search

dauparas / ProteinMPNN

Code for the ProteinMPNN paper
MIT License
910 stars 278 forks source link

Warnings From Example Scripts? #81

Closed jamesrgraham closed 7 months ago

jamesrgraham commented 8 months ago

Hello,

What are these warnings ("NOT loaded") that I get when I run the example scripts? The scripts output data, but I'm concerned about the warnings. Also, is the line, source activate mlfold, not needed if you already have the Conda env activated?

./submit_example_4.sh: line 8: activate: No such file or directory
----------------------------------------
pssm_jsonl is NOT loaded
----------------------------------------
omit_AA_jsonl is NOT loaded
----------------------------------------
bias_AA_jsonl is NOT loaded
----------------------------------------
tied_positions_jsonl is NOT loaded
----------------------------------------
bias by residue dictionary is not loaded, or not provided
----------------------------------------
discarded {'bad_chars': 0, 'too_long': 0, 'bad_seq_length': 0}
----------------------------------------
Number of edges: 48
Training noise level: 0.2A
Generating sequences for: 3HTN
2 sequences of length 429 generated in 3.7705 seconds
Generating sequences for: 4YOW
2 sequences of length 693 generated in 6.6713 seconds

Thanks! james

mlnance commented 8 months ago

Hi James,

The warnings can be spooky, but they look fine in this case. The program is just letting you know that you didn't supply any of those files, which is usually fine. I'd only be concerned if, say, you did pass an omit_AA_jsonl or something and that same warning came up.

As for the activation part, also should be fine. It looks like your example script ran so your own conda environment should be fine.

I'm not a developer, but essentially don't worry about these warnings!

Hope it helps, Morgan

jamesrgraham commented 7 months ago

Thank you, Morgan! I missed the alerts saying you had commented.