Adjustment required to symbol visibility, otherwise carbons will be d…

…isplayed as '>CH' in the delocalised rings.
cdk · Dec 29, 2017 · 603bc2d · 603bc2d
1 parent 2ffa3e1
commit 603bc2d
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Showing 2 changed files with 39 additions and 2 deletions.
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
@@ -164,8 +164,23 @@ public boolean visible(IAtom atom, List<IBond> bonds, RendererModel model) {
         private static boolean isFourValent(IAtom atom, List<IBond> bonds) {
             Integer valence = atom.getImplicitHydrogenCount();
             if (valence == null) return true;
-            for (final IBond bond : bonds) {
-                valence += bond.getOrder().numeric();
+            if (atom.isAromatic()) {
+                boolean hasUnsetArom = false;
+                for (final IBond bond : bonds) {
+                    if (bond.getOrder() == IBond.Order.UNSET && bond.isAromatic()) {
+                        hasUnsetArom = true;
+                        valence++;
+                    } else {
+                        valence += bond.getOrder().numeric();
+                    }
+                }
+                // valence nudge, we're only dealing with neutral carbons here
+                // and if
+                if (hasUnsetArom)
+                    valence++;
+            } else {
+                for (final IBond bond : bonds)
+                    valence += bond.getOrder().numeric();
             }
             return valence == 4;
         }

diff --git a/display/render/src/test/java/org/openscience/cdk/renderer/SymbolVisibilityTest.java b/display/render/src/test/java/org/openscience/cdk/renderer/SymbolVisibilityTest.java
@@ -229,4 +229,26 @@ public void alwaysDisplayCharges() {
                                    .visible(a1, Collections.singletonList(bond1), new RendererModel()));
     }
 
+    @Test
+    public void delocalisedCarbons() {
+        IAtom a1 = new Atom("CH");
+        IAtom a2 = new Atom("CH");
+        IAtom a3 = new Atom("CH");
+
+        a1.setPoint2d(new Point2d(0, 0));
+        a2.setPoint2d(new Point2d(0.5, -0.5));
+        a3.setPoint2d(new Point2d(1, 0));
+
+        IBond bond1 = new Bond(a1, a2, IBond.Order.UNSET);
+        IBond bond2 = new Bond(a2, a3, IBond.Order.UNSET);
+        bond1.setIsAromatic(true);
+        bond2.setIsAromatic(true);
+        a1.setIsAromatic(true);
+        a2.setIsAromatic(true);
+        a3.setIsAromatic(true);
+
+        assertFalse(SymbolVisibility.iupacRecommendationsWithoutTerminalCarbon()
+                                    .visible(a2, Arrays.asList(bond1, bond2), new RendererModel()));
+    }
+
 }