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

[John J. Irwin]

Hi Andrew

You can find provisional cluster lists for ZINC subset 23 ("drugs-now")
online now. I say provisional, because the clustering is still running. 
The 60% and 70% are likely to change very little, perhaps 1-2% more
molecules. The 80% and 90% will change (grow) until they are finished. 
It can take weeks!

I thought you might like to have the provisional results now.

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
>>> ----------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------
>>>
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>>> Zinc-fans at docking.org
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