On Friday, June 13, 2003, at 04:34 PM, Miguel wrote:
Basically, what I have been told is that the algorithms are all published.
They mostly involve geometry ... angles and distances. And the problem is
that there are no open-source implementations.
So, I think it is well worth it to do some research ... literature search
for these algorithms.
One start for such research is the CORINA algorithm by the Gasteiger group. Miguel is correct that there are no open-source implementations. Other algorithms include CONCORD and COBRA.
CORINA webpages: http://www2.chemie.uni-erlangen.de/software/corina/xrayeval.html#001 http://www2.chemie.uni-erlangen.de/software/corina/corina_lit.html
Someone also told me that there are a few review articles on 3D structure generation that were helpful in writing an in-house implementation, but since this was an off-hand remark, I didn't have a chance to follow up.
I'd expect that any implementation will require some parameterization and/or database, in which case contacting several mailing lists of groups like JMol, CDK, Open Babel, JOELib, etc. should be helpful in providing some data for that effort.
This would be a great addition to the open-source chemical toolkit! -Geoff
-- -Geoff Hutchison <[EMAIL PROTECTED]> Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.northwestern.edu/
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