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[Cdk-commits] SF.net SVN: cdk: [10916] cdk/trunk/src
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From: <eg...@us...> - 2008-05-07 17:28:26
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Revision: 10916
http://cdk.svn.sourceforge.net/cdk/?rev=10916&view=rev
Author: egonw
Date: 2008-05-07 09:50:41 -0700 (Wed, 07 May 2008)
Log Message:
-----------
Added a PubChem Substance XML reader (yes, PubChem SubstanceS XML is basically what SDF is to MDL molfile)
Modified Paths:
--------------
cdk/trunk/src/main/org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java
Added Paths:
-----------
cdk/trunk/src/data/asn/pubchem/sid577309.xml
cdk/trunk/src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java
cdk/trunk/src/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
cdk/trunk/src/test/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java
Added: cdk/trunk/src/data/asn/pubchem/sid577309.xml
===================================================================
--- cdk/trunk/src/data/asn/pubchem/sid577309.xml (rev 0)
+++ cdk/trunk/src/data/asn/pubchem/sid577309.xml 2008-05-07 16:50:41 UTC (rev 10916)
@@ -0,0 +1,257 @@
+<?xml version="1.0"?>
+<PC-Substance
+ xmlns="http://www.ncbi.nlm.nih.gov"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema-instance"
+ xs:schemaLocation="http://www.ncbi.nlm.nih.gov ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem.xsd"
+>
+ <PC-Substance_sid>
+ <PC-ID>
+ <PC-ID_id>577309</PC-ID_id>
+ <PC-ID_version>2</PC-ID_version>
+ </PC-ID>
+ </PC-Substance_sid>
+ <PC-Substance_source>
+ <PC-Source>
+ <PC-Source_db>
+ <PC-DBTracking>
+ <PC-DBTracking_name>DTP/NCI</PC-DBTracking_name>
+ <PC-DBTracking_source-id>
+ <Object-id>
+ <Object-id_str>371097</Object-id_str>
+ </Object-id>
+ </PC-DBTracking_source-id>
+ </PC-DBTracking>
+ </PC-Source_db>
+ </PC-Source>
+ </PC-Substance_source>
+ <PC-Substance_synonyms>
+ <PC-Substance_synonyms_E>NSC371097</PC-Substance_synonyms_E>
+ </PC-Substance_synonyms>
+ <PC-Substance_comment>
+ <PC-Substance_comment_E>DTP/NCI from SANSS. Release-June 2007.</PC-Substance_comment_E>
+ <PC-Substance_comment_E>Structure Evaluation:No Comparision - Unparameterized Atom - Ge.</PC-Substance_comment_E>
+ <PC-Substance_comment_E>Deposition record created from database webdb on host dtpiv1.ncifcrf.gov on Feb 22, 2008</PC-Substance_comment_E>
+ </PC-Substance_comment>
+ <PC-Substance_xref>
+ <PC-XRefData>
+ <PC-XRefData_regid>371097</PC-XRefData_regid>
+ </PC-XRefData>
+ <PC-XRefData>
+ <PC-XRefData_dburl>http://dtp.nci.nih.gov/</PC-XRefData_dburl>
+ </PC-XRefData>
+ <PC-XRefData>
+ <PC-XRefData_sburl>http://dtp.nci.nih.gov/dtpstandard/servlet/dwindex?searchtype=NSC&outputformat=html&searchlist=371097</PC-XRefData_sburl>
+ </PC-XRefData>
+ </PC-Substance_xref>
+ <PC-Substance_compound>
+ <PC-Compounds>
+ <PC-Compound>
+ <PC-Compound_id>
+ <PC-CompoundType>
+ <PC-CompoundType_type value="deposited">0</PC-CompoundType_type>
+ </PC-CompoundType>
+ </PC-Compound_id>
+ <PC-Compound_atoms>
+ <PC-Atoms>
+ <PC-Atoms_aid>
+ <PC-Atoms_aid_E>1</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>2</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>3</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>4</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>5</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>6</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>7</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>8</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>9</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>10</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>11</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>12</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>13</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>14</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>15</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>16</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>17</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>18</PC-Atoms_aid_E>
+ <PC-Atoms_aid_E>19</PC-Atoms_aid_E>
+ </PC-Atoms_aid>
+ <PC-Atoms_element>
+ <PC-Element value="a">255</PC-Element>
+ <PC-Element value="a">255</PC-Element>
+ <PC-Element value="ge">32</PC-Element>
+ <PC-Element value="ge">32</PC-Element>
+ <PC-Element value="o">8</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ <PC-Element value="c">6</PC-Element>
+ </PC-Atoms_element>
+ <PC-Atoms_label>
+ <PC-AtomString>
+ <PC-AtomString_aid>1</PC-AtomString_aid>
+ <PC-AtomString_value>R</PC-AtomString_value>
+ </PC-AtomString>
+ <PC-AtomString>
+ <PC-AtomString_aid>2</PC-AtomString_aid>
+ <PC-AtomString_value>R</PC-AtomString_value>
+ </PC-AtomString>
+ </PC-Atoms_label>
+ </PC-Atoms>
+ </PC-Compound_atoms>
+ <PC-Compound_bonds>
+ <PC-Bonds>
+ <PC-Bonds_aid1>
+ <PC-Bonds_aid1_E>1</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>2</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>3</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>3</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>3</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>3</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>4</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>4</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>4</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>6</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>6</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>7</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>7</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>8</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>9</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>12</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>13</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>14</PC-Bonds_aid1_E>
+ <PC-Bonds_aid1_E>15</PC-Bonds_aid1_E>
