molprobity.py gives a TypeError

[jbibbe4]

The bug When I use the molprobity.py 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/molprobity.py", line 143, in <module> fout.write(line+'\n')
TypeError: can't concat str to bytes

This same error also happens in Python 3.7.10.

When I use Python 2.7.13, I get the following error:

Traceback (most recent call last):
File "/Users/jbibbe/software/haddock-tools/molprobity.py", line 137, in <module> hadded, process_error = run_molprobity(open_fhandle)
File "/Users/jbibbe/software/haddock-tools/molprobity.py", line 69, in run_molprobity tmp_file.write(cmd_stdin)
TypeError: expected a string or other character buffer object

Quick fix I fixed this for Python 3 by adding a line at line 138: hadded = hadded.decode() I haven’t tried to fix it for Python 2.7.13.

To Reproduce molprobity.py file.pdb

Expected behavior The script should return a list of the histidines in the protein structure, with their protonation states. Example:

## Executing Reduce to assign histidine protonation states
## Input PDB: 2J8S-renumbered-clean.pdb 
HIS ( 526 ) --> HISD
HIS ( 1042 )    --> HISD
HIS ( 2525 )    --> HISD
HIS ( 4526 )    --> HISD
HIS ( 338 ) --> HISE
HIS ( 505 ) --> HISE
HIS ( 525 ) --> HISE

Desktop:

• OS: MacOS Catalina (10.15.7)
• Python Version: 3.9.4, 3.7.10 and 2.7.13.

[JoaoRodrigues]

Good bug report, wrong repository :) @amjjbonvin @brianjimenez @rvhonorato?

[JoaoRodrigues]

@jbibbe4 you could try submitting a pull request with this change to haddocking/haddock-tools