Iván Pulido

One of the things we want to achieve here is that we probably want the HTF objects to have their own energy validation methods, more information in https://github.com/choderalab/perses/pull/1092#issuecomment-1226537892

Propagate input sdtags and output lambda=1 compounds SDF files with experimental and computed affinities.

It appears to be related to the new release of sphinx 5.0.0 rather than something that changed in our `docstrings`. More info https://readthedocs.org/projects/perses/builds/?page=2

Builds are working now https://readthedocs.org/projects/perses/builds/18321864/ . Closing

We have now support for biopolymers in the `openff-toolkit` with their [latest release](https://docs.openforcefield.org/projects/toolkit/en/stable/releasehistory.html#minor-release-forbidding-loading-radicals). Copying from discussions with @jchodera, some of the parts that we will benefit from using the `openff-toolkit`...

Related issue https://github.com/choderalab/perses/issues/1034 This one is aimed more towards having the sanity checkings inside the `_solvate` or `_handle_charge_changes` methods themselves, rather than implementing the sanity checks themselves.

Yes, we were thinking the same. I think it is better to handle this correctly after we have dealt with the API refactor first.

Ok, on a second thought after our dev sync, we decided to keep this for our next release, since we are already using it for some of our docker containers....

We need a small molecule example code (in vacuum) that does A to B and B to A so we can plug it in our CI tests. @dominicrufa can you...

I performed a quick/basic profiling using our current examples and according to the following figures, we might not gain much from optimizing the setup parts of our software. It calls...