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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