import java.util.ArrayList;
import java.io.*;

import chemaxon.reaction.*;
import chemaxon.formats.*;
import chemaxon.struc.*;

public class StandardizerDemo {
    static public void main(String[] args) throws Exception {
	if (args.length < 2) {
	    System.err.println("Usage: ");
	    System.err.println("  java StandardizerDemo <config file> <molecule file>");
	    return;
	}

	// create Standardizer object
	Standardizer standardizer = new Standardizer(new File(args[0]));

	// standardize molecules
	MolImporter importer = new MolImporter(args[1]);
	MolExporter exporter = new MolExporter(System.out, importer.getFormat());
	Molecule mol = null;
	while ((mol = importer.read()) != null) {
	    standardizer.standardize(mol);
	    exporter.write(mol);
	}
	importer.close();
	exporter.close();
    }
}