CDK (Chemistry Development Kit): GUI for Descriptor Calculation from USER INPUT SMILES

This Program takes a Smiles string as input and generates corresponding Descriptor Specification and Descriptor Value. It uses cdk1.3.7.jar and cdk-jchempaint-8.jar.

	import java.awt.Cursor;
	import java.awt.Dimension;
	import java.awt.Toolkit;
	import java.util.Iterator;
	import java.util.Map;
	import java.util.logging.Level;
	import java.util.logging.Logger;
	import javax.swing.table.DefaultTableModel;
	import org.openscience.cdk.DefaultChemObjectBuilder;
	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.qsar.descriptors.molecular.BCUTDescriptor;
	import org.openscience.cdk.smiles.SmilesParser;

	/**
	*
	* @author Hari
	*acknowledgement:cdk team,Ramachandran.T.C.
	*/
	public class Descriptor extends javax.swing.JFrame {

	/** Creates new form Descriptor */
	public Descriptor(String smile) {
	initComponents();
	Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
	Dimension dim = new Dimension(screenSize.width-8, screenSize.height-40);
	this.setMinimumSize(dim);
	this.validate();
	tmodel = (DefaultTableModel) jTable1.getModel();
	// jTextField1.setText(smile);
	}

	/** This method is called from within the constructor to
	* initialize the form.
	*
	*/
	@SuppressWarnings("unchecked")
	// <editor-fold defaultstate="collapsed" desc="Generated Code">
	private void initComponents() {

	jScrollPane1 = new javax.swing.JScrollPane();
	jTable1 = new javax.swing.JTable();
	jLabel1 = new javax.swing.JLabel();
	jTextField1 = new javax.swing.JTextField();
	jButton1 = new javax.swing.JButton();

	setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
	setTitle("Descriptor");

	jTable1.setModel(new javax.swing.table.DefaultTableModel(
	new Object [][] {

	},
	new String [] {
	"Descriptor Specification", "Descriptor Value"
	}
	) {
	boolean[] canEdit = new boolean [] {
	false, false
	};

	public boolean isCellEditable(int rowIndex, int columnIndex) {
	return canEdit [columnIndex];
	}
	});
	jTable1.getTableHeader().setReorderingAllowed(false);
	jScrollPane1.setViewportView(jTable1);
	jTable1.getColumnModel().getColumn(0).setMinWidth(200);
	jTable1.getColumnModel().getColumn(0).setMaxWidth(200);

	jLabel1.setText("Smile");

	jTextField1.setText("NC(CO)C(=O)O");

	jButton1.setText("Generate");
	jButton1.addActionListener(new java.awt.event.ActionListener() {
	public void actionPerformed(java.awt.event.ActionEvent evt) {
	jButton1ActionPerformed(evt);
	}
	});

	javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
	getContentPane().setLayout(layout);
	layout.setHorizontalGroup(
	layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
	.addGroup(layout.createSequentialGroup()
	.addContainerGap()
	.addComponent(jLabel1)
	.addGap(18, 18, 18)
	.addComponent(jTextField1, javax.swing.GroupLayout.PREFERRED_SIZE, 163, javax.swing.GroupLayout.PREFERRED_SIZE)
	.addGap(28, 28, 28)
	.addComponent(jButton1)
	.addContainerGap(93, Short.MAX_VALUE))
	.addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 413, Short.MAX_VALUE)
	);
	layout.setVerticalGroup(
	layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
	.addGroup(layout.createSequentialGroup()
	.addContainerGap()
	.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
	.addComponent(jLabel1)
	.addComponent(jTextField1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
	.addComponent(jButton1))
	.addGap(1, 1, 1)
	.addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 268, Short.MAX_VALUE))
	);

	pack();
	}// </editor-fold>

	private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {
	try {
	// TODO add your handling code here:
	setCursor(new Cursor(Cursor.WAIT_CURSOR));
	BCUTDescriptor descriptor = new BCUTDescriptor();
	// Molecule molecule = (Molecule) new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles("NC(CO)C(=O)O");
	Molecule molecule = (Molecule) new SmilesParser(DefaultChemObjectBuilder.getInstance()).parseSmiles(jTextField1.getText());
	// Second program
	DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR,new String[]{"lib/cdk-1.3.7.jar"});
	engine.process(molecule);
	/**
	* The function getProperties returns a Map value. Map represents a Key Value set.
	* It is retrieved using an iterator. Since the key is of DescriptorSpecification class and the
	* value is of type DescriptorValue we have to typecast the key and value with the same while retrieving.
	* since they have not override the same to String.
	*/
	Map i = molecule.getProperties();
	Iterator iterator = i.keySet().iterator();
	Object[] o = i.keySet().toArray();
	System.out.print("" + o.length + "\n\n");
	/**
	* The following prints the key and Value set.
	*/
	while (iterator.hasNext()) {
	Object l = iterator.next();
	String key = ((DescriptorSpecification) l).getSpecificationReference().toString();
	tmodel.addRow(new Object[]{key.substring(key.lastIndexOf("#") + 1), ((DescriptorValue) i.get((DescriptorSpecification)l)).getValue().toString()});
	}
	setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
	} catch (CDKException ex) {
	Logger.getLogger(Descriptor.class.getName()).log(Level.SEVERE, null, ex);
	}
	}

	/**
	* @param args the command line arguments
	*/
	public static void main(String args[]) {
	java.awt.EventQueue.invokeLater(new Runnable() {
	public void run() {
	new Descriptor(null).setVisible(true);
	}
	});
	}

	// Variables declaration - do not modify
	private javax.swing.JButton jButton1;
	private javax.swing.JLabel jLabel1;
	private javax.swing.JScrollPane jScrollPane1;
	private javax.swing.JTable jTable1;
	private javax.swing.JTextField jTextField1;
	// End of variables declaration

	DefaultTableModel tmodel;
	}