You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Traceback (most recent call last):
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/prefect/engine/task_runner.py", line 876, in get_task_run_state
value = prefect.utilities.executors.run_task_with_timeout(
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/prefect/utilities/executors.py", line 467, in run_task_with_timeout
return task.run(*args, **kwargs) # type: ignore
File "/home/migwell/Programming/DriveGenePipe/driverpipe/arpeggio_tasks.py", line 23, in arpeggio
return df.assign(arpeggio = df.apply(_row, axis=1))
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/pandas/core/frame.py", line 8833, in apply
return op.apply().__finalize__(self, method="apply")
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/pandas/core/apply.py", line 727, in apply
return self.apply_standard()
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/pandas/core/apply.py", line 851, in apply_standard
results, res_index = self.apply_series_generator()
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/pandas/core/apply.py", line 867, in apply_series_generator
results[i] = self.f(v)
File "/home/migwell/Programming/DriveGenePipe/driverpipe/arpeggio_tasks.py", line 17, in _row
i_complex = InteractionComplex(temp.name)
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/arpeggio/core/interactions.py", line 62, in __init__
self.ob_mol = self._read_openbabel(filename)
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/arpeggio/core/interactions.py", line 2046, in _read_openbabel
mol = protein_reader.read_mmcif_to_openbabel(path)
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/arpeggio/core/protein_reader.py", line 88, in read_mmcif_to_openbabel
mol = _parse_atom_site_openbabel(list(parsed.values())[0])
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/arpeggio/core/protein_reader.py", line 105, in _parse_atom_site_openbabel
table = ob.OBElementTable()
File "/home/migwell/miniconda3/envs/driverpipe/lib/python3.9/site-packages/openbabel/__init__.py", line 17, in __getattr__
raise AttributeError
AttributeError
We should therefore follow the advice:
"import openbabel" is deprecated, instead use "from openbabel import openbabel"'
The text was updated successfully, but these errors were encountered:
Gives me:
We should therefore follow the advice:
The text was updated successfully, but these errors were encountered: