/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2004-2007 Rajarshi Guha <rajarshi@users.sourceforge.net>
*
* 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 java.util.ArrayList;
import javax.vecmath.Point3d;
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.geometry.GeometryTools;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
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.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* IDescriptor characterizing the mass distribution of the molecule.
* Described by Katritzky et al. {@cdk.cite KAT96}.
* For modelling purposes the value of the descriptor is calculated
* both with and without H atoms. Furthermore the square and cube roots
* of the descriptor are also generated as described by Wessel et al. {@cdk.cite WES98}.
* <p/>
* The descriptor routine generates 9 descriptors:
* <ul>
* <li>GRAV-1 - gravitational index of heavy atoms
* <li>GRAV-2 - square root of gravitational index of heavy atoms
* <li>GRAV-3 - cube root of gravitational index of heavy atoms
* <li>GRAVH-1 - gravitational index - hydrogens included
* <li>GRAVH-2 - square root of hydrogen-included gravitational index
* <li>GRAVH-3 - cube root of hydrogen-included gravitational index
* <li>GRAV-4 - grav1 for all pairs of atoms (not just bonded pairs)
* <li>GRAV-5 - grav2 for all pairs of atoms (not just bonded pairs)
* <li>GRAV-6 - grav3 for all pairs of atoms (not just bonded pairs)
* </ul>
* <p/>
* <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>
*
* @author Rajarshi Guha
* @cdk.created 2004-11-23
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:gravitationalIndex
* @cdk.keyword gravitational index
* @cdk.keyword descriptor
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.GravitationalIndexDescriptorTest")
public class GravitationalIndexDescriptor implements IMolecularDescriptor {
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(GravitationalIndexDescriptor.class);
private class pair {
int x, y;
public pair() {
x = 0;
y = 0;
}
}
private static final String[] names = {
"GRAV-1", "GRAV-2", "GRAV-3",
"GRAVH-1", "GRAVH-2", "GRAVH-3",
"GRAV-4", "GRAV-5", "GRAV-6"
};
public GravitationalIndexDescriptor() {
}
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#gravitationalIndex",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the GravitationalIndexDescriptor object.
*
* @param params The new parameters value
* @throws CDKException Description of the Exception
* @see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
// no parameters for this descriptor
}
/**
* Gets the parameters attribute of the GravitationalIndexDescriptor object.
*
* @return The parameters value
* @see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// no parameters to return
return (null);
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* Gets the parameterNames attribute of the GravitationalIndexDescriptor object.
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no param names to return
return (null);
}
/**
* Gets the parameterType attribute of the GravitationalIndexDescriptor object.
*
* @param name Description of the Parameter
* @return The parameterType value
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return (null);
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
int ndesc = getDescriptorNames().length;
DoubleArrayResult results = new DoubleArrayResult(ndesc);
for (int i = 0; i < ndesc; i++) results.add(Double.NaN);
return new DescriptorValue(getSpecification(), getParameterNames(),
getParameters(), results, getDescriptorNames(), e);
}
/**
* Calculates the 9 gravitational indices.
*
* @param container Parameter is the atom container.
