// ******************************************************************************
   //
   // 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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  // permission to link this library with independent modules to produce an
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  package ffx.algorithms.optimize.manybody;
  
  import ffx.algorithms.mc.MCMove;
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.potential.bonded.Residue;
  import java.util.ArrayList;
  import java.util.List;
  import java.util.Random;
  
  /** This implements single-rotamer changes in the framework of the rotamer energy matrices. */
  public class RotamerMatrixMove implements MCMove {
  
    private final boolean useAllElims;
    /**
     * CurrentRots should point to the same array as being used in the overlying MetropolisMC
     * implementation.
     */
    private final int[] currentRots;
  
    private final List<Integer> allowedRes;
    private final List<List<Integer>> allowedRots;
    private final int nAllowed;
    private final RotamerOptimization rotamerOptimization;
    private final boolean monteCarloTesting;
    /** When we take a step, we need to remember which rotamer of which residue was changed. */
    private int changedRes;
  
    private int changedRot;
  
    /**
     * Constructs the RotamerMatrixMove set; at present, a new object must be made if rotamers or
     * residues are changed outside the scope of this class.
     *
     * @param useAllElims Use eliminated pair/triple info.
     * @param rotamers Initial rotamer set.
     * @param residues Array of residues.
     * @param rotamerOptimization RotamerOptimization instance.
     * @param eliminatedRotamers Eliminated rotamers instance.
     * @param monteCarloTesting True for MC testing.
     */
    public RotamerMatrixMove(boolean useAllElims, int[] rotamers, Residue[] residues,
        RotamerOptimization rotamerOptimization, EliminatedRotamers eliminatedRotamers,
        boolean monteCarloTesting) {
      this.useAllElims = useAllElims;
      this.rotamerOptimization = rotamerOptimization;
      this.monteCarloTesting = monteCarloTesting;
  
      int nRes = rotamers.length;
      currentRots = rotamers;
  
      allowedRes = new ArrayList<>(nRes);
      allowedRots = new ArrayList<>(nRes);
  
      for (int i = 0; i < nRes; i++) {
        ArrayList<Integer> resAllowed = new ArrayList<>();
  
        int lenRi = residues[i].getRotamers().length;
        for (int ri = 0; ri < lenRi; ri++) {
          if (!eliminatedRotamers.check(i, ri)) {
            resAllowed.add(ri);
          }
        }
 
       if (resAllowed.size() > 1) {
         resAllowed.trimToSize();
         allowedRes.add(i);
         allowedRots.add(resAllowed);
       }
     }
 
     ((ArrayList<Integer>) allowedRes).trimToSize();
     nAllowed = allowedRes.size();
   }
 
   @Override
   public void move() {
     boolean validMove = !useAllElims;
     int indexI;
     int indexRI;
     do {
       // resI and rotI correspond to their positions in allowedRes and
       // allowedRots. indexI and indexRI correspond to their numbers
       // in the rotamer matrix.
 
       Random rand = new Random();
       if (monteCarloTesting) {
         rand.setSeed(nAllowed);
       }
       int resI = rand.nextInt(nAllowed);
       indexI = allowedRes.get(resI);
       List<Integer> allowedRotsI = allowedRots.get(resI);
       int lenRi = allowedRotsI.size();
       int rotI = rand.nextInt(lenRi);
       indexRI = allowedRotsI.get(rotI);
       if (useAllElims) {
         validMove = rotamerOptimization.checkValidMove(indexI, indexRI, currentRots);
       }
     } while (!validMove);
 
     changedRes = indexI;
     changedRot = currentRots[indexI];
 
     currentRots[indexI] = indexRI;
   }
 
   @Override
   public void revertMove() {
     currentRots[changedRes] = changedRot;
   }
 
   @Override
   public String toString() {
     return "Rotamer moves utilizing a rotamer energy matrix";
   }
 }