biotite 0.39.0__cp312-cp312-macosx_11_0_arm64.whl → 0.41.0__cp312-cp312-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/pubchem/download.py +23 -23
  4. biotite/database/pubchem/query.py +7 -7
  5. biotite/database/rcsb/download.py +19 -14
  6. biotite/file.py +17 -9
  7. biotite/sequence/align/banded.c +256 -235
  8. biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
  9. biotite/sequence/align/cigar.py +60 -15
  10. biotite/sequence/align/kmeralphabet.c +241 -220
  11. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  12. biotite/sequence/align/kmersimilarity.c +213 -194
  13. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  14. biotite/sequence/align/kmertable.cpp +231 -203
  15. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  16. biotite/sequence/align/localgapped.c +256 -235
  17. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  18. biotite/sequence/align/localungapped.c +233 -212
  19. biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
  20. biotite/sequence/align/multiple.c +253 -232
  21. biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
  22. biotite/sequence/align/pairwise.c +272 -251
  23. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  24. biotite/sequence/align/permutation.c +213 -194
  25. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  26. biotite/sequence/align/selector.c +215 -195
  27. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  28. biotite/sequence/align/tracetable.c +213 -193
  29. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  30. biotite/sequence/annotation.py +2 -2
  31. biotite/sequence/codec.c +233 -212
  32. biotite/sequence/codec.cpython-312-darwin.so +0 -0
  33. biotite/sequence/io/fasta/convert.py +27 -24
  34. biotite/sequence/phylo/nj.c +213 -194
  35. biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
  36. biotite/sequence/phylo/tree.c +225 -200
  37. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  38. biotite/sequence/phylo/upgma.c +213 -194
  39. biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
  40. biotite/structure/__init__.py +2 -0
  41. biotite/structure/basepairs.py +7 -12
  42. biotite/structure/bonds.c +1435 -1277
  43. biotite/structure/bonds.cpython-312-darwin.so +0 -0
  44. biotite/structure/celllist.c +215 -195
  45. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  46. biotite/structure/charges.c +1050 -1099
  47. biotite/structure/charges.cpython-312-darwin.so +0 -0
  48. biotite/structure/dotbracket.py +2 -0
  49. biotite/structure/filter.py +30 -37
  50. biotite/structure/info/__init__.py +5 -8
  51. biotite/structure/info/atoms.py +31 -68
  52. biotite/structure/info/bonds.py +47 -101
  53. biotite/structure/info/ccd/README.rst +8 -0
  54. biotite/structure/info/ccd/amino_acids.txt +1663 -0
  55. biotite/structure/info/ccd/carbohydrates.txt +1135 -0
  56. biotite/structure/info/ccd/components.bcif +0 -0
  57. biotite/structure/info/ccd/nucleotides.txt +798 -0
  58. biotite/structure/info/ccd.py +95 -0
  59. biotite/structure/info/groups.py +90 -0
  60. biotite/structure/info/masses.py +21 -20
  61. biotite/structure/info/misc.py +78 -25
  62. biotite/structure/info/standardize.py +17 -12
  63. biotite/structure/integrity.py +19 -70
  64. biotite/structure/io/__init__.py +2 -4
  65. biotite/structure/io/ctab.py +12 -106
  66. biotite/structure/io/general.py +167 -181
  67. biotite/structure/io/gro/file.py +16 -16
  68. biotite/structure/io/mmtf/__init__.py +3 -0
  69. biotite/structure/io/mmtf/convertarray.c +217 -196
  70. biotite/structure/io/mmtf/convertarray.cpython-312-darwin.so +0 -0
  71. biotite/structure/io/mmtf/convertfile.c +215 -195
  72. biotite/structure/io/mmtf/convertfile.cpython-312-darwin.so +0 -0
  73. biotite/structure/io/mmtf/decode.c +223 -202
  74. biotite/structure/io/mmtf/decode.cpython-312-darwin.so +0 -0
  75. biotite/structure/io/mmtf/encode.c +213 -194
  76. biotite/structure/io/mmtf/encode.cpython-312-darwin.so +0 -0
  77. biotite/structure/io/mmtf/file.py +34 -26
  78. biotite/structure/io/mol/__init__.py +4 -2
  79. biotite/structure/io/mol/convert.py +71 -7
  80. biotite/structure/io/mol/ctab.py +414 -0
  81. biotite/structure/io/mol/header.py +116 -0
  82. biotite/structure/io/mol/{file.py → mol.py} +69 -82
  83. biotite/structure/io/mol/sdf.py +909 -0
  84. biotite/structure/io/npz/__init__.py +3 -0
  85. biotite/structure/io/npz/file.py +21 -18
  86. biotite/structure/io/pdb/__init__.py +3 -3
  87. biotite/structure/io/pdb/file.py +89 -34
  88. biotite/structure/io/pdb/hybrid36.c +63 -43
