On 2017-09-13 10:17, Markus Sitzmann wrote:
Canonical SMILES are only a very rough approximation for "unique molecule" as they usually don't work well for tautomeric forms of compound.
InChI or Standard InChI is much better although also not perfect.

ALATIS I linked to above does impose a stable consistent ordering for everything including hydrogens. The downside is it's garbage in - garbage out: you need to start with a 3D structure, otherwise it has an option to addHs and gen3D but no guarantee it'll generate the one you want.


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