org.openscience.cdk.FragmentAtom Maven / Gradle / Ivy

/* Copyright (C) 2006-2007  Egon Willighagen 
 *
 * Contact: [email protected]
 *
 * 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;

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

/**
 * Class to represent an IPseudoAtom which embeds an IAtomContainer. Very much
 * like the MDL Molfile Group concept.
 *
 * @cdk.module data
 * @cdk.githash
 *
 * @author egonw
 */
public class FragmentAtom extends PseudoAtom implements IFragmentAtom {

    private static final long serialVersionUID = -6144605920605752463L;

    private IAtomContainer    fragment;
    private boolean           isExpanded;

    public FragmentAtom() {
        fragment = this.getBuilder().newInstance(IAtomContainer.class);
        isExpanded = false;
    }

    @Override
    public boolean isExpanded() {
        return isExpanded;
    }

    @Override
    public void setExpanded(boolean bool) {
        this.isExpanded = bool;
    }

    @Override
    public IAtomContainer getFragment() {
        return fragment;
    }

    @Override
    public void setFragment(IAtomContainer fragment) {
        this.fragment = fragment;
    }

    @Override
    public void setExactMass(Double mass) {
        throw new IllegalAccessError("Cannot set the mass of a IFragmentAtom.");
    }

    /**
     * The exact mass of an FragmentAtom is defined as the sum of exact masses
     * of the IAtom's in the fragment.
     */
    @Override
    public Double getExactMass() {
        double totalMass = 0.0;
        for (IAtom atom : fragment.atoms()) {
            totalMass += atom.getExactMass();
        }
        return totalMass;
    }

    @Override
    public String toString() {
        StringBuffer buffer = new StringBuffer(50);
        buffer.append("FragmentAtom{").append(hashCode());
        buffer.append(", A=").append(super.toString());
        if (fragment != null) {
            buffer.append(", F=").append(fragment.toString());
        }
        buffer.append('}');
        return buffer.toString();
    }

    @Override
    public IFragmentAtom clone() throws CloneNotSupportedException {
        IFragmentAtom cpy = (IFragmentAtom) super.clone();
        cpy.setFragment(fragment.clone());
        cpy.setExpanded(isExpanded);
        return cpy;
    }
}