search

dauparas / ProteinMPNN

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

Omit AAs per resiude #65

Closed Cookiemaster33 closed 11 months ago

Cookiemaster33 commented 11 months ago

Hi there.

I was wondering how to use the "--omit_AA_jsonl" flag. It seems that it would be possible to define the omission of certain amino acids per residue. Is there a helper script that can generate the .json file, or do I have to write that myselfe?

Thanks for your help.

Toby

dauparas commented 11 months ago

Hi Toby,

Have a look at this helper script: https://github.com/dauparas/ProteinMPNN/blob/main/helper_scripts/other_tools/make_omit_AA.py

Cookiemaster33 commented 11 months ago

Thank you so much. Should have looked more closely in the scripts folder. Sorry about that. I was able to adapt the script and it runs perfectly fine. When I run my main script however, it gives me the message "omit_AA_jsonl is no NOT loaded". Not sure what I am doing wrong. This is the command I am using:

python ~/Programs/ProteinMPNN/protein_mpnn_run.py \ --jsonl_path $path_for_parsed_chains \ --chain_id_jsonl $path_for_assigned_chains \ --fixed_positions_jsonl $path_for_fixed_positions \ --out_folder $output_dir \ --num_seq_per_target 1000 \ --backbone_noise $noise \ --sampling_temp $temperature \ --seed 6 \ --batch_size 100 \ --tied_positions_jsonl $path_for_tied_positions --omit_AA_jsonl 'inputs/omit_AA.jsonl'

Thanks for your help.

Best Toby