TBD - #8
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- Multi-copy ligand alerts now gate on genuine per-copy binding-site
divergence (>1 distinct site_ref, fail-closed on missing sites) rather
than crystallographic copy count; per-copy role divergence is advisory.
- Separate native G-protein alpha subtype ambiguity from genuine chimeras:
when the alpha5 helix confirms the family but cannot resolve the member
(e.g. Gi1 vs Gi2), emit an advisory "[G-ALPHA SUBTYPE UNRESOLVED]" note
instead of a critical "[CHIMERIC G PROTEIN]" warning; non-human orthologs
("[G-ALPHA SPECIES UNVERIFIED]"), model-declared chimeras, and unverified
constructs remain gated. g_proteins.csv columns are unchanged.
- Stop mistaking peptide agonists and fusion/tag chains for receptors:
extend the non-receptor slug-prefix list (collision-checked against the
receptor set) so they no longer trigger the suspicious-7TM alert; the
alert and its guidance are unchanged.
- De-noise validation gating: route already-corrected PubChem-mismatch
notes and apo-placeholder site disagreements to advisory; make the
apo-with-molecules check role-aware (advisory only when coexisting
molecules are all structural cofactors/ions/lipids); add a source-side
reconcile that downgrades gating records pointing at entities absent from
the shipped output, behind a bracket-safe, fail-closed guard.
- Add unit tests for the new gating branches; full suite green.
Co-Authored-By: Claude Opus 4.8 <[email protected]>
… single receptor Adds a chain-total check on the all-single stoichiometry proxy, scans every candidate assembly for a homo-oligomer record, and skips entries whose cited evidence only recites that assembly.
A fusion or splice construct can fragment the UniProt alignment so only five TM helices map, all of them resolved. The absolute six-helix threshold read that as missing density; requiring resolved == total with at least five annotated separates a mapping artefact from a genuinely unbuilt helix.
…etes a heterotrimer Also stops reporting a relocation when the subunit is already recorded on that chain: nothing is recovered there, so the bucket entry is left in place rather than deleted and neither channel describes a move that did not happen.
The silent no-op path is for beta and gamma only. An auxiliary entry sharing the G-alpha chain is what a receptor-Galpha fusion or a dominant-negative chimera looks like, so alpha keeps its review, matching the split this function applies elsewhere.
The weak-match branch is the one place the sequence check returns nothing about G-alpha identity, so a slug asserted there ships unverified. An asserted slug now raises a conflict; an honest abstention stays a note, since there is no claim to check.
The compound row cannot record which copy sits at which site; mirror the gating alert so that table opens for review.
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