/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2006-2007 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.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAminoAcid;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
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.IntegerArrayResult;
import org.openscience.cdk.templates.AminoAcids;
import java.util.List;
/**
* Class that returns the number of each amino acid in an atom container.
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td></td>
* <td></td>
* <td>no parameters</td>
* </tr>
* </table>
*
* Returns 20 values with names of the form <i>nX</i>, where <i>X</i> is the short versio
* of the amino acid name
*
* @author egonw
* @cdk.created 2006-01-15
* @cdk.module qsarprotein
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:aminoAcidsCount
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.AminoAcidCountDescriptorTest")
public class AminoAcidCountDescriptor implements IMolecularDescriptor {
private IAtomContainerSet substructureSet;
private static String[] names;
/**
* Constructor for the AromaticAtomsCountDescriptor object.
*/
public AminoAcidCountDescriptor() {
IAminoAcid[] aas = AminoAcids.createAAs();
substructureSet = aas[0].getBuilder().newAtomContainerSet();
for (IAminoAcid aa : aas) {
substructureSet.addAtomContainer(aa);
}
names = new String[substructureSet.getAtomContainerCount()];
for (int i = 0; i < aas.length; i++) names[i] = "n"+aas[i].getProperty(AminoAcids.RESIDUE_NAME_SHORT);
}
/**
* 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/#aminoAcidsCount",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the AminoAcidsCountDescriptor object.
*
* @param params The new parameters value
* @exception CDKException if more than one parameter or a non-Boolean parameter is specified
* @see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// no parameters exist
}
/**
* Gets the parameters attribute of the AminoAcidsCountDescriptor object.
*
* @return The parameters value
* @see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
return null;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* Determine the number of amino acids groups the supplied {@link IAtomContainer}.
*
* @param ac The {@link IAtomContainer} for which this descriptor is to be calculated
* @return the number of aromatic atoms of this AtomContainer
*
* @see #setParameters
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer ac) {
int resultLength = substructureSet.getAtomContainerCount();
IntegerArrayResult results = new IntegerArrayResult(resultLength);
IAtomContainer substructure;
for (int i=0; i<resultLength; i++) {
substructure = substructureSet.getAtomContainer(i);
List maps;
try {
maps = UniversalIsomorphismTester.getSubgraphMaps(ac, substructure);
} catch (CDKException e) {
// TODO is it OK to cast Double.NaN to int?
for (int j = 0; j < resultLength; j++) results.add((int) Double.NaN);
return new DescriptorValue(getSpecification(), getParameterNames(),
getParameters(), results, getDescriptorNames(),
new CDKException("Error in substructure search: "+e.getMessage()));
}
if (maps != null) {
results.add(maps.size());
}
}
return new DescriptorValue(getSpecification(), getParameterNames(),
getParameters(), results, 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 IntegerArrayResult(20);
}
/**
* Gets the parameterNames attribute of the AromaticAtomsCountDescriptor object.
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
return new String[0];
}
/**
* Gets the parameterType attribute of the AromaticAtomsCountDescriptor object.
*
* @param name Description of the Parameter
* @return An Object of class equal to that of the parameter being requested
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return null;
}
}