biotite 1.1.0__cp313-cp313-macosx_11_0_arm64.whl → 1.3.0__cp313-cp313-macosx_11_0_arm64.whl

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Files changed (160) hide show
  1. biotite/application/application.py +3 -3
  2. biotite/application/autodock/app.py +1 -1
  3. biotite/application/blast/webapp.py +1 -1
  4. biotite/application/clustalo/app.py +1 -1
  5. biotite/application/localapp.py +2 -2
  6. biotite/application/msaapp.py +10 -10
  7. biotite/application/muscle/app3.py +3 -3
  8. biotite/application/muscle/app5.py +3 -3
  9. biotite/application/sra/app.py +0 -5
  10. biotite/application/util.py +21 -1
  11. biotite/application/viennarna/rnaalifold.py +8 -8
  12. biotite/application/viennarna/rnaplot.py +10 -8
  13. biotite/application/viennarna/util.py +1 -1
  14. biotite/application/webapp.py +1 -1
  15. biotite/database/afdb/__init__.py +12 -0
  16. biotite/database/afdb/download.py +191 -0
  17. biotite/database/entrez/dbnames.py +10 -0
  18. biotite/database/entrez/download.py +9 -10
  19. biotite/database/entrez/key.py +1 -1
  20. biotite/database/entrez/query.py +5 -4
  21. biotite/database/pubchem/download.py +6 -6
  22. biotite/database/pubchem/error.py +10 -0
  23. biotite/database/pubchem/query.py +12 -23
  24. biotite/database/rcsb/download.py +3 -2
  25. biotite/database/rcsb/query.py +2 -3
  26. biotite/database/uniprot/check.py +2 -2
  27. biotite/database/uniprot/download.py +2 -5
  28. biotite/database/uniprot/query.py +3 -4
  29. biotite/file.py +14 -2
  30. biotite/interface/__init__.py +19 -0
  31. biotite/interface/openmm/__init__.py +20 -0
  32. biotite/interface/openmm/state.py +93 -0
  33. biotite/interface/openmm/system.py +227 -0
  34. biotite/interface/pymol/__init__.py +201 -0
  35. biotite/interface/pymol/cgo.py +346 -0
  36. biotite/interface/pymol/convert.py +185 -0
  37. biotite/interface/pymol/display.py +267 -0
  38. biotite/interface/pymol/object.py +1226 -0
  39. biotite/interface/pymol/shapes.py +178 -0
  40. biotite/interface/pymol/startup.py +169 -0
  41. biotite/interface/rdkit/__init__.py +19 -0
  42. biotite/interface/rdkit/mol.py +490 -0
  43. biotite/interface/version.py +94 -0
  44. biotite/interface/warning.py +19 -0
  45. biotite/sequence/align/__init__.py +0 -4
  46. biotite/sequence/align/alignment.py +33 -11
  47. biotite/sequence/align/banded.cpython-313-darwin.so +0 -0
  48. biotite/sequence/align/banded.pyx +22 -22
  49. biotite/sequence/align/cigar.py +2 -2
  50. biotite/sequence/align/kmeralphabet.cpython-313-darwin.so +0 -0
  51. biotite/sequence/align/kmeralphabet.pyx +2 -2
  52. biotite/sequence/align/kmersimilarity.cpython-313-darwin.so +0 -0
  53. biotite/sequence/align/kmertable.cpython-313-darwin.so +0 -0
  54. biotite/sequence/align/kmertable.pyx +6 -6
  55. biotite/sequence/align/localgapped.cpython-313-darwin.so +0 -0
  56. biotite/sequence/align/localgapped.pyx +47 -47
  57. biotite/sequence/align/localungapped.cpython-313-darwin.so +0 -0
  58. biotite/sequence/align/localungapped.pyx +10 -10
  59. biotite/sequence/align/matrix.py +12 -3
  60. biotite/sequence/align/multiple.cpython-313-darwin.so +0 -0
  61. biotite/sequence/align/multiple.pyx +1 -2
  62. biotite/sequence/align/pairwise.cpython-313-darwin.so +0 -0
  63. biotite/sequence/align/pairwise.pyx +37 -39
  64. biotite/sequence/align/permutation.cpython-313-darwin.so +0 -0
  65. biotite/sequence/align/selector.cpython-313-darwin.so +0 -0
  66. biotite/sequence/align/selector.pyx +2 -2
  67. biotite/sequence/align/statistics.py +1 -1
  68. biotite/sequence/align/tracetable.cpython-313-darwin.so +0 -0
  69. biotite/sequence/alphabet.py +2 -2
  70. biotite/sequence/annotation.py +19 -13
  71. biotite/sequence/codec.cpython-313-darwin.so +0 -0
  72. biotite/sequence/codon.py +1 -2
  73. biotite/sequence/graphics/alignment.py +25 -39
  74. biotite/sequence/graphics/dendrogram.py +4 -2
