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.cli;
39
40 import static java.lang.System.arraycopy;
41
42 import ffx.potential.ForceFieldEnergy;
43 import ffx.potential.MolecularAssembly;
44 import picocli.CommandLine.Option;
45
46 /**
47 * Represents command line options for scripts that save a structure to disc.
48 *
49 * @author Michael J. Schnieders
50 * @author Jacob M. Litman
51 * @since 1.0
52 */
53 public class SaveOptions {
54
55 /**
56 * -c or --constrain Apply geometric constraints before saving.
57 */
58 @Option(names = {"-c", "--constrain"}, paramLabel = "false", defaultValue = "false",
59 description = "Apply geometric constraints before saving.")
60 public boolean constrain = false;
61
62 private double[] x;
63 private double[] outputX;
64
65 /**
66 * Performs key operations prior to saving to disc, such as application of geometric constraints.
67 *
68 * @param molecularAssembly A MolecularAssembly.
69 */
70 public void preSaveOperations(MolecularAssembly molecularAssembly) {
71 preSaveOperations(molecularAssembly.getPotentialEnergy());
72 }
73
74 /**
75 * Performs key operations prior to saving to disc, such as application of geometric constraints.
76 *
77 * @param forceFieldEnergy A ForceFieldEnergy.
78 */
79 public void preSaveOperations(ForceFieldEnergy forceFieldEnergy) {
80 if (constrain) {
81 int nVars = forceFieldEnergy.getNumberOfVariables();
82 if (x == null) {
83 x = new double[nVars];
84 outputX = new double[nVars];
85 }
86 x = forceFieldEnergy.getCoordinates(x);
87 arraycopy(x, 0, outputX, 0, nVars);
88 forceFieldEnergy.applyAllConstraintPositions(x, outputX);
89 forceFieldEnergy.setCoordinates(outputX);
90 }
91 }
92 }