I wonder if Rosetta can cluster docked poses based on two atoms distance in a pdb? or someone can guide me where I can find the tool in Rosetta?
To be clarified, I have a set of PDBs, protein A with ligand docked on protein B. In these PDBs, protein B shares the same coords, while protein A and ligand are around protein B. I want to cluster these PDBs based on the distance between an atom in ligand to one atom in protein B. If possible, I wound to further cluster these PDBs based on differnent selection (location of atom) on protein B to ligand