biotite 1.5.0__cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

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  1. biotite/__init__.py +18 -0
  2. biotite/application/__init__.py +69 -0
  3. biotite/application/application.py +276 -0
  4. biotite/application/autodock/__init__.py +12 -0
  5. biotite/application/autodock/app.py +500 -0
  6. biotite/application/blast/__init__.py +14 -0
  7. biotite/application/blast/alignment.py +92 -0
  8. biotite/application/blast/webapp.py +428 -0
  9. biotite/application/clustalo/__init__.py +12 -0
  10. biotite/application/clustalo/app.py +223 -0
  11. biotite/application/dssp/__init__.py +12 -0
  12. biotite/application/dssp/app.py +216 -0
  13. biotite/application/localapp.py +342 -0
  14. biotite/application/mafft/__init__.py +12 -0
  15. biotite/application/mafft/app.py +116 -0
  16. biotite/application/msaapp.py +363 -0
  17. biotite/application/muscle/__init__.py +13 -0
  18. biotite/application/muscle/app3.py +227 -0
  19. biotite/application/muscle/app5.py +163 -0
  20. biotite/application/sra/__init__.py +18 -0
  21. biotite/application/sra/app.py +447 -0
  22. biotite/application/tantan/__init__.py +12 -0
  23. biotite/application/tantan/app.py +199 -0
  24. biotite/application/util.py +77 -0
  25. biotite/application/viennarna/__init__.py +18 -0
  26. biotite/application/viennarna/rnaalifold.py +310 -0
  27. biotite/application/viennarna/rnafold.py +254 -0
  28. biotite/application/viennarna/rnaplot.py +208 -0
  29. biotite/application/viennarna/util.py +77 -0
  30. biotite/application/webapp.py +76 -0
  31. biotite/copyable.py +71 -0
  32. biotite/database/__init__.py +23 -0
  33. biotite/database/afdb/__init__.py +12 -0
  34. biotite/database/afdb/download.py +197 -0
  35. biotite/database/entrez/__init__.py +15 -0
  36. biotite/database/entrez/check.py +60 -0
  37. biotite/database/entrez/dbnames.py +101 -0
  38. biotite/database/entrez/download.py +228 -0
  39. biotite/database/entrez/key.py +44 -0
  40. biotite/database/entrez/query.py +263 -0
  41. biotite/database/error.py +16 -0
  42. biotite/database/pubchem/__init__.py +21 -0
  43. biotite/database/pubchem/download.py +258 -0
  44. biotite/database/pubchem/error.py +30 -0
  45. biotite/database/pubchem/query.py +819 -0
  46. biotite/database/pubchem/throttle.py +98 -0
  47. biotite/database/rcsb/__init__.py +13 -0
  48. biotite/database/rcsb/download.py +161 -0
  49. biotite/database/rcsb/query.py +963 -0
  50. biotite/database/uniprot/__init__.py +13 -0
  51. biotite/database/uniprot/check.py +40 -0
  52. biotite/database/uniprot/download.py +126 -0
  53. biotite/database/uniprot/query.py +292 -0
  54. biotite/file.py +244 -0
  55. biotite/interface/__init__.py +19 -0
  56. biotite/interface/openmm/__init__.py +20 -0
  57. biotite/interface/openmm/state.py +93 -0
  58. biotite/interface/openmm/system.py +227 -0
  59. biotite/interface/pymol/__init__.py +201 -0
  60. biotite/interface/pymol/cgo.py +346 -0
  61. biotite/interface/pymol/convert.py +185 -0
  62. biotite/interface/pymol/display.py +267 -0
  63. biotite/interface/pymol/object.py +1228 -0
  64. biotite/interface/pymol/shapes.py +178 -0
  65. biotite/interface/pymol/startup.py +169 -0
  66. biotite/interface/rdkit/__init__.py +19 -0
  67. biotite/interface/rdkit/mol.py +490 -0
  68. biotite/interface/version.py +94 -0
  69. biotite/interface/warning.py +19 -0
  70. biotite/sequence/__init__.py +84 -0
  71. biotite/sequence/align/__init__.py +199 -0
  72. biotite/sequence/align/alignment.py +702 -0
  73. biotite/sequence/align/banded.cpython-313-x86_64-linux-gnu.so +0 -0
  74. biotite/sequence/align/banded.pyx +652 -0
  75. biotite/sequence/align/buckets.py +71 -0
  76. biotite/sequence/align/cigar.py +425 -0
  77. biotite/sequence/align/kmeralphabet.cpython-313-x86_64-linux-gnu.so +0 -0
  78. biotite/sequence/align/kmeralphabet.pyx +595 -0
  79. biotite/sequence/align/kmersimilarity.cpython-313-x86_64-linux-gnu.so +0 -0
  80. biotite/sequence/align/kmersimilarity.pyx +233 -0
  81. biotite/sequence/align/kmertable.cpython-313-x86_64-linux-gnu.so +0 -0
  82. biotite/sequence/align/kmertable.pyx +3411 -0
  83. biotite/sequence/align/localgapped.cpython-313-x86_64-linux-gnu.so +0 -0
  84. biotite/sequence/align/localgapped.pyx +892 -0
  85. biotite/sequence/align/localungapped.cpython-313-x86_64-linux-gnu.so +0 -0
  86. biotite/sequence/align/localungapped.pyx +279 -0
  87. biotite/sequence/align/matrix.py +631 -0
  88. biotite/sequence/align/matrix_data/3Di.mat +24 -0
  89. biotite/sequence/align/matrix_data/BLOSUM100.mat +31 -0
  90. biotite/sequence/align/matrix_data/BLOSUM30.mat +31 -0
  91. biotite/sequence/align/matrix_data/BLOSUM35.mat +31 -0
  92. biotite/sequence/align/matrix_data/BLOSUM40.mat +31 -0
  93. biotite/sequence/align/matrix_data/BLOSUM45.mat +31 -0
  94. biotite/sequence/align/matrix_data/BLOSUM50.mat +31 -0
  95. biotite/sequence/align/matrix_data/BLOSUM50_13p.mat +25 -0
  96. biotite/sequence/align/matrix_data/BLOSUM50_14.3.mat +25 -0
  97. biotite/sequence/align/matrix_data/BLOSUM50_5.0.mat +25 -0
  98. biotite/sequence/align/matrix_data/BLOSUM55.mat +31 -0
  99. biotite/sequence/align/matrix_data/BLOSUM60.mat +31 -0
  100. biotite/sequence/align/matrix_data/BLOSUM62.mat +31 -0
  101. biotite/sequence/align/matrix_data/BLOSUM62_13p.mat +25 -0
  102. biotite/sequence/align/matrix_data/BLOSUM62_14.3.mat +25 -0
  103. biotite/sequence/align/matrix_data/BLOSUM62_5.0.mat +25 -0
  104. biotite/sequence/align/matrix_data/BLOSUM65.mat +31 -0
  105. biotite/sequence/align/matrix_data/BLOSUM70.mat +31 -0
  106. biotite/sequence/align/matrix_data/BLOSUM75.mat +31 -0
  107. biotite/sequence/align/matrix_data/BLOSUM80.mat +31 -0
  108. biotite/sequence/align/matrix_data/BLOSUM85.mat +31 -0
  109. biotite/sequence/align/matrix_data/BLOSUM90.mat +31 -0
  110. biotite/sequence/align/matrix_data/BLOSUMN.mat +31 -0
  111. biotite/sequence/align/matrix_data/CorBLOSUM49_5.0.mat +25 -0
  112. biotite/sequence/align/matrix_data/CorBLOSUM57_13p.mat +25 -0
  113. biotite/sequence/align/matrix_data/CorBLOSUM57_14.3.mat +25 -0
  114. biotite/sequence/align/matrix_data/CorBLOSUM61_5.0.mat +25 -0
  115. biotite/sequence/align/matrix_data/CorBLOSUM66_13p.mat +25 -0
  116. biotite/sequence/align/matrix_data/CorBLOSUM67_14.3.mat +25 -0
  117. biotite/sequence/align/matrix_data/DAYHOFF.mat +32 -0
  118. biotite/sequence/align/matrix_data/GONNET.mat +26 -0
  119. biotite/sequence/align/matrix_data/IDENTITY.mat +25 -0
