Thanks, Greg-
>
>> What is the correct treatment of bond stereochemistry at centers for
>> which a hydrogen is required in order to specify the bond stereochemistry?
>> For example, an imine with a hydrogen substituent (trivial example,
>> F/C=N/[H]).
>>
>
> In these cases the H cannot be implicit. The double bond stereochemistry
> is always defined relative to atoms bonded to the double-bonded atoms (more
> complex to write than it actually is) and there’s just no way to do this if
> either of those atoms is implicit.
>
Ok. It sounds like the correct treatment for my schrodinger/rdkit
translation layer is to leave these hydrogens explicit.
> I notice that when I use the smiles constructor, or if I read from an SDF
>> file using the SDMolSupplier, the C=N bond in the example shown above is
>> not recognized as having stereochemistry. However, if I use
>> removeHydrogens=False in the SDMolSupplier, the bond *is* recognized as
>> Z.
>>
>
> I need to confirm it (I’m on my phone at the moment), but I think this is
> a bug: removeHs() should not remove atoms that determine stereochemistry.
> This might be something I can get fixed before the next release.
>
Reading from SMILES in RDKit also loses this hydrogen:
Python 3.6.2 (default, Sep 26 2017, 17:33:28)
[GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)] on darwin
>>> import rdkit.Chem
>>> rdkit.__version__
'2017.03.1'
>>> m = rdkit.Chem.MolFromSmiles('F/C=N/[H]')
>>> rdkit.Chem.MolToSmiles(m, isomericSmiles=True)
'N=CF'
Would it be useful for me to file a bug report?
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