Rosetta 3.4
Todo List

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
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