biotite 0.38.0__cp311-cp311-win_amd64.whl → 0.40.0__cp311-cp311-win_amd64.whl

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Files changed (124) hide show
  1. biotite/__init__.py +3 -3
  2. biotite/application/application.py +33 -28
  3. biotite/application/dssp/app.py +18 -18
  4. biotite/application/sra/__init__.py +5 -0
  5. biotite/application/sra/app.py +337 -55
  6. biotite/database/entrez/__init__.py +2 -1
  7. biotite/database/entrez/check.py +14 -3
  8. biotite/database/entrez/download.py +20 -13
  9. biotite/database/entrez/key.py +44 -0
  10. biotite/database/entrez/query.py +38 -34
  11. biotite/database/pubchem/query.py +44 -44
  12. biotite/database/rcsb/download.py +19 -14
  13. biotite/database/rcsb/query.py +46 -46
  14. biotite/sequence/align/__init__.py +5 -1
  15. biotite/sequence/align/banded.c +1408 -1025
  16. biotite/sequence/align/banded.cp311-win_amd64.pyd +0 -0
  17. biotite/sequence/align/buckets.py +69 -0
  18. biotite/sequence/align/cigar.py +389 -0
  19. biotite/sequence/align/kmeralphabet.c +3220 -2850
  20. biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd +0 -0
  21. biotite/sequence/align/kmersimilarity.c +713 -663
  22. biotite/sequence/align/kmersimilarity.cp311-win_amd64.pyd +0 -0
  23. biotite/sequence/align/kmertable.cp311-win_amd64.pyd +0 -0
  24. biotite/sequence/align/kmertable.cpp +68398 -0
  25. biotite/sequence/align/localgapped.c +1507 -1074
  26. biotite/sequence/align/localgapped.cp311-win_amd64.pyd +0 -0
  27. biotite/sequence/align/localungapped.c +1143 -833
  28. biotite/sequence/align/localungapped.cp311-win_amd64.pyd +0 -0
  29. biotite/sequence/align/multiple.c +1569 -1092
  30. biotite/sequence/align/multiple.cp311-win_amd64.pyd +0 -0
  31. biotite/sequence/align/pairwise.c +1612 -1212
  32. biotite/sequence/align/pairwise.cp311-win_amd64.pyd +0 -0
  33. biotite/sequence/align/permutation.c +33259 -0
  34. biotite/sequence/align/permutation.cp311-win_amd64.pyd +0 -0
  35. biotite/sequence/align/primes.txt +821 -0
  36. biotite/sequence/align/{kmertable.c → selector.c} +9129 -16497
  37. biotite/sequence/align/selector.cp311-win_amd64.pyd +0 -0
  38. biotite/sequence/align/tracetable.c +685 -646
  39. biotite/sequence/align/tracetable.cp311-win_amd64.pyd +0 -0
  40. biotite/sequence/codec.c +1159 -841
  41. biotite/sequence/codec.cp311-win_amd64.pyd +0 -0
  42. biotite/sequence/graphics/alignment.py +212 -2
  43. biotite/sequence/io/genbank/annotation.py +11 -11
  44. biotite/sequence/phylo/nj.c +684 -636
  45. biotite/sequence/phylo/nj.cp311-win_amd64.pyd +0 -0
  46. biotite/sequence/phylo/tree.c +970 -673
  47. biotite/sequence/phylo/tree.cp311-win_amd64.pyd +0 -0
  48. biotite/sequence/phylo/upgma.c +672 -626
  49. biotite/sequence/phylo/upgma.cp311-win_amd64.pyd +0 -0
  50. biotite/structure/__init__.py +1 -1
  51. biotite/structure/atoms.py +1 -1
  52. biotite/structure/basepairs.py +7 -12
  53. biotite/structure/bonds.c +3861 -3749
  54. biotite/structure/bonds.cp311-win_amd64.pyd +0 -0
  55. biotite/structure/celllist.c +727 -707
  56. biotite/structure/celllist.cp311-win_amd64.pyd +0 -0
  57. biotite/structure/charges.c +1561 -1560
  58. biotite/structure/charges.cp311-win_amd64.pyd +0 -0
  59. biotite/structure/filter.py +30 -37
  60. biotite/structure/info/__init__.py +5 -8
  61. biotite/structure/info/atoms.py +25 -67
  62. biotite/structure/info/bonds.py +46 -100
  63. biotite/structure/info/ccd/README.rst +8 -0
  64. biotite/structure/info/ccd/amino_acids.txt +1646 -0
  65. biotite/structure/info/ccd/carbohydrates.txt +1133 -0
  66. biotite/structure/info/ccd/components.bcif +0 -0
  67. biotite/structure/info/ccd/nucleotides.txt +797 -0
  68. biotite/structure/info/ccd.py +95 -0
  69. biotite/structure/info/groups.py +90 -0
  70. biotite/structure/info/masses.py +21 -20
  71. biotite/structure/info/misc.py +11 -22
  72. biotite/structure/info/standardize.py +17 -12
  73. biotite/structure/io/__init__.py +2 -4
