When I use the script to predict the His protonation states, it gives a TypeError (Python 3.9.4 on MacOS Catalina, 10.15.7):
## Executing Reduce to assign histidine protonation states
## Input PDB: e2aP2_1f3g-clean.pdb
Traceback (most recent call last):
File "/Users/jbibbe/software/haddock-tools/", line 143, in <module> fout.write(line+'\n')
TypeError: can't concat str to bytes

When I use Python 2.7.13, I get the following error:
Traceback (most recent call last):
File "/Users/jbibbe/software/haddock-tools/", line 137, in <module> hadded, process_error = run_molprobity(open_fhandle)
File "/Users/jbibbe/software/haddock-tools/", line 69, in run_molprobity tmp_file.write(cmd_stdin)
TypeError: expected a string or other character buffer object

I fixed this by adding a line at line 138:
hadded = hadded.decode()
Then it works in Python 3.9.4 again. I haven’t tried to fix it for Python 2.7.13.

Should I report this in GitHub some way? I don’t know how that works.

Thanks for looking into this.
I would suggest to open an issue in GitHub