Dear Pierluigi and Otis,OPSIN as a Java library and via its JSON api (e.g. http://opsin.ch.cam.ac.uk/opsin/benzene.json) can return standard or non-standard InChI.
The non-standard InChI OPSIN produces differs from StdInChI by including the fixed hydrogen layer (i.e. tautomer information). The reasoning for this is that IUPAC names are typically tautomer specific so at the time I initially added InChI support (quite a few years ago now) I thought it would be useful to retain this information. As InChI is hierarchical one can get an InChI with identical layers as StdInChI by stripping the fixed hydrogen layer (using the InChI toolkit or otherwise). Obviously the same is not true in reverse as StdInChI (intentionally) lacks tautomer information.
In practice utilisation of the layered nature of InChI is rare and virtually all sites with InChI now use StdInChI...so perhaps I should change opsin.ch.cam.ac.uk to display StdInChI in the GUI.
Standard InChIKey is used as this is the format of InChI key used in various internet databases hence allowing one to Google for a specific structure.
As pointed out earlier the NCI's chemical identifier resolver uses a copy of OPSIN internally....albeit I think the version is quite may now be quite out of date.
My main goal while developing OPSIN was to use it in automated text-mining. As a result while I aim to keep to an absolute minimum cases where the resultant structure is not in agreement with the name, I do tolerate minor errors in the input e.g. missing/extra spaces. As names like "5-chlorohexane" only have one plausible interpretation trying to flag these as "incorrect" was a low priority. I'm not actually aware of any existing name to structure algorithm that would reject that name. I think to solve the general case (e.g. 2-propylbutane ["incorrect"] vs 3-methylhexane [correct]) you'd have to written a fair chunk of a chemical structure to name algorithm to know that it was incorrect!
Daniel "For reasons that I do not fully understand, OPSIN returns InChI - not standard InChI. It does, however, return standard InChIKey! In general, I’d be very nervous about comparing InChI strings created by different resources."
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