biotite 0.39.0__cp312-cp312-win_amd64.whl → 0.41.0__cp312-cp312-win_amd64.whl

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Files changed (121) hide show
  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.cp312-win_amd64.pyd +0 -0
  9. biotite/sequence/align/cigar.py +60 -15
  10. biotite/sequence/align/kmeralphabet.c +241 -220
  11. biotite/sequence/align/kmeralphabet.cp312-win_amd64.pyd +0 -0
  12. biotite/sequence/align/kmersimilarity.c +213 -194
  13. biotite/sequence/align/kmersimilarity.cp312-win_amd64.pyd +0 -0
  14. biotite/sequence/align/kmertable.cp312-win_amd64.pyd +0 -0
  15. biotite/sequence/align/kmertable.cpp +231 -203
  16. biotite/sequence/align/localgapped.c +256 -235
  17. biotite/sequence/align/localgapped.cp312-win_amd64.pyd +0 -0
  18. biotite/sequence/align/localungapped.c +233 -212
  19. biotite/sequence/align/localungapped.cp312-win_amd64.pyd +0 -0
  20. biotite/sequence/align/multiple.c +253 -232
  21. biotite/sequence/align/multiple.cp312-win_amd64.pyd +0 -0
  22. biotite/sequence/align/pairwise.c +272 -251
  23. biotite/sequence/align/pairwise.cp312-win_amd64.pyd +0 -0
  24. biotite/sequence/align/permutation.c +213 -194
  25. biotite/sequence/align/permutation.cp312-win_amd64.pyd +0 -0
  26. biotite/sequence/align/selector.c +215 -195
  27. biotite/sequence/align/selector.cp312-win_amd64.pyd +0 -0
  28. biotite/sequence/align/tracetable.c +213 -193
  29. biotite/sequence/align/tracetable.cp312-win_amd64.pyd +0 -0
  30. biotite/sequence/annotation.py +2 -2
  31. biotite/sequence/codec.c +233 -212
  32. biotite/sequence/codec.cp312-win_amd64.pyd +0 -0
  33. biotite/sequence/io/fasta/convert.py +27 -24
  34. biotite/sequence/phylo/nj.c +213 -194
  35. biotite/sequence/phylo/nj.cp312-win_amd64.pyd +0 -0
  36. biotite/sequence/phylo/tree.c +225 -200
  37. biotite/sequence/phylo/tree.cp312-win_amd64.pyd +0 -0
  38. biotite/sequence/phylo/upgma.c +213 -194
  39. biotite/sequence/phylo/upgma.cp312-win_amd64.pyd +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.cp312-win_amd64.pyd +0 -0
  44. biotite/structure/celllist.c +215 -195
  45. biotite/structure/celllist.cp312-win_amd64.pyd +0 -0
  46. biotite/structure/charges.c +1050 -1099
  47. biotite/structure/charges.cp312-win_amd64.pyd +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.cp312-win_amd64.pyd +0 -0
  71. biotite/structure/io/mmtf/convertfile.c +215 -195
  72. biotite/structure/io/mmtf/convertfile.cp312-win_amd64.pyd +0 -0
  73. biotite/structure/io/mmtf/decode.c +223 -202
  74. biotite/structure/io/mmtf/decode.cp312-win_amd64.pyd +0 -0
  75. biotite/structure/io/mmtf/encode.c +213 -194
  76. biotite/structure/io/mmtf/encode.cp312-win_amd64.pyd +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.cp312-win_amd64.pyd +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.cp312-win_amd64.pyd +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.cp312-win_amd64.pyd +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/__init__.py CHANGED
@@ -120,9 +120,11 @@ from .mechanics import *
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  from .molecules import *
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  from .pseudoknots import *
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  from .rdf import *
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+ from .repair import *
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  from .residues import *
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  from .chains import *
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  from .sasa import *
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+ from .sequence import *
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  from .sse import *
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  from .superimpose import *
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  from .transform import *
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):
386
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387
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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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  """
543
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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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680
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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):
846
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847
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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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  """
852
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@@ -1190,12 +1190,7 @@ def _match_base(nucleotide, min_atoms_per_base):
1190
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  # Match the selected std_base to the base.
1192
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  _, transformation = superimpose(nucleotide_matched, std_base_matched)
1193
-
1194
- # Transform the vectors
1195
- trans1, rot, trans2 = transformation
1196
- vectors += trans1
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- vectors = np.dot(rot, vectors.T).T
1198
- vectors += trans2
1193
+ vectors = transformation.apply(vectors)
1199
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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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1256
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  References
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  ----------
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-
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+
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  .. footbibliography::
1260
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  """
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  # Check if the residue is a 'standard' nucleotide