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.realspace.cli;
39
40 import ffx.potential.MolecularAssembly;
41 import ffx.realspace.RealSpaceData;
42 import ffx.realspace.parsers.RealSpaceFile;
43 import ffx.xray.RefinementEnergy;
44 import ffx.xray.RefinementMinimize.RefinementMode;
45 import ffx.xray.cli.DataRefinementOptions;
46
47 import java.util.ArrayList;
48 import java.util.List;
49 import java.util.logging.Logger;
50
51 import picocli.CommandLine.Option;
52
53 /**
54 * Represents command line options for scripts that utilize a real-space density map.
55 *
56 * @author Michael J. Schnieders
57 * @author Soham Ali
58 * @since 1.0
59 */
60 public class RealSpaceOptions extends DataRefinementOptions {
61
62 private static final Logger logger = Logger.getLogger(RealSpaceOptions.class.getName());
63
64 /**
65 * The refinement mode to use.
66 */
67 public RefinementMode refinementMode = RefinementMode.COORDINATES;
68
69 /**
70 * -X or --data Specify input data filename and weight applied to the data (wA).
71 */
72 @Option(names = {"-X", "--data"}, arity = "2",
73 description = "Specify input data filename and its weight (wA) (e.g. -X filename 1.0).")
74 String[] data = null;
75
76 /**
77 * Process input to collect Real Space Files.
78 *
79 * @param filenames Input filenames (first filename is ignored).
80 * @param molecularAssembly Currently open molecularAssembly.
81 * @return a list of Real Space File instances.
82 */
83 public List<RealSpaceFile> processData(List<String> filenames, MolecularAssembly molecularAssembly) {
84
85 logger.info("\n");
86
87 // set up real space map data (can be multiple files)
88 List<RealSpaceFile> mapfiles = new ArrayList<>();
89 if (filenames.size() > 1) {
90 RealSpaceFile realspacefile = new RealSpaceFile(filenames.get(1), wA);
91 mapfiles.add(realspacefile);
92 }
93 if (data != null) {
94 for (int i = 0; i < data.length; i += 2) {
95 double w = wA;
96 if (data.length > i + 1) {
97 try {
98 w = Double.parseDouble(data[i + 1]);
99 } catch (Exception e) {
100 //
101 }
102 }
103 RealSpaceFile realspacefile = new RealSpaceFile(data[i], w);
104 mapfiles.add(realspacefile);
105 }
106 }
107
108 if (mapfiles.isEmpty()) {
109 RealSpaceFile realspacefile = new RealSpaceFile(molecularAssembly, wA);
110 mapfiles.add(realspacefile);
111 }
112
113 return mapfiles;
114 }
115
116 /**
117 * Process input from opened molecular assemblies to a RefinementEnergy
118 *
119 * @param filenames All filenames included in the real-space data.
120 * @param molecularAssemblies Array of MolecularAssembly instances.
121 * @return An assembled RefinementEnergy with real-space energy.
122 */
123 public RefinementEnergy toRealSpaceEnergy(List<String> filenames, MolecularAssembly[] molecularAssemblies) {
124
125 RealSpaceFile[] mapFiles = processData(filenames, molecularAssemblies[0]).toArray(new RealSpaceFile[0]);
126 RealSpaceData realspaceData = new RealSpaceData(molecularAssemblies, molecularAssemblies[0].getProperties(),
127 molecularAssemblies[0].getParallelTeam(), mapFiles);
128
129 return new RefinementEnergy(realspaceData, RefinementMode.COORDINATES);
130 }
131 }