Examples of Standard Rosetta and SS-Rosetta's inputs and outputs are found in the corresponding folders.
Folder Script_for_fragment_files contains three SH files (Unix/Linux Shell executable files) that amend 9-mers and 3-mers files based on the SS-Rosetta method.
Each folder contains its own Readme file
Very soon, there will be one python script that, once fed with the secondary strucutre prediciton, creates those three batch files without the need to adjust them manually.