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vinay
Hi 
  Noel,
          Thanks a lot for your reply, i have referred SMARTS_InteLigand.txt, even then i could not screen unwanted functional groups.
One more thing, why do we have two different codes obprop and obrotamer, is it possible to include print rotatable bonds by running obprop , can we do that.
Thanks a lot 
vinay


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Re: (no subject)

Geoffrey Hutchison
> One more thing, why do we have two different codes obprop and  
> obrotamer, is it possible to include print rotatable bonds by  
> running obprop , can we do that.

The definition of rotatable bonds is slightly different. The obprop  
program uses a general rule -- think of it as indicating the  
approximate number of rotatable bonds (based on cheminformatics). The  
obrotamer program actually generates rotamers/conformers. So it has a  
set of patterns for what bonds can be rotated.

Hope that helps,
-Geoff

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