Sorry guys for the late reply,
The code is available from here: https://gitlab.ebi.ac.uk/pdbe/ccdutils/blob/master/pdbeccdutils/core/depictions.py Hope you will find any use of it. The class you are after is DepictionValidator. Presently, I have a few changes on the development branch, which are soon to be merged to master (basically I started to calculate angle between two bonds if they share common atom because of this http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/CPT). Let me know if you would have any questions, or suggestions. Lukas From: Thomas Evangelidis <teva...@gmail.com> Date: Tuesday, 9 April 2019 at 15:43 To: Lukas Pravda <lpra...@ebi.ac.uk> Cc: Jose Manuel Gally <jose.manuel.ga...@gmail.com>, RDKIT mailing list <rdkit-discuss@lists.sourceforge.net> Subject: Re: [Rdkit-discuss] Which method to prefer for computing 2D coordinates 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 Prague, Czech Republic & CEITEC - Central European Institute of Technology Brno, Czech Republic email: teva...@gmail.com website: https://sites.google.com/site/thomasevangelidishomepage/
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