Lester Hedges
Lester Hedges
Thanks, @kexul, I'll look into this. Given that we use the same tools behind the scenes it should be easy enough to implement (or test) the approach that you suggest....
@jmichel80: The prematch approach won't work since there's no way to use it as a _seed_ for the MCS. Unfortunately we just use it retrospectively, i.e. checking that the MCS...
I see the RDKit MCS code has an `InitialSeed` option. Perhaps we could try matching with heavy atoms only, then using the MCS as a seed for a full atom...
As found [here](https://github.com/alchemistry/alchemlyb/issues/336), a workaround is to pin the version of `pymbar` to 4.0.2. Currently version 4.0.1 is pulled in by default, which pulls in an incompatible version of `jaxlib`....
Closing as this hasn't been an issue recently. I still don't think it's properly fixed, but the issue (and solution) is searchable.
I looked at this but there appears to be a mind boggling amount of options etc. for bespoke fit. I imagine we wouldn't need all of these, but it might...
Yes, I think some examples would help. I guess people might be unaware that you can mix things in BioSimSpace, i.e. you don't need everything to be in one topology...
I agree with that, my issue was more that there didn't (yet) appear to be a "standard" protocol to follow, so it wasn't clear what options to expose and what...
Great. I haven't looked for quite a while so it might be that things are more standardised now.
Thanks for reporting. Could you possibly upload the `test.pdb` file referenced in your issue so that I can debug?