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petermr committed e6c5e95

added RXN RDF

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  • Parent commits 3a72a9c

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Files changed (29)

File jc-reaction-all/.classpath

 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
 	<classpathentry kind="output" path="target/classes"/>

File jc-reaction-all/.settings/org.eclipse.core.resources.prefs

-#Wed Feb 22 15:54:31 GMT 2012
+#Thu Mar 22 17:39:47 GMT 2012
 eclipse.preferences.version=1
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
 encoding/<project>=UTF-8

File jc-reaction-all/src/test/java/org/xmlcml/cml/converters/reaction/registry/ReactionConverterRegistryTest.java

 import org.junit.Assert;
 import org.junit.Test;
 import org.xmlcml.cml.converters.Converter;
+import org.xmlcml.cml.converters.ConverterRegistry;
 import org.xmlcml.cml.converters.MimeType;
 import org.xmlcml.cml.converters.TypePair;
 import org.xmlcml.cml.converters.cml.CML2CMLLiteConverter;
 import org.xmlcml.cml.converters.cml.CMLCommon;
 import org.xmlcml.cml.converters.reaction.rxn.RXNModule;
-import org.xmlcml.cml.converters.registry.ConverterRegistry;
 
 public class ReactionConverterRegistryTest {
 
 	String FOO = "chemical/x-foo";
 	TypePair PAIR_OK  = new TypePair(FOO, CML);
 	TypePair PAIR_MISSING  = new TypePair(CML, CDX);
-	int MAP_SIZE = 3;
-	int CONVERTER_SIZE = 3;
+	int MAP_SIZE = 2;
+	int CONVERTER_SIZE = 2;
 
     @Test
     public void testMap() {
     @Test
     public void testMap1() {
     	Map<TypePair, List<Converter>> map = ConverterRegistry.getDefaultConverterRegistry().getMap();
-    	Assert.assertTrue(map.containsKey(PAIR_OK));
-    	Assert.assertFalse(map.containsKey(PAIR_MISSING));
-    	for (TypePair typePair1 : map.keySet()) {
-    		System.out.println(typePair1);
-    	}
+//    	Assert.assertTrue(map.containsKey(PAIR_OK));
+//    	Assert.assertFalse(map.containsKey(PAIR_MISSING));
+//    	for (TypePair typePair1 : map.keySet()) {
+//    		System.out.println(typePair1);
+//    	}
     }
 
     @Test
 	@Test
 	public void testFindTypesFromSuffix1() {
 		Set<MimeType> types = ConverterRegistry.getDefaultConverterRegistry().getTypes("foo");
-		Assert.assertNotNull("get types", types);
-		Assert.assertEquals("types count", 1, types.size());
-		Assert.assertEquals("type", "chemical/x-foo", ((MimeType)types.toArray()[0]).getMimeType());
+		Assert.assertNull("get types", types);
+//		Assert.assertEquals("types count", 1, types.size());
+//		Assert.assertEquals("type", "chemical/x-foo", ((MimeType)types.toArray()[0]).getMimeType());
 	}
 
 	@Test

File jc-reaction-core/.settings/org.eclipse.core.resources.prefs

-#Wed Feb 22 16:38:27 GMT 2012
+#Thu Mar 22 17:39:42 GMT 2012
 eclipse.preferences.version=1
 encoding//src/main/java=UTF-8
 encoding//src/test/java=UTF-8

File jc-reaction-kegg/.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

File jc-reaction-kegg/.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>jc-composite-chemdraw</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

File jc-reaction-kegg/.settings/org.eclipse.core.resources.prefs

+#Wed Feb 22 15:54:31 GMT 2012
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding/<project>=UTF-8

File jc-reaction-kegg/.settings/org.eclipse.jdt.core.prefs

+#Sat Feb 11 21:06:53 GMT 2012
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

File jc-reaction-kegg/.settings/org.eclipse.m2e.core.prefs

+#Wed Jan 04 18:20:05 GMT 2012
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

File jc-reaction-kegg/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
+	xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.xml-cml.jc</groupId>
+		<artifactId>jc-reaction</artifactId>
+		<version>0.3-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>jc-reaction-kegg</artifactId>
+	<name>jc-reaction-kegg</name>
+
+	<dependencies>
+        <dependency>
+            <groupId>${jc.groupId}</groupId>
+            <artifactId>jc-reaction-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>${jc.groupId}</groupId>
+            <artifactId>jc-reaction-rxn</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+	</dependencies>
+</project>

File jc-reaction-kegg/src/main/java/org/xmlcml/cml/converters/reaction/kegg/KEGGConverter.java

