Bob,
OK, I think I get it. To use log capability, I must use the signed applet.
It's about time I set up a signed applet test page anyway. It is,
indeed, a neat script.
Otis
Otis Rothenberger
chemagic.com
On 11/16/2010 8:38 AM, Robert Hanson wrote:
OK, OK.
Here's a neat script. -- A chiral octahedral compound generator!
It opens $SF6 -- from the NIH CACTVS server, and for 1000 cycles it
then randomly changes ligands, looking for errors in the algorithm by
matching the structure to the stereochemical SMILES that Jmol creates
for it. In addition, it switches chirality and checks to see if those
are the same. If not, it reports a line that can be used to load that
chiral compound for inspection. Logs to JmolLog_testSmiles.log
Requires Jmol 12.1.24_dev
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Bob
On Mon, Nov 15, 2010 at 11:53 PM, Robert Hanson <hans...@stolaf.edu
<mailto:hans...@stolaf.edu>> wrote:
Otis,
Sure enough -- I forgot about (all trans)-XA2B2C2 and trans-XA2B4.
You would think you wouldn't need @ or @@ for cases like that, but
you do. Even though @ and @@ are the same! Because they still
represent specific stereoisomers, and that is the only way with
SMILES that you can specify the ordering of the bonds around the
central atom. As far as I can tell, the only cases you do NOT need
@ for are XA6, XA5B, and XA5. Even though it is not necessary for
XA5B, it's too much of a trouble to figure out that is what it is,
so I'm just letting Jmol indicate @ for XA5B as well. At least for
now.
Wow, this is really going to be something when the bugs are worked
out! I'll bet you anything this has never been done before.
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.jar
should take care of that. Please check. Uploading now...
--
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
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today
http://p.sf.net/sfu/msIE9-sfdev2dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
