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_CustomNonbondedForce_addExclusion;
41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_addGlobalParameter;
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_addInteractionGroup;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_addParticle;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_addPerParticleParameter;
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_create;
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_destroy;
47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_setCutoffDistance;
48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_setNonbondedMethod;
49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_setSwitchingDistance;
50 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomNonbondedForce_setUseSwitchingFunction;
51
52 /**
53 * Custom Non-bonded Force.
54 */
55 public class CustomNonbondedForce extends Force {
56
57 public CustomNonbondedForce(String energy) {
58 pointer = OpenMM_CustomNonbondedForce_create(energy);
59 }
60
61 /**
62 * Add a global parameter.
63 *
64 * @param name The parameter name.
65 * @param value The parameter value.
66 */
67 public void addGlobalParameter(String name, double value) {
68 OpenMM_CustomNonbondedForce_addGlobalParameter(pointer, name, value);
69 }
70
71 /**
72 * Add a per particle parameter.
73 *
74 * @param name The parameter name.
75 */
76 public void addPerParticleParameter(String name) {
77 OpenMM_CustomNonbondedForce_addPerParticleParameter(pointer, name);
78 }
79
80 /**
81 * Add a particle to the force.
82 *
83 * @param parameters The particle parameters.
84 */
85 public void addParticle(DoubleArray parameters) {
86 OpenMM_CustomNonbondedForce_addParticle(pointer, parameters.getPointer());
87 }
88
89 /**
90 * Add an interaction group.
91 *
92 * @param group1 The first group.
93 * @param group2 The second group.
94 */
95 public void addInteractionGroup(IntSet group1, IntSet group2) {
96 OpenMM_CustomNonbondedForce_addInteractionGroup(pointer, group1.getPointer(), group2.getPointer());
97 }
98
99 /**
100 * Set the nonbonded method.
101 *
102 * @param method The nonbonded method.
103 */
104 public void setNonbondedMethod(int method) {
105 OpenMM_CustomNonbondedForce_setNonbondedMethod(pointer, method);
106 }
107
108 /**
109 * Set the cutoff distance.
110 *
111 * @param off The cutoff distance.
112 */
113 public void setCutoffDistance(double off) {
114 OpenMM_CustomNonbondedForce_setCutoffDistance(pointer, off);
115 }
116
117 /**
118 * Flag to contol use of a switching function.
119 *
120 * @param useSwitchingFunction If 1, the switching function is used.
121 */
122 public void setUseSwitchingFunction(int useSwitchingFunction) {
123 OpenMM_CustomNonbondedForce_setUseSwitchingFunction(pointer, useSwitchingFunction);
124 }
125
126 /**
127 * Set the switching distance.
128 *
129 * @param switchingDistance The switching distance.
130 */
131 public void setSwitchingDistance(double switchingDistance) {
132 OpenMM_CustomNonbondedForce_setSwitchingDistance(pointer, switchingDistance);
133 }
134
135 /**
136 * Add an exclusion.
137 *
138 * @param particle1 The first particle.
139 * @param particle2 The second particle.
140 */
141 public void addExclusion(int particle1, int particle2) {
142 OpenMM_CustomNonbondedForce_addExclusion(pointer, particle1, particle2);
143 }
144
145 /**
146 * Destroy the force.
147 */
148 public void destroy() {
149 if (pointer != null) {
150 OpenMM_CustomNonbondedForce_destroy(pointer);
151 pointer = null;
152 }
153 }
154 }