from rdkit import Chem
smiles_source = "smiles_list.smi"
grand_total = 0

# example pattern to identify and count:
functional_group = Chem.MolFromSmarts('[CH3]')  #  methyl group

# alternative examples:
#functional_group = Chem.MolFromSmarts('c1ccccn1')  # for a pyridine
#functional_group = Chem.MolFromSmarts('C1CCCCC1')  # for cyclohexane

with open(smiles_source, mode="r") as source_file:
    for index, line in enumerate(source_file, start=1):
        molecule = Chem.MolFromSmiles(line.strip())
        match = molecule.GetSubstructMatches(functional_group)

        print("{:3} matches in entry {:2}: {}.".format(
            len(match), index, line.strip()))

        grand_total += len(match)

print("\nIn total {} instances were identified.".format(grand_total))