1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
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 }