diamin_enumerator.py

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


raw_smiles = ['NCCN']
smiles_list = ['NCCN']
rxn_smarts_list = ['[C:1][*:2][C:3]>>[C:1]1[*:2][C:3]1','[C:1][C:2]>>[C:1][C][C:2]']
molecules = []
mol = Chem.MolFromSmiles(smiles_list[0])
molecules.append(mol)

substitutions = 6

for i in range(substitutions):
    for smiles in islice(raw_smiles,i,len(raw_smiles)):
        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 raw_smiles:
                    raw_smiles.append(new_smiles)

for smiles in raw_smiles:
    try:
        mol = Chem.MolFromSmiles(smiles)
    except:
        continue
    if mol != None:
        smiles = Chem.MolToSmiles(Chem.MolFromSmiles(smiles))
        if smiles not in smiles_list:
            smiles_list.append(smiles)
            molecules.append(mol)

print len(smiles_list)