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Specifying residue ranges does not work for TrueMultimer "quick mode" #463

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jkosinski opened this issue Nov 21, 2024 · 0 comments
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@jkosinski
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I am getting the following error when trying to run the TrueMultimer "quick mode"

Traceback (most recent call last):
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/bin/run_structure_prediction.py", line 283, in <module>
    app.run(main)
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/lib/python3.11/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
             ^^^^^^^^^^
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/bin/run_structure_prediction.py", line 267, in main
    object_to_model, flags_dict, postprocess_flags, output_dir = pre_modelling_setup(interactors, FLAGS, output_dir = FLAGS.output_directory[index])
                                                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/bin/run_structure_prediction.py", line 184, in pre_modelling_setup
    object_to_model = MultimericObject(
                      ^^^^^^^^^^^^^^^^^
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/lib/python3.11/site-packages/alphapulldown/objects.py", line 472, in __init__
    self.create_multimeric_template_features()
  File "/g/kosinski/kosinski/software/envs/AlphaPulldown2betaNoAlphaLink/lib/python3.11/site-packages/alphapulldown/objects.py", line 569, in create_multimeric_template_features
    curr_monomer = self.monomers_mapping[monomer_name]
                   ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
KeyError: 'P04051'

for a complex like this:

P32349;P32910;P17890;P47076;P35718;P04051,1-550,872-927,1083-1139,1317-1560;P22276,1028-1149;P20434

Maybe this is because monomer_name is P04051 while the key in self.monomers_mapping is P04051,1-550,872-927,1083-1139,1317-1560

@jkosinski jkosinski added the bug Something isn't working label Nov 21, 2024
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