[Rdkit-discuss] warnings when exporting pandas tables with molecules to hdf
Open-Source Cheminformatics and Machine Learning
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From: Jose M. G. <jos...@gm...> - 2019-02-15 13:33:57
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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) |