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 42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_append; 43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_create; 44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_destroy; 45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_get; 46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_getSize; 47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_resize; 48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_DoubleArray_set; 49 50 /** 51 * DoubleArray wrapper. 52 */ 53 public class DoubleArray { 54 55 private final PointerByReference pointer; 56 57 /** 58 * Constructor. 59 * 60 * @param size The size of the array. 61 */ 62 public DoubleArray(int size) { 63 pointer = OpenMM_DoubleArray_create(size); 64 } 65 66 /** 67 * Append a double value to the array. 68 * 69 * @param value The value to append. 70 */ 71 public void append(double value) { 72 OpenMM_DoubleArray_append(pointer, value); 73 } 74 75 /** 76 * Set a value in the array. 77 * 78 * @param index The index of the value. 79 * @param value The value. 80 */ 81 public void set(int index, double value) { 82 OpenMM_DoubleArray_set(pointer, index, value); 83 } 84 85 /** 86 * Destroy the array. 87 */ 88 public void destroy() { 89 OpenMM_DoubleArray_destroy(pointer); 90 } 91 92 /** 93 * Resize the array. 94 * 95 * @param size The new size. 96 */ 97 public void resize(int size) { 98 OpenMM_DoubleArray_resize(pointer, size); 99 } 100 101 /** 102 * Get the size of the array. 103 * 104 * @return The size. 105 */ 106 public int getSize() { 107 return OpenMM_DoubleArray_getSize(pointer); 108 } 109 110 /** 111 * Get a value from the array. 112 * 113 * @param index The index of the value. 114 * @return The value. 115 */ 116 public double get(int index) { 117 return OpenMM_DoubleArray_get(pointer, index); 118 } 119 120 /** 121 * Get the pointer to the array. 122 * 123 * @return The pointer. 124 */ 125 public PointerByReference getPointer() { 126 return pointer; 127 } 128 129 }