Hi,
I am currently working on using your tool for the comparison of a number of predicted protein structures.
Initially, I hand-picked five enzymes as an example case, and the tool worked without issue.
However, I then downloaded a set of 200 enzymes to further evaluate the performance of DeeplyTough, and on this set, the preprocessing script stops when the code arrives at the line I have pasted below while working on the second protein.
""
# process pdb -> pdbqt (output written to output_dir)
try:
subprocess.run(['/bin/bash', '-ic', mgl_command.format(pdb_path_tempdir1)], cwd=output_dir, check=True)
""
This does not seem to be a problem in the form of a corrupted file, because if I run the same command again, one more protein is preprocessed before it stops when trying to preprocess the next one.
I have taken a subset of five enzymes from this larger set to see if the number of proteins is the problem, but also for this subset of five the same thing happens.
I do not get any error information with it, as the htmd logging set up fails. See the full output below.
""
HTMD: Logging setup failed
INFO:misc.utils: Pre-processing /home/user/Data/test_structures/B0S0K3_AF_93_clean.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
INFO:misc.utils: Pre-processing /home/user/Data/test_structures/C1FNF9_AF_96_clean.pdb with HTMD...
[2]+ Stopped python $DEEPLYTOUGH/deeplytough/scripts/custom_evaluation.py --dataset_subdir ''test_structures" --output_dir "/mnt/c/Users/user/Data/results" --device 'cpu' --nworkers 1 --net $DEEPLYTOUGH/networks/deeplytough_toughm1_test.pth.tar
"""
Do you have any suggestions as to what could be the problem here? I am primarily stumped as it worked without issue before, and in principle there is no difference between both sets of structures, from a file perspective. Thank you in advance.
Hi,
I am currently working on using your tool for the comparison of a number of predicted protein structures.
Initially, I hand-picked five enzymes as an example case, and the tool worked without issue.
However, I then downloaded a set of 200 enzymes to further evaluate the performance of DeeplyTough, and on this set, the preprocessing script stops when the code arrives at the line I have pasted below while working on the second protein.
""
# process pdb -> pdbqt (output written to
output_dir)try:
subprocess.run(['/bin/bash', '-ic', mgl_command.format(pdb_path_tempdir1)], cwd=output_dir, check=True)
""
This does not seem to be a problem in the form of a corrupted file, because if I run the same command again, one more protein is preprocessed before it stops when trying to preprocess the next one.
I have taken a subset of five enzymes from this larger set to see if the number of proteins is the problem, but also for this subset of five the same thing happens.
I do not get any error information with it, as the htmd logging set up fails. See the full output below.
""
HTMD: Logging setup failed
INFO:misc.utils: Pre-processing /home/user/Data/test_structures/B0S0K3_AF_93_clean.pdb with HTMD...
setting PYTHONHOME environment
adding gasteiger charges to peptide
INFO:misc.utils: Pre-processing /home/user/Data/test_structures/C1FNF9_AF_96_clean.pdb with HTMD...
[2]+ Stopped python $DEEPLYTOUGH/deeplytough/scripts/custom_evaluation.py --dataset_subdir ''test_structures" --output_dir "/mnt/c/Users/user/Data/results" --device 'cpu' --nworkers 1 --net $DEEPLYTOUGH/networks/deeplytough_toughm1_test.pth.tar
"""
Do you have any suggestions as to what could be the problem here? I am primarily stumped as it worked without issue before, and in principle there is no difference between both sets of structures, from a file perspective. Thank you in advance.