// ******************************************************************************
   //
   // 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.potential.terms;
  
  import ffx.potential.bonded.BondedTerm;
  import ffx.potential.bonded.RestrainDistance;
  import ffx.potential.parameters.BondType;
  
  import javax.annotation.Nullable;
  import java.util.ArrayList;
  import java.util.Collection;
  import java.util.Collections;
  import java.util.List;
  import java.util.logging.Logger;
  
  /**
   * Restrain-Distance potential energy term using {@link ffx.potential.bonded.RestrainDistance} instances.
   *
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class RestrainDistancePotentialEnergy extends EnergyTerm {
  
    private static final Logger logger = Logger.getLogger(RestrainDistancePotentialEnergy.class.getName());
  
    /**
     * Log the details of Restrain Distance interactions.
     */
    @Override
    public void log() {
      if (getNumberOfRestrainDistances() <= 0) {
        return;
      }
      logger.info("\n Restrain Distance Interactions:");
      for (RestrainDistance restrainDistance : getRestrainDistances()) {
        logger.info(" Restrain Distance \t" + restrainDistance.toString());
      }
    }
  
    /**
     * Internal list of RestrainDistance instances.
     */
    private final List<RestrainDistance> restrainDistances = new ArrayList<>();
  
    /**
     * Create a RestrainDistancePotentialEnergy with the provided name.
     *
     * @param name Name for this term.
     */
    public RestrainDistancePotentialEnergy(String name) {
      super(name);
    }
  
    /**
     * Create a RestrainDistancePotentialEnergy with the provided name and force group.
     *
     * @param name       Name for this term.
     * @param forceGroup Integer force group identifier.
     */
    public RestrainDistancePotentialEnergy(String name, int forceGroup) {
      super(name, forceGroup);
    }
  
    /**
    * Create a RestrainDistancePotentialEnergy initialized with a list of terms and force group.
    *
    * @param name              Name for this term.
    * @param forceGroup        Force group identifier.
    * @param restrainDistances List of RestrainDistance instances (null-safe).
    */
   public RestrainDistancePotentialEnergy(String name, int forceGroup, List<RestrainDistance> restrainDistances) {
     super(name, forceGroup);
     if (restrainDistances != null) {
       Collections.sort(restrainDistances);
       this.restrainDistances.addAll(restrainDistances);
       logger.info(String.format("  Restrain Distances:                 %10d", getNumberOfRestrainDistances()));
     }
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int getNumberOfTerms() {
     return getNumberOfRestrainDistances();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public BondedTerm[] getBondedTermsArray() {
     return getRestrainDistanceArray();
   }
 
   /**
    * Create a RestrainDistancePotentialEnergy initialized with a collection of terms.
    *
    * @param name              Name for this term (may be null).
    * @param restrainDistances Collection of RestrainDistance instances to add (null-safe).
    */
   public RestrainDistancePotentialEnergy(String name, Collection<RestrainDistance> restrainDistances) {
     super(name);
     if (restrainDistances != null) {
       this.restrainDistances.addAll(restrainDistances);
     }
   }
 
   /**
    * Add a RestrainDistance to this term.
    *
    * @param restrainDistance RestrainDistance to add (ignored if null).
    * @return true if it was added.
    */
   public boolean addRestrainDistance(RestrainDistance restrainDistance) {
     if (restrainDistance == null) {
       return false;
     }
     return restrainDistances.add(restrainDistance);
   }
 
   /**
    * Add an array of RestrainDistances to this term.
    *
    * @param restrainDistances Array of RestrainDistance instances to add.
    * @return true if they were added.
    */
   public boolean addRestrainDistances(RestrainDistance[] restrainDistances) {
     if (restrainDistances == null) {
       return false;
     }
     Collections.addAll(this.restrainDistances, restrainDistances);
     return true;
   }
 
   /**
    * Add a list of RestrainDistances to this term.
    *
    * @param restrainDistances List of RestrainDistance instances to add.
    * @return true if they were added.
    */
   public boolean addRestrainDistances(List<RestrainDistance> restrainDistances) {
     if (restrainDistances == null) {
       return false;
     }
     this.restrainDistances.addAll(restrainDistances);
     return true;
   }
 
   /**
    * Remove a RestrainDistance from this term.
    *
    * @param restrainDistance RestrainDistance to remove (ignored if null).
    * @return true if it was present and removed.
    */
   public boolean removeRestrainDistance(RestrainDistance restrainDistance) {
     if (restrainDistance == null) {
       return false;
     }
     return restrainDistances.remove(restrainDistance);
   }
 
   /**
    * Get the RestrainDistance at a given index.
    *
    * @param index Index in the internal list.
    * @return RestrainDistance at the specified index.
    * @throws IndexOutOfBoundsException if index is invalid.
    */
   public RestrainDistance getRestrainDistance(int index) {
     return restrainDistances.get(index);
   }
 
   /**
    * Get an unmodifiable view of the RestrainDistances in this term.
    *
    * @return Unmodifiable List of RestrainDistances.
    */
   public List<RestrainDistance> getRestrainDistances() {
     return Collections.unmodifiableList(restrainDistances);
   }
 
   /**
    * Get an array of RestrainDistances in this term.
    *
    * @return Array of RestrainDistances.
    */
   public RestrainDistance[] getRestrainDistanceArray() {
     return restrainDistances.toArray(new RestrainDistance[0]);
   }
 
   /**
    * Get the number of RestrainDistances in this term.
    *
    * @return The number of RestrainDistances.
    */
   public int getNumberOfRestrainDistances() {
     return restrainDistances.size();
   }
 
   /**
    * Returns a list of restraint distances filtered by the specified bond function. If the bondFunction
    * is null, it returns all restrained bonds.
    *
    * @param bondFunction the type of bond function.
    * @return a {@link java.util.List} object.
    */
   public List<RestrainDistance> getRestrainDistances(@Nullable BondType.BondFunction bondFunction) {
     // If the bondFunction is null, return all restrained bonds.
     if (bondFunction == null) {
       return restrainDistances;
     }
     // Otherwise, return only the restraint bonds with the specified bond function.
     List<RestrainDistance> list = new ArrayList<>();
     for (RestrainDistance restrainDistance : restrainDistances) {
       if (restrainDistance.getBondType().bondFunction == bondFunction) {
         list.add(restrainDistance);
       }
     }
     if (!list.isEmpty()) {
       return list;
     }
     return null;
   }
 
   @Override
   public String toPDBString() {
     if (getNumberOfRestrainDistances() <= 0) {
       return "";
     }
     return String.format("REMARK   3   %s %g (%d)\n", "RESTRAIN DISTANCE          : ", getEnergy(), getNumberOfRestrainDistances());
   }
 
   @Override
   public String toString() {
     return String.format("  %s %20.8f %12d %12.3f\n", "Restrain Distance ",
         getEnergy(), getNumberOfRestrainDistances(), getTime());
   }
 }