Added a test case for GeometryTools.has2DCoordinatesNew where a mol f…

…ile has a single atom with 0,0,0 as coordinate. This is not considered a 2d coordinate right now, but in a way it is one.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

src/test/data/mdl/with000coordinate.mol

@@ -0,0 +1,6 @@
+
+  CDK    1/12/10,12:20
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 N   0  0  0  0  0  3  0  0  0  0  0  0
+M  END

src/test/org/openscience/cdk/geometry/GeometryToolsTest.java

@@ -36,6 +36,7 @@
 import org.openscience.cdk.Molecule;
 import org.openscience.cdk.Reaction;
 import org.openscience.cdk.config.Elements;
+import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
@@ -89,6 +90,15 @@ public class GeometryToolsTest extends CDKTestCase {
     	Assert.assertFalse(GeometryTools.has2DCoordinates((IAtomContainer)null));
     }
 
+    @Test public void testHas2DCoordinates_With000() throws CDKException {
+        String filenameMol = "data/mdl/with000coordinate.mol";
+        InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filenameMol);
+        Molecule molOne=null;
+        MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
+        molOne = (Molecule)reader.read(new Molecule());
+        Assert.assertEquals(2,GeometryTools.has2DCoordinatesNew(molOne));
+    }
+
     @Test public void testTranslateAllPositive_IAtomContainer() {
 		IAtomContainer container = new NNAtomContainer();
 		IAtom atom = new NNAtom(Elements.CARBON);