It's been a while since I've seen one of these, but could it be that you
either haven't imported rdkit.Chem (in Python) before calling the function
that returns the RDKit molecule or that your extension module is linked
against a different rdkit library than the rdkit extension module that
you're using?
-greg
On Sun, Jul 16, 2017 at 4:40 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:
>
> Hi,
>
> I'd like to bring to python a function that returns a list (or vector?) of
> RDKit molecules. But I am lost in boost::python.
>
> BOOST_PYTHON_MODULE(pyrogen) {
> def("extract_ligands_from_coords_file", coot::extract_ligands_from_coo
> rds_file);
> }
>
> boost::python::list
> coot::extract_ligands_from_coords_file(const std::string &file_name) {
>
> boost::python::list rdkit_mols_list;
> std::vector<RDKit::ROMol *> mols_vec = my_get_mols(file_name);
> for(unsigned int i=0; i<mols_vec.size(); i++) {
> rdkit_mols_list.append(mols_vec[i]);
> }
> return rdkit_mols_list;
> }
>
> When I try to use it:
>
> >>> m = pyrogen.extract_ligands_from_coords_mol('test.pdb')
> TypeError: No to_python (by-value) converter found for C++ type:
> RDKit::ROMol
>
> I am not sure what I should do (instead). At a guess, maybe I need to
> convert/wrap the mols_vec[i] before using it in append()? Please advise.
>
> Thanks,
>
> Paul.
>
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