Hi,
the core of the coordgen method is based on this paper
https://pubs.acs.org/doi/abs/10.1021/ci050550m
<https://pubs.acs.org/doi/abs/10.1021/ci050550m>
> On 2 Jun 2018, at 15:59, Greg Landrum <[email protected]> wrote:
>
> Hi Jason,
>
> On Sat, Jun 2, 2018 at 3:41 PM Jason Biggs <[email protected]
> <mailto:[email protected]>> wrote:
>
> This would be a question for both Greg and Nicola: What would be good words
> to describe the layout methods used by coordgen vs rdkit? I want to have an
> option for the user, Molecule[ <arguments>, DiagramLayout -> "MethodName"],
> but just using "RDKit" and "CoordGen" isn't right because it doesn't describe
> the underlying algorithm, just the library that implements them.
>
> Would it be wrong to call the rdkit method "DistanceGeometry"? What is the
> main distinction between the two methods?
>
> The RDKit uses distance geometry for 3D conformations. For 2D coordinates
> it's using an internal algorithm that hasn't really been described anywhere.
> I think it's fine to call it the "RDKit depiction algorithm" or "RDKit layout
> algorithm" if you prefer.
>
> -greg
>
> <PastedGraphic-2.tiff><image.png>
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