On 29/04/2015 13:39, Rajarshi Guha wrote:
The pharmacophore matching was described in a CDK News issue - but all
the links I have seem to be dead. It's very simplistic in fact -
pharmacophore query atoms and bonds are defined as subclasses of
SMARTS atoms and bonds. The query is parsed into a pharmacophore
molecule and then a match is identified via subgraph isomorphism.
Currently only distance and angle constraints are supported. The code
really should be extended to support dihedrals and excluded volumes
So this isn't clear to me. "subgraph isomorphism" makes is sound like
its using 2D pharmacophores, whereas "distance and angle constraints"
(and what follows) makes it sound like its 3D pharmacophores.
Regarding the details of the definition file - are you referring to
the definition in this particular case? Or just, generally how to
define a pharmacophore? If the former, it's probably best to get in
touch with John Van Drie directly.
I was wanting to know what the contents of the definition file were e.g.
how to create a new definition.
Tim
Egon/Chris - do we have old versions of CDK News somewhere?
On Wed, Apr 29, 2015 at 3:36 AM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Nice!
Is there any information available about the methodology involved
and on the details (not xml schema) of the pharmacophore
definition file?
Tim
On 28/04/2015 23:34, Rajarshi Guha wrote:
I recently updated the CDK pharmacophore search tool
(https://github.com/rajarshi/cdkpcore) and got this comment from
a very happy user :)
Kudos to everybody who contributed to the significant
improvements in the CDK.
---------- Forwarded message ----------
From: *John H Van Drie* <j...@vandrieresearch.com
<mailto:j...@vandrieresearch.com>>
Date: Tue, Apr 28, 2015 at 4:58 PM
Subject: CDKPsearch speed
To: rajarshi.g...@gmail.com <mailto:rajarshi.g...@gmail.com>
Rajarshi
I'm amazed at the speed of CDKPsearch now. 1 million confs in 3
min, using 15 processors. It's not compute-bound, so I think if
I shift things to my fastest disk things will be even better.
Almost interactive!
Of course, now I'll want to use more confs/mol...
John
Van Drie Research LLC
www.vandrieresearch.com <http://www.vandrieresearch.com>
--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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NIH Center for Advancing Translational Science
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