I have an experiment that I did loop modeling on for 6 loops in each PDB. Energy vs. to_native_RMSD of the lowest energies are awful, so I now need the individual energies for each loop.
What I am trying to get is basically the total residue energy and the 2 body contributions of each of the loop residues' neighbors. Having trouble in a few different areas.
First, using score.eval_ci_2b and observing the non-zero energies gives the same scoretypes, with different energies as eval_cd_2b. This makes no sense...VDW, fa_pair, hack_elec are all ci_2b energies...
Second, is there a method to return residue neighbors? I tried to access protocols::toolbox::NeighborsByDistanceCalculator from pyrosetta, and nothing...
Finally, any idea of how to get Hbond energies of residues or between residues?