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devalab / DeepPocket

Ligand Binding Site detection using Deep Learning
MIT License
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The number of pocket in types file #19

Closed fengyuewuya closed 1 year ago

fengyuewuya commented 1 year ago

Hi, I read the train.types like seg_scPDB_train0.types. The first few lines are as follows: 1 -18.161927039784217 32.606813980669806 85.32244760620364 10mh_1/protein_0.gninatypes 10mh_1/cavity6.mol2 1 -11.51310276710522 28.98620689253697 91.02771812783796 10mh_1/protein_0.gninatypes 10mh_1/cavity6.mol2 1 14.198903210849663 9.972515184884662 25.079490147212237 12gs_1/protein_0.gninatypes 12gs_1/cavity6.mol2 1 6.117556524238361 -2.4037784058248697 32.47945066104617 12gs_1/protein_0.gninatypes 12gs_1/cavity6.mol2

My confusion is that for this PDB 10mh_1 , it seems that there is only one cavity in the source folder "scPDB/10mh_1/", but there are two lines about 10mh_1 in seg_scPDB_train0.types. image

RishalAggarwal commented 1 year ago

Some proteins have more than 1 pocket (albeit under different folder names), the types files ensures that the structures have all the relevant pockets matched

fengyuewuya commented 1 year ago

Get, Thx

mainguyenanhvu commented 1 year ago

@fengyuewuya 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.