7QINbdNgDMYknW9PJ6GVRUdtM,32248
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+ biotite/structure/io/pdbx/component.py,sha256=jBFoQ9X6Sj-rSi1wBud2JebjlcsUr-KmqSQpfkJ28xQ,8080
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+ biotite/structure/io/pdbx/encoding.c,sha256=5aMg_2VMjcM0cwZEm1TH9ZGIwN5EoY6ccnx7YemUg80,4735611
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+ biotite/structure/io/npz/__init__.py,sha256=WBUmxbb3qaFjLdAQwzYhVI_vh8w7gMZRlcpNZBYBc0s,736
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+ biotite/structure/io/npz/file.py,sha256=5xrKj7raPsby5U7sIyeilfsbCx0w_bcR8QG8anE2eQQ,4958
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+ biotite/structure/io/pdbqt/file.py,sha256=mSeaAXfgYH0SDKTiIH-TvKgMbJeWkoUbqngE7RHKu7Q,26399
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+ biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so,sha256=Flq9Ei--VWf5-34PXT9cLT0gtnp1s3wCzEcQ2jeeYF4,211579
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+ biotite/structure/io/pdb/hybrid36.c,sha256=QnVrzSl-4F2C33KonKXRql1jPMhbywHQVUoMwwCwgfM,1110875
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- biotite/structure/io/mmtf/convertarray.c,sha256=vMVzYpHGN0DA3NpQugagr8C3BWpGb_eQzQkrljIRR4s,674027
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  biotite/structure/io/mmtf/assembly.py,sha256=HYVy2Knir1TqWT_NfvrmUmR2UX8eFNzVmQImSLZP-7w,8184
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- biotite/structure/io/mmtf/convertfile.c,sha256=xEiv7KXeX9i4Ex8qd2N4g8kTn8H11IItVwTuZ8HXldM,1553183
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- biotite/structure/info/misc.py,sha256=6xMO1yaWH2JxPeHqlDqC2SxAwKW9oVXE2omYHwUDdPk,2173
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- biotite/structure/info/carbohydrates.py,sha256=GQnIVS_hRK0zrlZ_o_xZD0TpNGPrH3_-Jv7hLXX_omI,1248
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  biotite/structure/info/atom_masses.json,sha256=WME4ezDPy-HrEIhxkOGxcmIMdgxf1x7e_xwBkFRdTsY,2383
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- biotite/structure/info/amino_acids.py,sha256=IDdvU79JMwLNwHA0fjoI4pVapbzTG1U5dqamrV4k9W0,1446
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- biotite/structure/info/amino_acids.json,sha256=W8QthUORbYGPBz8Y-xC6sfKE8hqKkk7PTu_6mm3OMNQ,12433
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- biotite/structure/info/nucleotides.json,sha256=Vp3vLEpNEgo1MLTRU3SDntxJQLKu3e3W1uIMm92VYLA,6104
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- biotite/structure/info/residue_masses.msgpack,sha256=KDZ4r82AcecK_CCD64bEnTZK3rur5Jq_fSBaiB3rB1M,459118
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- biotite/structure/info/residues.msgpack,sha256=yt9Nd0G3mnTorAfrNHAz34ZhgsvGwGWYRgG81Y3nuv4,73230917
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- biotite/structure/info/__init__.py,sha256=LnAvRskhphES4yfOT98EwcGWNKsH4TGkJqKTsUbEaPI,829
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+ biotite/structure/info/__init__.py,sha256=k57tfM03apKfR3UlJMoDXZHS6jilhkeni1DoQa_nWLs,702
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  biotite/structure/info/radii.py,sha256=GlTPOCvtqGy7PQJlTOZA57PXg7xPLwKYEy0wcrCmiEc,5648
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- biotite/structure/info/standardize.py,sha256=8LET7mOuNFCrLVMXjlHhj15ZDqzixZvGSw2TqxI_x-g,7573
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- biotite/structure/info/bonds.py,sha256=ugZitgA4Ajj3RcUrum4H_ZuqVcotr2-Df5vxkdVdPvo,6089
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- biotite/structure/info/carbohydrates.json,sha256=JfzMX_FwOBhzH3E0XEvJVjCP80d-bEjOiIFtgJpNd9U,8962
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- biotite/structure/info/link_types.msgpack,sha256=EO5H3hQFNuLs1tHft9zZf3HpN0-3O_XM3QA3HIY73PA,582272
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- biotite/structure/info/residue_names.msgpack,sha256=p8uLuHBVko6pbq-GDjqLIZMtc7_XEY1NUFZQt4YL-yA,2952002
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- biotite/structure/info/intra_bonds.msgpack,sha256=gdf7MGumNkEg6ToZnyI2_zL6z6gLVyi6k0kP5eFaDIo,16338340
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+ biotite/structure/info/standardize.py,sha256=AaYn7mx6Y6NylkeOg1kIpyNoI-KrWbGSXXu_GEcSAZw,7772
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+ biotite/structure/info/bonds.py,sha256=h32B-0-4zEs9e_ZrGyIXP_Rp4IXf6u_Cm0k-DgbC5pI,4644
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+ biotite/structure/info/masses.py,sha256=dnZbg4k_89SuTwFUulyTKAL6Mnk4POPMIVhJLl5xswA,4489
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+ biotite/structure/info/atoms.py,sha256=3a_Cp7sRKwRq6rzl1uvX9Ak1fzTzLdZdJdx4zXx_1JM,2427
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+ biotite/structure/info/ccd.py,sha256=26BnKJEGH6Bhmvkll_ev6HSCIi0hNx_cs_N9hqNXP-4,2754
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+ biotite/structure/info/ccd/components.bcif,sha256=2exbF1n0jReJ3JTI9YYPzjxCtrIu3Z6myll-w3JOQRU,35086693
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+ biotite/structure/info/ccd/amino_acids.txt,sha256=AC0v3vCBdzSzC0nQZ_jCXGviuBi_9PHUGqLe_regyMY,6591
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+ biotite/structure/info/ccd/README.rst,sha256=sfFRGesjpATIp5S8kiEV7cr-Jb51fWLGT4KypmzsoPM,342
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+ biotite/structure/info/ccd/carbohydrates.txt,sha256=2rAtgJ4vu_SPY_3dZOZkioBXs4lDPPY8FKfINPStFmk,4532
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+ biotite/structure/info/ccd/nucleotides.txt,sha256=x02Y7eWP4JiR-Fw5qXltSUd-UbTQxNWuQUjr67f46RM,3132
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  biotite/structure/graphics/__init__.py,sha256=YwMT8-c2DjrkcwyK6jPeDtAKxQda0OhElnwk8J0y3Hc,353
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  biotite/structure/graphics/rna.py,sha256=bhIHoB_9sFuZPrHQ8qQnToRiTCfgQ7JLVNIdsQVvkw8,11888
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  biotite/structure/graphics/atoms.py,sha256=nMhbmnjytxEDkxTTm2wHM2dObSw3izjvRbqssCW876E,8171
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: bdist_wheel (0.42.0)
2
+ Generator: bdist_wheel (0.43.0)
3
3
  Root-Is-Purelib: false
4
4
  Tag: cp312-cp312-macosx_11_0_arm64
5
5