Bob,
Some additional information to add some checks to this issue.
I pass the SMILES into Jmol Script from JavaScript, thus the // for / in
the DB. I thought I better check the console entry of SMILES on an example
that works. I was surprised by the results, but the NAD+ problem appears to
be a problem with the SMILES. Here's the test example:
With prostacyclin I2 in the Jmol window, I tried all variations of the
following, including changing "var z = {*}.find("SMILES",y);" to "var z =
x.find("SMILES",y);" With both finds, I think I tried every combination of
\\ and/or \. They all work! Do you have some type of auto correction for \
in the system?
var x =
"CCCCC[C@H](O)/C=C/[C@@H]1[C@@H]2[C@H]3O/C/4=C\CCCC(O)=O.C\42.[C@H](O)1C3";
var y =
"CCCCC[C@H](O)/C=C/[C@@H]1[C@@H]2[C@H]3O/C/4=C\CCCC(O)=O.C\42.[C@H](O)1C3";
var z = {*}.find("SMILES",y);
print @z
Anyway, the NAD+ problem remains. "var z = x.find("SMILES",y)" works,
including apparent \\ vs \ irrelevancy. The var "z = {*}.find("SMILES",y)"
with NAD+ in the window does not work.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Otis Rothenberger" <osrot...@chemagic.com>
Sent: Saturday, February 12, 2011 3:54 PM
To: jmol-users@lists.sourceforge.net
Subject: [Jmol-users] SMILES Problem
Bob,
For a model of NAD+, I have the following FIND problem.
SMILES strings are the same in both examples below.
THIS WORKS
var x =
"NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=
O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[
n]%11.[n]%12=c%10.O54.O98";var cks = x.find('SMILES',x);print @cks
THIS DOES NOT WORK
var x =
"NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=
O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[
n]%11.[n]%12=c%10.O54.O98";var cks = {*}.find('SMILES',x);print @cks
In the second case, "x" is pulled from a database via a query string query
to the DB.
If I examine "x" directly from the DB created JSON structure via:
alert(oChem.models[0].smiJ)
I get
NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=O
.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[n
]%11.[n]%12=c%10.O54.O98
which looks OK.
If I examine {*).find("SMILES") directly from the console, I get:
NC/1=O.C/2\1=C/[N+1]/3=C/C=C\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6=O
.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=[n
]%11.[n]%12=c%10.O54.O98
which also looks OK.
The actual DB text is escaped as follows:
NC/1=O.C/2\\1=C/[N+1]/3=C/C=C\\2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@]([O-1])6
=O.O6[P@](O)7=O.O7C[C@@H]8[C@@H](O)[C@@H](O)[C@@H]9[n]%10c%11=c%12c(N)=[n]c=
[n]%11.[n]%12=c%10.O54.O98
This is the single case in a 1630 record database that does not work. Do
you see anything in the above that might explain this? I'm stumped.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
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