ffx.xray.MTZFilterTest.java Source code

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Here is the source code for ffx.xray.MTZFilterTest.java

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/**
 * Title: Force Field X.
 *
 * Description: Force Field X - Software for Molecular Biophysics.
 *
 * Copyright: Copyright (c) Michael J. Schnieders 2001-2015.
 *
 * This file is part of Force Field X.
 *
 * Force Field X is free software; you can redistribute it and/or modify it
 * under the terms of the GNU General Public License version 3 as published by
 * the Free Software Foundation.
 *
 * Force Field X is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
 * details.
 *
 * You should have received a copy of the GNU General Public License along with
 * Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
 * Place, Suite 330, Boston, MA 02111-1307 USA
 *
 * Linking this library statically or dynamically with other modules is making a
 * combined work based on this library. Thus, the terms and conditions of the
 * GNU General Public License cover the whole combination.
 *
 * As a special exception, the copyright holders of this library give you
 * permission to link this library with independent modules to produce an
 * executable, regardless of the license terms of these independent modules, and
 * to copy and distribute the resulting executable under terms of your choice,
 * provided that you also meet, for each linked independent module, the terms
 * and conditions of the license of that module. An independent module is a
 * module which is not derived from or based on this library. If you modify this
 * library, you may extend this exception to your version of the library, but
 * you are not obligated to do so. If you do not wish to do so, delete this
 * exception statement from your version.
 */
package ffx.xray;

import java.io.File;

import org.apache.commons.configuration.CompositeConfiguration;
import org.junit.Test;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;

import ffx.crystal.Crystal;
import ffx.crystal.HKL;
import ffx.crystal.ReflectionList;
import ffx.crystal.Resolution;
import ffx.utilities.Keyword;

/**
 *
 * @author Timothy D. Fenn
 */
public class MTZFilterTest {

    String filename = "ffx/xray/structures/2DRM.mtz";
    ClassLoader cl = this.getClass().getClassLoader();
    File mtzFile = new File(cl.getResource(filename).getPath());
    // load any properties associated with it
    CompositeConfiguration properties = Keyword.loadProperties(mtzFile);
    // set up the crystal data
    Crystal crystal = new Crystal(29.97, 37.86, 44.51, 90.28, 90.11, 90.64, "P1");
    Resolution resolution = new Resolution(1.30);
    ReflectionList reflectionList = new ReflectionList(crystal, resolution);
    DiffractionRefinementData refinementData = new DiffractionRefinementData(properties, reflectionList);

    @Test
    public void testMTZReadFile() {
        MTZFilter mtzFilter = new MTZFilter();
        assertTrue("mtz file should be read in without errors",
                mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
    }

    @Test
    public void testMTZParams() {
        MTZFilter mtzFilter = new MTZFilter();
        assertTrue("mtz file should be read in without errors",
                mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
        assertEquals("mtz file number of columns", 6, mtzFilter.nColumns);
        assertEquals("mtz file number of reflections", 48115, mtzFilter.nReflections);
        assertEquals("mtz file space group number", 1, mtzFilter.sgnum);
    }

    @Test
    public void testMTZHKL() {
        MTZFilter mtzFilter = new MTZFilter();
        assertTrue("mtz file errors", mtzFilter.readFile(mtzFile, reflectionList, refinementData, null));
        HKL hkl = reflectionList.getHKL(-10, 1, 1);
        assertEquals("-10 1 1 FP value", 229.90, refinementData.getF(hkl.index()), 0.02);
        assertEquals("-10 1 1 SIGFP value", 2.50, refinementData.getSigF(hkl.index()), 0.02);
        assertEquals("-10 1 1 FREE value", 1, refinementData.getFreeR(hkl.index()));
        hkl = reflectionList.getHKL(-10, 1, 10);
        assertEquals("-10 1 10 FP value should be NaN", Double.NaN, refinementData.getF(hkl.index()), 0.1);
        assertEquals("-10 1 10 SIGFP value should be NaN", Double.NaN, refinementData.getSigF(hkl.index()), 0.1);
    }

    @Test
    public void testMTZReflectionList() {
        MTZFilter mtzFilter = new MTZFilter();
        ReflectionList tmp = mtzFilter.getReflectionList(mtzFile);
        assertNotNull("mtz file should return a reflection list", tmp);
        assertEquals("reflection list space group", 1, tmp.spaceGroup.number);
        assertEquals("reflection list cell dimension", 29.969, tmp.crystal.a, 0.01);
        assertEquals("reflection list resolution", 1.30, tmp.resolution.resolutionLimit(), 0.01);
    }
}