1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2024.
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_CustomCentroidBondForce_addBond;
41 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_addGroup;
42 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_addPerBondParameter;
43 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_create;
44 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_destroy;
45 import static edu.uiowa.jopenmm.OpenMMLibrary.OpenMM_CustomCentroidBondForce_setUsesPeriodicBoundaryConditions;
46
47 /**
48 * Custom Centroid Bond Force.
49 */
50 public class CentroidBondForce extends Force {
51
52 /**
53 * OpenMM CustomCentroidBondForce constructor.
54 *
55 * @param nGroups The number of particles in the bond.
56 * @param energy The energy expression.
57 */
58 public CentroidBondForce(int nGroups, String energy) {
59 pointer = OpenMM_CustomCentroidBondForce_create(nGroups, energy);
60 }
61
62 /**
63 * Add a per bond parameters
64 *
65 * @param name The parameter name.
66 */
67 public void addPerBondParameter(String name) {
68 OpenMM_CustomCentroidBondForce_addPerBondParameter(pointer, name);
69 }
70
71 /**
72 * Add a atoms of atoms to the force.
73 *
74 * @param atoms The group of atoms.
75 * @param weight The weight of each atom.
76 */
77 public void addGroup(IntArray atoms, DoubleArray weight) {
78 OpenMM_CustomCentroidBondForce_addGroup(pointer, atoms.getPointer(), weight.getPointer());
79 }
80
81 /**
82 * Add a bond between two groups to the force.
83 *
84 * @param groups The two groups.
85 * @param parameters The parameters of each groups.
86 */
87 public void addBond(IntArray groups, DoubleArray parameters) {
88 OpenMM_CustomCentroidBondForce_addBond(pointer, groups.getPointer(), parameters.getPointer());
89 }
90
91 /**
92 * Set whether to use periodic boundary conditions.
93 *
94 * @param periodic 1 if periodic boundary conditions should be used, 0 if not.
95 */
96 public void setUsesPeriodicBoundaryConditions(int periodic) {
97 OpenMM_CustomCentroidBondForce_setUsesPeriodicBoundaryConditions(pointer, periodic);
98 }
99
100 /**
101 * Destroy the OpenMM CustomCentroidBondForce.
102 */
103 public void destroy() {
104 OpenMM_CustomCentroidBondForce_destroy(pointer);
105 }
106
107 }