So I've being playing for a few days with the minimization of structures in Jmol, and I'm very happy with the result; I think it will make an excellent educational tool. I'm feeding Jmol with 2D structures drawn and then exported into MOL format. (All this runs within a single web page, though I'm not ready yet to go public with it.)
One thing I miss, and would be interesting to have, but likely not trivial to implement, is retention of the stereochemistry. Despite being 2D, formula drawing programs allow to put wedge bonds (up/down), and at least JChemPaint exports them correctly into MOL format. However, since the Z coordinate is zero for all atoms, that stereo info is lost. I can think of a way to set some positive or negative Z value on each atom depending on the type of stereo bond (even using Javascript) and so modifiy the MOL before giving it to Jmol, but then I'd need that Jmol retains that configuration, which it is not doing right now upon minimization. I realize the implications for the calculation are heavy, and it may even be undesirable to have it active by default --could be a toggle option--. Any insights? ------------------------------------------------------------------------- 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
