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.PointerByReference;
41 import edu.uiowa.jopenmm.OpenMM_Vec3;
42
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_create;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_create_2;
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_destroy;
46 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_getLocalPosition;
47 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_getOriginWeights;
48 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_getXWeights;
49 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_LocalCoordinatesSite_getYWeights;
50
51 /**
52 * This is a VirtualSite that computes the particle location based on a local coordinate system.
53 * The site is placed at a fixed position relative to a local coordinate system defined by
54 * other particles. This is useful for representing sites like lone pairs or pi-electron
55 * centers that have well-defined positions relative to the molecular framework.
56 * <p>
57 * The local coordinate system is defined by an origin and two direction vectors (x and y axes).
58 * Each of these is specified as a weighted average of particle positions. The z axis is taken
59 * to be the cross product of the x and y axes.
60 */
61 public class LocalCoordinatesSite extends VirtualSite {
62
63 /**
64 * Create a LocalCoordinatesSite using weighted averages to define the coordinate system.
65 *
66 * @param originWeights The weights for computing the origin as a weighted average of particle positions.
67 * @param xWeights The weights for computing the x direction as a weighted average of particle positions.
68 * @param yWeights The weights for computing the y direction as a weighted average of particle positions.
69 * @param zWeights The weights for computing the z direction as a weighted average of particle positions.
70 * @param localPosition The position of the virtual site in the local coordinate system.
71 */
72 public LocalCoordinatesSite(PointerByReference originWeights, PointerByReference xWeights,
73 PointerByReference yWeights, PointerByReference zWeights, OpenMM_Vec3 localPosition) {
74 super(OpenMM_LocalCoordinatesSite_create(originWeights, xWeights, yWeights, zWeights, localPosition));
75 }
76
77 /**
78 * Create a LocalCoordinatesSite using specific particles and vectors to define the coordinate system.
79 *
80 * @param particle1 The index of the first particle.
81 * @param particle2 The index of the second particle.
82 * @param particle3 The index of the third particle.
83 * @param originWeights The weights for the origin calculation.
84 * @param xdir The x direction vector.
85 * @param ydir The y direction vector.
86 * @param localPosition The position of the virtual site in the local coordinate system.
87 */
88 public LocalCoordinatesSite(int particle1, int particle2, int particle3, OpenMM_Vec3 originWeights,
89 OpenMM_Vec3 xdir, OpenMM_Vec3 ydir, OpenMM_Vec3 localPosition) {
90 super(OpenMM_LocalCoordinatesSite_create_2(particle1, particle2, particle3, originWeights, xdir, ydir, localPosition));
91 }
92
93 /**
94 * Destroy the virtual site.
95 */
96 @Override
97 public void destroy() {
98 if (pointer != null) {
99 OpenMM_LocalCoordinatesSite_destroy(pointer);
100 pointer = null;
101 }
102 }
103
104 /**
105 * Get the position of the virtual site in the local coordinate system.
106 *
107 * @return The local position of the virtual site.
108 */
109 public OpenMM_Vec3 getLocalPosition() {
110 return OpenMM_LocalCoordinatesSite_getLocalPosition(pointer);
111 }
112
113 /**
114 * Get the weights used for computing the origin of the local coordinate system.
115 *
116 * @param weights The weights for the origin calculation (output).
117 */
118 public void getOriginWeights(PointerByReference weights) {
119 OpenMM_LocalCoordinatesSite_getOriginWeights(pointer, weights);
120 }
121
122 /**
123 * Get the weights used for computing the x direction of the local coordinate system.
124 *
125 * @param weights The weights for the x direction calculation (output).
126 */
127 public void getXWeights(PointerByReference weights) {
128 OpenMM_LocalCoordinatesSite_getXWeights(pointer, weights);
129 }
130
131 /**
132 * Get the weights used for computing the y direction of the local coordinate system.
133 *
134 * @param weights The weights for the y direction calculation (output).
135 */
136 public void getYWeights(PointerByReference weights) {
137 OpenMM_LocalCoordinatesSite_getYWeights(pointer, weights);
138 }
139 }