Lester Hedges

Actually, the above doesn't work in all cases, e.g. fixes the `perturbable` issue, but fails for `water`. We'll need a different solution.

Okay, we can do the following: ```python try: # Query the Sire system. search_result = _SireMol.Select(query)(self._sire_object, property_map) except Exception as e: msg = "'Invalid search query: %r : %s" %...

Just to note that the following test is hanging locally for me [test/IO/test_openff_gromacs.py::test_molecule_combine](https://github.com/michellab/BioSimSpace/blob/fd7dc54be8a625fb39aeb8e29abe9b182601ac33/test/IO/test_openff_gromacs.py#L21). This passes on `devel`, using BioSImSpace built against Sire 2022.3.0. Quitting out of the test gives the...

Yes, most likely. I forgot to add that it did previously work locally, the hang occurred after a full rebuild and the latest edits. Will try again when I get...

Just to mention that, as reported [here](https://github.com/michellab/BioSimSpace/issues/383) this test hang is reproducible for Python 3.8 and Python 3.9 on both Linux and macOS (Python 3.7 passes). The issue isn't Sire...

It turns out that we now need to add [openff-interchange](https://anaconda.org/conda-forge/openff-interchange) as a dependency on Python 3.8+. I presume that they must have split out some functionality. I'll try to see...

Okay, I've made a few edits to remove some redundant imports and tidy some comments. One thing that I've noticed is that a search with no results now raises a...

Bah, it turns out that the behaviour is inconsistent, i.e. it sometimes returns an empty search if the string is valid but there is no result, but sometimes returns a...

Ah, this is because `BioSimSpace._SireWrappers.Molecule.search()` returns an empty result when the search fails, whereas the other wrappers raise the exception: ```python try: # Query the Sire molecule. search_result = query(self._sire_object,...

Okay, I've needed to make quite a few edits to handle the new search functionality. However, it looks like the existing searches used to find atoms when applying different types...