//******************************************************************************
   //
   // 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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  // 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
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  // permission to link this library with independent modules to produce an
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  //******************************************************************************
  package ffx.potential.commands;
  
  import ffx.crystal.Crystal;
  import ffx.numerics.Potential;
  import ffx.potential.MolecularAssembly;
  import ffx.potential.bonded.Atom;
  import ffx.potential.cli.PotentialCommand;
  import ffx.utilities.FFXBinding;
  import picocli.CommandLine.Command;
  import picocli.CommandLine.Parameters;
  
  import java.util.List;
  
  /**
   * Convert from Cartesian to fractional coordinates.
   * <p>
   * Usage:
   * ffxc Cart2Frac &lt;filename&gt;
   */
  @Command(name = "Cart2Frac", description = " Convert from Cartesian to fractional coordinates.")
  public class Cart2Frac extends PotentialCommand {
  
    /**
     * The final argument should be a file in PDB or XYZ format.
     */
    @Parameters(arity = "1", paramLabel = "file",
        description = "The atomic coordinate file in PDB or XYZ format.")
    private String filename = null;
  
    /**
     * Save a reference to the MolecularAssembly instances to destroy their potentials.
     */
    private MolecularAssembly[] molecularAssemblies;
  
    /**
     * Cartesian coordinate input.
     */
    private double[][][] cartCoordinates = null;
  
    /**
     * Fractional coordinate output.
     */
    private double[][][] fracCoordinates = null;
  
    public Cart2Frac() {
      super();
    }
  
    public Cart2Frac(FFXBinding binding) {
      super(binding);
    }
  
    public Cart2Frac(String[] args) {
      super(args);
    }
  
    /**
     * Return Cartesian Coordinate input.
     */
    public double[][][] getCart() {
      return cartCoordinates;
    }
 
   /**
    * Return Fractional Coordinate output.
    */
   public double[][][] getFrac() {
     return fracCoordinates;
   }
 
   @Override
   public Cart2Frac run() {
     if (!init()) {
       return this;
     }
 
     // Load one or more MolecularAssembly instances.
     molecularAssemblies = getActiveAssemblies(filename);
     if (activeAssembly == null) {
       logger.info(helpString());
       return this;
     }
 
     // Set the filename.
     filename = activeAssembly.getFile().getAbsolutePath();
 
     int num = molecularAssemblies.length;
     cartCoordinates = new double[num][][];
     fracCoordinates = new double[num][][];
 
     // Loop over each system.
     for (int i = 0; i < num; i++) {
       MolecularAssembly ma = molecularAssemblies[i];
       logger.info("\n Converting from Cartesian to fractional coordinates for " + ma);
       Crystal crystal = ma.getCrystal().getUnitCell();
 
       Atom[] atoms = ma.getAtomArray();
       int nAtoms = atoms.length;
       fracCoordinates[i] = new double[nAtoms][3];
       cartCoordinates[i] = new double[nAtoms][3];
 
       double[] frac = new double[3];
       double[] cart = new double[3];
 
       for (int index = 0; index < nAtoms; index++) {
         Atom atom = atoms[index];
         atom.getXYZ(cart);
         crystal.toFractionalCoordinates(cart, frac);
 
         // If the atom is at a special position, make sure it's active so the coordinates are updated.
         boolean active = atom.isActive();
         atom.setActive(true);
         atom.moveTo(frac);
         atom.setActive(active);
 
         cartCoordinates[i][index][0] = cart[0];
         cartCoordinates[i][index][1] = cart[1];
         cartCoordinates[i][index][2] = cart[2];
 
         fracCoordinates[i][index][0] = frac[0];
         fracCoordinates[i][index][1] = frac[1];
         fracCoordinates[i][index][2] = frac[2];
       }
     }
 
     saveByOriginalExtension(molecularAssemblies, filename);
 
     // Export results via Binding for compatibility.
     binding.setVariable("cart", cartCoordinates);
     binding.setVariable("frac", fracCoordinates);
 
     return this;
   }
 
   @Override
   public List<Potential> getPotentials() {
     return getPotentialsFromAssemblies(molecularAssemblies);
   }
 }