make_product_from_reactant.py

from rdkit import Chem
from rdkit.Chem import AllChem

#reactant_smiles = "C12=CC=CC=CC1CC=C2"
#reactant_smiles = "N#CC1(C#N)C2C=CC=CC=C2C=C1C3=CC=CC=C3"
reactant_smiles = "N#CC1(C#N)C2C=CC=C(C=CC=C3)C3=C2C=C1C4=CC=CC=C4"
reactant = Chem.MolFromSmiles(reactant_smiles)
print Chem.MolToSmiles(reactant)
Chem.Kekulize(reactant,clearAromaticFlags=True)

print Chem.MolToSmiles(reactant)

rxn_smarts = "[C:1]12=[C:2][C:3]=[C:4][C:5]=[C:6][C:7]1[C:8][C:9]=[C:10]2>>[C:8]=[C:9][C:10]=[C:1]1[C:2]=[C:3][C:4]=[C:5][C:6]=[C:7]1"
rxn = AllChem.ReactionFromSmarts(rxn_smarts)

product = rxn.RunReactants((reactant,))

print Chem.MolToSmiles(product[0][0])

molecules = []
molecules.append(reactant)
molecules.append(product[0][0])