[us-commits] [ehb54/ultrascan3] 251ce4: Propose hydration from pH 7 chemistry rules rather...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 251ce498b42c9b85c3bf1ee1c6c9114fa91eda97
      https://github.com/ehb54/ultrascan3/commit/251ce498b42c9b85c3bf1ee1c6c9114fa91eda97
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-08 (Sat, 08 Aug 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_hydration.h
    M us_somo/develop/perceiver/DECISIONS.md
    M us_somo/develop/perceiver/tests/builder.cpp
    M us_somo/develop/src/us_hydrodyn_hydration.cpp
    M us_somo/develop/src/us_hydrodyn_perceive_somo.cpp
    M us_somo/develop/src/us_hydrodyn_residue_builder.cpp

  Log Message:
  -----------
  Propose hydration from pH 7 chemistry rules rather than type averages

Mattia supplied the chemistry: at pH 7 an acidic side chain is a carboxylate,
with one oxygen double-bonded and neutral and the other deprotonated and
charged; an aliphatic amine is protonated; and the water a carboxylate carries
depends on the length of the aliphatic chain linking it to the backbone, which
is what separates aspartate from glutamate. No general pH machinery, just the
pH 7 assumption.

The residue table confirms this exactly. The ionised hydration is field 15 of
an atom line, not 13 as the layout first suggests, and reading it gives
aspartate 5 waters on its carboxylate against glutamate's 6, lysine 3 on its
ammonium, arginine 1 on each terminal guanidinium nitrogen. So aspartate's
runtime total of 6 and glutamate's 7 are carboxylate plus backbone amide, and
the difference between them really is the extra methylene.

The rules replace the previous per-hybrid-type majority vote, which could not
express residue-specific hydration and systematically under-predicted the
polar and charged side chains. Anything the rules do not recognise still falls
back to the observed averages and is flagged, so a novel group never receives
a confident-looking number by accident.

Hydration within half a water improves from roughly 69 of 145 residue types to
136 of 145 across seven structures, 48% to 94%, with lysozyme and both
ribonucleases now exact on every type. All fifteen applicable coded residues
reproduce exactly in the unit tests, including the aspartate/glutamate
methylene difference. Partial specific volume and anhydrous volume are
unchanged, and perception still scores 99.833%.

Validation also has to skip chain termini at both ends, not just the carboxy
end. An amino-terminal residue has a free protonated backbone nitrogen rather
than an amide, so an amino-terminal lysine genuinely carries two ammonium
groups and six waters where the tabulated internal residue has four. The rules
were right and the comparison was wrong.

Two rule edges the coded residues exposed: a disulfide sulfur has two heavy
neighbours just as a thioether does, so both partners must be carbon before it
counts as hydrated; and proline's tertiary ring amide nitrogen carries no
hydrogen, so amide nitrogens are identified by their carbonyl neighbour rather
than by hydrogen count.

Refs ehb54/ultrascan-tickets#980

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



To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications