Example below, I waited for 5 minutes, it never took more then a second for other compounds...
Best regards,
Martin
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IMolecule mol1 = sp.parseSmiles("O=C1OC=C(C=C1)C4CCC5(O)(C6CCC3=CC(OC2OC(C)C(O)C(O)C2(O))CCC3(C)C6(CCC45(C)))");
IMolecule mol2 = sp.parseSmiles("O=C1C=CC4(C(=C1)CCC3C5CC(C)C(O)(C(=O)COC2OC(CO)C(O)C(O)C2(O))C5(C)(CC(O)C34(F)))(C)");
UniversalIsomorphismTester.getOverlaps(mol1, mol2);
just noticed that my ticket reports get auto-assigned to chris steinbeck, changing that to none