all_chiral.py

from rdkit import Chem
import itertools

smiles = 'CNCC[NH+](C)CC(F)C'

mol = Chem.MolFromSmiles(smiles)

N_atoms = mol.GetSubstructMatches(Chem.MolFromSmarts('N([*])[*]'))
chiral = Chem.FindMolChiralCenters(mol, includeUnassigned=True)

chiral_atoms = [item[0] for item in N_atoms] + [item[0] for item in chiral if item[1]=='?']
chiral_atoms = list(set(chiral_atoms))

chiral_tags = len(chiral_atoms)*[[Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW,Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW]]
    
chiral_products = list(itertools.product(*chiral_tags))

mol_list = []
smiles_list = []
for chirality in chiral_products:
  newmol = Chem.Mol(mol)
  for atom, chiral_tag in zip(chiral_atoms,chirality):
    newmol.GetAtomWithIdx(atom).SetChiralTag(chiral_tag)
  new_smiles = Chem.MolToSmiles(newmol, isomericSmiles=True) 
  if new_smiles not in smiles_list:
    mol_list.append(newmol)
    smiles_list.append(new_smiles)

for newmol in mol_list:
  print Chem.MolToSmiles(newmol, isomericSmiles=True)