1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
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 static org.junit.Assert.assertEquals;
41 import static org.junit.Assert.assertNotNull;
42
43 import ffx.algorithms.misc.AlgorithmsTest;
44 import ffx.crystal.HKL;
45 import ffx.potential.bonded.Atom;
46 import ffx.potential.parameters.AtomType;
47 import org.junit.Before;
48 import org.junit.Test;
49
50 /**
51 * @author Timothy D. Fenn
52 */
53 public class FormFactorTest extends AlgorithmsTest {
54
55 private XRayFormFactor carbonFormFactor;
56
57 @Before
58 public void setUp() {
59 double[] d = new double[3];
60 double[] anisou = new double[6];
61 anisou[0] = anisou[1] = anisou[2] = 1.0;
62 anisou[3] = anisou[4] = anisou[5] = 0.0;
63 Atom carbon = new Atom(1, "C", 'A', d, "ALA", 1, 'A', 1.0, 20.0, "A");
64 AtomType atomType = new AtomType(1, 1, "C", null, 6, 12.01, 1);
65 carbon.setAtomType(atomType);
66 carbon.setAltLoc('A');
67 carbon.setAnisou(anisou);
68 carbonFormFactor = new XRayFormFactor(carbon, false);
69 }
70
71 @Test
72 public void testCarbonFF() {
73 assertNotNull(" Carbon form factors should exist", XRayFormFactor.getFormFactor("6"));
74 double[][] formFactor = XRayFormFactor.getFormFactor("6");
75
76 assertEquals(" Carbon form factors", 5, (int) formFactor[0][0]);
77 assertEquals(" Carbon form factors", 2.09921, formFactor[1][0], 0.0001);
78 assertEquals(" Carbon form factors", 13.18997, formFactor[2][0], 0.0001);
79 }
80
81 @Test
82 public void testCarbonfrho() {
83 HKL hkl = new HKL(1, 1, 1);
84 assertEquals("carbon (1 1 1) structure factor should be correct", 2.3986e-26,
85 carbonFormFactor.f(hkl), 1e-30);
86
87 double[] xyz = {1.0, 1.0, 1.0};
88 assertEquals("carbon (1 1 1) electron density should be correct", 0.081937,
89 carbonFormFactor.rho(0.0, 1.0, xyz), 0.000001);
90 }
91 }