Re: [Rdkit-discuss] SDMolSupplier warning 2023.9.2

[Jan H. J. <ja...@bi...>]

 > I could not figure out how Rdkit is guessing it as 2D structure, as 
there is no such information in SDF.


Ah, but there is, just a little hidden :-). The source-and-timestamp 
line of each molfile in the SDF contains that information. The line is 
the second line of the molfile and you can find the 2D/3D tag as the 
last two characters of that line. An example:

:MOLFILE_BEGINS:

   Mol2Comp0618061807*2D*

   1  0  0  0  0  0  0  0  0  0999 V2000
    10.2967   -1.5283    0.0000 Ar  0  0  0  0  0  0  0  0  0  0 0  0
M  END
:MOLFILE_ENDS:

Cheers
-- Jan

On 2023-12-13 03:39, Mandar Kulkarni wrote:
> Hello,
>
> I am using RDKit 2023.9.2's  SDMolSupplier to read docked SDF files 
> (V2000 formats, suppl  = Chem.SDMolSupplier(sdf_file);) and getting a 
> warning as:
>
> Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D.
>
> I could not figure out how Rdkit is guessing it as 2D structure, as 
> there is no such information in SDF.
> Is there any more information need to provide SDMolSupplier to make it 
> understand it's a 3D molecule?
> I kindly look forward to hearing to suggestions.
> TIhanks in advance,
> Mandar Kulkarni