Re: [Rdkit-discuss] Some of the fingerprint bit rendering code not working

[Greg L. <gre...@gm...>]

Hi Jan,

This is almost certainly being caused by the issue described in #3796:
https://github.com/rdkit/rdkit/issues/3796

If you switch to SVG for the output or update to 2020.09.3 or newer things
should be fine.
I'll try and fix the underlying problem for the 2020.09.5 patch release.

-greg


On Fri, Feb 19, 2021 at 3:07 PM Jan Halborg Jensen <jhj...@ch...>
wrote:

> Some of the fingerprint bit rendering code in this tutorial is no longer
> working with 2020.09.01
> https://rdkit.blogspot.com/2018/10/using-new-fingerprint-bit-rendering-code.html
>
>
> Draw.DrawMorganBit(epinephrine,589,bi)
>
> works, but
>
> tpls = [(epinephrine,x,bi) for x in fp.GetOnBits()]
> Draw.DrawMorganBits(tpls[:12],molsPerRow=4,legends=[str(x) for x in
> fp.GetOnBits()][:12])
>
> throws the error
>
> AtomKekulizeException: non-ring atom 3 marked aromatic
>
> It can be “fixed" by
>
> Chem.Kekulize(epinephrine,clearAromaticFlags=True)
>
> But now one gets different fingerprints of course.
>
> Has the usage changed since 2018 or did a bug sneak in?
>
> Best regards, Jan
>
>
>
>
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