Critical Patch: stereochemistry must be assigned after molecule has b…

…een flipped! Otherwise it may be wrong.
cdk · Jun 7, 2016 · 308c34e · 308c34e
1 parent e3c401d
commit 308c34e
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java
@@ -409,11 +409,16 @@ private void generateCoordinates(Vector2d firstBondVector, boolean isConnected,
             layoutCyclicParts();
         }
 
-        if (!isSubLayout)
-            assignStereochem(molecule);
+        // display reasonable error on failed layout, otherwise we'll have a NPE somewhere
+        if (iter == numAtoms && !AtomPlacer.allPlaced(molecule))
+            throw new CDKException("Could not generate layout? If a set of 'fixed' atoms were provided"
+                                       + " try removing these and regenerating the layout.");
 
         refinePlacement(molecule);
         finalizeLayout(molecule);
+
+        if (!isSubLayout)
+            assignStereochem(molecule);
     }
 
     /**