[Rdkit-discuss] MolFromInchi with Amides

[Jeff v. S. <jef...@sf...>]

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