RGroup.java

/*
 * Copyright (C) 2010  Mark Rijnbeek <mark_rynbeek@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.isomorphism.matchers;

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

/**
 * Represents a single substitute structure in an {@link RGroupList}. <P>
 * The order of attachment points is provided (first and second only, conform
 * RGFile spec). This order is relevant when the structure connects to the root
 * with more than one bond.
 * <P>
 * See also {@link RGroupList} and {@link RGroupQuery}.
 *
 * @cdk.module  isomorphism
 * @cdk.githash
 * @cdk.keyword Rgroup
 * @cdk.keyword R group
 * @cdk.keyword R-group
 * @author Mark Rijnbeek
 */
public class RGroup {

	/**
	 * Standard label/title to be used for the root atom container.  
	 */
	public final static String ROOT_LABEL="Root structure";

	/**
	 * Makes a label/title to be used for a substituent.
	 * @param rgroupNum R-Group number (1..32)
	 * @return label for substituent, like "R3"
	 */
	public static String makeLabel(int rgroupNum ) {
		return "(R"+rgroupNum+")";
	}
	
    IAtom firstAttachmentPoint;
    IAtom secondAttachmentPoint;
    IAtomContainer group;

    public void setFirstAttachmentPoint(IAtom firstAttachmentPoint) {
        this.firstAttachmentPoint = firstAttachmentPoint;
    }

    public IAtom getFirstAttachmentPoint() {
        return firstAttachmentPoint;
    }

    public void setSecondAttachmentPoint(IAtom secondAttachmentPoint) {
        this.secondAttachmentPoint = secondAttachmentPoint;
    }

    public IAtom getSecondAttachmentPoint() {
        return secondAttachmentPoint;
    }

    public void setGroup(IAtomContainer group) {
        this.group = group;
    }

    public IAtomContainer getGroup() {
        return group;
    }
}