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Date: Fri, 22 Apr 2005 19:02:08 -0400
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From: "Sean, , OBrien" <drseanobrien=at=yahoo.co.uk>
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Subject: W:Substructure matching 
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Hi All,

I am searching for some software that will help me to identify the atoms within a molecule that match a query substructure. For example I wish to find which atoms belong to an imidazole ring. The aim is to extract the matching substructure while keeping the original atomic coordinates.

I know that several substructure matching routines exist, and some are even freely available but I haven't found any that return the identity of the matching atoms. Some return the whole molecule or a tally of how many times the substructure is present. They obviously "know" which atoms match but I am having difficulty identifying them. Similarly matching strings in SMILES doesn't return the initial atom ids.

I would be very grateful for any routines that do this, or that can be modified for this purpose,

Many Thanks,

Sean O'Brien