Bob,
I was under the impression that canonical SMILES would be the same from one
program to another, not just from the same program. I participated in the Fall
2015 OLCC on cheminformatics, and that’s what I remember us teaching the
students. So the distinction you are making is reasonable to me but a new idea.
It’s wonderful to hear that Jmol could convert the SMILES to InChI with such an
easy process. Can it also do InChIKey? The cheminformatics guys made a big
deal over that being better than InChI in the OLCC course.
Jennifer
Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
600 West Walnut Street
Danville, KY 40422
jennifer.muz...@centre.edu<mailto:jennifer.muz...@centre.edu>
http://web.centre.edu/muzyka
http://organicers.org
859-238-5413
fax 859-236-7925
On Jul 22, 2016, at 9:01 AM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
Hi, Jennifer.
"Canonical" SMILES just means that a given version of a given program will
always report out the same string for a compound. Key words there are "same
program" and "same version". So if you used an earlier version of a program to
create a database of strings to compare, then you probably need to run through
that set with any newer version of JSME and require users use that version.
In developing the SMILES capabilities of Jmol I decided not to even attempt
canonicalization. It has not been important for any application I have seen,
short of what you are doing -- database lookup. But for that you can use InChI
keys. Jmol can deliver those either from the browser using inchi.js or by
remote calls to the NCI Resolver.
If you have only 3000 compounds, you could set up a little 5-line script that
will run in Jmol.jar that will probably take 10 minutes to convert all SMILES
to InChI.
Bob
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