1 // ******************************************************************************
2 //
3 // Title: Force Field X.
4 // Description: Force Field X - Software for Molecular Biophysics.
5 // Copyright: Copyright (c) Michael J. Schnieders 2001-2025.
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
39 package ffx.potential.parsers;
40
41 import org.apache.commons.io.FilenameUtils;
42
43 import javax.swing.filechooser.FileFilter;
44 import java.io.BufferedReader;
45 import java.io.File;
46 import java.io.FileReader;
47 import java.io.IOException;
48
49 import static java.lang.Double.parseDouble;
50 import static java.lang.Integer.parseInt;
51
52 /**
53 * The PDBFileFilter class is used to choose a Protein Databank (*.PDB) file.
54 *
55 * @author Michael J. Schnieders
56 * @since 1.0
57 */
58 public final class PDBFileFilter extends FileFilter {
59
60 /** Public Constructor. */
61 public PDBFileFilter() {}
62
63 /**
64 * This is a static version of the accept method.
65 *
66 * <p>This method return <code>true</code> if the file is a directory or Protein Databank File
67 * (*.PDB).
68 *
69 * @param file The File to examine.
70 * @return Returns true if this a PDB file.
71 */
72 public static boolean isPDB(File file) {
73 return new PDBFileFilter().accept(file);
74 }
75
76 /**
77 * {@inheritDoc}
78 *
79 * <p>This method return <code>true</code> if the file is a directory or Protein Databank File
80 * (*.PDB).
81 */
82 @Override
83 public boolean accept(File file) {
84 if (file.isDirectory()) {
85 return true;
86 }
87 String ext = FilenameUtils.getExtension(file.getName());
88 return ext.toUpperCase().startsWith("PDB");
89 }
90
91 /**
92 * acceptDeep Accepts a PDB file if it finds at least one parseable ATOM line.
93 *
94 * @param file a {@link java.io.File} object.
95 * @return Whether a valid PDB file.
96 */
97 public boolean acceptDeep(File file) {
98 try {
99 if (file == null || file.isDirectory() || !file.canRead()) {
100 return false;
101 }
102 try (BufferedReader br = new BufferedReader(new FileReader(file))) {
103 if (!br.ready()) {
104 return false;
105 }
106 String line = br.readLine();
107 if (line != null) {
108 line = line.trim();
109 } else {
110 return false;
111 }
112 while (line != null) {
113 line = line.trim();
114 if (line.startsWith("ATOM ") || line.startsWith("HETATM")) {
115 try {
116 parseInt(line.substring(6, 11).trim());
117 parseInt(line.substring(22, 26).trim());
118 String[] coordOccTempVals = line.substring(30, 66).trim().split(" +");
119 for (String value : coordOccTempVals) {
120 parseDouble(value);
121 }
122 return true;
123 } catch (NumberFormatException | StringIndexOutOfBoundsException ex) {
124 // Do nothing.
125 }
126 }
127 line = br.readLine();
128 }
129 }
130 } catch (IOException e) {
131 return false;
132 }
133 return false;
134 }
135
136 /**
137 * {@inheritDoc}
138 *
139 * <p>Provides a description of the PDBFileFilter.
140 */
141 @Override
142 public String getDescription() {
143 return "Protein Databank (*.PDB)";
144 }
145 }