On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER <
beren...@bioreg.kyushu-u.ac.jp> wrote:
> On 12/14/2017 05:15 AM, Sundar wrote:
> > Hi RDkit users,
> >
> > I encounter following sanitize issue while I was trying to load an SD
> > file using
> > Chem.SDMolSupplier('lig.sdf')
> >
> > Explicit valence for atom # 16 N, 4, is greater than permitted
> > ERROR: Could not sanitize molecule ending on line 3145
>
> I also encounter this exact error sometimes.
>
> Is there a way to tell rdkit to automatically correct this atom type?
>
The code currently only automatically corrects cases where it's really,
really obvious what the correction should be, like C-N(=O)=O ->
C-[N+](=O)[O-].
If there are additional commonly "misdrawn" functional groups, it would be
straightforward to add them
> I guess that sanitization failure means the molecule
> goes to the trash, which is terrible when there are so few molecules to
> learn from.
>
The philosophy taken in the RDKit is that it's better to have a bad
structure be rejected than it is to try and learn from it.
If you disagree with this, it is pretty easy to switch off the sanitization
checks and keep the bad molecules.
-greg
>
> > The molecule RDkit complains about has a charged N atom.
> > How do I sanitize it to fix these errors without losing its charge and
> > 3D coordinates?
> > Or how to disregard all these errors and get all the molecules read with
> > nothing missing?
> >
> > Thanks,
> > Sundar
> >
> >
> >
> >
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