1 // ****************************************************************************** 2 // 3 // Title: Force Field X. 4 // Description: Force Field X - Software for Molecular Biophysics. 5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025. 6 // 7 // This file is part of Force Field X. 8 // 9 // Force Field X is free software; you can redistribute it and/or modify it 10 // under the terms of the GNU General Public License version 3 as published by 11 // the Free Software Foundation. 12 // 13 // Force Field X is distributed in the hope that it will be useful, but WITHOUT 14 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 15 // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more 16 // details. 17 // 18 // You should have received a copy of the GNU General Public License along with 19 // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple 20 // Place, Suite 330, Boston, MA 02111-1307 USA 21 // 22 // Linking this library statically or dynamically with other modules is making a 23 // combined work based on this library. Thus, the terms and conditions of the 24 // GNU General Public License cover the whole combination. 25 // 26 // As a special exception, the copyright holders of this library give you 27 // permission to link this library with independent modules to produce an 28 // executable, regardless of the license terms of these independent modules, and 29 // to copy and distribute the resulting executable under terms of your choice, 30 // provided that you also meet, for each linked independent module, the terms 31 // and conditions of the license of that module. An independent module is a 32 // module which is not derived from or based on this library. If you modify this 33 // library, you may extend this exception to your version of the library, but 34 // you are not obligated to do so. If you do not wish to do so, delete this 35 // exception statement from your version. 36 // 37 // ****************************************************************************** 38 package ffx.openmm; 39 40 import com.sun.jna.ptr.PointerByReference; 41 import edu.uiowa.jopenmm.OpenMM_Vec3; 42 43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_append; 44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_create; 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_destroy; 46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_get; 47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_getSize; 48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_resize; 49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Vec3Array_set; 50 51 /** 52 * Vec3 Array. 53 */ 54 public class Vec3Array { 55 56 /** 57 * String vec3 array pointer. 58 */ 59 private PointerByReference pointer; 60 61 /** 62 * OpenMM Vec3 Array constructor. 63 * 64 * @param size The size of the String Array. 65 */ 66 public Vec3Array(int size) { 67 pointer = OpenMM_Vec3Array_create(size); 68 } 69 70 /** 71 * OpenMM Vec3 Array constructor. 72 * 73 * @param pointer The Vec3 Array pointer. 74 */ 75 public Vec3Array(PointerByReference pointer) { 76 this.pointer = pointer; 77 } 78 79 /** 80 * Get the pointer to the vec3 array pointer. 81 * 82 * @return The pointer to the vec3 array. 83 */ 84 public PointerByReference getPointer() { 85 return pointer; 86 } 87 88 /** 89 * Append a Vec3 to the Vec3Array. 90 * 91 * @param vec3 The Vec3 to append. 92 */ 93 public void append(OpenMM_Vec3.ByValue vec3) { 94 OpenMM_Vec3Array_append(pointer, vec3); 95 } 96 97 /** 98 * Get a Vec3 from the Vec3Array. 99 * 100 * @return The Vec3 at index i. 101 */ 102 public OpenMM_Vec3 get(int i) { 103 return OpenMM_Vec3Array_get(pointer, i); 104 } 105 106 /** 107 * Get the size of the Vec3Array. 108 * 109 * @return The size of the Vec3Array. 110 */ 111 public int getSize() { 112 return OpenMM_Vec3Array_getSize(pointer); 113 } 114 115 /** 116 * Resize the Vec3Array. 117 * 118 * @param size The new size of the Vec3Array. 119 */ 120 public void resize(int size) { 121 OpenMM_Vec3Array_resize(pointer, size); 122 } 123 124 /** 125 * Set a Vec3 in the Vec3Array. 126 * 127 * @param i The index of the Vec3 to set. 128 * @param vec3 The Vec3 to set. 129 */ 130 public void set(int i, OpenMM_Vec3.ByValue vec3) { 131 OpenMM_Vec3Array_set(pointer, i, vec3); 132 } 133 134 /** 135 * Destroy the Vec3Array. 136 */ 137 public void destroy() { 138 if (pointer != null) { 139 OpenMM_Vec3Array_destroy(pointer); 140 pointer = null; 141 } 142 } 143 144 /** 145 * Convert a double array to a Vec3Array. 146 * 147 * @param array The double array. 148 * @return The Vec3Array. 149 */ 150 public static Vec3Array toVec3Array(double[] array) { 151 Vec3Array vec3Array = new Vec3Array(0); 152 OpenMM_Vec3.ByValue vec3 = new OpenMM_Vec3.ByValue(); 153 for (int i = 0; i < array.length; i += 3) { 154 vec3.x = array[i]; 155 vec3.y = array[i + 1]; 156 vec3.z = array[i + 2]; 157 vec3Array.append(vec3); 158 } 159 return vec3Array; 160 } 161 162 /** 163 * Convert the Vec3Array to a double array. 164 * 165 * @return The double array. 166 */ 167 public double[] getArray() { 168 int size = getSize(); 169 double[] array = new double[size * 3]; 170 for (int i = 0; i < size; i++) { 171 OpenMM_Vec3 vec3 = get(i); 172 int index = i * 3; 173 array[index] = vec3.x; 174 array[index + 1] = vec3.y; 175 array[index + 2] = vec3.z; 176 } 177 return array; 178 } 179 180 }