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