Thanks, Diogo! Now the two files are essentially the same. Diogo Martins <diogo.stm...@gmail.com> escreveu no dia quarta, 15/06/2022 à(s) 20:53:
> Hi JSousa, > > Adding "removeHs=False" when reading from SDF should fix it. > > Best regards, > Diogo > > On Wed, 15 Jun 2022 at 01:24, J Sousa <jsousachemi...@gmail.com> wrote: > >> Hi Greg, >> >> Including the randomSeed argument in all instances didn't change the >> situation: >> AllChem.EmbedMolecule(mol,useRandomCoords=True,randomSeed=42) >> >> The descriptors are still different using the same randomSeed=42. And >> they are quite different (not just the normal fluctuations from different >> conformers). >> >> Best, >> J >> >> >> >> >> Greg Landrum <greg.land...@gmail.com> escreveu no dia quarta, 15/06/2022 >> à(s) 07:09: >> >>> Hi, >>> >>> I guess the differences you are seeing are arising because you have >>> different conformers of the molecule. >>> The conformer generation process in EmbedMolecule() uses a stochastic >>> procedure and if you want to be sure that you get the same results from >>> multiple runs you need to provide a random seed using the randomSeed >>> argument. >>> >>> Please give that a try and see if it helps, >>> -greg >>> >>> >>> >>> >>> On Tue, Jun 14, 2022 at 9:15 PM J Sousa <jsousachemi...@gmail.com> >>> wrote: >>> >>>> I'm trying RDKit to calculate 3D descriptors, but I get significant >>>> different descriptors if I read molecules from a SMILES file (and >>>> clean/optimize the 3D structure before calculating the descriptors) or if I >>>> read the SDF file obtained from exactly the same SMILES file using exactly >>>> the same code to optimize the structures. >>>> >>>> Scripts attached. >>>> >>>> Running smiltodesc_check.py produces descr_myfile.txt >>>> >>>> Running gen3D_check.py and then descr_from_sdf_check.py produces >>>> myfile_descr.txt >>>> >>>> But the two files are significantly different. >>>> >>>> Why aren't they the same? Which is wrong? >>>> >>>> JSousa >>>> _______________________________________________ >>>> 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 >> >
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