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 ffx.potential.MolecularAssembly;
41 import ffx.potential.utils.PotentialsFunctions;
42
43 import java.io.File;
44
45 import picocli.CommandLine.Option;
46
47 /**
48 * Represents command line options for scripts that periodically write out structures.
49 *
50 * @author Michael J. Schnieders
51 * @author Soham Ali
52 * @since 1.0
53 */
54 public class WriteoutOptions {
55
56 /**
57 * -F or --fileFormat Choose the file type to write [PDB/XYZ].
58 */
59 @Option(names = {"-F", "--fileFormat"}, paramLabel = "XYZ", defaultValue = "XYZ",
60 description = "Choose file type to write [PDB/XYZ].")
61 public String fileType = "XYZ";
62
63 public static String toArchiveExtension(String fileType) {
64 return Extensions.nameToExt(fileType).archive;
65 }
66
67 /**
68 * Getter for the field <code>fileType</code>.
69 *
70 * @return a {@link java.lang.String} object.
71 */
72 public String getFileType() {
73 return fileType;
74 }
75
76 /**
77 * Saves a single-snapshot file to either .xyz or .pdb, depending on the value of fileType.
78 *
79 * @param baseFileName Basic file name without extension.
80 * @param potentialsFunctions A PotentialFunctions object.
81 * @param molecularAssembly MolecularAssembly to save.
82 * @return File written to.
83 */
84 public File saveFile(String baseFileName, PotentialsFunctions potentialsFunctions,
85 MolecularAssembly molecularAssembly) {
86 String outFileName = baseFileName;
87 File outFile;
88 if (fileType.equalsIgnoreCase("XYZ")) {
89 outFileName = outFileName + ".xyz";
90 outFile = potentialsFunctions.versionFile(new File(outFileName));
91 potentialsFunctions.saveAsXYZ(molecularAssembly, outFile);
92 } else {
93 outFileName = outFileName + ".pdb";
94 outFile = potentialsFunctions.versionFile(new File(outFileName));
95 potentialsFunctions.saveAsPDB(molecularAssembly, outFile);
96 }
97 return outFile;
98 }
99
100 private enum Extensions {
101 XYZ("xyz", "arc"), PDB("pdb", "pdb");
102
103 private final String single;
104 private final String archive;
105
106 Extensions(String single, String archive) {
107 this.single = single;
108 this.archive = archive;
109 }
110
111 static Extensions nameToExt(String name) {
112 return switch (name.toUpperCase()) {
113 case "PDB" -> PDB;
114 default -> XYZ;
115 };
116 }
117 }
118 }