oh, good. On Tue, May 11, 2010 at 5:37 PM, Philip Bays <pb...@saintmarys.edu> wrote:
> 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 > > > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > 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
