b2bTools 3.0.6rc2__tar.gz → 3.0.7__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (273) hide show
  1. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/MANIFEST.in +8 -3
  2. {b2bTools-3.0.6rc2/b2bTools.egg-info → b2btools-3.0.7}/PKG-INFO +315 -206
  3. b2bTools-3.0.6rc2/PKG-INFO → b2btools-3.0.7/README.md +242 -232
  4. b2btools-3.0.7/b2bTools/__main__.py +182 -0
  5. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/Io.py +9 -9
  6. b2btools-3.0.7/b2bTools/multipleSeq/Predictor.py +153 -0
  7. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/multipleSeq/msa_core.py +9 -14
  8. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/multipleSeq/msa_plot.py +0 -3
  9. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftCrypt.py +0 -2
  10. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/utils.py +1 -18
  11. b2btools-3.0.7/b2bTools/requirements-dev.txt +11 -0
  12. b2btools-3.0.7/b2bTools/requirements.txt +14 -0
  13. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/agmata.py +11 -2
  14. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/sources/agmata_source.py +24 -10
  15. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/standalone.py +40 -15
  16. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/runpsipred_single.py +1 -1
  17. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/vettore_gen.py +1 -1
  18. b2btools-3.0.7/b2bTools/singleSeq/DynaMine/Predictor.py +236 -0
  19. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/EFoldMine/Predictor.py +38 -18
  20. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/PSPer/Predictor.py +1 -1
  21. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/PSPer/hmmer_research/hmmsearch_otf.py +4 -3
  22. b2btools-3.0.7/b2bTools/singleSeq/PSPer/phase_transition_hmm.py +919 -0
  23. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/PSPer/source/utils.py +0 -1
  24. b2btools-3.0.7/b2bTools/singleSeq/PSPer/standalone.py +182 -0
  25. b2btools-3.0.7/b2bTools/singleSeq/Predictor.py +158 -0
  26. b2btools-3.0.7/b2bTools/singleSeq/constants.py +41 -0
  27. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/single_core.py +1 -4
  28. b2btools-3.0.7/b2bTools/wrapper_source/metadata.py +296 -0
  29. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/wrapper_source/wrapper_utils.py +189 -89
  30. b2bTools-3.0.6rc2/README.md → b2btools-3.0.7/b2bTools.egg-info/PKG-INFO +341 -203
  31. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools.egg-info/SOURCES.txt +13 -1
  32. b2btools-3.0.7/b2bTools.egg-info/entry_points.txt +2 -0
  33. b2btools-3.0.7/b2bTools.egg-info/requires.txt +79 -0
  34. b2btools-3.0.7/b2bTools.egg-info/top_level.txt +2 -0
  35. b2btools-3.0.7/b2bTools_version/__init__.py +0 -0
  36. b2btools-3.0.7/b2bTools_version/versioning.py +2 -0
  37. b2btools-3.0.7/requirements-py310.txt +12 -0
  38. b2btools-3.0.7/requirements-py311.txt +10 -0
  39. b2btools-3.0.7/requirements-py312.txt +10 -0
  40. b2btools-3.0.7/requirements-py37.txt +11 -0
  41. b2btools-3.0.7/requirements-py38.txt +12 -0
  42. b2btools-3.0.7/requirements-py39.txt +12 -0
  43. b2btools-3.0.7/setup.py +90 -0
  44. b2bTools-3.0.6rc2/b2bTools/__main__.py +0 -148
  45. b2bTools-3.0.6rc2/b2bTools/multipleSeq/Predictor.py +0 -143
  46. b2bTools-3.0.6rc2/b2bTools/singleSeq/DynaMine/Predictor.py +0 -210
  47. b2bTools-3.0.6rc2/b2bTools/singleSeq/PSPer/phase_transition_hmm.py +0 -903
  48. b2bTools-3.0.6rc2/b2bTools/singleSeq/PSPer/standalone.py +0 -155
  49. b2bTools-3.0.6rc2/b2bTools/singleSeq/Predictor.py +0 -160
  50. b2bTools-3.0.6rc2/b2bTools/singleSeq/constants.py +0 -16
  51. b2bTools-3.0.6rc2/b2bTools.egg-info/requires.txt +0 -35
  52. b2bTools-3.0.6rc2/b2bTools.egg-info/top_level.txt +0 -1
  53. b2bTools-3.0.6rc2/setup.py +0 -86
  54. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/__init__.py +0 -0
  55. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/Util.py +0 -0
  56. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/__init__.py +0 -0
  57. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/File.py +0 -0
  58. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/SaveFrame.py +0 -0
  59. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/TagTable.py +0 -0
  60. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/Text.py +0 -0
  61. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/Utils.py +0 -0
  62. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/__init__.py +0 -0
  63. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/bmrb/base.py +0 -0
  64. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/__init__.py +0 -0
  65. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/__init__.py +0 -0
  66. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/general/Constants.py +0 -0
  67. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/general/Util.py +0 -0
  68. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/general/__init__.py +0 -0
  69. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/general/formatIO.py +0 -0
  70. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/__init__.py +0 -0
  71. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/chemShiftsIO.py +0 -0
  72. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/constants.py +0 -0
  73. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/coordinatesIO.py +0 -0
  74. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/csaIO.py +0 -0
  75. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/dihedralConstraintsIO.py +0 -0
  76. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/distanceConstraintsIO.py +0 -0
  77. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/generalIO.py +0 -0
  78. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/hBondConstraintsIO.py +0 -0
  79. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/hExchProtectionIO.py +0 -0
  80. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/hExchRateIO.py +0 -0
  81. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/hetNoeIO.py +0 -0
  82. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/jCouplingIO.py +0 -0
  83. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/nmrStarDict.py +0 -0
  84. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/orderParamIO.py +0 -0
  85. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/peopleAndCitationsIO.py +0 -0
  86. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/projectIO.py +0 -0
  87. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/rdcConstraintsIO.py +0 -0
