Table of Contents

Rosetta (not on) GPU

Introduction

This is the front page for the "internal" portion of the Rosetta documentation wiki. It provides convenient access to documentation pages which are primarily intended for the RosettaCommons community, but can be publically released. This is usually either things of primarily historical significance, developmental minutia, or in-work documentation which isn't ready for general consumption.

Documentation which is "internal-only" in nature should be placed on the internal password-protected RosettaCommons wiki (MediaWiki) instead.

See how to write documentation for more details.

Rosetta Build System

Core Class Modifications

If you change the API for a core class (particularly if you remove, rename, or alter an existing function), please make a note of it here to make it easy to communicate this to the development community and the PyRosetta community, and for future documentation in the release notes. Note that this applies to any API change in core.5 or below (numeric, basic, etc.). Such changes should be avoided if possible, but if such a change is unavoidable, please do the following:

E-mail the developer list. Developers need to know, and a conversation needs to happen. Do not proceed with the change without community approval.
If the change is approved, make sure that the Gray lab knows. The PyRosetta tutorials will need to change.
If possible, maintain an old function with the old interface, with a tracer warning that this function will be deprecated and that the new function should be used instead.
Document the change here, for future inclusion in the release notes:

Date	Author	Description	Reason
31 Aug 2016	Andy Watkins	[Example]: core::pose::Pose::n_residue() was renamed to core::pose::Pose::size().	An opportunity for maniacal laughter.

PyRosetta API changes

Since r59466 xyzMatrix now have .xy properties bound as 'data' instead of set/get functions. So if your code accessed this methods directly you will need to refactor it as m.xx( m.xy() ) --> m.xx = m.xy

Rosetta Code-Writing Documentation

Overview

RosettaAcademy

RosettaAcademy (or "Rosetta for Newbies") - An intro guide for new RosettaCommons users and developers.

Code Template Generation

Code Template Generation - How to use the template generator scripts to generate code templates of common Rosetta classes/apps/unit tests to save development time

Before Commit Check

Before commit check - Things to check before submission.

Code Review Guide

ReviewerTemplate - A template for reviewers of application documentation.

Documentation Template

App name - Template for Rosetta application documentation.
Template app documentation page - Alternative application documentation template.

Writing a New SimpleMetric

Creating a SimpleMetric instead of Filter or for general analysis

Global Objects-Singletons in Rosetta

Creating singletons that are threadsafe. Andrew

Rosetta Method Documentation

Computing SASA in Rosetta

Method for computing SASA in Rosetta written by Jared

Chemical XRW 2016

- Overview of File I/O Code

- Changes made post-XRW

JD3 -- version 3 of the JobDistributor system

TODO

Energy Function optimization

Seattle Group

Overview of Seattle Group energy function optimization project Updates beta july15 Updates beta nov15

Documentation for Specific Projects

Updating ResidueTypeSet to handle the full chemical repertoire of macromolecules

Overview of ResidueTypeSet
ResidueTypeFinder is new class to efficiently find ResidueTypes from a ResidueTypeSet for most (all?) queries.

Modeling membrane proteins with RosettaMP

Movers & Methods in development

Score Functions

Applications

Docking:
- Global Docking in the Membrane
Relax:
- Mutate Relax
- Quick Relax
De novo:
- Helix from sequence
Other:
- Mutate

Membrane Chemical Profiles Project

Design-specific scoring terms

Repeat stretch energy (aa_repeat_energy) -- A scoring term that penalizes long stretches of repeating sequence (e.g. poly-Q sequences).
Residue composition energy (aa_composition) -- A scoring term that penalizes deviation from a desired residue type composition (e.g. no more than 7% alanines; at least one aromatic; at least 40% hydrophobic).

Cyclic Peptides / Geometrically-Constrained Polymers Project

Peptide structure prediction with the simple_cycpep_predict app
Workflow
PeptideStubMover
DeclareBond
SetTorsion -- updated with new functionality; documentation needs to be written

Stepwise Assembly and Monte Carlo Project

General application documentation is publicly viewable.
Overview of stepwise enumeration and monte carlo, both accessed through stepwise application
Monte Carlo Moves and the move schedule
SampleAndScreen is a general class for enumerating or stochastically sampling residues (or rigid bodies)
Samplers are concatenated together to define the sampling loop, and can go through millions of poses.
Screeners are filters with some specialized features to 'fast-forward' through the sampling loop and prevent memory effects in the pose.
FullModelInfo is an important book-keeping object held by the pose used throughout the stepwise code.
Score terms calculate energies for a full model even if only subpieces are instantiated (other_pose, loop_close, free_side_chain).

Fragment assembly of RNA (FARNA) renovation, unification with stepwise

FARNA is Rosetta's original RNA de novo modeling code (dating back to Rosetta++). It is undergoing some updates in 2015-2016.

S.E.W.I.N.G. Protocol

Pilot Apps

This is documentation for not-yet-released applications

General

multi-residue-ligand-dock - Docking of multiple ligand residues
hotspot-hash - Documentation for Hotspot hashing
- hshash-utils - Utilities for Hotspot hashing
multistate-design-ga - DNA interface multistate design
RosettaPCS - Protein folding using Pseudo-Contact-Shift NMR restraints

Rosetta (not on) GPU

internal_documentation/Rosetta-GPU-conversation-transcription

Internal Documentation