  120. biotite/sequence/align/matrix_data/MATCH.mat +25 -0
  121. biotite/sequence/align/matrix_data/NUC.mat +25 -0
  122. biotite/sequence/align/matrix_data/PAM10.mat +34 -0
  123. biotite/sequence/align/matrix_data/PAM100.mat +34 -0
  124. biotite/sequence/align/matrix_data/PAM110.mat +34 -0
  125. biotite/sequence/align/matrix_data/PAM120.mat +34 -0
  126. biotite/sequence/align/matrix_data/PAM130.mat +34 -0
  127. biotite/sequence/align/matrix_data/PAM140.mat +34 -0
  128. biotite/sequence/align/matrix_data/PAM150.mat +34 -0
  129. biotite/sequence/align/matrix_data/PAM160.mat +34 -0
  130. biotite/sequence/align/matrix_data/PAM170.mat +34 -0
  131. biotite/sequence/align/matrix_data/PAM180.mat +34 -0
  132. biotite/sequence/align/matrix_data/PAM190.mat +34 -0
  133. biotite/sequence/align/matrix_data/PAM20.mat +34 -0
  134. biotite/sequence/align/matrix_data/PAM200.mat +34 -0
  135. biotite/sequence/align/matrix_data/PAM210.mat +34 -0
  136. biotite/sequence/align/matrix_data/PAM220.mat +34 -0
  137. biotite/sequence/align/matrix_data/PAM230.mat +34 -0
  138. biotite/sequence/align/matrix_data/PAM240.mat +34 -0
  139. biotite/sequence/align/matrix_data/PAM250.mat +34 -0
  140. biotite/sequence/align/matrix_data/PAM260.mat +34 -0
  141. biotite/sequence/align/matrix_data/PAM270.mat +34 -0
  142. biotite/sequence/align/matrix_data/PAM280.mat +34 -0
  143. biotite/sequence/align/matrix_data/PAM290.mat +34 -0
  144. biotite/sequence/align/matrix_data/PAM30.mat +34 -0
  145. biotite/sequence/align/matrix_data/PAM300.mat +34 -0
  146. biotite/sequence/align/matrix_data/PAM310.mat +34 -0
  147. biotite/sequence/align/matrix_data/PAM320.mat +34 -0
  148. biotite/sequence/align/matrix_data/PAM330.mat +34 -0
  149. biotite/sequence/align/matrix_data/PAM340.mat +34 -0
  150. biotite/sequence/align/matrix_data/PAM350.mat +34 -0
  151. biotite/sequence/align/matrix_data/PAM360.mat +34 -0
  152. biotite/sequence/align/matrix_data/PAM370.mat +34 -0
  153. biotite/sequence/align/matrix_data/PAM380.mat +34 -0
  154. biotite/sequence/align/matrix_data/PAM390.mat +34 -0
  155. biotite/sequence/align/matrix_data/PAM40.mat +34 -0
  156. biotite/sequence/align/matrix_data/PAM400.mat +34 -0
  157. biotite/sequence/align/matrix_data/PAM410.mat +34 -0
  158. biotite/sequence/align/matrix_data/PAM420.mat +34 -0
  159. biotite/sequence/align/matrix_data/PAM430.mat +34 -0
  160. biotite/sequence/align/matrix_data/PAM440.mat +34 -0
  161. biotite/sequence/align/matrix_data/PAM450.mat +34 -0
  162. biotite/sequence/align/matrix_data/PAM460.mat +34 -0
  163. biotite/sequence/align/matrix_data/PAM470.mat +34 -0
  164. biotite/sequence/align/matrix_data/PAM480.mat +34 -0
  165. biotite/sequence/align/matrix_data/PAM490.mat +34 -0
  166. biotite/sequence/align/matrix_data/PAM50.mat +34 -0
  167. biotite/sequence/align/matrix_data/PAM500.mat +34 -0
  168. biotite/sequence/align/matrix_data/PAM60.mat +34 -0
  169. biotite/sequence/align/matrix_data/PAM70.mat +34 -0
  170. biotite/sequence/align/matrix_data/PAM80.mat +34 -0
  171. biotite/sequence/align/matrix_data/PAM90.mat +34 -0
  172. biotite/sequence/align/matrix_data/PB.license +21 -0
  173. biotite/sequence/align/matrix_data/PB.mat +18 -0
  174. biotite/sequence/align/matrix_data/RBLOSUM52_5.0.mat +25 -0
  175. biotite/sequence/align/matrix_data/RBLOSUM59_13p.mat +25 -0
  176. biotite/sequence/align/matrix_data/RBLOSUM59_14.3.mat +25 -0
  177. biotite/sequence/align/matrix_data/RBLOSUM64_5.0.mat +25 -0
  178. biotite/sequence/align/matrix_data/RBLOSUM69_13p.mat +25 -0
  179. biotite/sequence/align/matrix_data/RBLOSUM69_14.3.mat +25 -0
  180. biotite/sequence/align/multiple.cpython-313-x86_64-linux-gnu.so +0 -0
  181. biotite/sequence/align/multiple.pyx +619 -0
  182. biotite/sequence/align/pairwise.cpython-313-x86_64-linux-gnu.so +0 -0
  183. biotite/sequence/align/pairwise.pyx +585 -0
  184. biotite/sequence/align/permutation.cpython-313-x86_64-linux-gnu.so +0 -0
  185. biotite/sequence/align/permutation.pyx +313 -0
  186. biotite/sequence/align/primes.txt +821 -0
  187. biotite/sequence/align/selector.cpython-313-x86_64-linux-gnu.so +0 -0
  188. biotite/sequence/align/selector.pyx +954 -0
  189. biotite/sequence/align/statistics.py +264 -0
  190. biotite/sequence/align/tracetable.cpython-313-x86_64-linux-gnu.so +0 -0
  191. biotite/sequence/align/tracetable.pxd +64 -0
  192. biotite/sequence/align/tracetable.pyx +370 -0
  193. biotite/sequence/alphabet.py +555 -0
  194. biotite/sequence/annotation.py +836 -0
  195. biotite/sequence/codec.cpython-313-x86_64-linux-gnu.so +0 -0
  196. biotite/sequence/codec.pyx +155 -0
  197. biotite/sequence/codon.py +476 -0
  198. biotite/sequence/codon_tables.txt +202 -0
  199. biotite/sequence/graphics/__init__.py +33 -0
  200. biotite/sequence/graphics/alignment.py +1101 -0
  201. biotite/sequence/graphics/color_schemes/3di_flower.json +48 -0
  202. biotite/sequence/graphics/color_schemes/autumn.json +51 -0
  203. biotite/sequence/graphics/color_schemes/blossom.json +51 -0
  204. biotite/sequence/graphics/color_schemes/clustalx_dna.json +11 -0
  205. biotite/sequence/graphics/color_schemes/clustalx_protein.json +28 -0
  206. biotite/sequence/graphics/color_schemes/flower.json +51 -0
  207. biotite/sequence/graphics/color_schemes/jalview_buried.json +31 -0
  208. biotite/sequence/graphics/color_schemes/jalview_hydrophobicity.json +31 -0
  209. biotite/sequence/graphics/color_schemes/jalview_prop_helix.json +31 -0
  210. biotite/sequence/graphics/color_schemes/jalview_prop_strand.json +31 -0
  211. biotite/sequence/graphics/color_schemes/jalview_prop_turn.json +31 -0
  212. biotite/sequence/graphics/color_schemes/jalview_taylor.json +28 -0
  213. biotite/sequence/graphics/color_schemes/jalview_zappo.json +28 -0
  214. biotite/sequence/graphics/color_schemes/ocean.json +51 -0
  215. biotite/sequence/graphics/color_schemes/pb_flower.json +40 -0
  216. biotite/sequence/graphics/color_schemes/rainbow_dna.json +11 -0
  217. biotite/sequence/graphics/color_schemes/rainbow_protein.json +30 -0
  218. biotite/sequence/graphics/color_schemes/spring.json +51 -0
  219. biotite/sequence/graphics/color_schemes/sunset.json +51 -0
  220. biotite/sequence/graphics/color_schemes/wither.json +51 -0
  221. biotite/sequence/graphics/colorschemes.py +170 -0
  222. biotite/sequence/graphics/dendrogram.py +231 -0
  223. biotite/sequence/graphics/features.py +544 -0
  224. biotite/sequence/graphics/logo.py +102 -0
