// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // 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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  package ffx.algorithms.optimize.manybody;
  
  import static ffx.crystal.SymOp.applyFracSymOp;
  import static ffx.potential.bonded.RotamerLibrary.applyRotamer;
  
  import ffx.crystal.Crystal;
  import ffx.crystal.SymOp;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.ResidueState;
  import ffx.potential.bonded.Rotamer;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Comparator;
  import java.util.List;
  
  /**
   * Contains a cell used for box optimization, its residues, the fractional coordinates within a
   * crystal it takes up, its overall (linear) index, and its indices along the a, b, and c crystal
   * axes.
   */
  public class BoxOptCell {
  
    // fracCoords indexed by 1-3 min x,y,z, 4-6 are max x,y,z
    private final double[] fracCoords = new double[6];
    private final int[] indexXYZ = new int[3];
    private final int linearIndex;
    private final ArrayList<Residue> residues = new ArrayList<>();
  
    /**
     * Constructs a BoxOptCell object, which takes up a set of fractional coordinates within the
     * Crystal, the Residues contained within, and the index of the cell along the crystal's a, b, and
     * c axes.
     *
     * @param fractionalCoordinates Fractional coordinates contained, indexed by 1-3 min x,y,z, 4-6
     *     max x,y,z
     * @param indices Index of cell along a, b, and c (x, y, and z).
     * @param linearIndex Index of box in linear box array.
     */
    public BoxOptCell(double[] fractionalCoordinates, int[] indices, int linearIndex) {
      System.arraycopy(fractionalCoordinates, 0, fracCoords, 0, fracCoords.length);
      System.arraycopy(indices, 0, indexXYZ, 0, indexXYZ.length);
      this.linearIndex = linearIndex;
    }
  
    /**
     * Add a residue to the box.
     *
     * @param residue Residue to be added.
     */
    public void addResidue(Residue residue) {
      residues.add(residue);
    }
  
    /**
     * Checks if any rotamer of a Residue is inside this BoxOptCell.
     *
     * @param residue Residue to check.
     * @param crystal A Crystal.
     * @param symOp A symmetry operator to apply.
     * @param variableOnly If using only variable (protein side-chain, nucleic acid backbone)
     *     atoms.
    * @return If contained inside this BoxOptCell.
    */
   public boolean anyRotamerInsideCell(Residue residue, Crystal crystal, SymOp symOp,
       boolean variableOnly) {
     ResidueState incomingState = residue.storeState();
     Rotamer[] rotamers = residue.getRotamers();
     boolean inside = Arrays.stream(rotamers).anyMatch((Rotamer r) -> {
       applyRotamer(residue, r);
       return residueInsideCell(residue, crystal, symOp, variableOnly);
     });
     residue.revertState(incomingState);
     return inside;
   }
 
   /**
    * Checks if an Atom would be contained inside this cell.
    *
    * @param atom Atom to check.
    * @param crystal A Crystal.
    * @param symOp A symmetry operator to apply.
    * @return If contained.
    */
   public boolean atomInsideCell(Atom atom, Crystal crystal, SymOp symOp) {
     double[] atXYZ = new double[3];
     atXYZ = atom.getXYZ(atXYZ);
     crystal.toFractionalCoordinates(atXYZ, atXYZ);
     moveValuesBetweenZeroAndOne(atXYZ);
     applyFracSymOp(atXYZ, atXYZ, symOp);
     return checkIfContained(atXYZ);
   }
 
   /**
    * Moves an array of doubles to be within 0.0 and 1.0 by addition or subtraction of a multiple of
    * 1.0. Typical use is moving an atom placed outside crystal boundaries from the symmetry mate back
    * into the crystal.
    *
    * @param valuesToMove Doubles to be moved between 0 and 1.
    */
   public static void moveValuesBetweenZeroAndOne(double[] valuesToMove) {
     for (int i = 0; i < valuesToMove.length; i++) {
       valuesToMove[i] = moveBetweenZeroAndOne(valuesToMove[i]);
     }
   }
 
   /**
    * Moves a double to be within 0.0 and 1.0 by addition or subtraction of a multiple of 1.0. Typical
    * use is moving an atom place outside crystal boundaries from the symmetry mate back into the
    * crystal.
    *
    * @param value Double to be moved between 0 and 1.
    * @return Shifted double.
    */
   private static double moveBetweenZeroAndOne(double value) {
     if (value < 0.0) {
       int belowZero = (int) (value);
       belowZero = 1 + (-1 * belowZero);
       value = value + belowZero;
     } else {
       value = value % 1.0;
     }
     return value;
   }
 
   /**
    * Returns the linear index of this Box.
    *
    * @return Linear index.
    */
   public int getLinearIndex() {
     return linearIndex;
   }
 
   /**
    * Returns an array of the Residues contained within the cell.
    *
    * @return Array of Residues.
    */
   public Residue[] getResidues() {
     return (Residue[]) residues.toArray();
   }
 
   /**
    * Returns a copy of the ArrayList of residues.
    *
    * @return ArrayList of Residues in the cell.
    */
   public ArrayList<Residue> getResiduesAsList() {
     return new ArrayList<>(residues);
   }
 
   /**
    * Returns the x, y, and z indices of this box.
    *
    * @return Box indices.
    */
   public int[] getXYZIndex() {
     int[] returnedIndices = new int[3];
     System.arraycopy(indexXYZ, 0, returnedIndices, 0, returnedIndices.length);
     return returnedIndices;
   }
 
   /**
    * Checks if a Residue is inside this BoxOptCell.
    *
    * @param residue Residue to check.
    * @param crystal A Crystal.
    * @param symOp A symmetry operator to apply.
    * @param variableOnly If using only variable (protein side-chain, nucleic acid backbone)
    *     atoms.
    * @return If contained inside this BoxOptCell.
    */
   public boolean residueInsideCell(Residue residue, Crystal crystal, SymOp symOp,
       boolean variableOnly) {
     List<Atom> atoms = variableOnly ? residue.getVariableAtoms() : residue.getAtomList();
     return atoms.stream().anyMatch(a -> atomInsideCell(a, crystal, symOp));
   }
 
   /** Sorts residues in the box. */
   public void sortBoxResidues() {
     Comparator<Residue> comparator = Comparator.comparing(Residue::getChainID)
         .thenComparingInt(Residue::getResidueNumber);
     residues.sort(comparator);
   }
 
   /**
    * Check if an atom's fractional coordinates would be contained by the box.
    *
    * @param atomFracCoords Atomic fractional coordinates
    * @return If contained.
    */
   private boolean checkIfContained(double[] atomFracCoords) {
     for (int i = 0; i < 3; i++) {
       if ((fracCoords[i] > atomFracCoords[i]) || (fracCoords[i + 3] < atomFracCoords[i])) {
         return false;
       }
     }
     return true;
   }
 }