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
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
|
/*
* $Id: ConformerTests.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 org.junit.Test;
public class ConformerTests extends GraphMolTest {
@Test
public void test0Conformers() {
ROMol mol = RWMol.MolFromSmiles("CC");
Conformer conf = new Conformer(2);
conf.setAtomPos(0, new Point3D(-0.5, 0.0, 0.0));
conf.setAtomPos(1, new Point3D(1.0, 0.0, 0.0));
conf.setId(0);
long cid = mol.addConformer(conf);
assertEquals(0, cid);
Conformer conf2 = mol.getConformer(0);
assertEquals(cid, conf2.getId());
Point3D pt1 = conf2.getAtomPos(0);
assertPointEquals(pt1, new Point3D(-0.5, 0.0, 0.0));
Point3D pt2 = conf2.getAtomPos(1);
assertPointEquals(pt2, new Point3D(1.0, 0.0, 0.0));
// conf and conf2 now reference the same object
conf.setAtomPos(1, new Point3D(2.0, 0.0, 0.0));
pt2 = conf2.getAtomPos(1);
assertEquals(2.0, pt2.getX(), defaultDoubleTol);
conf = new Conformer(2);
conf.setAtomPos(0, new Point3D(-0.5, 0.0, 0.0));
conf.setAtomPos(1, new Point3D(1.0, 0.0, 0.0));
conf.setId(2);
cid = mol.addConformer(conf, false);
assertEquals(2, cid);
}
@Test
public void test0AddHds() {
ROMol mol = RWMol.MolFromSmiles("CC");
Conformer conf = new Conformer(1);
conf.setAtomPos(0, new Point3D(-0.5, 0.0, 0.0));
conf.setAtomPos(1, new Point3D(1.0, 0.0, 0.0));
long cid = mol.addConformer(conf);
Conformer conf2 = mol.getConformer((int) cid);
assertEquals(2, conf2.getNumAtoms());
ROMol nmol = mol.addHs(false, true);
Conformer conf3 = nmol.getConformer();
assertEquals(8, conf3.getNumAtoms());
assertEquals(2, conf2.getNumAtoms());
double[][] targetCoords = { { -0.5, 0.0, 0.0 }, { 1.0, 0.0, 0.0 },
{ -0.8667, 0.0, 1.03709 }, { -0.8667, 0.8981, -0.5185 },
{ -0.8667, -0.8981, -0.5185 }, { 1.3667, 0.0, -1.0371 },
{ 1.36667, 0.8981, 0.5185 }, { 1.36667, -0.8981, 0.5185 } };
for (int i = 0; i < targetCoords.length; i++) {
Point3D pt = conf3.getAtomPos(i);
assertPointEquals(pt, new Point3D(targetCoords[i][0], targetCoords[i][1],
targetCoords[i][2]));
}
}
@Test
public void test2Issue217() {
String smi = "c1ccccc1";
RWMol m = RWMol.MolFromSmiles(smi);
m.addConformer(new Conformer(m.getNumAtoms()));
assertEquals(1,m.getNumConformers());
// We don't want an exception here
m.MolToMolBlock();
}
@Test (expected=GenericRDKitException.class)
public void test3Exceptions() {
String smi = "c1ccccc1";
RWMol m = RWMol.MolFromSmiles(smi);
m.addConformer(new Conformer());
assertEquals(1,m.getNumConformers());
// We just want the exception to be thrown
m.getConformer(2);
}
@Test
public void test4ConfTuple() {
String smi = "c1ccccc1";
RWMol m = RWMol.MolFromSmiles(smi);
for (int i = 0; i < 10; i++) {
Conformer c = new Conformer(m.getNumAtoms());
c.setId(i);
m.addConformer(c, false);
}
assertEquals(10, m.getNumConformers());
for (int i = 0; i < m.getNumConformers(); i++)
for (int j = 0; j < m.getConformer(i).getNumAtoms(); j++) {
Point3D pt = m.getConformer(i).getAtomPos(j);
assertPointEquals(pt, new Point3D(0.0, 0.0, 0.0));
}
for (int i = 0; i < 10; i++)
m.removeConformer(i);
assertEquals(0, m.getNumConformers());
}
public static void main(String args[]) {
org.junit.runner.JUnitCore.main("org.RDKit.ConformerTests");
}
}
|
