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.uniprot.txt ADDED Viewed

@@ -0,0 +1,2901 @@
+# SURFY human surfaceome — UniProt accessions, one per line.
+#
+# Bausch-Fluck et al., 'The in silico human surfaceome', PNAS 2018, doi:10.1073/pnas.1808790115
+# Licence: none stated by the source; the article it accompanies is CC BY-NC-ND 4.0.
+# Redistributed here as a table of identifiers, with attribution.
+#
+# 2886 accessions, resolved from 2886 SURFY entry names.
+# Sources: https://wollscheidlab.org/SURFY/surfaceome_ids.txt
+#          https://rest.uniprot.org/uniprotkb (entry name -> accession)
+# Retrieved: 2026-07-29 (191 name(s) needed an individual lookup)
+#
+# Generated by scripts/build_surfy_list.py — do not edit by hand.
+# The upstream .xlsx is no longer retrievable (the host serves an HTML
+# page; the mirror serves a Git-LFS pointer), which is why this list is
+# vendored rather than downloaded at run time.
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