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devalab / DeepPocket

Ligand Binding Site detection using Deep Learning
MIT License
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segmentation fault #7

Closed WangLiguo-DP closed 2 years ago

WangLiguo-DP commented 2 years ago

when predicting binding sites given a .pdb file of a protein using: python predict.py -p pdb/1alb_A.pdb -c first_model_fold1_best_test_auc_85001.pth.tar -s seg0_best_test_IOU_91.pth.tar -r 3

I meet this bug : 'segmentation fault' after POCKET HUNTING BEGINS POCKET HUNTING ENDS

I used gdb to view the core file : 'Failed to read a valid object file image from memory. Core was generated by `python3 predict.py -p pdb/1alb_A.pdb -c first_model_fold1_best_test_auc_85001.p'. Program terminated with signal 11, Segmentation fault.'

RishalAggarwal commented 2 years ago

Hey,

Could you share the PDB file to reproduce the error

WangLiguo-DP commented 2 years ago

OK，I used 1ALB_A in RCSB PDB, but I couldn't upload this pdb file in github issu, so upload the txt file instead 1alb_A.txt

RishalAggarwal commented 2 years ago

Hey sorry, it was a busy week. However, I am not able to reproduce the error, my best guess is that your environment may not be set for it. If you just want the output files on this protein I have uploaded them here: https://drive.google.com/drive/folders/1G8-0Apxn7NEs7pnV0FPvUmQzY4s0vF4h?usp=sharing

mainguyenanhvu commented 1 year ago

Hello @WangLiguo-DP have you re-run data preparation for a custom data? If yes, please help me.

I am trying to use the instruction to prepare data for training a new classifier. I have stuck in make_types step because I can't find train.txt and test.txt files.

Moreover, I have 4 questions:

  1. If I want to add several pdb files to the available scPDB dataset, how can I complete it?
  2. The instruction for preparing data only works for a single pdb file, does it? If not, I need to write a pipeline to wrap up it.
  3. How to prepare train.txt and test.txt files to run make_types.py?
  4. Could you please show me which file/folder needed inputting from previous to each step?

I am tried on this pdb.

Thank you very much.

p.s: I have asked in the issue https://github.com/devalab/DeepPocket/issues/26.