  225. biotite/sequence/graphics/plasmid.py +712 -0
  226. biotite/sequence/io/__init__.py +12 -0
  227. biotite/sequence/io/fasta/__init__.py +22 -0
  228. biotite/sequence/io/fasta/convert.py +283 -0
  229. biotite/sequence/io/fasta/file.py +265 -0
  230. biotite/sequence/io/fastq/__init__.py +19 -0
  231. biotite/sequence/io/fastq/convert.py +117 -0
  232. biotite/sequence/io/fastq/file.py +507 -0
  233. biotite/sequence/io/genbank/__init__.py +17 -0
  234. biotite/sequence/io/genbank/annotation.py +269 -0
  235. biotite/sequence/io/genbank/file.py +573 -0
  236. biotite/sequence/io/genbank/metadata.py +336 -0
  237. biotite/sequence/io/genbank/sequence.py +173 -0
  238. biotite/sequence/io/general.py +201 -0
  239. biotite/sequence/io/gff/__init__.py +26 -0
  240. biotite/sequence/io/gff/convert.py +128 -0
  241. biotite/sequence/io/gff/file.py +449 -0
  242. biotite/sequence/phylo/__init__.py +36 -0
  243. biotite/sequence/phylo/nj.cpython-313-x86_64-linux-gnu.so +0 -0
  244. biotite/sequence/phylo/nj.pyx +221 -0
  245. biotite/sequence/phylo/tree.cpython-313-x86_64-linux-gnu.so +0 -0
  246. biotite/sequence/phylo/tree.pyx +1169 -0
  247. biotite/sequence/phylo/upgma.cpython-313-x86_64-linux-gnu.so +0 -0
  248. biotite/sequence/phylo/upgma.pyx +164 -0
  249. biotite/sequence/profile.py +561 -0
  250. biotite/sequence/search.py +117 -0
  251. biotite/sequence/seqtypes.py +720 -0
  252. biotite/sequence/sequence.py +373 -0
  253. biotite/setup_ccd.py +197 -0
  254. biotite/structure/__init__.py +135 -0
  255. biotite/structure/alphabet/__init__.py +25 -0
  256. biotite/structure/alphabet/encoder.py +332 -0
  257. biotite/structure/alphabet/encoder_weights_3di.kerasify +0 -0
  258. biotite/structure/alphabet/i3d.py +109 -0
  259. biotite/structure/alphabet/layers.py +86 -0
  260. biotite/structure/alphabet/pb.license +21 -0
  261. biotite/structure/alphabet/pb.py +170 -0
  262. biotite/structure/alphabet/unkerasify.py +128 -0
  263. biotite/structure/atoms.py +1562 -0
  264. biotite/structure/basepairs.py +1403 -0
  265. biotite/structure/bonds.cpython-313-x86_64-linux-gnu.so +0 -0
  266. biotite/structure/bonds.pyx +2036 -0
  267. biotite/structure/box.py +724 -0
  268. biotite/structure/celllist.cpython-313-x86_64-linux-gnu.so +0 -0
  269. biotite/structure/celllist.pyx +864 -0
  270. biotite/structure/chains.py +310 -0
  271. biotite/structure/charges.cpython-313-x86_64-linux-gnu.so +0 -0
  272. biotite/structure/charges.pyx +520 -0
  273. biotite/structure/compare.py +683 -0
  274. biotite/structure/density.py +109 -0
  275. biotite/structure/dotbracket.py +213 -0
  276. biotite/structure/error.py +39 -0
  277. biotite/structure/filter.py +591 -0
  278. biotite/structure/geometry.py +817 -0
  279. biotite/structure/graphics/__init__.py +13 -0
  280. biotite/structure/graphics/atoms.py +243 -0
  281. biotite/structure/graphics/rna.py +298 -0
  282. biotite/structure/hbond.py +425 -0
  283. biotite/structure/info/__init__.py +24 -0
  284. biotite/structure/info/atom_masses.json +121 -0
  285. biotite/structure/info/atoms.py +98 -0
  286. biotite/structure/info/bonds.py +149 -0
  287. biotite/structure/info/ccd.py +200 -0
  288. biotite/structure/info/components.bcif +0 -0
