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.parsers;
39
40 import static java.lang.Double.parseDouble;
41 import static java.lang.Integer.parseInt;
42
43 import ffx.potential.MolecularAssembly;
44 import ffx.potential.bonded.Atom;
45 import java.io.BufferedReader;
46 import java.io.File;
47 import java.io.FileReader;
48 import java.util.List;
49 import java.util.logging.Logger;
50
51 /**
52 * The InducedFilter class parses TINKER Induced Dipole (*.*U) files.
53 *
54 * @author Michael J. Schnieders
55 * @since 1.0
56 */
57 public class InducedFilter {
58
59 private static final Logger logger = Logger.getLogger(InducedFilter.class.getName());
60 File file;
61 private final MolecularAssembly molecularAssembly;
62
63 /**
64 * Constructor for InducedFilter.
65 *
66 * @param s a {@link ffx.potential.MolecularAssembly} object.
67 * @param f a {@link java.io.File} object.
68 */
69 public InducedFilter(MolecularAssembly s, File f) {
70 molecularAssembly = s;
71 file = f;
72 }
73
74 /**
75 * read
76 *
77 * @return a boolean.
78 */
79 public boolean read() {
80 if (!file.exists() || !file.canRead()) {
81 return false;
82 }
83 try (BufferedReader br = new BufferedReader(new FileReader(file))) {
84 String data = br.readLine();
85 String[] tokens = data.trim().split(" +");
86 if (tokens.length == 0) {
87 return false;
88 }
89 int numAtoms = parseInt(tokens[0]);
90 if (numAtoms != molecularAssembly.getAtomList().size()) {
91 return false;
92 }
93 // Read the Induced Dipoles
94 double[][] x = new double[numAtoms][3];
95 for (int i = 0; i < numAtoms; i++) {
96 data = br.readLine().trim();
97 tokens = data.split(" +");
98 if (tokens.length != 5) {
99 return false;
100 }
101 x[i][0] = parseDouble(tokens[2]);
102 x[i][1] = parseDouble(tokens[3]);
103 x[i][2] = parseDouble(tokens[4]);
104 }
105 List<Atom> atoms = molecularAssembly.getAtomList();
106 double max = 0.0d;
107 for (Atom a : atoms) {
108 int j = a.getIndex() - 1;
109 // a.setInducedDipole(-x[j][0], -x[j][1], -x[j][2]);
110 }
111 logger.warning("Max Induced: " + max);
112 } catch (Exception e) {
113 return false;
114 }
115 return true;
116 }
117 }