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identifying functional groups
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Lauren

Joined: 06 Feb 2015
Posts: 7

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Link to postPosted: Thu Mar 12, 2015 3:27 pmPost subject: identifying functional groups Reply with quote

Is there a way to identify and catagorise the H-bond donor / acceptor functional group from a large dataset without having to specify a filter?

Daniel
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Joined: 22 Jan 2012
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Link to postPosted: Tue Mar 17, 2015 2:00 pmPost subject: Reply with quote

Dear Lauren,

You can use our cxcalc command line tool to solve this problem. I give you an example, in which molecules are read from a SMILES file, and writes the acceptor multiplicity for each atom in the molecule into a string. I put this string as an SDF property (named ACCEPTOR) and write it to SDF output (acc.sdf):

  cxcalc -S -t ACCEPTOR -o acc.sdf hbda -t acc nci700.smiles

You can also use the Chemical Terms evaluator function to calculate for lots of molecules, a whole JChem table for example:

 evaluate -e "acceptor()" -S -t ACCEPTOR -o acc.sdf nci700.smiles
You can calculate the donor multiplicity in the same way. I hope this helps. 

Daniel
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