Specifying encoding in CheckPDBatoms.py

[isty2e]

In line 281:

with open('log.txt', 'a') as log:

This can be changed as the following for the sake of safety:

with open('log.txt', 'a', encoding="utf8") as log:

This should not raise any exception normally, but I have encountered an issue when trying to use it after processing with pdbfixer. When adding missing atoms with pdbfixer (which I have used to add missing main chain atoms), the OpenMM minimization step inside it somehow magically changes the encoding to ASCII (related issue). Then the en dash in L288 causes the following error:

  File ".../conda/envs/py310/lib/python3.10/site-packages/Pras_Server/CheckPDBatoms.py", line 283, in checkpdbAtoms
    log.write('When using files generated by this program in a publication,'
UnicodeEncodeError: 'ascii' codec can't encode character '\u2013' in position 349: ordinal not in range(128)

This is a problem in OpenMM, but without knowing how to fix it for now, I think it is a safe solution for now.

[osita-sunday-nnyigide]

Hello, I have effected the correction in line 281 of CheckPDBatoms.py.

Thank you very much!