// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2023.
   //
   // 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
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.algorithms.mc;
  
  import static java.lang.System.arraycopy;
  
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.ResidueState;
  import org.apache.commons.math3.distribution.NormalDistribution;
  
  /**
   * The CoordShakeMove class implements a simplistic atomic coordinate shake. At present, simply adds
   * a random number from a normal distribution to each Cartesian coordinate; in the future, will use
   * a move in polar coordinates.
   *
   * @author Michael J. Schnieders
   * @author Jacob M. Litman
   * @since 1.0
   */
  public class CoordShakeMove implements MCMove {
  
    private Atom[] atoms;
    private double[][] originalCoords;
    private double sigma = 0.001;
    private NormalDistribution dist;
  
    /**
     * Constructor for CoordShakeMove.
     *
     * @param assembly a {@link ffx.potential.MolecularAssembly} object.
     */
    public CoordShakeMove(MolecularAssembly assembly) {
      this(assembly.getAtomArray());
    }
  
    /**
     * Constructor for CoordShakeMove.
     *
     * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
     */
    public CoordShakeMove(Atom[] atoms) {
      int nAtoms = atoms.length;
      this.atoms = new Atom[nAtoms];
      arraycopy(atoms, 0, this.atoms, 0, nAtoms);
      originalCoords = ResidueState.storeAtomicCoordinates(this.atoms);
      dist = new NormalDistribution(0, sigma);
    }
  
    /** {@inheritDoc} */
    @Override
    public void move() {
      originalCoords = ResidueState.storeAtomicCoordinates(atoms);
      // Perform the shake.
      for (Atom atom : atoms) {
        double[] xyz = new double[3];
        atom.getXYZ(xyz);
        for (int j = 0; j < 3; j++) {
          xyz[j] += dist.sample();
        }
        atom.setXYZ(xyz);
      }
    }
  
   /** {@inheritDoc} */
   @Override
   public void revertMove() {
     ResidueState.revertAtomicCoordinates(atoms, originalCoords);
   }
 
   /**
    * Setter for the field <code>atoms</code>.
    *
    * @param atoms an array of {@link ffx.potential.bonded.Atom} objects.
    */
   public void setAtoms(Atom[] atoms) {
     int nAtoms = atoms.length;
     this.atoms = new Atom[nAtoms];
     arraycopy(atoms, 0, this.atoms, 0, nAtoms);
     originalCoords = ResidueState.storeAtomicCoordinates(atoms);
   }
 
   /**
    * Setter for the field <code>sigma</code>.
    *
    * @param sigma a double.
    */
   public void setSigma(double sigma) {
     this.sigma = sigma;
     dist = new NormalDistribution(0, sigma);
   }
 
   /** {@inheritDoc} */
   @Override
   public String toString() {
     return String.format(
         " Coordinate randomization: normal distribution with sigma %10.6f.", sigma);
   }
 }