[us-commits] [ehb54/ultrascan3] 407436: perceiver: chain-embedded test residues with a kno...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 407436af5535e101ff8b633b0a1029996fcb40e0
      https://github.com/ehb54/ultrascan3/commit/407436af5535e101ff8b633b0a1029996fcb40e0
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-09 (Sun, 09 Aug 2026)

  Changed paths:
    A us_somo/develop/perceiver/data/non-coded/8RATNC.pdb
    A us_somo/develop/perceiver/data/non-coded/8RAT_gap3.pdb
    A us_somo/develop/perceiver/data/non-coded/8RAT_run3.pdb
    A us_somo/develop/perceiver/tools/make_noncoded_variant.py

  Log Message:
  -----------
  perceiver: chain-embedded test residues with a known answer

Every non-coded structure in the test set so far is a free ligand -- citrate,
benzamidine, sulfate -- so nothing exercises a non-coded residue INSIDE a
chain, and nothing has a ground truth to check the computed numbers against.

us_somo/somo/demo/8RATNC.pdb is 8RAT with LYS 31 renamed to LYD, done by hand
upstream. That trick is the useful one: the atoms are untouched, so whatever
the perceiver derives can be compared directly against the coded entry for
the residue it really is. Add it here and generalise it.

  tools/make_noncoded_variant.py IN.pdb OUT.pdb A:31=LYZ ...

renames residues by chain and resSeq, refusing to write if a spec matched
nothing -- a silently unmodified file would quietly pass any test built on
it. Two shapes beyond the single-residue case, both aimed at the chain
handling rather than the chemistry:

  8RAT_run3.pdb   LYS31/SER32/ARG33 -> LYZ/SEZ/ARZ, an unbroken run
  8RAT_gap3.pdb   LYS31/ARG33/LEU35 -> LYZ/ARZ/LEZ, alternating with coded

Coded values to check against (somo.residue.new):
  LYS vbar 0.818 molvol 167.30 hydration 4.0
  SER vbar 0.628 molvol  95.40 hydration 2.0
  ARG vbar 0.698 molvol 194.00 hydration 3.0
  LEU vbar 0.898 molvol 164.00 hydration 1.0

Expect a systematic offset rather than a match: the perceiver treats a
residue as an isolated unit, while the coded amino-acid entries describe it
in a chain.



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