Prioritise non-pseudo atoms for wedge labelled bonds.

cdk · Feb 1, 2016 · 38abffc · 38abffc
1 parent 66f406e
commit 38abffc
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java b/tool/sdg/src/main/java/org/openscience/cdk/layout/NonplanarBonds.java
@@ -437,6 +437,12 @@ boolean hasPriority(int focus, int i, int j) {
         if (!iCyclic && jCyclic) return true;
         if (iCyclic && !jCyclic) return false;
 
+        // avoid placing on pseudo atoms
+        if (container.getAtom(i).getAtomicNumber() > 0 && container.getAtom(j).getAtomicNumber() == 0)
+            return true;
+        if (container.getAtom(i).getAtomicNumber() == 0 && container.getAtom(j).getAtomicNumber() > 0)
+            return false;
+
         // prioritise atoms with fewer neighbors
         if (graph[i].length < graph[j].length) return true;
         if (graph[i].length > graph[j].length) return false;