Merge pull request #271 from cdk/patch/27Feb17

Looks good.
johnmay · Feb 27, 2017 · 20c1122 · 20c1122
2 parents f1e1e2c + c57989a
commit 20c1122
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java b/...tandard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
@@ -670,7 +670,8 @@ public static IAtomContainer suppressHydrogens(IAtomContainer org) {
 
         // we need fast adjacency checks (to check for suppression and
         // update hydrogen counts)
-        final int[][] graph = GraphUtil.toAdjList(org);
+        GraphUtil.EdgeToBondMap bondmap = GraphUtil.EdgeToBondMap.withSpaceFor(org);
+        final int[][] graph = GraphUtil.toAdjList(org, bondmap);
 
         final int nOrgAtoms = org.getAtomCount();
         final int nOrgBonds = org.getBondCount();
@@ -685,7 +686,7 @@ public static IAtomContainer suppressHydrogens(IAtomContainer org) {
         // be suppressed
         for (int v = 0; v < nOrgAtoms; v++) {
             final IAtom atom = org.getAtom(v);
-            if (suppressibleHydrogen(org, graph, v)) {
+            if (suppressibleHydrogen(org, graph, bondmap, v)) {
                 hydrogens.add(atom);
                 incrementImplHydrogenCount(org.getAtom(graph[v][0]));
             } else {
@@ -891,7 +892,7 @@ private static void incrementImplHydrogenCount(final IAtom atom) {
      * @param v         vertex (atom index)
      * @return the atom is a hydrogen and it can be suppressed (implicit)
      */
-    private static boolean suppressibleHydrogen(final IAtomContainer container, final int[][] graph, final int v) {
+    private static boolean suppressibleHydrogen(final IAtomContainer container, final int[][] graph, final GraphUtil.EdgeToBondMap bondmap, final int v) {
 
         IAtom atom = container.getAtom(v);
 
@@ -903,6 +904,8 @@ private static boolean suppressibleHydrogen(final IAtomContainer container, fina
         if (atom.getMassNumber() != null && atom.getMassNumber() != 1) return false;
         // hydrogen is either not attached to 0 or 2 neighbors
         if (graph[v].length != 1) return false;
+        // non-single bond
+        if (bondmap.get(v, graph[v][0]).getOrder() != Order.SINGLE) return false;
 
         // okay the hydrogen has one neighbor, if that neighbor is a
         // hydrogen (i.e. molecular hydrogen) then we can not suppress it

diff --git a/display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java b/display/render/src/main/java/org/openscience/cdk/renderer/SymbolVisibility.java
@@ -128,10 +128,12 @@ public boolean visible(IAtom atom, List<IBond> bonds, RendererModel model) {
             if (mass != null && !isMajorIsotope(element.number(), mass)) return true;
 
             // no kink between bonds to imply the presence of a carbon and it must
-            // be displayed
-            if (hasParallelBonds(atom, bonds)) {
-                // TODO only when both bonds are single?
-                return true;
+            // be displayed if the bonds have the same bond order
+            if (bonds.size() == 2 &&
+                    bonds.get(0).getOrder() == bonds.get(1).getOrder()) {
+                IBond.Order bndord = bonds.get(0).getOrder();
+                if (bndord == IBond.Order.DOUBLE || hasParallelBonds(atom, bonds))
+                    return true;
             }
 
             // special case ethane