Fixed proton isotope perception.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
cdk · Mar 23, 2013 · 421345b · 421345b
1 parent c273930
commit 421345b
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Showing 2 changed files with 36 additions and 12 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -925,14 +925,14 @@ private void fixHydrogenIsotopes(IMolecule molecule,IsotopeFactory isotopeFactor
                 if ("D".equals(pseudo.getLabel())) {
 					IAtom newAtom = molecule.getBuilder().newInstance(IAtom.class,atom);
 					newAtom.setSymbol("H");
-                    IIsotope isotope = molecule.getBuilder().newInstance(IIsotope.class,"H", 2);
-                    isotopeFactory.configure(newAtom, isotope);               
+                    IIsotope isotope = molecule.getBuilder().newInstance(IIsotope.class, 1, "H", 2, 2.014101778, 0.0115);
+					isotopeFactory.configure(newAtom, isotope);
 					AtomContainerManipulator.replaceAtomByAtom(molecule, atom, newAtom);
                 } else if ("T".equals(pseudo.getLabel())) {
                     IAtom newAtom = molecule.getBuilder().newInstance(IAtom.class,atom);
 					newAtom.setSymbol("H");
-				    IIsotope isotope = molecule.getBuilder().newInstance(IIsotope.class,"H", 3);
-				    isotopeFactory.configure(newAtom, isotope);               
+				    IIsotope isotope = molecule.getBuilder().newInstance(IIsotope.class, 1, "H", 3, 3.016049278, 0d);
+				    isotopeFactory.configure(newAtom, isotope);
 					AtomContainerManipulator.replaceAtomByAtom(molecule, atom, newAtom);
 				}
 			}

diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -25,9 +25,18 @@
 package org.openscience.cdk.io;
 
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringReader;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+
 import org.junit.Assert;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
 import org.openscience.cdk.CDKConstants;
 import org.openscience.cdk.ChemFile;
 import org.openscience.cdk.ChemModel;
@@ -49,14 +58,6 @@
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
 
-import java.io.InputStream;
-import java.io.StringReader;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
-
 
 /**
  * TestCase for the reading MDL mol files using one test file.
@@ -865,6 +866,18 @@ public void testDeuterium() throws Exception {
         Assert.assertEquals(3, deuteriumCount);
     }
 
+	@Test
+	public void testDeuteriumProperties() throws Exception {
+		String filename = "data/mdl/chemblMolregno5369.mol";
+		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+		MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.RELAXED);
+		IAtomContainer molecule = new AtomContainer();
+		molecule = reader.read(molecule);
+		IAtom deuterium = molecule.getAtom(molecule.getAtomCount() - 1);
+		Assert.assertTrue(1 == deuterium.getAtomicNumber());
+		Assert.assertTrue(2.014101778 == deuterium.getExactMass());
+	}
+
     @Test public void testTritium() throws Exception {
         String filename = "data/mdl/chemblMolregno7039.mol";
         InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
@@ -878,6 +891,17 @@ public void testDeuterium() throws Exception {
         Assert.assertEquals(1, tritiumCount);
     }
 
+	@Test public void testTritiumProperties() throws Exception {
+		String filename = "data/mdl/chemblMolregno7039.mol";
+		InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+		MDLV2000Reader reader = new MDLV2000Reader(ins);
+		IAtomContainer molecule = new AtomContainer();
+		molecule = reader.read(molecule);
+		IAtom tritium = molecule.getAtom(molecule.getAtomCount() - 1);
+		Assert.assertTrue(1 == tritium.getAtomicNumber());
+		Assert.assertTrue(3.016049278 == tritium.getExactMass());
+	}
+
     /**
      * Test that R-groups at higher atom numbers (>9) are read correctly
      */