I'm not sure if this the best place to ask, but I couldn't think of anywhere better:
I read and was really impressed by the conclusions of Koga, et al. "Principles for designing ideal protein structures". One thing that really intrigued me was the step in the process described as filtering for "local sequence structure comparability". Neither the article nor the example code seem to indicate how this filtering was done. The example RosettaScripts code simply indicates
## The filter for local sequence structure compatibility was done without using RosettaScripts
Can someone here provide a lead for how this step was done?