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 static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_addBond;
41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_create;
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_updateParametersInContext;
43
44 /**
45 * Harmonic Bond Force.
46 */
47 public class HarmonicBondForce extends Force {
48
49 public HarmonicBondForce() {
50 pointer = OpenMM_HarmonicBondForce_create();
51 }
52
53 /**
54 * Add a Harmonic Bond.
55 *
56 * @param i1 Index of the first atom.
57 * @param i2 Index of the second atom.
58 * @param length The equilibrium bond length.
59 * @param k The force constant.
60 */
61 public void addBond(int i1, int i2, double length, double k) {
62 OpenMM_HarmonicBondForce_addBond(pointer, i1, i2, length, k);
63 }
64
65 /**
66 * Set the bond parameters.
67 *
68 * @param i The bond index.
69 * @param i1 Index of the first atom.
70 * @param i2 Index of the second atom.
71 * @param length The equilibrium bond length.
72 * @param k The force constant.
73 */
74 public void setBondParameters(int i, int i1, int i2, double length, double k) {
75 OpenMM_HarmonicBondForce_addBond(pointer, i1, i2, length, k);
76 }
77
78 /**
79 * Update the parameters in the OpenMM Context.
80 *
81 * @param context The OpenMM Context.
82 */
83 public void updateParametersInContext(Context context) {
84 if (context.hasContextPointer()) {
85 OpenMM_HarmonicBondForce_updateParametersInContext(pointer, context.getPointer());
86 }
87 }
88
89 }