On Thu, Jun 11, 2020 at 4:04 PM Bennion, Brian <benni...@llnl.gov> wrote:
> Thank you for the explanation Greg. When the smiles strings are viewed I
> see the E designation for them two trans double bonds. What other double
> bond is missing ?
>
>
How do you view the SMILES strings? The way you are currently constructing
the molecule (without sanitization) means that the RDKit doesn't see the
stereochemistry information that's present in them.
Also, is it possible within RDKit to activate the fixedH layer in the inchi
> creation?
>
Sure, all of the InChI options can be provided just like you would on the
command line to the InChI executable:
In [54]: m1 = Chem.MolFromSmiles('CC1=CNC=N1')
In [55]: m2 = Chem.MolFromSmiles('CC1=CN=CN1')
In [58]: Chem.MolToInchi(m1,options='/FixedH')
Out[58]: 'InChI=1/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)/f/h5H'
In [59]: Chem.MolToInchi(m2,options='/FixedH')
Out[59]: 'InChI=1/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)/f/h6H'
In [60]: Chem.MolToInchi(m1)==Chem.MolToInchi(m2)
Out[60]: True
Best,
-greg
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