Hi Nick,

When you import IPythonConsole it monkey patches the substructure function
so that it saves info about the results when you do a substructure search
on a molecule.
The data member is called __sssAtoms, and if you delete that you should no
longer get the coloring:
Heres a bit of demo:

In [1]: from rdkit import Chem

In [2]: from rdkit.Chem.Draw import IPythonConsole

In [3]: m = Chem.MolFromSmiles('CCOC')

In [4]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
Out[4]: (1, 2)

In [5]: m.__sssAtoms
Out[5]: [1, 2]

In [7]: del m.__sssAtoms


You, of course, need to check that the data member is there.

If you're unlikely to want to see highlighting at all, it's easier to just
turn if off:

In [12]: IPythonConsole.highlightSubstructs=False

In [13]: m.GetSubstructMatch(Chem.MolFromSmiles('CO'))
Out[13]: (1, 2)

In [14]: m.__sssAtoms
Out[14]: []



I hope this helps,
-greg



On Thu, Nov 23, 2017 at 2:05 PM, Nicholas Firth <nfi...@evartech.co.uk>
wrote:

> Howdy RDKitters,
>
> Been a while since I used this list, so forgive me if my question is
> silly.
>
> I'm seeing some weird behaviour from drawing molecules. I've got some
> wrapper classes that I'm using to write some de novo design code, which
> involves fragmenting molecules, and I've obviously been fairly lax with my
> namespacing. Essentially when I fragment my molecule the first bond that is
> cut is highlighted when I draw the original molecule but the rest of the
> cuts aren't (because I reassign variables). There's an example of what I
> mean here <https://i.imgur.com/kvb3YyG.png> (https://i.imgur.com/
> kvb3YyG.png)
>
> I tried to ClearComputedProps on the molecule but it still highlights the
> bond, does anyone know of a way to clear this from the molecule so that it
> doesn't get drawn? I'm going to clear up my programming issues to stop this
> particular artefact, but it would definitely be helpful to understand this
> for the rest of my code.
>
> Cheers,
> Nick
>
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