BioJava based 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.)

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.

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

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

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

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

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.

The current primary projects defined for the ''RCSB Viewers'' are:

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''.

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.''

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.

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.

''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:

• [[RCSB Viewers:Developer Environment]]
• [[RCSB Viewers:Architectural Overview|Architectural Overview]]
• [[RCSB Viewers:Projects Overview|Projects Overview]]
• [[RCSB Viewers:Source Division|Source Division]]

• [[RCSB Viewers:MBT Libs:Bonds and Nucleic Acid Identification^Classification|Bonds and Nucleic Acid Identification/Classification]]
• [[RCSB Viewers:MBT Libs:Fragment (Secondary Structure) Definition|Fragment (Secondary Structure) Definition]]
• [[RCSB Viewers:MBT Libs:PDBToNdbConverter|PDBToNdbConverter]]

• [[RCSB Viewers:Viewer Framework:General Rendering|General Rendering]]
• [[RCSB Viewers:Viewer Framework:Picking|Picking]]