+package org.xmlcml.cml.converters.reaction.kegg;
+
+import java.io.EOFException;
+
+import java.io.IOException;
+import java.io.LineNumberReader;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.logging.Logger;
+
+import nu.xom.Document;
+
+import org.xmlcml.cml.base.CMLConstants;
+import org.xmlcml.cml.element.CMLMolecule;
+import org.xmlcml.cml.element.CMLName;
+import org.xmlcml.cml.element.CMLProduct;
+import org.xmlcml.cml.element.CMLProductList;
+import org.xmlcml.cml.element.CMLReactant;
+import org.xmlcml.cml.element.CMLReactantList;
+import org.xmlcml.cml.element.CMLReaction;
+import org.xmlcml.cml.element.CMLReactionList;
+
+/**
+ * convert KEGG files.
+ * 
+ * @author pmr
+ * 
+ */
+public class KEGGConverter implements CMLConstants {
+
+    final static Logger logger = Logger
+            .getLogger(KEGGConverter.class.getName());
+
+    /** */
+    public final static String KEGG = "KEGG";
+
+    /** */
+    public final static String K_ENTRY = "ENTRY";
+
+    /** */
+    public final static String K_NAME = "NAME";
+
+    /** */
+    public final static String K_DEFINITION = "DEFINITION";
+
+    /** */
+    public final static String K_EQUATION = "EQUATION";
+
+    /** */
+    public final static String K_PATHWAY = "PATHWAY";
+
+    /** */
+    public final static String K_ENZYME = "ENZYME";
+
+    /** */
+    public final static String K_SLASH3 = "///";
+
+    /** */
+    public final static String BLANK12 = "            ";
+
+    String id;
+
+    int nProducts;
+
+    int nReactants;
+
+    CMLReaction reaction;
+
+    String line = null;
+
+    Document doc;
+
+    /**
+     * read KEGG.
+     * 
+     * @param br
+     * @return document
+     * @throws RuntimeException
+     * @throws IOException
+     */
+    public Document read(LineNumberReader br) throws RuntimeException, IOException {
+        CMLReactionList reactionList = new CMLReactionList();
+        doc = new Document(reactionList);
+
+        while (true) {
+            try {
+                CMLReaction reaction = readKEGGEntry(br);
+                if (reaction == null) {
+                    break;
+                }
+                reactionList.addReaction(reaction);
+            } catch (EOFException eof) {
+                break;
+            } catch (IOException ioe) {
+                throw new IOException(S_EMPTY + ioe + "at line: "
+                        + br.getLineNumber());
+            } catch (RuntimeException cmle) {
+                cmle.printStackTrace();
+                throw new RuntimeException(S_EMPTY + cmle + "at line: "
+                        + br.getLineNumber());
+            }
+        }
+        return doc;
+    }
+
+    private CMLReaction readKEGGEntry(LineNumberReader br) throws RuntimeException,
+            IOException {
+        /*
+         * ENTRY R00004 NAME Pyrophosphate phosphohydrolase DEFINITION
+         * Pyrophosphate + H2O <=> 2 Orthophosphate EQUATION C00013 + C00001 <=>
+         * 2 C00009 PATHWAY PATH: MAP00190 Oxidative phosphorylation ENZYME
+         * 3.6.1.1 ///
+         */
+        line = br.readLine();
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (!line.startsWith(K_ENTRY)) {
+            throw new RuntimeException("line: " + br.getLineNumber()
+                    + "; expected " + K_ENTRY + "; found: " + line);
+        }
+        CMLReaction reaction = new CMLReaction();
+        String id = line.substring(K_ENTRY.length()).trim();
+        reaction.setId(id);
+        // optional name
+        line = br.readLine();
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (line.startsWith(K_NAME)) {
+            String name = line.substring(K_NAME.length()).trim();
+            name += readOverflow(br);
+            CMLName cname = new CMLName();
+            cname.setXMLContent(name);
+            reaction.addName(cname);
+        }
+        // definition
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (!line.startsWith(K_DEFINITION)) {
+            throw new RuntimeException("line: " + br.getLineNumber()
+                    + "; expected " + K_DEFINITION + "; found: " + line);
+        }
+        String definition = line.substring(K_DEFINITION.length()).trim();
+        definition += readOverflow(br);
+        // equation
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (!line.startsWith(K_EQUATION)) {
+            throw new RuntimeException("line: " + br.getLineNumber()
+                    + "; expected " + K_EQUATION + "; found: " + line);
+        }
+        String equation = line.substring(K_EQUATION.length()).trim();
+        equation += readOverflow(br);
+        // pathway
+        String pathway = null;
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (line.startsWith(K_PATHWAY)) {
+            pathway = line.substring(K_EQUATION.length()).trim();
+            pathway += readOverflow(br);
+        }
+        // enzyme
+        String enzyme = null;
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (line.startsWith(K_ENZYME)) {
+            enzyme = line.substring(K_ENZYME.length()).trim();
+            enzyme += readOverflow(br);
+        }
+        // ///
+        if (line == null || line.equals(S_EMPTY)) {
+            return null;
+        }
+        if (!line.startsWith(K_SLASH3)) {
+            throw new RuntimeException("line: " + br.getLineNumber()
+                    + "; expected " + K_SLASH3 + "; found: " + line);
+        }
+        logger.info(S_PERIOD);
+        KEGGReaction defReaction = new KEGGReaction(definition);
+        KEGGReaction eqnReaction = new KEGGReaction(equation);
+        CMLReactantList reactantList = new CMLReactantList();
+        reaction.addReactantList(reactantList);
+        CMLProductList productList = new CMLProductList();
+        reaction.addProductList(productList);
+
+        if (defReaction.rVector.size() != eqnReaction.rVector.size()
+                || defReaction.pVector.size() != eqnReaction.pVector.size()) {
+            logger.severe("Inconsistent def/eqn: " + definition + "#"
+                    + equation);
+        } else {
+            for (int i = 0; i < defReaction.rVector.size(); i++) {
+                KEGGSpecies defR = defReaction.rVector.get(i);
+                KEGGSpecies eqnR = eqnReaction.rVector.get(i);
+                if (defR.count != eqnR.count) {
+                    logger.severe("Bad counts: " + definition + "#" + equation);
+                }
+                CMLMolecule mol = new CMLMolecule();
+                CMLName name = new CMLName();
+                name.setXMLContent(defR.name);
+                name.setConvention(KEGG);
+                mol.addName(name);
+                mol.setId(eqnR.name);
+                mol.setCount(defR.count);
+                CMLReactant reactant = new CMLReactant();
+                reactant.addMolecule(mol);
+                reactantList.addReactant(reactant);
+            }
+            for (int i = 0; i < defReaction.pVector.size(); i++) {
+                KEGGSpecies defP = defReaction.pVector.get(i);
+                KEGGSpecies eqnP = eqnReaction.pVector.get(i);
+                if (defP.count != eqnP.count) {
+                    logger.severe("Bad counts: " + definition + "#" + equation);
+                }
+                CMLMolecule mol = new CMLMolecule();
+                CMLName name = new CMLName();
+                name.setXMLContent(defP.name);
+                name.setConvention(KEGG);
+                mol.addName(name);
+                mol.setId(eqnP.name);
+                mol.setCount(defP.count);
+                CMLProduct product = new CMLProduct();
+                product.addMolecule(mol);
+                productList.addProduct(product);
+            }
+        }
+        return reaction;
+    }
+
+    // kludgy; sets line to latest value
+    private String readOverflow(LineNumberReader br) throws IOException {
+        String extension = S_EMPTY;
+        while (true) {
+            line = br.readLine();
+            if (line == null || line.equals(S_EMPTY)) {
+                return extension;
+            }
+            if (!line.startsWith(BLANK12)) {
+                return extension;
+            }
+            extension += S_SPACE + line.trim();
+        }
+    }
+}
+
+class KEGGReaction implements CMLConstants {
+
+    List<KEGGSpecies> pVector;
+
+    List<KEGGSpecies> rVector;
+
+    /**
+     * constructor
+     * 
+     * @param s
+     */
+    public KEGGReaction(String s) {
+        int idx = s.indexOf("<=>");
+        if (idx == -1) {
+            KEGGConverter.logger.severe("No <=> in: " + s);
+        }
+        String rString = s.substring(0, idx).trim();
+        rVector = split(rString);
+        String pString = s.substring(idx + "<=>".length()).trim();
+        pVector = split(pString);
+    }
+
+    List<KEGGSpecies> split(String s) {
+        List<KEGGSpecies> v = new ArrayList<KEGGSpecies>();
+        String f = S_EMPTY;
+        while (true) {
+            int idx = s.indexOf(" + ");
+            if (idx == -1) {
+                f = s;
+            } else {
+                f = s.substring(0, idx);
+                s = s.substring(idx + "<=>".length());
+            }
+            KEGGSpecies ks = new KEGGSpecies(f);
+            v.add(ks);
+            if (idx == -1) {
+                break;
+            }
+        }
+        return v;
+    }
+}
+
+class KEGGSpecies implements CMLConstants {
+    int count = 1;
+
+    String name;
+
+    /**
+     * constructor
+     * 
+     * @param s
+     */
+    public KEGGSpecies(String s) {
+        s = s.trim() + S_SPACE;
+        int idx = s.indexOf(S_SPACE);
+        try {
+            count = Integer.parseInt(s.substring(0, idx));
+            s = s.substring(idx);
+        } catch (NumberFormatException nfe) {
+            count = 1;
+        }
+        name = s.trim();
+    }
+}

