/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.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.DoubleResult;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
/**
* This Class contains a method that returns the number failures of the
* Lipinski's Rule Of 5.
* See <a href="http://www.lifechemicals.com/eng/services/HTS/five/">http://www.lifechemicals.com/eng/services/HTS/five/</a>.
*
* <p>This descriptor uses these parameters:
* <table border="1">
* <tr>
* <td>Name</td>
* <td>Default</td>
* <td>Description</td>
* </tr>
* <tr>
* <td>checkAromaticity</td>
* <td>false</td>
* <td>True is the aromaticity has to be checked</td>
* </tr>
* </table>
*
* Returns a single value named <i>LipinskiFailures</i>.
*
* @author mfe4
* @cdk.created 2004-11-03
* @cdk.module qsarmolecular
* @cdk.githash
* @cdk.set qsar-descriptors
* @cdk.dictref qsar-descriptors:lipinskifailures
*
* @cdk.keyword Lipinski
* @cdk.keyword rule-of-five
* @cdk.keyword descriptor
*/
@TestClass("org.openscience.cdk.qsar.descriptors.molecular.RuleOfFiveDescriptorTest")
public class RuleOfFiveDescriptor implements IMolecularDescriptor {
private boolean checkAromaticity = false;
private static final String[] names = {"LipinskiFailures"};
/**
* Constructor for the RuleOfFiveDescriptor object.
*/
public RuleOfFiveDescriptor() { }
/**
* Returns a <code>Map</code> which specifies which descriptor
* is implemented by this class.
*
* These fields are used in the map:
* <ul>
* <li>Specification-Reference: refers to an entry in a unique dictionary
* <li>Implementation-Title: anything
* <li>Implementation-Identifier: a unique identifier for this version of
* this class
* <li>Implementation-Vendor: CDK, JOELib, or anything else
* </ul>
*
* @return An object containing the descriptor specification
*/
@TestMethod("testGetSpecification")
public DescriptorSpecification getSpecification() {
return new DescriptorSpecification(
"http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#lipinskifailures",
this.getClass().getName(),
"$Id$",
"The Chemistry Development Kit");
}
/**
* Sets the parameters attribute of the RuleOfFiveDescriptor object.
*
* There is only one parameter, which should be a Boolean indicating whether
* aromaticity should be checked or has already been checked. The name of the paramete
* is checkAromaticity.
*
*@param params Parameter is only one: a boolean.
*@throws CDKException if more than 1 parameter or a non-Boolean parameter is specified
*@see #getParameters
*/
@TestMethod("testSetParameters_arrayObject")
public void setParameters(Object[] params) throws CDKException {
if (params.length != 1) {
throw new CDKException("RuleOfFiveDescriptor expects one parameter");
}
if (!(params[0] instanceof Boolean)) {
throw new CDKException("The first parameter must be of type Boolean");
}
// ok, all should be fine
checkAromaticity = (Boolean) params[0];
}
/**
* Gets the parameters attribute of the RuleOfFiveDescriptor object.
*
*@return The parameters value
*@see #setParameters
*/
@TestMethod("testGetParameters")
public Object[] getParameters() {
// return the parameters as used for the descriptor calculation
Object[] params = new Object[1];
params[0] = checkAromaticity;
return params;
}
@TestMethod(value="testNamesConsistency")
public String[] getDescriptorNames() {
return names;
}
/**
* the method take a boolean checkAromaticity: if the boolean is true, it means that
* aromaticity has to be checked.
*
*@param mol AtomContainer for which this descriptor is to be calculated
*@return The number of failures of the Lipinski rule
*/
@TestMethod("testCalculate_IAtomContainer")
public DescriptorValue calculate(IAtomContainer mol) {
int lipinskifailures = 0;
IMolecularDescriptor xlogP = new XLogPDescriptor();
Object[] xlogPparams = {
checkAromaticity,
Boolean.TRUE,
};
try {
xlogP.setParameters(xlogPparams);
double xlogPvalue = ((DoubleResult) xlogP.calculate(mol).getValue()).doubleValue();
IMolecularDescriptor acc = new HBondAcceptorCountDescriptor();
Object[] hBondparams = {checkAromaticity};
acc.setParameters(hBondparams);
int acceptors = ((IntegerResult) acc.calculate(mol).getValue()).intValue();
IMolecularDescriptor don = new HBondDonorCountDescriptor();
don.setParameters(hBondparams);
int donors = ((IntegerResult) don.calculate(mol).getValue()).intValue();
IMolecularDescriptor mw = new WeightDescriptor();
Object[] mwparams = {""};
mw.setParameters(mwparams);
double mwvalue = ((DoubleResult) mw.calculate(mol).getValue()).doubleValue();
IMolecularDescriptor rotata = new RotatableBondsCountDescriptor();
rotata.setParameters(hBondparams);
int rotatablebonds = ((IntegerResult) rotata.calculate(mol).getValue()).intValue();
if (xlogPvalue > 5.0) {
lipinskifailures += 1;
}
if (acceptors > 10) {
lipinskifailures += 1;
}
if (donors > 5) {
lipinskifailures += 1;
}
if (mwvalue > 500.0) {
lipinskifailures += 1;
}
if (rotatablebonds > 10.0) {
lipinskifailures += 1;
}
} catch (CDKException e) {
new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new IntegerResult((int) Double.NaN),
getDescriptorNames(), e);
}
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(lipinskifailures),
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 IntegerResult(1);
}
/**
* Gets the parameterNames attribute of the RuleOfFiveDescriptor object.
*
*@return The parameterNames value
*/
@TestMethod("testGetParameterNames")
public String[] getParameterNames() {
String[] params = new String[1];
params[0] = "checkAromaticity";
return params;
}
/**
* Gets the parameterType attribute of the RuleOfFiveDescriptor object.
*
*@param name The name of the parameter. In this case it is 'checkAromaticity'.
*@return An Object of class equal to that of the parameter being requested
*/
@TestMethod("testGetParameterType_String")
public Object getParameterType(String name) {
return true;
}
}