Oh good grief...
I did a bit of googling: "python::object RDKit::ROMol" to see if I could find someone having
similar problems:
The first non-rdkit page was this:
ftp://ftp.ccp4.ac.uk/ccp4/7.0/unpacked/checkout/coot-0.8.2/lbg/qed-interface.cc
i.e... Just what I needed - hooray - it was the same problem!
But... Hmm... that's not surprising - it's code I had written 5 years ago and had forgotten
about (quite likely after having asked on the list a similar question :-)).
Cheers,
Paul.
On 16/07/2017 16:58, Greg Landrum wrote:
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
<mailto: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_coords_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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