Allow acyclic carbon to be kekulized correctly - providing the valenc…

…e is OK.
johnmay · Jul 22, 2024 · 0360978 · 0360978
1 parent a850353
commit 0360978
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/core/src/main/java/uk/ac/ebi/beam/Localise.java b/core/src/main/java/uk/ac/ebi/beam/Localise.java
@@ -192,7 +192,7 @@ else if (e.bond().order() > 2) {
             case Boron:
                 return (q == 0) && deg == 3;
             case Carbon:
-                return (q == 1 || q == -1) && deg == 3;
+                return ((q == 1 || q == -1) && deg == 3) || (q == 0 && deg == 4);
             case Silicon:
             case Germanium:
                 return q < 0;

diff --git a/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java b/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
@@ -360,6 +360,14 @@ public void mixing_aromatic_and_aliphatic() throws Exception {
         test("c1cc(c([n+]c1)N)[N+](=O)[O-]",
              "C1=CC(=C([N+]=C1)N)[N+](=O)[O-]");
     }
+
+    @Test public void acyclicValence() throws Exception {
+        test("[cH3]cc", "[CH3]C=C");
+        test("[cH2+][cH2-]", "[CH2+][CH2-]");
+        test("[cH+][cH-]", "[CH+]=[CH-]");
+        test("[nH2]cc", "[NH2]C=C");
+        test("[oH]cc", "[OH]C=C");
+    }
 
     @Test public void smallRingTest_5() throws Exception {
         Graph g = Graph.fromSmiles("C1CCCC1");