Dear Greg,
When you say as closely as I could, do you mean that all the paramaters are the
sames in ECFP and Morgan but the only divergence between them is on the way
RDKit/Pipeline handle aromaticity + hashing ?
Thanks
Guillaume
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: mercredi 30 septembre 2015 08:01
To: Jing Lu
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] Difference between ECFP and MorganFingerprint
On Wed, Sep 30, 2015 at 6:47 AM, Greg Landrum
<greg.land...@gmail.com<mailto:greg.land...@gmail.com>> wrote:
On Tue, Sep 29, 2015 at 8:22 PM, Jing Lu
<ajin...@gmail.com<mailto:ajin...@gmail.com>> wrote:
I was treating AllChem.GetMorganFingerprint(m1,2) the same as ECFP4. I am
writing a paper for a open source tool, so I need to be very accurate. I have
seen one open source implementation for ECFP, which is from CDK. Most
researchers are using Pipeline Pilot to calculate ECFP. But, Pipeline Pilot is
not open source.
To be very clear: the only implementation of ECFP is the one in Pipeline Pilot.
The other implementations like the one in the CDK and the RDKit, may have
followed the algorithm description that was published, but due to differences
in aromaticity perception and hashing algorithms the results will not be
exactly the same.
Sorry, should have been more explicit here: when I did the Morgan fingerprint
implementation for the RDKit, I followed the published algorithm description as
closely as I could.
-greg
**********************************************************************
DISCLAIMER
This email and any files transmitted with it, including replies and forwarded
copies (which may contain alterations) subsequently transmitted from Firmenich,
are confidential and solely for the use of the intended recipient. The contents
do not represent the opinion of Firmenich except to the extent that it relates
to their official business.
**********************************************************************
------------------------------------------------------------------------------
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
