I left minor comments, more for me to understrand than for suggesting changes. I removed the duplicated comments, but in case we decide to change something we need to remember that it may be in multiple files.

Sorry, I was actually meaning to leave references to some of these changes when I made the PR, but then forgot :)

I added them now in reply to your comments

3 additional changes:

1. I used from __future__ import annotations to avoid the quotation marks around some of the type hints
2. I improved docstrings and their formatting according to this convention: https://realpython.com/documenting-python-code/#class-docstrings.
3. I moved SingleResidueVariant into residue.py as they are closely related classes.
   • I even wonder if it would make sense to make it a child class of Residue instead of taking the Residue as an attribute (but that would require more coding than I am currently willing to do for this).

You should be able to go through the commits one by one to see each change in isolation, which might make reviewing easier.

Note that because I have "automatic import sorting upon save" turned on, some additional imports are switched around as well.

3 additional changes:

1. I used from __future__ import annotations to avoid the quotation marks around some of the type hints

2. I improved docstrings and their formatting according to this convention: https://realpython.com/documenting-python-code/#class-docstrings.

3. I moved SingleResidueVariant into residue.py as they are closely related classes.

   • I even wonder if it would make sense to make it a child class of Residue instead of taking the Residue as an attribute (but that would require more coding than I am currently willing to do for this).

You should be able to go through the commits one by one to see each change in isolation, which might make reviewing easier.

Note that because I have "automatic import sorting upon save" turned on, some additional imports are switched around as well.

Regarding 3., JFYTK, we're using the Google Style convention for docstrings. Nice that you moved SingleResidueVariant into residue.py, makes more sense. Regarding the possibility of making it a child of Residue, that also makes sense, not sure how much it's worth to spend time on doing it

3 additional changes:

1. I used from __future__ import annotations to avoid the quotation marks around some of the type hints

2. I improved docstrings and their formatting according to this convention: https://realpython.com/documenting-python-code/#class-docstrings.

3. I moved SingleResidueVariant into residue.py as they are closely related classes.

   • I even wonder if it would make sense to make it a child class of Residue instead of taking the Residue as an attribute (but that would require more coding than I am currently willing to do for this).

You should be able to go through the commits one by one to see each change in isolation, which might make reviewing easier.
Note that because I have "automatic import sorting upon save" turned on, some additional imports are switched around as well.

Regarding 3., JFYTK, we're using the Google Style convention for docstrings. Nice that you moved SingleResidueVariant into residue.py, makes more sense. Regarding the possibility of making it a child of Residue, that also makes sense, not sure how much it's worth to spend time on doing it

Thanks for the ref to google convention. It does still follow that as well. I wasn't sure whether the class itself should get a docstring or only the init method. But in both style guides, they each get a docstring.