Christopher Woods

@lohedges - thanks for all of your work to merge this in. @msuruzhon - thanks for reviewing and for your understanding for this merge. I've tried my best to create...

Yes, the BioSimSpace integration is a little janky because BioSimSpace uses the `Select` object directly. This returns a `SelectResult` that isn't processed down to the smallest molecule view type. In...

I've taken a look and it isn't a problem with the new search functionality. The change is because now Sire *always* iterates over atoms in a molecule. I had changed...

I've added the equivalent `.atoms()`, `.residues()` etc functions to BioSimSpace's `SearchResult` object. The test passes in the main branch locally. I will look to do the same fix in the...

That's strange - I believe that the test passes when run in GitHub Actions? Could it be an issue with your local environment?

Excellent - hopefully this will reduce the frequency of weird conda issues... ;-)

A virtual site in Sire is an atom that has null properties for the things that are not necessary (eg bonds, LJ etc). We treat them in the same way...

There are two options: 1. We have SireMol::GeometryPerturbations that are used to compute and update the coordinates of atoms as constraints. Currently these are constraints applied based on bond, angle...

Agree - we can add a BioSimSpace node at another time that wraps up different algorithms for adding hydrogens to crystal waters (which do typically appear as lone oxygen atoms...

The collaboration with syngenta was to port their BEE code for auto-setup of absolute binding free energy calculations in gromacs into BioSimSpace. I can show you the code and ideas...