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pierrepo / grodecoder

GroDecoder extracts and identifies the molecular components of a structure file (PDB or GRO) issued from a molecular dynamics simulation.
https://grodecoder.streamlit.app/
BSD 3-Clause "New" or "Revised" License
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Error with `is_lipid()` function #42

Closed pierrepo closed 2 months ago

pierrepo commented 2 months ago

When running the script, one get an error related to the is_lipid() function:

$ python grodecoder.py --input data/examples/barstar.gro
2024-05-20 19:07:52.112 | SUCCESS  | __main__:main:1023 - Bond threshold: 2.04 Angstrom
2024-05-20 19:07:52.936 | INFO     | __main__:remove_hydrogene:657 - Found 18,699 atoms
2024-05-20 19:07:52.937 | INFO     | __main__:remove_hydrogene:660 - Removing H atoms...
2024-05-20 19:07:53.497 | INFO     | __main__:remove_hydrogene:668 - Found 6,479 atoms remaining
[...]
2024-05-20 19:08:07.591 | INFO     | __main__:extract_protein_sequence:894 - Extracting protein sequence...
Traceback (most recent call last):
  File "/home/pierre/grodecoder/grodecoder.git/grodecoder.py", line 1161, in <module>
    main(
  File "/home/pierre/grodecoder/grodecoder.git/grodecoder.py", line 1070, in main
    if is_lipid():
       ^^^^^^^^^^
TypeError: is_lipid() missing 1 required positional argument: 'graph'