From d0c2b50f4641043e6aeca622448ddec50bcabe94 Mon Sep 17 00:00:00 2001
From: Egon Willighagen <egonw@users.sourceforge.net>
Date: Tue, 6 Oct 2009 15:35:07 +0200
Subject: [PATCH] Added read/write of IAtom.symbol in RDF

---
 .../openscience/cdk/libio/jena/Convertor.java | 45 ++++++++++++++++---
 .../cdk/io/rdf/CDKOWLWriterTest.java          |  2 +
 .../cdk/libio/jena/ConvertorTest.java         | 10 +++++
 3 files changed, 50 insertions(+), 7 deletions(-)

diff --git a/src/main/org/openscience/cdk/libio/jena/Convertor.java b/src/main/org/openscience/cdk/libio/jena/Convertor.java
index 1a73a4d49eb..9f4d51cc8fb 100644
--- a/src/main/org/openscience/cdk/libio/jena/Convertor.java
+++ b/src/main/org/openscience/cdk/libio/jena/Convertor.java
@@ -22,12 +22,17 @@
  */
 package org.openscience.cdk.libio.jena;
 
+import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IMolecule;
 
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ResIterator;
 import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.vocabulary.RDF;
 
 /**
@@ -42,22 +47,48 @@
 public class Convertor {
 
     public static Model molecule2Model(IMolecule molecule) {
-        Model model = ModelFactory.createOntologyModel();
-        model.setNsPrefix("cdk", "http://cdk.sourceforge.net/model.owl#");
+        Model model = createCDKModel();
         Resource subject = model.createResource(
             "http://cdk.sf.net/model/molecule/" + 1
         );
-        model.add(
-            subject, RDF.type,
-            model.createResource("cdk:Molecule")
-        );
+        model.add(subject, RDF.type, CDK.Molecule);
+        int atomCounter = 0;
+        for (IAtom atom : molecule.atoms()) {
+            atomCounter++;
+            Resource rdfAtom = model.createResource(
+                "http://cdk.sf.net/model/atom/" + atomCounter
+            );
+            model.add(rdfAtom, RDF.type, CDK.Atom);
+            model.add(rdfAtom, CDK.symbol, atom.getSymbol());
+            model.add(subject, CDK.hasAtom, rdfAtom);
+        }
         return model;
     }
 
     public static IMolecule model2Molecule(Model model,
         IChemObjectBuilder builder) {
-        IMolecule mol = builder.newMolecule();
+        ResIterator mols =
+            model.listSubjectsWithProperty(RDF.type, CDK.Molecule);
+        IMolecule mol = null;
+        if (mols.hasNext()) {
+            Resource rdfMol = mols.next();
+            mol = builder.newMolecule();
+            StmtIterator atoms = rdfMol.listProperties(CDK.hasAtom);
+            while (atoms.hasNext()) {
+                Statement rdfAtom = atoms.nextStatement();
+                IAtom atom = builder.newAtom();
+                Statement symbol = rdfAtom.getProperty(CDK.symbol);
+                if (symbol != null) atom.setSymbol(symbol.getString());
+                mol.addAtom(atom);
+            }
+        }
         return mol;
     }
 
+    private static Model createCDKModel() {
+        Model model = ModelFactory.createOntologyModel();
+        model.setNsPrefix("cdk", "http://cdk.sourceforge.net/model.owl#");
+        return model;
+    }
+
 }
diff --git a/src/test/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java b/src/test/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java
index e8e91416d14..81deeb43318 100644
--- a/src/test/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java
+++ b/src/test/org/openscience/cdk/io/rdf/CDKOWLWriterTest.java
@@ -30,6 +30,7 @@
 import org.junit.Test;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.io.ChemObjectWriterTest;
+import org.openscience.cdk.nonotify.NNAtom;
 import org.openscience.cdk.nonotify.NNMolecule;
 
 /**
@@ -48,6 +49,7 @@ public class CDKOWLWriterTest extends ChemObjectWriterTest {
         CDKOWLWriter writer = new CDKOWLWriter(output);
 
         IMolecule mol = new NNMolecule();
+        mol.addAtom(new NNAtom("C"));
         writer.write(mol);
         String outputString = output.toString();
         Assert.assertTrue(outputString.contains(
diff --git a/src/test/org/openscience/cdk/libio/jena/ConvertorTest.java b/src/test/org/openscience/cdk/libio/jena/ConvertorTest.java
index 3233ac1d138..1d41a884c1f 100644
--- a/src/test/org/openscience/cdk/libio/jena/ConvertorTest.java
+++ b/src/test/org/openscience/cdk/libio/jena/ConvertorTest.java
@@ -28,6 +28,7 @@
 import org.openscience.cdk.CDKTestCase;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.nonotify.NNAtom;
 import org.openscience.cdk.nonotify.NNMolecule;
 import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
 import org.openscience.cdk.tools.diff.AtomContainerDiff;
@@ -50,4 +51,13 @@ public class ConvertorTest extends CDKTestCase {
         Assert.assertEquals(0, diff.length());
     }
 
+    @Test public void roundtripAtom() {
+        IMolecule mol = new NNMolecule();
+        mol.addAtom(new NNAtom("C"));
+        Model model = Convertor.molecule2Model(mol);
+        IMolecule rtMol = Convertor.model2Molecule(model, builder);
+        String diff = AtomContainerDiff.diff(mol, rtMol);
+        Assert.assertEquals("Unexpected diff: " + diff, 0, diff.length());
+    }
+
 }