Caitlin Bannan

Thanks @isayev I'm not going to bother with ased3 then for now. I'm happy to put in a PR with the changes I mentioned above.

> I'll try to get that set up this weekend in http://github.com/omnia-md/basic-python-project-example or similar. @jchodera 404 error here... I didn't look closely at the cookie cutter example yet, but MolSSI...

Updating - I'm looking more closely at cookiecutter and it seems much more robust

My most recent pull request removed most of the files in filter_molecule_sets if that helps.

I'm trying to think through the logistics of using a SMARTS string for this purpose. The typical idea behind SMARTS is that they describe a substructure of a molecule. SMILES...

I think that makes the sense, I wasn't sure if you were suggesting replacing the SMILES with a SMARTS.

This sounds really useful, should we make a list of things that would need to be included in the `ChemistryFixer`? I'm thinking at least: * Charging * Aromaticity perception *...

Hi @UnixJunkie I managed to get something working back in 2019 for some benchmarking. However, I haven't used it since that summer so I don't remember what I did exactly....

> It would be ideal if there was an invertible one-to-one mapping between ChemicalEnvironment objects and SMIRKS strings. How hard do you think that is? SMIRKS to Chemical Environments is...

@davidlmobley that does make sense, I'm sure we'll have to discuss it in more detail later. Also I realized I didn't comment on this in general, I think the API...