`Model` object has no attribute decode in HelixFold
bernym12 opened this issue · comments
Stepped through this issue and I've found that <simtk.openmm.app.internal.pdbstructure.Model object at 0x7f424e6f6750> is passed in to this method within openmm that expects a file object. It is possible this is an openmm issue but this is currently blocking my usage of HelixFold. I have verified that I have the latest versions of both openmm and pdbfixer and also have recently pulled the updated setup_env file that made changes to the linking of openmm into simtek.
Traceback (most recent call last): File "run_helixfold.py", line 375, in <module> main(args) File "run_helixfold.py", line 280, in main random_seed=random_seed) File "run_helixfold.py", line 160, in predict_structure output_dir, 0, timings) File "/home/common/proj/FoldingBenchMarks/HelixFold/apps/protein_folding/helixfold/alphafold_paddle/model/model.py", line 283, in postprocess relaxed_pdb_str = relaxer.process(prot=prot)[0] File "/home/common/proj/FoldingBenchMarks/HelixFold/apps/protein_folding/helixfold/alphafold_paddle/relax/relax.py", line 63, in process max_outer_iterations=self._max_outer_iterations) File "/home/common/proj/FoldingBenchMarks/HelixFold/apps/protein_folding/helixfold/alphafold_paddle/relax/amber_minimize.py", line 939, in run_pipeline pdb_string = clean_protein(prot, checks=checks) File "/home/common/proj/FoldingBenchMarks/HelixFold/apps/protein_folding/helixfold/alphafold_paddle/relax/amber_minimize.py", line 187, in clean_protein as_file = openmm_app.PDBFile(pdb_structure) File "/home/grads/bernardm/.conda/envs/helixfold/lib/python3.7/site-packages/simtk/openmm/app/pdbfile.py", line 96, in __init__ pdb = PdbStructure(inputfile, load_all_models=True, extraParticleIdentifier=extraParticleIdentifier) File "/home/grads/bernardm/.conda/envs/helixfold/lib/python3.7/site-packages/openmm/app/internal/pdbstructure.py", line 153, in __init__ self._load(input_stream) File "/home/grads/bernardm/.conda/envs/helixfold/lib/python3.7/site-packages/openmm/app/internal/pdbstructure.py", line 161, in _load if not isinstance(pdb_line, str): AttributeError: 'Model' object has no attribute 'decode'
Hi there, thanks for the feedback. Could you try using openmm==7.5.1 as before or predicting the structure without relaxation?
Thank you for getting back to me so soon. That appears to have resolved my issue.