biotite 1.0.1__cp311-cp311-win_amd64.whl → 1.2.0__cp311-cp311-win_amd64.whl

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Files changed (177) 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/dssp/app.py +13 -3
  6. biotite/application/localapp.py +36 -2
  7. biotite/application/msaapp.py +10 -10
  8. biotite/application/muscle/app3.py +5 -18
  9. biotite/application/muscle/app5.py +5 -5
  10. biotite/application/sra/app.py +0 -5
  11. biotite/application/util.py +22 -2
  12. biotite/application/viennarna/rnaalifold.py +8 -8
  13. biotite/application/viennarna/rnaplot.py +9 -3
  14. biotite/application/viennarna/util.py +1 -1
  15. biotite/application/webapp.py +1 -1
  16. biotite/database/afdb/__init__.py +12 -0
  17. biotite/database/afdb/download.py +191 -0
  18. biotite/database/entrez/dbnames.py +10 -0
  19. biotite/database/entrez/download.py +9 -10
  20. biotite/database/entrez/key.py +1 -1
  21. biotite/database/entrez/query.py +5 -4
  22. biotite/database/pubchem/download.py +6 -6
  23. biotite/database/pubchem/error.py +10 -0
  24. biotite/database/pubchem/query.py +12 -23
  25. biotite/database/rcsb/download.py +3 -2
  26. biotite/database/rcsb/query.py +8 -9
  27. biotite/database/uniprot/check.py +22 -17
  28. biotite/database/uniprot/download.py +3 -6
  29. biotite/database/uniprot/query.py +4 -5
  30. biotite/file.py +14 -2
  31. biotite/interface/__init__.py +19 -0
  32. biotite/interface/openmm/__init__.py +16 -0
  33. biotite/interface/openmm/state.py +93 -0
  34. biotite/interface/openmm/system.py +227 -0
  35. biotite/interface/pymol/__init__.py +198 -0
  36. biotite/interface/pymol/cgo.py +346 -0
  37. biotite/interface/pymol/convert.py +185 -0
  38. biotite/interface/pymol/display.py +267 -0
  39. biotite/interface/pymol/object.py +1226 -0
  40. biotite/interface/pymol/shapes.py +178 -0
  41. biotite/interface/pymol/startup.py +169 -0
  42. biotite/interface/rdkit/__init__.py +15 -0
  43. biotite/interface/rdkit/mol.py +490 -0
  44. biotite/interface/version.py +71 -0
  45. biotite/interface/warning.py +19 -0
  46. biotite/sequence/align/__init__.py +0 -4
  47. biotite/sequence/align/alignment.py +49 -14
  48. biotite/sequence/align/banded.cp311-win_amd64.pyd +0 -0
  49. biotite/sequence/align/banded.pyx +26 -26
  50. biotite/sequence/align/cigar.py +2 -2
  51. biotite/sequence/align/kmeralphabet.cp311-win_amd64.pyd +0 -0
  52. biotite/sequence/align/kmeralphabet.pyx +19 -2
  53. biotite/sequence/align/kmersimilarity.cp311-win_amd64.pyd +0 -0
  54. biotite/sequence/align/kmertable.cp311-win_amd64.pyd +0 -0
  55. biotite/sequence/align/kmertable.pyx +58 -48
  56. biotite/sequence/align/localgapped.cp311-win_amd64.pyd +0 -0
  57. biotite/sequence/align/localgapped.pyx +47 -47
  58. biotite/sequence/align/localungapped.cp311-win_amd64.pyd +0 -0
  59. biotite/sequence/align/localungapped.pyx +10 -10
  60. biotite/sequence/align/matrix.py +284 -57
  61. biotite/sequence/align/matrix_data/3Di.mat +24 -0
  62. biotite/sequence/align/matrix_data/PB.license +21 -0
  63. biotite/sequence/align/matrix_data/PB.mat +18 -0
  64. biotite/sequence/align/multiple.cp311-win_amd64.pyd +0 -0
  65. biotite/sequence/align/pairwise.cp311-win_amd64.pyd +0 -0
  66. biotite/sequence/align/pairwise.pyx +35 -35
  67. biotite/sequence/align/permutation.cp311-win_amd64.pyd +0 -0
  68. biotite/sequence/align/selector.cp311-win_amd64.pyd +0 -0
  69. biotite/sequence/align/selector.pyx +2 -2
  70. biotite/sequence/align/statistics.py +1 -1
  71. biotite/sequence/align/tracetable.cp311-win_amd64.pyd +0 -0
  72. biotite/sequence/alphabet.py +5 -2
  73. biotite/sequence/annotation.py +19 -13
  74. biotite/sequence/codec.cp311-win_amd64.pyd +0 -0
  75. biotite/sequence/codon.py +1 -2
  76. biotite/sequence/graphics/alignment.py +25 -39
  77. biotite/sequence/graphics/color_schemes/3di_flower.json +48 -0
  78. biotite/sequence/graphics/color_schemes/pb_flower.json +2 -1
  79. biotite/sequence/graphics/colorschemes.py +44 -11
  80. biotite/sequence/graphics/dendrogram.py +4 -2
  81. biotite/sequence/graphics/features.py +2 -2
  82. biotite/sequence/graphics/logo.py +10 -12
  83. biotite/sequence/io/fasta/convert.py +1 -2
  84. biotite/sequence/io/fasta/file.py +1 -1
  85. biotite/sequence/io/fastq/file.py +3 -3
  86. biotite/sequence/io/genbank/file.py +3 -3
  87. biotite/sequence/io/genbank/sequence.py +2 -0
  88. biotite/sequence/io/gff/convert.py +1 -1
