/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
/**
* IDescriptor based on the number of atoms of a certain element type.
*
* It is
* possible to use the wild card symbol '*' as element type to get the count of
* all atoms.
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>elementName</td>
* <td>*</td>
* <td>Symbol of the element we want to count</td>
* </tr>
* </table>
*
* Returns a single value with name <i>nX</i> where <i>X</i> is the atomic symbol. If *
* is specified then the name is <i>nAtom</i>
*
* @author mfe4
* @cdk.created 2004-11-13
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:atomCount
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.AtomCountDescriptorTest")
public class AtomCountDescriptor implements IMolecularDescriptor {
private String elementName = "*";
/**
* Constructor for the AtomCountDescriptor object.
*/
public AtomCountDescriptor() {
elementName = "*";
}
/**
* 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/#atomCount",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the AtomCountDescriptor object.
*
*@param params The new parameters value
*@throws CDKException if the number of parameters is greater than 1
*or else 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("AtomCount only expects one parameter");
}
if (!(params[0] instanceof String)) {
throw new CDKException("The parameter must be of type String");
}
elementName = (String) params[0];
}
/**
* Gets the parameters attribute of the AtomCountDescriptor 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 = "n";
if (elementName.equals("*")) name = "nAtom";
else name += elementName;
return new String[]{name};
}
/**
* This method calculate the number of atoms of a given type in an {@link IAtomContainer}.
*
*@param container The atom container for which this descriptor is to be calculated
*@return Number of atoms of a certain type is returned.
*/
// it could be interesting to accept as elementName a SMARTS atom, to get the frequency of this atom
// this could be useful for other descriptors like polar surface area...
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
int atomCount = 0;
if (container == null) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN), getDescriptorNames(),
new CDKException("The supplied AtomContainer was NULL"));
}
if (container.getAtomCount() == 0) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN), getDescriptorNames(),
new CDKException("The supplied AtomContainer did not have any atoms"));
}
if (elementName.equals("*")) {
for (int i = 0; i < container.getAtomCount(); i++) {
// we assume that UNSET is equivalent to 0 implicit H's
Integer hcount = container.getAtom(i).getHydrogenCount();
if (hcount != CDKConstants.UNSET) atomCount += hcount;
}
atomCount += container.getAtomCount();
} else if (elementName.equals("H")) {
for (int i = 0; i < container.getAtomCount(); i++) {
if (container.getAtom(i).getSymbol().equals(elementName)) {
atomCount += 1;
} else {
// we assume that UNSET is equivalent to 0 implicit H's
Integer hcount = container.getAtom(i).getHydrogenCount();
if (hcount != CDKConstants.UNSET) atomCount += hcount;
}
}
}
else {
for (int i = 0; i < container.getAtomCount(); i++) {
if (container.getAtom(i).getSymbol().equals(elementName)) {
atomCount += 1;
}
}
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult(atomCount), 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 IntegerResult(1);
}
/**
* Gets the parameterNames attribute of the AtomCountDescriptor object.
*
*@return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "elementName";
return params;
}
/**
* Gets the parameterType attribute of the AtomCountDescriptor 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 "";
}
}