  88. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/rdcIO.py +0 -0
  89. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/sequenceIO.py +0 -0
  90. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/t1RelaxIO.py +0 -0
  91. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/t1RhoRelaxIO.py +0 -0
  92. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/t2RelaxIO.py +0 -0
  93. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/format/nmrStar/util.py +0 -0
  94. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/general/Constants.py +0 -0
  95. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/general/__init__.py +0 -0
  96. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/universal/Constants.py +0 -0
  97. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/universal/Io.py +0 -0
  98. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/universal/Util.py +0 -0
  99. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/ccpn/universal/__init__.py +0 -0
  100. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/parsers/__init__.py +0 -0
  101. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/parsers/alignments.py +0 -0
  102. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/parsers/fasta.py +0 -0
  103. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/parsers/nef.py +0 -0
  104. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/parsers/nmr_star.py +0 -0
  105. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/general/plotter.py +0 -0
  106. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/multipleSeq/__init__.py +0 -0
  107. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/multipleSeq/mapToMSA.py +0 -0
  108. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/multipleSeq/msa_quantification.py +0 -0
  109. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/__init__.py +0 -0
  110. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/Predictor.py +0 -0
  111. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/__init__.py +0 -0
  112. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/alignment.py +0 -0
  113. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/__init__.py +0 -0
  114. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_NH.mtorch +0 -0
  115. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_NH_p27.mtorch +0 -0
  116. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_NH_p37.mtorch +0 -0
  117. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_commons.mtorch +0 -0
  118. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_commons_p27.mtorch +0 -0
  119. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_commons_p37.mtorch +0 -0
  120. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_full.mtorch +0 -0
  121. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_full_p27.mtorch +0 -0
  122. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/models/new_full_p37.mtorch +0 -0
  123. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/__init__.py +0 -0
  124. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/autoenc_solo4.py +0 -0
  125. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/autoenchoder_standalone_version.py +0 -0
  126. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/chemical_shifts_custom_model.py +0 -0
  127. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/parser.py +0 -0
  128. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/nmr/shiftCrypt/shiftcrypt_pkg/shiftcrypt_parser.py +0 -0
  129. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/Predictor.py +0 -0
  130. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/__init__.py +0 -0
  131. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/bin/__init__.py +0 -0
  132. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/bin/agmata_c_final_linux +0 -0
  133. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/bin/agmata_c_final_mac +0 -0
  134. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/marshalled/__init__.py +0 -0
  135. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/marshalled/agmata_discriminative_converted.m +0 -0
  136. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/marshalled/discriminative.m +0 -0
  137. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/marshalled/model_parameters.m +0 -0
  138. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/Agmata/sources/__init__.py +0 -0
  139. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/Predictor.py +0 -0
  140. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/__init__.py +0 -0
  141. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/disomine_converted.mtorch +0 -0
  142. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/gru80_final.mtorch +0 -0
  143. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/torch_NN_gru_80AUC_prova.py +0 -0
  144. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/.DS_Store +0 -0
  145. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/__init__.py +0 -0
  146. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/.DS_Store +0 -0
  147. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/__init__.py +0 -0
  148. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/__init__.py +0 -0
  149. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/linux/__init__.py +0 -0
  150. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/linux/chkparse +0 -0
  151. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/linux/psipass2 +0 -0
  152. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/linux/psipred +0 -0
  153. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/linux/seq2mtx +0 -0
  154. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/osx/__init__.py +0 -0
  155. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/osx/chkparse +0 -0
  156. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/osx/psipass2 +0 -0
  157. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/osx/psipred +0 -0
  158. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/bin/osx/seq2mtx +0 -0
  159. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/data/__init__.py +0 -0
  160. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/data/weights.dat +0 -0
  161. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/data/weights.dat2 +0 -0
  162. {b2bTools-3.0.6rc2 → b2btools-3.0.7}/b2bTools/singleSeq/DisoMine/vector_builder/psipred/data/weights.dat3 +0 -0
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{b2bTools-3.0.6rc2 → b2btools-3.0.7}/MANIFEST.in RENAMED
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