aminoacidmanipulator.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $ 
 * $Date: 2007-02-07 20:28:54 +0100 (Wed, 07 Feb 2007) $
 * $Revision: 7879 $
 * 
 * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 * 
 * Contact: [e-mail]
 * 
 * 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.tools.manipulator;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAminoAcid;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.exception.CDKException;

/**
 * Class with convenience methods that provide methods to manipulate
 * AminoAcid's.
 *
 * @cdk.module  standard
 *
 * @author      Egon Willighagen
 * @cdk.created 2005-08-19
 */
public class AminoAcidManipulator {

	/**
	 * Removes the singly bonded oxygen from the acid group of the AminoAcid.
	 * 
	 * @param acid AminoAcid from which to remove the oxygen
	 * @throws CDKException when the C-terminus is not defined for the given AminoAcid 
	 */
	public static void removeAcidicOxygen(IAminoAcid acid) throws CDKException {
		if (acid.getCTerminus() == null) 
			throw new CDKException("Cannot remove oxygen: C-terminus is not defined!");
		
		java.util.List bonds = acid.getConnectedBondsList(acid.getCTerminus());
		// ok, look for the oxygen which is singly bonded
		for (int i=0; i<bonds.size(); i++) {
			IBond bond = (IBond)bonds.get(i);
			if (bond.getOrder() == CDKConstants.BONDORDER_SINGLE) {
				for (int j=0; j<bond.getAtomCount(); j++) {
					if (bond.getAtom(j).getSymbol().equals("O")) {
						// yes, we found a singly bonded oxygen!
						acid.removeAtomAndConnectedElectronContainers(bond.getAtom(j));
					}
				}
			}
		}
	}

	/**
	 * Adds the singly bonded oxygen from the acid group of the AminoAcid.
	 * 
	 * @param  acid         AminoAcid to which to add the oxygen
	 * @throws CDKException when the C-terminus is not defined for the given AminoAcid 
	 */
	public static void addAcidicOxygen(IAminoAcid acid) throws CDKException {
		if (acid.getCTerminus() == null) 
			throw new CDKException("Cannot add oxygen: C-terminus is not defined!");

		IAtom acidicOxygen = acid.getBuilder().newAtom("O");
		acid.addAtom(acidicOxygen);
		acid.addBond(
			acid.getBuilder().newBond(acid.getCTerminus(), 
			acidicOxygen,
			CDKConstants.BONDORDER_SINGLE)
		);
	}
}