forlilab/scrubber

Issues with --out_fname

Opened this issue · 1 comments

althea-hansel commented

--out_fname decoys_.sdf:
Observed behavior:

(scrubber) althea@pixar:~/Documents/dev/cryokit/ALK$ scrub.py --in_fname decoys.smi --out_mode split --out_naming name --out_fname decoys_.sdf
[ initializing multiprocessing pipeline ]
[ storage initialized in FILE MODE ]
[ 32 geometry workers initialized ]
[ ▇|▅|▆|▆|▄|▃|▄|▁|▆|▅|▇|▃|▆|▆|▄|▄|▄|█|▇|▁|▃|▅|▇|▅|▅|▇|▄|▄|▄|▅|▆|▄ processing input mol. 4 ]  Process MoleculeStorage:
Traceback (most recent call last):
  File "/home/althea/programs/miniconda3/envs/scrubber/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/home/althea/programs/scrubber/scrubber/storage.py", line 374, in run
    outfname = self._get_outfname(mol)
  File "/home/althea/programs/scrubber/scrubber/storage.py", line 416, in _get_outfname
    os.makedirs(dirname)
  File "/home/althea/programs/miniconda3/envs/scrubber/lib/python3.10/os.py", line 225, in makedirs
    mkdir(name, mode)
FileNotFoundError: [Errno 2] No such file or directory: ''
[ ▄|▇|▄|▄|█|▃|▆|▅|▃|▃|▄|▇|▃|▃|▄|▄|▄|▅|▆|▄|▅|▁|▃|▅|▁|▆|▄|▆|▃|█|▆|▇ processing input mol. 116 ]  ( 23.587 mol/sec.)
  • program freezes
    Expected behavior:
  • program runs and places files in directory named "decoys"

--out_fname ./decoys_.sdf:
Observed behavior:

  • program completes, all expected file written
  • written in working directory

Expected behavior:

  • program runs and places files in directory named "decoys"