Now this is actually supported in BEAM the semantics are different. A '*' atom in an aromatic system is presumed to have a conjugated double bond. Previously this example was allowed because '*' was always aliphatic but this was not by design. Update the example with the same intended behavior.

johnmay · johnmay · commit e2c6356da4e1 · 2019-02-03T18:02:54.000Z
diff --git a/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java b/base/test-standard/src/test/java/org/openscience/cdk/fingerprint/FingerprinterTest.java
@@ -394,8 +394,8 @@ public static void main(String[] args) throws Exception {
 
     @Test public void pseudoAtomFingerprintArom() throws CDKException {
         final SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance());
-        final String query  = "*1cccc1";
-        final String indole = "o1cccc1";
+        final String query  = "*1cnccc1";
+        final String indole = "n1cnccc1";
         IAtomContainer queryMol  = smipar.parseSmiles(query);
         IAtomContainer indoleMol = smipar.parseSmiles(indole);
         Fingerprinter fpr = new Fingerprinter();
