sub-structure search

I noticed that with the topology analysis feature, Marvin determines the number of aromatic rings, etc. contained in a chemical structure. Is there any way to extend this feature for arbitrary substructures as defined by the user? I may want to determine if a certain structure contains a carboxyl group and/or other predetermined substructures (and perhaps break the molecule down into these substructures), or in reverse I may want to specify a substructure, say an alkyl group, and return molecules in a database containing such a group. Seeing as there is already some structure searching going on in the topology analysis feature, it seems like the former could be possible, though the latter may be hard to implement. Anyway, please let me know if this is possible in Marvin.





Thanks a ton.

Topology Analyser is not based on substructure searching, although it performs aromatic ring recognition. For chemical substructure searching purposes I recommend you checking the JChem toolkit, especially the JChem Base tool. It contains very advanced substructure searching functions in files and databases as well. We provide you the API as well so you can integrate it in your application if you want to. For more information please visit: http://www.chemaxon.com/jchem/

Thanks.