The case that you have 3D information available for a molecule dataset is rare,
if you want it trustworthy it gets even worse than that. And what is the point
then to generate the configuration of a molecule first if you can not trust
that either?
-------------------------------------
| Markus Sitzmann
| markus.sitzm...@gmail.com
> On 13. Sep 2017, at 17:58, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote:
>
>> 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.
>
> Dima
>
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