// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2026.
   //
   // 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,
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  // ******************************************************************************
  package ffx.potential.terms;
  
  import ffx.crystal.Crystal;
  import ffx.numerics.switching.ConstantSwitch;
  import ffx.numerics.switching.UnivariateFunctionFactory;
  import ffx.numerics.switching.UnivariateSwitchingFunction;
  import ffx.potential.bonded.Atom;
  import ffx.potential.bonded.BondedTerm;
  import ffx.potential.bonded.RestrainDistance;
  import ffx.potential.parameters.BondType;
  import org.apache.commons.configuration2.CompositeConfiguration;
  
  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;
  
  import static java.lang.String.format;
  
  /**
   * 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());
   }
 
   /**
    * Method to parse the restrain-distance records.
    *
    * @param properties Configuration properties.
    */
   public static RestrainDistance[] configureRestrainDistances(
       CompositeConfiguration properties,
       Atom[] atoms, Crystal crystal, boolean lambdaTerm) {
     List<RestrainDistance> restrainDistanceList = new ArrayList<>();
     String[] bondRestraints = properties.getStringArray("restrain-distance");
     for (String bondRest : bondRestraints) {
       try {
         String[] toks = bondRest.split("\\s+");
         if (toks.length < 2) {
           throw new IllegalArgumentException(
               format(" restrain-distance value %s could not be parsed!", bondRest));
         }
         // Internally, everything starts with 0, but restrain distance starts at 1, so that 1 has to
         // be subtracted
         int at1 = Integer.parseInt(toks[0]) - 1;
         int at2 = Integer.parseInt(toks[1]) - 1;
 
         double forceConst = 100.0;
         double flatBottomRadius = 0;
         Atom a1 = atoms[at1];
         Atom a2 = atoms[at2];
 
         if (toks.length > 2) {
           forceConst = Double.parseDouble(toks[2]);
         }
         double dist;
         switch (toks.length) {
           case 2:
           case 3:
             double[] xyz1 = new double[3];
             xyz1 = a1.getXYZ(xyz1);
             double[] xyz2 = new double[3];
             xyz2 = a2.getXYZ(xyz2);
             // Current distance between restrained atoms
             dist = crystal.minDistOverSymOps(xyz1, xyz2);
             break;
           case 4:
             dist = Double.parseDouble(toks[3]);
             break;
           case 5:
           default:
             double minDist = Double.parseDouble(toks[3]);
             double maxDist = Double.parseDouble(toks[4]);
             dist = 0.5 * (minDist + maxDist);
             flatBottomRadius = 0.5 * Math.abs(maxDist - minDist);
             break;
         }
 
         UnivariateSwitchingFunction switchF;
         double lamStart = RestrainDistance.DEFAULT_RB_LAM_START;
         double lamEnd = RestrainDistance.DEFAULT_RB_LAM_END;
         if (toks.length > 5) {
           int offset = 5;
           if (toks[5].matches("^[01](?:\\.[0-9]*)?")) {
             offset = 6;
             lamStart = Double.parseDouble(toks[5]);
             if (toks[6].matches("^[01](?:\\.[0-9]*)?")) {
               offset = 7;
               lamEnd = Double.parseDouble(toks[6]);
             }
           }
           switchF = UnivariateFunctionFactory.parseUSF(toks, offset);
         } else {
           switchF = new ConstantSwitch();
         }
 
         RestrainDistance restrainDistance = createRestrainDistance(a1, a2, dist,
             forceConst, flatBottomRadius, lamStart, lamEnd, switchF, lambdaTerm, crystal);
         restrainDistanceList.add(restrainDistance);
       } catch (Exception ex) {
         logger.info(format(" Exception in parsing restrain-distance: %s", ex));
       }
     }
     if (!restrainDistanceList.isEmpty()) {
       return restrainDistanceList.toArray(new RestrainDistance[0]);
     } else {
       return null;
     }
   }
 
   /**
    * setRestrainDistance
    *
    * @param a1                a {@link ffx.potential.bonded.Atom} object.
    * @param a2                a {@link ffx.potential.bonded.Atom} object.
    * @param distance          a double.
    * @param forceConstant     the force constant in kcal/mole.
    * @param flatBottom        Radius of a flat-bottom potential in Angstroms.
    * @param lamStart          At what lambda does the restraint begin to take effect?
    * @param lamEnd            At what lambda does the restraint hit full strength?
    * @param switchingFunction Switching function to use as a lambda dependence.
    * @param lambdaTerm        Restrain distance is a function of lambda.
    * @param crystal           The unit cel and space group information.
    */
   private static RestrainDistance createRestrainDistance(Atom a1, Atom a2, double distance, double forceConstant,
                                                          double flatBottom, double lamStart, double lamEnd,
                                                          UnivariateSwitchingFunction switchingFunction,
                                                          boolean lambdaTerm, Crystal crystal) {
     boolean rbLambda = !(switchingFunction instanceof ConstantSwitch) && lambdaTerm;
     RestrainDistance restrainDistance = new RestrainDistance(a1, a2, crystal, rbLambda, lamStart, lamEnd, switchingFunction);
     int[] classes = {a1.getAtomType().atomClass, a2.getAtomType().atomClass};
     if (flatBottom != 0) {
       BondType bondType = new BondType(classes, forceConstant, distance,
           BondType.BondFunction.FLAT_BOTTOM_HARMONIC, flatBottom);
       restrainDistance.setBondType(bondType);
     } else {
       BondType bondType = new BondType(classes, forceConstant, distance,
           BondType.BondFunction.HARMONIC);
       restrainDistance.setBondType(bondType);
     }
     return restrainDistance;
   }
 }