Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?

[Greg Landrum]

My approach to this would depend on what you're trying to accomplish in the
end.

If you just want all the aromatic atoms you can just use "[a]". Unless you
do some extra work when you read in the molecules, any aromatic atom will
be in a ring. If you want to be really sure, you can do "[a;r]"
If you want all the aromatic bonds, it's "[a]:[a]"

If you want the rings themselves and you want to just use SMARTS, you have
to enumerate. Python makes getting the patterns pretty easy:

In [8]: patts = ["[a]:1"+":[a]"*i+":[a]:1" for i in range(3,22)] # 24 is
the max aromatic ring size

In [9]: patts[:3]
Out[9]:
['[a]:1:[a]:[a]:[a]:[a]:1',
 '[a]:1:[a]:[a]:[a]:[a]:[a]:1',
 '[a]:1:[a]:[a]:[a]:[a]:[a]:[a]:1']


The rest is just some calls to MolFromSmarts() and then
mol.GetSubstructMatches() for the molecules you want to test.

-greg



On Thu, Sep 21, 2017 at 3:56 AM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:

> Jason,
>
> Thanks!  I just thought of that for a 6-membered ring.  A 5-membered
> ring would be [a]1[a][a][a][a]1.
>
> Hmmm... I was thinking of using "r" to specify a ring, but I don't
> think
> that would be necessary.  Correct?
>
> Regards,
> Jim Metz
>
>
>
>
> -Original Message-
> From: Jason Biggs 
> To: James T. Metz 
> Cc: RDKit Discuss 
> Sent: Wed, Sep 20, 2017 8:36 pm
> Subject: Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?
>
> if you don't care what type of atom it is, just that it's aromatic, you
> should use [a],
>
> so [a]1[a][a][a][a][a]1 would match any 6-membered aromatic ring
>
> Jason Biggs
>
>
> On Wed, Sep 20, 2017 at 7:57 PM, James T. Metz via Rdkit-discuss <
> rdkit-discuss@lists.sourceforge.net> wrote:
>
> Hello,
>
> I would like to write a SMARTS that will match all of the individual
> atoms
> in all possible heteroaromatic rings.  Does anyone know of an elegant,
> compact way to do this?
>
> If one SMARTS will not work, I can concatenate SMARTS using
> a vertical pipe, "|", as I proposed in an earlier message in this forum.
>
> I am (perhaps) expecting SMARTS something like
> [c]1[c][n][c][c]1
> etc
> [c]1[c][c][c][c][c]1
> [c]1[c][n][c][c][c]1
> etc.
>
> Perhaps there is a very elegant way to specify the possible
> patterns.  I can't think of a way to do it, other than exhaustive
> enumeration.
>
> Any ideas?
>
> Regards,
> Jim Metz
>
>
>
>
>
> 
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Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?

[James T. Metz via Rdkit-discuss]

Jason,


Thanks!  I just thought of that for a 6-membered ring.  A 5-membered
ring would be [a]1[a][a][a][a]1.


Hmmm... I was thinking of using "r" to specify a ring, but I don't think

that would be necessary.  Correct?


Regards,

Jim Metz







-Original Message-
From: Jason Biggs 
To: James T. Metz 
Cc: RDKit Discuss 
Sent: Wed, Sep 20, 2017 8:36 pm
Subject: Re: [Rdkit-discuss] SMARTS for heteroaromatic rings?



if you don't care what type of atom it is, just that it's aromatic, you should 
use [a],


so [a]1[a][a][a][a][a]1 would match any 6-membered aromatic ring



Jason Biggs




On Wed, Sep 20, 2017 at 7:57 PM, James T. Metz via Rdkit-discuss 
 wrote:

Hello,


I would like to write a SMARTS that will match all of the individual atoms

in all possible heteroaromatic rings.  Does anyone know of an elegant, 
compact way to do this?


If one SMARTS will not work, I can concatenate SMARTS using 

a vertical pipe, "|", as I proposed in an earlier message in this forum.


I am (perhaps) expecting SMARTS something like

[c]1[c][n][c][c]1
etc
[c]1[c][c][c][c][c]1
[c]1[c][n][c][c][c]1
etc.


Perhaps there is a very elegant way to specify the possible

patterns.  I can't think of a way to do it, other than exhaustive
enumeration.  


Any ideas?



Regards,

Jim Metz










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[Rdkit-discuss] SMARTS for heteroaromatic rings?

[James T. Metz via Rdkit-discuss]

Hello,


I would like to write a SMARTS that will match all of the individual atoms

in all possible heteroaromatic rings.  Does anyone know of an elegant, 
compact way to do this?


If one SMARTS will not work, I can concatenate SMARTS using 

a vertical pipe, "|", as I proposed in an earlier message in this forum.


I am (perhaps) expecting SMARTS something like

[c]1[c][n][c][c]1
etc
[c]1[c][c][c][c][c]1
[c]1[c][n][c][c][c]1
etc.


Perhaps there is a very elegant way to specify the possible

patterns.  I can't think of a way to do it, other than exhaustive
enumeration.  


Any ideas?



Regards,

Jim Metz









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[Rdkit-discuss] Drawing options for the new drawing code to change background color

[Michał Nowotka]

Hi,

In the old drawing code it was possible to pass drawing options to the
MolToImage method.

Lookng at the C++ signature of the new DrawMolecule

DrawMolecule( (MolDraw2D)self, (Mol)mol, (object)highlightAtoms,
(object)highlightBonds [, (object)highlightAtomColors=None [,
(object)highlightBondColors=None [, (object)highlightAtomRadii=None [,
(int)confId=-1 [, (str)legend='']) -> None

I can see it's possible to change higlight colors but I need to be
able to change background color of the png image. I want to to be
transparent by default but I should be able to set it to any other
solid color, is that possible?

Cheers,
Michał

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