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 >
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