bindsight 0.3.5__py3-none-any.whl

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Files changed (106) hide show
  1. bindsight/README.md +44 -0
  2. bindsight/__init__.py +15 -0
  3. bindsight/benchmark/__init__.py +71 -0
  4. bindsight/benchmark/core.py +497 -0
  5. bindsight/benchmark/defaults.py +28 -0
  6. bindsight/benchmark/designer_bench.py +899 -0
  7. bindsight/benchmark/outcomes.py +508 -0
  8. bindsight/benchmark/panel.py +621 -0
  9. bindsight/benchmark/rediscovery.py +1153 -0
  10. bindsight/benchmark/statistics.py +622 -0
  11. bindsight/benchmark/study.py +1153 -0
  12. bindsight/benchmark/study_figures.py +164 -0
  13. bindsight/benchmark/study_report.py +607 -0
  14. bindsight/cli.py +2429 -0
  15. bindsight/config.py +451 -0
  16. bindsight/cost.py +258 -0
  17. bindsight/deg/__init__.py +7 -0
  18. bindsight/deg/pydeseq2_runner.py +285 -0
  19. bindsight/design/__init__.py +23 -0
  20. bindsight/design/_common.py +501 -0
  21. bindsight/design/bindcraft.py +78 -0
  22. bindsight/design/boltzgen.py +79 -0
  23. bindsight/design/developability.py +140 -0
  24. bindsight/design/embeddings.py +165 -0
  25. bindsight/design/prescreen.py +169 -0
  26. bindsight/design/protocol.py +111 -0
  27. bindsight/design/rfdiff_mpnn.py +93 -0
  28. bindsight/epitopes/__init__.py +7 -0
  29. bindsight/epitopes/surface_bind.py +134 -0
  30. bindsight/export/__init__.py +7 -0
  31. bindsight/export/ro_crate.py +595 -0
  32. bindsight/io/__init__.py +19 -0
  33. bindsight/io/cbioportal.py +118 -0
  34. bindsight/io/gdc.py +343 -0
  35. bindsight/io/paths.py +124 -0
  36. bindsight/pipelines/__init__.py +9 -0
  37. bindsight/pipelines/caveats.py +60 -0
  38. bindsight/pipelines/discover.py +1443 -0
  39. bindsight/pipelines/full_run.py +410 -0
  40. bindsight/plugins.py +335 -0
  41. bindsight/provenance/__init__.py +34 -0
  42. bindsight/provenance/append.py +199 -0
  43. bindsight/provenance/fragments.py +216 -0
  44. bindsight/provenance/manifest.py +506 -0
  45. bindsight/rank/__init__.py +7 -0
  46. bindsight/rank/scoring.py +355 -0
  47. bindsight/report/__init__.py +39 -0
  48. bindsight/report/format.py +100 -0
  49. bindsight/report/html.py +645 -0
  50. bindsight/report/showcase.py +653 -0
  51. bindsight/report/templates/report.css +67 -0
  52. bindsight/report/templates/report.html.j2 +420 -0
  53. bindsight/report/theme.py +231 -0
  54. bindsight/report/web/__init__.py +35 -0
  55. bindsight/report/web/app.py +624 -0
  56. bindsight/report/web/static/binder_viewer.js +245 -0
  57. bindsight/report/web/static/bindsight.css +455 -0
  58. bindsight/report/web/static/charts.js +425 -0
  59. bindsight/report/web/static/vendor/3Dmol-min.js +2 -0
  60. bindsight/report/web/static/vendor/3Dmol.LICENSE +90 -0
  61. bindsight/report/web/static/your_data_check.js +370 -0
  62. bindsight/report/web/templates/base.html.j2 +48 -0
  63. bindsight/report/web/templates/evidence.html.j2 +341 -0
  64. bindsight/report/web/templates/overview.html.j2 +140 -0
  65. bindsight/report/web/templates/runs.html.j2 +125 -0
  66. bindsight/report/web/templates/try.html.j2 +155 -0
  67. bindsight/report/web/templates/your_data.html.j2 +46 -0
  68. bindsight/runners/__init__.py +7 -0
  69. bindsight/runners/colab.py +158 -0
  70. bindsight/runners/job_exec.py +1110 -0
  71. bindsight/runners/kaggle.py +425 -0
  72. bindsight/runners/kaggle_kernel.py +489 -0
  73. bindsight/runners/local_docker.py +154 -0
  74. bindsight/runners/mock.py +167 -0
  75. bindsight/runners/modal_runner.py +199 -0
  76. bindsight/runners/notebook.py +116 -0
  77. bindsight/runners/notebook_content.py +217 -0
  78. bindsight/runners/protocol.py +81 -0
  79. bindsight/runners/source_wheel.py +104 -0
  80. bindsight/runners/tools.py +997 -0
  81. bindsight/structures/__init__.py +7 -0
  82. bindsight/structures/alphafolddb.py +93 -0
  83. bindsight/structures/plddt.py +92 -0
  84. bindsight/structures/topology.py +227 -0
  85. bindsight/surfaceome/__init__.py +42 -0
  86. bindsight/surfaceome/data/surfaceome_extended.tsv +4814 -0
  87. bindsight/surfaceome/data/surfy_offline.txt +17 -0
  88. bindsight/surfaceome/data/surfy_v1.ensembl.tsv +3380 -0
  89. bindsight/surfaceome/data/surfy_v1.uniprot.txt +2901 -0
  90. bindsight/surfaceome/surfy.py +441 -0
  91. bindsight/targets/__init__.py +7 -0
  92. bindsight/targets/ensembl_uniprot.py +56 -0
  93. bindsight/targets/gtex.py +250 -0
  94. bindsight/targets/open_targets.py +239 -0
  95. bindsight/validate/__init__.py +7 -0
  96. bindsight/validate/af2_ig.py +49 -0
  97. bindsight/validate/boltz2.py +256 -0
  98. bindsight/validate/chai1r.py +42 -0
  99. bindsight/validate/protocol.py +188 -0
  100. bindsight-0.3.5.data/data/bindsight_demo/config.yaml +54 -0
  101. bindsight-0.3.5.dist-info/METADATA +495 -0
  102. bindsight-0.3.5.dist-info/RECORD +106 -0
  103. bindsight-0.3.5.dist-info/WHEEL +4 -0
  104. bindsight-0.3.5.dist-info/entry_points.txt +20 -0
  105. bindsight-0.3.5.dist-info/licenses/COPYRIGHT +24 -0
  106. bindsight-0.3.5.dist-info/licenses/LICENSE +681 -0
bindsight/surfaceome/data/surfy_offline.txt ADDED
@@ -0,0 +1,17 @@
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+ # Offline-test fallback subset of the SURFY surfaceome list.
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+ # This is NOT the full SURFY table — it is a tiny curated list of widely-cited
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+ # human surface antigens used for unit tests and `--allow-offline` smoke runs.
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+ # For production discovery runs, populate the cache from
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+ # https://wlab.ethz.ch/surfaceome (no licence stated by the source).
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+ #
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+ # One UniProt accession per line. Lines starting with '#' are ignored.
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+ P04626
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+ P00533
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+ P56747
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+ Q13421
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+ P10747
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+ P16410
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+ Q9NZQ7
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+ P09038
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+ P10275
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+ P19838