[us-commits] [ehb54/ultrascan3] 34d7c5: perceiver: never compute a psv from unidentified e...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 34d7c5b303f2d8b0ee75f4c88c13badba270c3f3
      https://github.com/ehb54/ultrascan3/commit/34d7c5b303f2d8b0ee75f4c88c13badba270c3f3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-10 (Mon, 10 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_perceive_elements.h
    M us_somo/develop/perceiver/tests/tests_unit.cpp
    M us_somo/develop/src/us_hydrodyn_perceive_somo.cpp
    M us_somo/develop/src/us_hydrodyn_psv.cpp

  Log Message:
  -----------
  perceiver: never compute a psv from unidentified elements

A PDB with an empty element column (77-78) produced psv values of 0.001,
-0.068, -0.087 -- meaningless numbers that still look like numbers.
1AO6-compl_monA.pdb in the demo set is such a file, which is how it surfaced.

Two independent defects, either alone enough:

1. The atom-name fallback used norm_element(), which only strips
   non-alphabetics. So the alpha carbon "CA" became CALCIUM, "NE2" became
   NEON, and "CB", "CG", "OD1" matched no element at all. Every atomic volume
   increment then evaluated to zero and the sum collapsed to roughly the
   electrostriction terms. element_from_atom_name() takes the leading letter,
   accepting a two-letter element only when the atom name equals the residue
   name -- HETATM "CA" in residue "CA" is calcium, "CA" in "ALA" is carbon.

2. somo_psv::compute() reported ok on a residue containing atoms it had no
   increment for. It now counts them, records why in the review block, and
   returns ok == false, so the caller emits no psv rather than a plausible
   figure. An unidentified element is not a small error; it is not a volume.

The grid volume was unaffected and still looked sensible (Ala 77.45 A^3),
which is precisely why this was not obvious from the output.

tests_unit.cpp gains the case that catches it: CA/CB/CG1/OD1/NE2/NZ/SD/OXT
must resolve by leading letter, while CA-in-CA, FE-in-FE, ZN-in-ZN, MG-in-MG
resolve as the two-letter element. 69 checks, 0 failures.



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