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gabriellareggiano / MEDIC

MEDIC (model error detection in cryo-EM)
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While processing 8faz_refined_r0001.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__' #9

Open tomgoddard opened 1 year ago

tomgoddard commented 1 year ago

Running detect_errors.py on standard PDB and EMDB file

detect_errors.py --pdb 8faz.pdb --map emd_28961.map --reso 2.3 -j 1

on macOS 13.3.1, Python 3.9, in Conda environment, complete details in Github issue #8 produces the following error

While processing 8faz_refined_r0001.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute 'mul'

Here is the full run output. See Github issue #8 for the full MEDIC install output.

$ detect_errors.py --pdb 8faz.pdb --map emd_28961.map --reso 2.3 -j 1
PyRosetta-4 2023 [Rosetta PyRosetta4.conda.m1.cxx11thread.serialization.python39.Release 2023.21+release.9b3660a893207250b5c6735d08f5a4dcd45633c5 2023-05-26T08:14:51] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
PyRosetta-4 2023 [Rosetta PyRosetta4.conda.m1.cxx11thread.serialization.python39.Release 2023.21+release.9b3660a893207250b5c6735d08f5a4dcd45633c5 2023-05-26T08:14:51] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
rho_calc 7331 of 7331
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rho_calc 7331 of 7331
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rho_calc 7331 of 7331
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rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
rho_calc 7331 of 7331
PyRosetta-4 2023 [Rosetta PyRosetta4.conda.m1.cxx11thread.serialization.python39.Release 2023.21+release.9b3660a893207250b5c6735d08f5a4dcd45633c5 2023-05-26T08:14:51] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
PyRosetta-4 2023 [Rosetta PyRosetta4.conda.m1.cxx11thread.serialization.python39.Release 2023.21+release.9b3660a893207250b5c6735d08f5a4dcd45633c5 2023-05-26T08:14:51] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
[ WARNING ] Resetting the global tracer options, which have already been set.
[ WARNING ] This will not affect Tracers which are already initialized.
While processing 8faz_refined_r0001.features.npz: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'
Feature file does not exist: 8faz_refined_r0001.features.npz
Traceback (most recent call last):
  File "/Users/goddard/miniconda3/envs/medic/bin/detect_errors.py", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/Users/goddard/ucsf/medic/MEDIC/detect_errors.py", line 194, in <module>
    commandline_main()
  File "/Users/goddard/ucsf/medic/MEDIC/detect_errors.py", line 161, in commandline_main
    errors = run_error_detection(input_pdb, args.map, args.reso, processes=args.processors, verbose=args.verbose)
  File "/Users/goddard/ucsf/medic/MEDIC/detect_errors.py", line 91, in run_error_detection
    dat = compile_data(pdbf, mapf, reso, verbose=verbose, processes=processes,
  File "/Users/goddard/ucsf/medic/MEDIC/detect_errors.py", line 38, in compile_data
    deepAccNet_scores = broken_DAN.calc_lddts(pdbf, WINDOW_LENGTH, 
  File "/Users/goddard/ucsf/medic/MEDIC/medic/broken_DAN.py", line 214, in calc_lddts
    main_lddts[i] = run_dan(p,k)
  File "/Users/goddard/ucsf/medic/MEDIC/medic/broken_DAN.py", line 158, in run_dan
    return lddt_cpu[query_sequence_indices[0]:query_sequence_indices[1]+1]
UnboundLocalError: local variable 'lddt_cpu' referenced before assignment
detect_errors.py --pdb 8faz.pdb --map emd_28961.map --reso 2.3 -j 1  480.18s user 9.04s system 100% cpu 8:04.82 total
(medic) $
ccgauvin94 commented 1 week ago

Having this issue as well.