Re: [Cdk-user] [Cdk-devel] pharmacophore representation and matching now available

[Christoph S. <er...@do...>]

Rajarshi,

thanks. I think your posting did not receive the excitement that it
deserved :-)
The start of a pharmacophore package is as large a step for CDK as was
the start of QSAR development.
Although your question regarding incorporation into CDK got unanswered,
it seems that some things happened behind the scenes because the code is
already in SVN :-)

It would be absolutely great to see a small CDK News article with
examples on how to use this package.

Cheers,

Chris


Rajarshi Guha wrote:
> Hi, I have gotten pharmacophore representation and matching working -  
> the code is currently outside of the CDK, but if people agree I'll  
> move it into it's own package (pharmacophore) in the CDK hierarchy.
> 
>  From the user point of view there are two components:
> 
> 1. Creating a pharmacophore query - ideally this would be done  
> graphically, but the current classes allow programmatic access to  
> creating a query. A query consists of pharmacophore groups (a.k.a  
> pharmacophore atoms) and distances between pharmacophore groups  
> (a.k.a pharmacophore bonds).
> 
> A pharmacophore group is defined by a SMARTS pattern and a label. The  
> pharmacophore bonds are defined by  2 pharmacophore groups and either  
> an exact distance or distance range.
> 
> Note that queries general to an extent - you can use pharmacophore  
> triads, quads etc. However right now only Euclidean distances between  
> pharmacophore groups are considered - no torsions etc.
> 
> 2. Matching a query against a given 3D structure - this is performed  
> in a manner analogous to the SMARTSQueryTool. Supply a 3D structure  
> and a pharmacophore query and get back the matching groups. Note that  
> the return value is a set of matching pharmacophore groups. But since  
> each group contains the matching atoms from the actual target  
> molecule, you can identify/color etc the matching atoms easily.
> 
> Internally it uses the UniversalIsomorphismTester to perform the 3D  
> isomorphism matching. Currently, it's designed so that you have to  
> loop over every molecule in a set of conformers. The next step is to  
> perform matching on a set of conformers more efficiently.
> 
> The main thing that needs to be checked is the correctness of the  
> SMARTS parser (errors are still occuring due to incorrect implicit  
> hydrogens)
> 
> -------------------------------------------------------------------
> Rajarshi Guha  <rg...@in...>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04  06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> Q:  Why did the mathematician name his dog "Cauchy"?
> A:  Because he left a residue at every pole.
> 
> 
> 
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-- 
PD Dr. Christoph Steinbeck
Lecturer in Chemoinformatics
Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071-29-78978   Fax: (+49/0) 7071-29-5091

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..