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_CustomCompoundBondForce_addBond;
41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_addGlobalParameter;
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_addPerBondParameter;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_create;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_destroy;
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_setBondParameters;
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCompoundBondForce_updateParametersInContext;
47
48 /**
49 * Custom Compound Bond Force.
50 */
51 public class CustomCompoundBondForce extends Force {
52
53 public CustomCompoundBondForce(int i, String energy) {
54 pointer = OpenMM_CustomCompoundBondForce_create(i, energy);
55 }
56
57 /**
58 * Add a per-bond parameter to the OpenMM System.
59 *
60 * @param name The name of the parameter.
61 */
62 public void addPerBondParameter(String name) {
63 OpenMM_CustomCompoundBondForce_addPerBondParameter(pointer, name);
64 }
65
66 /**
67 * Add a global parameter.
68 *
69 * @param name The parameter name.
70 * @param value The parameter value.
71 */
72 public void addGlobalParameter(String name, double value) {
73 OpenMM_CustomCompoundBondForce_addGlobalParameter(pointer, name, value);
74 }
75
76 /**
77 * Add a Custom Compound Bond to the OpenMM System.
78 *
79 * @param particles The indices of the particles.
80 * @param parameters The bond parameters.
81 */
82 public void addBond(IntArray particles, DoubleArray parameters) {
83 OpenMM_CustomCompoundBondForce_addBond(pointer, particles.getPointer(), parameters.getPointer());
84 }
85
86 /**
87 * Set the parameters for a Custom Compound Bond.
88 *
89 * @param index The index of the bond.
90 * @param particles The indices of the particles.
91 * @param parameters The bond parameters.
92 */
93 public void setBondParameters(int index, IntArray particles, DoubleArray parameters) {
94 OpenMM_CustomCompoundBondForce_setBondParameters(pointer, index, particles.getPointer(), parameters.getPointer());
95 }
96
97 /**
98 * Update the parameters in the OpenMM Context.
99 *
100 * @param context The OpenMM Context.
101 */
102 public void updateParametersInContext(Context context) {
103 if (context.hasContextPointer()) {
104 OpenMM_CustomCompoundBondForce_updateParametersInContext(pointer, context.getPointer());
105 }
106 }
107
108 /**
109 * Clean up.
110 */
111 public void destroy() {
112 OpenMM_CustomCompoundBondForce_destroy(pointer);
113 }
114
115 }