- getDihedrals a program to get phi/psi and chi angles of a given structure. Can also give you probabilities and propensities for each angle.
- repackSideChains a program to repack sidechains
- energyTable a program to generate an energy table for repacking and/or designing sidechains
- optimizeMC a program to optimize an energy table (selects minimum energy side chains for repack/design runs)