biotite 0.39.0__cp312-cp312-macosx_11_0_arm64.whl → 0.40.0__cp312-cp312-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 +256 -235
  5. biotite/sequence/align/banded.cpython-312-darwin.so +0 -0
  6. biotite/sequence/align/kmeralphabet.c +241 -220
  7. biotite/sequence/align/kmeralphabet.cpython-312-darwin.so +0 -0
  8. biotite/sequence/align/kmersimilarity.c +213 -194
  9. biotite/sequence/align/kmersimilarity.cpython-312-darwin.so +0 -0
  10. biotite/sequence/align/kmertable.cpp +231 -203
  11. biotite/sequence/align/kmertable.cpython-312-darwin.so +0 -0
  12. biotite/sequence/align/localgapped.c +256 -235
  13. biotite/sequence/align/localgapped.cpython-312-darwin.so +0 -0
  14. biotite/sequence/align/localungapped.c +233 -212
  15. biotite/sequence/align/localungapped.cpython-312-darwin.so +0 -0
  16. biotite/sequence/align/multiple.c +253 -232
  17. biotite/sequence/align/multiple.cpython-312-darwin.so +0 -0
  18. biotite/sequence/align/pairwise.c +272 -251
  19. biotite/sequence/align/pairwise.cpython-312-darwin.so +0 -0
  20. biotite/sequence/align/permutation.c +213 -194
  21. biotite/sequence/align/permutation.cpython-312-darwin.so +0 -0
  22. biotite/sequence/align/selector.c +215 -195
  23. biotite/sequence/align/selector.cpython-312-darwin.so +0 -0
  24. biotite/sequence/align/tracetable.c +213 -193
  25. biotite/sequence/align/tracetable.cpython-312-darwin.so +0 -0
  26. biotite/sequence/codec.c +233 -212
  27. biotite/sequence/codec.cpython-312-darwin.so +0 -0
  28. biotite/sequence/phylo/nj.c +213 -194
  29. biotite/sequence/phylo/nj.cpython-312-darwin.so +0 -0
  30. biotite/sequence/phylo/tree.c +225 -200
  31. biotite/sequence/phylo/tree.cpython-312-darwin.so +0 -0
  32. biotite/sequence/phylo/upgma.c +213 -194
  33. biotite/sequence/phylo/upgma.cpython-312-darwin.so +0 -0
  34. biotite/structure/basepairs.py +7 -12
  35. biotite/structure/bonds.c +1173 -1224
  36. biotite/structure/bonds.cpython-312-darwin.so +0 -0
  37. biotite/structure/celllist.c +215 -195
  38. biotite/structure/celllist.cpython-312-darwin.so +0 -0
  39. biotite/structure/charges.c +1050 -1099
  40. biotite/structure/charges.cpython-312-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 +217 -196
  60. biotite/structure/io/mmtf/convertarray.cpython-312-darwin.so +0 -0
  61. biotite/structure/io/mmtf/convertfile.c +215 -195
  62. biotite/structure/io/mmtf/convertfile.cpython-312-darwin.so +0 -0
  63. biotite/structure/io/mmtf/decode.c +223 -202
  64. biotite/structure/io/mmtf/decode.cpython-312-darwin.so +0 -0
  65. biotite/structure/io/mmtf/encode.c +213 -194
  66. biotite/structure/io/mmtf/encode.cpython-312-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-312-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 +112803 -0
  81. biotite/structure/io/pdbx/encoding.cpython-312-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 +213 -194
  86. biotite/structure/sasa.cpython-312-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/basepairs.py CHANGED
@@ -15,7 +15,7 @@ import numpy as np
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  import warnings
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  from enum import IntEnum
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  from .atoms import Atom, array
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- from .superimpose import superimpose, superimpose_apply
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+ from .superimpose import superimpose
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  from .filter import filter_nucleotides
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  from .celllist import CellList
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  from .hbond import hbond
@@ -386,7 +386,7 @@ def base_pairs_edge(atom_array, base_pairs):
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  References
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  ----------
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-
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+
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  .. footbibliography::
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  """
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  # Result-``ndarray`` matches the dimensions of the input array
@@ -537,7 +537,7 @@ def base_pairs_glycosidic_bond(atom_array, base_pairs):
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  References
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  ----------
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-
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+
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  .. footbibliography::
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  """
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  results = np.zeros(len(base_pairs), dtype='uint8')
@@ -679,7 +679,7 @@ def base_stacking(atom_array, min_atoms_per_base=3):
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  References
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  ----------
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-
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+
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  .. footbibliography::
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  """
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  # Get the stacking candidates according to a cutoff distance, where
@@ -846,7 +846,7 @@ def base_pairs(atom_array, min_atoms_per_base = 3, unique = True):
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  References
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  ----------
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-
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+
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  .. footbibliography::
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  """
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@@ -1190,12 +1190,7 @@ def _match_base(nucleotide, min_atoms_per_base):
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  # Match the selected std_base to the base.
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  _, transformation = superimpose(nucleotide_matched, std_base_matched)
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-
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- # Transform the vectors
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- trans1, rot, trans2 = transformation
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- vectors += trans1
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- vectors = np.dot(rot, vectors.T).T
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- vectors += trans2
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+ vectors = transformation.apply(vectors)
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  # Normalize the base-normal-vector
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  vectors[1,:] = vectors[1,:]-vectors[0,:]
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  norm_vector(vectors[1,:])
@@ -1255,7 +1250,7 @@ def map_nucleotide(residue, min_atoms_per_base=3, rmsd_cutoff=0.28):
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  References
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  ----------
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-
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+
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  .. footbibliography::
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  """
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  # Check if the residue is a 'standard' nucleotide