Ah, HA! Found it. It was in the SMILES reader translating indicated
stereochemistry to actual 3D positions when a new component mark "." was
followed by a stereochemistry indicator with H, "[...@h]", which was followed
immediately with the SECOND ring bond connection number. Wow. That's
obscure. One little line in the code.... Amazing. Good test, Otis!
version=12.1.22_dev
# bug fix: SMILES matching string with "....@h]1" reads stereochemistry
incorrectly
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
On Thu, Nov 11, 2010 at 10:27 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
> 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.
>>
>>
>
>
>
> --
> 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
>
--
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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