// ******************************************************************************
   //
   // 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.
  //
  // 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.potential;
  
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.MSNode;
  import ffx.potential.bonded.MultiResidue;
  import ffx.potential.bonded.Residue;
  import ffx.potential.bonded.ResidueState;
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * The AssemblyState class stores the chemical and coordinate state of a Molecular Assembly. Not
   * robust to any chemical perturbation except for mutation of MultiResidues.
   *
   * @author Michael J. Schnieders
   * @author Jacob M. Litman
   * @since 1.0
   */
  public class AssemblyState {
    private final MolecularAssembly mola;
    private final Residue[] residues;
    private final ResidueState[] resStates;
    private final Atom[] otherAtoms;
    private final double[][] otherCoords;
  
    /**
     * Construct a snapshot of a MolecularAssembly. Currently accounts for the coordinates of all
     * entities, and the chemical state of MultiResidues. Does not include velocities, etc.
     *
     * @param assembly To store state of.
     */
    public AssemblyState(MolecularAssembly assembly) {
      mola = assembly;
  
      List<Residue> residueList = mola.getResidueList();
      List<Residue> copyResList = new ArrayList<>(residueList);
      // Remove all Residue nodes, including subnodes of a MultiResidue, from otherNodeList.
      List<MSNode> otherNodeList = mola.getNodeList();
      otherNodeList.removeAll(residueList);
  
      // Remove any Residue nodes which are beneath a MultiResidue.
      for (Residue res : copyResList) {
        if (res instanceof MultiResidue) {
          List<Residue> subResidues = ((MultiResidue) res).getConsideredResidues();
          residueList.removeAll(subResidues);
        }
      }
  
      residues = residueList.toArray(new Residue[0]);
      resStates = ResidueState.storeAllCoordinates(residues);
  
      List<Atom> otherAtomList = new ArrayList<>();
      for (MSNode node : otherNodeList) {
        otherAtomList.addAll(node.getAtomList());
      }
      int nOtherAtoms = otherAtomList.size();
      otherAtoms = new Atom[nOtherAtoms];
      otherAtomList.toArray(otherAtoms);
      otherCoords = ResidueState.storeAtomicCoordinates(otherAtoms);
    }
  
    /**
    * Copies an AssemblyState. Note: side effects possible if they occur between applying the state
    * to be copied and reverting to the pre-method-call state.
    *
    * @param state AssemblyState to copy.
    * @return A copied AssemblyState.
    */
   public static AssemblyState copyState(AssemblyState state) {
     MolecularAssembly assembly = state.getMolecularAssembly();
     AssemblyState orig = new AssemblyState(assembly);
     state.revertState();
     AssemblyState copiedState = new AssemblyState(assembly);
     orig.revertState();
     return copiedState;
   }
 
   /**
    * Returns the MolecularAssembly associated with this AssemblyState.
    *
    * @return The associated MolecularAssembly.
    */
   public MolecularAssembly getMolecularAssembly() {
     return mola;
   }
 
   /**
    * Revert the state of the associated MolecularAssembly, assuming no chemical changes were made
    * except to MultiResidues.
    */
   public void revertState() {
     int nResidues = residues.length;
     for (int i = 0; i < nResidues; i++) {
       residues[i].revertState(resStates[i]);
     }
 
     int nOthers = otherAtoms.length;
     for (int i = 0; i < nOthers; i++) {
       otherAtoms[i].setXYZ(otherCoords[i]);
     }
   }
 }