CalculateDescriptors

public class CalculateDescriptors
{
  private static void forTrainingSet(String smileFile)
    throws FileNotFoundException
  {
    IteratingSMILESReader reader = new IteratingSMILESReader(new FileInputStream(smileFile), DefaultChemObjectBuilder.getInstance());
    while (reader.hasNext())
    {
      IAtomContainer molecule = reader.next();
      ToxDescriptor desc = new ToxDescriptor();
      desc.setHBondAcceptors(CDKUtil.Molecule.getHBondAcceptorCount(molecule));
      desc.setHBondDonors(CDKUtil.Molecule.getHBondDonorCount(molecule));
      desc.setHeteroAtoms(CDKUtil.Molecule.getHeteroAtomCount(molecule));
      desc.setMolecularWeight(CDKUtil.Molecule.getExactMass(molecule));
      desc.setRotatableBonds(CDKUtil.Molecule.getRotatableBondCount(molecule));
      desc.setRuleOfFive(CDKUtil.Molecule.obeysRuleOfFive(molecule));
      desc.setTPSA(CDKUtil.Molecule.getTPSA(molecule));
      desc.setXLogP(CDKUtil.Molecule.getXLogP(molecule));
      
      System.out.println(desc.toString());
    }
  }
  
  public static void main(String[] args)
  {
    String file = "/home/vishal/charite/tox21/all_targets_sdf/nr-aromatase.smi";
    try
    {
      forTrainingSet(file);
    }
    catch (FileNotFoundException ex)
    {
      Logger.getLogger(CalculateDescriptors.class.getName()).log(Level.SEVERE, null, ex);
    }
  }
}