[us-commits] [ehb54/ultrascan3] af08ed: perceiver: add tracked test structures containing ...

[emre brookes]

  Branch: refs/heads/ehb54-issue-980
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af08ed5cadd29d5f6f9fd89e48596027a2531562
      https://github.com/ehb54/ultrascan3/commit/af08ed5cadd29d5f6f9fd89e48596027a2531562
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-08-09 (Sun, 09 Aug 2026)

  Changed paths:
    M us_somo/develop/perceiver/.gitignore
    M us_somo/develop/perceiver/README.md
    A us_somo/develop/perceiver/data/non-coded/1MBO.pdb
    A us_somo/develop/perceiver/data/non-coded/2CMD.pdb
    A us_somo/develop/perceiver/data/non-coded/3PTB.pdb
    A us_somo/develop/perceiver/data/non-coded/5PTI.pdb
    A us_somo/develop/perceiver/data/non-coded/README.md
    M us_somo/develop/perceiver/examples/perceive.somo

  Log Message:
  -----------
  perceiver: add tracked test structures containing non-coded residues

The demo structures under perceiver/data/ are all fully coded, so nothing in
the tree exercised the path the perceiver exists for. Add four structures that
do, tracked in git since they are copies of nothing else here (the parent
data/*.pdb ignore rule is deliberately non-recursive).

  1MBO  SO4 only -- heme and O2 are coded, so it also shows selectivity
  2CMD  citrate, 13 atoms, 3 flagged for review -- the clean first test
  3PTB  benzamidine -- the only case reaching SSSR/ring-decrement and
        electrostriction; its Ca2+ is coded and correctly left alone
  5PTI  neutron/deuterated -- 50 instances across 18 types, the stress case
        for "Skip all remaining" (residue matching fails on atom count, not
        chemistry: the perceiver excludes hydrogens by design)

data/non-coded/README.md records the expected scan output for each so a
regression is visible without rerunning everything.

Also correct the example gui_script: paths must be absolute, since SOMO
changes directory during startup and a shell-relative path fails to resolve.



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