1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
|
/*
* $Id: ChemBondTests.java 131 2011-01-20 22:01:29Z ebakke $
*
* Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
*
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above
* copyright notice, this list of conditions and the following
* disclaimer in the documentation and/or other materials provided
* with the distribution.
* * Neither the name of Novartis Institutes for BioMedical Research Inc.
* nor the names of its contributors may be used to endorse or promote
* products derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
* OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
* SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
* LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
* DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
* THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
package org.RDKit;
import static org.junit.Assert.*;
import java.io.File;
import org.junit.*;
public class ChemBondTests extends GraphMolTest {
private ROMol m;
@Before public void setUp() {
String smiles="CCCC1=CC=C1";
m = RWMol.MolFromSmiles(smiles);
}
// testing GetBond
@Test
public void test1Get() {
assertNotNull( m.getBondBetweenAtoms(0, 1) );
}
// Testing setting bond props
@Test
public void test2Setters() {
Bond b = m.getBondBetweenAtoms(0,1);
assertEquals(Bond.BondType.SINGLE, b.getBondType());
b.setBondDir(Bond.BondDir.BEGINWEDGE);
assertEquals(Bond.BondDir.BEGINWEDGE,m.getBondBetweenAtoms(0,1).getBondDir());
}
// Testing bond props
@Test
public void test3Props() {
Bond b = m.getBondBetweenAtoms(0,1);
assertEquals(Bond.BondType.SINGLE,b.getBondType());
assertEquals(m.getAtomWithIdx(0).getIdx(),b.getBeginAtom().getIdx());
assertEquals(0,b.getBeginAtomIdx());
assertEquals(m.getAtomWithIdx(1).getIdx(),b.getEndAtom().getIdx());
assertEquals(1,b.getEndAtomIdx());
}
// Testing more bond props
@Test
public void test4Props2() {
Bond b = m.getBondBetweenAtoms(3,4);
assertEquals(Bond.BondType.DOUBLE,b.getBondType());
Bond b2 = m.getBondBetweenAtoms(1,2);
assertEquals(Bond.BondType.SINGLE,b2.getBondType());
assertTrue (b.getIsConjugated());
assertFalse (b2.getIsConjugated());
}
// Testing more bond props
@Test
public void test5BondIters() {
// Traversing through bond list of a molecule
BondIterator it = m.beginBonds();
int iCount = 0;
while ( it.ne(m.endBonds()) ) {
final Bond bond = it.getBond();
final Bond.BondType type = bond.getBondType();
final Atom atomStart = bond.getBeginAtom();
final Atom atomEnd = bond.getEndAtom();
// some silly tests
assertEquals(atomStart.getIdx(),bond.getBeginAtomIdx());
assertEquals(atomEnd.getIdx(),bond.getEndAtomIdx());
it = it.next();
iCount++;
}
assertEquals(iCount,m.getNumBonds());
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.ChemBondTests");
}
}
|
