libRosetta

libRosetta is a library of object-oriented components for use in the Rosetta biomolecular structure prediction and design application. These components are designed to provide Rosetta with a modern framework that reduces software obstacles to research.

This Document

This libRosetta Users Guide is intended to provide an introduction to libRosetta and some general background and usage information. It is not intended to provide a complete API reference: the doxygen-generated documentation or a good class browser are currently the best sources for the current complete documentation of the full libRosetta API.

libRosetta uses services from other libraries including the numeric, utility, and ObjexxFCL libraries distributed with it and documented separately as well as zlib. Other libraries such as Boost may be used in the future but are not yet actively used or required.

Status

libRosetta currently contains components providing a conformational representation of polymer structures and their constituents and the capability to alter the conformations of those structures and to score those structures with the Rosetta scoring algorithms. The protein/amino support is fully functional and the DNA/nucleic support is ~ 75% complete. Ligand, interface, and other important subsystems are partially designed but not yet implemented. The conformational and scoring layers have met the design goals and attained substantial performance and scalability gains over the existing code.

This libRosetta core is being integrated into Rosetta and should be active by mid-2007. The libRosetta objects will be available to modules written to use them and will be used for the internal conformational representation and for scoring. When existing Rosetta modules have been migrated to work with libRosetta components the parallel array-based representations can be retired.

Supporting Institutions

Rosetta and libRosetta are developed by the Rosetta Commons consortium that includes the following institutions:

University of Washington
University of California Santa Cruz
University of California San Francisco
Johns Hopkins University
University of North Carolina, Chapel Hill
Vanderbilt University

The development of libRosetta and other refactoring and maintenance work has been supported under NIH grant _______.

Design & Development

Much of the libRosetta design and development was performed by Objexx Engineering, Inc. Ion Yannopoulos collaborated on the design and developed the PDB reader/builder system. Other contributors include Sergey Lyskov and the researchers in the Rosetta Commons institutions.

Authors

This document was written by Stuart G. Mentzer of Objexx Engineering, Inc.. Contributed materials from other authors are attributed on the pages where they occur.

What's New

» Compact energy tables
» Options system
» PDB reader/builder
   » Corrects common ATOM errors
» H bonds/energy support
» Inter-residue energy support
» Intra-residue energy support
   » Protonation energy