Test to make sure the SMILES parser gets the formal neighbor counts c…

…orrect Change-Id: Ib7c4909fdeb31d1fadde46a6685b1dd20a7959f8
cdk · Feb 25, 2012 · 5b1654d · 5b1654d
1 parent 516edbb
commit 5b1654d
Showing 1 changed file with 18 additions and 3 deletions.
diff --git a/src/test/org/openscience/cdk/smiles/SmilesParserTest.java b/src/test/org/openscience/cdk/smiles/SmilesParserTest.java
@@ -20,6 +20,9 @@
  */
 package org.openscience.cdk.smiles;
 
+import java.util.Iterator;
+import java.util.List;
+
 import org.junit.Assert;
 import org.junit.Assume;
 import org.junit.Ignore;
@@ -54,9 +57,6 @@
 import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
 import org.openscience.cdk.tools.manipulator.BondManipulator;
 
-import java.util.Iterator;
-import java.util.List;
-
 /**
  * Please see the test.gui package for visual feedback on tests.
  * 
@@ -2309,6 +2309,21 @@ public void testAromaticBoron() throws CDKException {
         Assert.assertNotNull(mol);
     }
 
+    @Test
+    public void testFormalNeighborBount() throws CDKException, CloneNotSupportedException {
+        SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+        IMolecule mol = sp.parseSmiles("Oc1ccc(O)cc1");
+        Assert.assertEquals("O.sp3", mol.getAtom(0).getAtomTypeName());
+        Assert.assertEquals(2, mol.getAtom(0).getFormalNeighbourCount().intValue());
+        Assert.assertEquals("C.sp2", mol.getAtom(1).getAtomTypeName());
+        Assert.assertEquals(3, mol.getAtom(1).getFormalNeighbourCount().intValue());
+        IMolecule clone = (IMolecule)mol.clone();
+        Assert.assertEquals("O.sp3", clone.getAtom(0).getAtomTypeName());
+        Assert.assertEquals(2, clone.getAtom(0).getFormalNeighbourCount().intValue());
+        Assert.assertEquals("C.sp2", clone.getAtom(1).getAtomTypeName());
+        Assert.assertEquals(3, clone.getAtom(1).getFormalNeighbourCount().intValue());
+    }
+
     /**
      * Counts aromatic atoms in a molecule.
      * @param mol molecule for which to count aromatic atoms.