On 12/14/2017 02:10 PM, Greg Landrum wrote:
> 
> On Thu, Dec 14, 2017 at 4:22 AM, Francois BERENGER
> <beren...@bioreg.kyushu-u.ac.jp <mailto: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-].

Where is this in the code?
I might have a look one day.

> 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.

I understand. I also guess unsanitized molecules would make some things
crash, just later.

> -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
>     >
>     >
>     >
>     >
>     >
>     
> ------------------------------------------------------------------------------
>     > Check out the vibrant tech community on one of the world's most
>     > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>     >
>     >
>     >
>     > _______________________________________________
>     > Rdkit-discuss mailing list
>     > Rdkit-discuss@lists.sourceforge.net
>     <mailto:Rdkit-discuss@lists.sourceforge.net>
>     > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>     <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
>     >
> 
>     
> ------------------------------------------------------------------------------
>     Check out the vibrant tech community on one of the world's most
>     engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>     _______________________________________________
>     Rdkit-discuss mailing list
>     Rdkit-discuss@lists.sourceforge.net
>     <mailto:Rdkit-discuss@lists.sourceforge.net>
>     https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>     <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
> 
> 

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Reply via email to