//******************************************************************************
   //
   // 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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  // combined work based on this library. Thus, the terms and conditions of the
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  // permission to link this library with independent modules to produce an
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  //******************************************************************************
  package ffx.xray.commands;
  
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.MinimizeOptions;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.cli.AtomSelectionOptions;
  import ffx.potential.cli.PotentialCommand;
  import ffx.utilities.FFXBinding;
  import ffx.xray.DiffractionData;
  import ffx.xray.RefinementMinimize;
  import ffx.xray.cli.XrayOptions;
  import ffx.xray.refine.RefinementMode;
  import ffx.xray.refine.RefinementModel;
  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 Minimize script.
   * <br>
   * Usage:
   * <br>
   * ffxc xray.Minimize [options] &lt;filename [file2...]&gt;
   */
  @Command(description = " Refine an X-ray/Neutron target.", name = "xray.Minimize")
  public class Minimize extends AlgorithmsCommand {
  
    @Mixin
    private XrayOptions xrayOptions;
  
    @Mixin
    AtomSelectionOptions atomSelectionOptions;
  
    @Mixin
    private MinimizeOptions minimizeOptions;
  
    /**
     * -t or --threeStage Perform refinement in 3 stages: coordinates, b-factors, and then occupancies (overrides mode setting if true).
     */
    @Option(names = {"-t", "--threeStage"}, paramLabel = "false",
        description = "Perform refinement in 3 stages: coordinates, b-factors, and then occupancies (overrides mode setting if true)")
    private boolean threeStage = false;
  
    /**
     * -E or --eps3 RMS gradient convergence criteria for three stage refinement (default of -1.0 automatically determine eps for each stage).
     */
    @Option(names = {"-E", "--eps3"}, paramLabel = "-1.0", arity = "3",
        description = "RMS gradient convergence criteria for three stage refinement (default of -1.0 automatically determines eps for each stage).")
    private double[] eps3 = {-1.0, -1.0, -1.0};
  
    /**
    * -c or --cycles Number of refinement cycles.
    */
   @Option(names = {"-c", "--cycles"}, paramLabel = "1", defaultValue = "1",
       description = "Number of refinement cycles.")
   private int ncycles = 1;
 
   /**
    * --mtz Write out MTZ containing structure factor coefficients.
    */
   @Option(names = {"--mtz"}, paramLabel = "false",
       description = "Write out an 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 MolecularAssembly[] molecularAssemblies;
   private DiffractionData diffractionData;
 
   /**
    * Minimize constructor.
    */
   public Minimize() {
     super();
   }
 
   /**
    * Minimize constructor that sets the command line arguments.
    *
    * @param args Command line arguments.
    */
   public Minimize(String[] args) {
     super(args);
   }
 
   /**
    * Minimize constructor.
    *
    * @param binding The Binding to use.
    */
   public Minimize(FFXBinding binding) {
     super(binding);
   }
 
   @Override
   public Minimize 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.getFirst());
       activeAssembly = molecularAssemblies[0];
     } else if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     } else {
       molecularAssemblies = new MolecularAssembly[]{activeAssembly};
     }
 
     // Update the active filename
     filename = activeAssembly.getFile().getAbsolutePath();
 
     // Apply active atom flags.
     for (MolecularAssembly molecularAssembly : molecularAssemblies) {
       atomSelectionOptions.setActiveAtoms(molecularAssembly);
     }
 
     logger.info("\n Running xray.Minimize on " + filename);
 
     // 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);
 
     // Log the energy of each MolecularAssembly
     algorithmFunctions.energy(molecularAssemblies);
 
     // RMS gradient convergence criteria for three stage refinement
     double coordinateEPS = eps3[0];
     double bfactorEPS = eps3[1];
     double occupancyEPS = eps3[2];
 
     // The number of corrections used in the BFGS update.
     int nBFGS = minimizeOptions.getNBFGS();
 
