I've CC'd to the cdk-user list since this is an interesting problem On Nov 16, 2007, at 11:15 AM, aziz yasri wrote:
> Example: > > > Reacts1 > = ["CCCN", "COCN","c1ccccc1N","C(O)CCN"] > # list of amines smiles > > > Reacts2 > = ["CCC(=O)Cl","CNC(=O)Cl ","CC(CC)(=O)Cl "] # > list of acyl chlorides smiles > > Reaction > = "*CN.*C(=O)Cl>>*CNC(=O)*" # the reaction in smirks code, amide > formation. > I want to perform the reaction using the reactants list and then get the products in smiles > string format. The CDK does not have SMIRKS supports, so you can't do this automatically. However this is actually quite easy to do with a bit of string (and SMARTS) manipulation. The basic idea is to take each reagent and replace the reacting group with a ring closure symbol. So your amines would become: CC%91, CO%91 etc and your acyl chlorides would be: CC%90, CN%90 etc Now, you product can be written as RC(=O)NCR (generally the two R's will be different) Thus if you rewrite the backbone with ring closure symbols C%90(=O)NC%91 and then catenate each pair of reagents as C%90(=O)NC%91.CC%90.CC%91 C%90(=O)NC%91.CO%90.CC%91 etc, you will get your combinatorial library. Any proper SMILES parser will process these cases and can generate a 'clean' SMILES if you want So after generating the fragment SMILES, it is simply a matter of string concatenation. This is the method used in http://www.chembiogrid.org/cheminfo/ combilib/vl and the java code that generates the reagent fragments can be found getFragmentWithClosure() at http://cicc-grid.svn.sourceforge.net/viewvc/cicc-grid/cicc-grid/cdkws/ trunk/src/net/sf/ciccgrid/cdkws/Utility.java?revision=341&view=markup Certainly not as efficient or elegant as SMIRKS, MQL etc, but gets the job done ------------------------------------------------------------------- Rajarshi Guha <[EMAIL PROTECTED]> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- If you believe in telekinesis, raise my hand. ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
