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.amoeba;
39
40 import com.sun.jna.ptr.IntByReference;
41 import com.sun.jna.ptr.PointerByReference;
42 import ffx.openmm.Force;
43
44 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_addTorsionTorsion;
45 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_create;
46 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_destroy;
47 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_getNumTorsionTorsionGrids;
48 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_getNumTorsionTorsions;
49 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_getTorsionTorsionGrid;
50 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_getTorsionTorsionParameters;
51 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_setTorsionTorsionGrid;
52 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_setTorsionTorsionParameters;
53 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_setUsesPeriodicBoundaryConditions;
54 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_AmoebaTorsionTorsionForce_usesPeriodicBoundaryConditions;
55 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_Boolean.OpenMM_True;
56
57 /**
58 * This class implements the Amoeba torsion-torsion interaction.
59 * <p>
60 * To use it, create an AmoebaTorsionTorsionForce object then call addTorsionTorsion() once for each torsion-torsion. After
61 * a torsion-torsion has been added, you can modify its force field parameters by calling setTorsionTorsionParameters().
62 */
63 public class TorsionTorsionForce extends Force {
64
65 /**
66 * Create an AmoebaTorsionTorsionForce.
67 */
68 public TorsionTorsionForce() {
69 super(OpenMM_AmoebaTorsionTorsionForce_create());
70 }
71
72 /**
73 * Add a torsion-torsion term to the force field.
74 *
75 * @param particle1 the index of the first particle connected by the torsion-torsion
76 * @param particle2 the index of the second particle connected by the torsion-torsion
77 * @param particle3 the index of the third particle connected by the torsion-torsion
78 * @param particle4 the index of the fourth particle connected by the torsion-torsion
79 * @param particle5 the index of the fifth particle connected by the torsion-torsion
80 * @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
81 * @param gridIndex the index to the grid to be used
82 * @return the index of the torsion-torsion that was added
83 */
84 public int addTorsionTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) {
85 return OpenMM_AmoebaTorsionTorsionForce_addTorsionTorsion(pointer, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex);
86 }
87
88 /**
89 * Destroy the Amoeba Torsion-Torsion Force.
90 */
91 @Override
92 public void destroy() {
93 if (pointer != null) {
94 OpenMM_AmoebaTorsionTorsionForce_destroy(pointer);
95 pointer = null;
96 }
97 }
98
99 /**
100 * Get the number of torsion-torsion terms in the potential function
101 *
102 * @return the number of torsion-torsion terms
103 */
104 public int getNumTorsionTorsions() {
105 return OpenMM_AmoebaTorsionTorsionForce_getNumTorsionTorsions(pointer);
106 }
107
108 /**
109 * Get the number of torsion-torsion grids
110 *
111 * @return the number of torsion-torsion grids
112 */
113 public int getNumTorsionTorsionGrids() {
114 return OpenMM_AmoebaTorsionTorsionForce_getNumTorsionTorsionGrids(pointer);
115 }
116
117 /**
118 * Get the force field parameters for a torsion-torsion term.
119 *
120 * @param index the index of the torsion-torsion for which to get parameters
121 * @param particle1 the index of the first particle connected by the torsion-torsion
122 * @param particle2 the index of the second particle connected by the torsion-torsion
123 * @param particle3 the index of the third particle connected by the torsion-torsion
124 * @param particle4 the index of the fourth particle connected by the torsion-torsion
125 * @param particle5 the index of the fifth particle connected by the torsion-torsion
126 * @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
127 * @param gridIndex the grid index
128 */
129 public void getTorsionTorsionParameters(int index, IntByReference particle1, IntByReference particle2,
130 IntByReference particle3, IntByReference particle4, IntByReference particle5,
131 IntByReference chiralCheckAtomIndex, IntByReference gridIndex) {
132 OpenMM_AmoebaTorsionTorsionForce_getTorsionTorsionParameters(pointer, index, particle1, particle2, particle3,
133 particle4, particle5, chiralCheckAtomIndex, gridIndex);
134 }
135
136 /**
137 * Get the torsion-torsion grid at the specified index
138 *
139 * @param index the grid index
140 * @return grid return grid reference
141 */
142 public PointerByReference getTorsionTorsionGrid(int index) {
143 return OpenMM_AmoebaTorsionTorsionForce_getTorsionTorsionGrid(pointer, index);
144 }
145
146 /**
147 * Set the force field parameters for a torsion-torsion term.
148 *
149 * @param index the index of the torsion-torsion for which to set parameters
150 * @param particle1 the index of the first particle connected by the torsion-torsion
151 * @param particle2 the index of the second particle connected by the torsion-torsion
152 * @param particle3 the index of the third particle connected by the torsion-torsion
153 * @param particle4 the index of the fourth particle connected by the torsion-torsion
154 * @param particle5 the index of the fifth particle connected by the torsion-torsion
155 * @param chiralCheckAtomIndex the index of the particle connected to particle3, but not particle2 or particle4 to be used in chirality check
156 * @param gridIndex the grid index
157 */
158 public void setTorsionTorsionParameters(int index, int particle1, int particle2, int particle3,
159 int particle4, int particle5, int chiralCheckAtomIndex, int gridIndex) {
160 OpenMM_AmoebaTorsionTorsionForce_setTorsionTorsionParameters(pointer, index, particle1, particle2, particle3,
161 particle4, particle5, chiralCheckAtomIndex, gridIndex);
162 }
163
164 /**
165 * Set the torsion-torsion grid at the specified index
166 *
167 * @param gridIndex the index of the torsion-torsion for which to get parameters
168 * @param grid either 3 or 6 values may be specified per grid point. If the derivatives
169 * are omitted, they are calculated automatically by fitting a 2D spline to
170 * the energies.
171 * grid[x][y][0] = x value
172 * grid[x][y][1] = y value
173 * grid[x][y][2] = energy
174 * grid[x][y][3] = dEdx value
175 * grid[x][y][4] = dEdy value
176 * grid[x][y][5] = dEd(xy) value
177 */
178 public void setTorsionTorsionGrid(int gridIndex, PointerByReference grid) {
179 OpenMM_AmoebaTorsionTorsionForce_setTorsionTorsionGrid(pointer, gridIndex, grid);
180 }
181
182 /**
183 * Set whether this force should apply periodic boundary conditions when calculating displacements.
184 * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
185 *
186 * @param periodic if true, periodic boundary conditions will be used
187 */
188 public void setUsesPeriodicBoundaryConditions(boolean periodic) {
189 OpenMM_AmoebaTorsionTorsionForce_setUsesPeriodicBoundaryConditions(pointer, periodic ? 1 : 0);
190 }
191
192 /**
193 * Returns whether or not this force makes use of periodic boundary
194 * conditions.
195 *
196 * @return true if force uses PBC and false otherwise
197 */
198 @Override
199 public boolean usesPeriodicBoundaryConditions() {
200 int pbc = OpenMM_AmoebaTorsionTorsionForce_usesPeriodicBoundaryConditions(pointer);
201 return pbc == OpenMM_True;
202 }
203 }