[Rdkit-devel] Python vs C++ exceptions

[<gi...@gm...>]

While reading some SD molecules in python, I've got on the console
messages like:

[15:18:47] Explicit valence for atom # 0 N, 4, is greater than permitted
[15:18:47] ERROR: Could not sanitize molecule ending on line 48
[15:18:47] ERROR: Explicit valence for atom # 0 N, 4, is greater than permitted

Then my script breaks (rightfully) when accessing the structure which
is not loaded

Traceback (most recent call last):
  File "importdata.py", line 23, in <module>
    molecule = Chem.MolToSmiles(sup[0])
Boost.Python.ArgumentError: Python argument types in
    rdkit.Chem.rdmolfiles.MolToSmiles(NoneType)
did not match C++ signature:
    MolToSmiles(RDKit::ROMol {lvalue} mol, bool isomericSmiles=False,
bool kekuleSmiles=False, int rootedAtAtom=-1)


I've checked the C++ code and it seems the error comes from the
calcExplicitValence() method in Code/GraphMol/Atom.cpp

Now my question is: since the method throws MolSanitizeException(msg);
maybe there should be a way from python to catch it?

-- 
Gianluca Sforna

http://morefedora.blogspot.com
http://identi.ca/giallu - http://twitter.com/giallu