With the current parser it is impossible to match a pharmacophore because
it does not provide the recursive smart search.
And determining the environment within a molecule without recursive search
would be very unacceptable.
Hi, I have gotten pharmacophore representation and matching working -
 
Sure, this is the next step after substructure search.
 
From the user point of view there are two components:
 
How the pharmacphore is being detected in both the step.
 
 
The main thing that needs to be checked is the correctness of the
SMARTS parser (errors are still occuring due to incorrect implicit
hydrogens)
 
Not only this there are 7 kind of errors and 4 limitation in the present parser.
 
 
 

 

 
 

 

 
On 7/25/07, Rajarshi Guha <rguha@indiana.edu> 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  <rguha@indiana.edu >
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-------------------------------------------------------------------
Q:  Why did the mathematician name his dog "Cauchy"?
A:  Because he left a residue at every pole.



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sushil ronghe
Application Scientist
Connexios Life Science
India
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