Re: [Open Babel] : PAINS filtering

[Chris Swain]

If you are planning to annotate very large data sets it might be worth looking 
at Vortex.

http://macinchem.org/reviews/vortex/tut24/scripting_vortex24.php

Pains matching PubChem 67M structures took under 4 hours.

Chris


> 
> Message: 6
> Date: Tue, 15 Mar 2016 10:54:11 -0700
> From: Stefano Forli <fo...@scripps.edu>
> Subject: Re: [Open Babel] PAINS filtering
> To: mirix <miromo...@gmail.com>,
>   "openbabel-discuss@lists.sourceforge.net"
>   <openbabel-discuss@lists.sourceforge.net>
> Message-ID: <56e84c43.4010...@scripps.edu>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
> 
> About that, a while ago I had compiled an OB-compatible data file with the 
> three pattern 
> classes (L15, L150 and M150) from Raj Gua [1].
> 
> Dirt cheap implementation with Pybel works fine, but the main issue is 
> timing. Processing 
> a Mol2 file with 1000 random molecules from the ZINC database takes about 13 
> seconds.
> Not bad, but not even fast: to process a pretty large library for virtual 
> screning  (e.g, 
> ChemBridge library, 1.5M compounds) would take about 5.4 hours.
> 
> I'm not sure if there's a way to speed up the process, but if so, it should 
> be definitely 
> considered.
> 
> Anyway, let me know what would be the best way to share the files, and I'll 
> do it.
> 
> Cheers,
> 
> S
> 
> 
> [1] http://blog.rguha.net/?p=850
> 


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Re: [Open Babel] PAINS filtering

[Maciek Wójcikowski]

Hi,
There are improved SMARTS for PAINS in RDKit.
https://github.com/rdkit/rdkit/tree/master/Data/Pains
http://rdkit.blogspot.com/2015/08/curating-pains-filters.html


You can also use ODDT to do the filtering
http://oddt.readthedocs.org/en/latest/#oddt-command-line-interface-cli
example #2. (although currently it uses Rajarshi's SMARTS definition). I
have to update those to Greg's revised version.

Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

2016-03-15 18:54 GMT+01:00 Stefano Forli :

> About that, a while ago I had compiled an OB-compatible data file with the
> three pattern
> classes (L15, L150 and M150) from Raj Gua [1].
>
> Dirt cheap implementation with Pybel works fine, but the main issue is
> timing. Processing
> a Mol2 file with 1000 random molecules from the ZINC database takes about
> 13 seconds.
> Not bad, but not even fast: to process a pretty large library for virtual
> screning  (e.g,
> ChemBridge library, 1.5M compounds) would take about 5.4 hours.
>
> I'm not sure if there's a way to speed up the process, but if so, it
> should be definitely
> considered.
>
> Anyway, let me know what would be the best way to share the files, and
> I'll do it.
>
> Cheers,
>
> S
>
>
> [1] http://blog.rguha.net/?p=850
>
>
> On 03/15/2016 08:21 AM, mirix wrote:
> > There you go:
> >
> > http://pastebin.ca/raw/3401877 
> >
> > This comes from here:
> >
> > http://blog.rguha.net/?p=850
> >
> >
> >
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/PAINS-filtering-tp4659223p4659226.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
> --
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> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >
>
> --
>
>   Stefano Forli, PhD
>
>   Assistant Professor of Integrative
>   Structural and Computational Biology,
>   Molecular Graphics Laboratory
>
>   Dept. of Integrative Structural
>and Computational Biology, MB-112A
>   The Scripps Research Institute
>   10550  North Torrey Pines Road
>   La Jolla,  CA 92037-1000,  USA.
>
>  tel: +1 (858)784-2055
>  fax: +1 (858)784-2860
>  email: fo...@scripps.edu
>  http://www.scripps.edu/~forli/
>
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
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Re: [Open Babel] PAINS filtering

[Stefano Forli]

About that, a while ago I had compiled an OB-compatible data file with the 
three pattern 
classes (L15, L150 and M150) from Raj Gua [1].

Dirt cheap implementation with Pybel works fine, but the main issue is timing. 
Processing 
a Mol2 file with 1000 random molecules from the ZINC database takes about 13 
seconds.
Not bad, but not even fast: to process a pretty large library for virtual 
screning  (e.g, 
ChemBridge library, 1.5M compounds) would take about 5.4 hours.

I'm not sure if there's a way to speed up the process, but if so, it should be 
definitely 
considered.

Anyway, let me know what would be the best way to share the files, and I'll do 
it.

Cheers,

S


[1] http://blog.rguha.net/?p=850


On 03/15/2016 08:21 AM, mirix wrote:
> There you go:
>
> http://pastebin.ca/raw/3401877 
>
> This comes from here:
>
> http://blog.rguha.net/?p=850
>
>
>
>
> --
> View this message in context: 
> http://forums.openbabel.org/PAINS-filtering-tp4659223p4659226.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
> --
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785231=/4140
> ___
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

-- 

  Stefano Forli, PhD

  Assistant Professor of Integrative
  Structural and Computational Biology,
  Molecular Graphics Laboratory

  Dept. of Integrative Structural
   and Computational Biology, MB-112A
  The Scripps Research Institute
  10550  North Torrey Pines Road
  La Jolla,  CA 92037-1000,  USA.

 tel: +1 (858)784-2055
 fax: +1 (858)784-2860
 email: fo...@scripps.edu
 http://www.scripps.edu/~forli/

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Re: [Open Babel] PAINS filtering (mirix)

[Geoffrey Hutchison]

> Have a look at http://www.macinchem.org/reviews/pains/painsFilter.php

This reminds me that we should integrate the Silicos tools into the main OB 
distribution.

Thanks,
-Geoff
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Re: [Open Babel] PAINS filtering

[mirix]

There you go:

http://pastebin.ca/raw/3401877   

This comes from here:

http://blog.rguha.net/?p=850




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Re: [Open Babel] PAINS filtering

[Geoffrey Hutchison]

> I am able to filter my SDF file using one SMARTS pattern at a time, but I
> was wondering if OB provides a simple way of filtering all PAINS in one go.

At the moment, no. But if someone posts the set of SMARTS patterns, it’s easy 
to add this as a filter to plugindefines.txt.

-Geoff
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Re: [Open Babel] PAINS filtering (mirix)

[Chris Swain]

Have a look at http://www.macinchem.org/reviews/pains/painsFilter.php

Cheers

Chris
> On 15 Mar 2016, at 12:10, openbabel-discuss-requ...@lists.sourceforge.net 
> wrote:
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> Today's Topics:
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>   1. PAINS filtering (mirix)
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> 
> Message: 1
> Date: Mon, 14 Mar 2016 08:36:56 -0700 (PDT)
> From: mirix 
> Subject: [Open Babel] PAINS filtering
> To: openbabel-discuss@lists.sourceforge.net
> Message-ID: <1457969816409-4659223.p...@n4.nabble.com>
> Content-Type: text/plain; charset=us-ascii
> 
> Hello,
> 
> I have downloaded a subset of the PubChem database in SDF format. On the
> other hand, I have a file containing SMARTS for about 500 undesirable
> functionalities.
> 
> I am able to filter my SDF file using one SMARTS pattern at a time, but I
> was wondering if OB provides a simple way of filtering all PAINS in one go.
> 
> Kind regards,
> 
> Miro
> 
> 
> 
> 
> --
> View this message in context: 
> http://forums.openbabel.org/PAINS-filtering-tp4659223.html
> Sent from the General discussion mailing list archive at Nabble.com.
> 
> 
> 
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