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 
 */
public class HydrogenAtom extends SMARTSAtom {
	/**
	 * Local copy of IAtomContainer. 
	 */
	private IAtomContainer atomContainer;

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

	/* (non-Javadoc)
	 * @see org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom#matches(org.openscience.cdk.interfaces.IAtom)
	 */
	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.
	 */
	public IAtomContainer getAtomContainer() {
		return atomContainer;
	}

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