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.potential.openmm;
39
40 import ffx.openmm.DoubleArray;
41 import ffx.openmm.Force;
42 import ffx.openmm.IntArray;
43 import ffx.openmm.CustomCompoundBondForce;
44 import ffx.potential.bonded.AngleTorsion;
45 import ffx.potential.bonded.Atom;
46
47 import java.util.logging.Level;
48 import java.util.logging.Logger;
49
50 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_KJPerKcal;
51 import static edu.uiowa.jopenmm.OpenMMAmoebaLibrary.OpenMM_RadiansPerDegree;
52 import static java.lang.String.format;
53
54 /**
55 * OpenMM Angle-Torsion Force.
56 */
57 public class AngleTorsionForce extends CustomCompoundBondForce {
58
59 private static final Logger logger = Logger.getLogger(AngleTorsionForce.class.getName());
60
61 /**
62 * Create an OpenMM Angle-Torsion Force.
63 *
64 * @param openMMEnergy The OpenMM Energy instance that contains the Angle-Torsions.
65 */
66 public AngleTorsionForce(OpenMMEnergy openMMEnergy) {
67 super(4, AngleTorsion.angleTorsionForm());
68 AngleTorsion[] angleTorsions = openMMEnergy.getAngleTorsions();
69 if (angleTorsions == null || angleTorsions.length < 1) {
70 // Free the memory created by the call to super.
71 destroy();
72 return;
73 }
74 addGlobalParameter("phi1", 0);
75 addGlobalParameter("phi2", Math.PI);
76 addGlobalParameter("phi3", 0);
77 for (int m = 1; m < 3; m++) {
78 for (int n = 1; n < 4; n++) {
79 addPerBondParameter(format("k%d%d", m, n));
80 }
81 }
82 for (int m = 1; m < 3; m++) {
83 addPerBondParameter(format("a%d", m));
84 }
85 for (AngleTorsion angleTorsion : angleTorsions) {
86 double[] constants = angleTorsion.getConstants();
87 DoubleArray parameters = new DoubleArray(0);
88 for (int m = 0; m < 2; m++) {
89 for (int n = 0; n < 3; n++) {
90 int index = (3 * m) + n;
91 parameters.append(constants[index] * OpenMM_KJPerKcal);
92 }
93 }
94 Atom[] atoms = angleTorsion.getAtomArray(true);
95 parameters.append(angleTorsion.angleType1.angle[0] * OpenMM_RadiansPerDegree);
96 parameters.append(angleTorsion.angleType2.angle[0] * OpenMM_RadiansPerDegree);
97
98 IntArray particles = new IntArray(0);
99 for (int i = 0; i < 4; i++) {
100 particles.append(atoms[i].getXyzIndex() - 1);
101 }
102
103 addBond(particles, parameters);
104 parameters.destroy();
105 particles.destroy();
106 }
107
108 int forceGroup = openMMEnergy.getMolecularAssembly().getForceField().getInteger("ANGLE_TORSION_FORCE_GROUP", 0);
109
110 setForceGroup(forceGroup);
111
112 logger.log(Level.INFO, format(" Angle-Torsions \t%6d\t\t%1d", angleTorsions.length, forceGroup));
113 }
114
115 /**
116 * Convenience method to construct an OpenMM Angle-Torsion Force.
117 *
118 * @param openMMEnergy The OpenMM Energy instance that contains the angle-torsions.
119 * @return An OpenMM Stretch-Bend Force, or null if there are no angle-torsion.
120 */
121 public static Force constructForce(OpenMMEnergy openMMEnergy) {
122 AngleTorsion[] angleTorsions = openMMEnergy.getAngleTorsions();
123 if (angleTorsions == null || angleTorsions.length < 1) {
124 return null;
125 }
126 return new AngleTorsionForce(openMMEnergy);
127 }
128 }