Resolution for bug1269 - stop the hydrogen placer attempting to place…

… hydrogens on null atoms. Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jun 8, 2013 · 3207c58 · 3207c58
1 parent 7c47f79
commit 3207c58
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Showing 2 changed files with 21 additions and 22 deletions.
diff --git a/src/main/org/openscience/cdk/layout/HydrogenPlacer.java b/src/main/org/openscience/cdk/layout/HydrogenPlacer.java
@@ -61,12 +61,13 @@ public  void placeHydrogens2D(IAtomContainer atomContainer, double bondLength){
 	    for (int f = 0; f < atomContainer.getAtomCount();f++)
 	    {
 	        atom = atomContainer.getAtom(f);
-//	        if (!atom.getSymbol().equals("H"))
-//	        {
+            // only place hydrogens when for atoms which have coordinates
+	        if (atom.getPoint2d() != null)
+	        {
 	            if (debug1) System.out.println("Now placing hydrogens at atom " + f);
 	            logger.debug("Now placing hydrogens at atom " + f);
 	            placeHydrogens2D(atomContainer, atom, bondLength);
-//	        }
+	        }
 	    }
 	    logger.debug("Hydrogen Placement finished");
 	}

diff --git a/src/test/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java b/src/test/org/openscience/cdk/layout/StructureDiagramGeneratorTest.java
@@ -942,25 +942,23 @@ public void testBug1234() throws Exception {
 
     }
 
-  /**
-   * Tests case where calling generateExperimentalCoordinates
-   * threw an NPE.
-   * 
-   * @throws Exception if the test failed
-   * @cdk.bug 1269
-  */
-@Test (timeout=5000, expected=CDKException.class)
-public void testBug1269() throws Exception {
-
-     SmilesParser sp = 
-         new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
-     String smiles = "O=C(O)[C@H](N)C"; // L-alanine, but any [C@H] will do
-     IMolecule mol = sp.parseSmiles(smiles);
-
-     StructureDiagramGenerator sdg = new StructureDiagramGenerator();
-     sdg.setMolecule(mol);
-     sdg.generateExperimentalCoordinates(new Vector2d(0, 1));
-}
+    /**
+     * Tests case where calling generateExperimentalCoordinates threw an NPE.
+     *
+     * @cdk.bug 1269
+     */
+    @Test(timeout = 5000)
+    public void testBug1269() throws Exception {
+
+        SmilesParser sp =
+                new SmilesParser(NoNotificationChemObjectBuilder.getInstance());
+        String smiles = "O=C(O)[C@H](N)C"; // L-alanine, but any [C@H] will do
+        IMolecule mol = sp.parseSmiles(smiles);
+
+        StructureDiagramGenerator sdg = new StructureDiagramGenerator();
+        sdg.setMolecule(mol);
+        sdg.generateExperimentalCoordinates(new Vector2d(0, 1));
+    }
 
   /**
    * Does the SDG handle non-connected molecules?