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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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Bug with current version #85

Closed pierrepo closed 3 months ago

pierrepo commented 3 months ago

As of commit e816c72e31 we have the following issue:

$ python grodecoder.py --input data/examples/1BRS.gro 
2024-07-17 22:18:22.070 | INFO     | __main__:remove_hydrogene:750 - Found 146,910 atoms in data/examples/1BRS.gro
2024-07-17 22:18:22.070 | INFO     | __main__:remove_hydrogene:753 - Removing hydrogen atoms...
[...]
2024-07-17 22:18:57.107 | INFO     | __main__:extract_protein_sequence:1149 - Extracting protein sequence...
Traceback (most recent call last):
  File "/home/pierre/grodecoder/grodecoder.py", line 1710, in <module>
    main(
  File "/home/pierre/grodecoder/grodecoder.py", line 1585, in main
    elif is_nucleic_acid(graph):
         ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/pierre/grodecoder/grodecoder.py", line 1461, in is_nucleic_acid
    return len(set_key_amino_acid_resname.intersection(set_res_name_graph)) > 1
               ^^^^^^^^^^^^^^^^^^^^^^^^^^
NameError: name 'set_key_amino_acid_resname' is not defined. Did you mean: 'set_key_amino_acid_mda'?

Could you please have a look @KarinDuong ?