// ******************************************************************************
   //
   // 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
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  // ******************************************************************************
  package ffx.potential.terms;
  
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.Bond;
  import ffx.potential.bonded.BondedTerm;
  import ffx.potential.bonded.Torsion;
  import ffx.potential.parameters.ForceField;
  import ffx.potential.parameters.TorsionType;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  import java.util.ArrayList;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.EmptyStackException;
  import java.util.List;
  import java.util.logging.Logger;
  
  /**
   * Restrain-Torsion potential energy term using {@link ffx.potential.bonded.Torsion} instances.
   * Method names are specific to restrain torsions for clarity.
   */
  public class RestrainTorsionPotentialEnergy extends EnergyTerm {
  
    private static final Logger logger = Logger.getLogger(RestrainTorsionPotentialEnergy.class.getName());
  
    /**
     * Internal list of Torsion instances for restrain torsions.
     */
    private final List<Torsion> restrainTorsions = new ArrayList<>();
  
    /**
     * Create a RestrainTorsionPotentialEnergy with the provided name.
     *
     * @param name Name for this term.
     */
    public RestrainTorsionPotentialEnergy(String name) {
      super(name);
    }
  
    /**
     * Create a RestrainTorsionPotentialEnergy with the provided name and force group.
     *
     * @param name       Name for this term.
     * @param forceGroup Integer force group identifier.
     */
    public RestrainTorsionPotentialEnergy(String name, int forceGroup) {
      super(name, forceGroup);
    }
  
    /**
     * Create a RestrainTorsionPotentialEnergy initialized with a list of torsions and force group.
     *
     * @param name             Name for this term.
     * @param forceGroup       Force group identifier.
     * @param restrainTorsions List of Torsion instances to add (null-safe).
     */
    public RestrainTorsionPotentialEnergy(String name, int forceGroup, List<Torsion> restrainTorsions) {
      super(name, forceGroup);
      if (restrainTorsions != null) {
        Collections.sort(restrainTorsions);
        this.restrainTorsions.addAll(restrainTorsions);
        logger.info(String.format("  Restrain Torsions:                   %10d", getNumberOfRestrainTorsions()));
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int getNumberOfTerms() {
     return getNumberOfRestrainTorsions();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public BondedTerm[] getBondedTermsArray() {
     return getRestrainTorsionArray();
   }
 
   /**
    * Create a RestrainTorsionPotentialEnergy initialized with a collection of torsions.
    *
    * @param name             Name for this term (may be null).
    * @param restrainTorsions Collection of Torsion instances to add (null-safe).
    */
   public RestrainTorsionPotentialEnergy(String name, Collection<Torsion> restrainTorsions) {
     super(name);
     if (restrainTorsions != null) {
       this.restrainTorsions.addAll(restrainTorsions);
     }
   }
 
   /**
    * Add a single restrain torsion.
    *
    * @param torsion Torsion to add (ignored if null).
    * @return true if added.
    */
   public boolean addRestrainTorsion(Torsion torsion) {
     if (torsion == null) {
       return false;
     }
     return restrainTorsions.add(torsion);
 
   }
 
   /**
    * Add an array of restrain torsions.
    *
    * @param torsions Array of Torsion instances to add.
    * @return true if added.
    */
   public boolean addRestrainTorsions(Torsion[] torsions) {
     if (torsions == null) {
       return false;
     }
     Collections.addAll(this.restrainTorsions, torsions);
     return true;
   }
 
   /**
    * Add a list of restrain torsions.
    *
    * @param torsions List of Torsion instances to add.
    * @return true if added.
    */
   public boolean addRestrainTorsions(List<Torsion> torsions) {
     if (torsions == null) {
       return false;
     }
     this.restrainTorsions.addAll(torsions);
     return true;
   }
 
   /**
    * Remove a restrain torsion.
    *
    * @param torsion Torsion to remove (ignored if null).
    * @return true if removed.
    */
   public boolean removeRestrainTorsion(Torsion torsion) {
     if (torsion == null) {
       return false;
     }
     return restrainTorsions.remove(torsion);
   }
 
   /**
    * Get a restrain torsion at an index.
    *
    * @param index Index.
    * @return Torsion.
    * @throws IndexOutOfBoundsException if invalid index.
    */
   public Torsion getRestrainTorsion(int index) {
     return restrainTorsions.get(index);
   }
 
   /**
    * Get an unmodifiable view of restrain torsions.
    *
    * @return List of Torsion.
    */
   public List<Torsion> getRestrainTorsions() {
     return Collections.unmodifiableList(restrainTorsions);
   }
 
   /**
    * Get an array of restrain torsions.
    *
    * @return Array of Torsion.
    */
   public Torsion[] getRestrainTorsionArray() {
     return restrainTorsions.toArray(new Torsion[0]);
   }
 
   /**
    * Get the number of restrain torsions.
    *
    * @return Number of restrain torsions.
    */
   public int getNumberOfRestrainTorsions() {
     return restrainTorsions.size();
   }
 
   @Override
   public String toPDBString() {
     if (getNumberOfRestrainTorsions() <= 0) {
       return "";
     }
     return String.format("REMARK   3   %s %g (%d)\n", "RESTRAIN TORSION           : ", getEnergy(), getNumberOfRestrainTorsions());
   }
 
   @Override
   public String toString() {
     return String.format("  %s %20.8f %12d %12.3f\n", "Restrain Torsion  ",
         getEnergy(), getNumberOfRestrainTorsions(), getTime());
   }
 
   /**
    * Log the details of Restrain Torsion interactions.
    */
   @Override
   public void log() {
     if (getNumberOfRestrainTorsions() <= 0) {
       return;
     }
     logger.info("\n Restrain Torsion Interactions:");
     for (Torsion torsion : getRestrainTorsions()) {
       logger.info(" Restrain Torsion \t" + torsion.toString());
     }
   }
 
   /**
    * Method to parse the restrain-torsion records.
    *
    * @param properties Configuration properties.
    * @param forceField Force field properties.
    * @param atoms      Array of atoms in the system.
    * @param torsions   Array of torsions in the system.
    * @return An array of restrain torsions, or null if none were found.
    */
   public static Torsion[] configureRestrainTorsions(CompositeConfiguration properties,
                                                     ForceField forceField,
                                                     Atom[] atoms,
                                                     Torsion[] torsions) {
     StringBuilder restrainLog = new StringBuilder("\n  Restrain-Torsions");
 
     String[] restrainTorsions = properties.getStringArray("restrain-torsion");
     double torsionUnits = forceField.getDouble("TORSIONUNIT", TorsionType.DEFAULT_TORSION_UNIT);
     List<Torsion> restrainTorsionList = new ArrayList<>(restrainTorsions.length);
     for (String restrainString : restrainTorsions) {
       // Add the key back to the input line.
       restrainString = "restrain-torsion " + restrainString;
       // Split the line on the pound symbol to remove comments.
       String input = restrainString.split("#+")[0];
       // Split the line on whitespace.
       String[] tokens = input.trim().split(" +");
       // Restrain torsion records have a similar form as torsion records.
       // The first four tokens are atom indices instead of atom classes.
       TorsionType torsionType = TorsionType.parse(input, tokens);
       torsionType.torsionUnit = torsionUnits;
 
       // Collect the atom indices.
       int[] atomIndices = torsionType.atomClasses;
       int ai1 = atomIndices[0] - 1;
       int ai2 = atomIndices[1] - 1;
       int ai3 = atomIndices[2] - 1;
       int ai4 = atomIndices[3] - 1;
       Atom a1 = atoms[ai1];
       Atom a2 = atoms[ai2];
       Atom a3 = atoms[ai3];
       Atom a4 = atoms[ai4];
 
       // Collect the bonds between the atoms making up the restrain torsion.
       Bond firstBond = a1.getBond(a2);
       Bond middleBond = a2.getBond(a3);
       Bond lastBond = a3.getBond(a4);
       Torsion torsion = new Torsion(firstBond, middleBond, lastBond);
       torsion.setTorsionType(torsionType);
       restrainTorsionList.add(torsion);
       restrainLog.append("\n   ").append(torsion);
     }
 
     // Apply the property "restrain-all-torsions".
     restrainTorsionList.addAll(restrainAllTorsions(torsions, properties));
 
     if (!restrainTorsionList.isEmpty()) {
       logger.info(restrainLog.toString());
       return restrainTorsionList.toArray(new Torsion[0]);
     } else {
       return null;
     }
   }
 
   /**
    * Method to parse the restrain-torsion-cos records.
    *
    * @param torsions   Array of torsions.
    * @param properties Configuration properties.
    * @return An array of restrain torsions, or null if none were found.
    */
   private static List<Torsion> restrainAllTorsions(Torsion[] torsions,
                                                    CompositeConfiguration properties) {
 
     List<Torsion> restrainTorsionList = new ArrayList<>();
 
     String restrainTorsions;
     boolean noHydrogenTorsions = false;
     if (properties.containsKey("restrain-all-torsions")) {
       restrainTorsions = properties.getString("restrain-all-torsions");
     } else if (properties.containsKey("restrain-heavy-torsions")) {
       restrainTorsions = properties.getString("restrain-heavy-torsions");
       noHydrogenTorsions = true;
     } else {
       return restrainTorsionList;
     }
 
     logger.info(" Restrain torsions " + restrainTorsions);
     // Split the line on the pound symbol to remove comments.
     String input = restrainTorsions.split("#+")[0];
     // Split the line on whitespace.
     String[] tokens = input.trim().split(" +");
     double forceConstant = Double.parseDouble(tokens[0]);
     logger.info(" Force constant %10.6f".formatted(forceConstant));
 
     for (Torsion torsion : torsions) {
       // Skip torsions with hydrogen
       if (noHydrogenTorsions && torsion.containsHydrogen()) {
         continue;
       }
 
       // Re-use current atom classes (they will not be used).
       TorsionType torsionType = torsion.torsionType;
       int[] atomClasses = torsionType.atomClasses.clone();
       // Single term in the Fourier series.
       double[] amplitude = {forceConstant};
       double[] phase = {torsion.measure() + 180.0};
       int[] periodicity = {1};
 
       // Create the new TorsionType for the restraint.
       TorsionType newTorsionType = new TorsionType(atomClasses, amplitude, phase, periodicity);
       newTorsionType.torsionUnit = torsionType.torsionUnit;
 
       Bond b1 = torsion.getBond(0);
       Bond b2 = torsion.getBond(1);
       Bond b3 = torsion.getBond(2);
       Torsion newTorsion = new Torsion(b1, b2, b3);
       newTorsion.setTorsionType(newTorsionType);
 
       restrainTorsionList.add(newTorsion);
     }
 
     return restrainTorsionList;
   }
 }