[Zinc-fans] Subset 'Clustering and Diversity' Lists Broken Links

[John J. Irwin]

Hi Andrew

Thanks for pointing this out.  I've started the clustering. The 60% will
be done first, perhaps in a day or two.  The 90% can take a month.  Yes,
I realize this is insane. We have really good ideas to make this faster.
For now, this is what we can offer.  Of course, you are welcome to
download the entire SMILES and cluster it yourself if prefer.

Thanks for your helpful feedback, and your patience.

John
UCSF ZINC Team

T. Andrew Binkowski wrote:
> John,
> I notices that the Clustering and Diversity lists for subset 23 are
> broken.  Here is what I tried to download:
>
> http://zinc.docking.org/subset1/23/23_t70.smi
>
> Here is the response:
>
> Error 404 - file not found. 
> You are in a twisty website of broken documents, all alike...
>
> Thanks,
> Andrew Binkowski
>
> On Jul 1, 2009, at 8:52 PM, John J. Irwin wrote:
>
>> Hi Andrew
>>
>> A new version of "drugs now" appeared on the website today and is
>> ready for download.
>>
>> Here is the blog entry about it: http://docking.org/?q=node/118
>>
>> John
>> UCSF ZINC Team
>>
>>
>> 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
>>> ----------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Zinc-fans mailing list
>>> Zinc-fans at docking.org
>>> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>>>   
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20090707/ac39941c/attachment-0001.html