On Jul 31, 2011, at 5:18 PM, Robert Hanson wrote: > Here's an idea IF you can provide a reference compound with known R/S > stereochemistry assignments. That, I think, would mean that it is in a > database somewhere (such as NCI) > > Jmol can compare two SMILES strings or a SMILES string and a molecule or two > molecules and distinguish stereoisomers and can certainly compare individual > centers for chiral similarity. Then it's just a matter of checking individual > stereocenters for similarity between the model of interest and the reference > compound. > > Or do you need to do this de novo -- for any possible structure?
Yes, any 3D structure as a .mol file. > > Rich, you say: > > "I have the luxury of having access to non-commercial proprietary software > to do this" > > Can you tell us what that means? You have proprietary software that > implements full CIP analysis? Or what sort of limitations does that have? Yes. There is a module in the modeling software (developed years ago in-house) that implements full CIP analysis. I have never had a case where it gave an incorrect result. I provide it a file with my crystallographic results along with standard Tripos-like bond-order definitions and I get back a list of atom names and R/S assignments. Similar in a way to what Platon provides but without the limitations of the incomplete implementation in that program. Rich ------------------------------------------------------------------------------ Got Input? Slashdot Needs You. Take our quick survey online. Come on, we don't ask for help often. Plus, you'll get a chance to win $100 to spend on ThinkGeek. http://p.sf.net/sfu/slashdot-survey _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
