Increase `protein-ligand` interaction calculation speed through threshold of `protein` `mda.AtomGroup`

[talagayev]

Calulcation time enhancement .

Currently for the PLIP interaction calculation we write out the PDB files with such an AtomGroup selection:

        atoms_selected = self.pdb_md.select_atoms(
            f"protein or nucleic or resname {self.lig_name} or (resname HOH and around 10 resname {self.lig_name}) or resname {self.special}"
        )

here we have the full protein, but only look at the area around the ligand. We can make such a selection:

        atoms_selected = self.pdb_md.select_atoms(
            f"((protein or nucleic) and around 20 resname {self.lig_name}) or "
            f"(resname {self.lig_name}) or "
            f"((resname HOH) and around 10 resname {self.lig_name}) or "
            f"(resname {self.special})"
        )

to make the amount of atoms that we write out smaller, increasing the speed