From samo.turk at ffa.uni-lj.si  Mon Jan 14 00:53:21 2008
From: samo.turk at ffa.uni-lj.si (Samo Turk)
Date: Mon, 14 Jan 2008 09:53:21 +0100
Subject: [Zinc-fans] Making your own subset
Message-ID: <20080114095321.67579f24@vhts.ffa.si>

Dear zinc-fans,

I noticed that generation of user subsets doesn't work. 
What is the easiest way to make your own subset? I downloaded compounds
of 4 different vendors (~million compounds) from ZINC and now I'd like
to extract those that fall in certain logP and molecular mass interval.
I tried to write a bash script which uses Open Babel for calculating
logP and molecular mass and then extracts relevant compounds, but it is
painfully slow. It would need few weeks to filter all compounds. Has
anyone written more effective script or knows of a program that can do
this in reasonable time.

Best regards,
Samo Turk

From stelzer at umich.edu  Wed Jan 16 11:07:26 2008
From: stelzer at umich.edu (Andrew Stelzer)
Date: Wed, 16 Jan 2008 14:07:26 -0500
Subject: [Zinc-fans] does ZINC8 use AMSOL
Message-ID: <02DEAFDD-9BA6-4059-A485-C9756104F8B8@umich.edu>

Hello all,

Does the new version ZINC8 use AMSOL to calculate partial atomic  
charges or is MMFF94 still used?

Take Care,
Andrew


From jji at cgl.ucsf.edu  Wed Jan 16 11:19:17 2008
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Wed, 16 Jan 2008 11:19:17 -0800
Subject: [Zinc-fans] does ZINC8 use AMSOL
In-Reply-To: <02DEAFDD-9BA6-4059-A485-C9756104F8B8@umich.edu>
References: <02DEAFDD-9BA6-4059-A485-C9756104F8B8@umich.edu>
Message-ID: <478E58B5.7000709@cgl.ucsf.edu>

Hi Andrew

All versions of ZINC from 6 on use AMSOL for partial atomic charges. 
ZINC5 used MMFF94, but that was an oversight.

Good luck!

John
UCSF ZINC Team


Andrew Stelzer wrote:
> Hello all,
>
> Does the new version ZINC8 use AMSOL to calculate partial atomic  
> charges or is MMFF94 still used?
>
> Take Care,
> Andrew
>
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>   

From jji at cgl.ucsf.edu  Wed Jan 16 16:13:35 2008
From: jji at cgl.ucsf.edu (John J. Irwin)
Date: Wed, 16 Jan 2008 16:13:35 -0800
Subject: [Zinc-fans] Making your own subset
In-Reply-To: <20080114095321.67579f24@vhts.ffa.si>
References: <20080114095321.67579f24@vhts.ffa.si>
Message-ID: <478E9DAF.8030809@cgl.ucsf.edu>

If you use mitools (molinspiration.com) to compute properties it will 
process around 200K to 500K molecules per hour on a modern CPU. But you 
can also just download the precomputed properties from ZINC as a table 
and write a script to pick codes within your filter criteria.

Samo Turk wrote:
> Dear zinc-fans,
>
> I noticed that generation of user subsets doesn't work. 
> What is the easiest way to make your own subset? I downloaded compounds
> of 4 different vendors (~million compounds) from ZINC and now I'd like
> to extract those that fall in certain logP and molecular mass interval.
> I tried to write a bash script which uses Open Babel for calculating
> logP and molecular mass and then extracts relevant compounds, but it is
> painfully slow. It would need few weeks to filter all compounds. Has
> anyone written more effective script or knows of a program that can do
> this in reasonable time.
>
> Best regards,
> Samo Turk
> _______________________________________________
> Zinc-fans mailing list
> Zinc-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans
>   

From stelzer at umich.edu  Thu Jan 17 11:16:38 2008
From: stelzer at umich.edu (Andrew Stelzer)
Date: Thu, 17 Jan 2008 14:16:38 -0500
Subject: [Zinc-fans] Molecular weight cutoff
Message-ID: <25587099-873D-44F1-BF2A-ADE03EBE9940@umich.edu>

When calculating protonation states and partial charges using the  
upload feature can one specify to ignore certain filtering  
restrictions such as MW, chiral centers etc?

Andrew


From bije_br at yahoo.com.br  Thu Jan 31 18:05:04 2008
From: bije_br at yahoo.com.br (Josmar R. da Rocha)
Date: Thu, 31 Jan 2008 23:05:04 -0300 (ART)
Subject: [Zinc-fans] all-purchasable subset
Message-ID: <269670.12485.qm@web55402.mail.re4.yahoo.com>

Dear Zinc-fans,

I noticed that the subset "all-purchasable" that could be downloaded from Zinc 7 is no longer available in Zinc 8. I'd Like to know if the only way to get this subset would be by downloading each one of the files found in " By vendor /in stock" subsets.

Thanks in advance!

Josmar Rocha
       
---------------------------------
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