Re: [Joelib-devel] Re: [Joelib-help] Canonified version?

[Joerg K. W. <we...@in...>]

Hi Xinshan,

> I am a new user of the package, and I have a kind of
> similar problem to Andreas'.  Thanks for the info. you
> have provided in this thread.  One remaining question
> I have regarding to Morgan routine is:  will each
> molecule end up the same unique numbering no matter
> what initial values are assigned?  The reason is that
> I did a test to convert between SDF and SMILES back
> and forth a couple times, and every time there is a
> portion of molecules in the collection show different
> SMILES strings compared to the previous rounds.  Any
> information is appreciated.
There are still ties, and there are also publications using other 
canonizations. Of course Morgan is not perfect. If you are interested 
you can send a support request to the JOELib project.
Please give details for the structures used (if possible), otherwise 
such things can get never fixed.

Please note that canonization has at least polynominal runtime and this 
is not an easy task for molecular graphs. The best solution would be to 
create a test data set with uniqueSMILES -> index scrambling -> 
uniqueSMILES, then we can measure the improvement rate for better tie 
resolvers, but at the moment i've no time for such things.

Any helping hand is highly welcome.

Kind regards, Joerg
-- 
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW:    http://www-ra.informatik.uni-tuebingen.de
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