Predict drug susceptibility for HIV mutant using XMPP service

hivpred.js

/*******************************************************************************
 * Script to predict the susceptibility of an HIV protease sequence for seven 
 * drugs based on the proteochemometric model described in:
 * Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JE. 
 * Proteochemometric modeling of HIV protease susceptibility,
 * BMC Bioinformatics. 2008 Apr 10;9:181. . 
 *
 * Script accepts a 99 aa sequence as input and delivers susceptbiliy values 
 * for the drugs Amprenavir, Atazanavir, Indinavir, Lopinavir, Nelfinavir, 
 * Ritonavir, and Saquinavir.
 *
 * Script author: Ola Spjuth <ola.spjuth@farmbio.uu.se>
 *     
 ******************************************************************************/

//Define input sequence and XMPP service and -function
var seq="PQITLWQRPIVTIKIGGQLREALLDTGADNTVLEEMNLPGRWKPKMIVGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRDLLTQIGCTLNF";
var predictionServer="hivpred.ws1.bmc.uu.se";
var predictionFunction="predictSusceptibility";

//Connect if not connected (requires JID and password in preferences)
if (!(xmpp.isConnected()))
	xmpp.connect();

//Set up function
var func = xmpp.getFunction(predictionServer, predictionFunction);

var iof;
if (xmpp.existsIoFactory(func))				//Check if binding exists
	iof=xmpp.getIoFactory(func);			//Try to load generated binding
if (iof==null){
	var ios = func.getIoSchemataSync(20000);	//Get schema from service
	iof = xmpp.getIoFactory(ios);		        //Generate binding
}

//Create input document
var inputDoc=iof.createHIVPredInputDocument();
var inputObject = inputDoc.addNewHIVPredInput();
inputObject.setSequence(seq);

//Invoke service on document
var result = func.invokeSync(inputDoc, 20000);

//Handle results
var resultDoc = iof.getOutputObject(result);
js.print("Predicted susceptibility:\n\n " + resultDoc.toString())