// ******************************************************************************
   //
   // 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.OutOfPlaneBend;
  import ffx.potential.parameters.OutOfPlaneBendType;
  
  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;
  import static org.apache.commons.math3.util.FastMath.PI;
  
  /**
   * Out-of-Plane Bend potential energy term using {@link ffx.potential.bonded.OutOfPlaneBend} instances.
   */
  public class OutOfPlaneBendPotentialEnergy extends EnergyTerm {
  
    private static final Logger logger = Logger.getLogger(OutOfPlaneBendPotentialEnergy.class.getName());
  
  
    /**
     * Internal list of OutOfPlaneBend instances.
     */
    private final List<OutOfPlaneBend> outOfPlaneBends = new ArrayList<>();
  
    /**
     * Create an OutOfPlaneBendPotentialEnergy with the provided name.
     *
     * @param name Name for this term.
     */
    public OutOfPlaneBendPotentialEnergy(String name) {
      super(name);
    }
  
    /**
     * Create an OutOfPlaneBendPotentialEnergy with the provided name and force group.
     *
     * @param name       Name for this term.
     * @param forceGroup Integer force group identifier.
     */
    public OutOfPlaneBendPotentialEnergy(String name, int forceGroup) {
      super(name, forceGroup);
    }
  
    /**
     * Create an OutOfPlaneBendPotentialEnergy initialized with a list of terms and force group.
     *
     * @param name            Name for this term.
     * @param forceGroup      Force group identifier.
     * @param outOfPlaneBends List of OutOfPlaneBend instances to add (null-safe).
     */
    public OutOfPlaneBendPotentialEnergy(String name, int forceGroup, List<OutOfPlaneBend> outOfPlaneBends) {
      super(name, forceGroup);
      if (outOfPlaneBends != null) {
        Collections.sort(outOfPlaneBends);
        this.outOfPlaneBends.addAll(outOfPlaneBends);
        logger.info(format("  Out-of-Plane Bends:                %10d", getNumberOfOutOfPlaneBends()));
      }
    }
  
   /**
    * {@inheritDoc}
    */
   @Override
   public int getNumberOfTerms() {
     return getNumberOfOutOfPlaneBends();
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public BondedTerm[] getBondedTermsArray() {
     return getOutOfPlaneBendArray();
   }
 
   /**
    * Create an OutOfPlaneBendPotentialEnergy initialized with a collection of terms.
    *
    * @param name            Name for this term (may be null).
    * @param outOfPlaneBends Collection of OutOfPlaneBend instances to add (null-safe).
    */
   public OutOfPlaneBendPotentialEnergy(String name, Collection<OutOfPlaneBend> outOfPlaneBends) {
     super(name);
     if (outOfPlaneBends != null) {
       this.outOfPlaneBends.addAll(outOfPlaneBends);
     }
   }
 
   /**
    * Add an OutOfPlaneBend to this term.
    *
    * @param outOfPlaneBend OutOfPlaneBend to add (ignored if null).
    * @return true if it was added.
    */
   public boolean addOutOfPlaneBend(OutOfPlaneBend outOfPlaneBend) {
     if (outOfPlaneBend == null) {
       return false;
     }
     return outOfPlaneBends.add(outOfPlaneBend);
   }
 
   /**
    * Add an array of OutOfPlaneBends to this term.
    *
    * @param outOfPlaneBends Array of OutOfPlaneBend instances to add.
    * @return true if they were added.
    */
   public boolean addOutOfPlaneBends(OutOfPlaneBend[] outOfPlaneBends) {
     if (outOfPlaneBends == null) {
       return false;
     }
     Collections.addAll(this.outOfPlaneBends, outOfPlaneBends);
     return true;
   }
 
   /**
    * Add a list of OutOfPlaneBends to this term.
    *
    * @param outOfPlaneBends List of OutOfPlaneBend instances to add.
    * @return true if they were added.
    */
   public boolean addOutOfPlaneBends(List<OutOfPlaneBend> outOfPlaneBends) {
     if (outOfPlaneBends == null) {
       return false;
     }
     this.outOfPlaneBends.addAll(outOfPlaneBends);
     return true;
   }
 
