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_HarmonicBondForce_addBond;
48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_create;
49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_destroy;
50 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_getBondParameters;
51 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_getNumBonds;
52 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_setBondParameters;
53 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_setUsesPeriodicBoundaryConditions;
54 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_updateParametersInContext;
55 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_HarmonicBondForce_usesPeriodicBoundaryConditions;
56
57 /**
58 * This class implements an interaction between pairs of particles that varies harmonically with the distance
59 * between them. To use it, create a HarmonicBondForce object then call addBond() once for each bond. After
60 * a bond has been added, you can modify its force field parameters by calling setBondParameters(). This will
61 * have no effect on Contexts that already exist unless you call updateParametersInContext().
62 */
63 public class HarmonicBondForce extends Force {
64
65 /**
66 * Create a new HarmonicBondForce.
67 */
68 public HarmonicBondForce() {
69 super(OpenMM_HarmonicBondForce_create());
70 }
71
72 /**
73 * Add a bond term to the force field.
74 *
75 * @param i1 The index of the first particle connected by the bond.
76 * @param i2 The index of the second particle connected by the bond.
77 * @param length The equilibrium length of the bond, measured in nm.
78 * @param k The harmonic force constant for the bond, measured in kJ/mol/nmˆ2.
79 * @return The index of the bond that was added.
80 */
81 public int addBond(int i1, int i2, double length, double k) {
82 return OpenMM_HarmonicBondForce_addBond(pointer, i1, i2, length, k);
83 }
84
85 /**
86 * Destroy the force.
87 */
88 @Override
89 public void destroy() {
90 if (pointer != null) {
91 OpenMM_HarmonicBondForce_destroy(pointer);
92 pointer = null;
93 }
94 }
95
96 /**
97 * Get the force field parameters for a bond term.
98 *
99 * @param index The index of the bond for which to get parameters.
100 * @param i1 The index of the first particle connected by the bond (output).
101 * @param i2 The index of the second particle connected by the bond (output).
102 * @param length The equilibrium length of the bond, measured in nm (output).
103 * @param k The harmonic force constant for the bond, measured in kJ/mol/nmˆ2 (output).
104 */
105 public void getBondParameters(int index, IntByReference i1, IntByReference i2,
106 DoubleByReference length, DoubleByReference k) {
107 OpenMM_HarmonicBondForce_getBondParameters(pointer, index, i1, i2, length, k);
108 }
109
110 /**
111 * Get the force field parameters for a bond term.
112 *
113 * @param index The index of the bond for which to get parameters.
114 * @param i1 The index of the first particle connected by the bond (output).
115 * @param i2 The index of the second particle connected by the bond (output).
116 * @param length The equilibrium length of the bond, measured in nm (output).
117 * @param k The harmonic force constant for the bond, measured in kJ/mol/nmˆ2 (output).
118 */
119 public void getBondParameters(int index, IntBuffer i1, IntBuffer i2,
120 DoubleBuffer length, DoubleBuffer k) {
121 OpenMM_HarmonicBondForce_getBondParameters(pointer, index, i1, i2, length, k);
122 }
123
124 /**
125 * Get the number of bonds.
126 *
127 * @return The number of bonds.
128 */
129 public int getNumBonds() {
130 return OpenMM_HarmonicBondForce_getNumBonds(pointer);
131 }
132
133 /**
134 * Set the force field parameters for a bond term.
135 *
136 * @param i The index of the bond for which to set parameters.
137 * @param i1 The index of the first particle connected by the bond.
138 * @param i2 The index of the second particle connected by the bond.
139 * @param length The equilibrium length of the bond, measured in nm.
140 * @param k The harmonic force constant for the bond, measured in kJ/mol/nmˆ2.
141 */
142 public void setBondParameters(int i, int i1, int i2, double length, double k) {
143 OpenMM_HarmonicBondForce_setBondParameters(pointer, i, i1, i2, length, k);
144 }
145
146 /**
147 * Set whether this force should apply periodic boundary conditions when calculating displacements.
148 *
149 * @param periodic If true, periodic boundary conditions will be applied.
150 */
151 public void setUsesPeriodicBoundaryConditions(boolean periodic) {
152 OpenMM_HarmonicBondForce_setUsesPeriodicBoundaryConditions(pointer, periodic ? 1 : 0);
153 }
154
155 /**
156 * Update the parameters in the OpenMM Context.
157 *
158 * @param context The OpenMM Context.
159 */
160 public void updateParametersInContext(Context context) {
161 if (context.hasContextPointer()) {
162 OpenMM_HarmonicBondForce_updateParametersInContext(pointer, context.getPointer());
163 }
164 }
165
166 /**
167 * Check if the force uses periodic boundary conditions.
168 *
169 * @return True if the force uses periodic boundary conditions.
170 */
171 @Override
172 public boolean usesPeriodicBoundaryConditions() {
173 int pbc = OpenMM_HarmonicBondForce_usesPeriodicBoundaryConditions(pointer);
174 return pbc == OpenMM_True;
175 }
176 }