org.openscience.cdk.SingleElectron Maven / Gradle / Ivy
/* Copyright (C) 2004-2007 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.
*
* 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 java.io.Serializable;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.ISingleElectron;
/**
* A Single Electron is an orbital which is occupied by only one electron.
* A radical in CDK is represented by an AtomContainer that contains an Atom
* and a SingleElectron type ElectronContainer:
*
* AtomContainer radical = new AtomContainer();
* Atom carbon = new Atom("C");
* carbon.setImplicitHydrogens(3);
* radical.addElectronContainer(new SingleElectron(carbon));
*
*
* @cdk.module data
* @cdk.githash
*
* @cdk.keyword radical
* @cdk.keyword electron, unpaired
*/
public class SingleElectron extends ElectronContainer implements Serializable, ISingleElectron, Cloneable {
/**
* Determines if a de-serialized object is compatible with this class.
*
* This value must only be changed if and only if the new version
* of this class is incompatible with the old version. See Sun docs
* for details.
*/
private static final long serialVersionUID = 7796574734668490940L;
/** Number of electron for this class is defined as one. */
protected final int electronCount = 1;
/** The atom with which this single electron is associated. */
protected IAtom atom;
/**
* Constructs an single electron orbital on an Atom.
*
* @param atom The atom to which the single electron belongs.
*/
public SingleElectron(IAtom atom) {
this.atom = atom;
}
/**
* Constructs an single electron orbital with an associated Atom.
*/
public SingleElectron() {
this.atom = null;
}
/**
* Returns the number of electrons in this SingleElectron.
*
* @return The number of electrons in this SingleElectron.
*/
@Override
public Integer getElectronCount() {
return this.electronCount;
}
/**
* Returns the associated Atom.
*
* @return the associated Atom.
*
* @see #setAtom
*/
@Override
public IAtom getAtom() {
return this.atom;
}
/**
* Sets the associated Atom.
*
* @param atom the Atom this SingleElectron will be associated with
*
* @see #getAtom
*/
@Override
public void setAtom(IAtom atom) {
this.atom = atom;
notifyChanged();
}
/**
* Returns true if the given atom participates in this SingleElectron.
*
* @param atom The atom to be tested if it participates in this bond
* @return true if this SingleElectron is associated with the atom
*/
@Override
public boolean contains(IAtom atom) {
return this.atom.equals(atom);
}
/**
* Returns a one line string representation of this SingleElectron.
* This method is conform RFC #9.
*
* @return The string representation of this SingleElectron
*/
@Override
public String toString() {
StringBuffer stringContent = new StringBuffer();
stringContent.append("SingleElectron(");
stringContent.append(this.hashCode());
if (atom != null) {
stringContent.append(", ");
stringContent.append(atom.toString());
}
stringContent.append(')');
return stringContent.toString();
}
/**
* Clones this SingleElectron object, including a clone of the atom for which the
* SingleElectron is defined.
*
* @return The cloned object
*/
@Override
public Object clone() throws CloneNotSupportedException {
SingleElectron clone = (SingleElectron) super.clone();
// clone the Atom
if (atom != null) {
clone.atom = (IAtom) ((IAtom) atom).clone();
}
return clone;
}
}