[us-commits] [ehb54/ultrascan3] 104ed9: somo/grpy: optionally write and display a bead mod...

[emre brookes]

  Branch: refs/heads/ehb54-issue-984
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 104ed92bc56aef41aaa36f39ccb10212f3422f74
      https://github.com/ehb54/ultrascan3/commit/104ed92bc56aef41aaa36f39ccb10212f3422f74
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-07 (Fri, 07 Aug 2026)

  Changed paths:
    M us_somo/develop/grpy/grpy_exposure.hpp
    M us_somo/develop/grpy/grpy_shell.hpp
    M us_somo/develop/grpy/tests/test_shell.cpp
    M us_somo/develop/include/us_hydrodyn.h
    M us_somo/develop/include/us_hydrodyn_hydro.h
    A us_somo/develop/revision.sh
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydro.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    A us_somo/develop/us_saxs_cmds_t/moc_predefs.h
    A us_somo/develop/us_saxs_cmds_t/moc_us_cmdline_app.cpp
    M us_somo/somo/doc/manual/somo/somo_hydro.html

  Log Message:
  -----------
  somo/grpy: optionally write and display a bead model of each shell rung

A "Save shell bead models" checkbox in the GRPY Shell Reduction box. When set,
the reduced model used at each ladder rung is written and opened in the viewer,
so the shell can be seen thickening as the ladder converges and the retained
beads inspected directly. For validating the reduction by eye; off by default.

Files go to <somo>/tmp as <model>-shell-rung-<n>, overwritten without prompting
-- they are regenerated every run, and prompting per rung would add a modal
dialog per rung to a diagnostic.

The mapping from the shell report back to beads was the part worth care.
ShellReport now records the indices its ranking selected (ShellOptions::
record_subsets, off by default, so nothing is paid when unused), and those
index the bead list handed to GRPY -- i.e. the .grpy file, which holds the
beads that are active and, unless buried beads are included, not buried, in
`use_model` order. That order is NOT bead_model order: bead_output.sequence == 1
reorders into exposed-sidechain / exposed-main-chain / buried. Taking
bead_model order would therefore have written models of the wrong beads,
silently and plausibly.

To make that impossible rather than merely correct today, the ordering is
extracted from write_bead_model() into US_Hydrodyn::bead_model_output_order()
and both callers use it. The writer also refuses and says so if an index falls
outside the rebuilt list, rather than emitting a wrong picture.

Selection now returns indices (reduce_top_frac_idx), which also removes the old
coordinate-matching rebuild -- O(keep*N), some 32M comparisons on an
11328-bead model -- with reduce_top_frac kept as a wrapper so existing callers
and tests are unaffected.

Tests: recorded subsets are sized to their rung, in range, unique, nested
(each rung contains the previous), complete on the full rung, absent unless
requested, and identical to the ranking's own selection.

Fixes ehb54/ultrascan-tickets#984

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



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