biotite 1.0.0__cp312-cp312-macosx_11_0_arm64.whl → 1.1.0__cp312-cp312-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-312-darwin.so +0 -0
  13. biotite/sequence/align/banded.pyx +5 -5
  14. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  15. biotite/sequence/align/kmeralphabet.pyx +17 -0
  16. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  17. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  18. biotite/sequence/align/kmertable.pyx +52 -42
  19. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  20. biotite/sequence/align/localungapped.cpython-312-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-312-darwin.so +0 -0
  26. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  27. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  28. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  29. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  30. biotite/sequence/alphabet.py +3 -0
  31. biotite/sequence/codec.cpython-312-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-312-darwin.so +0 -0
  36. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  37. biotite/sequence/phylo/upgma.cpython-312-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-312-darwin.so +0 -0
  52. biotite/structure/bonds.pyx +72 -21
  53. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  54. biotite/structure/charges.cpython-312-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-312-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-312-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-312-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
@@ -1,12 +1,13 @@
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- biotite-1.0.0.dist-info/RECORD,,
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- biotite-1.0.0.dist-info/WHEEL,sha256=RuH0OSSkE2iFFCiqpmSxZqGj3WHRpMHdUp0bulkW7xo,105
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- biotite-1.0.0.dist-info/METADATA,sha256=C6tIVbg8HfB-DgcNYsM7sb56iNpH-n4EulEWtL_-2fQ,7111
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- biotite-1.0.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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- biotite/version.py,sha256=DGJ4pj32xs3_DRJhSzQwCiRNnAQrMgo09USYpyMZsKc,411
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+ biotite-1.1.0.dist-info/RECORD,,
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+ biotite-1.1.0.dist-info/WHEEL,sha256=RuH0OSSkE2iFFCiqpmSxZqGj3WHRpMHdUp0bulkW7xo,105
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+ biotite-1.1.0.dist-info/METADATA,sha256=AWoJEvD_xouBG2_P5lKh-FPZOZQ9C12cRsO8GsBMBfE,7224
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+ biotite-1.1.0.dist-info/licenses/LICENSE.rst,sha256=ZuNQuB65Dxf0rDB_5LxvA4SVQJBWxRZyvbjbvE-APWY,1534
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+ biotite/version.py,sha256=CqDGE4B1ZqZ-56mxeOFcXRTmlxrdOh4ayrjbcPjziE4,411
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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=EYUBKgeNrkPI53f7L4T893NMmLWgBp07aO2XFcdpYTU,10012
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  biotite/file.py,sha256=TQLcN1FzEbEEOLdR0RUfHr9WPIkmULifHG_LoEWZV3w,6524
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+ biotite/setup_ccd.py,sha256=sWHyRm78imJybCzPu_W-gKR_itxrVwEEGJxMq6YlzIE,6051
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  biotite/database/error.py,sha256=3xyutl2nPzgBZqe5fpejOp6AQXAvtxO2hy_oWRrlcKI,410
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  biotite/database/entrez/check.py,sha256=5ITmnDoV6-lmfxux-HpXCUjcnI0dyYBwr-mqGkIb5e0,1853
@@ -15,30 +16,30 @@ biotite/database/entrez/key.py,sha256=JS9GxvUMSYYmb2wU5uQduKUjITXRfY62aFyUH7_OMT
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  biotite/database/entrez/download.py,sha256=RsB1xgcVSY_fjM1v2CMGwjImWG5e5qFg4_pttdgBxq4,7376
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  biotite/database/entrez/dbnames.py,sha256=57WUYPlTtPRne74fypNgFnE0cl91_WSRwzkoQsGjR6Q,2620
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- biotite/database/uniprot/check.py,sha256=7ShClNBBHZkKw09Cewl4drr4C0we7oFGJGHBbgINt50,1292
