Definitely not set up for Fischer projections.

Calculate Hydrogens was just broken on my local copy where I was working on implementing sp3d and sp3d2 hybridization and {...}.shape ("tetrahedral", "trigonal planar", "T-shaped", etc.)

Bob

On Sun, Aug 29, 2010 at 1:25 PM, Otis Rothenberger <osrothen@chemagic.com> wrote:
Bob,

Sorry about the lack of specificity. Verbose not concise is my major writing flaw! The Fisher projections were definitely bond wedge, albeit two solid wedges per carbon as per the FP convention.

I'm using 12.1.7. calculate H seems OK there.


Otis
Otis Rothenberger
chemagic.com

On 8/29/2010 1:12 PM, Robert Hanson wrote:
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 <osrothen@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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phone: 507-786-3107


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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