xlogpdescriptortest.java

化学图形处理软件

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-01-04 17:32:54 +0000 (Do, 04 Jan 2007) $
 * $Revision: 7635 $
 * 
 * Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
 * 
 * Contact: [e-mail]
 * 
 * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. 
 */
package org.openscience.cdk.test.qsar.descriptors.molecular;

import junit.framework.Test;
import junit.framework.TestSuite;

import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.descriptors.molecular.XLogPDescriptor;
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.test.CDKTestCase;
import org.openscience.cdk.tools.HydrogenAdder;

/**
 * TestSuite that runs all QSAR tests.
 *
 * @cdk.module test-qsar
 */

public class XLogPDescriptorTest extends CDKTestCase {

    public XLogPDescriptorTest() {
    }

    public static Test suite() {
        return new TestSuite(XLogPDescriptorTest.class);
    }

//	public void testXLogPDescriptor() throws ClassNotFoundException, CDKException, java.lang.Exception {
//	
//	// each test is for one or more atom types:
//	// 1. Test for cumarine
//	IMolecularDescriptor descriptor = new XLogPDescriptor();
//	Object[] params = {new Boolean(true)};
//	descriptor.setParameters(params);
//	SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
//	IMolecule mol = sp.parseSmiles("COc1ccccc1C(C3=C(O)c2ccccc2CC3=O)c5c(O)c4ccccc4oc5=O"); // a cumarine
//	HydrogenAdder hAdder = new HydrogenAdder();
//	hAdder.addExplicitHydrogensToSatisfyValency(mol);
//	logger.debug("Cumarine:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue());
//	//assertEquals(4.54, ((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
//	
//	
//}

    public void testno688() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=C(O)c1[nH0]cccc1"); // xlogp training set molecule no688
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no688:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(-1.69, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno1596() throws ClassNotFoundException, CDKException, java.lang.Exception {
        // the xlogp program value is 0.44 bevause of paralleled donor pair correction factor
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("Nc2ccc(S(=O)(=O)c1ccc(N)cc1)cc2"); // xlogp training set molecule no1596
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1596:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(0.86, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno367() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=C(O)C(N)CCCN"); // xlogp training set molecule no367
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no367:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(-3.30, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno1837() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("O=P(N1CC1)(N2CC2)N3CC3"); // xlogp training set molecule no1837
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1837:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(-1.19, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno87() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("c1cc2ccc3ccc4ccc5cccc6c(c1)c2c3c4c56"); // xlogp training set molecule no87
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no87:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(7.00, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno1782() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("S1C2N(C(=O)C2NC(=O)C(c2ccccc2)C(=O)O)C(C(=O)O)C1(C)C"); // xlogp training set molecule no30
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no1782:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(1.84, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16
    }

    public void testno30() throws ClassNotFoundException, CDKException, java.lang.Exception {
        IMolecularDescriptor descriptor = new XLogPDescriptor();
        Object[] params = {new Boolean(true), new Boolean(false)};
        descriptor.setParameters(params);
        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
        IMolecule mol = sp.parseSmiles("C(#Cc1ccccc1)c1ccccc1"); // xlogp training set molecule no30
        HydrogenAdder hAdder = new HydrogenAdder();
        hAdder.addExplicitHydrogensToSatisfyValency(mol);
        //logger.debug("no30:"+((DoubleResult)descriptor.calculate(mol).getValue()).doubleValue()+"\n");
        assertEquals(4.62, ((DoubleResult) descriptor.calculate(mol).getValue()).doubleValue(), 0.1); //at:  16