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
