I am trying to calculate all residue-residue pairwise energies for a given conformation. It doesn't appear that these are stored when the score is computed, and that I need to access them directly for every residue pair. I have a few questions regarding this:
1) There appear to be edge iterators for the energy graph obtained by pose.energies().energy_graph().edge_list_begin(). While this method is exposed to PyRosetta, it doesn't appear that I can do anything with the iterator. In the C++ code the ++ operator is overloaded to advance the iterator, but there is no similar method for the Python code.
2) Alternatively I can check all pairs of residues, which is kind of slow. With two residues rsd1 and rsd2 I can call the functions scorefxn.eval_ci_2b() and scorefxn.eval_cd_2d(). What is the difference between the "context dependent" and "context independent" energies (e.g. what is the context)? For precomputing energies on a fixed backbone which is correct? Are these weighted? And finally, how do these differ from the eval_*_2d_bb_sc() methods which compute backbone-sidechain energies?