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_CustomBondForce_addBond;
41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_addGlobalParameter;
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_addPerBondParameter;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_create;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_destroy;
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_setBondParameters;
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomBondForce_updateParametersInContext;
47
48 /**
49 * Custom Bond Force.
50 */
51 public class CustomBondForce extends Force {
52
53 /**
54 * Custom Bond Force Constructor.
55 *
56 * @param energy The definition of the Energy.
57 */
58 public CustomBondForce(String energy) {
59 pointer = OpenMM_CustomBondForce_create(energy);
60 }
61
62 /**
63 * Add a bond to the OpenMM System.
64 *
65 * @param i1 The index of the first atom.
66 * @param i2 The index of the second atom.
67 * @param parameters The bond parameters.
68 */
69 public void addBond(int i1, int i2, DoubleArray parameters) {
70 OpenMM_CustomBondForce_addBond(pointer, i1, i2, parameters.getPointer());
71 }
72
73 /**
74 * Add a per-bond parameter to the CustomBondForce.
75 *
76 * @param name The name of the parameter.
77 */
78 public void addPerBondParameter(String name) {
79 OpenMM_CustomBondForce_addPerBondParameter(pointer, name);
80 }
81
82 /**
83 * Add a global parameter to the CustomBondForce.
84 *
85 * @param name The name of the parameter.
86 * @param value The value of the parameter.
87 */
88 public void addGlobalParameter(String name, double value) {
89 OpenMM_CustomBondForce_addGlobalParameter(pointer, name, value);
90 }
91
92 /**
93 * Set the parameters for one bond in the OpenMM System.
94 *
95 * @param index The index of the bond.
96 * @param i1 The index of the first atom.
97 * @param i2 The index of the second atom.
98 * @param parameters The bond parameters.
99 */
100 public void setBondParameters(int index, int i1, int i2, DoubleArray parameters) {
101 OpenMM_CustomBondForce_setBondParameters(pointer, index, i1, i2, parameters.getPointer());
102 }
103
104 /**
105 * Update the parameters in the OpenMM Context.
106 *
107 * @param context The OpenMM Context.
108 */
109 public void updateParametersInContext(Context context) {
110 if (context.hasContextPointer()) {
111 OpenMM_CustomBondForce_updateParametersInContext(pointer, context.getPointer());
112 }
113 }
114
115 /**
116 * Destroy the OpenMM CustomBondForce.
117 */
118 public void destroy() {
119 if (pointer != null) {
120 OpenMM_CustomBondForce_destroy(pointer);
121 pointer = null;
122 }
123 }
124
125 }