biotite 1.3.0__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 (52) 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/interface/pymol/object.py +3 -1
  6. biotite/interface/rdkit/mol.py +5 -5
  7. biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
  8. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  9. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  10. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  11. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  12. biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
  13. biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
  14. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  15. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  16. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  17. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  18. biotite/sequence/codec.cpython-312-darwin.so +0 -0
  19. biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
  20. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  21. biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
  22. biotite/structure/atoms.py +1 -1
  23. biotite/structure/bonds.cpython-312-darwin.so +0 -0
  24. biotite/structure/bonds.pyx +67 -6
  25. biotite/structure/box.py +1 -1
  26. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  27. biotite/structure/chains.py +34 -0
  28. biotite/structure/charges.cpython-312-darwin.so +0 -0
  29. biotite/structure/compare.py +2 -0
  30. biotite/structure/filter.py +2 -1
  31. biotite/structure/geometry.py +164 -2
  32. biotite/structure/info/atoms.py +8 -0
  33. biotite/structure/info/components.bcif +0 -0
  34. biotite/structure/io/pdb/convert.py +1 -0
  35. biotite/structure/io/pdb/file.py +31 -7
  36. biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so +0 -0
  37. biotite/structure/io/pdbx/bcif.py +7 -4
  38. biotite/structure/io/pdbx/cif.py +6 -3
  39. biotite/structure/io/pdbx/compress.py +15 -11
  40. biotite/structure/io/pdbx/convert.py +42 -26
  41. biotite/structure/io/pdbx/encoding.cpython-312-darwin.so +0 -0
  42. biotite/structure/io/pdbx/encoding.pyx +39 -8
  43. biotite/structure/residues.py +173 -1
  44. biotite/structure/rings.py +117 -1
  45. biotite/structure/sasa.cpython-312-darwin.so +0 -0
  46. biotite/structure/segments.py +39 -3
  47. biotite/structure/util.py +14 -22
  48. biotite/version.py +16 -3
  49. {biotite-1.3.0.dist-info → biotite-1.5.0.dist-info}/METADATA +1 -1
  50. {biotite-1.3.0.dist-info → biotite-1.5.0.dist-info}/RECORD +52 -52
  51. {biotite-1.3.0.dist-info → biotite-1.5.0.dist-info}/WHEEL +0 -0
  52. {biotite-1.3.0.dist-info → biotite-1.5.0.dist-info}/licenses/LICENSE.rst +0 -0
@@ -1,4 +1,8 @@
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- biotite/version.py,sha256=qDtcPZdKzxLpd8vVl6fpIFIMkWt2HK_cO9gLDwaHEdk,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
@@ -21,23 +25,23 @@ 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
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  biotite/interface/warning.py,sha256=rU1F-b1MeIj1OWaK6wMeuM_YE-WKNGqo2TehjTr10KM,577
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  biotite/interface/pymol/startup.py,sha256=8W0wIx13MGqGNvwTTT7ogmgypXCO48PI5w-DVPdS9jw,4619
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  biotite/interface/pymol/shapes.py,sha256=Q34C5H5PkH4XbnyymwbJYp9iFD2Idj2a_qzDRA8tohQ,6066
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- biotite/interface/pymol/object.py,sha256=5_zG4rn-sjreAHGdRLW45IxK9A096zXjgxn1cEgOVag,44193
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+ biotite/interface/pymol/object.py,sha256=c0BxeD2rxyPNonXBTA1iLINSRA4_Ljn1_Tzpf4_rLYg,44280
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  biotite/interface/pymol/convert.py,sha256=ldLXSiFdwhEkoZkTtLFOMvymIh9oLniChve54SbHJLA,6044
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  biotite/interface/pymol/__init__.py,sha256=bOX95ek4eKSgZFYynrfcuZFRgjADYvhbrVWCR6ok7yc,6648
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  biotite/interface/pymol/display.py,sha256=KJfCM9-hzvFdC5KFxvG5-oEXd0MIaf3Ocr3dMQVoipY,8458
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  biotite/interface/pymol/cgo.py,sha256=wlG1GkbHAGYVdzaOUPQ5KzI-29lrDkutt0NRw7PIq-8,9859
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  biotite/interface/rdkit/__init__.py,sha256=K2gVw_wrbIU0v-I3RgRvrihdtcpFfL9_t-IlObLuCMk,532
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- biotite/interface/rdkit/mol.py,sha256=T4Nnc3ttQFfy-4YbbSRLuTpcAhahWjqQGwM7fypouEs,19644
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+ biotite/interface/rdkit/mol.py,sha256=iMPR8U5girjnCa2-xLHQG1duw-tR3bUruVQRa1O27fc,19629
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  biotite/interface/openmm/system.py,sha256=V-SDc1YDa6nKHcREXz1cGAN7jZJ2X1cPf0gazz_Gv6s,7018
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  biotite/interface/openmm/__init__.py,sha256=ZcLsA9PPsrFDtY7rTMspizpCCQ_Fnm7vqwY-E5xTw6k,587
