biotite 0.39.0__cp311-cp311-macosx_11_0_arm64.whl → 0.40.0__cp311-cp311-macosx_11_0_arm64.whl

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  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-311-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.c +243 -222
  7. biotite/sequence/align/kmeralphabet.cpython-311-darwin.so +0 -0
  8. biotite/sequence/align/kmersimilarity.c +215 -196
  9. biotite/sequence/align/kmersimilarity.cpython-311-darwin.so +0 -0
  10. biotite/sequence/align/kmertable.cpp +233 -205
  11. biotite/sequence/align/kmertable.cpython-311-darwin.so +0 -0
  12. biotite/sequence/align/localgapped.c +258 -237
  13. biotite/sequence/align/localgapped.cpython-311-darwin.so +0 -0
  14. biotite/sequence/align/localungapped.c +235 -214
  15. biotite/sequence/align/localungapped.cpython-311-darwin.so +0 -0
  16. biotite/sequence/align/multiple.c +255 -234
  17. biotite/sequence/align/multiple.cpython-311-darwin.so +0 -0
  18. biotite/sequence/align/pairwise.c +274 -253
  19. biotite/sequence/align/pairwise.cpython-311-darwin.so +0 -0
  20. biotite/sequence/align/permutation.c +215 -196
  21. biotite/sequence/align/permutation.cpython-311-darwin.so +0 -0
  22. biotite/sequence/align/selector.c +217 -197
  23. biotite/sequence/align/selector.cpython-311-darwin.so +0 -0
  24. biotite/sequence/align/tracetable.c +215 -195
  25. biotite/sequence/align/tracetable.cpython-311-darwin.so +0 -0
  26. biotite/sequence/codec.c +235 -214
  27. biotite/sequence/codec.cpython-311-darwin.so +0 -0
  28. biotite/sequence/phylo/nj.c +215 -196
  29. biotite/sequence/phylo/nj.cpython-311-darwin.so +0 -0
  30. biotite/sequence/phylo/tree.c +227 -202
  31. biotite/sequence/phylo/tree.cpython-311-darwin.so +0 -0
  32. biotite/sequence/phylo/upgma.c +215 -196
  33. biotite/sequence/phylo/upgma.cpython-311-darwin.so +0 -0
  34. biotite/structure/basepairs.py +7 -12
  35. biotite/structure/bonds.c +1175 -1226
  36. biotite/structure/bonds.cpython-311-darwin.so +0 -0
  37. biotite/structure/celllist.c +217 -197
  38. biotite/structure/celllist.cpython-311-darwin.so +0 -0
  39. biotite/structure/charges.c +1052 -1101
  40. biotite/structure/charges.cpython-311-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-311-darwin.so +0 -0
  61. biotite/structure/io/mmtf/convertfile.c +217 -197
  62. biotite/structure/io/mmtf/convertfile.cpython-311-darwin.so +0 -0
  63. biotite/structure/io/mmtf/decode.c +225 -204
  64. biotite/structure/io/mmtf/decode.cpython-311-darwin.so +0 -0
  65. biotite/structure/io/mmtf/encode.c +215 -196
  66. biotite/structure/io/mmtf/encode.cpython-311-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-311-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-311-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-311-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/io/pdbqt/file.py CHANGED
@@ -42,48 +42,48 @@ class PDBQTFile(TextFile):
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  >>> mask = file.set_structure(ligand, rotatable_bonds="all")
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  >>> # Print removed nonpolar hydrogen atoms
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  >>> print(ligand[~mask])
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- HET 0 BTN H101 H 3.745 1.171 0.974
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- HET 0 BTN H102 H 4.071 1.343 -0.767
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- HET 0 BTN H91 H 2.802 -0.740 -1.211
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- HET 0 BTN H92 H 2.476 -0.912 0.530
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- HET 0 BTN H81 H 1.289 1.265 0.523
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- HET 0 BTN H82 H 1.616 1.437 -1.218
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- HET 0 BTN H71 H 0.346 -0.646 -1.662
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- HET 0 BTN H72 H 0.020 -0.818 0.079
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- HET 0 BTN H2 H -0.838 1.576 -1.627
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- HET 0 BTN H61 H -3.797 1.837 1.286
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- HET 0 BTN H62 H -3.367 2.738 -0.205
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- HET 0 BTN H5 H -4.307 0.812 -1.205
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- HET 0 BTN H4 H -2.451 -0.038 -2.252
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+ HET 0 BTN H101 H 3.740 1.170 0.970
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+ HET 0 BTN H102 H 4.070 1.340 -0.770
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+ HET 0 BTN H91 H 2.800 -0.740 -1.210
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+ HET 0 BTN H92 H 2.480 -0.910 0.530
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+ HET 0 BTN H81 H 1.290 1.260 0.520
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+ HET 0 BTN H82 H 1.620 1.440 -1.220
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+ HET 0 BTN H71 H 0.350 -0.650 -1.660
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+ HET 0 BTN H72 H 0.020 -0.820 0.080
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+ HET 0 BTN H2 H -0.840 1.580 -1.630
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+ HET 0 BTN H61 H -3.800 1.840 1.290
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+ HET 0 BTN H62 H -3.370 2.740 -0.200
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+ HET 0 BTN H5 H -4.310 0.810 -1.210
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+ HET 0 BTN H4 H -2.450 -0.040 -2.250
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  >>> print(file)
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  ROOT
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- HETATM 1 C11 BTN 0 5.089 -0.280 0.173 1.00 0.00 0.258 C
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- HETATM 2 O11 BTN 0 4.956 -1.473 0.030 1.00 0.00 -0.264 OA
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+ HETATM 1 C11 BTN 0 5.090 -0.280 0.170 1.00 0.00 0.258 C
