Hello, developers
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
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Generally speaking, if you're interested in doing a complex clustering calculation you're probably better off calculating the pairwise distance matrix (e.g. by using features in PyRosetta), and then using some external clustering program (e.g. one of the algorithms provided by scikit learn).