[us-commits] [ehb54/ultrascan3] 41f898: Fix cross-structure state leak and add Skip all re...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 41f898a605969d7a4fa9a98ac6b2acad9948ece5
      https://github.com/ehb54/ultrascan3/commit/41f898a605969d7a4fa9a98ac6b2acad9948ece5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-09 (Sun, 09 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_perceive_dialog.h
    M us_somo/develop/perceiver/DECISIONS.md
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_perceive_dialog.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp

  Log Message:
  -----------
  Fix cross-structure state leak and add Skip all remaining

Two defects found while preparing structures for GUI testing, both visible
only when perceive is run over more than the demo set.

Running perceive twice in one session reported the previous structure's
non-coded residues against the new one. Ubiquitin alone has none, but after
malate dehydrogenase it reported two, which were citrate's. SOMO fills
unknown_residues during model building and never clears it, so the set
accumulates across loads. The emitted entries were still right, since a stale
name absent from the new model produces nothing, but the reported counts
described a structure that was no longer open. Both the script command and the
GUI slot now intersect that set with the residue names actually present in the
loaded model.

The second is a usability failure with real consequences. 5PTI is a neutron
structure carrying heavy water and explicit deuteriums, so its residues have
more atoms than the table's entries and SOMO matches none of them: fifty-five
non-coded instances across eighteen types, which meant eighteen modal dialogs
in succession with no way out but to dismiss each one. The dialog now offers
Skip all remaining, which abandons the review and leaves everything to the
Automatic Bead Builder, with a tooltip naming the likely cause so a user
seeing an implausible count suspects the file rather than the tool. The caller
honours it and reports how many residues went unreviewed.

Worth noting that the perceiver itself handles these structures correctly, as
it excludes hydrogens from bond perception by design. It is SOMO's residue
matching that fails on the atom count. Making that match hydrogen-agnostic
would be the real fix.

Refs ehb54/ultrascan-tickets#980

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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