Rosetta 3.3
Fragments Directory

Table of Contents

Overview of Directory

Fragments contains Classes and Functions related to modeling with fragments of structure.

Important Classes/Files in this Directory

users will only need to be familar with these classes

Lateral Dependencies

Email Oliver asking him to fill in this section.

Readmes, Code Snippets, and Tutorials

This section should contain links for Readmes, Code Snippets, and Tutorials enabling developers to use the code/files located in this directory.

Code Design, Extension, and Comments

FragSet

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

frame->steal(pose);

//add the frame to a fragset

fragset->add(frame);

the fragset now contains the fragment and can be used by a FragmentMover.

Planned Extensions, Known Limitations, Wish List of things needed

None at this point

Index of Directory

Files

BBTorsionAndAnglesSRFD

BBTorsionSRFD

BaseCacheUnit

ConstantLengthFragSet

ConstantLengthFragSetIterator_

FragCache

FragData

FragID

FragID_Iterator

FragSet

FragSetCollection

FragmentIO

Frame

FrameIterator

FrameIteratorWorker_

FrameList

FrameListIterator_

JumpSRFD

JumpingFrame

OrderedFragSet

OrderedFragSetIterator_

README

SRFD_Implementations

SecstructSRFD

SingleResidueFragData

TorsionSRFD

core/fragment/util

Directory

core/fragment/io/

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