/* $Revision$ $Author$ $Date: 2007-01-04 18:46:10 +0100 (gio, 04 gen 2007)$
*
* Copyright (C) 2007 Federico
*
* 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.ChemObject;
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.graph.matrix.TopologicalMatrix;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This class calculates ATS autocorrelation descriptor, where the weight equal
* to the scaled atomic mass {@cdk.cite Moreau1980}.
*
* @author Federico
* @cdk.created 2007-02-08
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.AutocorrelationDescriptorMassTest")
public class AutocorrelationDescriptorMass implements IMolecularDescriptor{
private final static String[] names = {"ATSm1", "ATSm2", "ATSm3", "ATSm4", "ATSm5"};
private final static double CARBON_MASS = 12.010735896788;
private static double scaledAtomicMasses(IElement element)
throws java.io.IOException, ClassNotFoundException {
IsotopeFactory isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
double realmasses = isofac.getNaturalMass(element);
return (realmasses / CARBON_MASS);
}
private static double[] listConvertion(IAtomContainer container)
throws java.io.IOException, ClassNotFoundException{
int natom = container.getAtomCount();
double[] scalated = new double[natom];
for (int i = 0; i < natom; i++) {
scalated[i] = scaledAtomicMasses(container.getAtom(i));
}
return scalated;
}
/**
* This method calculate the ATS Autocorrelation descriptor.
*/
@TestMethod("test1")
public DescriptorValue calculate(IAtomContainer atomContainer) {
IAtomContainer container;
try {
container = (IAtomContainer) atomContainer.clone();
container = AtomContainerManipulator.removeHydrogens(container);
} catch (CloneNotSupportedException e) {
DoubleArrayResult result = new DoubleArrayResult(5);
for (int i = 0; i < 5; i++) result.add(Double.NaN);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
result, getDescriptorNames(),
new CDKException("Error during cloner: " + e.getMessage(), e));
}
try {
double[] w = listConvertion(container);
int natom = container.getAtomCount();
int[][] distancematrix = TopologicalMatrix.getMatrix(container);
double[] masSum = new double[5];
for (int k = 0; k < 5; k++) {
for (int i = 0; i < natom; i++) {
for (int j = 0; j < natom; j++) {
if (distancematrix[i][j] == k) {
masSum[k] += w[i] * w[j];
} else masSum[k] += 0.0;
}
}
if (k > 0) masSum[k] = masSum[k] / 2;
}
DoubleArrayResult result = new DoubleArrayResult(5);
for (double aMasSum : masSum) {
result.add(aMasSum);
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
result, getDescriptorNames());
} catch (Exception ex) {
DoubleArrayResult result = new DoubleArrayResult(5);
for (int i = 0; i < 5; i++) result.add(Double.NaN);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
result, getDescriptorNames(),
new CDKException("Error while calculating the ATS_mass descriptor: " + ex.getMessage(), ex));
}
}
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
return new String[0];
}
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return null;
}
@TestMethod("testGetParameters")
public Object[] getParameters() {
return null;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#autoCorrelationMass",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
@TestMethod("testGetDescriptorResultType")
public IDescriptorResult getDescriptorResultType() {
return new DoubleArrayResultType(5);
}
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
}
}