// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // 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
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  // 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
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  // exception statement from your version.
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  // ******************************************************************************
  package ffx.xray.parsers;
  
  import static org.junit.Assert.assertEquals;
  import static org.junit.Assert.assertNotNull;
  import static org.junit.Assert.assertNull;
  import static org.junit.Assert.assertTrue;
  
  import ffx.algorithms.misc.AlgorithmsTest;
  import ffx.crystal.Crystal;
  import ffx.crystal.HKL;
  import ffx.crystal.ReflectionList;
  import ffx.crystal.Resolution;
  import ffx.utilities.Keyword;
  import ffx.xray.DiffractionRefinementData;
  
  import java.io.File;
  
  import org.apache.commons.configuration2.CompositeConfiguration;
  import org.junit.Test;
  
  /**
   * Test the CIF Filter.
   *
   * @author Timoth D. Fenn
   */
  public class CIFFilterTest extends AlgorithmsTest {
  
    @Test
    public void testCIFFilter2DRM() {
      File cifFile = getResourceFile("2DRM.cif");
      // load any properties associated with it
      CompositeConfiguration properties = Keyword.loadProperties(cifFile);
  
      CIFFilter cifFilter = new CIFFilter();
      ReflectionList reflectionList = cifFilter.getReflectionList(cifFile);
      assertNull(" Reflection list should be null", reflectionList);
  
      Crystal crystal = new Crystal(29.969, 37.861, 44.506, 90.28, 90.11, 90.64, "P1");
      Resolution resolution = new Resolution(1.30);
      reflectionList = new ReflectionList(crystal, resolution);
      DiffractionRefinementData refinementData =
          new DiffractionRefinementData(properties, reflectionList);
  
      assertTrue(
          " CIF data not read correctly",
          cifFilter.readFile(cifFile, reflectionList, refinementData, properties));
  
      HKL hkl = reflectionList.getHKL(-21, -6, 7);
      assertEquals("-21 -6 7 F", 18.6, refinementData.getF(hkl.getIndex()), 0.01);
      assertEquals("-21 -6 7 sigF", 3.6, refinementData.getSigF(hkl.getIndex()), 0.01);
      assertEquals("-21 -6 7 freeR value", 0, refinementData.freeR[hkl.getIndex()]);
  
      hkl = reflectionList.getHKL(-21, -6, 8);
      assertEquals("-21 -6 7 F", 20.2, refinementData.getF(hkl.getIndex()), 0.01);
      assertEquals("-21 -6 7 sigF", 5.0, refinementData.getSigF(hkl.getIndex()), 0.01);
      assertEquals("-21 -6 7 freeR value", 1, refinementData.freeR[hkl.getIndex()]);
    }
  
    @Test
    public void testCIFFilter3DYC() {
      File cifFile = getResourceFile("3DYC.ent");
      // load any properties associated with it
     CompositeConfiguration properties = Keyword.loadProperties(cifFile);
 
     CIFFilter cifFilter = new CIFFilter();
     ReflectionList reflectionList = cifFilter.getReflectionList(cifFile);
     assertNotNull(" Reflection list should not be null", reflectionList);
     DiffractionRefinementData refinementData =
         new DiffractionRefinementData(properties, reflectionList);
 
     assertTrue(
         " CIF data not read in correctly",
         cifFilter.readFile(cifFile, reflectionList, refinementData, properties));
 
     HKL hkl = reflectionList.getHKL(58, 0, 13);
     assertEquals("58 0 13 F", 99.7, refinementData.getF(hkl.getIndex()), 0.01);
     assertEquals("58 0 13 sigF", 69.7, refinementData.getSigF(hkl.getIndex()), 0.01);
     assertEquals("58 0 13 freeR value", 1, refinementData.freeR[hkl.getIndex()]);
 
     hkl = reflectionList.getHKL(28, 20, 5);
     assertEquals("28 20 5 F", 428.1, refinementData.getF(hkl.getIndex()), 0.01);
     assertEquals("28 20 5 sigF", 10.1, refinementData.getSigF(hkl.getIndex()), 0.01);
     assertEquals("28 20 5 freeR value", 0, refinementData.freeR[hkl.getIndex()]);
   }
 }