Hi all,
I have some questions about how remit handles amides. For context, I am
working with a large set of molecules, many of which contain peptides. I
have been running into a problem with using rdkit, in that when I try to
load a molecule from the InChI, the wrong tautomer is loaded. As a
simple example consider acetamide:
"""
FromInchi = Chem.MolFromInchi('InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)')
print(rdMolDescriptors.CalcNumAmideBonds(FromInchi))
> 0
print(Chem.MolToSmiles(FromInchi))
> CC(=N)O
FromSmiles = Chem.MolFromSmiles('CC(=O)N')
print(rdMolDescriptors.CalcNumAmideBonds(FromInchi))
> 1
print(Chem.MolToSmiles(FromSmiles))
> CC(=N)O
"""
I realize that Standard InChi does not have a mechanism for
distinguishing between the two tautomers, so I am wondering why rdkit
considers the iminol to be a better representation? Also, there is
anyway to get the amide instead? (Without using MolVS)
Thanks,
Jeff
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