It seems to me offhand RDKit's choice is analogous the way carboxylates are generally notated:
R-C(=O)O- rather than R-C+(O-)O- . Both are legitimate and in fact equivalent upon application of chemical knowledge, but do you prefer the second representation for carboxylates? -P. On Thu, Jan 21, 2021 at 2:06 PM Jason Biggs <jasondbi...@gmail.com> wrote: > The RDKit will always convert iodate from the form on the left, with an > expanded octet on iodine and a single negative charge, into the form on the > right with all single bonds and a charge on every atom (image here > https://i.stack.imgur.com/hq3St.png). This happens no matter how I > import the molecule, from SMILES or from a file. The only way to avoid it > is to skip sanitization, which I'd rather avoid. > > Is this the desired behavior? > > Thanks > Jason > > [image: image.png] > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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