Very cool! :-) I'd be for having this in Open Babel. In fact, I think
you should also consider it as an output format. In Cinfony, I use the
CIR to return 1 or multiple names for a compound (could be controlled
by an output option), or the IUPAC name.
Regarding the specifics, I'm just wondering whether the format should
be renamed to include the word "web", so that it would alert the user
that the data will be sent across the web - a big "no no" in pharma.
Also, you may want to include a parameter in the HTTP request so that
Markus knows that it's Open Babel ("&requester=OpenBabel231" or so)
and can track it.
- Noel
On 7 December 2011 20:48, Chris Morley <c.mor...@gaseq.co.uk> wrote:
> 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
>
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