Hi Jason,
On Sat, Jun 2, 2018 at 3:41 PM Jason Biggs <[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
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