import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;

import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.ChemObject;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
import org.openscience.cdk.io.*;

/** MolToSmiles 
 *
 * Command-line utility that translates MDL mol files to SMILES
 * strings
 * 
 *
 * @author  irilenia
 * @version 27/02/2005 compiled with CDK 25/01/2005 
 *
 */

public class MolToSmiles {

   public static void main(String[] args) {
      if (args.length <1) {
         System.err.println("syntax: MolToSmiles <mol_file>");
         System.exit(0);
      }

      // check the first argument - must be a file
      String mol_filename = args[0];
      File mol_file = new File(mol_filename);
      if (!(mol_file.isFile())) {
         System.err.println("Error: First argument must be a file! " + "Argument 1= " + args[0]);
         System.exit(0);
      }

      // create a reader and read the contents of the query file
      // only allow one molecule in the query file!
      try {
      Molecule mol =null; 

      ChemObjectReader reader = new ReaderFactory().createReader(new FileReader(mol_file));
      if (reader.accepts(new Molecule())) {
         ChemFile content = (ChemFile)reader.read((ChemObject)new ChemFile());
         AtomContainer[] containers = ChemFileManipulator.getAllAtomContainers(content);
         //will only read the first container and ignore the rest!
         if (containers.length<1) {
            System.err.println("Error: No molecules were found in " + mol_file.getName());
            System.exit(0);
         }
         mol = new Molecule(containers[0]);
         if (mol == null) {
            System.err.println("Error: Molecule returned is null from file " + mol_file.getName());
            System.exit(0);      
         }
         if (HueckelAromaticityDetector.detectAromaticity(mol)) { //REQUIRED to recognise aromatic flags
            //System.out.println("Query is aromatic!");
         }
      } 
      else {
         System.err.println("Error: Could not read molecule from file " + mol_file.getName());
         System.exit(0);
      }
  
      //print out the target molecule
      SMILESWriter writer = new SMILESWriter(new FileWriter(new File("target.smi")));
      writer.write(mol);
      writer.close();
      }//try
      catch (Exception exception) {
          exception.printStackTrace();
      }


   } //main

   
}