Re: [Cdk-devel] [ cdk-Patches-2687014 ] Implementation of Pubchem fingerprints

[Rajarshi Guha <rguha@in...>]

On Mar 14, 2009, at 1:15 PM, richard apodaca wrote:

>
> Hello Rajarshi,
>
> Interesting. Have you had a chance to do any benchmarking against  
> the existing CDK fingerprints in terms of hitset enrichment and/or  
> speed?


Haven't done that yet - but given that it involves doing 618 SMARTS  
queries per molecule, it will be slower than the MACCS keys, which is  
slower than the hashed fp's.

I plan to rerun the enrichment experiments in a few days

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Rajarshi Guha  <rguha@...>
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Re: [Cdk-devel] [ cdk-Patches-2687014 ] Implementation of Pubchem fingerprints

[richard apodaca <rich_apodaca@ya...>]

Hello Rajarshi,

Interesting. Have you had a chance to do any benchmarking against the existing CDK fingerprints in terms of hitset enrichment and/or speed?

Rich
___________________________________

Richard L. Apodaca

http://depth-first.com      Blog
http://metamolecular.com    Company


--- On Sat, 3/14/09, SourceForge.net <noreply@...> wrote:

> From: SourceForge.net <noreply@...>
> Subject: [Cdk-devel] [ cdk-Patches-2687014 ] Implementation of Pubchem fingerprints
> To: noreply@...
> Date: Saturday, March 14, 2009, 8:42 AM
> Patches item #2687014, was opened at
> 2009-03-14 11:42
> Message generated for change (Tracker Item Submitted) made
> by Item Submitter
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2687014&group_id=20024
> 
> Please note that this message will contain a full copy of
> the comment thread,
> including the initial issue submission, for this request,
> not just the latest update.
> Category: None
> Group: Needs Review
> Status: Open
> Resolution: None
> Priority: 5
> Private: No
> Submitted By: Rajarshi Guha (rajarshi)
> Assigned to: Egon Willighagen (egonw)
> Summary: Implementation of Pubchem fingerprints
> 
> Initial Comment:
> The pubchemfp branch implements the Pubchem fingerprint and
> is based on the public domain code provided by the NCGC
> using JChem. The current branch converts the code to CDK and
> also rewrites some of the SMARTS to use <Hn> based
> matching rather than explicit H matching.
> 
> Added several unit tests taken from Pubchem entries. The
> class also provides a helper method to decode Base64 encoded
> pubchem fp's (which can be found in the PubChem SD files).
> 
> To get this code, pull from my git repo by doing
> 
> git pull git://rguha.ath.cx/cdk pubchemfp
> 
> ----------------------------------------------------------------------
> 
> You can respond by visiting: 
> https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2687014&group_id=20024
> 
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[Cdk-devel] [ cdk-Patches-2687014 ] Implementation of Pubchem fingerprints

[SourceForge.net <noreply@so...>]

Patches item #2687014, was opened at 2009-03-14 11:42
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2687014&group_id=20024

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: Needs Review
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Rajarshi Guha (rajarshi)
Assigned to: Egon Willighagen (egonw)
Summary: Implementation of Pubchem fingerprints

Initial Comment:
The pubchemfp branch implements the Pubchem fingerprint and is based on the public domain code provided by the NCGC using JChem. The current branch converts the code to CDK and also rewrites some of the SMARTS to use <Hn> based matching rather than explicit H matching.

Added several unit tests taken from Pubchem entries. The class also provides a helper method to decode Base64 encoded pubchem fp's (which can be found in the PubChem SD files).

To get this code, pull from my git repo by doing

git pull git://rguha.ath.cx/cdk pubchemfp

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2687014&group_id=20024