  89. biotite/structure/io/pdb/hybrid36.cpython-312-darwin.so +0 -0
  90. biotite/structure/io/pdbqt/file.py +32 -32
  91. biotite/structure/io/pdbx/__init__.py +12 -6
  92. biotite/structure/io/pdbx/bcif.py +648 -0
  93. biotite/structure/io/pdbx/cif.py +1032 -0
  94. biotite/structure/io/pdbx/component.py +246 -0
  95. biotite/structure/io/pdbx/convert.py +858 -386
  96. biotite/structure/io/pdbx/encoding.c +112803 -0
  97. biotite/structure/io/pdbx/encoding.cpython-312-darwin.so +0 -0
  98. biotite/structure/io/pdbx/legacy.py +267 -0
  99. biotite/structure/molecules.py +151 -151
  100. biotite/structure/repair.py +253 -0
  101. biotite/structure/sasa.c +213 -194
  102. biotite/structure/sasa.cpython-312-darwin.so +0 -0
  103. biotite/structure/sequence.py +112 -0
  104. biotite/structure/superimpose.py +618 -116
  105. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/METADATA +3 -3
  106. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/RECORD +109 -103
  107. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/WHEEL +1 -1
  108. biotite/structure/info/amino_acids.json +0 -1556
  109. biotite/structure/info/amino_acids.py +0 -42
  110. biotite/structure/info/carbohydrates.json +0 -1122
  111. biotite/structure/info/carbohydrates.py +0 -39
  112. biotite/structure/info/intra_bonds.msgpack +0 -0
  113. biotite/structure/info/link_types.msgpack +0 -1
  114. biotite/structure/info/nucleotides.json +0 -772
  115. biotite/structure/info/nucleotides.py +0 -39
  116. biotite/structure/info/residue_masses.msgpack +0 -0
  117. biotite/structure/info/residue_names.msgpack +0 -3
  118. biotite/structure/info/residues.msgpack +0 -0
  119. biotite/structure/io/pdbx/file.py +0 -652
  120. {biotite-0.39.0.dist-info → biotite-0.41.0.dist-info}/LICENSE.rst +0 -0
  121. {biotite-0.39.0.dist-info → biotite-0.41.0.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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42
  >>> 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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58
  >>> print(file)
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59
  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
62
62
  ENDROOT
63
63
  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
65
+ HETATM 17 HO2 BTN 0 7.030 -0.390 0.520 1.00 0.00 0.221 HD
66
66
  ENDBRANCH 1 3
67
67
  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
68
+ HETATM 4 C10 BTN 0 3.900 0.630 0.040 1.00 0.00 0.105 C
69
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
71
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
74
- HETATM 7 C7 BTN 0 0.196 -0.106 -0.727 1.00 0.00 0.016 C
74
+ HETATM 7 C7 BTN 0 0.200 -0.110 -0.730 1.00 0.00 0.016 C
75
75
  BRANCH 7 8
76
- HETATM 8 C2 BTN 0 -1.015 0.819 -0.863 1.00 0.00 0.065 C
77
- HETATM 9 S1 BTN 0 -1.419 1.604 0.751 1.00 0.00 -0.154 SA
78
- 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
86
- HETATM 19 HN2 BTN 0 -1.462 -1.982 -0.843 1.00 0.00 0.132 HD
76
+ HETATM 8 C2 BTN 0 -1.020 0.820 -0.860 1.00 0.00 0.065 C
77
+ HETATM 9 S1 BTN 0 -1.420 1.600 0.750 1.00 0.00 -0.154 SA
78
+ HETATM 10 C6 BTN 0 -3.200 1.830 0.370 1.00 0.00 0.090 C
79
+ 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
82
+ 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
84
+ 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
87
  ENDBRANCH 7 8
88
88
  ENDBRANCH 6 7
89
89
  ENDBRANCH 5 6
biotite/structure/io/pdbx/__init__.py CHANGED
@@ -3,15 +3,21 @@
3
3
  # information.
4
4
 
5
5
  """
6
- This subpackage provides support for the the modern PDBx/mmCIF file
7
- format. The :class:`PDBxFile` class provides dictionary-like access to
8
- every field in PDBx/mmCIF files.
9
- Additional utility functions allow conversion of these dictionaries to
10
- :class:`AtomArray` and :class:`AtomArrayStack` objects and vice versa.
6
+ This subpackage provides support for the the modern PDBx file formats.
7
+ The :class:`CIFFile` class provides dictionary-like access to
8
+ every field in text-based *mmCIF* files.
9
+ :class:`BinaryCIFFile` provides analogous functionality for the
10
+ *BinaryCIF* format.
11
+ Additional utility functions allow reading and writing structures
12
+ from/to these files.
11
13
  """
12
14
 
13
15
  __name__ = "biotite.structure.io.pdbx"
14
16
  __author__ = "Patrick Kunzmann"
15
17
 
16
18
  from .convert import *
17
- from .file import *
19
+ from .bcif import *
20
+ from .cif import *
21
+ from .component import *
22
+ from .encoding import *
23
+ from .legacy import *