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- biotite/database/uniprot/query.py,sha256=dXjrBTeqpfrVOSoHVN4vdbZYR4ZtNvZTf0v_WfVwi4k,7563
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- biotite/database/uniprot/download.py,sha256=MZan2nFyYWSWgFL-VU3MOJOwp6g9h25_65zFfBr-Kww,4320
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+ biotite/database/uniprot/check.py,sha256=TJeIGnPGVOEXrvn4V4EIJs0NEXnvWDfXDAgZzSs2evY,1373
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+ biotite/database/uniprot/query.py,sha256=XZHNAARmrJP2zDVrdL3kmRl-LK_rTPweIGseBogCcqU,7551
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+ biotite/database/uniprot/download.py,sha256=HmWrYpNzpSvGGZP26xk0nzAv4fwzhA8mDZ4moexWgc4,4308
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  biotite/database/pubchem/error.py,sha256=_-SE2w-Jx5HqL8ll5deiaXAKAeEPC0ysSG6F3Mm8AGA,713
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- biotite/database/rcsb/query.py,sha256=ztyNlUs72vwjdG3Ci1Mj6UTJb9yupcRray8pYogPbw8,32902
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+ biotite/database/rcsb/query.py,sha256=DAXZJbI8lUey80MuA1QNetqv3MgqaAaY3jM9MhrjrTg,32919
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- biotite/application/util.py,sha256=zDxqVUWcINdTgnLMdC004GXygIUeYWSemwEALk8xrGo,2095
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- biotite/application/localapp.py,sha256=uvktgVp67gAyus4LR6dXjEc23y8M5n_K5e-ncWzwx-c,9286
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+ biotite/application/util.py,sha256=8iReyUmCizsbhkUv1t5QKx5tH9M101ebKy4EnviP2v4,2111
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+ biotite/application/localapp.py,sha256=JeiqQxP9JgV_kCaYXi14I_cfsxZZDEieymNaN_5sKqw,10270
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  biotite/application/dssp/__init__.py,sha256=lUf-A2rJzPLJYZQZGpZUt7HtA0M59KaX6zQSCrkhfF4,323
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- biotite/application/dssp/app.py,sha256=zhuHcUihTz9b9iOcYJ8ROAPYu-_0gW61d5fEXle2fHI,4840
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+ biotite/application/dssp/app.py,sha256=tHoG8uFmX8WaBHm0Fhjc7D0NXEaMa-zkLvwFzyP4FQk,5323
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  biotite/application/viennarna/rnaalifold.py,sha256=DmsHVi18izXS0ee6FN6MfgrCEScw9v9qSvkGOjHs8IU,10608
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- biotite/application/viennarna/rnaplot.py,sha256=IPZ-AOMwblQHoF1Y6xBtN84RqWfDMkMpn8Kiws-7w4E,6327
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+ biotite/application/viennarna/rnaplot.py,sha256=Z8TdKvd3mYAdUOdPLdsY10aeHVDsoXKJxsiChWkfjy8,6416
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@@ -53,20 +54,20 @@ biotite/application/mafft/__init__.py,sha256=VQPqkbQPAvGePLTb-Kgd1exMxDT5onbab34
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- biotite/application/muscle/app3.py,sha256=-T6AmkGlBE0EAxp3ZG--tvcxUVBTkBdr7W5qzUrDTXE,8085
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+ biotite/application/muscle/app3.py,sha256=C-W7MOHjwfb4ioKtVeVSAOD9sbO58bCdG8rRhy_vxzU,7613
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- biotite/application/muscle/app5.py,sha256=cjK26uAcL3dblyxa8WzfJE8FXzo3FZ0p5jn8ttu8YNc,4426
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- biotite/sequence/profile.py,sha256=VtRfHP3f4Ymw7tgV5wPvde22nH1KwOkkKXToHLkbl5Q,17126
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- biotite/sequence/alphabet.py,sha256=OiUxnsbTaxuDjAiB96sVHYTOqG3XvwF5ceJ3tvViqh4,17190
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+ biotite/sequence/codec.cpython-312-darwin.so,sha256=sG87Qj7g0XAXbJBFW95rTxVSrjOzxuXcLzpCenvQVg4,284488
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+ biotite/sequence/alphabet.py,sha256=IqZnJZtUku9HPcRwx8ta7dRaK7knmoNW1quMcf-2ZAs,17245
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+ biotite/sequence/align/matrix_data/PB.license,sha256=OkDCfXO06BfooLXYC3iF7LXXB_Uqqex1B2gjUEFdUZI,1091
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+ biotite/sequence/phylo/tree.cpython-312-darwin.so,sha256=U7VPm6TkUNY9_I4Dd-Lc1FGKFAp2e__28a6M-i4Q7o4,282216
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+ biotite/sequence/phylo/upgma.cpython-312-darwin.so,sha256=RwnV2iOkQ9U4a3ALhG56PlWRuat98d2RML6ozJVists,209224
