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HydrogenAtom.java

/* $Revision$ $Author$ $Date$
 * 
 * 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 org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;

import java.util.List;

/**
 * This matches Hydrogen atoms.
 *
 * @cdk.module  smarts
 * @cdk.githash
 * @cdk.keyword SMARTS 
 */
00035 public class HydrogenAtom extends SMARTSAtom {
      /**
       * Local copy of IAtomContainer. 
       */
00039       private IAtomContainer atomContainer;

      /**
       * Creates a new instance.
       *
       */
00045       public HydrogenAtom() {
            super();
      }

      /* (non-Javadoc)
       * @see org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom#matches(org.openscience.cdk.interfaces.IAtom)
       */
00052       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<IAtom> list = atomContainer.getConnectedAtomsList(atom);
            for (IAtom connAtom: list) {
                  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] or tritium etc
        if (atom.getMassNumber() != null) {
            if (getMassNumber().intValue() == atom.getMassNumber().intValue()) return true;
        } else {
            // target atom is [H], so make sure query atom has mass number = 1
            if (getMassNumber() == 1) return true;
        }
            
            return false;
      }

      /**
       * Returns local copy of IAtomContainer.
       */
00088       public IAtomContainer getAtomContainer() {
            return atomContainer;
      }

      /**
       * Sets IAtomContainer.
       */
00095       public void setAtomContainer(IAtomContainer atomContainer) {
            this.atomContainer = atomContainer;
      }     
}

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