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hariaimar/print descriptor into excel files.java

Created February 16, 2011 12:08
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print descriptor into excel files.java
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Iterator;
import java.util.Map;
import jxl.Workbook;
import jxl.write.Label;
import jxl.write.WritableSheet;
import jxl.write.WritableWorkbook;
import jxl.write.WriteException;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
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.SmilesGenerator;
import org.openscience.cdk.smiles.SmilesParser;
/**
*
* @author Hari
*acknowledgement CDK team,Ramachandran T.C
*/
public class Main {
/**
* @param args the command line arguments
*/
public static void main(String[] args) throws FileNotFoundException, CDKException, IOException, WriteException {
// TODO code application logic here
File sdfFile = new File("/hari/home/Downloads/CID_241.sdf");
WritableWorkbook workbook = Workbook.createWorkbook(new File("output.xls"));
WritableSheet sheet = workbook.createSheet("Sheet1",0);
IteratingMDLReader reader = new IteratingMDLReader(new FileInputStream(sdfFile), DefaultChemObjectBuilder.getInstance());
SmilesGenerator sg = new SmilesGenerator();
String smile = "";
int k = 0;
while (reader.hasNext()) {
IMolecule mol = (IMolecule)reader.next();
smile = sg.createSMILES(mol);
System.out.print(smile+"\n");
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(smile);
// Second program
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
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();
/**
* The following prints the key and Value set.
*/
Label label0 = new Label(1, k, smile);
sheet.addCell(label0);
k++;k++;
while (iterator.hasNext()) {
Object l = iterator.next();
String key = ((DescriptorSpecification) l).getSpecificationReference().toString();
Label label1 = new Label(1,k,key.substring(key.lastIndexOf("#") + 1));
sheet.addCell(label1);
Label label2 = new Label(2,k,((DescriptorValue) i.get((DescriptorSpecification)l)).getValue().toString());
sheet.addCell(label2);
k++;
}
k++;k++;
}
workbook.write();
workbook.close();
System.out.print(k+"\n");
}
}
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