Bob Hanson wrote: > that's next. I have an idea but no time to work on it. It would involve > the MOL2 format bond stereochemistry designations.
I can't find anything about stereochemistry in the MOL2 specs, but MOL has "up", "down", "none" and "nonspecified" bond types (and JChemPaint exports the first 3 into MOL). > Try at least setting Z values differently for the different atoms. Are > all the H atoms there? It will help a lot if the H atoms are on the > carbons that might otherwise invert. I've tested applying this: bondType = 1 (up) ==> Z= 1 bondType = 6 (down) ==> Z= -1 all the others have Z=0 and although not infallible, it does improve stereo retention during minimization. ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
