On Fri, Jan 22, 2021 at 9:01 AM Ivan Tubert-Brohman <
ivan.tubert-broh...@schrodinger.com> wrote:
> I think there was some confusion between left and right in the original
> message, but RDKit prefers the representation that preserves the octet at
> the expense of having more formal charges:
>
I think there was some confusion between left and right in the original
message, but RDKit prefers the representation that preserves the octet at
the expense of having more formal charges:
In [9]: mol = Chem.MolFromSmiles('O=I(=O)([O-])')
In [10]: Chem.MolToSmiles(mol)
Out[10]:
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
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
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