Hello! I have a large database of molecules where I have, for each molecule:

1. A geometry (element, x, y, z)
2. a SMILES string

and I would like to get the associated Chem.Mol structure. Of course,
there's no guarantee that the ordering of the atoms in the Mol will match
up with the order in my geometry list. I'm trying to figure out the right
way of turning this geometry into a valid conformation for my Mol. Is there
any reliable way of doing this? I know that going strictly from
geometry->Mol can be challenging (OBabel has some reasonable support, as
does the python library xyz2mol ) but those tools seem to depend largely on
bond-length heuristics, and it seems if I have the SMILES string it should
be possible to do a better job.

Thanks,

...Eric
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