  289. biotite/structure/info/groups.py +128 -0
  290. biotite/structure/info/masses.py +121 -0
  291. biotite/structure/info/misc.py +137 -0
  292. biotite/structure/info/radii.py +267 -0
  293. biotite/structure/info/standardize.py +185 -0
  294. biotite/structure/integrity.py +213 -0
  295. biotite/structure/io/__init__.py +29 -0
  296. biotite/structure/io/dcd/__init__.py +13 -0
  297. biotite/structure/io/dcd/file.py +67 -0
  298. biotite/structure/io/general.py +243 -0
  299. biotite/structure/io/gro/__init__.py +14 -0
  300. biotite/structure/io/gro/file.py +343 -0
  301. biotite/structure/io/mol/__init__.py +20 -0
  302. biotite/structure/io/mol/convert.py +112 -0
  303. biotite/structure/io/mol/ctab.py +420 -0
  304. biotite/structure/io/mol/header.py +120 -0
  305. biotite/structure/io/mol/mol.py +149 -0
  306. biotite/structure/io/mol/sdf.py +940 -0
  307. biotite/structure/io/netcdf/__init__.py +13 -0
  308. biotite/structure/io/netcdf/file.py +64 -0
  309. biotite/structure/io/pdb/__init__.py +20 -0
  310. biotite/structure/io/pdb/convert.py +389 -0
  311. biotite/structure/io/pdb/file.py +1380 -0
  312. biotite/structure/io/pdb/hybrid36.cpython-313-x86_64-linux-gnu.so +0 -0
  313. biotite/structure/io/pdb/hybrid36.pyx +242 -0
  314. biotite/structure/io/pdbqt/__init__.py +15 -0
  315. biotite/structure/io/pdbqt/convert.py +113 -0
  316. biotite/structure/io/pdbqt/file.py +688 -0
  317. biotite/structure/io/pdbx/__init__.py +23 -0
  318. biotite/structure/io/pdbx/bcif.py +674 -0
  319. biotite/structure/io/pdbx/cif.py +1091 -0
  320. biotite/structure/io/pdbx/component.py +251 -0
  321. biotite/structure/io/pdbx/compress.py +362 -0
  322. biotite/structure/io/pdbx/convert.py +2113 -0
  323. biotite/structure/io/pdbx/encoding.cpython-313-x86_64-linux-gnu.so +0 -0
  324. biotite/structure/io/pdbx/encoding.pyx +1078 -0
  325. biotite/structure/io/trajfile.py +696 -0
  326. biotite/structure/io/trr/__init__.py +13 -0
  327. biotite/structure/io/trr/file.py +43 -0
  328. biotite/structure/io/util.py +38 -0
  329. biotite/structure/io/xtc/__init__.py +13 -0
  330. biotite/structure/io/xtc/file.py +43 -0
  331. biotite/structure/mechanics.py +72 -0
  332. biotite/structure/molecules.py +337 -0
  333. biotite/structure/pseudoknots.py +622 -0
  334. biotite/structure/rdf.py +245 -0
  335. biotite/structure/repair.py +302 -0
  336. biotite/structure/residues.py +716 -0
  337. biotite/structure/rings.py +451 -0
  338. biotite/structure/sasa.cpython-313-x86_64-linux-gnu.so +0 -0
  339. biotite/structure/sasa.pyx +322 -0
  340. biotite/structure/segments.py +328 -0
  341. biotite/structure/sequence.py +110 -0
  342. biotite/structure/spacegroups.json +1567 -0
  343. biotite/structure/spacegroups.license +26 -0
  344. biotite/structure/sse.py +306 -0
  345. biotite/structure/superimpose.py +511 -0
  346. biotite/structure/tm.py +581 -0
  347. biotite/structure/transform.py +736 -0
  348. biotite/structure/util.py +160 -0
  349. biotite/version.py +34 -0
  350. biotite/visualize.py +375 -0
  351. biotite-1.5.0.dist-info/METADATA +162 -0
  352. biotite-1.5.0.dist-info/RECORD +354 -0
  353. biotite-1.5.0.dist-info/WHEEL +6 -0
  354. biotite-1.5.0.dist-info/licenses/LICENSE.rst +30 -0