Added (de)serialization of the IIsotope fields to RDF

cdk · Oct 17, 2010 · 3db0b71 · 3db0b71
1 parent 153fa7f
commit 3db0b71
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Showing 3 changed files with 80 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/libio/jena/CDK.java b/src/main/org/openscience/cdk/libio/jena/CDK.java
@@ -47,6 +47,7 @@ private static final Property property(String local) {
     public static final Resource ChemObject = resource("ChemObject");
     public static final Resource Element = resource("Element");
     public static final Resource AtomType = resource("AtomType");
+    public static final Resource Isotope = resource("Isotope");
 
     // IBond.Order
     public static final Resource SingleBond = resource("SingleBond");
@@ -77,5 +78,9 @@ private static final Property property(String local) {
     public static final Property hasAtomTypeName = property("hasAtomTypeName");
     public static final Property hasMaxBondOrder = property("hasMaxBondOrder");
     public static final Property hasFormalCharge = property("hasFormalCharge");
+    public static final Property hasMassNumber = property("hasMassNumber");
+    public static final Property hasExactMass = property("hasExactMass");
+    public static final Property hasNaturalAbundance =
+        property("hasNaturalAbundance");
 
 }
diff --git a/src/main/org/openscience/cdk/libio/jena/Convertor.java b/src/main/org/openscience/cdk/libio/jena/Convertor.java
@@ -25,12 +25,14 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomType;
 import org.openscience.cdk.interfaces.IBond;
 import org.openscience.cdk.interfaces.IChemObject;
 import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IElement;
+import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IMolecule;
 import org.openscience.cdk.interfaces.IAtomType.Hybridization;
 import org.openscience.cdk.interfaces.IBond.Order;
@@ -127,7 +129,7 @@ private static void deserializeElementFields(
 
     private static void serializeAtomTypeFields(Model model,
             Resource rdfObject, IAtomType type) {
-        serializeElementFields(model, rdfObject, type);
+        serializeIsotopeFields(model, rdfObject, type);
         if (type.getHybridization() != null) {
             Hybridization hybrid = type.getHybridization(); 
             if (hybrid == Hybridization.S) {
@@ -169,9 +171,32 @@ private static void serializeAtomTypeFields(Model model,
         }
     }
 
+    private static void serializeIsotopeFields(Model model, Resource rdfObject,
+            IIsotope isotope) {
+        serializeElementFields(model, rdfObject, isotope);
+        if (isotope.getMassNumber() != CDKConstants.UNSET) {
+            model.add(
+                 rdfObject, CDK.hasMassNumber,
+                 isotope.getMassNumber().toString()
+            );
+        }
+        if (isotope.getExactMass() != CDKConstants.UNSET) {
+            model.add(
+                 rdfObject, CDK.hasExactMass,
+                 isotope.getExactMass().toString()
+            );
+        }
+        if (isotope.getNaturalAbundance() != CDKConstants.UNSET) {
+            model.add(
+                 rdfObject, CDK.hasNaturalAbundance,
+                 isotope.getNaturalAbundance().toString()
+            );
+        }
+    }
+
     private static void deserializeAtomTypeFields(
             Resource rdfObject, IAtomType element) {
-        deserializeElementFields(rdfObject, element);
+        deserializeIsotopeFields(rdfObject, element);
         Statement hybrid = rdfObject.getProperty(CDK.hasHybridization);
         if (hybrid != null) {
             Resource rdfHybrid = (Resource)hybrid.getObject();
@@ -211,6 +236,21 @@ private static void deserializeAtomTypeFields(
             element.setFormalCharge(formalCharge.getInt());
     }
 
+    private static void deserializeIsotopeFields(Resource rdfObject,
+            IIsotope isotope) {
+        deserializeElementFields(rdfObject, isotope);
+        Statement massNumber = rdfObject.getProperty(CDK.hasMassNumber);
+        if (massNumber != null)
+            isotope.setMassNumber(massNumber.getInt());
+        Statement exactMass = rdfObject.getProperty(CDK.hasExactMass);
+        if (exactMass != null)
+            isotope.setExactMass(exactMass.getDouble());
+        Statement naturalAbundance =
+            rdfObject.getProperty(CDK.hasNaturalAbundance);
+        if (naturalAbundance != null)
+            isotope.setNaturalAbundance(naturalAbundance.getDouble());
+    }
+
     public static Order resource2Order(Resource rdfOrder) {
         if (rdfOrder.equals(CDK.SingleBond)) {
             return Order.SINGLE;

diff --git a/src/test/org/openscience/cdk/libio/jena/ConvertorTest.java b/src/test/org/openscience/cdk/libio/jena/ConvertorTest.java
@@ -122,6 +122,39 @@ private void roundtripBond_Order(IBond.Order order) {
         Assert.assertEquals("Unexpected diff: " + diff, 0, diff.length());
     }
 
+    @Test public void roundtripIsotope_ExactMass() {
+        IMolecule mol = new NNMolecule();
+        IAtom object = new NNAtom("C");
+        object.setExactMass(0.3);
+        mol.addAtom(object);
+        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());
+    }
+
+    @Test public void roundtripIsotope_MassNumber() {
+        IMolecule mol = new NNMolecule();
+        IAtom object = new NNAtom("C");
+        object.setMassNumber(13);
+        mol.addAtom(object);
+        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());
+    }
+
+    @Test public void roundtripIsotope_NaturalAbundance() {
+        IMolecule mol = new NNMolecule();
+        IAtom object = new NNAtom("C");
+        object.setNaturalAbundance(0.95);
+        mol.addAtom(object);
+        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());
+    }
+
     @Test public void roundtripAtomType_S() {
         roundtripAtomType_Hybridization(Hybridization.S);
     }