Bob: This looks quite interesting. I understand, or think I understand, what the new capability does. However, I do not quite understand what the examples in 129 are showing. And how do they relate to anything drawn or not drawn i the Jmol applet shown. Perhaps I am dense this morning:-(
I have been playing with another drawing program, Marvin Sketch, from ChamAxon. It has a lot more file format options for input and output. It also has the capability to generate a IUPAC name and to load a 2-D drawing from a name. I have found the names, including stereochemistry, of the rather simple organic structures I have been looking at to be accurate and consistent. The problem I run into with smiles and smarts is that if a student includes an implicit hydrogen in the structure, not matter what program I am looking at, that hydrogen is included into the string. How she puts it in, changes the string though it may not actually change the structure. But the stereochemically complete name is not changed (unless the hydrogen actually changes the stereochemistry. ) This seems a promising approach for me, but explain what your approach is doing. Is this incorporated into the Jmol.jar applet or is it a separate .jar file that can be called from Jmol or invoked from someplace else? On May 11, 2010, at 9:05 AM, Robert Hanson wrote: > 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 > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users J. Philip Bays Professor of Chemistry Science Hall 172 Saint Mary's College Notre Dame IN 46556 (574) 284-4663
------------------------------------------------------------------------------
_______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
