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.

Class protocols::relax::ClassicRelax

Crank and Wobble Moves - however there's little evidence that they are essential

Member protocols::scoring::Interface::pair_list ()

rename this to something more logical & give it a better return type

make a function that returns a vector1<pair<Size,Size> > containing all interacting pairs. This would be easy to implement.

Class protocols::simple_moves::BackboneMover

change this to some kind of 'protocol' so the MC is managed separately from conformational moves