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devalab / DeepPocket

Ligand Binding Site detection using Deep Learning
MIT License
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Question about classes #6

Closed elefps closed 2 years ago

elefps commented 2 years ago

Hello and congrats on your repo!

As I see at training segmentation, you have num_classes=1. That means that label=1 -> pocket and label->0 not pocket/?

RishalAggarwal commented 2 years ago

yup thats right

mainguyenanhvu commented 1 year ago

Hello @elefps 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.