Hello Eric, RDKit can assign bond orders from a smiles string to a PDB coordinate file.See chapter on 3D functionality in https://www.rdkit.org/docs/Cookbook.html. I assume that the coordinates need to have connectivity (but not bond order) information,which should not be too hard to compute as long as your coordinates are not too distorted. Hope this helps,Best wishes Maria Brandl On Thursday, 4 October 2018, 15:49:10 BST, Eric Jonas <[email protected]> wrote: 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_______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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