You are right, this is cool!!! Now to work on implementing it. And thanks of the sample page. I have been mucking around with an other applet today for which there are many example pages. The examples all work, but I learn best by taking an example and tinkering with it. When I load the example pages into a text editor, there is nothing there to se When I use the "View Source" option of the browser aI can get the code, copy it, and generate a new html file. However, when my file is placed in the same directory as the example came from, the applet does not load, though all of the explanatory text does.
Your examples actually work:-) 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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