Re: [Cdk-user] Substructure Searching, Fingerprints and cdk-1.3.7 Isomorphism Class

[Christoph S. <ste...@eb...>]

Hi Thomas, 

very interesting indeed. Thanks a lot. 

Cheers, 

Chris


On 21 Jan 2011, at 12:06, Thomas Strunz wrote:

> 
> Hi all,
> 
> just a few short comments if anyone is interested:
> 
> 	• I'm using multiple threads to read + create the Molecules. On an i7 870 @stock CPU (my personal desktop, 4 cores) search speed basically scales 100% going from 2 to 4 of such reader threads (while having only 1 that does the graph matching). In numbers: I'm searching for benzene in 65'000 records ( a subset of a subset of the Zinc Databasehttp://zinc.docking.org/). The search returns 37914 hits in about 22 s (2 threads) and about 11 s(4 threads).
>           The issue is that the search only returns the ID so all hits will have to be created a second time for displaying.
> 
> 	• I created SMILES from above Molecules. Creating Molecules from SMILES is slightly slower than from Molfiles, hence search speed is slower too. The difference is around 15%.
> 
> 	• I will probably make the source available some time. Have never done this and not sure how to proceed especially concerning licenses of all the used libraries and which one to use myself. Also I would probably need to create some kind of QuickStart Guide / Documentation to make it usable/understandable. So this could take some time.
> 
> Regards,
> 
> Thomas
> 
> 
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--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

Video meliora proboque deteriora sequor.
                ... Ovid, Metamorphoses VII, 20/21