Well, maybe not, but this is PRETTY COOL! *Jmol 12.0.RC11 allows unprecedented matching of non-canonical SMILES strings independent of any 3D structure. This includes both atom and bond stereochemistry, including cis/trans, allene, tetrahedral, square planar, trigonal bipyramidal, and octahedral stereochemistry. Starting with a SMILES string from some source, you can test for an equivalent structure WITHOUT any need for "canonicalization" of the SMILES (that is, turning it into some standard form). While canonicalization is important for database searching just in terms of speed, with this addition to Jmol, it is no longer necessary for pattern matching between two SMILES strings or pattern searching of a SMILES string using a SMARTS pattern. This feature is completely independent of any actual Jmol model (although that, too, can be tested against a SMILES or SMARTS string). Thus, for example, you can have a user create a 2D structure in JME and use Jmol to test its equivalence to some reference SMILES or SMARTS string you are expecting.
Think about it...I think this will open up all sorts of possibilities for student input of 2D or 3D structures. see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm **http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip * -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 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
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