Fragments contains Classes and Functions related to modeling with fragments of structure.
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Don't trust the following! This following is written by Kristian Kaufmann from impressions based on a cursory overview by Oliver.
FragSets contain the basic data required for Fragment based alterations of conformation in polymers. The FragSet contains Fragments for frames in the FoldTree. A Frame contains a list of FragData for a particular set of residues. Each FragData object constains a list of SingleResidueFragData objects. Each SingleResidueFragData object describes how the residue is related to the residue before and behind it in the FoldTree. There are different flavors of SingleResidueFragData (e.g. BBTorsionSRFD, TorsionSRFD, JumpSRFD) to account for the diverse number of FoldTree connections.
You can steal fragments for poses. Say you have a particular set of backbone torsions in one protein that you would like to be available for your modeling. You can extract that fragment from the pose in the following manner
//construct a Frame for the pos'th position of a pose with length len using BBTorsionSRFD (this is a rosetta++ like fragment)
FrameOP frame = new Frame( pos, new FragData( new BBTorsionSRFD, len) );
//steal the conformational data from pose
//add the frame to a fragset
the fragset now contains the fragment and can be used by a FragmentMover.
None at this point