Backbone standardization using RDKit could modify the nature of the functional groups

[josevlibera2010]

I am afraid that the standardization using RDKit when we only select the backbone for the analysis is affecting the nature of the bonds and producing non-logical results. I suggest you to create an index of functional groups/fragments for standard AAs, and only use RDKit for something else (giving the option of detailing the structure of unknown residues through a dict with resname:smiles). In this way, would be easier to provide ifps for backbone, sidechain, and else separately.