>
> 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 <shubbeymcb...@gmail.com>
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,&mol.getConformer());
> 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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