Added modifications and unit test for alias atom naming patch

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Dec 9, 2011 · bd4b094 · bd4b094
1 parent 23132a0
commit bd4b094
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -720,12 +720,19 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
             		int aliasAtomNumber = Integer.parseInt(line.replaceFirst("A\\s{1,4}", "")) - RGroupCounter;
             		line = input.readLine(); linecount++;
 					String[] aliasArray = line.split("\\\\");
-					// name of the alias atom like R1 odr R2 etc. 
+					// name of the alias atom like R1 or R2 etc. 
 					String alias = "";
 					for (int i = 0; i < aliasArray.length; i++) {
 						alias += aliasArray[i];
 					}
 					IAtom aliasAtom = molecule.getAtom(aliasAtomNumber);
+
+                    // skip if already a pseudoatom
+                    if(aliasAtom instanceof IPseudoAtom){
+                        ((IPseudoAtom) aliasAtom).setLabel(alias);
+                        continue;
+                    }
+
 					IAtom newPseudoAtom = molecule.getBuilder().newInstance(IPseudoAtom.class,alias);
 					if(aliasAtom.getPoint2d() != null) {
 						newPseudoAtom.setPoint2d(aliasAtom.getPoint2d());

diff --git a/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java b/src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -884,6 +884,24 @@ public void testDeuterium() throws Exception {
         MDLV2000Reader reader = new MDLV2000Reader(in);
         IMolecule molecule = DefaultChemObjectBuilder.getInstance().newInstance(IMolecule.class);
         reader.read(molecule);
-        Assert.assertEquals("R", molecule.getAtom(55).getSymbol() );
+        Assert.assertEquals("R", molecule.getAtom(55).getSymbol());
+    }
+
+    @Test
+    public void testAliasAtomNaming() throws Exception {
+        InputStream in = ClassLoader.getSystemResourceAsStream("data/mdl/mol_testAliasAtomNaming.mol");
+        MDLV2000Reader reader = new MDLV2000Reader(in);
+        IMolecule molecule = DefaultChemObjectBuilder.getInstance().newInstance(IMolecule.class);
+        reader.read(molecule);
+
+        IAtom[] atoms = AtomContainerManipulator.getAtomArray(molecule);
+
+
+        for (IAtom atom : atoms) {
+            if (atom instanceof IPseudoAtom) {
+                Assert.assertEquals("R1", ((IPseudoAtom) atom).getLabel());
+            }
+        }
+
     }
 }