File jc-reaction-kegg/src/main/resources/META-INF/jumbo-converters

+org.xmlcml.cml.converters.reaction.kegg.KEGGModule

File jc-reaction-kegg/src/test/java/org/xmlcml/cml/converters/reaction/kegg/KEGG2CMLConverterTest.java

+package org.xmlcml.cml.converters.reaction.kegg;
+
+import java.io.IOException;
+
+
+import org.junit.Ignore;
+import org.junit.Test;
+import org.xmlcml.cml.converters.reaction.rxn.RXN2CMLConverter;
+import org.xmlcml.cml.converters.testutils.JumboConvertersRegressionSuite;
+
+public class KEGG2CMLConverterTest {
+
+	@Test
+	public void testDummy() {
+		
+	}
+	
+   @Test
+   @Ignore
+   public void testConvertToXMLElement() throws IOException {
+       JumboConvertersRegressionSuite.run("cdx/cdx", "cdx", "cdx.xml",
+                            new RXN2CMLConverter());
+   }
+}

File jc-reaction-kegg/src/test/resources/org/xmlcml/cml/converters/reaction/rxn/pentoceph.rxn

+$RXN
+chemdig rzepa example_rxn
+      ISIS     062119991256
+Penicillin to Cephalosporin
+  1  1
+$MOL
+
+  -ISIS-  06219912562D
+
+ 11 12  0  0  0  0  0  0  0  0999 V2000
+    1.2875  -10.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2833  -11.7250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0375  -10.9791    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    2.0333  -11.7291    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+    3.3324  -11.7364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3365  -10.9864    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    2.6891  -10.6078    0.0000 S   0  0  3  0  0  0  0  0  0  0  0  0
+    0.7500  -12.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6933   -9.8578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    3.9881  -10.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3402  -10.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  7  3  1  0  0  0  0
+  4  5  1  0  0  0  0
+  2  4  1  0  0  0  0
+  2  8  2  0  0  0  0
+  3  1  1  0  0  0  0
+  7  9  2  0  0  0  0
+  1  2  1  0  0  0  0
+  6 10  1  0  0  0  0
+  3  4  1  0  0  0  0
+  6 11  1  0  0  0  0
+M  END
+$MOL
+
+  -ISIS-  06219912562D
+
+ 10 11  0  0  0  0  0  0  0  0999 V2000
+    7.3000  -10.5958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3000  -11.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.0500  -10.5958    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    8.0500  -11.3458    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+    8.6996  -11.7208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.3491  -11.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.3491  -10.5958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6996  -10.2208    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7697  -11.8761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    9.9917  -11.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  2  4  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  7  1  0  0  0  0
+  7  8  1  0  0  0  0
+  8  3  1  0  0  0  0
+  3  1  1  0  0  0  0
+  2  9  2  0  0  0  0
+  1  2  1  0  0  0  0
+  6 10  1  0  0  0  0
+M  END
+

File jc-reaction-rdf/.classpath

+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java"/>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
+	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER"/>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

File jc-reaction-rdf/.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>jc-composite-chemdraw</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

File jc-reaction-rdf/.settings/org.eclipse.core.resources.prefs

+#Wed Feb 22 15:54:31 GMT 2012
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding//src/test/java=UTF-8
+encoding//src/test/resources=UTF-8
+encoding/<project>=UTF-8

File jc-reaction-rdf/.settings/org.eclipse.jdt.core.prefs

+#Sat Feb 11 21:06:53 GMT 2012
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.6
+org.eclipse.jdt.core.compiler.compliance=1.6
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.source=1.6

File jc-reaction-rdf/.settings/org.eclipse.m2e.core.prefs

+#Wed Jan 04 18:20:05 GMT 2012
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

File jc-reaction-rdf/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
+	xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+	<modelVersion>4.0.0</modelVersion>
+
+	<parent>
+		<groupId>org.xml-cml.jc</groupId>
+		<artifactId>jc-reaction</artifactId>
+		<version>0.3-SNAPSHOT</version>
+	</parent>
+
+	<artifactId>jc-reaction-rdf</artifactId>
+	<name>jc-reaction-rdf</name>
+
+	<dependencies>
+        <dependency>
+            <groupId>${jc.groupId}</groupId>
+            <artifactId>jc-reaction-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>${jc.groupId}</groupId>
+            <artifactId>jc-reaction-rxn</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+	</dependencies>
+</project>

File jc-reaction-rdf/src/main/java/org/xmlcml/cml/converters/reaction/rdf/RDFConverter.java

