Refactor Query classes

[DaniBodor]

Create a parent class, which has an argument for the resolution and child classes for PPI and Variants.

[DaniBodor]

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

[github-actions]

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