Development Documentation

Getting Started

Build Documentation

Rosetta Tutorials

Rosetta Basics

Rosetta Applications

Rosetta Scripting Interfaces

Development Documentation

• Tests

• Tutorials

• Code structure

• Coding Conventions

• Common Errors

Internal Documentation

How to Write Documentation

FAQ

Glossary

RosettaEncyclopedia

Options list

Developing for Rosetta

• Rosetta overview - Explanations of key concepts in Rosetta.
• Glossary - Brief definitions of Rosetta-related terms
• Doxygen tips - How to work with Rosetta's in-code documentation.
• Writing an app - How to write your own Rosetta-based application.
• Making rosetta robust for running on large number of inputs
• Ensuring that Rosetta modules provide their own citations in Rosetta output

Where is the documentation for the various Rosetta libraries?

The documentation for the various libraries is a bit scattered. Here is a partially-complete list:

Internal libraries:

• Publicly available Doxygen code documentation describing the interface to Rosetta objects and functions
• Historical version of the documentation, including both user manual and code documentation.
  • The Rosetta 3.5 user manual, with documentation for the core and protocols libraries; curiously, this lacks RosettaScripts documentation
  • The Rosetta 3.4 user manual, with documentation for the core and protocols libraries and on RosettaScripts (an older version, for historical reference only)

For RosettaCommons developers, we have a version of the Doxygen documentation which also includes code. (Password protected access).

• Doxygen documentation of core and protocols (built frequently to reflect the latest commits to master)
• Doxygen documentation for the basic, numeric, utility, and ObjexxFCL (Fortran compatibility) libraries, (built frequently to reflect the latest commits to master)

External libraries:

• Boost 1.55.0 documentation (a very useful library intended to extend the standard C++ libraries with frequently-needed functionality)
• The Eigen library (used for linear algebra, matrix manipulations, Eigenvector problems, etc.)
• DAlphaBall information and references (but no documentation), which is used in Rosetta's holes score term

Code organization

A general scheme of Rosetta source code organization Large size file (poster size) can be downloaded from here

• Rosetta library structure - Overview of how the Rosetta library is structured.

• src index page - Overview of the src directory.

• Namespace core

  • Namespace core::chemical
  • Namespace core::conformation
    • Namespace core::conformation::idealization
  • Namespace core::io::pdb
  • Namespace core::scoring
  • Namespace core::fragments
• Namespace utility
  • Namespace utility::factory
  • Namespace utility::io
  • Namespace utility::keys
  • Namespace utility::options
• Namespace numeric
• Namespace objexxFCL

Rosetta style guidelines

• How to use pointers correctly - Working with Rosetta's smart pointer system.
• A note on parsing residue selections in movers and filters -- Using the residue selection parsing system to detect Rosetta numbering, PDB numbering, or ReferencePose numbering.

Using particular classes

• Owning pointers - Rosetta's shared-ownership intrusive reference counted smart pointer. Currently implemented using boost::shared_ptr.
  • Access pointers - An "owning pointer" which doesn't take ownership.
• Vector1 - Rosetta's 1-based indexing vector class.
  • Vector0 - A 0-based indexing version of vector1.
  • VectorL - The generalized L-based indexing vector, from which vector1 and vector0 are derived.

• Tracer - Using the tracer output class.

• Hbonds - Dealing with the Hbond energy terms.

• namespace-core-fragments - Using the classed located in src/core/fragments/

• xyzVector - A vector specialized for Cartesian coordinate use.

• xyzMatrix - A 3x3 matrix class specialized for Cartesian coordinate use.

How to extend Rosetta

• New energy method - How to add a new energy term.
• Resfile reader - How to extend the resfile reader.
• Multithreading - How to add support for multithreading.

Testing changes

See the

• Rosetta tests - A guide to running and writing tests for Rosetta
• Run unit test - How to run the unit tests.
• Write unit test - Writing unit tests.
• UTracer - How to use the UTracer tool in writing unit tests
• Mover test - How to write a unit test for a mover.
  
• Integration tests
• Scientific Benchmarks - How to create and run scientific tests

Visualization Tools

• PyMOL Resources for visualizing Rosetta simulations in PyMol
• Extending the PyMol Viewer Extending the PyMol Mover to add additional visualization features during Rosetta simulations

See Also

• Common Errors: Common errors seen when compiling Rosetta and how to fix them.
• RosettaEncyclopedia: Detailed descriptions of additional concepts in Rosetta.
• RosettaScripts: Wiki page for RosettaScripts, the Rosetta XML interface
• PyRosetta: Wiki page for PyRosetta, the independent Python interface to Rosetta
• Rosetta Timeline: History of Rosetta
• Getting Started: A page for people new to Rosetta
• Build Documentation: Information on building Rosetta
• Running Rosetta with options: Instructions for running Rosetta executables