Bob,
This is not a huge problem. For what we are doing, we depend mostly on
internal consistency of our SMILES library, and Jmol SMILES give us
that. The only place we run into this problem is with a link that
optimizes a model in the window by making a Resolver call.
Otis
Otis Rothenberger
chemagic.com
On 11/23/2010 7:39 AM, Robert Hanson wrote:
Sounds like a resolver issue. This is tricky, but not ambiguous.
C\2=C/C#C
indicates a trans connection ("down" to the other atom at connection
2; "up" to the triple bond)
More explicitly you would have:
o...@h]1[c@H]/2[C@@]34N[C@@H]5C/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C
but that first "/2" can be just "2" without any ambiguity.
Bob
On Mon, Nov 22, 2010 at 5:14 PM, Otis Rothenberger
<osrot...@chemagic.com <mailto:osrot...@chemagic.com>> wrote:
Bob,
I copied Markus with this problem because I don't know if it's a
Resolver of Jmol issue. I think it's a Resolver issue. While I
think the
backslash issue (Jmol to Resolver) is mostly under control, a general
slash issue seems to remain. By way of example:
o...@h]1[c@H]2[C@@]34N[C@@H]5C/C=C\C#C.C4CC1.C5CC3.C\2=C/C#C
In the above example, Resolver gets the .....C/C=C\..... right, but it
sees the ....C\2=C/.... (cis, I think) as ambiguous. This appears
to be
a general problem when either type of slash precedes a number.
As I type this, I am having a sense of deja vu. This might be an issue
that's already on the table.
Otis
--
Otis Rothenberger
chemagic.com <http://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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