Reminded by a question on Blue Obelisk Exchange
(http://blueobelisk.shapado.com/questions/converting-from-compound-name-to-chemical-structure),
I have tweaked up some code to access the NIH Chemical Identifier
Resolver from an input format in OpenBabel. There must be doubts as to
whether this sort of thing should be in OpenBabel at all, so I'll use
opportunity to demonstrate (on Windows) that OpenBabel can be extended
by plugins without having to rebuild the code.
Download http://gaseq.co.uk/OB/formats_web.obf and paste it into the
OpenBabel folder - probably C:\Program Files (x86)\OpenBabel-2.3.1. (You
will probably be prompted to do this as an Administrator.)
On opening the GUI you should find the nam input format. You can enter
your names, etc. directly when the input box is yellow or you can use
the attached file with some examples close to my heart. The NIH resolver
uses OPSIN for systematic names, its own or ChemSpider's database for
trivial names, and will also accept InChIKeys. On the command line it
would be something like:
obabel ResolverExamples.nam -osmi
Other ways of accessing this web service are the web site
http://cactus.nci.nih.gov/chemical/structure and via Cinfony/Webel. This
OpenBabel format doesn't add much value over these except possibly for
multiple names.
The code should be cross-platform and incorporates the lightweight
HappyHTML rather than loading some big library. I don't know whether
this is the right way to go, so I have held off putting the source code
into OpenBabel, and await advice.
Chris
#Names in NIH
Nicorandil
Clopidogrel
Atorvastatin
Candesartan
#Systematic name
acetylsalicylic acid Aspirin
#InChIKey
VHYCDWMUTMEGQY-UHFFFAOYSA-N Bisoprolol
#Name in Chem-Spider
rapamycin
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