Bob,
We've been working on a Fisher configuration proof student model
exercise using Jmol compare to have students follow the identity of the
aldoses as they hack away at glucose from the top down. Consequently, we
have good aldose SMILES and coordinates in an internal database. From
this, I noticed that there were problems with the NIH return of aldoses.
In addition to your observations, I've noted that there is lack of
cyclic vs acyclic hexose return consistency. Also while "glucose" loads
alpha-D-glucose (and water), "alpha-D-glucose" does not load
alpha-D-glucose. I see it as alpha-D-talose. "Talose" (and "tallose" to
be certain) is not recognized by the server. As a reminder that CAS
numbers may also be used, the server does recognize talose's CAS
(2595-98-4). Unfortunately, it loads mannose!
From the NIH docs, I see that the server has 68 million names linked to
16 million unique structures. The aldose confusion suggests that some of
my former students had a hand in this component of the database! Still,
16 million unique structures! I'm glad that you suggested that I write
these folks.
You can check me on the alpha-D-talose. I've been known to show the same
aldose confusion as some of my students.
Otis
Otis Rothenberger
chemagic.com
On 8/24/2010 7:41 PM, Robert Hanson wrote:
oh my oh my oh my....
I've changed the SMILES server url in 12.1 to this NIH server because
it is so very fast and I am SO impressed -- superb conversion to 3D,
even for steroids. Stereochemistry is good, conformation is good.
Allene stereochemistry is missing, but incorrect SMILES bond
stereochemistry is accepted graciously.
And this means you can now use:
load $cyclohexane
load $benzene
load $3-methoxytoluene
load $cholesterol
load $aspirin
load $taxol
load $viagra
wow!
BUT...
You do have to be careful. I also notice that these two give the same
return:
load $allose
load $mannose
giving C(O)[...@h]1[c@@H](O)[C@@H](O)[C@@H](O)[...@h](O)O1
which I believe is L-talose!
and
load $glucose
loads alpha-D-glucose with an extra H2O off to the side!
So there are a few issues there. But still, this is great!
Thank you, Otis!
Bob
--
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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