// ******************************************************************************
   //
   // 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
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  // 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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  // combined work based on this library. Thus, the terms and conditions of the
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  package ffx.algorithms.optimize.manybody;
  
  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 ffx.potential.nonbonded.NeighborList;
  import ffx.utilities.StringOutputStream;
  
  import java.util.*;
  
  import static ffx.crystal.SymOp.applyFracSymOp;
  import static ffx.potential.bonded.RotamerLibrary.applyRotamer;
  import static java.lang.String.format;
  import static java.lang.System.arraycopy;
  
  /**
   * A cell used for optimization of a subdomain, its residues, its extent in fractional coordinates,
   * its overall (linear) index, and its indices along the a, b, and c axes.
   */
  public class ManyBodyCell {
  
    /**
     * Cell extent in fractional coordinates.
     * fracCoords[0-2] contains min a, b and c
     * fracCoords[3-5] contains max a, b and c
     */
    private final double[] fracCoords = new double[6];
    /**
     * The a, b, and c indices of this cell.
     */
    private final int[] indices = new int[3];
    /**
     * The index of this cell.
     */
    private final int cellIndex;
    /**
     * The Residues contained within this cell.
     */
    private final ArrayList<Residue> residues = new ArrayList<>();
  
    /**
     * Constructs a ManyBodyCell instance, 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 Extent in fractional coordinates (0-2 are min a,b,c and 3-5 are max).
     * @param indices               Index of the cell along a, b, and c axes.
     * @param cellIndex             Index of the cell in linear array.
     */
    public ManyBodyCell(double[] fractionalCoordinates, int[] indices, int cellIndex) {
      arraycopy(fractionalCoordinates, 0, fracCoords, 0, fracCoords.length);
      arraycopy(indices, 0, this.indices, 0, this.indices.length);
      this.cellIndex = cellIndex;
    }
  
    /**
     * Returns a string representation of this BoxOptCell.
     *
     * @return String representation.
    */
   public String toString() {
     StringBuilder sb = new StringBuilder();
     sb.append(format(" Optimization Cell %2d (%2d, %2d, %2d)\n", cellIndex + 1, indices[0] + 1, indices[1] + 1, indices[2] + 1));
     int n = residues.size();
     if (n == 0) {
       sb.append("  Cell is Empty\n");
     } else if (n == 1) {
       sb.append(format("  Single Residue: %s\n", residues.getFirst()));
     } else {
       Residue firstResidue = residues.getFirst();
       Residue lastResidue = residues.getLast();
       sb.append(format("  %d Residues: %s ... %s\n", n, firstResidue.toString(), lastResidue.toString()));
     }
     sb.append("  Fractional Coordinates:\n");
     sb.append(format("   A-axis %5.3f to %5.3f\n", fracCoords[0], fracCoords[3]));
     sb.append(format("   B-axis %5.3f to %5.3f\n", fracCoords[1], fracCoords[4]));
     sb.append(format("   C-axis %5.3f to %5.3f", fracCoords[2], fracCoords[5]));
     return sb.toString();
   }
 
   /**
    * 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);
     applyFracSymOp(atXYZ, atXYZ, symOp);
     moveValuesBetweenZeroAndOne(atXYZ);
     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 within unit cell boundaries.
    *
    * @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 getCellIndex() {
     return cellIndex;
   }
 
   /**
    * 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 a, b, and c axis indices of this cell.
    *
    * @return Cell indices.
    */
   public int[] getABCIndices() {
     int[] returnedIndices = new int[3];
     arraycopy(indices, 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 sortCellResidues() {
     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 (atomFracCoords[i] < fracCoords[i] || atomFracCoords[i] > fracCoords[i + 3]) {
         // fracCoords[0-2] contain min a, b, and c-axes.
         // fracCoords[3-5] contain max a, b, and c-axes.
         return false;
       }
     }
     return true;
   }
 }