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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 2001-2025.
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  package ffx.potential.parsers;
39  
40  import org.w3c.dom.Document;
41  import org.w3c.dom.NodeList;
42  import org.xml.sax.ErrorHandler;
43  import org.xml.sax.SAXException;
44  import org.xml.sax.SAXParseException;
45  
46  import javax.xml.parsers.DocumentBuilder;
47  import javax.xml.parsers.DocumentBuilderFactory;
48  import javax.xml.parsers.ParserConfigurationException;
49  import java.io.File;
50  import java.io.IOException;
51  
52  /**
53   * PDBMLFilter class.
54   *
55   * @author Michael J. Schnieders
56   */
57  public class PDBMLFilter implements ErrorHandler {
58  
59    private static final String JAXP_SCHEMA_LANGUAGE =
60        "http://java.sun.com/xml/jaxp/properties/schemaLanguage";
61    private static final String W3C_XML_SCHEMA = "http://www.w3.org/2001/XMLSchema";
62    private static final String JAXP_SCHEMA_SOURCE =
63        "http://java.sun.com/xml/jaxp/properties/schemaSource";
64    private static final String PDBX_XSD = "pdbx.xsd";
65    private File pdbxFile = null;
66  
67    /** PDBML Constructor. */
68    public PDBMLFilter() {}
69  
70    /**
71     * Create an instance of the PDBML Filter
72     *
73     * @param args an array of {@link java.lang.String} objects.
74     */
75    public static void main(String[] args) {
76      if (args.length != 1) {
77        System.out.println("Usage: java PDBXFilter name.xml");
78      }
79      PDBMLFilter pdbx = new PDBMLFilter();
80      File pdbxFile = new File(args[0]);
81      pdbx.parse(pdbxFile);
82    }
83  
84    /** {@inheritDoc} */
85    @Override
86    public void error(SAXParseException e) throws SAXException {
87      parseMessage(e);
88    }
89  
90    /** {@inheritDoc} */
91    @Override
92    public void fatalError(SAXParseException e) throws SAXException {
93      parseMessage(e);
94    }
95  
96    /**
97     * parseMessage.
98     *
99     * @param e a {@link java.lang.Exception} object.
100    */
101   public void parseMessage(Exception e) {
102     System.out.println("Could not parse: " + pdbxFile + "\n" + e);
103   }
104 
105   /** {@inheritDoc} */
106   @Override
107   public void warning(SAXParseException e) throws SAXException {
108     parseMessage(e);
109   }
110 
111   private void parse(File pdbxml) {
112     pdbxFile = pdbxml;
113     try {
114       DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
115       dbf.setNamespaceAware(true);
116       dbf.setValidating(true);
117       dbf.setAttribute(JAXP_SCHEMA_LANGUAGE, W3C_XML_SCHEMA);
118       dbf.setAttribute(JAXP_SCHEMA_SOURCE, new File(PDBX_XSD));
119       DocumentBuilder db = dbf.newDocumentBuilder();
120       db.setErrorHandler(this);
121       Document doc = db.parse(pdbxFile);
122       NodeList list = doc.getElementsByTagName("PDBx:atom_site");
123       System.out.println("Number of Atoms: " + list.getLength());
124     } catch (ParserConfigurationException
125         | IllegalArgumentException
126         | SAXException
127         | IOException e) {
128       parseMessage(e);
129     }
130   }
131 }