Modification to a previous patch: cis/trans correction should be done…

… before refined by wedges should be done after.

tool/sdg/src/main/java/org/openscience/cdk/layout/StructureDiagramGenerator.java

@@ -542,11 +542,19 @@ private void generateCoordinates(Vector2d firstBondVector, boolean isConnected,
             throw new CDKException("Could not generate layout? If a set of 'fixed' atoms were provided"
                                        + " try removing these and regenerating the layout.");
 
+        if (!isSubLayout) {
+            // correct double-bond stereo, this changes the layout and in reality
+            // should be done during the initial placement
+            if (molecule.stereoElements().iterator().hasNext())
+                CorrectGeometricConfiguration.correct(molecule);
+        }
+
         refinePlacement(molecule);
         finalizeLayout(molecule);
 
         if (!isSubLayout)
             assignStereochem(molecule);
+
     }
 
     /**
@@ -705,10 +713,6 @@ private void assignStereochem(IAtomContainer molecule) {
         if (!molecule.stereoElements().iterator().hasNext())
             return;
 
-        // correct double-bond stereo, this changes the layout and in reality
-        // should be done during the initial placement
-        CorrectGeometricConfiguration.correct(molecule);
-
         // assign up/down labels, this doesn't not alter layout and could be
         // done on-demand (e.g. when writing a MDL Molfile)
         NonplanarBonds.assign(molecule);
@@ -950,6 +954,11 @@ private void generateFragmentCoordinates(IAtomContainer mol, List<IAtomContainer
                                      dest.x - curr.x, dest.y - curr.y);
         }
 
+        // correct double-bond stereo, this changes the layout and in reality
+        // should be done during the initial placement
+        if (molecule.stereoElements().iterator().hasNext())
+            CorrectGeometricConfiguration.correct(molecule);
+
         // finalize
         assignStereochem(mol);
         finalizeLayout(mol);