I think I'm coming pretty close to a definitive Jmol 3D-SEARCH SMARTS definition. See:
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/smiles/package.html I believe this comes VERY close to the Daylight definitions, with a few nice additions. Note that: -- "aromatic" is fully defined, with no ambiguity whatsoever. -- "Implicit hydrogen" is to be read as "a hydrogen that would be added by the Jmol 'calculate hydrogens' command" and is fully defined here. The only ambiguity that remains has to do with the models themselves -- if model bonds are left as "aromatic" or "partial" the primitives h (implicit hydrogen count) and X (total connections, including implicit hydrogens) are unreliable. And, of course, if model bonding is all single bonds (as in PDB files), although "aromatic" will be defined appropriately, implicit hydrogen counts on groups such as HIS will not necessarily be appropriate. (Jmol would add H atoms to BOTH N atoms of histidine.) In such cases, primitives h and X are disrecommended. Comments appreciated. Bob -- 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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