On Wed, Jul 6, 2011 at 3:26 PM, Christoph Steinbeck <steinb...@ebi.ac.uk> wrote:
> I'm not sure if CDK will give you quick results because of lacking atom types.

You may be interested in this post:

http://chembioinfo.wordpress.com/2011/07/06/improved-atom-typing-cdk/

I do not know when this will result in good patches, or when it will
be part of the 1.4.x series, but I think they have aluminum atom types
in there too...

Egon


-- 
Dr E.L. Willighagen
Postdoctoral Researcher
Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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