Fallback to placing across a bond with only one atom in the end point…

…s. Also only increment begIter when we have a bond to place it on.
cdk · Nov 30, 2015 · bf8ae70 · bf8ae70
1 parent cc52feb
commit bf8ae70
Showing 1 changed file with 9 additions and 1 deletion.
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
@@ -1788,11 +1788,18 @@ private void placePositionalVariation(IAtomContainer mol) {
                 shared.addAtom(atom);
             Point2d center = GeometryUtil.get2DCenter(shared);
 
+            // first priority bonds between selected atoms
             for (IBond bond : mol.bonds()) {
                 if (e.getKey().contains(bond.getAtom(0)) && e.getKey().contains(bond.getAtom(1))) {
                     bonds.add(bond);
                 }
             }
+            // second priority bonds adjacent to one of the atoms
+            for (IBond bond : mol.bonds()) {
+                if (e.getKey().contains(bond.getAtom(0)) || e.getKey().contains(bond.getAtom(1))) {
+                    bonds.add(bond);
+                }
+            }
 
             if (bonds.size() >= e.getValue().size()) {
 
@@ -1802,11 +1809,12 @@ private void placePositionalVariation(IAtomContainer mol) {
                 while (begIter.hasNext() && bndIter.hasNext()) {
 
                     final IBond bond = bndIter.next();
-                    final IAtom atom = begIter.next();
 
                     if (numRingBonds(mol, bond.getAtom(0)) > 2 && numRingBonds(mol, bond.getAtom(1)) > 2)
                         continue;
 
+                    final IAtom atom = begIter.next();
+
                     final Point2d newBegP = new Point2d(bond.getAtom(0).getPoint2d());
                     final Point2d newEndP = new Point2d(bond.getAtom(1).getPoint2d());