make_reactants.py

from rdkit import Chem
from rdkit.Chem import AllChem
from itertools import islice

smiles_list = ['C12=CC=CC=CC1CC=C2']
#smiles_list = ['C1=CC2CC=CC2=c2ccccc2=C1']
rxn_smarts_list = ['[CX3,cX3;H1:1]~[CX3,cX3;H1:2]>>[c:1]1[c:2]cccc1']
molecules = []
mol = Chem.MolFromSmiles(smiles_list[0])
molecules.append(mol)

substitutions = 1

for i in range(substitutions):
    for smiles in islice(smiles_list,i,len(smiles_list)):
        mol = Chem.MolFromSmiles(smiles)

        for rxn_smarts in rxn_smarts_list:
            rxn = AllChem.ReactionFromSmarts(rxn_smarts)
            new_mols = rxn.RunReactants((mol,))

            for new_mol in new_mols:
                new_smiles = Chem.MolToSmiles(new_mol[0])
                if new_smiles not in smiles_list:
                    smiles_list.append(new_smiles)
                    molecules.append(new_mol[0])