Watch out for cyclic cumulenes (bogus input) when checking for DB stereochemistry.

johnmay · johnmay · commit 8032dff72ed0 · 2021-04-20T08:32:08.000+01:00
diff --git a/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java b/storage/smiles/src/main/java/org/openscience/cdk/smiles/BeamToCDK.java
@@ -300,11 +300,19 @@ private void addDoubleBondStereochemistry(Graph g, IAtomContainer ac) {
                     List<Edge> edges = new ArrayList<>();
                     edges.add(e);
                     Edge f = findCumulatedEdge(g, v, e);
+                    int beg = v;
                     while (f != null) {
                         edges.add(f);
                         v = f.other(v);
                         f = findCumulatedEdge(g, v, f);
+                        if (beg == v) {
+                            beg = -1;
+                            break;
+                        }
                     }
+                    // cumulated loop
+                    if (beg < 0)
+                        continue;
                     // only odd number of cumulated bonds here, otherwise is
                     // extended tetrahedral
                     if ((edges.size() & 0x1) == 0)
diff --git a/storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java b/storage/smiles/src/test/java/org/openscience/cdk/smiles/BeamToCDKTest.java
@@ -512,6 +512,12 @@ public void extendedTetrahedral_cw() throws Exception {
                      "caffeine compound");
     }
 
+    /** GitHub Issue #723 */
+    @Test public void cumulatedCycle() throws Exception {
+        assertEquals(convert("C=1(=N(=C=1)(CC)CC)/N=C(/N1CCC(C2=CC=CC#C2)(CN2C(=NC3=C2C=CC=C3)C)CC1)\\NCC").getBondCount(),
+                     39);
+    }
+
     IAtomContainer convert(String smi) throws IOException {
         BeamToCDK g2c = new BeamToCDK(SilentChemObjectBuilder.getInstance());
         Graph g = Graph.fromSmiles(smi);
