[us-commits] [ehb54/ultrascan3] e94bcf: Add a GUI review dialog for non-coded residues

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e94bcfcd880bf374bb48742547448ef12606d6cc
      https://github.com/ehb54/ultrascan3/commit/e94bcfcd880bf374bb48742547448ef12606d6cc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn.h
    A us_somo/develop/include/us_hydrodyn_perceive_dialog.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/perceiver/DECISIONS.md
    A us_somo/develop/perceiver/run_dialog_test.sh
    A us_somo/develop/perceiver/tests/dialog_qt.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    A us_somo/develop/src/us_hydrodyn_perceive_dialog.cpp

  Log Message:
  -----------
  Add a GUI review dialog for non-coded residues

Everything built so far was reachable only from gui_script. A user working in
SOMO saw none of it, and a non-coded residue still fell silently to the
Automatic Bead Builder's averaged generic bead. This makes it visible and
correctable.

US_Hydrodyn_Perceive_Dialog presents one modal review per non-coded residue,
in the order Mattia laid out: view the residue in RasMol, confirm the
perceived atom table, edit the proposed per-atom hydration, check the
anhydrous volume, see the bead count and position, choose a bead colour, and
check the psv, with the somo.residue entry rebuilt live below so what is on
screen is exactly what Accept returns.

Only hydration is editable in the atom table. Name, hybrid, mass and radius
are perceived, and editing them would desynchronise the entry from the
geometry it came from. Hydration is editable because it is the weakest of the
three computed numbers; the residue total is shown beneath it and updates
live, with a note that the total is the quantity with literature backing while
the per-atom split is convention.

The colour combo is built from the manual's table and shows index, name and
meaning. The four reserved colours are never offered, since two of them mark a
bead for exclusion from the hydrodynamic computation and the other two are
assigned automatically during model generation.

Appending to somo.residue is opt-in and off by default, so accepting an entry
is per-session unless the user asks otherwise. After a save the user is told
to reload the structure, since hot-reloading the residue table would
invalidate indices the loaded model already holds.

The trigger is a Lookup Tables menu item rather than a hook inside model
building: check_for_missing_atoms runs per model and inside batch paths, so
opening a modal dialog from there would be invasive and wrong for scripted
runs. Skip leaves the residue to the Automatic Bead Builder exactly as before.

Testing a widget needs a widget test: run_dialog_test.sh builds the dialog
against the real library and exercises it under an offscreen Qt platform, so
it needs no display. Eighteen checks cover the proposal round-tripping through
parse and rebuild, a hydration edit propagating to both the atom line and the
bead total, a nonsense edit being rejected and the previous value restored,
read-only columns actually being read-only, the colour combo offering twelve
of the sixteen colours and defaulting to the configured one, and nothing being
marked accepted or saved until the user acts.

Refs ehb54/ultrascan-tickets#980

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



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