[us-commits] [ehb54/ultrascan3] 334282: Fix bead colour field in generated residue entries

[emre brookes]

  Branch: refs/heads/ehb54-issue-978
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 334282a13e665610a461cf04cad6af0cd9f17454
      https://github.com/ehb54/ultrascan3/commit/334282a13e665610a461cf04cad6af0cd9f17454
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_perceive.h
    M us_somo/develop/src/us_hydrodyn_perceive.cpp

  Log Message:
  -----------
  Fix bead colour field in generated residue entries

emit_residue() wrote the residue's atom count into the bead line's COLOUR
field. The bead line is hydration, colour, placing_method, chain, volume
(US_Hydrodyn::read_residue_file, us_hydrodyn_load.cpp:509), so a generated
entry's colour was whatever the atom count happened to be:

  - 6 atoms  -> colour 6, RESERVED brown, which marks a bead as buried and
                EXCLUDES it from the hydrodynamic computation
  - 7 atoms  -> colour 7, reserved for fused beads
  - 8 atoms  -> colour 8, reserved for beads found exposed on re-check
  - >15      -> out of range entirely

Six- to eight-atom ligands are common (glycerol has 6, phosphate 5), so this
silently dropped beads from models built with a generated entry.

Emit DEFAULT_BEAD_COLOR instead, defined once in us_hydrodyn_perceive.h with
the documented colour list from the SOMO manual (somo_residue.html, Panel 3)
and helpers bead_color_is_reserved() / bead_color_is_selectable() for the
residue-definition UI. Default is 10 (light green), which the manual records
as the Automatic Bead Builder's colour for non-coded residues; it is a single
named constant so the policy can be changed in one place.

Also spell out the remaining bead-line fields rather than emitting bare zeros.

Refs ehb54/ultrascan-tickets#978

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



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