It's been a VERY good week. First we get a working model kit for Jmol, and
now SMILES to 3D:
>From the application or SIGNED applet:
load SMILES "CC1C(C)c...@h]coc(=O)C1"
or, simply,
load $CC1C(C)c...@h]coc(=O)C1
($ indicates SMILES, like = indicates PDB)
and
print load("$CCCC")
or
Var x = load("$CCCC")
Need I say more? :)
see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?USEDSIGNED
Yes, I suppose I do need to say more.
This uses a web service at Indiana University
http://cheminfo.wikispaces.com/smi23d that appears to use PCMODEL for its
converter. The idea is similar to the way "=xxxx" goes to the RCSB site.
The implementation is not entirely reliable, at least I noticed that it did
double-bond stereochemistry wrong for some simple conjugated systems. For
example:
F/C=C/C=C\C
gives the expected E,Z configuration, but
F/C=C/C=C/C
ALSO gives that configuration.
To get E,E you have to use
F/C=C/\C=C/C
But that's not a valid SMILES string, as far as I know.
So something is amiss there. And certain atoms such as [Na] aren't
recognized. Also, formal charge is not recognized, for example [C+] doesn't
result in fewer H atoms.
C60's SMILES string didn't work.
So it's definitely not a perfect solution. But it's a start.
We need to do more testing on this, of course.
Bob
--
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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