Phil,
Bob can correct me if I'm wrong, but I think, for example:
"o...@](F)(Cl)I".find("smiles","[C@@](O)(Cl)(F)I")
returns 1 if it's a match and 0 if it's not a match.
Using a message call back, you should be able to feed the returned
information to a JavaScript grading routine.
For example, both SMILES above are (R)-chloro(fluoro)iodomethanol.
The one below is (S)-chloro(fluoro)iodomethanol:
[...@](O)(Cl)(F)I
So try print "o...@](F)(Cl)I".find("smiles","[...@](O)(Cl)(F)I") in the
command window. It results in 0
Otis
On 5/11/2010 11:07 AM, Philip Bays wrote:
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
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J. Philip Bays
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Saint Mary's College
Notre Dame IN 46556
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chemagic.com
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