biotite 0.39.0__cp310-cp310-macosx_11_0_arm64.whl → 0.40.0__cp310-cp310-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 +258 -237
  5. biotite/sequence/align/banded.cpython-310-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.c +243 -222
  7. biotite/sequence/align/kmeralphabet.cpython-310-darwin.so +0 -0
  8. biotite/sequence/align/kmersimilarity.c +215 -196
  9. biotite/sequence/align/kmersimilarity.cpython-310-darwin.so +0 -0
  10. biotite/sequence/align/kmertable.cpp +233 -205
  11. biotite/sequence/align/kmertable.cpython-310-darwin.so +0 -0
  12. biotite/sequence/align/localgapped.c +258 -237
  13. biotite/sequence/align/localgapped.cpython-310-darwin.so +0 -0
  14. biotite/sequence/align/localungapped.c +235 -214
  15. biotite/sequence/align/localungapped.cpython-310-darwin.so +0 -0
  16. biotite/sequence/align/multiple.c +255 -234
  17. biotite/sequence/align/multiple.cpython-310-darwin.so +0 -0
  18. biotite/sequence/align/pairwise.c +274 -253
  19. biotite/sequence/align/pairwise.cpython-310-darwin.so +0 -0
  20. biotite/sequence/align/permutation.c +215 -196
  21. biotite/sequence/align/permutation.cpython-310-darwin.so +0 -0
  22. biotite/sequence/align/selector.c +217 -197
  23. biotite/sequence/align/selector.cpython-310-darwin.so +0 -0
  24. biotite/sequence/align/tracetable.c +215 -195
  25. biotite/sequence/align/tracetable.cpython-310-darwin.so +0 -0
  26. biotite/sequence/codec.c +235 -214
  27. biotite/sequence/codec.cpython-310-darwin.so +0 -0
  28. biotite/sequence/phylo/nj.c +215 -196
  29. biotite/sequence/phylo/nj.cpython-310-darwin.so +0 -0
  30. biotite/sequence/phylo/tree.c +227 -202
  31. biotite/sequence/phylo/tree.cpython-310-darwin.so +0 -0
  32. biotite/sequence/phylo/upgma.c +215 -196
  33. biotite/sequence/phylo/upgma.cpython-310-darwin.so +0 -0
  34. biotite/structure/basepairs.py +7 -12
  35. biotite/structure/bonds.c +1175 -1226
  36. biotite/structure/bonds.cpython-310-darwin.so +0 -0
  37. biotite/structure/celllist.c +217 -197
  38. biotite/structure/celllist.cpython-310-darwin.so +0 -0
  39. biotite/structure/charges.c +1052 -1101
  40. biotite/structure/charges.cpython-310-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 +219 -198
  60. biotite/structure/io/mmtf/convertarray.cpython-310-darwin.so +0 -0
  61. biotite/structure/io/mmtf/convertfile.c +217 -197
  62. biotite/structure/io/mmtf/convertfile.cpython-310-darwin.so +0 -0
  63. biotite/structure/io/mmtf/decode.c +225 -204
  64. biotite/structure/io/mmtf/decode.cpython-310-darwin.so +0 -0
  65. biotite/structure/io/mmtf/encode.c +215 -196
  66. biotite/structure/io/mmtf/encode.cpython-310-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-310-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 +112813 -0
  81. biotite/structure/io/pdbx/encoding.cpython-310-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 +215 -196
  86. biotite/structure/sasa.cpython-310-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
biotite/structure/info/nucleotides.py DELETED
@@ -1,39 +0,0 @@
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- # This source code is part of the Biotite package and is distributed
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- # under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
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- # information.
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-
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- __name__ = "biotite.structure.info"
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- __author__ = "Tom David Müller"
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- __all__ = ["nucleotide_names"]
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-
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- import json
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- import numpy as np
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- from os.path import join, dirname, realpath
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-
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-
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- _info_dir = dirname(realpath(__file__))
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- # Data is taken from
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- # ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif
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- # (2022/09/17)
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- # The json-file contains all three-letter-codes of the components where
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- # the data item `_chem_comp.type` is equal to one of the following
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- # values:
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- # DNA LINKING; DNA OH 3 PRIME TERMINUS; DNA OH 3 prime terminus;
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- # DNA OH 5 prime terminus; DNA linking; L-DNA LINKING; L-DNA linking;
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- # L-RNA LINKING; L-RNA linking; RNA LINKING; RNA OH 3 prime terminus;
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- # RNA OH 5 prime terminus; RNA linking
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- with open(join(_info_dir, "nucleotides.json"), "r") as file:
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- _nucleotides = json.load(file)
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-
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- def nucleotide_names():
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- """
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- Get a list of nucleotide three-letter codes according to the PDB
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- chemical compound dictionary.
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-
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- Returns
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- -------
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- nucleotide_names : list
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- A list of three-letter-codes containing residues that are
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- DNA/RNA monomers.
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- """
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- return _nucleotides