BODRIsotopeDumper.java

/* Copyright (C) 2007,2011  Egon Willighagen <egonw@users.sf.net>
 *
 * Contact: cdk-devel@lists.sourceforge.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 */
package net.sf.cdk.tools.bodr;

import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;

import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.config.Isotopes;
import org.openscience.cdk.config.XMLIsotopeFactory;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.silent.SilentChemObjectBuilder;

/**
 * Support class that converts a BODR CML file with isotope data into a CDK-specific
 * test file. This class uses the {@link XMLIsotopeFactory} to creates input for the
 * {@link Isotopes} class.
 *
 * @author egonw
 */
public class BODRIsotopeDumper {

	/**
	 * Creates output to STDOUT which can be copied into the isotopes.txt file.
	 *
	 * @param args         Ignored command line parameters
	 * @throws IOException thrown when the input text file cannot be read
	 */
	public static void main(String[] args) throws IOException {
		String path = "src/main/org/openscience/cdk/config/data/isotopes.dat";
		IsotopeFactory fac = XMLIsotopeFactory.getInstance(SilentChemObjectBuilder.getInstance());
		IIsotope[] isotopes = fac.getIsotopes();
		ByteBuffer bout = ByteBuffer.allocate(50000); // file is < 50kB
		System.out.println("Put length: " + isotopes.length);
		bout.putInt(isotopes.length);
		for (IIsotope isotope : isotopes) {
			// chars a little more tricky
			bout.put((byte)isotope.getAtomicNumber().intValue());
			bout.putShort((short)isotope.getMassNumber().intValue());
			bout.putDouble(isotope.getExactMass());
			if (isotope.getNaturalAbundance() == 0.0) {
				bout.put((byte) 0);
			} else {
				bout.put((byte) 1);
				bout.putDouble(isotope.getNaturalAbundance());
			}
		}
		bout.limit(bout.position()).position(0);
		FileOutputStream out = new FileOutputStream(path);
        FileChannel fc = out.getChannel();
        fc.write(bout);
        fc.close();
        out.close();
	}

}