Hello, I have this sdf:
example SciTegic06111912192D 2 0 0 0 0 0 999 V2000 2.4541 -4.8083 0.0000 Cd 0 1 3.9125 -4.8083 0.0000 Sb 0 7 M CHG 2 1 3 2 -3 M END $$$$ When I use this code: from rdkit import Chem sdfile = Chem.SDMolSupplier('example.sdf') print(sdfile[0]) smistring = Chem.MolToSmiles(sdfile[0]) print(smistring) molecule = Chem.MolFromSmiles(smistring) print(molecule) The result is: <rdkit.Chem.rdchem.Mol object at 0x7f5c93689030> [Cd+3].[SbH6-3] [12:53:33] Explicit valence for atom # 1 Sb, 9, is greater than permitted None My question is how can I save the molecule as a smiles string, in a way that it will be read as a molecule also in the future. Benny
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss