I would suggest Cl everywhere. X is bad because it can not be used in smiles notation. At leaast mod does not like it:

mod.mod_.InputError: Error in graph loading from smiles string, 'X'.

Please get the updated, better named and all around fancier rules with:

$ scp -r prak10.bioinf.uni-leipzig.de:~/Documents/corerules/ ./

In there you find a runAsSets.py. Try a

$ cd corerules
$ mod -f runAsSets.py

and after that

$ atril summary/summary.pdf &

For more detail on how to use runAsSets, see documentation runAsSets

We do not really know but mod does not accept your rule. Please fix it. Also tell us about it, please. Come to PRAK05 or PRAK01.

All reactions are referred to by their respective reaction numbers as given here. Replace . with _ . If you want to try reactions 4.5 and 1.1 for example you would do something like

strat = (
    >> addSubset(inputgraphs)
    >> repeat[3](revive({r4_5, r1_1}))
)

For a more thorough description see