biotite 0.38.0__cp310-cp310-win_amd64.whl → 0.40.0__cp310-cp310-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.cp310-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.cp310-win_amd64.pyd +0 -0
  21. biotite/sequence/align/kmersimilarity.c +713 -663
  22. biotite/sequence/align/kmersimilarity.cp310-win_amd64.pyd +0 -0
  23. biotite/sequence/align/kmertable.cp310-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.cp310-win_amd64.pyd +0 -0
  27. biotite/sequence/align/localungapped.c +1143 -833
  28. biotite/sequence/align/localungapped.cp310-win_amd64.pyd +0 -0
  29. biotite/sequence/align/multiple.c +1569 -1092
  30. biotite/sequence/align/multiple.cp310-win_amd64.pyd +0 -0
  31. biotite/sequence/align/pairwise.c +1612 -1212
  32. biotite/sequence/align/pairwise.cp310-win_amd64.pyd +0 -0
  33. biotite/sequence/align/permutation.c +33259 -0
  34. biotite/sequence/align/permutation.cp310-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.cp310-win_amd64.pyd +0 -0
  38. biotite/sequence/align/tracetable.c +685 -646
  39. biotite/sequence/align/tracetable.cp310-win_amd64.pyd +0 -0
  40. biotite/sequence/codec.c +1159 -841
  41. biotite/sequence/codec.cp310-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.cp310-win_amd64.pyd +0 -0
  46. biotite/sequence/phylo/tree.c +970 -673
  47. biotite/sequence/phylo/tree.cp310-win_amd64.pyd +0 -0
  48. biotite/sequence/phylo/upgma.c +672 -626
  49. biotite/sequence/phylo/upgma.cp310-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.cp310-win_amd64.pyd +0 -0
  55. biotite/structure/celllist.c +727 -707
  56. biotite/structure/celllist.cp310-win_amd64.pyd +0 -0
  57. biotite/structure/charges.c +1561 -1560
  58. biotite/structure/charges.cp310-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.cp310-win_amd64.pyd +0 -0
  79. biotite/structure/io/mmtf/convertfile.c +725 -676
  80. biotite/structure/io/mmtf/convertfile.cp310-win_amd64.pyd +0 -0
  81. biotite/structure/io/mmtf/decode.c +1070 -754
  82. biotite/structure/io/mmtf/decode.cp310-win_amd64.pyd +0 -0
  83. biotite/structure/io/mmtf/encode.c +727 -677
  84. biotite/structure/io/mmtf/encode.cp310-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.cp310-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.cp310-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.cp310-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