/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.atomic;
import java.io.IOException;
import javax.vecmath.Point3d;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Inductive atomic softness of an atom in a polyatomic system can be defined
* as charge delocalizing ability. Only works with 3D coordinates, which must be calculated beforehand. <p>
*
* This descriptor uses these parameters:
* <tableborder="1">
*
* <tr>
*
* <td>
* Name
* </td>
*
* <td>
* Default
* </td>
*
* <td>
* Description
* </td>
*
* </tr>
*
* <tr>
*
* <td>
*
* </td>
*
* <td>
*
* </td>
*
* <td>
* no parameters
* </td>
*
* </tr>
*
* </table>
*
*
*@author mfe4
*@cdk.created 2004-11-03
*@cdk.module qsaratomic
* @cdk.githash
*@cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:atomicSoftness
*/
@TestClass(value="org.openscience.cdk.qsar.descriptors.atomic.InductiveAtomicSoftnessDescriptorTest")
public class InductiveAtomicSoftnessDescriptor implements IAtomicDescriptor {
private static final String[] names = {"indAtomSoftness"};
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(InductiveAtomicSoftnessDescriptor.class);
private AtomTypeFactory factory = null;
/**
* Constructor for the InductiveAtomicSoftnessDescriptor object
*
*@exception IOException Description of the Exception
*@exception ClassNotFoundException Description of the Exception
*/
public InductiveAtomicSoftnessDescriptor() throws IOException, ClassNotFoundException {
}
/**
* Gets the specification attribute of the InductiveAtomicSoftnessDescriptor
* object
*
*@return The specification value
*/
@TestMethod(value="testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#atomicSoftness",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* This descriptor does have any parameter.
*/
@TestMethod(value="testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
}
/**
* Gets the parameters attribute of the InductiveAtomicSoftnessDescriptor
* object
*
* @return The parameters value
* @see #setParameters
*/
@TestMethod(value="testGetParameters")
public Object[] getParameters() {
return null;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
private DescriptorValue getDummyDescriptorValue(Exception e) {
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(Double.NaN),
names, e);
}
/**
* It is needed to call the addExplicitHydrogensToSatisfyValency method from
* the class tools.HydrogenAdder, and 3D coordinates.
*
*@param atom The IAtom for which the DescriptorValue is requested
*@param ac AtomContainer
*@return a double with polarizability of the heavy atom
*/
@TestMethod(value="testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
if (factory == null)
try {
factory = AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt",
ac.getBuilder()
);
} catch (Exception exception) {
return getDummyDescriptorValue(exception);
}
java.util.Iterator allAtoms = ac.atoms().iterator();
double atomicSoftness;
double radiusTarget;
atomicSoftness = 0;
double partial;
double radius;
String symbol;
IAtomType type;
try {
symbol = atom.getSymbol();
type = factory.getAtomType(symbol);
radiusTarget = type.getCovalentRadius();
} catch (Exception execption) {
logger.debug(execption);
return getDummyDescriptorValue(execption);
}
while (allAtoms.hasNext()) {
IAtom curAtom = (IAtom)allAtoms.next();
if (atom.getPoint3d() == null || curAtom.getPoint3d() == null) {
return getDummyDescriptorValue(new CDKException("The target atom or current atom had no 3D coordinates. These are required"));
}
if (!atom.equals(curAtom)) {
partial = 0;
symbol = curAtom.getSymbol();
try {
type = factory.getAtomType(symbol);
} catch (Exception exception) {
logger.debug(exception);
return getDummyDescriptorValue(exception);
}
radius = type.getCovalentRadius();
partial += radius * radius;
partial += (radiusTarget * radiusTarget);
partial = partial / (calculateSquareDistanceBetweenTwoAtoms(curAtom, atom));
//logger.debug("SOFT: atom "+symbol+", radius "+radius+", distance "+calculateSquareDistanceBetweenTwoAtoms(allAtoms[i], target));
atomicSoftness += partial;
}
}
atomicSoftness = 2 * atomicSoftness;
atomicSoftness = atomicSoftness * 0.172;
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(atomicSoftness),
names);
}
private double calculateSquareDistanceBetweenTwoAtoms(IAtom atom1, IAtom atom2) {
double distance;
double tmp;
Point3d firstPoint = atom1.getPoint3d();
Point3d secondPoint = atom2.getPoint3d();
tmp = firstPoint.distance(secondPoint);
distance = tmp * tmp;
return distance;
}
/**
* Gets the parameterNames attribute of the InductiveAtomicSoftnessDescriptor object.
*
* @return The parameterNames value
*/
@TestMethod(value="testGetParameterNames")
public String[] getParameterNames() {
return new String[0];
}
/**
* Gets the parameterType attribute of the InductiveAtomicSoftnessDescriptor object.
*
* @param name Description of the Parameter
* @return An Object of class equal to that of the parameter being requested
*/
@TestMethod(value="testGetParameterType_String")
public Object getParameterType(String name) {
return null;
}
}