[us-commits] [ehb54/ultrascan3] 94b65c: Wire the computed properties into SOMO and add a h...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 94b65c74df263037724748131118d4736d9c7b4a
      https://github.com/ehb54/ultrascan3/commit/94b65c74df263037724748131118d4736d9c7b4a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_perceive_somo.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/perceiver/DECISIONS.md
    M us_somo/develop/src/us_hydrodyn_perceive_somo.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp

  Log Message:
  -----------
  Wire the computed properties into SOMO and add a headless perceive

libus_somo.pro did not list the four sources added since the perceiver work
resumed, so the grid volume, psv engine, hydration lookup and residue builder
were never compiled into the library at all. Registered, and the symbols are
confirmed present in the built dylib.

The Qt adapter now takes the bond graph from the new perceive overload and
goes through somo_residue_builder, so a proposal made inside SOMO carries
vbar, molvol and hydration rather than zeros. Tentative gained those three
fields for callers that want the numbers instead of the text block. The
hydration lookup is built from SOMO's own loaded residue_list, so a proposal
is always consistent with the user's tables rather than a snapshot compiled
into the binary.

"perceive auto <pdb>" is the headless sub-command: every default accepted,
nothing prompted, nothing written back to somo.residue. It also prints how
many atoms were flagged, since in a pipeline nobody is watching the REVIEW
block go past.

Defaults are pinnable through gparams in the same way as covolume:
perceive_psv, perceive_volume, perceive_hydration, perceive_volume_probe,
perceive_volume_grid and perceive_bead_color. A reserved bead colour is a
hard error rather than a silent substitution, because two of the reserved
values exclude a bead from the hydrodynamic computation and accepting one
would quietly produce a model missing beads.

Verified end to end through us3_somo -g on 2CMD, whose citrate is genuinely
not coded: vbar 0.542, molvol 186.56, and seven review flags. On the residue
basis SOMO stores, that vbar corresponds to 0.607 for the free molecule
against a literature value near 0.59 to 0.62. The proposed hydration of zero
for a triacid is plainly too low, and all four hydroxyl oxygens come back
flagged at 49% agreement, which is the intended behaviour: propose, then say
what cannot be supported.

Refs ehb54/ultrascan-tickets#980

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



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