Re: [Jmol-users] SMILES Problem

[Robert H. <ha...@st...>]

Otis,

I got it -- very interesting -- two obscure bugs, both relating to cationic
aromatic nitrogen. Wow. Good find! Fixed for both Jmol 12.1.35 and 12.0.32.
Uploading http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

Jmol was generating an incorrect SMILES string for NAD+ both in the sense
that the nicotinamide ring should have been shown as aromatic and also that
the double bond / \ markings should not be there. This was due to the fact
that the aromatic ring contained a cationic nitrogen atom. We now have:

$ load $NAD
$ show smiles

NC1=O.c21=c[n+1]3=cc=c2.[C@H]43[C@H](O)[C@H](O)[C@H]5CO[P@](O)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 checks out now:

$ print {*}.find(smiles, script("show smiles"))

({0:71})


Bob


On Sat, Feb 12, 2011 at 9:49 PM, Otis Rothenberger <osr...@ch...>wrote:

> 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" <osr...@ch...>
> *Sent*: Saturday, February 12, 2011 3:54 PM
> *To*: jmo...@li...
> *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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-- 
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