On Tue, 28 Jan 2014 12:22:34 +0000
Michał Nowotka <[email protected]> wrote:

> According to the documentation
> (http://www.rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#Cleanup):
> 
> "cleans up certain common bad functionalities in the molecule"
> 
> What are those 'certain common bad functionalities' that are being cleaned
> up?

Until Greg comes up with a more apt answer, I think you can find some
pointers by looking through comments of in $RDBASE/Code/GraphMol/MolOps.cpp.

Functions cleanUp() and nitrogenCleanUp() are defined at the beginning of the
source file.

Best,

-- 
Mikołaj Kowalik

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