//******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // 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,
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  //******************************************************************************
  package ffx.xray.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.utilities.FFXBinding;
  import ffx.xray.DiffractionData;
  import ffx.xray.cli.XrayOptions;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Option;
  import picocli.CommandLine.Parameters;
  
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.List;
  import java.util.stream.Collectors;
  
  import static java.lang.String.format;
  import static org.apache.commons.io.FilenameUtils.removeExtension;
  
  /**
   * The X-ray ModelvsData script.
   * <br>
   * Usage:
   * <br>
   * ffxc xray.ModelvsData [options] &lt;filename [file2...]&gt;
   */
  @Command(description = " Compare the PDB model to the diffraction data.", name = "xray.ModelvsData")
  public class ModelvsData extends AlgorithmsCommand {
  
    @Mixin
    private XrayOptions xrayOptions;
  
    @Mixin
    AtomSelectionOptions atomSelectionOptions;
  
    /**
     * -p or --maps Output sigmaA weighted 2Fo-Fc and Fo-Fc maps.
     */
    @Option(names = {"-p", "--maps"}, paramLabel = "false",
        description = "Output sigmaA weighted 2Fo-Fc and Fo-Fc maps.")
    private boolean maps = false;
  
    /**
     * -n or --normalize Normalize maps to a standard deviation of 1.0.
     */
    @Option(names = {"-n", "--normalize"}, paramLabel = "false",
        description = "Normalize maps to a standard deviation of 1.0.")
    private boolean normalize = false;
  
    /**
     * -t or --timings Perform FFT timings.
     */
    @Option(names = {"-t", "--timings"}, paramLabel = "false",
        description = "Perform FFT timings.")
    private boolean timings = false;
  
    /**
    * -w or --mtz Write out MTZ containing structure factor coefficients.
    */
   @Option(names = {"-w", "--mtz"}, paramLabel = "false",
       description = "write out MTZ containing structure factor coefficients.")
   private boolean mtz = false;
 
   /**
    * One or more filenames.
    */
   @Parameters(arity = "1..*", paramLabel = "files", description = "PDB and Diffraction input files.")
   private List<String> filenames;
   private DiffractionData diffractionData;
   private MolecularAssembly[] molecularAssemblies;
 
   /**
    * ModelvsData constructor.
    */
   public ModelvsData() {
     super();
   }
 
   /**
    * ModelvsData constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public ModelvsData(String[] args) {
     super(args);
   }
 
   /**
    * ModelvsData constructor.
    *
    * @param binding The Binding to use.
    */
   public ModelvsData(FFXBinding binding) {
     super(binding);
   }
 
   @Override
   public ModelvsData run() {
 
     if (!init()) {
       return this;
     }
 
     xrayOptions.init();
 
     String filename;
     if (filenames != null && !filenames.isEmpty()) {
       // Each alternate conformer is returned in a separate MolecularAssembly.
       molecularAssemblies = algorithmFunctions.openAll(filenames.get(0));
       activeAssembly = molecularAssemblies[0];
       filename = filenames.get(0);
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     } else {
       molecularAssemblies = new MolecularAssembly[]{activeAssembly};
       filename = activeAssembly.getFile().getAbsolutePath();
     }
 
     logger.info(format("\n Running xray.ModelvsData on %s", filename));
 
     // Apply active atom flags.
     for (MolecularAssembly molecularAssembly : molecularAssemblies) {
       atomSelectionOptions.setActiveAtoms(molecularAssembly);
     }
 
     // Combine script flags (in parseResult) with properties.
     CompositeConfiguration properties = activeAssembly.getProperties();
     xrayOptions.setProperties(parseResult, properties);
 
     // Set up diffraction data (can be multiple files)
     diffractionData = xrayOptions.getDiffractionData(filenames, molecularAssemblies, properties);
 
     boolean useHydrogen = properties.getBoolean("use-hydrogen", true);
     if (!useHydrogen) {
       Atom[] atoms = activeAssembly.getAtomArray();
       for (Atom atom : atoms) {
         if (atom.isHydrogen()) {
           atom.setOccupancy(0.0);
           // atom.setUse(false);
         }
       }
     }
 
     diffractionData.scaleBulkFit();
     diffractionData.printStats();
     algorithmFunctions.energy(molecularAssemblies);
 
     if (mtz) {
       diffractionData.writeData(removeExtension(filename) + "_ffx.mtz");
     }
 
     if (maps) {
       diffractionData.writeMaps(removeExtension(filename), normalize);
     }
 
     if (timings) {
       diffractionData.timings();
     }
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return getPotentialsFromAssemblies(molecularAssemblies);
   }
 
   @Override
   public boolean destroyPotentials() {
     return diffractionData == null ? true : diffractionData.destroy();
   }
 }