I am looking for computational tools to get a score/measurement of goodness of fit/binding affinity/any other metric to present a binding between a protein and a peptide, preferably via Pymol.
I think you can use molecular docking tools like AutoDock or AutoDock Vina to calculate the binding affinity between a protein and a peptide. PyMOL can be used for visualization but not for calculating affinity. I hope this helps!