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.DoubleByReference;
41 import com.sun.jna.ptr.IntByReference;
42
43 import java.nio.DoubleBuffer;
44 import java.nio.IntBuffer;
45
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Boolean.OpenMM_True;
47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_addTorsion;
48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_create;
49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_destroy;
50 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_getNumTorsions;
51 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_getTorsionParameters;
52 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_setTorsionParameters;
53 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_setUsesPeriodicBoundaryConditions;
54 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_updateParametersInContext;
55 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_RBTorsionForce_usesPeriodicBoundaryConditions;
56
57 /**
58 * This class implements an interaction between groups of four particles that varies with the torsion angle between them
59 * according to the Ryckaert-Bellemans potential. To use it, create an RBTorsionForce object then call addTorsion() once
60 * for each torsion. After a torsion has been added, you can modify its force field parameters by calling setTorsionParameters().
61 * This will have no effect on Contexts that already exist unless you call updateParametersInContext().
62 */
63 public class RBTorsionForce extends Force {
64
65 /**
66 * Create a new RBTorsionForce.
67 */
68 public RBTorsionForce() {
69 super(OpenMM_RBTorsionForce_create());
70 }
71
72 /**
73 * Add a torsion to the force.
74 *
75 * @param particle1 The index of the first particle forming the torsion.
76 * @param particle2 The index of the second particle forming the torsion.
77 * @param particle3 The index of the third particle forming the torsion.
78 * @param particle4 The index of the fourth particle forming the torsion.
79 * @param c0 The C0 RB parameter.
80 * @param c1 The C1 RB parameter.
81 * @param c2 The C2 RB parameter.
82 * @param c3 The C3 RB parameter.
83 * @param c4 The C4 RB parameter.
84 * @param c5 The C5 RB parameter.
85 * @return The index of the torsion that was added.
86 */
87 public int addTorsion(int particle1, int particle2, int particle3, int particle4,
88 double c0, double c1, double c2, double c3, double c4, double c5) {
89 return OpenMM_RBTorsionForce_addTorsion(pointer, particle1, particle2, particle3, particle4,
90 c0, c1, c2, c3, c4, c5);
91 }
92
93 /**
94 * Destroy the force.
95 */
96 @Override
97 public void destroy() {
98 if (pointer != null) {
99 OpenMM_RBTorsionForce_destroy(pointer);
100 pointer = null;
101 }
102 }
103
104 /**
105 * Get the number of torsions in the force.
106 *
107 * @return The number of torsions.
108 */
109 public int getNumTorsions() {
110 return OpenMM_RBTorsionForce_getNumTorsions(pointer);
111 }
112
113 /**
114 * Get the parameters for a torsion.
115 *
116 * @param index The index of the torsion for which to get parameters.
117 * @param particle1 The index of the first particle forming the torsion (output).
118 * @param particle2 The index of the second particle forming the torsion (output).
119 * @param particle3 The index of the third particle forming the torsion (output).
120 * @param particle4 The index of the fourth particle forming the torsion (output).
121 * @param c0 The C0 RB parameter (output).
122 * @param c1 The C1 RB parameter (output).
123 * @param c2 The C2 RB parameter (output).
124 * @param c3 The C3 RB parameter (output).
125 * @param c4 The C4 RB parameter (output).
126 * @param c5 The C5 RB parameter (output).
127 */
128 public void getTorsionParameters(int index, IntByReference particle1, IntByReference particle2,
129 IntByReference particle3, IntByReference particle4,
130 DoubleByReference c0, DoubleByReference c1, DoubleByReference c2,
131 DoubleByReference c3, DoubleByReference c4, DoubleByReference c5) {
132 OpenMM_RBTorsionForce_getTorsionParameters(pointer, index, particle1, particle2, particle3, particle4,
133 c0, c1, c2, c3, c4, c5);
134 }
135
136 /**
137 * Get the parameters for a torsion.
138 *
139 * @param index The index of the torsion for which to get parameters.
140 * @param particle1 The index of the first particle forming the torsion (output).
141 * @param particle2 The index of the second particle forming the torsion (output).
142 * @param particle3 The index of the third particle forming the torsion (output).
143 * @param particle4 The index of the fourth particle forming the torsion (output).
144 * @param c0 The C0 RB parameter (output).
145 * @param c1 The C1 RB parameter (output).
146 * @param c2 The C2 RB parameter (output).
147 * @param c3 The C3 RB parameter (output).
148 * @param c4 The C4 RB parameter (output).
149 * @param c5 The C5 RB parameter (output).
150 */
151 public void getTorsionParameters(int index, IntBuffer particle1, IntBuffer particle2,
152 IntBuffer particle3, IntBuffer particle4,
153 DoubleBuffer c0, DoubleBuffer c1, DoubleBuffer c2,
154 DoubleBuffer c3, DoubleBuffer c4, DoubleBuffer c5) {
155 OpenMM_RBTorsionForce_getTorsionParameters(pointer, index, particle1, particle2, particle3, particle4,
156 c0, c1, c2, c3, c4, c5);
157 }
158
159 /**
160 * Set the parameters for a torsion.
161 *
162 * @param index The index of the torsion for which to set parameters.
163 * @param particle1 The index of the first particle forming the torsion.
164 * @param particle2 The index of the second particle forming the torsion.
165 * @param particle3 The index of the third particle forming the torsion.
166 * @param particle4 The index of the fourth particle forming the torsion.
167 * @param c0 The C0 RB parameter.
168 * @param c1 The C1 RB parameter.
169 * @param c2 The C2 RB parameter.
170 * @param c3 The C3 RB parameter.
171 * @param c4 The C4 RB parameter.
172 * @param c5 The C5 RB parameter.
173 */
174 public void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4,
175 double c0, double c1, double c2, double c3, double c4, double c5) {
176 OpenMM_RBTorsionForce_setTorsionParameters(pointer, index, particle1, particle2, particle3, particle4,
177 c0, c1, c2, c3, c4, c5);
178 }
179
180 /**
181 * Set whether this force should apply periodic boundary conditions when calculating displacements.
182 *
183 * @param periodic If true, periodic boundary conditions will be applied.
184 */
185 public void setUsesPeriodicBoundaryConditions(boolean periodic) {
186 OpenMM_RBTorsionForce_setUsesPeriodicBoundaryConditions(pointer, periodic ? 1 : 0);
187 }
188
189 /**
190 * Update the parameters in the OpenMM Context.
191 *
192 * @param context The OpenMM Context.
193 */
194 public void updateParametersInContext(Context context) {
195 if (context.hasContextPointer()) {
196 OpenMM_RBTorsionForce_updateParametersInContext(pointer, context.getPointer());
197 }
198 }
199
200 /**
201 * Check if the force uses periodic boundary conditions.
202 *
203 * @return True if the force uses periodic boundary conditions.
204 */
205 @Override
206 public boolean usesPeriodicBoundaryConditions() {
207 int pbc = OpenMM_RBTorsionForce_usesPeriodicBoundaryConditions(pointer);
208 return pbc == OpenMM_True;
209 }
210 }