//******************************************************************************
   //
   // 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,
  // 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.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Residue;
  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.Parameters;
  
  import java.util.List;
  
  import static org.apache.commons.io.FilenameUtils.removeExtension;
  
  /**
   * The SaveConformerPDB script saves alternate conformers with proper alt loc labels.
   * <br>
   * Usage:
   * <br>
   * ffxc xray.SaveConformerPDB [options] &lt;filename&gt;
   */
  @Command(description = " Discrete optimization using a many-body expansion and elimination expressions.", name = "xray.SaveConformerPDB")
  public class SaveConformerPDB extends AlgorithmsCommand {
  
    @Mixin
    private XrayOptions xrayOptions;
  
    /**
     * One or more filenames.
     */
    @Parameters(arity = "1..*", paramLabel = "files", description = "PDB and Real Space input files.")
    private List<String> filenames;
    private MolecularAssembly[] molecularAssemblies;
    private DiffractionData diffractionData;
  
    /**
     * SaveConformerPDB constructor.
     */
    public SaveConformerPDB() {
      super();
    }
  
    /**
     * SaveConformerPDB constructor that sets the command line arguments.
     * @param args Command line arguments.
     */
    public SaveConformerPDB(String[] args) {
      super(args);
    }
  
    /**
     * SaveConformerPDB constructor.
     * @param binding The Binding to use.
     */
    public SaveConformerPDB(FFXBinding binding) {
      super(binding);
    }
  
   @Override
   public SaveConformerPDB 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();
     }
 
     if (molecularAssemblies.length == 1) {
       logger.info("No alternate conformers");
       return this;
     }
 
     // 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);
     diffractionData.scaleBulkFit();
     diffractionData.printStats();
     algorithmFunctions.energy(molecularAssemblies);
 
     List<Residue> residuesA = molecularAssemblies[0].getResidueList();
     List<Residue> residuesB = molecularAssemblies[1].getResidueList();
 
     for (int j = 0; j < residuesA.size(); j++) {
       List<Atom> atomsA = residuesA.get(j).getAtomList();
       List<Atom> atomsB = residuesB.get(j).getAtomList();
       for (int i = 0; i < atomsA.size(); i++) {
         Atom atomA = atomsA.get(i);
         Atom atomB = atomsB.get(i);
 
         if (atomA.getAltLoc() == null || atomA.getAltLoc() == ' ') {
           atomA.setAltLoc('A');
         }
         if (atomB.getAltLoc() == null || atomB.getAltLoc() == ' ') {
           atomB.setAltLoc('B');
         }
       }
     }
 
     logger.info(" ");
     diffractionData.writeModel(removeExtension(filename) + ".pdb");
     diffractionData.writeData(removeExtension(filename) + ".mtz");
 
     return this;
   }
 }