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.IntByReference;
41 import com.sun.jna.ptr.PointerByReference;
42
43 import java.nio.IntBuffer;
44
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_append;
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_create;
47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_destroy;
48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_get;
49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_getSize;
50 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_resize;
51 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_BondArray_set;
52
53 /**
54 * Bonds are specified by pairs of integers (the atom indices).
55 */
56 public class BondArray {
57
58 private PointerByReference pointer;
59
60 /**
61 * Create a new bond array.
62 *
63 * @param size The size of the bond array.
64 */
65 public BondArray(int size) {
66 pointer = OpenMM_BondArray_create(size);
67 }
68
69 /**
70 * Append a bond to the bond array.
71 *
72 * @param i1 The first atom index.
73 * @param i2 The second atom index.
74 */
75 public void append(int i1, int i2) {
76 OpenMM_BondArray_append(pointer, i1, i2);
77 }
78
79 /**
80 * Set the bond at index to i1 and i2.
81 *
82 * @param index The index of the bond to set.
83 * @param i1 The first atom index.
84 * @param i2 The second atom index.
85 */
86 public void set(int index, int i1, int i2) {
87 OpenMM_BondArray_set(pointer, index, i1, i2);
88 }
89
90 /**
91 * Get the size of the bond array.
92 *
93 * @return The size of the bond array.
94 */
95 public int getSize() {
96 return OpenMM_BondArray_getSize(pointer);
97 }
98
99 /**
100 * Resize the bond array.
101 *
102 * @param size The new size of the bond array.
103 */
104 public void resize(int size) {
105 OpenMM_BondArray_resize(pointer, size);
106 }
107
108 /**
109 * Get the bond at index.
110 *
111 * @param index The index of the bond to get.
112 * @param i1 The first atom index.
113 * @param i2 The second atom index.
114 */
115 public void get(int index, IntBuffer i1, IntBuffer i2) {
116 OpenMM_BondArray_get(pointer, index, i1, i2);
117 }
118
119 /**
120 * Get the bond at index.
121 *
122 * @param index The index of the bond to get.
123 * @param i1 The first atom index.
124 * @param i2 The second atom index.
125 */
126 public void get(int index, IntByReference i1, IntByReference i2) {
127 OpenMM_BondArray_get(pointer, index, i1, i2);
128 }
129
130 /**
131 * Get the pointer to the bond array.
132 *
133 * @return The pointer to the bond array.
134 */
135 public PointerByReference getPointer() {
136 return pointer;
137 }
138
139 /**
140 * Destroy the bond array.
141 */
142 public void destroy() {
143 if (pointer != null) {
144 OpenMM_BondArray_destroy(pointer);
145 pointer = null;
146 }
147 }
148
149 }