PyPI - bindsight - Versions diffs - 0.3.5__py3-none-any.whl - Mend

bindsight 0.3.5__py3-none-any.whl

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 (106) hide show

bindsight/README.md +44 -0
bindsight/__init__.py +15 -0
bindsight/benchmark/__init__.py +71 -0
bindsight/benchmark/core.py +497 -0
bindsight/benchmark/defaults.py +28 -0
bindsight/benchmark/designer_bench.py +899 -0
bindsight/benchmark/outcomes.py +508 -0
bindsight/benchmark/panel.py +621 -0
bindsight/benchmark/rediscovery.py +1153 -0
bindsight/benchmark/statistics.py +622 -0
bindsight/benchmark/study.py +1153 -0
bindsight/benchmark/study_figures.py +164 -0
bindsight/benchmark/study_report.py +607 -0
bindsight/cli.py +2429 -0
bindsight/config.py +451 -0
bindsight/cost.py +258 -0
bindsight/deg/__init__.py +7 -0
bindsight/deg/pydeseq2_runner.py +285 -0
bindsight/design/__init__.py +23 -0
bindsight/design/_common.py +501 -0
bindsight/design/bindcraft.py +78 -0
bindsight/design/boltzgen.py +79 -0
bindsight/design/developability.py +140 -0
bindsight/design/embeddings.py +165 -0
bindsight/design/prescreen.py +169 -0
bindsight/design/protocol.py +111 -0
bindsight/design/rfdiff_mpnn.py +93 -0
bindsight/epitopes/__init__.py +7 -0
bindsight/epitopes/surface_bind.py +134 -0
bindsight/export/__init__.py +7 -0
bindsight/export/ro_crate.py +595 -0
bindsight/io/__init__.py +19 -0
bindsight/io/cbioportal.py +118 -0
bindsight/io/gdc.py +343 -0
bindsight/io/paths.py +124 -0
bindsight/pipelines/__init__.py +9 -0
bindsight/pipelines/caveats.py +60 -0
bindsight/pipelines/discover.py +1443 -0
bindsight/pipelines/full_run.py +410 -0
bindsight/plugins.py +335 -0
bindsight/provenance/__init__.py +34 -0
bindsight/provenance/append.py +199 -0
bindsight/provenance/fragments.py +216 -0
bindsight/provenance/manifest.py +506 -0
bindsight/rank/__init__.py +7 -0
bindsight/rank/scoring.py +355 -0
bindsight/report/__init__.py +39 -0
bindsight/report/format.py +100 -0
bindsight/report/html.py +645 -0
bindsight/report/showcase.py +653 -0
bindsight/report/templates/report.css +67 -0
bindsight/report/templates/report.html.j2 +420 -0
bindsight/report/theme.py +231 -0
bindsight/report/web/__init__.py +35 -0
bindsight/report/web/app.py +624 -0
bindsight/report/web/static/binder_viewer.js +245 -0
bindsight/report/web/static/bindsight.css +455 -0
bindsight/report/web/static/charts.js +425 -0
bindsight/report/web/static/vendor/3Dmol-min.js +2 -0
bindsight/report/web/static/vendor/3Dmol.LICENSE +90 -0
bindsight/report/web/static/your_data_check.js +370 -0
bindsight/report/web/templates/base.html.j2 +48 -0
bindsight/report/web/templates/evidence.html.j2 +341 -0
bindsight/report/web/templates/overview.html.j2 +140 -0
bindsight/report/web/templates/runs.html.j2 +125 -0
bindsight/report/web/templates/try.html.j2 +155 -0
bindsight/report/web/templates/your_data.html.j2 +46 -0
bindsight/runners/__init__.py +7 -0
bindsight/runners/colab.py +158 -0
bindsight/runners/job_exec.py +1110 -0
bindsight/runners/kaggle.py +425 -0
bindsight/runners/kaggle_kernel.py +489 -0
bindsight/runners/local_docker.py +154 -0
bindsight/runners/mock.py +167 -0
bindsight/runners/modal_runner.py +199 -0
bindsight/runners/notebook.py +116 -0
bindsight/runners/notebook_content.py +217 -0
bindsight/runners/protocol.py +81 -0
bindsight/runners/source_wheel.py +104 -0
bindsight/runners/tools.py +997 -0
bindsight/structures/__init__.py +7 -0
bindsight/structures/alphafolddb.py +93 -0
bindsight/structures/plddt.py +92 -0
bindsight/structures/topology.py +227 -0
bindsight/surfaceome/__init__.py +42 -0
bindsight/surfaceome/data/surfaceome_extended.tsv +4814 -0
bindsight/surfaceome/data/surfy_offline.txt +17 -0
bindsight/surfaceome/data/surfy_v1.ensembl.tsv +3380 -0
bindsight/surfaceome/data/surfy_v1.uniprot.txt +2901 -0
bindsight/surfaceome/surfy.py +441 -0
bindsight/targets/__init__.py +7 -0
bindsight/targets/ensembl_uniprot.py +56 -0
bindsight/targets/gtex.py +250 -0
bindsight/targets/open_targets.py +239 -0
bindsight/validate/__init__.py +7 -0
bindsight/validate/af2_ig.py +49 -0
bindsight/validate/boltz2.py +256 -0
bindsight/validate/chai1r.py +42 -0
bindsight/validate/protocol.py +188 -0
bindsight-0.3.5.data/data/bindsight_demo/config.yaml +54 -0
bindsight-0.3.5.dist-info/METADATA +495 -0
bindsight-0.3.5.dist-info/RECORD +106 -0
bindsight-0.3.5.dist-info/WHEEL +4 -0
bindsight-0.3.5.dist-info/entry_points.txt +20 -0
bindsight-0.3.5.dist-info/licenses/COPYRIGHT +24 -0
bindsight-0.3.5.dist-info/licenses/LICENSE +681 -0

bindsight/surfaceome/data/surfy_v1.ensembl.tsv ADDED Viewed

@@ -0,0 +1,3380 @@
+# Ensembl gene id -> UniProt accession, for the SURFY surfaceome.
+# Generated by scripts/build_surfy_gene_map.py from the UniProt
+# cross-references of reviewed human proteins. Versionless gene ids,
+# matching how GDC STAR-Counts tables are keyed.
+# 3375 pairs covering 2706 of 2886 accessions.
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