Looks like you guys have this one answered, but just for the sake of
completeness here's a bit of explanation.
the cleanUp() function currently makes the following modifications:
1) neutral 5 coordinate N with a double bond to O is converted to
the charge-separated form. This cleans up nitro groups and N oxides.
Examples: N(=O)=O -> -[N+](-[O-)=O and C1=CC=CN(=O)=C1 ->
C1=CC=C[N+]([O-])=C1
2) neutral 5 coordinate N with a triple bond to an N to
the charge-separated form, example: -N=N#N -> -N=[N+]=[N-]
3) perchlorate to the charge-separated form: Cl(=O)(=O)(=O)[O-] ->
[Cl+3]([O-])([O-])([O-])[O-]
The theme is to convert certain unambiguous "hypervalent" representations
into something where a Lewis dot structure can be drawn.
-greg
On Tue, Jan 28, 2014 at 4:41 PM, Michał Nowotka <[email protected]> wrote:
> Yes Mikołaj, thank you very much for your very helpful advice of
> reading the code. Excellent pointers!
>
> Cheers,
>
> Michał
>
> On Tue, Jan 28, 2014 at 3:20 PM, Mikolaj Kowalik <[email protected]> wrote:
> > 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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