On Tue, Nov 16, 2010 at 2:57 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> Bob,
>
> I'm trying to make your script work on a local (served) file. There are
> two file references in your script. I don't understand the second one,
> and I suspect my substitution (below) is causing problems:
>
> var s = "/*\t"+ i + "\t" + ept + " " + elements[ept] + "\t" + pt +
> "\t" + atoms + "\t" + x + "\t*/\tload ../models/octahedral.txt;
>
> rotate x 20;set echo top left; echo " + i + ";"
>
> What's going on in this variable definition?
>
> This is just information that I was printing and also sending to the log
file. Looks like a correct change to me.
The version I sent you depends upon the SMILES string returning @@ (which is
what that $SF6 does), but in general, you want the following to switch
chirality:
x = x.replace("@","@@").replace("@@@@", "@")
instead of
x = x.replace("@@","@")
Even that depends upon
Bob
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
> >
> >
>
>
>
>
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--
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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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
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