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.
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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!
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)