Re: [Rdkit-discuss] Different 3D descriptors depending on mol reading method

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 wrote: > Hi Greg, > > Including the randomSeed argument in all instances didn't change the > situation: >

Re: [Rdkit-discuss] Different 3D descriptors depending on mol reading method

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

Re: [Rdkit-discuss] Different 3D descriptors depending on mol reading method

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