[Rdkit-discuss] Which method to prefer for computing 2D coordinates

[Jose Manuel Gally]

Dear all,

This might sound naive, but I want to compute 2D coordinates for a set 
of molecules.

For now I am considering the 3 methods below [1].

I was wondering if there was any recommendation to use one method over 
another in some cases?

For instance, very large rings are not displayed round for CoordGen but 
sometimes this method performs worse than the default (AllChem).

Computational time is not really an issue here as I generate those 
coordinates on the fly for a very small set of compounds.

Here is a gist with a few examples: 
https://gist.github.com/jose-manuel/0f2a5e8eae8bf2a72c0faad7f2f2a263

Thanks in advance, any suggestion is welcome!

Cheers,
Jose Manuel

[1] Methods:

1) rdkit.AllChem.Compute2dCoors (equivqlent to 
rdkit.Chem.rdDepictor.Compute2DCoords)
2) rdkit.Avalon.pyAvalonTools.Generate2DCoords
3) rdkit.Chem.rdCoordGen.AddCoords + rescale





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