[us-commits] [ehb54/ultrascan3] 2ee2c6: perceiver: element inference must key on the resid...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2ee2c6af7d1ce944ea384d34deff28ac864df569
      https://github.com/ehb54/ultrascan3/commit/2ee2c6af7d1ce944ea384d34deff28ac864df569
  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

  Log Message:
  -----------
  perceiver: element inference must key on the residue, not the atom name

The previous rule took the leading letter unless the atom name equalled the
residue name. That is right for proteins and wrong for ligands -- exactly the
population this code exists for. Six of fifteen test cases failed:

    FE in HEM -> F   (fluorine)      CU in CUA -> C
    CL in CIT -> C                   SE in MSE -> S
    NA in XYZ -> N                   BR in LIG -> B

so a heme iron contributed a fluorine volume, silently.

The discriminator is the RESIDUE. In a standard residue the naming convention
is fixed and the element is always the leading letter: CA is the alpha carbon,
NE2 a nitrogen, SD a sulfur. In a ligand it is not, and a two-letter atom name
that matches a known element is that element.

Residual ambiguity, stated in the header: a ligand carbon named bare "CA"
reads as calcium. Ligand carbons are normally C1/CAA/CB1, and the psv now
refuses to compute rather than guessing when an element cannot be resolved,
so the failure is visible either way.

Answers the question directly: with this, a PDB with no element column is
handled correctly for proteins AND for ligands with two-letter elements.
Without it, only proteins were safe.

79 checks, 0 failures.



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