RDF, Jena, Bioclipse, Eclipse, Zest #2: icons and an extension point

Jonathan worked this week on new features for the Bioclipse RDF editor (see these two earlier items). This version still does not edit, but only display using Zest. Jonathan created for me an extension point so that anyone can make the editor aware of domain objects, by simply registering the extension implementation along with the rdf:Class URI of the rdf:type of an object. This fixes the problem of having to hardcode dependencies of the RDF editor on all the domain code, as was the case earlier.

For example, the cheminformatics IMolecule object is now linked to the rdf:type <http://www.bioclipse.net/structuredb/#Molecule>:

<extension point="net.bioclipse.rdf.rdf2bioobjectfactory">
  <Factory
    instance="net.bioclipse.rdf.ui.RDFToCDKMoleculeFactory"
    uri="http://www.bioclipse.net/structuredb/#Molecule" >
  </Factory>
</extension>

The API for this factory looks like:

public IBioObject rdfToBioObject( Model model, Resource res );
public ImageDescriptor getImageDescriptor();

This is very much tied into the Jena data model, so not entirely clean, but has to do for now. The first method converts RDF content into a Bioclipse IBioObject, such as an IMolecule (see this list of currently supported objects). The second method returns an icon, which makes the editor more visually pleasing, and provides a nice way to see when you can double click the RDF node to have it open in an domain specific editor:

For example, double clicking the ron:mol2 node, would open up a JChemPaint editor.

Chemistry in Eclipse: Bioclipse-JChemPaint

The Uppsala and EBI CDK-teams have been working hard on finishing the rewrite of JChemPaint I started with Niels earlier. While the EBI-team focused on the applet (and Swing application), the Uppsala team, obviously, focused on the SWT side, for integration into Bioclipse. The new JChemPaint is reaching a useful state, and below is a quick update screenshot something Arvid has been working on:

It shows a periodic table which allows you to drag any element type onto the JChemPaint drawing area. It is using regular drag and drop functionality, allowing you to create any arbitrary pseudo atom too. This also paves the way for a template system, allowing you to drag-n-drop fragments onto an active JChemPaint editor.

Scripting JChemPaint

Stefan, Gilleain, Arvid and I had a JChemPaint Developers Workshop in Uppsala, to sprint the development of JChemPaint3, for which Niels layed out the foundation already a long time ago.

Gilleain and Arvid merged their branches into a single code base, while Stefan worked on the Swing application and applet. The Bioclipse SWT-based widget is being developed for Bioclipse2.

The new design separates widget/graphics toolkit specifics from the chemical drawing and editing logic. Regarding the editing functionality, this basically comes down to have a semantically meaningful edit API. This allows us to convert both Swing and SWT mouse events into things like addAtom("C", atom), which would add a carbon to an already existing atom. However, without too much phantasy, it allows adding a scripting language. This is what I have been working on. Right now, the following API is available from the Bioclipse2 JavaScript console (via the jcp namespace, in random order):

• ICDKMolecule jcp.getModel()
• IAtom getClosestAtom(Point2d)
• setModel(ICDKMolecule) (for really fancy things)
• removeAtom(IAtom)
• IBond getClosestBond(Point2d)
• updateView() (all edit command issue this automatically)
• addAtom(String,Point2d)
• addAtom(String,IAtom) (which works out coordinates automatically)
• Point2d newPoint2d(double,double)
• updateImplicitHydrogenCounts()
• moveTo(IAtom, Point2d)
• setSymbol(IAtom,String)
• setCharge(IAtom,int)
• setMassNumber(IAtom,int)
• addBond(IAtom,IAtom)
• moveTo(IBond,Point2d)
• setOrder(IBond,IBond.Order)
• setWedgeType(IBond,int)
• IBond.Order getOrder(int)
• zap() (sort of sudo rm -Rf /*)
• cleanup() (calculate 2D coordinates from scratch)
• addRing(IAtom,int)
• addPhenyl(IAtom)

This API (many more method will follow) is not really aimed at the end user, who will simply point and click. The goal of this scripting language is, at least at this moment, to test the underlying implementation using Bioclipse. Future applications, however, may include simple scripts which use some logic to convert the editor content. For example, replacing a t-butyl fragment into a pseudo atom "t-Bu". The key thing to remember, is that this will allow Bioclipse to have non-CDK-based programs act on the JChemPaint editor content (e.g. using getModel() and setModel(ICDKMolecule)). More on that later.

A simple script could look like: Or, as screenshot: