/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
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.DoubleArrayResult;
import org.openscience.cdk.qsar.result.DoubleArrayResultType;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import java.util.ArrayList;
/**
* Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs;
* a description is given at: http://www.chemcomp.com/Journal_of_CCG/Features/descr.htm#KH :
* "they are intended to capture different aspects of molecular shape. Note that hydrogens are ignored.
* In the following description, n denotes the number of atoms in the hydrogen suppressed graph,
* m is the number of bonds in the hydrogen suppressed graph. Also, let p2 denote the number of paths of length 2
* and let p3 denote the number of paths of length 3".
* <p/>
* Returns three values in the order
* <ol>
* <li>Kier1 - First kappa shape index
* <li>Kier2 - Second kappa shape index
* <li>Kier3 - Third kappa (κ) shape index
* </ol>
* <p/>
* <p>This descriptor does not have any parameters.
*
* @author mfe4
* @cdk.created 2004-11-03
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:kierValues
* @cdk.keyword Kappe shape index
* @cdk.keyword descriptor
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.KappaShapeIndicesDescriptorTest")
public class KappaShapeIndicesDescriptor implements IMolecularDescriptor {
private static final String[] names = {"Kier1", "Kier2", "Kier3"};
/**
* Constructor for the KappaShapeIndicesDescriptor object
*/
public KappaShapeIndicesDescriptor() {
}
/**
* Gets the specification attribute of the
* KappaShapeIndicesDescriptor object
*
* @return The specification value
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#kierValues",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the
* KappaShapeIndicesDescriptor object
*
* @param params The new parameters value
* @throws CDKException Description of the Exception
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// no parameters for this descriptor
}
/**
* Gets the parameters attribute of the
* KappaShapeIndicesDescriptor object
*
* @return The parameters value
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// no parameters to return
return (null);
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* calculates the kier shape indices for an atom container
*
* @param container AtomContainer
* @return kier1, kier2 and kier3 are returned as arrayList of doubles
* @throws CDKException Possible Exceptions
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
IAtomContainer atomContainer;
try {
atomContainer = (IAtomContainer) container.clone();
} catch (CloneNotSupportedException e) {
DoubleArrayResult kierValues = new DoubleArrayResult(3);
kierValues.add(Double.NaN);
kierValues.add(Double.NaN);
kierValues.add(Double.NaN);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), kierValues,
getDescriptorNames());
}
atomContainer = AtomContainerManipulator.removeHydrogens(atomContainer);
//org.openscience.cdk.interfaces.IAtom[] atoms = atomContainer.getAtoms();
java.util.List firstAtomNeighboors;
java.util.List secondAtomNeighboors;
java.util.List thirdAtomNeighboors;
DoubleArrayResult kierValues = new DoubleArrayResult(3);
double bond1;
double bond2;
double bond3;
double kier1;
double kier2;
double kier3;
double atomsCount = atomContainer.getAtomCount();
ArrayList<Double> singlePaths = new ArrayList<Double>();
ArrayList<String> doublePaths = new ArrayList<String>();
ArrayList<String> triplePaths = new ArrayList<String>();
double[] sorterFirst = new double[2];
double[] sorterSecond = new double[3];
String tmpbond2;
String tmpbond3;
for (int a1 = 0; a1 < atomsCount; a1++) {
bond1 = 0;
firstAtomNeighboors = atomContainer.getConnectedAtomsList(atomContainer.getAtom(a1));
for (int a2 = 0; a2 < firstAtomNeighboors.size(); a2 ++) {
bond1 = atomContainer.getBondNumber(atomContainer.getAtom(a1), (IAtom) firstAtomNeighboors.get(a2));
if (!singlePaths.contains(new Double(bond1))) {
singlePaths.add(bond1);
java.util.Collections.sort(singlePaths);
}
secondAtomNeighboors = atomContainer.getConnectedAtomsList((IAtom) firstAtomNeighboors.get(a2));
for (int a3 = 0; a3 < secondAtomNeighboors.size(); a3 ++) {
bond2 = atomContainer.getBondNumber((IAtom) firstAtomNeighboors.get(a2), (IAtom) secondAtomNeighboors.get(a3));
if (!singlePaths.contains(new Double(bond2))) {
singlePaths.add(bond2);
}
sorterFirst[0] = bond1;
sorterFirst[1] = bond2;
java.util.Arrays.sort(sorterFirst);
tmpbond2 = sorterFirst[0] + "+" + sorterFirst[1];
if (!doublePaths.contains(tmpbond2) && (bond1 != bond2)) {
doublePaths.add(tmpbond2);
}
thirdAtomNeighboors = atomContainer.getConnectedAtomsList((IAtom) secondAtomNeighboors.get(a3));
for (int a4 = 0; a4 < thirdAtomNeighboors.size(); a4 ++) {
bond3 = atomContainer.getBondNumber((IAtom) secondAtomNeighboors.get(a3), (IAtom) thirdAtomNeighboors.get(a4));
if (!singlePaths.contains(new Double(bond3))) {
singlePaths.add(bond3);
}
sorterSecond[0] = bond1;
sorterSecond[1] = bond2;
sorterSecond[2] = bond3;
java.util.Arrays.sort(sorterSecond);
tmpbond3 = sorterSecond[0] + "+" + sorterSecond[1] + "+" + sorterSecond[2];
if (!triplePaths.contains(tmpbond3)) {
if ((bond1 != bond2) && (bond1 != bond3) && (bond2 != bond3)) {
triplePaths.add(tmpbond3);
}
}
}
}
}
}
if (atomsCount == 1) {
kier1 = 0;
kier2 = 0;
kier3 = 0;
} else {
kier1 = (((atomsCount) * ((atomsCount - 1) * (atomsCount - 1))) / (singlePaths.size() * singlePaths.size()));
if (atomsCount == 2) {
kier2 = 0;
kier3 = 0;
} else {
if (doublePaths.size() == 0) kier2 = Double.NaN;
else
kier2 = (((atomsCount - 1) * ((atomsCount - 2) * (atomsCount - 2))) / (doublePaths.size() * doublePaths.size()));
if (atomsCount == 3) {
kier3 = 0;
} else {
if (atomsCount % 2 != 0) {
if (triplePaths.size() == 0) kier3 = Double.NaN;
else
kier3 = (((atomsCount - 1) * ((atomsCount - 3) * (atomsCount - 3))) / (triplePaths.size() * triplePaths.size()));
} else {
if (triplePaths.size() == 0) kier3 = Double.NaN;
else
kier3 = (((atomsCount - 3) * ((atomsCount - 2) * (atomsCount - 2))) / (triplePaths.size() * triplePaths.size()));
}
}
}
}
kierValues.add(kier1);
kierValues.add(kier2);
kierValues.add(kier3);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), kierValues,
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 DoubleArrayResultType(3);
}
/**
* Gets the parameterNames attribute of the
* KappaShapeIndicesDescriptor object
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no param names to return
return (null);
}
/**
* Gets the parameterType attribute of the
* KappaShapeIndicesDescriptor object
*
* @param name Description of the Parameter
* @return The parameterType value
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return (null);
}
}