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HydrogenAtom.java

/* $Revision: 8245 $ $Author: djiao $ $Date: 2007-04-22 17:20:57 -0400 (Sun, 22 Apr 2007) $
 * 
 * Copyright (C) 2004-2007  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.
 *
 * 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.isomorphism.matchers.smarts;

import java.util.List;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;

/**
 * This matches Hydrogen atoms
 *
 * @cdk.module extra
 */
00033 public class HydrogenAtom extends SMARTSAtom {
      private IAtomContainer atomContainer;

      public HydrogenAtom() {
      }

00039       public boolean matches(IAtom atom) {
            if (!atom.getSymbol().equals("H")) {
                  return false;
            }
            
            if (atom.getFormalCharge() == 1) { // proton matches
                  return true;
            }
            
            // hydrogens connected to other hydrogens, e.g., molecular hydrogen
            List list = atomContainer.getConnectedAtomsList(atom);
                for (int i=0; i<list.size(); i++) {
                    IAtom connAtom = (IAtom)list.get(i);
                  if (connAtom.getSymbol().equals("H")) {
                        return true;
                  }
            }
            
            // hydrogens connected to other than one other atom, e.g., bridging hydrogens
            if (atom.getFormalNeighbourCount() > 1) {
                  return true;
            }
            
            //isotopic hydrogen specifications, e.g. deuterium [2H] 
            if (atom.getMassNumber() > 1) { 
                  return true;
            }
            
            return false;
      }

      public IAtomContainer getAtomContainer() {
            return atomContainer;
      }

      public void setAtomContainer(IAtomContainer atomContainer) {
            this.atomContainer = atomContainer;
      }     
}

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