Here's a reply from Nic Zonta, the coordgen author: As for suggestions, I’d say that the strength of coordgen at the moment is in macrocycles handling, so if for instance E/Z stereo in a macrocycle is important I’d say that’s a good idea, and the weak point is intrinsically 3d systems and in performance, but the best way to get quality would still probably generate coordinates with all different approaches and coming up with some automated tests of the results to pick the best one
I don't have a whole lot to add to that. If I had to pick a single method, and the runtime was not important: I would go with coordgen in most circumstances. -greg On Tue, Apr 9, 2019 at 3:35 PM Jose Manuel Gally < jose.manuel.ga...@gmail.com> wrote: > 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 > > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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