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+ HETATM 2 O11 BTN 0 4.960 -1.470 0.030 1.00 0.00 -0.264 OA
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  ENDROOT
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  BRANCH 1 3
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- HETATM 3 O12 BTN 0 6.299 0.233 0.444 1.00 0.00 -0.331 OA
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- HETATM 17 HO2 BTN 0 7.034 -0.391 0.517 1.00 0.00 0.221 HD
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+ HETATM 3 O12 BTN 0 6.300 0.230 0.440 1.00 0.00 -0.331 OA
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+ HETATM 17 HO2 BTN 0 7.030 -0.390 0.520 1.00 0.00 0.221 HD
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66
  ENDBRANCH 1 3
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  BRANCH 1 4
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- HETATM 4 C10 BTN 0 3.896 0.631 0.039 1.00 0.00 0.105 C
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+ HETATM 4 C10 BTN 0 3.900 0.630 0.040 1.00 0.00 0.105 C
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69
  BRANCH 4 5
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- HETATM 5 C9 BTN 0 2.651 -0.200 -0.276 1.00 0.00 0.010 C
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+ HETATM 5 C9 BTN 0 2.650 -0.200 -0.280 1.00 0.00 0.010 C
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71
  BRANCH 5 6
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- HETATM 6 C8 BTN 0 1.440 0.725 -0.412 1.00 0.00 0.002 C
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+ HETATM 6 C8 BTN 0 1.440 0.720 -0.410 1.00 0.00 0.002 C
73
73
  BRANCH 6 7
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- HETATM 7 C7 BTN 0 0.196 -0.106 -0.727 1.00 0.00 0.016 C
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+ HETATM 7 C7 BTN 0 0.200 -0.110 -0.730 1.00 0.00 0.016 C
75
75
  BRANCH 7 8
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- HETATM 8 C2 BTN 0 -1.015 0.819 -0.863 1.00 0.00 0.065 C
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- HETATM 9 S1 BTN 0 -1.419 1.604 0.751 1.00 0.00 -0.154 SA
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- HETATM 10 C6 BTN 0 -3.205 1.827 0.371 1.00 0.00 0.090 C
79
- HETATM 11 C5 BTN 0 -3.530 0.581 -0.476 1.00 0.00 0.091 C
80
- HETATM 12 N1 BTN 0 -3.970 -0.507 0.412 1.00 0.00 -0.239 NA
81
- HETATM 13 C3 BTN 0 -3.141 -1.549 0.271 1.00 0.00 0.272 C
82
- HETATM 14 O3 BTN 0 -3.271 -2.589 0.888 1.00 0.00 -0.259 OA
83
- HETATM 15 N2 BTN 0 -2.154 -1.343 -0.612 1.00 0.00 -0.239 NA
84
- HETATM 16 C4 BTN 0 -2.289 0.010 -1.175 1.00 0.00 0.093 C
85
- HETATM 18 HN1 BTN 0 -4.738 -0.474 1.004 1.00 0.00 0.132 HD
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- HETATM 19 HN2 BTN 0 -1.462 -1.982 -0.843 1.00 0.00 0.132 HD
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+ HETATM 8 C2 BTN 0 -1.020 0.820 -0.860 1.00 0.00 0.065 C
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+ HETATM 9 S1 BTN 0 -1.420 1.600 0.750 1.00 0.00 -0.154 SA
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+ HETATM 10 C6 BTN 0 -3.200 1.830 0.370 1.00 0.00 0.090 C
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+ HETATM 11 C5 BTN 0 -3.530 0.580 -0.480 1.00 0.00 0.091 C
80
+ HETATM 12 N1 BTN 0 -3.970 -0.510 0.410 1.00 0.00 -0.239 NA
81
+ HETATM 13 C3 BTN 0 -3.140 -1.550 0.270 1.00 0.00 0.272 C
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+ HETATM 14 O3 BTN 0 -3.270 -2.590 0.890 1.00 0.00 -0.259 OA
83
+ HETATM 15 N2 BTN 0 -2.150 -1.340 -0.610 1.00 0.00 -0.239 NA
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+ HETATM 16 C4 BTN 0 -2.290 0.010 -1.170 1.00 0.00 0.093 C
85
+ HETATM 18 HN1 BTN 0 -4.740 -0.470 1.000 1.00 0.00 0.132 HD
86
+ HETATM 19 HN2 BTN 0 -1.460 -1.980 -0.840 1.00 0.00 0.132 HD
87
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  ENDBRANCH 7 8
88
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  ENDBRANCH 6 7
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  ENDBRANCH 5 6
biotite/structure/io/pdbx/__init__.py CHANGED
@@ -3,15 +3,22 @@
3
3
  # information.
4
4
 
5
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  """
6
- This subpackage provides support for the the modern PDBx/mmCIF file
7
- format. The :class:`PDBxFile` class provides dictionary-like access to
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- every field in PDBx/mmCIF files.
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- Additional utility functions allow conversion of these dictionaries to
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- :class:`AtomArray` and :class:`AtomArrayStack` objects and vice versa.
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+ This subpackage provides support for the the modern PDBx file formats.
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+ The :class:`CIFFile` class provides dictionary-like access to
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+ every field in text-based *mmCIF* files.
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+ :class:`BinaryCIFFile` provides analogous functionality for the
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+ *BinaryCIF* format.
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+ Additional utility functions allow reading and writing structures
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+ from/to these files.
11
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  """
12
14
 
13
15
  __name__ = "biotite.structure.io.pdbx"
14
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  __author__ = "Patrick Kunzmann"
15
17
 
16
18
  from .convert import *
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- from .file import *
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+ from .bcif import *
20
+ from .cif import *
21
+ from .component import *
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+ from .encoding import *
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+ from .error import *
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+ from .legacy import *