[Rdkit-discuss] warnings when exporting pandas tables with molecules to hdf

[Jose M. G. <jos...@gm...>]

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)