On Thu, Nov 11, 2010 at 7:37 PM, Otis Rothenberger <osrot...@chemagic.com>wrote:
> Bob is the master of Jmol SMILES, so I'll direct the second question to
> him.
>
> The SMILES on these compounds present another problem in Jmol. By way of
> example, if we construct an unconnected ferrocene in SPARTAN and then
> edit the molfile connection table so that the cyclopentadienyl anion
> carbons are assigned "aromatic" and the coordinate bonds to iron are
> assigned as type 8 ("any", evidently interpreted by Jmol as partial ),
> then we get the following SMILES from Jmol:
>
> [...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H]16[C@
> @H]5[C@@h]...@h]23
>
>
looks like ferrocene to me.... ;)
> The NIH Resolver reads this and returns evidence that it understands the
> bond connections - correctly connected 2D molfile and correctly
> connected GIF image. This appears to be a correct SMILES for the
> ferrocene that we constructed. It appears that the SMILES is very
> confused about the geometry of the cylopentadienyl anion hydrogens, but
> the connections are correct.
>
>
I'll have to look at it this weekend. There's a bug I just fixed that Jmol
doesn't escape the % there. But when I fix that, I do get
ferrocene from:
load $...@h]12[fe]3456789%10[c@H]%11[C@@H]%10[C@@H]9[C@@h]...@h]%117.[c@H
]16[C@@H]5[C@@h]...@h]23
but you need to rotate each ring:
select atomno < 11; rotate x 90
select atomno > 11; rotate x 90
Unfortunately, Jmol does not seem to recognize what it created.
yes, it's fouling up the stereochemistry. Probably has to do with the fact
that the C, H, and adjacent C atoms are all in a plane. Should be fixable.
Could we just call it "resolver SMILES" and "Jmol SMILES". When you say
"unique SMILES" it makes it sound like there's something special there. It's
just the SMILES that the resolver generates. Unique to it, I guess....
Bob
> Help!
>
> 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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