// ******************************************************************************
   //
   // 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.
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  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
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  // ******************************************************************************
  package ffx.algorithms.optimize.manybody;
  
  import static java.lang.System.arraycopy;
  
  import ffx.algorithms.mc.BoltzmannMC;
  import ffx.algorithms.optimize.RotamerOptimization;
  import ffx.potential.bonded.Residue;
  import java.util.Arrays;
  
  /** Monte Carlo driver for DEE-MC. */
  public class RotamerMatrixMC extends BoltzmannMC {
  
    private final int[] currentRots;
    private final int[] oldRots;
    private final int nRes;
    private final Residue[] residues;
    private final RotamerOptimization rotamerOptimization;
    private final boolean useFullAMOEBAEnergy;
  
    /**
     * The Rotamers array must be the same array as passed to any MCMove objects used (and not a
     * copy).
     *
     * @param rotamers Array of rotamers.
     * @param residues Array of residues.
     * @param useFullAMOEBAEnergy If true, re-evaluate AMOEBA energy for each conformation.
     * @param rotamerOptimization RotamerOptimization instance.
     */
    public RotamerMatrixMC(int[] rotamers, Residue[] residues, boolean useFullAMOEBAEnergy,
        RotamerOptimization rotamerOptimization) {
      currentRots = rotamers; // This is intentional.
      nRes = rotamers.length;
      oldRots = new int[nRes];
      arraycopy(rotamers, 0, oldRots, 0, nRes);
      this.residues = residues;
      this.useFullAMOEBAEnergy = useFullAMOEBAEnergy;
      this.rotamerOptimization = rotamerOptimization;
    }
  
    @Override
    public void revertStep() {
      arraycopy(oldRots, 0, currentRots, 0, nRes);
    }
  
    /**
     * If useFullAMOEBAEnergy is set to true, explicitly evaluates energy, else computes energy from
     * the rotamer energy matrices.
     *
     * @return Energy at the current state
     */
    @Override
    protected double currentEnergy() {
      try {
        try {
          return useFullAMOEBAEnergy ? rotamerOptimization.currentEnergyWrapper(
              Arrays.asList(residues))
              : rotamerOptimization.computeEnergy(residues, currentRots, false);
        } catch (ArithmeticException ex) {
          return 1E100;
        }
      } catch (NullPointerException ex) {
        // If using the rotamer energy matrix, and there is some missing
       // energy term, just return a default, very large energy.
       return 1e100;
     }
   }
 
   @Override
   protected void storeState() {
     arraycopy(currentRots, 0, oldRots, 0, nRes);
   }
 }