That's with the latest CDK jar 1.0.4 from
http://sourceforge.net/project/showfiles.php?group_id=20024&package_id=35118&release_id=630392

> On Mon, Nov 3, 2008 at 3:23 PM, Mark Rijnbeek <[EMAIL PROTECTED]> wrote:
>   
>> I attached an example test below. mol1 and mol2 are both Indole and
>> therefore sub graphs of each other.
>> However if you uncomment the fingerprinter line, the sub graph test
>> returns false. So it looks like the ExtendedFingerprinter is actually
>> changing mol2.
>>     
>
> That would be rather nasty.. :( Which CDK version?
>
> Egon
>
>   


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