Issues with selecting multiple residues with REST

[mb2055]

Hi,

There seems to be an issue when selecting multiple residues within rest2_selection, with an error of ERROR | somd2.runner._runner:run_window:413 - Error running λ = 0.0: list.remove(x): x not in list being raised when more than one residue is selected.
The issue seems to be coming from this line in sire not returning the expected shape.

I've attached a small example containing a host-guest system that runs succesfully when rest2_selection is either molidx 0 or molidx -1 (the indices of the host and guest respectively), but fails when the selection is set to molidx0 or molidx -1.
I can also confirm that the issue also arises in protein-ligand systems.

Versions:
somd2 version: 2026.2.0.dev+62.g0583678
sire version: 2026.2.0.dev+g35efd4a

Tagging @marcobICR as he found the issue.

example.tar.gz

[lohedges]

Thanks, Matthew. I should be able to take a look at this tomorrow. We have a bunch of tests for valid and invalid REST2 selections so I'll add this one once I figure out what the issue is.

[lohedges]

Just to say that the logic should be that the selection adds extra atoms to the default REST2 region, i.e. on top of those in the perturbable region. When the selection includes atoms from the perturbable region, then only those atoms are included, i.e. not the whole perturbable region. As such, if you want protein and ligand you should only need to include the protein in the selection. There's clearly a logic issue here regardless, but I just wanted to clarify what your selection means, and that you'd get host plus guest when only specifying the host.

[lohedges]

This is now fixed in Sire here. This issue will automatically be closed once the PR is merged. Updated conda packages will be available a few hours afterwards.

Thanks again for reporting.