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?
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 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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