How to use Python RDKit to remove stereochemistry, salts and molecules with undesirable atoms or groups?

Question

I am not a chemist, I come from a computer science background. Bung et al. [1] say in the Data preprocessing part that they used Python RDKit to remove stereochemistry, salts, and molecules with undesirable atoms or groups.

I was looking for a way to do so in the RDKit documentation but couldn't find any. Can anyone give a code example to achieve this?

Reference

1. Bung, N.; Krishnan, S. R.; Bulusu, G.; Roy, A. De Novo design of new chemical entities for SARS-CoV-2 using artificial intelligence. Future Med. Chem. 2021, 13 (6), 575–585. DOI: 10.4155/fmc-2020-0262. (Free Access)

Answer 1

Here's the code in Python

from rdkit import Chem
from rdkit.Chem.SaltRemover import SaltRemover

smiles = "Cl.C[C@@]1(O)CCCN1"
mol = Chem.MolFromSmiles( smiles )

print( Chem.MolToSmiles( mol  ) ) # mol
#>>> C[C@@]1(O)CCCN1.Cl

# remove salt
# remover = SaltRemover( defnData="[Cl,Br]" ) # define custom list, No spaces allowed
remover = SaltRemover() # use default saltremover
stripped = remover.StripMol( mol ) # strip salts
print( Chem.MolToSmiles( stripped ) ) #  mol w/o salt
#>>> C[C@@]1(O)CCCN1

# remove stereo
Chem.RemoveStereochemistry( stripped ) 
print( Chem.MolToSmiles( stripped ) ) # mol w/o salt & stereo
#>>> CC1(O)CCCN1

# check for specific atom
atomlist =  [ atom.GetAtomicNum() for atom in stripped.GetAtoms() ]
print( 8 in atomlist ) # check for atom for removal
#>>> True