Hi Soren,
On Thu, Mar 19, 2015 at 5:03 PM, Soren Wacker <[email protected]> wrote:
>
> when generating molecules from smiles and drawing them sometimes show
> little red squares around certain atoms. I guess, this means that the
> connectivity is wrong. Is there a way to identify and potentially repair
> these molecules in rdkit?
>
>
The red squares are indicating pairs of atoms that are very close to each
other in the drawing. They are just there to let you know that there is a
risk of confusion.
-greg
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