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 static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_OutOfPlaneSite_create;
41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_OutOfPlaneSite_destroy;
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_OutOfPlaneSite_getWeight12;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_OutOfPlaneSite_getWeight13;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_OutOfPlaneSite_getWeightCross;
45
46 /**
47 * This is a VirtualSite that computes the particle location based on three other
48 * particles' locations. If r<sub>1</sub> is the location of particle 1,
49 * r<sub>12</sub> is the vector from particle 1 to particle 2, and
50 * r<sub>13</sub> is the vector from particle 1 to particle 3, then the virtual
51 * site location is given by
52 * <p>
53 * r<sub>1</sub> + w<sub>12</sub>r<sub>12</sub> + w<sub>13</sub>r<sub>13</sub> + w<sub>cross</sub>(r<sub>12</sub> x r<sub>13</sub>)
54 * <p>
55 * The three weight factors are user-specified. This allows the virtual site location
56 * to be out of the plane of the three particles. Note that while w<sub>12</sub> and
57 * w<sub>13</sub> are unitless, w<sub>cross</sub> has units of inverse distance.
58 */
59 public class OutOfPlaneSite extends VirtualSite {
60
61 /**
62 * Create an OutOfPlaneSite.
63 *
64 * @param particle1 The index of the first particle.
65 * @param particle2 The index of the second particle.
66 * @param particle3 The index of the third particle.
67 * @param weight12 The weight for the vector from particle1 to particle2.
68 * @param weight13 The weight for the vector from particle1 to particle3.
69 * @param weightCross The weight for the cross product of the two vectors.
70 */
71 public OutOfPlaneSite(int particle1, int particle2, int particle3,
72 double weight12, double weight13, double weightCross) {
73 super(OpenMM_OutOfPlaneSite_create(particle1, particle2, particle3, weight12, weight13, weightCross));
74 }
75
76 /**
77 * Destroy the virtual site.
78 */
79 @Override
80 public void destroy() {
81 if (pointer != null) {
82 OpenMM_OutOfPlaneSite_destroy(pointer);
83 pointer = null;
84 }
85 }
86
87 /**
88 * Get the weight for the vector from particle1 to particle2.
89 *
90 * @return The weight12 parameter.
91 */
92 public double getWeight12() {
93 return OpenMM_OutOfPlaneSite_getWeight12(pointer);
94 }
95
96 /**
97 * Get the weight for the vector from particle1 to particle3.
98 *
99 * @return The weight13 parameter.
100 */
101 public double getWeight13() {
102 return OpenMM_OutOfPlaneSite_getWeight13(pointer);
103 }
104
105 /**
106 * Get the weight for the cross product of the two vectors.
107 *
108 * @return The weightCross parameter.
109 */
110 public double getWeightCross() {
111 return OpenMM_OutOfPlaneSite_getWeightCross(pointer);
112 }
113 }