+ </PC-Bonds_aid1>
+ <PC-Bonds_aid2>
+ <PC-Bonds_aid2_E>4</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>5</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>5</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>6</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>12</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>13</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>7</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>14</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>15</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>8</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>9</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>10</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>11</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>10</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>11</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>16</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>17</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>18</PC-Bonds_aid2_E>
+ <PC-Bonds_aid2_E>19</PC-Bonds_aid2_E>
+ </PC-Bonds_aid2>
+ <PC-Bonds_order>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="double">2</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="double">2</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="double">2</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ <PC-BondType value="single">1</PC-BondType>
+ </PC-Bonds_order>
+ </PC-Bonds>
+ </PC-Compound_bonds>
+ <PC-Compound_coords>
+ <PC-Coordinates>
+ <PC-Coordinates_type>
+ <PC-CoordinateType value="twod">1</PC-CoordinateType>
+ <PC-CoordinateType value="submitted">3</PC-CoordinateType>
+ </PC-Coordinates_type>
+ <PC-Coordinates_aid>
+ <PC-Coordinates_aid_E>1</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>2</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>3</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>4</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>5</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>6</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>7</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>8</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>9</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>10</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>11</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>12</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>13</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>14</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>15</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>16</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>17</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>18</PC-Coordinates_aid_E>
+ <PC-Coordinates_aid_E>19</PC-Coordinates_aid_E>
+ </PC-Coordinates_aid>
+ <PC-Coordinates_conformers>
+ <PC-Conformer>
+ <PC-Conformer_x>
+ <PC-Conformer_x_E>4.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2</PC-Conformer_x_E>
+ <PC-Conformer_x_E>3.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>3.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>3.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>3.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>4.366</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2.634</PC-Conformer_x_E>
+ <PC-Conformer_x_E>4.366</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2.634</PC-Conformer_x_E>
+ <PC-Conformer_x_E>3.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>4.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>3.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2.5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>4.366</PC-Conformer_x_E>
+ <PC-Conformer_x_E>5</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2.634</PC-Conformer_x_E>
+ <PC-Conformer_x_E>2</PC-Conformer_x_E>
+ </PC-Conformer_x>
+ <PC-Conformer_y>
+ <PC-Conformer_y_E>-2</PC-Conformer_y_E>
+ <PC-Conformer_y_E>2.866</PC-Conformer_y_E>
+ <PC-Conformer_y_E>2</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-2</PC-Conformer_y_E>
+ <PC-Conformer_y_E>2</PC-Conformer_y_E>
+ <PC-Conformer_y_E>1</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-1</PC-Conformer_y_E>
+ <PC-Conformer_y_E>0.5</PC-Conformer_y_E>
+ <PC-Conformer_y_E>0.5</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-0.5</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-0.5</PC-Conformer_y_E>
+ <PC-Conformer_y_E>3</PC-Conformer_y_E>
+ <PC-Conformer_y_E>2</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-3</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-2</PC-Conformer_y_E>
+ <PC-Conformer_y_E>3.5</PC-Conformer_y_E>
+ <PC-Conformer_y_E>2.866</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-3.5</PC-Conformer_y_E>
+ <PC-Conformer_y_E>-2.866</PC-Conformer_y_E>
+ </PC-Conformer_y>
+ </PC-Conformer>
+ </PC-Coordinates_conformers>
+ </PC-Coordinates>
+ </PC-Compound_coords>
+ <PC-Compound_charge>0</PC-Compound_charge>
+ </PC-Compound>
+ </PC-Compounds>
+ </PC-Substance_compound>
+</PC-Substance>
+
Added: cdk/trunk/src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java (rev 0)
+++ cdk/trunk/src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java 2008-05-07 16:50:41 UTC (rev 10916)
@@ -0,0 +1,149 @@
+/* $Revision: 10774 $ $Author: egonw $ $Date: 2008-05-03 08:50:01 +0200 (Sat, 03 May 2008) $
+ *
+ * Copyright (C) 2008 Egon Willighagen <eg...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.io.formats.IResourceFormat;
+import org.openscience.cdk.io.formats.PubChemSubstanceXMLFormat;
+import org.openscience.cdk.io.pubchemxml.PubChemXMLHelper;
+import org.xmlpull.v1.XmlPullParser;
+import org.xmlpull.v1.XmlPullParserFactory;
+
+/**
+ * Reads an object from ASN formated input for PubChem Compound entries. The following
+ * bits are supported: atoms.aid, atoms.element, bonds.aid1, bonds.aid2. Additionally,
+ * it extracts the InChI and canonical SMILES properties.
