RCSB Viewers:About

From BioJava
Jump to: navigation, search

Contents

About RCSB Viewers

The RCSB Viewers suite of frameworks provides the capability of creating 3-d viewing applications. The libraries are Java based, and rely on JOGL (Java OpenGL) to do the 3d rendering. Currently, there are four supported viewers implemented over the suite (see below.)

History

The RCSB Viewers were initially implemented as a set of viewers over the MBT (Molecular Biology Toolkit) Library, developed at the San Diego Super Computing Center. The MBT Library provided the base-level support for structure definition, loading, and viewing.

Since then, as part of a major re-architecting effort, the visualization and application functionality have been lifted out of the MBT Library, with a view towards replacing it with BioJava. As a result, the MBT Library (renamed and factored in this distribution as the RCSB MBT Libs) has been reduced to simply the structure definition and loading frameworks - the UI application and 3d visualization frameworks have been factored into discrete projects.

Current Viewers

The current set of viewers that are based on the framework are as follows:

RCSB Simple Viewer

A basic viewer with no UI, except a menubar that allows for loading of files and saving the current image to a file.

SimpleViewerOverview.png

RCSB Protein Workshop

A viewer that provides tools to manipulate and examine parts of the structure, as well as change the rendering styles.

ProteinWorkshopOverview.png

RCSB Ligand Explorer

This viewer explores relationships between ligands (or other non-protein chains/residues) and the containing protein.

LigandExplorerOverview.png

RCSB PDB Kiosk

The Kiosk viewer is a full screen viewer that provides a slide show of a set of structures, smoothly animating the camera for each structure shown to view it from different angles and perspectives. It can also focus on non-protein chains/residues, if present in the molecule.

Current Projects

The current primary projects defined for the RCSB Viewers are:

RCSB MBT Libs
this project contains the modules to define and carry the 'model', defined as a set of structures. It has been mostly preserved directly from the original MBT Library project. It also contains modules to load files (currently only PDB and XML files are supported.) It is expected this will be replaced by BioJava.
RCSB UIApp Framework
this project contains modules required to make an actual UI (windowing) application. It defines a singleton application class, mainframe (document frame) class, various controllers to tie the pieces together and direct program flow. The UI aspect is based on Swing.
RCSB Viewer Framework
this is the project that carries the 3d modules and derived/modified classes to enable creation of 3d applications. The 3d rendering is provided by JOGL (Java OpenGL), directly.
RCSB Simple Viewer, RCSB Protein Workshop, RCSB Ligand Explorer, RCSB PDB Kiosk
projects for the end viewer applications.

In addition, there are several minor projects for updating datasets, documentation, and tests. See the SVN repository for further information.

Documentation

Javadoc documentation is generated from all the sources, and is provided here (provide link.)

In addition, there are several operational/architectural topic pages as follows:

General:

RCSB MBT Libs:

RCSB Viewer Framework

Personal tools
Namespaces
Variants
Actions
Documentation
Community
Toolbox