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