Development Documentation

Developing for Rosetta

• Rosetta overview
• Using Git - Basic steps to working with git and committing code
• Doxygen tips - How to work with Rosetta's in-code documentation.
• Writing an app - How to write your own Rosetta-based application.
• Packer Task - Controlling which side chains can vary during rotamer optimization
• Making rosetta robust for running on large number of inputs

Code organization

• 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 utility
  • Namespace utility::factory
  • Namespace utility::io
  • Namespace utility::keys
  • Namespace utility::options
• Namespace numeric
• Namespace objexxFCL

Rosetta style guidelines

• Owning pointer usage guidlines - Working with Rosetta's smart pointer system.

Using particular classes - Some of this documention may be out of date.

• Owning pointers - Rosetta's shared-ownership intrusive reference counted smart pointer.
  • Access pointers - An "owning pointer" which doesn't take ownership.
  • ReferenceCount - How owning pointers are implemented.
  • ReferenceCountMI - ReferenceCount for multiple inheritance.
• 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.

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

• xyzVector - A vector specialized for Cartesian coordinate use.

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

How to extend Rosetta

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

Testing changes

• 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.
  
• Scientific test - How to create and run scientific tests