Documentation for SMILES and SMARTS and Jmol bioSMILES/bioSMARTS are at
http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/smiles/package.html
I'll be the first to admit that is obscure! And I see the change of code
location in SourceForge broke that link in the documentation.
On Wed, Jan 22, 2014 at 4:16 AM, Mike Casey <[email protected]> wrote:
> The SMILES/SMARTS comparison in Jmol is great! As Bob says, you don’t
> have to worry about the origin of the SMILES strings (as long as they are
> valid, of course), Jmol will get the comparison right every time.
>
>
>
> One useful additional feature that is not mentioned in the interactive
> scripting documentation page, is that Jmol can ignore stereochemical
> information present in the strings using the /nostereo/ option, e.g.
>
>
>
> var result = Jmol.evaluate(myJSmol, '"' + studentSMILES +
> '".find("SMILES","/nostereo/' + correctSMILES + '")');
>
>
>
> where ‘studentSMILES’ and ‘correctSMILES’ are variables containing SMILES
> strings.
>
>
>
> The /nostereo/ option must be documented in one of Bob’s other
> demonstration pages, I can’t remember which one. It can be very useful
> because users sometimes use dashed/wedged bonds where they are not needed.
>
>
>
> Mike
>
>
>
> *From:* Robert Hanson [mailto:[email protected]]
> *Sent:* 22 January 2014 03:10
> *To:* [email protected]
> *Subject:* Re: [Jmol-users] Jmol 14.0.6 released
>
>
>
> The nice thing about Jmol's SMILES comparisons is that it is totally
> independent of what program was used to make the SMILES string in the first
> place. There is no need for a "canonical" string for our purposes (as there
> might be for database look-ups). Thus, it matches any matching structure,
> regardless of method of construction. And it can detect isomerism. So it's
> really a very convenient solution to this problem of checking answers.
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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