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  biotite/interface/openmm/state.py,sha256=jmdLw1xc7TQbgeOnZGgSgdmD_rR9VEnMqhX0Wnw_1Jo,2723
@@ -48,7 +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
@@ -79,7 +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=KcCMZjc_9IZs6HPzpEuDykK0rWQzyl-m6E55UlUll-0,284488
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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
@@ -100,33 +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=PdT5P3RTHfsbcBo6xlDtyt5IS062rPDC75tgSq9TWX0,564880
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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=YLT0FqlUyShpdMM39iay2CxbsmzYtwkLz2raX1XBd3U,1062304
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- biotite/sequence/align/banded.cpython-312-darwin.so,sha256=tcOcwqpHQV3HgKteA0LJw-stemspC22Ep5_OdAa2ARw,527760
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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/localungapped.cpython-312-darwin.so,sha256=Xd5r4fmpaAyIff83NmWFanIqphrEduKByvn4fRqezu0,303984
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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=19sAMd8C4CaUwz6gO5fQkrPcqLX-gA0D23QqvTocfqY,231024
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- biotite/sequence/align/multiple.cpython-312-darwin.so,sha256=2UGuxoG7gYtWDQT19NmnjctxkOoxCeVHb7UZvfM-b7I,493952
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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=cwCv531KfE9dNX5NtvV2_De4ELQu0mPUiIQe3mHkULs,229544
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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=vdovy5HedLeoR-cX66U35dj_7AhNWqd8pULSn7dzc54,203344
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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=aNsV5UKbQXp5EZ9fS7RhmG4G8q5Dmpi2Rx8INktrOjI,323040
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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=-ArqKECpQBpPy4AmNPrGzgURm-RvgWSTpuoaihoDaoc,401824
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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=orIU4HMt_GuP5E5unEDi7Gz4F8vR_x2JMQI_GgDVUbA,684048
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+ biotite/sequence/align/kmertable.cpython-312-darwin.so,sha256=Nd60gxzhzS9ZvF2V5N22_KG6FF-0Q8hbY5pg0tUXFWw,756224
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@@ -246,25 +250,25 @@ biotite/sequence/graphics/color_schemes/autumn.json,sha256=usp-Y70tk39LCJV64vi7t
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- biotite/sequence/phylo/tree.cpython-312-darwin.so,sha256=ZiMyJOVu8V3Z4GF9X_Ei_CyLRC4v5i6c2GVLdrGRaFo,282216
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- biotite/sequence/phylo/upgma.cpython-312-darwin.so,sha256=ys6xNo46LXbJAO9eGC9uuClB_96eQo9U4yoLoWjscew,209224
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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/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/filter.py,sha256=3K8Xr4CgwlesldchvlEo0EC8NL_sWiFFfRnbunfc_xQ,18126
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+ biotite/structure/bonds.pyx,sha256=Bjjc5bTxFmbMUWeYNf1FMfHJ8DB4V02_DRFwrsqtdno,71791
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+ biotite/structure/rings.py,sha256=pdxrBNtuvOE1hi9sxtI1EamUFtGnqprpkjzZpUi7jgs,15584
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@@ -298,13 +302,13 @@ biotite/structure/io/dcd/__init__.py,sha256=tYiiTSmqDrsSgg_sZaoQgx2D8N9OeqlooxH4
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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/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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@@ -321,10 +325,10 @@ biotite/structure/io/mol/__init__.py,sha256=WvcNPDdf9W1zPyJ0tjTvGNxA83ht18uRQA8B
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+ biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so,sha256=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=4N6E-iNhSvbZ98HmvcS-dI9qUCnwoZD4NqxrfwGMMx4,53635
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+ biotite/structure/io/pdb/file.py,sha256=GCS8qD-efyXswe5acr2Erz3qurGfY52J60n06BqA7jc,54557
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@@ -334,7 +338,7 @@ biotite/structure/alphabet/encoder.py,sha256=2BWLMdGBr2bHw09vMhbzPztMKSnVt8UhUf8
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+ biotite/structure/info/components.bcif,sha256=mQrO6PEOkPNw2i1DHp5qugNyDx0g-2d_uV-T4KD1bwI,62070945
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@@ -343,12 +347,8 @@ 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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- biotite-1.3.0.dist-info/RECORD,,
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- biotite-1.3.0.dist-info/WHEEL,sha256=RemoLmiEETQWaDnkABcjmbI83SdF_gEdwFAlYn6e9o8,133
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- biotite-1.3.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534