While developing tutorials for variants (PR #435) I noticed that the logic behind the distance_cutoff parameter across different query types is not very linear and clear, at least from my perspective.

In variant query classes, the residues/atoms of interest are selected with the radius (via get_surrounding_residues) around the variant.

In PPIs query classes, distance_cutoff is used for _load_ppi_atoms (I guess selecting the interface, within the distance cutoff).

Then, in all queries logic, build_residue_graph (or build_atomic_graph) builds a graph of the selected elements, and takes the distance cutoff as input, which in build_residue_graph is defined as the shortest interatomic distance between two residues.

• Actually, looking into build_residue_graph, then distances < the distance cut off are selected, making the cutoff distance actually the max and not the min.
• build_residue_graph (and build_atomic_graph) selects distances < the distance cut off, but at least for PPIs this should have been done already in _load_ppi_atoms (and for variants in get_surrounding_residues). Can we remove this parameter from build_residue_graph?
• Graph class has cutoff_distance param as well, but again I don't think it's needed (never used in the Graph class).

Your feedback here would be very useful :) @DaniBodor