Mini Rosetta Documentation

This is the main page for Mini Rosetta Documentation. It is the first page that users see when they go to the Doxygen documentation. We should put links to commonly referred to documentation pages here.

Developer Guides

• Symmetry User's Guide.
• A Guide to the Structure of the Rosetta Library
• An Introduction to Important Rosetta Concepts
• A Guide to Developing in Rosetta
• Tips for writing doxygen documentation
• Coding Guidelines
  • List of things you should check in your code before committing it in to svn
  • Guidelines on Owning pointers usage
  • Option list with description/range/default values
• How to make mini 'robust' against badly formatted PDBs
• How to use combined RNA-protein poses (not possible by default!)
• How to prepare structures for use in Rosetta
• How to prepare ligands for use in Rosetta

Core Tutorial and Reference

• kinematics
  • AtomTree overview and concepts
  • FoldTree overview and concepts
• optimization
  • Minimization overview and concepts
• pack
  • How to use the PackerTask
  • Resfile syntax and conventions
  • How to write new resfile commands
• scoring
  • How to add a new scoring term
  • Constraints file formats
  • How to score structures using electron density data
• util
  • Tracer, tool for debug IO
• fragment
  • core::fragment::picking_old User's Guide.
• symmetry
  • Symmetry User's Guide.
• io
  • brief summary of atomtree diff format and silent file extraction
  • Support for database input and output

Protocol Library Tutorial and Reference

• New job distributor README

Numeric Library Tutorial and Reference

• Numeric Library page has a (very) brief introduction to the numeric library

Tests Tutorial and Reference

• Unit test and Performance test Mini Rosetta Documentation
• Mover test HOWTO
• Different way to run unit tests
• How to create and run scientific tests

Documentations for applications

• Index Page for Pilot Application Documentation
• Documentation for the ligand_dock application
• Documentation for the RNA 3D modeling applications
• Documentation for RNA fixed backbone design
• Documentation for RNA loop modeling (lock-and-key problem) with Stepwise Assembly
• Documentation for remodeling RNA crystallographic models with electron density constraint
• Documentation for the extract_atomtree_diffs application (use with ligand_dock)
• Documentation for kinematic loop modeling
• Documentation for next-generation KIC
• Documentation for CCD / fragment loop modeling
• Boinc minirosetta application usage and overview
• Documentation for the docking application
• Documentation for docking prepack application
• Documentation for the fixed backbone design application
• Documentation for the fixed backbone design application with the hpatch score term
• Documentation for the fragment picker application
• Commands for the relax application
• Commands for the cluster application
• Commands for the scoring application
• Commands collection for pilot and public applications
• Backrub application documentation
• Docking Design Scripting documentation
• Documentation for the enzyme design application
  • Documentation for the matcher
• Documentation for the membrane ab initio application
• Documentation for the Flexible Peptide Docking Refinement and ab-initio protocols
• Documentation for the sequence_tolerance application
• Documentation for the symmetric docking application
• Documentation for the Fold-and-Dock application
• Documentation for the InterfaceAnalyzer application
• Documentation for the ddg_monomer application
• Documentation for the multistate design application
• Documentation for the sequence recovery application
• Documentation for the FloppyTail application
• Documentation for the AnchoredDesign application
  • Documentation for the AnchoredPDBCreator application (part of AnchoredDesign)
  • Documentation for the AnchorFinder application (part of AnchoredDesign)
• Documentation for the UBQ conjugation suite of applications, including UBQ_E2_thioester, UBQ_Gp_CYD-CYD, UBQ_Gp_CYX-Cterm, UBQ_Gp_LYX-Cterm
• Documentation for the pepspec application
• Documentation for the comparative modeling application
• Documentation for the point mutant scan application
• Documentation for RosettaRemodel
• Documentation for the oligooxopiperazine (oop) design app
• Documentation for the hydrogen bond surrogate (hbs) design app

Important Namespaces

• core
  • core::pose
  • core::chemical
• utility
• numeric

Important Classes

• core::pose::Pose
• core::conformation::Residue
• core::chemical::ResidueType

To create a new additional page, just make a .dox file with a "@page ..." command in it, somewhere under the doc/ directory. These pages will show up under the "Related Pages" tab automatically, but you may add a "@ref" to them here also.