Lester Hedges

Yes, that's the correct branch. The way in which I search for disulphides is quite flexible to allow for non-ideal configurations. It would be good to know if it's _too_...

Related to other discussions [here](https://github.com/michellab/BioSimSpace/issues/369) and [here](https://github.com/michellab/Sire/issues/409), I've made some improvements to the `Sire.IO.PDB2` parser to improve the handling of `TER` and `HETATM` records,which should hopefully make parameterisation more robust....

Oh, and I have now added a `bonds` option to appropriate parameterisation functions. This takes a list/tuple of atom pairs, which are then used to generate the `LEaP` bond directives....

Okay, I've realised that I can match the atom coordinates from the `Sire.System` to those in the PDB file that is written in order to obtain the correct atom numbers...

Hi @JenkeScheen . I think this is a very good idea, and nicely fits the BioSimSpace philosophy, i.e. providing simplified wrappers around external tools, but given power-users full access to...

Even if we do just go via intermediate files for the time being, we could certainly abstract this from the user.

FYI: We also do multiple conversions behind the scenes for the OpenFF support, i.e. BSS --> RDKit --> OpenFF --> OpenMM --> ParmEd --> BSS. (Not all are 1:1 and...

Thanks, that's essentially the approach that we already take internally, e.g. see [here](https://github.com/michellab/BioSimSpace/blob/devel/python/BioSimSpace/Align/_align.py#L256) in the MCS routine of `BioSimSpace.Align`. The one issue with file conversion is that RDKit has internal...

I don't think this solves the problem since we are not directly parsing SMILES into a molecular structure, rather using OFF to generate a "molecule" behind the scenes using whatever...

Thanks for this, I should be able to merge in within the next few days.