1 /* Copyright (C) 2010  Egon Willighagen <egonw@users.sf.net>
2  *
3  * Contact: cdk-devel@lists.sourceforge.net
4  *
5  * This program is free software; you can redistribute it and/or
6  * modify it under the terms of the GNU Lesser General Public License
7  * as published by the Free Software Foundation; either version 2.1
8  * of the License, or (at your option) any later version.
9  *
10  * This program is distributed in the hope that it will be useful,
11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
13  * GNU Lesser General Public License for more details.
14  *
15  * You should have received a copy of the GNU Lesser General Public License
16  * along with this program; if not, write to the Free Software
17  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
18  */
19 package org.openscience.cdk.qsar.descriptors.molecular;
20 
21 import org.junit.Assert;
22 import org.junit.Before;
23 import org.junit.Test;
24 import org.openscience.cdk.AtomContainer;
25 import org.openscience.cdk.interfaces.IAtom;
26 import org.openscience.cdk.interfaces.IAtomContainer;
27 import org.openscience.cdk.interfaces.IBond;
28 import org.openscience.cdk.interfaces.IChemObjectBuilder;
29 import org.openscience.cdk.qsar.result.IntegerResult;
30 import org.openscience.cdk.silent.SilentChemObjectBuilder;
31 import org.openscience.cdk.smiles.SmilesParser;
32 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
33 
34 /**
35  * @cdk.module test-qsarmolecular
36  */
37 public class BasicGroupCountDescriptorTest extends MolecularDescriptorTest {
38 
39     @Before
setUp()40     public void setUp() throws Exception {
41         setDescriptor(BasicGroupCountDescriptor.class);
42     }
43 
44     @Test
testConstructor()45     public void testConstructor() throws Exception {
46         Assert.assertNotNull(new BasicGroupCountDescriptor());
47     }
48 
49     @Test
testAmine()50     public void testAmine() throws Exception {
51         SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
52         IAtomContainer mol = sp.parseSmiles("NC");
53         IntegerResult result = (IntegerResult) descriptor.calculate(mol).getValue();
54         Assert.assertEquals(1, result.intValue());
55     }
56 
57     @Test(expected = IllegalStateException.class)
uninitalisedError()58     public void uninitalisedError() {
59         new BasicGroupCountDescriptor().calculate(new AtomContainer());
60     }
61 
62     /**
63      * @cdk.inchi InChI=1S/C2H4N2/c1-4-2-3/h2-3H,1H2
64      */
65     @Test
test()66     public void test() throws Exception {
67         IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance();
68         IAtomContainer mol = builder.newInstance(IAtomContainer.class);
69         IAtom a1 = builder.newInstance(IAtom.class, "N");
70         mol.addAtom(a1);
71         IAtom a2 = builder.newInstance(IAtom.class, "N");
72         mol.addAtom(a2);
73         IAtom a3 = builder.newInstance(IAtom.class, "C");
74         mol.addAtom(a3);
75         IAtom a4 = builder.newInstance(IAtom.class, "C");
76         mol.addAtom(a4);
77         IAtom a5 = builder.newInstance(IAtom.class, "H");
78         mol.addAtom(a5);
79         IAtom a6 = builder.newInstance(IAtom.class, "H");
80         mol.addAtom(a6);
81         IAtom a7 = builder.newInstance(IAtom.class, "H");
82         mol.addAtom(a7);
83         IAtom a8 = builder.newInstance(IAtom.class, "H");
84         mol.addAtom(a8);
85         IBond b1 = builder.newInstance(IBond.class, a1, a3, IBond.Order.SINGLE);
86         mol.addBond(b1);
87         IBond b2 = builder.newInstance(IBond.class, a1, a4, IBond.Order.DOUBLE);
88         mol.addBond(b2);
89         IBond b3 = builder.newInstance(IBond.class, a2, a3, IBond.Order.DOUBLE);
90         mol.addBond(b3);
91         IBond b4 = builder.newInstance(IBond.class, a2, a8, IBond.Order.SINGLE);
92         mol.addBond(b4);
93         IBond b5 = builder.newInstance(IBond.class, a3, a5, IBond.Order.SINGLE);
94         mol.addBond(b5);
95         IBond b6 = builder.newInstance(IBond.class, a4, a6, IBond.Order.SINGLE);
96         mol.addBond(b6);
97         IBond b7 = builder.newInstance(IBond.class, a4, a7, IBond.Order.SINGLE);
98         mol.addBond(b7);
99 
100         AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
101         addImplicitHydrogens(mol);
102 
103         IntegerResult result = (IntegerResult) descriptor.calculate(mol).getValue();
104         // two SMARTS matches
105         Assert.assertEquals(2, result.intValue());
106     }
107 }
108