Tutorial for ppi

[mvfferraz]

Hey all,

First of all congratulations on this amazing work. I don't know if I'm being too early here as this is the first topic on discussion, but I have had some problems to reproduce the tutorial for PPI.

I have installed deeprank2 locally and everything seems to run fine. I'm running the JN for "data_generation_ppi.ipynb".
All the command works except for queries processing. I have the following error:

"Graph/Query with ID residue-ppi:M-P:BA-105857 ran into an Exception (ValueError: chain ['M', 'P'] not found in the structure), and it has not been written to the hdf5 file. More details below:
chain ['M', 'P'] not found in the structure
Traceback (most recent call last):
File "/home/matheus/miniconda3/envs/deeprank2/lib/python3.10/site-packages/deeprank2/query.py", line 477, in _process_one_query
graph = query.build(self._feature_modules)
File "/home/matheus/miniconda3/envs/deeprank2/lib/python3.10/site-packages/deeprank2/query.py", line 202, in build
graph = self._build_helper()
File "/home/matheus/miniconda3/envs/deeprank2/lib/python3.10/site-packages/deeprank2/query.py", line 364, in _build_helper
contact_atoms = get_contact_atoms(
File "/home/matheus/miniconda3/envs/deeprank2/lib/python3.10/site-packages/deeprank2/utils/buildgraph.py", line 176, in get_contact_atoms
atom_indexes = interface.get_contact_atoms(cutoff=influence_radius, chain1=chain_id1, chain2=chain_id2)
File "/home/matheus/miniconda3/envs/deeprank2/lib/python3.10/site-packages/pdb2sql/interface.py", line 82, in get_contact_atoms
raise ValueError(
ValueError: chain ['M', 'P'] not found in the structure
The queries processing is done. The generated HDF5 files are in data_processed/ppi/residue.
"

However, I'm using the input provided in the tutorial for peptide-MHC systems, in which the chains are indeed M and P.

Has anyone faced this problem before? I'd really appreciate thoughts on this matter.

Best,
Matheus

[gcroci2]

Hi @mvfferraz, sorry for the delay, somehow I missed your post.

This seems more like a topic for a new issue (which may be an installation error or a bug) than for the Discussions tab. Please fill out this form here, we will pick it up asap.

[mvfferraz]

Dear Giulia, thank you for the reply.

I've managed to fix this issue, but I still have some problems trying to reproduce the GNN training tutorial. I'll fill out the form in the proper venue.

Thank you and have a nice day.