  75. biotite/sequence/graphics/features.py +2 -2
  76. biotite/sequence/graphics/logo.py +10 -12
  77. biotite/sequence/io/fasta/convert.py +1 -2
  78. biotite/sequence/io/fasta/file.py +1 -1
  79. biotite/sequence/io/fastq/file.py +3 -3
  80. biotite/sequence/io/genbank/file.py +3 -3
  81. biotite/sequence/io/genbank/sequence.py +2 -0
  82. biotite/sequence/io/gff/convert.py +1 -1
  83. biotite/sequence/io/gff/file.py +1 -2
  84. biotite/sequence/phylo/nj.cpython-313-darwin.so +0 -0
  85. biotite/sequence/phylo/tree.cpython-313-darwin.so +0 -0
  86. biotite/sequence/phylo/upgma.cpython-313-darwin.so +0 -0
  87. biotite/sequence/profile.py +19 -25
  88. biotite/sequence/search.py +0 -1
  89. biotite/sequence/seqtypes.py +12 -5
  90. biotite/sequence/sequence.py +1 -2
  91. biotite/structure/__init__.py +2 -0
  92. biotite/structure/alphabet/i3d.py +1 -2
  93. biotite/structure/alphabet/pb.py +1 -2
  94. biotite/structure/alphabet/unkerasify.py +8 -2
  95. biotite/structure/atoms.py +35 -27
  96. biotite/structure/basepairs.py +39 -40
  97. biotite/structure/bonds.cpython-313-darwin.so +0 -0
  98. biotite/structure/bonds.pyx +8 -5
  99. biotite/structure/box.py +159 -23
  100. biotite/structure/celllist.cpython-313-darwin.so +0 -0
  101. biotite/structure/celllist.pyx +83 -68
  102. biotite/structure/chains.py +17 -55
  103. biotite/structure/charges.cpython-313-darwin.so +0 -0
  104. biotite/structure/compare.py +420 -13
  105. biotite/structure/density.py +1 -1
  106. biotite/structure/dotbracket.py +31 -32
  107. biotite/structure/filter.py +8 -8
  108. biotite/structure/geometry.py +15 -15
  109. biotite/structure/graphics/rna.py +19 -16
  110. biotite/structure/hbond.py +18 -21
  111. biotite/structure/info/atoms.py +11 -2
  112. biotite/structure/info/ccd.py +0 -2
  113. biotite/structure/info/components.bcif +0 -0
  114. biotite/structure/info/groups.py +0 -3
  115. biotite/structure/info/misc.py +0 -1
  116. biotite/structure/info/radii.py +92 -22
  117. biotite/structure/info/standardize.py +1 -2
  118. biotite/structure/integrity.py +4 -6
  119. biotite/structure/io/general.py +2 -2
  120. biotite/structure/io/gro/file.py +8 -9
  121. biotite/structure/io/mol/convert.py +1 -1
  122. biotite/structure/io/mol/ctab.py +33 -28
  123. biotite/structure/io/mol/mol.py +1 -1
  124. biotite/structure/io/mol/sdf.py +39 -13
  125. biotite/structure/io/pdb/convert.py +86 -5
  126. biotite/structure/io/pdb/file.py +90 -24
  127. biotite/structure/io/pdb/hybrid36.cpython-313-darwin.so +0 -0
  128. biotite/structure/io/pdbqt/file.py +4 -4
  129. biotite/structure/io/pdbx/bcif.py +22 -7
  130. biotite/structure/io/pdbx/cif.py +20 -7
  131. biotite/structure/io/pdbx/component.py +6 -0
  132. biotite/structure/io/pdbx/compress.py +71 -34
  133. biotite/structure/io/pdbx/convert.py +429 -77
  134. biotite/structure/io/pdbx/encoding.cpython-313-darwin.so +0 -0
  135. biotite/structure/io/pdbx/encoding.pyx +39 -23
  136. biotite/structure/io/trajfile.py +9 -6
  137. biotite/structure/io/util.py +38 -0
  138. biotite/structure/mechanics.py +0 -1
  139. biotite/structure/molecules.py +0 -15
  140. biotite/structure/pseudoknots.py +13 -19
  141. biotite/structure/repair.py +2 -4
  142. biotite/structure/residues.py +20 -48
  143. biotite/structure/rings.py +335 -0
  144. biotite/structure/sasa.cpython-313-darwin.so +0 -0
  145. biotite/structure/sasa.pyx +30 -30
  146. biotite/structure/segments.py +123 -9
  147. biotite/structure/sequence.py +0 -1
  148. biotite/structure/spacegroups.json +1567 -0
  149. biotite/structure/spacegroups.license +26 -0
  150. biotite/structure/sse.py +0 -2
  151. biotite/structure/superimpose.py +75 -253
  152. biotite/structure/tm.py +581 -0
  153. biotite/structure/transform.py +232 -26
  154. biotite/structure/util.py +3 -3
  155. biotite/version.py +9 -4
