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