From 0360978d3eb5c31dd645427c93543fc14e3f47d4 Mon Sep 17 00:00:00 2001
From: John Mayfield <john@nextmovesoftware.com>
Date: Mon, 22 Jul 2024 12:28:43 +0100
Subject: [PATCH] Allow acyclic carbon to be kekulized correctly - providing
 the valence is OK.

---
 core/src/main/java/uk/ac/ebi/beam/Localise.java     | 2 +-
 core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java | 8 ++++++++
 2 files changed, 9 insertions(+), 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
index 0c4297b..70a1cb6 100644
--- 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
index a92e791..f09ec01 100644
--- 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");