It's not a limit in *parsing*. It's a limit in *writing* the SMILES. Open Babel 
will read in any length SMILES. At the moment, it stops before exporting a 
molecule > 1000 atoms.

Since there's interest, I just committed a patch to the github "master" to 
remove this limit. Please give me feedback.
http://github.com/openbabel/openbabel

As for InChI, any limit isn't on our side. The InChI code is a mess, so you're 
better off asking the InChI Trust (IUPAC) what the problem is.

-Geoff
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