//******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2026.
   //
   // 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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  // library, you may extend this exception to your version of the library, but
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  //******************************************************************************
  package ffx.algorithms.commands;
  
  import edu.rit.pj.Comm;
  import ffx.algorithms.cli.AlgorithmsCommand;
  import ffx.algorithms.cli.ManyBodyOptions;
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.algorithms.optimize.TitrationManyBody;
  import ffx.numerics.Potential;
  import ffx.potential.ForceFieldEnergy;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.LambdaInterface;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.RotamerLibrary;
  import ffx.potential.cli.AlchemicalOptions;
  import ffx.potential.parsers.PDBFilter;
  import ffx.utilities.FFXBinding;
  import org.apache.commons.configuration2.CompositeConfiguration;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Mixin;
  import picocli.CommandLine.Parameters;
  
  import java.io.File;
  import java.util.ArrayList;
  import java.util.Collections;
  import java.util.HashSet;
  import java.util.List;
  import java.util.Set;
  
  import static ffx.potential.bonded.NamingUtils.renameAtomsToPDBStandard;
  import static java.lang.String.format;
  
  /**
   * The ManyBody script performs a discrete optimization using a many-body expansion and elimination expressions.
   * <br>
   * Usage:
   * <br>
   * ffxc ManyBody [options] &lt;filename&gt;
   */
  @Command(description = " Run ManyBody algorithm on a system.", name = "ManyBody")
  public class ManyBody extends AlgorithmsCommand {
  
    @Mixin
    private ManyBodyOptions manyBodyOptions;
  
    @Mixin
    private AlchemicalOptions alchemicalOptions;
  
    /**
     * An XYZ or PDB input file.
     */
    @Parameters(arity = "1", paramLabel = "file",
        description = "XYZ or PDB input file.")
    private String filename;
  
    private ForceFieldEnergy potentialEnergy;
    private TitrationManyBody titrationManyBody;
  
    /**
     * ManyBody Constructor.
     */
    public ManyBody() {
     super();
   }
 
   /**
    * ManyBody Constructor.
    * @param binding The Binding to use.
    */
   public ManyBody(FFXBinding binding) {
     super(binding);
   }
 
   /**
    * ManyBody constructor that sets the command line arguments.
    * @param args Command line arguments.
    */
   public ManyBody(String[] args) {
     super(args);
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public ManyBody run() {
 
     if (!init()) {
       return this;
     }
 
     // Atomic clashes are expected and will be handled using direct induced dipoles.
     System.setProperty("sor-scf-fallback", "false");
     System.setProperty("direct-scf-fallback", "true");
 
     // This flag is for ForceFieldEnergyOpenMM and must be set before reading files.
     // It enforces that all torsions include a Fourier series with 6 terms.
     // Otherwise, during titration the number of terms for each torsion can change and
     // cause updateParametersInContext to throw an exception.
     double titrationPH = manyBodyOptions.getTitrationPH();
 
     if (manyBodyOptions.getTitration()) {
       System.setProperty("manybody-titration", "true");
     }
 
     // Turn on computation of lambda derivatives if softcore atoms exist.
     boolean lambdaTerm = alchemicalOptions.hasSoftcore();
     if (lambdaTerm) {
       // Turn on softcore van der Waals
       System.setProperty("lambdaterm", "true");
       // Turn off alchemical electrostatics
       System.setProperty("elec-lambdaterm", "false");
       // Turn on intra-molecular softcore
       System.setProperty("intramolecular-softcore", "true");
     }
 
     // Load the MolecularAssembly.
     activeAssembly = getActiveAssembly(filename);
 
     if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     String listResidues = "";
     if (manyBodyOptions.getOnlyTitration() ||
         manyBodyOptions.getInterestedResidue() != -1 && manyBodyOptions.getInclusionCutoff() != -1) {
       listResidues = manyBodyOptions.selectInclusionResidues(activeAssembly.getResidueList(),
           manyBodyOptions.getInterestedResidue(), manyBodyOptions.getOnlyTitration(), manyBodyOptions.getInclusionCutoff());
       manyBodyOptions.setListResidues(listResidues);
     }
 
     CompositeConfiguration properties = activeAssembly.getProperties();
 
     // Application of rotamers uses side-chain atom naming from the PDB.
     if (properties.getBoolean("standardizeAtomNames", false)) {
       renameAtomsToPDBStandard(activeAssembly);
     }
 
     activeAssembly.getPotentialEnergy().setPrintOnFailure(false, false);
     potentialEnergy = activeAssembly.getPotentialEnergy();
 
