A TypeError of one function in chemutils.py

[limaosen0]

Dear Wengong:

I test some functions in your code to learn some functions of Rdkit, and I met one TypeError which cannot be solved by myself.

The run function is in chemutils.py:

def get_clique_mol(mol, atoms):
smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)
new_mol = Chem.MolFromSmiles(smiles, sanitize=False)
new_mol = copy_edit_mol(new_mol).GetMol()
new_mol = sanitize(new_mol) #We assume this is not None
return new_mol

The line is 'smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)'

---

TypeError Traceback (most recent call last)
in ()
----> 1 new_mol2 = chu.get_clique_mol(mol,atoms)

/DATA3_DB7/data/msli/graph_net/MolGAN/chemutils.pyc in get_clique_mol(mol, atoms)
67 def get_clique_mol(mol, atoms):
68
---> 69 smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)
70 new_mol = Chem.MolFromSmiles(smiles, sanitize=False)
71 new_mol = copy_edit_mol(new_mol).GetMol()

TypeError: No registered converter was able to produce a C++ rvalue of type int from this Python object of type Atom.

I believe that it is not your mistake, but I am a new learner of RDkit, please forgive me and help me.
Thank you very much!