I would like to add that the CDK *did* develop a 3D generator in the mean time. It works similar to the the Bustr3d approach and can be tested on http://www.chemistry-development-kit.org Note that there is currently a bug with the ring perception.
Cambridge and the CDK team had plans of merging the two approaches, but so far we did not do that. Cheers, Chris peter murray-rust wrote: > At 21:08 13/01/2007, Dan Willenbring wrote: >> Dear Dr. Peter Murray Rust, > > Thanks very much - I'm taking the liberty of copying your message to the > Blue Obelisk list > >> I ran across a pretty old Cdk-devel message ( http://sourceforge.net/ >> mailarchive/message.php?msg_id=5267361 ) where you were discussing a >> possible open source implementation of 3D structure generation. I am >> working on a project where I need to generate several thousand sets >> of crude 3D coordinates (for further optimization with Gaussian03) >> from structures presently in a ChemDraw document. > I am assuming these are primarily organic > > Sam Adams here created Bustr3D - which used a fragment-based approach > derived from the NCI dataset. BUSTR is being rewritten to allow for > easier distribution and maintenance. > > Nick Day has a library of many thousand fragments from the > crystallographic literature which we are soon going to release. > >> Do you know if there has been any progress made in this area? Is >> there a project I have yet to run across that I could work on to suit >> my needs? > > We would be delighted if you were able to give some help in this area. > It might be an idea to see the sorts of molecules you have. Our approach > is particularly geared to ring nuclei joined by short linkers - it is > not a conformational analysis system. > > Best > > P. > > >> Thank you, >> Dan Willenbring >> >> Tantillo Group >> University of California, Davis >> Department of Chemistry >> One Shields Ave >> Davis, CA 95616 >> >> [EMAIL PROTECTED] >> 530 304 0971 > > Peter Murray-Rust > Unilever Centre for Molecular Sciences Informatics > University of Cambridge, > Lensfield Road, Cambridge CB2 1EW, UK > +44-1223-763069 > _______________________________________________ > Blue-obelisk mailing list > Blue-obelisk@hardly.cubic.uni-koeln.de > http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Head of the Research Group for Molecular Informatics Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. _______________________________________________ Blue-obelisk mailing list Blue-obelisk@hardly.cubic.uni-koeln.de http://hardly.cubic.uni-koeln.de/mailman/listinfo/blue-obelisk
