On Tue, Oct 26, 2010 at 8:26 AM, Tobias Girschick <[email protected]> wrote: >>> In fact, given the substructure you must perform a substructure search to >>> get the mapping of the target atoms to the substructure atoms and use that >>> mapping to remove the target atoms. > > Well, that's the thing I wanted to prevent...as I already have performed > some kind of substructure search. Is there a way to map the substructure on > on the molecule so that I can afterwards remove the overlapping atoms?
Assuming you did the substructure search using the CDK, you can find the atoms matching the query and then either mark those atoms for later removal, or remove them then and there See the Javadocs for SMARTSQueryTool for some example code that would let you identify the matching atoms -- Rajarshi Guha NIH Chemical Genomics Center ------------------------------------------------------------------------------ Nokia and AT&T present the 2010 Calling All Innovators-North America contest Create new apps & games for the Nokia N8 for consumers in U.S. and Canada $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store http://p.sf.net/sfu/nokia-dev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
