[us-commits] [ehb54/ultrascan3] bb17af: perceiver: readable table headers, and stop flaggi...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb17af1bcaf6164b068ae745e30cca99b1222cb1
      https://github.com/ehb54/ultrascan3/commit/bb17af1bcaf6164b068ae745e30cca99b1222cb1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-12 (Wed, 12 Aug 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_hydration.cpp
    M us_somo/develop/src/us_hydrodyn_perceive_dialog.cpp

  Log Message:
  -----------
  perceiver: readable table headers, and stop flagging plain carbonyl oxygens

Two things from Mattia's screenshot of 8RAT_gap3 / LYZ.

Headers unreadable: QHeaderView paints its sections with Button/ButtonText, not
Window/WindowText. perceive_palette() set only the text, so the section background
stayed inherited and the headers came out dark on dark. Button is now an explicit
light grey, and the palette is applied to the table and its header widget -- neither
inherits the frame's -- with the header in bold so it reads as one.

Spurious review flag: an oxygen with no hydrogen that is not part of a carboxyl --
a backbone carbonyl, an ester, an ether, a phosphate O -- matched no rule and fell
through to "no pH 7 rule for this group", so nearly every entry was flagged for its
own backbone. Every O1H0 in somo.residue carries 0 waters (36 backbone O, plus
O2/O4/O6/OP1/OP2 and the rest), so that is a confident zero and is now stated as one.

LYZ in 8RAT_gap3 goes from 3 flagged items to 1, the remaining one being the real
ASA placeholder note.

Tests unchanged: unit 86/0, hydration 37/0, psv 60/0. libus_somo builds clean.

Co-Authored-By: Claude Opus 5 <noreply at anthropic.com>


  Commit: 71f1ee61a3daf2baf4560952ef17abf67f8c6c8e
      https://github.com/ehb54/ultrascan3/commit/71f1ee61a3daf2baf4560952ef17abf67f8c6c8e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-12 (Wed, 12 Aug 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_perceive_dialog.cpp

  Log Message:
  -----------
  perceiver: show both hydration totals, and point at the module from the load

Two from Mattia's testing.

Hydration total read 1 for 2CMD. That is the PROTONATED total and it is correct as
far as it goes -- since ionizable atoms started carrying their waters in the
deprotonated alternate, citrate's three carboxyls contribute 0 each and only the
central hydroxyl's 1 remains. But at pH 7 citrate is deprotonated, so the number
that matters is 16, and showing only the neutral one is misleading. The label now
gives both, and only when the entry actually has an ionizable atom:

    Residue hydration total: 1.00 waters neutral, 16.00 ionized

Missing perceiver warning: no such message has ever existed in this branch -- I
searched the history for one and there is none -- so this is a gap rather than a
regression, but the gap is real. The load reports non-coded residues, the bead
builder then represents each by a single crude bead, and nothing told the user an
entry could be derived from the coordinates first. check_for_missing_atoms now says
so once unknown_residues is final, naming the residues it means.

libus_somo builds clean.

Co-Authored-By: Claude Opus 5 <noreply at anthropic.com>


Compare: https://github.com/ehb54/ultrascan3/compare/8b715d0c3744...71f1ee61a3da

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