     // Maximum number of refinement cycles.
     int maxIterations = minimizeOptions.getIterations();
 
     for (int cycle = 0; cycle < ncycles; cycle++) {
       if (ncycles > 1) {
         logger.info(format("\n Refinement Cycle: %d\n", cycle + 1));
       }
       diffractionData.scaleBulkFit();
       diffractionData.printStats();
 
       if (threeStage) {
         // Coordinates
         RefinementModel refinementModel = diffractionData.getRefinementModel();
         RefinementMode refinementMode = RefinementMode.COORDINATES;
         refinementModel.setRefinementMode(refinementMode);
         if (refinementModel.getNumCoordParameters() > 0) {
           RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData);
           if (coordinateEPS < 0.0) {
             coordinateEPS = refinementMode.getDefaultEps();
           }
           if (maxIterations < Integer.MAX_VALUE) {
             logger.info(format("\n RMS gradient convergence criteria: %8.5f, Maximum iterations %d",
                 coordinateEPS, maxIterations));
           } else {
             logger.info(format("\n RMS gradient convergence criteria: %8.5f", coordinateEPS));
           }
           refinementMinimize.minimize(nBFGS, coordinateEPS, maxIterations);
           algorithmFunctions.energy(molecularAssemblies);
         }
 
         // B-factors
         refinementMode = RefinementMode.BFACTORS;
         refinementModel.setRefinementMode(refinementMode);
         if (refinementModel.getNumBFactorParameters() > 0) {
           RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData);
           if (bfactorEPS < 0.0) {
             boolean hasAnisous = refinementModel.getNumANISOU() > 0;
             bfactorEPS = refinementMode.getDefaultEps(hasAnisous);
           }
           if (maxIterations < Integer.MAX_VALUE) {
             logger.info(format("\n RMS gradient convergence criteria: %8.5f, Maximum iterations %d",
                 bfactorEPS, maxIterations));
           } else {
             logger.info(format("\n RMS gradient convergence criteria: %8.5f", bfactorEPS));
           }
           refinementMinimize.minimize(nBFGS, bfactorEPS, maxIterations);
         }
 
         // Occupancies
         refinementMode = RefinementMode.OCCUPANCIES;
         refinementModel.setRefinementMode(refinementMode);
         if (refinementModel.getNumOccupancyParameters() > 0) {
           RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData);
           if (occupancyEPS < 0.0) {
             occupancyEPS = refinementMode.getDefaultEps();
           }
           if (maxIterations < Integer.MAX_VALUE) {
             logger.info(format("\n RMS gradient convergence criteria: %8.5f, Maximum iterations %d",
                 occupancyEPS, maxIterations));
           } else {
             logger.info(format("\n RMS gradient convergence criteria: %8.5f", occupancyEPS));
           }
           refinementMinimize.minimize(occupancyEPS, maxIterations);
         } else {
           logger.info("Occupancy refinement not necessary, skipping");
         }
       } else {
         RefinementMinimize refinementMinimize = new RefinementMinimize(diffractionData);
         RefinementModel refinementModel = diffractionData.getRefinementModel();
         RefinementMode refinementMode = refinementModel.getRefinementMode();
         double eps = minimizeOptions.getEps();
         if (eps < 0.0) {
           boolean hasAnisous = refinementModel.getNumANISOU() > 0;
           eps = refinementMode.getDefaultEps(hasAnisous);
         }
         if (maxIterations < Integer.MAX_VALUE) {
           logger.info(format("\n RMS gradient convergence criteria: %8.5f, Maximum iterations %d", eps,
               maxIterations));
         } else {
           logger.info(format("\n RMS gradient convergence criteria: %8.5f", eps));
         }
         refinementMinimize.minimize(eps, maxIterations);
       }
     }
 
     diffractionData.scaleBulkFit();
     diffractionData.printStats();
 
     // Print the final energy of each conformer.
     algorithmFunctions.energy(molecularAssemblies);
 
     logger.info(" ");
     diffractionData.writeModel(removeExtension(filename) + ".pdb");
     if (mtz) {
       diffractionData.writeData(removeExtension(filename) + ".mtz");
     }
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return getPotentialsFromAssemblies(molecularAssemblies);
   }
 
   @Override
   public boolean destroyPotentials() {
     return diffractionData == null ? true : diffractionData.destroy();
   }
 }