For the isopeptide move of TAMC, I am not sure what is gained by requiring that the c-terminal residue of the flexible region come before the lysine residue. Having this requirement mean there has to be a test in the input filter to check that the requirement is satisfied. But if a test is already going to be run to check the input, why not include that test as input parsing, thereby reducing the input constraints? More specifically, what is gained by throwing an error rather than classifying each of the two input residues? This change would make it so user are required to remember one less thing.
For the isopeptide move of TAMC, I am not sure what is gained by requiring that the c-terminal residue of the flexible region come before the lysine residue. Having this requirement mean there has to be a test in the input filter to check that the requirement is satisfied. But if a test is already going to be run to check the input, why not include that test as input parsing, thereby reducing the input constraints? More specifically, what is gained by throwing an error rather than classifying each of the two input residues? This change would make it so user are required to remember one less thing.