     // Collect residues to optimize.
     List<Residue> residues = manyBodyOptions.collectResidues(activeAssembly);
     if (residues == null || residues.isEmpty()) {
       logger.info(" There are no residues in the active system to optimize.");
       return this;
     }
 
     // Handle rotamer optimization with titration.
     if (manyBodyOptions.getTitration()) {
       logger.info("\n Adding titration hydrogen to : " + filename + "\n");
 
       // Collect residue numbers.
       List<Integer> resNumberList = new ArrayList<>();
       for (Residue residue : residues) {
         resNumberList.add(residue.getResidueNumber());
       }
 
       // Create new MolecularAssembly with additional protons and update the ForceFieldEnergy
       titrationManyBody = new TitrationManyBody(filename, activeAssembly.getForceField(),
           resNumberList, titrationPH, manyBodyOptions);
       activeAssembly = titrationManyBody.getProtonatedAssembly();
       potentialEnergy = activeAssembly.getPotentialEnergy();
     }
 
     if (lambdaTerm) {
       alchemicalOptions.setFirstSystemAlchemistry(activeAssembly);
       LambdaInterface lambdaInterface = potentialEnergy;
       double lambda = alchemicalOptions.getInitialLambda();
       logger.info(format(" Setting ManyBody softcore lambda to: %5.3f", lambda));
       lambdaInterface.setLambda(lambda);
     }
 
     RotamerOptimization rotamerOptimization = new RotamerOptimization(activeAssembly,
         potentialEnergy, algorithmListener);
     rotamerOptimization.setPHRestraint(manyBodyOptions.getPHRestraint());
     rotamerOptimization.setpH(titrationPH);
 
     manyBodyOptions.initRotamerOptimization(rotamerOptimization, activeAssembly);
     List<Residue> residueList = rotamerOptimization.getResidues();
 
     logger.info("\n Initial Potential Energy:");
     potentialEnergy.energy(false, true);
 
     logger.info("\n Initial Rotamer Torsion Angles:");
     RotamerLibrary.measureRotamers(residueList, false);
 
     // Run the optimization.
     rotamerOptimization.optimize(manyBodyOptions.getAlgorithm(residueList.size()));
 
     boolean isTitrating = false;
     Set<Atom> excludeAtoms = new HashSet<>();
     int[] optimalRotamers = rotamerOptimization.getOptimumRotamers();
     if (manyBodyOptions.getTitration()) {
       isTitrating = titrationManyBody.excludeExcessAtoms(excludeAtoms, optimalRotamers, residueList);
     }
 
     // Log the final result on rank 0.
     int rank = Comm.world().rank();
     if (rank == 0) {
       logger.info(" Final Minimum Energy");
       double energy = potentialEnergy.energy(false, true);
       if (isTitrating) {
         double phBias = rotamerOptimization.getEnergyExpansion().getTotalRotamerPhBias(residueList,
             optimalRotamers, titrationPH, manyBodyOptions.getPHRestraint());
         logger.info(format("\n  Rotamer pH Bias    %16.8f", phBias));
         logger.info(format("  Potential with Bias%16.8f\n", phBias + energy));
       }
 
       // Prevent residues from being renamed based on the existence of hydrogen
       // atoms (i.e. hydrogen that are excluded from being written out).
       properties.setProperty("standardizeAtomNames", "false");
       File modelFile = saveDirFile(activeAssembly.getFile());
       PDBFilter pdbFilter = new PDBFilter(modelFile, activeAssembly, activeAssembly.getForceField(),
           properties);
       if (manyBodyOptions.getTitration()) {
         String remark = format("Titration pH: %6.3f", titrationPH);
         if (!pdbFilter.writeFile(modelFile, false, excludeAtoms, true, true, new String[]{remark})) {
           logger.info(format(" Save failed for %s", activeAssembly));
         }
       } else {
         if (!pdbFilter.writeFile(modelFile, false, excludeAtoms, true, true)) {
           logger.info(format(" Save failed for %s", activeAssembly));
         }
       }
     }
 
     if (manyBodyOptions.getTitration()) {
       System.clearProperty("manybody-titration");
     }
 
     return this;
   }
 
   /**
    * Get ManyBodyOptions to access script parameters.
    */
   public ManyBodyOptions getManyBodyOptions() {
     return manyBodyOptions;
   }
 
   /**
    * Returns the potential energy of the active assembly. Used during testing assertions.
    * @return potentialEnergy Potential energy of the active assembly.
    */
   public ForceFieldEnergy getPotential() {
     return potentialEnergy;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public List<Potential> getPotentials() {
     List<Potential> potentials;
     if (potentialEnergy == null) {
       potentials = Collections.emptyList();
     } else {
       potentials = Collections.singletonList(potentialEnergy);
     }
     return potentials;
   }
 
 }