> So now with the replace function in python I can easily remove
> sterochem information from the molecule.
>
> smiles_corrected = smiles_broken.replace("@","")
>
> Once I remove the stereochemistry , libcheck does the right thing and
> gives me the right 3D coordinates.
This doesn't make chemical sense, though. If libcheck is operating on a SMILES
without stereochemistry, there's no way it can always give "the right 3D"
coordinates. If you have "N" stereo centers, the chance of a correct 3D
structure will be (0.5)^N.
I'd suggest using a different tool. For example, the upcoming Open Babel 2.3
will handle 3D coordinate generation while ensuring stereochemistry.
But you don't have to use OB -- I'm just saying that your 3D coordinates won't
respect stereo with your approach.
-Geoff
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