We have a real need to generate structures from 1-D connection tables and there is no tried and trusted Blue Obelisk coordinate generator (e.g. we use CDK for 2D coordinates and have run it over 200,000 structures).
Here are the possibilities: * look it up in crystaleye. This will work instantly for molecules which have been done in the last 5-10 years. I suspect this will be very good for common solvents, anions and cations, etc. Nick now has this under OpenBabel search with SMARTS - try it out. * use RDKIT. * create a 2D picture, scale to 1.5 A bond length and optimize it in PM3. Not as silly as it sounds. It will work well for flat molecules. It may also be possible to distort the tetrahedral centres sufficiently to give the correct chirality. * hybrids. For anything with metal centres, and probably also complex rings, use crystaleye moieties to start with. It may need some substitution or addition. Then sprout some rough ligands. BUSTR (Sam Adams) did/does this. It works, but needs reengineering. After that use PM3. Ideally we should mount this as web services. P. Peter Murray-Rust Unilever Centre for Molecular Sciences Informatics University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK +44-1223-763069 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
