However, 3.5 is not officially supported anymore so we could easily drop it from PROPKA 3.2.0, just needs changes in PR #61
cd /tmp
curl https://files.rcsb.org/download//2bem.pdb.gz | gzip -dc > 2bem.pdb
propka31 2bem.pdb
... and I get the following error
Traceback (most recent call last):
File "~/.virtualenvs/propka/lib/python3.5/site-packages/propka/input.py", line 27, in open_file_for_reading
file_ = open(input_file, 'rt')
TypeError: invalid file: PosixPath('2bem.pdb')
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "~/.virtualenvs/propka/bin/propka31", line 8, in <module>
sys.exit(main())
File "~/.virtualenvs/propka/lib/python3.5/site-packages/propka/run.py", line 21, in main
my_molecule = read_molecule_file(pdbfile, my_molecule)
File "~/.virtualenvs/propka/lib/python3.5/site-packages/propka/input.py", line 51, in read_molecule_file
input_path, mol_container.version.parameters, mol_container)
File "~/.virtualenvs/propka/lib/python3.5/site-packages/propka/input.py", line 288, in read_pdb
for (name, atom) in lines:
File "~/.virtualenvs/propka/lib/python3.5/site-packages/propka/input.py", line 127, in get_atom_lines_from_pdb
lines = open_file_for_reading(pdb_file).readlines()
File "~/.virtualenvs/propka/lib/python3.5/site-packages/propka/input.py", line 29, in open_file_for_reading
raise IOError('Cannot find file {0:s}'.format(input_file))
TypeError: non-empty format string passed to object.__format__