+ *
+ * @cdk.module io
+ * @cdk.svnrev $Revision: 10774 $
+ *
+ * @cdk.keyword file format, PubChem Compound ASN
+ */
+public class PCSubstanceXMLReader extends DefaultChemObjectReader {
+
+ private Reader input;
+ private XmlPullParser parser;
+ private PubChemXMLHelper parserHelper;
+ private IChemObjectBuilder builder;
+
+ IMolecule molecule = null;
+
+ /**
+ * Construct a new reader from a Reader type object.
+ *
+ * @param input reader from which input is read
+ */
+ public PCSubstanceXMLReader(Reader input) throws Exception {
+ setReader(input);
+ }
+
+ public PCSubstanceXMLReader(InputStream input) throws Exception {
+ setReader(input);
+ }
+
+ public PCSubstanceXMLReader() throws Exception {
+ this(new StringReader(""));
+ }
+
+ public IResourceFormat getFormat() {
+ return PubChemSubstanceXMLFormat.getInstance();
+ }
+
+ public void setReader(Reader input) throws CDKException {
+ try {
+ XmlPullParserFactory factory = XmlPullParserFactory.newInstance(
+ System.getProperty(XmlPullParserFactory.PROPERTY_NAME), null
+ );
+ factory.setNamespaceAware(true);
+ parser = factory.newPullParser();
+ this.input = input;
+ parser.setInput(input);
+ } catch (Exception exception) {
+ throw new CDKException("Error while creating reader: " + exception.getMessage(), exception);
+ }
+ }
+
+ public void setReader(InputStream input) throws CDKException {
+ setReader(new InputStreamReader(input));
+ }
+
+ public boolean accepts(Class classObject) {
+ Class[] interfaces = classObject.getInterfaces();
+ for (int i=0; i<interfaces.length; i++) {
+ if (IMolecule.class.equals(interfaces[i])) return true;
+ }
+ return false;
+ }
+
+ public IChemObject read(IChemObject object) throws CDKException {
+ if (object instanceof IMolecule) {
+ try {
+ parserHelper = new PubChemXMLHelper(object.getBuilder());
+ builder = object.getBuilder();
+ return readMolecule((IMolecule)object);
+ } catch (IOException e) {
+ throw new CDKException("An IO Exception occured while reading the file.", e);
+ } catch (CDKException e) {
+ throw e;
+ } catch (Exception e) {
+ throw new CDKException("An error occured: " + e.getMessage(), e);
+ }
+ } else {
+ throw new CDKException("Only supported is reading of ChemFile objects.");
+ }
+ }
+
+ public void close() throws IOException {
+ input.close();
+ }
+
+ // private procedures
+
+ private IMolecule readMolecule(IMolecule file) throws Exception {
+ boolean foundCompound = false;
+ while (parser.next() != XmlPullParser.END_DOCUMENT) {
+ if (parser.getEventType() == XmlPullParser.START_TAG) {
+ if (parser.getName().equals("PC-Compound")) {
+ foundCompound = true;
+ break;
+ }
+ }
+ }
+ if (foundCompound) {
+ return parserHelper.parseMolecule(parser, builder);
+ }
+ return null;
+ }
+
+}
Added: cdk/trunk/src/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java (rev 0)
+++ cdk/trunk/src/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java 2008-05-07 16:50:41 UTC (rev 10916)
@@ -0,0 +1,79 @@
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (C) 2008 Egon Willighagen <eg...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io.formats;
+
+import org.openscience.cdk.tools.DataFeatures;
+
+/**
+ * @cdk.module io
+ * @cdk.svnrev $Revision$
+ * @cdk.set io-formats
+ */
+public class PubChemSubstanceXMLFormat implements IChemFormatMatcher {
+
+ private static IResourceFormat myself = null;
+
+ private PubChemSubstanceXMLFormat() {}
+
+ public static IResourceFormat getInstance() {
+ if (myself == null) myself = new PubChemSubstanceXMLFormat();
+ return myself;
+ }
+
+ public String getFormatName() {
+ return "PubChem Substance XML";
+ }
+
