Grrr...
Isoprene was another hand editing issue. I had:
"smiJ": "C/C/1=C.C\1=C", "smiR": "CC(=C)C=C",
It should have been:
"smiJ": "C/C/1=C.C\\1=C", "smiR": "CC(=C)C=C",
The smiles strings are handed to Jmol script via JavaScript, so the
database has to store \\ for \.
I now have Jmol script automatically creating the correct database
entries, but I have 300 of these that predate this approach. I'm trying
to clean this up by hand.
SmiR is unique, but I want a Jmol SMILES reference in the database.
That's the reason for the two entries.
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
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