you might be better off not storing the molecule RDkit objects themselves in the hdf file; but rather some other representation of the molecule. If you need 3D atom coordinates, you could call MolToMolBlock() on each of the rdkit mols, and then MolFromMolBlock later to regenerate them. If you don't need 3D atom coordinates to get saved, SMILES strings would work well.
PyTables is expecting each entry to be something like an 'int', 'string', 'float64', etc. So the RDKit mol object is a fairly odd data structure for that library; and it's just warning you that it will have to use Python's `pickle` module to serialize it. On Fri, Feb 15, 2019 at 6:35 AM Jose Manuel Gally < jose.manuel.ga...@gmail.com> wrote: > Hi all, > > I am working on some molecules in a pandas DataFrame and have to export > them to a hdf file. > > This works just fine but I get a warning about Performance due to mixed > types. (1) > > Why are RDKIT Mol objects causing this warning in the first place? Am I > doing something wrong? > > Please find attached a small notebook with an example. > > For now I set the type of hdf to 'table', but I'm unsure this is the > best work-around. > > Also, invoking pytest with --disable-warnings flag removes the message > but the warning itself remains. > > Thanks in advance for any hindsight! > > Cheers, > Jose Manuel > > (1) PerformanceWarning: > your performance may suffer as PyTables will pickle object types that it > cannot > map directly to c-types [inferred_type->mixed,key->values] [items->None] > > return pytables.to_hdf(path_or_buf, key, self, **kwargs) > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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