Hi Greg,

That's perfect. Thank you!

Cheers,
Nick

On Fri, 24 Nov 2017, 16:40 Greg Landrum, <greg.land...@gmail.com> wrote:

> 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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