Bob,
That's clearly my mistake. A lot of the kekule aromatic entries in my
database came from JME, and I hand edited JME's upper case aromatic "C"
to lower case aromatic "c" for Jmol comparison. I clearly hand edited a
non-aromatic here. I'll check the isoprene again to see if there is
anything obvious.
Otis
Otis Rothenberger
chemagic.com
On 11/9/2010 12:35 PM, Robert Hanson wrote:
what's with the lower case (c=O)?
On Tue, Nov 9, 2010 at 11:03 AM, Otis Rothenberger
<[email protected] <mailto:[email protected]>> wrote:
Bob,
I think the following are two correct SMILES for 3-methyl
benzaldehyde:
c12=cc=cc(C)=c2.C1=O
c1(c=O)=cc=cc(C)=c1
With the first being generated by the current model window and the
second coming from a database, the following fails:
var cks = {*}.find('SMILES','c1(c=O)=cc=cc(C)=c1');echo @cks
The following, of course, does not fail:
var cks = {*}.find('SMILES','c12=cc=cc(C)=c2.C1=O');echo @cks
Without giving the data here, I have a reciprocal case (failure) with
isoprene - i.e. the dot notation is in the database and the current
model is producing a non-dot SMILES.
Is this just a fact of life with the dot notation, or is this a
correctable problem? By the way, Resolver reads all of this just fine.
My problem is making my local database check the model in the window
using Jmol script.
One more question, probably naive: With the FIND that worked above, I
was surprised by the result:
{0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15}
I take it that the elements and the "=" are being matched (found)
- not
the dot??
Otis
--
Otis Rothenberger
chemagic.com <http://chemagic.com>
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Robert M. Hanson
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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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