Very interesting, Otis. Yes, the \\ business is a real nuisance. That's
exactly what you have to do. (Of course, you could do it on the original
long two-molecule string instead.)
Fischer projections -- are those with stereochemistry or without?
By the way, I think I just broke "calculate hydrogens..."
Bob
On Sun, Aug 29, 2010 at 10:41 AM, Otis Rothenberger
<osrot...@chemagic.com>wrote:
> I don't think this is a documented capability, but it seems to work
> well. It also may not be unexpected, but it pleasantly surprised me. If
> you draw two structures in a JME editor that is hooked to Jmol, then the
> following compare works when you parse the two JME SMILES in the
> original JME SMILES string:
>
> var y = compare(smi1, smi2, 'ISOMER'); echo @y;
>
> smi1 and smi2 are simply the JME SMILES fed to Jmol Script via
> JavaScript variables. While there are issues (aromatics, maybe
> others(?)) cross comparing JME and Jmol SMILES, this internal JME/JME
> seems to work as well as Jmol/Jmol comparisons.
>
> My reason for this use of compare is related to an aldose SMILES mess
> (unrelated to Jmol) that I'm trying to clean up in our application. When
> I decided to generalize the approach, I only ran into one issue. In
> passing the JME SMILES from JavaScript to Jmol Script, I lost the "\"
> character in e/z alkenes. This was corrected by the following:
>
> jmolScript("smi1 = '" + smils[0].replace(/\\/g, '\\\\') + "';")
> jmolScript("smi2 = '" + smils[1].replace(/\\/g, '\\\\') + "';")
>
> smils[0] and smils[1] are the JavaScript array variables resulting from
> a split of the original JME SMILES in the "." character.
>
> While passing the actual models to Jmol is a comparison option, I found
> this direct approach allowed me to quickly check and edit structures
> with multiple chiral centers. In addition, UFF doesn't always get it
> right. Passing D-glucose from JME to Jmol (Fisher Projections) directly
> results in the rendering of D-galactose. The recently added NIH
> rendering does, however, get this correct.
>
> Related Issue:
> I'm going to check on this next point. I think the NIH molfile return on
> a name query is database directed (i.e. sometimes wrong). I think (and
> I'll check this) that the molfile return on a SMILES is computed.
>
> Otis
>
> --
> Otis Rothenberger
> chemagic.com
>
>
>
>
>
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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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