Bioclipse2 Scripting #3: XLogP calculatation using a XMPP CDK cloud service

In preparation of the CDK workshop next week, here is a small Bioclipse2 script to calculate the XLogP value for a given SMILES, using the a CDK-based XMPP service:

	// connect to the XMPP hive
	xmpp.connect();
	// we are going to call the XLogP function of the descriptor service
	service = xmpp.getService("descriptor.ws1.bmc.uu.se");
	service.discoverSync(5000);
	service.getFunctions();
	f = service.getFunction("XLogP");
	// we use Bioclipse to create a CML document, starting from a SMILES
	smiles = "COC";
	propane = cdk.fromSMILES(smiles);
	js.clear();
	js.print("Molecule SMILES: " + smiles + "\n");
	result = f.invokeSync(propane.getCML(), 900000);
	cmlReturned = xmpp.toString(result);
	// convert the returned CML into CMLXOM and extract the value
	propertyList = cml.fromString(cmlReturned);
	xlogp = propertyList.getPropertyElements().get(0).
	getScalarElements().get(0).getValue()
	js.print("XLogP: " + xlogp + "\n")

view raw Calculates the XLogP for ethoxyethane using XMPP and the CDK.js hosted with ❤ by GitHub

Earlier in this series:

• Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol
• Bioclipse2 Scripting #2: searching PubChem

Multiple inheritence for content types?

Bioclipse is an environment for handling and processing life sciences data. This data is present in files with a wide variety of formats, each of which can contain a particular data type. For example, a we can have a single molecule in MDL molfile and in CML.

The latter is particularly interesting, as I do not know how to work that out... Firstly, I want the CML (Single Molecule) content type extend the CML content type, so that a validating CML editor can open it with the proper schema, but at the same time I would like to extend it a content type representation a Single Molecule. Hence, the multiple inheritance.

This is what the plugin.xml currently looks like:

<extension
  point="org.eclipse.core.runtime.contentTypes">

  <content-type
    base-type="net.bioclipse.contenttypes.cml"
    id="net.bioclipse.contenttypes.cml.singleMolecule2d"
    name="CML (Single 2D Molecule)"
    priority="high">
    <describer class="net.bioclipse.cml.contenttypes.CmlFileDescriber">
      <parameter
        name="dimension"
        value="2D"/>
      <parameter
        name="cardinality"
        value="single"/>
    </describer>
  </content-type>

</extension>

Very clearly, a single base-type. Is there any option of multiple inheritance?

Bioclipse: a powerful Jmol application

While Bioclipse is much more, it could be an interesting alternative to the Jmol application. It offers:

• a scripting console
• a file browser (the Eclipse way)
• an outline of the file content which allows selections
• a script editor

The underlying RCP toolkit has many other interesting features for a Jmol application, but the above is up and running: