//******************************************************************************
   //
   // 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.
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  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
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  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
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  // 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
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  //******************************************************************************
  package ffx.algorithms.commands.test;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.ManyBodyOptions;
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.RotamerLibrary;
  import ffx.utilities.FFXBinding;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Parameters;
  
  import java.util.List;
  
  import static ffx.potential.bonded.NamingUtils.renameAtomsToPDBStandard;
  
  /**
   * The IdentifyRotamers script attempts to identify which rotamer each Residue in the system is in.
   * <br>
   * Usage:
   * <br>
   * ffxc test.IdentifyRotamers [options] &lt;filename&gt;
   */
  @Command(description = " Identify the rotamers a system is in.", name = "test.IdentifyRotamers")
  public class IdentifyRotamers extends AlgorithmsCommand {
  
    @Mixin
    private ManyBodyOptions mbOpts;
  
    /**
     * The final argument(s) should be one or more filenames.
     */
    @Parameters(arity = "1", paramLabel = "files",
        description = "The atomic coordinate file in PDB or XYZ format.")
    private List<String> filenames;
  
    /**
     * IdentifyRotamers Constructor.
     */
    public IdentifyRotamers() {
      super();
    }
  
    /**
     * IdentifyRotamers Constructor.
     * @param binding The Binding to use.
     */
    public IdentifyRotamers(FFXBinding binding) {
      super(binding);
    }
  
    /**
     * IdentifyRotamers constructor that sets the command line arguments.
     * @param args Command line arguments.
     */
    public IdentifyRotamers(String[] args) {
      super(args);
    }
  
    /**
     * {@inheritDoc}
    */
   @Override
   public IdentifyRotamers run() {
 
     if (!init()) {
       return this;
     }
 
     mbOpts.setOriginalCoordinates(false);
 
     if (filenames != null && !filenames.isEmpty()) {
       MolecularAssembly[] assemblies = new MolecularAssembly[]{algorithmFunctions.open(filenames.get(0))};
       activeAssembly = assemblies[0];
       if (Boolean.parseBoolean(System.getProperty("standardizeAtomNames", "false"))) {
         renameAtomsToPDBStandard(activeAssembly);
       }
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     activeAssembly.getPotentialEnergy().setPrintOnFailure(false, false);
 
     RotamerOptimization rotopt = new RotamerOptimization(
         activeAssembly, activeAssembly.getPotentialEnergy(), algorithmListener);
     mbOpts.initRotamerOptimization(rotopt, activeAssembly);
 
     List<Residue> residues = rotopt.getResidues();
     RotamerLibrary rLib = mbOpts.getRotamerLibrary(false);
 
     for (Residue residue : residues) {
       RotamerLibrary.RotamerGuess guess = rLib.guessRotamer(residue);
       logger.info(guess.toString());
     }
 
     return this;
   }
 }