/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project
*
* 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.qsar.descriptors.molecular;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IIsotope;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
/**
* IDescriptor based on the weight of atoms of a certain element type.
*
* If the wild-card symbol *
* is specified, the returned value is the molecular weight.
* If an invalid element symbol is specified, the return value is
* 0 and no exception is thrown
* <p>
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>elementSymbol</td>
* <td>*</td>
* <td>If *, returns the molecular weight, otherwise the weight for the given element</td>
* </tr>
* </table>
*
* Returns a single value named <i>wX</i> where <i>X</i> is the chemical symbol
* or <i>MW</i> if * is specified as a parameter.
*
* @author mfe4
* @cdk.created 2004-11-13
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:weight
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.WeightDescriptorTest")
public class WeightDescriptor implements IMolecularDescriptor {
private String elementName = "*";
/**
* Constructor for the WeightDescriptor object.
*/
public WeightDescriptor() { }
/**
* Returns a <code>Map</code> which specifies which descriptor is implemented by this class.
*
* These fields are used in the map:
* <ul>
* <li>Specification-Reference: refers to an entry in a unique dictionary
* <li>Implementation-Title: anything
* <li>Implementation-Identifier: a unique identifier for this version of
* this class
* <li>Implementation-Vendor: CDK, JOELib, or anything else
* </ul>
*
* @return An object containing the descriptor specification
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#weight",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the WeightDescriptor object.
*
*@param params The new parameters value
*@throws CDKException if more than 1 parameter is specified or if the parameter
*is not of type String
*@see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length > 1) {
throw new CDKException("weight only expects one parameter");
}
if (!(params[0] instanceof String)) {
throw new CDKException("The parameter must be of type String");
}
// ok, all should be fine
elementName = (String) params[0];
}
/**
* Gets the parameters attribute of the WeightDescriptor object.
*
* @return The parameters value
* @see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[1];
params[0] = elementName;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
String name = "w";
if (elementName.equals("*")) name = "MW";
else name += elementName;
return new String[]{name};
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
return new DescriptorValue(getSpecification(), getParameterNames(),
getParameters(), new DoubleResult(Double.NaN), getDescriptorNames(), e);
}
/**
* Calculate the weight of specified element type in the supplied {@link IAtomContainer}.
*
* @param container The AtomContainer for which this descriptor is to be calculated. If 'H'
* is specified as the element symbol make sure that the AtomContainer has hydrogens.
*@return The total weight of atoms of the specified element type
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
double weight = 0;
if (elementName.equals("*")) {
try {
for (int i = 0; i < container.getAtomCount(); i++) {
//logger.debug("WEIGHT: "+container.getAtomAt(i).getSymbol() +" " +IsotopeFactory.getInstance().getMajorIsotope( container.getAtomAt(i).getSymbol() ).getExactMass());
weight += IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass();
Integer hcount = container.getAtom(i).getHydrogenCount();
if (hcount == CDKConstants.UNSET) hcount = 0;
weight += (hcount * 1.00782504);
}
} catch (Exception e) {
return getDummyDescriptorValue(e);
}
}
else if (elementName.equals("H")) {
try {
IIsotope h=IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope("H");
for (int i = 0; i < container.getAtomCount(); i++) {
if (container.getAtom(i).getSymbol().equals(elementName)) {
weight += IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass();
}
else {
weight += (container.getAtom(i).getHydrogenCount() * h.getExactMass());
}
}
} catch (Exception e) {
return getDummyDescriptorValue(e);
}
}
else {
try {
for (int i = 0; i < container.getAtomCount(); i++) {
if (container.getAtom(i).getSymbol().equals(elementName)) {
weight += IsotopeFactory.getInstance(container.getBuilder()).getMajorIsotope( container.getAtom(i).getSymbol() ).getExactMass();
}
}
} catch (Exception e) {
return getDummyDescriptorValue(e);
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(weight), getDescriptorNames());
}
/**
* Returns the specific type of the DescriptorResult object.
* <p/>
* The return value from this method really indicates what type of result will
* be obtained from the {@link org.openscience.cdk.qsar.DescriptorValue} object. Note that the same result
* can be achieved by interrogating the {@link org.openscience.cdk.qsar.DescriptorValue} object; this method
* allows you to do the same thing, without actually calculating the descriptor.
*
* @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating
* the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object
*/
@TestMethod("testGetDescriptorResultType")
public IDescriptorResult getDescriptorResultType() {
return new DoubleResult(0.0);
}
/**
* Gets the parameterNames attribute of the WeightDescriptor object.
*
*@return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "elementSymbol";
return params;
}
/**
* Gets the parameterType attribute of the WeightDescriptor object.
*
*@param name Description of the Parameter
*@return An Object whose class is that of the parameter requested
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return "";
}
}