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 >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
