>> The SMILES parser has an explicit 1000-atom limit.  It's unfortunate.
> 
> So does the the inchi one -- I ran a couple more tests...

I'm willing to hear suggestions as far as SMILES and InChI limits, but I don't 
even know if a 1000-atom SMILES would be particularly useful. That, plus the 
potential for overwhelming the computer (i.e., the computer would "hang" while 
it computes the SMILES and InChI) were the reason for these particular limits.

I suspect it's quite similar for 2D depiction.

There are no hard limits in the core -- indeed, the atom index was changed to 
an unsigned integer, good for approx. 4 billion atoms. As I mentioned, I 
routinely convert, e.g. PDBs with tens of thousands of atoms to other formats.

Thoughts?
-Geoff 
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