/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2001-2007 Christoph Steinbeck <steinbeck@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.
*
* 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.config;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.isotopes.IsotopeReader;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Used to store and return data of a particular isotope. As this class is a
* singleton class, one gets an instance with:
* <pre>
* IsotopeFactory ifac = IsotopFactory.getInstance(new IChemObject().getBuilder());
* </pre>
*
* <p>Data about the isotopes are read from the file
* org.openscience.cdk.config.isotopes.xml in the cdk-standard
* module. Part of the data in this file was collected from
* the website <a href="http://www.webelements.org">webelements.org</a>.
*
* <p>The use of this class is exemplified as follows. To get information
* about the major isotope of hydrogen, one can use this code:
* <pre>
* IsotopeFactory factory = IsotopeFactory.getInstance(DefaultChemObjectBuilder.getInstance());
* Isotope major = factory.getMajorIsotope("H");
* </pre>
*
* @cdk.module core
* @cdk.githash
*
* @author steinbeck
* @cdk.created 2001-08-29
* @cdk.keyword isotope
* @cdk.keyword element
*/
@TestClass("org.openscience.cdk.config.IsotopeFactoryTest")
public class IsotopeFactory
{
private static IsotopeFactory ifac = null;
private List<IIsotope> isotopes = null;
private HashMap<String, IIsotope> majorIsotopes = null;
private boolean debug = false;
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(IsotopeFactory.class);
/**
* Private constructor for the IsotopeFactory object.
*
*@exception IOException A problem with reading the isotopes.xml
* file
* @param builder The builder from which we the factory will be generated
*/
private IsotopeFactory(IChemObjectBuilder builder) throws IOException {
logger.info("Creating new IsotopeFactory");
InputStream ins;
// ObjIn in = null;
String errorMessage = "There was a problem getting org.openscience.cdk." +
"config.isotopes.xml as a stream";
try {
String configFile = "org/openscience/cdk/config/data/isotopes.xml";
if (debug) logger.debug("Getting stream for ", configFile);
ins = this.getClass().getClassLoader().getResourceAsStream(configFile);
} catch (Exception exception) {
logger.error(errorMessage);
logger.debug(exception);
throw new IOException(errorMessage);
}
if (ins == null) {
logger.error(errorMessage);
throw new IOException(errorMessage);
}
IsotopeReader reader = new IsotopeReader(ins, builder);
//in = new ObjIn(ins, new Config().aliasID(false));
isotopes = reader.readIsotopes();
if (debug) logger.debug("Found #isotopes in file: ", isotopes.size());
/* for (int f = 0; f < isotopes.size(); f++) {
Isotope isotope = (Isotope)isotopes.elementAt(f);
} What's this loop for?? */
majorIsotopes = new HashMap<String, IIsotope>();
}
/**
* Returns an IsotopeFactory instance.
*
* @param builder ChemObjectBuilder used to construct the Isotope's
* @return The instance value
* @exception IOException Description of the Exception
*/
@TestMethod("testGetInstance_IChemObjectBuilder")
public static IsotopeFactory getInstance(IChemObjectBuilder builder)
throws IOException {
if (ifac == null) {
ifac = new IsotopeFactory(builder);
}
return ifac;
}
/**
* Returns the number of isotopes defined by this class.
*
*@return The size value
*/
@TestMethod("testGetSize")
public int getSize()
{
return isotopes.size();
}
/**
* Gets an array of all isotopes known to the IsotopeFactory for the given
* element symbol.
*
*@param symbol An element symbol to search for
*@return An array of isotopes that matches the given element symbol
*/
@TestMethod("testGetIsotopes_String")
public IIsotope[] getIsotopes(String symbol) {
ArrayList<IIsotope> list = new ArrayList<IIsotope>();
for (IIsotope isotope : isotopes) {
if (isotope.getSymbol().equals(symbol)) {
try {
IIsotope clone = (IIsotope) isotope.clone();
list.add(clone);
} catch (CloneNotSupportedException e) {
logger.error("Could not clone IIsotope: ", e.getMessage());
logger.debug(e);
}
}
}
return list.toArray(new IIsotope[list.size()]);
}
/**
* Returns the most abundant (major) isotope with a given atomic number.
*
* <p>The isotope's abundancy is for atoms with atomic number 60 and smaller
* defined as a number that is proportional to the 100 of the most abundant
* isotope. For atoms with higher atomic numbers, the abundancy is defined
* as a percentage.
