Merge pull request #249 from cdk/patch/layout_091116

Patch/layout 091116
johnmay · Nov 9, 2016 · a46646d · a46646d
2 parents 1ec0d36 + 15e2c81
commit a46646d
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/...src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java b/...src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java
@@ -1241,7 +1241,7 @@ static int winding(IBond bond1, IBond bond2) {
      */
     static Map<IBond, IAtomContainer> ringPreferenceMap(IAtomContainer container) {
 
-        final IRingSet relevantRings = Cycles.relevant(container).toRingSet();
+        final IRingSet relevantRings = Cycles.sssr(container).toRingSet();
         final List<IAtomContainer> rings = AtomContainerSetManipulator.getAllAtomContainers(relevantRings);
 
         Collections.sort(rings, new RingBondOffsetComparator());

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
@@ -526,7 +526,9 @@ private void generateCoordinates(Vector2d firstBondVector, boolean isConnected,
         // coordinates to simplest: 0,0. See bug #780545
         logger.debug("Entry point of generateCoordinates()");
         logger.debug("We have a molecules with " + numAtoms + " atoms.");
-        if (numAtoms == 1) {
+        if (numAtoms == 0) {
+            return;
+        } if (numAtoms == 1) {
             molecule.getAtom(0).setPoint2d(new Point2d(0, 0));
             return;
         } else if (molecule.getBondCount() == 1 && molecule.getAtomCount() == 2) {
@@ -1501,7 +1503,7 @@ private int layoutRingSet(Vector2d firstBondVector, IRingSet rs) {
         int result = 0;
 
         // Check for an exact match (identity) on the entire ring system
-        if (lookupRingSystem(rs, molecule, !macro || rs.getAtomContainerCount() > 1)) {
+        if (!macro && lookupRingSystem(rs, molecule, rs.getAtomContainerCount() > 1)) {
             for (IAtomContainer container : rs.atomContainers())
                 container.setFlag(CDKConstants.ISPLACED, true);
             rs.setFlag(CDKConstants.ISPLACED, true);