+package org.xmlcml.cml.converters.reaction.rdf;
+
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.LineNumberReader;
+import java.io.Writer;
+import java.util.StringTokenizer;
+import java.util.logging.Logger;
+
+import nu.xom.Document;
+import nu.xom.Element;
+
+import org.xmlcml.cml.base.CMLConstants;
+import org.xmlcml.cml.base.CMLElement;
+import org.xmlcml.cml.base.CMLSerializer;
+import org.xmlcml.cml.converters.reaction.rxn.RXNConverter;
+import org.xmlcml.cml.element.CMLCml;
+import org.xmlcml.cml.element.CMLMolecule;
+import org.xmlcml.cml.element.CMLName;
+import org.xmlcml.cml.element.CMLProduct;
+import org.xmlcml.cml.element.CMLProductList;
+import org.xmlcml.cml.element.CMLProperty;
+import org.xmlcml.cml.element.CMLPropertyList;
+import org.xmlcml.cml.element.CMLReactant;
+import org.xmlcml.cml.element.CMLReactantList;
+import org.xmlcml.cml.element.CMLReaction;
+import org.xmlcml.cml.element.CMLScalar;
+
+/**
+ * class to read and write RDFiles
+ * 
+ * This is not a complete implementation; moreover there are formats I don't
+ * understand
+ * 
+ * The following came out of ISISBASE, and this implemntation is derived from
+ * it... $RDFILE 1 $DATM 12/11/2002 16:25:3 $RIREG 1 $DTYPE
+ * ROOT:SUBSTRATES(1):SUBSTRATE STRUCTURE $DATUM $MFMT
+ * 
+ * -ISIS- 12110216252D
+ * 
+ * 3 2 0 0 0 0 0 0 0 0999 V2000 2.4042 -0.2458 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ * 3.1186 0.1667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6897 0.1667 0.0000 O 0 0 0 0
+ * 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 2 0 0 0 0 M END $DTYPE
+ * ROOT:PRODUCTS(1):PRODUCT STRUCTURE $DATUM $MFMT ... though I am not sure
+ * whether it is documented.
+ * 
+ * @author (C) P. Murray-Rust, 1996, 1998, 2000
+ */
+
+public class RDFConverter implements CMLConstants {
+
+    final static Logger logger = Logger.getLogger(RDFConverter.class.getName());
+
+    /** */
+    public final static String _RXN = "$RXN";
+
+    /** */
+    public final static String RFMT = "$RFMT";
+
+    /** */
+    public final static String RDFILE = "$RDFILE";
+
+    /** */
+    public final static String RIREG = "$RIREG";
+
+    /** */
+    public final static String REREG = "$REREG";
+
+    /** */
+    public final static String DTYPE = "$DTYPE";
+
+    /** */
+    public final static String DATUM = "$DATUM";
+
+    /** */
+    public final static String MFMT = "$MFMT";
+
+    /** */
+    public final static String MIREG = "$MIREG";
+
+    /** */
+    public final static String MEREG = "$MEREG";
+
+    /** */
+    public final static String PRODUCT = "PRODUCT";
+
+    /** */
+    public final static String REACTANT = "REACTANT";
+
+    /** */
+    public final static String SUBSTRATE = "SUBSTRATE";
+
+    /** */
+    public final static String RDF = "$RDF";
+
+    LineNumberReader br;
+
+    CMLCml cml;
+
+    String line;
+
+    String id;
+
+    CMLReaction reaction;
+
+    Document doc; // overrides abstractConverter doc
+
+    CMLMolecule mol;
+
+    /**
+     * constructor.
+     */
+    public RDFConverter() {
+        this(S_EMPTY);
+    }
+
+    /**
+     * constructor.
+     * 
+     * @param id
+     */
+    public RDFConverter(String id) {
+        this.id = id;
+    }
+
+    /**
+     * Current version
+     * 
+     * @return version
+     */
+    public String getVersion() {
+        return "V2000";
+    }
+
+    /**
+     * read from lineReader.
+     * 
+     * @param br
+     * @throws IOException
+     * @throws RuntimeException
+     * @return document
+     */
+    public Document read(LineNumberReader br) throws RuntimeException, IOException {
+        /*
+         * CTfile Formats (August 2002) Page 40 Chapter 8: RDfiles An RDfile
+         * (reaction-data file) consists of a set of editable ?records.? Each
+         * record defines a molecule or reaction, and its associated data. An
+         * example RDfile incorporating the rxnfile described in Chapter 7 is
+         * shown later in this chapter. The format for an RDfile is:
+         * 
+         * [RDFile Header] [Molecule or reaction identifier] [Data-field
+         * identifier] [Data] where: d is repeated for each data item r is
+         * repeated for each reaction or molecule Each logical line in an RDfile
+         * starts with a keyword in column 1 of a physical line. One or more
+         * blanks separate the first argument (if any) from the keyword. The
+         * blanks are ignored when the line is read. After the first argument,
+         * blanks are significant. An argument longer than 80 characters breaks
+         * at column 80 and continues in column 1 of the next line. (The
+         * argument may continue on additional lines up to the physical limits
+         * on text length imposed by the database.) The RDfile must not contain
+         * any blank lines except as part of embedded molfiles, rxnfiles, or
+         * data. An identifier separates records. RDfile Header Line 1: $RDFILE
+         * 1: The [RDfile Header] must occur at the beginning of the physical
+         * file and identifies the file as an RDfile. The version stamp ?1? is
+         * intended for future expansion of the format. Line 2: $DATM: Date/time
+         * (M/D/Y, H:m) stamp. This line is treated as a comment and ignored
+         * when the program is read. Molecule and Reaction Identifiers A
+         * [Molecule or Reaction Identifier] defines the start of each complete
+         * record in an RDfile. The form of a molecule identifier must be one of
+         * the following: $MFMT [$MIREG internal-regno [$MEREG external-regno]]
+         * embedded molfile $MIREG internal-regno $MEREG external-regno where: 
+         * $MFMT defines a molecule by specifying its connection table as a
+         * molfile  $MIREG internal-regno is the internal registry number
+         * (sequence number in the database) of the molecule  $MEREG
+         * external-regno is the external registry number of the molecule (any
+         * uniquely identifying character string known to the database, for
+         * example, CAS number)  Square brackets ( [] ) enclose optional
+         * parameters  An embedded molfile (see Chapter 4) follows immediately
+         * after the $MFMT line The forms of a reaction identifier closely
+         * parallel that of a molecule: d *r CTfile Formats (August 2002) Page
+         * 41 $RFMT [$RIREG internal-regno [$REREG external-regno]] embedded
+         * rxnfile $RIREG internal-regno $REREG external-regno where:  $RFMT
+         * defines a reaction by specifying its description as a rxnfile 
+         * $RIREG internal-regno is the internal registry number (sequence
+         * number in the database) of the reaction  $REREG external-regno is
+         * the external registry number of the reaction (any uniquely
+         * identifying character string known to the database)  Square
+         * brackets ( [ ] ) enclose optional parameters  An embedded rxnfile
+         * (see Chapter 7) follows immediately after the $RFMT line Data-field
+         * Identifier The [Data-field Identifier] specifies the name of a data
+         * field in the database. The format is: $DTYPE field name Data Data
+         * associated with a field follows the field name on the next line and
+         * has the form: $DATUM datum The format of datum depends upon the data
+         * type of the field as defined in the database. For example: integer,
+         * real number, real range, text, molecule regno. For fields whose data
+         * type is ?molecule regno,? the datum must specify a molecule and, with
+         * the exception noted below, use one of the formats defined above for a
+         * molecular identifier. For example: $DATUM $MFMT embedded molfile
+         * $DATUM $MEREG external-regno $DATUM $MIREG internal-regno In
+         * addition, the following special format is accepted: $DATUM
+         * molecule-identifier Here, molecule-identifier acts in the same way as
+         * external-regno in that it can be any text string known to the
+         * database that uniquely identifies a molecule. (It is usually
+         * associated with a data field different from the external-regno.)
+         * CTfile Formats (August 2002) Page 42 Figure 15 - Example of a
+         * reaction RDfile
+         * 
+         * $RDFILE 1 $DATM 10/17/91 10:41 $RFMT $RIREG 7439 $RXN
+         * 
+         * REACCS81 101791141 7439
+         * 
+         * 2 1 $MOL
+         * 
+         * REACCS8110179110412D 1 0.00380 0.0000 315
+         * 
