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.algorithms.cli;
39
40 import ffx.potential.MolecularAssembly;
41 import picocli.CommandLine.ArgGroup;
42 import picocli.CommandLine.Option;
43
44 /**
45 * Represents command line options for scripts that create randomized unit cells.
46 *
47 * @author Michael J. Schnieders
48 * @author Jacob M. Litman
49 * @since 1.0
50 */
51 public class RandomUnitCellOptions {
52
53 /**
54 * The ArgGroup keeps the Random SymOp Options together when printing help.
55 */
56 @ArgGroup(heading = "%n Random Unit Cell Options%n", validate = false)
57 private final RandomUnitCellOptionGroup group = new RandomUnitCellOptionGroup();
58
59 /**
60 * Randomize the unit cell for a MolecularAssembly.
61 *
62 * @param assembly a {@link ffx.potential.MolecularAssembly} object.
63 */
64 public void randomize(MolecularAssembly assembly) {
65 if (group.randomSymOp >= 0) {
66 assembly.applyRandomSymOp(group.randomSymOp);
67 }
68 if (group.randomUnitCell > 0) {
69 assembly.applyRandomDensity(group.randomUnitCell);
70 }
71 }
72
73 /**
74 * A random SymOp with translation range -X/2 .. X/2 (0 for random placement in the unit cell,
75 * negative for no SymOp).
76 *
77 * @return Returns the random SymOp translation.
78 */
79 public double getRandomSymOp() {
80 return group.randomSymOp;
81 }
82
83 public void setRandomSymOp(double randomSymOp) {
84 group.randomSymOp = randomSymOp;
85 }
86
87 /**
88 * Random unit cell parameters will be used achieve the specified density (g/cc) (no default
89 * density).
90 *
91 * @return Returns the density target for the random unit parameters.
92 */
93 public double getRandomUnitCell() {
94 return group.randomUnitCell;
95 }
96
97 public void setRandomUnitCell(double randomUnitCell) {
98 group.randomUnitCell = randomUnitCell;
99 }
100
101 /**
102 * Collection of Random Unit Cell Options.
103 */
104 private static class RandomUnitCellOptionGroup {
105
106 /**
107 * --rsym or --randomSymOp Apply a random SymOp with translation range -X/2 .. X/2 (0 for random
108 * placement in the unit cell, negative for no SymOp).
109 */
110 @Option(names = {"--rsym", "--randomSymOp"}, paramLabel = "-1.0", defaultValue = "-1.0",
111 description = "Apply a random SymOp with translation range -X/2 .. X/2 (0 for random placement in the unit cell, negative for no SymOp)")
112 private double randomSymOp = -1.0;
113
114 /**
115 * --ruc or --randomUnitCell Random unit cell parameters will be used achieve the specified
116 * density (g/cc) (no default density).
117 */
118 @Option(names = {"--ruc", "--randomUnitCell"}, paramLabel = "-1.0", defaultValue = "-1.0",
119 description = "Apply random unit cell parameters to achieve the specified density (g/cc).")
120 private double randomUnitCell = -1.0;
121 }
122 }