/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2007 Rajarshi Guha <rajarshi@users.sf.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.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* 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 Jama.Matrix;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.geometry.GeometryTools;
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.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import javax.vecmath.Point3d;
/**
* Evaluates length over breadth descriptors.
* <p/>
* The current implementation reproduces the results obtained from the LOVERB descriptor
* routine in ADAPT. As a result ti does not perform any orientation and only considers the
* X & Y extents for a series of rotations about the Z axis (in 10 degree increments).
* <p/>
* The class gives two descriptors
* <ul>
* <li>LOBMAX - The maximum L/B ratio
* <li>LOBMIN - The L/B ratio for the rotation that results in the minimum area
* (defined by the product of the X & Y extents for that orientation)
* </ul>
* <B>Note:</B> The descriptor assumes that the atoms have been configured.
*
* @author Rajarshi Guha
* @cdk.created 2006-09-26
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:lengthOverBreadth
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.LengthOverBreadthDescriptorTest")
public class LengthOverBreadthDescriptor implements IMolecularDescriptor {
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(LengthOverBreadthDescriptor.class);
private static final String[] names = {"LOBMAX", "LOBMIN"};
/**
* Constructor for the LengthOverBreadthDescriptor object.
*/
public LengthOverBreadthDescriptor() {
}
/**
* Gets the specification attribute of the PetitjeanNumberDescriptor object
*
* @return The specification value
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#lengthOverBreadth",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the PetitjeanNumberDescriptor object
*
* @param params The new parameters value
* @throws org.openscience.cdk.exception.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 PetitjeanNumberDescriptor object
*
* @return The parameters value
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
return (null);
// no parameters to return
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
DoubleArrayResult result = new DoubleArrayResult(2);
result.add(Double.NaN);
result.add(Double.NaN);
return new DescriptorValue(getSpecification(), getParameterNames(),
getParameters(), result, getDescriptorNames(), e);
}
/**
* Evaluate the descriptor for the molecule.
*
* @param atomContainer AtomContainer
* @return A {@link org.openscience.cdk.qsar.result.DoubleArrayResult} containing LOBMAX and LOBMIN in that
* order
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer atomContainer) {
if (!GeometryTools.has3DCoordinates(atomContainer))
return getDummyDescriptorValue(new CDKException("Molecule must have 3D coordinates"));
double angle = 10.0;
double maxLOB = 0;
double minArea = 1e6;
double mmLOB = 0;
double lob, bol, area;
double[] xyzRanges;
double[][] coords = new double[atomContainer.getAtomCount()][3];
for (int i = 0; i < atomContainer.getAtomCount(); i++) {
coords[i][0] = atomContainer.getAtom(i).getPoint3d().x;
coords[i][1] = atomContainer.getAtom(i).getPoint3d().y;
coords[i][2] = atomContainer.getAtom(i).getPoint3d().z;
}
// get the com
Point3d com = GeometryTools.get3DCentreOfMass(atomContainer);
if (com == null) return getDummyDescriptorValue(new CDKException("Error in center of mass calculation"));
// translate everything to COM
for (int i = 0; i < coords.length; i++) {
coords[i][0] -= com.x;
coords[i][1] -= com.y;
coords[i][2] -= com.z;
}
int nangle = (int) (90 / angle);
for (int i = 0; i < nangle; i++) {
rotateZ(coords, Math.PI / 180.0 * angle);
try {
xyzRanges = extents(atomContainer, coords, true);
} catch (CDKException e) {
return getDummyDescriptorValue(e);
}
lob = xyzRanges[0] / xyzRanges[1];
bol = 1.0 / lob;
if (lob < bol) {
double tmp = lob;
lob = bol;
bol = tmp;
}
area = xyzRanges[0] * xyzRanges[1];
if (lob > maxLOB) maxLOB = lob;
if (area < minArea) {
minArea = area;
mmLOB = lob;
}
}
DoubleArrayResult result = new DoubleArrayResult(2);
result.add(maxLOB);
result.add(mmLOB);
return new DescriptorValue(getSpecification(),
getParameterNames(), getParameters(),
result, 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(2);
}
private void rotateZ(double[][] coords, double theta) {
int natom = coords.length;
Matrix rZ = new Matrix(4, 4);
rZ.set(0, 0, Math.cos(theta));
rZ.set(0, 1, Math.sin(theta));
rZ.set(1, 0, -1 * Math.sin(theta));
rZ.set(1, 1, Math.cos(theta));
rZ.set(2, 2, 1);
rZ.set(3, 3, 1);
Matrix newCoord = new Matrix(4, natom);
for (int i = 0; i < 3; i++) {
for (int j = 0; j < natom; j++) {
newCoord.set(i, j, coords[j][i]);
newCoord.set(3, j, 1.0);
}
}
newCoord = rZ.times(newCoord);
newCoord = newCoord.transpose();
for (int i = 0; i < natom; i++) {
for (int j = 0; j < 3; j++)
coords[i][j] = newCoord.get(i, j);
}
}
private double[] extents(IAtomContainer atomContainer, double[][] coords, boolean withRadii) throws CDKException {
double xmax = -1e30;
double ymax = -1e30;
double zmax = -1e30;
double xmin = 1e30;
double ymin = 1e30;
double zmin = 1e30;
int natom = atomContainer.getAtomCount();
for (int i = 0; i < natom; i++) {
double[] coord = new double[coords[0].length];
System.arraycopy(coords[i], 0, coord, 0, coords[0].length);
if (withRadii) {
IAtom atom = atomContainer.getAtom(i);
double radius = org.openscience.cdk.tools.periodictable.PeriodicTable.getCovalentRadius(atom.getSymbol());
xmax = Math.max(xmax, coord[0] + radius);
ymax = Math.max(ymax, coord[1] + radius);
zmax = Math.max(zmax, coord[2] + radius);
xmin = Math.min(xmin, coord[0] - radius);
ymin = Math.min(ymin, coord[1] - radius);
zmin = Math.min(zmin, coord[2] - radius);
} else {
xmax = Math.max(xmax, coord[0]);
ymax = Math.max(ymax, coord[1]);
zmax = Math.max(zmax, coord[2]);
xmin = Math.min(xmin, coord[0]);
ymin = Math.min(ymin, coord[1]);
zmin = Math.min(zmin, coord[2]);
}
}
double[] ranges = new double[3];
ranges[0] = xmax - xmin;
ranges[1] = ymax - ymin;
ranges[2] = zmax - zmin;
return ranges;
}
/**
* Gets the parameterNames attribute of the PetitjeanNumberDescriptor object
*
* @return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
// no param names to return
return (null);
}
/**
* Gets the parameterType attribute of the PetitjeanNumberDescriptor object
*
* @param name Description of the Parameter
* @return The parameterType value
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return (null);
}
}