[Rdkit-discuss] DeleteSubstructs vs ReplaceSubstructs

[Popov, M. (Ext) <max...@no...>]

Dear RDKit users,

I am trying to remove a common substructure from a number of molecules (with AllChem.DeleteSubstructs). My problem is best illustrated by this short code:


from rdkit import Chem
from rdkit.Chem import AllChem

m=Chem.MolFromSmiles('C1(C2=NC=CC=C2)=CC=CC(C)=C1')
ss = Chem.MolFromSmiles('C1=CC=CC(C)=C1')
hyd=Chem.MolFromSmiles('[H]')
print("Substituting substructure with hydrogen")
frags = AllChem.ReplaceSubstructs(m, ss,hyd)
for frag in frags:
    print(Chem.MolToSmiles(frag))
print("\nDeleting substructure")
frag = AllChem.DeleteSubstructs(m, ss)
print(Chem.MolToSmiles(frag))

I create a toluene connected to pyridine and try to remove toluene.

When replacing toluene substructure with hydrogen (AllChem.ReplaceSubstructs), I receive two sets of results: pyridine (with explicit hydrogen) and single carbon plus single hydrogen plus aromatic open chain (what is left from pyridine after removing one ring atom).

When deleting the toluene substructure (AllChem.DeleteSubstructs), I receive just the open chain of ex-pyridine (corresponding to second set of the ReplaceSubstructs results).

Is there a way of directing DeleteSubstructs method to a specific variant (in this case, leaving pyridine as a ring seems to be logical).

Best regards,

Maxim