Re: [Rdkit-discuss] Stop bond highlights

2017-11-27 Thread Nicholas Firth 
Hi Greg,

That's perfect. Thank you!

Cheers,
Nick

On Fri, 24 Nov 2017, 16:40 Greg Landrum,  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 
> 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)
>>
>> 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
>>
>>
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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Re: [Rdkit-discuss] Stop bond highlights

2017-11-24 Thread Greg Landrum 
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 
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)
>
> 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
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
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[Rdkit-discuss] Stop bond highlights

2017-11-23 Thread Nicholas Firth 
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
)

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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss