org.openscience.cdk.Element Maven / Gradle / Ivy
/*
* Copyright (C) 1997-2013 Christoph Steinbeck
* Egon Willighagen
* John May
* Rajarshi Guha
* miguelrojasch
*
* 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 com.google.common.base.Objects;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.tools.periodictable.PeriodicTable;
import java.io.Serializable;
/**
* Implements the idea of an element in the periodic table.
*
* Use the IsotopeFactory to get a ready-to-use elements
* by symbol or atomic number:
*
* IsotopeFactory if = IsotopeFactory.getInstance(new Element().getNewBuilder());
* Element e1 = if.getElement("C");
* Element e2 = if.getElement(12);
*
*
* @cdk.module data
* @cdk.githash
*
* @cdk.keyword element
*
* @see org.openscience.cdk.config.XMLIsotopeFactory
*/
public class Element extends ChemObject implements Serializable, IElement, 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 = 3062529834691231436L;
/** The element symbol for this element as listed in the periodic table. */
protected String symbol;
/** The atomic number for this element giving their position in the periodic table. */
protected Integer atomicNumber = (Integer) CDKConstants.UNSET;
/**
* Constructs an empty Element.
*/
public Element() {
super();
this.symbol = null;
}
/**
* Constructs an empty by copying the symbol, atomic number,
* flags, and identifier from the given IElement. It does
* not copy the listeners and properties.
*
* @param element IElement to copy information from
*/
public Element(IElement element) {
super(element);
this.symbol = element.getSymbol();
this.atomicNumber = element.getAtomicNumber();
}
/**
* Constructs an Element with a given
* element symbol.
*
* @param symbol The element symbol that this element should have.
*/
public Element(String symbol) {
this(symbol, PeriodicTable.getAtomicNumber(symbol));
}
/**
* Constructs an Element with a given element symbol,
* atomic number and atomic mass.
*
* @param symbol The element symbol of this element.
* @param atomicNumber The atomicNumber of this element.
*/
public Element(String symbol, Integer atomicNumber) {
this.symbol = symbol;
this.atomicNumber = atomicNumber;
}
/**
* Returns the atomic number of this element.
*
* Once instantiated all field not filled by passing parameters
* to the constructor are null. Elements can be configured by using
* the IsotopeFactory.configure() method:
*
*
* Element element = new Element("C");
* IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
* if.configure(element);
*
*
* @return The atomic number of this element
*
* @see #setAtomicNumber
*/
@Override
public Integer getAtomicNumber() {
return this.atomicNumber;
}
/**
* Sets the atomic number of this element.
*
* @param atomicNumber The atomic mass to be assigned to this element
*
* @see #getAtomicNumber
*/
@Override
public void setAtomicNumber(Integer atomicNumber) {
this.atomicNumber = atomicNumber;
notifyChanged();
}
/**
* Returns the element symbol of this element.
*
* @return The element symbol of this element. Null if unset.
*
* @see #setSymbol
*/
@Override
public String getSymbol() {
return this.symbol;
}
/**
* Sets the element symbol of this element.
*
* @param symbol The element symbol to be assigned to this atom
*
* @see #getSymbol
*/
@Override
public void setSymbol(String symbol) {
this.symbol = symbol;
notifyChanged();
}
@Override
public String toString() {
StringBuffer resultString = new StringBuffer(32);
resultString.append("Element(").append(hashCode());
if (getSymbol() != null) {
resultString.append(", S:").append(getSymbol());
}
if (getID() != null) {
resultString.append(", ID:").append(getID());
}
if (getAtomicNumber() != null) {
resultString.append(", AN:").append(getAtomicNumber());
}
resultString.append(')');
return resultString.toString();
}
@Override
public Object clone() throws CloneNotSupportedException {
return super.clone();
}
/**
* Compares an Element with this Element.
*
* @param object Object of type AtomType
* @return true if the atom types are equal
*/
@Override
public boolean compare(Object object) {
if (!(object instanceof Element)) {
return false;
}
if (!super.compare(object)) {
return false;
}
Element elem = (Element) object;
return Objects.equal(atomicNumber, elem.atomicNumber) && Objects.equal(symbol, elem.symbol);
}
}