// ******************************************************************************
   //
   // 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.openmm;
  
  import com.sun.jna.ptr.PointerByReference;
  import edu.uiowa.jopenmm.OpenMM_Vec3;
  
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_append;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_create;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_destroy;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_get;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_getSize;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_resize;
  import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_set;
  
  /**
   * Vec3 Array.
   */
  public class Vec3Array {
  
    /**
     * String vec3 array pointer.
     */
    private PointerByReference pointer;
  
    /**
     * OpenMM Vec3 Array constructor.
     *
     * @param size The size of the String Array.
     */
    public Vec3Array(int size) {
      pointer = OpenMM_Vec3Array_create(size);
    }
  
    /**
     * OpenMM Vec3 Array constructor.
     *
     * @param pointer The Vec3 Array pointer.
     */
    public Vec3Array(PointerByReference pointer) {
      this.pointer = pointer;
    }
  
    /**
     * Append a Vec3 to the Vec3Array.
     *
     * @param vec3 The Vec3 to append.
     */
    public void append(OpenMM_Vec3.ByValue vec3) {
      OpenMM_Vec3Array_append(pointer, vec3);
    }
  
    /**
     * Destroy the Vec3Array.
     */
    public void destroy() {
      if (pointer != null) {
        OpenMM_Vec3Array_destroy(pointer);
        pointer = null;
      }
    }
  
    /**
     * Get a Vec3 from the Vec3Array.
    *
    * @return The Vec3 at index i.
    */
   public OpenMM_Vec3 get(int i) {
     return OpenMM_Vec3Array_get(pointer, i);
   }
 
   /**
    * Convert the Vec3Array to a double array.
    *
    * @return The double array.
    */
   public double[] getArray() {
     int size = getSize();
     double[] array = new double[size * 3];
     for (int i = 0; i < size; i++) {
       OpenMM_Vec3 vec3 = get(i);
       int index = i * 3;
       array[index] = vec3.x;
       array[index + 1] = vec3.y;
       array[index + 2] = vec3.z;
     }
     return array;
   }
 
   /**
    * Get the pointer to the vec3 array pointer.
    *
    * @return The pointer to the vec3 array.
    */
   public PointerByReference getPointer() {
     return pointer;
   }
 
   /**
    * Get the size of the Vec3Array.
    *
    * @return The size of the Vec3Array.
    */
   public int getSize() {
     return OpenMM_Vec3Array_getSize(pointer);
   }
 
   /**
    * Resize the Vec3Array.
    *
    * @param size The new size of the Vec3Array.
    */
   public void resize(int size) {
     OpenMM_Vec3Array_resize(pointer, size);
   }
 
   /**
    * Set a Vec3 in the Vec3Array.
    *
    * @param i    The index of the Vec3 to set.
    * @param vec3 The Vec3 to set.
    */
   public void set(int i, OpenMM_Vec3.ByValue vec3) {
     OpenMM_Vec3Array_set(pointer, i, vec3);
   }
 
   /**
    * Convert a double array to a Vec3Array.
    *
    * @param array The double array.
    * @return The Vec3Array.
    */
   public static Vec3Array toVec3Array(double[] array) {
     Vec3Array vec3Array = new Vec3Array(0);
     OpenMM_Vec3.ByValue vec3 = new OpenMM_Vec3.ByValue();
     for (int i = 0; i < array.length; i += 3) {
       vec3.x = array[i];
       vec3.y = array[i + 1];
       vec3.z = array[i + 2];
       vec3Array.append(vec3);
     }
     return vec3Array;
   }
 
 }