TO DO (if updates to this list are needed, will be done in #492 instead of here)

Move parameters to parent class
Switch to dataclasses
Unify atomic and residue version of each query into one
- fix all tests, linting, READMEs, notebooks until here
Move as much as possible into parent class
- Make main build function in parent, have specific helper functions in child classes.
- Remove unbound functions or make them methods or parent if still useful.
- Unify build methods for PPI and SVR (if possible)
Make sure all tests and external modules work with new classes
Update docstrings
- Check how this should work with inheritance, what is listed in which docstring, etc
- Check if it's possible to inherit docstrings.
  - Haven't found a nice way of doing this beyond the default for (data) classes
- Check for all methods as well (not all necessarily require one).
Remove code related to inlcuding hydrogens
- check that this is indeed OK
Clarify distance_cutoff vs radius across different Query classes (see here)
- Moved to PR feature: separate max edge distance from interaction radius throughout #504 instead
- Add radius parameter for PPI
- rename the parameters to avoid confusion
- remove it as a Graph attribute
- allow for setting them to 0 to mean include all??
  - Create tests for this
Resolve conflicts with docs: type hinting and docstrings in molstruct #497
- Potentially others
Check all #TODOs throughout script
Refactor duplicate code from buildgraph module
- Will be a new PR.
- Unify build_atomic_graph and build_residue_graph into single function with resolution kw
- Check for other instances

Refactor Query classes #480

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