This is a cool quote from the paper, "Parsing TEX into Mathematics":
We agree that there are good reasons for trying to come up with a
single universal grammar and semantics for mathematics notation, but
we are concerned that any efforts to find a fixed and complete
notation must founder on the shoals of ambiguity. Even granted some
oracle of disambiguation, it appears that total generality must
require fairly substantial extensibility and the ability to
incorporate context into interpretation. One simply cannot expect to
represent all past and especially all future mathematics with a fixed
set of notations. Therefore one must provide tools for extension that
are sufficiently "universal" for all further work.
Can you do painless TEX molecular modeling I wonder? I must google...