[Python] Why does ReplaceSubstructs() always replace the last C atom?

I'm trying to use ReplaceSubstructs() function to combine two SMILES string together by replacing a carbon (C) atom in the first molucule with second molecule. However, no matter what c_options I pick, the RDKit always replace the first or last C atom, and the indices of the atoms also seem to get shuffled.

Here is my code:

from rdkit import Chem

def combine_smile(smile1, smile2, c_options=1):
mol1 = Chem.MolFromSmiles(smile1) mol2 = Chem.MolFromSmiles(smile2)
if mol1 is None or mol2 is None:
raise ValueError("One or both SMILES strings are invalid.")

index_mol1 = mol_with_atom_index(mol1)

combined_mol = Chem.ReplaceSubstructs(index_mol1, Chem.MolFromSmarts("[CH3]"), mol2)[c_options]
combined_smiles = Chem.MolToSmiles(combined_mol)

print(combined_smiles)

def mol_with_atom_index( mol ):
atoms = mol.GetNumAtoms() for idx in range( atoms ): mol.GetAtomWithIdx( idx ).SetProp( 'molAtomMapNumber', str( mol.GetAtomWithIdx( idx ).GetIdx() ) )
return mol

if name == "main":
mol1_smiles = "CC(C)(C)Cl"
mol2_smiles = "CN(C)C"

combine_smile(mol1_smiles, mol2_smiles)


Output:

CN(C)C[C:1]([CH3:2])([CH3:3])[Cl:4] # for c_options=0
CN(C)C[C:1]([CH3:0])([CH3:3])[Cl:4] # for c_options=1
CN(C)C[C:1]([CH3:0])([CH3:2])[Cl:4] # for c_options=2


Desired Output:

CN(C)C[C:1]([CH3:2])([CH3:3])[Cl:4] # for c_options=0
[CH3:0][C:1](CN(C)C)([CH3:3])[Cl:4] # for c_options=1
[CH3:0][C:1]([CH3:2])(CN(C)C)[Cl:4] # for c_options=2

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