Aromatic phosphorus should be treated the same as nitrogen.

johnmay · Mar 15, 2023 · aafd244 · aafd244
1 parent d79481f
commit aafd244
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Showing 2 changed files with 7 additions and 2 deletions.
diff --git a/core/src/main/java/uk/ac/ebi/beam/Localise.java b/core/src/main/java/uk/ac/ebi/beam/Localise.java
@@ -159,8 +159,9 @@ static boolean predetermined(Graph g, int v) {
             for (int j = 0; j < d; ++j) {
                 Edge e = g.edgeAt(v, j);
                 if (e.bond() == Bond.DOUBLE) {
-                    if (q == 0 && (a.element() == Element.Nitrogen || (a.element() == Element.Sulfur && deg > 3))
-                            )
+                    if (q == 0 && (a.element() == Element.Nitrogen ||
+                                   a.element() == Element.Phosphorus ||
+                                  (a.element() == Element.Sulfur && deg > 3)))
                         return false;
                     return true;
                 }

diff --git a/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java b/core/src/test/java/uk/ac/ebi/beam/LocaliseTest.java
@@ -385,6 +385,10 @@ public void mixing_aromatic_and_aliphatic() throws Exception {
         test("*1ccccc1", "*1=CC=CC=C1");
     }
 
+    @Test public void aromphos() throws Exception {
+      test("O=p1ccccc1", "O=P1=CC=CC=C1");
+    }
+
     static void test(String delocalised, String localised) throws Exception {
         Graph g = Graph.fromSmiles(delocalised);
         Graph h = Localise.localise(g);