+ public String getMIMEType() {
+ return null;
+ }
+ public String getPreferredNameExtension() {
+ return getNameExtensions()[0];
+ }
+ public String[] getNameExtensions() {
+ return new String[]{"xml"};
+ }
+
+ public String getReaderClassName() {
+ return null;
+ }
+ public String getWriterClassName() {
+ return null;
+ }
+
+ public boolean isXMLBased() {
+ return true;
+ }
+
+ public int getSupportedDataFeatures() {
+ return DataFeatures.NONE;
+ }
+
+ public int getRequiredDataFeatures() {
+ return DataFeatures.NONE;
+ }
+
+ public boolean matches(int lineNumber, String line) {
+ if (lineNumber == 2 && line.startsWith("<PC-Substance") &&
+ !line.startsWith("<PC-Substances")) return true;
+ return false;
+ }
+}
Modified: cdk/trunk/src/main/org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java
===================================================================
--- cdk/trunk/src/main/org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java 2008-05-07 16:25:42 UTC (rev 10915)
+++ cdk/trunk/src/main/org/openscience/cdk/io/pubchemxml/PubChemXMLHelper.java 2008-05-07 16:50:41 UTC (rev 10916)
@@ -156,9 +156,14 @@
if (EL_ELEMENT.equals(parser.getName())) {
int atomicNumber = Integer.parseInt(parser.nextText());
IElement element = factory.getElement(atomicNumber);
- IAtom atom = molecule.getBuilder().newAtom(element.getSymbol());
- atom.setAtomicNumber(element.getAtomicNumber());
- molecule.addAtom(atom);
+ if (element == null) {
+ IAtom atom = molecule.getBuilder().newPseudoAtom();
+ molecule.addAtom(atom);
+ } else {
+ IAtom atom = molecule.getBuilder().newAtom(element.getSymbol());
+ atom.setAtomicNumber(element.getAtomicNumber());
+ molecule.addAtom(atom);
+ }
}
}
}
Added: cdk/trunk/src/test/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java
===================================================================
--- cdk/trunk/src/test/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java (rev 0)
+++ cdk/trunk/src/test/org/openscience/cdk/io/PCSubstanceXMLReaderTest.java 2008-05-07 16:50:41 UTC (rev 10916)
@@ -0,0 +1,75 @@
+/* $Revision: 10838 $ $Author: egonw $ $Date: 2008-05-05 23:03:59 +0200 (Mon, 05 May 2008) $
+ *
+ * Copyright (C) 2006-2007 Egon Willighagen <eg...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io;
+
+import java.io.InputStream;
+
+import junit.framework.Test;
+import junit.framework.TestSuite;
+
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.Molecule;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.tools.LoggingTool;
+
+/**
+ * @cdk.module test-io
+ */
+public class PCSubstanceXMLReaderTest extends CDKTestCase {
+
+ private LoggingTool logger;
+
+ public PCSubstanceXMLReaderTest(String name) {
+ super(name);
+ logger = new LoggingTool(this);
+ }
+
+ public static Test suite() {
+ return new TestSuite(PCSubstanceXMLReaderTest.class);
+ }
+
+ public void testAccepts() throws Exception {
+ PCSubstanceXMLReader reader = new PCSubstanceXMLReader();
+ assertTrue(reader.accepts(Molecule.class));
+ }
+
+ public void testReading() throws Exception {
+ String filename = "data/asn/pubchem/sid577309.xml";
+ logger.info("Testing: " + filename);
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ PCSubstanceXMLReader reader = new PCSubstanceXMLReader(ins);
+ IMolecule molecule = (IMolecule)reader.read(new Molecule());
+ assertNotNull(molecule);
+
+ // check atom stuff
+ assertEquals(19, molecule.getAtomCount());
+ assertTrue(molecule.getAtom(0) instanceof IPseudoAtom);
+
+ // check bond stuff
+ assertEquals(19, molecule.getBondCount());
+ assertNotNull(molecule.getBond(3));
+ }
+}
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