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- biotite/structure/segments.py,sha256=_yotEX4cr9WbxHdezLmoak5M3306PZZmPAxcO-tqSHU,5546
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+ biotite/structure/util.py,sha256=ywK8N5Po74uwTim2KuXOFIh5ivV0_pCc1W1oiZT_9sA,4956
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- biotite/structure/__init__.py,sha256=r2CR-UtCLVqbAygpKCri0pXD1FCe2M9wZSOi1Szp700,5324
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+ biotite/structure/bonds.cpython-312-darwin.so,sha256=5wJeNc6m3Oep58RLNXBz7Nk9nNDkV3ik6UZSumQylhs,560840
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+ biotite/structure/__init__.py,sha256=VSJMdPML_2MJPcSnmfRCyAcIpFlJRN8MLrHpj7RqQQ4,5449
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+ biotite/structure/celllist.cpython-312-darwin.so,sha256=YdfSF9xcQUKaXdJ9Y5qvIGMNS-sAHrFTaqhrVdIDJzY,302960
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+ biotite/structure/geometry.py,sha256=U7xtFwM6OTB0sjgyN3jhxPTXQn6_NmwW6ueNsdc6Zn4,23423
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+ biotite/structure/molecules.py,sha256=dQ1Ad7_rX8HRpEHfIhfLWq1-ydalpjwPEPHrEtDPBy4,15504
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+ biotite/structure/filter.py,sha256=X2Mj5_Z0_lk1LxuJudlztxuu7VkVF_ObtV_FCrXyHhg,17967
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+ biotite/structure/bonds.pyx,sha256=ILmU-8m_3yj_ZBMhMvS4Z5hl7hbugyDnzP20lnH6-sk,69546
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+ biotite/structure/atoms.py,sha256=ZcCvMUjBVGjdJuwqMrXXTjgZYQozWPRUPXvqnJyofao,50458
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+ biotite/structure/sasa.cpython-312-darwin.so,sha256=XfQ5AsLhN_sMNsl_8m4b83ND3xDKgTCB1O-KsGTvuV0,264008
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@@ -268,25 +273,26 @@ biotite/structure/hbond.py,sha256=4y2FXeAXl7g2EDnwb1uDXFieGpZPQhnnkdATBechvW8,15
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+ biotite/structure/io/pdbx/bcif.py,sha256=TU8qz07kSxPK1GRzZK_t-wdkS5KlnvN7kmIwZdgag9E,20638
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+ biotite/structure/io/pdbx/convert.py,sha256=HdgQpVRqE_q99IsjnAIbvL8PUE5dRt1PYscFmvBp6F8,65635
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+ biotite/structure/io/pdbx/encoding.pyx,sha256=ySywnGIvlDER4tcQzFMEgWkQJN_sMzB__MHbRQ0-wxc,31184
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+ biotite/structure/io/pdbx/__init__.py,sha256=DlVXhrcuAF9A6Gim_JMccz-j8jDZuF2liDDA5cZxzx8,717
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+ biotite/structure/io/pdbx/compress.py,sha256=-v-lpJDxeEyYtXK3tGwQFwqm73355ZocT4U6L1bZcmk,11800
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+ biotite/structure/io/pdbx/cif.py,sha256=va3C2ANDFSuyY72gWWboY9TPUA1DlTB3zjQVeV80b2A,34506
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@@ -296,27 +302,31 @@ biotite/structure/io/mol/convert.py,sha256=sj7V7pdBlGQAAaXl7fAVf8JZC4Fd-z0gjne_0
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- biotite/structure/io/pdb/convert.py,sha256=fzXkfm-SN9HswZ8srj0v15RRec9hq0BtB3gCgNIlk9s,10602
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+ biotite/structure/io/mol/sdf.py,sha256=bAfypU7QBrP4DhHDf9Qi5eKGHU_bjC4Ox0xHSlYuPxQ,32314
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+ biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so,sha256=40dqmKCofL0K8oYvjvfhyz0tNHdC8ZZeVFvPJRCqGas,209760
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+ biotite/structure/io/pdb/convert.py,sha256=xuodAbfXe3BOuETPhV0x3D1ogJwaba9KFXr4mWuzNqo,10720
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- biotite/structure/info/misc.py,sha256=GIdFhRtzWInhynVXNQwQpJszowmZ_0Jdqh9R706CB_Y,3512
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+ biotite/structure/alphabet/pb.py,sha256=gtGuWDpMhJUkVUO30GHhlgNhwwzycGkkGNykw32FUjU,5995
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+ biotite/structure/alphabet/unkerasify.py,sha256=Ri7rAxBDG7_xlddpReBJkNZrl5ues3_bygpC2gDb3XY,3201
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+ biotite/structure/alphabet/encoder_weights_3di.kerasify,sha256=m4JF4oVWBbiu6r8DM9ONQ5Bmcbqwr5dxKfqYThOmHpk,1032
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+ biotite/structure/alphabet/__init__.py,sha256=tUAybrggScCsom1b_EXQ63pA88L_PmQpcYS-MnqKavM,928
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+ biotite/structure/alphabet/encoder.py,sha256=2BWLMdGBr2bHw09vMhbzPztMKSnVt8UhUf85g5M1xnY,11383
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+ biotite/structure/alphabet/i3d.py,sha256=eIcm3l0GLkjxm17bykrfwtKpS5AYDAsDiChLOyMVCu0,3010
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+ biotite/structure/alphabet/pb.license,sha256=OkDCfXO06BfooLXYC3iF7LXXB_Uqqex1B2gjUEFdUZI,1091
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+ biotite/structure/alphabet/layers.py,sha256=Y1Y8G2LqqzC7M0kNUv8k-EXTVVKGLnPDJKdRrVEf3H4,2087
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+ biotite/structure/info/components.bcif,sha256=wwalqJIJBcRDT7wXyzWbn89uSsum-4Ah87ImtfpDMVE,57915331
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+ biotite/structure/info/misc.py,sha256=rfNLLm21FPq-Ugpf3J8tX77fxkQsotZbOY-_vbWmGP0,3429
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+ biotite/structure/info/__init__.py,sha256=k08kdsKlrxaVQ9x8MjEXoVFaXl1J8OcpLf6iG7dUgOY,698
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+ biotite/structure/info/groups.py,sha256=dX9kK5KGyLvH38-5L7y_oaaI1poR2FIARrzfBXGSwPQ,3187
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- biotite/structure/info/standardize.py,sha256=mF8N112nB5LLo6fZNOxlviZzccDD9ouFKefhR4NhSX0,7713
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- biotite/structure/info/bonds.py,sha256=Nv-OKSjBblrGfOsYVYbE6uDs18nIvXr8l-g-7YLmXtM,4501
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- biotite/structure/info/masses.py,sha256=kIMc-_NdEushTskuTszdd9FdrPUeqEO9EczOA9sAT7g,4483
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- biotite/structure/info/atoms.py,sha256=vBtjGVSLjnh69nFJYJ3s9Li_cnyBDTTijTiD77CLUbc,2622
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- biotite/structure/info/ccd.py,sha256=ZMaICtIrkUMLZ6Lvmo5riML1H9JETJqulk6ovJlafMk,3002
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- biotite/structure/info/ccd/components.bcif,sha256=xgvErxils9GNg5s0sGI33B7w4lWeUBZRksPer3japnE,35649254
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- biotite/structure/info/ccd/amino_acids.txt,sha256=RUyolncqbsplkY2hlajjOSciigyZEYL1GCx_f63jXx4,6669
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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=bh5Vc84tETB-FKUm6H1brBN6zM5a2zzzwuWyb0MXaLA,4544
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- biotite/structure/info/ccd/nucleotides.txt,sha256=Q7Zjz45BAO6c2QDAgvYdKtWAqmjQxy2NQ6r-bsZRqv4,3136
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+ biotite/structure/info/standardize.py,sha256=hWsxKSo7xdiGRyOoQcay0mslPTtb9cQuQds5IsWG8Xg,7759
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+ biotite/structure/info/bonds.py,sha256=6pXAZPeKPL2pwFi5fhSyTwh_gd5fToIgvwguGffrE-0,4644
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+ biotite/structure/info/masses.py,sha256=HOdaeFZkd5LSrl00025S1MwXT7im8V-s0bU54tr1te8,4555
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+ biotite/structure/info/atoms.py,sha256=RniEQ9e_ocMV3sPdpTokm4s-V8A49n0W0ZsYoEv4YVI,2622
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+ biotite/structure/info/ccd.py,sha256=EBSqvzgIXl7U5wxSVOFPSaLQLBRP2E_mUVXEwsRyOO4,5853
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@@ -1,8 +0,0 @@
1
- These files are based on the
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- `Chemical Component Dictionary <https://www.wwpdb.org/data/ccd>`_
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- and were created using ``setup_ccd.py``.
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-
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- To keep the size of the repository small, the original commit should be
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- rewritten, if the formats of the affected files are compatible with the
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- original ones.
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- The name of the commit is ``Add CCD dataset``.