// ******************************************************************************
   //
   // 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.
  //
  // 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.ui.commands;
  
  import ffx.potential.MolecularAssembly;
  import ffx.potential.Utilities.FileType;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Bond;
  import ffx.potential.parameters.AtomType;
  import ffx.potential.parsers.SystemFilter;
  import java.io.File;
  import java.util.ArrayList;
  import java.util.Hashtable;
  import java.util.Vector;
  
  /**
   * The SimulationFilter class parses system data sent by FFXServer to FFXClient.
   *
   * @author Michael J. Schnieders
   */
  public final class SimulationFilter extends SystemFilter {
  
    SimulationDefinition system;
    Hashtable<Integer, AtomType> atomTypes = new Hashtable<Integer, AtomType>();
  
    /**
     * Constructor for SimulationFilter.
     *
     * @param sys a {@link ffx.ui.commands.SimulationDefinition} object.
     * @param m a {@link ffx.potential.MolecularAssembly} object.
     */
    public SimulationFilter(SimulationDefinition sys, MolecularAssembly m) {
      super(new File(""), m, null, null);
      system = sys;
      fileType = FileType.SIM;
      fileRead = false;
    }
  
    @Override
    public void closeReader() {
      // logger.fine(" Reading trajectories not yet supported for MergeFilter");
      // No logger set for SimulationFilter.
    }
  
    /** {@inheritDoc} */
    @Override
    public boolean readFile() {
      // Create Molecular Mechanics Data Objects from the SimulationDefinition
      // information
      for (int i = 0; i < system.numatoms; i++) {
        AtomType atomType = atomTypes.get(system.types[i]);
        if (atomType == null) {
          atomType =
              new AtomType(
                  system.types[i],
                  -1,
                  system.name[i],
                  system.story[i],
                  system.atomic[i],
                  system.mass[i],
                  0);
          atomTypes.put(system.types[i], atomType);
        }
      }
     atomList = new ArrayList<Atom>();
     Vector<Integer> bonds1 = new Vector<Integer>();
     Vector<Integer> bonds2 = new Vector<Integer>();
     double[] d = new double[3];
     int[] b = new int[4];
     for (int i = 0; i < system.numatoms; i++) {
       d[0] = system.coordinates[0][i];
       d[1] = system.coordinates[1][i];
       d[2] = system.coordinates[2][i];
       String s = "" + system.types[i];
       AtomType atomType = atomTypes.get(s);
       Atom a = new Atom(i + 1, "" + atomType.type, atomType, d);
       atomList.add(a);
       int b1 = i + 1;
       b[0] = system.connectivity[0][i];
       b[1] = system.connectivity[1][i];
       b[2] = system.connectivity[2][i];
       b[3] = system.connectivity[3][i];
       int j = 0;
       while (j < 4 && b[j] != 0) {
         int b2 = b[j];
         bonds1.add(b1);
         bonds2.add(b2);
         j++;
       }
     }
     bondList = new ArrayList<Bond>();
     for (int i = 0; i < bonds1.size(); i++) {
       int a1 = bonds1.get(i);
       int a2 = bonds2.get(i);
       if (a1 < a2) {
         Atom atom1 = atomList.get(a1 - 1);
         Atom atom2 = atomList.get(a2 - 1);
         bondList.add(new Bond(atom1, atom2));
       }
     }
     setFileRead(true);
     return true;
   }
 
   @Override
   public boolean readNext(boolean resetPosition) {
     return false;
   }
 
   @Override
   public boolean readNext(boolean resetPosition, boolean print) {
     return false;
   }
 
   @Override
   public boolean readNext(boolean resetPosition, boolean print, boolean parse) {
     return false;
   }
 
   @Override
   public boolean readNext() {
     return readNext(false);
   }
 
   /** {@inheritDoc} */
   @Override
   public boolean writeFile(File saveFile, boolean append, String[] extraLines) {
     return false;
   }
 }