catch exactly what's thrown below ControllerHub.generateNewCoords; ad…

…d test for JChemPaint#165 = CDK1269

src/main/org/openscience/jchempaint/controller/ControllerHub.java

@@ -1280,7 +1280,7 @@ public static void generateNewCoordinates(IAtomContainer container) {
 				container.getAtom(i).setPoint2d(
 						cleanedMol.getAtom(i).getPoint2d());
 			}
-		} catch (Exception e) {
+		} catch (CDKException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 		}

src/test/org/openscience/jchempaint/AllJCPTests.java

@@ -15,6 +15,7 @@
         BugSF70Test.class,
         BugSF75Test.class,
         BugSF80Test.class,
+        CDK1269Test.class,
         CDK1272Test.class,
         Issue4Test.class,
         Issue8Test.class,

src/test/org/openscience/jchempaint/CDK1269Test.java

@@ -0,0 +1,43 @@
+package org.openscience.jchempaint;
+
+import org.fest.swing.fixture.JPanelFixture;
+import org.junit.Assert;
+import org.junit.Test;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+/**
+ * @author Ralf Stephan <[email protected]>
+ *
+ * Tests chiral SMILES input with following cleanup. 
+ * See also #165.
+ */
+public class CDK1269Test extends AbstractAppletTest {
+
+    @Test public void testCDK1269() {
+        JPanelFixture jcppanel=applet.panel("appletframe");
+        JChemPaintPanel panel = (JChemPaintPanel)jcppanel.target;
+        try {
+        	jcpApplet.setSmiles("O=C(O)[C@H](N)C"); // L-alanine
+        	panel.get2DHub().updateView();
+    	    applet.panel("renderpanel").robot.waitForIdle();
+        	panel.get2DHub().cleanup();
+        	panel.get2DHub().updateView();
+    	    applet.panel("renderpanel").robot.waitForIdle();
+		} catch (Throwable e) {
+			Assert.fail();
+		}
+/*        
+        int atomCount=0, bondCount=0, implicitHCount=0;
+		for(IAtomContainer atc : panel.getChemModel().getMoleculeSet().atomContainers()) {
+			for (IAtom a : atc.atoms())
+				implicitHCount += a.getImplicitHydrogenCount();
+			atomCount+=atc.getAtomCount();
+			bondCount+=atc.getBondCount();
+		}
+		Assert.assertEquals(7, atomCount);
+        Assert.assertEquals(6, bondCount);
+        Assert.assertEquals(6, implicitHCount);*/
+    }
+
+}