   /**
    * Remove an OutOfPlaneBend from this term.
    *
    * @param outOfPlaneBend OutOfPlaneBend to remove (ignored if null).
    * @return true if it was present and removed.
    */
   public boolean removeOutOfPlaneBend(OutOfPlaneBend outOfPlaneBend) {
     if (outOfPlaneBend == null) {
       return false;
     }
     return outOfPlaneBends.remove(outOfPlaneBend);
   }
 
   /**
    * Get the OutOfPlaneBend at a given index.
    *
    * @param index Index in the internal list.
    * @return OutOfPlaneBend at the specified index.
    * @throws IndexOutOfBoundsException if index is invalid.
    */
   public OutOfPlaneBend getOutOfPlaneBend(int index) {
     return outOfPlaneBends.get(index);
   }
 
   /**
    * Get an unmodifiable view of the OutOfPlaneBends in this term.
    *
    * @return Unmodifiable List of OutOfPlaneBends.
    */
   public List<OutOfPlaneBend> getOutOfPlaneBends() {
     return Collections.unmodifiableList(outOfPlaneBends);
   }
 
   /**
    * Get an array of OutOfPlaneBends in this term.
    *
    * @return Array of OutOfPlaneBends.
    */
   public OutOfPlaneBend[] getOutOfPlaneBendArray() {
     return outOfPlaneBends.toArray(new OutOfPlaneBend[0]);
   }
 
   /**
    * Get the number of OutOfPlaneBends in this term.
    *
    * @return The number of OutOfPlaneBends.
    */
   public int getNumberOfOutOfPlaneBends() {
     return outOfPlaneBends.size();
   }
 
 
   /**
    * Get a string representation of the Out-of-Plane Bend energy expression.
    * @return A formatted string representing the energy expression for Out-of-Plane Bends.
    */
   public String getOutOfPlaneEnergyString() {
     OutOfPlaneBendType outOfPlaneBendType = outOfPlaneBends.getFirst().outOfPlaneBendType;
     String energy = format(""" 
             k*(theta^2 + %.15g*theta^3 + %.15g*theta^4 + %.15g*theta^5 + %.15g*theta^6);
             theta = %.15g*pointangle(x2, y2, z2, x4, y4, z4, projx, projy, projz);
             projx = x2-nx*dot;
             projy = y2-ny*dot;
             projz = z2-nz*dot;
             dot = nx*(x2-x3) + ny*(y2-y3) + nz*(z2-z3);
             nx = px/norm;
             ny = py/norm;
             nz = pz/norm;
             norm = sqrt(px*px + py*py + pz*pz);
             px = (d1y*d2z-d1z*d2y);
             py = (d1z*d2x-d1x*d2z);
             pz = (d1x*d2y-d1y*d2x);
             d1x = x1-x4;
             d1y = y1-y4;
             d1z = z1-z4;
             d2x = x3-x4;
             d2y = y3-y4;
             d2z = z3-z4
             """,
         outOfPlaneBendType.cubic, outOfPlaneBendType.quartic,
         outOfPlaneBendType.pentic, outOfPlaneBendType.sextic, 180.0 / PI);
     return energy;
   }
 
   /**
    * Log the details of Out-of-Plane Bend interactions.
    */
   @Override
   public void log() {
     if (getNumberOfOutOfPlaneBends() <= 0) {
       return;
     }
     logger.info("\n Out-of-Plane Bend Interactions:");
     for (OutOfPlaneBend outOfPlaneBend : getOutOfPlaneBends()) {
       logger.info(" Out-of-Plane Bend \t" + outOfPlaneBend.toString());
     }
   }
 
   @Override
   public String toPDBString() {
     if (getNumberOfOutOfPlaneBends() <= 0) {
       return "";
     }
     return format("REMARK   3   %s %g (%d)\n", "OUT-OF-PLANE BEND          : ", getEnergy(), getNumberOfOutOfPlaneBends());
   }
 
   @Override
   public String toString() {
     return format("  %s %20.8f %12d %12.3f\n", "Out-of-Plane Bend ",
         getEnergy(), getNumberOfOutOfPlaneBends(), getTime());
   }
 }