  156. biotite/visualize.py +111 -1
  157. {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/METADATA +8 -36
  158. {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/RECORD +160 -138
  159. {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/WHEEL +3 -1
  160. {biotite-1.1.0.dist-info → biotite-1.3.0.dist-info}/licenses/LICENSE.rst +0 -0
@@ -1,119 +1,132 @@
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@@ -206,12 +219,12 @@ biotite/sequence/align/matrix_data/PAM340.mat,sha256=9rV5CU441SuU-MhTIOFBHbg2i6b
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+ biotite/sequence/graphics/alignment.py,sha256=IvwMusuZ72eDPl-VDPQGmu1GMS3uo9xtPcvDgK8hsVQ,39368
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+ biotite/sequence/graphics/features.py,sha256=SJ81q33R7ZJSaJiVMJoie2IjWXUydU0eWCy_E10vzdE,17297
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@@ -234,99 +247,108 @@ biotite/sequence/graphics/color_schemes/jalview_zappo.json,sha256=V0IJ-GsT8G8-J9
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  biotite/structure/io/pdb/__init__.py,sha256=5NbUMDRKIe7jJ2ByRHpMhJzY_vIasjSgO63Zxrpq8BM,733
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  biotite/structure/io/pdb/hybrid36.pyx,sha256=BKV7oh0xrrjqVrkhTn7KEolon57fUhlG4Yf0Tf22wuU,8036
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  biotite/structure/alphabet/encoder_weights_3di.kerasify,sha256=m4JF4oVWBbiu6r8DM9ONQ5Bmcbqwr5dxKfqYThOmHpk,1032
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  biotite/structure/alphabet/__init__.py,sha256=tUAybrggScCsom1b_EXQ63pA88L_PmQpcYS-MnqKavM,928
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  biotite/structure/alphabet/encoder.py,sha256=2BWLMdGBr2bHw09vMhbzPztMKSnVt8UhUf85g5M1xnY,11383
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+ biotite/structure/alphabet/i3d.py,sha256=SLJkVWiKl-EXMcsv8gcKF4zujoR5L8sQRyo9fnrETPM,3009
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  biotite/structure/alphabet/pb.license,sha256=OkDCfXO06BfooLXYC3iF7LXXB_Uqqex1B2gjUEFdUZI,1091
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  biotite/structure/alphabet/layers.py,sha256=Y1Y8G2LqqzC7M0kNUv8k-EXTVVKGLnPDJKdRrVEf3H4,2087
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  biotite/structure/info/atom_masses.json,sha256=WME4ezDPy-HrEIhxkOGxcmIMdgxf1x7e_xwBkFRdTsY,2383
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  biotite/structure/info/__init__.py,sha256=k08kdsKlrxaVQ9x8MjEXoVFaXl1J8OcpLf6iG7dUgOY,698
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  biotite/structure/info/bonds.py,sha256=6pXAZPeKPL2pwFi5fhSyTwh_gd5fToIgvwguGffrE-0,4644
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  biotite/structure/info/masses.py,sha256=HOdaeFZkd5LSrl00025S1MwXT7im8V-s0bU54tr1te8,4555
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- biotite/structure/info/ccd.py,sha256=EBSqvzgIXl7U5wxSVOFPSaLQLBRP2E_mUVXEwsRyOO4,5853
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  biotite/structure/graphics/__init__.py,sha256=YwMT8-c2DjrkcwyK6jPeDtAKxQda0OhElnwk8J0y3Hc,353
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- biotite/structure/graphics/rna.py,sha256=w7zFMKo2ZZ4n60SkbkupEXPxe3-KUNa261PF784ry8k,12016
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+ biotite/structure/graphics/rna.py,sha256=1fa-_ROxHIdCQu4nFEmDWqWnQlXA6iZDZDprKST_h_g,11842
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  biotite/structure/graphics/atoms.py,sha256=988_URX4hfTE3oBOYgAvZruOrzogMPcFKiTT5RJL01E,8116
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+ biotite-1.3.0.dist-info/RECORD,,
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@@ -1,4 +1,6 @@
1
1
  Wheel-Version: 1.0
2
- Generator: hatchling 1.25.0
2
+ Generator: hatchling 1.27.0
3
3
  Root-Is-Purelib: false
4
4
  Tag: cp313-cp313-macosx_11_0_arm64
5
+ Generator: delocate 0.13.0
6
+