// ******************************************************************************
   //
   // 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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  package ffx.crystal;
  
  import static java.lang.String.format;
  
  import java.util.List;
  import java.util.Objects;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  import org.apache.commons.math3.linear.MatrixUtils;
  import org.apache.commons.math3.linear.RealMatrix;
  
  /**
   * The NCSCrystal class extends Crystal to support non-crystallographic symmetry (NCS). The NCS
   * operators can be obtained from the BIOMT records of a PDB file, and are permuted with the space
   * group symmetry operators.
   *
   * @author Aaron J. Nessler
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class NCSCrystal extends Crystal {
  
    /** The logger. */
    private static final Logger logger = Logger.getLogger(NCSCrystal.class.getName());
    /** The base unit cell for the system being simulated. */
    private final Crystal unitCell;
    /** The non-crystallographic symmetry operators needed to be applied to the unit cell. */
    private final List<SymOp> NCSsymOps;
  
    /**
     * Constructor for a NCSCrystal.
     *
     * @param unitCell The base unit cell.
     * @param NCSsymOps Non-crystallographic symmetry operators applied to the unit cell.
     * @since 1.0
     */
    private NCSCrystal(Crystal unitCell, List<SymOp> NCSsymOps) {
      super(
          unitCell.a,
          unitCell.b,
          unitCell.c,
          unitCell.alpha,
          unitCell.beta,
          unitCell.gamma,
          unitCell.spaceGroup.shortName);
      this.unitCell = unitCell;
      this.NCSsymOps = NCSsymOps;
  
      /*
       At this point, the NCSCrystal references a SpaceGroup instance
       that is lacking symmetry operators. This is corrected by generating symmetry
       operators to fill up the non-crystallographic, which is added to the unit
       cell based on the asymmetric unit.
      */
      updateNCSOperators();
    }
  
    /**
     * Returns an NCSCrystal by expanding the orignal unit cell with the symmetry operators provided
     * by the BIOMT records in the PDB files. See REMARK 350.
     *
     * @param unitCell The unit cell of the crystal.
    * @param symOps Symmetry operators for non-crystallographic symmetry
    * @return A Crystal or NCSCrystal
    */
   public static Crystal NCSCrystalFactory(Crystal unitCell, List<SymOp> symOps) {
 
     if (unitCell == null || unitCell.aperiodic()) {
       return unitCell;
     } else {
       return new NCSCrystal(unitCell, symOps);
     }
   }
 
   /**
    * Change the cell parameters for the base unit cell, which is followed by an update of the
    * ReplicateCrystal parameters and possibly the number of replicated cells.
    *
    * @param a The length of the a-axis for the base unit cell (in Angstroms).
    * @param b The length of the b-axis for the base unit cell (in Angstroms).
    * @param c The length of the c-axis for the base unit cell (in Angstroms).
    * @param alpha The angle between the b-axis and c-axis (in Degrees).
    * @param beta The angle between the a-axis and c-axis (in Degrees).
    * @param gamma The angle between the a-axis and b-axis (in Degrees).
    * @return True is returned if the unit cell and replicates cell are updated successfully.
    */
   @Override
   public boolean changeUnitCellParameters(
       double a, double b, double c, double alpha, double beta, double gamma) {
     // First, update the parameters of the unit cell.
     if (unitCell.changeUnitCellParameters(a, b, c, alpha, beta, gamma)) {
 
       // Then, update the parameters of the NCSCrystal.
       if (super.changeUnitCellParameters(a, b, c, alpha, beta, gamma)) {
         // Finally, update the NCS operators.
         updateNCSOperators();
         return true;
       }
     }
     return false;
   }
 
   /** Two crystals are equal only if all unit cell parameters are exactly the same. */
   @Override
   public boolean equals(Object o) {
     if (this == o) return true;
     if (o == null || getClass() != o.getClass()) return false;
     NCSCrystal ncsCrystal = (NCSCrystal) o;
     return (Objects.equals(unitCell, ncsCrystal.unitCell)
         && a == ncsCrystal.a
         && b == ncsCrystal.b
         && c == ncsCrystal.c
         && alpha == ncsCrystal.alpha
         && beta == ncsCrystal.beta
         && gamma == ncsCrystal.gamma
         && spaceGroup.number == ncsCrystal.spaceGroup.number
         && spaceGroup.symOps.size() == ncsCrystal.spaceGroup.symOps.size());
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Returns the unit cell for this NCSCrystal. This is useful for the reciprocal space portion
    * of PME that operates on the unit cell.
    */
   @Override
   public Crystal getUnitCell() {
     return unitCell;
   }
 
   /**
    * {@inheritDoc}
    *
    * <p>Include information about the base unit cell and NCS cell.
    */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder(unitCell.toString());
     sb.append("\n\n Non-Crystallographic Cell\n");
     sb.append(format("  A-axis:                              %8.3f\n", a));
     sb.append(format("  B-axis:                              %8.3f\n", b));
     sb.append(format("  C-axis:                              %8.3f\n", c));
     sb.append(format("  Alpha:                               %8.3f\n", alpha));
     sb.append(format("  Beta:                                %8.3f\n", beta));
     sb.append(format("  Gamma:                               %8.3f\n", gamma));
     sb.append(
         format("  UnitCell Symmetry Operators:         %8d\n", unitCell.spaceGroup.symOps.size()));
     sb.append(format("  NCS Symmetry Operators:              %8d\n", NCSsymOps.size()));
     sb.append(format("  Total Symmetry Operators:            %8d", spaceGroup.getNumberOfSymOps()));
     return sb.toString();
   }
 
   /**
    * Update the list of symmetry operators to contain the non-crystallographic operations as well.
    */
   private void updateNCSOperators() {
     List<SymOp> symOps = spaceGroup.symOps;
 
     // First, we remove the existing symmetry operators.
     symOps.clear();
 
     /*
      Symmetry operators are produced that are the combination of the non-crystallographic and the unit cell symmetry operations.
      Note that the first symOp is still equivalent to the asymmetric unit and the first set of
      symOps are still equivalent to the unit cell.
     */
     int ii = 0;
     int soRemoved = 0;
     for (SymOp NCSsymOp : NCSsymOps) {
       // All UC symOps seem to have collision issues... Use 1st (identity) for now...
       for (SymOp symOp : unitCell.spaceGroup.symOps) {
         //            SymOp symOp=unitCell.spaceGroup.symOps.get(0); //Identity matrix is standard
         // first matrix. (P1)
         double[] NCSTrans = new double[3];
         RealMatrix NCS = MatrixUtils.createRealMatrix(NCSsymOp.rot);
         RealMatrix UC = MatrixUtils.createRealMatrix(symOp.rot);
         RealMatrix result = NCS.multiply(UC); // Abelian groups order doesnt matter...
         double[][] NCSRot = result.getData();
         NCSTrans[0] = symOp.tr[0] + NCSsymOp.tr[0];
         NCSTrans[1] = symOp.tr[1] + NCSsymOp.tr[1];
         NCSTrans[2] = symOp.tr[2] + NCSsymOp.tr[2];
         SymOp NCSSymOp = new SymOp(NCSRot, NCSTrans);
         if (!symOps.contains(NCSSymOp)) {
           symOps.add(NCSSymOp);
         } else {
           soRemoved++;
         }
         if (logger.isLoggable(Level.FINEST)) {
           logger.finest(format("\n SymOp: %d", ii));
           logger.finest(NCSSymOp.toString());
         }
         ii++;
       }
     }
     if (soRemoved != 0) {
       logger.warning(format("\n NCS Replicated SymOps Removed: %d", soRemoved));
     }
   }
 }