Open mainguyenanhvu opened 1 year ago
Hey, thanks for your interest.
1) To add more files to the scpdb dataset you will have to create new types/molcache files for training 2) The first 4 steps are for a single pdb yes. 3) I believe the train.txt and test.txt files just need to contain the protein-ligand complexes you are training/testing on. 4) I'm not sure what you mean here, but you need to ensure (unfortunately in the scripts) that all the file paths are valid.
Let me know if you are facing any errors in the process.
Thank for your reply. I added a code to deploy data preparation pipeline, and made a pull request. If you have time, please check it whether or not I might make some mistakes.
To reply your answer:
Besides, I would like to ask you:
==============================
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 79-80 should contain charge of the atom
but OpenBabel found ' 0' (atom 5489).
==============================
*** Open Babel Warning in parseAtomRecord
WARNING: Problems reading a PDB file
Problems reading a HETATM or ATOM record.
According to the PDB specification,
columns 79-80 should contain charge of the atom
but OpenBabel found ' 0' (atom 5490).
Please help me. Thank you very much.
Thank you for the pull request, I will check it when I get more time.
I am trying to use your 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:
I am tried on this pdb.
Thank you very much.