File CentroidDisulfideEnergyContainer.hh: This file was taken with minimal modifications from FullatomDisulfideEnergyContainer.hh. It might be a good idea to move some code into a superclass inheritted by both.
Class core::scoring::disulfides::CentroidDisulfideNeighborIterator: Given the proper options, include all residues in the vicinity which could form a bond, not just the best one. Maybe even include non-cysteines!
Class core::scoring::disulfides::DisulfideMatchingNeighborIterator: Given the proper options, include all residues in the vicinity which could form a bond, not just the best one. Maybe even include non-cysteines!
File DisulfideMatchingEnergyContainer.hh: This file was taken with minimal modifications from FullatomDisulfideEnergyContainer.hh. It might be a good idea to move some code into a superclass inheritted by both.