On 7/23/11 8:28 AM, Greg Landrum wrote: > I've spent a while beating my head against this without much success, > so I figured I'd ask around. > > The attached mol file contains a chiral phosphorus center; I'm trying > to figure out whether the label for that center should be R or S. > My usual approach to this is to draw the thing in Marvin Sketch and/or > Chemdraw and see what they say. Both agree that the P is (R). > The problem I have with that is that I can't really figure out why. > I'm sure the answer is simple, but I haven't been able to find it. > > I've been singularly unsuccessful at coming up with the right search > phrase to google for a result. I don't have an answer, but I do have an editorial. This is why Dave Weininger abandoned the R/S notation for SMILES. I recall something about how if you actually implement the rules as a computer algorithm, the solution takes time proportional to a high-order polynomial, or maybe it's even exponential -- i.e. you can wait all day for an answer. (WLN had the same problem.) By adopting an atom-centered approach, SMILES only requires you to consider the atom and it's immediate neighbors in order to create a valid, correct SMILES.
The R/S notation is really a form of canonicalization, and Weininger decided to leave that to the computer. Craig ------------------------------------------------------------------------------ Storage Efficiency Calculator This modeling tool is based on patent-pending intellectual property that has been used successfully in hundreds of IBM storage optimization engage- ments, worldwide. Store less, Store more with what you own, Move data to the right place. Try It Now! http://www.accelacomm.com/jaw/sfnl/114/51427378/ _______________________________________________ Blueobelisk-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
