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
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_VirtualSite_getNumParticles;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_VirtualSite_getParticle;
44
45 /**
46 * A VirtualSite describes the rules for computing a particle's position based on
47 * other particles. This is an abstract class. Subclasses define particular rules.
48 * To define a virtual site, create an instance of a VirtualSite subclass and then
49 * call setVirtualSite() on the System.
50 */
51 public abstract class VirtualSite {
52
53 /**
54 * The pointer is allocated and deallocated by classes that extend VirtualSite.
55 */
56 protected PointerByReference pointer;
57
58 /**
59 * Create a VirtualSite from an existing pointer.
60 *
61 * @param pointer The pointer to the OpenMM VirtualSite.
62 */
63 public VirtualSite(PointerByReference pointer) {
64 this.pointer = pointer;
65 }
66
67 /**
68 * Destroy the virtual site.
69 */
70 public abstract void destroy();
71
72 /**
73 * Get the number of particles this virtual site depends on.
74 *
75 * @return The number of particles.
76 */
77 public int getNumParticles() {
78 return OpenMM_VirtualSite_getNumParticles(pointer);
79 }
80
81 /**
82 * Get the index of a particle this virtual site depends on.
83 *
84 * @param particle the particle to get (between 0 and getNumParticles())
85 * @return the index of the particle in the System
86 */
87 public int getParticle(int particle) {
88 return OpenMM_VirtualSite_getParticle(pointer, particle);
89 }
90
91 /**
92 * Get the pointer to the OpenMM VirtualSite.
93 *
94 * @return The pointer to the OpenMM VirtualSite.
95 */
96 public PointerByReference getPointer() {
97 return pointer;
98 }
99 }