From BioclipseWiki

Plugins are central to Bioclipse: the plugins implement functionality. The [Ghemical] plugin adds functionality from this open source molecular mechanics (MM), quantum mechanics (QM) and molecular dynamics (MD) program to Bioclipse. Ghemical is GPL and written in C++, so either the command line can be used as interface, or JNI.

Bioclipse already uses Jmol for 3D graphics, so Ghemical is used as calculation engine only. Additionally, the already existing JChemPaint plugin provides a 2D structure editor for setting up the chemical input for calculations. Bioclipse uses the Eclipse Rich-Client-Platform, and the plugin would make heavy use of this technology, making this project an excellent way to learn about the Eclipse RCP architecture.

Contents 1 The implementation 1.1 Running the Plug-in 1.2 Architecture 2 About the project 2.1 Goals 2.2 Status

The implementation

Running the Plug-in

 Testing purpose only, software still under development

• Make sure your are using Eclipse 3.2 or higher
• [Retrieve Bioclipse] as usual
• Download the bc_compute and bc_ghemical from the trunk
• In Eclipse goto Run->Run and select your Bioclipse target
• Select the tab page "Plug-ins" and select "net.bioclipse.plugins.bc_compute" and "net.bioclipse.plugins.bc_ghemical"
• Run

Architecture

About the project

Goals

• write interface to Ghemical, using JNI or command line
• allow setting up QM/MM/MD calculations, using the RCP preference system
• use the RCP monitoring system to track calculation progress

On an architectural level, these goals have to be persued too:

• define an 'QM/MM' extension point
• define a 'MD' extension point

Status

August 14, 2006

• Split the general computation engine and formalised in bc_compute. Which is an adaption of the 'New' wizard in Eclipse, to select and configure a computation using a wizard.
• Added demo wizards for bc_compute.
• Molecular Mechanics computations are running, ready to be tested (Linux).
• Quantum Mechanics computations are not working yet, Ghemical needs to be linked against the MOPAC7 lib.
• Geometric Optimization computations are added, not finished yet.
• Molecular Dynamics computations are added, not finished yet.
• Added help

July 10, 2006

• Linux support added.
• Native binaries loading is improved. Loading is now triggered at plugin startup.
• The progress of calculations is now tracked using the Progress View.
• Added a plugin logger.

July 1, 2006

• Added Plugin project to the Bioclipse trunk
• Added a Preference Store Page, where users can select the calculation method they want to use (MM/QM).
• Added a Help TOC + near empty documentation page.
• Added an action, wich is hooked to the CDKResources in the BioResource Navigator and upon activation calculates the energy for the selected CDKResource(s).
• Added a progress monitor to track the progress of the calculation of the selected resources.
• Added an empty test project.
• Made a stub library (dll) that takes the place of the LibGhemical until that is working correct.