Angel Herraez wrote: >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). > > > maybe I was thinking "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. > > Good - so then maybe "up from up" gives Z=2? "down from down" gives Z=-2? I was thinking about something like that. > >------------------------------------------------------------------------- >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 > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- 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
