[Cdk-user] pharmacophore representation and matching now available

[Rajarshi G. <rg...@in...>]

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)

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Rajarshi Guha  <rg...@in...>
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