MDLMolConvention.java

/* $Revision$ $Author$ $Date$
 *
 * Copyright (C) 1997-2007  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 org.openscience.cdk.io.cml;

import org.openscience.cdk.interfaces.IChemFile;
import org.xml.sax.Attributes;

/**
 * Implementation of the MDLMol Covention for CML.
 *
 * @cdk.module io
 * @cdk.githash
 *
 * @author Egon Willighagen <egonw@sci.kun.nl>
 */
public class MDLMolConvention extends CMLCoreModule {

    public MDLMolConvention(IChemFile chemFile) {
        super(chemFile);
    }

    public MDLMolConvention(ICMLModule conv) {
        super(conv);
    }

    public void startDocument() {
        super.startDocument();
//        cdo.startObject("Frame");
        currentChemModel = currentChemFile.getBuilder().newChemModel();
    }

    public void startElement(CMLStack xpath, String uri, String local, String raw, Attributes atts) {
        logger.debug("MDLMol element: name");
        super.startElement(xpath, uri, local, raw, atts);
    }

    public void characterData(CMLStack xpath, char ch[], int start, int length) {
        String s = new String(ch, start, length).trim();
        if (xpath.toString().endsWith("string/") && BUILTIN.equals("stereo")) {
            stereoGiven = true;
            if (s.trim().equals("W")) {
                logger.debug("CML W stereo found");
                bondStereo.add("1");
            } else if (s.trim().equals("H")) {
                logger.debug("CML H stereo found");
                bondStereo.add("6");
            }
        } else {
            super.characterData(xpath, ch, start, length);
        }
    }
}