Critical bug, in some cases the firstBondVector get's passed down to the AtomPlacer where it is modified. Since we used a static default there was a race condition generating malformed coordinates.

johnmay · johnmay · commit 0e52fa9947e4 · 2019-07-03T10:52:29.000+01:00
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
@@ -604,6 +604,10 @@ public void generateCoordinates(Vector2d firstBondVector) throws CDKException {
      */
     private void generateCoordinates(Vector2d firstBondVector, boolean isConnected, boolean isSubLayout) throws CDKException {
 
+        // defensive copy, vectors are mutable!
+        if (firstBondVector == DEFAULT_BOND_VECTOR)
+            firstBondVector = new Vector2d(firstBondVector);
+
         final int numAtoms = molecule.getAtomCount();
         final int numBonds = molecule.getBondCount();
         this.firstBondVector = firstBondVector;