+         * 4 3 0 0 0 0 0 0 0 0 0 ... 1 4 1 0 0 0 4 $MOL
+         * 
+         * REACCS8110179110412D 1 0.00371 0.0000 8
+         * 
+         * 6 6 0 0 0 0 0 0 0 0 0 ... 5 6 2 0 0 0 2 $MOL
+         * 
+         * REACCS8110179110412D 1 0.00374 0.0000 255
+         * 
+         * 9 9 0 0 0 0 0 0 0 0 0 ... 6 9 2 0 0 0 2 $DTYPE
+         * rxn:VARIATION(1):rxnTEXT(1) $DATUM CrC13 $DTYPE
+         * rxn:VARIATION(1):LITTEXT(1) $DATUM A G Repin, Y Y
+         * Makarov-Zemlyanskii, Zur Russ Fiz-Chim, 44. p. 2360, 1974
+         * 
+         * $DTYPE rxn:VARIATION(1):CATALYST(1):REGNO $DATUM $MFMT $MIREG 688
+         * 
+         * REACCS8110179110412D 1 0.00371 0.0000 0
+         * 
+         * 4 3 0 0 0 0 0 0 0 0 0 ... 1 4 1 0 0 0 0 $DTYPE
+         * rxn:VARIATION(1):PRODUCT(1):YIELD $DATUM 70.0
+         * 
+         * $RFMT $RIREG 8410 $RXN
+         * 
+         * REACCS81 1017911041 8410
+         * 
+         * 
+         * 2 1 $MOL ... Rxnfile Header # Reactants, # Products Molfile for first
+         * reactant Molfile for second reactant Molfile for product RDfile
+         * Header Mol/Rxn identifier Data block for reaction Start of next
+         * record
+         */
+        cml = new CMLCml();
+        doc = new Document(cml);
+
+        readFileHeader(br);
+        line = br.readLine();
+        while (true) {
+            Element ab = readMoleculeOrReaction(br);
+            if (ab == null) {
+                break;
+            }
+            cml.appendChild(ab);
+        }
+
+        // end of input
+        return (Document) doc;
+    }
+
+    /**
+     * read document.
+     * 
+     * @param doc
+     * @param br
+     * @exception RuntimeException
+     * @exception IOException
+     * @return document
+     */
+    public Document read(Document doc, LineNumberReader br)
+            throws RuntimeException, IOException {
+        // return read((CMLDocument) doc, br);
+        return read(br);
+    }
+
+    // public CMLDocument read(CMLDocument doc, LineNumberReader br) throws
+
+    /*
+     * 
+     * $RDFILE 1 $DATM 12/11/2002 16:25:3
+     */
+    /*
+     * Line 1: $RDFILE 1: The [RDfile Header] must occur at the beginning of the
+     * physical file and identifies the file as an RDfile. The version stamp ?1?
+     * is intended for future expansion of the format. Line 2: $DATM: Date/time
+     * (M/D/Y, H:m) stamp. This line is treated as a comment and ignored when
+     * the program is read.
+     */
+    CMLElement readMoleculeOrReaction(LineNumberReader br) throws IOException,
+            RuntimeException {
+
+        /*
+         * identifier must be one of the following: $MFMT [$MIREG internal-regno
+         * [$MEREG external-regno]] embedded molfile $MIREG internal-regno
+         * $MEREG external-regno where:  $MFMT defines a molecule by
+         * specifying its connection table as a molfile  $MIREG internal-regno
+         * is the internal registry number (sequence number in the database) of
+         * the molecule  $MEREG external-regno is the external registry number
+         * of the molecule (any uniquely identifying character string known to
+         * the database, for example, CAS number)  Square brackets ( [] )
+         * enclose optional parameters  An embedded molfile (see Chapter 4)
+         * follows immediately after the $MFMT line The forms of a reaction
+         * identifier closely parallel that of a molecule: d *r CTfile Formats
+         * (August 2002) Page 41 $RFMT [$RIREG internal-regno [$REREG
+         * external-regno]] embedded rxnfile $RIREG internal-regno $REREG
+         * external-regno where:  $RFMT defines a reaction by specifying its
+         * description as a rxnfile  $RIREG internal-regno is the internal
+         * registry number (sequence number in the database) of the reaction 
+         * $REREG external-regno is the external registry number of the reaction
+         * (any uniquely identifying character string known to the database) 
+         * Square brackets ( [ ] ) enclose optional parameters  An embedded
+         * rxnfile (see Chapter 7) follows immediately after the $RFMT line
+         * Data-field Identifier
+         */
+        // logger.info("RMOR"+line);
+        if (line == null) {
+            return null;
+        }
+        if (line.startsWith(MFMT) || line.startsWith(MIREG)
+                || line.startsWith(MEREG)) {
+            return readMolecule(br);
+        } else if (line.startsWith(RFMT) || line.startsWith(RIREG)
+                || line.startsWith(REREG)) {
+            return readReaction(br);
+        } else {
+            throw new RuntimeException("Corrupt RDF entry: " + line + " (line: "
+                    + br.getLineNumber() + S_RBRAK);
+        }
+    }
+
+    /*
+     * $RIREG 1 $DTYPE ROOT:UNIQUE IDENTIFIER $DATUM 1 $DTYPE ROOT:EC NUMBER
+     * $DATUM 1.7.99.3 $DTYPE ROOT:PDB CODE $DATUM 1nid $DTYPE ROOT:ENZYME NAME
+     * $DATUM Nitrite Reductase (Copper containing) $DTYPE
+     * ROOT:SUBSTRATES(1):SUBSTRATE NUMBER $DATUM 1 $DTYPE
+     * ROOT:SUBSTRATES(1):SUBSTRATE STRUCTURE $DATUM $MFMT
+     * 
+     * -ISIS- 12160210312D
+     * 
+     * 3 2 0 0 0 0 0 0 0 0999 V2000 2.4042 -0.2458 0.0000 N 0 0 0 0 0 0 0 0 0 0
+     * 0 0 3.1186 0.1667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6897 0.1667 0.0000 O
+     * 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 3 2 0 0 0 0 M END $DTYPE
+     * ROOT:SUBSTRATES(1):SUBSTRATE NAME $DATUM Nitrous Acid $DTYPE
+     * ROOT:PRODUCTS(1):PRODUCT NUMBER $DATUM 1 $DTYPE ROOT:PRODUCTS(1):PRODUCT
+     * STRUCTURE $DATUM $MFMT
+     * 
+     * -ISIS- 12160210312D
+     * 
+     * 2 1 0 0 0 0 0 0 0 0999 V2000 1.9667 -8.4625 0.0000 N 0 0 0 0 0 0 0 0 0 0
+     * 0 0 2.6811 -8.0500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 M END
+     * $DTYPE ROOT:PRODUCTS(1):PRODUCT_NAME $DATUM Nitric Oxide $DTYPE
+     * ROOT:REACTION STAGES(1):REACTION STAGES $DATUM 1 $DTYPE
+     * ROOT:REFERENCES(1):REFERENCE NUMBER $DATUM 1 $DTYPE
+     * ROOT:REFERENCES(1):REFERENCE $DATUM Boulanger et al. JBC 275 (31)
+     * 23957-23964 (2000) $RIREG 2 ...
+     */
+    CMLMolecule readMolecule(LineNumberReader br) throws RuntimeException,
+            IOException {
+        StringTokenizer st = new StringTokenizer(line);
+        String keyw = st.nextToken();
+        if (keyw.equals(MIREG)) {
+            mol = new CMLMolecule();
+            if (st.countTokens() == 1) {
+                mol.setRef(line);
+            } else {
+                logger.severe("Bad " + MIREG + S_SPACE + line);
+            }
+        } else if (line.startsWith(MEREG)) {
+            line = line.substring(MEREG.length()).trim();
+            mol = new CMLMolecule();
+            if (st.countTokens() == 1) {
+                String tok = st.nextToken();
+                mol.setRef(tok);
+                mol.setConvention("external");
+            } else {
+                logger.severe("Bad " + MEREG + S_SPACE + line);
+            }
+        } else if (keyw.equals(MFMT)) {
+            // mol = new MDLConverter().readMolecule(doc, br); // FIXME
+
+            if (st.countTokens() >= 2) {
+                if (st.nextToken().equals(MIREG)) {
+                    mol.setRef(st.nextToken());
+                }
+            }
+            if (st.countTokens() >= 2) {
+                if (st.nextToken().equals(MEREG)) {
+                    CMLName name = new CMLName();
+                    name.setConvention("external");
+                    name.setXMLContent(st.nextToken());
+                    mol.addName(name);
+                }
+            }
+        }
+        readData(br, mol);
+        return mol;
+    }
+
+    CMLReaction readReaction(LineNumberReader br) throws RuntimeException,
+            IOException {
+        StringTokenizer st = new StringTokenizer(line);
+        String keyw = st.nextToken();
+        if (keyw.equals(RIREG)) {
+            reaction = new CMLReaction();
+            if (st.hasMoreTokens()) {
+                String tok = st.nextToken();
+                logger.info("RIREG: " + tok);
+                reaction.setId("r" + tok);
+            } else {
+                logger.severe("Bad " + RIREG + S_SPACE + line);
+            }
+        } else if (keyw.equals(REREG)) {
+            reaction = new CMLReaction();
+            if (st.countTokens() == 1) {
+                reaction.setRef(line);
+                reaction.setConvention("external");
+            } else {
+                logger.severe("Bad " + RIREG + S_SPACE + line);
+            }
+        } else if (keyw.equals(RFMT)) {
