Yes, I will try it. The -1 results because my text editor converted C@ to the copyright sign and the text was too small for me to detect when I pasted it in:-(
Phil On May 11, 2010, at 6:30 PM, Robert Hanson wrote: > Phil, here's the idea. I'm pretty sure this a comprehensive solution for you. > > 2D or 3D: > > It doesn't matter how you draw the structure. > > It doesn't matter if you include extra hydrogen atoms or not, because what > Jmol is doing is creating a topologically (though not dimensionally) correct > model from the SMILES string, then checking it. So it doesn't matter how you > indicate H atoms or what order the stereochemical notation of the SMILES > string ends up being. It should work. > > Jmol should give a definitive answer as to whether the structure drawn > matches your specified SMILES string, as long as your string is valid. Or, if > you wish, it can tell you if a subset of the SMILES string is some particular > grouping of atoms, with or without stereochemistry. > > JmolSmilesApplet.jar > ----------------------------- > > You can see a demo of this at > http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolSmiles.htm > > This page uses a mini-version of Jmol that I just made that JUST does ONE > THING -- checks SMILES strings for patterns. It's just 41K in size. But you > can use Jmol itself if you want. This mini version just has one function: > > var retValue = document.getElementById("JmolSmiles1").find("pattern", > "smilesString", asSMARTS, isAll) > > where > > asSMARTS (true or false) indicates whether you want a substructure search > (SMARTS, true) or an exact search (SMILES, false) > > isAll indicates whether you want Jmol to return the total number of matches > or just the number 1 indicating a match and 0 indicating no match. (-1 means > there was an error handling the string) > > > 3D: > > Jmol will also check a 3D model against a SMILES string or a SMARTS pattern. > Within Jmol, this is done within the SELECT command using the smiles() > function (for exact match) or using the search() function (for a substructure > search). You can also use this construct within Jmol: > > Var x = {*/1.1}.find("smarts","C=O", true) > > This function is actually VERY powerful and can return either a set of all > matching atoms (false) or a list of sets of atoms (true). I've added one bit > to SMARTS -- so I'm calling it now "3D-SEARCH" -- that allows you to select > out WHICH atoms you want returned. To do this, just add { } around the atoms > you want returned. > > So, for example: > > print {*}.find("a") # all aromatic atoms > > print {*}.find("{C}=O") # all carbonyl carbons > > print {*}.find("{C}=CC(=O)[O,N]") # all beta carbons on alpha-beta > conjugated esters or amides > > Cool, huh? > > The only problem with matching a 3D structure may be with what other programs > use to define "aromatic". Jmol should do just fine with structures that are > typically aromatic. In addition, though, it will assign all the ring carbons > of quinone to be aromatic as well (which is what JME does). Basically it > defines aromatic as "flat ring that is all sp2-hybridized" regardless of what > the bonding indicates. (This is kind of cool, because you can then use it in > PDB files to find all the aromatic rings in HIS, TYR, TRP, A, T, C, G, etc.) > > Bob > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > 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 > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Professor of Chemistry Department of Chemistry and Physics Saint Mary's College Notre Dame, IN 46556 (574) 284-4663 pb...@saintmarys.edu
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