  74. biotite/structure/io/ctab.py +1 -1
  75. biotite/structure/io/general.py +37 -43
  76. biotite/structure/io/mmtf/__init__.py +3 -0
  77. biotite/structure/io/mmtf/convertarray.c +528 -365
  78. biotite/structure/io/mmtf/convertarray.cp311-win_amd64.pyd +0 -0
  79. biotite/structure/io/mmtf/convertfile.c +725 -676
  80. biotite/structure/io/mmtf/convertfile.cp311-win_amd64.pyd +0 -0
  81. biotite/structure/io/mmtf/decode.c +1070 -754
  82. biotite/structure/io/mmtf/decode.cp311-win_amd64.pyd +0 -0
  83. biotite/structure/io/mmtf/encode.c +727 -677
  84. biotite/structure/io/mmtf/encode.cp311-win_amd64.pyd +0 -0
  85. biotite/structure/io/mmtf/file.py +34 -26
  86. biotite/structure/io/npz/__init__.py +3 -0
  87. biotite/structure/io/npz/file.py +21 -18
  88. biotite/structure/io/pdb/__init__.py +3 -3
  89. biotite/structure/io/pdb/file.py +72 -70
  90. biotite/structure/io/pdb/hybrid36.c +540 -478
  91. biotite/structure/io/pdb/hybrid36.cp311-win_amd64.pyd +0 -0
  92. biotite/structure/io/pdbqt/file.py +82 -68
  93. biotite/structure/io/pdbx/__init__.py +13 -6
  94. biotite/structure/io/pdbx/bcif.py +649 -0
  95. biotite/structure/io/pdbx/cif.py +1028 -0
  96. biotite/structure/io/pdbx/component.py +243 -0
  97. biotite/structure/io/pdbx/convert.py +707 -359
  98. biotite/structure/io/pdbx/encoding.c +112813 -0
  99. biotite/structure/io/pdbx/encoding.cp311-win_amd64.pyd +0 -0
  100. biotite/structure/io/pdbx/error.py +14 -0
  101. biotite/structure/io/pdbx/legacy.py +267 -0
  102. biotite/structure/molecules.py +151 -151
  103. biotite/structure/residues.py +40 -40
  104. biotite/structure/sasa.c +713 -644
  105. biotite/structure/sasa.cp311-win_amd64.pyd +0 -0
  106. biotite/structure/superimpose.py +158 -115
  107. biotite/visualize.py +9 -11
  108. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/METADATA +2 -2
  109. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/RECORD +112 -102
  110. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/WHEEL +1 -1
  111. biotite/structure/info/amino_acids.json +0 -1556
  112. biotite/structure/info/amino_acids.py +0 -42
  113. biotite/structure/info/carbohydrates.json +0 -1122
  114. biotite/structure/info/carbohydrates.py +0 -39
  115. biotite/structure/info/intra_bonds.msgpack +0 -0
  116. biotite/structure/info/link_types.msgpack +0 -1
  117. biotite/structure/info/nucleotides.json +0 -772
  118. biotite/structure/info/nucleotides.py +0 -39
  119. biotite/structure/info/residue_masses.msgpack +0 -0
  120. biotite/structure/info/residue_names.msgpack +0 -3
  121. biotite/structure/info/residues.msgpack +0 -0
  122. biotite/structure/io/pdbx/file.py +0 -652
  123. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/LICENSE.rst +0 -0
  124. {biotite-0.38.0.dist-info → biotite-0.40.0.dist-info}/top_level.txt +0 -0
@@ -1,10 +1,10 @@
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- biotite/__init__.py,sha256=LGd3I_NCGIkCs_3vSFb-zLC75ElWgrtFb84uBX3r7_0,543
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+ biotite/__init__.py,sha256=idLYRVttRoHGTws624jHvtwxXEg0zyjQek4xaHbip1s,541
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  biotite/copyable.py,sha256=bS6JvqiG2G-8Kav7hzJb2mhO0mSpgjFvm_LD_t9dTLA,2042
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  biotite/file.py,sha256=M7FlQdNOUjDOBjkLMrzPq-xljwEFe93jFCLrFV6rprw,7578
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  biotite/temp.py,sha256=zROAfIdwaqso8_cvpVkCM37LNtzpke-XIoidHZkDnuY,2130
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- biotite/visualize.py,sha256=kwOd6IKxfNrIQHNu8XNSDFyuVYaompOVuUUCN6UtloQ,10223
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+ biotite/visualize.py,sha256=yuQJEwZhfbXPR8tWKUywusP1puFlLc_DAbctY_nCrhM,10092
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  biotite/application/__init__.py,sha256=k1y1IgbK_vZJdHbQt4cgNgR1auc-riGcjrb5rkhyQuQ,1778
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- biotite/application/application.py,sha256=VMWjLuQzlQX-LaAKaKA_ofCy6hrwiUM2rwgkunCOEFs,8363
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+ biotite/application/application.py,sha256=MsmH0iopsHenUDoijuDcbE9TGQBPgWgOFp9N5XD4tEU,8393
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  biotite/application/localapp.py,sha256=B4OdFmn6UaKXB9KEP1fKDnvXuO0qJqe2UFpZs1twA_0,9755
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@@ -17,14 +17,14 @@ biotite/application/blast/webapp.py,sha256=J_uRQMFMdCOyGP-kEaXRNLgDHopUU68Wcuru5
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  biotite/application/clustalo/__init__.py,sha256=11hGCckaAM6MOv9krf585L5-7JAgRMJv2bxv3UlrgAQ,336
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  biotite/application/dssp/__init__.py,sha256=ILnVuoQhzPQRXDyDVVu2_I4xCejdRtQY8PbsM1UExos,333
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- biotite/application/dssp/app.py,sha256=l9J7VxfXP5WlpoCa-GZiNT1Vv5Tsyt73IwdbtsVkMd0,5081
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+ biotite/application/dssp/app.py,sha256=g2z5u8bty5NxVNufaYavBECg65UlqWpSn98BShblxFg,4980
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  biotite/application/mafft/__init__.py,sha256=AtmjXcE6WsWc8JxbcmUtIHDqPBh8cH1XTZrxWlEihx8,325
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  biotite/application/muscle/__init__.py,sha256=22UWh76stefAwlwMayawfD9kJTjlsXdUfgrsnVze8Bw,349
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  biotite/application/muscle/app5.py,sha256=nERqI3e3sVk8dJOPQlP5QgE2M-HOSR3jB06403iJbZk,4970
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- biotite/application/sra/__init__.py,sha256=ksyjhj-V-SIWJJfDoixA4GVpCgzafKpdzmqNNEiVQ7w,355
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- biotite/application/sra/app.py,sha256=H0ezpFIn4dCF9-8IuuUlQKerYOJw4sw3VcIwz4a4Qdo,6713
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+ biotite/application/sra/__init__.py,sha256=NVKKZ3jXNG5Iiz0NEXnRgqc0Cnu1GA8YicZfym3UK04,569
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+ biotite/application/sra/app.py,sha256=CBLpjc3PGkBXCqLBJuZhhmBpIHp7Zvx_EKGDb8tI0D0,16353
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  biotite/application/tantan/__init__.py,sha256=OM2nQgJMs1a67VhZfZf7OoZX8E5ftlunKWqJeyiTNbk,338
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@@ -34,19 +34,20 @@ biotite/application/viennarna/rnaplot.py,sha256=f6huuTtb6ocAMYAx0isrYTmlQ4x9pMDF
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- biotite/database/entrez/__init__.py,sha256=CFQUvB2h_AersTS_rJXxaMctuNVivygKoZGPAkYy9Lo,381
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- biotite/database/entrez/check.py,sha256=qNJJfvHQ7dn_twuGoDtSVPHAxAQiwdN163YdmiNbjVU,1546
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+ biotite/database/entrez/__init__.py,sha256=bV79S80mgbqSs7wnWyRzMzWuKfYDNd3D7DOJCnoPVYg,401
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+ biotite/database/entrez/check.py,sha256=9GZlumJwjj6f68l-tgwOtTYBtgd1HV5RQknbncLCY9g,1898
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- biotite/database/entrez/download.py,sha256=Mjmt1sJ6Ty3JtqSImFkpe5DNkuMytXY29_at4RNMeUI,7435
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- biotite/database/entrez/query.py,sha256=ygWtjUTXiSL1G6KMZhQbsvKISoisDtB2IBpa8m61Jno,7026
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+ biotite/database/entrez/download.py,sha256=Ieqx9Rx_A36RZiEMzuY1pw8CXEnofHguLQ9qRDDY0gI,7647
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+ biotite/database/entrez/key.py,sha256=XSaqJT7IhbGI1UUZNmgbu0elKJ9KWRvxHhOS6aw8QhI,1154
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+ biotite/database/entrez/query.py,sha256=n55TM0yhJVhywTA60o159_GDrnff3kfxXrS5MbrE76o,7245
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- biotite/database/pubchem/query.py,sha256=GaktG4ZwmlXP6319cnkHYFvCTvmc7e9t1sy_JomuGSE,27437
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+ biotite/database/pubchem/query.py,sha256=JhmrlulVF0FAFf92fmCipXkMALqTZgv9EV93pDcDxvs,27267