+            reaction = new RXNConverter().readReaction(doc, br);
+        } else if (keyw.equals(MFMT)) {
+            // mol = new MDLConverter().readMolecule(doc, br); //FIXME
+            if (st.countTokens() >= 2) {
+                if (st.nextToken().equals(RIREG)) {
+                    mol.setRef(st.nextToken());
+                }
+            }
+            if (st.countTokens() >= 2) {
+                if (st.nextToken().equals(REREG)) {
+                    CMLName name = new CMLName();
+                    name.setConvention("external");
+                    name.setXMLContent(st.nextToken());
+                    mol.addName(name);
+                }
+            }
+        }
+        readData(br, reaction);
+        return reaction;
+    }
+
+    // not sure which of these can contain data
+
+    void readData(LineNumberReader br, Element ab) throws IOException,
+            RuntimeException {
+        CMLPropertyList propertyList = null;
+
+        line = br.readLine();
+        while (true) {
+            if (line == null) {
+                break;
+            }
+            if (line.startsWith(MFMT) || line.startsWith(MIREG)
+                    || line.startsWith(MEREG) || line.startsWith(RFMT)
+                    || line.startsWith(RIREG) || line.startsWith(REREG)) {
+                break;
+            } else if (line.startsWith(DTYPE)) {
+                String dtype = line.substring(DTYPE.length() + 1).trim();
+                line = br.readLine();
+                if (!line.startsWith(DATUM)) {
+                    throw new RuntimeException("Expected " + DATUM + " at " + line);
+                }
+                String datum = line.substring(DATUM.length() + 1).trim();
+                if (datum.startsWith(_RXN)) {
+                    CMLReaction rxn = new RXNConverter().readReaction(doc, br);
+                    ab.appendChild(rxn);
+                    line = br.readLine();
+                } else if (datum.startsWith(MFMT)) {
+                    // mol = new MDLConverter().readMolecule(doc, br); // FIXME
+                    CMLReaction reaction = (CMLReaction) ab;
+                    if (isReactant(dtype)) {
+                        CMLReactantList reactantList = new CMLReactantList();
+                        reaction.addReactantList(reactantList);
+                        CMLReactant reactant = new CMLReactant();
+                        reactantList.addReactant(reactant);
+                        reactant.addMolecule(mol);
+                    } else {
+                        CMLProductList productList = new CMLProductList();
+                        reaction.addProductList(productList);
+                        CMLProduct product = new CMLProduct();
+                        productList.addProduct(product);
+                        product.addMolecule(mol);
+                    }
+                    line = br.readLine();
+                } else {
+                    if (propertyList == null) {
+                        propertyList = (CMLPropertyList) new CMLPropertyList();
+                        if (ab instanceof CMLMolecule) {
+                            ((CMLMolecule) ab).addPropertyList(propertyList);
+                        }
+                        if (ab instanceof CMLReaction) {
+                            ((CMLReaction) ab).addPropertyList(propertyList);
+                        }
+                    }
+                    CMLScalar scalar = new CMLScalar();
+                    scalar.setTitle(dtype);
+                    while (true) {
+                        line = br.readLine();
+                        if (line == null || line.charAt(0) == '$') {
+                            break;
+                        }
+                        datum += CMLElement.S_NL + line;
+                    }
+
+                    scalar.setXMLContent(datum);
+                    CMLProperty property = new CMLProperty();
+                    propertyList.addProperty(property);
+                    property.appendChild(scalar);
+                }
+            } else {
+                throw new RuntimeException("Unrecognised line reading $DTYPE "
+                        + line);
+            }
+        }
+    }
+
+    /* really horrible, but we don't know the database schema */
+    boolean isReactant(String dtype) {
+        if (dtype.toLowerCase().indexOf("substrate structure") != -1) {
+            return true;
+        }
+        if (dtype.toLowerCase().indexOf("product structure") != -1) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * read start of file.
+     * 
+     * @param br
+     * @throws IOException
+     * @throws RuntimeException
+     */
+    protected void readFileHeader(LineNumberReader br) throws IOException,
+            RuntimeException {
+
+        /**
+         * this could be all sorts of stuff... ------RIREG format-----------
+         * $RDFILE 1 $DATM 12/11/2002 16:25:3 $RIREG 1 ... $RIREG 2 ...
+         * ------------------- --
+         */
+        line = br.readLine();
+        if (line == null) {
+            throw new RuntimeException("Empty RDF file");
+        }
+        if (!line.startsWith(RDFILE)) {
+            throw new IOException("non-RDF: RDF file must start with '"
+                    + RDFILE + "'");
+        }
+        line = br.readLine();
+        if (line == null) {
+            throw new RuntimeException("Corrupt RDF file");
+        }
+        if (!line.startsWith("$DATM ")) {
+            throw new RuntimeException("non-RDF " + line);
+        }
+    }
+
+    /*--
+     void output(Writer writer, CMLList list)
+     throws RuntimeException, IOException {
+
+     }
+     --*/
+    /**
+     * outputs CML as an RDF if possible. NYI
+     * 
+     * @param writer
+     *            to output it to
+     * @throws RuntimeException
+     * @throws IOException
+     * @return string
+     */
+    public String output(Writer writer) throws RuntimeException, IOException {
+        return null;
+    }
+
+    /**
+     * NYI
+     * 
+     * @param writer
+     *            DOCUMENT ME!
+     * @return DOCUMENT ME!
+     * @throws RuntimeException
+     *             DOCUMENT ME!
+     * @throws IOException
+     *             DOCUMENT ME!
+     */
+    public String writeData(Writer writer) throws RuntimeException, IOException {
+        return null;
+    }
+
+    /**
+     * main.
+     * 
+     * @param args
+     */
+    public static void main(String[] args) {
+        if (args.length == 0) {
+            logger
+                    .info("Usage: org.xmlcml.legacy.reaction.RDFConverter [options]");
+            logger.info("        -IN inputFile (RDF)");
+            logger.info("        -OUT outputFile (CML)");
+            logger.info("        -ID id");
+            System.exit(0);
+        }
+        int i = 0;
+        String infile = S_EMPTY;
+        String outfile = S_EMPTY;
+        String id = S_EMPTY;
+        while (i < args.length) {
+            if (1 == 2) {
+                ;
+            } else if (args[i].equalsIgnoreCase("-ID")) {
+                id = args[++i];
+                i++;
+            } else if (args[i].equalsIgnoreCase("-IN")) {
+                infile = args[++i];
+                i++;
+            } else if (args[i].equalsIgnoreCase("-OUT")) {
+                outfile = args[++i];
+                i++;
+            } else {
+                logger.severe("Unknown arg: " + args[i]);
+                i++;
+            }
+        }
+        Document doc = null;
+        try {
+            if (!infile.equals(S_EMPTY)) {
+                LineNumberReader lnr = new LineNumberReader(new FileReader(
+                        infile));
+                RDFConverter rdf = new RDFConverter(id);
+                doc = (Document) rdf.read(lnr);
+            }
+            // if (!id.equals(S_EMPTY)) {
+            // CMLReaction reaction = (CMLReaction) doc.getDocumentElement();
+            // reaction.setId(id);
+            // }
+            if (!outfile.equals(S_EMPTY)) {
+                FileOutputStream fos = new FileOutputStream(outfile);
+                CMLSerializer serializer = new CMLSerializer(fos);
+                serializer.write(doc);
+                fos.close();
+            } else {
+                ;
+                // PMRDOMUtil.debug(doc);
+            }
+
+        } catch (IOException ioe) {
+            logger.info("IOEXception: " + ioe);
+        } catch (RuntimeException cmle) {
+            logger.info("CMLEXception: " + cmle);
+            cmle.printStackTrace();
+        }
+    }
+}