  89. biotite/sequence/io/gff/file.py +1 -2
  90. biotite/sequence/phylo/nj.cp311-win_amd64.pyd +0 -0
  91. biotite/sequence/phylo/tree.cp311-win_amd64.pyd +0 -0
  92. biotite/sequence/phylo/upgma.cp311-win_amd64.pyd +0 -0
  93. biotite/sequence/profile.py +105 -29
  94. biotite/sequence/search.py +0 -1
  95. biotite/sequence/seqtypes.py +136 -8
  96. biotite/sequence/sequence.py +1 -2
  97. biotite/setup_ccd.py +197 -0
  98. biotite/structure/__init__.py +6 -3
  99. biotite/structure/alphabet/__init__.py +25 -0
  100. biotite/structure/alphabet/encoder.py +332 -0
  101. biotite/structure/alphabet/encoder_weights_3di.kerasify +0 -0
  102. biotite/structure/alphabet/i3d.py +109 -0
  103. biotite/structure/alphabet/layers.py +86 -0
  104. biotite/structure/alphabet/pb.license +21 -0
  105. biotite/structure/alphabet/pb.py +170 -0
  106. biotite/structure/alphabet/unkerasify.py +128 -0
  107. biotite/structure/atoms.py +163 -66
  108. biotite/structure/basepairs.py +26 -26
  109. biotite/structure/bonds.cp311-win_amd64.pyd +0 -0
  110. biotite/structure/bonds.pyx +79 -25
  111. biotite/structure/box.py +19 -21
  112. biotite/structure/celllist.cp311-win_amd64.pyd +0 -0
  113. biotite/structure/celllist.pyx +83 -67
  114. biotite/structure/chains.py +5 -37
  115. biotite/structure/charges.cp311-win_amd64.pyd +0 -0
  116. biotite/structure/compare.py +420 -13
  117. biotite/structure/density.py +1 -1
  118. biotite/structure/dotbracket.py +27 -28
  119. biotite/structure/filter.py +8 -8
  120. biotite/structure/geometry.py +74 -127
  121. biotite/structure/hbond.py +17 -19
  122. biotite/structure/info/__init__.py +1 -0
  123. biotite/structure/info/atoms.py +24 -15
  124. biotite/structure/info/bonds.py +12 -6
  125. biotite/structure/info/ccd.py +125 -34
  126. biotite/structure/info/{ccd/components.bcif → components.bcif} +0 -0
  127. biotite/structure/info/groups.py +62 -19
  128. biotite/structure/info/masses.py +9 -6
  129. biotite/structure/info/misc.py +15 -22
  130. biotite/structure/info/radii.py +92 -22
  131. biotite/structure/info/standardize.py +4 -4
  132. biotite/structure/integrity.py +4 -6
  133. biotite/structure/io/general.py +2 -2
  134. biotite/structure/io/gro/file.py +8 -9
  135. biotite/structure/io/mol/convert.py +1 -1
  136. biotite/structure/io/mol/ctab.py +33 -28
  137. biotite/structure/io/mol/mol.py +1 -1
  138. biotite/structure/io/mol/sdf.py +80 -53
  139. biotite/structure/io/pdb/convert.py +4 -3
  140. biotite/structure/io/pdb/file.py +85 -25
  141. biotite/structure/io/pdb/hybrid36.cp311-win_amd64.pyd +0 -0
  142. biotite/structure/io/pdbqt/file.py +36 -36
  143. biotite/structure/io/pdbx/__init__.py +1 -0
  144. biotite/structure/io/pdbx/bcif.py +54 -15
  145. biotite/structure/io/pdbx/cif.py +92 -66
  146. biotite/structure/io/pdbx/component.py +15 -4
  147. biotite/structure/io/pdbx/compress.py +321 -0
  148. biotite/structure/io/pdbx/convert.py +410 -75
  149. biotite/structure/io/pdbx/encoding.cp311-win_amd64.pyd +0 -0
  150. biotite/structure/io/pdbx/encoding.pyx +98 -17
  151. biotite/structure/io/trajfile.py +9 -6
  152. biotite/structure/io/util.py +38 -0
  153. biotite/structure/mechanics.py +0 -1
  154. biotite/structure/molecules.py +141 -156
  155. biotite/structure/pseudoknots.py +7 -13
  156. biotite/structure/repair.py +2 -4
  157. biotite/structure/residues.py +13 -24
  158. biotite/structure/rings.py +335 -0
  159. biotite/structure/sasa.cp311-win_amd64.pyd +0 -0
  160. biotite/structure/sasa.pyx +2 -1
  161. biotite/structure/segments.py +69 -11
  162. biotite/structure/sequence.py +0 -1
  163. biotite/structure/sse.py +0 -2
  164. biotite/structure/superimpose.py +74 -62
  165. biotite/structure/tm.py +581 -0
  166. biotite/structure/transform.py +12 -25
  167. biotite/structure/util.py +76 -4
  168. biotite/version.py +9 -4
  169. biotite/visualize.py +111 -1
  170. {biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/METADATA +6 -2
  171. {biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/RECORD +173 -143
  172. biotite/structure/info/ccd/README.rst +0 -8
  173. biotite/structure/info/ccd/amino_acids.txt +0 -1663
  174. biotite/structure/info/ccd/carbohydrates.txt +0 -1135
  175. biotite/structure/info/ccd/nucleotides.txt +0 -798
  176. {biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/WHEEL +0 -0
  177. {biotite-1.0.1.dist-info → biotite-1.2.0.dist-info}/licenses/LICENSE.rst +0 -0