Hi Jean-Marc,

The answer is in the error message, once you know how to read it, which
isn't really trivial:

On Wed, Dec 14, 2016 at 5:35 PM, Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:

> Traceback (most recent call last):
>    File "glmap.py", line 11, in <module>
>      matches = mol.GetSubstructMatches(skel)
> Boost.Python.ArgumentError: Python argument types in
>      Mol.GetSubstructMatches(Mol, str)
> did not match C++ signature:
>      GetSubstructMatches(class RDKit::ROMol self, class RDKit::ROMol
> query, bool uniquify=True, bool useChirality=False, bool
> useQueryQueryMatches=False, unsigned int maxMatches=1000)

It's telling you that you called Mol.GetSubstructMatches was called with a
Mol and a string  (the "Mol" is the object you're calling "mol" and the
string is the  object you are calling "skel"). It expects, however, to be
called with a Mol and a Mol.

If you convert skel into an RDKit molecule everything should work.

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