Dear RDKitters, I am struggling with working organometals and coordination complexes. with a small team, we are creating a series of recommendations to draw correctly organometals (catalyst, complexes, etc), so that we can use them in our chemoinformatics pipeline.
I know it is a horrible mess out there, but we are trying to achieve some consistency, rather than full correctness. I guess there is something with the accepted valence for Mg. Now the purpose of this is to have a smiles representation of these metal complexes that are not fragmented (with the dot) so that I keep the notion of bond where there is (or I believe) one for instance, for the edta complex this smiles works fine: [Na+].[Na+].[Mg++].[O-]C(=O)CN(CCN(CC([O-])=O)CC([O-])=O)CC([O-])=O but I would really distinguish the fact that there is a bond between the [O-]/N and the [Mg++ ] while there is none with the two [Na+] [image: image.png] I can read it in without sanitization, but it fails for everything I nato to do after with the molecules. in theory, dative bonds should not affect the valence of receiving atoms, right? any suggestion for reading in the enclosed v3000 molfile and keeping the bonding info? or sharing what you are doing with metals Thanks a lot in advance, kind regards Marco f1 = 'edta_case.mol' rdmol = Chem.MolFromMolFile(f1, sanitize=True) print(rdmol) Chem.MolToSmiles(rdmol) the rdmol is None in my case
edta_case.mol
Description: Binary data
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