Hello Lukas, I am also struggling with 2D coordinate generation quite a long time as well as what criteria to use for choosing the most appropriate. Therefore, I would be very interest to use your code for 2D coordinate selection.
With best regards, Thomas PS: very nice notebook Jose. I also wanted to write something similar but never really found enough time to finish it. On Tue, 9 Apr 2019 at 16:31, Lukas Pravda <lpra...@ebi.ac.uk> wrote: > Hi Jose, > > As you have shown there is no single method which would be perfect for > everything. If you don’t care that much about speed, the possible solution > could be to compute coordinates with all three approaches and then simply > select the best conformer based on some criteria. > > The solution I use is to generate 2D coordinates using multiple approaches > and then I have a set of methods which computes number of bond collisions > and atoms being close to each other using KD-tree. Altogether this all is > expressed as penalty score, where the lower is better. > > Should you need any code, let me know. > > Lukas > > On 09/04/2019, 14:35, "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 > > > > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology <https://www.ceitec.eu/> Brno, Czech Republic email: teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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