Dear all, I'm new to RDKit and cheminformatics in general. I'm using the latest RDKit libraries. Any suggestions you can offer would be kindly received.
Using the canonical SMILES C(C1C(C(C(C(O1)[S-])O)O)O)O.[Au+] of Aurothioglucose (Pubchem CID: 454937) I've generated a 3D structure using the python RDKit code: mol = Chem.MolFromSmiles(self.canonicalSMILES) mol3D = Chem.AddHs(mol) AllChem.EmbedMolecule(mol3D) AllChem.MMFFOptimizeMolecule(mol3D) Unfortunately, the mol3D representation has Au+ right in the middle of and in the plane of the benzene rings, too far from the negatively charged sulfur. I'm new at generating structures from SMILES. Are there any steps I'm missing that could help correct the placement of Au+? Thanks Anthony
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