Use RDKit normalization method on all residue definitions

[Yoshanuikabundi]

Is your feature request related to a problem?

And at some point in the future, consider shifting to NAGL's version

https://www.rdkit.org/docs/source/rdkit.Chem.MolStandardize.rdMolStandardize.html

Describe the solution you'd like

Describe alternatives you've considered

Additional context

[Yoshanuikabundi]

#62 points out that if this happens too early, it may stop residue definitions from matching PDBs with formal charges.