[Zinc-fans] User-created subset download

[John J. Irwin]

Hi Sergio

Thanks for your email and your interest in ZINC.  Sorry it has taken so
long to get back to you.

Sergio Mares-Samano wrote:
> Dear John,
>
> Thank you very much for such an amazing database like zinc; it's
> fantastic! Also, I'm grateful for responding my question regarding the
> use of the smiles in the JME applet in the ZINC search page. I have
> one more question though, it is about how to download a user-created
> subset. This is the issue:
>
>    1. After conducting a search, I created a subset using the "Create
>       subset" button on the results browser of the ZINC search
>       facility. The subset did not contain more than 2000 compounds.
>    2. Even though it is a relatively small subset, I waited more than
>       24 h for all the files to be generated.
>    3. wget http://zinc.docking.org/subset2/86378/usual.sdf.csh
>    4. csh usual.sdf.csh # At this point, this message comes up in the
>       konsole: "No URLs found in -."
>    5. I confirmed this by opening the 'usual.sdf.csh' file using a
>       text editor; it only contains: "wget
>       --base=http://blaster.docking.org/zinc8/subset1/86378/ -i - <<++"
>    6. The whole procedure was carried out before the stated date in
>       which the subset would be removed ("delete after" date).
>
> I've tried other subsets created by other users getting the same
> problem. However, when trying the "by property subsets" it works fine;
> I am able to download the files.
>
> Obviously, I am missing something, I still haven't found out what is
> the problem though.

The problem is that ZINC subset creation is flawed.   Here is a
pragmatic workaround until we fix it.

1. Perform the search you want.
2. Download SMILES at the top of the search results page.  This contains
the ZINC ids of the compounds you want.
3. Use a script to download individual entries for each molecule
separately. Use the script and method cited in Question 3 of a ZINC FAQ:

http://wiki.compbio.ucsf.edu/wiki/index.php/ZINC:FAQ

4. Hint 1: This is general for any number of ZINC molecules, so you can
combine searches into one monster search.
5. Hint 2: You can also download the properties and purchasing info at
the same time as the SMILES, which may come in handy later.

I hope this is useful.

John
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