Generalize ff interaction

[ehhartmann]

Deal with problems discussed in #359 and facilitate future addition of non-amber force-fields to kimmdy.

• expose reference to residuetypes file in config
• add optional radicals section to config
• add tests

[ehhartmann]

2 failed, 94 passed, ready for review

[jmbuhr]

Which are the failing tests? tox looks fine. I'd advise to run black before the review so that we have common formatting, otherwise we might get confused with line numbers during it.

[ehhartmann]

Integration as always. It's formatted with the latest black version now. To me the docs action failure looks like some parts of the action are outdated.

[ehhartmann]

To use the new features of this PR, the plugins (at least both HAT ones) would have to be updated as well

[jmbuhr]

ah, looks like the doc parser is now attempting to parse every heading in the docstring as a proper semantic section, but https://github.com/hits-mbm-dev/kimmdy/blob/ce1daf0e68627c04e16c878e0d4d8f897ad5c833/src/kimmdy/parsing.py#L108-L109 is just a random heading I threw in, so this just has to not be a section by removing the ---.

[jmbuhr]

would you like me to do small fixes directly in the PR when I review or just comment instead?

[ehhartmann]

Just change it

[jmbuhr]

looking good, just some minor questions I can then also fix myself if you approve.

[ehhartmann]

For radicals, the workflow is different between writing radicals: '' and not having a radicals section at all (#59) because in the missing section case, we use the bondorder to guess radicals. For the modify-top tool I thought it was a reasonable default to say there are no radicals but I wouldn't do that for a kimmdy run. If you want to have it consistent, I would have no default in both.

Regarding residuetypes, it is similar. No section means we want to use the one in the force field. Having aminoacids.rtp as default would mean we need it in the rundir.

Feel free to rename the functions for finding and setting the atoms attribute. If you find ways to make the same logic more elegant I would be happy. It felt quite awkward to do it like this.