[us-commits] [ehb54/ultrascan3] 10d48c: somo: add a "Skip deuterium atoms" PDB parsing option

[emre brookes]

  Branch: refs/heads/ehb54-issue-1000
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 10d48cec080b53d282c4412ccfa6b46a44349c9f
      https://github.com/ehb54/ultrascan3/commit/10d48cec080b53d282c4412ccfa6b46a44349c9f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-10 (Mon, 10 Aug 2026)

  Changed paths:
    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_pdb_parsing.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/etc/somo.config.new
    M us_somo/etc/somo.defaults.new
    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: add a "Skip deuterium atoms" PDB parsing option

Neutron structures carry deuterium where an X-ray structure carries hydrogen -
5PTI has 103 of them in the protein, on top of its D2O.  The hydrogen test the
readers apply matches names beginning with H only, so those deuteriums survived
parsing and arrived as unknown atoms; somo.residue codes them no better than it
codes hydrogens.

New option below "Skip hydrogen atoms", default on, applied in the same four
readers.  Unlike the hydrogen option it is live rather than greyed out, so the
old behaviour is still reachable, with the deuteriums then falling to the
missing atoms setting.

Deuterium is recognized from the wwPDB element field (columns 77-78) where the
file supplies it and from the atom name otherwise - a name test alone cannot
tell a deuterium from the second letter of a two-letter element, "CD  " being
cadmium.

Persisted through the JSON config alongside the other parsing options, and added
to the somo.config/somo.defaults templates.  Configs written before this option
existed simply take the default, since load_config_json() lays down the
hard-coded defaults before reading.



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