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FingerPrinter.java

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-04-21 02:36:13 +0200 (Sat, 21 Apr 2007) $
 * $Revision: 8227 $
 *
 * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 *
 * 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.
 *
 * 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 org.openscience.cdk.applications;

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

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.iterator.IteratingMDLReader;
import org.openscience.cdk.tools.LoggingTool;

/**
 * Command line utility that will generate fingerprints for a set of files.
 *
 * @cdk.module applications
 *
 * @author  Egon Willighagen
 * @cdk.created 2003-08-14
 */
00045 public class FingerPrinter {

      /*
       *  This is a command line application            *
       *  Do not convert these System.out/err.println() *
       *  to logger statements
       */
      
    public static void main(String[] args) {
        if (args.length < 1) {
            System.err.println("syntax: FingerPrinter <file> <file2> ...");
            System.exit(0);
        }

        // to make sure the CDK LoggingTool is configured
        LoggingTool logger = new LoggingTool();
        LoggingTool.configureLog4j();
        logger.dumpSystemProperties();

        Fingerprinter fingerprinter = new Fingerprinter();

        // loop over all files
        for (int i=0; i<args.length; i++) {
            String ifilename = args[i];
            try {
                File input = new File(ifilename);
                if (!input.isDirectory()) {
                    IteratingMDLReader reader = new IteratingMDLReader(new FileReader(input),
                        DefaultChemObjectBuilder.getInstance());
                    IMolecule molecule;
                    while (reader.hasNext()) {
                        molecule = (Molecule)reader.next();
                        try {
                            String print = fingerprinter.getFingerprint(molecule).toString();
                            System.out.println("Hit molecule's remark: " +
                                molecule.getProperty(CDKConstants.REMARK));
                            System.out.println("Fingerprint=" + print);
                        } catch (Exception exception) {
                            logger.debug(exception);
                            System.err.println(ifilename + ": error=");
                            exception.printStackTrace();
                        }
                    }
                }
            } catch (Exception exception) {
                logger.debug(exception);
                System.err.println(ifilename + ": error=");
                exception.printStackTrace();
            }
        }
    }

}

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