[us-commits] [ehb54/ultrascan3] fbd259: somo: ask about open RasMol windows on exit, and s...

[emre brookes]

  Branch: refs/heads/ehb54-issue-1000
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fbd25903bcbb082bfa6ecbdb0ab776e277329c8a
      https://github.com/ehb54/ultrascan3/commit/fbd25903bcbb082bfa6ecbdb0ab776e277329c8a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-09 (Sun, 09 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn.h
    M us_somo/develop/include/us_hydrodyn_pdb_parsing.h
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_parsing.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/somo/doc/manual/somo/somo_pdb_parsing.html
    M us_somo/somo/doc/manual/somo/somo_pdb_parsing_expert_mode.html

  Log Message:
  -----------
  somo: ask about open RasMol windows on exit, and skip heavy water

Two housekeeping fixes for ehb54/ultrascan-tickets#1000.

RasMol viewers are started by model_viewer() with startDetached(), so nothing
held on to them.  closeEvent() only ever looked at the legacy `rasmol` QProcess
member, which is allocated but never started - its one launch() call sits inside
#if defined( TODO_FIX_MOVIE_FRAME ) and uses a Qt3 API - so the check never
fired and every viewer SOMO opened was left behind.  Track the detached pids and
ask on exit whether to close them or leave them open.  Liveness and termination
go through small portable helpers rather than QProcess, since a detached child
has no QProcess to ask.

"Skip solvent water molecules" now means light and heavy water everywhere.  The
main GUI reader already listed DOD, but the headless reader, the hydro reader,
1D SAXS, the PDB editor and the BEST/DMD exclusion lists each tested for HOH
alone, so the same structure parsed differently depending on the route - 5PTI,
63 D2O residues, keeps 728 atoms instead of 539 through those paths.  All of
them now share one definition in us_hydrodyn_pdb_parsing.h.  WAT stays out of
it: that is SOMO's own explicit hydration water, not solvent to discard.



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