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.algorithms.optimize.manybody;
39
40 import ffx.algorithms.mc.BoltzmannMC;
41 import ffx.algorithms.optimize.RotamerOptimization;
42 import ffx.potential.bonded.Residue;
43
44 import java.util.Arrays;
45
46 import static java.lang.System.arraycopy;
47
48 /** Monte Carlo driver for DEE-MC. */
49 public class RotamerMatrixMC extends BoltzmannMC {
50
51 private final int[] currentRots;
52 private final int[] oldRots;
53 private final int nRes;
54 private final Residue[] residues;
55 private final RotamerOptimization rotamerOptimization;
56 private final boolean useFullAMOEBAEnergy;
57
58 /**
59 * The Rotamers array must be the same array as passed to any MCMove objects used (and not a
60 * copy).
61 *
62 * @param rotamers Array of rotamers.
63 * @param residues Array of residues.
64 * @param useFullAMOEBAEnergy If true, re-evaluate AMOEBA energy for each conformation.
65 * @param rotamerOptimization RotamerOptimization instance.
66 */
67 public RotamerMatrixMC(int[] rotamers, Residue[] residues, boolean useFullAMOEBAEnergy,
68 RotamerOptimization rotamerOptimization) {
69 currentRots = rotamers; // This is intentional.
70 nRes = rotamers.length;
71 oldRots = new int[nRes];
72 arraycopy(rotamers, 0, oldRots, 0, nRes);
73 this.residues = residues;
74 this.useFullAMOEBAEnergy = useFullAMOEBAEnergy;
75 this.rotamerOptimization = rotamerOptimization;
76 }
77
78 @Override
79 public void revertStep() {
80 arraycopy(oldRots, 0, currentRots, 0, nRes);
81 }
82
83 /**
84 * If useFullAMOEBAEnergy is set to true, explicitly evaluates energy, else computes energy from
85 * the rotamer energy matrices.
86 *
87 * @return Energy at the current state
88 */
89 @Override
90 protected double currentEnergy() {
91 try {
92 try {
93 return useFullAMOEBAEnergy ? rotamerOptimization.currentEnergyWrapper(
94 Arrays.asList(residues))
95 : rotamerOptimization.computeEnergy(residues, currentRots, false);
96 } catch (ArithmeticException ex) {
97 return 1E100;
98 }
99 } catch (NullPointerException ex) {
100 // If using the rotamer energy matrix, and there is some missing
101 // energy term, just return a default, very large energy.
102 return 1e100;
103 }
104 }
105
106 @Override
107 protected void storeState() {
108 arraycopy(currentRots, 0, oldRots, 0, nRes);
109 }
110 }