Hi Nina,

Very strange, it would seem it could be related. Here was the differences.

{9, 14, 15, 143,                 148, 149,                 284, 285, 300, 351, 358, 376, 387, 416, 418, 422, 442, 449, 477, 485, 499, 515, 547, 569}
{9, 14, 15, 143, 145, 146,                 255, 256, 284, 285, 300, 351,                         416, 418, 422, 442, 449, 477, 485, 499, 515, 547, 569}

145	>= 1 saturated or aromatic nitrogen-containing ring size 5
146	>= 1 saturated or aromatic heteroatom-containing ring size 5
148	>= 1 unsaturated non-aromatic nitrogen-containing ring size 5
149	>= 1 unsaturated non-aromatic heteroatom-containing ring size 5
etc...

I've tested again with the following code and the 1,2,3-triazole now produces the same fingerprint twice. Interestingly when the atom typing/aromaticity detection is missing the fingerprints are different.

        IAtomContainer mol = MoleculeFactory.make123Triazole();
        IFingerprinter fp = new PubchemFingerprinter();

        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
        CDKHueckelAromaticityDetector.detectAromaticity(mol);

        BitSet bs1 = fp.getBitFingerprint(mol).asBitSet();
        BitSet bs2 = fp.getBitFingerprint(mol).asBitSet();

        System.out.println(bs1);
        System.out.println(bs2);


On 14 Dec 2012, at 09:01, Nina Jeliazkova <jeliazkova.nina@gmail.com> wrote:

John, All,

It might not be at all related, but I have noticed some time ago
PubChemFingerprinter results differ if applied more than once on the
exactly same molecule instance. For example this test is failing.

IMolecule mol = MoleculeFactory.make123Triazole();
IFingerprinter fp = new PubchemFingerprinter();
BitSet bs1 = fp.getFingerprint(mol);
BitSet bs2 = fp.getFingerprint(mol);
Assert.assertEquals(bs1,bs2);

junit.framework.AssertionFailedError: expected:<{9, 14, 15, 143, 148,
149, 284, 285, 300, 351, 358, 376, 387, 416, 418, 422, 442, 449, 477,
485, 499, 515, 547, 569}> but was:<{9, 14, 15, 143, 145, 146, 255,
256, 284, 285, 300, 351, 358, 376, 387, 416, 418, 422, 442, 449, 477,
485, 499, 515, 547, 569}>


If this is the expected behaviour, it at least should be documented
why it is so (may be some preprocessing)?  Or the code above is wrong?

Regards,
Nina

On 14 December 2012 10:51, John May <john.wilkinsonmay@gmail.com> wrote:
Yep you are right. Looking a bit deeper I found that it was to do with
checking if there were any atoms in an unsaturated ring of a certain size.
The second one finds there is an unsaturated ring of size 6 (Bit 181) where
as the first one does not.

Thanks,
J

On 14 Dec 2012, at 06:55, Egon Willighagen <egon.willighagen@gmail.com>
wrote:

On Thu, Dec 13, 2012 at 7:52 PM, John May <johnmay@ebi.ac.uk> wrote:

Say for example we query the structures for the following fragment


BTW, these two fragments are both present in both structures...

Egon


--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Cdk-devel mailing list
Cdk-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-devel



------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Cdk-devel mailing list
Cdk-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-devel




--
--
Dr. Nina Jeliazkova
Technical Manager
4 A.Kanchev str.
IdeaConsult Ltd.
1000 Sofia, Bulgaria
Phone: +359 886 802011
http://www.ideaconsult.net

------------------------------------------------------------------------------
LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial
Remotely access PCs and mobile devices and provide instant support
Improve your efficiency, and focus on delivering more value-add services
Discover what IT Professionals Know. Rescue delivers
http://p.sf.net/sfu/logmein_12329d2d
_______________________________________________
Cdk-devel mailing list
Cdk-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-devel