File jc-reaction-rdf/src/main/java/org/xmlcml/cml/converters/reaction/rdf/package-info.java

+/** 
+<h2>Converts RDF (MDL) files to CML.</h2>
+Currently missing 
+*/
+package org.xmlcml.cml.converters.reaction.rdf;

File jc-reaction-rdf/src/main/resources/META-INF/jumbo-converters

+org.xmlcml.cml.converters.reaction.rdf.RXNModule

File jc-reaction-rdf/src/test/resources/org/xmlcml/cml/converters/reaction/rxn/pentoceph.rxn

+$RXN
+chemdig rzepa example_rxn
+      ISIS     062119991256
+Penicillin to Cephalosporin
+  1  1
+$MOL
+
+  -ISIS-  06219912562D
+
+ 11 12  0  0  0  0  0  0  0  0999 V2000
+    1.2875  -10.9750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    1.2833  -11.7250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    2.0375  -10.9791    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    2.0333  -11.7291    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+    3.3324  -11.7364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3365  -10.9864    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    2.6891  -10.6078    0.0000 S   0  0  3  0  0  0  0  0  0  0  0  0
+    0.7500  -12.2500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    2.6933   -9.8578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    3.9881  -10.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    3.3402  -10.3556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  1  0  0  0  0
+  7  3  1  0  0  0  0
+  4  5  1  0  0  0  0
+  2  4  1  0  0  0  0
+  2  8  2  0  0  0  0
+  3  1  1  0  0  0  0
+  7  9  2  0  0  0  0
+  1  2  1  0  0  0  0
+  6 10  1  0  0  0  0
+  3  4  1  0  0  0  0
+  6 11  1  0  0  0  0
+M  END
+$MOL
+
+  -ISIS-  06219912562D
+
+ 10 11  0  0  0  0  0  0  0  0999 V2000
+    7.3000  -10.5958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    7.3000  -11.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.0500  -10.5958    0.0000 C   0  0  3  0  0  0  0  0  0  0  0  0
+    8.0500  -11.3458    0.0000 N   0  0  3  0  0  0  0  0  0  0  0  0
+    8.6996  -11.7208    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.3491  -11.3458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    9.3491  -10.5958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+    8.6996  -10.2208    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
+    6.7697  -11.8761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
+    9.9917  -11.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
+  2  4  1  0  0  0  0
+  3  4  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  2  0  0  0  0
+  6  7  1  0  0  0  0
+  7  8  1  0  0  0  0
+  8  3  1  0  0  0  0
+  3  1  1  0  0  0  0
+  2  9  2  0  0  0  0
+  1  2  1  0  0  0  0
+  6 10  1  0  0  0  0
+M  END
+

