Regarding using JSON as a new file format...
This discussion has focussed on the syntax of JSON, but completely
overlooks the real problem with ALL chemical file formats: how do you
handle all of the cases where a simple connection-table ("ball and stick")
doesn't capture reality? Things like aromaticity, tautomers,
organo-metallic bonds, boron-hydrogen cages, distributed bonds (ferrocenes
and the like) ... these are the problems.
If we could solve these problems, it wouldn't much matter which file format
we picked ... they'd all be equivalent and sufficient. Without solving
these problems, a new file format doesn't really matter very much. All it
does is make another parser with yet-another-interpretation of these hard
problems.
If JSON is a need, I suggest that you embed an existing chemical format
(see my previous note that uses SMILES) into a JSON object.
Craig
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