*
* @param atomicNumber The atomicNumber for which an isotope is to be returned
* @return The isotope corresponding to the given atomic number
*
* @see #getMajorIsotope(String symbol)
*/
@TestMethod("testGetMajorIsotope_int")
public IIsotope getMajorIsotope(int atomicNumber) {
IIsotope major = null;
for (IIsotope isotope : isotopes) {
if (isotope.getAtomicNumber() == atomicNumber) {
try {
if (major == null) {
major = (IIsotope) isotope.clone();
} else {
if (isotope.getNaturalAbundance() > major.getNaturalAbundance()) {
major = (IIsotope) isotope.clone();
}
}
} catch (CloneNotSupportedException e) {
logger.error("Could not clone IIsotope: ", e.getMessage());
logger.debug(e);
}
}
}
if (major == null) logger.error("Could not find major isotope for: ", atomicNumber);
return major;
}
/**
* Checks whether the given element exists.
*
* @param elementName The element name to test
* @return True is the element exists, false otherwise
*/
@TestMethod("testIsElement_String")
public boolean isElement(String elementName) {
return (getElement(elementName) != null);
}
/**
* Returns the most abundant (major) isotope whose symbol equals element.
*
*@param symbol Description of the Parameter
*@return The Major Isotope value
*/
@TestMethod("testGetMajorIsotope_String")
public IIsotope getMajorIsotope(String symbol) {
IIsotope major = null;
if (majorIsotopes.containsKey(symbol)) {
major = majorIsotopes.get(symbol);
} else {
for (IIsotope isotope : isotopes) {
if (isotope.getSymbol().equals(symbol)) {
try {
if (major == null) {
major = (IIsotope) isotope.clone();
} else {
if (isotope.getNaturalAbundance() > major.getNaturalAbundance()) {
major = (IIsotope) isotope.clone();
}
}
} catch (CloneNotSupportedException e) {
logger.error("Could not clone IIsotope: ", e.getMessage());
logger.debug(e);
}
}
}
if (major == null) {
logger.error("Could not find major isotope for: ", symbol);
} else {
majorIsotopes.put(symbol, major);
}
}
return major;
}
/**
* Returns an Element with a given element symbol.
*
*@param symbol The element symbol for the requested element
*@return The configured element
*/
@TestMethod("testGetElement_String")
public IElement getElement(String symbol)
{
return getMajorIsotope(symbol);
}
/**
* Returns an element according to a given atomic number.
*
*@param atomicNumber The elements atomic number
*@return The Element
*/
@TestMethod("testGetElement_int")
public IElement getElement(int atomicNumber)
{
return getMajorIsotope(atomicNumber);
}
/**
* Returns the symbol matching the element with the given atomic number.
*
* @param atomicNumber The elements atomic number
* @return The symbol of the Element
*/
@TestMethod("testGetElementSymbol_int")
public String getElementSymbol(int atomicNumber) {
IIsotope isotope = getMajorIsotope(atomicNumber);
return isotope.getSymbol();
}
/**
* Configures an atom. Finds the correct element type
* by looking at the atoms element symbol.
*
*@param atom The atom to be configured
*@return The configured atom
*/
@TestMethod("testConfigure_IAtom")
public IAtom configure(IAtom atom)
{
IIsotope isotope = getMajorIsotope(atom.getSymbol());
return configure(atom, isotope);
}
/**
* Configures an atom to have all the data of the
* given isotope.
*
*@param atom The atom to be configure
*@param isotope The isotope to read the data from
*@return The configured atom
*/
@TestMethod("testConfigure_IAtom_IIsotope")
public IAtom configure(IAtom atom, IIsotope isotope)
{
atom.setMassNumber(isotope.getMassNumber());
atom.setSymbol(isotope.getSymbol());
atom.setExactMass(isotope.getExactMass());
atom.setAtomicNumber(isotope.getAtomicNumber());
atom.setNaturalAbundance(isotope.getNaturalAbundance());
return atom;
}
/**
* Configures atoms in an AtomContainer to
* carry all the correct data according to their element type.
*
*@param container The AtomContainer to be configured
*/
@TestMethod("testConfigureAtoms_IAtomContainer")
public void configureAtoms(IAtomContainer container)
{
for (int f = 0; f < container.getAtomCount(); f++)
{
configure(container.getAtom(f));
}
}
/**
* Gets the natural mass of this element, defined as average of masses of isotopes,
* weighted by abundance.
*
* @param element Description of the Parameter
* @return The natural mass value
*/
@TestMethod("testGetNaturalMass_IElement")
public double getNaturalMass(IElement element){
IIsotope[] isotopes = getIsotopes(element.getSymbol());
double summedAbundances = 0;
double summedWeightedAbundances = 0;
double getNaturalMass = 0;
for (int i = 0; i < isotopes.length; i++) {
summedAbundances += isotopes[i].getNaturalAbundance();
summedWeightedAbundances += isotopes[i].getNaturalAbundance() * isotopes[i].getExactMass();
getNaturalMass = summedWeightedAbundances / summedAbundances;
}
return getNaturalMass;
}
}