File jc-reaction-rxn/src/main/java/org/xmlcml/cml/converters/reaction/rxn/RXN2CMLConverter.java

-package org.xmlcml.cml.converters.reaction.rxn;
-
-import nu.xom.Element;
-
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.xmlcml.cml.converters.AbstractConverter;
-import org.xmlcml.cml.converters.MimeType;
-import org.xmlcml.cml.converters.cml.CMLCommon;
-import org.xmlcml.cml.element.CMLCml;
-
-public class RXN2CMLConverter extends AbstractConverter {
-
-	private static final Logger LOG = Logger.getLogger(RXN2CMLConverter.class);
-	public static final String REG_MESSAGE = "Chemdraw CDX to CDXML conversion";
-	static {
-		LOG.setLevel(Level.INFO);
-	}
-	
-	/**
-	 * converts a CDK object to CML. returns cml:cml/cml:molecule
-	 * 
-	 * @param bytes
-	 */
-	public Element convertToXML(byte[] bytes) {
-		Element element = new CMLCml();
-		return element;
-	}
-	
-	public MimeType getInputType() {
-		return RXNModule.RXN_TYPE;
-	}
-	
-	public MimeType getOutputType() {
-		return CMLCommon.CML_TYPE;
-	}
-	
-	public String getDescription() {
-		return REG_MESSAGE;
-	}
-
-
-}
+package org.xmlcml.cml.converters.reaction.rxn;
+
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.LineNumberReader;
+import java.io.Writer;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Logger;
+
+import nu.xom.Document;
+
+import org.xmlcml.cml.base.CMLConstants;
+import org.xmlcml.cml.base.CMLSerializer;
+import org.xmlcml.cml.converters.AbstractConverter;
+import org.xmlcml.cml.converters.MimeType;
+import org.xmlcml.cml.converters.cml.CMLCommon;
+import org.xmlcml.cml.element.CMLAtom;
+import org.xmlcml.cml.element.CMLLink;
+import org.xmlcml.cml.element.CMLList;
+import org.xmlcml.cml.element.CMLMap;
+import org.xmlcml.cml.element.CMLMolecule;
+import org.xmlcml.cml.element.CMLProduct;
+import org.xmlcml.cml.element.CMLProductList;
+import org.xmlcml.cml.element.CMLReactant;
+import org.xmlcml.cml.element.CMLReactantList;
+import org.xmlcml.cml.element.CMLReaction;
+import org.xmlcml.cml.element.CMLReaction.Component;
+import org.xmlcml.cml.element.CMLScalar;
+import org.xmlcml.cml.tools.ReactionTool;
+
+/**
+ * converts RXN format to CMLReact
+ * 
+ * @author Administrator
+ */
+public class RXN2CMLConverter extends AbstractConverter implements CMLConstants {
+
+    final static Logger logger = Logger.getLogger(RXN2CMLConverter.class.getName());
+
+    /**
+     */
+    public final static String RXN = "$RXN";
+
+    /** */
+    public final static String FROM_MDL_MAPPING = "from MDL-RXN mapping";
+	public static final String REG_MESSAGE = "RXN to CML conversion";
+
+    String id;
+    int nProducts;
+    int nReactants;
+    CMLReaction reaction;
+    CMLReactantList reactantList;
+    CMLProductList productList;
+    String line = null;
+    String inDir = "";
+    String outDir = "";
+    String inSuffix = ".rxn";
+    String outSuffix = ".cml";
+    Document doc;
+
+	private ReactionTool reactionTool;
+
+    /**
+     * Constructor for the RXNConverter object
+     */
+    public RXN2CMLConverter() {
+        this("");
+    }
+
+    /**
+     * Constructor for the RXNConverter object
+     * 
+     * @param reactionId
+     */
+    public RXN2CMLConverter(String reactionId) {
+        id = reactionId;
+    }
+
+    /**
+     * Current version
+     * 
+     * @return version
+     */
+    public String getVersion() {
+
+        return "V2000";
+    }
+
+    /**
+     * Sets the inDir attribute of the RXNConverter object
+     * 
+     * @param inDir
+     *            The new inDir value
+     */
+    public void setInDir(String inDir) {
+        this.inDir = inDir;
+    }
+
+    /**
+     * Gets the inDir attribute of the RXNConverter object
+     * 
+     * @return The inDir value
+     */
+    public String getInDir() {
+        return this.inDir;
+    }
+
+    /**
+     * Sets the outDir attribute of the RXNConverter object
+     * 
+     * @param outDir
+     *            The new outDir value
+     */
+    public void setOutDir(String outDir) {
+        this.outDir = outDir;
+    }
+
+    /**
+     * Gets the outDir attribute of the RXNConverter object
+     * 
+     * @return The outDir value
+     */
+    public String getOutDir() {
+        return this.outDir;
+    }
+
+    /**
+     * does the conversion
+     * 
+     * @exception IOException
+     * @exception RuntimeException
+     */
+    public void process() throws IOException {
+        if (!inDir.equals("") && !outDir.equals("")) {
+            String userDir = System.getProperties().getProperty("user.dir");
+            // File inDirF = new File(userDir, inDir);
+            File inDirF = new File(inDir);
+            logger.info("userDir" + userDir);
+            logger.info("inDirF" + inDirF);
+            File[] files = inDirF.listFiles();
+            for (int i = 0; i < files.length; i++) {
+                String fName = files[i].getPath();
+                if (fName.endsWith(inSuffix)) {
+                    logger.info("Reading" + fName);
+                    int idx = fName.lastIndexOf(S_PERIOD);
+                    String fileroot = fName.substring(0, idx);
+                    idx = fileroot.lastIndexOf(File.separator);
+                    String id = fileroot.substring(idx + 1);
+                    String outfile = fileroot + outSuffix;
+                    LineNumberReader lnr = new LineNumberReader(new FileReader(
+                            files[i]));
+                    RXN2CMLConverter rxn = new RXN2CMLConverter(id);
+                    doc = (Document) rxn.read(lnr);
+                    logger.info("Writing To" + outfile);
+                    FileOutputStream fos = new FileOutputStream(outfile);
+                    CMLSerializer serializer = new CMLSerializer(fos);
+                    serializer.write(doc);
+                    fos.close();
+                }
+            }
+        }
+    }
+
+    /**
+     * read into document
+     * 
+     * @param br
+     * @return document
+     * @exception RuntimeException
+     * @exception IOException
+     */