phdymz / proteinmae Goto Github PK

Hi~thanks for your nice model. I am trying to get the embedding of a whole protein from the pretrained model, but i'm little confused about which part i should take, do you have any suggestions? Thanks. @phdymz

Hi, thank you for your work! This is an inspiring project and I really wonder when it will be open-sourced. I would really appreciate it if you can also release your code for training downstream tasks. Best wishes!

Arguments.py seems taken from the dMaSIF code, which had the same issue. In Argsparse, setting type=bool and default=True does not give what you initially expect. Eg, you cannot turn off the search using --search False. This could have implications on how the model was trained too?

Example:

args.py

import argparse
parser = argparse.ArgumentParser(description="Network parameters")  
parser.add_argument(
    "--search_wrong",
    type=bool,
    default=True,
    help="Predict matching between two partners",
)  
parser.add_argument(
    "--search_wrongFalse",
    type=bool,
    default=False,
    help="Predict matching between two partners",
)
parser.add_argument('--search_right', action=argparse.BooleanOptionalAction)  

test.py

from args import parser

# Parse the arguments
args = parser.parse_args()
print('search wrong, set to True in args.py')
print(args.search_wrong)
print('search_right, set as boolean action in args.py')
print(args.search_right)

Run python test.py
search wrong, set to True in args.py
True
search wrongFalse, set to False in args.py
False
search_right, set as boolean action in args.py
None

Run python test.py --search_wrong False --search_wrongFalse True --search_right
search wrong, set to True in args.py
True
search wrongFalse, set to False in args.py
True
search_right, set as boolean action in args.py
True

Run python test.py --search_wrong False --search_wrongFalse True --no-search_right
search wrong, set to True in args.py
True
search wrongFalse, set to False in args.py
True
search_right, set as boolean action in args.py
False

The only flag that gives exactly what you think it would is --search_right vs --no-search_right. It also works if you set the flag as boolean with False as default, but that is not the case in the current Arguments.py.

Hello, could you please provide the code to process protein PDB files into NPZ files?

Hello,
From the README, it is not clear how to supply a protein or a list thereof for training/inference. Could you clarify:

• how to supply inputs (proteins for --site, protein pairs for --search)
• the format of those inputs (pdb file, or processed tensor? If tensor, how to preprocess the -I suppose- pdb input?)

Thank you, the software looks promising!