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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 java.io.BufferedReader;
44  import java.io.File;
45  import java.io.FileReader;
46  import java.io.IOException;
47  import javax.swing.filechooser.FileFilter;
48  import org.apache.commons.io.FilenameUtils;
49  
50  /**
51   * The XYZFileFilter class is used to choose a TINKER Cartesian Coordinate (*.XYZ) file.
52   *
53   * @author Michael J. Schnieders
54   * @since 1.0
55   */
56  public final class XYZFileFilter extends FileFilter {
57  
58    /** Public Constructor. */
59    public XYZFileFilter() {
60    }
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 TINKER Cartesian
66     * coordinate (*.XYZ) file.
67     *
68     * @param file The File to examine.
69     * @return Returns true if this an XYZ file.
70     */
71    public static boolean isXYZ(File file) {
72      return new XYZFileFilter().accept(file);
73    }
74  
75    /**
76     * {@inheritDoc}
77     *
78     * <p>This method return <code>true</code> if the file is a directory or TINKER Cartesian
79     * coordinate (*.XYZ) file.
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("XYZ");
88    }
89  
90    /**
91     * acceptDeep
92     *
93     * @param file a {@link java.io.File} object.
94     * @return a boolean.
95     */
96    public boolean acceptDeep(File file) {
97      if (file == null || file.isDirectory() || !file.canRead()) {
98        return false;
99      }
100 
101     try (BufferedReader br = new BufferedReader(new FileReader(file))) {
102       if (!br.ready()) {
103         return false;
104       }
105 
106       /*
107        If the first token is not an integer this file is not a TINKER
108        Cartesian Coordinate File.
109       */
110       String rawdata = br.readLine();
111       String[] header = rawdata.trim().split(" +");
112       if (header.length == 0) {
113         return false;
114       }
115       try {
116         parseInt(header[0]);
117       } catch (Exception e) {
118         return false;
119       }
120       /*
121        If the the first line does not begin with an integer (an Atom Line)
122        or a double (a unit cell parameter line) and contain at least
123        six tokens, this is not a TINKER cartesian coordinate file.
124       */
125       String firstAtom = br.readLine();
126       if (firstAtom == null) {
127         return false;
128       }
129       String[] data = firstAtom.trim().split(" +");
130       if (data.length < 6) {
131         return false;
132       }
133       try {
134         parseInt(data[0]);
135       } catch (NumberFormatException e) {
136         try {
137           parseDouble(data[0]);
138         } catch (NumberFormatException e2) {
139           return false;
140         }
141       }
142       return true;
143     } catch (IOException e) {
144       return true;
145     }
146   }
147 
148   /**
149    * {@inheritDoc}
150    *
151    * <p>Provides a description of the XYZFileFilter.
152    */
153   @Override
154   public String getDescription() {
155     return "TINKER Cartesian Coordinates (*.XYZ)";
156   }
157 }