PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
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run.single pdbfile argument ignored #82
Closed
IAlibay closed 4 years ago
Expected
Passing a file and some arguments to
run.single
should work:i.e.
Actual behaviour
The above worked in 3.1, however moving to 3.2 this leads to a
SystemExit
caused by agparse.Causes
From what I can tell, the following are causing this behaviour:
1) single calls loadOptions whose argparse call expects an
input_pdb
entry.2) pdbfile is overwritten by the return value of options.filenames.pop(0)
https://github.com/jensengroup/propka/blob/01debbf63dd51a7edac38e18d96b406abd532351/propka/run.py#L59
Possible fix
One quick fix here would be to switch single to have a behaviour similar to what is done in: https://github.com/jensengroup/propka/blob/01debbf63dd51a7edac38e18d96b406abd532351/tests/test_basic_regression.py#L60-L84