1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025.
6 //
7 // This file is part of Force Field X.
8 //
9 // Force Field X is free software; you can redistribute it and/or modify it
10 // under the terms of the GNU General Public License version 3 as published by
11 // the Free Software Foundation.
12 //
13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT
14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
16 // details.
17 //
18 // You should have received a copy of the GNU General Public License along with
19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
20 // Place, Suite 330, Boston, MA 02111-1307 USA
21 //
22 // Linking this library statically or dynamically with other modules is making a
23 // combined work based on this library. Thus, the terms and conditions of the
24 // GNU General Public License cover the whole combination.
25 //
26 // As a special exception, the copyright holders of this library give you
27 // permission to link this library with independent modules to produce an
28 // executable, regardless of the license terms of these independent modules, and
29 // to copy and distribute the resulting executable under terms of your choice,
30 // provided that you also meet, for each linked independent module, the terms
31 // and conditions of the license of that module. An independent module is a
32 // module which is not derived from or based on this library. If you modify this
33 // library, you may extend this exception to your version of the library, but
34 // you are not obligated to do so. If you do not wish to do so, delete this
35 // exception statement from your version.
36 //
37 // ******************************************************************************
38 package ffx.xray;
39
40 import ffx.algorithms.misc.AlgorithmsTest;
41 import ffx.xray.commands.test.Gradient;
42 import org.junit.Test;
43
44 import static org.junit.Assert.assertEquals;
45
46 /**
47 * Tests X-Ray Gradient.
48 *
49 * @author Michael J. Schnieders
50 */
51 public class XRayGradientTest extends AlgorithmsTest {
52
53 @Test
54 public void testAlametXYZGradient() {
55 // Set-up the input arguments.
56 String[] args = {
57 "-m", "coordinates",
58 "--sol", "none",
59 "--aRadBuffer", "3.0",
60 "-G", "0.5",
61 "--tol", "1.0e-2",
62 "--params", "1-2",
63 getResourcePath("alamet.pdb_2"),
64 getResourcePath("alamet.mtz")
65 };
66 binding.setVariable("args", args);
67 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
68
69 // alamet.pdb was refined with CNS
70 // alamet.pdb_2 was refined with FFX
71
72 // Construct and evaluate the Gradient script.
73 Gradient gradient = new Gradient(binding).run();
74 algorithmsScript = gradient;
75 assertEquals(" Number of failed gradient components.", 0, gradient.nFailures);
76 }
77
78 @Test
79 public void test1N7SXYZGradient() {
80 // Set-up the input arguments.
81 String[] args = {
82 "-m", "coordinates",
83 "--aRadBuffer", "4.0",
84 "--params", "1-2",
85 getResourcePath("1N7S.pdb"),
86 getResourcePath("1N7S.cif")
87 };
88 binding.setVariable("args", args);
89 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
90
91 // Construct and evaluate the Gradient script.
92 Gradient gradient = new Gradient(binding).run();
93 algorithmsScript = gradient;
94 assertEquals(" Number of failed gradient components.", 0, gradient.nFailures);
95 }
96
97 @Test
98 public void test1N7SBFactorsGradient() {
99 // Set-up the input arguments.
100 String[] args = {
101 "-m", "bfactors",
102 "--aRadBuffer", "4.0",
103 "--params", "1-2",
104 getResourcePath("1N7S.pdb"),
105 getResourcePath("1N7S.cif")
106 };
107 binding.setVariable("args", args);
108 binding.setVariable("baseDir", registerTemporaryDirectory().toFile());
109
110 // Construct and evaluate the Gradient script.
111 Gradient gradient = new Gradient(binding).run();
112 algorithmsScript = gradient;
113 assertEquals(" Number of failed gradient components.", 0, gradient.nFailures);
114 }
115
116 @Test
117 public void testGradientHelp() {
118 // Set-up the input arguments for the Biotype script.
119 String[] args = {"-h"};
120 binding.setVariable("args", args);
121
122 // Construct and evaluate the Gradient script.
123 Gradient gradient = new Gradient(binding).run();
124 algorithmsScript = gradient;
125 }
126 }