Re: [Rdkit-discuss] Question about WedgeMolBonds

[Peter S. Shenkin]

(or by means of an optional argument :-) )

-P.
Sent from a cell phone. Please forgive brvty and m1St@kes.

On Feb 26, 2017 00:36, "Greg Landrum"  wrote:

>
>
> On Sat, Feb 25, 2017 at 7:23 PM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>> Is there something that the compute2DCoords() is doing that makes it a
>>> dependency for WedgeMolBonds()
>>
>>
>> Yes, calculating 2D coordinates. Look at these two molecules, they are
>> the same but the atoms have been positioned differently in 2D and hence the
>> wedging needs to be different. Therefore you need 2D coordinates before you
>> can (re)assign wedges.
>> [image: Inline images 3]
>>
>
> John is exactly right here.
>
>
>> In truth since the two (2D layout and wedging) are dependant I'd probably
>> make the layout call the wedging automatically
>>
>
> Not a bad idea, but the RDKit doesn't do it since you don't always need
> the bond wedging information.
>
> -greg
>
>
> 
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Re: [Rdkit-discuss] Question about WedgeMolBonds

[John Mayfield]

>
> Is there something that the compute2DCoords() is doing that makes it a
> dependency for WedgeMolBonds()


Yes, calculating 2D coordinates. Look at these two molecules, they are the
same but the atoms have been positioned differently in 2D and hence the
wedging needs to be different. Therefore you need 2D coordinates before you
can (re)assign wedges.
[image: Inline images 3]
In truth since the two (2D layout and wedging) are dependant I'd probably
make the layout call the wedging automatically

John

On 25 February 2017 at 03:39, Shubbey McBean 
wrote:

> Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations,
> roughly:
>
>   // ... read in 3D mol
>   assignChiralTypesFrom3D(mol);
>   assignStereochemistry(mol,true,true);
>   WedgeMolBonds(mol,());
>   compute2DCoords(...)
>
> However, this does not produce an accurate result.  In order to "fix"
> this, I need to reverse the last two calls (calling the 3D->2D _before_
> WedgeMolBonds). This seems counter-intuitive to me.  Is there something
> that the compute2DCoords() is doing that makes it a dependency for
> WedgeMolBonds()?  Or am I going about this the wrong way?  The specifics of
> my situation make it preferable to order things as stated, but it's not a
> deal-breaker.  Mostly I am just a bit stuck as to what is going on here.
>
> Thanks!
>
>
>
> 
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[Rdkit-discuss] Question about WedgeMolBonds

[Shubbey McBean]

Hi, I am using WedgeMolBonds() to label converted 3D->2D conformations,
roughly:

  // ... read in 3D mol
  assignChiralTypesFrom3D(mol);
  assignStereochemistry(mol,true,true);
  WedgeMolBonds(mol,());
  compute2DCoords(...)

However, this does not produce an accurate result.  In order to "fix" this,
I need to reverse the last two calls (calling the 3D->2D _before_
WedgeMolBonds). This seems counter-intuitive to me.  Is there something
that the compute2DCoords() is doing that makes it a dependency for
WedgeMolBonds()?  Or am I going about this the wrong way?  The specifics of
my situation make it preferable to order things as stated, but it's not a
deal-breaker.  Mostly I am just a bit stuck as to what is going on here.

Thanks!
--
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