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- biotite/database/rcsb/download.py,sha256=aZkP5KrrEChhhZgOv-PKnAiVmfbVBxRTI-lJrRLutL8,5949
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- biotite/database/rcsb/query.py,sha256=e7qy1I_nUj_XHxBTevWjq6H_lmOndXPHxRyiE8k2KEc,34221
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+ biotite/database/rcsb/download.py,sha256=ZlbYbAvCsri4NnpDvaLeCSTJUSlz6etQOExd_301rN0,6163
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+ biotite/database/rcsb/query.py,sha256=CzV9YOujbyjmIv-2OuLVJN3iHC4WiOAaNcZfnPC7muc,34023
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+ biotite/sequence/codec.c,sha256=iJ3FkIQFGXipN-KD7huu2VENylRb8IVFFPPgEXASq-s,1529118
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+ biotite/sequence/codec.cp311-win_amd64.pyd,sha256=hcjET8vMIlIfswXmX6nb1xB4Cb7nYtnM-77oozZowsU,240640
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- biotite/sequence/align/__init__.py,sha256=NrTZtqlkeTEN8zdIw9-yDuQ4RDuChlBS76_Yp51Xhmk,1654
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+ biotite/sequence/align/__init__.py,sha256=0nXg-din6JaXqPAZsv9yf0F7YICjNsXTc4erZotaF10,1752
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- biotite/sequence/align/banded.c,sha256=kC85Y4MX6uhgc0QNWApO4BCu0utwn4ygaUZLxG6yKY0,2565453
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- biotite/sequence/align/banded.cp311-win_amd64.pyd,sha256=Od5H_9dtJvdwb6biCAGYDnxhq1XCCmoeaZ7uzqtETro,492032
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- biotite/sequence/align/kmeralphabet.c,sha256=2C3kgACxQELv3CFS4gBSb5QLFPULFco4GhfuXkU6ceU,1900240
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- biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd,sha256=jLOi1OteSf3IfMJt45VGcW8UKDKDkzkeVyCE2tsytdc,306688
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- biotite/sequence/align/kmersimilarity.c,sha256=Kt19QCJrhmtyg26pdnfyCXoW_vCm4RnPbkI5jf2-iIc,1250571
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- biotite/sequence/align/kmersimilarity.cp311-win_amd64.pyd,sha256=RFvbRJVQWrUKb86_SqFsaObyl_ZmKnN4o-ZBQ4YmhVA,172544
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- biotite/sequence/align/kmertable.c,sha256=WcgHAm5i0bFAZ81A35e6kbujnvr8zYMeKzU5Fjqilj4,2008084
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+ biotite/sequence/align/primes.txt,sha256=XcNX2_hYQI4H-8MPvZH1oiYeQ1lfxU8rBvuwMlcQa3Y,10961
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+ biotite/sequence/align/tracetable.c,sha256=sVZt-oEryd7dlxDt3CwwP5Xx5ts6z19IQTuAeoSWLVU,1219044
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@@ -208,7 +216,7 @@ biotite/sequence/io/fastq/__init__.py,sha256=9gwrwPLZ-2-3AU-PIBKxJfs9DmB4I9mCMup
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- biotite/sequence/io/genbank/annotation.py,sha256=F7sBzDSRGZ6o0e9ebdBpJYy7MULCNLAYLGhj8OPI7YI,9773
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+ biotite/sequence/io/genbank/annotation.py,sha256=945xm68XyzKWodNSwlBxZi1TMCCIHiK-G3U1crZHWvg,9731
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+ biotite/sequence/phylo/nj.c,sha256=ZGjmXblCfqNkRuw0jEwzoMyhHG0fv-eG_C49hQoA0nQ,1221174
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- biotite/structure/charges.cp311-win_amd64.pyd,sha256=MRxQy5PFEEVROe20RpCOSnoELDc5cKFFjJoTg0IiRDI,215552
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+ biotite/structure/charges.c,sha256=gd8CizGGVI6dxTsH6_pzd6m4xKSKUm5G5ZnfmYLUB0I,1410335
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+ biotite/structure/superimpose.py,sha256=DRGkXYeHOX1sM4S_xHBOY_mrLGoFy5hvOGeuCybFKVc,9352
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+ biotite/structure/info/__init__.py,sha256=zIRFQGmBG-XWfuID8Xr2vp6o70DdbdH1x8QXMn78MUY,727
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- biotite/structure/info/carbohydrates.json,sha256=kc6-oNoMKzoagwbOJDyeF0cN-HGB7twhXGrCFQmramY,10083
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