Updated OB note and robustified unit tests

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Aug 1, 2010 · 2b96512 · 2b96512
1 parent dbd6df4
commit 2b96512
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/io/Mol2Reader.java b/src/main/org/openscience/cdk/io/Mol2Reader.java
@@ -295,6 +295,8 @@ private IMolecule readMolecule(IMolecule molecule) throws CDKException {
                         String atomTypeStr = tokenizer.nextToken();
 
                         // fix OpenBabel atom type codes to SYBYL specification
+                        // this addresses wrong types that were output by OB (but is now fixed)
+                        // see https://sourceforge.net/tracker/index.php?func=detail&aid=1650239&group_id=40728&atid=428740
                         if ("S.o2".equals(atomTypeStr)) atomTypeStr = "S.O2";
                         if ("S.o".equals(atomTypeStr)) atomTypeStr = "S.O";
 

diff --git a/src/test/org/openscience/cdk/io/Mol2ReaderTest.java b/src/test/org/openscience/cdk/io/Mol2ReaderTest.java
@@ -125,7 +125,7 @@ public class Mol2ReaderTest extends SimpleChemObjectReaderTest {
      * 
      * @throws Exception if an error occurs
      */
-     public void testNCIfeb03_2D() throws Exception {
+     @Test public void testNCIfeb03_2D() throws Exception {
         Assume.assumeTrue(runSlowTests());
 
         String filename = "data/mol2/NCI_feb03_2D.mol2.gz";
@@ -155,6 +155,8 @@ public void testMultiMol() throws Exception {
         IChemFile chemFile = reader.read(new ChemFile());
         List<IAtomContainer> mols = ChemFileManipulator.getAllAtomContainers(chemFile);
         Assert.assertEquals(30, mols.size());
+        Assert.assertEquals(25, mols.get(0).getAtomCount());
+        Assert.assertEquals(24, mols.get(29).getAtomCount());
     }
 
     @Test
@@ -167,6 +169,7 @@ public void testMultiMolButSingle() throws Exception {
         IChemFile chemFile = reader.read(new ChemFile());
         List<IAtomContainer> mols = ChemFileManipulator.getAllAtomContainers(chemFile);
         Assert.assertEquals(1, mols.size());
+        Assert.assertEquals(12, mols.get(0).getAtomCount());
 
     }