How to do SMARTS reaction substructure mapping with RDKit

Question

I have been trying to use the RDKit's reaction substructure matching for some time. I want to match all reactions where a C-H bond is being broken to form a new C-C bond.

This is my code:

from rdkit.Chem import AllChem
from rdkit.Chem import rdChemReactions

c_h_template = AllChem.ReactionFromSmarts('[#6:1]-[#1]>>[#6:1]~[#6]')
x = AllChem.ReactionFromSmarts('C1=[CH:1]C=CC=C1.C[CH:2]=C.[Pd]>>C[C:2](=C)[CH:1]1=CC=CC=C1',useSmiles=True)
result = rdChemReactions.HasReactionSubstructMatch(x,c_h_template)
print(result) # always False

The result is always False, even though the reaction pattern should match.

The template, and the reaction are shown below (in jupyter notebook):

I am not sure what I am doing wrong here. I have read about SMARTS from daylight website, and I think the atom mapping is correct, and it should match. Any help is greatly appreciated.

Answer 1

I changed the c_h_template to also use smiles and the substructMatch returns True.

I am using rdkit version number: 2022.9.4

Here is the full reproducible code.

from rdkit.Chem import AllChem
from rdkit.Chem import rdChemReactions
c_h_template = AllChem.ReactionFromSmarts('[CH:1]>>[C:1]~[C:2]', useSmiles=True)
rxn = AllChem.ReactionFromSmarts('C1=[CH:1]-C=CC=C1.C[CH:2]=C.[Pd]>>C[C:2](=C)[CH:1]1=CC=CC=C1',useSmiles=True)

result = rdChemReactions.HasReactionSubstructMatch(x,c_h_template)
print(result) # returns True