[Zinc-fans] Clarification on Single and Usual Downloading

[John J. Irwin]

Hello Andrew

Thanks for your email and your interest in ZINC.  You are quite correct
- the "drugs now" subset is incomplete in mol2 format. I have started a
fresh export.  It should be ready by Friday.

Thanks for your helpful feedback, and your patience.

John
UCSF ZINC Team

(As a result of your enquiry, I am going through all the other subsets
and checking for completeness)



T. Andrew Binkowski wrote:
> Hi,
> I have a question on clarification of what 'single' and 'usual' mean
> and how to deal with them.  Here is my scenario:
>
> In the 70% clustering "drugs now" subset, it lists the following compound:
>
> 23_t70.smi  -- C(C(F)(F)F)OC(F)F ZINC01995123
>
> I downloaded the entire "drugs now - usual" subset and ZINC01995123
> was not present.  It was not present in the "single" subset either.
>
> If I use the wget techniques in the FAQ:
>   wget http://zinc8.docking.org/fget2.pl?f=m&l=1&z=ZINC01995123
> <http://zinc8.docking.org/fget2.pl?f=m&l=1&z=ZINC01995123> returns
> nothing.
> wget http://zinc8.docking.org/fget2.pl?f=m&l=0&z=ZINC01995123
> <http://zinc8.docking.org/fget2.pl?f=m&l=0&z=ZINC01995123> returns the
> molecule.
>
>
> So, my questions:
> 1) Is this the correct behavior or an error for this particular compound?
> 2) Are the 'usual' compounds only present for a subset of the single
> compounds (e.g. all compounds in zinc have a 'single' state, but not
> necessarily a 'usual' state?
> 3) What is the best (most reliable) way to download a compound from a
> subset list?  Download from single first and then check for 'usuals'?
>  Or check for usual, if none, then download from single?
>
> Thanks,
> Andrew
>
> ----------------------------------------------------------------------------
> T. Andrew Binkowski, Ph.D.
> Center for Structural Genomics of Infectious Diseases &
>  Midwest Center for Structural Genomics
> Biosciences Division, Argonne National Laboratory
> 9700 S. Cass Av. Argonne, IL 60439
> Telephone: 630-252-3927 Fax: 630-252-6991
> ----------------------------------------------------------------------------
>
> ------------------------------------------------------------------------
>
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