1 /*
2  * Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
3  *
4  * Contact: cdk-devel@lists.sourceforge.net
5  *
6  * This program is free software; you can redistribute it and/or
7  * modify it under the terms of the GNU Lesser General Public License
8  * as published by the Free Software Foundation; either version 2.1
9  * of the License, or (at your option) any later version.
10  *
11  * This program is distributed in the hope that it will be useful,
12  * but WITHOUT ANY WARRANTY; without even the implied warranty of
13  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
14  * GNU Lesser General Public License for more details.
15  *
16  * You should have received a copy of the GNU Lesser General Public License
17  * along with this program; if not, write to the Free Software
18  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
19  */
20 package org.openscience.cdk.qsar.descriptors.molecular;
21 
22 import java.io.InputStream;
23 import java.util.List;
24 
25 import org.junit.Assert;
26 import org.junit.Before;
27 import org.junit.Test;
28 import org.openscience.cdk.ChemFile;
29 import org.openscience.cdk.ChemObject;
30 import org.openscience.cdk.DefaultChemObjectBuilder;
31 import org.openscience.cdk.exception.CDKException;
32 import org.openscience.cdk.exception.InvalidSmilesException;
33 import org.openscience.cdk.interfaces.IAtomContainer;
34 import org.openscience.cdk.io.HINReader;
35 import org.openscience.cdk.io.ISimpleChemObjectReader;
36 import org.openscience.cdk.qsar.DescriptorValue;
37 import org.openscience.cdk.qsar.result.DoubleArrayResult;
38 import org.openscience.cdk.smiles.SmilesParser;
39 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
40 
41 /**
42  * TestSuite that runs all QSAR tests.
43  *
44  * @cdk.module test-qsarmolecular
45  */
46 
47 public class MomentOfInertiaDescriptorTest extends MolecularDescriptorTest {
48 
MomentOfInertiaDescriptorTest()49     public MomentOfInertiaDescriptorTest() {}
50 
51     @Before
setUp()52     public void setUp() throws Exception {
53         setDescriptor(MomentOfInertiaDescriptor.class);
54     }
55 
56     /**
57      * @cdk.bug 1956139
58      * @throws InvalidSmilesException
59      */
60     @Test
testMOIFromSmiles()61     public void testMOIFromSmiles() throws InvalidSmilesException {
62         SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
63         IAtomContainer mol = sp.parseSmiles("CCCC");
64         DescriptorValue value = descriptor.calculate(mol);
65         Assert.assertNotNull("The Exception should be non-null since we don't have 3D coords", value.getException());
66 
67     }
68 
69     @Test
testMomentOfInertia1()70     public void testMomentOfInertia1() throws ClassNotFoundException, CDKException, java.lang.Exception {
71         String filename = "data/hin/gravindex.hin";
72         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
73         ISimpleChemObjectReader reader = new HINReader(ins);
74         ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
75         List cList = ChemFileManipulator.getAllAtomContainers(content);
76         IAtomContainer ac = (IAtomContainer) cList.get(0);
77 
78         DoubleArrayResult retval = (DoubleArrayResult) descriptor.calculate(ac).getValue();
79 
80         Assert.assertEquals(1820.692519, retval.get(0), 0.00001);
81         Assert.assertEquals(1274.532522, retval.get(1), 0.00001);
82         Assert.assertEquals(979.210423, retval.get(2), 0.00001);
83         Assert.assertEquals(1.428517, retval.get(3), 0.00001);
84         Assert.assertEquals(1.859347, retval.get(4), 0.00001);
85         Assert.assertEquals(1.301592, retval.get(5), 0.00001);
86         Assert.assertEquals(5.411195, retval.get(6), 0.00001);
87     }
88 
89     @Test
testMomentOfInertia2()90     public void testMomentOfInertia2() throws ClassNotFoundException, CDKException, java.lang.Exception {
91         String filename = "data/hin/momi2.hin";
92         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
93         ISimpleChemObjectReader reader = new HINReader(ins);
94         ChemFile content = (ChemFile) reader.read((ChemObject) new ChemFile());
95         List cList = ChemFileManipulator.getAllAtomContainers(content);
96         IAtomContainer ac = (IAtomContainer) cList.get(0);
97 
98         DoubleArrayResult retval = (DoubleArrayResult) descriptor.calculate(ac).getValue();
99 
100         Assert.assertEquals(10068.419360, retval.get(0), 0.00001);
101         Assert.assertEquals(9731.078356, retval.get(1), 0.00001);
102         Assert.assertEquals(773.612799, retval.get(2), 0.00001);
103         Assert.assertEquals(1.034666, retval.get(3), 0.00001);
104         Assert.assertEquals(13.014804, retval.get(4), 0.00001);
105         Assert.assertEquals(12.578745, retval.get(5), 0.00001);
106         Assert.assertEquals(8.2966226, retval.get(6), 0.00001);
107     }
108 
109 }
110