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 42 import ffx.algorithms.misc.AlgorithmsTest; 43 import ffx.numerics.Potential; 44 import ffx.xray.groovy.ManyBody; 45 import java.util.List; 46 import org.junit.Test; 47 48 /** 49 * Tests X-Ray many body optimization and the X-Ray many body groovy script under varying 50 * parameters. 51 * 52 * @author Mallory R. Tollefson 53 */ 54 public class XRayManyBodyTest extends AlgorithmsTest { 55 56 // @Test 57 public void testManyBodyGlobal() { 58 // Set-up the input arguments for the script. 59 String[] args = { 60 "-a", "2", 61 "-L", "2", 62 "--sR", "1", 63 "--fR", "5", 64 getResourcePath("5awl.pdb"), 65 getResourcePath("5awl.mtz") 66 }; 67 binding.setVariable("args", args); 68 binding.setVariable("baseDir", registerTemporaryDirectory().toFile()); 69 70 // Construct and evaluate the ManyBody script. 71 ManyBody manyBody = new ManyBody(binding).run(); 72 algorithmsScript = manyBody; 73 74 List<Potential> list = manyBody.getPotentials(); 75 double expectedPotential = 35106.252654189106; 76 double actualPotential = list.get(0).getTotalEnergy(); 77 double tol = 1.0E-4 * expectedPotential; 78 assertEquals(expectedPotential, actualPotential, tol); 79 manyBody.getManyBodyOptions().getRestartFile().delete(); 80 } 81 82 @Test 83 public void testManyBodyHelp() { 84 // Set-up the input arguments for the Biotype script. 85 String[] args = {"-h"}; 86 binding.setVariable("args", args); 87 88 // Construct and evaluate the ManyBody script. 89 ManyBody manyBody = new ManyBody(binding).run(); 90 algorithmsScript = manyBody; 91 } 92 }