CDK QSARs of Peptides

I was doing some working in CDK and was pleasantly surprised at how easy it is to calculate descriptors on short peptides. The code to do this is actually only three lines! Adding in a bug fix though, it becomes four. Here's the code to calculate every QSAR descriptor on a peptide

	String textString="GG";//two glycines
	BioPolymer peptide = ProteinBuilderTool.createProtein(textString);
	//Need to get rid of BioPolymer class since there is a bug in its clone implementation
	Molecule mpeptide = new Molecule(peptide);
	DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
	engine.process(mpeptide);

view raw gistfile1.java hosted with ❤ by GitHub

The complete code with imports and outputting the results is shown below:

	import java.io.IOException;
	import org.openscience.cdk.BioPolymer;
	import org.openscience.cdk.Molecule;
	import org.openscience.cdk.exception.CDKException;
	import org.openscience.cdk.qsar.DescriptorEngine;
	import org.openscience.cdk.qsar.DescriptorSpecification;
	import org.openscience.cdk.qsar.DescriptorValue;
	import org.openscience.cdk.smiles.SmilesGenerator;
	import org.openscience.cdk.tools.ProteinBuilderTool;
	public class PepQSAR {
	public static void main(String[] args) throws
	CloneNotSupportedException, CDKException, IOException {
	String textString="GG";
	BioPolymer peptide = ProteinBuilderTool.createProtein(textString);
	//Need to get rid of BioPolymer class since there is a bug in its clone
	Molecule mpeptide = new Molecule(peptide);
	DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
	engine.process(mpeptide);
	for(DescriptorSpecification sp : engine.getDescriptorSpecifications()) {
	int rcount = mpeptide.getProperty(sp) == null ?
	0 :
	((DescriptorValue) (mpeptide.getProperty(sp))).getValue().length();
	if(rcount > 0) {
	String[] results =
	((DescriptorValue) (mpeptide.getProperty(sp))).getValue().toString().split(",", rcount);
	for(int i = 0; i < rcount; i++) {
	System.out.println(sp.getImplementationTitle() + i + " : " + results[i]);
	}
	}
	}
	}

view raw gistfile1.java hosted with ❤ by GitHub