* @return An ArrayList containing 9 elements in the order described above
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer container) {
if (!GeometryTools.has3DCoordinates(container))
return getDummyDescriptorValue(new CDKException("Molecule must have 3D coordinates"));
IsotopeFactory factory = null;
double mass1;
double mass2;
try {
factory = IsotopeFactory.getInstance(container.getBuilder());
} catch (Exception e) {
logger.debug(e);
}
double sum = 0;
for (int i = 0; i < container.getBondCount(); i++) {
IBond bond = container.getBond(i);
if (bond.getAtomCount() != 2) {
return getDummyDescriptorValue(new CDKException("GravitationalIndex: Only handles 2 center bonds"));
}
mass1 = factory.getMajorIsotope(bond.getAtom(0).getSymbol()).getMassNumber();
mass2 = factory.getMajorIsotope(bond.getAtom(1).getSymbol()).getMassNumber();
Point3d p1 = bond.getAtom(0).getPoint3d();
Point3d p2 = bond.getAtom(1).getPoint3d();
double x1 = p1.x;
double y1 = p1.y;
double z1 = p1.z;
double x2 = p2.x;
double y2 = p2.y;
double z2 = p2.z;
double dist = (x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2);
sum += (mass1 * mass2) / dist;
}
// heavy atoms only
double heavysum = 0;
for (int i = 0; i < container.getBondCount(); i++) {
IBond b = container.getBond(i);
if (b.getAtomCount() != 2) {
return getDummyDescriptorValue(new CDKException("GravitationalIndex: Only handles 2 center bonds"));
}
if (b.getAtom(0).getSymbol().equals("H") ||
b.getAtom(1).getSymbol().equals("H")) continue;
mass1 = factory.getMajorIsotope(b.getAtom(0).getSymbol()).getMassNumber();
mass2 = factory.getMajorIsotope(b.getAtom(1).getSymbol()).getMassNumber();
Point3d point0 = b.getAtom(0).getPoint3d();
Point3d point1 = b.getAtom(1).getPoint3d();
double x1 = point0.x;
double y1 = point0.y;
double z1 = point0.z;
double x2 = point1.x;
double y2 = point1.y;
double z2 = point1.z;
double dist = (x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2);
heavysum += (mass1 * mass2) / dist;
}
// all pairs
ArrayList<Integer> x = new ArrayList<Integer>();
for (int i = 0; i < container.getAtomCount(); i++) {
if (!container.getAtom(i).getSymbol().equals("H")) x.add(i);
}
int npair = x.size() * (x.size() - 1) / 2;
pair[] p = new pair[npair];
for (int i = 0; i < npair; i++) p[i] = new pair();
int pcount = 0;
for (int i = 0; i < x.size() - 1; i++) {
for (int j = i + 1; j < x.size(); j++) {
int present = 0;
int a = x.get(i);
int b = x.get(j);
for (int k = 0; k < pcount; k++) {
if ((p[k].x == a && p[k].y == b) ||
(p[k].y == a && p[k].x == b)) present = 1;
}
if (present == 1) continue;
p[pcount].x = a;
p[pcount].y = b;
pcount += 1;
}
}
double allheavysum = 0;
for (pair aP : p) {
int atomNumber1 = aP.x;
int atomNumber2 = aP.y;
mass1 = factory.getMajorIsotope(container.getAtom(atomNumber1).getSymbol()).getMassNumber();
mass2 = factory.getMajorIsotope(container.getAtom(atomNumber2).getSymbol()).getMassNumber();
double x1 = container.getAtom(atomNumber1).getPoint3d().x;
double y1 = container.getAtom(atomNumber1).getPoint3d().y;
double z1 = container.getAtom(atomNumber1).getPoint3d().z;
double x2 = container.getAtom(atomNumber2).getPoint3d().x;
double y2 = container.getAtom(atomNumber2).getPoint3d().y;
double z2 = container.getAtom(atomNumber2).getPoint3d().z;
double dist = (x1 - x2) * (x1 - x2) + (y1 - y2) * (y1 - y2) + (z1 - z2) * (z1 - z2);
allheavysum += (mass1 * mass2) / dist;
}
DoubleArrayResult retval = new DoubleArrayResult(9);
retval.add(heavysum);
retval.add(Math.sqrt(heavysum));
retval.add(Math.pow(heavysum, 1.0 / 3.0));
retval.add(sum);
retval.add(Math.sqrt(sum));
retval.add(Math.pow(sum, 1.0 / 3.0));
retval.add(allheavysum);
retval.add(Math.sqrt(allheavysum));
retval.add(Math.pow(allheavysum, 1.0 / 3.0));
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
retval, 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(9);
}
}