lbm-epfl / pesto Goto Github PK

Dear Authors,

Thanks for developing this very useful tool. I did a test on a PDB structure. The tool generated 5 files (with names of *_i[0-4].pdb). The b factor column in each of the five files is different. I didn't find documents about the these files. Please advise on how to use the files for interface inference, such as meaning of b factor column in each file, and cutoffs (like the mean values in a window and size of window to call interface, etc. Thanks!

Hi,

I am trying to install the environment with your .yml file it do not seems to work. Do you have an idea why ?

Modules are not called according to the repository structure, eg:
from model import Model
should be
from model.model import Model

Also, example data missing:
dataset = Dataset("datasets/contacts_rr5A_64nn_8192.h5")

I could suggest to rerun all .ipynb files in a fresh conda enviroment with a cloned git, to ensure they work?

Dear authors,

Thanks for developing this very useful tool. I am testing PeSTo, and got an error with numpy:

model/save/i_v4_1_2021-09-07_11-21/src/structure.py", line 99, in tag_hetatm_chains
structure = tag_hetatm_chains(structure)
AttributeError: module 'numpy' has no attribute 'object'

This is perhaps a numpy version issue. When I created the environment, conda automatically installed numpy 1.25. Can you please tell the numpy version that works? Or even better specify versions in pesto.yml file? Thanks.

I have tried to run PeSTo/md_analysis/apply_model_md.ipynb.
The folder "model" does not exist here, but I copied it from the root directory.
The from X import statements need to refer to "model."

In
from CLoNe.clone import CLoNe
"CLoNe" does not exist

The data "meta" does not exist, so the data_manager.py just throws a
FileNotFoundError: [Errno 2] No such file or directory: 'database/meta'

Also, the symlink for directory
datasets/
points to an non-existent location

Could you upload the data, for testing?

Hello,
Thank you for sharing such a good job PeSTo.
I'm doing some work about protein-lipid interactions.
Is it convenient for you to tell me how can I get these protein-lipid data in PeSTo ?
Thanks !
CJ Wu

Is there a ready-made docker image ？
the conda install is Very time-consuming

Hi,
the following files are missed in this repo.
training_exclusion_lists = [ # "data/lists/ppdb5_set.txt", # "data/lists/masif-site_test_set.txt", # "data/lists/skempi_v2.txt", # "data/lists/memcplxdb.txt", # "data/lists/excluded.txt" ]
would you like to upload them?
Best,
Zhangzhi

Hello, I noticed that some module calls do not match the directory structure in the .ipynb file.
Eg.
from config import config_model, config_data
should be (according to the github structure)
from model.config import config_model, config_data

Also, the benchmark data is missing in the github. Where could I retrieve it from?
dataset = Dataset("datasets/contacts_rr5A_64nn_8192.h5")

The results file below is missing from the repository, so the .ipynb notebook cannot be run:

results/interface_ppi_cuda_profiling.csv